y2006 annual report

ISSO

THE INSTITUTE FOR SPACE SYSTEMS OPERATIONS

Y 2 0 0 6 A N N U A L R E P O RT

UNIVERSITY OF HOUSTON | UNIVERSITY OF HOUSTON-CLEAR LAKE NASA-JOHNSON SPACE CENTER

ISSO | SPRING 2007

COVER—Aiyaz Paniwala, pursuing a master’s degree in computer science at the University of Houston-Clear Lake, studies the components of a wireless sensor in the laboratory of Dr. T. Andrew Yang. Paniwala earned his B.E. in computer engineering at the University of Mubai, India.

ISSO Institute for Space Systems Operations University of Houston University of Houston-Clear Lake NASA-Johnson Space Center Y2006 Annual Report

University of Houston Jay Gogue, Ph.D. President, Chancellor of UH System Donald J. Foss, Ph.D. Provost, Senior Vice-President and Vice-Chancellor for Academic Affairs Donald L. Birx, Ph.D. Vice-President and Vice-Chancellor for Research

University of Houston-Clear Lake William A. Staples, Ph.D. President Edward J. Hayes, Ph.D. Senior Vice-President and Provost

The Institute for Space Systems Operations (ISSO) of the Houston Partnership for Space Exploration (HPSE) David R. Criswell, Ph.D. Director Phone: 713 743-9135; FAX 713 743-3589 E-mail: [email protected] The Institute for Space Systems Operations—ISSO 617 Science & Research Bldg 1, Rm 629F University of Houston Houston, TX 77204-5005

Editorial Office Irving N. Rothman, Ph.D., Editor Matthew Dulin Associate Editor and Chief Graphic Designer Ann V. Nunes, Ph.D. Assistant Editor Debbie V. Bush Consultant Photography—Irving N. Rothman, Matthew Dulin 504 Science & Research Bldg University of Houston Houston, TX 77204-5006 Phone: 713 743-9138; FAX: 713 743-9134 E-mail: [email protected]

OPPOSITE—NASA tracks space experiments through an extensive field of satellite dishes at the Johnson Space Center.

TA B L E O F C O N T E N T S ISSO Director’s Report • 1 David R. Criswell PDAF REPORTS—POST-DOCTORAL AEROSPACE FELLOWSHIPS Development of Micro Column Arrays (MCA) for Thermal Management Applications • 8 Abdelhak Bensaoula, UH Center for Advanced Materials [CAM] and Pranob Misra, NASA-JSC PI UWB Tracing System Design with TDOA Algorithm for Space Applications • 11 Edward T. Dickerson, UHCL Science and Computer Engineering; G. Dickey Arndt and David (Jianjun) Ni, NASA-JSC Effects of Simulated Microgravity on Microbial Gene Expression • 17 George E. Fox, UH Department of Biology and Biochemistry; and Duane L. Pierson, NASA-JSC Martian Soil Biosensors Based on Dielectric Spectroscopy • 21 John H. Miller, Jr., UH Department of Physics, and David Warmflash, NASA-JSC MINI-GRANTS Micro-Integrated Super Broadband Stellar Simulator Optical Calibration Sources • 28 Abdelhak Bensaoula, Chris Boney, and Nasr Medelci, UH Center for Advanced Materials (CAM) Optimizing Quality-of-Service in Adaptive Optics Systems and Other (m,k)-Firm Real-Time Systems • 30 Albert M. K. Cheng, UH Department of Computer Science Prototype Micro-Manipulator of Space Robotics Applications • 37 James B. Dabney, UHCL School of Science and Computer Engineering; and Thomas L. Harman, UHCL Department of Computer Engineering Bacillus Pumilus SAFR-032: A Model for Planetary Protection Research • 40 George E. Fox, UH Department of Biology and Biochemistry Origin of Structure in the Early Universe from Gravitation in Radiation • 43 David Garrison, UHCL School of Science and Computer Engineering Superior Adsorbents for Aerospace Applications • 46 Jack Y. Lu, UHCL School of Science and Computer Engineering The Solar Eclipse of April 22, 1715, and Family Quarrels in Daniel Defoe’s The Family Instructor • 48 Irving N. Rothman, UH Department of English Computational Methods in Non-Smooth Mechanics: Application to Dry Friction Constrained Motions • 53 LieJune Shiau, UHCL School of Science and Computer Engineering Efficient Space Radiation Computation with Parallel FPGA • 56 Liwen Shih, UHCL Department of Computer Engineering Fault Tolerant Control of a Truss Structure Using MR Dampers • 62 Gangbing Song and Linsheng Huo, UH Department of Mechanical Engineering

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FOLLOW-UP REPORTS: INNOVATIONS AND NEW DEVELOPMENTS Natural Language Interface Models for Fast Responsiveness Applications • 68 Hisham Al-Mubaid, UHCL Department of Computer Information Systems A Text-Mining Technique for Literature Profiling and Information Extraction from Biomedical Literature • 69 Hisham Al-Mubaid, UHCL Department of Computer Information Systems Investigation of III-Nitride Materials for Space-Based Solar Cells • 70 Abdelhak Bensaoula and Chris Boney, UH Center for Advanced Materials [CAM] Miniature Optical Sensors for Detection of Water and Air Contamination • 71 Abdelhak Bensaoula, David Starikov, and Chris Boney, UH Center for Advanced Materials [CAM] The Impact of Chromosome Lineage upon Genetic Program Modeling • 72 Gary D. Boetticher and Kim Kaminsky, UHCL Division of Computing and Mathematics Progress on Three Projects: Systems for Spacecrafts, Rovers, and Station Crew Return Vehicles • 74 Albert M. K. Cheng, UH Department of Computer Science Real-Time Active Loading of Piezoelectric Ultrasonic Motors for Simulating Space Robotics Applications • 76 James B. Dabney and Thomas Harman, UHCL School of Science and Computer Engineering Early Genetic Systems • 79 George E. Fox, UH Department of Biology and Biochemistry A Unique Camera System To Study the High-Speed Dynamics of Premixed Flames • 81 Michael Gorman, UH Department of Physics A Theoretical Analysis of Vibrational Modes Aimed at Their Use as Measures of Bone Damage • 82 Gemunu Gunaratne and Chamith Rajapakse, UH Department of Physics Raman Scattering Test of Mechanical and Sensor Properties of Advanced Nanocomposites • 83 Viktor G. Hadjiev, Leonard Yowell, and Sivaram Arepalli, Texas Center for Superconductivity at UH [TCSUH] Development of Quantum-Cascade Laser-Based Biosensor Technology • 85 Thomas L. Harman, UHCL Department of Computer Engineering The Effect of Martian Dust on Radiator Performance • 88 D. Keith Hollingsworth, Larry C. Witte, and Ashley Higgins, UH Department of Mechanical Engineering Mechanical Foot Stimulation Results in Lower Limb Muscle Activation • 90 Charles S. Layne, UH Department of Health and Human Performance Contaminant Removal from Fuel Cells for Aerospace Applications • 91 Jack Y. Lu, UHCL Department of Computer Engineering Energy-to-Peak Induced Norm Upper Bound Control Approach for Collocated Structural Systems • 92 Mona Meisami-Azad, Javad Mohammadpour, and Karolos M. Grigoriadis, UH Mechanical Engineering Electromagnetic Probes of Molecular Motors (2005) and Low-Frequency Dielectric Spectroscopy of Martian Soil Samples (2004) • 95 John H. Miller, Jr., UH Department of Physics Space Radiation Shielding Modeling Consortium • 96 Lawrence S. Pinsky, UH Department of Physics High-Performance Martian Space Radiation Mapping • 104 Liwen Shih, UHCL Department of Computer Engineering An AC-DC-AC Converter with Smaller DC-Link Capacitor for Space Power Distribution Systems • 106 Wajiha Shireen, UH Department of Engineering Technology Dielectrophoresis of Biological Cells and Single-Walled Carbon Nanotubes • 108 Jaroslaw (Jarek) Wosik, Divya Padmaraj, Chinmay Darne, and Wandd Zagozdozon-Wosik, Texas Center for Superconductivity at UH [TCSUH] Development of Wireless Stations for Distributed Field Operations • 111 T. Andrew Yang and Sadegh Davari, UHCL School of Science and Computer Engineering Roster of Principal Investigators, NASA-JSC Co-PI's, Post-Doctoral Aerospace Fellows • 113 ISSO Student Researchers • 120 ISSO Research Projects • 122

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The Director’s Report by David R. Criswell

T

HE INSTITUTE FOR

SPACE SYSTEMS OPERATIONS In 2006, the prior and currently fund(ISSO) is the operating agency for the ed UH and UHCL faculty reported Houston Partnership for Space Exploration submitting 37 proposals applying for (HPSE) at the University of Houston and the $15,470,000 of external funding. University of Houston-Clear Lake. UH and UHCL They report obtaining $2,850,000 for are also members of the Texas Space Grant these external proposals and proposConsortium. ISSO works through TSGC on a als submitted the prior year. The 2006 statewide level. Dr. David R. Criswell directs ISSO ISSO State of Texas funds were and is responsible for both UH and UHCL activities. leveraged by a factor of ~8. In the academic year 2005-06, HPSE continued Leveraging of the 2006 funds will funding under a State of Texas Line Item for continue to increase as more propos$355,986 that allocated $278,990 to operations at als are submitted based on follow-up the University of Houston and $76,996 at the results of the 2006 projects. University of Houston-Clear Lake. As reported by In 2006, ISSO investigators the faculty in the following research articles, the reported submitting 120 professionAY2005 ISSO State of Texas funds were leveraged al papers, delivering 110 professionby a factor of 7.8 to 1. al presentations and interviews. Six ISSO projects have established solid professional undergraduates participated in the links between NASA, the Johnson Space Center research activities. Twenty-nine David R. Criswell (JSC), the Houston aerospace community, and UH master’s level students and 17 docand UHCL. ISSO provides the flexibility and toral candidates participated in ISSO resources for UH and UHCL faculty to fully participate in the research projects along with 14 post-doctoral fellows. rapidly evolving national space program. Since 1991, faculty Thirty-five UH System faculty participated in the ISSO supported by ISSO research funds have reported obtaining research along with eight professors from other universities, $23,800,000 of external funding and thus leveraged the research nine NASA researchers, and 14 from other non-profit organizafunds by 4.7 to 1 over the life of the program. tions and companies. In addition to JSC, 15 other organizations This report summarizes the 2006 accomplishments by ISSO and/or their employees participated: supported researchers. A short synopsis of each research activity is presented within six study areas. The joint UH/UHCL• Baylor College of Medicine NASA JSC Post-Doctoral Aerospace Fellowship projects, • Boeing - Houston approved as of August 31, 2006, are listed in the last section • Centre for European Radiation Nuclear (CERN) along with a description of a new request for proposals for • Harbin Institute of Technology, China Space Cluster projects. • Lockheed Martin - Houston • Montreal Bio-Processing Laboratory Summary of the 2006 Program • NASA- Langley Research Center The primary activities of ISSO are the unique Post Doctoral • Prairie View - A&M Aerospace Fellowship (PDAF) program between UH/UHCL • Rice University Electrical and Computer Engineering and the NASA-Johnson Space Center seed-level funds awarded • Smalley Inst. For Nanoscale Science and Technology to UH and UHCL faculty for development of new aerospace • Stanford Linear Accelerator Center research projects. Prior ISSO reports, available on request as • University of Quebec published reports and on the web at http://www.isso. • University of Singapore uh.edu, provide detailed descriptions of both programs. The • University of Texas at Dallas PDAF program started in 1995. It operated through a • University of Texas Medical Branch Memorandum of Understanding between JSC and the university on the main campus and the campus at Clear Lake. The MOU ISSO maintains a website of all reports and uses that website was converted to a Space Act Agreement in early 2006. to announce proposals and fellowship opportunities. In 2006, ISSO provided $308,300 in research funds to 16 UH ISSO worked at UH with four colleges and Deans J. Bear and UHCL faculty to support nine new seed-grant projects, five (Natural Science & Mathematics), R. Flumerfelt (Engineering), PDAF projects, the director’s research, and for program docu- W. E. Fitzgibbon (Technology), and R. K. Wimpelberg mentation. ISSO requires investigators to report results on proj- (Education) and with Dr. A. Ignatiev (SVEC) and the newly ects for five years after completion of funding of a given project. reformed Center for Advanced Materials (CAM). ISSO thanks

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them for their support in the research projects. At UHCL, ISSO worked primarily with the School of Science and Computer Engineering. Thanks are sincerely extended to Dean C. McKay (retired) and E. A. Dickerson (interim). Summary of ISSO Research Projects Six major themes identify the 14 research projects funded in 2006 and the follow-up results of 42 projects first funded between 2003 and 2005: Astrobiology and Life Sciences Space Radiation Modeling Computer Science and Communications Physical Sciences, Cosmology, and Defoe Engineering and Sensors Post-doctoral Aerospace Fellowship Projects (2006) and Related Follow-up Projects Professor A. Bensaoula (UH: Center for Advanced Materials), Dr. Pranob Misra (Fellow), and Dr. Andenet Alemu (prior Fellow, now with the UH Advanced Materials Center) and Dr. Bran Mayeaux (JSC: Materials Processing Branch) conducted research on the “Development of Micro Column Arrays (MCA) for Thermal Management Applications” (p. 8) and report both current progress and new results from the initiation of the grant in 2003. They have fabricated and demonstrated micro column arrays exhibiting low reflectance, high emissivity, and large effective surface areas by pulsed laser ablation on several metals, ceramics, and semiconductor materials. In addition to their use for emissive-based thermal management, MCA can produce enhanced bonding and brazing strength when applied to either identical or dissimilar materials. Some of the specific applications that can benefit from this and other aspects of MCA technology are space, defense, avionics, laser systems, and high performance computers. Professor G. E. Fox (UH: Biology and Biochemistry) and Dr. Duane Pierson (JSC) report on the results of the third and final year of the Post-Doctoral Aerospace Fellowship project concerning the “Effects of Simulated Microgravity on Microbial Gene Expression” (p. 17). Dr. Victor Stepanov completed his PDAF. Dr. Madhan R. Tirumalai is the new Post-Doctoral Aerospace Fellow. Bacteria can leave and thrive in an extremely wide range of environmental conditions. Unusual conditions can lead to unexpected bacterial responses that can not be predicted even if their genetic map is completely described. Wild type E. coli MG1655 were grown for 1,000 generations in a rotating environment that simulates zero-gravity. Researchers found that E. coli chemotactic and flagellar genes as well as genes involved in the acid tolerance response were up-regulated. Refer to the report for details of the methodology, equipment, and an extended discussion. Professor G. Fox also provided a follow-up report on his 2004 and 2005 seed-grant projects on early genetic systems: “Early Origins of Genetic Systems” and “Remnants of the RNA World: RNA Structures Associated with Gene Regulation” (p. 79). These two projects focused on different aspects of the hypothesis that DNA-based Earth life arose

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from an earlier RNA world. A detailed study of the RNAs and proteins associated with the translation machinery was carried out, and many remnants of early evolution were identified. Professor J. H. Miller (UH: Physics and TCSAM) and Dr. D. S. McKay (JSC: Planetary Sciences) participated with the ISSO Fellow, Dr. David Warmflash, and Prof. J. Wosik (UH: Electrical and Computer Engineering) and Dr. J. A. Jones (JSC: Flight Medicine) to develop electronic means of detecting life on Mars (p. 21). F. Karouia (JSC) is pursuing a doctoral degree on the project in the UH Biology and Biochemistry Department. They have found that dielectric spectroscopy measurements at different temperatures can distinguish live organisms from nonliving complex macromolecules and may eventually be suitable for in situ astrobiology studies on the surface of Mars or in the liquid ocean beneath the ice of Europa. Dr. Dickey Arndt (NASA-JSC) and UHCL Post-Doctoral Aerospace Fellow Dr. Jianjun Ni worked with Prof. E. Dickerson (UHCL: Acting Dean of the College of Science and Computer Engineering) on the second and final year of the development and demonstration of an “Ultra-Wideband Two-Cluster AngleOf-Arrival Tracking System Design for Space Exploration” (p. 11). The system is being studied for use in tracking of Lunar/Mars rovers during early exploration missions when satellite navigation systems (such as GPS) are not available. Field tests were conducted jointly with the SCOUT vehicle at the Meteor Crater in Arizona to test the tracking capability for a moving target. These tests demonstrated that the UWB tracking system can co-exist with other RF communication systems onboard SCOUT, and that a tracking resolution less than one percent of the range (range up to 2000 feet) can be achieved. Seed Grants (2006) and Follow-up Results (2003) Astrobiology and Life Sciences Professor G. Fox (UH: Biology and Biochemistry) investigated the Bacillus pumilus SAFR-032 as a model for protecting other planets from contamination by Earth’s micro-organisms carried on spacecraft (p. 40). As a first step toward understanding the biology of these strains that are extremely resistant to decontamination procedures, research scientists determined the whole genome sequence of one isolate, B. pumilus SAFR-032. Prof. Fox collaborated with the Baylor College of Medicine Human Genome Sequencing Center (HGSC). Professor Jaroslaw Wosik (UH: Electrical and Computer Engineering) led a 2005 and 2006 seed grant funded collaboration with UH professors J. H. Miller (Physics) and W. Zagozdzon-Wosik (ECE) and Rice University professor J. M. Tour (Mechanical Engineering and Materials and the Smalley Institute For Nanoscale Science and Technology), and four doctoral students and one master’s student on “Dielectrophoresis of Biological Cells and Single-walled Carbon Nanotubes” (p. 108). The general goal is to develop miniaturized sensors aimed at cellular analysis and bio-diagnostics. Such sensors are expected to play a very prominent role in space missions. The sensors were used to characterize the electromagnetic properties of biological and solid state materials, as well as electromagnetic properties of neutral (reference) par-

ticles, single-wall nanotubes, and the microorganism S. Cerevisiae and S. pombe. Results of these preliminary experiments are described. Professor C. Layne (UH: Health and Human Performance, College of Education) completed his Post-Doctoral Fellowship Program in 2003 on “Using Dynamic Foot Pressure as a Countermeasure to Muscle Atrophy” (p. 90). The ISSO Fellow Katharine Forth continues her work as a post-doctoral fellow at UH. Dr. Andrew Abercromby completed his doctoral program and now works for Wyle Life Sciences at NASA-JSC. Space Radiation Modeling Professors L. Pinsky and B. Mayers (UH: Physics) participated under ISSO special funding for 2005 in an international “Space Radiation Shielding Modeling Consortium” (p. 96). Two postdoctoral fellows (A. Empl and V. Anderson), three Ph.D. candidates, along with three master’s candidates and two undergraduates, also participated. Dr. Tom Wilson (NASA-JSC), Dr. A. Fasso (Stanford Linear Accelerator Consortium), five members of CERN, and six faculty of INFN (Italy) were also members. The objective was to provide a Monte Carlo-based software tool to model the radiation environment in space that will enable the evaluation of radiation shielding materials. In particular, they proposed to cooperate with the other members of the consortium to develop an event generator for Nucleus-Nucleus interactions that is accurate to within 25 percent in any significant channel over energies that are relevant for the evaluation of space radiation shielding issues. As a result of the efforts of the Houston Group in concert with the FLUKA team at CERN and in the INFN Milan Group, the analysis tool FLUKA now embeds two of the most respected heavy ion event generators in existence, RQMD and DPMJET. The past year has also seen significant progress in the primary effort of the UH Group to enhance the models within FLUKA and the user interfaces to the FLUKA code itself. Please refer to the full report for descriptions of the many other major accomplishments of the consortium. Space radiation is likely to be the ultimate limiting factor for future human deep space exploration. Prof. Liwen Shih (UHCL: Computer Engineering) worked with seven UHCL master’s level students, one Ph.D. candidate (UH: Aerospace Engineering), Dr. Robert Singleterry, Jr. (NASALangley), and the JSC MARIE Team via Dr. P. Saganti of Lockheed Martin and Prairie View A&M on the 2006 seed grant “Efficient Space Radiation Computations with Parallel FPGA” (p. 56). The team has identified major bottlenecks that slow down the running of the code HZETRN on several types of parallel computing systems. They are seeking further improvement, semantic application-, methodologyand algorithm-specific thread mapping optimization. Better understanding of the numerical models of nuclear physics theory with the help of LaRC Nuclear physics researchers is needed to further optimize parallel mapping. They note that as Earth’s ozone depletion continues, space radiation study could lead to dual-use countermeasures that will, in turn, protect human health from the radiation/aging effect in general, e.g., slowing down cataract development. Other critical

NEW CANDIDATE—Marius Dettmar, a doctoral student from the University of Bochun, Germany, is introduced to equipment designed to prevent muscle atrophy in astronauts who suffer from the loss of muscle tone when assigned for a lengthy period of time in an atmosphere free of gravity. The technology has been applied with success to bedridden and hospitalized patients.

CLUSTER/GRID—Team members focused on high-performance computing (HPC) are (l. to r.) Victor Shum, Ph.D. candidate in Aerospace Engineering, Thang Nguyen Toan, M.S. student, Dr. Liwen Shih, UHCL professor of computer engineering, and Susan Strasser, M.S. student in the Computer Engineering Department.


medical cures, e.g., proton cancer radiation treatment, are evolving. Dr. Shih also provides a follow-up on the initial ISSO seed grant “High-Performance Martian Space Radiation Mapping” (p. 104). Computer Science and Communications Adaptive optics systems used in surveillance satellites/air/spacecrafts, and astronomical observatories provide high-resolution imaging through Earth’s atmosphere. Professor Albert M. K. Cheng (UH: Computer Science) conducted the study “Optimizing Quality-of-Service in Adaptive Optics Systems and Other (m, k)-Firm Real-Time Spacecraft Control Systems” (p. 30). This preliminary study proved that the problem is NP-hard. He proposes a simple heuristic solution. “Greedily” increasing the QoS level of the tasks with the maximal “reward ratio” is possible as long as all the other tasks have their minimum service level. In 2003, 2004, and 2005, Prof. Cheng conducted three successive seed grant projects related to the ultimate goal of building fully-verified space vehicles that are (1) reliable, (2) energy-efficient, and (3) schedule-optimized (p. 74). Professor H. Al-Mubaid (UHCL: Computer Engineering) provides a combined progress report on two 2005 seed grants (p. 68). The first deals with “Natural Language Interface Models for Fast Responsiveness Applications” such as needed in Virtual Reality (VR) training programs, real-time text messaging applications, and mission-critical systems like aerospace applications. He designed and implemented word disambiguation and prediction techniques to solve the NL ambiguity problem. In “A Text-Mining Technique for Literature Profiling and Information Extraction from Biomedical Literature,” methods based on machine learning were used for a word classification task. Feature extraction techniques like MI (mutual information) and X2 (Chi-square) selected the key features in the contexts of the terms of interest. The methods were evaluated extensively with a large number of experiments. One of the challenges in data mining is to provide sufficient coverage of the search space in order to produce an acceptable model. Solving large problems using genetic programs (GPs) consumes excessive amounts of computer resources. Professor G. D. Boetticher (UHCL: Computer Science and Engineering) asked the questions, “Does chromosome lineage information provide any insight into the effectiveness of solving problems? If so, how could these insights be utilized to make better breeding decisions?” Experiments reveal that higher pedigree chromosomes can be identified leading to more efficient searches (p. 72). He participated with faculty of Rice University and the University of Texas Medical Branch in proposals to the Department of Defense and to the Severe Asthma Research Program. More accurate friction models are needed for software that simulates the motion of mechanical systems, such as the remote manipulators of the Space Shuttle or the International Space Station. Prof. LieJune Shiau (UHCL: School of Science and Computer Engineering) worked with Prof. R. Glowinski (UH: Mathematics), and UHCL Research Assistant M. Sheppard in the third seed grant devoted to “Computational Methods in Non-Smooth Mechanics: Applications to Dry Friction Constrained Motions” (p. 53). They formulated a friction-


constrained motion model to describe some remote manipulator system simulators with finite numbers of degree of freedom. The formulation addressed the need for computational efficiency required for high degree-of-freedom models. They have published results of low degree-of-freedom. The current study resulted in the new publication of higher degree-of-freedom generalized test systems proposed by NASA engineers. Professors T. Andrew Yang and S. Davrai (UHCL: Science and Computer Engineering) provide a follow-up on their 2004 ISSO seed-grant “Development of Wireless Stations for Distributed Field Operations” (p. 111). They specifically investigated the security and performance issues of wireless stations in mobile ad hoc networks, with a focus on the public key management system using certificates. One of the main issues to consider in a certificate-based scheme is the secure distribution of the public keys to all the nodes in the network. In addition, they were awarded a two-year Advanced Research Programs (ARP) grant by the Texas Higher Education Coordinating Board for the project “SOCO—Secure and Optimized Communication & Organization for Target Tracking in Wireless Sensor Networks.” Physical Sciences, Cosmology, and Defoe Professors J. D. Dabney and T. L. Harman (UHCL: School of Science and Computer Engineering) investigated a “Prototype Micro-Manipulator for Space Robotics Applications” (p. 37). This type of actuator has great potential for space-based robots because of their inherent low mass, simplicity, and immunity from magnetic fields. In this study, a piezoelectric actuator, position sensor, driver, and sensor amplifier were assembled. LabView software was applied to monitor the performance of the system. Dabney and Harman also provide an update (p. 76) of results from their 2003-2005 seed grants for the application of piezoelectric devices to the sensing and control of motion of mechanical systems such as robotic manipulators. The combustion front of an engine or a gas turbine combustor near its lean burn limit can become unstable to dynamic modes of propagation in which the steady front is replaced by a front that varies in both space and time. Professor M. Gorman (UH: Physics) utilizes “A Unique Camera System To Study the High-Speed Dynamics of Premixed Flames” (p. 81). He presents examples of the greater details visible in the rotating flame fronts in viewing at 60 Hz versus 250 Hz imaging rates. Professor D. Garrison (UHCL: Physics) is developing mathematical models for the “Origin of Structure in the Early Universe from Gravitational Radiation” (p. 43). Relatively little work has been done within standard cosmology on the impacts of structures in the early universe due to interactions between initial high-energy plasmas and gravitational radiation. The open-source computational tool CACTUS will be applied using the 30 2-GHz Pentium-4 based Linux machines and a small 16-node Beowulf cluster housed at the UHCL computational laboratory. This 2006 seed grant has already resulted in two proposals to NSF. Professor I. Rothman (UH: English) provides a delightful history of Daniel Defoe’s writings opposing the English Schism Act of 1714. He made use of Edward Halley’s prediction of the April 22, 1715 eclipse of the sun by the moon over southern England

FLUIDS & MAGNETICS—Dr. Gangbing Song (l.) and Dr. L. Huo (r.), Post-Doctoral Fellow, are writing a proposal to the National Science Foundation on handling vibration-sensitive instruments in space, utilizing a fluid whose viscosity responds to an applied magnetic field. Instruments are affixed to low-mass truss structures.

and Wales to satirize this act of Parliament (p. 48). Defoe explored the complex interactions between the populace, parliament, predictive astronomy, religion, and a husband and wife. Engineering and Sensors Professor A. Bensaoula provided follow-up reports on 2003 and 2005 seed grant projects “Miniature Optical Sensors for Detection of Water and Air-Contaminations” and “Investigation of IIINitride Materials for Space-Based Solar Cells” (pp. 71, 70). He also provided a report on the 2006 seed-grant project “MicroIntegrated Super Broadband Stellar Simulator Optical Calibration Source” (p. 28). Thermal radiators are required to let waste heat flow away from operating equipment, such as rovers that are used to explore Mars. Dust suspended in the atmosphere of Mars or churned up by driving across Mars can land on radiators and inhibit the flow of heat from the radiator. Professors K. Hollingsworth and L. C. Witte (UH: Mechanical Engineering) conducted a 2005 seed grant project on “The Effect of Martian Dust on Radiator Performance” (p. 88). This follow-up paper describes their progress implementing an automatic system to conduct long-duration measurements of the temperature and heater voltage of a thermal test station for radiator coupons. Metal-organic polymers have been found to have wide range of applications such as molecular separation and pollution prevention in air, liquid and water systems, where they can be used as ion exchangers and molecular sieves. Professor J. Y. Lu (UHCL: Chemistry) conducted experiments under a 2006 seed grant to

develop “Superior Adsorbents for Aerospace Applications” (p. 46). He also provides a follow-up report on the 2005 seed grant “Contaminant Removal From Fuel Cells for Aerospace Applications” (p. 91). Proposals were submitted in 2006 to the Texas Higher Education Coordinating Board ARP and the Welch Foundation that focused on water quality after a disaster and the adsorption properties of porous compounds. A proposal is planned for fall 2007 to the NSF. Equipment used to condition electric power onboard spacecraft can be a significant fraction of the mass of the overall electrical power system. The 2004 seed grant research on “An AC-DC-AC Converter with Smaller DC-Link Capacitor for Space Power Distribution Systems” conducted by Professor W. Shireen (UH: Engineering Technology) and graduate research assistant S. Vanapalli (M.S., 2004) continues to yield publications and is supported by an NSF grant through 2007 (p. 106). They demonstrate and test an experimental prototype of an AC-DC-AC converter that consists of a diode rectifier, DC-link, and a PWM inverter used in a closed loop V/Hz motor drive. Dr. Gangbing Song (UH: Mechanical Engineering) and Dr. L. Huo (UH post-doctoral fellow) conducted the 2006 seed grant “Fault Tolerant Control of a Truss Structure Using MR Dampers” (p. 62). Very low-mass truss structures are used in space to support and position vibration-sensitive instruments such as interferometers, antennas, cameras, or remote devices. This work focuses on techniques to suppress truss vibrations inducted by motions and vibrations of the spacecraft, environmental changes (changing sun angle), or driven motion of the truss or of the devices the truss supports. They examine the use of a magneto-rheological (MR) damper that uses a fluid whose viscosity responds to an applied magnetic field. They have developed mathematical models and applied them to data on a vibrating laboratory 8-bay truss supplied by Prof. Dr. S. Nagarajaiah of the Civil and Environmental Engineering Department at Rice University. They find that the designed fault tolerant controller can achieve a fair vibration reduction ratio, though there are partial faulty signals in the outputs of the sensors. A proposal is being prepared for submission to NSF. Follow-up reports were not received from: Prof. M. S. F. Clarke (Health and Human Performance) 2005: Validation of a Novel Micro-capillary Array Fluid Collection Technology for the Determination of Biomarkers of Bone Metabolism in Human Sweat 2004: Development of a Microgravity-Compatible Slide Staining Device Professors H. Malki (Technology) and K. Grigoriadis (Mechanical Engineering): 2005: PWM Control of Formation Flying Space Vehicle 2004: A Neural-Network-based Approach for Control of Vibration in a Black Hawk Helicopter These will be provided in future ISSO Annual Reports and on the ISSO website as they are received. Follow-up reports on the following subjects indicate sustained effort: Prof. M. Gorman’s study of the dynamics of premixed flames, (p. 81); Prof. G. Gunaratne’s study of measures of bone damage, (p. 82); Prof. V. Hadjiev’s


“Raman Scattering Test of the Properties of Nanocomposites,” (p. 83); Prof. T. Harman’s development laser-based biosensor technology, (p. 85); Prof. K. Grigoriadis’s approach for collocated structural systems, (p. 92); Prof. J. Miller’s studies of molecular motors and Martian soil samples, (p. 95). Post Doctoral Program for 2006 – 2009 ISSO invited proposals for new two-year duration Post-Doctoral Aerospace Fellowship projects in early 2006. Six proposals were received from UH/UHCL faculty and NASA-JSC co-investigators. Four were accepted: • Prof. G. E. Fox (UH: Biology and Biochemistry) and Dr. D. Pierson (JSC) – “Bacterial Adaptation to the Space Environment.” • Prof. R. Krishnamoorti (UH: Chemical Engineering) and Dr. L. Yowell (JSC) – “Active Nanocomposites: Multifunctional Aerospace Structures.” • Prof. L. H. Rhode (UHCL: Physics) – “Biological Effects of Shielding Parameters Across the Bragg Curve of Energetic Protons and Fe ions.” • Prof. E. A. Bering (UH: Physics) and Dr. D. S. Winter (JSC) – “Study of Mechanics of Plasma Detachment in a Magnetic Nozzle.” Two existing PDAF projects were renewed for their third and final year: • Prof. A. Bensaoula (UH: Center for Advanced Materials) and Dr. Brian Mayeaux (JSC: Materials Processing Branch) – “Development of Micro Column Arrays (MCA) for Thermal Management Applications.” • Prof. J. H. Miller, Jr. (UH: Physics), Dr. D. S. McKay (JSC: Planetary Sciences), and Dr. J. A. Jones (JSC: Flight Medicine), and Dr. D. Warmflash (UH: PDAF) – “Martian Soil Biosensors Based on Dielectric Spectroscopy.” The ISSO program is evolving in response to the evolving objectives of the University of Houston System. In past years, ISSO has requested mini-grant proposals from UH and UHCL faculty members. Each selected principal investigator received funds for summer research that would enable the professor, sometimes including a co-investigator, and one or more students to prepare better individual proposals to external organizations. In the fall of 2006, Dr. D. L. Birx (Vice Chancellor and Vice President for Research and Intellectual Property) challenged the UH System faculty to form large teams that could more effectively identify and pursue major research programs offered by external government and private organizations. In the spring of 2007, ISSO is requesting Space Exploration Cluster Pre-proposals from faculty teams of the UH System. Each team pre-proposal must be from a group of faculty committed to working as a team through 2008 to pursue major external funding in the very broad field of space exploration and development. Each pre-proposal must list specific external agencies and funding opportunities that exist as of May 1, 2007. Each proposal should also list highly probable proposing opportunities anticipated during 2007 and early 2008.


Director’s Research and Administrative Activities Dr. D. R. Criswell directs the Institute for Space Systems Operations at the University of Houston and the University of Houston-Clear Lake. His primary research interests are in industrial development of the moon and the economic benefits to Earth of a sustainable global solar power grid. Dr. Criswell works extensively with Dr. Helen Lane (Director of University Programs at the Johnson Space Center), Dr. Kamlesh P. Lulla (University Program Officer), and Dr. Donn Sickorez (University Affairs Officer) coordinating the ISSO research program with primary program goals of NASA-JSC. Since April 2006, he has provided interviews to members of the general and aerospace press and one invited editorial on solar power from space. Presentations and papers from September 2005 through March 2006 are listed in the ISSO 2006 Annual Report. Interviews Interview with Ms. C. Tumiel, San Antonio Express-News, “Lunar Solar Power and the Supply of Commercial Power to Earth” (May 23, 2006). Interview and filming by Mr. Brian Solari (Production Manager), The Future Channel, “Lunar Solar Power” (May 10, 2006). Interview with Ms. M. Chandler, CBS San Antonio, “Lunar Solar Power” (May 23, 2006). Interview with Mr. T. Hamilton (Energy Reporter/Tech Columnist), Toronto Star (July 6, 2006). Interview with Mr. N. Davidson, British Broadcasting Company (TV), (July 24, 2006). Publications Criswell, D. R. “The Sun, the Moon, and Sustainable Global Prosperity,” Energy Biz Magazine, July/August 2006, p. 54 (also available online; invited editorial). ISSO Program Documents Criswell, D. R. (Director), Rothman, I. (Editor), and Bush, D. (Associate Editor) (2006 Spring) Y2005 Annual Report, the Institute for Space Systems Operations of the University of Houston and the University of Houston-Clear Lake, 136pp., Houston, TX. Criswell D.R. (director) and H. Lane (JSC) (2006, 9 May) Peer Review of proposals submitted by University of Houston and University of Houston-Clear Lake faculty to ISSO Post Doctoral Aerospace Fellowship projects by faculty and research staff from UH, UHCL, and NASA-Johnson Space Center. Criswell, D.R. (2005 August - December) Worked with UH System Office of the General Counsel and NASA-JSC to renew the existing Memorandum of Understanding for the UH/UHCLJSC Post-Doctoral Aerospace Fellowship Program and then (2006, January - to date) convert it to a Space Act Agreement.

TEAM MEMBERS—Researchers working on micro column arrays (MCA) for thermal management applications (l. to r.) Nasr Medelci, Ph.D.; Rajeev Pillai, Ph.D. candidate in electric engineering; Dr. Abdelhak Bensaoula, Ph.D., Principal Investigator; and Sujay Paranjape, master’s student in mechanical engineering.

PDAF REPORTS (POST-DOCTORAL AEROSPACE FELLOWSHIPS)

Development of Micro Column Arrays (MCA) for Thermal Management Applications by Abdelhak Bensaoula and Pranob Misra

T

MANof advanced thermal agement of and structural materials ABSTRACT—Micro Column spacecraft and to one another. Arrays (MCA) have been space station environformed on thin metal foils, ments is an important Methodology selected ceramics, and semiissue in both manned MCAs are produced by conductor materials. The forand unmanned explopulsed laser ablation of mation process by pulsed ration of space. Typical the substrate material laser ablation is being refined active systems based on combined with mechanto produce MCA structures large, liquid-based heat ical translation of the tailored for different applicaexchange systems add sample to create conetions. Such applications of extra weight to the shaped micro tips interMCA include: possible passpacecraft and rely on digitated with conesive cooling components mechanical components shaped micro cavities.2,3 which would collect or remove which can malfunction, The formation of the heat by radiative absorption thus affecting maxicone-shaped micro color emission though their mum payloads and the umns protruding above near-blackbody nature, eleclifetime of a mission. A the surface by about 10tronics based on field emitpossible alternative is a 20 µm is a result of reters, and enhancement of passive cooling system distribution of the surAbdelhak Bensaoula bond strength between similar in which thin coatings face material which is or dissimilar materials. Results or foils would collect or made molten by ablaon the bonding of various metallic and ceramic plates with various remove heat by radiation with a sufficiently epoxies indicated an increase of up to four times in the bonding tive absorption or emislong sequence of laser strength for joints that employed MCA versus the ones without. sion. In order for a radipulses. The most imporation-based system to tant parameter in this be feasible, the foil or coating would have a high emissivity process is the laser fluence, which should provide heating near and/or absorptance. Additionally, newer materials based on or slightly above the solid melting threshold. The second parammetal matrix composites like aluminum silicon carbide, ceram- eter is the number of laser shots applied to the same surface ics like silicon carbide and aluminum nitride, and graphite struc- spot, which should exceed a threshold value (>103). For this tures with the characteristics of pyrolytic graphite and foamed project, MCA have been investigated on SiC, Si, Ta, Ti, Tigraphite are all being used to improve thermal performance alloys, ceramics, and stainless steel materials. An example of without adding weight. However, there are strength and stabili- the effect on the number of shots and the laser power is shown ty issues when trying to integrate these materials with standard in Fig. 1 for fabrication of MCA on silicon. structural materials. For bond strength enhancement investigations, fabrication of A technology for the successful fabrication of Micro Column MCA on Ti/Ti alloys and various ceramics was performed. Arrays (MCA) on various materials has recently been develb oped in conjunction with Integrated Micro Sensors, Inc. (IMS) a of Houston, Texas. MCAs consist of densely packed micro cones separated by cone-shaped micro cavities. They exhibit low reflectance (0.978) over a wide spectral range in a very close approximation of blackbody behavior.1 Employment of MCA is expected to enhance the strength and stability between materials due, in part, to a large increase in the effective surface area of the bond joint. This project seeks to explore MCA structures from thin foils as a possible passive cooling system which would collect or Figure 1. Effects of the laser fluence and number of laser shots on remove heat by radiative absorption or emission though their MCA fabrication on silicon: (a) 2400 shots, 23 J/cm2 ; (b) 3200 near-blackbody nature. Also under investigation is the bonding shots, 32 J/cm2. HERMAL


a

b

Figure 2. SEM images showing the progress of MCA parameter optimization on ceramics and Ti-based materials. (a) parameters optimized for traditional ceramic -> traditional ceramic parameters used on high strength ceramic -> optimized parameters for high strength ceramics; (b) optimized for Ti -> Ti parameters used Ti alloy -> optimized parameters for Ti alloy.

Figure 3. Titanium alloy coupon brazed to a high-strength ceramic coupon using a conventional brazing furnace.

These materials are widely used in military and space applications. Conventional brazing of MCA-structured and unstructured Ti alloy and ceramic coupons was performed in a vacuum tube furnace and the resulting coupons tested for bond strength in a single lap configuration. Equipment A Baasel LBI 6000 Nd:YAG Laser (Ï = 1064 nm) and a NEAT computer-controlled XYZ Stage have been used to fabricate MCA structures from several semiconductor and metal materials. In addition to this stage, we have implemented a small processing chamber accessory for the laser which will provide pumping to low vacuum, or purging with various gases such as dry air or with an inert gas, such as nitrogen or argon. We have also built a small liquid pumped cuvette for laser ablation of the samples in liquids (water, ethanol, methanol). The chamber or the cuvette can be displaced under the laser beam by the same computer-driven X-Y-Z stage as used for in-air processing. Results and Discussion A majority of the activity on this project has been to optimize MCA formation on the Ti/Ti alloys and on several relevant ceramic materials. This involved transfer of the MCA fabrication parameters previously developed for traditional ceramics and Ti metal to those applicable to the alloys under consideration. Significantly different parameters were needed because of the substantial differences in the chemical composition between these materials resulting in higher melting temperatures,

thermal conductivity and changes in optical characteristics. Figure 2a and 2b show SEM images from samples illustrating the progress on the transfer of the MCA fabrication process from a ceramic to a reinforced ceramic sample (a) and from Ti to Ti-alloy (b), respectively, through optimization of the process ambient and scanning parameters. Figure 3 is an example of a finished single lap test coupon, consisting of a Ti-alloy plate brazed to a ceramic plate, both of which have been MCA processed. Similar coupons, along with non-MCA textured structures, were tested for bond strength. The results achieved from testing of these samples (Fig. 4) indicate an average of about 53 percent increase in the bond strength when using the MCA structuring. The advanced features of the MCA-structured surfaces that contribute to the strength and stability of the brazed joints are: (1) the interlocking of the braze material between micro columns, (2) a more than a 10-fold increase in the specific surface area, (3) the inherent elasticity of the micro cones that could compensate for the difference in thermal expansion or for the shear stresses between the bonded materials and the braze material, (4) the repeated bend contours of the surface preventing hydrothermal failure, (5) the improved wettability of the surfaces by the braze material. There are several advantages of the MCA process over other optical coating technologies and surface treatments. In theory, generation of the MCA structures can be accomplished directly on the surface of virtually any material, including flexible materials, metal foils, plastic films, and on surfaces with a complex shape. The coatings are robust with long-life and can either resemble the


Baburaj, e.g., D. Starikov, J. Evans, G.A. Shafeev, and A. Bensaoula. “Enhancement of Adhesive Joint Strength by Laser Surface Modification,” J of Adhesion and Adhesives (In press). Presentations Starikov, D., N. Medelci, S. Paranjape, F. Attia, B. Eranezhuth, C. Joseph, and A. Bensaoula. “Enhanced Metal-Ceramic Brazed Bond Strength Using Micro/Nano Structured Surfaces and Nanofoil Technologies,” Material Science and Technology Conference 2007 (MS&T’07®). Sept. 16–20, 2007, Detroit, MI. (submitted).

Figure 4. Stress-Elongation graph showing bond strength for a plain sample versus a MCA-structured sample (~ 53% average increase).

properties of the base material or can be automatically coated with the base material oxide. Finally, the MCA fabrication process is environmentally safe and low cost with high scalability.

Funding and Proposals Starikov, D. “A Novel Manufacturing Process for Ultrastrong, Intelligent Adhesive Bonds,” NSF-NIRT, $450,000 (CAM/IMS; declined). Starikov, D. “Ultra-Strong High-Temperature Bonding of Titanium to Ceramic Materials,” DOD (MDA), (IMS/CAM; Phase I funded $100,000; Phase II approved). Starikov, D. “Universal Method of Bonding Steel Repairs to Aluminum Structures,” Air Force Phase I SBIR, $100,000 (IMS/CAM; submitted).

Conclusions Micro column arrays exhibiting low reflectance, high emissivity, and large effective surface areas have been fabricated by pulsed laser ablation on several metals, ceramics, and semiconductor materials. In addition to its use for emissive-based thermal management, MCA can produce enhanced bonding and brazing strength when used for either identical or dissimilar materials. By testing samples of non-textured and MCA processed metal to ceramic braze joints, we have achieved an approximately 50 percent increase in strength when MCA are present. Some of the specific applications that can benefit from this and other aspects of MCA technology include space, defense, avionics, laser systems, and high-performance computers. References 1 D. Starikov, C. Boney, R. Pillai, A. Bensaoula, G.A. Shafeev, and A.V. Simakin, “Spectral and Surface Analysis of Heated Micro Column Arrays Fabricated by Laser-Assisted Surface Modification,” Infrared Physics and Technology 45 (2004): 159-67. 2 F. Sánchez, J. L. Morenza, R. Aguiar, J. C. Delgado, and M. Varela, “Whiskerlike Structure Growth on Silicon Exposed to ArF Excimer Laser Irradiation,” Appl. Phys. Lett. 69 (1996): 620-22. 3 Dolgaev, S.I., S.V. Lavrishev, A.A. Lyalin, A.V. Simakin, V.V. Voronov, and G.A. Shafeev, “Formation of Conical Microstructures upon Laser Evaporation of Solids,” Appl. Phys. Lett. A 73.2 (2001): 177-81. Publications Adjim, M, A. Saidane, R. Pillai, A. Bensaoula, C. Boney, and D. Starikov. “Thermal Analysis of Micro Column Arrays for precise Temperature Control in Space,” ASME J. of Heat Transfer. (To be published Spring 2007).


LASER SYSTEM—Sujay Paranjape, master’s student in mechanical engineering, studies methods for bonding metallic materials for lightweight space-based cooling systems in the UH Center for Advanced Materials. Parnjape earned his bachelor’s degree in mechanical engineering at Pune University in India.

Ultra-Wideband Two-Cluster Angle-Of-Arrival Tracking System Design for Space Exploration By Dickey Arndt, Edward Dickerson, and Jianjun Ni

R

ESEARCH SCIENTISTS

are exploiting ABSTRACT—This UWB technology study describes a to implement a UWB design effort for a protracking system with its totype UWB (ultrafine-time resolution on the wideband) tracking order of picoseconds, its system currently under low-power spectral densidevelopment at the ty, which allows the sysNASA-Johnson Space tem to coexist with other Center. The system is communication systems, being studied for its and its resistance to multipractical use in procepath interference. In addidures for tracking tion, the high data rate Lunar/Mars rovers capability of UWB produring early explovides a multimedia comration missions when munication channel that satellite navigation can support a passive systems (such as GPS) tracking system with very are not available. The Jianjun Ni little increase in system Dickey Arndt Science Crew Operacomplexity, cost, or power tions Utility Testbed requirements. A two-cluster (SCOUT) vehicle under development at JSC provides a testbed for the utilization of the Angle-of-Arrival (AOA) UWB tracking system in the space environment. Field tests were conducted jointly with tracking method, using the SCOUT vehicle at the Meteor Crater in Arizona to test the tracking capability for a Time Difference of Arrival moving target. These maneuvers showed the compatibility of the UWB tracking system (TDOA) information, is under simulated conditions. utilized for implementation of the tracking system, not only to exploit the achievable fine time resolution of onboard SCOUT and that a tracking resolution less than one UWB signals, but also to eliminate the need for synchronization percent of the range (range up to 2000 feet) can be achieved. between the transmitter and the receiver. The UWB radio at each cluster is used to obtain the TDOA estimates from the Introduction UWB signal sent from the target. Assuming this is a long-range Researchers at the NASA-Johnson Space Center (JSC) are application, the TDOA data can be carefully converted to AOA developing a manned Lunar/Mars rover prototype known as the data to find the angle of arrival. Since the distance between two Science Crew Operations and Utility Testbed (SCOUT). For clusters is known, the target position is computed by a simple space exploration, after a Lunar/Mars outpost has been established, it will be necessary to track the rover or astronauts’ positriangulation. To evaluate tracking performance of the AOA algorithm, sev- tions while they work off the base. In early exploration phases, eral Matlab simulations have been conducted. These simulation there were no satellite navigation systems (such as GPS satelresults reveal that the tracking resolution is a function of the lites) available around the moon or Mars. Hence, a RF tracking TDOA estimate noise level, the baseline receiver configuration, system is needed which can co-exist with other communication and the tracking range. Simulations show that the AOA algo- systems used by the landing vehicle and other spacecrafts. A UWB R&D Group has been formed at NASA/JSC to develrithm achieves fine resolution with a low estimation noise level of TDOA data. This provides valuable guidance for design of op and evaluate communication and tracking systems using UWB technology. In this report, we document a research effort the tracking system. Field tests were conducted jointly with the SCOUT vehicle at that exploits UWB technology to meet the tracking system the Meteor Crater in Arizona to test the tracking capability for a design challenges posed by the complex operational environmoving target. These tests demonstrated that the UWB tracking ments of NASA prototypes such as the SCOUT vehicle. The remainder of this report is organized first with an system can co-exist with other RF communication systems


overview of the UWB technology. Next, a tracking methodology Angle of Arrival (AOA) will be introduced and the simulation results discussed. The last section will discuss the field test results and provide some concluding remarks. UWB Technology Ultra-wideband (UWB), also known as impulse or carrier-free radio technology, is a promising new technology. It has been utilized for decades by the military and law enforcement agencies for fine-resolution ranging, covert communications, and ground-penetrating radar applications. In February 2002, the Federal Communications Commission (FCC) approved the deployment of this technology in the commercial sector under Part 15 of its regulations.1 More researchers are recognizing that UWB technology holds great potential to provide significant benefits in many applications such as precise positioning, shortrange multimedia services, and high-speed mobile wireless communications. The DARPA (Defense Advanced Research Project Agency) study panel that coined the term ultra-wideband in the 1990s defines it as a system with a fractional bandwidth greater than 25 percent. Later, the FCC defined the term UWB to describe any signal with bandwidth equal to or in excess of 500 MHz or a fractional bandwidth greater than 0.2. The basic concept of current UWB technology is to develop, transmit and receive an extremely short duration burst of RF energy — typically a few tens of picoseconds to a few nanoseconds in duration. Whereas conventional continuous sine wave radio systems operate within a relatively narrow bandwidth, UWB operates across a wide range of frequencies (a few GHz) by transmitting a series of low-power impulsive signals. For the emerging technology of UWB radar and UWB wireless communications, the transmitted signal can be regarded as a uniform train of pulses represented as ,

(1)

where Tr is the pulse repetition interval, and P(t) is the pulseshaping waveform, which is often a Gaussian monocycle. In the time domain, the Gaussian monocycle is mathematically similar to the first derivative of a Gaussian function. It takes the form ,

(2)

where t is the duration of the monocycle. Figure 1 shows an ideal monocycle centered at 2 GHz in both the time and frequency domains.2 Conveying information over impulse-like radio waveform, UWB is characterized by several uniquely attractive features: • Low-power carrier-free ultra-wide bandwidth signal transmissions • Low impact on other RF systems due to its extremely low-power spectral densities • Immunity to interference from narrow band RF systems due to its ultra-wide bandwidth • Multipath immunity to fading due to ample multipath diversity (RAKE receiver)


Figure 1. Gaussian Monocycle in Time and Frequency Domains

• Capability of precise positioning due to fine-time resolution • Capability for a high data rate, multi-channel performance • Low-complexity low-power baseband transceivers without intermediate frequency stage At present, there are many UWB product manufactures. In 2003, there were only two companies, Time Domain Corporation3 and XtremeSpectrum, Inc.4 (acquired by Freescale Corporation in November 2003), offering commercially available products. In this research effort, we investigated their chipsets and exploited them to design the tracking systems. Time Domain was the first to miniaturize UWB technology to a silicon solution, marketed as PulsON. PulsON systems use pulse position modulation. PulsON 100 is the first generation of UWB silicon chipsets that powered a variety of UWB product prototypes and demonstrations. In 2001, Time Domain launched the first commercial UWB chipset solution, PulsON 200, for many potential applications of UWB. The PulsON 200 chipset is comprised of three components:5 • The PulsON Dual Timer, which precisely slices time into picoseconds • The PulsON Quad Correlator, the receiver cast in SiGe • The PulsON CMOS Logic Chip, a software-definable RF processor. PulsON chipsets are available to customers as part of the PulsON Evaluation Kit (EVK), a comprehensive product development platform that supports the full range of UWB capabilities, including wireless communications, tracking, and radar. XtremeSpectrum named its product TRINITY because it is a high-speed, low-power and low-cost chipset. The XtremeSpectrum XSI100 TRINITY chipset provides full wireless connectivity, implementing bi-phase modulated ultra-wideband and the IEEE 802.15.3 MAC protocol. In June 2002, the company demonstrated that TRINITY delivers up to a 100 Mbps data rate supporting applications such as streaming video, streaming audio, and high-rate data transfer at very low levels of power consumption. The four-chip set consists of an RF Front End, an RF transceiver, a digital baseband and a MAC. The potential advantages of a UWB system for this application, including high-speed video transmission, multipath resistance, ease of interoperability with other RF systems, and precision tracking characteristics, together with the availability of

Figure 2. AOA Localization in 2-D Space

commercial UWB products, makes this technology a good choice for implementation of the communication and tracking system. Rapid technological advances have enabled cost-effective implementation of UWB radar, communication, and tracking systems. Furthermore, array beam forming and space–time processing techniques promise further advancement in the operational capabilities of UWB technology to achieve long-range coverage, high capacity, and interference-free quality of reception.6 Hence, UWB technology is proposed with confidence to implement the communications and tracking system for space applications investigated in this research effort. The UWB radios (PulsON 200 EVK) from Time Domain Corporation have been chosen as the core hardware for the design of the tracking system since it was the only available evaluation and development platform in the UWB field when this project began. The latest available UWB products (such as PulsON 210 EVK from Time Domain Corporation) and next generation UWB development platforms will be utilized to enhance the system in the future work. Tracking Methodology Many different approaches can be applied to estimate the location of a radio source, including angle of arrival (AOA), time of arrival (TOA), time difference of arrival (TDOA), relative signal strength (RSS), and various hybrids of these parameters. For close-in applications, the TDOA approach has been chosen as the tracking method since it does not require synchronization between the transmitter and receiver but can still exploit the fine time resolution available with UWB signals.7,8 For long-range applications, the AOA approach can be applied to estimate the location of a target since the approximation error under the far field assumption is relatively small. The AOA technique is discussed briefly below. A two-dimensional AOA tracking case is illustrated in Fig. 2. Two receivers are used to locate the transmitter in this 2-D space by a simple triangulation. Two receivers’ positions (Rx1(0,0), Rx2(d,0)) are assumed known. If the angle of arrival from the target to each receiver (i.e., θ 1 and θ 2) can be estimated, the transmitter’s position can be computed using the Law of Sine as follows,

Figure 3. Tracking Error with Perfect TDOA Estimates

In order to find the AOA information (θ1 and θ2), two antennas spaced by distance a are connected with each receiver. Since the UWB signal has fine time resolution, the TDOA information (τ12 and τ43) has been measured and carefully converted to the AOA information as follows. Since electromagnetic waves travel with constant velocity c in free space, the distance between the transmitter and the receiver’s antenna is directly proportional to the propagation time of the signal. Under the long-range assumption (r1, r2 >> a), cτ12 ≈ a cosθ1 θ1 ≈ arcos (cτ12 /a); similarly, cτ43 ≈ a cosθ2 θ2 ≈ arcos (cτ43 /a); The advanced signal processing techniques are developed to estimate the TDOA information (τ12 and τ43) from the pulses transmitted from the target UWB radio.9 The TDOA estimates are then fed into the above AOA algorithm to locate the target. Tracking Simulations In order to analyze the tracking error behavior and gain some insight regarding achievable tracking resolution, several Matlab simulations were performed using the AOA tracking method described under “UWB Technology.” The results of two of these simulations are discussed below. Tracking error with perfect TDOA estimates In order to transform TDOA estimates to AOA data, a far field assumption (r1, r2 >> d so that the lines from the target to two antennas at each receiver are approximately parallel) is made. A 2-D tracking simulation is presented to illustrate the impact of


Figure 4. Tracking Error with Noisy TDOA Estimates

this far field assumption on tracking performance. The simulation setup is as follows: • Baseline configuration: two receivers are 50 meters apart (d=50m) and two antennas at each receiver are 15 meters apart (a=15m). • Transmitter trajectory: the transmitter moves in a semi-circular orbit (from 0 degrees to 180 degrees) with a radius of 610 meters (=610m). • TDOA noise level: the TDOA estimates are assumed perfect. The simulated tracking error due to the parallel approximation is plotted in Fig. 3. The simulation result shows that the tracking error due to approximation has a W-shape pattern. In general, this approximation error is relatively small with the average about 0.05 meters. The tracking error at certain trajectory range (angle of target from 30 degrees to 150 degrees) is below the average error.

Figure 5. Tracking Error vs. Cluster Size

Figure 6. Tracking Error vs. Baseline Size

Tracking error with noisy TDOA estimates A similar simulation with noisy TDOA estimates (standard derivation σ = 10 picoseconds) is conducted and the error analysis (from 30 degrees to 150 degrees) is illustrated in Fig. 4. The simulation shows that the tracking error is random and the average tracking error at range of 610 meters is 2.7595 meters, less than 0.5% of the tracking range. Tracking error vs. affecting parameters It can be shown that the tracking error MSE (Mean Squared Error) is a function of parameters a, d, r1 and σ. Several simulations have been conducted to study how these parameters affect the tracking resolution. The default values of these parameters are as follows: a=15m, d=50m, r1=610m, σ = 10 picoseconds. First, the relationship between the tracking error (MSE) and the cluster size (a) has been studied for both perfect TDOA estimates and noisy TDOA estimates. In Fig. 5, simulation results show that the tracking error increases as the cluster size increases for perfect TDOA estimates while the tracking error decreases as the cluster size increases for noisy TDOA estimates.


Figure 7. Tracking Error vs. Tracking Range

SCOUT Camp

EC/Suit Camp

Figure 8. Tracking Error vs. TDOA Noise Level

Second, the relationship between the tracking error (MSE) and the baseline size (d) has been studied for both perfect TDOA estimates and noisy TDOA estimates. In Fig. 6, simulation results show that the tracking error does not change as the baseline size changes for perfect TDOA estimates, while the tracking error decreases as the baseline size increases for noisy TDOA estimates. Third, the relationship between the tracking error (MSE) and the tracking range (r1) has been studied for both perfect TDOA estimates and noisy TDOA estimates. In Fig. 7, simulation results show that the tracking error decreases as the tracking range increases for perfect TDOA estimates while the tracking error increases as the tracking range increases for noisy TDOA estimates. Finally, the relationship between the tracking error (MSE) and the TDOA noise level (σ) has been studied for noisy TDOA estimates. In Fig. 8, simulation results show that the tracking error does not change when the TDOA noise level is low (e.g., less than 0.1 picoseconds) while the tracking error increases dramatically as the TDOA noise increases to picoseconds level. The above simulation results in Fig. 8 show that the tracking resolution can be further improved by increasing the cluster size and the baseline size, if it is feasible, and by decreasing the TDOA noise level. Outdoor Tests Outdoor tests have been conducted to test the UWB tracking capability with extended range in an operational environment. A joint tracking test was conducted with the SCOUT vehicle at the Meteor Crater in Arizona. Figure 9 shows the test site. Two camps (SCOUT Camp and EC/Suit Camp) were set up near the Meteor Crater. Twelve way points (WP) with GPS coordinates were put between two camps and beyond to define the SCOUT running trajectory. The configuration of the two-cluster UWB AOA tracking system is shown in Fig. 10. Due to the conservative FCC limit on the UWB emission power (-41.3dBm/MHz), the transmitting range is limited. In order to increase the tracking range,

Figure 9. Test Site – Meteor Crater in Arizona

Figure 10. Configuration of the Two-Cluster UWB AOA Tracking System

Figure 11. Tracking System Baseline Setup

Figure 12. Tracking Target – SCOUT Vehicle


four high-gain horn antennas are used as receiving antennas, AOA algorithm is relatively small and the tracking scheme and a low noise amplifier (LNA) is added at the receiving side can achieve the desired fine tracking resolution. Outdoor tests after each receiving antenna. Two clusters are connected to a have been conducted jointly with the SCOUT vehicle to test laptop computer through a hub. the tracking capability for a moving target. These tests The two-cluster UWB AOA tracking system baseline has the demonstrate that the UWB tracking system can co-exist with following setup (Fig. 11): two receivers are placed 50 meters other RF communication systems, and that a tracking resoluapart and two horn antennas at each receiver, 15 meters apart. tion less than one percent of the range (range up to 2000 feet) One UWB radio was integrated with the can be achieved. SCOUT vehicle as the transmitter (Fig. References 12). 1 FCC First Notice and Order, “Revision The objectives of the test were to: of Part 15 of the Commission’s Rules 1. Test the real-time tracking of a Regarding Ultra-wideband Transmission moving target. Systems,” ET-Docket, Feb. 2002. 2. Test the interference with other 2 Time Domain Corporation, “PulsON communication systems on vehicle. Technology Overview,” ing area. Figure 13 shows the tracking 3 Time Domain Corporation, accuracy compared to the differential ranges up to 610 meters (2000 feet). A 4 XtremeSpectrum, Inc., Fig. 14 demonstrates the real-time track5 K. Siwiak and M. Franklin, “Advances ing capability of the system. The tracking in Ultra-Wide Band Technology,” Radio update rate for the trajectory was approxSolutions, Commonwealth Conference & imately 5 Hz. No RF interference was Events Centre, London, Nov. 6–7, 2001. observed between the UWB tracking sys6 M. G. M. Hussain, “Principles of tem and other on-board SCOUT systems Edward Dickerson Space-Time Array Processing for (such as GPS at 1.6 GHz, video at 5.8 Ultrawide Band Impulse Radar and Radio GHz, voice at 140 MHz and telemetry at Edward Dickerson, former Communication,” IEEE Trans. on 2.4 GHz). dean of the UHCL College Vehicular Tech. 51 (2002): 393-403. of Computer Science and 7 J. Ni, D. Arndt, P. Ngo, C. Phan, and Conclusion Engineering, serves as coJ. Gross, “UWB Tracking System A prototype UWB tracking system has PI for a prototype UWB Design for Free-Flyers,” AIAA Space been designed, implemented, tested, and tracking system for space. 2004 Conference and Exposition, Sept. proven feasible for space applications. 28–30, 2004. UWB technology has been exploited to 8 J. Ni and R. Barton, “Design and implement the tracking system because of its properties such as high data rate, fine time resolution, and low power spectral Performance Analysis of a UWB Tracking System for Space density. The AOA tracking method using TDOA information Applications,” IEEE/ACES Intl. Conf. on Wireless has been employed to avoid synchronization problems Communications and Applied Computational Electromagnetics, between the transmitter and the receiver. A two-cluster system April 3–7, 2005. 9 J. Ni, D. Arndt, P. Ngo, C. Phan, and J. Gross, “UWB with high-gain horn antennas has been implemented to increase the tracking range. Simulations demonstrate that the Tracking System Design with TDOA Algorithm for Space approximation error due to the far field assumption for the Applications,” NASA/JSC Internal Report, August 2005.


The Effect of Simulated Microgravity on Microbial Gene Expression by George E. Fox and Duane Pierson

B

ACTERIAARE CAPABLE

of living in and ABSTRACT—The effect of long-term exposure to adapting to a far low-shear modeled microgravity (LSMMG) on larger range of environmicrobial gene expression and physiology is being mental conditions than are examined using functional genomics and molecular normally encountered in techniques in Escherichia coli. In short-term studies, the usual laboratory envireproducible changes in transcription were seen but ronments. Even with full no direct response to changes in the gravity vector knowledge of an organwas identified. Instead, absence of shear and a ranism’s gene content, it is domized gravity vector appeared to cause local currently impossible to extra-cellular environmental changes, which elicited predict how expression reproducible cellular responses. In minimal media, patterns will change in the majority of the significantly up- or down-regulatdifferent situations. Thus, ed genes of known function were associated with the usual laboratory growth cell envelope. Comparison with earlier studies of conditions may not invoke Salmonella enterica serovar Typhimurium conducted key aspects of an organunder similar growth conditions revealed essentially ism’s potential response. no similarity in genes, which were significantly up or Such studies thereby may down-regulated. Given the substantial overlap in conceal behaviors that in a George Fox gene content between these closely related organdifferent environment isms, this result clearly demonstrates that different may contribute to undesirorganisms may dramatically differ in their responses to medically significant low-shear able phenomena such as and space environments. Current efforts are focused on assessing the extent to which the pathogenesis. One such response changes over the long-term as a result of evolutionary adaptation. To this end, case is the low-shear, lowa cell line has now been cultured in the LSMMG environment for 1000 generations and turbulence environments is currently being studied. The project is part of a larger effort to identify, monitor, and present in utero, at the assess the effect of exposure on microorganisms in spacecraft environments. brush border microvilli of epithelial cells, and other medically important host environments.1 Another example is the response to LSMMG. Thus, it is essential to better underspace environment characterized by microgravity and high stand both the long- and short-term effect of the microgravibackground radiation. In this case, the absence of gravity also ty environment on bacterial behavior. produces a low shear environment, which likely results in microorganisms having difficulty in removing themselves from Methodology immediate surroundings that have been nutrient depleted and Wild type E. coli MG1655 (CGSC7740) was grown aerobically at 37oC, in rich (LB) and minimal MOPS plus glucose have received waste products.2 In order to adapt to life in a low shear world, bacteria like- medium in low shear modeled microgravity (LSMMG) and a ly express different combinations of genes than they do in normal gravity vector control environment. They were commore usual laboratory environments and may ultimately pared with each other as well as in control experiments conmake evolutionary adaptations, as well. Thus, a particular ducted with a normal gravity vector. bacterium may exhibit properties such as antibiotic resistIn order to conduct long-term studies, a sterilization proceance, biofilm formation, or virulence that are not generally dure was developed in which two reactors were alternatively associated with it. It is not certain, therefore, which organ- used. The reactor not in use was rinsed with an antibiotic soluisms may be problematic. For example, a recent study3 tion and exposed to UV light. This protocol has allowed culshowed that Salmonella enterica serovar Typhimurium tures to be maintained for more than 1000 generations. grown under low-shear modeled microgravity (LSMMG) Thirteen separate minimal MOPS and 16 LB medium growth appeared to have increased virulence potential in a murine experiments were performed. Total RNA was extracted from model system. A follow-up study4 revealed that a significant cells and labeled following removal of ribosomal RNA, number of the genes are transcriptionally regulated in radioactively. Whole genome transcriptional assays were per-


formed using matched pairs of PCR-product DNA macroarrays (Panorama E. coli Gene Arrays; Sigma-Genosys, Houston, TX). The hybridized membrane phosphorimages were imported into image analysis software. Data were normalized by reporting each spot as a percentage of the sum of intensities of all spots on the array image. Significant changes in gene expression were identified based on three previously documented criteria: (1) an overall p-value of < 0.05 which implies a 95 percent probability that a change in expression between strains or media was significant; (2) a log ratio of gene expression which differed from the mean of the log ratios by > 3.0 standard deviations giving a 99.9 percent confidence in gene expression; and (3) similar gene expression in all three biological replicates. Online databases were used for gene nomenclature, gene location and orientation, putative co-transcription, product function, and presence in S. Typhimurium. The Colibiri WWW Server v3.1 (http://genolist.pasteur.fr/Colibri/ genome.cgi) was used to determine individual gene locations and orientations in the E. coli genome as well as possible cotranscription with other expressed genes. EcoCyc (Institute for Genomic Research, University of California; San Diego, CA (http://ecocyc.org/) and EcoSearch (University of Miami School of Medicine; Miami, FL (http://bmb.med.miami.edu/ search.htm) were used in determining gene names / synonyms and gene product function. Researchers used the coliBase website (http://colibase.bham.ac.uk/) to identify genes significantly expressed in this study that are present or have an orthologue in S. Typhimurium. Separately, following growth in the LSMMG environment, the cultures were subjected to antibiotic sensitivity and stress resistance studies to determine if their response had been changed by the exposure to the LSMMG environment. Antibiotics employed were ampicillin, kanamycin, polymyxin E, chloramphenicol and rifampicin. Stress conditions included acidic and basic conditions, oxidative stress, osmotic stress, alcohol stress, and heat shock. Culture survival was compared to controls that had not been grown under LSMMG conditions. Equipment/Special Technology The project takes advantage of the High aspect rotating vessel (HARV) bioreactor which was originally developed by NASA scientists5 to minimize fluid motion for tissue culture differentiation, while maintaining culture aeration through a gas permeable membrane. The HARV’s rotation also has the effect of randomizing the gravity vector, by rotating in the plane of gravity, producing the LSMMG environment. To obtain this environment, the HARV device is rotated at a speed sufficient to maintain cell suspension in the media and completely filled, thereby preventing gas bubbles from causing solution turbulence (i.e., shear). The HARV apparatus approximates the physiological and transcriptional changes occurring in space flight due to microgravity, while allowing Earth-based culturing. Used in conjunction with commercially available functional genomics technology (Panorama Gene Arrays, Sigma-Genosys), the HARV makes it possible to


study microbial gene expression on a genome-wide basis under LSMMG. Results Statistical analysis identified 19 up-regulated and 24 downregulated genes in LSMMG compared to the control during the mid-log phase of growth in minimal MOPS medium. Of these, one up-regulated and 12 down-regulated genes coded for hypothetical proteins. Among the up-regulated genes of known or putative function in LSMMG are genes involved in the E. coli acid tolerance response: transcriptional regulator gadE, the putative chaperone hdeA, and associated genes hdeB, hdeD and dctR, flg and fli genes involved in cell motility, chemotaxis regulating genes cheY, cheZ and tar, and the phage related gene ydfD. Among the MOPS LSMMG down-regulated genes were five genes involved in heavy metal efflux (CusCFBA and copA). Other LSMMG down-regulated genes included five putative bacteriaphage lambda homologs, four genes involved in various stress responses, the drug resistance gene emrE, the acetylCoA carboxylase subunit accB, and the putative NAD(P) binding enzyme ybeM. Two of the MOPS LSMMG down-regulated genes (cpxP and yfiA) were regulators. CpxP serves as repressor of the Cpx envelope / extracytoplasmic toxicity stress response system, protects the cell from toxic, transitory stresses, is involved in adhesion and virulence of pathogenic E. coli, and may also act as a periplasmic chaperone. Yfia stabilizes 30S rRNA under cold shock conditions. Possible co-transcribed genes of putative operons were identified based on genomic location and orientation. Physical mapping of the LSMMG MOPS regulated genes found 34 of 43 genes in four gene clusters. Similar analysis of the LB LSMMG cultures identified seven down-regulated genes in LSMMG. These genes were mostly involved in biosynthesis and energy utilization. No significant change in response relative to the controls was seen with any of the antibiotics or stresses that were tested. Salmonella Typhimurium is an evolutionarily very close relative of E. coli and its response to LSMMG had been studied previously.4 In fact, the majority of the E. coli MG1655 LSMMG up- and down-regulated genes have homologues or orthologues in S. Typhimurium. We, therefore, reduced the statistical stringency of our analysis so that a direct comparison could be made with the earlier Salmonella results. When individual genes were intercompared, it was abundantly clear that the vast majority of genes affected by LSMMG in E. coli MG1655 and S. Typhimurium were not affected in the same manner in the other organism. Discussion The primary differences between the LSMMG environment and the control are the randomized gravity vector and low shear present in LSMMG. In attempting to interpret the differences seen, one must consider that they might be due to either or both of these factors or as an indirect effect of one or both. In minimal MOPS medium, E. coli chemotactic and flagellar genes, as well as genes involved in the acid tolerance

S. Typhimurium appears to be responding to LSMMG by activating genes associated with adhesion in an attempt to promote colonization in the low-shear environment. These are the same genes usually associated with pathogenicity. In contrast, E. coli MG1655 is a commensal that lacks many of these genes and hence adhesion in preparation for colonization is apparently not its preferred response to LSMMG. Conclusions Bacteria, having lived on the Earth for billions of years, have not typically encountered microgravity and hence it would seem unlikely that genes governing a direct response to variations in gravity would have evolved. With specific reference to the LSMMG environment then, it would be anticipated that low-shear is more important in the bacterial transcriptional response than a direct effect of the randomized gravity vector. The experiments to date have confirmed this conclusion. In addition, our studies have reinforced the notion that the cell envelope is superlative in sensing changes in its local environment and able to rapidly respond to the changes in a multifaceted way. Future time course studies of the LSMMG response to minimal media in cells preadapted to the HARV control environment may allow detailed study of how the genes involved are coordinated. However, the dramatically different response to LSMMG that is observed between E. coli MG1655 and S. Typhimurium emphasizes that different species can respond to LSMMG in very different ways. This is a frustrating conclusion for those seeking to ascertain the effect of exposure to low-shear or the space environment for microorganisms in general.

CONTRIBUTOR—Dr. Duane L. Pierson, NASA-JSC, conducts seminars on bacteria in space focusing on the characterization of E. coli grown in a low-shear modeled microgravity environment.

response, were up-regulated in LSMMG. It is attractive to theorize that the LSMMG up-regulation of flagellar and chemotactic genes in minimal medium is related to a cellular requirement for relocation away from zones of local nutrient depletion and excreted waste hypothesized to occur in the low mixing environment of space.6 The majority of minimal medium LSMMG down-regulated genes are involved in metal or drug transport, cell lysis, or in regulating cellular stress responses, which alludes to the importance of the cell envelope in regulating the LSMMG response in minimal medium grown E. coli MG1655. More generally, all of the LSMMG up-regulated genes and a majority of the down-regulated genes of known function are present in or involved with regulation of the cellular envelope. This suggests that the cell envelope is superlative in sensing changes in its local environment and able to rapidly respond to the changes in a multifaceted way. Future time course studies of the LSMMG response to minimal media in cells preadapted to the HARV control environment may allow detailed study of how the genes involved are coordinated.

Acknowledgments We would like to thank Dr. Yuriy Folfanov in the Department of Computer Science at the University of Houston for his advice and assistance in performing statistical analysis on the microarray data. References 1 U. A. Stock and J. P. Vacanti, “Cardiovascular Physiology during Fetal Development and Implications for Tissue Engineering,” Tissue Eng. 7 (2001): 1-7. 2 J. M Jessup and N. R. Pellis, “NASA Biotechnology: Cell Science in Microgravity,” In Vitro Cell Dev. Biol. Anim. 37 (2001): 61-63. 3 C. A. Nickerson, C. M. Ott, S. J. Mister, B. J. Morrow, L. Burns-Keliher, and D. L. Pierson, “Microgravity as a Novel Environmental Signal Affecting Salmonella Enterica Serovar Typhimurium Virulence,” Infect. Immun. 68 (2000): 3147-52. 4 J. W. Wilson, R. Ramamurthy, S. Porwollik, M. McClelland, T. Hammond, P. Allen, C. M. Ott, D. L. Pierson, and C. A. Nickerson, “Microarray Analysis Identifies Salmonella Genes Belonging to the Low-Shear Modeled Microgravity Regulon,” Proceedings Natl. Acad. Sci. U. S. A. 99 (2002): 13807-12. 5 T. L. Prewett, T. J. Goodwin, and G. F. Spaulding, “ThreeDimensional Modeling of T-24 Human Bladder Carcinoma Cell Line: A New Simulated Microgravity Culture Vessel,” J. of Tiss. Cult. Methods 15 (1993): 29-36. 6 P. Todd and D. M. Klaus, “Theories and Models on the Biology of Cells in Space,” Adv. Space Res. 17 (1996): 3-10.


Publications Chumakova S, C. Bepapurkara, C. Putoni, T. B. Li, B. M. Pettitt, G. E. Fox, R. C. Willson, and Y. Fofanov. “Theoretical Basis for Universal Identification Systems for Bacteria and Viruses,” J. Biological Phys. and Chem. 5 (2005):121-28. Jackson, G. W., R. J. McNichols, G. E. Fox, and R. C. Willson. “Bacterial Genotyping by 16S rRNA Mass Cataloging,” BMC-Bioinformatics 7 (2006): 321. Larios-Sanz M, K. E. Kourentzi, D. Warmflash , J. Jones, R. C. Willson, D. L. Pierson, and G. E. Fox. “16S rRNA Beacons for Bacterial Monitoring in Craft and Habitat Modules in Human Space Missions,” Aviation Space and Environmental Medicine (2007). (In press.) Murphy, J. C., T. Cano, G. E. Fox, and R. C. Willson. “Compaction Agent Protection of Nucleic Acids during Mechanical Lysis,” Biotechnology Progress 22 (2006): 519-22. Potty, A. S., J. Y. Fu, S. Balan, B. L. Haymore, D. J. Hill, G. E. Fox, and R. C. Willson. “Neutral Additives Enhance the Metal-Chelate Affinity Adsorption of Nucleic Acids,” J. of Chromatography 1115 (2006): 88-92. Putonti, C., S. Chumakov, R. Mitra, G. E. Fox, R. C. Willson, and Y. Fofanov. “Human-Blind Probes and Primers for Dengue Virus Identification: Exhaustive Analysis of Subsequences Present in the Human and 83 Dengue Genome Sequences,” FEBS J. 273 (2006): 398-408. Tucker D. L., F. Karouia, J. Wang, Y. Luo, T. B. Li, R. C. Willson, Y. Fofanov, and G. E. Fox. “The Effect of an Artificial RNA Marker on Gene Expression in Escherichia Coli,” Applied Environmental Microbiology 71 (2005): 4156-59. Zhang, Z., G. W. Jackson, G. E. Fox, and R. C. Willson. “Microbial Identification by Mass Cataloging,” BMCBioinformatics 7 (2006): 117. Zhu D., Y. Fofanov, R. C. Willson, and G. E. Fox. “A Parallel Computing Algorithm for 16S rRNA Probe Design,” J. of Parallel and Distributed Computing 66 (2006):1546-51. Zhu D, Y. Fofanov, R. C. Willson, and G. E. Fox. “ProkProbePicker (PPP): a Fast Program to Extract 16S rRNA-Targeted Probes for Prokaryotes,” Proc. 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, June 20–23, 2005. Las Vegas, Nevada (2005): 41-47. Presentations Fox, G. E. “Mars Genetic Inventory of Spacecraft Analysis,” Planetary Biology Workshop Jet Propulsion Laboratory, Pasadena, CA, Feb. 28–March 1, 2006. Fox, G. E., G. W. Jackson, and R. C. Willson. “Identification of Unknown Bacteria by Mass Spectroscopy,” Planetary Biology Workshop “Mars Genetic Inventory of Spacecraft Analysis,” JPL, Pasadena, CA., Feb. 28–March 1, 2006. Fox, G. E., D. L. Tucker, R. C. Willson, C. M. Ott, and D. L. Pierson. “Characterization of E. Coli Grown in a Low-Shear Modeled Microgravity Environment,” Bacteria in Space: 15th Humans in Space Symposium, Graz, Austria, May 22–25, 2005 (Invited presentation).


Jackson, G. W., Z. Zhang, G. E. Fox, and R. C. Willson. “Rapid Microbial Identification by MALDI-TOF Mass Spectrometry of 16S Ribosomal RNA,” 22nd Annual Meeting, Houston Society for Engineering in Medicine and Biology, Houston, TX, Feb. 11, 2005. Liu Y., V. G. Stepanov, and G. E. Fox. ”Stress-Driven in Vivo Selection of Functional RNAS and Peptides by Random Sampling of the Sequence Space,” Sealy Structural Biology Symposium, Galveston, TX, May 19–20, 2006. Potty, A., S. Balan, G. E. Fox, and R. C. Willson. “Neutral Additive Effects on Metal Affinity Adsorption of Nucleic Acids,” 229th National Meeting American Chemical Society, San Diego, CA, March 13–17, 2005. Tucker, D. L., D. Zhu, G. W. Jackson, M. Anez, T. Cano, I. DasGupta, A. Potty, F. Karouia, C. M. Ott, Y. Fofanov, D. L. Pierson, R. C. Willson, and G. E. Fox. “Microbes in the Spacecraft Environment,” Poster, Bioastronautics Investigators’ Workshop, Galveston, TX, Jan. 10–12, 2005. Warmflash, D., J. Miller Jr., D. S. McKay, G. E. Fox, and N. Keerthi. “In Situ Detection of Extant Microbial Life in Extraterrestrial Settings Using Dielectric Spectroscopy,” Biennial Meeting of the NASA Astrobiology Institute, University of Colorado, Boulder, CO, April 10–14, 2005. Astrobiology Abstract 641 5.2 ( 2005). Warmflash, D., J. Siefert, and G. E. Fox. “Detection of Life Forms in Soil using D and L Glucose,” Astrobiology Science Conference, Washington, D.C., March 26–30, 2006. Abstract 355 (2006). Zhu D, Y. Fofanov, R. C.Willson, and G. E. Fox., “ProkProbePicker (PPP): a Fast Program to Extract 16S rRNA-Targeted Probes for Prokaryotes,” The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, NV, June 20–23, 2005. Funding and Proposals Fox, G. E. “Chiral-Selective Planetary Chemistries as a Marker for Life,” NASA ASTID Program, Aug. 1, 2005–July 31, 2007, $429,920. Fox, G. E. and K. Venkateswaran, “Comparative Genome Analysis and the Resistance Properties of Various Bacillus Species,” NASA Planetary Protection Program, Feb. 1, 2005–Jan. 1, 2008, UH Total Costs: $226,723. Fox, G. E. and R. C. Willson, “Microorganisms in the Spacecraft Environment,” NASA Office of Exploration Research, June 7, 2004–March 31, 2007, $904,809. Miller, J. H. Jr. and Fox, G. E. “Biosensors Based on Dielectric Response: A Non-Geocentric Approach for in situ Life Detection,” NASA_ASTEP Program, Jan. 1, 2005-Dec. 31, 2008, UH Total Costs: $794,864 (Not funded). Venkateswaran, K. and G. E. Fox. “Microbial Ecological Perspectives of Space-Exposed Microbes: A Genetic Approach,” NASA Human Support Technology, April 1, 2005–March 31, 2008, UH Subcontract: $120,000 (Not funded).

Martian Soil Biosensors Based on Dielectric Spectroscopy by John H. Miller, Jr., and David Warmflash

M

ARS HAS BEEN A

candidate for the ABSTRACT—Researchers are studying the elecpossible existence tromagnetic responses of live organisms, and the of life, either in the distant potential of such measurements to develop biosenpast or at present,1 for many sors with applications in astrobiology and medidecades. If life were to be discine. For example, dielectric spectroscopy meascovered on Mars, the scientifurements at different temperatures can distinguish ic implications would be prolive organisms from nonliving complex macromolfound for the distribution of ecules and may eventually be suitable for in situ life in the cosmos and the evoastrobiology studies on the surface of Mars or in lution of life on Earth. In the liquid ocean beneath the ice of Europa. More 1976, the Viking program recent studies have involved nonlinear (harmonic made an attempt to detect evigeneration) responses of biological systems to oscildence for living or fossilized latory electric fields. Some results suggest that organisms in Martian soil, active biological motors and other enzyme comwhich yielded ambiguous, plexes generate harmonics over specific frequency somewhat negative results.2 ranges. These include complexes in the mitochonThe exciting, and more recent, drial inner membrane, such as the molecular turstudies3 of the Martian metebine ATP synthase and pumps in the outer plasma orite Allan Hills 84001 John H. Miller, Jr. membrane. In addition, the harmonic generation (ALH84001) suggest that spectra of chloroplasts, responsible for photosynmicrobial life existed on Mars thesis in plants, exhibit light-activated features. This provides evidence that the techabout four billion years ago. nique detects physiologically active processes, which could lead to fundamental Reported evidence includes advances in understanding of biochemical and other complex macromolecular systems. magnetite (Fe3O4) crystals found in carbonate globules and their associated rims in the meteorite.4 About one fourth of on frequency and on each enzyme’s charge distribution, structure, these tens-of-nanometer sized magnetites are nearly identical to and state of activity. The resulting motion of charged macromolthose produced by magnetotactic bacteria on Earth and are not ecules leads to a nonlinear response and to the generation of highexpected to be produced by abiotic means. It has thus been argued er harmonics, providing a powerful functional spectroscopy tool. that such Martian magnetite crystals are magnetofossils, which, if This hypothesis is supported by the following observations. true, would constitute evidence of the oldest life forms known.5 First, oscillatory fields induce ac components of transmemFurther studies indicate that subsurface Martian life could brane potentials that add to the intrinsic potentials.12 A low-frepotentially survive even today.6 There is geological evidence that quency electric field polarizes live cells or macromolecules,13 ice was once deposited in the regolith, where it may be present resulting in enormous dielectric responses, and also modulates above mid-latitudes.7 This ice, which could extend several kilome- the membrane potential of each cell.14 Second, sinusoidal fields ters below the surface, might be a source of liquid water near mag- can induce membrane pumps to translocate cations15,16 and genmatic intrusions.8 On Earth, the biomass of subterranean organ- erate harmonics.17 Membrane proteins exhibit nonlinear behavisms may even exceed that at the surface.9 These organisms can ior18 since domains with dipole moments interact with the live in highly saline conditions at temperatures from 115°C to induced transmembrane potential, driving them to change con–20°C.10,11 Such conditions might prevail beneath the surface in an formation. The combination of conformational changes and ion aquifer or hydrothermal system. Therefore, there is considerable translocation creates a nonlinear response. For example, cation interest in developing new techniques for detecting subsurface life pumps such as P-type ATPases,19 have been reported to generon Mars. Furthermore, the likelihood that oceans of liquid water ate harmonics.20 We have developed a sensitive method,21 using exist below the icy surfaces of Europa and other moons make superconducting quantum interference devices (SQUIDs) to these exciting candidates for possible extraterrestrial life. measure the harmonics produced by such membrane pumps at This research is further motivated by the hypothesis that an low frequencies. Further support is provided by our recent haroscillatory field induces proteins and other macromolecules to monic generation spectroscopy measurements, which will be change conformation. The rate of conformational change depends discussed in the section “Results and Discussion.”


Goal of the Project The goal of this project is to study dielectric spectroscopy22 and related methods, such as harmonic generation spectroscopy,23 for the detection of live organisms. Toward this end, the project aims to identify and explain possible signatures of active macromolecular complexes unique to living biological systems. Possible signatures include unusual behavior, distinct from those of inanimate materials, in the frequency- and temperature-dependent dielectric response, and in harmonic generation spectroscopy, in which generated harmonics are plotted vs. frequency and amplitude. Methodology Previous reports focused on variable temperature dielectric spectroscopy of live organisms and Martian soil simulants. Our experiments on linear dielectric response employed a Solartron Impedance Analyzer, which measures complex admittance at frequencies up to 32 MHz. In this report, we report on harmonic generation spectroscopy measurements that suggest a potentially unique method of detecting physiologically active processes. A four-electrode setup is employed in conjunction with a Stanford Research SR780 signal analyzer, operated as a spectrum analyzer, for measurements at kilohertz frequencies. A function generator applies a sinusoidal signal to the outer electrodes, while the voltage difference between the inner electrodes is fed into Channel 1 of the SR780, which records the induced harmonics. A reference spectrum is acquired using a supernatant, whose conductivity has been adjusted (with distilled water, to compensate for the volume fraction of the cells present in the sample) to be identical to that of the sample at the frequency of the point of interest. The supernatant typically consisted of an aqueous solution of ~1- 10 mM NaCl. Two different types of control files are used, depending upon whether the reference is to be logged using the same set of electrodes or a separate matched reference cell. In either case, the logging, windowing, and Fourier Transform routines were identical and provide a power spectrum of the reference cell, which is also recorded as a data file in the computer. Finally, the sample power spectrum obtained from the sample (e.g., cell suspension or soil sample) of interest is divided by the reference power spectrum, and also stored. The entire procedure is automated using LabVIEW data acquisition software. The power of this approach stems from the fact that it allows the researcher to deconvolve the effects of nonlinearities within the electrochemical system from those attributed to the biological cells themselves. Equipment and Special Technology Most of our experiments at kilohertz frequencies employ the 4electrode configuration shown in Fig. 1, where electrodes are immersed into a suspension of cells or organelles. In Fig. 1, the waveform generator applies a sinusoidal voltage of high spectral purity to the two outer electrodes, while the response across the inner electrodes is measured with a Stanford Research SR780, which shows the generated higher harmonics. Typically, the second or third harmonic generated by the suspension is recorded vs. amplitude and frequency, and all measurements are automated with LabVIEW software. Experiments have been carried out on suspensions of whole


Figure 1. Schematic diagram of 4-electrode setup for in vitro measurements, in which platinum electrodes are immersed directly into a suspension (expanded scale) of cells, organelles, or reconstituted vesicles. The spacing between the outer electrodes is about 1 cm and the housing rests on a magnetic stirrer. The Agilent 33220A Waveform Generator produces a sinusoidal voltage of high spectral purity, while the Stanford Research SR780 Dynamic Signal Analyzer is operated as an FFT (fast Fourier transform) spectrum analyzer. Both instruments are interfaced to a computer (not shown) using a GPIB (general purpose interface bus). The experiments are automated with LabVIEW software. The oxygen sensor enables one to monitor the rate of oxygen consumption (or production for the case of chloroplasts), which can be correlated with the generation of harmonics created by enzymatic activity.

cells, mitochondria, and chloroplasts, the latter of which provide validation and are of fundamental interest since the photosynthetic enzyme complexes are light activated. Many of these measurements have been carried out in collaboration with the group headed by Prof. William R. Widger in the Department of Biology and Biochemistry at the University of Houston. Additional experiments have been performed on whole organisms, such as plants and earthworms. Results and Discussion Some examples of observed harmonic generation spectra in the kHz range are illustrated by Fig. 2, which shows generated harmonics vs. applied frequency for S. cerevisiae, which lacks mitochondrial complex I, and uncoupled mammalian mitochondria, in which complexes I, III, and IV have been activated by glutamate malate but ATP synthase (complex V) is inactive due to the lack of a transmembrane potential. (We observed similar, though not identical, behavior by activating complexes II, III, and IV with succinate.) Several features of the harmonic spectra are noteworthy. First, the spectral features generated by S. cerevisiae increase with cell concentration (upper left). We also find that potassium cyanide, which binds to complex IV and completely shuts down ATP production, suppresses the observed spectral features, as seen in the B. indicas data shown here. Second, the higher frequency feature (~12 kHz) observed in S. cerevisiae and B. indicas is not seen in uncoupled mitochondria, in which

Figure 2. Harmonic generation spectra (applied field amplitude = 5 V/cm) of suspensions of budding yeast (S. cerevisiae, top), a relative of the mitochondrial ancestor (B. indicas, lower left, and uncoupled mammalian mitochondria, in which ETC complexes I, III, and IV have been activated by adding glutamate malate (lower right). The data were obtained with the 4-electrode setup shown in Fig. 2, in which a sinusoidal voltage is applied across the outer two electrodes and the induced harmonics measured across the two inner electrodes with a spectrum analyzer. The spectral features generated by S. cerevisiae are observed to increase with cell concentration (upper left).

Figure 3. (Left) Generated second harmonic vs. fundamental frequency (applied field amplitude = 5 V/cm) of a suspension of uncoupled mammalian mitochondria, in which ETC complexes I, III, and IV are activated by adding glutamate malate (closed circles) and subsequently inhibited (open circles) by adding rotenone, which binds to complex I. Here the second harmonic was by far the largest of the higher harmonics, and the magnitude of the second harmonic response (2-40 kHz) was measured for applied frequencies ranging from 1 to 20 kHz. (Right) Generated second harmonic vs. fundamental frequency (field amplitude = 1 V/cm, 4-electrode method) of a suspension of uncoupled mammalian mitochondria before (open circles) and after (closed circles) activating ETC complexes II, III, and IV with succinate.

ATP synthase (complex V) is inactive. We hypothesize that the higher frequency feature is generated during ATP production by this molecular turbine. Finally, note that, although a lower frequency (~3 kHz) peak in harmonic generation spectra is present in S. cerevisiae, B. indicas, and uncoupled mitochondria, this feature is significantly smaller in S. cerevisiae. There could be at least two possible reasons for this. One is that complex I is missing in S. cerevisiae, and it may contribute to the more pronounced feature seen in B. indicas and mitochondria. This is consistent with data obtained from uncoupled mitochondria, Fig. 3, in which either complexes I, III, and IV or complexes II, III, and IV are activated. In addition, the plasma membrane of a eukarote, such as S. cerevisiae, acts as a high-pass filter due to its finite capacitance. The data in Fig. 3 was also obtained with the 4electrode method, in which a sinusoidal voltage is applied across

the outer two electrodes and the induced harmonics measured across the two inner electrodes with a spectrum analyzer. We find that potassium cyanide, which binds to complex IV and completely shuts down ATP production, suppresses the observed spectral features, as seen in the B. indicas data shown here. The higher frequency feature (~12 kHz) observed in whole cells is not seen in uncoupled mitochondria, where ATP synthase (complex V) is inactive. We hypothesize that the higher frequency feature is generated during ATP production by this molecular turbine. Photosynthetic organisms have also proven extremely useful for validation of the technique, since photosynthesis and ATP production are activated by light. Figure 4 shows examples of the second harmonic generation spectra of a whole leaf and a suspension of spinach chloroplasts, which show dramatic differences between the spectra with and without light activation.


Figure 4. Light activated responses in the 2nd harmonic generation spectra of a whole leaf (left) and a suspension of spinach chloroplasts (right) in which the photosynthetic ETC has been activated by an electron acceptor (ferricyanide).

Conclusions Our studies thus far have encompassed both linear (impedance, dielectric) and nonlinear (harmonic generation, mixing) responses of biological systems to oscillatory electric fields. Some results suggest that active biological motors and other enzyme complexes generate harmonics over specific frequency ranges. These include complexes in the mitochondrial inner membrane, such as the molecular turbine ATP synthase, and pumps in the outer plasma membrane. In addition, the harmonic generation spectra of chloroplasts, responsible for photosynthesis in plants, exhibit light-activated features. This provides evidence that the technique detects physiologically active processes, which could lead to fundamental advances in understanding of biochemical and other complex macromolecular systems. Moreover, the method could eventually play an important role in the search for extant life elsewhere in the solar system. References 1 B. M. Jakosky and E. L. Shock, “The Biological Potential of Mars, the Early Earth, and Europa,” J. Geophys. Res. 103 (1998): 19,359-19,364. 2 L. Margulis, P. Mazur, E. S. Barghoorn, H. O. Halvorson, T. H. Jukes, and I. R. Kaplan, “The Viking Mission: Implications for Life on Mars,” J. Mol. Evol. 14 (1979): 223-32. 3 D. S. McKay, E. K. Gibson Jr., K. L. Thomas-Keprta, H. Vali, C. S. Romanek, S. J. Clemett, X. D. F. Chillier, C. R. Maechling, and R. N. Zare, “Search for Past Life on Mars: Possible Relic Biogenic Activity in Martian Meteorite ALH84001,” Science 273 (1996): 924-930. 4 K. L. Thomas-Keprta, S. J. Clemett, D. A. Bazylinksi, J. L. Kirschvink, D. S. McKay, S. J. Wentworth, H. Vali, E. K. Gibson, Jr., M. F. McKay, and C. S. Romanek, “Truncated Hexaoctahedral Magnetite Crystals in ALH84001: Presumptive Biosignatures,” Proc. Nat. Acad. Sci. USA 98 (2001): 2164-69. 5 K. L. Thomas-Keprta, S. J. Clemett, D. A. Bazylinksi, J. L. Kirschvink, D. S. McKay, S. J. Wentworth, H. Vali, E. K.


Gibson, Jr., and C. S. Romanek, “Magnetofossils from Ancient Mars: A Robust Biosigniture in the Martian Meteorite ALH84001,” Applied & Environmental Microbiology 68 (2002): 3663-3672. 6 B. P. Weiss, Y. L. Yung, and K. H. Nealson, “Atmospheric Energy for Subsurface Life on Mars?” Proc. Nat. Acad. Sci. USA 97 (2000): 1395-1399. 7 M. T. Mellon and B. M. Jakosky, “Geographic Variations in the Thermal and Diffusive Stability of Ground Ice on Mars,” J. Geophys. Res. 98 (1993): 3345-64. 8 M. H. Carr, Water on Mars. New York: Oxford Univ. P., 1996. 9 W. B. Whitman, D. C. Coleman, and W. J. Wiebe, “Prokaryotes: The Unseen Majority,” Proc. Nat. Acad. Sci. USA 95 (1998): 6578-83. 10 K. H. Nealson, “The Limits of Life on Earth and Searching for Life on Mars,” J. Geophys. Res. 102 (1997): 23,675-86. 11 J. C. Priscu, C. H. Fritsen, E. E. Adams, S. J. Giovannoni, H. W. Paerl, C. P. McKay, P. T. Doran, D. A. Gordon, B. D. Lanoil, and J. L. Pinckney, “Perennial Antarctic Lake Ice: An Oasis for Life in a Polar Desert,” Science 280 (1998): 2095-98. 12 H. P. Schwan. “Electrical Properties of Tissues and Cells,” Adv. Biol. Med.Phys. 5 (1957): 147-209. 13 H. Sanabria, J. H. Miller, Jr., A. Mershin, R. F. Luduena, A. A. Kolomenski, H. A. Schuessler, and D. V. Nanopoulos, “Impedance Spectroscopy of a-b Tubulin Heterodimer Suspensions,” Biophys J. 90 (2006): 4644-50. 14 C. Grosse and H. P. Schwan. “Cellular Membrane Potentials Induced by Alternating Fields,” Biophys J. 63 (1992): 1632-164. 15 R. D. Astumian, “Effects of Time-dependent Electric Fields on Membrane Transport,” Biophys J. 64 (1993): 7-8. 16 R. D. Astumian and I. Derényi, “Fluctuation Driven Transport and Models of Molecular Motors and Pumps,” Eur. Biophys. J. 27 (1998): 474-89. 17 A. M. Woodward and D. B. Kell, “On the Nonlinear Dielectric Properties of Biological Systems. Saccharomyces cerevisiae,” Bioelectrochem. Bioenerg. 24 (1990): 83-100.

D. Nawarathna, J. R. Claycomb, J. H. Miller, Jr., and M. J. Benedik, “Nonlinear Sielectric Spectroscopy of Live Cells Using Superconducting Quantum Interference devices,” Appl. Phys. Lett. 86 (2005): 023902-1-3. 23

ELECTROMAGNETIC RESPONSES—Hans Infante, graduate student in physics, takes in-vitro measurements of electromagnetic responses of living cell suspensions utilizing superconducting quantum interference devices.

A. M. Woodward, A. Jones, X.-Z. Zhang, J. J. Rowland, and D. B. Kell. “Rapid and Non-invasive Quantification of Metabolic Substrates in Biological Cell Suspensions Using Nonlinear Dielectric Spectroscopy with Multivariate Calibration and Artificial Neural Networks. Principles and applications,” Bioelectrochem. Bioenerg. 40 (1996): 99-132. 19 W. Kühlbrandt. “Structure, and Mechanism of P-type ATPases,” Nat. Rev. Mol. Cell Biol. 5 (2004): 282-95. 20 A. M. Woodward and D. B. Kell. “Confirmation Using Mutant Strains that the Membrane-bound H+-ATPase is the Major Source of Nonlinear Dielectricity in Saccharomyces cerevisiae,” FEMS Microbiol Lett. 84 (1991): 91-96. 21 D. Nawarathna, J.R. Claycomb, J.H. Miller, Jr. and M.J. Benedik. “Nonlinear Dielectric Spectroscopy of Live Cells Using Superconducting Quantum Interference Devices,” Appl. Phys. Lett. 86 (2005): 023902–1-3. 22 K. Asami, “Characterization of Biological Cells by Dielectric Spectroscopy,” J. of Non-crystaline Solids 305 (2002): 268-77. 18

Publications Sanabria, Hugo, John H. Miller, Jr., Andreas Mershin, Richard F. Luduena, Alexandre A. Kolomenski, Hans A. Schuessler, and Dimitri V. Nanopoulos, “Impedance Spectroscopy of α−β Tubulin Heterodimer Suspensions,” Biophysical Journal 90 (2006): 4644-4650. Nawarathna, D., J. R. Claycomb, G. Cardenas, J. Gardner, D. Warmflash, J. H. Miller, Jr., and W. R. Widger, “Harmonic Generation by Yeast Cells in Response to Low-Frequency Electric Fields,” Physical Review E 73 (2006): 051914-1—6. Claycomb, James R. and John H. Miller, Jr., “Superconducting and High-Permeability Shields Modeled for Biomagnetism and Nondestructive Testing,” IEEE Trans. on Magnetics 42 (2006): 1694-1702. Sanabria, Hugo and John H. Miller, Jr., “Relaxation Processes Due to the Electrode-Electrolyte Interface in Ionic Solutions,” Physical Review E 74 (2006): 051505—1-9. Mershin, Andreas, Hugo Sanabria, John H. Miller, Dharmakeerthna Nawarathna, Efthemios M. C. Skoulakis, Nikolaos E. Mavromatos, Alexandre A. Kolomenskii, Hans A. Schuessler, Richard F. Luduena, and Dimitri V. Nanopoulos, “Towards Experimental Tests of Quantum Effects in Cytoskeletal Proteins,” Chapter 4 of The Emerging Physics of Consciousness, ed. Jack A. Tuszynski. The Frontiers Collection. N. Y.: Springer, Berlin, Heidelberg, 2006. 95-170. (Invited book chapter.)

Presentations Nawarathna, D., J. Gardner, G. Cardenas, J. R. Claycomb, J. H. Miller, Jr., and W. R. Widger, “Electromagnetic Probing of Mitochondria and Chloroplasts Reveals Unique Harmonics Due to Specific Components of the Electron Transport Chain,” Biophysical Society 50th Annual Meeting, Feb. 18–20, 2006, Salt Lake City, UT. Nawarathna, Dharmakirthi, Jeffrey Gardner, Gustavo Cardenas, David Warmflash, John Miller, William Widger, and James Claycomb, “Nonlinear Electromagnetic Responses of Active Molecular Motors in Live Cells and Organelles,” Bull. Am. Phys. Soc. 51, 200 (2006), March Meeting of the American Physical Society, Session B29, Focus Session on Microorganism Motility, March 13–17, 2006; Baltimore, MD. Vajrala, Vijayanand, James Claycomb, and John H. Miller, Jr., “Analytical Model of Induced Transmembrane Potentials in Cells and Organelles,” Bull. Am. Phys. Soc. 51, 1524 (2006), March Meeting of the American Physical Society, Session Y26, Focus Session on the Physics of Physiological Systems, March 13–17, 2006; Baltimore, MD.


Miller, J. H., Jr., D. Warmflash, D. Nawarathna, J. Gardner, G. Cardenas, and W. R. Widger, “Low-Frequency Electromagnetic Probes of Live Organisms,” Session on Biogeophysics, 2006 Joint Assembly between the American Geophysical Union, Geochemical Society, Microbeam Analysis Society, Mineralogical Society of America, Society of Exploration Geophysicists, and Unión Geofísica Mexicana, May 23–26, 2006, Baltimore, MD (Invited talk). Funding and Proposals Miller, John H., Jr. “Dielectric Spectroscopy of Chemical and Biological Systems,” Robert A. Welch Foundation, June 1, 2004–May 31, 2007. $165,000. Miller, John H. Miller, Jr., PI, William R. Widger, Co-I, “Noninvasive Sensors of Metabolic Activity,” NIH, RFA-HL07-007, Bioengineering Approaches to Energy Balance and Obesity (R21), $150K/yr of direct costs requested for 3 years. Additional co-investigators/collaborators include Dale J. Hamilton, MD, and Richard J. Robbins, MD, of Methodist Hospital. Miller, John H., Jr., PI, “Nonlinear Impedance Spectroscopy of Chemical and Biological Systems,” Robert A. Welch Foundation, renewal of E-1221, $60,000/year direct costs requested for three years. Funding Initiative NIH (R01), United Mitochondrial Disease Foundation and American Diabetes Assoc.: Marin Laughlin, an NIDDK program director in NIH, and others in NIBIB and NHLBI have expressed considerable interest in UH ideas and methodology for detecting mitochondrial function.

SPECTROSCOPY—Dr. John H. Miller Jr. supervises Shih-Ying Hsu, a Taiwanese doctoral student in biophysics, in a study of electromagnetic responses of living cell suspensions.

SCIENCE AND ENGINEERING—The Science and Engineering Research and Classroom Complex on the UH main campus is a 200,000-sq. ft. facility offering five floors of laboratory space capable of supporting an estimated 40 research laboratories.


Mini-Grants

Micro-Integrated Super Broadband Stellar Simulator Optical Calibration Sources by Abdelhak Bensaoula, Chris Boney, and Nasr Medelci

ABSTRACT—This project involves the development, fabrication, and testing of miniature solid-state highstability integrated super broadband semiconductor optical emission sources for field and in-flight calibration of stellar photometers and spectrometers. In this project, we will combine expertise in the area of SiC avalanche light emitting diodes fabrication available through our Houston-based collaborator, Integrated Micro Sensors Inc.—a firm currently working on a related NSF-funded project—with our new achievements in III nitride materials growth, characterization, and processing to demonstrate a prototype device with the specified characteristics.

O

PTICAL SPECTROSCOPY IS A POWERFUL TECHNIQUE TO

analyze emissions from galaxies and explore stellar populations. Existing lamps and blackbody simulators used for optical calibration are power hungry, bulky, and can be used only in laboratory conditions. At present, no miniature and stable solid-state optical calibration sources are available for simulation of the stellar-related radiation measured by photo and spectrometric equipment in a broad optical range of the spectrum. Avalanche electroluminescence-based LEDs have numerous advantages over lamps and injective LEDs including unusually broad emission spectrum, lack of spectral dependence on the input current, similarity to solar radiation spectrum, high thermal and temporal stability, and miniaturization in size.1,2 Intraband hot electron transitions participating in the avalanche process result in unusually broad spectrum and stable optical emission, which can be used either to simulate standard spectra of various class stars or for broad-band calibration of photodetectors in spectroscopic and photometric applications. Goals The band gap of ternary compounds based on III nitrides can be tuned from 0.7 to 6 eV allowing for optoelectronic devices capable of performing in a spectral range from 200 nm to 1.77 μm. Spectral tuning of such devices can be provided by changing the composition of the active layers in these devices as well as by integrating layers of various materials on a single chip. For example, the possibility of III nitride growth on either sapphire, silicon carbide, or silicon can result in devices that would take advantage of the characteristics of each of the materials used in the device structure.3 A new approach relies on the employment of stacked III nitride materials with band gaps increasing from the bottom, allowing for optical emission virtu-


ally in the range from 0.2 to 5 μm as shown in Fig. 1. As a first step toward realizing the essential structures of the device, our first project task was focused on the optimization of the growth of GaN and AlGaN layers with various Al content on Si and sapphire substrates using Radio-Frequency Molecular Beam Epitaxy (RF MBE). Results The III-Nitride layers in our investigation were grown in a custom-made molecular beam epitaxy (MBE) chamber equipped with standard effusion cells for Group III and dopant flux delivery, which includes Ga, Al, In, Si, and Mg. Active nitrogen species are generated by an EPI Uni-Bulb radio-frequency (RF) plasma source. The sample manipulator is compatible with 2” diameter substrates and operating temperatures of 900°C. The chamber is pumped with a 2200 L/s turbomolecular pump and reaches a base pressure of 0. If mi = 0, all jobs of Ti are optional similarly); otherwise, it is optional. Quan et al. improve the result of overload management with enhanced fixed-priority scheduling.4, 7 We use the evenly-distributed-mandatory pattern in our preliminary experiments since it has been reported that this pattern exhibits relatively good schedulability.4, 7 Regarding the scheduling method, we adopt the earliest-deadline-first (EDF) algorithm because it is expected to provide good schedulability. In mandatory/optional job scheduling, the mandatory jobs of each task are assigned the priority according to the deadline-monotonic (DM) or EDF algorithm, and all optional jobs of every task are assigned the lowest priority. If two or more optional jobs compete for the processor when no mandatory jobs are eligible to run, the one with the earliest deadline executes first. If they happen to have the same deadline, any arbitrary priority assignment can be used to break the ties. West and Poellabauer3 present a necessary and sufficient condition for the deeply-red task set to determine schedulability. They claim that the worst case occurs on the first job of each task. We can use the time-demand analysis method proposed by Lehoczky9 to calculate the response time for each task. Please note that only mandatory workloads are incurred in the calculations. Quan et al.17 present a sufficient and necessary condition for the evenly-distributed-mandatory pattern by using the EDF algorithm to schedule the jobs. Let R be the set of mandatory jobs. R is (m,k)-firm schedulable with EDF if and only if all the mandatory jobs within the first busy interval [0, t] can meet their


deadlines. The end point of the first busy intercal can be easily found by observing that it must be the smallest t such that the accumulated mandatory workload within interval [0, t] equals t, that is,

One can easily compute the end point for the first busy interval by using fixed-point iteration on this formula with the initial value of t set to a small number larger than 0, e.g., 1. The fixedpoint iteration will converge rapidly as long as the task set is schedulable. We can always set the upper bound of the busy interval length to be the least common multiple (LCM) of the tasks’ periods. If the busy interval length is longer than the LCM of the tasks’ periods, the task set is not schedulable. System Model and Objectives Here is an example showing that carefully selecting the (m,k) constraint, hence the guaranteed granularity of QoS for each task, is important to the system’s overall performance. Consider a task set of three tasks: T1 = (10, 2, 1, 2, [10, 30]), T2 = (15, 6, 1, 2, [20, 50]), T3 = (60, 30, 1, 1, [50]). Since the utilization of the task set is 1.10, this task set is not schedulable without using (m,k) constraints. With the help of (m,k) constraints, the schedule of meeting all mandatory deadlines of the jobs is shown in Fig. 1(a). Note that in this case, using either the deeply-red pattern or evenly-distributed pattern produces the same result. It is not difficult to see that all tasks in Fig. 1(a) only attain their minimum GQoS-reward, and the total reward of the system for this case is 10+20+50 = 80. However, with a more in-depth analysis, the total GQoS-reward can be increased by adjusting the (m,k) constraints used at run-time. In fact, for this example, we can increase either m1 to 2 or m2 to 2. In both cases, they all raise the total GQoS-reward while satisfying the new (m,k)-related rules. Figure 1(b) shows the schedule of giving m2 one increment and the schedule in Fig. 1(c) has m1 increased by 1. In addition to improving the overall granularity of QoS, several interesting phenomena can be observed in the example. First, one idle interval (from 56 to 60) is left within the schedule in Fig. 1(a). The effective processor utilization (EPU) of this schedule is the lowest among the three schedules because several optional job(s) which, in fact, can be executed as mandatory job(s) have to be blocked by other mandatory jobs, while there are some idle intervals after executing the leftover optional jobs. Another phenomenon is well known although it is not reflected in our example: EDF performs very poorly under overload.16 Second, note that the output produced from the schedule in Fig. 1(a) is non-stable. However, after increasing m of k for some task, EPU and output stability are all enhanced for the schedules in Fig. 1(b) and Fig. 1(c). As a result of these observations, we expect that our idea has positive effects on these soft/firm real-time performance metrics. The rationale behind our conjecture is that since we reserve as much CPU time as possible for important mandatory jobs, the space for the source of the negative factor, overloaded optional jobs, is compressed.


Figure 1. (a) Schedule obtained by satisfying the original (m,k) constraints, that is, (m1, k1) = (1, 2), (m2, k2) = (1, 2), (m3, k3) = (1, 1). (b) Schedule obtained by increasing m2 by 1, (m2, k2) = (2, 2) or (1, 1). (c) Schedule obtained by increasing m1 by 1, (m1, k1) = (2, 2) or (1, 1).

Hence, the maximum effect of the possible degradation is minimized, and consequently, it is very likely that the soft/firm realtime performance can be improved. According to the relative importance among all tasks in the task set, each task Ti has a multi-version GQoS rewards. The number of versions in task Ti is dependent on the (mi, ki) parameter and then it equals ki - mi + 1. Our goal is to determine the version of GQoS for each task such that the total GQoS reward is maximized while satisfying the corresponding (m,k)-firm deadline requirements. Formally, the problem can be defined as: Maximize

subject to:

(1) the task set is schedulable by the re-defined (m,k)-firm constraints: {(m1, k1)…. (mn, kn)} corresponding to {r1…rn}, and (2) ri ∈ {ri(0)…ri(ki – mi)}. Complexity of the GQoS-Reward Optimization Problem By using patterns where the first job of every task is mandatory and has the worst-case execution time, we can use Lehoczky’s time-demand analysis method9 to check if the task set is schedulable for those given (m,k)-patterns. However, the

problem of selecting the best version of GQoS for each task to ensure that the total reward is maximized and all mandatory jobs are schedulable is an NP-hard problem. This can be shown by using a reduction from the 0-1 constrained knapsack maximization problem,11 which is defined as follows: Maximize pi xi subject to wi xi ≤ M, where xi ∈ {0, 1}. Given an instance of the 0-1 constrained knapsack problem P = {p1, p2,…, pn}, W = {w1, w2,…, wn}, we construct an instance of the GQoS-reward maximization problem: each task Ti has a worst-case execution time ei = wi . The period and relative deadline of each task are all equal to M. The number of granularities of QoS for each task is 2, represented as (mi, ki) = (0,1) and (1,1). The reward for the case of (0,1) is trivial, which is 0. The reward for the case of (1, 1) for task Ti is pi . Therefore, if xi = 1, pi xi means the GQoS-reward of selecting the (1, 1)-version of granularity of QoS for Ti. Otherwise, (0, 1) is selected instead. It is not difficult to see that pi xi is maximized in the 0-1 constrained knapsack problem if and only if the total GQoS-reward is maximized in the GQoS-reward maximization problem. Since the transformation between the given instance of 0-1constrained knapsack problem and the instance of GQoS-reward maximization problem can be performed in polynomial time, we thus know that the GQoS-reward maximization problem is also NP-hard. Results If the number of tasks in a task set and the number of versions of each task are not large, an exhaustive search method similar to that in Seto, Lehoczky et al. can be used.6 First, to guarantee that each task Ti is schedulable, a set of feasible (mj, kj) parameters, where Pj Pi, is determined, e.g., in the motivational example, the feasible set for task T3 is {(m1, k1)-(m2, k2)(m3, k3) | (1, 2)-(1, 2)-(1, 1), (1, 2)-(2, 2)-(1, 1), (2, 2)-(1, 2)(1, 1)}. Next, we intersect the sets of feasible granularities. After this intersection, we have all feasible combinations of (m, k) parameters in the task set which can be used at run-time. Finally, we traverse these combinations to determine the optimal selection which maximizes the total GQoS-reward. Although we can use the Branch-and-Bound strategy to ease the work slightly, the number of possible combinations of GQoS increases exponentially with the number of tasks or the total number of granularity versions in all tasks. If the task set is very large, it is impossible to perform this calculation within a reasonable length of time. Thus, we have to look for some other sub-optimal solutions to solve the problem efficiently. Our idea is to define a heuristic method based on sorting all versions of GQoS by a metric to be determined. The metric should reflect a relatively large reward and has a small negative effect on schedulability. Hence, we can solve the problem suboptimally in polynomial time (the time for sorting plus the time for a linear search). Selecting a good heuristic is very important to the final results. A good choice is prone to a larger value-density task10 which focuses on values and execution times of the task. However, for our problem, the effects of the (m,k) parameters and task periods also need to be considered. For example, increasing different mi by one increment has different effects on task schedulability. This project will design the heuristics and

Algorithm 1: Select the best (m,k) parameter for each task while keeping the task set schedulable. 1. 2.

3.

Input: Periodic task set T with tasks having firm deadlines and GQoS-rewards assigned properly. Output: Version of QoS represented by the (m,k) parameter used at runtime for each task to maximize the total GQoS-reward. Sort all the versions according to their nonincreasing values of i = 1,…, n, j = 0,…, ki – mi.

4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16.

U = set containing the sorted versions. Vi = minimum required version for task Ti. Remove the minimum versions from U. while U ≠ Ø do temp = the head of U use temp to replace corresponding Vi to check the feasibility of the task set if schedulable then Vi = temp remove all versions not finer than Vi in U for Ti else remove the version at the head end if end while Return Vi, i = 1, … , n

Figure 2. Algorithm for Selecting the Best (m,k) Parameter

perform experiments on a variety of control, multimedia, and networking applications to evaluate different heuristic functions. In our preliminary experiments, metrics which do not consider these parameters fail to give good approximations of the optimal total rewards. Hence, we design the versions of granularity so that they are ordered non-increasingly according to the values of i = 1, … , n, j = 0, … , ki – mi, initially. We next present the

algorithm applying this principle for selecting the best (m,k) parameter. It works like the greedy approach, always choosing the schedulable version of GQoS which has the largest reward to resource demand ratio. If one version for a task should be chosen, the coarser versions for that task are removed from the sorted list and only finer versions are left. By accomplishing this process, the “surplus” computing resource is reserved for relatively important tasks as much as possible. Experimental Results and Evaluation We use simulation experiments to demonstrate the effectiveness of our heuristic method to solve the GQoS-reward optimization problem, and discover the positive effects of maximizing gran-


ularities of QoS. In the first part, we simulate our heuristic algorithm on the same task sets whose sizes are relatively small with up to eight (8) tasks each. The task sets are divided evenly into nine (9) groups by their effective utilizations in the interval 0.1 –1.0. Each group contains at least 100 randomly generated task sets.

Then we compare our solution with the optimal solution that is obtained with an exhaustive search. Figure 3 shows the optimal total GQoS-reward and our approximated total GQoS-reward normalized to the initial total GQoS-reward (the granularities of QoS over the system with the original (m, k) parameters). One can see that our heuristic solutions are very close to the optimal results. Actually, in these preliminary experiments, our algorithm finds the optimal solution most of the time. In the second part, we want to determine the relationship between the optimization of the granularities of QoS and the performance of a soft/firm real-time system. We adopt several popular soft/firm real-time system performance metrics from the literature such as EPU19 and instability.15 In the experiments, 500 task sets are randomly generated. The periods are randomly selected between 10 and 150, and the deadlines are assumed to be the same as their periods. The worst-case execution time (WCET) of a task is uniformly distributed from 1 to its deadline. Similar to the experiments in the first part, the task sets are divided into 9 groups according to their effective utilizations. To reduce statistical errors, we ensure that each group contains at least 20 schedulable task sets. To measure EPU and instability, the task sets are simulated within the K-LCMs (least common multiple of Pi* ki). EPUs are obtained by calculating the fraction of time during the interval in which the processor executes tasks that complete by their deadlines. To calculate instabilities, the idea in Brandt (2001) is used, which sees the instability of a task as a discrete sum of changes on the number of the task completions between any two consecutive distinct intervals. To accommodate the requirements of the (m, k)-constrained model, we define the length of the intervals for a task to be the same as the parameter k for that task and the intervals are overlapped. We expect that our algorithm can improve the soft/firm real-time performance on both EPU and instability. Figure 4 shows the comparison results on EPU. Compared with the results that are not optimized, our proposed technique has significant improvements when the effective utilization of the system is relatively low. As utilization increases, improvement decreases because the space for improvement becomes less available. However, it is very attractive that our strategy always keeps the average EPU around 95 percent. For instability, an amazingly huge improvement can be seen in Fig. 5. The average instability is maintained at a very low level; hence, this response supports the fact that simulated systems are very stable in QoS using our method. Discussion In order to discover the effects of our optimization strategy more thoroughly, we also investigate the comparisons on accumulated value (AV) although this metric is not very good


Figure 3. Total Reward Ratio

Figure 4. EPU Comparison

for the (m,k)-constrained model since it lacks enforcement on granularity. We assign each task in the experiment a value and assign the GQoS-rewards according to this value; we calculate the total accumulated value that is in the same sense of the total weighted completion count (CC). (See Baruha et al. and Ramanathan.) In our experiments, about 85 percent of the cases improve the results; consequently, the average case with our technique is slightly better than the case without using it (Table 1). The reason for the small improvement, on average, is that after we increase m of k for some relatively important tasks, we, in fact, increase the priority of some jobs in the tasks by changing them into mandatory tasks. However, since those jobs could be run even if they were optional but block some other optional jobs after being re-categorized as mandatory, the system may lose accumulated rewards in total for

References M. Hamdaoui and P. Ramanathan, “A Dynamic Priority Assignment Technique for Streams with (m,k)-Firm Deadlines,” IEEE Trans. on Computers 44 (1995): 1443-51. 2 G. Koren and D. Shasha, “Skip-over: Algorithms and Complexity for Overloaded Systems That Allow Skips,” IEEE Real-Time Systems Symposium [RTSS] (1995): 110-17. 3 R. West and C. Poellabauer, “Analysis of a WindowConstrained Scheduler for Real-Time and Best-Effort Packet Streams,” Proc. IEEE RTSS (2000): 239-48. 4 P. Ramanathan, “Overload Management in Real-Time Control Applications Using (m,k)-Firm Guarantee,” IEEE Trans. on Parallel and Distributed Systems 10.6 (1999): 549-59. 5 D. B. Seto, J. P Lehoczky, L. Sha, and K. G. Shin, “On Task Schedulability in Real-Time Control Systems,” IEEE RTSS (1996): 13-21. 6 D. B. Seto, J. P Lehoczky, and L. Sha, “Task Period Selection and Schedulability in Real-Time Systems,” IEEE RTSS (1998): 188-98. 7 Q. Quan and X. Hu, “Enhanced Fixed-Priority Scheduling with (m,k)-Firm Guarantee,” IEEE RTSS (2000): 79-88. 8 M. Lloyd-Hart, “Taking the Twinkle out of Starlight,” IEEE Spectrum (2003): 22-29. 9 Lehoczky, J. P., L. Sha, and Y. Ding, “The Rate-Monotonic Scheduling Algorithm: Exact Characterization and Average Case Behavior,” IEEE RTSS (1989): 166-71. 10 G. Buttazzo, M. Spuri, and F. Sensini, “Value vs. Deadline Scheduling in Overload Conditions,” IEEE RTSS (1995): 90-99. 11 M. R. Garey and D. S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. New York: Freeman, 1979. 12 A. M. K. Cheng, Real-Time Systems: Scheduling, Analysis and Verification. Wiley-Interscience, 2002. 13 S. K. Baruah and Jayant R. Haritsa, “Scheduling for Overload in Real-Time Systems,” IEEE Trans. on Computers 46 (1997): 1034-1039. 14 S. Baruah, J. Haritsa, and N. Sharma, “On-Line Scheduling to Maximize Task Completions,” IEEE RTSS (1994): 228-37. 15 S. A. Brandt, “Performance Analysis of Dynamic Soft Real-Time Systems,” IEEE IPCCC (2001): 379-86. 16 J. Haritsa, M. Carey, and M. Livny. “Earliest-Deadline Scheduling for Real-Time Database Systems,” IEEE RTSS (1991): 232-43. 17 G. Quan, L. Niu and J. P. Davis, “Power Aware Scheduling for Real-Time Systems with (m,k) Guarantee,” CNDS (2004). 18 J. Lin, A. M. K. Cheng, “Maximizing Guaranteed QoS in (m, k)-firm Real-time Systems," 12th IEEE Intl. Conf. on Embedded and Real-Time Computing Systems and Applications (2006): 402-10. 19 P. Ramanathan, “Overload Management in Real-Time Control Applications Using (m,k)-Firm Guarantee,” IEEE Trans. on Parallel and Distributed Systems, 10.6 (1999): 549-59. 20 Bernat, G. and R. Cayssials, “Guaranteed on-Line Weakly-Hard Real-Time Systems,” Proc. IEEE 22nd Real-Time Systems Symposium (2001): 25-35. 21 D. Liu, X. S. Hu, M. D. Lemmon, and Q. Ling, “Firm Real-Time 1

Figure 5. Instability Comparison Effective Utilization

Average AV without our strategy

Average AV using our strategy

0.1 – 0.2

100

113

0.2 – 0.3

100

118

0.3 – 0.4

100

114

0.4 – 0.5

100

112

0.5 – 0.6

100

107

0.6 – 0.7

100

104

0.7 – 0.8

100

105

0.8 – 0.9

100

104

0.9 – 1.0

100

104

Table 1. Normalized Average Total Accumulated Values (AV)

some cases. Nonetheless, while considering this together with other performance perspectives, enhancement in the overall performance is apparent using our optimization strategy. Conclusions We have introduced the problem of maximizing the guaranteed quality of service while maintaining the schedulability of a task set in an (m,k)-firm real-time system. We proved that the problem is NP-hard and proposed a simple heuristic solution — by greedily increasing the QoS level of the tasks with the maximal “reward ratio” as long as all the other tasks have their minimum service level. Our preliminary study has evaluated the solution using the Granularity-of-Quality-of-Service Rewards, effective processor utilization, total accumulated reward, and instability as performance measures. We like the simplicity of the heuristics and the good performance with regard to its minimizing the instability in an overloaded system.


System Scheduling Based on a Novel QoS Constraint,” IEEE Trans. on Computers, 55.3 (2006): 320-33 Publications Andrei, S. and A. M. K. Cheng. “Faster Verification of RTL-Specified Systems via Decomposition and Constraint Extension,’’ Proc. IEEECS Real-Time Systems Symposium (RTSS), Rio de Janeiro, Brazil, December 2006. Andrei, S. and A. M. K. Cheng. “Optimization of Real-Time Systems Timing Specifications,’’ Proc. 12th IEEE-CS Intl. Conf. on Embedded and Real-Time Computing Systems and Applications, Sydney, Australia, 2006. Andrei, S., W.-N. Chin, A. M. K. REAL-TIME TEAM—(l. to r.) Computer scientists Bin Lu, master’s student, Yingwei Kuo, Ph.D. Cheng, and M. Lupu. “Automatic candidate, Dr. Albert M. K. Cheng and Jian Lin, Ph.D. candidate, focused their study on optiDebugging of Real-Time Systems mizing real-time task processing and minimizing instability in overloaded computer systems. Based on Incremental Satisfiability Counting,’’ IEEE Transactions on Collector that Considers Time, Space, and Energy,’’ IEEE-CS Computers 55.7 (2006): 830-43. (Accepted February 2006, Real-Time Systems Symposium (RTSS) WIP Session, Rio de selected as this issue’s featured article.) Janeiro, Brazil, December 2006. Aruchamy, G. and A. M. K. Cheng. “Translating Real-Time UML Timing Constraints into Real-Time Logic Lin, J. and A. M. K. Cheng. “Maximizing Guaranteed QoS in (m,k)-firm Real-time Systems,’’ Proc. 12th IEEE-CS Intl. Conf. Formulas,’’ IEEE-CS Real-Time Systems Symposium on Embedded and Real-Time Computing Systems and (RTSS) WIP Session, Rio de Janeiro, Brazil, December Applications, Sydney, Australia, August 2006. 2006. Cheng, A. M. K. “Intrusion Detection via Automatic Rule- Lin, J. and Albert M. K. Cheng. “Maximizing Guaranteedf QoS within (m,k)-Firm Real-time Constraints,’’ Proc. IEEE-CS Base Generation and Semantic Analysis,” Proc. SCISS, Real-Time and Embedded Technology and Applications Houston, TX, April 2006. Symposium (RTAS) WIP Session, San Jose, CA, April 2006. Cheng, A. M. K. “On-Time and Scalable Intrusion Detection in Embedded Systems,’’ Proc. Workshop on Research Zhang, W., A. M. K. Cheng, B. Fang, and M. Hu. “An Adaptive Multisite Scheduling Algorithm for Parallel Jobs in Directions for Security and Networking in Critical RealComputational Grid Environments,’’ Proc. Third HighTime and Embedded Systems, in conjunction with IEEEPerformance Grid Computing Workshop, in conjunction with CS Real-Time and Embedded Technology and Applications International Parallel and Distributed Processing Symposium. Symposium (RTAS), San Jose, CA, April 2006. Rhodes Island, Greece, April 29, 2006. Cheng, A. M. K. and F. Shang. “Priority-Driven Coding and Transmission of Progressive JPEG Images for Real-Time Applications.’’ (Accepted May 2006; forthcoming in J of Presentations VLSI Signal Processing - Systems for Signal, Image and Cheng, A. M. K., Tutorial Speaker, “Parallel and Distributed Embedded/Real-Time Systems,” The 18th IASTED Intl. Video Technology, 2007. (Accepted May 2006.) Conf. on Parallel and Distributed Computing and Systems Cheng, A. M. K. and Z. Zhang. “Improving Web Server (PDCS), Dallas, TX, Nov. 14, 2006. Performance with Adaptive Proxy Caching in Soft RealTime Mobile Applications,’’ (Accepted, Dec. 2006; forth- Cheng, A. M. K., Tutorial Speaker, “Analysis and Verification of Real-Time Embedded Software and Systems,” Formal coming in J. of VLSI Signal Processing Systems for Signal, Methods Symposium, McMaster University, Hamilton, Image, and Video Technology, 2007.) Canada, Aug. 21–27, 2006. Cheng, A. M. K. and Z. Zhang. “Improving Web Server Performance in Soft Real-Time Mobile Applications with Adaptive Proxy Caching,’’ Proc. MobEA IV-Empowering Proposals the Mobile Web, Collocated with ACM WWW External, NSF, “Optimizing Quality of Service in Firm RealTime Systems,” $325,000, June 1, 2007–May 31, 2010. Conference, Edinburgh, Scotland, May 2006. (Submitted). Lewis, Q. S. and A. M. K. Cheng, “3D GC: Towards a Garbage


Prototype Micromanipulator of Space Robotics Applications by James B. Dabney and Thomas L. Harman

P

IEZOELECTRIC ACTUATORS HAVE CONSIDER-

able potential for space-based robots. This research produced a prototype singledegree-of-freedom (DOF) micromanipulator consisting of a piezoelectric bending actuator and a capacitive position measuring system. The actuator will facilitate research to solve open issues in piezoelectric actuator control, particularly in hysteresis modeling and control. Premises of the Project Piezoelectric actuation is ideal for spacebased robotics applications requiring inherent lightweight features, simplicity, and immunity from magnetic fields. End effectors for miniature space-based robots must also be simple and lightweight and can also benefit from immunity from magnetic fields. Therefore, a piezoelectric actuator is an ideal candidate for an end effector. A piezoelectric bending actuator (Fig. 1) consists of two layers of piezoelectric material bonded together with opposite polarity in the form of a cantilever beam. The application of an electric field to the actuator causes one layer to extend slightly and the other layer to contract slightly.1 The differential length causes the beam to bend toward the contracting layer. By controlling the applied electric field precisely, it is possible to control the movement of the beam tip. The tip of this particular actuator has a range of motion of ±0.5 millimeters. Labview version 6.0 is used to generate voltages in the range +5V to –5V which are, in turn, supplied to a piezo-linear amplifier. The piezo-linear amplifier is used as a high voltage drive source for the piezoelectric actuating device. The capacitive sensor2 senses the motion and produces an analog voltage proportional to the distance between the capacitive probe and the piezoelectric actuator. Labview 6.0 is used to record the capacitive sensor output. Laboratory Apparatus The UHCL micromanipulator system will facilitate research in dynamics and control of micromanipulators. The device uses a piezoelectric bending actuator that has a range of

James B. Dabney

Thomas L. Harman

ABSTRACT—Piezoelectric actuators offer dramatic improvements in a variety of space-based robotics applications. Bending piezoelectric actuators offer a simple, lightweight, and reliable means for actuating end effectors. This research produced a single degree-of-freedom micromanipulator prototype which can be used to solve open issues in bending actuator control, especially in hysteresis modeling and control.

Figure 1. Schematic of the Principle of Operation


Figure 2. Block Diagram of the Experimental Setup

Figure 3. Micromanipulator Experimental Setup

motion of approximately ±0.5mm. A block diagram of the apparatus is shown in Fig. 2. The apparatus consists of the piezoelectric bending actuator mounted to a mechanical breadboard and driven by a piezo-linear amplifier (Model EPA 007). The EPA-007 is a very compact high voltage linear non-inverting amplifier, which is used as a high voltage drive source for the piezoelectric actuating device. The manipulator position is measured using a commercial high-resolution capacitive position sensor (Series 4000 Capacitec amplifier) mounted to the mechanical breadboard. Labview version 6.0 is used to generate drive voltages to the piezo driver and measure capacitive sensor output. The experimental laboratory setup is shown in Fig. 3. Research Plan The main components of the prototype micromanipulator were available commercially. They were integrated mechanically,


and a hardware-software interface was developed to permit experimentation. Three main research issues were addressed: • To design and implement the actuator and capacitive sensor mounting system. • To design and implement circuitry to power and control the actuator and to record sensor output via Labview 6.0 software. • To develop a Labview 6.0 user interface to generate control signals for the actuator and record key parameters and tip position from the capacitive sensor. Results The actuator, capacitive position sensor, actuator driver, and sensor amplifier were assembled as shown in Fig. 3. Labview 6.0 software was developed to control the actuator driver and capture the sensor amplifier output. Using Labview software, preliminary experiments were performed to verify the operation of the system throughout the actuator range of motion.

J. Yan, R. J. Wood, S. Avadhanula, M. Sitti, and R. S. Fearing, “Towards Flapping Wing Control for a Micromechanical Flying Insect,” 2001 Intl. Conf. on Robotics and Automation, Seoul, Korea, 2001. 4

Publications Garud A., J. B. Dabney, and T. L. Harman, “Micromanipulator Modeling and Control: Initial Experiments,” UHCL Systems Engineering Laboratory Report, 2007.

Figure 4. Response of Piezoactuator as a Function of Drive Voltage

Funding Dabney, J. B., “Gulf Coast Consortium of Control and Dynamics Interactive Remote Laboratory,” NSF Collaborative Proposal, $54,000 (Joint proposal with UH, Rice, UH-Downtown). (Not funded.) Dabney, J. B., A. J. Meade (co-PI), “Micro Air Vehicle Modeling and Control,” Air Force Office of Scientific Research, $81,694. (Pending.)

For example, the approximate linear input-output relationship between the commanded position (actuator driver command voltage) and position (amplified capacitive sensor output voltage) was measured, as diagrammed in Fig. 4. Future Work An extensive literature is available on the control of piezoelectric micromanipulators. Among the control techniques studied are standard linear, non-model-based techniques such as proportional-integral-derivative control, linear control techniques including robust control, and adaptive control. The inherent precision feasible with piezoelectric micromanipulators is not attainable using these techniques because the piezoelectric actuators exhibit significant hysteresis. Preliminary results on dealing with the hysteresis have recently been reported3 but the techniques discussed in the literature deal only with repetitive motion. Therefore significant work remains in order to achieve the potential of these actuators for space-based robotics and other applications. Piezoelectric bending actuators are also ideal for flappingwing micro air vehicles. Among the issues to resolve are precise control of flapping amplitude and tailoring of flapping motion. Acknowledgments This study was supported by an ISSO mini-grant for the summer of 2006. References 1 M. Novotny and P. Ronkanen, “Piezoelectric Actuators,” 2 M. A. Ayer, Operation/Maintenance Manual: Series 4000 Capacitec Amplifiers and Rack Accessories, Ayer, MA: Capacitec, Inc., 1998. 3 J. Zhong and B. Yao, “Adaptive Robust Repetitive Control of Piezoelectric Actuators,” 2005 International Mechanical Engineering Conference and Exposition, Orlando, FL, 2005.


Bacillus Pumilus SAFR-032L: A Model for Planetary Protection Research by George E. Fox

ABSTRACT—In order to prevent forward contamination of Mars, it is necessary to minimize the bio-burden on spacecraft that will contact the Martian surface. Bacillus pumilus strains whose spores are unusually resistant to ultraviolet light and other means of sterilization have been consistently found in the clean rooms used in space craft assembly as well as on space craft. In order to better understand the origin of these organisms and to develop effective means for eliminating them, the complete genome of Bacillus pumilus SAFR032 is being sequenced in collaboration with the Baylor College of Medicine Human Genome Sequencing Center (HGSC). The sequence is in the finishing stage, and annotation is nearly complete. Comparisons of the genes involved in the sporulation process and UV repair are being intercompared in detail to identify genomic features that might be responsible for the unusual resistances that this organism exhibits.

A PRIMARY OBJECTIVE OF THE SPACE SCIENCES IS TO SEARCH for evidence of living systems in the universe. The most tractable target for such efforts has been and for the near future will continue to be the planet Mars. Having ratified the 1967 Outer Space Treaty, the United States is obliged to avoid harmful contamination of celestial bodies that might harbor life. Spacecraft that land on Mars but are not equipped with lifedetection experiments must minimize the bio-burden they bring to the planet. Thus, the components are subjected to rigorous cleaning and must be assembled in a Class 100,000 clean room or better. If the mission contains life-detection experiments, a sterilization process must be applied as good as or better than that applied to the landers used in the 1967 Viking missions. In preparing that protocol, researchers argued that the organisms most likely to be resistant to sterilization would be endospore-forming bacteria of the genera Bacillus and Clostridium. Hence, a spore assay was developed to evaluate the effectiveness of the sterilization process using Bacillus subtilis as the model organism. Given this background, modern planetary protection research focuses on two issues: (1) development of cleaning and sterilization technologies and better methods of evaluating their success and (2) the assessment of which terrestrial microorganisms are most likely to survive cleaning and sterilization and hence possibly confound tests for life done on the Martian surface or contaminate returned samples. Spacecraft are assembled in clean rooms which employ sterilants including vapor-phase hydrogen peroxide (VHP), a


BIO-BURDEN—Dr. George Fox (l.) and Dr. Duane L. Pierson, director of the NASA-JSC Microbiology Laboratory, work to prevent man’s biological contamination of Mars and other planets.

strong oxidizing agent, and UV, in addition to physical containment to obtain and maintain the necessary pristine surfaces. While conducting a microbial census of NASA spacecraft assembly facilities, Venkateswaran and his colleagues discovered that strict contamination control measures did not provide an absolute barrier to microbial contamination but, instead, established a series of selective “bottlenecks” which are sufficient to prevent the penetration or survival of all but the hardiest microbes into the interior assembly area.1 The predominant isolates repeatedly found to have penetrated deepest within the cleanest parts of the spacecraft assembly facilities were spore-forming bacteria, especially strains of Bacillus pumilus, B. nealsonii,2,3 and a closely related grouping recently named B. odysseyi because it was first isolated from the surface of the Mars Odyssey spacecraft.4 B. pumilus strains have also regularly been isolated from space craft including hardware from the International Space Station (ISS). In comparison with the model organism B. subtilis, which is used in the standard spore assay, B. odysseyi spores had survival times that were 3 times, 10 times and 6 times longer when exposed to UV, gamma radiation, and hydrogen peroxide. The most resistant strain isolated to date, B. pumilus SAFR-032 (Space Craft Assembly Facility Resistant Isolate 32) has at least a 10fold increase in its resistance to Mars UV radiation conditions

than the standard B. subtilis. In view of these findings, it is clear that assays for cleanliness and survival potential will be more meaningful if they are based on the organisms that are likely to be problematic such as B. pumilus and B. oddysseyi. Of the various resistant Bacillus strains that were isolated, the SAFR-032 isolate is the most resistant and has been selected for two key follow-up studies. First, a flight experiment was proposed and has been selected for a study of the effect of radiation resistance on this organism. This experiment will be carried out aboard the ISS using the European Technology Exposure Platform and Experiment Facility (EXPOSE). Second, the complete sequence of the genome of SAFR-032 is currently being determined by investigators at the Baylor College of Medicine Human Genome Sequencing Center (HGSC) with funding from the National Science Foundation (NSF). Methodology The SAFR-032 genome is essentially complete, and the HGSC group is currently conducting finishing studies in order to finalize the assembly of several very large reliable contigs. In addition, partial data were obtained for a second strain, F036B. A high-quality manual annotation is in progress using the HGSCdeveloped CONAN interface. Possible open reading frames are initially predicted by Glimmer5 and GeneMarkS6 and then automatically examined for similarity to known COGS, protein domains and other annotated genes (i.e., pre-run BLAST searches). The annotator looks at all the data and in some cases literature references before assigning a name and if possible a likely function for the open reading frame.7 Each gene is annotated separately by two annotators and the resulting annotations compared automatically. Differences are subsequently resolved by conference between the annotators with input from the group as a whole when needed. The initial analysis will identify genes that are shared or not shared with Bacillus subtilis8 and other Bacillus genomic sequences. Of special interest will be genes known to be involved in spore resistance9-12, DNA repair,13-15 and sporulation in general.16,17 Examination of shared genes will allow us to assess whether regulatory signals, e.g., promoter sequences for various sigma factors, are changed or not. In particular, genes known to be associated with particular sigma factors can be used to define recognition sites in SAFR-032. With this knowledge in place, genes that are uniquely present or absent in SAFR-032 will be broken into two groups, those associated with known sporulation genes and regulons and those not so associated. The leader regions of unique genes not associated with known sporulation operons will be further examined to see if they are likely to be transcribed by any of the sigma factors associated with sporulation.18 A second analysis will be a detailed comparison of the SAFR-032 gene organization with the well established operon structure of B. subtilis19 to identify possible regulatory differences. The most promising changes here will likely be operons whose structure is uniquely changed in SAFR-032 relative to the other known Bacillus genomes, all lacking resistant spores.

Results As a first step toward understanding the biology of these unique strains, the whole genome sequence of one isolate, B. pumilus SAFR-032, was determined. The B. pumilus SAFR-032 genome is 3.62 MB in size with approximately 3950 genes. Sequence alignment and subsequent construction of a tree of phylogenetic relationship for multiple housekeeping genes revealed that among published complete genomes, SAFR-032 is most closely related to B. subtilis and B. licheniformis, thereby rendering these organisms of greatest relevance for comparison. Since the sporulation machinery of B. subtilis has been extensively studied, this is an especially favorable outcome. A similar analysis of the F036B strain of B. pumilus revealed that it is much closer to SAFR-032 than the latter is to B. subtilis or B. licheniformis. A comparison of gene order between SAFR-032 and B. licheniformis revealed substantial co-linearity. This is important because one can scan local clusters for gene additions or losses that may correlate with changes in regulation. Discussion Despite the substantial similarity to B. licheniformis and B. subtilis, there are, nevertheless, many coding regions in SAFR-032 with no obvious homolog in these other organisms. Genes known to be involved in the sporulation processes, including regulation, spore protection, and germination, were compared with their homologs in B. subtilis and B. licheniformis in order to identify unusual absences and changes in gene order. The largest number of such changes are associated with genes involved in the generation of the spore coat protein which has likely been redesigned in B. pumilus relative to its sister species. Genes encoding the small acid soluble proteins, which are not only crucial for spore DNA protection but also known to be highly conserved within and across species, have interesting sequence variation, as compared to those of other Bacillus strains. Further, detailed comparative analysis revealed that several proteins annotated as hypothetical in B. subtilis/B. licheniformis, could actually be classified as functional genes (such as families of transporters, transcriptional regulator proteins etc.), genes unique to B. pumilus. Researchers found also that gene clusters encoding the polyketide pathway have substantial sequence variation from those of other Bacillus strains. Conclusions Results obtained here will in the short term generate multiple candidate genomic features that may separately or in combination be responsible for the unusual resistance associated with B. pumilus spores. In the immediate future it will be of interest to explore these alternative possibilities by comparing gene expression patterns in resistant and non-resistant strains. Funding for this purpose will be sought from the National Science Foundation and other federal agencies. In the longer view, the processes by which non-resistant strains readily evolve resistance to UV will be a useful model system for studying evolution. References M. J. Kempf, F. Chen, R. Kern, and K. Venkateswaran, “Recurrent Isolation of Hydrogen Peroxide-Resistant Spores

1


of Bacillus pumilus from a Spacecraft Assembly Facility,” Astrobiology 5 (2005): 391-405. 2 K. M. Venkateswaran, M. Satomi, S. Chung, R. Kern, R. Koukol, C. Basic, and D. White. “Molecular Microbial Diversity of a Spacecraft Assembly Facility,” Systematic and Applied Microbiology, 24 (2001): 311-20. 3 K. Venkateswaran, M. J. Kempf, F. Chen, W. Nicholson, and R. Kern, “Description of Bacillus nealsonii sp., Nov., Isolated from Spacecraft Assembly Facility, Whose Spores Are Radiation Resistant,” Intl. J. of Systematic and Evolutionary Microbiology 53 (2003): 165-72. 4 M. T. La Duc, M. Satomi, and K. Venkateswaran, “Bacillus odysseyi Sp. Nov., a Round-Spore-Forming Bacillus Isolated from the Mars Odyssey Spacecraft,” Intl. J. of Systematic and Evolutionary Microbiology 54 (2004): 195-201. 5 A. L. Delcher, D. Harmon, S. Kasif, O. White, and S. L. Salzberg, “Improved Microbial Gene Identification with GLIMMER,” Nucleic Acids Research 27 (1999): 4636-41. 6 J. Besemer J., A. Lomsadze, and M. Borodovsky, “GeneMarkS: A Self-Training Method for Regulatory Regions,” Nucleic Acids Research 29 (2001): 2607-18. 7 M. P. McLeod, S. E. Karpathy, J. Gioia, X. Qin, S. K. Highlander, G. E. Fox, T. Z. McNeil, H. Jiang, D. Muzny, L. S. Jacob, A. C. Hawes, E. Sodergren, R. Gill, J. Hume, M. Morgan, C. Hong, X. Yu, D. H. Walker, and G. M. Weinstock, “The Complete Genome of Rickettsia Typhi and Comparison with R. Prowazekii and R. Conorii,” J. of Bacteriology 186 (2004): 5842-55. 8 I. Moszer, L. M. Jones, S. Moreira, C. Fabry, and A. Danchin, “SubtiList: The Reference Database for the Bacillus subtilis Genome,” Nucleic Acids Research 30 (2002): 62-5. 9 P. Setlow, “Spores of Bacillus subtilis: Their Resistance to and Killing by Radiation, Heat, and Chemicals,” J. Appl. Microbiol. 101.3 (2006): 514-25. 10 T. A. Slieman, and W. L. Nicholson, “Role of Dipicolinic Acid in Survival of Bacillus subtilis Spores Exposed to Artificial and Solar UV Radiation,” Appl. and Environmental Microbiology, 67 (2001): 1274-79. 11 P. Setlow, “Resistance of Spores of Bacillus Species to Ultraviolet Light,” Environmental Molecular Mutagenesis 38 (2002): 97-104. 12 P. Setlow, “Spores of Bacillus subtilis: Their Resistance to and Killing by Radiation, Heat and Chemicals,” J. of Applied Microbiology 101 (2006): 514-25. 13 Y.M. Xue and W. L. Nicholson, “The Two Major Spore DNA Repair Pathways, Nucleotide Excision Repair and Spore Photoproduct Lyase, Are Sufficient for the Resistance of Bacillus subtilis Spores to Artificial UV-C and UV-B but not to Solar Radiation,” Appl. Environ. Microb. 62.7 (1996): 2221-7. 14 M. A. Ross, and P. Setlow, “The Bacillus subtilis HBsu Protein Modifies the Effects of Alpha/beta-Type, Small Acid-Soluble Spore Proteins on DNA,” J. of Bacteriology 182 (2000): 1942-48. 15 C. S. Hayes and P. Setlow, “An Alpha/Beta-Type, Small, AcidSoluble Spore Protein Which Has Very High Affinity for DNA Prevents Outgrowth of Bacillus subtilis Spores,” J. of Bacteriology 183 (2001): 2662-66. 16 D. W. Hilbert and P. J. Piggot, “Compartmentalization of Gene


Expression during Bacillus subtilis Spore Formation,” Microbiology and Molecular Biology Reviews 68 (2004): 234-62. 17 Makita, Y., M. Nakao, N. Ogasawara, and K. Nakai, “DBTBS: Database of Transcriptional Regulation in Bacillus subtilis and Its Contribution to Comparative Genomics,” Nucleic Acids Research 32 (2004): D75-77. 18 D. W. Hilbert and P. J. Piggot, 2004, 234-62. 19 M. J. De Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, and S. Miyano, “Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance and Gene Expression Information,” Pacific Symposium on Biocomputing (2004): 276-87. Publications Gioia, J., X. Qin, H. Jiang, K. Clinkenbeard, R. Lo, Y. Liu, G. E. Fox, M. P. McLeod, T. Z. McNeil, L. Hemphill, E. Sodergren, G. M. Weinstock, and S. K. Hightower. “The Genome Sequence of Mannheimia Haemolytica A1: Insights into Virulence, Natural Competence and Pasteurellaceae Phylogeny,” J of Bacteriology 188 (2006): 7257-66. Petrosino, J.F., Q. Xiang, S. E. Karpathy, H. Jiang, S. Yerrapragada, Y. Liu, J. Gioia, L. Hemphill, A. Gonzalez, T. M. Raghaven, A. Suman, G. E. Fox, S. K. Highlander, M. Reichard, R. J. Morton, K. D. Clinkenbeard, and G. W. Weinstock. “Chromosome Rearrangements and Diversification of Francisella Tularensis Revealed by the Type B (OSU18) Genome Sequence,” J. of Bacteriology 188 (2006): 6977-85. Viswanath, L., Y. Lu, and G. E. Fox. “Genome Display Tool: Visualizing Possible Correlations in Complex Data Sets,” Source Code for Biology and Medicine (2007). (In Press.) Presentations Fox, G. E. “Overview of the B. Pumilus Genome Sequencing Project,” Planetary Biology Workshop Entitled Mars Genetic Inventory of Spacecraft Analysis, JPL, Pasadena, CA, February 28–March 1, 2006. Tirumalai, M. R., Y. Yerrapragada, J. Gioia, I. DaGupta, L. Bokhetache, Y. Liu, P. E. Moorthy, B. D. McWilliams, J. Siefert, F. Karouia, A. A. Olowu, K. D. Clinkenbeard, A. Verma, P. Buzombo, H. Zwiya, O. Igboeli, A. Suman, X. Qin, H. Jiang, S. K. Highlander, K Venkateswaran, G. E. Fox, and G. M. Weinstock. “Whole Genome Sequence of a Bacillus pumilus strain isolated from a Spacecraft Assembly Facility,” 107th American Society of Microbiology General Meeting, May 21–25, 2007, Toronto, Canada. (Forthcoming). Funding and Proposals Venkateswaran, Kasthuri, JPL. “Microbial Ecological Perspectives of Space-Exposed Microbes: A Genetic Approach,” NASA: Human Support Technology, April 1, 2005-March 31,2008. UH Subcontract Total Costs: $120,000. (Not funded.) Fox, G. E. “Comparative Genome Analysis and the Resistance Properties of Various Bacillus Species,” NASA-Planetary Protection Program: Feb. 1, 2005–Jan. 31, 2008. UH Total Costs: $226,723. (Not funded.)

Origin of Structure in the Early Universe from Gravitational Radiation by David Garrison

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TANDARD COSMO-

given these initial conlogical theory ditions and evolve a set ABSTRACT—Cosmology has holds that fields of coupled General become an exciting topic in of homogenous highRelativistic and Magrecent years due to many new energy plasma and neto-Hy d r o d y n a m i c discoveries and theories. Howgravitational radiation equations. This GRMHD ever, no one has successfully populated the early code can be used to simulated the creation of universe. However, solve a variety of astrostructure in the universe from relatively little work physics problems, but, a smooth inflationary stage has been done which for this project, we will using a fully-relativistic-nonexamines the impact of focus on the problem of linear-dynamical code. Cosmic the interaction becosmic structure formastructure formation is usually tween these fields on tion. Consequently, we simulated using linear codes in the evolution of the expect to simulate the which structures evolve from universe. For example, formation of certain scalar quantum fluctuations. work by Kodama and structures from an iniThis work will focus on the Sasaki1 examined how tially homogenous plasinteraction between the priscalar, vector and tenma field and a field of mordial plasma and gravitasor perturbations digravitational radiation. tional wave fields as a cause of rectly resulted in densiThese structures inDavid Garrison cosmic structure formation. ty fluctuations but negclude: magnetic fields, We will examine whether or lected the dynamical density and temperature not gravitational waves lead to plasma turbulence and will preeffects caused by these variations, and seconddict the spectrum of the resulting relic waves. perturbations. Adding ary gravitational waves. dynamical effects such The spectrum and as turbulence will significantly reduce or eliminate the role of polarization of the resulting gravitational waves should be cold dark matter in early universe structure formation. We are, observable by future gravitational wave observatories such as therefore, working to examine the effects of primordial gravita- LISA and advanced LIGO. tional waves on structure formation in the early universe through dynamic interactions with the plasma field. Methodology We are currently examining the effects of both isotropic and As with any other numerical project, our first step is to develbirefringent gravitational waves on the plasma field. An exten- op initial data for the code. The initial data used will be based sive literature search reveals that a study such as this has never on initial conditions that involve the state of both the plasma been attempted. Our hypothesis is that General Relativistic field and the spacetime. The initial time chosen for this study is Magneto-hydrodynamic (GRMHD) turbulence contributed sig- three minutes after inflation in order to avoid significant quannificantly to structure formation in the early universe. The goal tum effects. We utilize the framework developed by Duez2,3 in of this work is to identify and evolve the initial conditions for order to classify the variables needed for the initial data and for the standard model that led to the development of the observed evolution equations. Initial conditions for the plasma field mass concentration in clusters and super-clusters of galaxies. include mass density, magnetic field, velocity, pressure, and The initial conditions are selected so that alignment with energy density for the magneto-fluid. Initial conditions for the observed values of the spectrum and isotropy of the cosmic spacetime include the scale factor, Hubble parameter, tensor background radiation are preserved as the solution evolves for- perturbations, gauge conditions and the Stress-Energy Tensor ward in time. calculated from the initial plasma conditions. The goal is to This project is a computational study of GRMHD turbulence. model the homogenous plasma described by the standard model For this work we use Cactus, an open-source framework for of cosmology on top of a perturbed Freidman-Robertsoncomputational physics. This tool will prove useful in the devel- Walker (FRW) spacetime. Various assumptions must be made in order to calculate these opment of a cosmic simulation program capable of recreating many of the conditions found in the early universe shortly after initial conditions; therefore our choice of initial conditions is the inflationary period. This code will solve Einstein’s equations not unique. These initial conditions will be continuously refined


and improved throughout this experiment. Dark Matter or Scalar Fields may be added as the project develops. Our plan is to use a General Relativistic MagnetoHydrodynamic computer code (GRMHD) to simulate the early universe during the classical plasmafilled regime. This code must be developed and tested as part of the project. The Cactus framework will be utilized for this work. Cactus is an open-source, problem-solving environment designed for scientists and engineers. The Cactus framework, which was originally developed for numerical relativity research, has become an extremely powerful and flexible tool. It originated in the academic research community, where it has been developed and used over many years by a large international collaboration of physicists and computational scientists. Its modular structure easily enables parallel computation across different architectures and collaborative code development between different individuals or groups. The advantage of this modular approach to software development in an educational environment is that it significantly reduces the learning curve for students working on the project and leads to greater research productivity in a shorter amount of time. Each student will be able to concentrate on developing his or her section of the project while treating the rest of the code like a collection of objects. I have been working with the students involved in this project to develop a code called Cosmo. Cosmo is an arrangement for Cactus and contains the MHD thorns, the basic unit of the Cactus framework. This code is capable of modeling the Magneto-Hydrodynamic (MHD) equations in a curved space-time and interacting with other BEOWULF—PI David Garrison stands at the secondary Beowulf cluster Cactus thorns resulting in a fully dynamical built by Lee Morin, an astronaut currently working on his master’s degree in GRMHD code. In particular, Cosmo interacts physics. Morin built the unit in his garage and at the Advanced Space with the BSSN_MOL thorn developed by the Propulsion Laboratory, Netural Bouyancy Laboratory. Albert Einstein Institute in Germany. BSSN_MOL then models Einstein’s equations in order to the Stress-Energy Tensor from the MHD evolution variables, evolve the spacetime. Because the early universe is considered as well as a technique called “divergence cleaning” to mainto be homogenous and isotropic, it is assumed that the simula- tain physical values for the B-field. Optimizing and improving tion domain is a homogenous slice of the early universe, and these solvers are essential to developing a stable code. In addiperiodic boundary conditions are applied to the simulation tion, preliminary results show that a large computational grid domain. Also, both linear and logarithmic scales are used for is required to accurately produce gravitational wave-induced calculating data in the simulation domain, making it possible MHD waves. Incorporating techniques such as adaptive mesh to compare results at multiple length scales. This program can refinement (AMR) into the evolution code have proven effectherefore effectively model the dynamic plasma-filled tive in other numerical relativity projects and may also be useFriedman-Robertson-Walker (FRW) universe. ful for this project. The use of AMR will allow us to effectiveThere are many challenges to evolving the numerical code. ly create a large computational grid with minimal computaFirst, there are the standard difficulties of dealing with a non- tional resources. linear finite-differenced relativity code. We utilize periodic Much of the data analysis work will involve the addition of boundary conditions in order to eliminate boundary errors. new analysis routines to the code as well as the use of thirdHowever, we may also need to develop more advanced gauge party software. Visualization of Cactus-generated data will be conditions to create a truly stable code. Second, additional done using a variety of open-source software such as OpenDX, challenges are created by the GRMHD code’s utilization of a xgraph, ygraph and gnuplot. OpenDX will require the writing of nonlinear “primitive variable” solver to recover elements of implementation scripts. These scripts will tell the visualization


program how to convert the Cactus-generated data files into the proper analysis format. These may include Fast Fourier Transforms (FFT) or Hilbert-Huang Transforms (HHT) for spectral analysis of the data. This part of the project will require significant data visualization resources. The real test of how structure was created in the early universe will occur after the results of the code can be shown to reasonably match those of the analytic results. At this stage, we will be refining the initial conditions so that they more accurately represent the early universe’s homogenous MHD field on a perturbed FRW background spacetime. As these numerical experiments are being performed, the students and I will be analyzing the output. We will look for variations in the density, temperature and magnetic field of the output data. If such variations are seen, a spectral analysis and phase space portrait of the data will be used to determine the relative size and distribution of these structures. Gravitational waves in the simulation domain will be extracted in order to determine the spectrum and relative amplitude of secondary gravitational waves created as a result of the development of the structures. Numerical experiments will then be repeated for different scales and initial conditions. We have outlined the process of evolving the GRMHD conditions for the early universe using an established framework. A numerical simulation of the initial conditions is designed to model the early life of the universe after the creation of subatomic particles, when a relativistic plasma field could describe the universe. It is expected that these conditions will result in fluctuations of the density of the plasma, growing seed magnetic fields and a modified spectrum of primordial gravity waves that we predict will one day be seen by observatories such as LISA. We may also witness the development of inhomogenities in the background temperature of the plasma field in agreement with that observed in the cosmic microwave background by WMAP. Equipment and Special Technology We currently have a computational laboratory with 30 2-GHz Pentium-4 based Linux machines and a small 16-node Beowulf cluster. In addition, we recently acquired a Beowulf cluster consisting of 48 dual processor nodes powered by 1.4 GHz PIII’s. The Beowulf has a 1.0 TB raid storage unit. This machine is linked to an educational grid of similar machines bringing the total computational availability to more than 600 processors. Once the code has been tested and science data runs begin, we can utilize faster supercomputers. We use a variety of software including OpenDX, xgraph, ygraph and gnuplot to visualize the output data. Results We expect the continued development of the Cosmo arrangement to be a long-term project with constant improvements as new data are generated. We began multiprocessor runs and testing of the code in the summer of 2006. The analysis of the data began soon after and the code is continuously being tested and improved. During the spring of 2007, FRW spacetimes should replace the analytically known solutions used to test the numerical code. We should begin seeing the results of this

work by summer 2007. At that time, significant effort will be required to analyze and visualize the data. Discussion To date, much of our work on this project has consisted of code development, computer hardware development, and software testing. We are currently pursuing external grants to finish this work and begin science runs. The focus of this project is to create a numerical simulation of initial conditions, which are designed to model the early life of the universe after the creation of subatomic particles, when a relativistic plasma field can describe the universe. It is expected that these conditions will result in fluctuations of the density of the plasma, growing seed magnetic fields, and a modified spectrum of primordial gravity waves that may one day be seen by observatories such as LISA. We may also witness the development of inhomogenities in the background temperature of the plasma field in agreement with that observed in the cosmic microwave background by WMAP. References 1 H. Kodama and M. Sasaki, “Cosmological Perturbation Theory,” Prog. Theor. Phys. Suppl. 78 (1985): 1-166. 2 M. D. Duez, Y. T. Liu, S. T. Shapiro, and B. C. Stephens, “Relativistic Magnetohydrodynamics in Dynamical Spacetimes: Numerical Methods and Tests,” Phys. Rev. D72 (2005): 024028. 3 M. D. Duez, Y. T. Liu, S. T. Shapiro, and B. C. Stephens, “Excitation of MHD Codes with Gravitational Waves: A Testbed for Numerical Codes,” Phys. Rev. D72 (2005): 024029. Publications Garrison, D., C. Ballard, R. de la Torre, and J. Hamilton. “Initial Conditions for Numerical Cosmic Evolution Using GRMHD Equations,” Classical and Quantum Gravity (2006). (Submitted for publication.) Presentations Garrison, D. “Cosmic Structure Formation via Gravitational Radiation,” University of Oregon Invited Talk, May 11, 2006. Garrison, D. “Initial Conditions for Cosmic Evolution Using GRMHD Equations,” 2006 American Physical Society April Meeting, April 22, 2006. Garrison, D. “Cosmic Structure Formation From Gravitational Radiation,” 2006 National Society of Black Physicists Meeting, Feb. 17, 2006. Garrison, D. “Cosmic Structure Formation From Gravitational Radiation,” Physics Department Seminars, UH-Clear Lake, 2006. Proposals Garrison, D. “Origin of Structure in the Early Universe from Gravitational Radiation,” National Science Foundation, June 1, 2007–May 31, 2010. $291,861. (Submitted.) Garrison, D. “Cosmic Structure Formation from Gravitational Radiation,” The Research Corporation, June 1, 2007–Aug. 31, 2008. $53,684. (Submitted.)


Superior Adsorbents for Aerospace Applications by Jack Y. Lu

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YNTHESIS OF FUNCTIONAL MATERIALS REPRESENTS ONE OF

the current challenges in chemical research. The metalorganic polymers have been found to have a wide range of applications such as molecular separation and pollution prevention in air, liquid and water systems, where they can be used as ion exchangers and molecular sieves. The objective of the proposal is a design and synthesis of new superior adsorbents that can be used to protect aerospace personnel from unhealthy environments. Experimental Activity, Results and Discussion Among the polymeric materials synthesized in our laboratory, 1 [Cd(NA)2], a new two-dimensional coordination polymer, has been synthesized under hydrothermal reaction conditions. The two-dimensional networks (Fig. 1) show a paired stacking arrangement and define how 2-D networks are stabilized via interdigitation and π-π interactions. [Cu(BPY)(NO3)2]n was reacted with additional 4,4’-bipy, resulting in a new self-assembled metal-organic network structure featuring the first two-fold interpenetrating 3-D 42.84 network structure: 2

{[Cu(BPY)2(H2O)2][Cu(BPY)2(H2O)(NO3)]}(NO3)3·12H2O.

The two independent 3-D networks in this compound, when minimally interpenetrating, enable this 3-D open-channel structure to accommodate a large amount of water molecules and nitrate anions. Such inclusion phenomena in interpenetrating open-frameworks are very suggestive of practical applications, especially in those open-channel structures with minimum interpenetrating frameworks (Fig.2). References 1 J. Y. Lu, M. A. Achten, and A. Zhang, “A 2-D CadmiumCentered Polymer and Its Isomers,” Inorg. Chem. Commun. 10 (2006): 114-16 (In press.) 2 J. Y Lu, A. A. Fernandez, Zh. Ge, and K. A. Abboud, “A Novel Two-Fold Interpenetrating 3-D 42.84 Network SelfAssembled from a New 1-D Coordination Polymer,” New J. Chem. 29 (2005): 434-38. Publications Lu, J. Y, A. A. Fernandez, Zh. Ge, and K. A. Abboud. “A Novel Two-Fold Interpenetrating 3-D 42.84 Network SelfAssembled from a New 1-D Coordination Polymer,” New J. Chem. 29 (2005): 434-38. Lu, J. Y. and Zh. Ge. “Synthesis and Structures of Two New Metal-Organic Polymers Containing Imidazoldicarboxylate Ligands for Hydrogen Bonding Networks, One with a Covalent Pleated Sheet Conformation,” Inorg. Chim. Acta, 358 (2005): 828-33.


ABSTRACT— Superior adsorbents have been important topics in current chemical and materials research because they have been found to have a wide range of applications. Research on adsorbents focuses on the rational design and synthesis of new materials that can be used for space applications. Jack Y. Lu The development of a new twodimensional coordination polymer indicates the potential of UHCL laboratories.

Lu, J. Y. and Chen, L. “The First Bromonicotinato-Coordinated Metal-Organic Polymer Featuring Covalent 2-D Layer Alternately Sandwiched by 1-D Intra-Hydrogen Bonding Networks,” Inorg. Chem. Commun. 7 (2004) 350-54. Lu, J. Y. “Crystal Engineering of Cu-Containing Metal-Organic Coordination Polymers Under Hydrothermal Conditions,” Coord. Chem. Rev. 246 (2003): 345-65. Lu, J. Y. and Babb, A. M. “A Unique Eclipsed 2-D Coordination Polymer with Removable Iodine Molecules in the OpenChannel Structure,” Chem. Commun. (2003): 1346-47. Lu, J. Y. and V. E. J. Schauss. “A Novel Nanostructured OpenChannel Coordination Polymer with an Included FusedPolyiodide Ring,” Inorg. Chem. (2002): 1945-48. Lu, J. Y. and E. E. Kohler. “A Non-Interpenetrating 3-D Coordination Polymer Built From Binuclear Cd Units Elaborated With Square-Pyramidal Geometry of Cadmium,” Inorg. Chem. Commun. 5 (2002) 196-99. Lu, J. Y. and A. M. Babb. “A Simultaneous Reduction, Substitution and Self-Assembly Reaction Under Hydrothermal Conditions Afforded the First Diiodopyridine Copper(I) Coordination Polymer,” Inorg. Chem. 41 (2002) 1339-41. Lu, J. Y. and A. M. Babb. “An Extremely Stable OpenFramework Metal-Organic Polymer With Expandable Structure and Selective Adsorption Capability,” Chem. Commun. 13 (2002): 1340-41.

Fig. 1. Non-perspective view of a section of the 2-D plane of the structure.

Figure 2. View of the 3-D open-framework linkages in complex 2. The “bending” part of the square-grid is differentiated from copper atoms dispersed throughout the model.

Lu, J. Y. and A. M. Babb. “An Unprecedented Interpenetrating Structure with Two Covalent-Bonded Open-Framework of Different Dimensionality,” Chem. Commun. (2001) 821-22. Lu, J. Y, C. Norman, K. A. Abboud, and A. Ison. “Crystal Engineering of An Inclusion Coordination Polymer with Cationic Pocket-Like Structure and Its Property to Form Metal-Organic Nanofibers,” Inorg. Chem. Commun. 4 (2001) 459-62. Lu, J. Y. and A. M. Babb. “The First Triple-Layer 2-D Coordination Polymer: [Cu3(bpen)(IN)6(H2O)2],” Inorg. Chem. 40 (2001): 3261-63. Lu, J. Y. and A. M. Babb. “Self-Assembly of Two-Dimensional Coordination Polymers with Rigid and Flexible Building Blocks,” Inorg. Chim. Acta 318 (2001) 186. Lu, J. Y., K. A. Runnels, and C. Norman. “A New MetalOrganic Polymer with Large Grid Acentric Structure Created by Unbalanced Inclusion Species and Its Electrospun Nanofibers,” Inorg. Chem. 40 (2001) 4516-18.


NASA photo of a solar eclipse, December 4, 2002, with the solar image taken in Ceduna, south Australia. Credit: NASA/Goddard Space Flight Center Scientific Visualization Studio. Apogee camera eclipse image by Jay Pasachoff, Bryce Babcock, Steven Souza, Daniel Seaton, Lisa Ong, and Jesse Dill. .


The Solar Eclipse of April 22, 1715, and Family Quarrels in Daniel Defoe’s The Family Instructor By Irving N. Rothman

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is exempt from the author’s view. Thus, is to interpret sociOn April 22, 1715, the Defoe, who draws upon ety’s mannerisms in population of England the knowledge of saila way that might urge readand Wales experienced a ers to reflect upon their own ing in Robinson Crusoe, solar eclipse for the first the machinations of a experience. In eighteenthtime in 500 years. The business woman seekcentury literature, the theoevent, described in advance ries of John Locke endorsed ing security in Moll by William Whiston and the primary importance of Flanders, and the ecoEdmond Halley, captured nomics of the slave individual experience.1 If, the imagination of the indeed, humans were born trade in Colonel Jack, nation. It was spread to a has the capability to with a clean slate, a tabula popular audience in the engage the latest scirasa, a lifetime of adventure new medium of the broador misadventure filled that ence. In the second volside, a one-page low-cost blank page with descriptions ume of The Family handout. The image of the of the paradoxical nature of Instructor, the newly moon as a dark object human conduct. Among the established science of hiding the splendor of the most successful realistic eclipses of the moon sun allowed Daniel Defoe novelists, Daniel Defoe provides a telling metain the second volume of mesmerized readers with the phor for the experiences Irving N. Rothman The Family Instructor experiences of a shipof one family’s dysfunc(1718) to draw an analowrecked sailor on a deserted tional behavior. gy between a rancorous wife, envisioned as the moon, and a island, in Robinson Crusoe frustrated husband, described as the sun. The wife’s angry Dramatic Narrative (1719), with the plight of a behavior eclipsed the husband’s expectation of a family willwoman born in Newgate At the beginning of the ing to submit to religious discipline. prison to a mother transportsecond volume of The ed to America, in Moll FlanFamily Instructor, Defoe describes a man of ders (1722), and with the success of an indentured servant who proved to his master that moral conduct whose discipline is undermined and who African natives treated kindly could improve the productivity of despairs of raising a family responsive to his beliefs and his a slave owner’s plantation, as narrated in Colonel Jack (1723). commands. His actions are, at the worst, eclipsed, by a termagant But before Robinson Crusoe and his other novels, Daniel wife who quarrels with him constantly and prevents family peace. Defoe provided English society with a conduct book that pref- Defoe tells us that the man is so frustrated by his wife’s actions that aced these great novels that have earned him lasting fame. In his he has thrown aside all reason and finds himself “conversing with conduct books, Daniel Defoe exposed conflict in family life and himself . . . without calling his Reason and Conscience of Duty to sought remedies for family dissension, arguments between hus- his Assistance” (p. 1). He laments the fact that neither his wife nor bands and wives, and the disobedience of children. In 1715, his children are paying attention to his demand for obedience or Defoe wrote The Family Instructor. The book was so popular demonstrating moral conduct: that in 1718 he issued a second volume, a sequel, providing additional stories about family disharmony. What can I do, says he, when a Woman is arriv’d to such a These conduct books, intended to answer political and social height as to make a Mock of me in my own Family? She has brought Things to such a pass, that I do not think it is conflicts, also had political ramifications in voicing opposition to my Duty to pray among them any more; she openly told the Schism Act (1714) which sought to empower the Anglican me, before my Children, that I need not give my self the Church and disenfranchise dissenting religions.2 The fictional nature of Defoe’s narratives sought to mask his political opposiTrouble to keep up the Ceremony; that they none of them tion to Queen Anne’s law, which was passed at the time of her value it; that they hate the Offering for the sake of the death and never actually took effect, finally being withdrawn in Priest; and that they care not to join with me . . . (2). 1718. To a writer, filling up the metaphorical blank page with real text on an actual printed page is a challenge. No experience That night he met his family, pretending to be little concerned NE AIM OF A WRITER


about his family’s intransigence. His wife ignored him after supper and, calling her “Maid to bring her a Candle . . . away she goes to Bed, taking no Notice of him, or of the usual FamilyOrder.” Thus, Defoe presents a situation where the husband ignores the wife and the wife ignores her husband, illustrating a family conflict that can only grow worse as it proceeds. Defoe explains the “Breach was now made, and every thing contributed to make it wider” (3). Defoe describes the growing animosity between husband and wife: “they were continually quarrelling, and falling out with one another; their Humours jostled in every Trifle, upbraiding one another’s Sincerity, Affection, Integrity, on every little Occasion; reproaching the least Miscarriage, reviling one another with Bitterness, and forgetting nothing that might tend to make them disagreeable to one another; peevish, waspish and fretful, even when they agreed best, and scandalously furious, and hot when they fell out” (4). One has only to read the daily newspapers reporting family conflict, abuse, separation, and divorce to understand that readers of the twenty-first century are not unfamiliar with the feelings expressed in Defoe’s era. The consequence of their argument led to confusion in the household as children and servants sided with one parent or the other, further contributing to the dissension of the household: Hardly any Discourse happen’d between them however mildly it began, but it ended in a Broil; she would thwart him in every thing he said, and he contradict her as often . . . that, it was impossible to preserve any Harmony among the Children; two of them, one Son and one Daughter, taking part with the Father; and another Son and two Daughters with the Mother; so that as the Father and Mother differed, the children differed, and that with such Heat, as to fill the House with Disorder (4). The conflict takes on momentum as a consequence of a solar eclipse that occurred on April 22, l715. Defoe explains that “the Eclipse of the Sun was the Subject of all Conversation at that time, having been, as is well known, so Total, and the Darkness so great, as that the like had not been known in that Age, or some hundreds of Years before” (5). When the wife asks her husband to explain the nature of an eclipse, he uses the opportunity to continue his tirade against his wife. Defoe has the husband explain “that the Moon was like a cross Wife, that when she was out of Humour, could Thwart and Eclipse her Husband whenever she pleased; and that if an ill Wife stood in the Way, the brightest Husband could not shine” (5). Readers who eagerly sought to learn details of solar eclipses were all the more willing to apply their new knowledge to an age-old problem, family conflict. The wife turns the debate upon her husband, complaining that he thinks wives gain their sparkle only if they acquiesce to their husbands and live in their husbands’ limelight. Defoe presents the story as a playwright with the wittiest dialogue: She flew in a Passion at this, and being of a sharp Wit, you do well, says she, to carry your Emblem to a suitable height; I warrant, you think a Wife, like the Moon, has no


light but what she borrows from her Husband, and that we can only shine by Reflection; it is necessary then you should know, she can Eclipse him when she pleases. Ay, ay, says the Husband, but you see when she does, she darkens the whole House, she can give no light without him. [Upon this she came closer to him.] Wife. I suppose you think you have been Eclips’d lately, we don’t see the House is the darker for it. Husband. That’s because of your own Darkness; I think the House has been much the darker. Wife. None of the Family are made sensible of it, we don’t miss your Light. Husb. It’s strange if they don’t, for I see no Light you give in the room of it. Wife. We are but as dark as we were before; for we were none of us the better for all your Hypocritical shining. Husb. Well, I have done shining, you see; the Darkness be at your Door. . . . Wife. At my Door! am I the Master of the Family! don’t lay your Sins to my Charge. Husb. No, no; but your own I may; It is the Retrograde Motion of the Moon that causes an Eclipse. Wife. Where all was dark before, there can be no Eclipse. Husb. Your Sin is, that my Light is your Darkness. (5-6) The father concludes his argument with political innuendo. He says, “If Half the Family, or any of the Family separate, it is a Schism in the House; and the Unity being broke, the rest is but private Worship, and may as well be done alone” (7). The reference here is to the Schism Act of l714 which forbade the Dissenters (Protestants separate from the Anglican church) from bringing a family instructor into their homes. Defoe sought to circumvent the law by bringing into peoples’ homes a book—not a forbidden human tutor or clergyman—that could render instruction to families.2 Thus, he sought to breach the conflict between the high church and the Dissenters, between Tory and Whig. April 22, 1715 Eclipse Defoe’s decision to bring the eclipse of April 22, 1715, into his narrative proved an astute move. His conduct book with its political implications offered an argument that sought to ameliorate religious conflict by addressing domestic problems. To impress his point, he introduced a scientific phenomenon that had captured the attention of the nation. Although his use of the eclipse in his story is satirical and ironic, his verbal ingenuity renders it an original metaphor for the psychology of human conduct. His facility with words—his clever wit and his ability to provide credible dialogue—turns the episode into a memorable study of family conflict. When he has the wife described like the moon hiding the transcendence of the sun, he shows the wife emasculating her husband. The husband who radiates light is prevented from doing so by the wife whose impiety keeps the family in the dark. The wife, of course, objects to the idea that women gain their strength, fortitude, knowledge, and perseverance only by virtue of their husband’s grace. The wife/moon and husband/sun metaphor does not hold up, of course, if one grants Locke’s premise that all can achieve understanding by the accumulation of knowledge through sensational apprehension and

500-YEAR ECLIPSE—Englishmen thought the world was coming to an end with the eclipse. In The Black-day, or, A prospect of doomsday, exemplified in the great and terrible eclipse, which will happen on Friday the 22d of April, 1715: . . . According to. . . Mr. Halley . . . and Mr. Whiston. London: J. Reed and R. Burleigh, [1715?].

the association of ideas. But the ill-tempered frustration of the husband and the rancorous nature of the wife fuel an argument enriched by the striking nature of the eclipse that had occurred three years earlier. Edward Halley and Daniel Defoe were contemporaries. Halley (1656-1742), who first determined how to predict eclipses, was born four years before Defoe (1660-1731) and lived eleven years after Defoe’s death. Defoe who read everything and followed reports of the Royal Society of London doubtlessly followed Halley’s career. A year before the eclipse of 1715, Halley had produced a paper showing how one could readily compute and thus predict the advent of the eclipses of the sun and moon.3 Halley drew from recent scientific developments. In 1605, Johann Kepler (1571-1630) had described the nature of the corona of the sun in an eclipse. Giovanni Domenico Cassini (1625-1712) attempted a more detailed description of the corona in 1706, but they both appeared to have thought that the corona was a lunar phenomenon lit by the sun behind it.4 That this interpretation does not enter Defoe’s description suggests Defoe’s sophisticated understanding of scientific data. In The Family Instructor, the wife responds in anger to her husband: “you think a Wife, like the Moon, has no light but what she borrows from her Husband.” Defoe might well have been a reader of detailed scientific studies, such as Newton’s study of optics (1664) when sunlight was defined by the separation of its colors in a prism.5 He does not grant to the moon a separate source of light. It represents darkness and blackness and, in the case of the wife, the moon anthropomorphizes into a dark vision with a black heart. Halley predicted “that in 1715 a total solar eclipse would sweep across southern England and Wales, the first time that London has been so-visited since 1140 (and 878 before that).”6 What affected religionists so markedly was a detailed map that Halley issued “entitled The Black Day” which offered “a prospect of Doomsday” and anticipated a “great and terrible eclipse which will happen on 22nd of April 1715.”7 Faced with the oppression of the government in the passage of the Schism Act, which was forced through Parliament by the will of Queen Anne, Dissenters might have felt the end was near. They could

not have known at the time of passage that Queen Anne’s death would essentially vitiate the intent of the Act. Apart from the domestic crisis in The Family Instructor, portending the doom of family unity, and with Dissenters facing penalties for violations of the Schism Act, the English also concerned themselves with apocalyptic change resulting from the end of the Stuart throne. With no heirs, Queen Anne (16651714) was the last of the Anglican Stuarts. Any number of Roman Catholic Stuarts could have ascended the throne had the English wanted to restore the throne to the descendants of the exiled James II (1633-1701), but they did not want a Roman Catholic ruler. Thus, the English throne reverted to the Austrian Hanovers. Jacobites who refused to accept the legitimacy of the Hanover court surely thought the world was coming to an end in the spring of 1715. The eclipse seemed a sign of impending doom.8 Halley contacted numerous colleagues who would be positioned as witnesses throughout Wales and southern England in a 138-mile swath at the width of the country to report the events of April 22.9 Halley also published a new document, estimated to have been published in March 1715, designed to provide an advanced description of the nature of the eclipse,10 entitled A Description of the Passage of the Shadow of the Moon over England, In the Total Eclipse of the SUN, on the 22d Day of April 1715 in the Morning.11 Apart from his actually being able to view the eclipse in London, Defoe had a number of broadsides available to him before the event, as had the general public, as well as Halley’s account of the event and reportage in the Philosophical Transactions of the Royal Society. Halley and the scientific world also had access to a wealth of information through data collected at the Greenwich Observatory which, however, never gained publication.12 One can imagine the trepidation Englishmen felt with the anticipation of doomsday occurrences threatening them and a series of broadsides flooding the market in a new venture to popularize and disseminate newsworthy events. The country had reached a state of hysteria. Broadsides, printed single-sheet documents, made text and illustrations available to the general public at low cost, the equivalent today of an internet web page. According to Walters, William Whiston (1667-1752) and the printer John Senex (1678-1740) “had pioneered the production of broadsides intended for the public presentation of astronomy.”13 Among broadsides that enticed the populous were William Whiston’s Scheme of the Solar System (1712), on sale for 2s 6d; Whiston’s Calculation of the Great Eclipse of the Sun (1715) at 6d; Edmond Halley’s Description of the Passage of the Shadow of the Moon over England (1715), 6d; Whiston’s Compleat Account of the Great Eclipse of the Sun (1715), 1s; and Halley’s Description of the Passage of the Shadow of the Moon (1715), 6d. Not until 1718 did Halley provide the general public a detailed report of the events of 1715 in An Exact Description of the Total and Visible Eclipse of the Moon, at 6d, although his full account appeared not in a broadside but in the Philosophical Transactions (1714-1716).14 In his narration of the wife’s acrimonious response, Defoe does not accord to the moon an independent light source. In fact, the “darkness” attributed to the moon serves inexorably to illustrate the wife’s moral decay, her iconoclastic vacuity, and the


darkness that informs her negative response to moral instruction. The wife tries to declare herself independent of her husband, but eighteenth-century society does not allow the division. She functions, as does the moon, with its diurnal cycle and its purposefulness in comprehending distinctions to be drawn between night and day, with the implicit understanding that the wife cannot divorce herself from duties required throughout the day and into the night. She serves to fulfill cyclical events. Feministic imagery allows interpretation comparing the monthly graduation of the moon’s growth with menstrual cycles. Paglia interprets this ontology of cyclic menstruation:15 Woman does not dream of transcendental or historical escape from natural cycle, since she is that cycle. Her sexual maturity means marriage to the moon, waxing and waning in lunar phases. Moon, month, menses: same word, same world. The ancients knew that woman is bound to nature’s calendar, an appointment she cannot refuse. . . She knows there is no free will, since she is not free. . . . Whether she desires motherhood or not, nature yokes her into the brute inflexible rhythm of procreative law. Menstrual cycle is an alarming clock that cannot be stopped until nature wills it. Indeed, mythology has granted the moon feminine qualities with Cynthia, the goddess of the moon, anticipating childbirth. The epithalamium, the classical poem celebrating marriage, features Cynthia at the beginning before the marriage anticipating the union of the couple and the subsequent celebration of new birth.16 Thus, in traditional literature, the moon has been linked to family. In Defoe’s The Family Instructor, where family is destroyed by wanton willfulness and obdurate behavior, the darkness of the moon, as representative of a miscreant wife, confirms the husband’s impression that his ideology—his ambition, his patriarchy, his faith, and his exemplary conduct—has been stifled and his light obscured.17 If the eighteenth-century population was terrorized by the prospects of the solar eclipse with its doomsday prediction, it also found terror in a hapless marriage. Endnotes 1 John Locke, An Essay Concerning Human Understanding. Collated and annotated by Alexander Campbell Fraser. 2 vols. New York: Dover Publications, Inc., 1894. 2 Irving N. Rothman, “Defoe’s The Family Instructor: A Response to the Schism Act,” PBSA 74 (1980): 212-20. 3 Duncan Steel, Eclipse: The Celestial Phenomenon That Changed the Course of History (Washington, D.C.: The Joseph Henry Press, 2001), 90. 4 Steel, 138; 5Steel, 139; 6Steel 166. 7 The Black-Day, or, a Prospect of Doomsday. Exemplified in the Great and Terrible Eclipse, which will happen on Friday the 22d of April 1715. . . . According to the most exact calculation by Mr. Halley . . . and Mr. Whiston. . . . London: Printed and sold by J. Read and R. Burleigh, 1715? 8 Alice N. Walters, “Ephemeral Events: English Broadsides of Early Eighteenth-Century Solar Eclipses,” Hist. Sci. 37 (1999): 11, fn. 22: Nicholas Rogers, “Popular Protest in Early


Hanoverian London,” Past and Present, no. 79 (1978): 70-100. 9 Steel, 167. 10 Walters, 39, fn.20. The document is dated April 10, 1715, in the Harvard Houghton copy, probably the date on which Nicholas Luttrell, collector of ephemera, purchased the piece (in Steel, 167). 12

Steel, 166. 13 Walters, 21. 14 Edmond Halley, “Observations of the Late Total Eclipse of the Sun on the 22d of April Last Past . . .,” Philosophical Transactions, 29 (1714-16): 245-62, in Walters, 4. 15 Camille Paglia, Sexual Personae: Art and Decadence from Nefertiti to Emily Dickinson. New York: Yale University Press, 1990. 10. 16 Edward O’Neil, “Cynthia and the Moon,” Classical Philology 53.1 (January 1958): 1-8. 17 See James A. S. McPeek, “The Major Sources of Spenser’s ‘Epithalamion,’” JEGP 35 (1936): 183-213; Robert Hope Case, English Epithalamia. London: Lane; Chicago: McClung, 1896; and Irving N. Rothman, “Fielding’s Comic Prose Epithalamium in Joseph Andrews: A Spenserian Imitation,” MLR 93.3 (1998): 609-28. Publication This study will be republished in the “Headnotes” of the definitive edition of The Famiily Instructor, ed. Irving N. Rothman, Stoke Newington Daniel Defoe Edn.; General. eds., Jim Springer Borck, Maximillian E. Novak, John G. Peters, and Manuel Schonhorn (N.Y.: AMS Press). Indebtedness is owed the UH Small Grant Program for support in studies of scientific literature of the eighteenth century in the summer 2006 at the Hubbard Collection, Univ. of Michigan, Special Collections, the Boston Public Library, and the Houghton Library, Harvard University. Funding “Scientific Sources of the Literary Imagination in the Long Eighteenth Century (1660-1830),” Small Grant Program, Office of Sponsored Programs, University of Houston, 2006, $3000. (Funded.) “Stylometric Study of Daniel Defoe’s Texts,” with Blake Whitaker, undergraduate researcher, Dr. Rakesh Verma, Professor of Computer Science, and Dr. Thomas M. Woodell, Associate Professor of Linguistics, the Martha Gano Houstoun Foundation, Department of English, Spring 2006, $1200. (Funded.) “Stylometric Study of Daniel Defoe’s Texts,” Provost’s Summer Undergraduate Research Fellowship, Blake Whitaker, junior, with their donation of computer and linguistic analysis, ” Dr. Rakesh Verma, Professor of Computer Science, and Dr. Thomas M. Woodell, Associate Professor of Linguistics, $2800. (Funded.) Textual Study of Variants in the Writings of Daniel Defoe, the Martha Gano Houstoun Foundation, Department of English, assistance provided by Karl Roppel, M.A. student and Ann V. Nunes, Ph.D., independent scholar, 2007, $1200. (Funded.)

Computational Methods in Non-Smooth Mechanics: Applications to Dry Friction Constrained Motions by LieJune Shiau

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OTIVATED BY THE NEED FOR REAL-TIME SIMULATION OF

elasto-dynamical systems with friction, researchers seek to mathematically analyze and numerically simulate the solution of non-smooth mechanical problems. Special attention is given to those differential equations and inequalities modeling1,2,3 elasto-dynamical systems with dryfriction. Thus, a family of numerical schemes with the existence of a friction multiplier is currently being analyzed and studied. This family of numerical schemes is subsequently engaged in solving the existence of the new friction multiplier as well as the solutions. Furthermore, with improved numerical computational techniques, higher dimensional problems can be simulated and resolved more efficiently.

ABSTRACT— NASA space science researchers need more sophisticated friction models and computational techniques. New models offer a better description of system behavior when velocities are close to zero. With improved numerical computational techniques, science can better solve higherdimensional problems.

Methodology We formulate the following friction constrained motion model to describe some remote manipulator system simulators with finite number of degree of freedom: LieJune Shiau

models by implementing more sophisticated friction models and computational techniques. In a higher degree-of-freedom case, the computational efficiency becomes an important issue. We then incorporate the penalty/Newton methodology developed in Dacorogna, et al. and Glowinski and his University of Houston colleagues to resolve this obstacle. We illustrate an example of the 3-D test problem, as follows:

Starting modestly, we initially modeled one-degree and twodegree-of-freedom generalized systems.4,5 Since higher degree models give a better prediction of the system behavior when velocities are near zero, we are then ready to move our focus to higher degree of freedom models. The methodology we successfully utilized in the study of one- or two-degree-of-freedom models is extended to the study of higher degree-of-freedom

(Equation continues on following page)


Our schemes are applied to this test problem including the improved penalty/Newton method studied. No more than four Newton’s iterations were required at each time-step, making this approach much faster than the previous algorithms without the improvement. Numerical results are shown in Figs. 1-3. Results Our motivation to investigate such problems is driven by two main factors: the applications of such problems and the computational methodology necessary to solve such problems. Presently, practitioners are limited to the use of existing inhouse software, which is fundamentally inadequate, to model and implement their simulation process. Hence, the proposed research will produce important results of interest to various government agencies, especially NASA. We have published results of a low degree of freedom. The current study resulted in the new publication of higher degree of freedom generalized test systems proposed by NASA engineers. These results are very promising.4,5,6,7 The development and analysis of higher number degrees of freedom models, typically allowing 10 to 20 degrees of freedom, and a subsequent evolution to beam-based flexible systems (some ODEs become PDEs) will undoubtedly be of more significance and benefit to NASA’s needs and practices. Therefore it is essential to ensure that the rate of convergence on the multiplier is efficient; it is the main focus of the future study. In the future, we will also investigate theoretically the extension of the method in the first step to the simulation of visco-plastic particulate flow encountered in oil drilling technologies. The computer implementation of the methods resulting from these investigations will be part of another project. Among consideration in the difficulty of these problems is the solution of 3-dimensional non-smooth generalizations of the Navier-Stokes equations.


References 1 E. J. Dean, R. Glowinski, Y. M. Kuo, and G. Nasser, “Multiplier Techniques for Some Dynamical System with Dry Friction,” C. R. Acad. Sc., Paris, T. 314, Série I (1992): 153-59. 2 E. J. Dean, R. Glowinski, Y. M. Kuo, and G. Nasser, “On the Discretization of Some Second Order in Time Differential Equations—Applications to Nonlinear Wave Problems, in Computational Techniques,” in Identification and Control of Flexible Flight Structures. Ed. A.V. Balakrisknan. Los Angeles: Optimization Software, Inc., 1990. 199-246. 3 G. Duvaut, J.-L. Lions, Inequalities in Mechanics and Physics. Berlin: Springer-Verlag, 1976. 4 R. Glowinski, L. J. Shiau, Y .M. Kuo, and G. Nasser, “The Numerical Simulation of Friction Constrained Motions (I): One Degree of Freedom Models,” Appl. Mathematics Lett. 17.7 (2004): 801-07. 5 R. Glowinski, L. J. Shiau, Y. M. Kuo, and G. Nasser, “On the Numerical Simulation of Friction Constrained Motions(II): Multiple Degrees of Freedom Models,” Appl. Mathematics Lett. 18.10 (2005): 1108-15. 6 L. J. Shiau and R. Glowinski, “Operator Splitting Method for Friction Constrained Dynamical Systems,” AIMS Proceedings (2005) 806-15. 7 R. Glowinski, L. J. Shiau, Y. M. Kuo, and G. Nasser, “On the Numerical Simulation of Friction Constrained Motions,” Nonlinearity 19 (2006): 195-216. 8 B. Dacorogna, R. Glowinski, Y. Kuznetsov, and T .W. Pan, “On a Conjugate Gradient/Newton/Penalty Method for the Solution of Obstacle Problem: Application to the Solution of an Eikonal System with Dirichlet Boundary Conditions,” in Conjugate Gradient Algorithms and Finite Element Methods. Ed. M. Kvrivzek, P. Neittaanmaki, R. Glowinski, and S. Korotov. Berlin: Springer, (2004): 263-83. 9 R. Glowinski, Y. Kuznetsov, and T. W. Pan, “On a Penalty/ Newton/Conjugate Gradient Method for the Solution of Obstacle Problems,” C.R. Acad. Sci. Paris, Série I 336.5 (2003): 435-40. Publications Glowinski, R., L.J. Shiau, Y.M. Kuo, G. Nasser, “On the Numerical Simulation of Friction Constrained Motions,” Nonlinearity 19 (2006): 195-216. Presentations Glowinski, R., L. J. Shiau, “Operator Splitting Method for Friction Constrained Dynamical Systems,” AIMS Conference, Poitier, France, June 2006. Proposals Shiau, L. J. (P.I.) and R. Glowinski (CO-PI), “Computational Methods in Non-Smooth Mechanics: Application to Dry Friction Constrained Motions,” ARP 2005. (Unfunded.)

SHELVING—Scientific periodicals in the University library.

Figure 1.Left, the computed x1(t); middle, the computed x2(t); right, the computed x3(t)

Figure 2.Left, the computed v1(t); middle, the computed v2(t); right, the computed v3(t)

Figure 3. (Left) the computed λ1(t); (middle) the computed λ2(t); (right) the computed λ3(t).


Efficient Space Radiation Computation with Parallel FPGA by Liwen Shih

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ASA HAS, ACCORDING TO RECENT MISSION OBJECTIVES, developed several long-range goals for human exploration of space, including missions to the moon and Mars in the near future. In addition, the deep space environment and the long-term duration of spaceflight require a thorough understanding of all hazards and dangers that both astronauts and spacecraft materials will encounter over such missions. Space radiation is among the foremost dangers of such missions. As such, Space Radiation Modeling is of paramount concern to NASA design engineers, scientists, and mission planners when considering and estimating radiation dosage to both human beings and spacecraft materials. Space radiation consists of galactic cosmic rays, solar particle events, trapped radiation, and ions over a wide energy range. These ions penetrate Figure 1. HZE particles cause spacecraft materials producing more harm to DNA in living nuclear fragments and second- tissue than X-rays. ary particles that damage materials, tissue, and electronics. See Fig. 1. Among the various deep space particles, GCR particles modeled by HZETRN code are the most dangerous forms of known space radiation based on their relative biological effectiveness (RBE), an index of radiation dosage as it affects biological tissue. In order to simulate the dosage effects of these High Charge and Energy Particles (HZE) NASA Langley Research Center (LaRC) scientists have created nuclear transport software to model these particles. This code is identified by its nomenclature, the High Charge and Energy Transport Code (HZETRN). It was developed in the early 1990s to provide dosage parameters to design engineers. HZETRN was written in FORTRAN-77 for a VAX 4000 Mainframe platform. NASA LaRC made the source code available to UHCL in April 2005 hoping for urgently needed modernization and improvement in performance.

models the dosage of these particles using deterministic models (as opposed to stochastic models such as the Monte Carlo method used in FLUKA code). A fundamental summary of HZETRN has been provided by the physicists who developed the code as follows: HZETRN is high charge and energy transport code. This code calculates particle transport deterministically using approximate solutions to the Bolztmann transport equation. It is much faster than Monte Carlo codes and can be used to calculate the transport of the heavy ions found in the GCR as well as light ions and neutrons. The current version of HZETRN uses a straight-ahead approximation and models the 3-dimensional nature of radiation transport by calculating the transport along rays from a large number of different directions and averaging the fluencies.1 The fundamental numerical algorithm used by HZETRN is a version of the time-independent Bolztmann Nuclear Transport Equation, which describes neutral and charged particle transport:

HZETRN Theory A typical high-energy particle of radiation found in the space environment is ionized itself. As it passes through material such as human tissue, it disrupts the electronic clouds of the constituent molecules and leaves a path of ionization in its wake. These particles are either singly charged protons or more highly charged nuclei called “HZE” particles. HZETRN

Although Monte Carlo simulation universally is viewed as the most accurate method for solving complex three-dimensional radiation transport problems, deterministic methods such as


Liwen Shih

ABSTRACT—Space radiation is likely to be the ultimate limiting factor for future deep space exploration by humans. NASA’s Radiation Dosage/Flux Software HZETRN is currently used to simulate highenergy nuclear transport across all materials being tested for a space mission. We are currently collaborating with NASA LaRC to establish an SAA to modernize and optimize radiation analysis.

Figure 3. MARIE (gray spikes) vs. HZETRN (black curve) Data Figure 2. HZETRN Algorithm and Program Structure

HZETRN offer a faster alternative to Monte Carlo simulation. They often provide an accurate enough solution for engineering decisions or provide a ‘benchmark’ comparison. HZETRN Algorithm and Program Structure The HZETRN numerical algorithm involves interpolation, integration and extrapolation with the program controlling truncation and propagation errors. Flux and dosimetric results are output for six charge groups of HZE particles ranging from (Z = 0, 1,2, 3-10, 11-20 and 21-28). In addition, dose equivalent is also calculated for tissue material (which is approximated using water, since biological tissue is 80 percent water). HZETRN code was developed in 1992 as a combination of previous nuclear transport codes by physicists at NASALangley and was written in FORTRAN-77 for the VAX platform. As such, it contains numerous inefficiencies in coding that increase the run time of the code and decrease performance. Optimization of HZETRN code can have direct benefits in space radiation research. For example, HZETRN code is a major part of the MARIE (Martian Atmosphere Radiation Experiment) carried on the 2001 Mars Odyssey spacecraft. Current results indicate that HZETRN underestimates dosage data partly because of code inefficiency. Methodology: High-performance/ Parallel HZETRN Code Optimization Before the HZETRN source was available to UHCL for analysis in Spring 2005, HZETRN methodology was studied in search of run-time bottlenecks and code optimization possibilities. In particular, after communicating with scientists responsible for HZETRN development, we identified the numerical algorithms for interpolation and integration as being the optimal candidates for runtime bottlenecks, where integration also calls the interpolation routine. FPGA based numerical methods prototypes were developed for research into adapting the HZETRN numerical ker-

nel onto an FPGA based computer, which showed an increased speed of up to 325 to 600 times for the bottleneck routines. In April 2005, UHCL researchers were given approval to access the HZETRN1995 source code by NASA LaRC and were thus able to begin in-depth analysis of the code and undertake actual code optimization. Steps toward Efficient Parallelization of HZETRN Code The ultimate goal of our research involves speeding-up the runtime of the HZETRN code by parallelization of the code and by running it on a distributed computing environment However, this process of parallelizing legacy code requires a number of intermediate steps: first, determining the static code structure, next evaluating runtime bottlenecks and inefficiencies/redundancies, then cleaning up the original code to prepare it for translation to a parallel environment, and, finally, conducting serial optimizations so that the code runs well even on a single processor. HZETRN, being written in FORTRAN-77, which is an outdated version of the FORTRAN, is not by itself directly suited to high-performance optimization: 1. Algorithm review (not well documented). 2. Analysis of source code and data files (Data files contain sparse matrices amenable to performance improvement). 3. Portability study (not portable to modern platforms even though it was designed to be platform-independent). 4. Static analysis (We generated a detailed HTML report documenting HZETRN source code functions and structure of subroutine calls). 5. Runtime analysis (Analysis revealed that the PHI interpolation function is the major bottleneck function. The natural logarithm intrinsic function is also a performance issue). 6. Serial optimization of code (FPGA to implement core routines in one instruction cycle). 7. Parallel optimization of code (Parallel FPGA and/or Cluster/Grid Computing needed).


High-Performance Intrinsic Math Library (instead of standard math functions) HZETRN code performance was evaluated using an Intel 9.0 FORTRAN complier on an Intel Pentium platform. Since HZETRN functions make an extremely large number of intrinsic function calls (with the natural log being the major math function called), we considered using high performance versions of these intrinsic math functions. For example, there are substantial performance advantages over scalar implementations with Intel® MKL 8.0 VML (Vector Math Library) functions that operate on real vector arguments versus LibM functions on Pentium 4. For example Exp and Log10 can be improved from ~90 to ~30 CPE, where Clocks Per Element (CPE) is the number of clock cycles that are required to execute a single element of the vector.2

Figure 4. HZETRN Runtime Profile Analysis

Figure 5. Algorithm-Specific FPGA

HZETRN Runtime Analysis We examined the runtime performance of the standard HZETRN code. Statistics included average runtime and most called functions. Not surprisingly, analysis confirmed our previous study even before we received the source code, that interpolation and intrinsic math function calls consumed most of HZETRN runtime. Function Bottlenecks: The PHI Interpolation Function More than 70 percent of runtime is devoted to three functions with the PHI function taking up most of the runtime (approximately 34.5 percent time spent in calls to this interpolation function). Therefore, we determined that the PHI interpolation function was the most attractive target to aim for in code optimization. Starting with the PHI function, we removed extraneous function calls, cleaned up “messy code,” SAVE statements, and evaluated the use of faster intrinsic functions for expf and logf to replace the archaic ALOG function called in HZETRN. The effort resulted in a 10 percent overall increase in runtime performance improvement.


HPC Technology The performance profile of HZETRN code determined that 34.5 percent of the run time spent on the PHI/interpolation function confirms previous results. There is much inefficiency and redundancy in the code itself. By cleaning up minor programs, we obtained an overal speedup of about 10 percent. Much more can be improved if the PHI Function is updated. The current running environment (requiring changing parameters in the code, recompiling, then running again) is not user friendly. Next, we continue to explore parallel FPGA and parallel grid/clusters to improve the critical portion of the computation. NASA LaRC can arrange to provide Parallel FPGA hypercomputers for our study. Parallel FPGA – Hypercomputing (supercomputing in a box): Xilinx’s radiation tolerant FPGAs are playing a critical role in the successful NASA/JPL Mars exploration mission for the Spirit Rover and the Opportunity MER rover. Cray XD1™ supercomputers will support the latest generation of Xilinx® Virtex-4 FPGAs, including the Virtex™-4 LX and SX platforms. The Starbridge Hypercomputer uses high-end Xilinx Virtex-II FPGAs, each containing more than six million gates. Various Hypercomputer configurations comprise between 7 and 22 Virtex-II FPGAs, providing from 36 million gates to 124 million gates, that can be employed simultaneously to implement massively parallel computational pipelines for powerful algorithm execution. NASA – Scientists at NASA’s Langley Research Center use a Starbridge Hypercomputer for projects that push traditional computational boundaries, including radiation analyses, digital signal processing, and atmospheric studies. NASA nuclear physics engineers need our computer engineering expertise to help them apply these powerful emerging technologies effectively. LaRC has indicated the possibility of providing UHCL with a hypercomputer HC-38 with 10 Virtex-II FPGAs (60 million gates). Parallel Clusters: Texas Learning & Computational Center (TLC2) The computational resources of the Advanced Computing Laboratory at the UH Central Campus is considered the “flag-

ship” of the Texas Learning & Computational Center (TLC2). Three computer clusters are available: Two have Itanium2 CPUs as the workhorses (the Atlantis and Eldorado clusters); and the computational power of the third, the small Medusa cluster, utilizes the Opteron CPUs. The Atlantis and Eldorado feature distributed memory architecture with 4 GB of memory per node. With the Itanium2’s excellent floating point and good integer performance and a relatively fast network interconnect, the Atlantis/Eldora- Figure 6. (l.) Atlantis Cluster (Gimli), (r.) Medusa at TLC2 do systems are suitable for almost any kind of scientific computing that can be efficiently parallelized/partitioned on a Linux cluster. for easier navigation of the source code. We also tried The Atlantis/Eldorado clusters can be “clustered” together also to organize the source in HTML and spreadsheet forinto one, resulting in 445 CPUs. Perhaps their only limitation for mats. (HZETRN2005 is trying to make the code betthis sized cluster is the lack of a high-speed file system such as a ter modularized.) GPFS/Lustre/PVFS file system. 5. Need better user interface: A parameter change is The third cluster, Medusa, is a 21-node Opteron cluster that is required in the source code to recompile between partially owned by the Advanced Computing Research runs. (NASA is also fixing this problem now.) Laboratory and the Texas Learning and Computation Center. The small size of the Medusa cluster does not allow its use for Spring 2006:After this detailed performance profiling and jobs that require a large number of nodes, but the Opteron CPUs diagnosis of the HZETRN, we started to attack these bottledo well at both integer and floating point calculations. The necks by approaching the treatment of both top-down parallel Medusa Cluster would be effective for a problem that might be grid computing among the particles tracking and bottom-up latency-sensitive and/or bandwidth-intensive, but does not FPGA in time-consuming routines. Our UHCL HPC team conrequire a large amount of CPUs. A job that the user might continues to meet weekly to analyze the HZETRN code for sider to be I/O bound may do well on Medusa, while using par- improvement. A spreadsheet to categorize all routines is mainallel I/O like MPI I/O or similar. tained. Large flow charts were generated by software analysis tools for inspection. Preliminary Result – Parallel Space Radiation Summer 2006: Our UHCL HPC team used the parallel comSpace radiation work at UHCL so far is summarized: puter clusters to run the HZETRN in parallel. OpenMP was used first and MPI has just been started. A study of the more accurate 2004:Performed general space radiation problem study and but time consuming FLUKA Monte Carlos method was also made connection with LaRC researchers. performed during the summer. Spring 2005: FPGA prototype achieved up to 600 times speed Fall 2006: The FPGA developed in the spring of 2005 was up on HZETRN bottleneck routines. Obtained HZETRN1995 specially designed for a reduced 8-bit floating point format to source code in 4/2005. accommodate the limitation of pins. A general purposed IEEEFall 2005: HZETRN portability, performance profile study: 754 32-bit Floating Point Core has been designed and specified 1. HZETRN is not portable, most encounter syntax error in VHDL (VHSIC Hardware Description Language). It is sysin PHTOD routine. tematically designed to scale to future needs. It will be further 2 HZETRN Performance Profile: Bottleneck routines tested and implemented on FPGA hardware. Eventually it will are PHI, then logf, then expf. (All three routines take be extended to perform the bottleneck function of interpolation. up ~70 percent of HZETRN run time). During the FPGA redesign an error in the 2005 VHDL was 2a.Hand optimized PHI function (10 percent speedup in found and corrected, where two variables were mistakenly HZETRN run time). swapped. 2b.logf and expf: Table lookup did not help memory In other words, the HPC team at UHCL has completed most of time increase. the HZETRN “diagnosis” and has begun the parallel moderniza3. Opportunities available for sparse data matrix techtion “treatment” of the code. Support for this effort is still greatly niques and HZETRN application-specific limited needed to demonstrate this effort. To conduct syntax code thread data value range. analysis, we need to perform data flow analysis either from the 4. Need modulization: We tried to modularize the code code or algorithm design. To further optimize parallel mapping


and semantic application-, methodology- and algorithm-specific thread mapping optimization, a better understanding of the numerical models of nuclear physics theory is needed. Help is being sought from LaRC nuclear physics researchers. Discussion Since the performance profile revealed bottleneck routines such as PHI, we can try to model/simulate/estimate how much speedup can be achieved for various ways of improvement and determine the most promising direction for research: • Replace PHI and other bottleneck routine with FPGA or updated algorithms/data-structure/operations. • Produce data-flow and control flow charts of HZETRN. • Perform data-flow/thread analysis to determine the best mapping (data/function partition) from HZETRN to either cluster, grid, parallel FPGA (Viva/Hypercomputing) or VHDL/Xlinx ML-310 with bottleneck code on FPGA and non-bottleneck code compiled to the built-in power-PC core on FPGA. If we work more closely with NASA nuclear physics scientists to help us better understand the physics/math application of the radiation model, we can further improve the algorithm, data structure, and code design. If the application-specific data range were known, we could replace some complex computations with simple tables (while controlling memory access time increase), or we could replace current methodology with faster equivalent calculation for the hardware. The mode of execution can be improved also, such as conducting a multiple run in one or by reusing partial results from a previous run. If we can better understand the radiation model, we can monitor/deduce the cumulative computation errors to improve the precision. The current model predicting accuracy is low, and three days of data may require up to a day of CPU time to analyze. When the speed is improved, we might be able to improve the data size, resolution, to expand beyond straight-ahead simplification for better accuracy. Conclusions NASA LaRC is currently working on establishing a Space Act Agreement (SAA) between NASA and UHCL for a long-term collaboration to enable computer engineers to work with NASA nuclear scientists and engineers to modernize computer application and optimize space radiation computation. The SAA has been reviewed by UH System general counsel and is currently been revised at NASA Langley. After SAA is signed, we expect to gain access to the newest HZETRN2005 code for optimization within two weeks. An essential step toward a more efficient and cost effective solution to the radiation-shielding problem is the development of accurate, efficient and fast tools for modeling radiation transport. We hope that HZETRN code improvement can benefit design and engineering of lighter and more cost-effective shielding material for use in NASA spacecraft. As earth’s ozone depletion continues, space radiation study


could lead to dual-use countermeasures that will, in turn, protect human health from radiation/aging effect in general, e.g., slowing down cataract development. Other evolving critical medical technology, e.g., proton cancer radiation treatment, is being realized for its cures. Personnel Computer Engineering Professor Liwen Shih specialized in optimizing computation-machine matching with AI and parallel techniques. Dr. Shih regularly teaches High-Performance Computer Architecture, Machine Intelligence, and Parallel Processing. Uniquely innovated approaches in knowledge delivery often result in full enrollment despite the national downtrend in computer science majors. Dr. Shih has supervised all or most of UHCL’s recent computer engineering master’s capstone research projects. The recent emphasis in critical medical applications has resulted in several presentations in the worldwide forum. Dr. Shih and students successfully improved the performance of scientific/image modeling, including the speedup of Medical Image Texture Analysis from eight days CPU time on VAX per image to within 10 seconds on a PC platform (70,000 times speedup). Dr. Shih and students are very enthusiastic in applying the high-performance computing expertise to participate in the great space expedition to the moon and Mars. Acknowledgments NASA LaRC researcher Dr. Robert Singleterry Jr. and the NASA JSC MARIE Team (Dr. Premkumar Saganti of Lockheed-Martin and physics professor at Prairie View A&M) worked with us to understand the space radiation modeling and analysis. NASA LaRC will provide UHCL researchers the parallel FPGA Hypercomputer STARBRIDGE HC-38 with the VIVA software. The School of SCE at UHCL provides faculty and students space and computer needs, including the Athena TxGrid Texas Education Grid and FPGA lab. Dr. Shih and students/associates have access to labs and clusters/grids at such resources as the Texas Education Grid, UH TLC2, UT ACC, etc. References Singleterry, R. C. et al. Physica Medica Vol. XVII, Suppl. 1: 90-93; 2001. M. S. Clowdsley et al. NASA TP-2000-209856, 2000. [MARIE 05] “Martian Radiation Environment Experiment” MARIE, Oct. 27, 2003, NASA-JSC, March 7, 2005 . “Hypercomputer Parallel FPGA with VIVA Graphic Programming” “Starbridge Hypercomputers Complement Linux Clusters” Xilinx ML410 Embedded kit with Power PC core Advance Computing Laboratory at Texas Learning & Computational Center (TLC2)

Shih, L., T. Gilbert, A. Kadari and S. Kodali, “HighPerformance Martian Space Radiation Mapping,” NASA/UHCL/UH-ISSO Y2004 annual report, Spring 2005, PP. 145-149. Shih, L,, S. J. Larrondo, K. Katikaneni, A. Khan, T. Gilbert, S. Kodali, and ., Kadari, “High-Performance Martian Space Radiation Mapping” NASA/UHCL/UH-ISSO Y2005 annual report, Spring 2006, pp. 121-122 Wilson, J. W., F. F. Badavi, F. A. Cucinotta, J. L. Shinn, G. D. Badhwar, R. Silberberg, C. H. Tsao, L. W. Townsend, and R. K. Tripathi, “HZETRN: Description of a Free-Space Ion and Nucleon Transport and Shielding Computer Program,” Publications & Presentations Gilbert, T. and L. Shih. “High-Performance Martian Space Radiation Mapping,” Proc. Computer Application Conference, IEEE/ACM/UHCL 2005 Johnson, A. (supervised by Liwen Shih). “32-bit IEEE Compliant Floating Point FPGA Core Design,” UHCL Master Capstone Project Report & Presentation, Fall 2006. Kadari, A., S. Kodali, T. Gilbert and L. Shih. “HighPerformance Space Radiation Analysis with FPGA,” Proc. Computer Application Conference, IEEE/ACM/UHCL 2005 Kodali, S., A. Kadari, T. Gilbert, and L. Shih. “Space Radiation Analysis with FPGA” UHCL Master Capstone Project Report and Website, Spring 2005 . Larrondo, S. and A. Johnson (supervised by Liwen Shih). “Space Radiation HZETRN Architecture and FPGA System Selection via Weighted Scores,” UHCL Parallel Processing Project Report & Presentation, Fall 2006. Shum, V., S. Strasser and R. Chua (supervised by Liwen Shih). “Space Radiation HZETRN on Parallel Cluster,” UHCL Parallel Processing Project Report & Presentation, Spring 2005.

FLEXIBILITY—Researchers seek to mathematically analyze and numerically simulate the solution of non-smooth mechanical problems seeking higher levels of freedom. With Dr. Shih are Romeo Chua from the Phillipines (l.), M.S. student in software engineering, and Victor Shum from Hong Kong, Ph.D. student in aerospace engineering system assembly, with the ARES Corp.

Funding Shih, L., R. Singleterry, Jr. “Starbridge HC-38 (Viva FPGA machine)” and “HZETRN2005 (the newest version of NASA Space Radiation code)” – an on-going Space Act Agreement (SAA) between NASA-Langley and UHCL (Shih) to analyze/improve NASA’s HZETRN2005 code that utilizes the newer computational devices. (in progress, currently being reviewed/revised by UH/NASA) Shih, L. “Parallel Space Radiation Computation with Cluster and FPGA,” NASA Langley Contract Statement of Work, Jan. 1–May 31, 2007, $15,000 (submitted). Shih, L., “Efficient Space Radiation Computation with Parallel FPGA” ISSO Mini-Grant 2006, $16,950 Shih, L., “Partitioning Space Radiation Analysis/Simulation Code for High-Performance Execution with Parallel Computing Techniques,” granted support for student RA, UHCL Faculty Research and Support Fund, June–December


Fault-Tolerant Control of a Truss Structure Using MR Dampers by Gangbing Song and Linsheng Huo

T

RUSS-TYPE STRUCTURES ARE OFTEN USED IN

space applications. These structures can support interferometer, antenna, and other vibration-sensitive instrumentation. Launch constraints mandate these truss structures be lightweight. The combination of large and lightweight design results in these space structures being flexible and having low-frequency fundamental modes. These modes might be excited in a variety of tasks such as slewing, pointing maneuvers, and docking with other spacecraft. The induced vibration must be effectively suppressed to satisfy stringent requirements for attitude control and vibration sensitive missions, such as space-based interferometer. Various active vibration suppression strategies have been proposed in the past to suppress vibration of the truss structures. One semi-active device Gangbing Song Linsheng Huo that appears to be particularly promising for truss applications is the Magneto-Rheological ABSTRACT—In recent years, Magneto-Rheological (MR) dampers (MR) damper. have been used for structural control. This research presents a new MR dampers have been developed in recent years as semi-active vibration devices.1, 2, 3 For approach to vibration control of a space truss structure using MR their operating fluid, they use a Magnetodampers with system faults. The new approach uses an H∞-based Fault Rheological fluid, a material which responds Detection and Isolation (FDI) algorithm to identify the faults and an H∞ to applied magnetic fields. MR fluids alter -based Fault Tolerant Controller (FTC) to achieve satisfactory vibratheir viscosity according to the applied magtion suppression in the presence of the faults. Simulation results of the netic field and exhibit nonlinear properties proposed FDI algorithm and FTC controller shows its effectiveness for like a typical Bingham fluid. In MR dampers, vibration suppression of a faulty truss for the faulty system. electromagnets are used to generate the required magnetic field. The force generated in the MR damper is therefore controlled by adjusting the and performance. Consequently, fault detection and isolation electric current supplied to the electromagnets.4 The advan- (FDI) and fault tolerant control (FTC) problems have received tage of this adaptive-passive system lies in its fail-safe considerable attention in the control systems literature.5 Recently developed analytical redundancy techniques use design. Unlike the active control, which requires active energy for vibration suppression, this MR fluid design will utilize the residue signals to monitor the health of systems. The term residue is defined as a signal that is zero when the system its passive damping properties in the event of energy loss. Fault tolerant schemes in engineering systems provide early functions properly and nonzero when some abnormal behavwarnings of faulty sensors, actuators, or system components. In ior is observed. This residual signal indicates the faulty inforthis research, a “component fault” refers to a change in the oper- mation in the system; it can be used not only for fault detecating behavior of a component such that the new behavior dif- tion, but also for fault identification. Furthermore, it provides fers significantly from what is defined as normal behavior for basic information for the fault tolerant control purpose of use. that component. Common examples of such faults include bias It is a natural way to cope with the FTC problem thereby errors in the output of a sensing device and loss of function for employing the fault diagnosis information online. There are several approaches to generating the residual sigan actuating device. Health monitoring systems are needed to provide early alarm nals and building the FTC scheme, such as the unknown input notification of faults before they lead to catastrophic failure, so observer, the H∞ method, the Kalman filter, and the H2/LQG that remedial actions can be carried out to retain system stability techniques.6 Among these approaches, H∞ optimization-based


Figure 1. Block Diagram of the H∞ Fault Detection Filter

Figure 2. Block Diagram of the Proposed FTC.8

methods have attracted much attention by their explicit address of robustness issues. In this work, an H∞ FDI filter is developed based on the system identification model of the truss. The main design goal of this FDI filter is to detect and identify sensors failure in the truss structure system. The linear matrix inequality formulation of the FDI H∞ filter is obtained based on the famous bounded real lemma.7 Researchers propose an FTC H∞ control scheme that successfully retains the vibration suppression level when the sensors on the truss partially fails.

input and the error of the fault estimation. Similarly, the problem raised in γ-suboptimal H∞ FDI filtering is to find, if there exists, a filter, F, such that , where γ is a given positive scalar. Using the linear fractional transformation (LFT), the space state realization of the transfer function (or transfer matrix) Tωe (see the black square in Fig. 1) can be obtained as

Methodology Consider the following state-space realization for a plant P given by

(4) ,

(1) , where where xp is the state vector, u is the control input, d is the disturbance input, f is the fault input, yp is the system output, and Ap, Bp, Ep, Fp, Cp, Dp, Gp and Hp are real matrices of appropriate dimensions. Suppose F is the unknown filter to be determined and has the following state-space representation,

and

(2) ,

where xf is the filter state vector, u is the control input, r is the output vector and Af, Bf, Ef, Cf, Df, and Hf are real matrices of appropriate dimensions. Define the generalized disturbance, ωT=[u, d, f]T, and estimation error, e= r -f, as shown in Fig. 1. The problem with the H∞ optimal filter is to find a dynamic filter to minimize the worst case estimation error energy over the energy of bounded generalized disturbance. That is,

Thus, the optimal or γ-suboptimal H∞ FDI filtering problem can be formulated as the standard H∞ control problem and then solved by the linear matrix inequality (LMI) approach. It is well known that the solution to the H∞ control problem is a powerful tool in solving the disturbance attenuation problem. The H∞ optimal fault tolerant control design requires a dynamic controller, C, to minimize the worst case performance output energy over the energy of bounded generalized disturbance, . That is,

(3)

(5)

The expression (3) is equivalent to minimizing the H∞ norm of the transfer function Tωe between the generalized disturbance

The control strategy of the H∞ control FTC controller is shown in Fig.2.

.


Figure 3. 8-Bay Truss at Rice University

Figure 4. Finite Element Model of the Truss

Fault-Tolerant Control of a Truss Structure The truss used in this research is located at Rice University as shown in Fig. 3. This 8-bay, planar aluminum truss structure consists of 109 rod elements connected at 36 nodes. The total length of the truss is 4m with each bay 0.5m long, and with road elements having a Young’s modulus of E=7.58 x 107 N/m2. All the members are 0.1 in. thick hollow tubes with an outer diameter of 0.5 in. The truss can be simplified as a finite element model with 36 nodes and 109 members as shown in Fig. 4. This truss has an electromechanical shaker mounted for excitation at node 4. Four accelerometers are mounted for monitoring of vibrations on the truss at node 1, 9, 13 and 17. A Magneto-Rheological (MR) damper is installed between node 32 and 36 to reduce the vibration of the truss. Determining the transfer function using the mathematical modeling and finite element analysis is complex. The finite element models sometimes are not feasible for control purposes because their orders are too high to achieve the desired accuracy. However, the system identification technique based on experimentation offers a rather simplistic approach to obtain the transfer function of the system. Input and output signals from the system are analyzed in order to obtain a model. In this work, the system identification algorithm used to identify the system is based on the Subspace method. A linear system can be represented in the state space innovations form as

formed as linear combinations of the k step ahead of predicted outputs. The predictor, in this method, can be determined using the k step ahead of predictors by projections from the observed data sequences. The above model derived from the subspace method is then used as a base model for further refining the model by the prediction error method (PEM). In the time domain, the above system can be represented by using the shift operator q as (7)

where G(q) is the transfer function of the system, e(t) is the innovation, and I is the identity matrix. From the observed data of input, u, and output, y, the prediction errors can be computed as .

(8)

The above error can now be parameterized by the state space matrices derived by the subspace method. The common parametric identification method is to determine estimates of G and H by minimizing .

(9)

(6) , i.e., where e(t) is the innovation (i.e., the part of the output that cannot be predicted from the past data), x(t) is the state vector, y(t) is output, u(t) is the input and K is the Kalman gain. The subspace method can be used to estimate the A, B, C, D and K matrices. Assuming that x(t), y(t) , and u(t) are known, equation (6) becomes a linear regression. This will enable us to estimate the matrices C and D by the least square method and will lead us to determine e(t). Again, e(t) can be treated as a known signal, and this will lead to the determination of A, B and K using the least squares method. The Kalman gain K is computed using the Riccati equation. In the above method, initially it is assumed that states x(t) are known, but they need to be determined. The states x(t) can be


This algorithm forms the basis for the prediction error method. The model is first initialized and further adjusted by optimizing the prediction error fit. Substantial details for system identification can be found in the MATLAB reference manual. MATLAB has the System Identification toolbox to perform the above algorithm. The prediction error method first initializes the model by using the subspace algorithm and then minimizes the prediction error. In this research, a state space realization that does not model the noise properties (i.e., an output error model, K = 0), is considered. Thus, the implications will be derived from the predictors which will be based only on the past inputs. Using the truss structure discussed above, the shaker is excited at node 4 by a sweep sine signal of frequency ranging

Figure 5. Fault ID in Sensor 1








from 5 Hz to 20 Hz for 100 seconds. Using the MATLAB System Identification toolbox, we obtain a state space model of second order. The validation results of the identified models from the shaker to sensors are with the fit of 88.44%, 87.83%, 87.49% and 87.16%, respectively. Similarly, the validation results of the identified models from the controllers to sensors are with the fit of 88.09%, 89.45%, 90.55% and 92.21%, respectively. Results Some research on the FTC turns to the design of an integrated filter and controller. Such methods usually lead to very high order integrated filter/controllers. To ease the implementation of the FTC, we designed the H∞ FDI filter and H∞ FTC separately. In the literature regarding H∞ norm analysis and design, the weight function selection is a highly problem-dependent, iterative process. Usually, we repeat the trial-and-error procedure until the desired performance and robustness objectives are achieved. In this research, the control objective is to suppress the first mode vibration of the smart structure. The disturbance input weight, Wd, is used to shape the worst case disturbance. It can be a low pass shape, or it can stress the amplitude at the frequency of the first mode. In this research, we use the a sine wave with the frequency of the first mode of the structure as the disturbance input. So the disturbance input weight is set to scalar 1. The performance or error weight, We, is used to specify the performance objectives of the resulting filter from the H∞ optimization, e.g., bandwidth, steady-state requirements, and attenuation/amplification of signals at certain frequency ranges. Typically, the actuator fault input weight, Wf, has low-pass characteristics to emphasize the

effects of faults on the low-frequency domain. The identified structure model combined with the weights yields the augmented model, P, as shown in the black square in Fig. 1. Using the developed LMI method, the following four stable, 3rd order H∞ filters for sensors are obtained. Using the a similar technique, the reduced 3rd H∞ controller is obtained. The truss was continuously excited by the sine wave at 85.95 rad/sec, which is the worst case disturbance input. Residual responses to different faulty inputs were examined. First, a faulty signal of square wave with different varying amplitude was introduced into four sensors at 10 sec. Filter outputs are shown in Fig. 5 to Fig. 8. From these figures, we can see that the residual signal clearly identified the square wave. For comparison, another simulation with the sine wave faulty input was conducted. Fig. 9 to Fig. 12 shows the faulty input signal and the residual signal. It can be seen that within one second of the occurrence of the fault, the residual signal clearly indicated the fault. Next, the designed H∞ FTC controller was examined using the MR damper. The structure was excited by a sine wave at 85.95 rad/sec. To simulate the partial failure of sensors, the outputs of the sensor 1, 2, 3 and 4 were reduced to 10%, 20%, 30%, and 40%, respectively, after 5 seconds had elapsed. The semi-active control law of the MR damper is:


Figure 13. Displacement at Tip of Truss (With Faults)

Figure 14. Displacement at Tip of Truss (Without Faults)

where ud is the control force applied by the MR damper and u is the optimal force acquired by FTC. The parameters of the MR damper are:

and . The displacement at the tip of the truss is shown in Fig. 13. It can be seen that the response of the closed-loop system with the FTC controller is reduced by about 50 percent, though there are partial faulty signals in the output of the sensors. The result of the FTC Controller without faults in sensors is shown in Fig. 14. Comparing the two figures, it can be clearly seen that the system with FTC controller remained almost unchanged when a failure occurred in the sensors. Conclusions In this research, a model-based fault detection and isolation (FDI) and the solution of the fault tolerant control problem using H∞ techniques are considered for the vibration control of truss structures. A linear matrix inequality (LMI) formulation is obtained to design a full order robust H∞ filter to estimate the faulty input signals. FDI LMI synthesis conditions are obtained by applying the Bounded Real Lemma to the closed loop system. A feasible solution for these conditions forms a convex problem for the full order filter, which is solved via LMI optimization techniques. A fault tolerant H∞ controller, which minimizes the control objective selected in the presence of disturbances and faults, has been designed for the combined system of plant and filter. An 8-bay truss structure has been used in validation of the FDI filter and FTC controller designs. A MR damper was installed in the truss to reduce the vibration of the truss using the FTC controller. To assist control system design, system identification was conducted for the first vibration mode of the truss. The state space model from system identification was used for the H∞ filter design. Residuals obtained from the filter through simulation are seen following the faults signals. The result shows that the designed FTC controller can achieve a fair vibration reduction ratio, though there are partial faulty signals in the output of sensors.


References 1 B. F. Spencer Jr., S. J. Dyke, M. K. Sain and J. D. Carlson, “Phenomenological Model for Magnetorheological Dampers,” J. of Engineering Mechanics 123 (1997): 230-38. 2 H-U Oh and J. Onoda, “An Experimental Study of a Semiactive Magneto-rheological Fluid Variable Damper for Vibration Suppression of Truss Structures,” Smart Materials and Structures 11 (2002): 156-62. 3 S. J. Dyke and B. F. Spencer Jr., M. K. Sain and J. D. Carlson, “Modeling and Control of Magnetorheological Dampers for Seismic Response Reduction,” Smart Materials and Structures 5 (1996): 565-75. 4 H. Sodeyama and K. Sunakoda, “Dynamic Tests and Simulation of Magneto-rheological Damper,” Computer-Aided Civil and Infrastructure Engineering 18 (2003): 45-57. 5 D. Diallo, M.E.H. Benbouzid and A. Makouf, “A FaultTolerant Control Architecture for Induction Motor Drives in Automotive Applications,” IEEE Trans. On Vehicular Technology, 53 (2004): 1847-55 6 E. Eryurek and B.R. Upadhyaya, “Fault-tolerant Control and Diagnostic for Large-Scale Systems,” IEEE Con. Sys. Mag., 15 (1995): 34-42. 7 Y. Bai, “Advanced Controls of Large Scale Structural Systems Using Linear Matrix Inequality Methods,” Ph.D. dissertation, Department of Mechanical Engineering, University of Houston, 2006. 8 Y. Bai, K. Grigoriadis, G. Song, “Active Fault-tolerant Control of a Flexible Beam,” Proc. of 2007 SPIE Intl. Symposium on Smart Structures and Materials, San Diego, CA, 2007. Acknowledgments We would like to thank Dr. Satish Nagarajaiah in the Department of Civil and Environmental Engineering at Rice University for providing the data of the truss model in this research. The authors also benefited from discussions with Dr. Grigoriadis and Dr. Bai.

Follow-Up Reports

Natural Language Interface Models for Fast Responsiveness Applications by Hisham Al-Mubaid

Figure 1. Basic Structure of the Proposed Model

U

HCL RESEARCHERS STUDY EFFICIENT MODELS OF interfaces with natural language (NL) capabilities for fast responsiveness systems. A fast responsiveness system is a system that incurs minimum latency and produces high throughput and quick responses. Interacting with such systems requires smart interfaces with capabilities to maintain and support fast responses. The smart interfaces of these systems require natural language (NL) capabilities and a natural language processing (NLP) component. Examples of fast responsiveness systems include Virtual Reality (VR) training programs, real-time text messaging applications, mission-critical systems like aerospace applications, and applications in which immediate responses are needed. The NLP component constitutes an important part of the interface, but it is the hard part since working with NL will lead to facing the difficult problem of NL ambiguity. In addition, having an efficient NL component is very appealing for fast responsiveness applications. An important part of the interface is the language disambiguation component. The language disambiguation component is based on integrating adaptive and supervised Machine Learning (ML) techniques. ML techniques have demonstrated outstanding success in many similar problems. The basic structure of the proposed design is shown in Fig. 1. The language disambiguation module will be able to perform a number of tasks including the following: • Predicting words and completion of user input: the system completes a word being typed by the user; thus, many keystrokes can be saved and text entry delay is reduced. • Correcting real word errors. • Suggesting words during text entry. We designed and implemented a word disambiguation and prediction techniques to solve the NL ambiguity problem. The proposed techniques allow for fast word prediction and completion in the NL interfaces of fast responsiveness applications. Experimental results are fairly impressive and encourage more work in this direction.


A Text-mining Technique for Literature Profiling and Information Extraction from Biomedical Literature by Hisham Al-Mubaid

Publications Al-Mubaid, H. and Nguyen H. A., “New Ontology-Based Semantic Simularity ASSIVE AMOUNTS OF BIOMEDICAL Measure for the Biomedical Domain,” literature are readily available IEEE Conf. on Granular Computing online to researchers in many GrC-2006. Atlanta, GA, May 10–12, forms: text abstracts, Medline with more than 2006. 16 million biomedical abstracts, full text Al-Mubaid H., “Context-Based Technique research articles, databases of protein interacfor Biomedical Term Classification,” tions, dictionaries of gene and protein names, Proc. 2006 IEEE Congress on and other electronic databases. Huge amounts Evolutionary Computation CEC-2006, of valuable knowledge and useful informaVancouver, BC, Canada, Abdelhak tion are embedded in these resources and Bensaoula, David Starikov, Chris Boney, available to be properly extracted, discovJuly 16–21, 2006. ered, and utilized. There is a great need for Al-Mubaid, H. and N. Ghaffari, “A New computational techniques to utilize and Gene Selection Technique Using Feature extract the useful knowledge from these Selection Methodology Gene Selection,” resources. A number of systems and software Proc. CATA-2006, 2006. tools have been developed to utilize these Al-Mubaid H. and H. A. Nguyen, extensive resources. Biomedical research has Hisham Al-Mubaid “Similarity Computation Using Multiple shown that text mining can be effective in UMLS Ontologies in a Unified Framework,” 22nd ACM this field, making text mining increasingly important and necesSymposium on Applied Computing SAC’07, 2007. sary for biology and medicine. This project aims at investigating and designing effective computational methods for literature profiling to extract and Presentation organize important information and related data from the bio- Al-Mubaid, H. and H. A. Nguyen, “New Ontology-based Semantic Similarity Measure for the Biomedical Domain,” medical literature. For that, we implemented new methods for IEEE Conference on Granular Computing, GrC-2006. identifying and classifying technical terms and entity names Atlanta, GA, May 10-12, 2006. 623-28. in biomedical texts. The methods are based on machine learning and can be viewed as a word classification task. We use feature extraction techniques like MI (mutual information) Funding and Proposals and X2 (Chi-square) to select the key features in the contexts Al-Mubaid, H., “Supervised and Adaptive Learning To Improve of the terms of interest. Methods were evaluated extensively text Entry for People with Physical Disabilities,” Proposal with a large number of experiments. submitted to NSF IIS, December 2006. (Under review.)

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SPIRIT OF THE WORLD—At the entrance to the UHCL Bayou Building, students see Spanish sculptor Pablo Serrano’s Spiritus Mundi.


Investigation of III-Nitride Materials for Space-based Solar Cells

of structural defects on the performance of the devices. Simulations verified that InGaN is theoretically a viable candidate for solar cell applications but that improvement in electrical and structural quality was necessary.

by Abdelhak Bensaoula and Chris Boney

INGaN MATERIAL SYSTEM HAS THE CAPABILITY OF covering almost all of the usable solar spectral range (0.5 – 3.0 eV) employed by solar cells. Based on the film composition, InGaN can cover from 0.70 eV up to 3.4 eV, which would be ideal for high efficiency solar cell applications. Also, it has recently been determined that the Nitride materials can offer exceptional radiation tolerance well beyond what can be achieved with conventional solar cell materials currently flown into space.1 However, InGaN is currently a much less mature technology than other III-V semiconductors used in conventional solar cells.

Results Growth of InxGa1-xN films by MBE under different growth conditions — such as In/Ga ratio, total III/N ratio, and film growth rate — have been performed. To date, we have realized a maximum indium mole fraction of approximately 51 percent based on room temperature and low temperature photoluminescence measurements. Thick InGaN for this project faced several challenges: large difference in volatility (evaporation) for indium compared to gallium, much lower growth temperatures needed for indium incorporation compared to pure GaN, and segregation of the indium during the growth which can cause compositional fluctuations. Currently, samples in the higher indium mole fraction range exhibit some compositional fluctuations and increased background conductivity, but it is expected that further growth refinements should be able to reduce or eliminate these effects. These refinements include improved deposition parameters and exploration of a flux modulation approach to the InGaN deposition. Modulating the arrival of the metal and nitrogen fluxes to the substrate can improve adatom mobility at the lower growth temperatures and help suppress compositional fluctuations.

Goal The goal of this ongoing project is to determine the feasibility of the InGaN material system for use in high efficiency single and multijunction solar cells. Previously, simulations of single junction InGaN solar cells were undertaken to predict the effect

References 1 J. W. Ager III, J. Wu, K. M. Yu, R. E. Jones, S. X. Li, W. Walukiewicz, E. E. Haller, H. Lu, and W. J. Schaff, “Group IIINitride Alloys as Photovoltaic Materials,” Proc. SPIE 5530 (2004): 308-15.

ABSTRACT—This project is investigating the suitability of the material InGaN as a candidate for photovoltaic space power generation. The effect of growth parameters on the properties of the films is under study.

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CERAMIC BONDING—Dr. Nasi Medelci, research scientist in electrical engineering, with the Center for Advanced Materials (CAM), modifies a ceramic chip with laser technology effective in the improvement of bonding between diverse materials. See report, p. 8.


Miniature Optical Sensors for Detection of Water and Air Contaminations by Abdelhak Bensaoula, David Starikov, and Chris Boney ABSTRACT—During the past years, several complex, bulky, and expensive spectroscopic instruments have been replaced by portable systems based on solid-state components. This project developed multi-band LED chips and solid-state photodetectors integrated into a miniature portable system capable of detection and quantification of a large variety of effluents in a gas, liquid, or solid form.

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LUORESCENCE INTENSITY MEASUREMENTS ARE NOW

utilized in hand-held compact sensors for detection of important compounds in various applications. However, the detection and quantification capabilities of these devices are still much lower than those of laboratory-based measurement systems. Any effluent that interacts with light in the range from near ultraviolet to near infrared in the form of at least one of the following phenomena — optical absorption, reflection, scattering, luminescence, or fluorescence — can be potentially identified and characterized by the system. System operation and signal acquisition rely upon the latest state-of-the-art developments in signal coding and electronic circuit design and allow measurements with an accuracy of few ppm. Identification and characterization of various compounds is based on the employment of artificial neural network architecture, built upon the principles of a human brain. The inherent spectral selectivity results in unique spectroscopic signal patterns from each tested effluent. These patterns are used to train the neural network first, in order to provide for their future identification by the system. Goal The goal of this current project is to further improve the performance of the portable system, based on light intensity, by the introduction of fluorescence lifetime (temporal) measurements, which are extremely sensitive to the specific compound signatures. Results Preliminary results have shown higher than 70% accuracy achieved in detecting E. coli bacteria without any knowledge of the tested environment. Under similar conditions, accuracies from important organic effluents exceeded 90%, and soared to 98-100% when data on the environment were fed into the neural network. The rapid development of semiconductor technology has enabled the solid-state components to satisfy critical requirements for lifetime measurements. Our first-of-a-kind portable

lifetime measurement system utilizes LEDs as excitation sources and fast photodiode or reverse-biased LEDs as photodetectors. This system can be tailored for specific applications as well as for universal use. The III nitride based components used in the sensor design allow for its operation in normal and superambient environments related to the following applications: detection and characterization of crude oil, oil in seawater, environmental pollution, bio-chemical hazards in military and industrial process control and monitoring, health monitoring in the biomedical field, identification and characterization of the variables in space applications, and the quality assurance of drugs in the pharmaceutical industry. A new high-sensitivity intelligent lifetime based prototype is currently under development in collaboration with the BioProcessing Laboratory at the University of Quebec at Montreal (UQAM). This project is supported by current US Air Force Phase II SBIR contract on the development of advanced fire/flame detectors. Publications Starikov, D., C. Boney, R. Pillai, and A. Bensaoula. “Solar-Blind Dual-Band UV/IR Photodetectors Integrated on a Single Chip,” Proc. of the 2006 NSTI Nanotechnology Conference and Trade Show, Nanotech 2006 3.1 (2006): 74-77. Presentations Boney, C., P. Misra, and A. Bensaoula. “Dependence of Impurity Incorporation on the Growth Temperature During GaN MBE Growth,” North American MBE Conference, Durham, North Carolina, Oct. 8–11, 2006. Joseph, C., M. Boukadoum, J. Charlson, D. Starikov, and A. Bensaoula. “High-Speed Front End for LED-Photodiode Based Fluorescence Lifetime Measurement System,” 2007 IEEE Intl. Symposium on Circuits and Systems, New Orleans, LA, May 27–30, 2007. (Accepted.) Starikov, D., C. Boney, R. Pillai, and A. Bensaoula. “Solar-Blind Dual-Band UV/IR Photodetectors Integrated on a Single Chip,” Proc. of the 2006 Nanotechnology Conference and Trade Show, Nanotech 2006 3.1 (2006): 74-77. Starikov, D., C. Boney, R. Pillai, and A. Bensaoula. “VisibleBlind UV/IR Photodetectors Integrated on Si Substrates,” Proc. of the 2006 MRS Spring Meeting, San Francisco, CA, April 17–21, 2006. (Accepted.) Tabari, K., M. Boukadoum, A. Bensaoula, and D. Starikov. “Neural Network Processor for a FPGA-based Multiband Fluorometer Device,” The International Workshop on Computer Architecture for Machine Perception and Sensing, Sept. 2006. Funding and Proposals Starikov, D. “Integrated Broad-Band Optical Calibration Sources for Star Simulation,” NSF Phase II SBIR project (IMS/CAM), $60,000 (Submitted.) Starikov, D. “Solid-State High Temperature Jet Engine Fire Detector,” Air Force Phase II SBIR project (IMS/CAM), 2005-2007, $250,000.


The Impact of Chromosome Lineage Upon Genetic Program Modeling

Original GP

Lineage-Based GP

Fitness

Final r2

Gen.

Fitness

Final r2

Gen.

591.8

0.8734

29.1

740.9

0.9315

28.5

210.9

0.7244

50.0

346.5

0.8069

48.6

by Gary D. Boetticher and Kim Kaminsky Table 1. Original vs. Lineage Approach

ABSTRACT—One of the challenges in data mining is to provide sufficient coverage of the search space in order to produce an acceptable model. Traditionally, genetic programs (GP) consider all chromosomes within a population for breeding purposes. Considering the enormous size of the search space, it is imperative to focus breeding efforts in genetic programs in order to attain a betGary D. Boetticher ter solution in less time. This research examines the lineage of genetic programs in order to identify any breeding patterns. Five separate experiments have been conducted where chromosomes are grouped into five classes. Lineage patterns are assessed for the best-, middle-, and worst-class parental chromosomes. Based upon the results, a new genetic programming process is proposed.

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(GPS) consumes excessive amounts of computer resources. Though genetic programs may successfully evolve solutions to complex problems, their use can be cost-prohibitive. What is desired is a more efficient approach to exploring the search space. This may be accomplished qualitatively by focusing the search efforts or, quantitatively, by increasing the number of searches. This research explores the qualitative approach by examining the breeding patterns of a GP. Key questions focused upon are: • Does chromosome lineage information provide any insight into the effectiveness of solving problems? • If so, how could these insights be utilized to make better breeding decisions? OLVING LARGE PROBLEMS USING GENETIC PROGRAMS

Goals of the project Gaining a better understanding about the lineage of a chromo-


Figure 1. Results from an Initial Experiment

some, in terms of how fitness values propagate over generations, is beneficial in several ways.1 Greater emphasis could be placed on those chromosomes that produce better offspring. Secondly, the utility of such a discovery could focus the search efforts, thus reducing training time, and requiring fewer computing resources. All of these benefits are immensely important when applying GPs to large, complex, noisy problem spaces. To explore the role chromosome lineage plays in the breeding process, five initial experiments have been conducted using synthetic datasets. Chromosomes are clustered into different classes (e.g., best, middle, and lower classes). Each of these classes has been tracked over a generation to determine whether certain classes are prone to producing good (or poor) solutions. Based upon the results of the initial set of experiments, an alternative breeding approach is proposed that focuses on those chromosomes with a solid pedigree. A second set of experiments examines this novel approach along with a traditional approach to determine the merit of focusing on a certain portion of a GP population. Results Figure 1 depicts the results from a typical experiment. The xaxis represents the number of GP generations (1 through 50) per trial. The y-axis shows the average fitness values for the bestclass, middle-class, and worst-class groups. The top line in the 300-400 range represents average fitness values of the offspring for the best-class parents. The middle line is the average fitness values of the offspring for the middle class parent chromosomes. The bottom line shows the average fitness values of the

offspring for the worst class parents. Figure 1 shows a clear distinction between best-, middle-, and worst-class groups. At no time do any of the group averages intersect. A t-test reveals these differences as statistically significant. These results in Fig. 1 are representative of all experiments. The next step applies the observed breeding habits to two equations. Table I shows the results after applying the lineage technique in 20 trials. These results show clearly that a lineage-based GP produces better models in terms of fitness and correlation in fewer generations. References 1 G. Boetticher and K. Kaminsky, “The Impact of Chromosome Lineage upon Genetic Program Modeling,” ISSO Annual Report, 2004. 122-27. Publications Boetticher, G. and K. Kaminsky. “The Assessment and Application of Lineage Information in Genetic Programs for Producing Better Models,” IEEE Information Reuse and Integration Conference 2006 (IRI), Big Island of Hawaii, September 2006. Presentations Boetticher, G. and K. Kaminsky. “The Assessment and Application of Lineage Information in Genetic Programs for Producing Better Models,” IEEE Information Reuse and Integration Conference 2006 (IRI), Big Island of Hawaii, September 2006.

SITES—Departmental offices for the College of Science and Computer Engineering at UHCL are located in the Bayou Building. The nearby Delta Building also houses experiments for NASA-JSC projects.


Progress on Three Projects: Systems for Spacecraft, Rovers, and Station Crew Return Vehicles by Albert M.K. Cheng ABSTRACT—Three projects are closely related with the ultimate goal of building fully-verified space vehicles that are (1) reliable, (2) energy-efficient, and (3) schedule-optimized. Timing response is a key issue.

1. Building and Verifying Fault-tolerant Autonomous Real-time Systems for Space Applications Premises of the project AUTONOMOUS SYSTEMS AND THEIR EMBEDDED AUTONOMY software in many NASA missions must perform correctly for an extended period of time and make real-time decisions that meet both logical and timing requirements. Furthermore, the autonomy software must tolerate implementation and environmentinduced faults. Developing and verifying these systems are especially difficult because of the large (and often infinite) state space and execution sequences as well as the uncertainties in the environment in which these systems operate. One focus of the NASA’s Automated Reasoning thrust is to “enhance the autonomous decision-making capabilities of robotic explorers, spacecraft, and mission management systems.” The objectives of this project are to address two key technology areas in the category of Automated Reasoning: (1) adding scalable fault-tolerance in the decision-making autonomy software of a real-time autonomous system and (2) augmenting the capability of formal verification strategies by providing an alternative based on scalable rulebase analysis to model checking and theorem proving. Results Since our approach can transform subsets of the code into selfstabilizing equivalents with different code modifications depending on their syntactic/semantic forms, it can be scaled to increasingly large and complex autonomy software systems. Coupled with the compositional analysis/verification strategy that identifies these syntactic/semantic code subsets applies to our overall approach further scales to deriving and verifying highly fault-tolerant autonomy software systems. Ongoing work evaluates this strategy on the modified Ganglia simulation platform.

2. Optimizing System Reward in BatteryPowered Spacecrafts and Rovers Premises of the project RECHARGEABLE BATTERIES ARE USED TO OPERATE MANY SPACECRAFTS and autonomous rovers; consequently, their operational periods


are limited by their battery supplies before the next recharge. How to use this battery-supplied energy efficiently is a critical issue. Most existing energy-conserving techniques are based on dynamic voltage scaling (DVS) and consider only timing or energy constraints. In a more realistic scenario, we should simultaneously consider three constraints: time, energy, and reward (quality-of-service). This project investigates two static methods (Greedy and Dynamic Programming) and an On-Line method for selecting tasks to optimize system reward while meeting timing constraints and conserving energy. We use simulation experiments to compare the performance of these methods with existing techniques. We have three static methods for selecting tasks from the task sets: (1) Simplified REW-Pack, (2) Greedy and (3) REW-Pack. We have compared the reward gained by these three methods. We found that our Greedy method often yields a larger total reward value than REW-Pack’s. Besides, the Greedy method is more efficient than REW-Pack. Results In this project, we have developed a static method to schedule an overloaded, battery-powered system. We compared our methods to a previous method. We compared the performance of these four methods in many situations. Our conclusion is that the Greedy method often has a better performance than REW-Pack, especially when the system has more of an energy limit, number of processor frequencies, and number of tasks. In a future project, we plan to develop a combined method which is more suitable in more situations. We also plan to investigate the best scheduling choice for each system environment. This project implements power-saving methods and investigates their performance by simulation. In particular, we have compared our static methods with REW-Pack, the only existing technique that deals with all three constraints (time, energy, and reward) but that does not perform well in overloaded systems. We believe that our algorithms are more suitable when the energy limit is higher when there is a larger set of processor frequencies, or whenever there is a larger number of tasks.

3. Timing Analysis and Scheduling of the X-38 Space Station Crew Return Vehicle and Other Space Vehicles Premises of the project THIS PROJECT HAS PERFORMED TIMING ANALYSIS AND SCHEDULING of the X-38 autonomous spacecraft built by NASA as a prototype of the International Space Station (ISS) Crew Return Vehicle (CRV). The avionics hardware and software design phase for this spacecraft requires tools for representing, analyzing, and verifying the hard real-time timing aspects of the system. To verify the planned performance of the safety-critical system functions, researchers have modeled a high-level specification of the X-38 multi-processor system task structure in Real-Time Logic (RTL) and Presburger Arithmetic representations. This timing analysis methodology can be applied to other space vehicles. Results

tool to represent many aspects of the system which may aid in timing, schedulability, fault, and safety analysis as well as verification. This methodology can be readily applied to verify the timing properties of other space vehicles. Publications Cheng, A. M. K. and F. Shang. “Priority-Driven Coding of Progressive JPEG Images for Transmission in Real-Time Applications,” Proc. 11th IEEECS Intl. Conf. on Embedded and Real-Time Computing Systems and Applications, Hong Kong, August 2005. Andrei, S. W., N. Chin, A. M. K. Cheng, and Y. Zhu. “RuntimeCoordinated Scalable Incremental Checksum Testing of Combinational Circuits based on #SAT Problem,” Proc. 11th IEEE-CS COMPUTER STUDENTS—Bin Lu (l.), master’s student and Yingwei Kuo, a Ph.D. candiIntl. Conf. on Embedded and date in computer science, focus upon the complex problem of programming computers Real-Time Computing Systems so that commands operate on a real-time basis. Many NASA missions rely on software and Applications, Hong Kong, that is able to make real-time decisions that meet both logical and timing requirements. August 2005. Andrei, S. W., N., Chin, A. M. K. We have investigated the X-38 201 vehicle avionics system Cheng, and M. Lupu. “Incremental Automatic Debugging of development through its requirements and design phases. Real-Time Systems Based on Satisfiability Counting,” IEEEAlthough the system is intentionally designed to reflect deterCS Real-Time and Embedded Technology and Applications ministic software timing relationships, one or more tools yet Symposium, San Francisco, March 2005. required for modeling and analyzing critical system performance throughout the life-cycle. A scheduling tool similar to Cheng, A. M. K. and F. Shang. “Priority-Driven Coding of Progressive JPEG Images for Transmission in Real-Time those evaluated is believed necessary to provide a means of easApplications,” Proc. 11th IEEE-CS International Conference ily analyzing possibly fluctuating workloads, to ensure that on Embedded and Real-Time Computing Systems and deadlines are met, and to provide a pictorial representation of Applications, Hong Kong, August 2005. the system timeline for communication. Although none of the tools met all evaluation requirements, it Cheng, A. M. K. and L. E. P. Williams. “Timing Analysis and Scheduling of the X-38 Space Station Crew Return Vehicle was decided that rather than building a custom tool for this projAvionics,” submitted to IEEE Transactions on Aerospace and ect, it would be best to choose one or more of the commercialElectronics Systems, 2004. ly available tools and try to extend it for our particular needs. RAPID RMA and TimeWiz were both chosen for further devel- Rice, L. E. P. and A. M. K. Cheng. “Timing Analysis of the X38 Space Station Crew Return Vehicle Avionics,” Proc. opment based upon their current state of development as well as IEEE-CS Real-Time and Embedded Technology and maintenance support. Applications Symposium, Vancouver, Canada, June 1999. In addition to a scheduling tool, the RTL representation seems to be a promising mechanism for satisfying similar timing Zu, M. and A. M. K. Cheng. “Real-Time Scheduling of Hierarchical Reward-Based Tasks,” Proc. IEEE-CS Realanalysis and verification tool requirements. The RTL represenTime Technology and Applications Symposium, Washington, tation presented here represents one aspect, task loop timing, of D.C., May 27–30, 2003. a complex avionic system. The specification language itself seems well-suited for representing this as well as possibly a broader range of areas of the system specification. For example, Presentations only one of the four FCC’s high-level task structure is modeled. Cheng, A. M. K. and S. Fang. “Study and Simulation of a Distributed Real-Time Fault-Tolerance Web Monitoring It may be possible to model redundancy aspects of the system as System,” Proc. IEEE-CS Real-Time Systems Symposium well as actual hardware devices in order to verify system fault (RTSS) WIP Session, Miami, FL, December 2005. tolerance. The RTL representation combined with the graphical constraint analysis mechanism seems to be a powerful enough


Real-Time Active Loading of Piezoelectric Ultrasonic Motors for Simulating Space Robotics Applications by James B. Dabney and Thomas L. Harman ABSTRACT—The next generation of robotic spacecraft will require simple, reliable, and lightweight robotic manipulators. This research enabled a new class of robotic actuators by successfully producing a prototype real-time model-based torque control system for a piezoelectric ultrasonic motor. Piezoelectric ultrasonic motors (PUMs) offer dramatic improvements to a variety of space-based robotics applications, if the problem of real-time torque control can be solved. This research used the UHCL PUM laboratory apparatus to develop, implement, and experimentally validate a real-time model-based PUM torque control law. PROGRAMMING—Thomas L. Harman, (l.) and James B. Dabney hold a copy of the new edition of their book, Mastering Simulink.

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PACE-BASED ROBOTS TYPICALLY REQUIRE ACTUATORS WITH

the advantages of high precision, light weight, and simplicity. Piezoelectric ultrasonic motors (PUM) are wellsuited to these requirements. PUM can achieve high precision as a result of low speed, its lack of gears and transmissions, and the freedom it affords from backlash. They are quite simple mechanically, consisting of a single moving part that provides the same functionality as motor, transmission, and brake in a conventional motor-driven system.1 A typical piezoelectric ultrasonic motor (Piezo Systems/Shinsei USR 30, Fig. 1)2 consists of a toothed piezoelectric disk (stator) in contact with a metal disk (rotor). Timevarying electric fields applied to the piezoelectric stator induce a traveling wave which is mechanically rectified, causing the rotor to rotate (Fig. 2).3 This mechanism produces relatively high torque at low rotor angular velocities, obviating the need for gearing. The friction between rotor and stator provides a passive holding torque typically larger than the rotating torque, eliminating the need for mechanical brakes or active holding torque. These motors can be built such that they neither produce nor are affected by magnetic fields, making them useful in highly magnetic environments and applications in which magnetic fields are harmful. The state of the art in control of PUM was not fully developed prior to this work. Good results had been achieved for applications requiring only speed regulation. Also, existing controller technology was adequate for positioning applications traditionally served by stepper motors. The new UHCL model-based torque control algorithm addresses the many important potential PUM applications requiring precise torque control.


Goals of the Project The ultimate goal of the PUM research conducted in the UHCL Systems Engineering Laboratory was to develop a PUM driver/controller unit that implements model-based real-time torque control algorithms. The goal was achieved this year in the form of a prototype driver/controller which implemented a model-based control law developed in the Systems Engineering Laboratory of the University of Houston-Clear Lake. Results PUM hardware is shown in Fig. 3. The PUM is mounted to a torque sensor and drives a flywheel which, in turn, drives a magnetic particle brake. The brake is connected by a flexible coupling to a laser encoder which measures the motor angular position. The magnetic particle brake produces a brake torque commanded by the dSpace software system. A system block diagram including the magnetic particle brake and driver is shown in Fig. 4. Previously, the experimental apparatus was used to characterize the relationship among drive signal frequency, motor speed, and motor torque, resulting in the torque surface shown in Fig. 5. Figure 1. Piezo Systems Ultrasonic A control law was imple- Motor (Shinsei USR30)

Figure 2. Traveling Wave Formation

Figure 3. Motor and Encoder Assembly

mented that inverts the torque surface shown in Fig. 5 to compute drive signal frequency as a function of instantaneous motor speed and commanded torque. The control law was implemented using the Simulink4 model shown in Fig. 6 and loaded into the dSpace real-time control system. Regulation and tracking experiments were performed to demonstrate that the control law is effective throughout the PUM operational range. Example tracking experiment results are shown in Fig. 7. In the tracking experiment, the control objective was to maintain constant torque magnitude of 0.01 NM, switching torque sign at +/-10 rad/sec. The brake torque was set to its residual value of 0.00015 NM (the brake produces approximately 0.00015 NM of drag torque when not energized). Examining Fig. 7, it is apparent that the motor torque deviates from commanded torque twice during each branch of the speed trajectory. The first deviation occurs when the commanded torque changes sign and is relatively small. The second deviation occurs when the motor direction of rotation changes sign and consequently when the motor switches from a braking mode to an accelerating mode. A factor that degraded tracking performance somewhat was drift in drive signal amplitude each time the drive signal phase (sense) switched. It is expected that an improved controller with more stable voltage regulation and greater frequency precision will improve tracking accuracy. Conclusions and Future Work This work has demonstrated the feasibility of model-based torque control for an important class of traveling wave piezoelectric ultrasonic motors. The model-based torque controller provides stable torque control at constant motor speed and convergent tracking during transient operation. The operation of the algorithm was demonstrated by simulation and experimention. Future work will entail development of a single degree of freedom haptic display using the present apparatus. The torque control performance can be improved by higher bandwidth control and increased resolution of frequency control.

Figure 4. Apparatus Schematic

Acknowledgments This work was partially supported by ISSO mini-grants for the summers of 2002, 2003, 2004, and 2005. Additional support was provided by the NASA Lyndon B. Johnson Space Center and by the UHCL Faculty Research Support Fund. A UHCL Systems Engineering Capstone team5 implemented the controller software. References 1 T. Shashida and T. Kenjo, An Introduction to Ultrasonic Motors. Oxford, UK: Clarendon Press, 1993. 2 Operating Manual: Ultrasonic Rotary Motor and Driver. Cambridge, MA: Piezo Systems, Inc., 2001. 3 N. W. Hagood and A. J. McFarland, “Modeling of a Piezoelectric Ultrasonic Motor,” IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 42.2 (1995): 210-31. 4 J. B. Dabney and T. L. Harman, Mastering Simulink. Upper Saddle River, NJ: Prentice-Hall, 2004. Figure 5. Example PUM Torque Surface


Figure 6. PUM Simulation Implementing Model-based Torque Control

Publications Dabney, J. B., T. L. Harman, F. H. Ghorbel, C. Aswatharanayan, M. Randolph-Gips, and J. J. Chakkungal. “Dynamic Response Modeling of Piezoelectric Ultrasonic Motors,” 2005 International Mechanical Engineering Conference and Exhibition, Orlando, FL, 2005. Dabney, J. B., T. L. Harman, F. H. Ghorbel, and J. J. Chakkungal. “Model-Based Torque Control of Piezoelectric Ultrasonic Motors,” International Mechanical Engineering Conference and Exposition, Chicago, IL, 2006. Dabney, J. B., and V. Tang. “Model-based Torque Control of Piezoelectric Ultrasonic Motors,” STTR Phase I Final Report, UHCL Systems Engineering Laboratory, 2005.

Figure 7. Tracking Response Using Model-based Torque Control

Presentations Wagner, C., J. Arceneaux, A. Vyvial. “Model-Based Torque Control of Piezoelectric Ultrasonic Motors,” Capstone Project Report, UHCL Systems Engineering Laboratory, 2005. Funding Dabney, J. B. “Model-Based Torque Control of Piezoelectric Ultrasonic Motors.” January, 2005, $600,000. (Not funded.) Dabney, J. B., “Robust Miniaturized Piezoelectric Motor Controller,” September 2005, $100,000. (Not funded.) Dabney, J. B., T. L. Harman. “Low Cost Haptic Display Using Piezoelectric Ultrasonic Motors,” Texas Advanced Research Program, February 2006, $66,000. (Not funded.)

STUDIES—Teamwork is an essential part of any research effort, exemplified by these students at work in the Bayou Building at UHCL.


Early Origins of Genetic Systems and Remnants of the RNA World By George E. Fox ABSTRACT—These two projects focused on different aspects of the hypothesis that DNA based Earth life arose from an earlier RNA World: (1) Early Origins of Genetic Systems and (2) Remnants of the RNA World: RNA Structures Associated with Gene Regulation.” Researchers conducted a detailed examination of modern genetic systems and found support for the notion that RNA catalyzed protein synthesis predates DNA replication and is at least as old as transcription. Thus, we concluded that living organisms as we know them likely emerged first with an RNA-based genetic system and only later with DNA as the genetic material The development of sophisticated translation machinery and its integration with RNA level regulation of transcription was therefore likely to have been a major driving force in the early history of life. A detailed study of the RNAs and proteins associated with translation machinery identified many remnants of early evolution.

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E SOUGHT TO COMPARE THE RELATIVE AGE OF MAJOR

cellular processes to translation as well as the relative age of components of the translation machinery. To this end, the r-proteins and RNAs associated with the large ribosomal subunit of archaeal and bacterial ribosomes were intercompared with particular attention paid to features unique to one or the other, as universal components are likely older than kingdom specific components. Likewise, those that are central to ribosome assembly are more likely older than those which are added at the end. These hypotheses about age were also evaluated within the context of gene organization. Components thought to be older were consistently found in more conserved gene clusters. The structures of many other cellular proteins are also known and these have been classified by the folds they contain, as summarized in the SCOP (structural classification of proteins) database at . We used this database as a starting point to identify non-r-proteins that share similarity with r-proteins. Results Multiple examples of r-proteins are related by insertion, fusion, and/or duplication events; in those cases, an interest is which protein is the predecessor. One key example is the very ancient protein L2 which is universal, early in the assembly process and in one of the most conserved r-protein gene clusters. This protein has two domains. One has an OB fold and the other an SH3 fold. These folds differ by the insertion/deletion of a single alpha helical element. Thus, a likely scenario is that L2 began as a single domain protein with an SH3 fold

which allowed it to interact with RNA. A subsequently duplication event followed by a second insertion event would then create a new second domain. The resulting OB fold, which may have originated with L2, is found in many modern membrane associated proteins. Among the most interesting findings is the observation that elongation factor G (EF-G) is largely a composite of several rprotein domains. EF-G has five structural domains. Domain II which is also shared with EF-Tu is seen in one of the oldest ribosomal proteins, L2. Domains III and V have the same ferredoxin-like fold seen in r-proteins S6 and S10. Domain IV has an alpha/beta structure as found in r-protein S9 and the central domain of r-protein S5. EF-G is involved in GTP cleavage and is a key component of ribosomal bioenergetics. In its absence, the rate of translation is dramatically slowed but not eliminated. In total, the evidence suggests that it is a relatively recent addition to the ribosomal machinery. Given its dramatic role in the rate of protein synthesis, its introduction may have been a major transition in the history of living systems. Another far more recent partial duplication event was detected for L15 and L18e. The former is a universal protein and therefore likely to be older, since the latter is not found in bacteria. The two proteins share significant sequence homology as well as structural similarity, but L15 has an extension that is missing in L18e. The binding site for L18e in the archaeal ribosomal RNA includes an inserted loop not present in bacterial rRNAs. Hence, the newer protein interacts with an added/newer feature in the RNA. There are, in fact, many such minor changes in the RNAs when kingdoms are compared. Some of these, like the L18e example, are associated with r-proteins unique to a kingdom. However, a more detailed examination revealed three large clusters of changes in which the variant RNA regions interact with either one another or with novel proteins. Thus, it is likely that the various components of each cluster co-evolved suggesting that various RNA and protein changes in the cluster are of a similar age. Discussion and Conclusions Results obtained from these studies have made it clear that it is possible to determine the relative age of many cellular components. It is generally thought that if two proteins or RNAs are similarly distributed among the various taxa that it would not be possible to show that characteristic despite the fact that many components are completely universal. One can nevertheless use data from multiple sources to assess the relative age of even these early components. In conclusion, a multifaceted study of protein and RNA that takes into account sequence structure, genetic regulation, and functional positioning can provide meaningful insight into the earliest history of cellular organization and evolution. Funding for this purpose was sought and obtained from NASA’s Exobiology program. These preliminary data also yield information on RNA structure that, in part, led to a funded project from the Texas Advanced Research Program. In addition, multiple publications are now in preparation.


Publications Hury J., U. Nagaswamy, M. Larios-Sanz, and G. E. Fox, “Ribosome Origins: The Relative Age of 23S rRNA Domains,” Origins Life & Evol. Biosphere 36 (2006): 421-29. Wang J., “From Genome to Structure: Comparative Studies of Archaeal Unique Ribosomal Proteins,” Ph. D. dissertation, University of Houston, Houston, TX, 2006. Presentations Fox, G. E., “Inferring Evolutionary History from Multiple Data Sets: Insights to the Origins of the Translation Machinery,” Invited Symposium Speaker, Computational Molecular Biology: The Future; University of Houston, Houston, TX, April 4, 2005. Dasgupta I., Y. Liu, J. Wang , H-C. Huang, U. Nagaswamy, G. E. Fox, “Conservation and Clustering of Translation Related Genes,” Cold Springs Harbor Meeting on Genome Informatics, Oct. 28–Nov. 1, 2005, Cold Springs Harbor, NY. Fox, G. E., “Origins of the Translation Machinery,” Invited Seminar Speaker, Planetary Protection Group, Jet Propulsion

Laboratory, Pasadena, CA. Dec. 8, 2005. Fox, G. E., “Unraveling the History of the Ribosome,” Invited Symposium Speaker, Houston Society for Engineering in Medicine and Biology 23rd Annual Conf. on Biomedical Engineering Research, Houston, TX, Feb. 9–10, 2006. Fox, G. E., “EF-G, A Key Historical Advance in Early Genetic Systems,” Invited speaker, Origin of Life Gordon Conf., Bates College, Lewiston, MN, July 23–28, 2006. Fox, G. E. “The Ribosome as a Model Nanomachine,” Invited seminar, Dept. of Chemical Engineering, Syracuse University, Syracuse, NY, April 20, 2007. Funding and Proposals Travisano, M. T., Fox, G. E. et al., “Shared Genomic Resources in Prokaryotic Evolution,” NSF-Frontiers in Biology Program, October 1, 2005–September 30, 2010. Total Costs: $7,612,114. (Not funded.). NASA Exobiology Program; “The Origins of Translation and Early Evolution of Life,” Aug. 15, 2005–Aug. 14, 2008. Total costs: $288,268. (Funded.) Texas ARP, “Artificial Stable RNA Sequestration of Heavy Metals,” Jan. 1, 2006–Aug. 31, 2008. Total costs: $176,076.

RESEARCH CAMPUS—At the heart of any great research university is an extensive library. UH’s M.D. Anderson Library, (far l.) which underwent a major expansion in 2005, provides the UH System necessary support for advanced study in the 21st century.


A Unique Camera System To Study the High-Speed Dynamics of Premixed Flames by Michael Gorman ABSTRACT— Instabilities of the reacting front of commercial combustion systems limit their performance, decrease their efficiencies, and increase their pollution. We have assembled a unique, high-speed camera system with a micro-channel plate intensifier to study this dynamics.

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these dynamics studies. These frames show counter-propagating hot spots, which collide and annihilate between frames 1 and 2. In frames 2-4, two free hot spots propagate in the clockwise direction and one bound hot spot. Figure 2 shows the dynamics of unusual pulsating states. These states form N-lobed structures which break along their mid-line into counter-propagating spiral arms, rotate, and annihilate with spiral arms from adjacent lobes. This dynamics is qualitatively different from other dynamics of pulsating flames in which the circular flame front oscillates in modes similar to those of a vibrating drumhead or in spirals rotating in a circular domain. These two examples are a fraction of the pulsating dynamic states that we have observed in these studies. Publications Gorman, M. and R. Brockman. “Structures—Hot Spots, Cool Spots, and Wave Trains—and Events in HydrocarbonOxygen Premixed Flames on an Annular Burner.” (Submitted to Physica D; under review.) Gorman, M., B. Pearson, and M. el-Hamdi. “The Dynamics of Four Ratcheting States of Cellular Flames: The Legacy States.” (Submitted to Chaos, under review.) Gorman, M. and S. Perrollier. “Unusual Pulsating States In Hydrocarbon-Oxygen Premixed Flames,” Chaos 16 (2007) (Forthcoming.)

INSTITUTE FOR Space Systems Michael Gorman Operations support for research in combustion dynamics continues to play a crucial role in our studies. The combustion front of an engine or a gas turbine combustor near its lean burn limit can become unstable to dynamic modes of propagation in which the steady front is replaced by a front that varies in both space and time. The characteristic oscillation frequencies are 25–75 Hz, which are above the Nyquist frequency of videotape, 15 Hz. As the frame rate of the camera is increased, the light per frame decreases. A micro-channel plate image intensifier, capable of gains adjustable to 60,000, is used to amplify the signal so that the images are clearly visible to the operator. The ISSO funds were used to repair this image intensifier, which had been damaged. Figure 1 is a sequence of images of the dynamics of an annular state taken at 60 Hz in (a) and 250 Hz in (b), demonstrating the importance of using a high-speed camera in Figure 1. Dynamics of Annular States HE

Figure 2. Dynamics of Unusual Pulsating States


A Theoretical Analysis of Vibrational Modes Aimed at their use as Measures of Bone Damage by Gemunu Gunaratne and Chamith Rajapakse

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CATTERING IS ONE OF THE MOST WIDELY

used techniques for probing the interior of solids. In order to adapt this Figure 1. The Linear Response to a methodology to extract material properties of Triangular Pulse cortical and trabecular bone tissue, we introduced a model system consisting of a porous Gemunu Gunaratne segment constructed from a digitized image of vertebral trabecular bone and a solid segment attached to it on Publications a side. In our calculations, the rear end will be held stationary Gunaratne, C. S. Rajapaksa, K. E. Bassler, K. K. Mohanty, while the solid front end will be subjected to a short-time pulse and S. J. Wimalawansa. “A Model for Bone Strength and of a known shape. The stress on the front end following the Osteoporotic Fracture,” Phys. Rev. Lett., 88 (2002): pulse will be calculated using an integration of the type adopt068101. ed for laborator procedures. Figure 1 shows an example of the Espinoza Ortiz, J. S., C. S. Rajapakse, and G. H. Gunaratne. calculated response for such a model system when the external“Strength Reduction in Electrical and Elastic Networks,” ly applied pulse is triangular. The question then is whether this Phys. Rev. B, 66 (2002): 144203. time-dependent response can be inverted to obtain “effective” Espinoza Ortiz, J. S. and G. H. Gunaratne. “Current material properties of cortical and trabecular segments. Distributions in Fused Electrical Networks,” Brazilian We approximated the system with a one-dimensional array Journal of Physics 33 (2003): 368-75. of springs-and-masses. The trabecular bone is represented by Song, Y., M. A. K. Liebschner, and G. H. Gunaratne. “A Study Ν1 identical objects of mass m1 connected by elastic elements of Age-Related Architectural Changes that are Most Damaging of spring constant k1, and are assumed to move in a medium to Bones,” Biophysical J. 87 (2004): 3642-47. with damping η1. Cortical bone is represented by η2 identical Song, Y. and G. H. Gunaratne. “A Method for Vibrational objects of mass m2 connected by elastic elements of spring Assessment of Solid Bone,” Chaos 16 (2006): 033102. constant k2, and are assumed to move in a medium with damping η2. The scattering problem assumes that the pulse Presentations sent inward is partially reflected back to the cortical bone and “How to Find When Bones May Break” Workshop on partially transmitted to the trabecular bone. Solving the probBiomechanics, Notre Dame University, November 2002; lem, one finds that the Fourier transform of the stress on the Georgia Institute of Technology, March 2003; Boston front end is given by University, February 2004; University of Connecticut, April 2004. “Summer School for Advanced Electronic and Bio-materials,” International Center for Materials Physics, Chinese Academy with the reflection coefficient of Sciences, Shenyang, China, June 2004; Dalian University, China, June 2004.

Here and for j=1 or 2, where

, and

is the Fourier transform of the pulse. We propose to develop inverse techniques to estimate c1, c2, γ1, γ2, k1 and k2 from the time behavior of c.


Proposals “Development of Analytical Tools for Vibrational Assessment of Bone,” Joint NSF/NIH program for Mathematical Biology, $1,467,000: NSF ranked the proposal in the “Highest Priority”, but it was not funded by the NIH. (The program officer requested that it be resubmitted in June 2006.) “Vibrational Response as a Measure of Trabecular bone Quality,” NIH, $1.471,000. (Not funded.) “Theoretical Analysis of Accoustical Assessment of Bone,” NSF, $220,000. (Not funded; to be resubmitted.)

Raman Scattering Test of Mechanical and Sensor Properties of Advanced Nanocomposites

The strain transfer is deduced from the Raman scattering test in which we simultaneously measure the changes in both the Gmode frequency and the surface strain εS ≈ εm (for low SWNT concentration nanocomposites), close to the laser spot, with varying external load. We measured a nanocomposite sample containing 0.001% SWNTs dispersed in Epon by Viktor G. Hadjiev, Leonard 682 and cured with W-agent in the presence Yowell, and Sivaram Arepalli of ~16 T magnetic field. Typically, nanocomposites of SWNTs prepared in a strong magnetic field contained well orientABSTRACT—In this report on the ed nanotubes along the field direction. project completed in 2004, we briefly To quantitatively assess the degree of the demonstrated that single wall carbon orientation of SWNTs, we measured a series nanotubes (SWNT) embedded in polyof Raman spectra for incident laser polarizamer matrix can be used as distributed, tion directions at various angles, 0 ≤ Ψ ≤ nano-scale, strain gauges measured Viktor Hadjiev 180°, with respect to the director (direction remotely by Raman spectroscopy. of the magnetic field). It is well known that the G-mode intensity of a SWNT varies with the angle Ψ between the incident laser polarization and the nanotube axes as N THE COURSE OF THE PROJECT, WE MEASURED LOAD TRANSFER 1,2 in various SWNT nanocomposites using the Raman scat- cos4Ψ. If all nanonotubes in the nanocomposite sample are pertering micromechanical test.3 As a result, it has been well fectly aligned in one direction, the resulting G-mode intensity documented that the G-mode frequency at 1590 cm-1 varies should follow cos4Ψ as well. Figures 1 and 2 show that the G-mode intensity change with linearly with nanotube’s axial strain εaxial. Specifically, the Ψ in the sample under study resembles that of cos4Ψ. These fractional G-mode frequency change is proportional to the data, however, allow more quantitative treatment, and we find axial strain the average degree of nanotube misalignment θ from the fit to , the dependence given in Fig. 2 with the expression5 where A~1 follows from an empirical model for chiral SWNT,3 and A~1-2 is found using the Local Density Approximation (LDA) calculations.4 In a nanocomposite containing SWNTs, any external load is transferred to the nanotubes through the where interfaces between the matrix and nanotubes. This process can also be described as a strain transfer S ≤ 1 given by are the second- and fourth-order orientation parameters. We obtained for the second-order parameter (see following page) , εm is the matrix strain.

I

BEFORE—TCSUH, the Texas Center for Superconductivity at UH, with discoveries that require more advanced measuring devices, updates its lab equipment in a periodic reinvestment program.

AFTER—Shipping cases (l. photo) were emptied of a new Raman microscope, which was reconstructed in the lab to perform precise chemical mapping and Raman imaging.


, which corresponds to misalignment of the nanotubes of no more than 25 degrees. In Fig. 3 we present the change in the G-mode Raman spectra under external compressive load along the director. The load created a matrix strain ε ≈ -0.004 measured by a strain gauge placed close to the laser spot. Given the measured fractional frequency change, , one obtains very good strain transfer S ≈ 0.88 in a 0.001 percent SWNT/epoxy sample. This value of S is characteristic for well dispersed nanotubes and for those that adhere to the matrix. In addition to the frequency shift, the G-mode Raman line in the sample under load becomes inhomogeneous broadened. This effect comes in part from the contribution of those nanotubes that are misaligned and therefore subjected to a reduced load. On the other hand, the nanocomposite contained different diameter nanotubes, which, although having approximately the same G-mode frequency, shifted differently under the load due to the different strength of coupling to epoxy. Currently, we are working on a refined approach to resolve these problems of misalignment. In this study, we demonstrated that in addition to reinforcement, well-dispersed nanotubes and those that adhere to the matrix can serve also as nano-scale strain gauges. Further improvement of the performance of the nano-gauges can be achieved by using nanotubes with narrow diameter distribution. References 1 V. G. Hadjiev, D. C. Lagoudas, E-S. Oh, P. Thakre, D. Davis, B. S. Files, L. Yowell, S. Arepalli, J. L. Bahr, and J. M. Tour, “Buckling Instabilities of Octadecylamine Functionalized Carbon Nanotubes Embedded in Epoxy,” Composites Science and Technology 66 (2006): 128. 2 V. G. Hadjiev, C. A. Mitchell, S. Arepalli, J. L. Bahr, J. M. Tour, and R. Krishnamoorti, “Thermal Mismatch Strains in Sidewall Functionalized Carbon Nanotubes/Polystyrene Nanocomposites,” J. of Chem. Phys. 122.12 (2005): 124708. 3 V. G. Hadjiev, M. N. Iliev, S. Arepalli, P. Nikolaev, B. S. Files, “Raman Scattering Test of Single-wall Carbon Nanotube composite,” Appl. Phys. Lett. 78 (2001): 3193. 4 Wu G., J. Zhou, and J. Dong, “Raman Modes of the Deformed Single-wall Carbon Nanotubes,” Phys. Rev. B 72, 1(2005): 15411. 5 Liu T. and S. Kumar, “Quantitative Characterization of SWNT Orientation by Polarized Raman Spectroscopy,” Chem. Phys. Lett. 378.3 (2003): 257.

Figure 1. G-mode Raman spectra of 0.001% SWNT/epoxy nanocomposite measured at various angles between the laser polarization and the direction of magnetic field applied during the curing process.

Figure 2. Variation of the G-mode intensity with angle (open circles) and the best fit to experimental points (solid line) using the expression 1.

Figure 3. G-mode Raman line in 0.001% SWNT/epoxy nanocomposite at zero stress (1592.4 cm-1) and an external load (the line shifted upward by 5.6 cm-1) that creates matrix strain.


Development of Quantum-Cascade Laser Based Biosensor Technology by Thomas Harman ABSTRACT—Researchers are developing new types of sensitive, selective, real-time gas sensors based on continuous wave and pulsed quantum cascade lasers for various chemical sensing applications, such as medical diagnostics, environmental monitoring, and industrial process control. Tunable laser absorption spectroscopy in the mid-infrared spectral region is a sensitive analytical technique for trace gas quantification. During the past year a nitric oxide (NO) gas sensor was developed based on a novel thermoelectrically cooled, continuous wave, distributed feedback quantum cascade lasers operating at 5.45 mm (1835 cm-1) and 5.22 mm (1916 cm-1), and off-axis integrated cavity output spectroscopy (OA-ICOS) combined with a wavelength modulation technique. Its purpose is to determine NO concentrations at the sub-ppbv levels that are essential for such applications. The sensor employs a 50 cm long high-finesse optical cavity that provides an effective pathlength of ~ 700 m. Research efforts achieved a noise equivalent (SNR = 1) minimum detection limit of 0.4 ppbv with a 1 second observation time.

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HE DEVELOPMENT OF COMPACT OPTICAL SENSORS FOR NITRIC

oxide detection is of interest for a number of applications, such as environmental monitoring,1 atmospheric chemistry,2 industrial process control,3 combustion studies,4 and medical diagnostics.5,6 NO is involved in many vital physiological processes in the human body. For example, an elevated level of NO in exhaled breath is correlated with airway inflammation in asthmatic patients. Knowledge of NO concentrations in the exhaled breath of these patients may allow health care providers to adjust therapeutic drug dosages.7,8 For medical diagnostics purposes, it is essential to time-resolve the NO concentration as a function of a breath cycle phase, because the corresponding air samples originate in the different parts of the respiratory tract. This application requires a sensor response time of £1 second and a NO minimum detection sensitivity of < 1 ppbv. Such high sensitivity, rapid response measurements are possible with laser absorption spectroscopy in the fundamental absorption band of NO. Distributed feedback quantum cascade lasers (DFB QCLs) operating in a pulsed or continuous wave (CW) mode are promising spectroscopic sources because of their narrow linewidths, single mode operation, tunability, output power, reliability, and compactness. Until recently, CW operation of QCLs was possible only at cryogenic temperatures, and room temperature (RT) operation was realized only with pulsed operation at a low duty cycle, but recent developments in QCL technology now permit

CW operation at room temperature or temperatures which can be obtained by thermoelectric cooling.9,10 Goals of the project In this research, we utilize a novel and now commercially available TEC, CW, DFB quantum cascade laser fabricated by our collaborating team from the University of Neuchatel, Switzerland.9 The DFB CW QCL characteristics, such as a narrow laser spectral width (£3 MHz,11 necessary for efficient laser to cavity coupling and high average power, make CW TEC QC lasers more suitable than pulsed QCLs for ICOS-based sensor platforms for real world applications. These systems avoid the size and complications of liquid nitrogen cooling required by earlier QC lasers. The basic sensor platform is an OA-ICOS configuration with a 50 cm long optical cavity. A wavelength modulation technique (harmonic detection) was implemented in order to reach sub-ppbv levels of NO detection sensitivity. Results Exhaled nitric oxide (NO) is an important biomarker in asthma and other respiratory disorders. We studied the optical performance of a NO/CO2 QCL-based sensor employing integrated cavity output spectroscopy capable of real-time NO and CO2 measurements in a single breath cycle. Furthermore, the off axis ICOS sensor performance was compared to a chemiluminescent NO analyzer and a non-dispersive infrared (NDIR) CO2 absorption capnograph. Differences between the gas analyzers were assessed by the Bland-Altman method to estimate the expected variability between the gas sensors. The OA-ICOS sensor measurements were in good agreement with the data acquired with the two commercial gas analyzers. The sensor had a noiseequivalent sensitivity (1Û) for NO of 0.4 ppbv with a 1-s averaging time. Potential improvements to the ICOS sensor include incorporating higher reflectivity mirrors and utilizing the stronger NO absorption line at 1900 cm-1. This work demonstrates the performance characteristics and merits of midinfrared spectroscopy for exhaled breath analysis. References 1 D. D. Nelson, J. H. Shorter, J. B. McManus, and M. S. Zahniser, “Sub-Part-per-Billion Detection of Nitric Oxide in Air Using a Thermoelectrically Cooled Mid-Infrared Quantum Cascade Laser Spectrometer,” Appl. Phys. B, 75 (2002): 343. 2 J. H. Steinfeld and S. N. Pandis, Atmospheric Chemistry and Physics: from Air Pollution to Climate Change. New York: Wiley 1998. 3 G. Wysocki, A. A. Kosterev, and F. K. Tittel, “Spectroscopic Trace-Gas Sensor with Rapidly Scanned Wavelengths of a Pulsed Quantum Cascade Laser for in situ NO Monitoring of Industrial Exhaust Systems,” Appl. Phys. B, 80 (2005): 617. 4 H. Gupta and L.-S. Fan, “Reduction of Nitric Oxide from Combustion Flue Gas by Bituminous Coal Char in the Presence of Oxygen,” Ind. Eng. Chem. Res. 42 (2003): 2536. 5 C. Roller, K. Namjou, J. D. Jeffers, W. Potter, P. J. McCann, and J. Grego, “Simultaneous NO and CO2 Measurement in Human Breath with a Single IV–VI Mid-Infrared Laser,” Opt. Lett. 27 (2002): 107.


C. Roller, K. Namjou, J. D. Jeffers, M. Camp, A. Mock, P. J. McCann, and J. Grego, “Nitric Oxide Breath testing by TunableDiode Laser Absorption Spectroscopy: Application in Monitoring Respiratory Inflammation,” Appl. Opt. 41 (2002): 6018. 7 “Breath Analysis for Clinical Diagnosis and Therapeutic Monitoring,” ed. A. Amann and D. Smith. World Scientific, Singapore, (2005): 575-84. 8 A. D. Smith, D. R. Taylor, “Is Exhaled Nitric Oxide Measurement a Useful Clinical Test in Asthma?” Current Opinion in Allergy and Clinical Immunology 5 (2005): 49. 9 S. Blaser, D. A. Yarekha, L. Hvozdara, Y Bonetti, A. Miller, M. Giovannini, and J. Faist, “Room-Temperature, ContinuousWave, Single Mode Quantum-Cascade Lasers at 5.4 mm,” Appl. Phys. Lett., 86, (2005): 041109-1. 10 S. Blaser, Y. Bonetti, L. Hvozdara, and A. Mueller (Alpes Laser, Neuchatel, Switzerland), “Quantum-Cascade Lasers for TDLS,” 5th International Conference on Tunable Diode Laser Spectroscopy, July 11–15, 2005, Florence, Italy. 11 A. A. Kosterev, A. L. Malinovsky, F. K. Tittel, C. Gmachl, F. Capasso, D. L. Sivco, J. N. Baillargeon, A. L. Hutchinson, and A. Y. Cho, “Cavity Ringdown Spectroscopic Detection of Nitric Oxide with Continuous-Wave Quantum-Cascade Laser,” Appl. Opt. 40 (2001): 5522. 6

Publications Bakhirkin, Y., A. A. Kosterev, R. Curl, F. K. Tittel, D. A. Yarekha, L. Hvozdara, M. Giovannini, and J. Faist. “Sub-ppbv Nitric Oxide Concentration Measurements Using CW RoomTemperature Quantum Cascade Laser-Based Integrated Cavity Spectroscopy,” Appl.Phys. B 82 (2006): 149-54. McCurdy M., Y. A. Bakhirkin, and F. K. Tittel. “Quantum Cascade Laser-Based Integrated Cavity Output Spectroscopy of Exhaled Nitric Oxide,” Applied Physics B 85 (2006): 445-52 McCurdy, M., Y. Bakhirkin, G. Wysocki, and F. K. Tittel. “Performance of an Exhaled Nitric Oxide and Carbon Dioxide Sensor Using Quantum Cascade Laser-Based Integrated Cavity Output Spectroscopy,” J. of Biomedical Optics (November 2006). (Submitted.) Miller, J. H., Y. A. Bakhirkin, T. Ajtai, F. K. Tittel, C. J. Hill, and R. Q. Yang. “Detection Of Formaldehyde Using Off-Axis Integrated Cavity Output Spectroscopy with an Interband Cascade Laser,” Applied Physics B 85 (2006): 391-96 Tittel, F. K., Y. Bakhirkin, A. Kosterev, and G. Wysocki. “Recent Advances in Trace Gas Detection Using Quantum and Interband Cascade Lasers,” The Review of Laser Engineering 34 (2006): 275-82 Tittel, F. K., Y. A Bakhirkin, R. F. Curl, A. A. Kosterev, M. M. McCurdy, S. G. So, and G. Wysocki. “Laser-Based Chemical Sensor Technology: Recent Advances and Applications,” Advanced Environmental Monitoring. Berlin: Springer Verlag, 2006. (Accepted.) Tittel, F. K., G. Wysocki, A. Kosterev, and Y. Bakhirkin. “Semiconductor Laser-Based Trace Gas Sensor Technology: Recent Advances and Applications,” Middle Infrared Coherent Sources and Applications, Eds. M. Ebrahimzadeh and I. Sorokina, Springer NATO Science Series, 2006. (Accepted).


SYSTEMS—M.S. student Anjana Garud, with her B.S. degree from Manipal Academy, India, studies systems engineering at UHCL.

Presentations Bakhirkin, Y. A., A. A. Kosterev, T. Ajtai, R. Q. Yang, and F. K. Tittel. “Quartz-Enhanced Photoacoustic Spectroscopy Based Formaldehyde Sensor Using a Mid-IR Interband Cascade Laser,” SPIE Optics East Conf., Boston, MA, Oct. 1–4, 2006. McCurdy, M., Y. A. Bakhirkin, F. K. Tittel, and A. Sharafkhaneh. “Quantum Cascade Laser-Based Nitric Oxide Detection in Exhaled Breath of Patients with Chronic Obstructive Pulmonary Disease,” Laser Application to Chemical Security and Environmental Analysis (LACSEA 2006), Incline Village, NV, Feb. 5–9, 2006. Miller, H. J, Y. A. Bakhirkin, T. Ajtai, F. K. Tittel, C. J. Hill, B. Yang, and R. Q. Yang. “Detection of Formaldehyde Using Off-Axis Integrated Cavity Output Spectroscopy with an Interband Cascade Laser,” Laser Application to Chemical Security and Environmental Analysis (LACSEA 2006), Incline Village, NV, Feb. 5–9, 2006. Miller, H. J., B. McAdrew, A. A. Kosterev, Y. A. Bakhirkin, G. Wysocki, F. K. Tittel, and R. Q. Yang. “Development of Optical Trace Gas Monitoring Technology for NASA Human Space Flight,” Habitation 2006, Orlando, FL, Feb. 5–8, 2006. Tittel, F. K., Y. A. Bakhirkin, A. A. Kosterev, M. McCurdy, S. So, and G. Wysocki. “Semiconductor Laser-Based Trace Gas Sensor Technology: Advances and Opportunities,” 36th Winter Colloquium on the Physics of Quantum Electronics, Snowbird, UT, Jan. 2–6, 2006. Tittel, F. K., Y. A. Bakhirkin, A. Kosterev, and R. F. Curl. “Advances and Applications of Semiconductor-Based Trace Gas Sensor Technology (Enviro & Biom),” Laser Application to Chemical Security and Environmental Analysis (LACSEA 2006), Incline Village, NV, Feb. 5–9, 2006. Tittel, F. K., Y. A. Bakhirkin, R. F. Curl, A. A. Kosterev, R. Lewicki, S. So, and G. Wysocki. “L-PAS Based Gas Sensor Development at Rice: Jan. 2005–May 2006,” PNNL L-PAS Team Meeting, Laguna Beach, CA, June 12, 2006.

Tittel, F. K., Y. Bakhirkin, R. F. Curl, A. A. Kosterev, R. Lewicki, M. McCurdy, S. So, and G. Wysocki. “Recent Advances and Applications of Semiconductor Laser-Based Gas Sensor Technology,” University of Duesseldorf, Germany, July 4, 2006. Tittel, F. K., Y. Bakhirkin, R. F Curl, A. A. Kosterev, R. Lewicki, M. McCurdy, S. So, G. Wysocki, R. Maulini, J. Faist, L. Diehl, M. Trocolli, and F. Cappasso. “High Resolution Spectroscopy and Trace-Gas Detection with Stateof-the Art Thermoelectrically-Cooled cw Mid-Infrared Quantum Cascade Lasers,” The 2nd International Workshop on Quantum Cascade Lasers, Brindisi, Italy, Sept. 6–9, 2006. Tittel, F. K., Y. A. Bakhirkin, A. A. Kosterev, G. Wysocki, and R. F. Curl. “Laser-Based Chemical Sensor Technology: Recent Advances and Applications,” The 6th International Symposium on Advanced Environmental Monitoring, Heidelberg, Germany, June 27–30, 2006. Funding and proposals Tittel, F. K. “Advanced Trace Gas Monitoring Technology for NASA Human Space Flight,” NASA, March 1, 2003–March 31, 2007. $414,242. Tittel, F. K. “Broadly Tunable Infrared Quantum Cascade Laser Technology for Remote Sensing,” Department of Energy, STTR Subaward from Aerodyne Inc., July 1, 2006–June 15, 2007. $50,000. Tittel, F. K. “Development of QEPAS-Based Sensor Systems and Applications,” National Science Foundation (MIRTHE ERC), May 1, 2006-April 30, 2007. $78,185. Tittel, F. K. “High Resolution Spectroscopy with Lasers,” Welch Foundation, June 1, 2003–May 31, 2006. Tittel, F. K. “Low-Cost Integrated IR Quartz- Enhanced Photoacoustic Gas Sensor,” NSF, STTR Subaward from Ekips Technologies, Jan. 1, 2006–Dec. 31, 2006. $50,000. Tittel, F. K., NASA-JSC Graduate Fellowship for Matt McCurdy, July 1, 2005–June 30, 2006. $24,000. Tittel, F. K. “Optical Carbon Dioxide Field Isotope Ratiometer Department of Energy,” SBIR Subaward from Vistaphotonics,” Aug. 1, 2006–July 31, 2008. $120,000. Tittel, F. K. “Quantum Cascade Laser-Based Sensors for Chemical and Environmental Analysis,” Texas Advanced Technology Program, Rice University PI., Jan. 1, 2003–Aug. 30, 2006. $187,380. Tittel, F. K. “Quantum Cascade Laser Photoacoustic Sensor for Chemical Warfare Agent Detection,” Pacific Northwest National Laboratory, Rice University, PI, Jan. 3, 2005–Sept. 30. 2006. $210,000. Tittel, F. K. “Quartz Enhanced Photoacoustic Spectroscopy Methane System Development,” Savannah River National Laboratory, May 31, 2006–Sept. 30, 2007. $135,674. Tittel, F. K. “Shipboard Atmospheric Propagation Measurements, Department of Defense, Subaward from Aculight Inc., Oct. 1, 2006–Feb. 22, 2007. $26,000. Tittel, F. K. “Ultra-Sensitive Detection of Aerosol Precursors Including Ammonia,” Aculight, Botthell, WA, Sept. 9, 2005–March 26, 2006. $26,000.

The original NASA Logo


The Effect of Martian Dust on Radiator Performance

than the test surface of the coupon. The system included an apparatus that deposited dust uniformly on multiple coupons in situ in the vacuum chamber. (An invention disclosure has been filed through NASA-JSC and UH.) Experiments were completed for seven temperature operating conditions under vacuum by D. Keith Hollingsworth, Larry C. Witte, and (10-6 torr). The effect of dust loading was dramatic: high-emittance surfaces see an approximately 50 percent reduction in Ashley Higgins emissive power as the surface emittance drops toward that of the dust simulant. The highest dust loading produced a thickABSTRACT—Thermal radiators are ness of roughly 100 microns. a critical element for lunar or Martian The weakest element of the system was habitation missions. Experiments by the manual temperature control used to University of Houston and NASA adjust the 16 heaters necessary to establish investigators have demonstrated a drathe eight coupons at steady-state conditions. matic degradation in radiator emitUnder the control of an experienced operatance attributed to the accumulation of tor, the system would require more than a Martian dust simulant. The ISSO three hours to stabilize at single set of conmini-grant funded the development of ditions. An automatic controller would an automated facility that will lower allow a significant reduction in the time operational costs for future tests. required for a single run. The ISSO mini-grant funded a conversion of this system to automatic control. The U S T I S E X P E C T E D TO B E A M A J O R idea is that the measured temperature and contributor to the local environmenheater voltage would be used to compute an tal conditions at the Martian surface estimated set point for each heater. That set and may also be a substantial problem for point would be communicated to the heater long-term equipment on the lunar surface. power supply electronically so that manual The ISSO Mini-grant afforded researchers adjustment via potentiometers of the heater D. Keith Hollingsworth funding intended to enhance an existing power would be replaced by transistor-gated University of Houston/NASA Johnson Space control of the heater power. Both the main Center effort to measure the radiative emittance of thermal radi- and guard heaters were automatically controlled so that the ator coatings laden with simulated Martian dust. This larger coupon arrives at the set point temperature with essentially a project—“The Mars Radiator Characterization Experimental zero temperature difference within the structure of the coupon. Program”—received NASA funding in 2002-2004 and produced measurements of the reduction in effective radiative Results emittance as (simulated) Martian dust accumulates on surfaces Each test coupon was driven by two heaters: a main heater that coated with high-emittance materials. This work was motivated provides the measured power to the radiator surface and a by the expectation that radiators will be a critical element in the guard heater that is set to maintain the remainder of the coupon thermal control system for future robotic and human explo- surface at the same temperature as the surface. Temperatures of ration missions to Mars. Radiator performance depends on the the test surface and of the surrounding structure were measured radiating surface area, the emittance and absorptance of the by resistance temperature devices (RTDs). The temperature of radiator surface, the temperature of the radiator, the effective the vacuum chamber walls was controlled by a separate system sky temperature surrounding the radiator, solar radiation, and operated by NASA staff. atmospheric irradiation levels. Radiative properties of the surFor all eight coupons there were a total of 16 RTDs to moniface are affected by dust accumulation and surface oxidation. tor and 16 heaters to adjust. An IoTech Daqbook data acquisition system collected the temperature and power data while sixProject goals teen precision DC power supplies provided manually-controlled During the original NASA project (Hollingsworth et. al., 2004 current to the heaters. Data from the IoTech were recorded on a and 2006), an apparatus was developed to measure the radia- laptop computer. The operator observed the 16 RTD readings and tive emittance of test coupons in the JSC Energy Systems adjusted the power supplies to arrive at the target temperature. Vacuum Chamber. The chamber produced a range of sky temTo implement automatic control, four IoTech digital-toperatures typical of Martian conditions. The Martian dust analog boards and associated power conditioning equipment “simulant” used by NASA is Carbondale red clay. Eight radia- were added to the data acquisition system. The power supply tor coupons were constructed so that two examples of each of for the coupon heaters was modified so that either transistor three candidate radiator coatings and a control surface could be control or potentiometer-control (manual operation) could be tested at each dust loading. The coupon design included active selected by a switch. guard heating that prevented heat loss from all surfaces other A custom-written software controller in the laptop generated

D


these follow-on efforts coincided with the redirection of NASA’s efforts away from a mission to Mars for which dust storms were an obvious problem and toward a lunar mission where the problems posed by dust require a new evaluation. Efforts to date for renewed funding have not been successful. Publications D. K. Hollingsworth, L. C. Witte, J. Hinke, and K. Hurlbert. “The Effect of Martian Dust on Radiator Performance,” Proc. ASME Summer Heat Transfer/Fluids Engineering Division Joint Conference: ASME HT-FED04-56577, 2004. D. K. Hollingsworth, L. C. Witte, J. Hinke, and K. Hurlbert. “Reduction in the Emittance of Thermal Radiator Coatings Caused by the Accumulation of Simulated Martian Dust,” Applied Thermal Engineering 26 (2006): 2383-92.

Figure 1. Heating of one coupon from room temperature to 320 K, cooling from 320 K to 305 K. For the heating case the 95% confidence uncertainty at steady state is ± 0.25 K. For the cooling case, the uncertainty during steady operation is ± 0.13 K.

appropriate heater settings which were then converted to analog voltages by the D-to-A boards. Those voltages drove power transistors which generated a current sufficient to drive the heaters at the desired power. The resulting heater voltages, along with the coupon and guard temperatures, were read by the data acquisition system and the process repeated. A proportional integral (PI) control strategy was implemented in the same VisualBasic code that handles the data acquisition. To demonstrate the automatic control system, scientists had one coupon exercised in room air in the laboratory. Operation of the system in room air is a more severe test of the control system than its operation in high vacuum. For the heating case shown in Fig. 1, the coupon is initially at room temperature and the system given a target of 320 K. The coupon temperature traversed the 25 K difference in roughly 9 minutes and was steady at an average of 319.8 K with a 95 percent (two-sigma) singlesample variation of ± 0.25 K. This uncertainty is 1.0 percent of the difference between the target and ambient temperatures and is on the order of the uncertainty produced by the measurement system. For the cooling example, the coupon was initially at 320 K and cooled by natural convection under automatic control to a target temperature of 305 K. The cooling process occurred over 6 minutes and the system achieves a steady state at 305.0 ± 0.13 K. This uncertainty is 1.3 percent of the mean rise above ambient. In vacuum, the heat transfer rate from the coupons would be much lower and the transients longer; however, response faster than the 2-3 hours per point typical of manual operation is expected. Automatic control proved to be a successful and worthwhile addition to the system. A new proposal for continued work featuring the strong potential of cost-savings produced by the improved system was submitted to both the NASA Johnson Space Center Director’s Discretionary Fund ($200,000) and to the NASA Constellation/Exploration Program. The timing of

Presentations D. K. Hollingsworth. “The Effect of Martian Dust on Radiator Performance,” NASA Contamination and Coatings Workshop, Aug. 3–4, 2005. D. K. Hollingsworth, L. C. Witte, and J. Hinke. “The Effect of Martian Dust on Thermal Radiators,” National Teleconference Meeting of the NASA Advanced Life Support Group, Johnson Space Center, Aug. 12, 2004. D. K. Hollingsworth, L. C. Witte, J. Hinke, and K. Hurlbert. “The Effect of Martian Dust on Thermal Radiators,” Poster HLS46, Habitation 2004, National Conference, Orlando, FL, Jan. 4–7, 2004. Proposals Project Managers: George Tuan, Katy Hurlbert; UH Investigators: D. Keith Hollingsworth, Larry C. Witte. “Dust Impact of Radiator Test Stand,” NASA Johnson Space Center Director’s Discretionary Fund, NASA JSC, Nov. 2005. FY 2006 and 2007. $200,000. (Status: Not funded by JSC CDDF.) Project Managers: George Tuan, Katy Hurlbert; UH Investigators: D. Keith Hollingsworth, Larry C. Witte. “Dust Impact of Radiator Test Stand,” NASA Constellation/Exploration Program, Level 2. (Status: Not funded.)

CREED—Inside the UH Cullen College of Engineering Building, the Engineers’ Creed reads, “As a professional engineer, I dedicate my professional knowledge and skill to the advancement and betterment of human welfare.”


Mechanical Foot Stimulation Results in Lower Limb Muscle Activation

Strategic Planning,” Texas Association for Health, Physical Education, Recreation, and Dance (TAHPERD), Galveston, TX, Dec., 2003. Layne, C. S., A. P. Mulavara, J. J. Bloomberg, K. E. Forth, M. F. Baxter, J. J. Houser, I. B. Kozlovskaya. “Using Dynamic Foot Stimulation During Space Flight as a Countermeasure to by Charles S. Layne Muscle Degradation,” 24th Annual Intl. Conf. of the IEEE/EMBS (Institute of Electrical and Electronics Engineers, Inc. and Engineering in Medicine and HE AIM OF INVESTIGATION IN 2005 WAS Biology and Annual Fall Meeting of the to determine the modulating effect BMES (Biomedical Engineering Society), of background muscle activity on Houston, TX, Oct., 2002.(Invited.) enhanced neuromuscular responses to mechLayne, C. S., K. E. Forth, and A. F. Abercromby. anical foot stimulation. A small solenoid “Spatial Factors Influence the Generation of embedded within a platform provided nonNeuromuscular Responses to Foot Stimunoxious stimulation to the lateral portion of the lation,” 14th Humans in Space Conf., Banff, sole for 100ms at 3mm protrusion. Stimulation Alberta, Canada, May, 2003. was applied during different contraction levels Layne, C. S., K. T. Nguyen, and K. E. Forth. of the homonymous muscle and of remote, “Muscle Contractions in Response to Foot Jendrassik-like contractions. We measured Stimulation as an Inflight Counter root mean square electromyography from the measure,” 16th Humans in Space Sympo soleus and lateral gastrocnemius. Homonysium of the Intl. Academy of Astronautics mous muscle contraction linearly increased the (IAA), May, 2007. neuromuscular response to foot stimulation, Nguyen, K. T. and Layne, C. S. “Identifying although no effect was exhibited from remote Neuromuscular Inhibition in the Human contractions. The levels of response to stimuLower Leg Using Mechanical Stimulation lation in all conditions were 80-100 percent of to the Foot,” The Houston Society for Charles S. Layne maximal contraction levels. The application of Engineering in Medicine and Biology, The mechanical foot stimulation can be used to 22nd Annual Houston Conf. on Biomedical Engineering elicit and enhance neuromuscular activity of the triceps surae musResearch, Feb., 2005. “Runner up” award: one out of four recogcles, particularly when combined with preexisting “background” nitions among 77 posters in Student Poster Competition. voluntary contractions. This activity could be used to attenuate neu-

T

romuscular degradation experienced during prolonged bedrest and during extended stays in microgravity. Publications Forth, K.E. and Layne, C.S. “The Influence of Loading and Postural Context on the Neuromuscular Response to Mechanical Foot Stimulation.” (Under review) Forth, K.E., and Layne, C.S. “Background Muscle Activity Enhances the Neuromuscular Response to Mechanical Foot Stimulation,” American J. of Physical Medicine & Rehabilitation, 86 (2006): 50-56. Presentations Forth, K. E. and C. S. Layne. “The Neuromuscular Response to Context-Specific Foot Stimulation,” The Houston Society for Engineering in Medicine and Biology, The 22nd Annual Houston Conf. on Biomedical Engineering Research, Feb., 2005. Forth, K. E. and C. S. Layne. “Spatial and Temporal Mechanical Foot Stimulation Parameters Influence Neuromuscular Responses in the Lower Limbs,” Sigma Xi Student Research Day, University of Houston, April, 2004. Layne, C. S., K. T. Nguyen, and K. E. Forth. “Muscle Contractions in Response to Foot Stimulation as an Inflight Countermeasure,” 16th Humans in Space Symposium of the Intl. Academy of Astronautics (IAA), May, 2007. Layne, C. S. “Budget Crunches and the Future: The Need for


Funding Layne, C. S. “Developmental Evaluation of a Dynamic Foot Stimulation Device,” National Aeronautics and Space Administration (NASA), Jan., 2004. $59,592 (direct costs). Contract modification, April 2004. $20,000 added. Layne, C. S. “Using Patterned Stimulation of the Soles to Prevent Muscle Degradation,” Faculty Research Opportunity Award (FROA), College of Education, University of Houston, Feb. 2003. $2,835. (Funded.) Student Researchers During the previous reporting period, ISSO-supported student Katharine E. Forth, who earned her Ph.D. in Motor Control from the Department of Health and Human Performance, University of Houston. She is continuing in her role as a post-doctoral fellow in the Neurosciences Laboratory at the NASA-Johnson Space Center. During the reporting period, Andrew Abercromby, who previously worked on the project, obtained his Ph.D. degree in Motor Control from the Department of Health and Human Performance, University of Houston. Dr. Abercromby is now employed by Wyle Life Sciences at NASA-JSC. Ms. Kimthu Nguyen in 2005 earned her M.S. in the exercise science program in the Department of Health and Human Performance, University of Houston.

Contaminant Removal from Fuel Cells for Aerospace Applications by Jack Y. Lu ABSTRACT—UHCL researchers focused on the rational design and synthesis of new MOF materials for a PEM FC fuel processing system in which the MOF material is an integral component and the key for contaminant removal in hydrocarbon or ammonia fuel processors. Design and synthesis of desirable MOF materials for uses in fuel processors will have immediate impact on a wide range of space applications.

S

YNTHESIS OF FUNCTIONAL MATERIALS REPRESENTS ONE OF

the great challenges in current research. The coordination polymers have been found with wide range of applications such as molecular separation and pollution prevention in air, liquid and water systems, where they can be used as ion exchangers and molecular sieves. The objective of the proposal was to design and develop robust metal-organic framework (MOF) materials that may selectively remove small molecule contaminant(s) produced by the fuel processing system of a fuel cell. Experimental Activity, Results and Discussion The reactions of Cd(NO3)2 • 4H2O with imidazol-4,5-dicarboxylic acid and 4, 4’- bipyridine under hydrothermal reaction conditions resulted in two new metal-organic polymers.1 The hydrogen-bonding linked a 3-D structure of complex 2 composed of covalent pleated sheets. The pleated sheet conformation here is derived from the bonding-mode of the tetradentate HIDC2- ligands and the rigid BPY spacers. The rectangular grids (BPY-Cd-HIDC2--Cd-HIDC2--Cd-BPY-CdHIDC2--Cd-HIDC2--Cd) in the 2-D covalent pleated sheet conformation network have corner metal to metal distances of 13.564 x 11.754 Å (Fig. 1).

Figure 1. View of the Rectangular Grids in the Structure

Lu, J. Y. and A. M. Babb. “An Extremely Stable OpenFramework Metal-Organic Polymer with Expandable Structure and Selective Adsorption Capability,” Chem. Commun. (2002): 1340-41. Lu, J. Y. and A. M. Babb. “An Unprecedented Interpenetrating Structure with Two Covalent-Bonded Open-Framework of Different Dimensionality,” Chem. Commun. (2001): 821-22. Lu, J. Y. and L. Chen. “The First Bromonicotinato-Coordinated Metal-Organic Polymer Featuring Covalent 2-D Layer Alternately Sandwiched by 1-D Intra-Hydrogen Bonding Networks,” Inorg. Chem. Commun. 7 (2004): 350-54. Lu, J. Y. and V. Schauss. “A Novel Nanostructured OpenChannel Coordination Polymer With an Included FusedPolyiodide Ring,” Inorg. Chem. (2002): 1945-48. Lu, J. Y. and Zh. Ge. “Synthesis and Structures of Two New Metal-Organic Polymers Containing Imidazoldicarboxylate Ligands for Hydrogen Bonding Networks, One with a Covalent Pleated Sheet Conformation,” Inorg. Chim. Acta 358 (2005): 828-33.

References 1 J. Y. Lu and Zh. Ge, “Synthesis and Structures of Two New Metal-Organic Polymers Containing Imidazoldicarboxylate Ligands for Hydrogen Bonding Networks, One with a Covalent Pleated Sheet Conformation,” Inorg. Chim. Acta, 358 (2005): 828-33. Publications Lu, J. Y. and A. M. Babb. “A Simultaneous Reduction, Substitution and Self-Assembly Reaction Under Hydrothermal Conditions Afforded the First Diiodopyridine Copper(I) Coordination Polymer,” Inorg. Chem. 41 (2002): 1339-41. Lu, J. Y. and A. M. Babb. “A Unique Eclipsed 2-D Coordination Polymer with Removable Iodine Molecules in the OpenChannel Structure,” Chem. Commun. (2003): 1346-47.

FLUID DESIGN—Prof. Jack Y. Lu stands at the Masuru Takiguchi marble sculpture, “The Ocean,” in the UHCL Bayou Building.


Energy-to-Peak Induced Norm Upper Bound Control Approach for Collocated Structural Systems

induced L2–L∞ norm of the system that can be calculated effectively. The qualifications of the proposed upper bound and the control design methodology are verified using a large scale model of the International Space Station (ISS). Consider a structural system with collocated sensors and actuators in a second order vector form represented by (1)

by Mona Meisami-Azad, Javad Mohammadpour, and Karolos M. Grigoriadis ABSTRACT—UH researchers determine an analytical upper bound for the energyto-peak gain or L2–L∞ induced norm of collocated structural systems. The proposed technique does not require solving Lyapunov equations or a set of LMIs usually needed to compute the L2–L∞ induced norm. Furthermore, an output feedback control law has been developed which ensures that the Karolos M. Grigoriadis closed loop system of the collocated structure and the output feedback control achieves a desired L2–L∞ norm bound.

A

USEFUL MEASURE OF PERFORMANCE OF A DYNAMICAL

system is the induced L2–L∞ or energy-to-peak norm that dictates the peak value (L∞norm) of the system subject to a bound on the energy (L2 norm) of the input.1 Computation of the L2–L∞ norm of a system using the linear matrix inequality (LMI) formulation or the Lyapunov equation approach can be very intensive, especially for large scale systems. The LMI problem has a polynomial time complexity with respect to the number of decision variables, while solution of Lyapunov equations is of quadratic complexity with respect to computations and storage requirements. Consequently, the use of these tools for performance analysis and control of large scale systems is limiting.2 The present work examines the induced L2–L∞ analysis problem and the corresponding output feedback control design for collocated structural systems. Toward this purpose, we consider the LMI analysis conditions that characterize the L2–L∞ norm of the system and propose a particular solution for the Lyapunov function in the LMIs. The proposed bound is shown to be exact for the one-degree-of-freedom structure. This work demonstrates the high accuracy of the proposed upper bound on the


, where

represent input disturbance matrix with full column rank, mass matrix, stiffness matrix, and damping matrix, respectively. The vectors and are the vector of displacements, control input, external/disturbance signal, and measured output, respectively. For a fixed initial condition x(0) = 0, the induced energy-topeak gain is defined as .

(2)

The following result provides an explicit formula for computation of the induced L2–L∞ norm upper bound of collocated structural systems that only needs the calculation of the maximum eigenvalue of matrices generated from the system data. Theorem 1: Consider the system in (1). This system has an induced L2–L∞ norm ν from the input u(t) to the output y(t) that satisfies the following bound .

(3)

It is worth mentioning that for the single degree-of-freedomcase (n=1), the proposed upper bound for the induced L2–L∞ performance is exactly the same as the actual induced L2–L∞ norm of the system.3 Next, consider the collocated system in (1) along with a controlled output equation .

(4)

The collocated L2–L∞ control synthesis problem is to design a symmetric static output feedback gain H = HT such that the output feedback control law (5) renders the closed-loop system stable with an L2–L∞ norm less than a prescribed scalar ν > 0, i.e. ,

(6)

where Tzw is the closed-loop transfer function mapping w(t) to z(t). We now present the following result that provides an explicit expression for the output feedback gain H that guarantees a closed-loop L2–L∞ norm less than a bound ν. Theorem 2: A control law as in (5) whose interconnection with the collocated system (1) satisfies the performance bound (6) is derived as following: a) If F is square and invertible, H can be computed as ,

(7)

where Figure 1: Assembly Phase 8A-OBS of the ISS Model

.

(8)

(b) If FFT is singular, H can be computed as ,

(9)

where η is given by (8). Results We apply the proposed L2–L∞ bound analysis and output controller design to a very large scale structural system model. We consider the finite element structural model for the assembly phase 8A-OBS of the International Space Station (ISS) with collocated control, Rayleigh damping, and 720 states, as shown in Fig. 1. Computation of the induced L2–L∞ (energy-to-peak) norm through solving the Lyapunov equation requires 16.548 seconds; the obtained norm is equal to 5.9051. However, it only takes 0.3607 seconds to calculate the norm bound via the proposed analytical bound approach which provides a bound equal to 5.935.We observed that the bound estimates the norm closely and its calculation is computationally efficient. Table 1 shows the results of the computations performed in order to determine the energy-to-peak feedback control gains and the required computational times for different desired closed-loop norm bounds. For instance, designing an output feedback controller to

guarantee that the energy-to-peak norm of the closed-loop system is less than or equal to 0.5 takes 0.2642 seconds. The actual norm of the closed-loop system with the designed controller has been determined to be 0.4998. It takes 9.1099 seconds to calculate this norm using MATLAB. This is almost 65 times longer than our proposed method to determine the energy-topeak norm bound computed in 0.1349 seconds. Notice that the computation of an L2–L∞ controller for this system using standard methods fails since a solution by Lyapunov equations or LMIs for a system of this size is computationally prohibitive. References 1 C. Scherer and S. Weiland. “Lecture Notes DISC Course on Linear Matrix Inequalities in Control,” Version 2.0, April 1999. 2 R.E. Skelton, T. Iwasaki, and K. M. Grigoriadis. A Unified Algebraic Approach to Linear Control Design. London; Bristol, PA: Taylor & Francis, 1998. 3 M. MeisamiAzad, J. Mohammadpour, and K.M. Grigoriadis. “Energy-to-Peak Norm Upper Bound for Collocated Structural Systems,” scheduled for publication in Proc. SPIE 14th Annual International Symposium on Smart Structures and Materials, San Diego, CA, March 2007.

Table 1: Results and Comparisons for the 8A-OBS ISS Model Desired closed-loop L2–L∞ norm bound

Time to calculate feedback Exact L2–L∞ norm of the gain using Th. 2 (sec) closed-loop system

Time to calculate exact L2–L∞ norm (sec)

Time to calculate L2–L∞ norm bound (sec)

5

0.2650

4.9910

9.1441

0.1294

1

0.2645

0.9993

9.1358

0.1406

0.5

0.2642

0.4998

9.1099

0.1349

0.1

0.2642

0.1

9.1034

0.1319


TRUSS—Dr. Heidar Malki (l.) and Dr. Karolos M. Grigoriadis have collaborated in past ISSO projects, including “A Neural-Network-Based Approach for Control of Vibration in a Black Hawk Helicopter.” Here, they stand with a mechanical truss used to simulate vibrations and measure their effects.

Publications Bai, Y., and K.M. Grigoriadis. “H∞ Collocated Control of Structural Systems: An Analytical Bound Approach,” AIAA Journal of Guidance, Control and Dynamics 28.5 (2005): 850853. Hiramoto, K., and K.M. Grigoriadis. “Integrated Design of Structural and Control Systems with a Homotopylike Iterative Method,” in Proc. American Control Conference, (2005). Hiramoto, K., Y. Bai, and K.M. Grigoriadis. “Upper Bound H∞ and H2 Control for Symmetric Mechanical Systems,” Proc. International Federation of Automatic Control World Congress, (2005). Hiramoto, K., and K.M. Grigoriadis. “Integrated Design of Structural and Control Systems with a Homotopylike Iterative Method,” International Journal of Control 79.9 (2006): 1062-73. MeisamiAzad, M., J. Mohammadpour, and K. M. Grigoriadis. “An H2 Upper Bound Approach for Control of Collocated Structural Systems,” Proc. American Control Conference, New York, NY, June 2007. (Accepted.) MeisamiAzad, M., J. Mohammadpour, and K. M. Grigoriadis. “Energy-to-Peak Norm Upper Bound for Collocated Structural Systems,” Proc. SPIE 14th Annual International Symposium on Smart Structures and Materials, San Diego, CA, March 2007. (Accepted.) Mohammadpour, J., M. Meisami-Azad, and K. M. Grigoriadis. “An Efficient Approach for Damping Parameter Design in Collocated Structural Systems Using An H2 Upper Bound,” Proc. American Control Conference, New York, NY, June 2007. (Accepted.) Mohammadpour, J., M. Meisami-Azad, and K. M. Grigoriadis. “An Efficient Approach for Integrated Design of Damping and Feedback Controllers: H2 and H∞ Perspectives,” Structural and Multidisciplinary Optimization, Feb. 2007. (To be submitted.) Presentations Hiramoto, K., and K.M. Grigoriadis. “Integrated Design of Structural and Control Systems with a Homotopy Like Iterative Method,” in Proc. American Control Conference, Portland, OR, 2005. Mehendale, C. and K. M. Grigoriadis. “Control of Timedelayed LPV Systems Using Delayed Feedback,” in Proc. International Federation of Automatic Control World Congress, Prague, Czech Republic, 2005.

RESEARCH HUB—Hoffman Hall is a major UH research center housing the Dept. of Computer Science, the Dept. of Mathematics, and the innovative Texas Learning and Computation Center (TLC2).


Electromagnetic Probes of Biological Molecular Motors (2005) and Low-Frequency Dielectric Spectroscopy of Martian Soil Samples (2004) by John H. Miller, Jr.

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ISSO-FUNDED PROJECTS ARE to (1) study the electromagnetic properties of active enzyme complexes in live organisms and (2) investigate Martian soil simulants and live cell suspensions using low-frequency dielectric spectroscopy and related techniques. Our studies have focused on both linear (dielectric) and nonlinear (harmonic) responses and include studies of whole cells, extracted organelles, such as mitochondria and chloroplasts, and whole organisms. Continuance of these studies has been aided by a Postdoctoral Aerospace Fellowship (PDAF) awarded to Dr. David Warmflash. Results are discussed in a companion report titled: “Martian Soil Biosensors Based on Dielectric Spectroscopy.” (p. 21) New resulting publications have benefited from both the previous mini-grant, as well as the ongoing PDAF program and are thus also listed here for convenience. HE AIMS OF THESE ONGOING

Publications Sanabria, Hugo, John H. Miller, Jr., Andreas Mershin, Richard F. Luduena, Alexandre A. Kolomenski, Hans A. Schuessler, and Dimitri V. Nanopoulos, “Impedance Spectroscopy of α-β Tubulin Heterodimer Suspensions,” Biophys. J. 90 (2006): 4644-50. Nawarathna, D., J. R. Claycomb, G. Cardenas, J. Gardner, D. Warmflash, J. H. Miller, Jr., and W. R. Widger, “Harmonic Generation by Yeast Cells in Response to Low-Frequency Electric Fields,” Physical Review E 73 (2006): 051914-1—6. Claycomb, James R. and John H. Miller, Jr., “Superconducting and High-Permeability Shields Modeled for Biomagnetism and Nondestructive Testing,” IEEE Trans. on Magnetics 42 (2006): 1694-1702. Sanabria, Hugo and John H. Miller, Jr., “Relaxation Processes Due to the Electrode-Electrolyte Interface in Ionic Solutions,” Physical Review E 74 (2006): 051505—1-9. Mershin, Andreas, Hugo Sanabria, John H. Miller, Dharmakeerthna Nawarathna, Efthemios M. C. Skoulakis, Nikolaos E. Mavromatos, Alexandre A. Kolomenskii, Hans A. Schuessler, Richard F. Luduena, and Dimitri V. Nanopoulos, “Towards Experimental Tests of Quantum Effects in Cytoskeletal Proteins,” Chapter 4 of The Emerging Physics of Consciousness, Ed. Jack A. Tuszynski. The Frontiers Collection. Springer Berlin Heidelberg, 2006, pp. 95-170. (Invited book chapter.) Presentations Nawarathna, D., J. Gardner, G. Cardenas, J. R. Claycomb, J. H. Miller, Jr., and W. R. Widger. “Electromagnetic Probing of Mitochondria and Chloroplasts Reveals Unique Harmonics Due to Specific Components of the Electron Transport

Chain,” Biophysical Society 50th Annual Meeting, Salt Lake City, UT, Feb. 18–22, 2006. Nawarathna, D., J. Gardner, G. Cardenas, D. Warmflash, J. Miller, W. Widger, and J. Claycomb. “Nonlinear Electromagnetic Responses of Active Molecular Motors in Live Cells and Organelles,” Bull. Am. Phys. Soc. 51.200 (2006), March Meeting of the American Physical Society, Session B29, Focus Session on Microorganism Motility, Baltimore, MD, March 13–17, 2006. Vajrala, Vijayanand, James Claycomb, and John H. Miller, Jr., “Analytical Model of Induced Transmembrane Potentials in Cells and Organelles,” Bull. Am. Phys. Soc. 51, 1524 (2006), March Meeting of the American Physical Society, Session Y26, Focus Session on the Physics of Physiological Systems, Baltimore, MD, March 13–17, 2006. Miller, J. H., Jr., D. Warmflash, D. Nawarathna, J. Gardner, G. Cardenas, and W. R. Widger, “Low-Frequency Electromagnetic Probes of Live Organisms,” Session on Biogeophysics, 2006 Joint Assembly between the American Geophysical Union, Geochemical Society, Microbeam Analysis Society, Mineralogical Society of America, Society of Exploration Geophysicists, and Unión Geofísica Mexicana, Baltimore, MD, May 23–26, 2006. (Invited Talk.) Funding and Proposals Miller, J. H., Jr. “Dielectric Spectroscopy of Chemical and Biological Systems,” Robert A. Welch Foundation, June 1, 2004–May 31, 2007. $165,000. Miller, J. H. Miller, Jr., PI, W. R. Widger, Co-I. Dale J. Hamilton, MD, and Richard J. Robbins, MD, of Methodist Hospital. “Noninvasive Sensors of Metabolic Activity,” NIH, Bioengineering Approaches to Energy Balance and Obesity (R21), $150,000/yr for three years. (Direct costs.) Miller, J. H., Jr., PI. “Nonlinear Impedance Spectroscopy of Chemical and Biological Systems,” Robert A. Welch Foundation, renewal of E-1221, $60,000/year for three years. (Direct costs.) Planned submissions NIH (R01), United Mitochondrial Disease Foundation and American Diabetes Assoc. Marin Laughlin, an NIDDK program director in NIH, and others in NIBIB and NHLBI have expressed considerable interest in our ideas for detecting mitochondrial function.


Space Radiation Shielding Modeling Consortium

ment performance. The need exists to understand the actual measurement of crew radiation doses recorded on current missions and to explore the predicted doses for future missions and new spacecraft designs. These planning tasks call for significant flexibility to simulate a wide variety of conditions such as those likely to exist within spacecraft in interplanetary space and on the surface by Lawrence S. Pinsky of the moon and Mars. In addition, many experiments need to simulate the effects that space radiation will have on their instruABSTRACT—Our objective is to proments. These effects can either be direct, as vide a Monte Carlo-based software tool part of the actual measurements, in the case of to model the radiation environment in experiments like MARIE or AMS (Alpha space that will enable the evaluation of Magnetic Spectrometer), or as a background, radiation shielding materials. The tool as in GLAST (Gamma-ray Large Area Space is to include the basic physics transport Telescope), HUBBLE, or the JWST. Further, code known as FLUKA embedded in a there can be operational concerns such as graphical user interface infrastructure degradation of instruments from radiation that includes the capability to provide damage or data interference, as in the case of the input for simulation and analysis single event upsets. tools needed to evaluate and display the Finally, the development of flight hardware results. The practical goal of this projto serve as active dosimeters onboard the next ect is to produce a code considerably generation of spacecraft will require Monte more accurate and user-friendly than Carlo-based codes as part of the design and existing Monte-Carlo-based tools for evaluation process, as well as their use during the evaluation of space radiation the subsequent analysis of the mission data. shielding. We will cooperate with other Improvement in the accuracy of the software members of the consortium to develop that NASA currently uses for these tasks will an event generator for Nucleusresult from this project. This research will Lawrence S. Pinsky Nucleus interactions that is accurate to substantially increase the reliability of the within 25 percent in any significant channel over enerprojected results. gies relevant for evaluating issues of space radiation. Summary of Task Accomplishments E HAVE CHOSEN TO ADAPT THE EXISTING FLUKA During the performance of this effort as part of the NASA Space Monte Carlo code to the task of simulating the radi- Radiation Modeling Consortium, the University of Houston ation environment in space. In a prior NASA-funded Group focused its attention upon tasks related to the FLUKA code project (NAG8-1648), we succeeded in embedding two existing and its evolution as a useful tool in the simulation of the Space event generators within FLUKA to allow the direct simulation Radiation environment. At present, the FLUKA code that has of nucleus-nucleus interactions. For energies above a few resulted from this project is the sole integrated Monte Carlo code GeV/nucleon, we chose the DPMJET event generator and for in the world that has the full capability to simulate the Space the energy range below that down to ~100MeV/nucleon we Radiation environment over the full range of energies up to those incorporated an existing version of the RQMD event generator. primary particles detected in air showers. This intermediate energy range is the focus of this project. The As a result of the efforts of the Houston Group in concert with principal tasks at hand for the current project are the develop- the FLUKA team at CERN and in the INFN Milan Group, ment of a more accurate replacement for the current RQMD FLUKA now embeds two of the most respected heavy ion event version and an extension down to the lowest threshold energies generators in existence, RQMD and DPMJET. Both of these for nucleus-nucleus inelastic interactions. Finally, we hope to event generators have been checked to validate their ability to be able to contribute to the task of creating a new graphics rep- replicate the available measurements of heavy ion interactions, resentation format optimized for transport type problems that including those made by our complementary NASA-sponsored can be used by a subsequent conversion tool from existing Measurement Consortium. Further, in developments in physics, CAD formats. The acronym FLEUR-S (FLuka Executing FLUKA now has the ability to provide detailed predictions of the Under Root-for Space applications) was adopted for the code post irradiation environment attributed to activation of the ambiduring prior development. That acronym will continue to be ent material. With respect to user interface, considerable effort employed during this project. has been expended in producing a user-friendly GUI interface to prepare FLUKA simulations and to analyze and view the results. Task Significance These user interface tools are designed to incorporate standard The ability to simulate the radiation environment in space and the space radiation fields of interest to NASA, such as the modulated transport of these particles through spacecraft shielding materials GCR environment, the trapped radiation environment, and modare crucial to concerns such as crew health and electronic equip- els for some of the benchmark prior solar particle events.

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Although this project is coming to a close, FLUKA will continue to be supported by the FLUKA Collaboration. Improvements will continue to evolve in physics-simulated tools, as well as in user-interface tools. Because of their prior support of this program, NASA has been assured continued access to these future improvements under the standard CERN/INFN FLUKA License. This past year has seen several major accomplishments by the UH group in support of the Modeling Consortium, in general, and our FLUKA-based tasks, in particular. The UH Group has long advocated acquiring data in the energy range above 1 GeV/A for several reasons. Not only is the primary Cosmic Ray flux still significant through these higher energies, but there is currently a wide disagreement between existing nucleus-nucleus interaction models in this regime. The decision was made to pursue measurements at the AGS during the summer of 2005, before the AGS floor itself was to become unavailable for several years. To that end and because of the lack of time and funding to develop additional detectors, the UH group agreed to employ existing detectors and expertise to enhance the date acquired during those runs. Additional funding was requested to cover expenses, and in concert with the LBL Measurement Consortium Group, an additional stipend had been awarded a graduate student to work on these measurements as his Ph.D. thesis. In addition, the UH group also participated in measurements at the HIMAC facility at NIRS in Chiba, Japan, this past February. Professor Billy Mayes of the Physics Department at UH has joined our effort for these measurements, along with Andrea Mairani, a graduate student. During the AGS run, data were taken with C, Si and Fe beams of ~3, 5 and 10 GeV/A incident on thin (~ 0.5 interaction length) targets of C, Al, Fe and Cu, as well as a number of thick and compound targets including polyethylene. Data taken during the process represent the Ph.D. thesis project for Najib Elkhayari; these data are currently being analyzed. That analysis is separately funded through 2007. The results of that effort will be made available to the FLUKA Collaboration to guide the needed modifications to the event generators. During the HIMAC run, data were acquired for Si at 800 MeV/A, Fe at 500 Mev/A and Oxygen at 270 MeV/A. Similar targets to those used at the AGS were used. The data taken will be analyzed by Mr. Mairani and also made available to the FLUKA Collaboration. Models within Fluka The past year has also seen significant progress in the primary effort of the UH Group to enhance the models within FLUKA and the user interfaces to the FLUKA code itself. While we are closely tied to the entire FLUKA team at CERN and INFN in Italy, and we have a significant influence on the direction that this broader team chooses to focus upon in its effort, the items reported here are exclusively those which have been directly supported by the funding received through the Modeling Consortium. Dr. Anton Empl has developed and released via the project website a ROOT-based GUI analysis tool to allow visualization of color-coded fluence plots superimposed on line drawings of the input geometry. Work is in progress to expand that capability to allow the plotting of all standard FLUKA scoring capabilities

via an entirely new GUI interface based on the use of the GTK graphics software. Significant progress has also been made on the coding of an XML-based GUI front-end tool, known as FLAIR, to enable the user to start and control FLUKA jobs completely from a GUI environment without the need for command-line interactions. Beta versions of that software are currently under test, and there should be a public release of this software in early 2007. In July, the long awaited release of the FLUKA source code under a CERN-INFN license agreement occurred. Along with that release, several improvements to the core FLUKA code were made, the most visible of which from the user’s standpoint is the elimination of the need to make an “EGS-like” pre-run to set up the so-called “pemf” file necessary for the implementation of electromagnetic interactions. That initialization activity is now seamlessly embedded within the core FLUKA code. NASA users thus have full access to the FLUKA Source code via the FLUKA Website and under the terms of the general public license agreement. Considerable work implemented and upgraded the treatment of electromagnetic dissociation in Nucleus-Nucleus interactions in FLUKA. In this effort, Dr. Georgi Smirnov made use of large volumes of data now accessible from Russian sources. This past year has also seen the extension of the capabilities in FLUKA to calculate directly dose rates owing to activation as a function of time after irradiation of material in any representable geometry. This capability has already been employed to predict the Positron Emission Tomography images from proton and heavy ion beam cancer therapy irradiations. Neal Zapp has continued to develop his Hamiltonian Molecular Dynamics-Based Nucleus-Nucleus Interaction code. He now has a working version that includes only the internal elastic scattering cross sections for the constituents. He is currently in the process of exploring the introduction of the inelastic cross sections for the constituent particles. Dr. Lawrence Pinsky has been working on the refinement of software tools to compare the direct output of event generator models and to identify flaws in the output of current versions of these codes that are employed within FLUKA. In addition, with the help of Kerry Lee, UH Ph.D. candidate, models of solar modulation of the GCR flux are being explored. Likewise, Dr. Victor Andersen of the UH group has been involved in modeling SPEs for inclusion in the standard FLUKA input package. Lee completed and defended his Ph.D. thesis utilizing FLUKA to simulate the response of the MARIE experiment. His Ph.D. degree was awarded May 14, 2006. Jeffrey Chancellor began his Ph.D. research by exploring comparisons between predictions of HZETRN and FLUKA for several benchmark incident fluxes. He will continue the development of FLUKA as a tool to model the response of proposed active dosimeters for use in spacecraft and space suits. Finally, efforts have been under way not only to improve the tools for the input of geometry information into FLUKA, but to develop a broad tool for general use in the conversion of CAD files into Monte Carlo Geometry input files. The Virtual Monte Carlo (VMC) project at CERN is progressing well. A version of FLUKA is currently being tested in that new environment. The


Generic ROOT-based geometry included in this package would be a strong candidate for the common Monte Carlo geometry targeted for such a conversion software code. Copies of all of the released software are being supplied as deliverables under the Consortium contract and are furnished under the general CERN/INFN License Agreement. Acronyms associated with this project AMS – Alpha Magnetic Spectrometer. A cosmic ray spectrometer experiment that has flown previously on the Space Shuttle scheduled to fly for several years on the International Space Station. ACCESS – A Cosmic-ray Composition Experiment planned for deployment on the International Space Station. This largeaperture experiment is being designed to determine the composition of the cosmic-ray flux at energies on the order of 100 TeV around the so-called “knee” in the energy spectrum. ALICE – A Large Ion Collider Experiment, one of the major experiments at the new Large Hadron Collider (LHC) facility at CERN. ALICE is primarily concerned with the measurement of relativistic heavy ion collisions and is similar to the STAR detector at RHIC. Because LHC will operate at considerably higher energies than RHIC, these two experiments are complementary. ALIROOT – (ALICE ROOT) ALIROOT is a software adaptation of the ROOT software infrastructure for the simulation of the ALICE (A Large Ion Collider Experiment) experiment at CERN. BME – Boltzmann Master Equation. A theory describing the preequilibrium deexcitation of the composite system created by the interaction of two ions at some tens of MeV/nucleon. CAD – Computer Aided Design. CAD generally refers to the software engineering drawing tools that have largely replaced mechanical drafting. The most sophisticated CAD tools allow the complete specification of geometric shapes and detailed compositions of mechanical and electronic assemblies. CERN – European Organization for Nuclear Research. Originally “Centre,” now “Organization” Europenne pour la Recherche Nucleaire (located in Geneva, Switzerland). CME – Coronal Mass Ejections. An eruptive phenomenon in the solar corona that results in the ejection of large numbers of particles. DPMJET – Dual Parton Model JET. A version of the DTUNUC event generator code. (See http://www.physik.unisiegen.de/ kolloquium/dpmjet.) DTUNUC – Dual-Parton-Model Two-component Universal NUCleus-Nucleus event generator. DTUNUC is a Monte Carlo event generator for high-energy hadron-hadron, hadronnucleus, nucleus-nucleus and photon-nucleus collisions. It is based on the Gribov-Glauber approach and treats both soft and hard scattering processes in a unified way. Professor Johannes Ranft, University of Leipzig (retired), is the principal author of the code. EVCPDS – External Vehicular Charged Particle Detector System – A charged particle spectrometer instrument similar to the MARIE instrument in design that has been deployed on the ISS to measure the charged particle spectrum between about 10


MeV/n and 450 MeV/n. Three such instruments are deployed externally pointing in different directions FLEUR-S – FLuka Executing Under Root-Space – The ROOTbased simulation application using FLUKA for simulating the space radiation environment that is the object of this project. FLUKA – FLUctuating KAskad. A Monte Carlo-based particle transport code initiated in 1964 by Professor Johannes Ranft at the University of Leipzig. The code has been continually improved and upgraded to include the latest physics and is now being maintained by Dr. Alfredo Ferrari and others. Although Dr. Ferrari holds a permanent appointment with INFN in Milan, Italy, he is currently based at CERN. GCR – Galactic Cosmic Rays, as distinguished from SEPs. GEANT – GEometry ANd Tracking. A Monte-Carlo based particle transport code that has been maintained at CERN since the early 1970’s. The best known previous version (GEANT3.21) was written by Dr. Rene Brun (one of the co-investigators on this project). The most recent version is titled GEANT4 and has incorporated an object-oriented structure. GeV (or MeV or TeV)–Giga (or Mega or Tera) electron Volts – 109 (Giga), 106 (Mega), and 1012 (Tera) electron volts. GUI – Graphical User Interface. A computer user interface that provides graphic interaction with a mouse and clickable buttons and menus, as opposed to a command line interface that requires the user to enter text commands. INC – Intra-Nuclear Cascade. This is an approach to modeling nucleus-nucleus collisions wherein individual nucleons are propagated through the collision using Monte Carlos techniques. When individual nucleons are deemed to have interacted using their free cross sections, either unchanged or modified in some way, the resulting final state is drawn from the free particle cross sections. In this model, other particles such as mesons can be included. The influence of the surrounding nuclear field is typically handled using a mean field approximation, which is one of the principal distinguishing characteristics between these models and QMD-based codes. INFN – Instituto Nazionale de Fisica Nucleare. The Italian National Nuclear Research Funding Agency. ISSO – Institute for Space Systems Operations. An institute at the University of Houston funded by the State of Texas to facilitate NASA-University programs. IVCPDS – Internal Vehicular Charged Particle Detector System. A charged particle spectrometer instrument similar to the MARIE instrument in design that has been deployed on the ISS to measure the charged particle spectrum between about 10 MeV/n and 450 MeV/n. This detector is complementary to the externally mounted EVCPDS instruments, but it is located internally within the ISS. Its location and orientation are variable and can be changed by the crew. JWST – James Webb Space Telescope. The Next Generation Space Telescope (NGST), which will be the follow-on optical on-orbit telescope to Hubble, was recently renamed in honor of former NASA Administrator James Webb. LBL – Lawrence Berkeley Laboratory. The Lawrence Berkeley National Laboratory in Berkeley, California, managed by the University of California under contract from the U.S. Department of Energy (DoE).

DOCIMETRY—Dr. Lawrence Pinsky, Physics Department chairman, shows a computer rendering captured from a newly designed docimeter which had been exposed to an alpha source. The circles on the display represent alpha particles hitting the detector.

LHC – Large Hadron Collider. The major new hadron collider facility being constructed at CERN. LHC will be used to accelerate both protons and relativistic heavy nuclei through Pb (lead) with center of mass energies up to 5.5 TeV/Nucleon. LHC was to have begun operation in 2005. MARIE – MArs Radiation envIronment Experiment. A charged particle spectrometer flown on the Mars Odyssey 01 mission to assess the radiation environment in the interplanetary medium and in the orbit of Mars. QMD – Quantum Molecular Dynamics. A microscopic model and the name of an event generator code to describe heavy ion reactions at low and intermediate energies that explicitly treat nuclear resonances. QMD can be used for incident projectile energies below a few GeV/n. RHIC – Relativistic Heavy Ion Collider. The new facility at the Brookhaven National Laboratory in Upton, Long Island (NY), that began operation in the summer of 2000. RHIC can provide beams of nuclei through Ag (gold) at center of mass energies up to 130 GeV/nucleon. rQMD – Relativistic Quantum Molecular Dynamics. A microscopic model and an event generator code to describe heavy ion reactions at ultrarelativistic energies that explicitly treat high nuclear resonances, string formation, strangeness production and that uses a relativistic covariant formalism for particle

propagation. RQMD can be used from below 1 GeV/n up to TeV energies. ROOT – Although not strictly an acronym, the “OO” in ROOT is motivated by Object-Oriented programming. ROOT is a software package originally developed by René Brun at CERN. It provides an object-oriented graphical user interface (GUI) data analysis infrastructure. SEP – Solar Energetic Particles. Space Radiation originating from the Sun as opposed to GCRs, which are galactic in origin. STAR – Solenoid Tracker At RHIC. STAR is one of the major RHIC experiments. Presentations Anderson, V., F. Ballarini, G. Battistoni, R. Brun, F. Cerutti, N. Elkahayari, A. Empl, A. Fassó, A. Ferrari, M. V. Garzelli, M. Gheata, M. K. Lebourgeois, K. Lee, B. Mayes, A. Ottolenghi, L. Pinsky, J. Ranft, S. Roesler, P. Sala, G. Smirnov, T. Wilson, V. Vlachoudis and N. Zapp. “FLUKA Status and Preliminary Results from the 3, 5 and 10 GeV/A AGS July Runs,” 10th Workshop on Radiation Measurements on the International Space Station (WRMISS), Chiba, Japan Sept., 7-9, 2005. Anderson, V., F. Ballarini, G. Battistoni, R. Brun, F. Cerutti, A. Empl, A. Fassó, A. Ferrari, M. V. Garzelli, M. Gheata, K. Lee, A. Ottolenghi, L. Pinsky, J. Ranft, S. Roesler, P. Sala, T. Wilson


and N. Zapp. “FLUKA: Status and Capabilities,” 9th Workshop on Radiation Measurements on the International Space Station (WRMISS), Vienna, Austria, Sept., 8-10, 2004. Ballarini, F., D. Alloni, G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, H. Paretzke, V. Parini, M. Pelliccioni, L. Pinsky, P. Sala, D. Scannicchio, and M. Zankl. “Modelling Human Exposure to Space Radiation with Different Shielding: the FLUKA Code Coupled with Anthropomorphic Phantoms,” The NPDC19 Conference, Pavia, 5-9 Sept. 2005. Ballarini, F., G. Battistoni, M. Campanella, M. Carboni, F. Cerutti, A. Empl, A. Fassó, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Mostacci, A., S. Muraro, A. Ottolenghi, M. Pelliccioni, L. Pinsky, J. Ranft, S. Roesler, P. Sala, D. Scannicchio, V. Vlachoudis, R. Villari, T. Wilson, and N. Zapp. “Using the FLUKA Monte Carlo Code To Simulate Extreme Radiation Environments,” Materials Research Society Annual Meeting, San Francisco, April 17-22, 2006. (Invited talk.) Ballarini, F., G. Battistoni, M. Campanella, M. Carboni, F. Cerutti, A. Empl, Fassó, A. Ferrari, E. Gadioli, M. V. Garzelli, M. Lantz, M. Liotta, A. Mairani, A. Mostacci, S. Muraro, A. Ottolenghi, M. Pelliccioni, L. Pinsky, J. Ranft, S. Roesler, P. Sala, D. Scannicchio, S. Trovati, R. Villari, T. Wilson, N. Zapp, V. Vlachoudis. “The FLUKA Code: an Overview,” J of Phys Conf Series 415, 2006 Ballarini, F., G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala , and S. Trovati. “Physics To Understand Biology: Monte Carlo Approaches To Investigate Space Radiation Doses and Their Effects on DNA and Chromosomes,” 11th International conference on Nuclear Reaction Mechanisms, Varenna, Italy, June 12-16, 2006. Ballarini, F., G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, V. Parini, M. Pelliccioni, L. Pinsky, P. Sala, D. Scannicchio. “Modeling the Action of Protons and Heavier Ions in Biological Targets: Nuclear Interactions in Hadrontherapy and Space Radiation Protection,” International Conference on Nuclear Data for Science , and Technology, Santa Fe, Sept. 26-Oct. 2004 Ballarini, F., G. Battistoni, F. Cerutti, A. Empl, A. Fassó, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, L. Pinsky, J. Ranft, S. Roesler, P. Sala, and G. Smirnov. “Nuclear Models in FLUKA: Present Capabilities, Open Problems and Future Improvements,” International Conference on Nuclear Data for Science , and Technology, Santa Fe, Sept. 26 -Oct. 2004 Ballarini, F., G. Battistoni, F. Cerutti, A. Empl, A. A. Fassó, E. Ferrari, E. Gadioli, M. V. Garzelli, L. Ottolenghi, L. Pinsky, J. Ranft, S. Roesler, P. Sala, D. Scannicchio, and V. Vlachoudis. “The FLUKA Code: Physics and Applications,” Plenary Talk and Procedures of Monte Carlo 2005, Chattanooga, Tennessee, April 19-22, 2005. Ballarini, F., G. Battistoni, F. Cerutti A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, V. Parini, M. Pelliccioni, L. Pinsky, P. Sala, D. Scannicchio. “Modeling the Action ofP and Heavier Ions in Biological Targets: Nuclear Interactions in Hadrontherapy and Space Radiation Protection,” American Inst. of Physics Conf. Procedures (2005): 1606-16.


Ballarini, F., F. Cerutti, A. Fassó, A. Ferrari, M. V. E. Gadioli, A. Garzelli, A. Ottolenghi, L. Pinsky, J. Ranft, and P. Sala. “Heavy-Ion Collisions in the FLUKA Monte Carlo Event Generator: Present and Perspectives,” INPC 2004, Goteborg, Sweden, June 2004. Ballarini, F., F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, Paretzke, H., V. Parini, M. Pelliccioni, L. Pinsky, P. Sala and M. Zankl. “Simulazione degli effetti della radiazione spaziale mediante integrazione tra il codice MC FLUKA e fantocci antropomorfi,” XC Congresso Nazionale Societ‡ Italiana di Fisica, Brescia, Italy, Sept. 20-25, 2004. Ballarini, F., F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, Parini, V., L. Pinsky, and P. Sala. “Modelling Radiation-induced Cellular Damage: Nuclear Models and Data Needed for Radiation Protection and Hadrontherapy.” 2004 Nuclear Data Conference, Santa Fe (NM, USA), Sept. 2004. (Invited talk.) Battistoni, G., F. Ballarini, A. Cerutti A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala and S. Trovati. “Nuclear Effects in Neutrino Interactions,” 11th Conf. on Nuclear Reaction Mechanisms, Varenna (Italy) June 12-16, 2006. Cerutti, F., F. Ballarini, G. Battistoni, P. Colleoni, A. Ferrari, F. Fortsch, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, and P. Sala. “Light Ion Iinteractions of Concern for Hadrontherapy,” Procedures of the VIth Latin American Symposium on Nuclear Physics and Applications, Iguazu, Argentina, Oct. 3-7, 2005. Cerutti, F., F. Ballarini, G. Battistoni, P. Colleoni, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala, D. Scannicchio, and G. F. Steyn. “Carbon-Iinduced Reactions at Low Incident Energies,” J of Phys Conf Series 4212, 2006. Cerutti, F., F. Ballarini, G. Battistoni, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala , and S. Trovati. “Low Energy Nucleus-Nucleus Interactions: the BME Approach and Its Interface to FLUKA,” 11th Conf. on Nuclear Reaction Mechanisms, Varenna (Italy) June 12-16, 2006. Ferrari, A., F. Ballarini, G. Battistoni, F. Cerutti, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala , and S. Trovati. “Recent Developments in the FLUKA Nuclear Reaction Models,” 11th Conf. on Nuclear Reaction Mechanisms, Varenna (Italy) June 12-16, 2006. Garzelli, M. V., F. Ballarini, G. Battistoni, F. A. Cerutti A. Ferrari, E. Gadioli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala, S. Trovati. “Heavy Ions Collisions Described by a New QMD Code Interfaced to FLUKA,” 11th Conf. on Nuclear Reaction Mechanisms, Varenna (Italy) June 12-16, 2006. Garzelli, M. V., F. Ballarini, G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala, and S. Trovati. “Heavy-Ion Collisions: Preliminary Results of a New QMD Model Coupled with FLUKA,” J of Phys Conf Series 4519, 2006. Lee, K., V. Anderson, L. Pinsky, W. Atwell, T. Cleghorn, F. Cucinotta, R. Turner, P. Saganti, C. Zeitlin. “MARIE Solar Quite Time Flux Measurements of H and He Ions Below 300 MeV/n,” 29th International Cosmic Ray Conference, Pune,

India, July, 2005. Lee, K, J. Flanders, E., Semones, T. Shelfer, F. Riman. “Preliminary Results of the CPDS Instruments Aboard the ISS,” 29th International Cosmic Ray Conference, Pune, India, 2005. (Procedures in press.) Mairani, F., A. Ottolenghi, H. Paretzke, V. Parini, M. Pelliccioni, L. Pinsky, P. Sala, D. Scannicchio, S. Trovati. S. and M. Zankl. “Modelling Human Exposure to Space Radiation with Different Shielding: the FLUKA Code Coupled with Anthropomorphic Phantoms,” Journal of Physics Conf Series 41 (2006):135. Pinsky, L., V. Anderson, A. Empl, K. Lee, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft And A. Fassó. “A FLUKA-Based Space Radiation Simulation Code,” International Conference on Radiation Protection, Funchal, Madeira Island, Portugal, May 10-14, 2004. Pinsky, L. “The FLUKA Team: Status and Efforts Within the Modeling and Measurements Consortia,” Space Radiation Shielding Program Review, Huntsville, Alabama, Aug. 19-20, 2004. Pinsky, L. “Surviving in Space: The Challenges of a Manned Mission to Mars,” CERN Academic Lecture Series, CERN, Geneva, Switzerland, Oct. 26-28, 2005. Conference Proceedings Aiginger, H., V. Anderson, F. Ballarini, G. Battistoni, M. Campanella, M. Carboni, F. Cerutti, A. Empl, W. Enghardt, A. Fassó E. Ferrari, E. Gadioli, M. V. Garzelli, K. Lee, A. Ottolenghi, K. Parodi, M. Pelliccioni, L. Pinsky, J. Ranft, S. Roesler, P. Sala, D. Scannicchio, G. Smirnov, F. Sommerer, T. Wilson and N. Zapp. “The FLUKA Code: New Developments and Application to 1 GeV/n Iron Beam,” Procedures of the 35th COSPAR Scientific Assembly, Paris, France, July 18-24, 2004. Andersen,V., N. Elkhayari, A. Empl, M. LeBourgeois, K. Lee, B. Mayes, L. L. Pinsky, G. Smirnov, N. Zapp, T. WilsonN., F. Ballarini, G. Battistoni, M. Campanella, M. Carboni, F. Cerutti, E. Gadioli, M. V. Garzelli, T. Rancati, S. Muraro, A. Ottolenghi, M. Pelliccioni, P. Sala, D. Scannocio, A. Ferrari, S. Roesler, V. Vlachoudis, J. Ranft, and A. Fassó. “Nuclear Physics Issues in Space Radiation Risk Assessment - The FLUKA Monte Carlo Transport Code Used for Space Radiation Measurement and Protection,” Procedures of the VIth Latin American Symposium on Nuclear Physics and Applications, Iguazu, Argentina, Oct. 3-7, 2005. Ballarini, F., G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, H. Paretzke, V. Parini, M. Pelliccioni, L. Pinsky, P. Sala, and M. Zankl. “Models and Monte Carlo simulations of GCR and SPE Organ Doses with Different Shielding, Based on the FLUKA Code Coupled with Anthropomorphic Phantoms,” Procedures of the 35th COSPAR Scientific Assembly, Paris, France, July 18-24, 2004. Ballarini, F., G. Battistoni, F. Cerutti A. Empl, A. Fassó, A. Ferrari, E. Gadioli, A. Garzelli, A. Ottolenghi, L. Pinsky, J.

Ranft, S. Roesler, P. Sala, G. Smirnov. “Nuclear Models in FLUKA: Present Capabilities, Open Problems and Future Improvements,” American Inst. of Physics Conf. Procedures (2005): 1197-1202. Battistoni, G., M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, Sala., P., A. Ferrari, S. Roesler, V. Vlachoudis, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft, L. Pinsky, V. Anderson, A. Empl, K. Lee, G. Smirnov, Zapp, N and A. Fassó. “Applications of the FLUKA Monte Carlo Code in High Energy and Accelerator Physics,” Procedures of the Computing in High Energy Physics Conference (CHEP04), Interlaken, Switzerland, Sept. 27-Oct. 2004. Battistoni, G., M. Cavinato, F. Cerutti, Clivio, A., Fabrici, E. Gadioli, E. Gadioli-Erba, E., M. V. Garzelli, A. Mairani, A. Ferrari, F. Ballarini, A. Ottolenghi, A. Empl, L. Pinsky, A. Fassó, J. Ranft, and P. Sala. “Heavy Ion Interactions from Coulomb Barrier to Few GeV-n: Boltzmann Master Equation Theory and FLUKA Code Performances,” Procedures of the V Latinamerican Symposium on Nuclear Physics - XXVI Reuni„o de Trabalho sobre FÌsica Nuclear no Brasil, Sept. 1-5, 2003, Santos, Brazil. Brazilian Journal of Physics 3 (2004): 897. Cerutti, F., F. Ballarini, G. Battistoni, P. Colleoni, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Mairani, A. Ottolenghi, L. Pinsky, P. Sala, D. Scannicchio. “Analysis of Carboninduced Reactions at Low Incident Energies,” The NPDC19 Conference, Pavia, 5-9 Sept. 2005. Cerutti, F., F. Ballarini, G. Battistoni, M. Cavinato, A. Empl, E. Fabrici, A. Fassó, A. Ferrari, E. Gadioli, E. Gadioli-Erba, M. V. Garzelli, A. Ottolenghi, V. Parini, L. Pinsky, J. Ranft, and P. Sala. “Toward a Comprehensive Description of Heavy Ion Reactions,” PROCEDURES of the NATO Advances Study Institute “Structure and Dynamics of Elementary Matter,” Kemer, Turkey, Sept. 22 - Oct. 2, 2003.. Ed. W. Greiner. (Norwell, MA: Kluwer Academic Publishers, 2004):255-63 . Cerutti, F., F. Ballarini, G. Battistoni, A. Fassó, A. A. Ferrari,E. Gadioli, M. V. Garzelli, A. Ottolenghi, L. Pinsky , J. Ranft, P. R. Sala, D. Scannicchio. “Il codice FLUKA per la radioprotezione nello spazio: caratterizzazione fisica dei prodotti di interazione ioni-schermatura,” XII Convegno nazionale della Societ‡ Italiana per le Ricerche sulle Radiazioni (SIRR), Genova, Italy, Nov. 9-12, 2004. In Radiazioni - Ricerca e Applicazioni, suppl. al vol. VII/2 (2004): 35. Ferrari, A., M. Loenzo-Sentis, S. Roesler, G. Smirnov, F. Sommerer, G. Theis, V. Vlachoudis, M. Carboni, A. Mostacci, M. Pelliccioni, R. Villari, V. Anderson, N. Elkhayari, A. Empl, Lee, K,. B. Mayes, L. Pinsky, N. Zapp, Parodi, K., Paganetti, H., T. Bortfeld, G. Battistoni, M. Campanella, F. Cerutti, P. Colleoni, E. Gadioli, M. V. Garzelli, M. Lanza, S. Muraro, A. Pepe, P. Sala, T. Wilson., D. Alloni, F. Ballarini, M. Liotta, A. Mairani, A. Ottolenghi, D. Scannicchio, S. Trovati, J. Ranft, and A. Fassó. “Update on the Status of the FLUKA Monte Carlo Transport Code,” CHEP í06, Mumbai (India) Feb., 2006. (Procedures published on the website.) Garzelli, M. V., P. Sala, G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, F. Ballarini, A. Ottolenghi, Fassó, A., L. Pinsky, J. Ranft. “Correlations in the Interactions of Ion Beams with


Matter,” 25th Conference on Nuclear Theory, Rila (Bulgaria) June 2006. (Procedures in press.) Lee, K., L. Pinsky, V. Anderson, C. Zeitlin, T. Cleghorn, F. Cucinotta, P. Saganti, W. Atwell, and R. Turner. “Helium Cosmic Ray Measurements at Mars,” Procedures of the 35th COSPAR Scientific Assembly, Paris, France, July 18-24, 2004. Pinsky, L. “NASAís Interest in Cosmic Rays as a Radiation Hazard to a Human Presence in SpaceóA Brief Introduction,” Procedures of the Vulcano Cosmic Ray Workshop, Vulcano Island, Sicily (Italy), May 24-28, 2004. Pinsky, L., V. Anderson, N. Elkhayari, A. Empl, K. Lee, B. Mayes, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft And A. Fassó. “FLUKA Status And Preliminary Results From the July-2005 AGS Run,” Procedures of the 2005 IEEE Aerospace Conference, Big Sky, Montana, March 6-10, 2006. Pinsky, L., V. Anderson, N. Elkhayari, A. Empl, K. Lee, B. Mayes, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft And A. Fassó. “FLUKA Status And Preliminary Results From the July-2005 AGS Run,” Procedures of the 2005 IEEE Aerospace Conference, Big Sky, Montana, March 6-10, 2006. Pinsky, L., V. Anderson, N. Elkhayari, A. Empl, K. Lee, B. Mayes, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft And A. Fassó. “FLUKA Status And Preliminary Results From the July-2005 AGS Run,” Procedures of the 2005 IEEE Aerospace Conference, Big Sky, Montana, March 6-10, 2006. Pinsky, L., V. Anderson, A. Empl, K. Lee, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft, and A. Fassó. “Event Generators for Simulating Heavy Ion Interactions To Evaluate the Radiation Risks in Spaceflight,” Procedures of the 2005 IEEE Aerospace Conference, Big Sky, Montana, March 7-12, 2005. Pinsky, L., V. Anderson, N. Elkhayari, A. Empl, K. Lee, B. Mayes, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft And A. Fassó. “FLUKA Status And Preliminary Results From the July-2005 AGS Run,” Procedures of the 2005 IEEE Aerospace Conference, Big Sky, Montana, March 6-10, 2006.


Pinsky, L., V. Anderson, A. Empl, K. Lee, G. Smirnov, N. Zapp, A. Ferrari, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson, J. Ranft And A. Fassó. “Update on the Status of the FLUKA Monte Carlo Code,” Procedures of the Computing in High Energy Physics Conference (CHEP04), Interlaken, Switzerland, Sept. 27-Oct. 2004. Pinsky, L., Anderson, V., A. Empl, K. Lee, G. Smirnov, N. Zapp, A. Ferrari, K. Tsoulou, S. Roesler, V. Vlachoudis, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, V. Parini, D. Scannicchio, M. Carboni, M. Pelliccioni, T. Wilson., J. Ranft, and A. Fassó “Update on the Status of the FLUKA Monte Carlo Transport Code,” Procedures of the Computing in High Energy Physics (CHEPí06) Conference, Mumbai, India, Feb. 13-17, 2006. Pinsky, L., A. Empl, A. Ferrari, G. Battistoni, P. Sala, F. Ballarini, A. Ottolenghi, J. Ranft, A. Fassó , H. Paretzke, and M. Zankl. “The Application of FLUKA to Dosimetry and Radiation Therapy,” Procedures of the International Conference on Radiation Protection, Madeira, Portugal, May 10-14, 2004. Pinsky, L., A. Empl, A. Ferrari, G. Battistoni, P. Sala, F. Ballarini, A. Ottolenghi, J. Ranft, A. Fassó , H. Paretzke, and M. Zankl. “The Use of Voxel-based Human Phantoms in FLUKA,” The Procedures of the Heavy Charged Particles in Biology and Medicine Workshop, Oropa, Italy, 2005. Pinsky, L., A. Empl, A. Ferrari, G. Battistoni, P. Sala, F. Ballarini, A. Ottolenghi, J. Ranft, Fassó , A., Paretzke, H., and M. Zankl. “The Use of Voxel-Based Human Phantoms in FLUKA,” Procedures of Monte Carlo 2005, Chattanooga, Tennessee, April 19-22, 2005. (Invited talk.) Wilson., T., N. Zapp, A. Empl, L. Pinsky, G. Battistoni, M. Campanella, F. Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, Ballarini, F., A. Ottolenghi, D. Scannicchio, A. A. Fassó Ferrari, S. Roesler, V. Vlachoudis, J. Ranft, M. Carboni, and M. Pelliccioni. “Space Applications of the FLUKA Monte-Carlo Code: Lunar and Planetary Exploration,” Procedures of the VIth Latin American Symposium on Nuclear Physics and Applications, Iguazu, Argentina, Oct. 3-7, 2005. (Procedures in press.) Wilson, T., N Zapp, L. Pinsky, A Empl, A Fassó, A Ferrari, S Roesler, V. Vlachoudis, G Battistoni, M Campanella, F Cerutti, E. Gadioli, M. V. Garzelli, S. Muraro, T. Rancati, P. Sala, F. Ballarini, A. Ottolenghi, D. Scannicchio, M. Carboni, M. Pelliccioni, J. Ranft. “Application of the FLUKA Monte-Carlo Transport Code to Lunar and Planetary Exploration,” Procedures of the Space Nuclear Conf. 2005, American Nuclear Society, San Diego, California, June 5-9 2005. Ed. S. Anghaie (2005), 553-62.

FOUNTAIN—Between classes, students sit at the NSM fountain, designed to lay a continuous film of water across metal plates.

Publications Aiginger, H., V. Anderson, F. Ballarini, G. Battistoni, M. Campanella, M. Carboni, F. Cerutti, A. Empl, Enghardt, W., Fassó, A., A. Ferrari, E. Gadioli, M. V. Garzelli, K. Lee, A. Ottolenghi, Parodi, K., M. Pelliccioni, L. Pinsky, J. Ranft, S. Roesler, P. Sala, D. Scannicchio, G. Smirnov, F. Sommerer, T. Wilson, and N. Zapp. “The FLUKA code: New Developments and Application to 1 GeV/n Iron beams,” Adv. Space Res. 35 (2005): 214-22. Ballarini, F., G. Battistoni, F. Cerutti, A. Ferrari, E. Gadioli, M. V. Garzelli, A. Ottolenghi, H. Paretzke, V. Parini, M. Pelliccioni, L. Pinsky, P. Sala, and M. Zankl. “GCR and SPE Organ Doses in Deep Space with Different Shielding: Monte Carlo

Simulations Based on the FLUKA Code Coupled to Anthropomorphic Phantoms,” Adv. Space Res. 37.9 (2006): 1791-97. Pinsky, L., A. Empl, A. Ferrari, G. Battistoni, P. Sala, F. Ballarini, A. Ottolenghi, J. Ranft, Fassó , A., Paretzke, H., and M. Zankl. “The Application of FLUKA to Dosimetry and Radiation Therapy,” Radiat. Prot. Dosimetry 116, (2005): 113- 17. Trovati, S., F. Ballarini, G. Battistoni, F. Cerutti, A. Fassó, A. Ferrari, E. Gadioli, E,. M. V. Garzelli, A. Mairani, A. Ottolenghi, H. Paretzke, V, Parini, M. Pelliccioni, L. Pinsky, P. Sala, D. Scannicchio, and M. Zankl. “Human Exposure to Space Radiation: Role of Primary and Secondary Particles,” Radiat. Prot. Dosim. 2006. (In press.)


High-Performance Martian Space Radiation Mapping by Liwen Shih ABSTRACT—For future safer, sooner, and cheaper deep space missions, we apply high-performance computer techniques to enable better space radiation analysis for the moon, Mars and beyond.

S

PACE RADIATION IS LIKELY TO BE THE ULTIMATE LIMITING

FACTOR for future human deep space exploration. Understanding the space radiation environment is essential for risk assessment of orbit/crew selection and provides the scientific basis of countermeasures for shielding materials (affecting flight weight/cost), radio-protectants, and pharmaceuticals. Every tissue/material/part installed on a space mission requires radiation risk analysis. HZETRN is the Space Radiation Dosage/Flux Software provided by NASA to simulate high-energy nuclear transport across materials being tested. The HZETRN model has been developed as an accurate scientific model, but the implementation of the model in FORTRAN-77 code using VAX machines is slow and inefficient. Radiation exposure is underestimated by 15-30 percent. HZETRN code is outdated and incompatible with most of the modern compilers/platforms that we tested so far and is broken at times. In the current HZETRN implementation, space radiation predicting accuracy is low, and three days of Mars data may take up to one day of CPU time to analyze. An essential step toward a more efficient and cost-effective solution to the radiationshielding problem is the development of accurate, efficient and fast tools for modeling radiation transport. We hope that HZETRN code improvement can benefit the design and engineering of lighter and more cost-effective shielding material for use in NASA spacecraft, e.g., CEV Orion. A probable key solution to the complex HZETRN computation would be to restructure the computation to match the newly developed resource of a parallel, multithreading network cluster/grid and reconfigurable FPGA (Field Programmable Gate Array) platform. We studied the current execution mode/platform of the NASA space radiation code, to determine the feasibility of finding a high-performance/parallel improvement that will make deep space missions possible. To modernize and optimize the HZETRN code, we analyzed the code using both static and runtime analysis tools. Specifically, we attacked the HZETRN performance problem from both ends: with top-down parallel thread mapping onto a cluster/grid, and bottom-up bottleneck function routines speeding up with a hardware co-processor performance-accelerator, e.g., FPGA. We examined multithread code optimization and parallel FPGA options for the major performance bottleneck functions in the source code, including the PHI/interpolation function.


Our preliminary FPGA prototypes for bottleneck functions showed up to 325 times speedup. With the newly emerging technology in parallel network clusters/grids and FPGA arrays, it is highly promising that a high-performance improvement of the HZETRN code can be developed that will enhance both speed and accuracy of space radiation analysis. In support of our space endeavor, our tireless HPC students and alumni volunteers team held weekly meetings throughout 2006 to complete the following tasks: • Perform HZETRN program flow analysis. • Study, investigate, and organize HZETRN routines in hypertext and spreadsheet. • Expand and redesign the FPGA floating point core performance accelerator from 8-bit (in 2005) to a current 32-bit IEEE-754 standard. • Compare and select hardware FPGA systems with weighted scores. • Experiment HZETRN with OpenMP on UH TLC2 parallel clusters. • Experiment with a parallel Monte Carlo FLUKA code in the UHCL Athena cluster. In conclusion, we performed HZETRN “diagnosis” and developed a plan for the parallel modernization “treatment” of the code. Support for this effort is still greatly needed. To conduct syntax code thread analysis, we need Data Flow analysis either from the software testing, source code, or algorithm design. To achieve further improvements in such techniques as semantic/application/methodology/algorithm-specific thread mapping optimization, we need a closer collaboration with LaRC nuclear physicists in order to advance a better understanding of how parallel optimization techniques can be applied to the physicists’ numerical models. With the ISSO min-grant and UHCL support, the UHCL team has demonstrated effort to NASA and was granted access to HZETRN1995 in April 2005. NASA LaRC is currently working on establishing a Space Act Agreement (SAA) between NASA and UHCL for a long-term collaboration to enable computer engineers to work with NASA nuclear scientists and engineers to modernize computer applications and to optimize space radiation computation. The SAA was reviewed by the UH System General Counsel and is being revised at NASA Langley. After the SAA is signed, we expect to receive the newest HZETRN2005 code for optimization within two weeks. The success of applying parallel techniques to enhance both complementing deterministic HZETRN and stochastic FLUKA Monte Carlo radiation transport analysis/simulation code used by NASA scientists will greatly enhance space radiation understanding for safer and cheaper missions sooner. As Earth’s ozone depletion continues, space radiation study could lead to dual-use countermeasures that will, in turn, protect human health from radiation/aging effect in general (earth/space), e.g., slowing down cataract development. Other evolving critical medical cures, e.g., the higher range-precision proton cancer radiation treatment, are becoming a reality. Radiation shielding study can also lead to safer nuclear energy for the future which in turn can bring about health, peace, economic growth and many emerging technology advancements on Earth.

References Shih, Liwen, Travis Gilbert, Arun Kadari and Shilpa Kodali. “High-Performance Martian Space Radiation Mapping,” ISSO Y2004 Annual Report, Spring (2005): 145-49 Shih, Liwen, Sergio J. Larrondo, Karthik Katikaneni, Ahmed Khan, Travis Gilbert, Shilpa Kodali, Arun Kadari. “HighPerformance Martian Space Radiation Mapping,” ISSO Y2005 Annual Report Spring (2006): 121-22. Wilson, J. W., F. F. Badavi, F. A. Cucinotta, J. L. Shinn, G. D. Badhwar, R. Silberberg, C. H. Tsao, L. W. Townsend, and R. K. Tripathi. “HZETRN: Description of a Free-Space Ion and Nucleon Transport and Shielding Computer Program,” 1995. Publications Gilbert, T., and L. Shih. “High-Performance Martian Space Radiation Mapping,” Proc. Computer Application Conference, IEEE/ACM/UHCL, 2005. Johnson, Adam (supervised by Liwen Shih). “32-Bit IEEE Compliant Floating Point FPGA Core Design,” UHCL Master Capstone Project Report & Presentation, Fall 2006. Kadari, Arun, Shilpa Kodali, Travis Gilbert, and Liwen Shih. “High-Performance Space Radiation Analysis with FPGA,” Proc. Computer Application Conf., IEEE/ACM/UHCL 2005. Kodali, Shilpa, Arun Kadari, Travis Gilbert, and Liwen Shih. “Space Radiation Analysis with FPGA” UHCL Master Capstone Project Report and Website, Spring 2005. Larrondo, Sergio, and Adam Johnson (supervised by Liwen Shih). “Space Radiation HZETRN Architecture and FPGA System Selection via Weighted Scores,” UHCL Parallel Processing Project Report & Presentation, Fall 2006. Shum, Victor, Susan Strasser, and Romeo Chua (supervised by Liwen Shih). “Space Radiation HZETRN on Parallel Cluster,” UHCL Parallel Processing Project Report & Presentation, Spring 2005. Grants, Contracts & Agreements Shih, Liwen., R. Singleterry, Jr. “Starbridge HC-38” and “HZETRN2005,” an on-going Space Act Agreement (SAA) between NASA-Langley and UHCL. (In progress, currently being reviewed/revised by UH/NASA). Shih, Liwen. “Parallel Space Radiation Computation with Cluster and FPGA,” NASA Langley Contract Statement of Work, Jan. 1–May 31, 2007. (Submitted.) Shih, Liwen. “Partitioning Space Radiation Analysis/ Simulation Code for High-Performance Execution with Parallel Computing Techniques,” UHCL Faculty Research and Support Fund, June–December 2005. $7,200. Shih, Liwen. “HZETRN1995,” Granted Access to NASA Langley Space Radiation Source Code, April 2005.

Lab Chips and Board Design Dr. Dabney’s and Dr. Harman’s team developed this power supply for a piezoelectric motor causing the rotor to rotate.

This micro-device was developed in Dr. Miller’s laboratory for taking in vitro measurements of living cell suspensions.

In Dr. Miller’s group, Dr. Bukahri developed this fentoampere amplifier to detect very weak oscillations in cells.

Dr. Bensaoula’s team used a brazing furnace to bond a titanium alloy to a ceramic coupon for MCA research.


An AC-DC-AC Converter with Smaller DC-link Capacitor for Space Power Distribution Systems by Wajiha Shireen ABSTRACT—The power conditioning equipment used in a space power system contributes to the total system mass, reliability, and cost. The focus of this research was to reduce the weight and improve the reliability of an ACDC-AC converter used in a large number of the power conditioning stages in a typical space power system.

T

Wajiha Shireen

HE POWER CONDITIONING STAGE BETWEEN THE SOURCE AND

distribution or between the distribution and the load efficiently interfaces various source types with different distribution systems and with a wide variety of load requirements in a typical space power system. In addition to providing flexible electric power of high quality, the power conditioning method and the associated equipment (power converters, filters

etc.), have a significant effect on the total power system affecting mass, reliability and cost in a space power system. In view of these issues, this research involved the study of a method for reducing the weight and improving the reliability of an AC-DCAC converter utilized in a large number of the power conditioning stages used in a typical space power system. The DC link in any AC-DC-AC converter is normally equipped with an electrolytic capacitor, which provides decoupling between the rectifier and the inverter. However, the DC link capacitor is a large, heavy and expensive component. Moreover, the DC bus capacitor is the prime factor of degradation of the system reliability. However, a cost effective and efficient solution is not yet available. For space power distribution systems, these problems may prove to be even more critical. Objectives Researchers hope to develop a Digital Signal Processor (DSP)based modified space vector pulse width modulation (PWM) technique that will allow the use of a smaller DC-link capacitor without affecting the output performance of the converter. The proposed method implemented in AC-DC-AC converter applications will result in the following advantages: • Reduced converter weight and volume. • Significant improvement in system reliability by the use of a smaller link capacitor. • Digital control by a DSP to provide fast transient response, high performance and increased reliability. • A digital controller insensitive to the environment, offering a stable operation under most operating conditions. Moreover, the DSP-based controller, being programmable, can also be easily upgraded or modified to meet the specific system requirements. Results Figure 1 shows the block diagram of the experimental set-up used to test and verify the proposed technique. The experimen-

Figure 1. A Closed Loop V/Hz Motor Drive System with the Proposed DSP-based Control


Fig. 2 Inverter output voltage magnitude when the DC bus voltage varies in the range of 25 V to 34 V (with 47 ÌF DC-link capacitor).

Fig. 3 Inverter output voltage magnitude when the DC bus voltage is varied in the range of 55 V to 110 V.

tal prototype of the AC-DC-AC converter consists of a diode rectifier, DC-link, and a PWM inverter used in a closed loop V/Hz motor drive. Researchers utilized the DSP-based controller (TMS320F240) to implement the proposed technique, which allowed the use of a smaller DC-link capacitor without affecting the output performance of the rectifier-inverter system. The use of smaller link capacitor introduced a ripple on the dc-bus voltage. The DC-link voltage ripple was sensed and fed as an input to the DSP controller. Figure 2 shows a plot of the recorded experimental data of the inverter output voltage magnitude, with the DC bus voltage varying in the range of 25 V to 34 V (when the DC-link capacitor is 47 ÌF), both with and without the proposed correction algorithm in effect. Without correction, the output voltage increases as the DC bus voltage is increased, but with the modified SVPWM correction in place the output voltage magnitude is maintained constant (at 12 V) regardless of the DC bus voltage. Figure 3 shows a plot of the recorded experimental data when the DC bus voltage is manually varied over a wider range (55 V to 110 V). The plot in Fig. 3 shows that with modified SVPWM control in effect, the output voltage magnitude is maintained constant (at 26 V ) even when the input DC voltage is varied over a wide range.

Shireen, W., S. Vanapalli, and H. R. Nene. “DSP-Based Inverter Control for Alternate Energy Systems,” J. of Power Sources, 2007. (Accepted.)

Publications Shireen, W., R. Kulkarni, and M. Arefeen. “Analysis and Minimization of Input Ripple Current in PWM Inverters for Designing Reliable Fuel Cell Power Systems,” J. of Power Sources 156.2 (2006): 448-54. Shireen, W. and H. R. Nene. “Active Filtering of Input Ripple Current To Obtain Efficient and Reliable Power from Fuel Cell Sources,” IEEE-INTELEC, Intl. Telecommunications Energy Conf., 2006. Shireen, W. and H. R. Nene. “Control and Design Aspects of Power Electronics Converters using PSpice,” J. of Advanced Technology for Learning 3.1, 2006. (Accepted.) Shireen, W., S. Vanapalli, and H. R. Nene. “A DSP-Based Utility Interactive Inverter for Alternate Energy Systems,” IEEEAPEC, 2006; 21st Annual IEEE Applied Power Electronics Conference and Exposition, APEC ‘06. (2006): 1099-03.

Presentations Shireen, W., S.Vanapalli, and H. R. Nene. “A DSP Based SVPWM Control for Utility Interactive Inverters Used in Alternate Energy Systems,” IEEE Applied Power Electronics Conference (APEC) Proc., 2006. Funding, Proposals, and Grants Shireen, W. “Development of a Modern DSP-Based Laboratory for Power Electronics Education,” National Science Foundation, $74,000. (Project ends September 2007.) Shireen, W. “Control of Power Converters in a Fuel Cell System Using a Single DSP Controller,” University of Houston GEAR Award, $20,000. (Project ended September 2006.)

POWER—Lakshmi Gopal, M.S. student in electrical engineering, earned her B.S. in electrical engineering at Anna University in Chennai. Tamil Nadu, India. Her ISSO-based research focuses on digital signal processors (DSPs) to control space power systems.


Dielectrophoresis of Biological Cells and Single-walled Carbon Nanotubes

through nanotechnology provides the venue for delivering these answers. Electrical phenomena play a considerable role in living organisms2 and can be used to modify, change, and also to interrogate biological samples in order to provide information on their structures and various kinetic processes in the cells3. By by Jaroslaw (Jarek) Wosik, Divya Padmaraj, interaction with electric and magnetic fields, the cells, through Chinmay Darne, and changes of electrical charges, conformation, polarization and conWanda Zagozdozon-Wosik ductivity, can provide structural information as well as data on functional and metabolic behavior in cell membranes, mitochondria, chloroplasts, motor proteins, and cytoskeletal proteins. ABSTRACT—Our research is a continEspecially important is the dependence of uation of the development and refinethese properties on frequency, which, in turn, ment of devices that can be used for the can help to identify various bio-physical and characterization of electromagnetic bio-chemical effects and parameters of livproperties of biological and nano-size ing organisms. Widely used methods for materials. In framing this approach, such measurements include frequency which is the follow-up of our earlier dependent capacitance/conductance and work on Martian Meteorite ALH84001 impedance performed using electrical test characterization, we have developed sevstructures made as part of fluidic systems eral capacitors with a gap between elecwith embedded electrodes. trodes of the order of tens nm. For cell Electrical characterization of biological and carbon nanotubes manipulation, we samples is difficult.4 Due to conductive losshave studied the technique of dieleces, there is a quite pronounced polarization trophoresis. Electrical phenomena play effect at the electrode/electrolyte interface, a role in living organisms. They can be which results from charge accumulation and used to modify and change biological distribution at the electrode site.5 It introsamples. duces an additional interfacial capacitance, which increases quickly at low frequencies thus obstructing the real picture of behavior Jaroslaw (Jarek) Wosik INIATURIZED SENSORS AIMED AT celof the sample. One way of alleviating this lular analysis and bio-diagnostics effect is to use capacitors with a very small dielectric thickness6, has become increasingly important in biomedical sci- 7 that would be comparable to Debye length, i.e., a parameter ences. They are expected to play an especially prominent role in characteristic of the electrical potential decay from the elecspace missions. If one can monitor responses of cells to effects trode. such as radiation or other deleterious effects related to toxicity Fabrication of such small nm range structures is also very difinduced by the space environment to access the mechanisms of ficult, especially if vertical structures are to be made. However, cells modification or degradation, our space missions not only they can be precisely controlled if horizontal structures are used will be safer but they will contribute a better understanding of such as those in Integrated Circuits (ICs). Planar capacitors with cellular mechanisms and processes to be used in medical fields a very small (nm) oxide thickness can be fabricated; after etchon Earth. ing a cavity around the electrode perimeter, it can be used to We continue the development and refinement of devices, entrap minute particles or fragments of bio samples. For other which can be used for characterization of electromagnetic propbiological samples, such as cells that are of the order of µm, erties of biological and solid state materials. In the scope of this these capacitors can be used for sensing the properties of cells approach, which is a continuation of our earlier work on Martian via their fringing electric fields. Also they can be used for charMeteorite ALH84001 characterization, we have developed sevacterization of smaller objects such as carbon nanotubes. eral probes for operation in the rf and microwave frequency To deliver cells to the site of this electric field, we used cell range. They work as broadband and single frequency probes and manipulation by a phenomenon called dielectrophoresis (DEP).8 are used for complex permittivity measurements of liquid susIt is a process that relies on electrical polarization of neutral parpended biological cells and also for biomedical applications of ticles present in a solution.9, 10 DEP occurs in a nonuniform elecoriented single-walled carbon nanotubes (SWNT).1 Our study tric field created by specially configured and patterned electrodes focused on the characterization and manipulation of biological operating under an ac signal condition. The process depends on cells and SWNT. Using silicon/silicon oxide integrated circuit dielectric and conductive properties of both the cells and solution technology, we fabricated structures needed for such a study. and is controlled by the signal amplitude and frequency.9, 10 Growing interest of dielectric properties of nano and micro Particles can migrate to the maximum of electric field in positive scale particles is a result of great expectations in understanding dielectrophoresis (p-DEP) or to the minimum of electric field in mechanisms that control many basic processes and phenomena negative dielectrophoresis (n-DEP). Additional effects affecting in live organisms and in the nanoworld of physics and chemthe motion of particles and their attachment to the electrode istry. At the same time, miniaturization of tools available now

M


Figure 1. Dielecrophoresis results in the polarization of a neutral particle (formation of a dipole). As a result, such a particle will move in an electric field either toward a positive or a negative electrode, depending on permittivity and conductivity parameters of the whole system.

include rotation, levitation, chain formation, and bubbles that are all affected by temperature, flow and concentration of solution. In Fig. 1, a sketch explaining DEP is shown. The goal of this part of the work is to use a controlled and effective entrapment of particles or cells for their further electrical interrogation. We designed test structures to attract, agglomerate, and attach particles to the electrodes and to perform electrical measurements of capacitance and conductance with high sensitivity. Capacitors were fabricated using Si technology where oxide layers of 17 nm and 150 nm were produced as dielectrics and electrodes were formed by doping and polysilicon deposition processes to ensure high conductivity (Fig. 2). Such structures have so small a gap between capacitor electrodes that even carbon nanotubes can be characterized this way. Structures of various geometries and dimensions, including interdigitated capacitors, were patterned by a photolithography process. We characterized these devices to verify proper electrical parameters prior testing of the samples. Using minute drops of sample electrolytes, we conducted tests of particulate entrapment and then measurements of capacitance and conductance as a function of DC electric field, frequency of probing ac signal, and as a function of time. By changing conductivity of the suspension of yeast cells (S. cerevisiae and S. pombe) and parameters of the ac power supply (amplitude and frequency), we obtained positive or negative DEP i.e., accumulation of cells at the highest or lowest E-field sites, respectively. Figure 3 shows an agglomeration of S. pombe aligned 3a) and misaligned 3b) in p-DEP around an elec-

trode. Orientation of cells is affected by DEP conditions (voltage and frequency). Similarly, we used single wall carbon nanotubes (SWNT) suspended in water with two surfactants (Pluronic™ F108 or SDBS) and samples with varying conductivity for measurements. SWCNT, first placed homogeneously over test structures with electrodes, were subjected to ac signals of frequencies up to 15 MHz and voltage amplitudes up to 10 Vpp until they dried up. The obtained patterns, recorded by scanning electron microscopy (SEM), show the agglomeration of SWCNT around the perimeters of electrodes in the regions of high electric fields (positive DEP) with SWCNT clearly aligned with the electric field (Fig. 4c). The electrodes in our structures acting for SWCNT manipulation were also used as capacitors for complex permittivity measurements as a function of frequency. We found that increasing frequency in DEP manipulation of SWCNT resulted in the increased capacitance and in larger conductance of the capacitors. We have correlated SEM recorded patterns with simulated applied electric field and resulting DEP force distribution over the electrodes of nanogap capacitors. The correlation and the obtained pattern of the DEP aligned SWCNT were found to be a function of applied frequency and the semiconducting/conducting nature of measured samples. Capacitance and conductance measurements of capacitors with entrapped cells and with SWNT done as a function of frequency when compared with non-trapped capacitors show differences indicating that there is an effect of the fringing electric field in probing the agglomerated particles. The efficiency of DEP in creating force-inducing motion of particles was verified using numerical simulations. The electrophoresis force that exerts on a nano-particle of radius R with dielectric constant ε2 and conductivity σ2 suspended in a liquid with dielectric constant ε1 and conductivity σ1, due to non uniform the electric field can be calculated as: .

(1)

The factor K is a Clausius-Mossetti coefficient, which is a function of frequency. It is determined by the electrical properties of the medium and particles. Its sign determines whether the force is attractive or repulsive. The last factor is the geometric gradient of the square of the field intensity, which means that the direction of the dielectrophoretic force is independent of the sign of the applied field. In this work we only analyze this field factor Figure. 2. Nanogap capacitor represented as a cartoon (a) and as a fabricated structure with 150 nm oxide (b).


Figure 3. Dielectrophoresis for S. pombe shows positive DEP behavior. Researchers obtain better alignment (circled) along the electric field lines (a) compared with less oriented entrapped cells (b).

with a special configuration of device. In our numerical calculation we used the normalized equation (1) and its corresponding boundary conditions. The results are shown in Fig. 5 (a, b), where an excellent agreement is shown between a pictured SWNT entrapment between two electrodes and the calculated electric field lines distribution and the force factor. Calculated electric field values showed very high electric fields on the edges of the electrodes, such as 5x108 V/m. The actual values of the field factor (which for given frequency and ε and σ parameters ) proportional to the force acting on nanotubes are 1.3x1022 V2/m3, and 4x1019 V2/m3, at inner and outer electrodes edges. In Fig. 4 we show the field factor values. References 1 N. Peng, Q. Zhang, J. Li, and N. Liu, “Influences of AC Electric Field on the Spatial Distribution of Carbon Nanotubes Formed Betweeen Electrodes,” J. Appl. Phys., 100 (2006): 024309. 2 M. B. Fox, D. C. Esveld, A. Valero, R. Luttge, H. C. Mastwijk, P. V. Bartels, A. van den Berg, and R. M. Boom, “Electroporation of Cells in Microfluidic Devices: A Review,” Anal. Bioanal. Chem. 385 (2006): 474-85. 3 P. Shea, B. Songb, X.-H. Xinga, M. van Loosdrechtc, and Z. Liu, Biochemical Eng. Journal 28 (2006): 23-29. 4 Y. Feldman, I. Ermolina, and Y. Hayashi, “Time Domain Dielectric Spectroscopy Study of Biological Systems,” IEEE Trans. on Dielectrics & Electrical Insulation 10 (2003): 728-53. 5 H. Berney, “Capacitance Affinity Biosensors,” in Ultrathin Electrochem. Chemo-and Biosensors, Vol. 2. Ed. M. Mirsky. Springer Series Chem. Sens. and Biosensors, 2004. 43-65. 6 M. Yi, K-H. Jeong, and L.P. Lee, “Biosensors and Bioelectronics,” 20.7 (2005): 1320-26. 7 C. Ionescu-Zanetti, J. T. Nevill, D. DiCarlo, K. H. Jeong, and L. P. Lee, “Nanogap Capacitors: Sensitivity to Sample Permittivity Changes,” J. Appl. Phys. 99 (2006): 024305 8 T. B. Jones, "Basic Theory of Dielectrophoresis and Electrorotation,” IEEE Eng Med Biol Mag. 22.6 (2003) :33-42. 9 W. M. Arnold and N. R. Franich, “Cell Isolation and Growth in Electric-Field Defined Micro-Wells,” Current Appl. Phys. 6.3 (2006): 371-74. 10 M. N. Castellarnau, M. N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid., Mat. Science and Eng. C 26 (2006): 405:10.


Figure 4. (a) The contour plot (in log scale) of the magnitude of electric field factor is shown. At center is the highest amplitude. (b) The plot of the vector of electric field factor distribution is shown according to equation (1). One can see clearly that the DEP forces are concentric toward the edge of the electrodes and that the force is the strongest toward the inner edge, weaker at the outer electrode edge. Because of the structure of the device in the gap region, particles experience a repelling force. (c) Entrapment of SWNT is seen in this SEM picture on a patterned electrode due to a positive DEP force at 10MHz at 10V peak-to-peak applied to the electrode.

M. Frenea, S. P. Faure, B. Le Pioufle, P. Coquet, and H. Fujita, “Positioning Living Cells on a High-Density Electrode Array by Negative Dielectrophoresis,” Mat. Science and Eng. C 23 (2003): 597-603. 11

Development of Wireless Stations for Distributed Field Operations by T. Andrew Yang and Sadegh Davari

D

ISTRIBUTED FIELD OPERATIONS INVOLVE

We have come up with an efficient WSN algorithm, entitled OCO (Optimized Communications and Organization), which proved to be very efficient in accurately detecting intruding objects while conserving energy use. To date, we have published our work on OCO in two refereed articles and have acquired a Texas Higher Education Coordination Board’s ARP (Advanced Research Program) grant to further our research in this area.

dispersed mobile units operating in a wide geographical area, such as battlefield operations or exploration on the Publications moon. One or more wireless stations may be Sadasivam, K., V. Changrani, and T. A. Yang. deployed for effective connectivity among “Scenario Based Performance Evaluation the units. In this project, we investigate the of Secure Routing in MANETs,” Proc. of security and performance issues of wireless the Second Int. Workshop on Mobile Ad stations in mobile ad hoc networks Hoc Networks and Interoperability Issues T. Andrew Yang (MANET), with a focus on the public key (MANETII’05). 2005. management system using certificates. One of the main issues to Sadasivam, K. and T. A. Yang. “Evaluation of Certificate-Based consider in a certificate-based scheme is the secure distribution of Authentication in Mobile Ad Hoc Networks,” Eds. M. H. the public keys to all the nodes in the network. The Public Key Hamza, P. Prapinmonkolkarn, and T. Angkaew. Proc. of the Infrastructure (PKI) defines methods for handling public key manIASTED Int. Multi-Conf. on Networks and Communication agement using X.509 certificates. In a wired network, there exists Systems (NCS 2005). 2005. a centralized certificate server which handles the creation, renew- Tran, S. P. M. and T. A. Yang. “Evaluations of Target Tracking al, and revocation of certificates. This is not feasible in mobile ad Methods in Wireless Sensor Networks,” Proc. of the 37th hoc networks (MANET), which are composed of mobile nodes ACM SIGCSE Technical Symposium on Computer Science that may be constantly moving in the geographical area, and do Education. SIGCSE, 2006. not have a fixed infrastructure or centralized management. Tran, S. P. M. and T. A. Yang. “OCO: Optimized Communication & Besides, due to the dynamic topology of the network, frequent Organization for Target Tracking in Wireless Sensor Networks,” link failures may occur, resulting in issues such as re-authenticaProc. of the IEEE International Conference on Sensor Networks, tion and timely communication with the certificate server. Ubiquitous, and Trustworthy Computing, 2006. Over the past year (2006), our work in mobile networks had led us to explore a related research area, the wireless sensor net- Grants work (WSN), which is a network composed of wireless sensor Yang, T. A. “SOCO: Secure and Optimized Communication & nodes. Each sensor node is a small computer with three modOrganization for Target Tracking in Wireless Sensor Networks,” ules: the energy module, the radio module, and the sensor modAdvanced Research Programs (ARP), Texas Higher Education ule. A WSN may be deployed to monitor a variety of phenomeCoordination Board (THECB), 2006-2008, $48,780. na, such as light, motion, humidity, moisture, wind speed, etc. WIRELESS—Dr. T. Andrew Yang is flanked by Aiyaz Paniwala (l.), B.E. in computer engineering from the U. of Mumbai (formerly Bombay), and Bengami Saurav (r.), B.E. in electronic and communications engineering, the U. of Rajasthan, India. Paniwala is pursuing an M.S. in computer science, and Saurav, an M.S. at UHCL with a focus on wireless field operations, useful on the moon and in battlefield operations.



UH UHCL NASA-JSC Principal Investigators & Co-Principal Investigators

ISSO

Principal and Co-Principal Investigators Dr. Hisham Al-Mubaid Assistant Professor Department of Computer Information Systems School of Science and Computer Engineering University of Houston-Clear Lake Houston, TX 77058 Phone: 281 283-3802; FAX: 281 283-3869 [email protected]

Dr. Abdelhak Bensaoula Research Professor of Physics and Electrical and Computer Engineering Center for Advanced Materials (CAM) University of Houston, 731 S&R1 Houston, TX 77204-5004 Phone: 713 743-3621; FAX: 713 747-7724 [email protected]

Dr. Andenet Alemu Post-Doctoral Aerospace Fellow Center for Advanced Materials University of Houston, 704 S&R1 Houston, TX 77204-5004 Phone: 713 743-3621; FAX: 713 747-7724 [email protected]

Dr. Gary D. Boetticher Associate Professor Division of Computing and Mathematics School of Science and Computer Engineering University of Houston-Clear Lake, D164 2700 Bay Area Blvd. Houston, TX 77058-1098 Phone: 281 283-3805; FAX: 281 283-3869 [email protected]

Dr. Victor Andersen Post-Doctoral Aerospace Fellow Department of Physics University of Houston Houston, TX 77204-5005 Phone: 713 743-8666; FAX: 713 743-3589 [email protected] Dr. Sivaram Arepalli NASA-JSC Collaborator National Aeronautics and Space Administration Lyndon B. Johnson Space Center 2101 NASA Road 1 Houston, TX 77058 [email protected] Dr. G. Dickey Arndt Co-Principal Investigator Avionics Systems Division NASA Johnson Space Center 2101 NASA Parkway, Code Houston, TX 77058 Phone: 281 483-1438 [email protected] Dr. Nacer Badi Research Assistant Professor Center for Advanced Materials (CAM) University of Houston, SR1 419B Houston, TX 77204-5005 Phone: 713 743-3621; FAX: 713 747-7724 [email protected]


Dr. Chris Boney Research Scientist Department of Physics University of Houston, SR 419A Houston, TX 77204-5004 Phone: 713 743-3621; FAX: 713 743-7724 [email protected] Debbie V. Bush Print and Graphics Consultant, ISSO University of Houston, S&R1 510G Houston, TX 77204-5006 Phone: 713 743-9138; FAX: 713 743-9134 [email protected] Dr. Angela Carreno Post-Doctoral Aerospace Fellow Center for Advanced Materials University of Houston, 735 S&R1 Houston, TX 77204-5004 Dr. Albert M. K. Cheng Associate Professor Department of Computer Science College of Natural Sciences and Mathematics University of Houston, PGH 534 Houston, TX 77204-3010 Phone: 713 743-3353; FAX: 713 743-3335 [email protected]

Dr. Mark S. F. Clarke Associate Professor Department of Health & Human Performance College of Education University of Houston Houston, TX 77204-6015 Phone: 713 743-9854; FAX: 713 743-9860 [email protected] Dr. David Criswell Director, The Institute for Space Systems Operations (ISSO) Houston Partnership for Space Exploration (HPSE) University of Houston, 629F S&R1 Houston, TX 77204-5006 Phone: 713 743-9135; FAX: 713 743-3589 [email protected] Dr. James B. Dabney Assistant Professor School of Science and Computer Engineering University of Houston-Clear Lake, D108 Houston, TX 77058-1098 Phone: 281 283-3852; FAX: 281 283-3707 [email protected] Dr. Sadegh Davari Professor and Interim Dean School of Science and Computer Engineering University of Houston-Clear Lake, D171 Houston, TX 77058-1098 Phone: 281 283-3865; FAX: 281 283-3870 [email protected] Jennifer J. Chin-Davis Department Business Administrator Department of Physics Institute for Space System Operations Mission-Oriented Seismic Research Program University of Houston, 617 S&R1 Houston, TX. 77204-5005 Phone: 713 743-3524; FAX: 713 743-3589 [email protected] Dr. Edward T. Dickerson School of Science and Computer Engineering University of Houston-Clear Lake, D114 2700 Bay Area Blvd Houston, TX 77058-1098 Phone: 281 283-3809; FAX: 281 283-3870 [email protected] Matthew Dulin Associate Editor and Chief Graphics Designer, ISSO 1403 Maygrove Dr. Sugar Land, TX 77478 Phone: 281 491-1769; FAX: 713 743-9134 [email protected]

Kathy Dupree Assistant Director, Office of Sponsored Programs University of Houston-Clear Lake 2700 Bay Area Blvd, Box 44 Houston, TX 77058 Phone: 281 283-2141; FAX: 281 283-2143 [email protected] Dr. Daniel L. Feeback Director, Muscle Research Laboratory Human Adaptation and Countermeasure Office Space and Life Sciences Directorate, NASA-JSC 2101 NASA Parkway, Code SK Houston, TX 77058 Phone: 281 483-7189; FAX: 281 483-2888 [email protected] Dr. Katharine E. Forth Post-Doctoral Fellow Department of Health and Human Performance Houston, TX 77204-5331 Phone: 713 743-9868; Fax: 713 743-9860 [email protected] Dr. George E. Fox Professor Department of Biology and Biochemistry College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5001 Phone: 713 743-8363; FAX: 713 743-8351 [email protected] Dr. Karen Frasier-Scott Department of Biology School of Science and Computer Engineering University of Houston-Clear Lake Houston, TX 77058 Phone: 281 283-3744; FAX: 281 283-3869 [email protected] Dr. David Garrison Assistant Professor School of Science and Computer Engineering University of Houston-Clear Lake, B3531 Houston, TX 77058 Phone: 281 283-3796; FAX: 281 283-3870 [email protected] Dr. Michael Gorman Professor Department of Physics College of Natural Sciences and Mathematics University of Houston, 531B S&R1 Houston, TX 77204-5005 Phone: 713 743-3558; FAX: 713 743-3589 [email protected]


Dr. John C. Graf NASA-JSC Co-PI Crew and Thermal Systems NASA Johnson Space Center Houston, TX 77058-3696 Phone: 281 483-9226; FAX: 281 483-5060 [email protected] Dr. Karolos Grigoriadis Professor Department of Mechanical Engineering University of Houston, ENG1 N206 Houston, TX 77204-4006 Phone: 713 743-4387; FAX: 713 743-5403 [email protected] Dr. Gemunu Gunaratne Associate Professor Department of Physics University of Houston, S&R1 629D Houston, TX 77204-5005 Phone: 713 743-3534; FAX: 713 743-3589 [email protected] Dr. Viktor Hadjiev Research Scientist Texas Center for Superconductivity at the University of Houston (TCSUH) University of Houston, UHSC 322 Houston, TX 77204-5002 Phone: 713 743-8442; FAX: 713 743-8201 [email protected]

RESEARCHER—Dr. David Warmflash, Post-Doctoral Aerospace Fellow, works with Dr. John H. Miller and Dr. George Fox at UH.

Dr. Thomas L. Harman Professor and Chair Computer Engineering Department School of Science and Computer Engineering University of Houston-Clear Lake, D104 Houston, TX 77058-1098 Phone: 281 283-3774; FAX: 281 283-3870 [email protected]

Dr. Linsheng Huo Post-Doctoral Aerospace Fellow Dept. of Mechanical Engineering Cullen College of Engineering Engineering Building One, N295-D University of Houston Houston, TX 77204-4006 Phone: 713 743-4498; FAX 713 743-4503 [email protected]

Dr. Hung-Chung Huang Post-Doctoral Research Associate Department of Biology and Biochemistry University of Texas at Dallas Richardson, TX 75083

Roberta Hohmann Office of Sponsored Programs University of Houston-Clear Lake 2700 Bay Area Boulevard, Box 44 Houston, TX 77058-1098 Phone: 281-283-3015; FAX: 281-283-2143 [email protected]

Dr. Keesu Jeon Post-Doctoral Researcher Department of Chemical and Biomedical Engineering Florida State University Tallahassee, FL 32306

Dr. D. Keith Hollingsworth Department of Mechanical Engineering Engineering Building One, N217 University of Houston Houston, Texas, 77204-4006 Phone: 713 743-4534; FAX: 713 743-4503 [email protected]

Dr. Jeffrey A. Jones, M.D. NASA-JSC Co-Investigator Space Medicine and Health Care Systems Medical Operations Division, NASA Johnson Space Center 2101 NASA Parkway, SD2 Houston, TX 77058 Phone: 281 483-4418; FAX: 281 244-7947 [email protected]


Fathi Karouia UH/NASA-JSC Co-Investigator Department of Biology & Biochemistry College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5001 Phone: 713 743-8365 [email protected]

Dr. Brian M. Mayeaux NASA-JSC Co-PI Materials and Processes Branch NASA Johnson Space Center 2101 NASA Parkway, Code MV6 Houston, TX 77058 Phone: 281 244-5802 [email protected]

Dr. Helen W. Lane Manager, University Research and Affairs Office NASA Johnson Space Center 2101 NASA Parkway, Code AD2 Houston, TX 77058 Phone: 281 483-7165; FAX: 281 483-2086 [email protected]

Dr. Billy Mayes Professor, Co-Investigator Department of Physics College of Natural Sciences and Mathematics Science and Research Building I, 406A Houston, TX 77204-5005 Phone: 713 743-3548; FAX: 713 743-3589 [email protected]

Dr. Charles S. Layne Professor Department of Health and Human Performance College of Education University of Houston, HHP 5331 Houston, TX 77204-5331 Phone: 713 743-9868; FAX: 713 743-9860 [email protected] Dr. Ho Jae Lee Visiting Assistant Professor Department of Electrical and Computer Engineering Cullen College of Engineering University of Houston Houston, TX 77204-4005 Phone: 713-743-4460 Dr. Jack Y. Lu School of Science and Computer Engineering University of Houston-Clear Lake, B3531 Houston, TX 77058-1098 Phone: 281 283-3780; FAX: 281 283-3707 [email protected] Dr. Kamlesh P. Lulla Deputy Manager University Research and Affairs Office AD2, NASA-JSC Houston, Texas 77058 Phone: 281 483-5066 [email protected] Dr. Heidar A. Malki Professor Department of Engineering Technology College of Technology University of Houston, 309B T2 Houston, TX 77204-4022 Phone: 713 743-4075; FAX: 713 743-4032 [email protected]

Dr. David S. McKay NASA-JSC Principal Investigator NASA Johnson Space Center 2101 NASA Parkway, Code KA Houston, TX 77058 Phone: 281 483-5048 [email protected] Dr. Nasr Medelci UH collaborator Center for Advanced Materials Science and Research I, 419C University of Houston Houston, TX 77204-5004 Phone: 713 743-3621; FAX: 713 743-7724 [email protected] Dr. John H. Miller, Jr. Associate Professor Texas Center for Superconductivity and Advanced Materials (TCSAM) and Department of Physics College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5005 Phone: 713 743-8257; FAX: 713 743-8201 [email protected] Dr. Pranob Misra Post-Doctoral Aerospace Fellow Center for Advanced Materials 432G Science and Research I University of Houston Houston, TX 77204-5004 Phone: 713 743-3621; FAX: 713 743-7724 [email protected]


Dr. David (Jianjun) Ni Post-Doctoral Aerospace Fellow NASA-Johnson Space Center 2101 NASA Parkway, Code EV4 Houston, TX 77058-3691 Phone: 281 483-1467; FAX: 281 483-5830 Dr. Charles Ott Co-Principal Investigator Life Science Research Laboratory, Medical Science Division NASA Johnson Space Center 2101 NASA Parkway, Code SD3/KI Houston, TX 77058 Phone: 281 483-7155 [email protected] Dr. Duane L. Pierson Director, Microbiology Laboratory Life Sciences Research Laboratory NASA-Johnson Space Center 2101 NASA Parkway, Code SD-4 Houston, TX 77058 Phone: 281 483-7166 [email protected]

Dr. Liwen Shih Associate Professor Computer Engineering Department School of Science and Computer Engineering University of Houston-Clear Lake, D117 2700 Bay Area Blvd. Houston, TX 77058 Phone: 281 283-3866; FAX: 281 283-3870 [email protected]

Dr. Lawrence S. Pinsky Professor and Chair, Department of Physics College of Natural Sciences and Mathematics University of Houston, SR1 412 Houston, TX 77204-5005 Phone: 713 743-3552; FAX: 713 743-3589 [email protected]

Dr. Wajiha Shireen Professor Department of Engineering Technology College of Technology University of Houston, 331 T2 Houston, TX 77204-4022 Phone: 713 743-4080; FAX: 713 743-4032 [email protected]

Dr. T. Madhan Raghaven Post-Doctoral Aerospace Fellow Dept. of Biology and Biochemistry College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5001 Phone: 713 743-8364; FAX: 713 743-8351 [email protected]

Dr. Donn G. Sickorez University Affairs Officer NASA-Johnson Space Center 2101 NASA Parkway, Code AE2 Houston, TX 77058 Phone: 281 483-4724; FAX: 281 483-4876 [email protected]

Dr. Irving N. Rothman Martha Gano Houstoun Research Professor in Literature, 2004-05 Department of English University of Houston, 232B-C, 510-G S&R1 Houston, TX 77204-3013 Phone: 713 743-2962; FAX: 713 743-3215 [email protected]

Dr. Gangbing Song Professor Dept. of Mechanical Engineering Cullen College of Engineering, N235-D University of Houston Houston, TX 77204-4006 Phone: 713 743-4525; FAX 713 743-4503 [email protected]

Dr. LieJune Shiau Associate Professor School of Science and Computer Engineering University of Houston-Clear Lake, B3521 Houston, TX 77058 Phone: 281 283-3724; FAX: 281 283-3707 [email protected]

Dr. David Starikov Research Associate Professor Center for Advanced Materials (CAM) University of Houston, 733 S&R1 Houston, TX 77204-5002 Phone: 713 743-3621; FAX: 713 743-8201 [email protected]


Dr. Viktor Stepanov Post-Doctoral Aerospace Fellow Department of Biology and Biochemistry College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5001 Phone: 713 743-8364; FAX: 713 743-8351 Dr. Madhan R Tirumalai Post-Doctoral Aerospace Fellow Department of Biology and Biochemistry College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5001 Phone: 713 743-8365; FAX: 713 743-2632 [email protected] Dr. James M. Tour Collaborator Depts. of Mechanical Engineering and Materials Sciences Smalley Institute for Nanoscale Science and Technology, Rice University Houston, TX 77251 Phone: 713 348-6346; FAX 713 348-6250 [email protected] Dr. Don L. Tucker NASA Johnson Space Center 2101 NASA Parkway, Code SF24 Houston, TX 77508 Phone: 281 483-0507; FAX: 281 483-3396 [email protected] Dr. David Warmflash, M.D. Post-Doctoral Aerospace Fellow TCSUH and Department of Biology and Biochemistry College of Natural Sciences and Mathematics University of Houston Houston, TX 77204-5002 [email protected] Dr. William R. Widger Associate Professor Department of Biology and Biochemistry University of Houston, 442 HSCHouston, TX 77204-5001 Phone: 713 743-8368 [email protected] Dr. Richard C. Willson Associate Professor Department of Chemical Engineering and Department of Biology and Biochemistry Cullen College of Engineering and the College of Natural Sciences and Mathematics University of Houston, Houston, TX 77204-4004 Phone: 713 743-4308; FAX: 713 743-4323 [email protected]

Dr. Thomas L. Wilson NASA-JSC Co-Investigator Earth Science and Solar System Exploration Division Space Science Branch NASA Johnson Space Center 2101 NASA Parkway, Code SN3 Houston, TX 77058 Phone: 281 483-2147 [email protected] Dr. Larry C. Witte Professor and Associate Dean of Graduate Studies Department of Mechanical Engineering Cullen College of Engineering Engineering Building One, N-224 University of Houston Houston, Texas, 77204-4006 Phone: 713 743-4501; FAX: 713 743-4503 [email protected] Dr. Jaroslaw (Jarek) Wosik Research Professor Texas Center for Superconductivity at the University of Houston (TCSUH) and Department of Electrical and Computer Engineering Cullen College of Engineering University of Houston Houston, TX 77204-5002 Phone: 713 743-8237; FAX: 713 743-8201 [email protected] Dr. T. Andrew Yang Associate Professor School of Science and Computer Engineering University of Houston-Clear Lake, D106 Houston, TX 77058-1098 Phone: 281 283-3835; FAX: 281 283-3870 [email protected] Leonard Yowell NASA-JSC Collaborator National Aeronautics and Space Administration Lyndon B. Johnson Space Center 2101 NASA Road 1 Houston, TX 77058 [email protected] Dr. Wanda Zagozdzon-Wosik Collaborator, Associate Professor Dept. of Electrical and Computer Engineering Cullen College of Engineering Engineering Building One, W330 University of Houston Houston, TX 77204-4005 Phone: 713 743-4427; FAX: 713 743-4444 [email protected]


Student Researchers

SAURAV BENGAMI

CHINMAY DARNE, HASHITRA KODALI, AND DIVYA PADMARAJ

Saurav Bengami, with a B.E. Univ. of Ragasthan, India, pursuing an M.S. in computer engineering at UH-Clear Lake, studying in Dr. Yang’s laboratory.

Chinmay Darne, M.S. electrical engineering, Mumbai U. (Bombay); Harshita Kodali (middle), M.S. in electrical engineering from Andhra Univ., India; Divya Padmaraj, B.S., electrical engineering, Univ. of Madras.

• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •

Andrew Abercromby, Ph.D. recipient, Dept. of Health and Human Performance [UH, Dr. Layne] Cindi Ballard, M.S. recipient, Dept. of Physics [UHCL, Dr. Garrison] Saurav Bengami, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Yang] Masroor Buikhari, Ph.D student, Dept. of Physics [UH, Dr. Miller] Jeffrey Chancellor, Ph.D. student, Dept. of Physics [UH, Dr. Pinsky] Vishal Changrani, M.S. student, Dept. of Computer Science [UHCL, Dr. Yang] David Chow, M.S. recipient, Dept. of Physics [UHCL, Dr. Garrison] Romeo Chua, M.S. recipient, Dept. of Computer Engineering [UHCL, Dr. Shih] James Claycomb, Ph.D. recipient, Dept. of Physics [UH, Dr. Miller] Katherine Covin, B.S. recipient, Dept. of Physics [UH, Dr. Pinsky] Chinmay Darne, Ph.D. student, Dept. of Electrical and Computer Engineering [UH, Dr. Wosik] Indrani DasGupta, Ph. D. student, Dept. of Biology and Biochemistry [UH, Dr. Fox] Rafael de la Torre, M.S. student, Dept. of Physics [UHCL, Dr. Garrison] Kevin Depaula, M.S. recipient, Dept. of Physics [UHCL, Dr. Garrison] Najib Elkhayari, Ph.D. student, Dept. of Physics [UH, Dr. Pinsky] Jie Fang, Ph.D. student, biophysics, Dept. of Physics [UH, Dr. Miller] Katharine E. Forth, Ph.D. recipient, Dept. of Health & Human Performance [UH, Dr. Layne] Lakshmi Gopal, M.S. student in electrical engineering [UH, Dr. Shireen] Anjana Garud, M.S. student in systems engineering, Dept. of Computer Science [UHCL, Dr. Dabney] Marlo Graves, M.S. student, Dept. of Physics [UHCL, Dr. Garrison] John Hamilton, M.S. recipient, Dept. of Physics [UHCL, Dr. Garrison] Muhammad Haq, senior, B.S. student, Dept. of Physics [UH, Dr. Miller] Ashley Higgins, M.S. student, Dept. of Mechanical Engineering [UH, Dr. Hollingsworth] Hans Infante, Ph.D. student, Dept. of Physics [UH, Dr. Miller] Shih-Ying Hsu, Ph.D. student, biophysics, Dept. of Physics [UH, Dr. Miller] Flora Ip, Ph.D candidate, Dept. of Electrical and Computer Engineering [UH, Dr. Wosik] Adam Johnson, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Shih] Maged Kamel, Ph.D. student, Dept. of Electrical and Computer Engineering [UH, Dr. Wosik] Fathi Karouia, Ph.D. student, Dept. of Biology and Biochemistry [UH, Dr. Miller] Ahmed Khan, B.S. recipient, Dept. of Computer Science [UHCL, Dr. Shih] Harshita Kodali, M.S. student, Dept. of Electrical and Computer Engineering [UH, Dr. Wosik] Hari Krishnareddy Kondapalli, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Shih] Yingwei Kuo, Ph.D.student, Dept. of Computer Science [UH, Dr. Cheng] Sergio J. Larrondo, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Shih]


MUHAMMAD HAQ

SEDJANA MARIC

SHIH-YING HSU

Muhammad Haq, pursuing a B.S. in physics, studying probes of biological molecular motors.

Sladjana Maric, M.S. from the University of Belgrade, currently a Ph.D. student in biophysics.

Shih-Ying Hsu, Ph.D. student in biophysics, from Chung-Hsing University, Taichung, Taiwan.

• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •

Matthew LeBourgeois, B.S. recipient, Dept. of Physics [UH, Dr. Pinsky] Kerry Lee, Ph.D. recipient, Dept. of Physics [UH, Dr. Pinsky] Jian Lin, Ph.D. student, Dept. of Computer Science [UH, Dr. Cheng] Yamei Liu, Ph. D. student, Dept. of Biology and Biochemistry, [UH, Dr. Fox] Bin Lu, M.S. student, Dept. of Computer Science [UH, Dr. Cheng] Andrea Mairani, M.S. student, Dept. of Physics [UH, Dr. Pinsky] Sladjana Maric, Ph.D. student, Dept. of Physics [UH, Dr. Miller] Mona Meisami-Azad, M.S. student, Dept. of Mechanical Engineering [UH, Dr. Grigoriadis] Javad Mohammadpour, Ph.D. student, Dept. of Mechanical Engineering [UH, Dr. Grigoriadis] Dharmakeerthi Nawarathna, Ph.D recipient, Dept. of Physics [UH, Dr. Miller] Mozhdeh Niazmand, Ph.D. student, biophysics, Dept. of Physics [UH, Dr. Miller] Kimthu Nguyen, M.S. recipient, Dept. of Health & Human Performance [UH, Dr. Layne] Divya Padmaraj, M.S. student, Dept. of Electrical and Computer Engineering [UH, Dr. Wosik] Aiyaz Paniwala, M.S. student, Dept. of Computer Science [UHCL, Dr. Yang] Sujay Paranjape, M.E. student, Dept. of Mechanical Engineering [UH, Dr. Bensaoula] Rajeev Pillai, Ph.D. student, Dept. of Electrical Engineering [UH, Dr. Bensaoula] Amir Pourmoghaddam, Ph.D. student, Dept. of Health & Human Performance [UH, Dr. Layne] Camelia Prodan, Ph.D. recipient, Dept. of Physics [UH, Dr. Miller] Chamith Rajapakse, Ph.D. recipient, Dept. of Physics [UH, Dr. Gunaratne] Brandon Reddell, Ph.D. student, Dept. of Physics [UH, Dr. Pinsky] Hari Krishnraeddy Chinnapu Reddy, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Shih] Karthik Sadasivam, M.S. student, Dept. of Computer Science [UHCL, Dr. Yang] Hugo Sanabria, Ph.D. recipient, Dept. of Physics [UH, Dr. Miller] Mark Sheppard, M.S. student, Dept. of Mathematics [UHCL, Dr. Shiau] Victor Shum, Ph.D. student, Dept. of Aerospace Engineering [UHCL, Dr. Shih] Tom Smith, M.S. recipient, Dept. of Physics [UHCL, Dr. Garrison] Susan Strasser, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Shih] Sam Phu Manh Tran, M.S. student, Dept. of Computer Engineering [UHCL, Dr. Yang] Srinivas Vanapalli, M.S. recipient, Dept. of Electrical and Computer Engineering [UH, Dr. Shireen] Vijay Vajrala, Ph.D. student, Dept. of Physics [UH, Dr. Miller] Jiachen Wang, Ph.D. recipient, Dept. of Biology and Biochemistry [UH, Dr. Fox] Lian Xue, Ph.D. student, Dept. of Electrical Engineering [UH, Dr. Wosik] Neal Zapp, Ph.D. student, Dept. of Physics [UH, Dr. Pinsky]


ISSO RESEARCH PROJECTS ISSO Director’s Report • 1 PDAF REPORTS—POST-DOCTORAL AEROSPACE FELLOWSHIPS Development of Micro Column Arrays (MCA) for Thermal Management Applications • 8 UWEB Tracing System Design with TDOA Algorithm for Space Applications • 11 Effects of Simulated Microgravity on Microbial Gene Expression • 17 Martian Soil Biosensors Based on Dielectric Spectroscopy • 21 Early Origins of Genetic Systems and Remnants of the RNA World • 79 ASTROBIOLOGY AND LIFE SCIENCES Bacillus Pumilus SAFR-032: A Model for Planetary Protection Research • 40 A Theoretical Analysis of Vibrational Modes Aimed at Their Use as Measures of Bone Damage • 82 Mechanical Foot Stimulation Results in Lower Limb Muscle Activation • 90 Dielectrophoresis of Biological Cells and Single-Walled Carbon Nanotubes • 108 SPACE RADIATION MODELLING Efficient Space Radiation Computation with Parallel FPGA • 56 Space Radiation Shielding Modeling Consortium • 96 High-Performance Martian Space Radiation Mapping • 104 COMPUTER SCIENCE AND COMMUNICATIONS Optimizing Quality-of-Service in Adaptive Optics Systems and Other (m,k)-Firm Real-Time Systems • 30 Computational Methods in Non-Smooth Mechanics: Application to Dry Friction Constrained Motions • 53 Natural Language Interface Models for Fast Responsiveness Applications • 68 The Impact of Chromosome Lineage upon Genetic Program Modeling • 72 Progress on Three Projects: Systems for Spacecrafts, Rovers, and Station Crew Return Vehicles • 74 Low-Frequency Dielectric Spectroscopy of Martian Soil Samples (2004) • 95 Electromagnetic Probes of Molecular Motors (2005) and High-Performance Martian Space Radiation Mapping • 104 Development of Wireless Stations for Distributed Field Operations • 111 PHYSICAL SCIENCES, COSMOLOGY, AND DEFOE Prototype Micro-Manipulator of Space Robotics Applications • 37 Origin of Structure in the Early Universe from Gravitation in Radiation • 43 The Solar Eclipse of April 22, 1715, and Family Quarrels in Daniel Defoe’s The Family Instructor • 48 A Text-Mining Technique for Literature Profiling and Information Extraction from Biomedical Literature • 69 Miniature Optical Sensors for Detection of Water and Air Contamination • 71 Real-Time Active Loading of Piezoelectric Ultrasonic Motors for Simulating Space Robotics Applications • 76 A Unique Camera System To Study the High-Speed Dynamics of Premixed Flames • 81 Raman Scattering Test of Mechanical and Sensor Properties of Advanced Nanocomposites • 83 ENGINEEERING AND SENSORS Micro-Integrated Super Broadband Stellar Simulator Optical Calibration Sources • 28 Superior Adsorbents for Aerospace Applications • 46 Fault Tolerant Control of a Truss Structure Using MR Dampers • 62 Investigation of III-Nitride Materials for Space-Based Solar Cells • 70 Development of Quantum-Cascade Laser-Based Biosensor Technology • 85 The Effect of Martian Dust on Radiator Performance • 88 Contaminant Removal from Fuel Cells for Aerospace Applications • 91 Energy-to-Peak Induced Norm Upper Bound Control Approach for Collocated Structural Systems • 92 An AC-DC-AC Converter with Smaller DC-Link Capacitor for Space Power Distribution Systems • 106 Roster of Principal Investigators, NASA-JSC Co-PI’s, Post-Doctoral Aerospace Fellows • 113 ISSO Student Researchers • 120


REHAB—ISSO Annual Report Associate Editor Matt Dulin meets with Dr. Adam Thrasher of Alberta, Canada, in the Laboratory of Integrated Physiology where practical experiments lead to devices designed to help astronauts maintain muscle tone in the vacuum of space. On Earth, these experiments conducted by Charles S. Layne and Mark F. S. Clarke, UH Dept. of Health and Human Performance, are proving beneficial, even essential, in the convalescence and rehabilitation of bedridden patients. For report, see p. 90.

BACK COVER—Antennas at NASA under study and in development by Edward Dickerson (UHCL), G. Dickey Arndt, NASA-JSC Co-PI, and PDAF David (Jianjun) Ni. See p. 11.


ISSO The Institute for Space Systems Operations University of Houston University of Houston-Clear Lake Houston, TX 77204-5005

Director—Phone: 713 743-9135 Editorial—Phone: 713 743-9138 E-mail: [email protected] http://www.isso.uh.edu