NeTS-NOSS: PARIS: A Framework for Privacy Augmented Relaying of Information from Sensors

Award Number: 435043

Program(s): , RES IN NETWORKING TECH and SYS

Start Date: 9/15/2004

Principal Investigator: Trappe, Wade

Co-PI Name(s): Yanyong Zhang

PI Email Address: trappe@winlab.rutgers.edu

Abstract: Abstract:

Providing privacy for sensor networks is an important problem that is complicated by the fact that it is easy for adversaries to observe communications between sensor nodes. A first line of defense for protecting sensor communications is cryptography. However, these methods cannot address the complete spectrum of privacy issues in sensor systems. Specifically, security solutions are inadequate for protecting the privacy of contextual information surrounding a sensor application, such as the source's location, or the time at which a measurement was made, or even the size of sensor data packets.

This project investigates the development of a framework for providing three critical types of contextual privacy to sensor communications: source location privacy, temporal privacy, and traffic privacy. The project takes the viewpoint that the existing network stack can be modified to protect privacy while maintaining desirable levels of resource-efficiency. This investigation will enhance the privacy levels achieved through the development of new routing protocols involving the use of directed random walk techniques to obfuscate the data source, the modification of the structure of sensor messages to prevent traffic analysis attacks, the introduction of delay in the delivery of messages to reduce temporal correlation attacks, and the introduction of modifications to physical layer communications and the sensor topology to prevent the localization of a communication source. Through dissemination of the research results in both archival publications and new curricula, this project will advance the development of sensor applications by addressing critical privacy issues before sensor systems become a communal asset.

NeTs-ProWin: High Performance Cognitive Radio Platform with Integrated Physical and Network Layer Capabilities

Award Number: 435370

Program(s): , RES IN NETWORKING TECH and SYS

Start Date: 9/15/2004

Principal Investigator: Ackland, Bryan

Co-PI Name(s): Michael Bushnell Christopher Rose Dipankar Raychaudhuri Tod Sizer

PI Email Address: bda@winlab.rutgers.edu

Abstract: NeTS-ProWiN: High Performance Cognitive Radio Platform with Integrated Physical and Network Layer Capabilities

Award 0435370

Bryan Ackland, Rutgers

Rutgers University, Georgia Institute of Technology and Lucent Bell Laboratories

The objective of this project is to build a high-performance experimental cognitive radio platform based on a novel network-centric architecture for software defined radios. Cognitive radio bands under consideration by the US FCC represent a new approach for co-existence between wireless devices based on intelligent adaptation to the observed radio frequency (RF) environment. Dynamic adaptation capabilities of cognitive radios range from frequency agility to more complex collaborative approaches in which radio nodes self-organize into an ad-hoc multi-hop network. In this project, we are developing an FPGA-based experimental platform which incorporates a number of cognitive radio capabilities including frequency agility, software-defined modulation, programmable etiquette and MAC protocols, and ad-hoc network routing. The hardware architecture contains a mix of software programmable and reconfigurable components, and incorporates a flexible packet processing engine for high-speed (~50 Mbps+) link and network layer functions.

This project is a team effort involving the Wireless Information Networks Laboratory (WINLAB) at Rutgers University (cognitive radio systems, SDR, and low-power VLSI), Georgia Institute of Technology (agile RF front end) and Lucent Bell Laboratories (flexible radio platforms). The research program has the following thrusts: (1) system-level investigation of cognitive radio spectrum sharing scenarios, (2) design of agile RF transceivers for efficient reconfiguration of frequency, bandwidth and power, (3) architecture, design and validation of baseband and protocol processing modules for a cognitive radio with integrated PHY and networking capabilities, and (4) development of experimental cognitive radio platforms for use in system prototyping and field evaluation of cognitive radio usage scenarios.

Collaborative Research: Algorithms for sparse data representations

Award Number: 354690

Program(s): COMPUTATIONAL MATHEMATICS, APPLIED MATHEMATICS

Start Date: 9/15/2004

Principal Investigator: Muthukrishnan, Shanmugavelayut

Co-PI Name(s):

PI Email Address: muthu@cs.rutgers.edu

Abstract: The investigators address the mathematical underpinnings of compressing large data sets using sparse representations over rich dictionaries and develop a foundation for classifying these problems in terms of their algorithmic complexity. The investigators also find efficient algorithms for computing high-quality sparse representations of data over sophisticated, commonly used dictionaries that provably perform as claimed with respect to both efficiency and correctness of output and are particularly well-suited for massive data set applications. The research proceeds at multiple levels of abstraction. It considers general factors of a representation class that guarantee or preclude such algorithms, it considers algorithms for specific common representation classes, and it finds algorithms for representation classes adapted to specific common (and diverse) applications, such as solutions of partial differential equations, image processing, and database query optimization.

Over the past ten years there has been a dramatic increase in data gathering mechanisms, as well as an ever-increasing demand for finer data analysis in applications that rely on scientific and geometric modeling. Each day, literally millions of large data sets are generated in medical imaging, surveillance, and scientific acquisition. In addition, the internet has become a communication medium with vast capacity, generating massive traffic data sets. The usefulness of these data sets rests on our ability to process them efficiently, whether it be for storage, transmission, visual display, fast on-line graphical query, correlation, or registration against data from other modalities. The current state of the art in data processing is far from providing the efficient and faithful representations required in emerging applications. With few exceptions, previous work has not provided algorithms whose efficiency or output quality, though typically validated experimentally, has been analyzed rigorously and thoroughly. The investigators carry out fundamental mathematical and algorithmic research to significantly increase our capacity to process and manage large data sets. The research makes significant mathematical progress in providing rigorous algorithmic results that are of great need in this field. The research also makes significant improvements through highly efficient algorithms in the sizes of data sets that are analyzable and in the types of data processing tasks that can be carried out. Finally, the investigators create a library of software for massive data processing applications.

Collaborative Research: SEI (EAR): Adaptive Fusion of Stochastic Information for Imaging Fractured Vadose Zones

Award Number: 430826

Program(s): ITR-INFORMATION INTEGRATION

Start Date: 9/15/2004

Principal Investigator: Parashar, Manish

Co-PI Name(s):

PI Email Address: parashar@caip.rutgers.edu

Abstract: A stochastic information fusion methodology is developed to assimilate electrical resistivity tomography, high-frequency ground penetrating radar, mid-range-frequency radar, pneumatic/gas tracer tomography, and hydraulic/tracer tomography to image fractures, characterize hydrogeophysical properties, and monitor natural processes in the vadose zone. The information technology research will develop: (1) mechanisms and algorithms for fusion of large data volumes; (2) parallel adaptive computational engines supporting parallel adaptive algorithms and multi-physics/multi-model computations; (3) adaptive runtime mechanisms for proactive and reactive runtime adaptation and optimization of geophysical and hydrological models of the subsurface; and (4) technologies and infrastructure for remote (pervasive) and collaborative access to computational capabilities for monitoring subsurface processes through interactive visualization tools.

The combination of the stochastic fusion approach and information technology can lead to a new level of capability for both hydrologists and geophysicists enabling them to "see" into the earth at greater depths and resolutions than is possible today. Furthermore, the new computing strategies will make high resolution and large-scale hydrological and geophysical modeling feasible for the private sector, scientists, and engineers who are unable to access supercomputers, i.e., it is an effective paradigm for technology transfer.

NeTS-ProWin: Cognitive Radios for Open Access to Spectrum

Award Number: 434854

Program(s): , RES IN NETWORKING TECH and SYS

Start Date: 9/15/2004

Principal Investigator: Mandayam, Narayan

Co-PI Name(s): Christopher Rose Roy Yates Predrag Spasojevic

PI Email Address: narayan@winlab.rutgers.edu

Abstract: NeTS-ProWiN: Cognitive Radios for Open Access to Spectrum

Award 0434854

Narayan Mandayam, Rutgers

Abstract

Spectrum regulation has traditionally been driven by improvements in technology, from improved filters to the sophisticated logic and radio techniques that created the cellular revolution. More recently, however, a new paradigm has emerged in which regulation has driven technology. A modest regulatory experiment in "open spectrum" that began in the ISM bands has spawned an impressive variety of important technologies and innovative uses, from cordless phones and wireless LANs to meter readers and home entertainment products. Since these systems must adapt to a wide variety of unpredictable conditions, the emerging technologies called "cognitive radio" offer significant potential benefits in system capacity and service quality.

This investigation begins with the forward-looking assumption that a perfect cognitive radio exists and can configure itself to any transceiver type. Under this assumption, a number of exemplary cognitive strategies are studied to identify the approaches that offer the greatest benefit at the least "cost". These strategies include: (1) discovery of available spectrum, (2) information to support efficient operation, (3) negotiation in situations of conflict, (4) coding for efficient sharing, and (5) domination in situations of conflict. Because these strategies are technologically diverse, their costs are measured against the common metrics of hardware and protocol complexity.

This work is carried out using a combination of fundamental analysis, computer simulation and physical emulation using testbeds developed at WINLAB. The results will identify the potential benefits and costs of a diverse set of design strategies, and will be disseminated via a workshop for practitioners in the field.

Relativistic Fields with Point Defects

Award Number: 406951

Program(s): APPLIED MATHEMATICS

Principal Investigator: Kiessling, Michael

Co-PI Name(s):

PI Email Address: miki@math.rutgers.edu

Abstract: This project is divided into a classical and a quantum physical part. The classical part is concerned with the rigorous analysis of the classical limit of a new dynamical theory of relativistic electromagnetic fields with topological point defects that represent point electrons. This theory combines the nonlinear Maxwell-Born-Infeld field equations with a novel Hamilton-Jacobi type law of motion for the point defects. The most important issue here is the special relativistic radiation reaction problem, which can now be investigated without any a priori regularization or renormalization. The principal investigator will also develop a general relativistic extension of this theory, which promises progress on the problem of motion of so-called naked singularities of space-time and the gravitational field. The theory has already been partly quantized; the quantum part of the project now is concerned with the completion of the quantization. In particular, the implementation of the physically important quantum effects of spin and photon are the primary goals. So far the theory is free of any of the notorious divergence problems that plague the prevailing electromagnetic theory (QED), and it is expected that the final theory will also be entirely well-behaved.

Electromagnetism is the most widely applicable part of fundamental physical theory. It touches everything from atomic physics, chemistry, and condensed matter physics to electronics and electrical engineering. The orthodox theory has certainly been hugely successful, yet it has also been plagued by infinities that have stood in the way of further progress on a number of issues. The research in this project involves a new formalism which is designed to overcome the problems of the orthodox electromagnetic theory and which has already overcome some of these. As a result of the new mathematically well-defined formalism under development, better quantitative, rigorous, computational simulation of electromagnetic phenomena may be expected. The classical version of the theory covers, for instance, the physics of high temperature plasma, with applications to space and laboratory (thermonuclear fusion) phenomena. A promising application of the new quantum theory is to positronium physics, which in particular may have medical applications in positron emission tomography.

Cone-Preserving Operators and Nonlinear Differential-Delay Equations

Award Number: 401100

Program(s): ANALYSIS PROGRAM

Principal Investigator: Nussbaum, Roger

Co-PI Name(s):

PI Email Address: nussbaum@math.rutgers.edu

Abstract: Abstract

Nussbaum

The research proposed here concerns two areas: (a) the dynamics of nonlinear differential-delay equations with state-dependent time lag(s) and (b) questions about cone-preserving operators. The immediate link between (a) and (b) is a recently discovered and unexpected connection between singular limits of differential-delay equations and generalized max-plus equations. The PI will continue this work in several directions. For example, is it possible to extend known results to the case of two or more state-dependent time lags? This is largely terra incognita, but numerical results suggest a variety of intriguing results.

The general problem of understanding the dynamics of nonlinear functional differential equations is important in both theory and practice. Many physical problems are best modeled by functional differential equations. Mathematical biology is a particularly rich source of examples. The methods developed here provide some insight into the models. Conversely, models in the sciences have traditionally motivated the choice of equations to study; Nicholson's model of blowfly population from fifty years ago is a typical example. Thus a broader impact of this proposal is obtaining a better understanding of models from the physical and biological sciences that involve functional differential equations.

Collaborative Research: I/UCRC: Ceramic and Composite Materials Center

Award Number: 436504

Program(s): , INDUSTRY/UNIV COOP RES CENTERS

Start Date: 9/1/2004

Principal Investigator: Haber, Richard

Co-PI Name(s):

PI Email Address: rhaber1@rci.rutgers.edu

Abstract: The Industry/University Cooperative Research Center for Ceramic and Composite Materials has met the program criteria over their first five year period. The Center's research now spans synthesis processing, microstructural characterization and properties from nanometer through the micron scale. The Center has added three new thrust areas, 1) ceramic armor materials; 2) catalysis and; 3) electrochemical and energy related materials.

Undergraduate Research Center for Chemistry and Closely Allied Fields

Award Number: 418772

Program(s): CHEMISTRY EDUCATION

Start Date: 9/1/2004

Principal Investigator: Herzog, Gregory

Co-PI Name(s): John Krenos Joseph Potenza Paul Schueler Diane Trainor

PI Email Address: herzog@rutchem.rutgers.edu

Abstract: The award from the Chemistry Division supports an Undergraduate Research Centers (URC) planning grant. The PI is Gregory Herzog. The co-PIs are John Krenos and Joseph Potenza from Rutgers, Paul Schueler from Raritan Valley Community College and Diane C. Trainor of Middlesex County Community College. The planning grant will work towards 1) improvement of a large first-year laboratory course by adding a research-oriented project carried out in small groups; 2) recruit students for a second semester research project; 3) match these students with an active research group; 4) create a new second semester 3-credit course with research and laboratory components. The project directors will assist students to find further research opportunities, supervise their final reports, evaluate the program elements for effectiveness and scale up, and initiate wide ranging discussions of the results. Student participants will be drawn from the two community colleges and the undergraduate colleges at Rutgers. Faculty research mentors will be drawn from several academic units at Rutgers and the University of Medicine and Dentistry of New Jersey. Industrial scientists from pharmaceutical companies in New Jersey will help to teach the new course.

Acquisition of Instruments for Biosample Analyses in Research and Teaching

Award Number: 421079

Program(s): MAJOR RESEARCH INSTRUMENTATION

Start Date: 9/1/2004

Principal Investigator: Martin, Joseph

Co-PI Name(s): John Dighton Pradip Sarkar Daniel Shain

PI Email Address: jomartin@camden.rutgers.edu

Abstract: This award supports purchase of three major instruments to be used for analytical biochemistry in research and teaching efforts at a predominantly undergraduate institution. The award, to a group of faculty with related interests in information processing in complex biological systems, will permit acquisition and operation of a high pressure liquid chromatography system, an elemental analyser, and a phospoimaging system. These instruments will be placed in a central shared laboratory where they will be maintained by an experienced research technician. Expected research uses include the following: studies of nutrient movement within fungal mycelia; long-term analysis of soil chemistry in the New Jersey Pinelands; analysis of the effects of circadian rhythms and sleep-waking cycles on distribution of thyroid hormones and related CNS neurotransmitters; clarification of the neurotransmitter histology of a unique feeding circuit in Pantadon buchholzi, a fish with an unusual eye that receives light simultaneously from air and water; and others. In addition, the equipment will be used to enhance numerous graduate and undergraduate course offerings in biology and chemistry. The availability of this equipment will allow student researchers at both graduate and undergraduate levels to have hands-on experience with sophisticated research instruments. Courses that will benefit from the new equipment include biochemistry, cell physiology, molecular biology, general ecology, practical field ecology, and a proposed laboratory course in neuroscience and others. The equipment will also benefit several outreach programs that bring participants into the research laboratories of Rutgers/Camden faculty.

BE MUSES: Towards Self-Sustaining High-Rise Buildings: Framework for an Analysis of Materials, Energy, Economic and Social Issues

Award Number: 424625

Program(s): BE-MAT USE:SCIENCE,ENG and SOCIETY, BE: NON-ANNOUNCEMENT RESEARCH

Start Date: 9/1/2004

Principal Investigator: Krogmann, Uta

Co-PI Name(s): Clinton Andrews

PI Email Address: krogmann@aesop.rutgers.edu

Abstract: This BE:MUSES planning grant will support activities directed at advancing research on green or sustainable construction. Sustainable building practices are intended to reduce resource consumption, energy consumption, life-cycle costs and production of pollutants and wastes, while improving human productivity. Ideally, self-sustaining buildings produce their own energy and engender safe, regenerative, closed-loop construction and operational materials flow. The primary objective of this planning project is to develop a preliminary framework for the analysis of a large, self-sustaining, high-rise building with a focus on the building's utilities.

This project will achieve its objectives by assembling an experienced, interdisciplinary team around the core team of a civil engineer, an urban planner and an architect, conducting a trade-off analysis with focus on the utility infrastructure for a speculative, self-sustaining, high-rise building, conducting a small, interdisciplinary workshop to review the trade-off analysis and discuss the inclusion of economic and policy aspects, and submitting a full proposal. Findings will be disseminated to practitioners via a web site and presentations and used as case studies in urban planning and waste management classes.

Building design choices have important environmental impacts and also dramatically affect users' quality of life. This project will establish an analytical framework for assessing how self-sustaining, high-rise buildings that can generate much of their own electricity and recycle much of their own water can contribute to reduced material and energy use. The project will develop methods to assess under what circumstances there would be sufficient return to justify such investments in self-sufficiency. This project will improve the intellectual basis for building design and for public policymaking that influences self-sustaining building practices.

This planning award will be co-managed and co-funded by CMS and SBE.

Collaborative Research: Magnetic Properties of Greenland and Antarctic Ice Cores

Award Number: 424940

Program(s): ARCTIC NATURAL SCIENCES, ANTARCTIC GLACIOLOGY

Start Date: 9/1/2004

Principal Investigator: Kent, Dennis

Co-PI Name(s):

PI Email Address: dvk@rci.rutgers.edu

Abstract: The Principal Investigators have successfully measured the concentration of ultra-fine magnetic particles in ice samples from different climatic intervals from the NorthGRIP core, Greenland, using low temperature (77K) isothermal remnant magnetization (IRM) analysis and compared it with the mass concentration of aerosol dust that varies by a factor of ten. The mean IRM intensity of the ice varies by a factor of three from glacial to interglacial intervals, being lower during interglacials. The magnetic measurements are reproducible and well above the IRM intensity of ultra-pure water ice made under clean lab conditions. The IRM acquisition curves of the ice samples are compatible with a mixture of magnetite and subsidiary hematite contributions, magnetic properties that are typical of pristine loess from the Chinese loess plateau, which is considered to have the same source in the eastern Asian deserts as dust in Greenland ice. Comparison of the IRM intensity and total dust mass of the ice shows a remarkably good correlation, but also reveals a large uncorrelated magnetization, which is essentially constant over the different climatic stages and is the dominant component during intervals with very low measured dust concentrations. The uncorrelated magnetization may be due to either a constant flux of highly magnetic interplanetary dust particles (IDPs) or the more general presence of ultrafine grain aerosol dust mass that were largely undetected in the Coulter Counter measurements. The latter would imply that the actual dust concentration contrast between glacial and interglacial intervals is much smaller than estimated. These alternative hypotheses can be evaluated by obtaining comparative data from ice cores from Antarctica, where the aerosol dust flux is radically different (concentration, source) than in Greenland whereas the flux of IDPs should be about the same. The Principal Investigators will measure the magnetization of a suite of samples representing the full range of glacial and interglacial dust concentrations from the Vostok ice core. IRM acquisition curves will be generated for about 10 samples from each of 12 distinct climatic intervals using a new pulse magnetizer capable of generating fields to 2.5 T on large (~50 cc) samples to achieve saturation and high signal level. Dust concentrations will be measured on the same samples using a Coulter Counter. Additional sets of samples from selected intervals with intermediate dust concentrations will be analyzed from North GRIP to solidify the magnetization vs. dust concentration curve from that region. SEM-EDXRF analyses will be done to characterize the dust. A comparison of the magnetization vs. dust concentration relationships between NorthGRIP and Vostok will allow them to make quantitative estimates of the contributions to the uncorrelated magnetization from the flux of extraterrestrial particles and possibly, the undetected aerosol dust mass. The outcome of these novel experiments is expected to have broad significance to our understanding of the role of dust in long-term climate change.

CompBio: Special Focus on Information Processing in Biology

Award Number: 432013

Program(s): , CISE EDUCAT RES and CURRIC DEVEL

Start Date: 9/1/2004

Principal Investigator: Roberts, Fred

Co-PI Name(s): Ronald Levy Wilma Olson Eduardo Sontag

PI Email Address: froberts@dimacs.rutgers.edu

Abstract: Increasingly, many aspects of biology can be viewed as involving the processing of information. Modern

information and computer science have played an important rolein such major biological accomplishments

as the sequencing of the human genome. On the other hand, biological ideas can inspire new concepts and

methods in information science. This project is motivated by these two observations. Progress in the field

of biological information processing will require interdisciplinary collaborations among computer scientists,

mathematicians, physicists, chemists, and biologists. The project is built around a series of workshops that

will enhance the interdisciplinary collaborations beginning to form and introduce outstanding junior people

to problems and topics at the forefront of research.

Intellectual Merit

The project will be organized around a series of workshops with four themes: (1) Algorithmic Approaches

to Biological Information Processing; (2) Computer Science, Engineering and Biology: Applications and

Analogies; (3) Biological Circuits and Cellular Signaling; (4) Proteomics. Two of these themes represent

approaches and two represent areas of application of these approaches. Under theme 1, planned workshops

are on Detecting and Processing Regularities in High Throughput Biological Data; Machine Learning Ap-

proaches for Understanding Gene Regulation; and Computational Tumor Modeling. Theme 2 workshops will

cover Nanotechnology and Biology; Control, Communication, and Computing in Biology; and The Mecha-

nism and Applications of the RNA Interference Process. For Theme 3, there will be workshops on Strategies

for Reverse Engineering Biological Circuits; Cell Communication and Information Processing in Developing

Tissues; Dynamics of Biological Networks; and Evolution of Gene Regulatory Networks. Theme 4 work-

shops will be on Information Processing by Protein Structures in Molecular Recognition; Proteome Network

Evolution; Functional Proteomics of Neurodegenerative Diseases; and Implications of Mathematical Models

of Infection and Molecular Modeling of Hepatitis B Virus. We expect that the workshops, scientific papers

and books coming out of the project will help to develop the long-term focus of the field, carefully define

problems and directions in computer science, mathematics, chemistry, andphysics of specific interest to and

designed in collaboration with biologists, and lead to new biological concepts that will in uence biological

and information science research in the future. In short, we expect the project to in uence the study of

biological information processing for years to come.

Broader Impacts

The ideas developed in this project will have impact on a myriad of fields and create cross-disciplinary

connections. A visitor program will encourage senior and junior researchers, including students, to participate

in collaborative research spawned by the workshops. Each workshop will have a fund for support of graduate

students and postdocs amd workshops will have a substantial educational component through talks of a

tutorial/expository nature. The topic lends itself well to undergraduate research and participating faculty

will coordinate topics with an undergraduate research program (REU program) already in existence. To give

the project widespread dissemination, each workshop will have awebsite with relevant references, problems,

and copies of presentations that can make it a resource for a large community. The project should significantly

in uence the careers of a large number of outstanding junior researchers and it should play an important

role in the training and development of scientists who are well-prepared to become leaders in the field of

biological information processing. The project is expected to have a long-term impact well beyond its four

year duration since the workshop, visitor, and dissemination components of the project will allow the ideas

developed to reach hundreds of people nationwide and worldwide.

QSB: Experimental and Computational Studies to Optimize Hepatocyte Function

Award Number: 424968

Program(s): MSPA-INTERDISCIPLINARY, BIOTECHNOLOGY, PROCESS and REACTION ENGINEERING

Start Date: 9/1/2004

Principal Investigator: Ierapetritou, Marianthi

Co-PI Name(s): Martin Yarmush Charles Roth

PI Email Address: marianth@sol.rutgers.edu

Abstract: Ierapetritou

0424968

The objective of this research is to develop systems-based quantitative approaches that consider the whole picture of cell metabolism, including intra and inter compartmental processes within a multi-objective framework. This is needed in order to investigate the characteristics of hepatocyte cells, the role of specific functions in bioartificial liver systems, and the optimization of their performance. Their hypothesis is that there is a finite number of hepatic functions which are most critical for patient survival, that it is possible to significantly upregulate these functions in hepatocyte cultures, and as a result, maximize cell function and reduce the cell mass required in the bioartificial liver. In particular, the specific aims for this research are: (1) to characterize and optimize substrate supplementation to enhance hepatocyte function, (2) to modulate the hepatocyte function through the use of antisense technology with the target to examine different substrates and validate the importance of different pathways as predicted by specific aim 1, and (3) to develop a quantitative analysis to study the effects of uncertainty considerations mainly due to variability of plasma concentration.

The role of histidine in plant development

Award Number: 419745

Program(s): FUNCTIONAL and REGULATORY SYS CL, INTEGRATIVE PLANT BIOLOGY

Start Date: 9/1/2004

Principal Investigator: Leustek, Thomas

Co-PI Name(s):

PI Email Address: leustek@aesop.rutgers.edu

Abstract: PROJECT SUMMARY

The proteins in all living organisms are constructed using a set of twenty different amino acids, and plants serve as the primary source of these protein building blocks in the human diet. Plants also use specific amino acids in a variety of other ways including combating insect pests, plant diseases, and surviving environmental hardship. Therefore, it is ultimately important to understand how plants supply amino acids to their various organs. One example of this importance relates to the nutritional quality of seeds. Amino acid content is an important factor affecting the nutritional value of seed crops. Knowing how amino acids are accumulated in seeds, whether they are produced endogenously or are delivered there from elsewhere in the plant, would be critical to devising strategies to improve nutritional quality.

This proposal focuses on the amino acid histidine. Examination of mutants of the plant species Arabidopsis thaliana that are unable to synthesize histidine showed that they die at the earliest stages of seed development. The mutants die even if they are borne by a maternal plant that is able to produce histidine. This observation suggests that the maternal plant cannot supply this amino acid to its seeds. The aim of the current proposal is to learn how histidine is accumulated in seeds. To address this issue a series of experiments are proposed to explore the following questions. If the parent plant cannot supply histidine, is it because this amino acid is actively excluded from developing seeds, or is it because the parent plant does not produce enough histidine to supply its seeds? If histidine is actively excluded, why is this so? Is it an indication that histidine plays some special role in seed development and if so, what is this function? If developing seeds produce their own histidine, what genes are necessary for the process and how does the expression of these genes control histidine production?

Intellectual Merit

The current proposal challenges common presumptions on how amino acids are supplied for seed development. Until now it was thought that all of them are supplied to developing seeds by the maternal plant. Apparently this is not true for histidine. Studying how plants allocate histidine will lead to insights into the allocation of other amino acids. Therefore, the proposed work will expand our understanding of how plants control synthesis and utilization of amino acids, processes that are essential for the growth and development of plants, and to human use of plant resources.

Broader Impacts

The proposed activities will provide research and training for a postdoctoral fellow, undergraduates, and high school students. Laboratory experiences for undergraduates and high school students in particular are critical for the training of future scientists, policy makers, and informed citizens. The P.I. has a strong track record of involving undergraduate and high school students in vibrant research projects. The students are frequently from demographic groups that are underrepresented in the biological sciences. Moreover, the "educational" mindset in the P.I.'s group translates into opportunities for the postdoctoral fellow to develop teaching skills.

Collaborative Research: Mercury isotope fractionation during microbial and abiotic redox transformations

Award Number: 433793

Program(s): BE-UF: BIOGEOSCIENCES, BE: NON-ANNOUNCEMENT RESEARCH

Start Date: 9/1/2004

Principal Investigator: Barkay, Tamar

Co-PI Name(s): John Reinfelder

PI Email Address: barkay@aesop.rutgers.edu

Abstract: EAR 0433793

BARKAY

An investigation of the isotope fractionation of mercury (Hg) by microbial and abiotic redox transformations is proposed herein. It is believed that this work fits appropriately within the Geosciences program: Research in Biogeosciences Opportunities in Geomicrobial Processes. Specifically, this research fits into Focus II of this program, which emphasizes developing new research techniques (including isotope proxies) to address questions generated at the intersection between biology and geology. Two of the PIs (Blum and Klaue) have worked for the past five years to develop an analytical method with high enough precision to allow measurement of natural variations in the isotopic composition of Hg. This group has demonstrated that they can routinely measure Hg isotope ratios to an accuracy of 0.02 permil per atomic mass unit (amu) and recent research by this group has explored Hg isotope variation in meteorites and ore deposits. A central question in the application of Hg isotopes to the study of Hg in the environment and as a biogeochemical proxy is the degree to which microbes fractionate Hg during various redox processes. To answer this question quantitatively requires a team with specialization in the microbiology of Hg transformations (PIs Barkay and Reinfelder at Rutgers), and specialization in the isotope geochemistry of Hg (PIs Blum and Klaue at Michigan). In preliminary experiments this team has demonstrated that a strain of Hg resistant Escherichia coli, which produce the mercuric reductase enzyme (MR), fractionate Hg isotopes during the reduction of Hg (II) to Hg(0). The magnitude of this fractionation is up to 1.5 permil per amu, (>50 times uncertainty) and it follows a Rayleigh law with a fractionation factor of 1.0006.

These initial results give the PIs great optimism that Hg isotopes will provide a powerful new tracer of Hg redox transformation in the environment, and a proxy record of changes in Hg redox processes through geological time. The objective of this study is to conduct a series of carefully controlled experiments to investigate Hg isotope fractionation during each of the major microbial and abiotic redox transformations. The specific processes that will be investigated include: 1) The reduction of Hg (II) to Hg(0) by the bacterial MR, by light-dependent and independent algal processes, by Fe(II)- dependent reduction in thiobacilli, and by photoreduction. 2) The oxidation of Hg (0) to Hg(II) by bacterial enzymes whose primary cellular role is protection against oxygen damage. 3) The methylation of Hg (II) to MeHg by sulfate reducing bacteria (SRB). 4) The degradation of MeHg to Hg (II) and CH4 and CO2 by the reductive and oxidative pathways, respectively. This project will set the groundwork for Hg isotope systematics and the use of Hg isotopes in geology and biogeochemistry. Once developed, the Hg isotope tool will allow future studies that address issues such as: 1) the tracking of sources, pathways and sinks of various Hg species in the environmental and in geological deposits, 2) the use of Hg isotopes as a paleo-redox proxy in lacustrine and marine deposits, and 3) the study of the evolution of Hg-microbe interactions in sediments and sedimentary rocks.

Intellectual Merit. The proposed research activity will lay the groundwork for a completely new methodology that has the potential to significantly enhance understanding of mercury biogeochemistry on scales ranging from microbial mechanisms to individual lakes to global cycles and finally to the geological record. The research team members have proven track records in studying Hg-microbe interactions (Rutgers PIs) and the isotope geochemistry and aquatic ecology of Hg (Michigan PIs) and are poised to make rapid advancements in this combined research area.

Broader Impacts. The proposed research will integrate students from both Rutgers and the

University of Michigan, giving them experience in advanced laboratory techniques and at the intellectual intersection between the biological and geological sciences where important, and sometimes paradigm- shifting, research advances are being made. A female PhD student at Rutgers, who has already completed the preliminary experiments, will work on the microbial experiments for her dissertation work and travel to Michigan to participate in the mass spectrometry and theoretical isotope geochemistry. An undergraduate student at Michigan will assist with the analytical geochemistry as part of a senior thesis research project. The cross-fertilization of methods and scientific approaches will be beneficial to all of the research participants and will likely lead to additional collaborations. Results will be published and disseminated broadly. As exposure to Hg remains a major public health concern this project will assist in the implementation of sound environmental practices to reduce Hg contamination and exposure.

Bioinformatics: The Rutgers Initiative in Teacher Enhancement (BRITE)

Award Number: 422902

Program(s): ITEST

Start Date: 9/1/2004

Principal Investigator: Sofer, William

Co-PI Name(s): Andrew Vershon Lenore Neigeborn

PI Email Address: sofer@waksman.rutgers.edu

Abstract: This project will implement a comprehensive project for teachers and students designed to integrate bioinformatics and structural biology into existing high school programs so that it becomes a permanent offering of the science curriculum. The BRITE project will engage high school teachers and students in a series of scientific challenges, the answers to which require using the computational tools of molecular biology, structural biology and bioinformatics. Over the 36-month period of the grant, BRITE will train up to 55 teachers in a local project at the Waksman Institute and over 100 teachers in a regional project conducted through distance learning on the Internet. Teachers will field-test challenges with students participating in summer institutes, then introduce the challenges into classroom science teaching. Each year approximately 5,500 students will benefit from their teachers' work in the local and regional projects.

Spectral Built-In Self-Testing for Mixed-Signal Systems-in-a-Package (SIP)

Award Number: 429743

Program(s): DES AUTO FOR MICRO and NANO SYS

Start Date: 9/1/2004

Principal Investigator: Bushnell, Michael

Co-PI Name(s): Vishwani Agrawal

PI Email Address: bushnell@caip.rutgers.edu

Abstract: PROPOSAL ID: 0429743

PI: Mike Bushnell (Rutgers U), Vishwani Agrawal (Auburn U)

TITLE: Spectral Built-In Self-Testing for Mixed-Signal Systems-in-a-Package

Abstract:

In this research the PIs propose a new application of the theory of signals and systems to testing digital systems-in-a-package (SIPs). Digital input signals are considered as a set of time-varying waveforms, characterized by a correlation matrix. The elements of this matrix are the auto-correlation and cross-correlation coefficients, determined from inputs that have known fault and error detection properties. The auto-correlation indicates how a signal resembles its own past, and the cross-correlation indicates how a signal resembles other signals.

The PIs propose a completely integrated built-in self-testing (BIST) system for huge digital hardware systems. Rather than inserting a full-scan chain and using combinational BIST, digital circuit spectral analysis techniques is used to determine which flip-flops (memory elements) to scan to simplify the testing. Subsequent topologically analysis of the digital part of the system is made to determine its necessary spectral testing frequencies in partial-scan mode at each primary input. Finally, one inserts low-overhead spectral BIST hardware to generate these frequencies and uses a novel response compacter for BIST, which calculates the cross-correlation between various primary outputs as a signature. Spectral BIST uses less hardware than the conventional BIST system, covers 8.4% more of the faults in sequential mode, but requires less than 10% of the patterns.

The benefits of these concepts would be drastically shorter test pattern sequences, compared with present-day BIST, but high fault coverage. This leads to economic benefits of a large power reduction in test mode, and shorter test time. Other benefits are simplified testing hardware and lower hardware overhead. We will create a spectral analysis method to insert the testing hardware into the sequential circuit to raise its fault coverage. The PIs plan to topologically analyze sequential circuits to determine the predominant spectra of their input responses. This is expected to accelerate spectral analysis, since one can avoid analyzing parts of the spectrum that the circuit could never generate.

Unquantized and Uncoded Channel State Information Feedback in Multiple Antenna Multiuser Wireless Systems

Award Number: 429724

Program(s): COMMUNICATIONS RESEARCH

Start Date: 9/1/2004

Principal Investigator: Mandayam, Narayan

Co-PI Name(s):

PI Email Address: narayan@winlab.rutgers.edu

Abstract: The potential and promise of multiple antenna techniques has now resulted in widespread considerations for the use of these in a variety of contexts: for wide area wideband wireless transmission in next generation cellular systems; for local area hot-spot data service overlays in cellular systems; for emerging short-range wireless LAN networks; for promoting efficient spectrum sharing in the unlicensed bands; and a variety of collaborative techniques in wireless adhoc networks. A key attribute required of any multiple antenna technique to be successful, in any of the above contexts, is the need for reliable and efficient channel state information (CSI). Delay requirements imposed by wireless applications and the time variations in the channel, require not only reliability in CSI information, but also that the feedback of such information be fast and frequent. This project studies the fundamental limits of CSI feedback schemes that can be used in multiple antenna multiuser wireless communication systems.

A fundamental issue studied is if it is necessary for reliable CSI feedback to be optimally quantized and encoded in a Shannon theoretic sense? Specifically, unquantized and uncoded (UQ-UC) CSI feedback schemes are studied, that have the attractive feature of avoiding the delays due to quantization and coding, while still being optimal in certain situations relating to the uplink and downlink of wireless channels. In cases where such "zero-delay" schemes are sub-optimal, enhancements that can substantially improve performance are studied via (a) performance bounds for UQ-UC CSI feedback in FDD and TDD systems, (b) CSI feedback receivers, (c) information capacity of transmitter optimization in multiple antenna multiuser systems, and (d) comparative evaluation of UQ-UC CSI feedback with practical coded transmission.

ITWF: Collaborative Research: Increasing the Representation of Undergraduate Women and Minorities in Computer Science

Award Number: 420433

Program(s): WORKFORCE

Start Date: 9/1/2004

Principal Investigator: Ryder, Barbara

Co-PI Name(s):

PI Email Address: ryder@cs.rutgers.edu

Abstract: Title: ITWF Collaborative Research: Increasing the Representation of Undergraduate Women and Minorities in Computer Science

CNS 0420436, PI Horwitz, Univ. of Wisconsin-Madison

CNS 0419340, PI Huss-Lederman, Beloit College

CNS 0420312, PI Munson, Univ. of Wisconsin-Milwaukee

CNS 0420337, PI Dunsmore, Purdue University

CNS 0420343, PI Rodger, Duke University

CNS 0420358, PI Binkley, Loyola College of Maryland

CNS 0420368, PI Biggers, Georgia Institute of Technology

CNS 0420433, PI Ryder, Rutgers University

This collaborative ITWF project implements a new approach to introductory computer science with the goal of increasing the enrollment and retention of women and under-represented minorities in undergraduate computer science degree programs. The project adapts the Emerging Scholars Program and the Peer-led Team Learning approaches, which have been proven successful in mathematics and other sciences, to computer science. It is a collaborative project between the University of Wisconsin-Madison, Beloit College, Duke University, Georgia Institute of Technology, Loyola College of Maryland, Purdue University, Rutgers University, and the University of Wisconsin-Milwaukee. The project includes targeted recruitment of students with strong mathematics and science backgrounds to the new course. The course includes students working in small groups on challenging problems with group facilitation by outstanding undergraduates.

The intellectual merit of this project lies in the strong basis on models that have been successful in other disciplines. The collaborative represents a team of investigators with significant expertise in educational reform and transformation. Implementation will take place at the diverse set of institutions represented by the collaborative partners, thus providing an excellent environment for evaluation of this innovative approach and illustrating the possibilities for replication and adoption by a wide range of institutions.

The broader impacts of the project lie with the potential increasing the participation of under-represented groups in computer science. The method to be tested is relative low cost and straightforward to implement, thus it has a high potential for broad impact across the country.