STEM for Education (STEM-E) Scholarship Program

Start Date: 1/1/2012

Award Number: 1136381

NSF Funding Organization: DUE

Principal Investigator: Laffey, Evelyn

Co-PI: Mohan Kalelkar, Thomas Papathomas, Eugenia Etkina, Keith Weber

Award Amount: $135417

Program(s): ROBERT NOYCE SCHOLARSHIP PGM

Abstract: The goal of the STEM for Education (STEM-E) Scholarship Program at Rutgers University is to recruit, retain, and maintain a community of engineers and physicists who are dedicated to teaching in high-needs school districts. Intellectual Merit is encompassed in an overarching theme of "STEM for Humanity" and the program (1) blends the physics and engineering undergraduate programs with the existing graduate physics and mathematics teacher preparation programs, (2) strengthens the focus on teaching physics and mathematics to students in high-needs districts, (3) includes an e-mentoring network between pre- and in-service teachers, and (4) infuses seminars that illustrate the impact of STEM on society. Fifteen STEM-E scholars are being prepared to graduate ready to teach in high-needs K-12 math and science classrooms with strong pedagogical content knowledge and deep understanding of the importance of STEM professionals. Additionally, the program offers long-term continuing professional development to ensure the success of new teachers. Broader Impacts are achieved in that STEM-E scholars will be the nation's leading educational change agents serving in high-need school districts as highly qualified math and science teachers who integrate engineering into their math and physics courses. A mixed-method evaluation plan includes formative and summative assessment of program goals and components. Results are disseminated through the program's website and presentations at conferences.

Application for Grant to support ISVD2012, the 9th International Symposium on Voronoi Diagrams in Science and Engineering, July 2012

Start Date: 1/1/2012

Award Number: 1143838

NSF Funding Organization: CCF

Principal Investigator: Kalantari, Bahman

Co-PI:

Award Amount: $10000

Program(s): ALGORITHMIC FOUNDATIONS

Abstract: ISVD 2012 will be the continuation of a highly successful and innovative series of conferences within the geometric modeling and computer graphics disciplines. The eight previous events were held in Tokyo, Japan; Seoul, Korea; Banff, Canada; Kiev, Ukraine; Copenhagen, Denmark; Quebec City, Canada, and Quin Dao, China. While many conferences in the areas of computational geometry, computer graphics and engineering have touched some topics covered by the proposed event, it is only recently that the Voronoi diagram research has formed into a separate discipline and the unique forum on Voronoi Diagrams in Science and Engineering was created. The goal of the International Conferences on Voronoi Diagrams in Science and Engineering is to concentrate specifically on unique aspects of the research into the Voronoi diagrams and on practical applications of this research to manufacturing engineering, VLSI design, communication, geomatics, GIS (geographical information systems), urban planning, medicine, bioinformatics, high-performance computing, education and other applications. Another unique aspect is that this year will also feature a Voronoi Art Symposium that runs concurrently with the conference and showcases artistic drawings and interpretations of the Voronoi concept. This event, without a doubt, bridges the gap between Sciences and Arts.

Full Jet Reconstruction In Relativistic Heavy Ion Collisions

Start Date: 7/15/2011

Award Number: 1067907

NSF Funding Organization: PHY

Principal Investigator: Salur, Sevil

Co-PI:

Award Amount: $282000

Program(s): NUCLEAR STRUCTURE & REACTIONS

Abstract: Quantum chromodynamics (QCD), the fundamental theory of the strong force, predicts the liberation of quarks and gluons to create a new phase of matter, the Quark Gluon Plasma (QGP). During the last 10 years, experiments performed at the Relativistic Heavy Ion Collider (RHIC) tested this prediction and explored the properties of this novel form of matter. While the naive interpretations of QCD calculations suggested that this QGP produced at RHIC should behave like a dilute gas, the experimental results provided evidence that it behaves more like a nearly `perfect' liquid, which is opaque to the passage of colored partons. In November 2010, LHC successfully delivered the first heavy ion collisions at an unprecedented center-of-mass energy of 2.76 TeV to explore new regions of the phase diagram. A wide variety of energetic hard probe measurements will be available over a broad extended kinematic range at LHC. These new measurements will quantify the fundamental properties of QGP. The intellectual merit of this proposal derives from the PI's focus on hard probes as a diagnostic tool to determine the detailed properties of the hot QCD matter. For a more complete, quantitative and discriminatory picture of quenching of the color partons and to avoid intrinsic biases of leading hadron measurements, the PI will reconstruct jets in relativistic heavy ion collisions at LHC using the CMS detector. She proposes to transform knowledge of the large color opaqueness of the QGP to the determination of its fundamental properties by the measurements of jet structure and its modification in terms of energy flow by an unbiased full jet reconstruction to measure nuclear modification ratios of jets. With these robust measurements, she will determine key features of QGP such as how hot QCD medium responds to jet energy loss and how QGP affects jet structures. For broader impacts of this project, the PI plans to establish a cultivating environment for a diverse and competitive work force in nuclear physics via integration of active research and education. She will recruit and mentor two minority and female junior undergraduates from Rutgers's Aresty program for the summer term and continue supporting them throughout the year. She plans to include these undergraduates in all phases of research, including data taking, analysis, presentation of results at meetings, and writing refereed papers.

Collaborative Research: Autotrophic carbon fixation at a shallow-water hydrothermal system: Constraining microbial activity, isotopic and geochemical

Start Date: 10/1/2011

Award Number: 1124141

NSF Funding Organization: OCE

Principal Investigator: Vetriani, Costantino

Co-PI:

Award Amount: $196665

Program(s): BIOLOGICAL OCEANOGRAPHY

Abstract: Currently, there is only limited information on the identity and activity of the microorganisms carrying out CO2-fixation in situ, despite the fact that these organisms form the basis of their respective ecosystems. Representatives that are able to grow autotrophically are known to exist in almost all major groups of prokaryotes, and these organisms play essential roles in ecosystems by providing a continuous supply of organic carbon for heterotrophs. Microorganisms present in extreme environments utilize CO2- fixation pathways other than the Calvin-Benson-Bassham (CBB) cycle. At present, five alternative autotrophic CO2 fixation pathways are known. Different carbon fixation pathways result in distinct isotopic signatures of the produced biomass due to the isotopic discrimination between light (12C) and heavy (13C) carbon by the carboxylating enzymes. Thus, inferences about the carbon fixation pathway predominantly utilized by the microbial community can also be made based on the stable carbon isotopic composition of the organic matter, in extant systems as well as in the geological record. However, at present little is known about the systematics and extents of fractionation during carbon fixation by prokaryotic organisms, and to our knowledge no studies exist that have systematically studied the relationship between the operation of different carbon fixation pathways and how this is reflected in the stable carbon isotopic composition in a natural system. This is a 2-year interdisciplinary, international research program that employs a powerful combination of cutting-edge research tools aiming to improve our understanding of autotrophic carbon fixation and its chemical and isotopic signature along environmental gradients in a natural hydrothermal system. The following hypotheses are addressed: 1. The diversity of microorganisms present along a thermal and redox gradient, and rates of CO2 fixation, will reflect adaptation to in situ temperatures and geochemical conditions 2. Microorganisms utilizing the CBB cycle for autotrophic CO2-fixation will represent a smaller percentage of the chemolithoautotrophic community at higher temperatures, where microorganisms utilizing alternative CO2-fixation pathways dominate 3. Isotopic values of biomass and specific biomarker molecules will vary along a thermal and redox gradient from zones characterized by a higher hydrothermal fluid flux and thus higher temperatures to the surrounding, cooler areas, corresponding to the physiology of the microorganisms utilizing different pathways for carbon fixation The PIs will use a multidisciplinary approach to delineate the relative contribution of the different carbon fixation pathways along an environmental gradient by combining metagenomic analyses coupled with: 1) an assessment of the frequency and the expression of specific key genes involved in carbon fixation, and 2) with the measurement of carbon fixation rates. These data will be integrated with the determination of stable C isotopic composition of biomass, DIC, and specific hydrocarbons/lipids. Due to its easy accessibility, well-established environmental gradients, and extensive background information, the shallow-water vents off Milos (Greece) will be used as a natural laboratory to perform these studies. Intellectual Merit. The data generated in this study will allow constraints on the relationship between autotrophic carbon fixation and the resulting isotopic signatures of biomass and specific biomarker molecules (e.g. CH4, C2+ alkanes, lipids) in a natural system.. This has implications for assessing the importance of carbon fixation in extant ecosystems, and it will also provide a tool to improve the interpretation of isotopic values in the geological record. Broader Impacts. This is an interdisciplinary and collaborative effort between US and foreign institutions, creating unique opportunities for networking and to foster international collaborations. This will also benefit the involved students (1 graduate, several undergraduates) and a postdoc. The PIs have been involved in several educational and public outreach activities over the years that have reached literally millions of individuals. Finally, the project fits with the focus of a number of multi-disciplinary and international initiatives, in which PIs are active members (e.g. SCOR working group on Hydrothermal energy and the ocean carbon cycle;and Deep Carbon Observatory at CIW).

International Collaboration in Chemistry: A Comprehensive Computational/Experimental Analysis of the Hofmeister Effect

Start Date: 10/1/2011

Award Number: 1124776

NSF Funding Organization: CHE

Principal Investigator: Romsted, Laurence

Co-PI: Ronald Sauers, David Case

Award Amount: $570626

Program(s): MACROMOLEC/SUPRAMOLEC/NANO

Abstract: This International Collaboration in Chemistry award, co-funded in France by the Agence Nationale de la Recherche (ANR) and in the United States by the National Science Foundation, through the Macromolecular, Supramolecular, and Nanochemistry Program of the Chemistry Division, supports an international collaboration between Drs. Laurence Romsted, David Case, and Ronald Sauers, all from Rutgers University, New Brunswick, and Drs. Reiko Oda, Michel Laguerre (both from the Institut Europeen de Chimie et de Biologie, France), and Dario Bassani (from the Institut des Science Molecularier CNRS, France). The fundamental goal of the project is the characterization of ion-specific effects on the properties of aqueous solutions of primarily gemini amphiphiles. The team will systematically vary amphiphile structure and use a wide variety of counterions to identify the shifts in the balance of forces controlling aggregate structure from the molecular level to bulk solution properties. Cationic gemini amphiphiles with decyl and dodecyl tails will be synthesized, with fully and partially methylated headgroups and a variety of counterions, e.g., the typical inorganic counterions of the Hofmeister series, but also organic counterions, such as alkylcarboxylates and alkylphosphates of various chain lengths. By using a combination of physical, chemical, and simulation methods, the researchers will determine correlations between physical properties (e.g., critical micelle concentration, ionization degree, and aggregation number and interfacial concentrations of the counterions and water), as determined by chemical trapping and by simulation using a combined molecular dynamics/density functional theory approach. The simulations will also provide new information on the overall organization of the tails, headgroups, counterions, and water within the aggregate. Parallel studies on single chain analogs will highlight the importance of the methylene bridge of the gemini surfactants. Because chemical trapping and molecular dynamic simulations make no assumptions about aggregate structure, correlations discovered between amphiphile structure, counterion type and aggregate physical properties will deepen current understanding and provide new insight into the delicate balance of forces that controls aggregation behavior of association colloids. One of the oldest, unresolved challenges in colloid and surface chemistry is a coherent explanation for ion-specific effects on the properties of colloids and biointerfaces, first demonstrated in 1888 by Hofmeister as a specific salt effect on the solubility of a protein. Since then, many empirically observed orders have been published including ion-specific effects on a variety of aqueous solution properties of self-assembling ionic association colloids such as micelles, microemulsions and vesicles. This collaborative project offers a systematic approach toward understanding the interplay of intermolecular forces controlling amphiphile aggregate structures. Results should have real-life impact by aiding in selection of amphiphiles for particular applications (currently a trial-and-error procedure) and should enhance the utility of soft materials, e.g., by tuning their structures simply by changing the counterion. This project's novel multidisciplinary approach benefits from the complementary expertise of six collaborators in two countries: Drs. Oda and Bassani will obtain precise physical property measurements on the aggregation; Dr. Romsted will use his group's chemical trapping method to determine interfacial water and counterion concentrations; simulations by Drs. Laguerre, Case, and Sauers should provide new insight into specific interactions between headgroups, counterions, and water at gemini micelle interfaces. This research collaboration will also provide advanced training for undergraduate and graduate students and postdoctoral fellows. They will be immersed in a fundamental and intellectually challenging project that includes experience with a variety of experimental approaches combined with simulations in laboratories in the US and France, and in discussions on characterizing amphiphile solutions at the aggregate and molecular levels.

International Collaboration in Chemistry: Structure and dynamics of amino acids adsorbed on coinage metal surfaces

Start Date: 10/1/2011

Award Number: 1124879

NSF Funding Organization: CHE

Principal Investigator: Hinch, Barbara

Co-PI:

Award Amount: $304006

Program(s): STRUCTURE,DYNAMICS &MECHANISMS

Abstract: With the support of the Chemical Structure, Dynamics and Mechanisms Program, Professor Hinch and her coworkers in the Department of Chemistry and Chemical Biology at Rutgers University are using high resolution angular diffraction and time of flight analysis of thermal helium scattering to investigate structure, assembly and low energy molecule surface vibrations of adsorbed amino acids. This International Collaboration in Chemistry award includes a collaborator, Professor Stephen J. Jenkins at Cambridge University in the United Kingdom. His work is supported by EPSRC in the United Kingdom. The interactions of alanine, glycine and proline adsorbates with coinage metal surfaces are the focus of this research. These systems are believed to adsorb as carboxylate species and the amino groups may or may not undergo protonation. Information about chirality and possible racemization of adsorbed phases will be evident in the surface sensitive diffraction measurements. The real time kinetics of film assembly of these molecules on the surfaces, determined with this non destructive probe, will provide an understanding of the long- and short- range intermolecular interactions. In transitioning from low to high coverage regimes, changes in the discrete vibrational modes, and the effective masses of the scattering centers, will elucidate the significance of hydrogen bonding in these self assembled films. The low energy vibrational spectra are also to determine the influence of coadsorbed hydrogen levels in film stability, kinetics of assembly and surface diffusion and reaction mechanisms. Through collaboration with Professor Jenkins' group at Cambridge University, the Hinch group at Rutgers will also be able to utilize high-resolution low-temperature scanning probe techniques for studies of amino acid films. The international collaboration also offers a powerful computational capability and understanding of the multi-dimensional potential energy surfaces governing vibrational motion in simple adsorbed amino acids. A mutual objective is to image, simulate, and measure the dynamics within hydrogen bonding networks established in the amino acid films. This research will advance the understanding of the behavior of molecules adsorbed on surfaces. The knowledge obtained will implications for a variety of fields and applications, including chirally-specific sensors, enantioselective chemical synthesis, and possibly medical implant materials with improved biocompatibility. The research also has considerable workforce development benefits, as graduate and undergraduate students and post-doctoral associates will engage in a richly interdisciplinary research experience, which entails a variety of experimental techniques as well as theory and computation. The student experience will be further augmented by the international exchange aspects; extended visits by Rutgers and Cambridge group researchers to the partnering laboratory will provide invaluable experience with research environments beyond each participant's home institution.

CDI-TYPE II--COLLABORATIVE RESEARCH: Using Algebraic Topology to Connect Models with Measurements in Complex Nonequilibrium Systems

Start Date: 10/1/2011

Award Number: 1125174

NSF Funding Organization: DMS

Principal Investigator: Mischaikow, Konstantin

Co-PI:

Award Amount: $704040

Program(s): CDI TYPE II

Abstract: Numerous complex systems in nature and in technology defy concise characterization because they exhibit strongly nonlinear behaviors that lack all symmetries and are highly non-periodic on a wide range of spatial and temporal scales. Characterization by detailed measurement (in lab experiments or direct numerical simulations) is now possible in many cases using modern measurement technologies or computational techniques. However, the resulting deluge of data often leads to little insight; in particular, there is frequently no good way to connect quantitatively experimental measurements of a particular complex system with the output from simulations/models of the same system. New, computationally-based, mathematical tools from algebraic topology have the potential to bridge the gap between measurements and models; the proposed research will explore the use of algebraic topology to link numerical simulations and laboratory experiments in situations where complexity arises because the system under study is driven out of thermodynamic equilibrium. The research focuses on an outstanding paradigm for nonequilibrium complexity: fluid flow driven by temperature gradients (thermal convection). The planned work brings three unique capabilities together in a single effort: (1) the experimental ability both to measure and to manipulate precisely complex, convective flows; (2) efficient methods for state-of-the-art, large scale, high-resolution numerical simulations of convective flow; (3) open source, general purpose, and efficient computational algorithms and software for computing algebraic topological invariants on large data sets. Topological tools will be developed both to characterize and to minimize model error as well as to compare and to quantify dynamical properties including Lyapunov exponents, dimensionality and bifurcations between complex spatiotemporal flow states. This effort should ultimately identify ways in which homology-based metrics can be used for building reduced order models that permit prediction and, perhaps, control of convective flow. More generally, we expect the metrics developed for convection should find broad application to PDE-modeled problems ranging from the control of cardiac arrythmias to the prediction of weather and climate. The behaviors of complex systems in the world around us can now both be measured with high fidelity using advanced sensing technologies and simulated with great realism using modern computer techniques. However, the enormous data sets typically produced in these cases are often difficult to interpret because there exist few good mathematical tools to connect quantitatively the experimental measurements of a given complex system with the output of computer simulations of that same system. The proposed research explores the use of the mathematics of topology to relate lab measurements to computer outputs in a particular complex system, thermal convection. The results of this work should lead to new ways to understand, to predict, and, perhaps, to control convective flow, which plays a direct role in natural processes (e.g., volcanism, earthquake dynamics, continential drift) and industrial applications (e.g., thermal regulation of many devices, the growth of semiconductor materials). Moreover, the topological tools developed for thermal convection should apply more generally to a wide variety of other problems involving complex systems including the forecasting of weather and climate; the dynamics of the biomass in the oceans; the onset of turbulence; the evolution of reagent patterns on a catalytic metal surface; and ventricular fibrillation in a human heart.

BIOME-A Bio-Robotic Infrastructure for Oceanic Microbial Ecology

Start Date: 10/1/2011

Award Number: 1131022

NSF Funding Organization: OCE

Principal Investigator: Kerkhof, Lee

Co-PI: Scott Glenn, Oscar Schofield , Jingang Yi

Award Amount: $826509

Program(s): OCEAN TECH & INTERDISC COORDIN

Abstract: The PI's request funding to develop BIOME, a Bio-Robotic Infrastructure for Oceanic Microbial Ecology. Coastal ecosystems are central to global biogeochemical cycles despite their relatively small size; therefore, biological oceanography has focused on understanding microbial bloom dynamics on continental shelves. Unfortunately, our concepts of how a diverse bacterial community transitions between seasons remain incomplete because of our inability to sample on the appropriate time and spaces scales to resolve the processes influencing the microbiota. In order to address this limitation, we are proposing a build a biological sampler compatible with the Slocum Glider. What is missing is a component capable of collecting and returning intact biomass to the laboratory for molecular ecology studies to delineate the mechanisms driving bacterial evolution in the sea. this project will provide a platform to define the metabolic and genomic properties and mechanisms responsible for microbial growth, adaptation, and survival in the oceanic environment. The BIOME research will address fundamental questions in marine ecology and elucidate the mechanisms supporting the diversity of microorganisms in the ocean. Broader Impacts: The potential broad impacts of this proposal are greater than average because the device being designed has potential to be deployed widely if it is successful and would lead to more accurate models of ocean microbial community structure and activity. The PIs propose to develop a K-12 lesson plan about bacteria in the Mid-Atlantic Bight with the help of an education outreach specialist associated with the Mid Atlantic Center for Ocean Science Education Excellence, and have included this aspect of the project in the budget. There is a plan for disseminating the lessons to K-12 teachers through a variety of on-line and summer teacher training programs, to the public through lectures at local library, and to kids through the Rutgers 4-H after school programs. The PIs also intend (though don't lay out any specific plan) to include underrepresented ethnic groups in summer research through the RISE @ Rutgers program.

Dimensions: Collaborative Research: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial

Start Date: 10/1/2011

Award Number: 1136451

NSF Funding Organization: OCE

Principal Investigator: Vetriani, Costantino

Co-PI:

Award Amount: $420434

Program(s): Dimensions of Biodiversity

Abstract: Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives: 1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities. 2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents. 3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents. 4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms. Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts. Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context. Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), http://www.whoi.edu/GBF-OOI/page.do?pid=41475)

MRI: Development of a Versatile High Energy Resolution Ion Nanosope for Nanoscale Ion Spectroscopy, Ion-based Materials Fabrication and Ion Milling

Start Date: 10/1/2011

Award Number: 1126468

NSF Funding Organization: DMR

Principal Investigator: Gustafsson, Torgny

Co-PI: Eva Andrei, Leonard Feldman, Adrian Mann, Laura Fabris

Award Amount: $1640493

Program(s): MAJOR RESEARCH INSTRUMENTATION

Abstract: Technical abstract: The development of a new research instrument for nanoscale elemental analysis and materials modification using scattering of noble gas ions creates opportunities for materials science unachievable to date. Intellectual challenges include the creation of the tool, understanding energetic ion-solid interactions with a nano-beam, and applications, both in materials analysis and materials modification. Our project integrates two recent technological developments: Focused nanoscale ion beams available as the Zeiss ORION® He microscope and picosecond timing electronics with high throughput by Ionwerks®. Analysis applications include the first ion beam interrogation of individual nanostructures and determinations of lateral film uniformity. The instrument will also be used for materials modifications such as graphene based counters for single molecule analysis, development of qubit based superconducting junctions for quantum computing and studies of the behavior of defects within nano-structured materials. Also included is the development of nanoscale Ne beams for materials modification and sample preparation, an entirely new ion beam capability. Such beams may be used for ion milling on the nm scale, semiconductor amorphization and implantation with nm precision, spatial control of 'single ion upsets' in electronic devices, new tests of inter-granular defects for fusion applications and the creation of new materials from ion-carved graphene and other two dimensional materials. Non-technical abstract: Nanoscale materials have an enormous impact on basic and applied science. Unanticipated phenomena and functionalities are being discovered and exploited commercially at an ever increasing pace. New experimental tools are therefore needed to reliably perform materials characterization and modification at the same level. This project introduces a significant advance through the development of a versatile ion beam facility for true nano-scale ion spectroscopy, ion beam materials modification and ion beam milling. The project integrates new ion beam technologies to allow analysis of individual nano-particles as well as materials modification of nanostructures and ion sculpting and milling with unprecedented spatial control, involving the development of a new, heavy ion nano-beam. This represents a leap in ion beam oriented materials science. New science and technology is anticipated such as the investigation of the ligand binding of gold nanoparticles used in cancer drug delivery, the creation of nanometer orifices to explore DNA sequencing and the formation of quantum structures for advanced computing and communications. The direct and visually oriented nature of the information from this instrument will illustrate the excitement of materials science to students ranging from middle school to advanced graduate students through a well developed local infrastructure. As Rutgers has an extraordinarily diverse student body, the project will be particularly useful in attracting underrepresented groups. The instrument will provide excellent opportunities for hands-on experience in the development and use of sophisticated scientific equipment for undergraduate students and enrich the graduate curriculum. The general public will be involved through open houses and lectures. As a 'one of a kind' instrument this instrument will attract world leaders in the diverse fields addressed by nano-materials. Together with other recent NSF awarded instrumentation, this instrument will establish Rutgers as a national center for nano-scale microscopy.

CDI-Type II: Mapping Complex Biomolecular Reactions with Large Scale Replica Exchange Simulations on National Production Cyberinfrastructure

Start Date: 10/1/2011

Award Number: 1125332

NSF Funding Organization: CHE

Principal Investigator: Levy, Ronald

Co-PI: Darrin York, Shantenu Jha

Award Amount: $1625000

Program(s): CDI TYPE II

Abstract: Large scale, realistic simulations of complex biological and chemical phenomena at the atomic level of resolution level present a grand challenge for molecular simulation. Effective sampling of conformational space may require large numbers of computationally intensive simulations which are coupled to one another. Enhanced conformational sampling algorithms based on the application of biasing forces and replica exchange generalized ensembles, whereby a large number of replicas of the system are simulated in parallel, among the most powerful methods to study a wide variety of physicochemical processes. Uncoupled methods currently in use are very slowly convergent and often of dubious reliability as the independent simulations are not in equilibrium with one another. The key aspect of replica exchange (RE) algorithms is that replicas of the system periodically exchange their state parameters allowing them to rapidly traverse conformational space and to enhance equilibration. Current synchronous formulations of the RE method in wide use, however, are highly limited in terms of scalability and control when many exchanging replicas are involved. This limitation precludes the use of RE simulations to new application areas that require the calculation of high-dimensional free energy surfaces, and necessitate the dynamic control of 103-104 replicas as the landscape evolves. This project involves the development of a robust adaptive force biasing procedure coupled with an asynchronous replica exchange method. The research team is developing a novel infrastructure, the Replica Exchange Frame work (REFW) to enable the execution of very large scale RE simulations on a broad range of production computational resources, including but not limited to NSF TeraGrid (and its successor XD), cloud and campus-level cluster environments, as well as the forthcoming Blue Waters supercomputer. The REFW is being applied to applications that present multiple levels of complexity, such as coupled ligand binding, conformational change and catalysis in the glmS ribozyme/riboswitch that were hitherto not possible. The cyberinfrastructure created by this research team enables realistic simulations of important biological processes that have relevance in many areas of biology, biophysics, medicinal chemistry, and biophysics with the potential to impact human health. Additionally, the REWF may be applied in many other scientific areas that increasingly rely on realistic simulation including catalysis, earthquake prediction and petroleum engineering. The project is also training the next generation of computational scientists to apply these methods to solve high-impact interdisciplinary research problems. The resulting technology and training enables the study of a host of new reactive chemical problems of unprecedented complexity, and greatly facilitates innovation and discovery through advanced computation. This is a Cyber-Enabled Discovery and Innovation Program award and is co-funded by the Division of Chemistry and the Division of Physics in the Directorate for Mathematical and Physical Sciences.

Studies in Statistical Mechanics

Start Date: 10/1/2011

Award Number: 1104501

NSF Funding Organization: DMR

Principal Investigator: Lebowitz, Joel

Co-PI:

Award Amount: $141000

Program(s): CONDENSED MATTER & MAT THEORY|MATHEMATICAL PHYSICS|APPLIED MATHEMATICS

Abstract: TECHNICAL SUMMARY The Division of Materials Research, the Division of Mathematical Sciences, and the Physics Division contribute funds to this award. This award supports theoretical research and education aimed at advancing understanding of the properties of macroscopic systems originating in the collective behavior of their microscopic constituents. The methods used range from exact mathematical analysis to computer simulation. They provide a bridge between rigorous results and applications, for both equilibrium and nonequilibrium phenomena. The research is highly interdisciplinary, bringing together physicists, mathematicians, chemists and those working in theoretical areas of the biological and social sciences. Topics of study include: 1) The effects of randomness in quantum systems will be elucidated. This will extend the recent proof that the addition of randomness to a quantum system rounds a first-order phase transition in the conjugate order parameter in 2 dimensions or less, or for cases involving the breaking of a continuous symmetry in 4 dimensions or less. New inequalities for random systems will be explored. 2) The phase diagram of general systems with spatially asymmetric long range interactions will be investigated, extending the exact solution of the three species ABC model in 1D. 3) Results on the phase diagram of lattice systems with multispin interactions will be extended. 4) Pattern formation such as stripes, in equilibrium and nonequilibrium systems, due to short range attractions and long range repulsions will be elucidated. 5) The evolution of the macrostate of an open system given by an autonomous equation will be investigated. In analogy to the Boltzmann entropy in an isolated system, the large deviation function, with respect to the stationary measure of the nonequilibrium stationary state, is a Lyapunov function for this evolution. This yields new Lyapunov functions for nonlinear diffusion equations. The deviation function, considered as a relative free energy of an open system, will be explored from both a microscopic and macroscopic point of view. 6) A rigorous determination of transport coefficients is an important objective of this research project. Domains of validity of Fourier's law in various systems, for example weakly anharmonic crystals with random masses, will be elucidated. When noise is added to the dynamics Fourier's law holds rigorously, but will a small amount of anharmonicity destroy phonon localization? Violations of Fourier's law for momentum conserving models in 1D and 2D will be investigated. 7) Criteria for "typicality" in realistic systems will be investigated: for a "typical" large isolated quantum system every initial wave function from an energy shell evolves in such a way that, for most time it is macroscopically equivalent to the micro-canonical density matrix. This award supports the PI's efforts to organize two conferences every year in which both core subjects and new developments in statistical mechanics are discussed in a collegial atmosphere. Graduate students, postdocs and minority scientists are encouraged to present talks on their work and interact with leaders in the field. They also serve as a clearing house for positions and often lead to new collaborations. In addition to many invited lectures at scientific conferences the PI has given public lectures and has written an article for Scholarpedia on Time's Arrow. NONTECHNICAL SUMMARY This award supports theoretical research and education in a variety of subfields of statistical mechanics. This work is jointly supported by the Division of Materials Research and the Division of Mathematical Sciences. The central theme of the effort is a better understanding of the properties of material systems originating in the collective behavior of their elementary atomic constituents. The methods used range from exact mathematical analysis to computer simulations. These approaches bridge the gap between rigorous results and applications. Topics of study range from classical physics to quantum physics, from highly formal to applications of technological relevance and even to dynamics of disease propagation. The project aims to advance the theory of systems that are far from the balance of equilibrium with an impact on biological systems, biomaterials, and materials more generally. The research activities are highly interdisciplinary, bringing together physicists, mathematicians, chemists and those working in theoretical areas of the biological and social sciences. The expected applications are in material science, complex fluids and in biological systems. The project also includes the organization of two conferences every year in which both core subjects and new developments in statistical mechanics are discussed in a collegial atmosphere. Graduate students, postdocs and minority scientists are involved and present talks on their work and interact with established researchers in the field. The conferences also serve as an opportunity for professional networking and can lead to new collaborations.

Collaborative Research: Using Transcriptomics to Understand Mechanisms of Stress Response and Toxin Production in Pathogenic and Toxigenic Microbes in

Start Date: 9/15/2011

Award Number: 1129203

NSF Funding Organization: OCE

Principal Investigator: Bhattacharya, Debashish

Co-PI:

Award Amount: $276857

Program(s): CHEMICAL OCEANOGRAPHY

Abstract: In this project an interdisciplinary research team from the University of Hawaii at Manoa, Stanford University, and Rutgers University will study the transcriptomes of Gambierdiscus, Staphylococcus aureus, and Enterococcus in Hawaiian coastal waters - toxin-producing species that pose significant health hazards to humans. Their goal is to elucidate the mechanisms associated with toxin production by Gambierdiscus and inactivation by sunlight of the bacterial pathogen, S. aureus, and the fecal indicator, Enterococcus. Because the transcriptome of an organism reflects the genes that are actively being expressed at any given time, this study, by elucidating levels of messenger RNA expression in the target organisms, should provide valuable insights into the mechanisms responsible for toxin production, responses to stress and/or subsequent bacterial inactivation. The research program will be organized around four working hypotheses: H1: Production of ciguatoxin by Gambierdiscus reflects the physiological condition of the culture as influenced by temperature, irradiance, and growth phase. H2: High throughput transcriptome analysis from toxin (+) and toxin (-) cultures will allow the identification of genes involved in ciguatoxin production and understanding of the light and nutrient conditions that favor this function. H3: Whereas E. faecalis is susceptible to indirect photoinactivation under exposure to sunlight in seawater, S. aureus is not. This is likely due to the presence of carotenoid pigments within the cells, which are able to quench reactive oxygen species. H4: E. faecalis and S. aureus respond to photo-stress in clear seawater by up-regulating genes that encode for proteins to repair cellular damage and mitigate oxidative stress; this "stressome" will change with increasing exposure to photostress, revealing the stress at which repair is no longer possible. Broader Impacts: The information that will be gathered in this study is expected to contribute significantly to advancing the field of risk management with respect to recreational water use and seafood consumption beyond reliance on empirical correlations and towards policies that are based on a mechanistic understanding of the threats these organisms pose to human health.

NeTS: Large: Collaborative Research: Closing the loop between traffic/pollution sensing and vehicle route control using traffic lights and navigators

Start Date: 9/15/2011

Award Number: 1111811

NSF Funding Organization: CNS

Principal Investigator: Iftode, Liviu

Co-PI: Badri Nath

Award Amount: $789543

Program(s): NETWORK SCIENCE & ENGINEERING

Abstract: Today, most urban traffic control is rudimentary: in smaller cities, many traffic signals remain isolated, and while most larger cities have integrated systems of signals, they are still not dynamically timed in response to real-time vehicle information. Congestion fees, which are increasingly popular as a traffic management tool, are usually based on historical traffic data rather than varying dynamically to reflect instantaneous conditions. Recent advances in communication, navigation, and sensor technologies present far more opportunities to increase the intelligence and efficiency of metropolitan streets than are in place today. This project focuses on designing a real-time networked sensing and actuation platform for future 'intelligent' metropolitan traffic management with the aim of simultaneously reducing congestion, pollution, and traveler delays. The pivotal element of the proposed Green City intelligent transport architecture is the ability to 'close the loop' between traffic/pollution sensing and traffic control; a system achieved through an incentivized collaboration between the central traffic management and the drivers. In this collaboration, the 'intelligent' traffic signals and the on-board navigators play key roles. Traffic signals sense traffic characteristics and vehicular emissions, collect data from vehicle sensors, and broadcast traffic advisories, routings, and restrictions to on-board navigators. The on-board navigators choose optimal routings taking into account drivers' preferences, local perceived traffic, and signal timing. All this is enabled by efficient vehicle to roadway infrastructure communications from 3G channels to DSRC radios. Broader Impact: This project is highly interdisciplinary; it benefits from the collaboration and expertise of computer science, atmospheric science, and urban planning faculty and students. New education opportunities will result from the multidisciplinary nature of the project.

Collaborative Research: Ionic Liquids- Cations in the Spotlight and Single Atom Changes with Large Consequences

Start Date: 9/15/2011

Award Number: 1112077

NSF Funding Organization: CHE

Principal Investigator: Castner, Edward

Co-PI:

Award Amount: $171000

Program(s): STRUCTURE,DYNAMICS &MECHANISMS

Abstract: The Chemical Structure, Dynamics and Mechanisms Program of the NSF Chemistry Division supports a Collaborative Research effort by Assoc. Prof. Claudio J. Margulis (P.I.) at the University of Iowa Dept. of Chemistry and by Prof. Edward W. Castner, Jr. (co-P.I.) at the Dept. of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey. The goal is to study in detail the structural and dynamical properties of ionic liquids using a combination of theoretical and computational methods from the Margulis group with experimental investigations done by the Castner group. Ionic liquids consist of flexible, asymmetric molecular cations and anions. Several reports have shown that very small modification of either the cation or the anion components of the ionic liquid can make dramatic changes to its properties. For example replacing the central nitrogen atom of a tetralkylammonium cation by a phosphorus atom can lead to a drop in the liquid viscosity by a factor of two. Our current understanding of these liquids does not provide a straightforward explanation of these results; our goal is to combine x-ray and NMR experiments on these liquids with detailed molecular simulations and theoretical analyses to explain this phenomenon. The observed x-ray scattering patterns from ionic liquids that all share the same bis(trifluoromethylsulfonyl)amide anion are remarkably similar. This is because the anions have more electron-rich atoms than the hydrocarbon-based cations. Thus, whereas the cations may be the most important organizational components in many liquids, the information content in the x-ray scattering provides mostly detailed information about the anions with information about the cations being obtained only indirectly. We will invert this circumstance by preparing ionic liquids with smaller anions such as nitrate, dicyanamide and acetate, so that the observed x-ray scattering patterns result predominantly from scattering by the cations. This will provide a new perspective on the structure of ionic liquids. It will also help in testing and designing better parameters for simulations. While the research is of a fundamental nature, the outcomes will inform the design, testing and selection of ionic liquids for a range of electrolyte applications and interaction with biological molecules and assemblies. These liquids are providing solutions to a number of significant challenges in energy storage, nanotechnology, processing of biomass, and pharmaceutical research. Undergraduate students, graduate students and postdoctoral researchers will receive training in the latest experimental methods, including synchrotron-based x-ray scattering experiments, two-dimensional NMR spectroscopy, molecular dynamics simulations, and theoretical methods applied to the statistical physics of complex liquids.