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Interactions leading to disordered ground states and unusual low-temperature behavior

Physical Review E 2009年第3期80卷 031105-031105页

作者： Robert D. Batten Frank H. Stillinger Salvatore Torquato Department of Chemical Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Materials Institute Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08544 USA

We have shown that any pair potential function v(r) possessing a Fourier transform V(k) that is positive and has compact support at some finite wave number K yields classical disordered ground states for a broad density range [R. D. Batten, F. H. Stillinger, and S. Torquato, J. Appl. Phys. 104, 033504 (2008)]. By tuning a constraint parameter χ (defined in the text), the ground states can traverse varying degrees of local order from fully disordered to crystalline ground states. Here, we show that in two dimensions, the “k-space overlap potential,” where V(k) is proportional to the intersection area between two disks of diameter K whose centers are separated by k, yields anomalous low-temperature behavior, which we attribute to the topography of the underlying energy landscape. At T=0, for the range of densities considered, we show that there is continuous energy degeneracy among Bravais-lattice configurations. The shear elastic constant of ground-state Bravais-lattice configurations vanishes. In the harmonic regime, a significant fraction of the normal modes for both amorphous and Bravais-lattice ground states have vanishing frequencies, indicating the lack of an internal restoring force. Using molecular-dynamics simulations, we observe negative thermal-expansion behavior at low temperatures, where upon heating at constant pressure, the system goes through a density maximum. For all temperatures, isothermal compression reduces the local structure of the system unlike typical single-component systems.

关键词： Ground state

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The Broad Institute-Six Years Later

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CHEMISTRY & BIOLOGY 2010年第4期17卷 311-312页

作者： McCarthy, Alice Main Text “In June 2003 the scientific and medical communities at MIT Harvard University and its affiliated hospitals and the Whitehead Institute banded together as collaborating partners to form the Eli and Edythe L. Broad Institute based in Cambridge MA. The Broad Institute established with initial funding from a $100 million philanthropic donation from the Los Angeles-based Broad family was primarily viewed as a marriage between the Whitehead Institute's Center for Genome Research (WICGR) and the Harvard Institute of Chemistry and Cell Biology (ICCB). Eli Broad founder and chairman of AIG SunAmerica Inc. explained “the purpose of the Broad Institute is to create a new type of research institute to build on the accomplishments of the human genome project and to move to clinical applications to both prevent and cure diseases.” Every Thursday morning we meet with perhaps 20 faculty members and 100 other researchers to discuss what we're all doing and should be doing next. -David Altschuler This paragraph was written five years ago when the Broad Institute was in its very earliest days as a life science research community (McCarthy 2005). Since that time “the Broad” as it's known has kept true to Eli Broad's vision having attracted a talented group of researchers faculty trainees and professional staff. This 1600 person research community known internally as “Broadies” includes faculty staff and students from throughout the MIT and Harvard biomedical research communities and beyond with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. “What is special about the Broad is that we have people from Harvard MIT and the Harvard hospitals come together and work on problems of shared interest that could not be solved in their own individuals labs” explains David Altshuler M.D. Ph.D. Deputy Director and one of the Broad's six core faculty members. “These problems require expertise beyond any one principal investigator and in

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An Integration Free Universal Approximation Method Based on Orthogonal Polynomials

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AIP Conference Proceedings 2008年第1期1048卷 601-604页

作者： İrem Yaman Metin Demiralp aİstanbul Technical University Informatics Institute Computational Science and Engineering Program 34469 İstanbul‐Turkey bİstanbul Technical University Informatics Institute Computational Science and Engineering Program 34469 Istanbul‐Turkey

In this work, we focus on the development of a novel polynomial approximation method, which is based on orthogonal expansion. Although the basis set elements of the expansion will be chosen polynomials or multinomials to this end, the method is open to any kind of complete set of basis functions. The projection integrals are replaced with certain quadratic forms over the matrix representation of the independent variable. This brings the universality and reduces the computational complexity drastically. Hence, it can be conjectured that this method will find quite large area of applicability. Another advantage of this technique is, that it is not limited to univariate cases, and can be used for the multivariate cases by taking necessary precautions to get efficiency

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Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

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Standards in genomic sciences 2010年第3期3卷 259-66页

作者： Carsten Kettner Dawn Field Susanna-Assunta Sansone Chris Taylor Jan Aerts Nigel Binns Andrew Blake Cedrik M Britten Ario de Marco Jennifer Fostel Pascale Gaudet Alejandra González-Beltrán Nigel Hardy Jan Hellemans Henning Hermjakob Nick Juty Jim Leebens-Mack Eamonn Maguire Steffen Neumann Sandra Orchard Helen Parkinson William Piel Shoba Ranganathan Philippe Rocca-Serra Annapaola Santarsiero David Shotton Peter Sterk Andreas Untergasser Patricia L Whetzel Beilstein-Institut Frankfurt am Main Germany Centre for Ecology & Hydrology UK Oxford e-Research Centre University of Oxford UK The European Bioinformatics Institute (EBI) UK Faculty of Engineering - ESAT/SCD Leuven University Leuven-Heverlee Belgium Division of Pathway Medicine University of Edinburgh Medical School Edinburgh UK MRC Harwell UK Medical Department University Medical Center Johannes Gutenberg University-Mainz Mainz Germany Consortium for Genomic Technology Milano Italy University of Nova Gorica Nova Gorica Slovenia NIEHS NIH US National Toxicology Program USA Swiss Institute of Bioinformatics Geneva Switzerland Computational and Systems Medicine and Department of Computer Science University College London London UK Department of Computer Science Aberystwyth University Aberystwyth UK Center for Medical Genetics Ghent University Ghent Belgium Department of Plant Biology University of Georgia Athens USA Department of Stress- and Developmental Biology Institute for Plant Biochemistry Halle Germany Peabody Museum of Natural History Yale University New Haven USA Macquarie University Sydney Australia National University of Singapore Singapore Cancer Pharmacology The Mario Negri Institute for Pharmacological Research Milan Italy Image Bioinformatics Research Group Department of Zoology University of Oxford Oxford UK Wellcome Trust Sanger Institute UK Zentrum für Molekulare Biologie der Universität Heidelberg Heidelberg Germany The National Center for Biomedical Ontology / Stanford Center for Biomedical Informatics Research Stanford University Stanford USA

This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://***/.

关键词： Minimum Information European Bioinformatics Institute Biomedical Ontology Stable Link Breakout Group

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Experiences in teaching and mentoring interdisciplinary graduate students of diversified backgrounds

Experiences in teaching and mentoring interdisciplinary grad...

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2008 ASEE Annual Conference and Exposition

作者： Mohan, Ram Kelkar, Vinaya Kelkar, Ajit North Carolina AandT State University Department of Computational Science and Engineering Graduate Program North Carolina AandT State University Department of Biology North Carolina AandT State University

The interdisciplinary master's degree program in computational science and engineering (CSE) at North Carolina A&T State University, Greensboro, NC is now more than 3 years old, and provides graduate education in several computational areas and the associated primary field disciplines. The CSE program since its inception has presently graduated more than 12 students who are currently placed in several major industries. Our CSE graduate program offers an interdisciplinary curriculum combining computational core areas along with various domain areas. The students enrolled in the program begin with diversified backgrounds (prior undergraduate studies in various fields such as engineering, physical sciences, life sciences, mathematics, business, etc), and are required to take four core courses relevant to CSE for their graduation in the areas of applied probability and statistics, comprehensive numerical analysis, Data structures and parallel programming, computational and scientific visualization irrespective of their prior background. The preparation level for the diversified group of students in these courses depends on their undergraduate major. This poses significant challenges to graduate faculty teaching these courses and mentoring these students with diversified backgrounds. Our experiences and observations with the course content and structure, teaching methods, evaluation and student performances in these courses with diversified graduate students and their mentoring for the past 3 years are presented. The performances of the students in these core courses are correlated to their background and analyzed. Our experiences indicate students with a lesser preparation level seem to get geared quickly via peer guidance from the stronger students. In several cases, the performances were not related to an individual's prior background, but on their motivation and willingness to strive and succeed. The experiences indicate that the students can benefit well with additi

关键词： Students

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Domain Formation in the Plasma Membrane: Roles of Nonequilibrium Lipid Transport and Membrane Proteins

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Physical Review Letters 2008年第17期100卷 178102-178102页

作者： Jun Fan Maria Sammalkorpi Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Compositional lipid domains (“lipid rafts”) in plasma membranes are believed to be important components of many cellular processes. The mechanisms by which cells regulate the sizes and lifetimes of these spatially extended domains are poorly understood at the moment. Here we show that the competition between phase separation in an immiscible lipid system and active cellular lipid transport processes naturally leads to the formation of such domains. Furthermore, we demonstrate that local interactions with immobile membrane proteins can spatially localize the rafts and lead to further clustering.

关键词： Lipids

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Quasicontinuum-like reduction of density functional theory calculations of nanostructures

Quasicontinuum-like reduction of density functional theory c...

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作者： Negrut, Dan Anitescu, Mihai El-Azab, Anter Zapol, Peter Materials Science Program Department of Mechanical Engineering University of Wisconsin Madison WI 53706 United States Mathematics and Computer Science Division Argonne National Laboratory Argonne IL 60439 United States School of Computational Science Florida State University Tallahassee FL 32306 United States Materials Science and Chemistry Divisions Argonne National Laboratory Argonne IL 60439 United States

Density functional theory can accurately predict chemical and mechanical properties of nanostructures, although at a high computational cost. A quasicontinuum-like framework is proposed to substantially increase the size of the nanostructures accessible to simulation. It takes advantage of the near periodicity of the atomic positions in some regions of nanocrystalline materials to establish an interpolation scheme for the electronic density in the system. The electronic problem embeds interpolation and coupled cross-domain optimization techniques through a process called electronic reconstruction. For the optimization of nuclei positions, computational gains result from explicit consideration of a reduced number of representative nuclei and interpolating the positions of the rest of nuclei following the quasicontinuum paradigm. Numerical tests using the Thomas-Fermi-Dirac functional demonstrate the validity of the proposed framework within the orbital-free density functional theory. Copyright © 2008 American Scientific Publishers All rights reserved.

关键词： Electronic structure

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Diffusion maps - A probabilistic interpretation for spectral embedding and clustering algorithms

Diffusion maps - A probabilistic interpretation for spectral...

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作者： Nadler, Boaz Lafon, Stephane Coifman, Ronald Kevrekidis, Ioannis G. Department of Computer Science and Applied Mathematics Weizmann Institute of Science Rehovot 76100 Israel Google Inc. United States Department of Mathematics Yale University New Haven CT 06520-8283 United States Department of Chemical Engineering Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 United States

ISBN: (纸本)9783540737490

Spectral embedding and spectral clustering are common methods for non-linear dimensionality reduction and clustering of complex high dimensional datasets. In this paper we provide a diffusion based probabilistic analysis of algorithms that use the normalized graph Laplacian. Given the pairwise adjacency matrix of all points in a dataset, we define a random walk on the graph of points and a diffusion distance between any two points. We show that the diffusion distance is equal to the Euclidean distance in the embedded space with all eigenvectors of the normalized graph Laplacian. This identity shows that characteristic relaxation times and processes of the random walk on the graph are the key concept that governs the properties of these spectral clustering and spectral embedding algorithms. Specifically, for spectral clustering to succeed, a necessary condition is that the mean exit times from each cluster need to be significantly larger than the largest (slowest) of all relaxation times inside all of the individual clusters. For complex, multiscale data, this condition may not hold and multiscale methods need to be developed to handle such situations.

关键词： Relaxation time

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Aircraft passenger cabin ECS-generated ventilation velocity and mass transport CFD simulation: Mass transport validation exercise

Journal of the IEST

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Journal of the IEST 2008年第1期51卷 90-113页

作者： Baker, A. Ericson, S. Orzechowski, J. Wong, K. Garner, R. Engineering Science Graduate Program University of Tennessee United States Computational Fluid Dynamics Laboratory University of Tennessee United States Joint Institute for Computational Science University of Tennessee United States Federal Aviation Administration Civil Aerospace Medical Institute United States

A collaborative research project established between the University of Tennessee (UT) computational fluid dynamics (CFD) lab and the Federal Aviation Administration (FAA) Civil Aerospace Medical Institute (CAMI) sought to validate CFD prediction of the environmental control system (ECS)-generated ventilation velocity vector field with induced mass transport. The results of the velocity field validation exercise were published previously. An FAA Cooperative Research and Development Agreement (CRADA) project generated an experimental database of time-dependent inserted mass distributions in the CAMI Aircraft Environmental Research Facility (AERF). The companion CFD mass transport simulations were conducted at the UT CFD Lab using both commercial and proprietary computer codes. This paper reports the qualified results of the mass transport validation exercise.

关键词： Cabins (aircraft)

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Midwest Structural sciences Center A University‐Government Partnership

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AIP Conference Proceedings 2008年第1期973卷 377-382页

作者： William A. Dick Executive Director Midwest Structural Sciences Center Computational Science and Engineering Program University of Illinois at Urbana‐Champaign 2270 Digital Computer Laboratory 1304 West Springfield Avenue Urbana Illinois 61801 USA

Strategic partnerships among universities, industry and government have been a trademark of the research environment in the United States for more than two decades. Each member of this research triad brings a set of unique perspectives and strengths to the table, as well as being hampered with an often equally daunting set of weaknesses. It is clear that given appropriate opportunities in specific technologies, university‐industry‐government collaboration is a “big winner.” Our observation, however, is that some federally‐funded research programs have failed to achieve the synergistic result envisioned by the funding agency, the host university, or collaborating industries. This paper introduces the relationships and highlights a new research program at the University of Illinois focused on the structural sciences necessary for next‐generation air vehicles. Keys to successful programs are realistic expectations on all sides, a clear focus on appropriate science and engineering technologies, flexibility on the part of the federal funding agency, and a strong university management team.

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