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ICCSA 2006: International Conference on computational science and Its Applications

作者： Chlebiej, Michal Mikolajczak, Pawel Nowiński, Krzysztof Ścislo, Piotr Bala, Piotr Department of Information Technology Institute of Computer Science Maria Curie-Sklodowska University Pl. M. Curie-Sklodowskiej 1 20-031 Lublin Poland Interdisciplinary Centre for Mathematical and Computational Modeling Warsaw University Pawińskiego 5a 02-106 Warsaw Poland Department of Cardiology Medical Academy of Warsaw 02-097 Warszawa Poland Faculty of Mathematics and Computer Science N. Copernicus University Chopina 12/16 87-100 Toruń Poland

ISBN: (纸本)3540340793

One of the most challenging problems in the modern cardiology is a correct quantification of the left ventricle contractility and synchronicity. Correct, quantitative assessment of these parameters, which could be changed in a course of many severe diseases of the heart (e.g. coronary artery disease and myocardial infarction, heart failure), is a key factor for the right diagnose and further therapy. Up to date, in clinical daily practice, most of these information is collected by transthoracic two dimensional echocardiography. Assessment of these parameters is difficult and depends on observer experience. However, quantification method of the contractility assessment based on strain and strain analysis are available, these methods still are grounded on 2D analysis. Real time 3D echocardiography gives physicians opportunity for real quantitative analysis of the left ventricle contractility and synchronicity. In this work we present a method for estimating heart motion from 4D (3D+time) echocardiographic images. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Echocardiography

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Self-assembly of the simple cubic lattice with an isotropic potential

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Physical Review E 2006年第2期74卷 021404-021404页

作者： Mikael C. Rechtsman Frank H. Stillinger Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology Materials Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Physics Princeton University Princeton New Jersey 08544 USA

Conventional wisdom presumes that low-coordinated crystal ground states require directional interactions. Using our recently introduced optimization procedure to achieve self-assembly of targeted structures [M. C. Rechtsman et al., Phys. Rev. Lett. 95, 228301 (2005); Phys. Rev. E 73, 011406 (2006)], we present an isotropic pair potential V(r) for a three-dimensional many-particle system whose classical ground state is the low-coordinated simple cubic lattice. This result is part of an ongoing pursuit by the authors to develop analytical and computational tools to solve statistical-mechanical inverse problems for the purpose of achieving targeted self-assembly. The purpose of these methods is to design interparticle interactions that cause self-assembly of technologically important target structures for applications in photonics, catalysis, separation, sensors, and electronics. We also show that standard approximate integral-equation theories of the liquid state that utilize pair correlation function information cannot be used in the reverse mode to predict the correct simple cubic potential. We report in passing optimized isotropic potentials that yield the body-centered-cubic and simple hexagonal lattices, which provide other examples of non-close-packed structures that can be assembled using isotropic pair interactions.

关键词： CRYSTALS CLUSTERS DENSE

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Collective coordinate control of density distributions

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Physical Review E 2006年第3期74卷 031104-031104页

作者： Obioma U. Uche Salvatore Torquato Frank H. Stillinger Department of Chemical Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied & Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Physics Princeton University Princeton New Jersey 08544 USA

Real collective density variables C(k) [cf. Eq. (1.3)] in many-particle systems arise from nonlinear transformations of particle positions, and determine the structure factor S(k), where k denotes the wave vector. Our objective is to prescribe C(k) and then to find many-particle configurations that correspond to such a target C(k) using a numerical optimization technique. Numerical results reported here extend earlier one- and two-dimensional studies to include three dimensions. In addition, they demonstrate the capacity to control S(k) in the neighborhood of ∣k∣=0. The optimization method employed generates multiparticle configurations for which S(k)∝∣k∣α, ∣k∣⩽K, and α=1, 2, 4, 6, 8, and 10. The case α=1 is relevant for the Harrison-Zeldovich model of the early universe, for superfluid He4, and for jammed amorphous sphere packings. The analysis also provides specific examples of interaction potentials whose classical ground states are configurationally degenerate and disordered.

关键词： STATISTICAL MECHANICS REALIZABILITY SYSTEM

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Fluid permeabilities of triply periodic minimal surfaces

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Physical Review E 2005年第5期72卷 056319-056319页

作者： Y. Jung S. Torquato Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

It has recently been shown that triply periodic two-phase bicontinuous composites with interfaces that are the Schwartz primitive (P) and diamond (D) minimal surfaces are not only geometrically extremal but extremal for simultaneous transport of heat and electricity. The multifunctionality of such two-phase systems has been further established by demonstrating that they are also extremal when a competition is set up between the effective bulk modulus and electrical (or thermal) conductivity of the bicontinuous composite. Here we compute the fluid permeabilities of these and other triply periodic bicontinuous structures at a porosity ϕ=1∕2 using the immersed-boundary finite-volume method. The other triply periodic porous media that we study include the Schoen gyroid (G) minimal surface, two different pore-channel models, and an array of spherical obstacles arranged on the sites of a simple cubic lattice. We find that the Schwartz P porous medium has the largest fluid permeability among all of the six triply periodic porous media considered in this paper. The fluid permeabilities are shown to be inversely proportional to the corresponding specific surfaces for these structures. This leads to the conjecture that the maximal fluid permeability for a triply periodic porous medium with a simply connected pore space at a porosity ϕ=1∕2 is achieved by the structure that globally minimizes the specific surface.

关键词： EXACT COMPUTATION FLOW SIMULATIONS COMPOSITES TRANSPORT SYSTEMS PHASES STEP

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Experiments on Random Packings of Ellipsoids

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Physical Review Letters 2005年第19期94卷 198001-198001页

作者： Weining Man Aleksandar Donev Frank H. Stillinger Matthew T. Sullivan William B. Russel David Heeger Souheil Inati Salvatore Torquato P. M. Chaikin Department of Physics and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemistry and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemical Engineering and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Psychology and Center for Neural Science New York University New York New York 10003 USA

Recent simulations indicate that ellipsoids can pack randomly more densely than spheres and, remarkably, for axes ratios near 1.25∶1∶0.8 can approach the densest crystal packing (fcc) of spheres, with a packing fraction of 74%. We demonstrate that such dense packings are realizable. We introduce a novel way of determining packing density for a finite sample that minimizes surface effects. We have fabricated ellipsoids and show that, in a sphere, the radial packing fraction ϕ(r) can be obtained from V(h), the volume of added fluid to fill the sphere to height h. We also obtain ϕ(r) from a magnetic resonance imaging scan. The measurements of the overall density ϕavr, ϕ(r) and the core density ϕ0=0.74±0.005 agree with simulations.

关键词： .ellipsoids Princeton New Jersey

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GAUGE METHOD FOR VISCOUS INCOMPRESSIBLE FLOWS

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Communications in Mathematical sciences 2003年第2期1卷 317-332页

作者： Weinan, E. Liu, Jian-Guo Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton 08544 NJ United States Institute for Physical Science and Technology and Department of Mathematics University of Maryland College Park 20742 MD United States

We present a new formulation of the incompressible Navier-Stokes equation in terms of an auxiliary field that differs from the velocity by a gauge transformation. The gauge freedom allows us to assign simple and specific boundary conditions for both the auxiliary field and the gauge field, thus eliminating the issue of pressure boundary condition in the usual primitive variable formulation. The resulting dynamic and kinematic equations can then be solved by standard methods for heat and Poisson equations. A normal mode analysis suggests that in contrast to the classical projection method, the gauge method does not suffer from the problem of numerical boundary layers. Thus the subtleties in the spatial discretization for the projection method are removed. Consequently, the projection step in the gauge method can be accomplished by standard Poisson solves. We demonstrate the efficiency and accuracy of the gauge method by several numerical examples, including the flow past cylinder © 2003 International Press

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Logic-based granular prototyping

Logic-based granular prototyping

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IEEE Annual International Computer Software and Applications Conference (COMPSAC)

作者： A. Bargiela W. Pedrycz K. Hirota Department of Computing and Mathematics Nottingham Trent University Nottingham UK Systems Research Institute Polish Academy of Sciences Warsaw Poland Department of Electrical and Computer Engineering University of Alberta Edmonton Canada Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Presto JST Tokyo Institute of Technology Yokohama Japan

A fuzzy logic based similarity measure is introduced as a criterion for the identification of structure in data. An important characteristic of the proposed approach is that cluster prototypes are formed and evaluated in the course of the optimization without any a-priori assumptions about the number of clusters. The intuitively straightforward compound optimization criterion of maximizing the overall similarity between data and the prototypes while minimizing the similarity between the prototypes is adopted. It is shown that the partitioning of the pattern space obtained in the course of the optimization is more intuitive than the one obtained for the standard FCM. The local properties of clusters (in terms of the ranking order of features in the multidimensional pattern space) are captured by the weight vector associated with each cluster prototype. The weight vector is then used for the construction of interpretable information granules.

关键词： Prototypes Data engineering Design engineering Fuzzy logic Data mining mathematics computational intelligence Electric variables measurement Pattern recognition Computer applications

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Contributory presentations/posters

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Journal of Biosciences 1999年第1期24卷 33-198页

作者： N. Manoj V. R. Srinivas A. Surolia M. Vijayan K. Suguna R. Ravishankar R. Schwarzenbacher K. Zeth Diederichs G. M. Kostner A. Gries P. Laggner R. Prassl Madhusudan Pearl Akamine Nguyen-huu Xuong Susan S. Taylor M. Bidva Sagar K. Saikrishnan S. Roy K. Purnapatre P. Handa U. Varshney B. K. Biswal N. Sukumar J. K. Mohana Rao A. Johnson Vasantha Pattabhi S. Sri Krishna Mira Sastri H. S. Savithri M. R. N. Murthy Bindu Pillai Kannan M. V. Hosur Mukesh Kumar Swati Patwardhan K. K. Kannan B. Padmanabhaa S. Sasaki-Sugio M. Nukaga T. Matsuzaki S. Karthikevan S. Sharma A. K. Sharma M. Paramasivam P. Kumar J. A. Khan S. Yadav A. Srinivasan T. P. Singh S. Gourinath Neelima Alam A. Srintvasan Vikas Chandra Punit Kaur Ch. Betzel S. Ghosh A. K. Bera S. Bhattacharya S. Chakraborty A. K. Pal B. P. Mukhopadhyay I. Dey U. Haldar Asok Baneriee Jozef Sevcik Adriana Solovicova K. Sekar M. Sundaralingam N. Genov Dong-cai Liang Tao Jiang Ji-ping Zhang Wen-rui Chang Wolfgang Jahnke Marcel Blommers S. C. Panchal R. V. Hosur Bindu Pillay Puniti Mathur S. Srivatsun Ratan Mani Joshi N. R. Jaganathan V. S. Chauhan H. S. Atreya S. C. Sahu K. V. R. Chary Girjesh Govil Elisabeth Adjadj Éric Quinjou Nadia Izadi-Pruneyre Yves Blouquit Joël Mispelter Bernadette Heyd Guilhem Lerat Philippe Milnard Michel Desmadreil Y. Lin B. D. Nageswara Rao Vidva Raghunathan Mei H. Chau Prashant Pesais Sudha Srivastava Evans Coutinho Anil Saran Leizl F. Sapico Jayson Gesme Herbert Lijima Raymond Paxton Thamarapu Srikrishnan C. R. Grace G. Nagenagowda A. M. Lynn Sudha M. Cowsik Sarata C. Sahu S. Chauhan A. Bhattacharya G. Govil Anil Kumar Maurizio Pellecchia Erik R. P. Zuiderweg Keiichi Kawano Tomoyasu Aizawa Naoki Fujitani Yoichi Hayakawa Atsushi Ohnishi Tadayasu Ohkubo Yasuhiro Kumaki Kunio Hikichi Katsutoshi Nitta V. Rani Parvathy R. M. Kini Takumi Koshiba Yoshihiro Kobashigawa Min Yao Makoto Demura Astushi Nakagawa Isao Tanaka Kunihiro Kuwajima Jens Linge Seán O. Donoghue Michael Nilges G. Chakshusmathi Girish S. Ratnaparkhi P. K. Madhu R. Varadarajan C. Tetreau Molecular Biophysics Unit Indian Institute of Science Bangalore India Austrian Academy of Sciences Institute of Biophysics and X-ray Structure Research Graz Austria Faculty of Biology University of Konstanz Germany Institute of Medical Biochemistry University of Graz Austria Howard Huges Medical Institute Department of Chemistry & Biochemistry University of California La Jolla USA Department of Chemistry & Biochemistry University of California San Diego La Jolla USA Molecular Biophysics Unit India Department of Microbiology &Cell Biology Indian Institute of Science Bangalore India Macromolecular Structure Laboratory NCI - Frederick Cancer Research and Development Center ABL - Basic Research Program Frederick USA Department of Crystallography and Biophysics University of Madras Chennai Biochemistry Department Indian Institute of Science Bangalore India Condensed Matter Physics Division B.A.R.C. Trombay Mumbai Condensed Matter Physics Division Bhabha Atomic Research Centre Trombay Mumbai IMCB The University of Tokyo Tokyo Japan Mitsubishi Chemical Corporation Yokohama Research Center Yokohama Japan Faculty of Pharmaceutical Sciences Chiba University Chiba Japan Department of Biophysics All India Institute of Medical Sciences New Delhi India Department of Biophysics All India Institute of Medical sciences New Delhi India Institüt Physiologische Chemie Hamburg Germany Biophysics Department Bose Institute Calcutta India Slovak Academy of Sciences Institute of Molecular Biology Bratislava Slovakia Indian Institute of Science Bioinformatics Centre Bangalore Departments of Chemistry and Biochemistry Biological Macromolecular Structure Center USA Bulgarian Academy of Sciences Institute of Organic Chemistry Sofia Bulgaria Chinese Academy of Sciences Institute of Biophysics Beijing China Novartis Pharma AG Preclinical Research Basel Switzerland Department of Chemical Sciences Tata Institute of Fundamental Research Mumbai India Solid State Physics Div

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computational Methods for Single-Cell RNA Sequencing

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Biomedical Data science 1000年第1期3卷 339-364页

作者： Brian Hie Joshua Peters Sarah K. Nyquist Alex K. Shalek Bonnie Berger Bryan D. Bryson 1Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA email: bab@mit.edu 3Ragon Institute of MGH MIT and Harvard Cambridge Massachusetts 02139 USA 2Department of Biological Engineering Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA email: bryand@mit.edu 4Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA 5Department of Chemistry Institute for Medical Engineering & Science (IMES) and Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA 6Department of Mathematics Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA

Single-cell RNA sequencing (scRNA-seq) has provided a high-dimensional catalog of millions of cells across species and diseases. These data have spurred the development of hundreds of computational tools to derive novel biological insights. Here, we outline the components of scRNA-seq analytical pipelines and the computational methods that underlie these steps. We describe available methods, highlight well-executed benchmarking studies, and identify opportunities for additional benchmarking studies and computational methods. As the biochemical approaches for single-cell omics advance, we propose coupled development of robust analytical pipelines suited for the challenges that new data present and principled selection of analytical methods that are suited for the biological questions to be addressed.

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