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A parallel accelerated adaptive mesh algorithm for the solution of electrical models of the heart

International Journal of High Performance Systems Architecture 2012年第2期4卷 89-100页

作者： Oliveira, Rafael Sachetto Rocha, Bernardo M. Burgarelli, Denise Meira Jr., Wagner Dos Santos, Rodrigo Weber Department of Computer Science Federal University of São João de Rei Av. Visconde do Rio Preto s/n Col. do Bengo São João del-Rei MG 36301-360 Brazil Department of Computer Science Federal University of Minas Gerais Av. Antônio Carlos 6627 Pampulha Belo Horizonte MG 31270-010 Brazil National Laboratory for Scientific Computing Avenida Getúlio Vargas 333 Petrópolis RJ 25651-076 Brazil Department of Computer Science Federal University of Juiz de Fora Campus Universitário Rua José Kelmer S/n Bairro São Pedro Juiz de Fora MG 36036-330 Brazil Department of Mathematics Federal University of Minas Gerais Av. Antônio Carlos 6627 Pampulha Belo Horizonte MG 31270-010 Brazil Department of Computer Science e Computational Modeling Program Federal University of Juiz de Fora Campus Universitário Rua José Kelmer S/n Bairro São Pedro Juiz de Fora MG 36036-330 Brazil

Computer models have become valuable tools for the study and comprehension of the complex phenomena of cardiac electrophysiology. However, the high complexity of the biophysical processes translates into complex mathematical and computational models. In this paper, we evaluate a parallel numerical algorithm based on mesh adaptivity and finite volume method aiming to accelerate these simulations. This is a very attractive approach since the spreading electrical wavefront corresponds only to a small fraction of the cardiac tissue. Usually, the numerical solution of the partial differential equations that model the phenomenon requires very fine spatial discretisation to follow the wavefront, which is approximately 0.2 mm. The use of uniform meshes leads to high computational cost as it requires a large number of mesh points. In this sense, the tests reported in this work show that simulations of two-dimensional models of cardiac tissue have been accelerated by more than 340 times using the adaptive mesh algorithm and parallel computing, with no significant loss in accuracy. Copyright © 2012 Inderscience Enterprises Ltd.

关键词： Wavefronts

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A Document Comparison Approach using Hybrid Keyword and Structured Full Text Vocabulary Searches

A Document Comparison Approach using Hybrid Keyword and Stru...

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2011 3rd International Conference on Computer Research and Development(ICCRD 2011)

作者： Kudachamai Boonsuk Peraphon Sophatsathit Technopreneurship and Innovation Management Program Graduate School Chulalongkorn UniversityBangkok 10330Thailand Advanced Virtual and Intelligent Computing (AVIC) Center Department of MathematicsFaculty of Science Chulalongkorn UniversityBangkok 10330Thailand

This paper proposes a systematic full text search on document using a combined keyword and structural similarity of documents under consideration. The approach operates in two steps. The first step uses a set of designated keywords to acquire potential desired documents by means of an open source tool. The second step builds a suffix tree of frequently used vocabulary to retrieve the most similar documents from the acquired documents. In so doing, variations on contextual matching of full text search can be mitigated, wherein the resulting performance turns out to be quite acceptable. The ultimate goal is to arrive at a platform independent full text search technique that can be realized. The benefits for this scheme are two folds. On the one hand, relevant document can be retrieved as close to the desired document as possible. On the other hand, suspect plagiarism can be identified to some extent, which is dependent on the effectiveness of the proposed approach with plenty of rooms for future improvement. The proposed work will eventually be put to real use for database retrieval in a small business enterprise.

关键词： Keywords full text search structural similarity suffix tre contextual matching plagiarism

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K, T and D-like fuzzy Kripke models

K, T and D-like fuzzy Kripke models

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Annual Meeting of The North American Fuzzy Information Processing Society

作者： Bedregal, Benjamin Santiago, Regivan H. N. Benevides, Mario Viana, Petrucio Group of Logic Language Information Theory and Applications - LoLITA Department of Informatics and Applied Mathematics Federal University of Rio Grande Do Norte 59072-970 Natal-RN Brazil Program of Engineering of Systems and Computing - PESC Department of Computer Science Federal University of Rio de Janeiro 21941-972 Rio de Janeiro-RJ Brazil Department of Analysis Fluminense Federal University 24020-140 Niterói-RJ Brazil

ISBN: (纸本)9781612849676

The idea of a Kripke semantics endowed with possibility/plausibility information is not new;in fact there are different approaches for that;see: [6], [13], [16], [19]. This paper follows the approach found in [6], but whereas [6] provides a fixed interpretation for connectives into [0,1] here we provide a characterization of a fuzzy semantics for connectives in such a way that the resulting fuzzy frames: K, T and D, are described precisely by the set of statements which also describes, respectively, the usual modal systems K, T and D. © 2011 IEEE.

关键词： Semantics

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Bio-inspired models of memory capacity, recall performance and theta phase precession in the hippocampus

Bio-inspired models of memory capacity, recall performance a...

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International Joint Conference on Neural Networks (IJCNN)

作者： Vassilis Cutsuridis Bruce P. Graham Stuart Cobb Michael E. Hasselmo Center for Memory and Brain Boston University Boston MA USA Institute of Computing Science and Mathematics University of Stirling UK Institute of Neuroscience and Psychology University of Glasgow UK Center for Memory and Brain Department of Psychology and Graduate Program in Neuroscience Boston University Boston MA USA

The hippocampus plays an important role in the encoding and retrieval of spatial and non-spatial memories. Much is known about the anatomical, physiological and molecular characteristics as well as the connectivity and synaptic properties of various cell types in the hippocampal circuits [1], but how these detailed properties of individual neurons give rise to the encoding and retrieval of memories remains unclear. Computational models play an instrumental role in providing clues on how these processes may take place. Here, we present three computational models of the region CA1 of the hippocampus at various levels of detail. Issues such as retrieval of memories as a function of cue loading, presentation frequency and learning paradigm, memory capacity, recall performance, and theta phase precession in the presence of dopamine neuromodulation and various types of inhibitory interneurons are addressed. The models lead to a number of experimentally testable predictions that may lead to a better understanding of the biophysical computations in the hippocampus.

关键词： Loading Firing Oscillators Hippocampus Encoding Nerve fibers Load modeling

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K, T and D-like fuzzy Kripke models

K, T and D-like fuzzy Kripke models

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Conference of the North American Fuzzy Information Processing Society - NAFIPS

作者： Benjamin Bedregal Regivan H. N. Santiago Mario Benevides Petrúcio Viana Group of Logic Language Information Theory and Applications-LoLITA Department of Informatics and Applied Mathematics Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Program of Engineering of Systems and Computing-PESC Department of Computer Science Federal University of Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil Department of Analysis Fluminense Federal University (UFF) Niteroi Rio de Janeiro Brazil

The idea of a Kripke semantics endowed with possibility/plausibility information is not new; in fact there are different approaches for that; see: [6], [13], [16], [19]. This paper follows the approach found in [6], but whereas [6] provides a fixed interpretation for connectives into [0,1] here we provide a characterization of a fuzzy semantics for connectives in such a way that the resulting fuzzy frames: K, T and D, are described precisely by the set of statements which also describes, respectively, the usual modal systems K, T and D.

关键词： Semantics Fuzzy sets Fuzzy logic Bismuth Electronic mail Uncertainty Reliability

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Collective Intelligence for the design of emergency response

Collective Intelligence for the design of emergency response

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International Conference on Computer Supported Cooperative Work in Design

作者： Vivacqua, Adriana S. Borges, Marcos R.S. PPGI/DCC-IM - Graduate Program in Informatics Department of Computer Science Institute of Mathematics UFRJ - Federal University of Rio de Janeiro Rio de Janeiro Brazil PPGI/DCC-IM - Graduate Program in Informatics Department of Computer Science Institute of Mathematics NCE - Electronic Computing Institute UFRJ - Federal University of Rio de Janeiro Rio de Janeiro Brazil

ISBN: (纸本)9781424467631

Collective Intelligence has received much attention in recent years, as organizations and businesses discover the power of crowds. With new technologies, such as blogs, twitter, wikis, photo sharing, collaborative tagging and social networking sites, people may create and disseminate content as never before. Many organizations are looking for ways to harness this power, which is being called collective intelligence. Additionally, many open-source initiatives have shown that it is possible to obtain high quality results from collectively produced work. In this paper, we consider the domain of emergency response. We have been working in this domain for a few years now, mostly focusing on small disaster relief groups and field command. One of the command problems is lack of information about the location where the disaster occurred. We believe some of this information could be crowdsourced, changing current practices and enabling more effective response to the situation. In this paper, we discuss the possibilities for crowdsourcing and present an initial proposal for harnessing collective intelligence for the fire department. © 2010 IEEE.

关键词： Emergency services

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$H(\mathrm {div})$ preconditioning for a mixed finite element formulation of the diffusion problem with random data

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mathematics of Computation 2010年第270期79卷 733-760页

作者： Elman, Howard Furnival, Darran Powell, Catherine Department of Computer Science and Institute for Advanced Computer Studies University of Maryland College Park Maryland 20742 Applied Mathematics and Scientific Computing Program University of Maryland College Park Maryland 20742 National Oceanographic Centre Southampton S014 32H School of Mathematics University of Manchester Oxford Road Manchester M13 9PL United Kingdom

Abstract: We study $H(\mathrm {div})$ preconditioning for the saddle-point systems that arise in a stochastic Galerkin mixed formulation of the steady-state diffusion problem with random data. The key ingredient is a multigrid V-cycle for an $H(\mathrm {div})$ operator with random weight function acting on a certain tensor product space of random fields with finite variance. We build on the Arnold-Falk-Winther multigrid algorithm presented in 1997 by varying the spatial discretization from grid to grid whilst keeping the stochastic discretization fixed. We extend the deterministic analysis to accommodate the modified $H(\mathrm {div})$ operator and establish spectral equivalence bounds with a new multigrid V-cycle operator that are independent of the spatial and stochastic discretization parameters. We implement multigrid within a block-diagonal preconditioner for the full saddle-point problem, derive eigenvalue bounds for the preconditioned system matrices and investigate the impact of all the discretization parameters on the convergence rate of preconditioned minres.

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computing H/D-Exchange rates of single residues from data of proteolytic fragments

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BMC Bioinformatics 2010年第1期11卷 1-12页

作者： Althaus, Ernst Canzar, Stefan Ehrler, Carsten Emmett, Mark R. Karrenbauer, Andreas Marshall, Alan G. Meyer-Bäse, Anke Tipton, Jeremiah D. Zhang, Hui-Min Institut für Informatik Fachbereich 08 Staudingerweg 9 55099 Mainz Germany Algorithmic Computational Biology Centrum Wiskunde and Informatica Amsterdam Netherlands Center for Bioinformatics Computer Science Department Saarland University 66041 Saarbrücken Germany Ion Cyclotron Resonance Program National High Magnetic Field Laboratory Florida State University 1800 East Paul Dirac Drive Tallahassee FL 32310-4005 United States Department of Chemistry and Biochemistry Florida State University 95 Chieftain Way Tallahassee FL 32306 United States Institute of Mathematics EPFL Station 8 1015 Lausanne Switzerland Department of Scientific Computing Florida State University Tallahassee FL 32306-4120 United States

Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein ***: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue ***: With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments. © 2010 Althaus et al;licensee BioMed Central Ltd.

关键词： Proteins

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Dislocation climb strengthening in systems with immobile obstacles: Three-dimensional level-set simulation study

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Physical Review B 2010年第5期81卷 054104-054104页

作者： Zi Chen Kevin T. Chu David J. Srolovitz Jeffrey M. Rickman Mikko P. Haataja Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08540 USA Princeton Institute for the Science and Technology of Materials (PRISM) Princeton University Princeton New Jersey 08540 USA Vitamin D Inc. Menlo Park California 94025 USA Institute of High Performance Computing Singapore Singapore Department of Materials Science and Engineering Lehigh University Bethlehem Pennsylvania 18015 USA Department of Physics Lehigh University Bethlehem Pennsylvania 18015 USA Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08540 USA

We employ a parallel, three-dimensional level-set code to simulate the dynamics of isolated dislocation lines and loops in an obstacle-rich environment. This system serves as a convenient prototype of those in which extended, one-dimensional objects interact with obstacles and the out-of-plane motion of these objects is key to understanding their pinning-depinning behavior. In contrast to earlier models of dislocation motion, we incorporate long-ranged interactions among dislocation segments and obstacles to study the effect of climb on dislocation dynamics in the presence of misfitting penetrable obstacles/solutes, as embodied in an effective climb mobility. Our main observations are as follows. First, increasing climb mobility leads to more effective pinning by the obstacles, implying increased strengthening. Second, decreasing the range of interactions significantly reduces the effect of climb. The dependence of the critical stress on obstacle concentration and misfit strength is also explored and compared with existing models. In particular, our results are shown to be in reasonable agreement with the Friedel-Suzuki theory. Finally, the limitations inherent in the simplified model employed here, including the neglect of some lattice effects and the use of a coarse-grained climb mobility, are discussed.

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Edge-Stress-Induced Warping of Graphene Sheets and Nanoribbons

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Physical Review Letters 2008年第24期101卷 245501-245501页

作者： V. B. Shenoy C. D. Reddy A. Ramasubramaniam Y. W. Zhang Division of Engineering Brown University Providence Rhode Island 02912 USA Institute of High Performance Computing Singapore 138632 Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Department of Materials Science and Engineering National University of Singapore Singapore 119260

We show that edge stresses introduce intrinsic ripples in freestanding graphene sheets even in the absence of any thermal effects. Compressive edge stresses along zigzag and armchair edges of the sheet cause out-of-plane warping to attain several degenerate mode shapes. Based on elastic plate theory, we identify scaling laws for the amplitude and penetration depth of edge ripples as a function of wavelength. We also demonstrate that edge stresses can lead to twisting and scrolling of nanoribbons as seen in experiments. Our results underscore the importance of accounting for edge stresses in thermal theories and electronic structure calculations for freestanding graphene sheets.

关键词： Nanoribbons

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