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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Katherine V. Wendeldorf Josep Bassaganya-Riera Keith Bisset Stephen Eubank Raquel Hontecillas Madhav Marathe Network Dynamics and Simulation Science Laboratory Center of Modeling Immunity to Enteric Pathogens Virginia Bioinformatics Institute Virginia Polytechnic Institute and University Blacksburg VA USA Nutritional Immunology and Molecular Medicine Laboratory Center of Modeling Immunity to Enteric Pathogens Virginia Bioinformatics Institute Virginia Polytechnic Institute and University Blacksburg VA USA Department of Computer Science Center of Modeling Immunity to Enteric Pathogens Virginia Bioinformatics Institute Virginia Polytechnic Institute and University Blacksburg VA USA

Clinical symptoms of gastrointestinal (GI) infections are often caused by the inflammatory response elicited to eliminate the invading microbe. Here we present ENISI, a simulator of GI immune mechanisms in response to resident commensal bacteria as well as invading pathogens and the effect on host clinical symptoms. ENISI is a tool for identifying treatment strategies that reduce inflammation-induced damage and, at the same time, ensure pathogen removal by allowing one to test plausibility of in vitro observed behavior as explanations for observations in vivo, propose behaviors not yet tested in vitro that could explain these tissue-level observations, and conduct low-cost, preliminary experiments of proposed interventions/ treatments. An example of such application is shown in which we simulate dysentery resulting from B. hyodysenteriae infection and identify aspects of the host immune pathways that lead to continued inflammation-induced tissue damage even after pathogen elimination.

关键词： Immune system Microorganisms Automata Pathogens Blood Tissue damage Computational modeling

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Towards a methodological approach to identify future M&S standard needs

Towards a methodological approach to identify future M&S sta...

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2011 Winter simulation Conference, WSC 2011

作者： Tolk, Andreas Balci, Osman Diallo, Saikou Y. Fishwick, Paul A. Hu, Xiaolin Loper, Margaret Petty, Mikel D. Reynolds Jr., Paul F. Sarjoughian, Hessam Zeigler, Bernard P. Old Dominion University Engineering Management and Systems Engineering 241 Kaufman Hall Norfolk VA 23529 United States Virginia Tech. Department of Computer Science 3160B Torgersen Hall Blacksburg VA 24061 United States Virginia Modeling Analysis and Simulation Center Old Dominion University 1030 University Blvd Suffolk VA 23435 United States University of Florida Digital Arts and Sciences CISE Department Gainesville FL 32611 United States Georgia State University Computer Science Department Atlanta GA 30303 United States Georgia Tech. Research Institute Information and Communications Laboratory Atlanta GA 30318 United States University of Alabama in Huntsville Shelby Center 144 301 Sparkman Drive Huntsville AL 35899 United States University of Virginia 151 Engineer's Way Charlottesville VA 22901 United States Arizona State University Center for Integrative Modeling and Simulation Tempe AZ 85271 United States RTSync Corp. 11900 Parklawn Dr. Rockville MD 20852 United States

ISBN: (纸本)9781457721083

Although modeling and simulation is successfully applied for several decades, the community only established a handful of M&S specific standards. Although the standards were applied enabling worldwide distributed simulation applications, in particular in the training application domain of military simulation systems, the general success of M&S standard efforts and their potential for general applicability has been debated repeatedly during several conferences and workshop. This collection of position statements discusses related questions, such as, "What makes M&S special that we need M&S standards," "Are M&S standards truly different from Software Engineering Standards," and "What metrics can be used to measure M&S standard success," and tries to contribute to establishing a methodological approach to identify future M&S standard needs. These position statements have been contributed in preparation of a panel discussion and edited for the supporting proceedings. © 2011 IEEE.

关键词： Military applications

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Towards a methodological approach to identify future M&S standard needs 11

Towards a methodological approach to identify future M&S sta...

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simulation Winter Conference

作者： Andreas Tolk Osman Balci Saikou Y. Diallo Paul A. Fishwick Xiaolin Hu Margaret Loper Mikel D. Petty Paul F. Reynolds Hessam Sarjoughian Bernard P. Zeigler Engineering Management & Systems Engineering Old Dominion University Norfolk VA USA Department of Computer Science Virginia Polytechnic Institute and State University Blacksburg VA USA Virginia Modeling Analysis & Simulation Center Old Dominion University Suffolk VA USA Digital Arts and Sciences CISE Department University of Florida Gainesville FL USA Computer Science Department Georgia State University Atlanta GA USA Information & Communications Laboratory Georgia Tech Research Institute Georgia Institute of Technology Atlanta GA USA University of Alabama-Huntsville Huntsville AL USA University of Virginia Charlottesville VA USA Center for Integrative Modeling and Simulation Arizona State University Tempe AZ USA RTSync Corp. Rockville MD USA

Although modeling and simulation is successfully applied for several decades, the community only established a handful of M&S specific standards. Although the standards were applied enabling worldwide distributed simulation applications, in particular in the training application domain of military simulation systems, the general success of M&S standard efforts and their potential for general applicability has been debated repeatedly during several conferences and workshop. This collection of position statements discusses related questions, such as, “What makes M&S special that we need M&S standards,” “Are M&S standards truly different from Software Engineering Standards,” and “What metrics can be used to measure M&S standard success,” and tries to contribute to establishing a methodological approach to identify future M&S standard needs. These position statements have been contributed in preparation of a panel discussion and edited for the supporting proceedings.

关键词： Standards USA Councils Biological system modeling Educational institutions Computational modeling

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Current Density Effects on the Structural and Magnetic Properties of CoNiFe Alloy Thin Films

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AIP Conference Proceedings 2011年第1期1349卷 781-782页

作者： K. Sundaram V. Dhanasekaran T. Mahalingam M. Raja Takeyu Kim Yong Deak Kim aDepartment of Physics Government Arts and Science College Melur ‐ 625 106 India bDepartment of Physics Alagappa University Karaikudi ‐ 630 003 India cDepartment of Physics Kalasalingam University Krishnankoil ‐ 626 790 India dCenter for Modeling and Simulation Studies Security Management Institute Seoul ‐ 135 871 Korea eDepartment of Electrical and Computer Engineering Ajou University Suwon‐443 749 Korea

CoNiFe alloy thin films with various current densities were galvano statically electro deposited on the pre‐cleaned copper substrates. The higher value of saturation magnetization (4πMs) and low value of coercivity ...

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Inside Back Cover: The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach (Angew. Chem. Int. Ed. 44/2012)

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Angewandte Chemie International Edition 2012年第44期51卷

作者： Andrew J. Thompson Dr. Jerome Dabin Javier Iglesias-Fernández Dr. Albert Ardèvol Dr. Zoran Dinev Assoc. Prof. Spencer J. Williams Dr. Omprakash Bande Dr. Aloysius Siriwardena Carl Moreland Dr. Ting-Chou Hu David K. Smith Prof. Harry J. Gilbert Prof. Carme Rovira Prof. Gideon J. Davies Department of Chemistry University of York Heslington York YO10 5DD (UK) Computer Simulation & Modeling Laboratory Parc Científic de Barcelona Baldiri Reixac 4 08028 Barcelona (Spain) Institut de Química Teòrica i Computacional (IQTCUB) (Spain) Present address: Departament de Química Orgànica Universitat de Barcelona Martí i Franquès 1 08028 Barcelona (Spain) Present address: Department of Chemistry and Applied Biosciences ETH Zurich USI Campus Via Giuseppe Buffi 13 CH-6900 Lugano (Switzerland) School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville (Australia) Université de Picardie Jules Vernes Laboratoire des Glucides (CNRS-FRE 3617) 33 Rue Saint Leu 80039 Amiens (France) Institute for Cell and Molecular Biosciences The Medical School Newcastle University Framlington Place Newcastle upon Tyne NE2 4HH (UK) Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 23 08020 Barcelona (Spain) Carme Rovira Computer Simulation & Modeling Laboratory Parc Científic de Barcelona Baldiri Reixac 4 08028 Barcelona (Spain) Gideon J. Davies Department of Chemistry University of York Heslington York YO10 5DD (UK)

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The attributed pi-calculus with priorities

The attributed pi-calculus with priorities

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作者： John, Mathias Lhoussaine, Cédric Niehren, Joachim Uhrmacher, Adelinde M. University of Rostock Institute of Computer Science Modeling and Simulation Group Germany University of Lille 1 France INRIA Lille France BioComputing Group LIFL IRI France

ISBN: (纸本)3642117112

We present the attributed π-calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The λ-calculus serves as a constraint language underlying the π-calculus. Interaction constraints subsume priorities, by which to express global aspects of populations. We present a non-deterministic and a stochastic semantics for the attributed π-calculus. We show how to encode the π-calculus with priorities and polyadic synchronization π-@ and thus dynamic compartments, as well as the stochastic π-calculus with concurrent objects spico. We illustrate the usefulness of the attributed π-calculus for modeling biological systems at two particular examples: Euglena's spatial movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda. Furthermore, population-based model is supported beside individual-based modeling. A stochastic simulation algorithm for the attributed π-calculus is derived from its stochastic semantics. We have implemented a simulator and present experimental results, that confirm the practical relevance of our approach. © 2010 Springer.

关键词： Stochastic systems

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The Reaction Coordinate of a Bacterial GH47 α‐Mannosidase: A Combined Quantum Mechanical and Structural Approach†

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Angewandte Chemie 2012年第44期124卷

作者： Andrew J. Thompson Jerome Dabin Javier Iglesias‐Fernández Albert Ardèvol Zoran Dinev Spencer J. Williams Omprakash Bande Aloysius Siriwardena Carl Moreland Ting‐Chou Hu David K. Smith Harry J. Gilbert Carme Rovira Gideon J. Davies Department of Chemistry University of York Heslington York YO10 5DD (UK) Computer Simulation & Modeling Laboratory Parc Científic de Barcelona Baldiri Reixac 4 08028 Barcelona (Spain) Institut de Química Teòrica i Computacional (IQTCUB) (Spain) Present address: Departament de Química Orgànica Universitat de Barcelona Martí i Franquès 1 08028 Barcelona (Spain) Present address: Department of Chemistry and Applied Biosciences ETH Zurich USI Campus Via Giuseppe Buffi 13 CH‐6900 Lugano (Switzerland) School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville (Australia) Université de Picardie Jules Vernes Laboratoire des Glucides (CNRS‐FRE 3617) 33 Rue Saint Leu 80039 Amiens (France) Institute for Cell and Molecular Biosciences The Medical School Newcastle University Framlington Place Newcastle upon Tyne NE2 4HH (UK) Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 23 08020 Barcelona (Spain)

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Innenrücktitelbild: The Reaction Coordinate of a Bacterial GH47 α‐Mannosidase: A Combined Quantum Mechanical and Structural Approach (Angew. Chem. 44/2012)

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Angewandte Chemie 2012年第44期124卷

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Editorial

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Theory in Biosciences 2008年第2期127卷 67-68页

作者： Jost, Jürgen Helbing, Dirk Lörincz, András Middendorf, Martin Max Planck Institute for Mathematics in the Sciences Leipzig Germany Department of Humanities and Social Sciences Chair of Sociology in particular of Modeling and Simulation ETH Zurich Zurich Switzerland Department of Information Systems Eötvös Loránd University Budapest Hunhary Department of Computer Science University of Leipzig Leipzig Germany

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Discrete event multi-level models for systems biology

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Lecture Notes in computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2005年 3380 LNBI卷 66-89页

作者： Uhrmacher, Adelinde M. Degenring, Daniela Zeigler, Bernard Institute for Computer Science University of Rostock Albert-Einstein-Str. 21 D-18059 Rostock Germany Arizona Center of Integrative Modeling and Simulation University of Arizona Tucson AZ 85721 United States

ISBN: (纸本)3540254226

Diverse modeling and simulation methods are being applied in the area of Systems Biology. Most models in Systems Biology can easily be located within the space that is spanned by three dimensions of modeling: continuous and discrete;quantitative and qualitative;stochastic and deterministic. These dimensions are not entirely independent nor are they exclusive. Many modeling approaches are hybrid as they combine continuous and discrete, quantitative and qualitative, stochastic and deterministic aspects. Another important aspect for the distinction of modeling approaches is at which level a model describes a system: is it at the "macro" level, at the "micro" level, or at multiple levels of organization. Although multi-level models can be located anywhere in the space spanned by the three dimensions of modeling and simulation, clustering tendencies can be observed whose implications are discussed and illustrated by moving from a continuous, deterministic quantitative macro model to a stochastic discrete-event semi-quantitative multi-level model. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Data structures

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