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Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems

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Membrane Computing (CMC 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6501))

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Abstract

The simulator software SRSim is presented here. It is constructed from the molecular dynamics simulator LAMMPS and a set of extensions for modeling rule-based reaction systems. The aim of this software is coping with reaction networks that are combinatorially complex as well as spatially inhomogeneous. On the one hand, there is a combinatorial explosion of necessary species and reactions that occurs when complex biomolecules are allowed to interact, e.g. by polymerization or phosphorilation processes. On the other hand, diffusion over longer distances in the cell as well as the geometric structures of sophisticated macromolecules can further influence the dynamic behavior of a system. Addressing the mentioned demands, the SRSim simulation system features a stochastic, particle based, spatial simulation of Brownian Dynamics in three dimensions of a rule-based reaction system.

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Authors and Affiliations

  1. Jena Center for Bioinformatics, Bio Systems Analysis Group, Institute of Computer Science, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1-4, 07743, Jena, Germany

    Gerd Grünert & Peter Dittrich

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  1. Gerd Grünert
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  2. Peter Dittrich
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Editors and Affiliations

  1. Department of Computer Science, University of Sheffield, Regent Court, Portobello Street, S1 4DP, Sheffield, UK

    Marian Gheorghe

  2. Department of Bioinformatics, School of Biology and Pharmacy, Friedrich Schiller University, Ernst-Abbe-Platz 1–4, 07743, Jena, Germany

    Thomas Hinze

  3. Institute of Mathematics of the Romanian Academy, P.O. Box 1-764, 014700, Bucureşti, Romania

    Gheorghe Păun

  4. Leiden Center of Advanced Computer Science (LIACS), Universiteit Leiden, Niels Bohrweg 1, 2333, CA Leiden, The Netherlands

    Grzegorz Rozenberg

  5. Turku Centre for Computer Science (TUCS), Leminkäisenkatu 14, 20520, Turku, Finland

    Arto Salomaa

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Grünert, G., Dittrich, P. (2010). Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems. In: Gheorghe, M., Hinze, T., Păun, G., Rozenberg, G., Salomaa, A. (eds) Membrane Computing. CMC 2010. Lecture Notes in Computer Science, vol 6501. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18123-8_19

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  • DOI: https://doi.org/10.1007/978-3-642-18123-8_19

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-18122-1

  • Online ISBN: 978-3-642-18123-8

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