263086 Recent Computational Tools for the Analysis of Complex Biochemical Reaction Networks

Wednesday, October 31, 2012: 8:48 AM
Westmoreland East (Westin )
Daniel Knight, Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, Haixia Ji, Mathematics, Ohio State University, Columbus, OH and Martin Feinberg, Ohio State University, Columbus, OH

Recent Computational Tools for the Analysis of Complex Biochemical Reaction Networks

Daniel Knight, Haixia Ji, Martin Feinberg

Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio

When studying biological systems, understanding of their dynamical properties is more readily inferred from knowledge of only the reaction network, as detailed kinetic information is generally not available with confidence. There are exemplary complex biochemical reaction networks with rich behavior (multiple steady states, oscillatory behavior, etc.), while others have relatively dull, stable dynamics. Recent theoretical developments1, 2 allow for powerful statements to be made about the dynamics of even very complex networks, provided the kinetics falls within a very general and natural class. In particular, it is possible to distinguish in a precise way between networks that might provide the basis for a bistable switch, and networks even very intricate ones that cannot. These recent theoretical developments have been incorporated into a freely available computer program, Chemical Reaction Network Toolbox (CRNT)3. The theory will be discussed, and examples of its implementation via the Toolbox will be given.

1. G. Shinar and M. Feinberg, Concordant Chemical Reaction Networks, 2011, available at www.arXiv.org/pdf/1109.2923v1.pdf.

2. G. Shinar and M. Feinberg, Concordant Chemical Reaction Networks and the Species-Reaction Graph, 2012, available at www.arXiv.org/pdf/1203.6560v3.pdf.

3. H. Ji, P. Ellison, D. Knight, and M. Feinberg, The chemical reaction network toolbox, version 2.1, 2011, available at http://www.chbmeng.ohiostate.edu/ feinberg/crntwin/.


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