Hill kinetics meets P systems: a case study on gene regulatory networks as computing agents in silico and in vivo

Authors:
Thomas Hinze;Sikander Hayat;Thorsten Lenser;Naoki Matsumaru;Peter Dittrich
Affiliations:
Friedrich-Schiller-Universität Jena, Jena, Germany;Universität des Saarlandes, Saarbrücken, Germany;Friedrich-Schiller-Universität Jena, Jena, Germany;Friedrich-Schiller-Universität Jena, Jena, Germany;Friedrich-Schiller-Universität Jena, Jena, Germany
Venue:
WMC'07 Proceedings of the 8th international conference on Membrane computing
Year:
2007

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Abstract

Modeling and simulation of biological reaction networks is an essential task in systems biology aiming at formalization, understanding, and prediction of processes in living organisms. Currently, a variety of modeling approaches for specific purposes coexists. P systems form such an approach which owing to its algebraic nature opens growing fields of application. Here, emulating the dynamical system behavior based on reaction kinetics is of particular interest to explore network functions. We demonstrate a transformation of Hill kinetics for gene regulatory networks (GRNs) into the P systems framework. Examples address the switching dynamics of GRNs acting as NAND gate and RS flip-flop. An adapted study in vivo experimentally verifies both practicability for computational units and validity of the system model.