Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents $in silico$ and $in vivo

• Published in: Membrane Computing Vol. 4860; pp. 320 - 335
• Main Authors: Hinze, Thomas, Hayat, Sikander, Lenser, Thorsten, Matsumaru, Naoki, Dittrich, Peter
• Format: Book Chapter
• Language: English
• Published: Germany Springer Berlin / Heidelberg 2007; Springer Berlin Heidelberg
• Series: Lecture Notes in Computer Science
• Subjects: Computational Unit; Computer science; Gene Regulatory Network; Mathematical theory of computation; NAND Gate; Quorum Sensing; Stochastic Simulation Algorithm; User interface design & usability
• ISBN: 3540773118; 9783540773115
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-540-77312-2_20

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.