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

  • Thomas Hinze
  • Sikander Hayat
  • Thorsten Lenser
  • Naoki Matsumaru
  • Peter Dittrich
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4860)


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.


Gene Regulatory Network Quorum Sensing Computational Unit Stochastic Simulation Algorithm NAND Gate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Thomas Hinze
    • 1
  • Sikander Hayat
    • 2
  • Thorsten Lenser
    • 1
  • Naoki Matsumaru
    • 1
  • Peter Dittrich
    • 1
  1. 1.Friedrich-Schiller-Universität Jena, Bio Systems Analysis Group, Ernst-Abbe-Platz 1–4, D-07743 JenaGermany
  2. 2.Universität des Saarlandes, Computational Biology Group, Center for Bioinformatics, P.O. Box 15 11 50, D-66041 SaarbrückenGermany

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