Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Stephan Menz, University of Potsdam, AG Huisinga

Title: Direct Hybrid Stochastic-Deterministic Solution of the Chemical Master Equation

Time: Wed, May 4, 2011, 10am

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
The chemical master equation (CME) is the fundamental evolution equation of the stochastic description of biochemical reaction kinetics. In contrast to deterministic models it accounts for the discrete and random nature of reaction processes in cells. Due to its high dimensionality, however, in most applications it is impracticable to compute direct solutions of the CME. Instead the CME is indirectly solved by Monte Carlo (MC) simulations of the underlying Markov jump process. Apart from the general problem of estimating the required number of realizations to meet a certain accuracy such indirect approaches become numerically inefficient when the system's dynamics include fast reaction processes or species with high copy numbers. In hybrid approaches, such parts of a reaction network are approximated as continuous processes or replaced by quasi-stationary distributions either in a stochastic or deterministic context. Current hybrid approaches, however, still rely on MC simulations of the stochastic part of the system. This talk first gives a brief recap of the stochastic and deterministic modeling approach of biochemical reaction kinetics. Then, a new direct hybrid approach is presented where a CME for the probability density function of species with low copy numbers is coupled to an evolution equation of deterministically approximated expectations of the remaining species. The performance of the proposed hybrid stochastic-deterministic description is illustrated in application to model systems of biological interest. This is joint work with J. Latorre and C. Schütte, FU Berlin, and W. Huisinga, University of Potsdam.

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Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


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