TU Darmstadt / ULB / TUbiblio

Improved Reaction Scheme for Spatial Stochastic Simulations with Single Molecule Detail

Klann, M. and Ganguly, A. and Koeppl, H. (2011):
Improved Reaction Scheme for Spatial Stochastic Simulations with Single Molecule Detail.
Tampere, Tampere University of Technology, In: Eighth International Workshop on Computational Systems Biology (WCSB 2011), [Online-Edition: http://www.wcsb2011.ethz.ch/programme],
[Conference or Workshop Item]

Abstract

We present an improved spatial simulation method to model intracellular reactions in detail. It combines the efficiency of the Gillespie algorithm for first order reactions with the spatial detail of particle tracking in molecule positions and bimolecular reactions. Bimolecular reactions depend on the collision of two molecules, but the time of a first order (e.g. decay) event can be pre-calculated at the time when the molecule is created. We applied this method to study the effect of scaffolds in MAPK signaling. Scaffolds co-localize the molecules of the signaling cascade and thus control the output of the signaling module.

Item Type: Conference or Workshop Item
Erschienen: 2011
Creators: Klann, M. and Ganguly, A. and Koeppl, H.
Title: Improved Reaction Scheme for Spatial Stochastic Simulations with Single Molecule Detail
Language: English
Abstract:

We present an improved spatial simulation method to model intracellular reactions in detail. It combines the efficiency of the Gillespie algorithm for first order reactions with the spatial detail of particle tracking in molecule positions and bimolecular reactions. Bimolecular reactions depend on the collision of two molecules, but the time of a first order (e.g. decay) event can be pre-calculated at the time when the molecule is created. We applied this method to study the effect of scaffolds in MAPK signaling. Scaffolds co-localize the molecules of the signaling cascade and thus control the output of the signaling module.

Volume: 57
Place of Publication: Tampere
Publisher: Tampere University of Technology
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Event Title: Eighth International Workshop on Computational Systems Biology (WCSB 2011)
Date Deposited: 04 Apr 2014 12:52
Official URL: http://www.wcsb2011.ethz.ch/programme
Related URLs:
Export:

Optionen (nur für Redakteure)

View Item View Item