TU Darmstadt / ULB / TUbiblio

Hybrid spatial Gillespie and particle tracking simulation

Klann, M. and Ganguly, A. and Koeppl, H. (2012):
Hybrid spatial Gillespie and particle tracking simulation.
In: Bioinformatics (Oxford, England), pp. i549, 28, (18), [Online-Edition: http://bioinformatics.oxfordjournals.org/content/28/18/i549....],
[Article]

Abstract

MOTIVATION: Cellular signal transduction involves spatial-temporal dynamics and often stochastic effects due to the low particle abundance of some molecular species. Others can, however, be of high abundances. Such a system can be simulated either with the spatial Gillespie/Stochastic Simulation Algorithm (SSA) or Brownian/Smoluchowski dynamics if space and stochasticity are important. To combine the accuracy of particle-based methods with the superior performance of the SSA, we suggest a hybrid simulation.

RESULTS: The proposed simulation allows an interactive or automated switching for regions or species of interest in the cell. Especially we see an application if for instance receptor clustering at the membrane is modeled in detail and the transport through the cytoplasm is included as well. The results show the increase in performance of the overall simulation, and the limits of the approach if crowding is included. Future work will include the development of a GUI to improve control of the simulation.

Item Type: Article
Erschienen: 2012
Creators: Klann, M. and Ganguly, A. and Koeppl, H.
Title: Hybrid spatial Gillespie and particle tracking simulation
Language: English
Abstract:

MOTIVATION: Cellular signal transduction involves spatial-temporal dynamics and often stochastic effects due to the low particle abundance of some molecular species. Others can, however, be of high abundances. Such a system can be simulated either with the spatial Gillespie/Stochastic Simulation Algorithm (SSA) or Brownian/Smoluchowski dynamics if space and stochasticity are important. To combine the accuracy of particle-based methods with the superior performance of the SSA, we suggest a hybrid simulation.

RESULTS: The proposed simulation allows an interactive or automated switching for regions or species of interest in the cell. Especially we see an application if for instance receptor clustering at the membrane is modeled in detail and the transport through the cytoplasm is included as well. The results show the increase in performance of the overall simulation, and the limits of the approach if crowding is included. Future work will include the development of a GUI to improve control of the simulation.

Journal or Publication Title: Bioinformatics (Oxford, England)
Volume: 28
Number: 18
Uncontrolled Keywords: Algorithms, Computer Simulation, Signal Transduction, Stochastic Processes
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
Date Deposited: 04 Apr 2014 12:51
Official URL: http://bioinformatics.oxfordjournals.org/content/28/18/i549....
Related URLs:
Export:

Optionen (nur für Redakteure)

View Item View Item