Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
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- Systems Biology Program, Graduate School of Media and Governance, Keio University, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
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This manuscript is a preprint. A published version is available at:
http://sites.google.com/site/ijcsis/july-2009 (Peer Reviewed) Arjunan SNV, Tomita M (2009) Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System. International Journal of Computer Science and Information Security 3(1):211–216- Document Type:
- Manuscript
- Date:
- Received 31 July 2009 15:41 UTC; Posted 31 July 2009
- Subjects:
- Developmental Biology, Microbiology, Bioinformatics
- Abstract:
The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in vivo dynamics of MinD and MinE and comparing their simulated localization patterns to the observations in experiments and previous computational work. In both cases, our simulation results are in good agreement.
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- License:
- This document is licensed to the public under the Creative Commons Attribution 3.0 License
- How to cite this document:
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Arjunan, Satya and Tomita, Masaru. Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3526.1> (2009)
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Published version:
http://sites.google.com/site/ijcsis/july-2009 (Peer Reviewed) Arjunan SNV, Tomita M (2009) Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System. International Journal of Computer Science and Information Security 3(1):211–216 -
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