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MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.

David Fange¹, Anel Mahmutovic, Johan Elf

¹Department of Cell & Molecular Biology, Science for Life Laboratory, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden.

Bioinformatics (Oxford, England)

|October 10, 2012

Summary

MesoRD is a new software tool that simulates complex reaction-diffusion systems. It enables physically consistent modeling of diffusion-controlled reactions, even at fine spatial scales.

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Area of Science:

Computational Biology
Biophysics
Systems Biology

Background:

MesoRD is a C++ software tool for simulating stochastic reaction-diffusion systems.
It is licensed under the GNU General Public License (GPL).
Downloadable at http://mesord.sourceforge.net with documentation and updates.

Purpose of the Study:

To introduce MesoRD, a tool for simulating reaction-diffusion systems.
To enhance the tool's capabilities for physically consistent modeling.
To support advanced features for diffusion-controlled reactions.

Main Methods:

Modeling stochastic reaction-diffusion systems using the reaction diffusion master equation.
Defining systems in Systems Biology Markup Language (SBML) with compartment geometries.
Implementing scale-dependent reaction rate constants and reactions between neighboring subvolumes.

Main Results:

MesoRD 1.0 enables simulation of stochastic reaction-diffusion systems.
The tool supports Systems Biology Markup Language (SBML) with custom compartment geometries.
New features allow for scale-dependent reaction rates and inter-compartmental reactions.

Conclusions:

MesoRD provides a robust tool for simulating reaction-diffusion systems.
The software facilitates physically consistent modeling of diffusion-controlled reactions.
Advanced features enable accurate simulations at fine spatial resolutions.