Brownian Dynamics Simulator Prototype

Prototype Brownian Dynamics simulation code for E-Cell

A Brownian Dynamics simulation code based on an improved version of Green's Function Reaction Dynamics (GFRD) algorithm is under development and will be released soon.

Green's Function Reaction Dynamics

GFRD algorithm is an accelerated brownian dynamics simulation method primarily having in mind applications to modeling and simulating biochemical network models with space. GFRD was originally proposed by van Zon and ten Wolde [1] [2] at The Institute for Atomic and Molecular Physics in Amsterdam (AMOLF) in 2005. Currently an improved version is being developed by Sorin Tanase-Nicola, Pieter Rein ten Wolde (AMOLF) and Koichi Takahashi (MSI, E-Cell Project).

The Simulator Code

Takahashi has been working on a high-performance implementation of the GFRD algorithm and its improved versions. The purpose of this prototype code written in mixed Python and C++ is to establish a solid and practical implementation of the algorithm, and to extend it into a form that is more suitable for biochemical and cell simulations.

The prototype will eventually be reorganized to be part of E-Cell System Version 4, of which one of the leading features will be multi-spatial representation, meaning that multiple sub-models with different classes and scales of representations of space can coexist and interplay in a simulation model.

This prototype code will be made publicly available as OpenSource software, and maintenance will continue until it is integrated into E-Cell 4. After that point the simulation code will be maintained by E-Cell developers.

More info will follow in this website. Please contact Koichi Takahashi <ktakahashi at molsci dot org> for further details on the code being developed.