An Accelerated Biochemical Brownian Dynamics Code Released

Details and a download link can be found here.

The E-Cell Project publicly released E-Cell Particle Dynamics Prototype (EPDP) version 0.3 for the first time on Dec 22nd, 2008, Japan Time. This is the first public release of the package after some internal releases for testing and debugging purposes.

This package implements a new Brownian Dynamics method called enhanced Greens Function Reaction Dynamics (eGFRD). eGFRD is exact (based directly on analytical solutions of the diffusion-reaction equation), high-performance (orders of magnitude faster than conventional BD methods), extendable (different types of diffusion and boundary conditions can be efficiently implemented) and thus opens a possibility to applications of exact particle methods to cellular-level problems which has previously been unrealistic due to high computational costs.

The purpose of this prototype code in EPDP 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 suitable for biochemical and cell simulations.

The prototype will eventually be reorganized to be part of the 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.

The novel simulation algorithm was devised by Pieter Rein ten Wolde (AMOLF, Amsterdam), Sorin Tanase-Nicola (U. Michigan), and Koichi Takahashi (RIKEN, Japan). The simulation code in the EPDP package was developed by Takahashi.