GFRD Simulator

E-Cell Particle Dynamics Prototype by Koichi Takahashi and Moriyoshi Koizumi. Adapted by Thomas Miedema, Laurens Bossen and Thomas Sokolowski.

Copyright (C) 2005-2008 The E-Cell Project

Copyright (C) 2009 FOM Institute AMOLF, The Netherlands.

About this package

This package is started of from version 0.3 of the E-Cell Particle Dynamics Prototype (epdp): http://www.e-cell.org/ecell/software/releases/epdp-0.3/epdp-0.3.tar.gz

Just as that package it implements the enhanced Greens Function Reaction Dynamics (eGFRD), and brute-force Brownian Dynamics (BD) simulation algorithms. Additionaly it support reaction-diffusion on and with 1D and 2D surfaces.

The code is implemented with the hope that it will eventually be included into the epdp package, and also function as a standalone GFRD implementation.

The eGFRD algorithm is used and described in the following paper: K. Takahashi, S. Tanase-Nicola, P.R. ten Wolde, 2009 (in preparation).

Building this package

See INSTALL.

History of the Code

Koichi Takahashi initially stated development of the code in 2005 to implement his prototype of Greens Function Reaction Dynamics simulation method invented by Jeroen van Zon and Pieter Rein ten Wolde in AMOLF, Amsterdam[1,2]. He gave a brief invited talk about performance evaluation and applicability of the method to yeast pheromon response pathway (the Alpha pathway) using the prototype in Third Annual Alpha Project Research Symposium (June 16-27, 2005, at UC Berkeley Art Museum).

Later, in December 2006, ten Wolde, Sorin Tanase-Nicola, and Takahashi decided to introduce the concept called first-passage processes inspired by a paper by Opplestrup et al.[3] to Greens Function Reaction Dynamics to further boost the performance and accuracy of the method. The new method was called eGFRD (enhanced Greens Function Reaction Dynamics). Takahashi implemented the single-body Greens function within the year. Tanase-Nicola derived the two-body Greens function, and Takahashi devised and implemented a neat yet complicated way to efficiently evaluate the function mostly in the first half of

2007. Takahashi also implemented the main part of the code, asynchronous discrete-event-driven kinetic monte-carlo, which has been mostly finished within 2007, and the dynamic switching between Greens function and brute-force Brownian Dynamics as a means to recover from particle squeezing conditions by April 2008. At this point, development and debugging of the initial version (version 0.1) of the code had been largely finished and had been used in simulation experiments in study of various biochemical systems including dual-phosphorylation pathways[4].

Thomas Miedema and Laurens Bossen, while masters students in the group of Pieter Rein ten Wolde at AMOLF, added support for reaction-diffusion on and with 1D and 2D surfaces. Laurens implemented the 1D and 2D Green's functions in C++, Thomas implemented the algorithm in Python.

In 2009 Thomas Sokolowski and Nils Becker joined the project. Thomas S. will extend the scheme to be able to simulate active transport processes via molecular motors. This requires the calculation of new Green's functions starting from the diffusion-drift equation. Nils B. recently started working on the interplay of DNA sliding and 3D diffusion.

List of features planned to be added:

• interactions between membrane proteins and proteins in solution
• diffusion-drift movement on one-dimensional structures to simulate active transport
• interaction of particles with arbitrary 2-dimensional manifolds

References:

• [1] Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space; van Zon and ten Wolde, J. Chem. Phys. 123 (2005).
• [2] Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics; van Zon and ten Wolde, Phys. Rev. Lett. 94 (2005).
• [3] First-Passage Monte Carlo Algorithm: Diffusion without All the Hops, Opplestrup et al., Phys. Rev. Lett. 97 (2006).
• [4] Spatio-temporal correlations can drastically change the response of a MAPK pathway; Takahashi, Tanase-Nicola, ten Wolde, arXiv:0907.0514v1 (2009)