:author: Koichi Takahashi


E-Cell Particle Dynamics Prototype

Copyright (C) 2008-2010 RIKEN
Copyright (C) 2009-2010 AMOLF
Copyright (C) 2005-2008 The Molecular Sciences Institute


About this package
========================

This package is tentatively named E-Cell Particle Dynamics Prototype
(EPDP).  It currently implements the enhanced Greens Function Reaction
Dynamics (eGFRD) algorithm and the reaction Brownian Dynamics (BD) simulation
algorithm.  Implementation of the original version of GFRD will
possibly be added in future.  The code is implemented with the hope
that it will eventually be part of the E-Cell System Version 4
multi-algorithm, multi-space simulation platform.

The purpose of this prototype code written in mixed Python and C++ is
to establish a solid and practical implementation of the algorithms,
and to extend it into a form that is suitable for large-scale
biochemical and cell simulations.

The eGFRD algorithm first appeared and be used in a paper by
Takahashi, Tanase-Nicola and ten Wolde [1], and will be described more
in detail in a forthcoming paper[2].

The reaction Brownian Dynamics algorithm is described in a paper by
Morrelli and ten Wolde[3].


Authors
========================

(alphabetical order)
Kazunari Kaizu
Moriyoshi Koizumi
Thomase Miedema
Koichi Takahashi


License
========================

This package is distributed under the terms of GNU General Public License
version 2.  See COPYING.


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[4].  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
the 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
introduced the concept called first-passage processes[5][6] to Greens
Function Reaction Dynamics by putting protective domains around
particles to further boost the performance and accuracy of the method.
The new method was named eGFRD (enhanced Greens Function Reaction
Dynamics).


Plans
=========================

Some features planned to be added are; surfaces, interactions between
membrane proteins and proteins in solution, optimistic discrete-event
scheduling for massive parallelization, connections to non-spatial 
simulation methods such as ODE and Gillespie methods.


[1] K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, PNAS doi:10.1073/pnas.0906885107 (2010).
[2] K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, in preparation. 
[3] M.J. Morelli and P.R. ten Wolde, J. Chem. Phys. 7;129(5):054112 (2008).
[4] van Zon and ten Wolde, Phys. Rev. Lett. 94 (2005).
[5] T. Opplestrup, V.V. Bulatov, G.H. Gilmer, M.H. Kalos, and B. Sadigh, Phys. Rev. Lett. 97 (2006).
[6] M.H. Kalos, D. Levesque and L. Verlet, Phys. Rev. A 9 (1974).