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Greens Function Reaction Dynamics simulation framework
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README

E-Cell Particle Dynamics Prototype

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


EGFRD Simulator
------------------------

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 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
------------------------
- Nils Becker
- Laurens Bossen
- Kazunari Kaizu
- Moriyoshi Koizumi
- Thomase Miedema
- Thomas Sokolowski
- 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).

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] 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).
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