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: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 , and will be described more in detail in a forthcoming paper. The reaction Brownian Dynamics algorithm is described in a paper by Morrelli and ten Wolde. 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. 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 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.  K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, PNAS doi:10.1073/pnas.0906885107 (2010).  K. Takahashi, S. Tanase-Nicola and P.R. ten Wolde, in preparation.  M.J. Morelli and P.R. ten Wolde, J. Chem. Phys. 7;129(5):054112 (2008).  van Zon and ten Wolde, Phys. Rev. Lett. 94 (2005).  T. Opplestrup, V.V. Bulatov, G.H. Gilmer, M.H. Kalos, and B. Sadigh, Phys. Rev. Lett. 97 (2006).  M.H. Kalos, D. Levesque and L. Verlet, Phys. Rev. A 9 (1974).