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AnalyticalPair.hpp
AnalyticalSingle.hpp
BDPropagator.hpp
BDSimulator.hpp
BasicNetworkRulesImpl.cpp
BasicNetworkRulesImpl.hpp
BasicReactionRecorderImpl.hpp
Box.hpp
COPYING
ChangeLog
ConsoleAppender.cpp
ConsoleAppender.hpp
CuboidalRegion.hpp
Cylinder.hpp
CylindricalBesselGenerator.cpp
CylindricalBesselGenerator.hpp
CylindricalSurface.hpp
Defs.hpp
Dockerfile
Domain.hpp
DomainFactory.hpp
DomainID.hpp
DomainUtils.hpp
DynamicPriorityQueue.hpp
EGFRDSimulator.hpp
EGFRDSimulatorFactory.hpp
EventScheduler.hpp
GSLRandomNumberGenerator.hpp
GreensFunction.hpp
GreensFunction1DAbsAbs.cpp
GreensFunction1DAbsAbs.hpp
GreensFunction1DRadAbs.cpp
GreensFunction1DRadAbs.hpp
GreensFunction3D.cpp
GreensFunction3D.hpp
GreensFunction3DAbs.cpp
GreensFunction3DAbs.hpp
GreensFunction3DAbsSym.cpp
GreensFunction3DAbsSym.hpp
GreensFunction3DRadAbs.cpp
GreensFunction3DRadAbs.hpp
GreensFunction3DRadAbsBase.cpp
GreensFunction3DRadAbsBase.hpp
GreensFunction3DRadInf.cpp
GreensFunction3DRadInf.hpp
GreensFunction3DSym.cpp
GreensFunction3DSym.hpp
HalfOrderBesselGenerator.hpp
INSTALL
Identifier.hpp
Logger.cpp
Logger.hpp
Makefile.am
MatrixSpace.hpp
Model.cpp
Model.hpp
Multi.hpp
NEWS
NetworkRules.cpp
NetworkRules.hpp
NetworkRulesWrapper.hpp
OldDefs.hpp
Pair.hpp
PairGreensFunction.hpp
Particle.hpp
ParticleContainer.hpp
ParticleContainerBase.hpp
ParticleID.hpp
ParticleModel.cpp
ParticleModel.hpp
ParticleSimulationStructure.hpp
ParticleSimulator.hpp
ParticleSimulatorFactory.hpp
PlanarSurface.hpp
Plane.hpp
Point.hpp
PyEventScheduler.hpp
README
ReactionRecord.hpp
ReactionRecorder.hpp
ReactionRule.hpp
ReactionRuleInfo.hpp
Region.hpp
SerialIDGenerator.hpp
Shape.hpp
ShapedDomain.hpp
Shell.hpp
ShellID.hpp
Single.hpp
SpeciesInfo.hpp
SpeciesType.cpp
SpeciesType.hpp
SpeciesTypeID.hpp
Sphere.hpp
SphericalBesselGenerator.cpp
SphericalBesselGenerator.hpp
SphericalSurface.hpp
Structure.hpp
StructureType.cpp
StructureType.hpp
StructureUtils.hpp
Surface.hpp
Transaction.hpp
Vector3.hpp
VolumeClearer.hpp
World.hpp
abstract_set.hpp
acinclude.m4
autogen.sh
bd.py
bessel.hpp
compat.h
configure.ac
constants.py
datafile.py
dumper.py
egfrd.py
exceptions.hpp
factorial.hpp
filters.hpp
findRoot.cpp
findRoot.hpp
freeFunctions.cpp
freeFunctions.hpp
funcSum.cpp
funcSum.hpp
generator.hpp
geometry.hpp
gfrdbase.py
gillespie.py
greens_function_wrapper.py
greens_functions.cpp
gsl_rng_base.hpp
legacy.py
linear_algebra.hpp
logger.py
make_cjy_table.py
make_sjy_table.py
model.py
multi.py
myrandom.py
pair.py
pyGFRD.cpp
pyport.patch
single.py
sorted_list.hpp
twofold_container.hpp
utils.cpp
utils.hpp
utils.py

README

: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).