Particle-Based Stochastic Simulators

[1]  Nicolas Le Novère,et al.  Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes , 2010, BMC Systems Biology.

[2]  Terrence J. Sejnowski,et al.  Multi-state Modeling of Biomolecules , 2014, PLoS Comput. Biol..

[3]  D. Ermak,et al.  Brownian dynamics with hydrodynamic interactions , 1978 .

[4]  Roger Brent,et al.  Detailed Simulations of Cell Biology with Smoldyn 2.1 , 2010, PLoS Comput. Biol..

[5]  Leslie M Loew,et al.  Spatial modeling of cell signaling networks. , 2012, Methods in cell biology.

[6]  Masaru Tomita,et al.  E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[7]  K. T. Blackwell,et al.  Approaches and tools for modeling signaling pathways and calcium dynamics in neurons , 2013, Journal of Neuroscience Methods.

[8]  Andreas Hellander,et al.  URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries , 2012, BMC Systems Biology.

[9]  Masaru Tomita,et al.  Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico , 2005, FEBS letters.

[10]  S. Andrews.  Methods for modeling cytoskeletal and DNA filaments , 2014, Physical biology.

[11]  P. R. ten Wolde,et al.  Spatio-temporal correlations can drastically change the response of a MAPK pathway , 2009, Proceedings of the National Academy of Sciences.

[12]  T. Bartol,et al.  Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Monika Heiner,et al.  Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481) , 2014, Dagstuhl Reports.

[14]  Frank Noé,et al.  Simulation tools for particle-based reaction-diffusion dynamics in continuous space , 2014, BMC biophysics.

[15]  Yoshihisa Kubota,et al.  Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology , 2010, Neuroinformatics.

[16]  Anton Khmelinskii,et al.  Analytical model for macromolecular partitioning during yeast cell division , 2014, BMC biophysics.

[17]  D. Lauffenburger,et al.  Physicochemical modelling of cell signalling pathways , 2006, Nature Cell Biology.

[18]  Frank Noé,et al.  ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments , 2013, PloS one.