Chen W, De Schutter E. (2017). Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers. Frontiers in neuroinformatics. 11 [PubMed]

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References and models cited by this paper

Andrews SS, Bray D. (2004). Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Physical biology. 1 [PubMed]

Anwar H, Hepburn I, Nedelescu H, Chen W, De Schutter E. (2013). Stochastic calcium mechanisms cause dendritic calcium spike variability. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]

Anwar H et al. (2014). Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models. Frontiers in cellular neuroscience. 8 [PubMed]

Baden SB, Balls GT. (2004). A large scale monte carlo simulator for cellular microphysiology Proceedings of the 18th International Parallel and Distributed Processing Symposium.

Baden SB, Fink SJ, Kohn SR. (1998). Efficient run-time support for irregular block-structured applications J. Parallel Distrib. Comput.. 50

Bruck J, Gibson MA. (2000). Efficient exact stochastic simulation of chemical systems with many species and many channels J. Phys. Chem.. 104

Coupez T, Digonnet H, Ducloux R. (2000). Parallel meshing and remeshing Appl. Math. Model.. 25

D'Agostino D et al. (2014). Parallel solutions for voxel-based simulations of reaction-diffusion systems. BioMed research international. 2014 [PubMed]

Dematté L. (2012). Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations. IEEE/ACM transactions on computational biology and bioinformatics. 9 [PubMed]

Dematté L, Mazza T. (2008). On Parallel Stochastic Simulation of Diffusive Systems Computational Methods in Systems Biology Lecture Notes in Computer Science.

Drawert B, Engblom S, Hellander A. (2012). URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. BMC systems biology. 6 [PubMed]

Et AL, Gladkov DV. (2011). Accelerating the Smoldyn spatial stochastic biochemical reaction network simulator using GPUs Proceedings of the 19th High Performance C. Symposia. Society for Computer Simulation International.

Gillespie DT. (1976). A General method for numerically simulating the stochastic time evolution of coupledchemical reactions J Comput Phys. 22

Gillespie DT. (2001). Approximate accelerated stochastic simulation of chemically reacting systems The Journal Of Chemical Physics. 115

Hattne J, Fange D, Elf J. (2005). Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics (Oxford, England). 21 [PubMed]

Hepburn I, Cannon R, De Schutter E. (2013). Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS. Frontiers in computational neuroscience. 7 [PubMed]

Hepburn I, Chen W, De Schutter E. (2016). Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations. The Journal of chemical physics. 145 [PubMed]

Hepburn I, Chen W, Wils S, De Schutter E. (2012). STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC systems biology. 6 [PubMed]

Hines ML et al. (2015). NTW-MT: a multi-threaded simulator for reaction diffusion simulations in neuron Proceedings of the 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (London, UK).

Kerr RA et al. (2008). FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES. SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics. 30 [PubMed]

Koh W, Blackwell KT. (2011). An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping. The Journal of chemical physics. 134 [PubMed]

Markram H. (2012). The human brain project. Scientific American. 306 [PubMed]

Marquez-Lago TT, Burrage K. (2007). Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics. The Journal of chemical physics. 127 [PubMed]

McDougal RA, Shepherd GM. (2015). 3D-printer visualization of neuron models. Frontiers in neuroinformatics. 9 [PubMed]

Oliveira RF et al. (2010). The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PloS one. 5 [PubMed]

Roberts E, Stone JE, Luthey-Schulten Z. (2013). Lattice Microbes: highperformance stochastic simulation method for the reaction-diffusion master equation J. Comput. Chem.. 34

Rodríguez JV, Kaandorp JA, Dobrzyński M, Blom JG. (2006). Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinformatics (Oxford, England). 22 [PubMed]

Schnakenberg J, Fricke T. (1991). Monte-Carlo simulation of an inhomogeneous reaction-diffusion system in the biophysics of receptor cells Z. Phy. B Condens. Matter. 83

Slepoy A, Thompson AP, Plimpton SJ. (2008). A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks. The Journal of chemical physics. 128 [PubMed]

Vigelius M, Lane A, Meyer B. (2011). Accelerating reaction-diffusion simulations with general-purpose graphics processing units. Bioinformatics (Oxford, England). 27 [PubMed]

Wang B, Zhao Y, Yao Y, Hou B, Peng S. (2009). Experimental analysis of optimistic synchronization algorithms for parallel simulation of reaction-diffusion systems International Workshop on High Performance Computational Systems Biology, (Trento).

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