The URDME manual Version 1.3
作者： Stefan Engblom , Pavol Bauer
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摘要: We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows more flexible handling complicated geometries and curved boundaries compared to simulations structured, cartesian The underlying algorithm is the next subvolume method, extended meshes by obtaining jump coefficients from finite element formulation corresponding macroscopic equation. This manual describes version 1.3 software. URDME includes support Comsol Multiphysics 5.x PDE Toolbox 1.5 above.
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harvard.edu参考文章(27)
Andreas Hellander, Numerical simulation of well stirred biochemical reaction networks governed by the master equation Uppsala University. ,(2008)
Stefan Engblom, Numerical Solution Methods in Stochastic Chemical Kinetics Acta Universitatis Upsaliensis. ,(2008)
Stefan Engblom, Galerkin spectral method applied to the chemical master equation Communications in Computational Physics. ,vol. 5, pp. 871- 896 ,(2009)
Paul Sjöberg, Numerical Methods for Stochastic Modeling of Genes and Proteins Acta Universitatis Upsaliensis. ,(2007)
Naama Barkai, Stanislas Leibler, Circadian clocks limited by noise Nature. ,vol. 403, pp. 267- 268 ,(2000) , 10.1038/35002258
Andreas Hellander, Brian Drawert, Stefan Engblom, Pavol Bauer, URDME v. 1.2: User's manual arXiv: Molecular Networks. ,(2009)
Harley H McAdams, Adam Arkin, None, It’s a noisy business! Genetic regulation at the nanomolar scale Trends in Genetics. ,vol. 15, pp. 65- 69 ,(1999) , 10.1016/S0168-9525(98)01659-X
Christopher V. Rao, Adam P. Arkin, Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm The Journal of Chemical Physics. ,vol. 118, pp. 4999- 5010 ,(2003) , 10.1063/1.1545446
J. Elf, M. Ehrenberg, Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases Systems Biology. ,vol. 1, pp. 230- 236 ,(2004) , 10.1049/SB:20045021