用于高效模拟随机反应扩散主方程的扩散有限状态投影算法。
The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.
机构信息
Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
出版信息
J Chem Phys. 2010 Feb 21;132(7):074101. doi: 10.1063/1.3310809.
Abstract
We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.
摘要
我们开发了一种用于准确高效模拟随机空间不均匀生物化学系统的计算框架。新的计算方法采用分数步混合策略。引入了一种新的有限状态投影 (FSP) 方法的公式，称为扩散 FSP 方法，用于有效准确地模拟扩散传输。反应由随机模拟算法处理。
相似文献
1
The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.用于高效模拟随机反应扩散主方程的扩散有限状态投影算法。
J Chem Phys. 2010 Feb 21;132(7):074101. doi: 10.1063/1.3310809.
2
Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm.基于随机模拟算法，通过快速自适应有限状态投影求解化学主方程。
Math Biosci. 2015 Nov;269:10-6. doi: 10.1016/j.mbs.2015.08.010. Epub 2015 Aug 28.
3
The finite state projection algorithm for the solution of the chemical master equation.用于求解化学主方程的有限状态投影算法。
J Chem Phys. 2006 Jan 28;124(4):044104. doi: 10.1063/1.2145882.
4
Fractional diffusion-reaction stochastic simulations.分数阶扩散-反应随机模拟。
J Chem Phys. 2013 Mar 14;138(10):104117. doi: 10.1063/1.4794696.
5
Multiscale Stochastic Reaction-Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations.多尺度随机反应扩散算法，结合马尔可夫链模型与随机偏微分方程。
Bull Math Biol. 2019 Aug;81(8):3185-3213. doi: 10.1007/s11538-019-00613-0. Epub 2019 Jun 4.
6
The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems.用于反应扩散系统离散随机模拟的多项模拟算法。
J Chem Phys. 2009 Mar 7;130(9):094104. doi: 10.1063/1.3074302.
7
A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems.一种用于反应扩散系统的微观介观随机模拟的混合方法。
Math Biosci. 2019 Jun;312:23-32. doi: 10.1016/j.mbs.2019.04.001. Epub 2019 Apr 15.
8
A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions.一种针对具有与生成时间相关的双分子速率函数的生化系统的主方程和矩方法。
J Chem Phys. 2014 Dec 7;141(21):214108. doi: 10.1063/1.4902239.
9
The Linear Noise Approximation for Spatially Dependent Biochemical Networks.具有空间相关性的生物化学网络的线性噪声逼近。
Bull Math Biol. 2019 Aug;81(8):2873-2901. doi: 10.1007/s11538-018-0428-0. Epub 2018 Apr 11.
10
An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems.一种用于生化系统随机模型灵敏度分析的高效有限差分策略。
Biosystems. 2017 Jan;151:43-52. doi: 10.1016/j.biosystems.2016.11.006. Epub 2016 Nov 30.
引用本文的文献
1
Accurate and efficient discretizations for stochastic models providing near agent-based spatial resolution at low computational cost.在低计算成本下提供接近基于主体的空间分辨率的随机模型的精确且高效的离散化。
J R Soc Interface. 2019 Oct 31;16(159):20190421. doi: 10.1098/rsif.2019.0421. Epub 2019 Oct 23.
2
BioSimulator.jl: Stochastic simulation in Julia.BioSimulator.jl：Julia 中的随机模拟。
Comput Methods Programs Biomed. 2018 Dec;167:23-35. doi: 10.1016/j.cmpb.2018.09.009. Epub 2018 Oct 10.
3
Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems.基于数据驱动的方法高效刻画生物化学系统稀有事件概率。
Bull Math Biol. 2019 Aug;81(8):3097-3120. doi: 10.1007/s11538-018-0509-0. Epub 2018 Sep 17.
4
Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.空间随机细胞内动力学：建模方法综述。
Bull Math Biol. 2019 Aug;81(8):2960-3009. doi: 10.1007/s11538-018-0443-1. Epub 2018 May 21.
5
MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.MOLNs：一个使用PyURDME在系统生物学中进行交互式、可重复且可扩展的空间随机计算实验的云平台。
SIAM J Sci Comput. 2016;38(3):C179-C202. doi: 10.1137/15M1014784. Epub 2016 Jun 1.
6
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.随机模拟服务：弥合计算专家与生物学家之间的差距。
PLoS Comput Biol. 2016 Dec 8;12(12):e1005220. doi: 10.1371/journal.pcbi.1005220. eCollection 2016 Dec.
7
SParSE++: improved event-based stochastic parameter search.SParSE++：改进的基于事件的随机参数搜索
BMC Syst Biol. 2016 Nov 25;10(1):109. doi: 10.1186/s12918-016-0367-z.
8
A framework for discrete stochastic simulation on 3D moving boundary domains.三维移动边界域上离散随机模拟的一个框架。
J Chem Phys. 2016 Nov 14;145(18):184113. doi: 10.1063/1.4967338.
9
A hybrid continuous-discrete method for stochastic reaction-diffusion processes.一种用于随机反应扩散过程的混合连续-离散方法。
R Soc Open Sci. 2016 Sep 14;3(9):160485. doi: 10.1098/rsos.160485. eCollection 2016 Sep.
10
Cox process representation and inference for stochastic reaction-diffusion processes.Cox 过程表示和随机反应扩散过程的推断。
Nat Commun. 2016 May 25;7:11729. doi: 10.1038/ncomms11729.
本文引用的文献
1
ANALYSIS AND DESIGN OF JUMP COEFFICIENTS IN DISCRETE STOCHASTIC DIFFUSION MODELS.离散随机扩散模型中跳跃系数的分析与设计
SIAM J Sci Comput. 2016;38(1):A55-A83. doi: 10.1137/15M101110X. Epub 2016 Jan 6.
2
Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients.基于空间梯度的酵母细胞极化诱导建模稳健性权衡。
PLoS One. 2008 Sep 1;3(9):e3103. doi: 10.1371/journal.pone.0003103.
3
Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions.反应扩散过程的随机建模：双分子反应算法
Phys Biol. 2009 Aug 21;6(4):046001. doi: 10.1088/1478-3975/6/4/046001.
4
The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems.用于反应扩散系统离散随机模拟的多项模拟算法。
J Chem Phys. 2009 Mar 7;130(9):094104. doi: 10.1063/1.3074302.
5
A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks.一种用于模拟大型生化反应网络的恒时动力学蒙特卡罗算法。
J Chem Phys. 2008 May 28;128(20):205101. doi: 10.1063/1.2919546.
6
Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.用于化学动力学的二项式τ跳跃空间随机模拟算法。
J Chem Phys. 2007 Sep 14;127(10):104101. doi: 10.1063/1.2771548.
7
Reduction and solution of the chemical master equation using time scale separation and finite state projection.使用时间尺度分离和有限状态投影对化学主方程进行约化与求解。
J Chem Phys. 2006 Nov 28;125(20):204104. doi: 10.1063/1.2397685.
8
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases.双稳态生化系统自发分离成相反相的空间域。
Syst Biol (Stevenage). 2004 Dec;1(2):230-6. doi: 10.1049/sb:20045021.
9
Stochastic simulation of chemical kinetics.化学动力学的随机模拟。
Annu Rev Phys Chem. 2007;58:35-55. doi: 10.1146/annurev.physchem.58.032806.104637.
10
Noise-induced Min phenotypes in E. coli.大肠杆菌中噪声诱导的微小表型。
PLoS Comput Biol. 2006 Jun 30;2(6):e80. doi: 10.1371/journal.pcbi.0020080. Epub 2006 May 18.
Zotero 插件