Approximate Exponential Algorithms to Solve the Chemical Master Equation

被引：1
|
作者：
Mooasvi, Azam [1 ]
Sandu, Adrian [1 ]
机构：
[1] Virginia Polytech Inst & State Univ, Dept Comp Sci, Sci Computat Lab, Blacksburg, VA 24060 USA
来源：
MATHEMATICAL MODELLING AND ANALYSIS | 2015年 / 20卷 / 03期
基金：
美国国家科学基金会;
关键词：
stochastic simulation algorithm; exact solution; tau-leap; stochastic chemical kinetics; chemical master equation; STOCHASTIC SIMULATION; STABILITY;
D O I：
10.3846/13926292.2015.1048760
中图分类号：
O1 [数学];
学科分类号：
0701 ; 070101 ;
摘要：
This paper discusses new simulation algorithms for stochastic chemical kinetics that exploit the linearity of the chemical master equation and its matrix exponential exact solution. These algorithms make use of various approximations of the matrix exponential to evolve probability densities in time. A sampling of the approximate solutions of the chemical master equation is used to derive accelerated stochastic simulation algorithms. Numerical experiments compare the new methods with the established stochastic simulation algorithm and the tau-leaping method.
引用
收藏
页码：382 / 395
页数：14
相关论文
共 50 条
  • [41] Using simulated annealing algorithms to solve the Schrodinger equation in muonic atoms
    Kardaras, I. S.
    Kosmas, O. T.
    [J]. 3RD INTERNATIONAL CONFERENCE ON MATHEMATICAL MODELING IN PHYSICAL SCIENCES (IC-MSQUARE 2014), 2015, 574
  • [42] Optimization of adaptive direct algorithms for approximate solution of integral equation
    Ma, W
    [J]. JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS, 2006, 315 (01) : 167 - 175
  • [43] RADIAL BASIS FUNCTION COLLOCATION FOR THE CHEMICAL MASTER EQUATION
    Zhang, Jingwei
    Watson, Layne T.
    Beattie, Christopher A.
    Cao, Yang
    [J]. INTERNATIONAL JOURNAL OF COMPUTATIONAL METHODS, 2010, 7 (03) : 477 - 498
  • [44] Sparse grids and hybrid methods for the chemical master equation
    Markus Hegland
    Andreas Hellander
    Per Lötstedt
    [J]. BIT Numerical Mathematics, 2008, 48
  • [45] Robust Moment Closure Method for the Chemical Master Equation
    Naghnaeian, Mohammad
    Del Vecchio, Domitilla
    [J]. 2017 IEEE CONFERENCE ON CONTROL TECHNOLOGY AND APPLICATIONS (CCTA 2017), 2017, : 967 - 972
  • [46] Reducing a chemical master equation by invariant manifold methods
    Roussel, MR
    Zhu, R
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (18): : 8716 - 8730
  • [47] MULTISCALE MODELING OF CHEMICAL KINETICS VIA THE MASTER EQUATION
    Macnamara, Shev
    Burrage, Kevin
    Sidje, Roger B.
    [J]. MULTISCALE MODELING & SIMULATION, 2008, 6 (04): : 1146 - 1168
  • [48] Modeling bursty transcription and splicing with the chemical master equation
    Gorin, Gennady
    Pachter, Lior
    [J]. BIOPHYSICAL JOURNAL, 2022, 121 (06) : 1056 - 1069
  • [49] Solving the chemical master equation by aggregation and Krylov approximations
    Vo, Huy D.
    Sidje, Roger B.
    [J]. 2016 IEEE 55TH CONFERENCE ON DECISION AND CONTROL (CDC), 2016, : 7093 - 7098
  • [50] Structure-preserving discretization of the chemical master equation
    Ludwig Gauckler
    Harry Yserentant
    [J]. BIT Numerical Mathematics, 2017, 57 : 753 - 770
12345