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Volumn 9, Issue 70, 2012, Pages 859-868

The two-regime method for optimizing stochastic reaction-diffusion simulations

Author keywords

Hybrid algorithm; Multi scale simulation; Reaction diffusion processes; Stochastic modelling

Indexed keywords

ALGORITHMS; CELL MEMBRANES; CYTOLOGY; DIFFUSION IN LIQUIDS; STOCHASTIC SYSTEMS;

EID: 84860779000     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2011.0574     Document Type: Article
Times cited : (95)

References (29)
  • 1
    • 72449190160 scopus 로고    scopus 로고
    • The role of spatial averaging in the precision of gene expression patterns
    • doi:10.1103/ PhysRevLett.103.258101
    • Erdmann, T., Howard, M. & ten Wolde, P. R. 2009 The role of spatial averaging in the precision of gene expression patterns. Phys. Rev. Lett. 103, 258101. (doi:10.1103/ PhysRevLett.103.258101)
    • (2009) Phys. Rev. Lett. , vol.103 , pp. 258101
    • Erdmann, T.1    Howard, M.2    Ten Wolde, P.R.3
  • 2
    • 77249093066 scopus 로고    scopus 로고
    • Spatio-temporal correlations can drastically change the response of a MAPK pathway
    • doi:10.1073/pnas.0906885107
    • Takahashi, K., Tǎ;nase-Nicola, S. & ten Wolde, P. R. 2010 Spatio-temporal correlations can drastically change the response of a MAPK pathway. Proc. Natl Acad. Sci. USA 107, 19 820-19 825. (doi:10.1073/pnas. 0906885107)
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 19820-19825
    • Takahashi, K.1    Tǎnase-Nicola, S.2    Ten Wolde, P.R.3
  • 3
    • 11144264728 scopus 로고    scopus 로고
    • Simulated diffusion of phosphorylated CHeY through the cytoplasm of Escherichia coli
    • doi:10.1128/JB.187.1.45-53.2005
    • Lipkow, K., Andrews, S. S. & Bray, D. 2005 Simulated diffusion of phosphorylated CHeY through the cytoplasm of Escherichia coli. J. Bacteriol. 187, 45-53. (doi:10.1128/JB.187.1.45-53.2005)
    • (2005) J. Bacteriol. , vol.187 , pp. 45-53
    • Lipkow, K.1    Andrews, S.S.2    Bray, D.3
  • 4
    • 33745591124 scopus 로고    scopus 로고
    • Noise-induced Min phenotypes in E. coli
    • doi:10.1371/journal.pcbi.0020080
    • Fange, D. & Elf, J. 2006 Noise-induced Min phenotypes in E. coli. PLoS Comput. Biol. 2, 637-648. (doi:10.1371/journal.pcbi.0020080)
    • (2006) PLoS Comput. Biol. , vol.2 , pp. 637-648
    • Fange, D.1    Elf, J.2
  • 5
    • 0035371624 scopus 로고    scopus 로고
    • Whole-cell simulation: A grand challenge of the 21st century
    • doi:10.1016/S0167-7799(01)01636-5
    • Tomita, M. 2001 Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19, 205-210. (doi:10.1016/S0167-7799(01)01636-5)
    • (2001) Trends Biotechnol. , vol.19 , pp. 205-210
    • Tomita, M.1
  • 7
    • 70350729439 scopus 로고    scopus 로고
    • Stochastic modelling of reaction-diffusion processes: Algorithms for bimolecular reactions
    • doi:10.1088/1478-3975/6/4/046001
    • Erban, R. & Chapman, J. 2009 Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions. Phys. Biol. 6, 046001. (doi:10.1088/1478-3975/6/4/046001)
    • (2009) Phys. Biol. , vol.6 , pp. 046001
    • Erban, R.1    Chapman, J.2
  • 8
    • 78650556702 scopus 로고    scopus 로고
    • Stochastic reaction-diffusion kinetics in the microscopic limit
    • doi:10.1073/pnas.1006565107
    • Fange, D., Berg, O. G., Sjöberg, P. & Elf, J. 2010 Stochastic reaction-diffusion kinetics in the microscopic limit. Proc. Natl Acad. Sci. USA 107, 19 820-19 825.(doi:10.1073/pnas.1006565107)
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 19820-19825
    • Fange, D.1    Berg, O.G.2    Sjöberg, P.3    Elf, J.4
  • 9
    • 20844432892 scopus 로고    scopus 로고
    • Stochastic reaction-diffusion simulation with MesoRD
    • doi:10.1093/bioinformatics/bti431
    • Hattne, J., Fange, D. & Elf, J. 2005 Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 21, 2923-2924. (doi:10.1093/ bioinformatics/bti431)
    • (2005) Bioinformatics , vol.21 , pp. 2923-2924
    • Hattne, J.1    Fange, D.2    Elf, J.3
  • 10
    • 14844328879 scopus 로고    scopus 로고
    • SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: Analysis of simple networks
    • doi:10.1049/sb:20045017
    • Ander, M. 2004 SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst. Biol. 1, 129-138. (doi:10.1049/sb:20045017)
    • (2004) Syst. Biol. , vol.1 , pp. 129-138
    • Ander, M.1
  • 11
    • 67649365828 scopus 로고    scopus 로고
    • The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target
    • doi:10.1137/070705039
    • Isaacson, S. A. 2009 The reaction-diffusion master equation as an asymptotic approximation of diffusion to a small target. SIAM J. Appl. Math. 70, 77-110. (doi:10.1137/070705039)
    • (2009) SIAM J. Appl. Math. , vol.70 , pp. 77-110
    • Isaacson, S.A.1
  • 12
    • 73649105850 scopus 로고    scopus 로고
    • Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials
    • doi:10.1103/Phys-RevE.80.066106
    • Isaacson, S. A. & Isaacson, D. 2009 Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials. Phys. Rev. E 80, 066106. (doi:10.1103/Phys-RevE.80.066106)
    • (2009) Phys. Rev. E , vol.80 , pp. 066106
    • Isaacson, S.A.1    Isaacson, D.2
  • 13
    • 33748520215 scopus 로고    scopus 로고
    • Stochastic simulation of chemical reactions with spatial resolution and single molecular detail
    • doi:10.1088/1478-3967/1/3/001
    • Andrews, S. S. & Bray, D. 2004 Stochastic simulation of chemical reactions with spatial resolution and single molecular detail. Phys. Biol. 1, 137-151. (doi:10.1088/1478-3967/1/3/001)
    • (2004) Phys. Biol. , vol.1 , pp. 137-151
    • Andrews, S.S.1    Bray, D.2
  • 14
    • 77950833499 scopus 로고    scopus 로고
    • Detailed simulations of cell biology with Smoldyn 2.1
    • doi:10.1371/journal.pcbi.1000705
    • Andrews, S. S., Addy, N. J., Brent, R. & Arkin, A. P. 2010 Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput. Biol. 6, e1000705. (doi:10.1371/journal.pcbi.1000705)
    • (2010) PLoS Comput. Biol. , vol.6
    • Andrews, S.S.1    Addy, N.J.2    Brent, R.3    Arkin, A.P.4
  • 15
    • 85057660342 scopus 로고    scopus 로고
    • Monte Carlo methods for simulating realistic synaptic microphysiology using MCell
    • ed. E. De Schutter, Boca Raton, FL: CRC Press
    • Stiles, J. R. & Bartol, T. M. 2001 Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In Computational neuroscience: realistic modeling for experimentalists (ed. E. De Schutter), pp. 87-127. Boca Raton, FL: CRC Press.
    • (2001) Computational Neuroscience: Realistic Modeling for Experimentalists , pp. 87-127
    • Stiles, J.R.1    Bartol, T.M.2
  • 16
    • 55149086309 scopus 로고    scopus 로고
    • Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces
    • doi:10.1137/070692017
    • Kerr, R. A., Bartol, T. M., Kaminsky, B., Dittrich, M., Chang, J.-C. J., Baden, S. B., Sejnowski, T. J. & Stiles, J. R. 2008 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM J. Sci. Comput. 30, 3126-3126. (doi:10.1137/070692017)
    • (2008) SIAM J. Sci. Comput. , vol.30 , pp. 3126-3126
    • Kerr, R.A.1    Bartol, T.M.2    Kaminsky, B.3    Dittrich, M.4    Chang, J.-C.J.5    Baden, S.B.6    Sejnowski, T.J.7    Stiles, J.R.8
  • 17
    • 18244404300 scopus 로고    scopus 로고
    • Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics
    • doi:10.1103/PhysRevLett.94.128103
    • van Zon, J. S. & ten Wolde, P. R. 2005 Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics. Phys. Rev. Lett. 94, 128103. (doi:10.1103/PhysRevLett.94.128103)
    • (2005) Phys. Rev. Lett. , vol.94 , pp. 128103
    • Van Zon, J.S.1    Ten Wolde, P.R.2
  • 18
    • 34147128541 scopus 로고    scopus 로고
    • Reactive boundary conditions for stochastic simulations of reaction-diffusion processes
    • doi:10.1088/1478-3975/4/1/003
    • Erban, R. & Chapman, J. 2007 Reactive boundary conditions for stochastic simulations of reaction-diffusion processes. Phys. Biol. 4, 16-28. (doi:10.1088/1478-3975/4/1/003)
    • (2007) Phys. Biol. , vol.4 , pp. 16-28
    • Erban, R.1    Chapman, J.2
  • 20
    • 0033031386 scopus 로고    scopus 로고
    • E-Cell software environment for whole-cell simulation
    • doi:10.1093/bioinformatics/15.1.72
    • Tomita, M. et al. 1999 E-Cell software environment for whole-cell simulation. Bioinformatics 15, 72-84. (doi:10.1093/bioinformatics/15.1.72)
    • (1999) Bioinformatics , vol.15 , pp. 72-84
    • Tomita, M.1
  • 21
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • doi:10.1021/j100540a008
    • Gillespie, D. 1977 Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361. (doi:10.1021/j100540a008)
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.1
  • 22
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and channels
    • doi:10.1021/jp993732q
    • Gibson, M. & Bruck, J. 2000 Efficient exact stochastic simulation of chemical systems with many species and channels. J. Phys. Chem. A 104, 1876-1889. (doi:10.1021/jp993732q)
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1876-1889
    • Gibson, M.1    Bruck, J.2
  • 23
    • 79960351109 scopus 로고    scopus 로고
    • Analysis of Brownian dynamics simulations of reversible biomolecular reactions
    • doi:10.1137/100794213
    • Lipkova, J., Zygalakis, K. C., Chapman, S. J. & Erban, R. 2011 Analysis of Brownian dynamics simulations of reversible biomolecular reactions. SIAM J. Appl. Math. 71, 714-730. (doi:10.1137/100794213)
    • (2011) SIAM J. Appl. Math. , vol.71 , pp. 714-730
    • Lipkova, J.1    Zygalakis, K.C.2    Chapman, S.J.3    Erban, R.4
  • 24
    • 70450285537 scopus 로고    scopus 로고
    • Accurate particle-based simulation of adsorption, desorption and partial transmission
    • doi:10.1088/1478-3975/6/4/046015
    • Andrews, S. S. 2009 Accurate particle-based simulation of adsorption, desorption and partial transmission. Phys. Biol. 6, 046015. (doi:10.1088/1478- 3975/6/4/046015)
    • (2009) Phys. Biol. , vol.6 , pp. 046015
    • Andrews, S.S.1
  • 26
    • 34247619844 scopus 로고    scopus 로고
    • Fundamental limits of position determination by concentration gradients
    • Tostevin, F., ten Wolde, P. R. & Howard, M. 2007 Fundamental limits of position determination by concentration gradients. PLoS Comput. Biol. 3, 0763-0771.
    • (2007) PLoS Comput. Biol. , vol.3 , pp. 0763-0771
    • Tostevin, F.1    Ten Wolde, P.R.2    Howard, M.3
  • 27
    • 33846958053 scopus 로고    scopus 로고
    • Pre-steady-state decoding of the bicoid morphogen gradient
    • Bergmann, S. et al. 2007 Pre-steady-state decoding of the bicoid morphogen gradient. PLoS Comput. Biol. 5, 0232-0242.
    • (2007) PLoS Comput. Biol. , vol.5 , pp. 0232-0242
    • Bergmann, S.1
  • 28
    • 61849164660 scopus 로고    scopus 로고
    • Simulation of stochastic reaction-diffusion processes on unstructured meshes
    • doi:10.1137/080721388
    • Engblom, S., Ferm, L., Hellander, A. & Lötstedt, P. 2009 Simulation of stochastic reaction-diffusion processes on unstructured meshes. SIAM J. Sci. Comput. 31, 1774-1797. (doi:10.1137/080721388)
    • (2009) SIAM J. Sci. Comput. , vol.31 , pp. 1774-1797
    • Engblom, S.1    Ferm, L.2    Hellander, A.3    Lötstedt, P.4
  • 29
    • 33751568004 scopus 로고    scopus 로고
    • Incorporating diffusion in complex geometries into stochastic chemical kinetics simulations
    • doi:10.1137/040605060
    • Isaacson, S. A. & Peskin, C. S. 2007 Incorporating diffusion in complex geometries into stochastic chemical kinetics simulations. SIAM J. Sci. Comput. 28, 47-74. (doi:10.1137/040605060)
    • (2007) SIAM J. Sci. Comput. , vol.28 , pp. 47-74
    • Isaacson, S.A.1    Peskin, C.S.2


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