-
1
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
10.1016/0021-9991(76)90041-3
-
D. T. Gillespie, " A general method for numerically simulating the stochastic time evolution of coupled chemical reactions.," J. Comput. Phys. 22 (4), 403-434 (1976). 10.1016/0021-9991(76)90041-3
-
(1976)
J. Comput. Phys.
, vol.22
, Issue.4
, pp. 403-434
-
-
Gillespie, D.T.1
-
2
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
10.1021/j100540a008
-
D. T. Gillespie, " Exact stochastic simulation of coupled chemical reactions.," J. Phys. Chem. 81 (25), 2340-2361 (1977). 10.1021/j100540a008
-
(1977)
J. Phys. Chem.
, vol.81
, Issue.25
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
3
-
-
0001455869
-
The relationship between stochastic and deterministic models for chemical reactions
-
10.1063/1.1678692
-
T. G. Kurtz, " The relationship between stochastic and deterministic models for chemical reactions.," J. Chem. Phys. 57 (7), 2976-2978 (1972). 10.1063/1.1678692
-
(1972)
J. Chem. Phys.
, vol.57
, Issue.7
, pp. 2976-2978
-
-
Kurtz, T.G.1
-
4
-
-
77952668745
-
From microscopic to macroscopic descriptions of cell migration on growing domains
-
10.1007/s11538-009-9467-x
-
R. E. Baker, C. A. Yates, and R. Erban, " From microscopic to macroscopic descriptions of cell migration on growing domains.," Bull. Math. Biol. 72 (3), 719-762 (2010). 10.1007/s11538-009-9467-x
-
(2010)
Bull. Math. Biol.
, vol.72
, Issue.3
, pp. 719-762
-
-
Baker, R.E.1
Yates, C.A.2
Erban, R.3
-
5
-
-
20844455677
-
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases
-
10.1049/sb:20045021
-
J. Elf and M. Ehrenberg, " Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases.," Syst. Biol. 1 (2), 230-236 (2004). 10.1049/sb:20045021
-
(2004)
Syst. Biol.
, vol.1
, Issue.2
, pp. 230-236
-
-
Elf, J.1
Ehrenberg, M.2
-
6
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
-
A. Arkin, J. Ross, and H. H. McAdams, " Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells.," Genetics 149 (4), 1633-1648 (1998).
-
(1998)
Genetics
, vol.149
, Issue.4
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
7
-
-
0022429106
-
R control system of bacteriophage lambda. A physical-chemical model for gene regulation
-
10.1016/0022-2836(85)90086-5
-
R control system of bacteriophage lambda. A physical-chemical model for gene regulation.," J. Mol. Biol. 181 (2), 211-230 (1985). 10.1016/0022-2836(85)90086-5
-
(1985)
J. Mol. Biol.
, vol.181
, Issue.2
, pp. 211-230
-
-
Shea, M.A.1
Ackers, G.K.2
-
8
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
10.1021/jp993732q
-
M. A. Gibson and J. Bruck, " Efficient exact stochastic simulation of chemical systems with many species and many channels.," J. Phys. Chem. A. 104 (9), 1876-1889 (2000). 10.1021/jp993732q
-
(2000)
J. Phys. Chem. A.
, vol.104
, Issue.9
, pp. 1876-1889
-
-
Gibson, M.A.1
Bruck, J.2
-
9
-
-
0035710725
-
Feedback regulation of the heat shock response in E. coli
-
in (IEEE), Vol
-
H. Kurata, H. El-Samad, T. M. Yi, M. Khammash, and J. Doyle, " Feedback regulation of the heat shock response in E. coli.," in Proceedings of the 40th IEEE Conference on Decision and Control (2001) (IEEE, 2001), Vol. 1, pp. 837-842.
-
(2001)
Proceedings of the 40th IEEE Conference on Decision and Control (2001)
, vol.1
, pp. 837-842
-
-
Kurata, H.1
El-Samad, H.2
Yi, T.M.3
Khammash, M.4
Doyle, J.5
-
10
-
-
23944491675
-
Avoiding negative populations in explicit Poisson tau-leaping
-
10.1063/1.1992473
-
Y. Cao, D. T. Gillespie, and L. R. Petzold, " Avoiding negative populations in explicit Poisson tau-leaping.," J. Chem. Phys. 123 (5), 054104 (2005). 10.1063/1.1992473
-
(2005)
J. Chem. Phys.
, vol.123
, Issue.5
, pp. 054104
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
11
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
10.1063/1.1378322
-
D. T. Gillespie, " Approximate accelerated stochastic simulation of chemically reacting systems.," J. Chem. Phys. 115 (4), 1716-1733 (2001). 10.1063/1.1378322
-
(2001)
J. Chem. Phys.
, vol.115
, Issue.4
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
12
-
-
79952080934
-
Look before you leap: A confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping
-
10.1063/1.3554385
-
C. A. Yates and K. Burrage, " Look before you leap: A confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping.," J. Chem. Phys. 134 (8), 084109 (2011). 10.1063/1.3554385
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.8
, pp. 084109
-
-
Yates, C.A.1
Burrage, K.2
-
13
-
-
84874889449
-
-
Note that in ste5 of the original DM algorithm and ste4 of our revised algorithm, in the case j = 1 we assume ∑j′=10=0
-
Note that in step 5 of the original DM algorithm and step 4 of our revised algorithm, in the case j = 1 we assume ∑j′=10=0.
-
-
-
-
14
-
-
36849077107
-
A modified next reaction method for simulating chemical systems with time dependent propensities and delays
-
10.1063/1.2799998
-
D. F. Anderson, " A modified next reaction method for simulating chemical systems with time dependent propensities and delays.," J. Chem. Phys. 127 (21), 214107 (2007). 10.1063/1.2799998
-
(2007)
J. Chem. Phys.
, vol.127
, Issue.21
, pp. 214107
-
-
Anderson, D.F.1
-
15
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
10.1063/1.1778376
-
Y. Cao, H. Li, and L. Petzold, " Efficient formulation of the stochastic simulation algorithm for chemically reacting systems.," J. Chem. Phys. 121 (9), 4059-4067 (2004). 10.1063/1.1778376
-
(2004)
J. Chem. Phys.
, vol.121
, Issue.9
, pp. 4059-4067
-
-
Cao, Y.1
Li, H.2
Petzold, L.3
-
16
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
10.1146/annurev.physchem.58.032806.104637
-
D. T. Gillespie, " Stochastic simulation of chemical kinetics.," Annu. Rev. Phys. Chem. 58 (1), 35-55 (2007). 10.1146/annurev.physchem.58.032806.104637
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, Issue.1
, pp. 35-55
-
-
Gillespie, D.T.1
-
17
-
-
31344458755
-
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
-
10.1016/j.compbiolchem.2005.10.007
-
J. M. McCollum, G. D. Peterson, C. D. Cox, M. L. Simpson, and N. F. Samatova, " The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior.," Comput. Biol. Chem. 30 (1), 39-49 (2006). 10.1016/j.compbiolchem.2005.10.007
-
(2006)
Comput. Biol. Chem.
, vol.30
, Issue.1
, pp. 39-49
-
-
McCollum, J.M.1
Peterson, G.D.2
Cox, C.D.3
Simpson, M.L.4
Samatova, N.F.5
-
19
-
-
84855375396
-
Fat vs. thin threading approach on GPUs: Application to stochastic simulation of chemical reactions
-
10.1109/TPDS.2011.157
-
G. Klingbeil, R. Erban, M. Giles, and P. K. Maini, " Fat vs. thin threading approach on GPUs: Application to stochastic simulation of chemical reactions.," IEEE Trans. Parallel Distrib. Syst. 23 (2), 280-287 (2012). 10.1109/TPDS.2011.157
-
(2012)
IEEE Trans. Parallel Distrib. Syst.
, vol.23
, Issue.2
, pp. 280-287
-
-
Klingbeil, G.1
Erban, R.2
Giles, M.3
Maini, P.K.4
-
20
-
-
84874907995
-
-
Note that the ordering of these steps is interchangeable in the original algorithm, but will not be so in our revised method
-
Note that the ordering of these steps is interchangeable in the original algorithm, but will not be so in our revised method.
-
-
-
-
21
-
-
34548237327
-
TestU01: A C library for empirical testing of random number generators
-
(article 22). 10.1145/1268776.1268777
-
P. L'Ecuyer and R. Simard, " TestU01: A C library for empirical testing of random number generators.," ACM Trans. Math. Softw. 33 (4) (2007) (article 22). 10.1145/1268776.1268777
-
(2007)
ACM Trans. Math. Softw.
, vol.33
, Issue.4
-
-
L'Ecuyer, P.1
Simard, R.2
-
24
-
-
84874825675
-
-
The Marsaglia Random Number CDROM, The Diehard Battery of Tests of Randomness
-
G. Marsaglia, The Marsaglia Random Number CDROM, The Diehard Battery of Tests of Randomness, 1995.
-
(1995)
-
-
Marsaglia, G.1
-
25
-
-
0347666758
-
Some difficult-to-pass tests of randomness
-
G. Marsaglia and W. W. Tsang, " Some difficult-to-pass tests of randomness.," J. Stat. Software 7 (3), 1-9 (2002).
-
(2002)
J. Stat. Software
, vol.7
, Issue.3
, pp. 1-9
-
-
Marsaglia, G.1
Tsang, W.W.2
-
26
-
-
84874928568
-
-
A statistical test suite for random and pseudorandom number generators for cryptographic applications
-
A. Rukhin, J. Soto, J. Nechvatal, M. Smid, and E. Barker, A statistical test suite for random and pseudorandom number generators for cryptographic applications, 2001.
-
(2001)
-
-
Rukhin, A.1
Soto, J.2
Nechvatal, J.3
Smid, M.4
Barker, E.5
-
27
-
-
38349167535
-
The SBML discrete stochastic models test suite
-
10.1093/bioinformatics/btm566
-
T. W. Evans, C. S. Gillespie, and D. J. Wilkinson, " The SBML discrete stochastic models test suite.," Bioinformatics 24 (2), 285-286 (2008). 10.1093/bioinformatics/btm566
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 285-286
-
-
Evans, T.W.1
Gillespie, C.S.2
Wilkinson, D.J.3
-
28
-
-
0037197850
-
Mechanisms of noise-resistance in genetic oscillators
-
10.1073/pnas.092133899
-
J. M. G. Vilar, H. Y. Kueh, N. Barkai, and S. Leibler, " Mechanisms of noise-resistance in genetic oscillators.," Proc. Natl. Acad. Sci. U.S.A. 99 (9), 5988-5992 (2002). 10.1073/pnas.092133899
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, Issue.9
, pp. 5988-5992
-
-
Vilar, J.M.G.1
Kueh, H.Y.2
Barkai, N.3
Leibler, S.4
-
30
-
-
0031599142
-
Mersenne twister: A 623-dimensionally equidistributed uniform pseudo-random number generator
-
10.1145/272991.272995
-
M. Matsumoto and T. Nishimura, " Mersenne twister: A 623-dimensionally equidistributed uniform pseudo-random number generator.," ACM Trans. Model. Comput. Simul. 8 (1), 3-30 (1998). 10.1145/272991.272995
-
(1998)
ACM Trans. Model. Comput. Simul.
, vol.8
, Issue.1
, pp. 3-30
-
-
Matsumoto, M.1
Nishimura, T.2
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