-
1
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
McAdams H., and Arkin A. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA 94 (1997) 814-819
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 814-819
-
-
McAdams, H.1
Arkin, A.2
-
2
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected escherichia coli cells
-
Arkin A., Ross J., and McAdams H. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected escherichia coli cells. Genetics 149 (1998) 1633-1648
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.3
-
3
-
-
0033083733
-
It's a noisy business!
-
McAdams H.H., and Arkin A. It's a noisy business!. Trends Genet. 15 2 (1999) 65-69
-
(1999)
Trends Genet.
, vol.15
, Issue.2
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
4
-
-
0037119578
-
Small numbers of big molecules
-
Fedoroff N., and Fontana W. Small numbers of big molecules. Science 297 (2002) 1129-1131
-
(2002)
Science
, vol.297
, pp. 1129-1131
-
-
Fedoroff, N.1
Fontana, W.2
-
5
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie D. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22 (1976) 403-434
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 403-434
-
-
Gillespie, D.1
-
6
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
-
(1977)
J. Phys. Chem.
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.1
-
7
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson M., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104 (2000) 1876
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 1876
-
-
Gibson, M.1
Bruck, J.2
-
8
-
-
4644266081
-
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
-
Cao Y., Li H., and Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J. Chem. Phys. 121 (2004) 4059-4067
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 4059-4067
-
-
Cao, Y.1
Li, H.2
Petzold, L.3
-
9
-
-
0004003433
-
-
SIAM, Philadelphia, Pa
-
Brenan K.E., Campbell S.L., and Petzold L.R. Numerical Solution of Initial-Value Problems in Differential-Algebraic Equations. second ed. (1996), SIAM, Philadelphia, Pa
-
(1996)
Numerical Solution of Initial-Value Problems in Differential-Algebraic Equations. second ed.
-
-
Brenan, K.E.1
Campbell, S.L.2
Petzold, L.R.3
-
10
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie D. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 (2001) 1716
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 1716
-
-
Gillespie, D.1
-
11
-
-
0942279178
-
Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method
-
Rathinam M., Petzold L., Cao Y., and Gillespie D. Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method. J. Chem. Phys. 119 (2003) 12784-12794
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 12784-12794
-
-
Rathinam, M.1
Petzold, L.2
Cao, Y.3
Gillespie, D.4
-
12
-
-
48849096900
-
-
Y. Cao, L. Petzold, Trapezoidal tau-leaping formula for the stochastic simulation of chemically reacting systems, in: Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), 2005, pp. 149-152.
-
Y. Cao, L. Petzold, Trapezoidal tau-leaping formula for the stochastic simulation of chemically reacting systems, in: Proceedings of Foundations of Systems Biology in Engineering (FOSBE 2005), 2005, pp. 149-152.
-
-
-
-
13
-
-
33748419488
-
Consistency and stability of tau leaping schemes for chemical reaction systems
-
Rathinam M., Petzold L., Cao Y., and Gillespie D. Consistency and stability of tau leaping schemes for chemical reaction systems. SIAM Multiscale Model. 4 (2005) 867-895
-
(2005)
SIAM Multiscale Model.
, vol.4
, pp. 867-895
-
-
Rathinam, M.1
Petzold, L.2
Cao, Y.3
Gillespie, D.4
-
14
-
-
31544465969
-
Efficient stepsize selection for the tau-leaping method
-
Cao Y., Gillespie D., and Petzold L. Efficient stepsize selection for the tau-leaping method. J. Chem. Phys. 124 (2006) 044109
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 044109
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
15
-
-
34250754425
-
The adaptive explicit-implicit tau-leaping method with automatic tau selection
-
Cao Y., Gillespie D., and Petzold L. The adaptive explicit-implicit tau-leaping method with automatic tau selection. J. Chem. Phys. 126 (2007) 224101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 224101
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
16
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
Haseltine E., and Rawlings J. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys. 117 (2002) 6959-6969
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 6959-6969
-
-
Haseltine, E.1
Rawlings, J.2
-
17
-
-
1342309249
-
Hybrid simulation of cellular behavior
-
Mattheyses T., and Simmons M. Hybrid simulation of cellular behavior. Bioinformatics 20 (2004) 316-322
-
(2004)
Bioinformatics
, vol.20
, pp. 316-322
-
-
Mattheyses, T.1
Simmons, M.2
-
18
-
-
0035710725
-
-
H. Kurata, H. El-Samad, T. Yi, M. Khammash, J. Doyle, Feedback regulation of the heat shock response in E. Coli, in: Proceedings of the 40th IEEE Conference on Decision and Control, 2001, pp. 837-842.
-
H. Kurata, H. El-Samad, T. Yi, M. Khammash, J. Doyle, Feedback regulation of the heat shock response in E. Coli, in: Proceedings of the 40th IEEE Conference on Decision and Control, 2001, pp. 837-842.
-
-
-
-
19
-
-
48849114166
-
-
H. Kurata, M. Khammash, J. Doyle, Stochastic analysis of the heat shock response in E. Coli, in: 3rd International Conference on Systems Biology, 2002.
-
H. Kurata, M. Khammash, J. Doyle, Stochastic analysis of the heat shock response in E. Coli, in: 3rd International Conference on Systems Biology, 2002.
-
-
-
-
20
-
-
0010484096
-
Partial chemical equilibrium in fluid dynamics
-
Ramshaw J.D. Partial chemical equilibrium in fluid dynamics. Phys. Fluid 23 (1980)
-
(1980)
Phys. Fluid
, vol.23
-
-
Ramshaw, J.D.1
-
21
-
-
0041386562
-
The partial-equilibrium approximation in reacting flows
-
Rein M. The partial-equilibrium approximation in reacting flows. Phys. Fluids A 4 (1992)
-
(1992)
Phys. Fluids A
, vol.4
-
-
Rein, M.1
-
22
-
-
0024731820
-
The quasi-steady-state assumption: a case study in perturbation
-
Segel L.A., and Slemrod M. The quasi-steady-state assumption: a case study in perturbation. SIAM Rev. 31 (1989)
-
(1989)
SIAM Rev.
, vol.31
-
-
Segel, L.A.1
Slemrod, M.2
-
23
-
-
0037444724
-
Stochastic chemical kinetics and the quasi steady-state assumption: application to the Gillespie algorithm
-
Rao C., and Arkin A. Stochastic chemical kinetics and the quasi steady-state assumption: application to the Gillespie algorithm. J. Chem. Phys. 118 (2003) 4999-5010
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 4999-5010
-
-
Rao, C.1
Arkin, A.2
-
24
-
-
22944480262
-
The slow-scale stochastic simulation algorithm
-
Cao Y., Gillespie D., and Petzold L. The slow-scale stochastic simulation algorithm. J. Chem. Phys. 122 (2005) 014116
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 014116
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
25
-
-
3142543968
-
Binomial leap methods for simulating stochastic chemical kinetics
-
Tian T., and Burrage K. Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys. 121 (2004) 10356-10364
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 10356-10364
-
-
Tian, T.1
Burrage, K.2
-
26
-
-
22944469465
-
Binomial distribution based tau-leap accelerated stochastic simulation
-
Chatterjee A., Vlachos D.G., and Katsoulakis M.A. Binomial distribution based tau-leap accelerated stochastic simulation. J. Chem. Phys. 122 (2005) 024112
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 024112
-
-
Chatterjee, A.1
Vlachos, D.G.2
Katsoulakis, M.A.3
-
27
-
-
33847663281
-
Multinomial tau-leaping method for stochastic kinetic simulation
-
Pettigrew M., and Resat H. Multinomial tau-leaping method for stochastic kinetic simulation. J. Chem. Phys. 126 (2007) 084101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 084101
-
-
Pettigrew, M.1
Resat, H.2
-
28
-
-
23944491675
-
Avoiding negative populations in explicit tau leaping
-
Cao Y., Gillespie D., and Petzold L. Avoiding negative populations in explicit tau leaping. J. Chem. Phys. 123 (2005) 054104
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 054104
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
29
-
-
0242425970
-
Improved leap-size selection for accelerated stochastic simulation
-
Gillespie D., and Petzold L. Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys. 119 (2003) 8229-8234
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 8229-8234
-
-
Gillespie, D.1
Petzold, L.2
-
31
-
-
0347306243
-
Decay of metastable states: mean relaxation time formulation
-
Drozdov A., and Brey J. Decay of metastable states: mean relaxation time formulation. J. Chem. Phys. (1999) 7133-7141
-
(1999)
J. Chem. Phys.
, pp. 7133-7141
-
-
Drozdov, A.1
Brey, J.2
-
32
-
-
33846185710
-
Accelerated stochastic simulation of the stiff enzyme-substrate reaction
-
Cao Y., Gillespie D., and Petzold L. Accelerated stochastic simulation of the stiff enzyme-substrate reaction. J. Chem. Phys. 123 (2005) 144917
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 144917
-
-
Cao, Y.1
Gillespie, D.2
Petzold, L.3
-
33
-
-
38949164415
-
Algorithms and software for stochastic simulation of biochemical reacting systems
-
Li H., Cao Y., Petzold L., and Gillespie D. Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol. Progr. 24 (2008) 56-61
-
(2008)
Biotechnol. Progr.
, vol.24
, pp. 56-61
-
-
Li, H.1
Cao, Y.2
Petzold, L.3
Gillespie, D.4
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