Solution of chemical master equations for nonlinear stochastic reaction networks
Tài liệu tham khảo
Ramkrishna, 2004, Mathematics in chemical engineering: a 50 year introspection, AIChE J, 50, 7, 10.1002/aic.10002
Bilous, 1955, Chemical reactor stability and sensitivity, AIChE J, 1, 513, 10.1002/aic.690010422
Bilous, 1956, Chemical reactor stability and sensitivity. II. Effect of parameters on sensitivity of empty tubular reactors, AIChE J, 2, 117, 10.1002/aic.690020124
Aris, 1958, An analysis of chemical reactor stability and control. I. The possibility of local control, with perfect or imperfect control mechanisms. II. The evolution of proportional control. III. The principles of programming reactor calculations. Some extensions, Chem Eng Sci, 5, 121, 10.1016/0009-2509(58)80019-6
Aris, 1965
McQuarrie, 1967, Stochastic approach to chemical kinetics, J Appl Prob, 4, 413, 10.2307/3212214
Moyal, 1949, Stochastic processes and statistical physics, J R Stat Soc Ser B: Methodol, 11, 150
Oppenheim, 1965, Master equations and Markov processes, Phys Rev, 138, 1007, 10.1103/PhysRev.138.B1007
Oppenheim, 1967, Stochastic theory of multistate relaxation processes, Adv Mol Relax Process, 1, 13, 10.1016/0001-8716(67)80003-8
Oppenheim, 1977
Gillespie, 2009, Moment closure approximations for mass-action models, IET Syst Biol, 3, 52, 10.1049/iet-syb:20070031
Sotiropoulos, 2011, Analytical derivation of moment equations in stochastic chemical kinetics, Chem Eng Sci, 66, 268, 10.1016/j.ces.2010.10.024
Smadbeck, 2012, Efficient moment matrix generation for arbitrary chemical networks, Chem Eng Sci, 84, 612, 10.1016/j.ces.2012.08.031
Gillespie, 1976, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, J Comp Phys, 22, 403, 10.1016/0021-9991(76)90041-3
Gillespie, 1977, Exact stochastic simulation of coupled chemical reactions, J Phys Chem, 81, 2340, 10.1021/j100540a008
Gibson, 2000, Efficient exact stochastic simulation of chemical systems with many species and many channels, J Phys Chem, 104, 1876, 10.1021/jp993732q
Haseltine, 2002, Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics, J Chem Phys, 117, 6959, 10.1063/1.1505860
Cao, 2004, Efficient formulation of the stochastic simulation algorithm for chemically reacting systems, J Chem Phys, 121, 4059, 10.1063/1.1778376
Chatterjee, 2005, Time accelerated Monte Carlo simulations of biological networks using the binomial {tau}-leap method, Bioinformatics, 21, 2136, 10.1093/bioinformatics/bti308
Tian, 2004, Binomial leap methods for simulating stochastic chemical kinetics, J Chem Phys, 121, 10356, 10.1063/1.1810475
Liu, 2005, Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates, J Chem Phys, 123, 194107, 10.1063/1.2109987
Munsky, 2006, The finite state projection algorithm for the solution of the chemical master equation, J Chem Phys, 124, 044104, 10.1063/1.2145882
Cao, 2005, Avoiding negative populations in explicit Poisson tau-leaping, J Chem Phys, 123, 054104, 10.1063/1.1992473
Chatterjee, 2006, Temporal acceleration of spatially distributed kinetic Monte Carlo simulations, J Comput Phys, 211, 596, 10.1016/j.jcp.2005.06.004
Harris, 2006, A “partitioned leaping” approach for multiscale modeling of chemical reaction dynamics, J Chem Phys, 125, 144107, 10.1063/1.2354085
Salis, 2005, Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions, J Chem Phys, 122, 1, 10.1063/1.1835951
Salis, 2005, Numerical simulation of stochastic gene circuits, Comput Chem Eng, 29, 577, 10.1016/j.compchemeng.2004.08.017
Salis, 2005, An equation-free probabilistic steady state approximation: dynamic application to the stochastic simulation of biochemical reaction networks, J Chem Phys, 123, 214106, 10.1063/1.2131050
Sotiropoulos, 2009, Model reduction of multiscale chemical Langevin equations: a numerical case study, IEEE Trans Comput Biol Bioinform, 6, 470, 10.1109/TCBB.2009.23
Contou-Carrere, 2011, Model reduction of multi-scale chemical Langevin equations, Syst Contr Lett, 60, 75, 10.1016/j.sysconle.2010.10.011
Smadbeck, 2012, Stochastic model reduction using a modified Hill-type kinetic law, J Chem Phys, 137, 234109, 10.1063/1.4770273
Sotiropoulos, 2008, An adaptive time step scheme for a system of SDEs with multiple multiplicative noise. Chemical Langevin equation, a proof of concept, J Chem Phys, 128, 014103, 10.1063/1.2812240
Salis, 2006, Multiscale Hy3S: hybrid stochastic simulations for supercomputers, BMC Bioinform, 7, 93, 10.1186/1471-2105-7-93
Hill, 2008, SynBioSS: the synthetic biology modeling suite, Bioinformatics, 24, 2551, 10.1093/bioinformatics/btn468
Weeding, 2010, SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs, Brief Bioinform, 11, 394, 10.1093/bib/bbq002
Tuttle, 2005, Model-driven design principles of gene networks: the oscillator, Biophys J, 89, 3873, 10.1529/biophysj.105.064204
Tomshine, 2006, Optimization of a stochastically simulated gene network model via simulated annealing, Biophys J, 91, 3196, 10.1529/biophysj.106.083485
Kaznessis, 2006, Multi-scale models for gene network engineering, Chem Eng Sci, 61, 940, 10.1016/j.ces.2005.06.033
Kaznessis, 2007, Models for synthetic biology, BMC Syst Biol, 1, 47, 10.1186/1752-0509-1-47
Ramalingam, 2009, Forward engineering of synthetic biological AND gates, Biochem Eng J, 47, 38, 10.1016/j.bej.2009.06.014
Volzing, 2011, proTeOn and proTeOff, new protein devices that inducibly activate bacterial gene expression, ACS Chem Biol, 6, 1107, 10.1021/cb200168y
Smadbeck, 2013, A closure scheme for chemical master equations, Proc Natl Acad Sci U S A, 110, 14261, 10.1073/pnas.1306481110
Schlögl, 1972, Chemical reaction models for non-equilibrium phase transition, Z Physik, 253, 147, 10.1007/BF01379769