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cond-mat.stat-mech2018
Model reduction methods for classical stochastic systems with fast-switching environments: reduced master equations, stochastic differential equations, and applications
Peter G. Hufton, Yen Ting Lin, Tobias Galla
We study classical stochastic systems with discrete states, coupled to switching external environments. For fast environmental processes we derive reduced dynamics for the system i…
q-bio.QM2018
Generalizing Gillespie's direct method to enable network-free simulations
Ryan Suderman, Eshan D. Mitra, Yen Ting Lin +3
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration…