[图书][B] An introduction to the numerical simulation of stochastic differential equations

D Higham, P Kloeden - 2021 - SIAM
For a function g (h), we write g (h)= O (hp) to mean that there exist constants h0> 0 and K> 0
(independent of h) such that| g (h)|< Khp for all| h|< h0. In words, this means that g (h) tends …

A practical guide to pseudo-marginal methods for computational inference in systems biology

DJ Warne, RE Baker, MJ Simpson - Journal of theoretical biology, 2020 - Elsevier
For many stochastic models of interest in systems biology, such as those describing
biochemical reaction networks, exact quantification of parameter uncertainty through …

Large deviations and exit-times for reflected McKean–Vlasov equations with self-stabilising terms and superlinear drifts

D Adams, G Dos Reis, R Ravaille, W Salkeld… - … Processes and their …, 2022 - Elsevier
Abstract We study reflected McKean–Vlasov diffusions over a convex, non-bounded domain
with self-stabilising coefficients that do not satisfy the classical Wasserstein Lipschitz …

Catalyst: fast biochemical modeling with Julia

TE Loman, Y Ma, V Ilin, S Gowda, N Korsbo, N Yewale… - bioRxiv, 2022 - biorxiv.org
We introduce Catalyst. jl, a flexible and feature-filled Julia library for modeling and high
performance simulation of chemical reaction networks (CRNs). Catalyst acts as both a …

Revisit of macroscopic dynamics for some non-equilibrium chemical reactions from a Hamiltonian viewpoint

Y Gao, JG Liu - Journal of Statistical Physics, 2022 - Springer
Most biochemical reactions in living cells are open systems interacting with environment
through chemostats to exchange both energy and materials. At a mesoscopic scale, the …

Catalyst: Fast and flexible modeling of reaction networks

TE Loman, Y Ma, V Ilin, S Gowda… - PLOS Computational …, 2023 - journals.plos.org
We introduce Catalyst. jl, a flexible and feature-filled Julia library for modeling and high-
performance simulation of chemical reaction networks (CRNs). Catalyst supports simulating …

A constrained Langevin approximation for chemical reaction networks

SC Leite, RJ Williams - 2019 - projecteuclid.org
Continuous-time Markov chain models are often used to describe the stochastic dynamics of
networks of reacting chemical species, especially in the growing field of systems biology …

Molecular communications with molecular circuit-based transmitters and receivers

H Awan, CT Chou - IEEE transactions on nanobioscience, 2019 - ieeexplore.ieee.org
The performance of a communication link can be improved by maximizing the mutual
information between the input and output signals. This paper considers this maximization …

Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions

D Cappelletti, A Ortiz-Muñoz, DF Anderson… - Theoretical Computer …, 2020 - Elsevier
We show that discrete distributions on the d-dimensional non-negative integer lattice can be
approximated arbitrarily well via the marginals of stationary distributions for various classes …

Simplest random walk for approximating Robin boundary value problems and ergodic limits of reflected diffusions

B Leimkuhler, A Sharma… - The Annals of Applied …, 2023 - projecteuclid.org
A simple-to-implement weak-sense numerical method to approximate reflected stochastic
differential equations (RSDEs) is proposed and analysed. It is proved that the method has …