Modeling and Simulating Chemical Reactions

From MaRDI portal
Publication:3503956

DOI10.1137/060666457zbMath1144.80011OpenAlexW2131766020MaRDI QIDQ3503956

Desmond J. Higham

Publication date: 10 June 2008

Published in: SIAM Review (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1137/060666457




Related Items (46)

A Hierarchy of Network Models Giving Bistability Under Triadic ClosureSpike timing precision of neuronal circuitsIdentifiability analysis for models of the translation kinetics after mRNA transfectionQuantitative comparison of the mean-return-time phase and the stochastic asymptotic phase for noisy oscillatorsModelling of DNA mismatch repair with a reversible process calculusExtending the multi-level method for the simulation of stochastic biological systemsRadiant heat transfer in nitrogen-free combustion environmentsModeling of chemical reaction systems with detailed balance using gradient structuresRapid Bayesian Inference for Expensive Stochastic ModelsStructure-preserving discretization of the chemical master equationDiscrete-state stochastic models of calcium-regulated calcium influx and subspace dynamics are not well-approximated by ODEs that neglect concentration fluctuationsMultifidelity multilevel Monte Carlo to accelerate approximate Bayesian parameter inference for partially observed stochastic processesProtein pattern formation induced by the joint effect of noise and delay in a multi-cellular systemIncorporating Computational Challenges into a Multidisciplinary Course on Stochastic ProcessesHeteroclinic cycling and extinction in May-Leonard models with demographic stochasticityNegative feedback contributes to the stochastic expression of the interferon-\(\beta\) gene in virus-triggered type I interferon signaling pathwaysClustered model reduction of positive directed networksA numerical characteristic method for probability generating functions on stochastic first-order reaction networksOptimal explicit stabilized postprocessed \(\tau\)-leap method for the simulation of chemical kineticsFirst passage times and minimum actions for a stochastic minimal bistable systemSolving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithmA spatiotemporal master equation model of morphogen transport: local accumulation times, noise measurement and diffusion forceExtinction models for cancer stem cell therapyNumerical stationary distribution and its convergence for nonlinear stochastic differential equationsMicrodomain [Ca2+ Fluctuations Alter Temporal Dynamics in Models of Ca2+-Dependent Signaling Cascades and Synaptic Vesicle Release] ⋮ Stochastic modelling of chromosomal segregation: errors can introduce correctionRobust stability and instability of biochemical networks with parametric uncertaintyStationary Distributions of Continuous-Time Markov Chains: A Review of Theory and Truncation-Based ApproximationsChemical master equation and Langevin regimes for a gene transcription modelMeasuring edge importance: a quantitative analysis of the stochastic shielding approximation for random processes on graphsWeak solution of stochastic differential equations with fractional diffusion coefficientApplications of Magnus expansions and pseudospectra to Markov processesSUPPLY CHAIN MODELED AS A METABOLIC PATHWAYMultifidelity Approximate Bayesian ComputationVariance reduction with array-RQMC for tau-leaping simulation of stochastic biological and chemical reaction networksHybrid modeling of homogenous gas-phase combustion reactionsAsymptotics of Stochastic Protein Assembly ModelsLyapunov Function Partial Differential Equations for Chemical Reaction Networks: Some Special CasesQuasi-Monte Carlo methods applied to tau-leaping in stochastic biological systemsFinite state projection for approximating the stationary solution to the chemical master equation using reaction rate equationsModeling fast diffusion processes in time integration of stiff stochastic differential equationsAlgebraic expressions of conditional expectations in gene regulatory networksMultiscale Global Sensitivity Analysis for Stochastic Chemical SystemsLocalization and Pseudospectra of Twisted Toeplitz Matrices with Applications to Ion ChannelsA first step to implement Gillespie's algorithm with rejection samplingKrylov subspace approximation for quadratic-bilinear differential system


Uses Software



This page was built for publication: Modeling and Simulating Chemical Reactions