Multiscale Simulation of Stochastic Reaction-Diffusion Networks
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Publication:4555225
DOI10.1007/978-3-319-62627-7_3zbMath1401.92091OpenAlexW2763982505MaRDI QIDQ4555225
Andreas Hellander, Stefan Engblom, Per Loetstedt
Publication date: 19 November 2018
Published in: Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/978-3-319-62627-7_3
Reaction-diffusion equations (35K57) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Systems biology, networks (92C42)
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Cites Work
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- A stochastic analysis of first-order reaction networks
- Multilevel hybrid Chernoff tau-leap
- A comparison of bimolecular reaction models for stochastic reaction-diffusion systems
- Flexible single molecule simulation of reaction-diffusion processes
- Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
- Product-form stationary distributions for deficiency zero chemical reaction networks
- Adaptive mesh refinement for stochastic reaction-diffusion processes
- Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
- Markovian dynamics on complex reaction networks
- Computing the moments of high dimensional solutions of the master equation
- Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
- Solving the chemical master equation for monomolecular reaction systems analytically
- A solver for the stochastic master equation applied to gene regulatory networks
- A first-passage kinetic Monte Carlo algorithm for complex diffusion-reaction systems
- Asymptotic analysis of multiscale approximations to reaction networks
- Spectral approximation of solutions to the chemical master equation
- Strong approximation theorems for density dependent Markov chains
- An analysis of operator splitting techniques in the stiff case
- Hybrid framework for the simulation of stochastic chemical kinetics
- Influence of the nuclear membrane, active transport, and cell shape on the Hes1 and p53-Mdm2 pathways: insights from spatio-temporal modelling
- The existence and uniqueness of steady states for a class of chemical reaction networks
- Stochastic simulation of coupled reaction-diffusion processes
- Separation of time-scales and model reduction for stochastic reaction networks
- Simulation of stochastic diffusion via first exit times
- A multiple time interval finite state projection algorithm for the solution to the chemical master equation
- A hierarchy of approximations of the master equation scaled by a size parameter
- An adaptive algorithm for simulation of stochastic reaction-diffusion processes
- Mesoscopic Modeling of Stochastic Reaction-Diffusion Kinetics in the Subdiffusive Regime
- Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
- Multilevel Monte Carlo for Continuous Time Markov Chains, with Applications in Biochemical Kinetics
- Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions
- Using Gene Expression Noise to Understand Gene Regulation
- Approximation and inference methods for stochastic biochemical kinetics—a tutorial review
- An Adaptive Wavelet Method for the Chemical Master Equation
- Incorporating Active Transport of Cellular Cargo in Stochastic Mesoscopic Models of Living Cells
- Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
- Jump-Diffusion Approximation of Stochastic Reaction Dynamics: Error Bounds and Algorithms
- Analysis and Design of Jump Coefficients in Discrete Stochastic Diffusion Models
- Strong Convergence for Split-Step Methods in Stochastic Jump Kinetics
- Parallel in Time Simulation of Multiscale Stochastic Chemical Kinetics
- Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes
- Quality Triangulations with Locally Optimal Steiner Points
- On Nonobtuse Simplicial Partitions
- Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation
- Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
- Weakened acute type condition for tetrahedral triangulations and the discrete maximum principle
- Pathwise Error Bounds in Multiscale Variable Splitting Methods for Spatial Stochastic Kinetics
- Stochastic reaction-diffusion kinetics in the microscopic limit
- Error Bound for Piecewise Deterministic Processes Modeling Stochastic Reaction Systems
- The Reaction-Diffusion Master Equation as an Asymptotic Approximation of Diffusion to a Small Target
- Modeling Subdiffusion Using Reaction Diffusion Systems
- Parallelization, Processor Communication and Error Analysis in Lattice Kinetic Monte Carlo
- Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations
- On the Construction and Comparison of Difference Schemes
- Solutions of ordinary differential equations as limits of pure jump markov processes
- Stochastic approach to chemical kinetics
- Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems
- A Multilevel Adaptive Reaction-splitting Simulation Method for Stochastic Reaction Networks
- Handbook of stochastic methods for physics, chemistry and the natural sciences.
- The random walk's guide to anomalous diffusion: A fractional dynamics approach
