A multiple time interval finite state projection algorithm for the solution to the chemical master equation
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Publication:2456722
DOI10.1016/J.JCP.2007.05.016zbMATH Open1131.82020OpenAlexW2171720907MaRDI QIDQ2456722FDOQ2456722
Authors: Brian Munsky, Mustafa Khammash 
Publication date: 19 October 2007
Published in: Journal of Computational Physics (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/j.jcp.2007.05.016
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Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Genetics and epigenetics (92D10)
Cites Work
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- Stochastic approach to chemical kinetics
- A multiple time interval finite state projection algorithm for the solution to the chemical master equation
- Stochastic modelling of gene regulatory networks
- Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems
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- Jump longer to jump less: improving dynamic boundary projection with \(h\)-scaling
- Assessing Markovian and delay models for single-nucleus RNA sequencing
- Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks
- Stochastic reaction networks in dynamic compartment populations
- Stochastically modeled weakly reversible reaction networks with a single linkage class
- Data-driven method for efficient characterization of rare event probabilities in biochemical systems
- Model-free reinforcement learning for branching Markov decision processes
- Multiscale Modeling of Chemical Kinetics via the Master Equation
- Analyzing oscillatory behavior with formal methods
- On evolution of solution times for the chemical master equation of the enzymatic futile cycle
- Algebraic expressions of conditional expectations in gene regulatory networks
- Computing cumulative rewards using fast adaptive uniformization
- Implementation of variable parameters in the Krylov-based finite state projection for solving the chemical master equation
- Exponential equilibration of genetic circuits using entropy methods
- A review of stochastic and delay simulation approaches in both time and space in computational cell biology
- A modified uniformization method for the solution of the chemical master equation
- Variance reduction in stochastic reaction networks using control variates
- Multiscale Simulation of Stochastic Reaction-Diffusion Networks
- Method of conditional moments (MCM) for the chemical master equation
- Analysis of Markov jump processes under terminal constraints
- State space truncation with quantified errors for accurate solutions to discrete chemical master equation
- Tensor numerical methods for multidimensional PDEs: theoretical analysis and initial applications
- A numerical characteristic method for probability generating functions on stochastic first-order reaction networks
- Hybrid models of chemotaxis with application to leukocyte migration
- A tensor decomposition algorithm for large ODEs with conservation laws
- Generalizing Gillespie's direct method to enable network-free simulations
- Conditional Monte Carlo for reaction networks
- Approximate exponential algorithms to solve the chemical master equation
- Hybrid discrete/continuum algorithms for stochastic reaction networks
- Stochastic nonlinear model for somatic cell population dynamics during ovarian follicle activation
- General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks
- Computational identification of irreducible state-spaces for stochastic reaction networks
- Parallelising the finite state projection method
- Markovian dynamics on complex reaction networks
- Simultaneous state-time approximation of the chemical master equation using tensor product formats.
- Krylov and steady-state techniques for the solution of the chemical master equation for the mitogen-activated protein kinase cascade
- A shift and invert reorthogonalization Arnoldi algorithm for solving the chemical master equation
- Solving the chemical master equation by a fast adaptive finite state projection based on the stochastic simulation algorithm
- Solving the chemical master equation for monomolecular reaction systems and beyond: a Doi-Peliti path integral view
- The exit time finite state projection scheme: bounding exit distributions and occupation measures of continuous-time Markov chains
- Tensor approximation of stationary distributions of chemical reaction networks
- Finite state projection for approximating the stationary solution to the chemical master equation using reaction rate equations
- A dynamical low-rank approach to the chemical master equation
- Structure-preserving discretization of the chemical master equation
- A multiple time interval finite state projection algorithm for the solution to the chemical master equation
- Unbiased Bayesian inference for population Markov jump processes via random truncations
- Spatial stochastic intracellular kinetics: a review of modelling approaches
- Multiscale stochastic modelling of gene expression
- The efficient computation of periodic states of cyclically operated chemical processes
- Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching Mechanisms
- Accurate chemical master equation solution using multi-finite buffers
- An improved finite state projection algorithm for the numerical solution of the chemical master equation with applications
- A solver for the stochastic master equation applied to gene regulatory networks
- Nonlinear Langevin model with product stochasticity for biological networks: the case of the Schnakenberg model
- Modeling of chemical reaction systems with detailed balance using gradient structures
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