Analytic solutions for stochastic hybrid models of gene regulatory networks

DOI10.1007/S00285-021-01549-7zbMATH Open1459.35362arXiv1812.07788OpenAlexW2903812525WikidataQ113905597 ScholiaQ113905597MaRDI QIDQ2223255FDOQ2223255

Authors: Pavel Kurasov, Delio Mugnolo, Verena Wolf 

Publication date: 28 January 2021

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: Discrete-state stochastic models are a popular approach to describe the inherent stochasticity of gene expression in single cells. The analysis of such models is hindered by the fact that the underlying discrete state space is extremely large. Therefore hybrid models, in which protein counts are replaced by average protein concentrations, have become a popular alternative. The evolution of the corresponding probability density functions is given by a coupled system of hyperbolic PDEs. This system has Markovian nature but its hyperbolic structure makes it difficult to apply standard functional analytical methods. We are able to prove convergence towards the stationary solution and determine such equilibrium explicitly by combining abstract methods from the theory of positive operators and elementary ideas from potential analysis.

Full work available at URL: https://arxiv.org/abs/1812.07788

Recommendations

• Stochastic hybrid models of gene regulatory networks -- a PDE approach
• Modelling Gene Regulatory Networks
• Stochastic modelling of gene regulatory networks
• A solver for the stochastic master equation applied to gene regulatory networks
• Time-dependent propagators for stochastic models of gene expression: an analytical method

zbMATH Keywords

positive \(C_0\)-semigroupspiecewise deterministic Markov processessystems of PDEsPetri networks

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20) Positive solutions to PDEs (35B09) PDEs in connection with biology, chemistry and other natural sciences (35Q92) PDEs with randomness, stochastic partial differential equations (35R60) Cell biology (92C37) Control/observation systems governed by partial differential equations (93C20) One-parameter semigroups and linear evolution equations (47D06) Initial-boundary value problems for systems of linear first-order PDEs (35F46)

Cites Work

• Title not available (Why is that?)
• Title not available (Why is that?)
• Elliptic partial differential equations of second order
• Title not available (Why is that?)
• One-Parameter Semigroups for Linear Evolution Equations
• One-parameter semigroups of positive operators
• A short course on operator semigroups
• Non-equilibrium thermodynamics of piecewise deterministic Markov processes
• Qualitative properties of certain piecewise deterministic Markov processes
• Title not available (Why is that?)
• Fluid stochastic Petri nets: Theory, applications, and solution techniques
• High cooperativity in negative feedback can amplify noisy gene expression
• Transcriptional bursting diversifies the behaviour of a toggle switch: hybrid simulation of stochastic gene expression
• Quantitative ergodicity for some switched dynamical systems
• Solving the chemical master equation for monomolecular reaction systems analytically
• Hybrid representation and simulation of stiff biochemical networks
• Positive semigroups of kernel operators
• DICHOTOMOUS MARKOV NOISE: EXACT RESULTS FOR OUT-OF-EQUILIBRIUM SYSTEMS
• Triviality of the peripheral point spectrum
• Autocatalytic genetic networks modeled by piecewise-deterministic Markov processes
• Gene expression in self-repressing system with multiple gene copies
• Convergence of positive operator semigroups
• A piecewise deterministic model for a prey-predator community
• Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
• Decomposition and tunability of expression noise in the presence of coupled feedbacks
• Stochastic hybrid models of gene regulatory networks -- a PDE approach
• Stochastic gene expression with a multistate promoter: breaking down exact distributions
• Limit theorems for generalized density-dependent Markov chains and bursty stochastic gene regulatory networks

Cited In (17)

• Heavy-tailed distributions in a stochastic gene autoregulation model
• Convergence of stochastic gene networks to hybrid piecewise deterministic processes
• Uniform convergence of solutions to stochastic hybrid models of gene regulatory networks
• Robust dynamics in minimal hybrid models of genetic networks
• Limit theorems for generalized density-dependent Markov chains and bursty stochastic gene regulatory networks
• Protein noise and distribution in a two-stage gene-expression model extended by an mRNA inactivation loop
• Stochastic analysis of a complex gene-expression model
• A kinetic finite volume discretization of the multidimensional PIDE model for gene regulatory networks
• Linear hyperbolic systems on networks: well-posedness and qualitative properties
• Numerical analysis of a method for a partial integro-differential equation model in regulatory gene networks
• Infection time in multistable gene networks. A backward stochastic variational inequality with nonconvex switch-dependent reflection approach
• Modelling Gene Regulatory Networks
• On the use of the Hill functions in mathematical models of gene regulatory networks
• Stochastic hybrid models of gene regulatory networks -- a PDE approach
• Hybrid simulation of autoregulation within transcription and translation
• Time-dependent propagators for stochastic models of gene expression: an analytical method
• An analytical study of the number of steady states in gene regulatory networks

This page was built for publication: Analytic solutions for stochastic hybrid models of gene regulatory networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2223255)