Stochastic reaction networks within interacting compartments
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Publication:6049022
Abstract: Stochastic reaction networks, which are usually modeled as continuous-time Markov chains on , and simulated via a version of the "Gillespie algorithm," have proven to be a useful tool for the understanding of processes, chemical and otherwise, in homogeneous environments. There are multiple avenues for generalizing away from the assumption that the environment is homogeneous, with the proper modeling choice dependent upon the context of the problem being considered. One such generalization was recently introduced in (Duso and Zechner, PNAS, 2020), where the proposed model includes a varying number of interacting compartments, or cells, each of which contains an evolving copy of the stochastic reaction system. The novelty of the model is that these compartments also interact via the merging of two compartments (including their contents), the splitting of one compartment into two, and the appearance and destruction of compartments. In this paper we begin a systematic exploration of the mathematical properties of this model. We (i) obtain basic/foundational results pertaining to explosivity, transience, recurrence, and positive recurrence of the model, (ii) explore a number of examples demonstrating some possible non-intuitive behaviors of the model, and (iii) identify the limiting distribution of the model in a special case that generalizes three formulas from an example in (Duso and Zechner, PNAS, 2020).
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Cites work
- A comparison of bimolecular reaction models for stochastic reaction-diffusion systems
- A constrained Langevin approximation for chemical reaction networks
- A Stochastic Compartmental Model for Fast Axonal Transport
- Basics of Applied Stochastic Processes
- Chemical diffusion master equation: Formulations of reaction–diffusion processes on the molecular level
- Compartmental Models in Epidemiology
- Editorial: Special issue on stochastic modelling of reaction-diffusion processes in biology
- Full classification of dynamics for one-dimensional continuous-time Markov chains with polynomial transition rates
- scientific article; zbMATH DE number 3951715 (Why is no real title available?)
- scientific article; zbMATH DE number 934443 (Why is no real title available?)
- Introduction to probability
- Markov Chains
- On constrained Langevin equations and (bio)chemical reaction networks
- Solving the chemical master equation for monomolecular reaction systems analytically
- Stability of Markovian processes III: Foster–Lyapunov criteria for continuous-time processes
- Stochastic analysis of biochemical systems
- Stochastic modelling for systems biology
- Stochastic reaction networks in dynamic compartment populations
- Strong approximation theorems for density dependent Markov chains
- Tier structure of strongly endotactic reaction networks
- Time-dependent product-form Poisson distributions for reaction networks with higher order complexes
Cited in
(12)- Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations
- A statistical mechanics description of environmental variability in metabolic networks
- A stochastic analysis of first-order reaction networks
- Stochastic reaction networks in dynamic compartment populations
- Stochastically modeled weakly reversible reaction networks with a single linkage class
- Cluster compartmentalization may provide resistance to parasites for catalytic networks
- A local polynomial moment approximation for compartmentalized biochemical systems
- A generic framework to coarse-grain stochastic reaction networks by abstract interpretation
- Hawkes process modelling for chemical reaction networks in a random environment
- Polynomial time reachable sequence computation in discrete state reaction networks
- Modeling compartmentalization within intracellular signaling pathway
- Scaling limits of spatial compartment models for chemical reaction networks
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