We consider stochastically modeled chemical reaction systems with mass-action kinetics and prove that a product-form stationary distribution exists for each closed, irreducible subset of the state space if an analogous deterministically modeled system with mass-action kinetics admits a complex balanced equilibrium. Feinberg's deficiency zero theorem then implies that such a distribution exists so long as the corresponding chemical network is weakly reversible and has a deficiency of zero. The main parameter of the stationary distribution for the stochastically modeled system is a complex balanced equilibrium value for the corresponding deterministically modeled system. We also generalize our main result to some non-mass-action kinetics.
In many applications, for example when computing statistics of fast subsystems in a multiscale setting, we wish to find the stationary distributions of systems of continuous time Markov chains. Here we present a class of models that appears naturally in certain averaging approaches whose stationary distributions can be computed explicitly. In particular, we study continuous time Markov chain models for biochemical interaction systems with non-mass action kinetics whose network satisfies a certain constraint. Analogous with previous related results, the distributions can be written in product f…
Deficiency zero is an important network structure and has been the focus of many celebrated results within reaction network theory. In our previous paper \textit{Prevalence of deficiency zero reaction networks in an Erd\H os-Rényi framework}, we provided a framework to quantify the prevalence of deficiency zero among randomly generated reaction networks. Specifically, given a randomly generated binary reaction network with $n$ species, with an edge between two arbitrary vertices occurring independently with probability $p_n$, we established the threshold function $r(n)=\frac{1}{n^3}$ such that…
Reaction networks are commonly used within the mathematical biology and mathematical chemistry communities to model the dynamics of interacting species. These models differ from the typical graphs found in random graph theory since their vertices are constructed from elementary building blocks, i.e., the species. In this paper, we consider these networks in an Erd\H os-Rényi framework and, under suitable assumptions, derive a threshold function for the network to have a deficiency of zero, which is a property of great interest in the reaction network community. Specifically, if the number of s…
We investigate a broad family of non weakly reversible stochastically modeled reaction networks (CRN), by looking at their steady-state distributions. Most known results on stationary distributions assume weak reversibility and zero deficiency. We first give explicitly product-form steady-state distributions for a class of non weakly reversible autocatalytic CRN of arbitrary deficiency. Examples of interest in statistical mechanics (inclusion process), life sciences and robotics (collective decision making in ant and robot swarms) are provided. The product-form nature of the steady-state then …
Stochastic reaction networks are dynamical models of biochemical reaction systems and form a particular class of continuous-time Markov chains on $\mathbb{N}^n$. Here we provide a fundamental characterisation that connects structural properties of a network to its dynamical features. Specifically, we define the notion of `stochastically complex balanced systems' in terms of the network's stationary distribution and provide a characterisation of stochastically complex balanced systems, parallel to that established in the 70-80ies for deterministic reaction networks. Additionally, we establish t…
The graph-related symmetries of a reaction network give rise to certain special equilibria (such as complex balanced equilibria) in deterministic models of dynamics of the reaction network. Correspondingly, in the stochastic setting, when modeled as a continuous-time Markov chain, these symmetries give rise to certain special stationary measures. Previous work by Anderson, Craciun and Kurtz identified stationary distributions of a complex balanced network; later Cappelletti and Wiuf developed the notion of complex balancing for stochastic systems. We define and establish the relations between …
We consider the relationship between stationary distributions for stochastic models of reaction systems and Lyapunov functions for their deterministic counterparts. Specifically, we derive the well known Lyapunov function of reaction network theory as a scaling limit of the non-equilibrium potential of the stationary distribution of stochastically modeled complex balanced systems. We extend this result to general birth-death models and demonstrate via example that similar scaling limits can yield Lyapunov functions even for models that are not complex or detailed balanced, and may even have mu…
In the setting of stochastic dynamical systems that eventually go extinct, the quasi-stationary distributions are useful to understand the long-term behavior of a system before evanescence. For a broad class of applicable continuous-time Markov processes on countably infinite state spaces, known as reaction networks, we introduce the inferred notion of absorbing and endorsed sets, and obtain sufficient conditions for the existence and uniqueness of a quasi-stationary distribution within each such endorsed set. In particular, we obtain sufficient conditions for the existence of a globally attra…
We examine reaction networks (CRNs) through their associated continuous-time Markov processes. Studying the dynamics of such networks is in general hard, both analytically and by simulation. In particular, stationary distributions of stochastic reaction networks are only known in some cases. We analyze class properties of the underlying continuous-time Markov chain of CRNs under the operation of join and examine conditions such that the form of the stationary distributions of a CRN is derived from the parts of the decomposed CRNs. The conditions can be easily checked in examples and allow recu…
Stochastic reaction networks (SRNs) provide models of many real-world networks. Examples include networks in epidemiology, pharmacology, genetics, ecology, chemistry, and social sciences. Here, we model stochastic reaction networks by continuous time Markov chains (CTMCs) and pay special attention to one-dimensional mass-action SRNs (1-d stoichiometric subspace). We classify all states of the underlying CTMC of 1-d SRNs. In terms of (up to) four parameters, we provide sharp checkable criteria for various dynamical properties (including explosivity, recurrence, ergodicity, and the tail asymptot…
This work reviews deterministic and diffusion approximations of the stochastic chemical reaction networks and explains their applications. We discuss the added value the diffusion approximation provides for systems with different phenomena, such as a deficiency and a bistability. It is advocated that the diffusion approximation can be considered as an alternative theoretical approach to study the reaction networks rather than a simulation shortcut. We discuss two examples in which the diffusion approximation is able to catch qualitative properties of reaction networks that the deterministic mo…
We consider the superposition of a symmetric simple exclusion dynamics, speeded-up in time, with a spin-flip dynamics in a one-dimensional interval with periodic boundary conditions. We prove the large deviations principle for the empirical measure under the stationary state. We deduce from this result that the stationary state is concentrated on the stationary solutions of the hydrodynamic equation which are stable.
We study stability of stationary solutions for a class of non-local semilinear parabolic equations. To this end, we prove the Feynman--Kac formula for a Lévy processes with time-dependent potentials and arbitrary initial condition. We propose sufficient conditions for asymptotic stability of the zero solution, and use them to the study of the spatial logistic equation arising in population ecology. For this equation, we find conditions which imply that its positive stationary solution is asymptotically stable. We consider also the case when the initial condition is given by a random field.
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor stochastic, discrete population, continuous time models. The stationary distributions provide snapshots of the model behavior at the stationary regime, and as such finding their expression in terms of the model parameters is of great interest. The aim of the present paper is to describe when the stationary distributions of the original model, whose state sp…
In 2010, Anderson, Craciun, and Kurtz showed that if a deterministically modeled reaction network is complex balanced, then the associated stochastic model admits a stationary distribution that is a product of Poissons \cite{ACK2010}. That work spurred a number of followup analyses. In 2015, Anderson, Craciun, Gopalkrishnan, and Wiuf considered a particular scaling limit of the stationary distribution detailed in \cite{ACK2010}, and proved it is a well known Lyapunov function \cite{ACGW2015}. In 2016, Cappelletti and Wiuf showed the converse of the main result in \cite{ACK2010}: if a reaction …
We study three basic diffusion-controlled reaction processes -- annihilation, coalescence, and aggregation. We examine the evolution starting with the most natural inhomogeneous initial configuration where a half-line is uniformly filled by particles, while the complementary half-line is empty. We show that the total number of particles that infiltrate the initially empty half-line is finite and has a stationary distribution. We determine the evolution of the average density from which we derive the average total number N of particles in the initially empty half-line; e.g., for annihilation \l…
The Togashi Kaneko model (TK model), introduced by Togashi and Kaneko in 2001, is a simple stochastic reaction network that displays discreteness-induced transitions between meta-stable patterns. Here we study a constrained Langevin approximation (CLA) of this model. The CLA, obtained by Anderson et al. in 2019, is an obliquely reflected diffusion process on the positive orthant and hence it respects the constrain that chemical concentrations are never negative. We show that the CLA is a Feller process, is positive Harris recurrent, and converges exponentially fast to the unique stationary dis…
The past few decades have seen robust research on questions regarding the existence, form, and properties of stationary distributions of stochastically modeled reaction networks. When a stochastic model admits a stationary distribution an important practical question is: what is the rate of convergence of the distribution of the process to the stationary distribution? With the exception of \cite{XuHansenWiuf2022} pertaining to models whose state space is restricted to the non-negative integers, there has been a notable lack of results related to this rate of convergence in the reaction network…
For reaction networks arising in systems biology, the capacity for two or more steady states, that is, multistationarity, is an important property that underlies biochemical switches. Another property receiving much attention recently is absolute concentration robustness (ACR), which means that some species concentration is the same at all positive steady states. In this work, we investigate the prevalence of each property while paying close attention to when the properties occur together. Specifically, we consider a stochastic block framework for generating random networks, and prove edge-pro…
We provide a theoretical analysis of some autocatalytic reaction networks exhibiting the phenomenon of discretely induced transitions (DITs). The family of networks that we address includes the celebrated Togashi and Kaneko model. We prove positive recurrence, finiteness of all moments, and geometric ergodicity of the models in the family. For some parameter values, we find the analytic expression for the stationary distribution, and discuss the effect of volume scaling on the stationary behavior of the chain. We find the exact critical value of the volume for which DITs disappear.
Consider the standard stochastic reaction network model where the dynamics is given by a continuous-time Markov chain over a discrete lattice. For such models, estimation of parameter sensitivities is an important problem, but the existing computational approaches to solve this problem usually require time-consuming Monte Carlo simulations of the reaction dynamics. Therefore these simulation-based approaches can only be expected to work over finite time-intervals, while it is often of interest in applications to examine the sensitivity values at the steady-state after the Markov chain has rela…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant, deterministically modeled mass-action systems [Shinar and Feinberg, Science, 2010]. We show here that fundamentally different conclusions about the long-term behavior of such systems are reached if the systems are instead modeled with stochastic dynamics and a discrete state space. Specifically, we characterize a large class of models that exhibit convergence to a po…
The probability distribution describing the state of a Stochastic Reaction Network evolves according to the Chemical Master Equation (CME). It is common to estimated its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases these simulations can take an impractical amount of computational time. Therefore many methods have been developed that approximate the Stochastic Process underlying the Chemical Master Equation. Prominent strategies are Hybrid Models that regard the firing of some reaction channels as being continuous and applying the quasi-sta…
