相关论文: Fixed Points for Stochastic Open Chemical Systems
In the classical stochastic resetting problem, a particle, moving according to some stochastic dynamics, undergoes random interruptions that bring it to a selected domain, and then, the process recommences. Hitherto, the resetting mechanism…
Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws…
Quantum collision models allow for the dynamics of open quantum systems to be described by breaking the environment into small segments, typically consisting of non-interacting harmonic oscillators or two-level systems. This work introduces…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…
In this paper we derive several quasi steady-state approximations (QSSAs) to the stochastic reaction network describing the Michaelis-Menten enzyme kinetics. We show how the different assumptions about chemical species abundance and…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
To model bio-chemical reaction systems with diffusion one can either use stochastic, microscopic reaction-diffusion master equations or deterministic, macroscopic reaction-diffusion system. The connection between these two models is not…
We investigate a class of stochastic chemical reaction networks with $n{\ge}1$ chemical species $S_1$, \ldots, $S_n$, and whose complexes are only of the form $k_iS_i$, $i{=}1$,\ldots, $n$, where $(k_i)$ are integers. The time evolution of…
The Boltzmann equation, a fundamental equation in kinetic theory, serves as a bridge between microscopic particle dynamics and macroscopic continuum mechanics. However, deriving closed macroscopic moment systems from the Boltzmann equation…
We study the time-evolution of cumulants of velocities and kinetic energies in the stochastic Kac model for velocity exchange of $N$ particles, with the aim of quantifying how fast these degrees of freedom become chaotic in a time scale in…
The recent advancements in mathematical modeling of biochemical systems have generated increased interest in sensitivity analysis methodologies. There are two primary approaches for analyzing these mathematical models: the stochastic…
Most literature on quantum collision models (CMs) usually considers periodic weak collisions featuring a fixed waiting time between two next collisions. Some works have yet addressed CMs with random waiting time and strong collisions…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state…
In these lecture notes, the basic principles of stochastic thermodynamics are developed starting with a closed system in contact with a heat bath. A trajectory undergoes Markovian transitions between observable meso-states that correspond…
Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…
This paper deals with the theory of structure, stability, robustness, and stabilization for an appealing class of nonlinear systems which arises in the analysis of chemical networks. The results given here extend, but are also heavily based…
We consider steady states of dynamics that have an underlying network structure. We study how a steady state responds to small perturbations in the network parameters and how this sensitivity is connected to the network structure. We…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…