A comparison of deterministic and stochastic modeling approaches for biochemical reaction systems: On fixed points, means, and modes

SK Hahl, A Kremling - Frontiers in genetics, 2016 - frontiersin.org
In the mathematical modeling of biochemical reactions, a convenient standard approach is
to use ordinary differential equations (ODEs) that follow the law of mass action. However …

Large deviations for multi-scale jump-diffusion processes

R Kumar, L Popovic - Stochastic Processes and their Applications, 2017 - Elsevier
We obtain large deviation results for a two time-scale model of jump-diffusion processes.
The processes on the two time scales are fully inter-dependent, the slow process has small …

Theoretical and computational tools to model multistable gene regulatory networks

F Bocci, D Jia, Q Nie, MK Jolly… - Reports on Progress in …, 2023 - iopscience.iop.org
The last decade has witnessed a surge of theoretical and computational models to describe
the dynamics of complex gene regulatory networks, and how these interactions can give rise …

Stationary distributions and condensation in autocatalytic reaction networks

L Hoessly, C Mazza - SIAM Journal on Applied Mathematics, 2019 - SIAM
We investigate a broad family of stochastically modeled reaction networks by looking at their
stationary distributions. Most known results on stationary distributions assume weak …

A minimal model of burst-noise induced bistability

J Falk, M Mendler, B Drossel - PloS one, 2017 - journals.plos.org
We investigate the influence of intrinsic noise on stable states of a one-dimensional
dynamical system that shows in its deterministic version a saddle-node bifurcation between …

Asymmetric autocatalytic reactions and their stationary distribution

C Gallinger, L Popovic - Royal Society Open Science, 2024 - royalsocietypublishing.org
We consider a general class of autocatalytic reactions, which has been shown to display
stochastic switching behaviour (discreteness-induced transitions (DITs)) in some parameter …

Constrained Langevin approximation for the Togashi-Kaneko model of autocatalytic reactions

WTL Fan, YJ Yang, C Yuan - arXiv preprint arXiv:2209.00426, 2022 - arxiv.org
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 …

A spatial measure-valued model for chemical reaction networks in heterogeneous systems

L Popovic, A Véber - The Annals of Applied Probability, 2023 - projecteuclid.org
We propose a novel measure valued process which models the behaviour of chemical
reaction networks in spatially heterogeneous systems. It models reaction dynamics between …

The statistics of fixation times for systems with recruitment

T Biancalani, L Dyson, AJ McKane - Journal of Statistical …, 2015 - iopscience.iop.org
We investigate the statistics of the time taken for a system driven by recruitment to reach
fixation. Our model describes a series of experiments where a population is confronted with …

Approximation methods for stochastic systems biology

A Sukys - 2024 - era.ed.ac.uk
Biochemical reactions involved in complex cellular mechanisms are driven by inherently
stochastic molecular interactions. Although the intrinsic noise is often negligible in the …