Related papers: A toy model solved by statistical mechanics for te…
We numerically and analytically investigate the behavior of a non-equilibrium phase transition in the second Schl\"ogl autocatalytic reaction scheme. Our model incorporates both an interaction-induced phase separation and a bifurcation in…
Virtually every biological rate depends on temperature, yet the resulting rate-temperature relationships often deviate strongly from simple Arrhenius behavior. In this first part of a two-part review, we survey phenomenological models used…
A system is glassy when the observation time is much smaller than the equilibration time. A unifying thermodynamic picture of the glassy state is presented. Slow configurational modes are in quasi-equilibrium at an effective temperature. It…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
Non-Maxwellian distributions are commonly observed across a wide range of systems and scales. While direct observations provide the strongest evidence for these distributions, they also manifest indirectly through their influence on…
We discuss several ways of illustrating fundamental concepts in statistical and thermal physics by considering various models and algorithms. We emphasize the importance of replacing students' incomplete mental images by models that are…
We present a toy theory that is based on a simple principle: the number of questions about the physical state of a system that are answered must always be equal to the number that are unanswered in a state of maximal knowledge. A wide…
We study the response of chemical reaction networks driven far from equilibrium to logarithmic perturbations of reaction rates. The response of the mean number of a chemical species is observed to be quantitively limited by number…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
Semiclassical instanton theory is a form of quantum transition-state theory which can be applied to computing thermal reaction rates for complex molecular systems including quantum tunneling effects. There have been a number of attempts to…
In the last decade, stochastic models have shown to be very useful for quantitative modelling of social processes. Here, a configurational master equation for the description of behavioral changes by pair interactions of individuals is…
Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviours. Here, we extend the theory to include incoherent light as a…
Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on…
Equilibrium statistical mechanics is intended to link the microscopic dynamics of particles to the thermodynamic laws for macroscopic quantities. However, the modern statistical theory is faced with significant difficulties, as applied to…
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…
Statistical models provide a powerful and useful class of approximations for calculating reaction rates by bypassing the need for detailed, and often difficult, dynamical considerations. Such approaches invariably invoke specific…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
The development of stochastic thermodynamics during the last decades prompted the discovery of novel nonequilibrium relations refining our understanding of the second law in small fluctuating systems and its connection with information…
In this paper, we propose a novel sequential data-driven method for dealing with equilibrium based chemical simulations, which can be seen as a specific machine learning approach called active learning. The underlying idea of our approach…