Related papers: Relaxation to statistical equilibrium in stochasti…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Biological networks have been recently found to exhibit many topological properties of the so-called complex networks. It has been reported that they are, in general, both highly skewed and directed. In this paper, we report on the dynamics…
For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…
Stochastic resetting breaks detailed balance and drives the formation of nonequilibrium steady states . Here, we consider a chain of diffusive processes $x_i(t)$ that interact unilaterally: at random time intervals, the process $x_n$…
Recent experiments indicate that electromagnetic hysteresis behavior can be exhibited at the molecular level.A MD simulation using 2-body potentials and switches to form and break bonds is implemented to determine whether chemical reaction…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
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…
We demonstrate the equilibration of isolated macroscopic quantum systems, prepared in non-equilibrium mixed states with significant population of many energy levels, and observed by instruments with a reasonably bound working range compared…
We study networks of biochemical reactions modelled by continuous-time Markov processes. Such networks typically contain many molecular species and reactions and are hard to study analytically as well as by simulation. Particularly, we are…
Enzyme kinetics is very often characterised by the irreversible Michaelis-Menten (MM) equation. However, in open chemical reaction networks such as metabolic pathways, this approach can lead to significant kinetic and thermodynamic…
Michaelis--Menten analysis is often conducted by nonlinear least squares under a constant-variance assumption, even though enzyme-kinetic data frequently display concentration-dependent heteroscedasticity and often include repeated or…
Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph…
An unified thermodynamical framework based in the use of a generalized Massieu-Planck thermodynamic potential is proposed and a new formulation of Boltzmann-Gibbs Statistical Mechanics is established. Under this philosophy a generalization…
Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical…
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…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, we identify structural network conditions that…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…