Related papers: Transition to the Most Probable Kinetic State in a…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
We consider a reaction-diffusion system including discontinuous hysteretic relay operators in reaction terms. This system is motivated by an epigenetic model that describes the evolution of a population of organisms which can switch their…
This paper deals with the energy transport properties of charged particles with time-dependent damping force. Based on the proposed nonlinear dimensionless mapping,the stability and dynamical evolution of the particle system is analyzed…
Driven-dissipative nonlinear systems exhibit rich critical behavior, related to bifurcation, bistability and switching, which underlie key phenomena in areas ranging from physics, chemistry and biology to social sciences and economics. The…
In this paper we perform a formal asymptotic analysis on a kinetic model for reactive mixtures in order to derive a reaction-diffusion system of Maxwell-Stefan type. More specifically, we start from the kinetic model of simple reacting…
A tribological system consisting of two contacting blocks has been considered. One of them is arranged between two springs, the other is driven periodically. The kinetics of the system has been studied in the boundary friction mode, when an…
We numerically examine a binary system of particles with repulsive interactions, where one species is driven by a rotating drive and the other is subjected either to a constant drive in a fixed direction or to a rotating drive that is out…
We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X. Assuming the distribution of reacting particles in the system volume to be uniform, we introduced the notion of the point model of reaction…
Open quantum walks often lead to a classical asymptotic behavior. Here, we look for a simple open quantum walk whose asymptotic behavior can be non-classical. We consider a discrete-time quantum walk on n-cycle subject to a random…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
A novel mechanism for the appearance of oriented processes is investigated with a flexible dynamical system overcoming barriers. Under non-equilibrium condition with external driving, reaction paths deviate from that at equilibrium with an…
We show that a reversible pumping mechanism operating between two states of a kinetic network can give rise to Poisson transitions between these two states. An external observer, for whom the pumping mechanism is not accessible, will…
Chaos is an inherently dynamical phenomenon traditionally studied for trajectories that are either permanently erratic or transiently influenced by permanently erratic ones lying on a set of measure zero. The latter gives rise to the final…
This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation…
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…
To be useful, steady state thermodynamics (SST) must be self-consistent and have predictive value. Although consistency of SST was recently verified for driven lattice gases under global weak exchange, I show here that it does not predict…
Metastable polymorphs often result from the interplay between thermodynamics and kinetics. Despite advances in predictive synthesis for solution-based techniques, there remains a lack of methods to design solid-state reactions targeting…