Related papers: Transition to the Most Probable Kinetic State in a…
Controlling complex reaction networks is a fundamental challenge in the fields of physics, biology, and systems engineering. Here, we prove a general principle for catalytic reaction systems with kinetics where the reaction order and the…
In this paper we study the kinetics of diffusion-limited, pseudo-first-order A + B -> B reactions in situations in which the particles' intrinsic reactivities vary randomly in time. That is, we suppose that the particles are bearing "gates"…
A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This…
An optimal finite-time process drives a given initial distribution to a given final one in a given time at the lowest cost as quantified by total entropy production. We prove that for system with discrete states this optimal process…
The mass-based Maxwell-Stefan approach to one-phase multicomponent reactive mixtures is mathematically analyzed. It is shown that the resulting quasilinear, strongly coupled reaction-diffusion system is locally well-posed in an…
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…
When an interacting many-body system, such as a magnet, is driven in time by an external perturbation, such as a magnetic field,the system cannot respond instantaneously due to relaxational delay. The response of such a system under a…
Extinction appears ubiquitously in many fields, including chemical reactions, population biology, evolution, and epidemiology. Even though extinction as a random process is a rare event, its occurrence is observed in large finite…
The work is presented, leading to the universal contact molecular mechanism of phase transitions and other reactions in solid state. The two components of the mechanism - nucleation and interface propagation - are investigated in detail and…
Increasing evidence suggests that active matter exhibits instances of mixed symmetry that cannot be fully described by either polar or nematic formalism. Here, we introduce a minimal model that integrates self-propulsion into the active…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…
A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is…
Rare transitions between long-lived metastable states underlie a great variety of physical, chemical and biological processes. Our quantitative understanding of reactive mechanisms has been driven forward by the insights of transition state…
Quantum mechanical motion of a particle in a periodic asymmetric potential is studied theoretically at zero temperature. It is shown based on semi-classical approximation that the tunneling probability from one local minimum to the next…
Depending on how the dynamical activity of a particle in a random environment is influenced by an external field $E$, its differential mobility at intermediate $E$ can turn negative. We discuss the case where for slowly changing random…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
This paper is a preliminary work to address the problem of dynamical systems with parameters varying in time. An idea to predict their behaviour is proposed. These systems are called \emph{transient systems}, and are distinguished from…