Related papers: Kinetics of quasi-isoenergetic transition processe…
Novel physical mechanism is proposed for explanation of temperature-independent transition reactions in molecular systems. The mechanism becomes effective in the case of conformation transitions between quasi-isoenergetic molecular states.…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
We study an ideal-gas-like model where the particles exchange energy stochastically, through energy conserving scattering processes, which take place if and only if at least one of the two particles has energy below a certain energy…
A microscopic model for thermal excitation of vibrational ground state of a molecule interacting with a condensed medium is developed. The master equation for evolution of occupancies of the vibrational levels is derived. The rate constant…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
More than a century has passed since van't Hoff and Arrhenius formulated their celebrated rate theories, but there are still elusive aspects in the temperature-dependent phase transition kinetics of molecular systems. Here I present a…
We review the non-zero temperature relaxational dynamics of quantum systems near a zero temperature, second-order phase transition. We begin with the quantum Ising chain, for which universal and exact results for the relaxation rates can be…
Transition to thermal equilibrium in a uniformly heated two-dimensional harmonic triangular lattice with nearest neighbor interactions is investigated. Initial conditions, typical for molecular dynamics simulations, are considered.…
We provide a stochastic thermodynamic description across scales for $N$ identical units with all-to-all interactions that are driven away from equilibrium by different reservoirs and external forces. We start at the microscopic level with…
Processes that break molecular bonds are typically observed with molecules occupying a mixture of quantum states and successfully described with quasiclassical models, while a few studies have explored the distinctly quantum mechanical…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
We investigate the nonequilibrium stationary state (NESS) of the two-dimensional Ising model under a stochastic dichotomous modulation of temperature, which alternates between $T_c \pm \delta$ around the critical temperature $T_c$ at a rate…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
A formalism for quantum many-body systems is proposed through a semiclassical treatment in phase space, allowing us to establish a stochastic thermodynamics incorporating quantum statistics. Specifically, we utilize a stochastic…
Understanding how fluctuations propagate across spatial scales is central to our understanding of inanimate matter from turbulence to critical phenomena. In contrast to physical systems, biological systems are organized into a hierarchy of…
Quasistatic evolutions of critical points of time-dependent energies exhibit piecewise smooth behavior, making them useful for modeling continuum mechanics phenomena like elastic-plasticity and fracture. Traditionally, such evolutions have…
This thesis is devoted to the theoretical study of slow thermodynamic processes in non-equilibrium stochastic systems. Its main result is a physically and mathematically consistent construction of relevant thermodynamic quantities in the…
At low temperature a thermodynamic system undergoes a phase transition when a physical parameter passes through a singularity point of the free energy, corresponding to formation of a new order. At high temperature the thermal fluctuations…
We present a new stochastic model, based on a 0-dimensional version of the well known biogeochemical flux model (BFM), which allows to take into account the temperature random fluctuations present in natural systems and therefore to…
Phase transitions which occur at zero temperature when some non-thermal parameter like pressure, chemical composition or magnetic field is changed are called quantum phase transitions. They are caused by quantum fluctuations which are a…