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Stochastic and dynamical processes lie at the heart of all physical, chemical, and biological systems. However, kinetic and thermodynamic properties which characterize these processes have largely been treated separately as they can be…
We consider the dynamics of a quantum system immersed in a dilute gas at thermodynamics equilibrium using a quantum Markovian master equation derived by applying the low-density limit technique. It is shown that the Gibbs state at the bath…
We study dynamics and thermodynamics of ion channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and lipids,…
General conditions are established under which reaction-cross-diffusion systems can undergo spatiotemporal pattern-forming instabilities. Recent work has focused on designing systems theoretically and experimentally to exhibit patterns with…
In order to determine what quantum operations and measurements are consistent with the laws of thermodynamics, one must start by allowing all processes allowed by the framework of quantum theory, and then impose the laws of thermodynamics…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
We present a multiscale atomistic-to-continuum method for ionic crystals with defects. Defects often play a central role in ionic and electronic solids, not only to limit reliability, but more importantly to enable the functionalities that…
It is well known that, for mass-action systems, complex-balanced equilibria are asymptotically stable. For generalized mass-action systems, even if there exists a unique complex-balanced equilibrium (in every stoichiometric class and for…
In this paper, we examine how to build coarse-grain transport models consistently from the kinetic to fluid regimes. The internal energy of the gas particles is described through a state-to-state approach. A kinetic equation allows us to…
Deep convection is one of the most important atmospheric transport mechanisms and associated with various severe weather phenomena. Manifestations of deep convection in the atmosphere are composed of a recurring fundamental building block,…
Realistic modeling of ionic systems necessitates taking explicitly account of many-body effects. In molecular dynamics simulations, it is possible to introduce explicitly these effects through the use of additional degrees of freedom. Here…
Over the past years, radiofrequency ion traps have become an attractive platform for studying chemical reactions as they enable a high degree of control over ion-molecule dynamics. In this review, we summarize techniques for the trapping…
Ion transport through nanoscale channels and pores is pivotal to numerous natural processes and industrial applications. Experimental investigation of the kinetics and mechanisms of such processes is, however, hampered by the limited…
From a mathematical model that describes a complex chemical kinetic system of $N$ species and $M$ elementrary reactions in a rapidly stirred vessel of size $V$ as a Markov process, we show that a macroscopic chemical thermodynamics emerges…
Ionic liquids offer unique bulk and interfacial characteristics as battery electrolytes. Our continuum approach naturally describes the electrolyte on a macroscale. An integral formulation for the molecular repulsion,which can be…
We consider a particle with a position-dependent mass, moving in a three-dimensional semi-infinite parallelepipedal or cylindrical channel under the influence of some hyperbolic potential. We show that the lack of uniformity in the…
Cold ions in anisotropic harmonic potentials can form ion chains of various sizes. Here, the density of ions is not uniform, thus the eigenmodes are not phononic-like waves. We study chains of N>>1 ions and evaluate analytically the long…
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…
A new class of models, generalizing Asymmetric Exclusion Process for many parallel interacting channels, is proposed. We couple the models with boundary reservoirs, study boundary-driven phase transitions and show that usually taken…
Under the assumption of mass-action kinetics, a dynamical system may be induced by several different reaction networks and/or parameters. It is therefore possible for a mass-action system to exhibit complex-balancing dynamics without being…