Related papers: Master Equation Approach to Molecular Motors
The Fokker-Planck equation is a partial differential equation which is a key ingredient in many models in physics. This paper aims to obtain a quantum counterpart of Fokker-Planck dynamics, as a means to describing quantum Fokker-Planck…
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. Based on a discrete kinetic network model, we use the integrated probability flux balance method to derive the…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
A generic method to investigate many-body continuous-variable systems is pedagogically presented. It is based on the notion of matrix product states (so-called MPS) and the algorithms thereof. The method is quite versatile and can be…
Markovian master equations provide a versatile tool for describing open quantum systems when memory effects of the environment may be neglected. As these equations are of an approximate nature, they often do not respect the laws of…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Boltzmann equation requires some alternative simpler kinetic model like BGK to replace the collision term. Such a kinetic model which replaces the Boltzmann collision integral should preserve the basic properties and characteristics of the…
We consider a system of globally coupled rotors, described by a set of Langevin equations, and examine stability of the incoherent phase. The corresponding Fokker-Planck equation, providing a unified description of microcanonical and…
The stochastic thermodynamics provides a framework for the description of systems that are out of thermodynamic equilibrium. It is based on the assumption that the elementary constituents are acted by random forces that generate a…
We develop a classical well-posedness and regularity theory on a finite connected weighted graph for an extended mean field game system, its associated master equation, and a Hamilton-Jacobi- Bellman equation on the probability simplex, all…
We propose a new kinetic BGK-type model for a mixture of four monatomic gases, undergoing a bimolecular and reversible chemical reaction. The elastic and reactive interactions are described separately by distinct relaxation terms and the…
Quantum systems coupled to environments exhibit intricate dynamics. The master equation gives a Markov approximation of the dynamics, allowing for analytic and numerical treatments. It is ubiquitous in theoretical and applied quantum…
We consider a Markov process in continuous time with a finite number of discrete states. The time-dependent probabilities of being in any state of the Markov chain are governed by a set of ordinary differential equations, whose dimension…
We model thermostatic devices using a stochastic hybrid description, and introduce an external actuation mechanism that creates random switch events in the discrete dynamics. We then conjecture the form of the Fokker-Planck equation and…
An expression for the energetic efficiency of a molecular motor is presented in terms of an effective temperature, which was defined based on the ratio of the correlation function to the susceptibility of its velocity. We also present a…
We examine a completely positive and trace preserving evolution of finite dimensional open quantum system, coupled to large environment via periodically modulated interaction Hamiltonian. We derive a corresponding Markovian Master Equation…
The stochastic systems without detailed balance are common in various chemical reaction systems, such as metabolic network systems. In studies of these systems, the concept of potential landscape is useful. However, what are the sufficient…
An extended variational principle providing the equations of motion for a system consisting of interacting classical, quasiclassical and quantum components is presented, and applied to the model of bilinear coupling. The relevant dynamical…
A multi-species Fokker-Planck model for simulating particle collisions in a plasma is presented. The model includes various parameters that must be tuned. Under reasonable assumptions on these parameters, the model satisfies appropriate…