Related papers: Multicanonical molecular dynamics by variable-temp…
We introduce an infinite particle system dynamics, which includes stochastic chemical kinetics models, the classical Kac model and free space movement. We study energy redistribution between two energy types (kinetic and chemical) in…
A consistent description of simultaneous heat and particle transport, including cross effects, and the associated entropy balance is given in the framework of a deterministic dynamical system. This is achieved by a multibaker map where,…
We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
We show that for any liquid or solid with strong correlation between its $NVT$ virial and potential-energy equilibrium fluctuations, the temperature is a product of a function of excess entropy per particle and a function of density,…
The crucial problem for better understanding the nature of glass transition and related relaxation phenomena is to find proper interrelations between molecular dynamics and thermodynamics of viscous systems. To gain this aim the recently…
Molecular dynamics simulations require barostats to be performed at constant pressure. The usual recipe is to employ the Berendsen barostat first, which displays a first-order volume relaxation efficient in equilibration but results in…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
The recently established connection between stochastic thermodynamics and fluctuating hydrodynamics is applied to a study of efficiencies in the coupled transport of heat and matter on a small scale. A stochastic model for a mesoscopic cell…
In systems with detailed balance, the stationary distribution and the equilibrium distribution are identical, creating a clear connection between energetic and entropic quantities. Many driven systems violate detailed balance and still pose…
Using molecular dynamics simulations we study the temperature-density phase diagram of a simple model system of particles in two dimensions. In addition to translational degrees of freedom, each particle has two internal states and…
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the thermodynamically-weighted activation-relaxation…
We introduce a reweighting technique which allows for a continuous sampling of temperatures in a single simulation and employ it to compute the temperature dependence of the QCD topological susceptibility at high temperatures. The method…
We consider numerical methods for thermodynamic sampling, i.e. computing sequences of points distributed according to the Gibbs-Boltzmann distribution, using Langevin dynamics and overdamped Langevin dynamics (Brownian dynamics). A wide…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
In the general case of a many-body Hamiltonian system, described by an autonomous Hamiltonian $H$, and with $K\geq 0$ independent conserved quantities, we derive the microcanonical thermodynamics. By a simple approach, based on the…
Descriptions of molecular systems usually refer to two distinct theoretical frameworks. On the one hand the quantum pure state, i.e. the wavefunction, of an isolated system which is determined to calculate molecular properties and to…
The molecular dynamics lattice gas method maps a molecular dynamics simulation onto a lattice gas using a coarse-graining procedure. This is a novel fundamental approach to derive the lattice Boltzmann method by taking a Boltzmann average…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…