Related papers: Maintaining the equipartition theorem in small het…
Statistical physics in equilibrium grants us one of its most powerful tools: the equipartition principle. It states that the degrees of freedom of a mechanical system act as a thermometer: temperature is equal to the mean variance of their…
We formulate a method for incorporating quantum fluctuations into molecular- dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous…
Molecular Dynamics (MD) simulations of standard systems of interacting particles ("atoms") give excellent agreement with the equipartition theorem for the average energy, but we find that these simulations exhibit finite-size effects in the…
We describe how the fast quasi-centroid molecular dynamics (f-QCMD) method can be applied to condensed phase systems by approximating the quasi-centroid potential of mean force as a sum of inter- and intra-molecular corrections to the…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
Impact phenomena of small clusters subject to thermal fluctuations are numerically investigated. From the molecular dynamics simulation for colliding two identical clusters, it is found that the restitution coefficient for head-on…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
The resolution of Brownian motion in simulations of micro-particle suspensions can be crucial to reproducing the correct dynamics of individual particles, as well as providing an accurate characterisation of suspension properties. Including…
We examine a biomolecular machine involving a driven, observable process coupled to a hidden process in a kinetically cooperative manner. A stochastic thermodynamics framework is employed to analyze a fluctuation theorem for the…
Molecular dynamics simulations of a quasi-harmonic solid are conducted to elucidate the meaning of temperature fluctuations in canonical systems and validate a well-known but frequently contested equation predicting the mean square of such…
A fluctuation theorem is examined for the first-passage time of a biomolecular machine (e.g., a motor protein or an enzyme) in a nonequilibrium steady-state. For such machines in which the driven, observable process is coupled to a hidden…
We extend the Exchange Fluctuation Theorem for energy exchange between thermal quantum systems beyond the assumption of molecular chaos, and describe the non-equilibrium exchange dynamics of correlated quantum states. The relation…
Recently a model of metric fluctuations has been proposed which yields an effective Schr\"odinger equation for a quantum particle with a modified inertial mass, leading to a violation of the weak equivalence principle. The renormalization…
Subensemble Acceptance Method (SAM) [1,2] is an essential link between measured event-by-event fluctuations and their grand canonical theoretical predictions such as lattice QCD. The method allows quantifying the global conservation law…
We consider a scalar QED model for the frictional force and the momentum fluctuations of a polarizable particle in thermal equilibrium with radiation or in hyperbolic motion in a vacuum. In the former case the loss of particle kinetic…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
We describe a fast implementation of the quasi-centroid molecular dynamics (QCMD) method in which the quasi-centroid potential of mean force is approximated as a separable correction to the classical interaction potential. This correction…
A fundamental principle of chaotic quantum dynamics is that local subsystems eventually approach a thermal equilibrium state. Large subsystems thermalize slower: their approach to equilibrium is limited by the hydrodynamic build-up of…
Fluctuation theorems are fundamental extensions of the second law of thermodynamics for small nonequilibrium systems. While work and heat are equally important forms of energy exchange, fluctuation relations have not been experimentally…
The fluctuation theorems have remained one of the cornerstones in the study of systems that are driven far out of equilibrium, and they provide strong constraints on the fraction of trajectories that behave atypically in light of the second…