相关论文: Single-ensemble nonequilibrium path-sampling estim…

Free energy perturbation (FEP) was proposed by Zwanzig more than six decades ago as a method to estimate free energy differences, and has since inspired a huge body of related methods that use it as an integral building block. Being an…

In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…

The equilibrium thermodynamics of the two dimensional Su-Schrieffer-Heeger Model is derived by means of a path integral method which accounts for the variable range of the electronic hopping processes. While the lattice degrees of freedom…

An estimator for the dynamical temperature in an arbitrary ensemble is derived in the framework of Bayesian statistical mechanics and the maximum entropy principle. We test this estimator numerically by a simulation of the two-dimensional…

We perform a thorough analysis on the choice of estimators for random series path integral methods. In particular, we show that both the thermodynamic (T-method) and the direct (H-method) energy estimators have finite variances and are…

We address the problem of the minus sign sampling for two electron systems using the path integral approach. We show that this problem can be reexpressed as one of computing free energy differences and sampling the tails of statistical…

We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution…

The modern theory of rare events is grounded in near equilibrium ideas, however many systems of modern interest are sufficiently far from equilibrium that traditional approaches do not apply. Using the recently developed variational path…

A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…

It has recently been shown that the Helmholtz free energy difference between two equilibrium configurations of a system may be obtained from an ensemble of finite-time (nonequilibrium) measurements of the work performed in switching an…

We employ the quantum jump trajectory approach to construct a systematic framework to study the thermodynamics at the trajectory level in a nonequilibrium open quantum system under discrete feedback control. Within this framework, we derive…

Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…

Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature, it has the potential to provide…

We introduce a new method to simulate the physics of rare events. The method, an extension of the Temperature Accelerated Molecular Dynamics, comes in use when the collective variables introduced to characterize the rare events are either…

Near equilibrium, thermodynamic intuition suggests that fast, irreversible processes will dissipate more energy and entropy than slow, quasistatic processes connecting the same initial and final states. Here, we test the hypothesis that…

All ensembles of statistical mechanics are equivalent in the sense that they give the equivalent thermodynamic functions in the thermodynamic limit. However, when investigating microscopic structures in the first-order phase transition…

We present a history-dependent Monte Carlo scheme for the efficient calculation of the free-energy of quantum systems, inspired by the Wang-Landau sampling and metadynamics method. When embedded in a path integral formulation, it is of…

We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from…

The nonequilibrium work relation, or Jarzynski equality, establishes a statistical relationship between a series of nonequilibrium experiments on a system subjected to thermal fluctuations and a hypothetical experiment at thermodynamic…

This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…