相关论文: Efficient Estimation of Transition Rates as Functi…
We present a method to estimate the transition rates of molecular systems under different environmental conditions which cause the formation or the breaking of bonds and require the sampling of the Grand Canonical Ensemble. For this…
The most efficient MC weights for the calculation of physical, canonical expectation values are not necessarily those of the canonical ensemble. The use of suitably generalized ensembles can lead to a much faster convergence of the…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other…
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…
Calculating thermodynamic potentials and observables efficiently and accurately is key for the application of statistical mechanics simulations to materials science. However, naive Monte Carlo approaches, on which such calculations are…
We describe a Monte Carlo scheme for simulating polydisperse fluids within the grand canonical ensemble. Given some polydisperse attribute $\sigma$, the state of the system is described by a density distribution $\rho(\sigma)$ whose form is…
Many experimentally-accessible, finite-sized interacting quantum systems are most appropriately described by the canonical ensemble of statistical mechanics. Conventional numerical simulation methods either approximate them as being coupled…
We describe a Monte Carlo scheme for the grand canonical simulation study of fluid phase equilibria in highly size-asymmetrical binary mixtures. The method utilizes an expanded ensemble in which the insertion and deletion of large particles…
We discuss problems associated with the notion of pH in heterogeneous systems. For homogeneous systems, standardization protocols lead to a well defined quantity, which although different from S\o rensen's original idea of pH, is well…
In any valid Monte Carlo sampling that realizes microcanonical property we can collect statistics for a transition matrix in energy. This matrix is used to determine the density of states, from which most of the thermodynamical averages can…
Monte Carlo simulations have boosted the numerical study of several different physical systems and in particular, the canonical ensemble has been especially useful because of the existence of easy and efficient relaxation algorithms…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We present a formalism of the transition matrix Monte Carlo method. A stochastic matrix in the space of energy can be estimated from Monte Carlo simulation. This matrix is used to compute the density of states, as well as to construct…
In complex systems with many degrees of freedom such as spin glass and biomolecular systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble performs a random…
Simulation within the grand canonical ensemble is the method of choice for accurate studies of first order vapour-liquid phase transitions in model fluids. Such simulations typically employ sampling that is biased with respect to the…
In this paper, we draw attention to the problem of phase transitions in systems with locally affine microcanonical entropy, in which partial equivalence of (microcanonical and canonical) ensembles is observed. We focus on a very simple spin…
A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic…
The aim of this tutorial is to analyze the equilibrium properties of some simple but widely used quantum systems. The canonical ensemble is used to evaluate the required properties here.
In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this…