Related papers: Replica-Permutation Method with the Suwa-Todo Algo…

We introduce a parallel Wang-Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of complex systems, we apply it to different spin models…

We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…

We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…

We present a new type of the Hamiltonian replica-exchange method, in which not temperatures but the van der Waals radius parameter is exchanged. By decreasing the van der Waals radii that control spatial sizes of atoms, this Hamiltonian…

This study develops an algorithm to reproduce reaction route maps (RRMs) in shape space from the outputs of potential search algorithms. To demonstrate this, GRRM is utilized as a potential search algorithm but the proposed algorithm should…

Although machine-learning potentials have recently had substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio…

A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…

In 1986, Swendsen and Wang proposed a replica Monte Carlo algorithm for spin glasses [Phys. Rev. Lett. 57 (1986) 2607]. Two important ingredients are present, (1) the use of a collection of systems (replicas) at different of temperatures,…

We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…

Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…

We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…

Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…

Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…

Computationally expensive Radiative Transfer Models (RTMs) are widely used} to realistically reproduce the light interaction with the Earth surface and atmosphere. Because these models take long processing time, the common practice is to…

We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models…

We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the…

The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in…

In this paper, we suggest a novel sampling method for Monte Carlo molecular simulations. In order to perform efficient sampling of molecular systems, it is advantageous to avoid extremely high energy configurations while also retaining the…

Nested sampling (NS) has emerged as a powerful tool for exploring thermodynamic properties in materials science. However, its efficiency is often hindered by the limitations of Markov chain Monte Carlo (MCMC) sampling. In strongly…

We propose a theoretical approach to estimate the permeability coefficient of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of…