Related papers: Mass-scaling replica-exchange molecular dynamics o…
Recent advances in diffusion models have demonstrated their strong capabilities in generating high-fidelity samples from complex distributions through an iterative refinement process. Despite the empirical success of diffusion models in…
We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of…
Diffusion distillation is central to accelerating image and video generation, yet existing methods are fundamentally limited by the denoising process, where step reduction has largely saturated. Partial timestep low-resolution generation…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
The nematic-isotropic (NI) phase transition of 4-cyano-4'-pentylbiphenyl (5CB) was simulated using the generalized replica-exchange method (gREM) based on molecular dynamics simulations. The effective temperature is introduced in gREM,…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…
We describe the study of thermodynamics of materials using replica-exchange Wang-Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang-Landau Monte Carlo method. To evaluate the performance and…
We describe the remapped particle-mesh method, a new mass-conserving method for solving the density equation which is suitable for combining with semi-Lagrangian methods for compressible flow applied to numerical weather prediction. In…
We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
A new approach to simulating rotational cooling using a direct simulation Monte Carlo (DSMC) method is described and applied to the rotational cooling of ammonia seeded into a helium supersonic jet. The method makes use of ab initio…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Deep learning-based recommendation models (DLRMs) are widely deployed in commercial applications to enhance user experience. However, the large and sparse embedding layers in these models impose substantial memory bandwidth bottlenecks due…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
In replica exchange Monte Carlo (REM), tuning of the temperature set and the exchange scheduling are crucial in improving the accuracy and reducing calculation time. In multi-dimensional simulated tempering, the first order phase transition…