Related papers: Mass-scaling replica-exchange molecular dynamics o…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
Langevin diffusion (LD) is one of the main workhorses for sampling problems. However, its convergence rate can be significantly reduced if the target distribution is a mixture of multiple densities, especially when each component…
By combining two generalized-ensemble algorithms, Replica-Exchange Wang-Landau (REWL) method and Multicanonical Replica-Exchange Method (MUCAREM), we propose an effective simulation protocol to determine the density of states with high…
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally…
Enhanced sampling techniques are essential for exploring biomolecular conformational dynamics that occur on timescales inaccessible to conventional molecular dynamics (MD) simulations. This study introduces a framework that combines…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
This paper presents a novel non-linear model reduction method: Probabilistic Manifold Decomposition (PMD), which provides a powerful framework for constructing non-intrusive reduced-order models (ROMs) by embedding a high-dimensional system…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
With the path integral approach, the thermal average in a multi-electronic-state quantum systems can be approximated by the ring polymer representation on an extended configuration space, where the additional degrees of freedom are…
The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients of the two-channel roaming reaction H + MgH. Both reaction channels, tight and roaming, are explicitly considered. This is a pioneering attempt…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Part of the success of diffusion models stems from their ability to perform iterative refinement, i.e., repeatedly correcting outputs during generation. However, modern masked discrete diffusion lacks this capability: when a token is…
Stochastic multi-scale modeling and simulation for nonlinear thermo-mechanical problems of composite materials with complicated random microstructures remains a challenging issue. In this paper, we develop a novel statistical higher-order…
Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving…
In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HS). The idea behind the proposal is expanding volume instead of…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown…
In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD).…
Diffusion Models have emerged as a leading class of generative models, yet their iterative sampling process remains computationally expensive. Timestep distillation is a promising technique to accelerate generation, but it often requires…