Related papers: Replica-Permutation Method with the Suwa-Todo Algo…
Sediment transport over an erodible sediment bed is studied by particle resolved simulations with a hybrid parallel approach. To overcome the challenges of load imbalance in the traditional domain decomposition method when encountering…
In this paper we propose an enhanced version of the residual sub-sampling method (RSM) in [9] for adaptive interpolation by radial basis functions (RBFs). More precisely, we introduce in the context of sub-sampling methods a maximum profile…
In this work we formulate and test a new procedure, the Multiscale Perturbation Method for Two-Phase Flows (MPM-2P), for the fast, accurate and naturally parallelizable numerical solution of two-phase, incompressible, immiscible…
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).…
We propose a novel scheme that allows MIMO system to modulate a set of permutation matrices to send more information bits, extending our initial work on the topic. This system is called Permutation Matrix Modulation (PMM). The basic idea is…
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…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms.…
We present a novel, generally applicable Monte Carlo algorithm for the simulation of fluid systems. Geometric transformations are used to identify clusters of particles in such a manner that every cluster move is accepted, irrespective of…
Reverse Osmosis(RO) membranes are widespread nowadays for separating the solvent from a solution. RO membranes are made of polymer matrix. Experiments show changes in relative interaction of solvent and solute with RO membrane matrix lead…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
There exist several methods for simulating biological and physical systems as represented by chemical reaction networks. Systems with low numbers of particles are frequently modelled as discrete-state Markov jump processes and are typically…
In this paper, the surface of revolution discrete element method (SR-DEM) is introduced to simulate systems of particles with closed surfaces of revolution. Due to the cylindrical symmetry of a surface of revolution, the geometry of any…
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…
Electrochemical energy storage always involves the capacitive process. The prevailing electrode model used in the molecular simulation of polarizable electrode-electrolyte systems is the Siepmann-Sprik model developed for perfect metal…
Super-Droplet Method (SDM) is a probabilistic Monte-Carlo-type model of particle coagulation process, an alternative to the mean-field formulation of Smoluchowski. SDM as an algorithm has linear computational complexity with respect to the…
The Hybrid Monte Carlo algorithm is adapted to the simulation of a system of classical degrees of freedom coupled to non self-interacting lattices fermions. The diagonalization of the Hamiltonian matrix is avoided by introducing a…
Replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around…