相关论文: A new method for reactive constant pH simulations
In this work, we examine sheath formation in the presence of bias potentials in the current saturation regime for pulsed power fusion experiments. It is important to understand how the particle and heat fluxes at the wall may impact the…
We introduce an Eulerian approach for problems involving one or more soft solids immersed in a fluid, which permits mechanical interactions between all phases. The reference map variable is exploited to simulate finite-deformation…
Simulations of chemical reaction probabilities in gas surface dynamics require the calculation of ensemble averages over many tens of thousands of reaction events to predict dynamical observables that can be compared to experiments. At the…
We present simulation results addressing the dynamics of a colloidal system with attractive interactions close to gelation. Our interaction also has a soft, long range repulsive barrier which suppresses liquid-gas type phase separation at…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
Molecular dynamics simulations are utilized to study the microwave heating of methane hydrate by the five-body rotation coordinate system with the TIP5P-Ewald model. The structure I of methane hydrate is constructed, and the ice and free…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary…
We present a new first-principles linear-response theory of changes due to perturbations in the quasiparticle self-energy operator within the $GW$ method. This approach, named $GW$ perturbation theory ($GW$PT), is applied to calculate the…
Adiabatic mixed quantum/classical molecular dynamics simulations were used to generate snapshots of the hydrated electron (e-) in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the e- were…
The recently published DeePMD model (https://github.com/deepmodeling/deepmd-kit), based on a deep neural network architecture, brings the hope of solving the time-scale issue which often prevents the application of first principle molecular…
Electrostatic correlation effects in inhomogeneous symmetric electrolytes are investigated within a previously developed electrostatic self-consistent (SC) theory (R.R. Netz and H. Orland, Eur. Phys.J. E 11, 301 (2003)). To this aim, we…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
We discuss the simulation of non-perturbative cavity-QED effects using systems of trapped ions. Specifically, we address the implementation of extended Dicke models with both collective dipole-field and direct dipole-dipole interactions,…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
We develop a computational method for modeling electrostatic interactions of arbitrarily-shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion…
We consider an electrolyte solution confined by semipermeable membranes in contact with a salt-free solvent. Membranes are uncharged, but since small counter-ions leak-out into infinite salt-free reservoirs, we observe a distance-dependent…
In this paper we propose a novel and general approach to design semi-implicit methods for the simulation of fluid-structure interaction problems in a fully Eulerian framework. In order to properly present the new method, we focus on the…
The dynamic structure factor and the eigenmodes of density fluctuations in the uniform liquid $^3$He are studied using a novel non-perturbative approach. This new version of the self-consistent method of moments invokes up to nine sum rules…
The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to…