相关论文: How wet should be the reaction coordinate for liga…
A molecular theory of liquid water is identified and studied on the basis of computer simulation of the TIP3P model of liquid water. This theory would be exact for models of liquid water in which the intermolecular interactions vanish…
We provide exact solutions of the Stokes equations for a squirming sphere close to a no-slip surface, both planar and spherical, and for the interactions between two squirmers, in three dimensions. These allow the hydrodynamic interactions…
A sequential of concepts developed in last decade has enabled a resolution to multiple anomalies of water ice and its low-dimensionality, particularly. Developed concepts include the coupled hydrogen bond oscillator pair, segmental specific…
Analysis of SFG vibrational spectra of OH stretching bands in four experimental configurations shows that orientational motion of water molecule at air/water interface is libratory within a limited angular range. This picture is…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
A general and local reactive boundary condition (RBC) for studying first-order equilibrium reactions using the lattice Boltzmann method (LBM) is presented. Its main characteristics are accurate reproduction of wall diffusion, invariance to…
Recently it was shown that the WAC model for liquid silica [L. V. Woodcock, C. A. Angell, and P. Cheeseman, J. Chem. Phys. 65, 1565 (1976)] is remarkably close to having a liquid-liquid critical point (LLCP). We demonstrate that increasing…
In an attempt to investigate the structures of ultra-relativistic jets injected into the intracluster medium (ICM) and the associated flow dynamics, such as shocks, velocity shear, and turbulence, we have developed a new special…
Trajectory optimization with contact-rich behaviors has recently gained attention for generating diverse locomotion behaviors without pre-specified ground contact sequences. However, these approaches rely on precise models of robot dynamics…
Microgrids are increasingly being utilized to improve the resilience and operational flexibility of power grids, and act as a backup power source during grid outages. However, it necessitates that the microgrid itself could provide power to…
This paper introduces two metrics (cycle-based and memory-based metrics), grounded on a dynamical game-theoretic solution concept called sink equilibrium, for the evaluation, ranking, and computation of policies in multi-agent learning. We…
A new consistent, spatially adaptive, smoothed particle hydrodynamics (SPH) method for Fluid-Structure Interactions (FSI) is presented. The method combines several attributes that have not been simultaneously satisfied by other SPH methods.…
We describe a technique for particle-based simulations of heterogeneous catalysis in open-cell foam structures, which is based on isotropic Stochastic Rotation Dynamics (iSRD) together with Constructive Solid Geometry (CSG). The approach is…
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
This article describes a set of methods for quickly computing the solution to the regularized optimal transport problem. It generalizes and improves upon the widely-used iterative Bregman projections algorithm (or Sinkhorn--Knopp…
We use stochastic rotation dynamics to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using SRD are compared to similar…
Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding…
We propose a theoretical framework for the dynamics of bulk isotropic hard-sphere systems in the presence of randomly pinned particles and apply this theory to supercooled water to validate it. Structural relaxation is mainly governed by…
Entropy regularization is an important idea in reinforcement learning, with great success in recent algorithms like Soft Q Network (SQN) and Soft Actor-Critic (SAC1). In this work, we extend this idea into the on-policy realm. We propose…
Second order perturbation solutions of profiles of bubbles suspended in liquid and liquid gas interfaces when liquid all sinks in the bottom under different accelerations are derived. Six procedures are developed based on these solutions,…