Related papers: Sparse Sampling of Water Density Fluctuations near…
The free energetics of water density fluctuations near a surface, and the rare low-density fluctuations in particular, serve as reliable indicators of surface hydrophobicity; the easier it is to displace the interfacial waters, the more…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing…
Water density fluctuations are an important statistical mechanical observable that is related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also…
We use molecular dynamics simulations of the SPC-E model of liquid water to derive probability distributions for water density fluctuations in probe volumes of different shapes and sizes, both in the bulk as well as near hydrophobic and…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
Sampling from unnormalized densities is analogous to the generative modeling problem, but the target distribution is defined by a known energy function instead of data samples. Because evaluating the energy function is often costly, a…
In this paper an approach for decreasing the computational effort required for the spectral simulations of the water waves is introduced. Signals with majority of the components zero, are known as the sparse signals. Like majority of the…
Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to…
Simulation within the grand canonical ensemble is the method of choice for accurate studies of first order vapour-liquid phase transitions in model fluids. Such simulations typically employ sampling that is biased with respect to the…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
Free energies as a function of a selected set of collective variables are commonly computed in molecular simulation and of significant value in understanding and engineering molecular behavior. These free energy surfaces are most commonly…
The expression of the free energy of a liquid in terms of an explicit decomposition of the particle configurations into local coordination clusters is examined. We argue that the major contribution to the entropy associated with structural…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive…
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…
We investigate the fluctuations around the average density profile in the weakly asymmetric exclusion process with open boundaries in the steady state. We show that these fluctuations are given, in the macroscopic limit, by a centered…