Related papers: xTRAM: Estimating equilibrium expectations from ti…
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram Analysis Method (WHAM) which is an iterative post-processing…
In modern computer experiment applications, one often encounters the situation where various models of a physical system are considered, each implemented as a simulator on a computer. An important question in such a setting is determining…
We present two algorithms by which a set of short, unbiased trajectories can be iteratively reweighted to obtain various observables. The first algorithm estimates the stationary (steady state) distribution of a system by iteratively…
We present extensive Monte Carlo simulations on a two-dimensional XY model with a modified form of interaction potential. Thermodynamic quantities other than energy, specific heat etc (such as magnetization, susceptibility, fourth order…
Stochastic nonlinear dynamical systems can undergo rapid transitions relative to the change in their forcing, for example due to the occurrence of multiple equilibrium solutions for a specific interval of parameters. In this paper, we…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
In comparison to numerous enhanced sampling methods for equilbrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many non-equilibrium processes can be described by suitable subsets of the equilibrium…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant…
A simple reweighting scheme is proposed for Monte Carlo simulations of interacting particle systems, permitting one to study various parameter values in a single study, and improving efficiency by an order of magnitude. Unlike earlier…
Computer simulations generate trajectories at a single, well-defined thermodynamic state point. Statistical reweighting offers the means to reweight static and dynamical properties to different equilibrium state points by means of analytic…
Inspired by biological swimming and flying with distributed sensing, we propose a data-driven approach for load estimation that relies on complex networks. We exploit sparse, real-time pressure inputs, combined with pre-trained transition…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in…
This paper presents a novel approach that leverages Transformer-based multivariate time series model and Machine Learning Ensembles to predict the quality of human sleep, emotional states, and stress levels. A formula to calculate the…
Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, including single-molecule pulling experiments and analogous computer…
We illustrate how finite-temperature charge and thermal Drude weights of one-dimensional systems can be obtained from the relaxation of initial states featuring global (left-right) gradients in the chemical potential or temperature. The…