Related papers: Combining Enhanced Sampling with Experiment Direct…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
Complex biological processes are usually experimented along time among a collection of individuals. Longitudinal data are then available and the statistical challenge is to better understand the underlying biological mechanisms. The…
Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly…
Enriched Dirichlet process mixture (EDPM) models are Bayesian nonparametric models which can be used for nonparametric regression and conditional density estimation and which overcome a key disadvantage of jointly modeling the response and…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
Online controlled experiments, also known as A/B testing, are the digital equivalent of randomized controlled trials for estimating the impact of marketing campaigns on website visitors. Stratified sampling is a traditional technique for…
Cosimulation methods allow combination of simulation tools of physical systems running in parallel to act as a single simulation environment for a big system. As data is passed across subsystem boundaries instead of solving the system as…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
Chemical space is so large that brute force searches for new interesting molecules are infeasible. High-throughput virtual screening via computer cluster simulations can speed up the discovery process by collecting very large amounts of…
Stochastic simulators are increasingly used to expand the frontier of scientific knowledge and inform decision-making across real-world contexts. Simulator calibration, a process by which internal model inputs are tuned to match some…
One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here I derive equations for the equilibrium distributions generated by…
Observations with distributed sensors are essential in analyzing a series of human and machine activities (referred to as 'events' in this paper) in complex and extensive real-world environments. This is because the information obtained…
Numerical modeling of turbulent spray combustion provides a promising tool for advanced engine design. In spray flames, the droplet evaporation not only reduces the ambient gas temperature, but also influences flame structure by generating…
A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…
Mechanistic simulation models are inverted against observations in order to gain inference on modeled processes. However, with the increasing ability to collect high resolution observations, these observations represent more patterns of…
Ultrasound-guided drug and gene delivery (usdg) enables controlled and spatially precise delivery of drugs and macromolecules, encapsulated in microbubbles (embs) and submicron gas vesicles (gvs), to target areas such as cancer tumors. It…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
A valuable step in the modeling of multiscale dynamical systems in fields such as computational chemistry, biology, materials science and more, is the representative sampling of the phase space over long timescales of interest; this task is…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…