Enhanced sampling methods for molecular dynamics simulations
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …
molecular dynamics simulations and allow the sampling of larger portions of the …
Driving and characterizing nucleation of urea and glycine polymorphs in water
Z Zou, ER Beyerle, ST Tsai… - Proceedings of the …, 2023 - National Acad Sciences
Crystal nucleation is relevant across the domains of fundamental and applied sciences.
However, in many cases, its mechanism remains unclear due to a lack of temporal or spatial …
However, in many cases, its mechanism remains unclear due to a lack of temporal or spatial …
[HTML][HTML] State predictive information bottleneck
The ability to make sense of the massive amounts of high-dimensional data generated from
molecular dynamics simulations is heavily dependent on the knowledge of a low …
molecular dynamics simulations is heavily dependent on the knowledge of a low …
A maximum caliber approach for continuum path ensembles
The maximum caliber approach implements the maximum entropy principle for trajectories
by maximizing a path entropy under external constraints. The maximum caliber approach …
by maximizing a path entropy under external constraints. The maximum caliber approach …
Transition path sampling as Markov chain Monte Carlo of trajectories: Recent algorithms, software, applications, and future outlook
PG Bolhuis, DWH Swenson - Advanced Theory and …, 2021 - Wiley Online Library
The development of enhanced sampling methods to investigate rare but important events
has always been a focal point in the molecular simulation field. Such methods often rely on …
has always been a focal point in the molecular simulation field. Such methods often rely on …
Data-driven path collective variables
Identifying optimal collective variables to model transformations using atomic-scale
simulations is a long-standing challenge. We propose a new method for the generation …
simulations is a long-standing challenge. We propose a new method for the generation …
Discovering collective variables of molecular transitions via genetic algorithms and neural networks
F Hooft, A Pérez de Alba Ortíz… - Journal of chemical theory …, 2021 - ACS Publications
With the continual improvement of computing hardware and algorithms, simulations have
become a powerful tool for understanding all sorts of (bio) molecular processes. To handle …
become a powerful tool for understanding all sorts of (bio) molecular processes. To handle …
[HTML][HTML] Classical molecular dynamics
This issue of JCP highlights both developments in and applications of classical molecular
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions
N Naleem, CRA Abreu, K Warmuz, M Tong… - The Journal of …, 2023 - pubs.aip.org
Determining collective variables (CVs) for conformational transitions is crucial to
understanding their dynamics and targeting them in enhanced sampling simulations. Often …
understanding their dynamics and targeting them in enhanced sampling simulations. Often …
[HTML][HTML] Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)
A method for obtaining appropriate reaction coordinates is required to identify transition
states distinguishing the product and reactant in complex molecular systems. Recently …
states distinguishing the product and reactant in complex molecular systems. Recently …