41 citations · 120 across the 6 of their papers we have counts for
6 papers
Good rates from bad coordinates: the exponential average time-dependent rate approach
Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio +1
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 confo…
Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods
Yuvraj Singh, Glen M. Hocky
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic…
Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate betwee…
Assessing models of force-dependent unbinding rates via infrequent metadynamics
Willmor J. Peña Ccoa, Glen M. Hocky
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and t…
Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data
Andrew D. White, Chris Knight, Glen M. Hocky +1
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties…
Equilibrium ultrastable glasses produced by random pinning
Glen M Hocky, Ludovic Berthier, David R. Reichman
Ultrastable glasses have risen to prominence due to their potentially useful material properties and the tantalizing possibility of a general method of preparation via vapor deposi…