148 citations · 745 across the 26 of their papers we have counts for
4 papers · 1 filter
Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton
Fatemah Mukadum, Willmor J. Pena Ccoa, Glen M. Hocky
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the…
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…
Computing equilibrium free energies through a nonequilibrium quench
Kangxin Liu, Grant M. Rotskoff, Eric Vanden-Eijnden +1
Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute e…
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…