162 citations · 330 across the 11 of their papers we have counts for
11 papers
Benchmarking optimality of time series classification methods in distinguishing diffusions
Zehong Zhang, Fei Lu, Esther Xu Fei +3
Statistical optimality benchmarking is crucial for analyzing and designing time series classification (TSC) algorithms. This study proposes to benchmark the optimality of TSC algor…
Order parameter prediction from molecular dynamics simulations in proteins
Juan R. Perilla, Thomas B. Woolf
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfort…
Folding is Not Required for Bilayer Insertion: Replica Exchange Simulations of an a-Helical Peptide with an Explicit Lipid Bilayer
Hugh Nymeyer, Thomas B. Woolf, Angel E. Garcia
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We obser…
Stochastic dynamics and the dynamic phase transition in thin ferromagnetic films
Hyunbum Jang, Malcolm J. Grimson, Thomas B. Woolf
The dynamic phase behavior of a classical Heisenberg spin system with a bilinear exchange anisotropy in a planar thin film geometry has been investigated by Monte Carlo simulations…
Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm
Daniel M. Zuckerman, Thomas B. Woolf
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure,…
Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities
Daniel M. Zuckerman, Thomas B. Woolf
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the…