49 citations · 85 across the 4 of their papers we have counts for
5 papers
Choice of Damping Coefficient in Langevin Dynamics
Robert D. Skeel, Carsten Hartmann
This article considers the application of Langevin dynamics to sampling and investigates how to choose the damping parameter in Langevin dynamics for the purpose of maximizing thor…
On the famous unpublished preprint "Methods of integration which preserve the contact transformation property of the Hamilton equations" by René De Vogelaere
Robert D. Skeel, Jan L. Cieśliński
The well known 1956 unpublished report by De Vogelaere, motivated by the physics of particle accelerators, is the first demonstration of the existence of numerical integrators (now…
Quasi-Reliable Estimates of Effective Sample Size
Youhan Fang, Yudong Cao, Robert D. Skeel
The efficiency of a Markov chain Monte Carlo algorithm might be measured by the cost of generating one independent sample, or equivalently, the total cost divided by the effective…
Compressible Generalized Hybrid Monte Carlo
Youhan Fang, Jesus-Maria Sanz-Serna, Robert D. Skeel
One of the most demanding calculations is to generate random samples from a specified probability distribution (usually with an unknown normalizing prefactor) in a high-dimensional…
Maximum Flux Transition Paths of Conformational Change
Ruijun Zhao, Juanfang Shen, Robert D. Skeel
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and…