25 citations · 49 across the 7 of their papers we have counts for
7 papers
Reducing Weighted Ensemble Variance With Optimal Trajectory Management
Won Hee Ryu, John D. Russo, Mats S. Johnson +7
Weighted ensemble (WE) is an enhanced path-sampling method that is conceptually simple, widely applicable, and statistically exact. In a WE simulation, an ensemble of trajectories…
Ferroelectric hydration shells around proteins: Electrostatics of the protein/water interface
David N. LeBard, Dmitry V. Matyushov
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The em…
Pretty Fast Analysis: An embarrassingly parallel algorithm for biological simulation analysis
David N. Lebard
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave algorithm, the software operates on AMBER generated t…
Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins
David N. LeBard, Dmitry V. Matyushov
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of…
Energetics and Kinetics of Primary Charge Separation in Bacterial Photosynthesis
David N. LeBard, Vitaliy Kapko, Dmitry V. Matyushov
We report the results of Molecular Dynamics (MD) simulations and formal modeling of the free energy surfaces and reaction rates of primary charge separation in the reaction center…
Redox Entropy of Plastocyanin: Developing a Microscopic View of Mesoscopic Polar Solvation
David N. LeBard, Dmitry V. Matyushov
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The…