41 citations · 79 across the 6 of their papers we have counts for
6 papers
Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning
Dhiman Ray, Trevor Gokey, David L. Mobley +1
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociatio…
Weighted Ensemble Milestoning (WEM): A Combined Approach for Rare Event Simulations
Dhiman Ray, Ioan Andricioaei
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist t…
Advancements in Milestoning II: Calculating Autocorrelation from Milestoning Data Using Stochastic Path Integrals in Milestone Space
Gianmarc Grazioli, Ioan Andricioaei
The Milestoning method has achieved great success in the calculation of equilibrium kinetic properties such as rate constants from molecular dynamics simulations. The goal of this…
Advancements in Milestoning I: Accelerated Milestoning via "Wind" Assisted Re-weighted Milestoning (WARM)
Gianmarc Grazioli, Ioan Andricioaei
The Milestoning algorithm created by Ron Elber et al. is a method for determining the time scale of processes too complex to be studied using brute force simulation methods. The fu…
Free energy landscape and characteristic forces for the initiation of DNA unzipping
Ahmet Mentes, Ana Maria Florescu, Elizabeth Brunk +3
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded…
Reconstructing Equilibrium Entropy and Enthalpy Profiles from Non-equilibrium Pulling
Daun Jeong, Ioan Andricioaei
The Jarzynski identity can be applied to instances when a microscopic system is pulled repeatedly but quickly along some coordinate, allowing the calculation of an equilibrium free…