5 papers
Improving sampling of binding free energy differences between covalently bound ligands in alternate binding pockets using MT-REXEE
Anika J. Friedman, Jerome M. Fox, Michael R. Shirts
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding comp…
Local ion environment in polyamide membranes revealed by molecular dynamics
Nathanael S. Schwindt, Anthony P. Straub, Michael F. Toney +1
In reverse osmosis (RO) and nanofiltration (NF) membranes, the polymer structure and interactions with solvent and solutes dictate the permeability and selectivity. However, these…
Molecular details and free energy barriers of ion de-coordination at elevated salinity and pressure and their consequences for membrane separations
Nathanael S. Schwindt, Razi Epsztein, Anthony P. Straub +2
Ion dehydration has been hypothesized to strongly influence separation performance in membrane systems and ion transport in nanoscale channels. However, the molecular details of io…
Multiple Topology Replica Exchange of Expanded Ensembles (MT-REXEE) for Multidimensional Alchemical Calculations
Anika J. Friedman, Wei-Tse Hsu, Michael R. Shirts
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To addr…
Interpreting effective energy barriers to membrane permeation in terms of a heterogeneous energy landscape
Nathanael S. Schwindt, Mor Avidar, Razi Epsztein +2
Major efforts in recent years have been directed towards understanding molecular transport in polymeric membranes, in particular reverse osmosis and nanofiltration membranes. Trans…