With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical
antidepressant effect. We discovered that the transmembrane domain of tyrosine kinase …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

The templating method holds great promise for fabricating surface nanopatterns. To
enhance the manufacturing capabilities of complex surface nanopatterns, it is important to …

Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

The ability of atomic interaction parameters generated using the Automated Topology
Builder and Repository version 3.0 (ATB3. 0) to predict experimental hydration free …

We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and
free energy methods in Amber18. Of particular interest is the development of alchemical free …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

Monovalent ions play significant roles in various biological and material systems. Recently,
four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved …