Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

Classical 3-point rigid water models are most widely used due to their computational
efficiency. Recently, we introduced a new approach to constructing classical rigid water …

Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Hydrophobicity is a phenomenon of great importance in biology, chemistry, and
biochemistry. It is defined as the interaction between nonpolar molecules or groups in water …

Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility
and its recognition by other macromolecules. Here we generate extensive atomic level …

The abnormal aggregation of α-synuclein (α-Syn) is closely associated with Parkinson's
disease. Different post-translational modifications of α-Syn have been identified and …

We investigate the effect of solvent models on the computed thermodynamics of protein
folding. Atomistic folding simulations of a fast-folding mini-protein, CLN025, were employed …

A recently introduced family of globally optimal water models, OPC, has shown promise in a
variety of biomolecular simulations, but properties of these water models outside of the liquid …

The accuracy of computational models of water is key to atomistic simulations of
biomolecules. We propose a computationally efficient way to improve the accuracy of the …