The issues of electronic polarizability in molecular dynamics simulations are discussed. We
argue that the charges of ionized groups in proteins, and charges of ions in conventional …

▪ Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge
transfer in a wide variety of systems including biology-and materials-oriented venues. We …

Implicit solvent models for biomolecular simulations are reviewed and their underlying
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …

Because of its unique properties, water drives many natural and biological processes. While
a detailed understanding of its precise role is still being unravelled, it is clear that the …

The dielectric constants of myoglobin, apomyoglobin, the B fragment of staphylococcal
protein A, and the immunoglobulin-binding domain of streptococcal protein G are calculated …

One of the most direct benchmarks for electrostatic models of macromolecules is provided
by the p K a's of ionizable groups in proteins. Obtaining accurate results for such a …

Ionizable residues play important roles in protein structure and activity, and proton binding is
a valuable reporter of electrostatic interactions in these systems. We use molecular …

A simple model for accounting for electronic polarization in molecular dynamics (MD)
simulations is discussed. In this model, called molecular dynamics electronic continuum …

Electrostatic interactions are the most relevant for understanding biochemical systems. Acid-
base and redox reactions create or destroy unit charges in biomolecules and can thus be …

We discuss a bottom up approach for modeling photosynthetic light-harvesting. Methods are
reviewed for a full structure-based parameterization of the Hamiltonian of pigment–protein …