paper 141228174126

Abstract

Understanding the behavior of biomolecules such as proteins requires understand- ing the critical influence of the surrounding fluid (solvent) environment — water with mobile salt ions such as sodium. Unfortunately, for many studies, fully atomistic simulations of biomolecules, surrounded by thousands of water molecules and ions are too computationally slow. Continuum- solvent models based on macroscopic dielectric theory (e.g., the Poisson equation) are popular alternatives, but their simplicity fails to capture well-known phenomena of functional signifi- cance. For example, standard theories predict that electrostatic response is symmetric with respect to the sign of an atomic charge, even though response is in fact strongly asymmetric if the charge is near the biomolecule surface. In this work, we present an asymmetric continuum theory that captures the essential physical mechanism — the finite size of solvent atoms — us- ing a nonlinear boundary condition (NLBC) at the dielectric interface between the biomolecule and solvent. Numerical calculations using boundary-integral methods demonstrate that the new NLBC model reproduces a wide range of results computed by more realistic, and expensive, all-atom molecular-dynamics (MD) simulations in explicit water. We discuss model extensions such as modeling dilute-electrolyte solvents with Debye-Huckel theory (the linearized Poisson- Boltzmann equation) and opportunities for the electromagnetics community to contribute to research in this important area of molecular nanoscience and engineering.

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Jaydeep P. Bardhan

Matthew G. Knepley

A. Ramaswamy

D. A. Tejani

N. S. Wieckowski