Biomolecular Applications of Poisson–Boltzmann Methods

Abstract

INTRODUCTION TO BIOMOLECULAR ELECTROSTATICSThroughout the 1990s, biomolecular simulation has become increasingly commonplace in biology and has gained acceptance as an important biophysical method for understanding molecular structure, dynamics, and function. The energetic properties of a biomolecule are determined by a combination of both short-and long-range forces. Short-range forces include several components, such as van der Waals, bonding forces, angular forces, and torsional interactions. Long-range forces, on the other hand, are typically dominated by electrostatic interactions. Because of their slow decay over distance, electrostatics cannot be neglected or truncated in biomolecular modeling; these forces contribute significantly to molecular interactions at all length scales. As such, methods that enable the accurate and efficient modeling of these interactions are of central importance in molecular simulation.The exact behavior of electrostatic interactions in a simulation is generally determined by four factors: molecular charge distributions, solute atomic radii, mobile ionic species, and solvent. Molecular charge distributions are

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