The Problem: Biomolecular structure and interactions in an aqueous environment are determined by a complicated interplay between physical and chemical forces including solvation, electrostatics, van der Waals forces, the hydrophobic effect, and covalent bonding. Electrostatic forces have received a great deal of study due to their longrange nature and the tradeoff between desolvation and interaction effects [1]. In addition, electrostatic interactions play a significant role within a biomolecule as well as between biomolecules, making the balance between the two vital to the understanding of macromolecular systems. Specifically, the goal of this work is to accurately and quickly compute the strength of electrostatic interactions for a biomolecule in an electrolyte solution, as well as the potential field that the molecule generates in all space.

The need to determine electrostatic fields in domains bounded by molecular surfaces arises in a number of nanotechnology applications including: biomolecule design, carbon nanotube simulation, and molecular electron transport analysis. Molecular surfaces are typically smooth, without the corners common in electrical interconnect problems, but are often so geometrically complicated that numerical evaluation of the associated electrostatic fields is extremely time-consuming. In this paper we describe and demonstrate a meshless spectrally-accurate integral equation method that only requires a description of the molecular surface in the form of a collection of surface points. Our meshless method is a synthesis of techniques, suitably adapted, including: spherical harmonic surface interpolation, spectral-element-like integral equation discretization, integral desingularization via variable transformation, and matrix-implicit iterative matrix solution. The spectral accuracy of this combined method is verified using analytically solvable sphere and ellipsoid problems, and then its accuracy and efficiency is demonstrated numerically by solving capacitance and coupled Poisson/linearized Poisson-Boltzmann problems associated with a commonly used model of a molecule in solution. The results demonstrate that for a tolerance of 10 −3 this new approach reduces the number of unknowns by as much as two orders of magnitude over the more commonly used flat panel methods.

Electrostatic analysis of complicated molecular surfaces arises in a number of nanotechnology applications including: biomolecule design, carbon nanotube simulation, and molecular electron transport. Molecular surfaces are typically smooth, without the corners common in electrical interconnect problems, and are candidates for methods with higher order convergence than that of the commonly used flat panel methods. In this paper we describe and demonstrate a spectrally accurate approach for analyzing molecular surfaces described by a collection of surface points. The method is a synthesis of several techniques, and starts by using least squares to fit a high order spherical harmonic surface representation to the given points. Then this analytic representation is used to construct a differentiable map from the molecular suface to a cube, an orthogonal basis is generated on the rectangular cube surfaces, and a change of variables is used to desingularize the required integrals of products of basis functions and Green's function. Finally, an efficient method for solving the discretized system using a matrix-implicit scheme is described. The combined method is demonstrated on an analytically solvable sphere problem, capacitance calculation of complicated molecular surface, and a coupled Poisson/Poisson-Boltzmann problem associated with a biomolecule. The results demonstrate that for a tolerance of 10-3 this new approach requires one to two orders of magnitude fewer unknowns than a flat panel method.

Electrostatic analysis of complicated molecular surfaces arises in a number of nanotechnology applications including: biomolecule design, carbon nanotube simulation, and molecular electron transport. Molecular surfaces are typically smooth, without the corners common in electrical interconnect problems, and are candidates for methods with higher order convergence than that of the commonly used flat panel methods. In this paper we describe and demonstrate a spectrally accurate approach for analyzing molecular surfaces described by a collection of surface points. The method is a synthesis of several techniques, and starts by using least squares to fit a high order spherical harmonic surface representation to the given points. Then this analytic representation is used to construct a differentiable map from the molecular suface to a cube, an orthogonal basis is generated on the rectangular cube surfaces, and a change of variables is used to desingularize the required integrals of products of basis functions and Green's function. Finally, an efficient method for solving the discretized system using a matrix-implicit scheme is described. The combined method is demonstrated on an analytically solvable sphere problem, capacitance calculation of complicated molecular surface, and a coupled Poisson/Poisson-Boltzmann problem associated with a biomolecule. The results demonstrate that for a tolerance of 10 −3 this new approach requires one to two orders of magnitude fewer unknowns than a flat panel method.