Molecular multiresolution surfaces

TL;DR

This paper introduces molecular multiresolution surfaces as a new multiscale modeling paradigm, generated via a novel diffusion map approach that unifies various molecular surface types.

Contribution

It presents a new concept and computational method for molecular surfaces using diffusion maps and a local spectral evolution kernel.

Findings

Unified framework for multiple molecular surfaces

Efficient numerical integration of diffusion equations

Potential applications in biological modeling

Abstract

The surface of a molecule determines much of its chemical and physical property, and is of great interest and importance. In this Letter, we introduce the concept of molecular multiresolution surfaces as a new paradigm of multiscale biological modeling. Molecular multiresolution surfaces contain not only a family of molecular surfaces, corresponding to different probe radii, but also the solvent accessible surface and van der Waals surface as limiting cases. All the proposed surfaces are generated by a novel approach, the diffusion map of continuum solvent over the van der Waals surface of a molecule. A new local spectral evolution kernel is introduced for the numerical integration of the diffusion equation in a single time step.