The Geometry of Biomolecular Solvation

Summary

Years of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molecular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.

Here we focus on the representation of biomolecules used in these simulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics.

In parallel, we review our own developments in mathematics and computer science on understanding the geometry of unions of balls, and their applications in molecular simulation.

1. Introduction

The molecular basis of life rests on the activity of biological macro-molecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between biology and geometry, focusing on hard sphere models of biomolecules.

The biomolecular revolution. Most living organisms are complex assemblies of cells, the building blocks for life. Each cell can be seen as a small chemical factory, involving thousands of different players with a large range of size and function. Among them, biological macro-molecules hold a special place.