Chapter 3 - Density functional theory and bridging to classical interatomic force fields

Abstract

The foundation for computational multiscale modeling of biological materials is in the quantum mechanical realm. At this scale, fundamental physical equations can be used to describe molecular systems and ab initio calculations can, in principle, be performed at the size scale of the electron. In practice, a number of assumptions are used to make computations tractable, such as those employed by density functional theory (DFT), and these assumptions allow for accurate results for the behavior of organic systems at the next scale up of individual molecules. These calculations can serve as the basis, via length-scale bridging for further simplifications used to motivate classical force field atomic models that are useful for molecular dynamics (MD) simulations on scales up to millions or even billions of atoms. This is in contrast to DFT, which is limited computationally to at most a few hundred atoms. In this chapter, we will briefly introduce the physics that governs molecular interactions at the smallest scale (electron) and the computational techniques used in solutions to these fundamental equations. We will then discuss the length-scale bridge between first principles (electron) calculation and classical force field models (atom). We will then review an existing formalism for modeling MD of biologically relevant molecules and demonstrate how it is informed by lower length-scale simulation. Finally, we will outline the process for developing new force fields using simple hydrocarbons as a model system.