Introduction to Computational Materials Science Fundamentals to Applications

In this chapter, we discuss how to extend the methods introduced in the previous chapters from atomic to macromolecular systems. The basic ideas are the same, but there are additional complexities that arise from the molecular shapes. The simulation of molecular systems, especially polymeric and biological materials, is a very active field and we barely touch the surface here. For more information, please see the texts in the Suggested reading section.

After a review of the basic properties of macromolecules, the chapter continues with a discussion of some of the common approaches to model the interaction between the molecules, followed by descriptions of how molecular dynamics and Monte Carlo methods can be applied to molecular systems. When discussing systems of large molecules, such as polymers or proteins, however, it becomes challenging to include the full complexity of the molecules within a calculation. Thus, various models that approximate the physics have been developed. The chapter ends with a discussion of some of these approximate methods.

INTRODUCTION

Polymers (macromolecules) are large molecules made up of long chains of monomer units. In some biological molecules, the number of monomers (N) can be quite high, e.g., in DNA N ˜ 108 in some cases. In other systems, N can be of the order of a few hundred. The identity of the monomer units defines the overall properties of the polymer – DNA and RNA are made up of nucleotides, proteins are made up of amino acids, etc.