Dynamics of macromolecules

Biological macromolecules carry out functions that require them to have very complex physical and chemical dynamics. Theoretical analysis of that dynamics has proven very difficult because the macromolecules are large systems whose dynamics is very nonlinear. The large size arises because the systems have many atoms which cannot be simply related by symmetry operations and the dynamics has to be analyzed down to motions on the atomic level to fully appreciate what is going on. This microscopic approach is important because macromolecules often function by changing their conformation on the atomic level. The nonlinearity results because many bonds are weak relative to physiological temperatures, in many biological processes bonds are broken and bonding rearranged. In this book we detail a method for studying macromolecular dynamics that is particularly well suited to large systems that are also highly nonlinear. With an additional operator included the method is particularly useful in studying the dissociation of chemical bonds in large nonlinear systems. We know of no other approach that can efficiently study the melting or bond disruption problem in such large systems on a microscopic scale. To date the majority of the applications of this method, and those presented in this book, are to problems of base pair separation in the DNA double helix. The advantages and disadvantages of the method and how it may be extended to other systems can, however, be seen in these applications.