Chapter 10 Atomistic and Mean Field Simulations of Lateral Organization in Membranes

Abstract

Publisher Summary This chapter provides an overview of molecular dynamics (MD) simulations of mixed lipid bilayer. The chapter shows how the data from MD simulations can be incorporated into a larger scale coarse-grained model that predicts lateral organization and phase properties over times and distances well beyond the reach of MD. The chapter discusses one of the most critical issues, the determination of the simulation force field parameters, describing new and highly accurate set of parameters developed. This phenomenon is studied by Pastor, MacKerell, and Klauda. Their effort is based on the inclusion of all hydrogen atoms on the lipids as well as the water, whereas the method discussed in the chapter uses a “united atom” approach for hydrogens on most lipid molecules. The chapter also describes the MD simulation of lipid bilayer of mixed composition and how the MD data from the mixed bilayer simulations can be used as input to construct a mean field-based coarse grained model that can serve as a predictive platform for the lateral organization of the membranes.