Molecular Dynamics Simulations of biopolymers within the cell environment: Minimalist models for the Nucleic Acids and Green Fluorescent Proteins in the cytoplasm

From the introduction: "... This thesis reports on simplified models (`coarse grained') of proteins and nucleic acids in which many degrees of freedom (DOF) are eliminated, to speed up the computation of the interactions. The resolution of these models is minimal, with respect to the representation of the phenomena studied, in order to extend the time and length scales accessible to atomistic simulations. Furthermore the existence of a coarse- to fine-grain backmapping ensures to switch between diff erent resolutions of the same system, naturally leading to an integrative approach used for multi-scale simulations. Careful parameterization and optimization of the interactions between the interactive centers additionally allow to overcome the limitations of the reductionist first stage by including directly experimental and theoretical data.