ABSTRACT
This chapter explains recent techniques to simulate the three-dimensional (3D) structure and dynamics of the genome of a model organism, budding yeast. It discusses the decomposition in diploid cells for general cases including both trans and cis interactions to construct a whole genome model of a higher organism. A genome is not an abstract one-dimensional sequence of alphabet but a physical entity embedded in 3D space. In recent years, intense efforts have been focused on constructing the 3D genome structures of various organisms using the data obtained by the chromatin-conformation-capture (3C)-based methods. To examine the dynamical genome hypothesis, not only the static average structure but also the dynamical movement of the genome should be analyzed. The chapter describes a straightforward application of the idea to construct computational models of genomes in haploid cells. Among the haploid cells, budding yeast is a model organism, for which data of intensive analyses have been accumulated.
