ABSTRACT
This chapter reviews the present status of modeling of chromatin and the relation of these models to experimental studies. It concentrates on coarse-grained (CG) modeling at the first level of chromatin compaction, namely the nucleosome core particle (NCP) and nucleosome arrays. The chapter discusses some of the approaches and models that have been used in recent years with a main focus on CG computer simulations methods based on producing trajectories that describe the ensemble of states of the system from which various average structural properties can be calculated. It gives the pertinent background on chromatin structure and dynamics with emphasis on the physical–chemical properties of the system. The presence of a compact, folded higher order structure of chromatin represses many deoxyribonucleic acid (DNA)-dependent activities such as transcription, replication, and repair. The chapter discusses the prospect of employing more detailed and rigorous CG modeling of chromatin using systematic multiscale approaches.
