The functions of biomolecules are associated with specific structures. Experimental methods can be used to determine native structures, but can hardly provide high-resolution dynamic information of the molecules, due to the limitation of current technologies. To fill the gap, computational methods, particularly Molecular Dynamics simulations, are applied to study the dynamics of molecules based on their static structures. In this thesis, nucleosome systems were used as examples to demonstrate potential applications of molecular dynamics simulation methods in structural biology.

Nucleosomes are the basic building blocks of chromatins. The histone tails in nucleosomes are important for the control of gene expression and chromatin structures, because the tails are under diverse posttranslational modifications that affect the tail functions. To study the functions of histone tails and posttranslational modification effects, a series of computational modeling and simulations were performed. Based on the simulation results, several control mechanisms of chromatin structure and gene expressions were proposed. Those hypotheses can be very useful for designing experiments to further study the roles of histone tails in nucleosome dynamics and packing.