Structure and Dynamics of Bio- and Macromolecules
Alexey V. Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov
in book
Dynamics of Systems on the Nanoscale
edited by
Ilia A. Solov'yov and Alexey V. Verkhovtsev and Andrei V. Korol and Andrey V. Solov'yov
This chapter overviews the computational techniques and theoreticalmodels used for exploring structure and dynamics of complex biomolecular systemsat the atomistic level of detail. Particular focus is put on the application of statisticalmechanics methods combined with the classical molecular mechanics approach to the description of phase transitions in polypetides and proteins. The molecular mechanics approach permits simulating a large variety of biomacromolecular systems (both in vacuum and in ubiquitous environments) and their transformations at different thermal and biologically relevant conditions as well as at various external stresses. This chapter presents several illustrative examples of such computational research related to protein folding, unbinding of protein-ligand complex, and DNA unzipping.