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Course description:
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Computer simulations: basics of statistical physics of macromolecules. Monte Carlo method and its modifications. Molecular Dynamics and Brownian Dynamics methods. Polymer models: continue models, full atom models, reduced models, lattice models. Potentials of interaction. Simulation of single chains: the Verdier-Stockmayer algorithm, flexible and stiff chains. Polymer solutions and melts. Different chain architectures. The transition coil-globule, adsorption, glass transition and crystalization. Local ordering, viscoelastic properties. Autocorrelation functions. Mechanisms of chain motion. Models of proteins: full atom models, reduced models, lattice models. Force fields. Statistical potentials. Simulation of globular proteins: native structures, trajectories of folding, all-or-none folding transition, thermodynamics of folding. The prediction of native structures: ab initio, with constraints. Simulation of many chain protein systems: associates, superhelices, receptor-ligand systems. Simple models of polypeptides (HP), DNA, RNA. The formation and stability of secondary structures.
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