Computer Simulations of Polymers and Biopolymers 1200-2SPEC172M
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, DLL, CMA and pivot algorithms, 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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Term 2023L:
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 |
Mode
Course coordinators
Learning outcomes
Student learns physicochemical basis of polymer, polypeptide and biopolymer theories, basic models and the most important calculation methods
Assessment criteria
Test (passed when over 60% correct)
Practical placement
does not concern
Bibliography
1. M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford 1989.
Encyclopedia of Computational Chemistry, Vol. I-V, ed. Paul von Ragué Schleyer, Chichester 1998.
2. Daan Frenkel, Berend Smit, Understanding Molecular Simulation, Academic Press, San Diego 2002.
3. Dieter W. Heermann, Podstawy symulacji komputerowych w fizyce, WNT, Warszawa 1997.
4. Simulation Methods for Polymers, ed. Michael Kotelyanskii and Doros N. Theodorou, Marcel Dekker, New York-Basel 2004.
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Term 2023L:
1. M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford 1989. |
Additional information
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