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Computer Simulations of Polymers and Biopolymers

General data

Course ID:	1200-2SPEC172M
Erasmus code / ISCED:	13.3 Kod klasyfikacyjny przedmiotu składa się z trzech do pięciu cyfr, przy czym trzy pierwsze oznaczają klasyfikację dziedziny wg. Listy kodów dziedzin obowiązującej w programie Socrates/Erasmus, czwarta (dotąd na ogół 0) – ewentualne uszczegółowienie informacji o dyscyplinie, piąta – stopień zaawansowania przedmiotu ustalony na podstawie roku studiów, dla którego przedmiot jest przeznaczony. / (0531) Chemistry The ISCED (International Standard Classification of Education) code has been designed by UNESCO.
Course title:	Computer Simulations of Polymers and Biopolymers
Name in Polish:	Symulacja komputerowa polimerów i biopolimerów
Organizational unit:	Faculty of Chemistry
Course groups:	(in Polish) Przedmioty do wyboru w semestrze 3M (S2-PRK-CHM) (in Polish) Wykłady specjalizacyjne w semestrze 2M
ECTS credit allocation (and other scores):	3.00 Basic information on ECTS credits allocation principles: the annual hourly workload of the student’s work required to achieve the expected learning outcomes for a given stage is 1500-1800h, corresponding to 60 ECTS; the student’s weekly hourly workload is 45 h; 1 ECTS point corresponds to 25-30 hours of student work needed to achieve the assumed learning outcomes; weekly student workload necessary to achieve the assumed learning outcomes allows to obtain 1.5 ECTS; work required to pass the course, which has been assigned 3 ECTS, constitutes 10% of the semester student load.
Language:	Polish
Mode:	Classroom
Short description:	The usage of simulation techniques, the knowledge of polymer and proteins models
Full description:	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
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.
Learning outcomes:	Student learns physicochemical basis of polymer, polypeptide and biopolymer theories, basic models and the most important calculation methods
Assessment methods and assessment criteria:	Test (passed when over 60% correct)
Practical placement:	does not concern

Classes in period "Summer semester 2023/24" (in progress)

Time span:	2024-02-19 - 2024-06-16	Selected timetable range: weekly course term Navigate to timetable MO TU W WYK-SPE TH FR
Type of class:	Specialised lecture, 30 hours, 30 places more information
Coordinators:	Andrzej Sikorski
Group instructors:	Andrzej Sikorski
Students list:	(inaccessible to you)
Examination:	Examination
Full description:	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
Bibliography:	1. M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford 1989. 2. Encyclopedia of Computational Chemistry, Vol. I-V, ed. Paul von Ragué Schleyer, Chichester 1998. 3. Daan Frenkel, Berend Smit, Understanding Molecular Simulation, Academic Press, San Diego 2002. 4. Dieter W. Heermann, Podstawy symulacji komputerowych w fizyce, WNT, Warszawa 1997. 5. Simulation Methods for Polymers, ed. Michael Kotelyanskii and Doros N. Theodorou, Marcel Dekker, New York-Basel 2004.

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