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Terminated in academic year 2019/2020

Molecular modeling and nanomaterials design

Type of study Follow-up Master
Language of instruction English
Code 9360-0141/02
Abbreviation MOLMOD
Course title Molecular modeling and nanomaterials design
Credits 5
Coordinating department CNT - Nanotechnology Centre
Course coordinator doc. Ing. Jonáš Tokarský, Ph.D.

Subject syllabus

The role of molecular simulations for understanding the relationship between structure and properties of materials and the importance of modeling in prediction of the structure and properties. Practical examples of nanomaterials development.

The principles of supramolecular chemistry. The nature of intermolecular interactions and their empirical description. Types of force fields.

Molecular mechanics. Binding energy in harmonic approximation. Anharmonicity of potentials, its manifestations and descriptions. Description of non-bond interactions. Atom-atom potential, hydrogen bond, electrostatic interactions. Methods for calculating charges. Optimizing the structure of molecular crystals.

Strategy of molecular modeling. Construction and parameterization of models. The problem of finding the global minimum. Geometry optimization and its strategy. Stochastic and deterministic methods. Selection of a suitable force field.

Molecular dynamics. Classical molecular dynamics, solving Newton's equations, stochastic methods (Monte Carlo), generating statistical ensembles. Study of dynamic processes and phase transitions.

The role of experiment in molecular modeling for verifying and interpreting the results. X-ray diffraction and IR spectroscopy as complementary methods in structure analysis of partially disordered materials.

Use of molecular modeling in the development of photocatalytic and antibacterial nanocomposites, drug carriers, and organo-inorganic hybrid nanostructures.

Literature

POSPÍŠIL, M. and M. VETEŠKA. Computational procedures in molecular dynamics. Materials Structure. 2012, vol. 19, no. 2, pp. 71-74.
COMBA, P. and T. W. HAMBLEY. Molecular modeling of inorganic compounds. 2nd ed. Weinheim: Wiley-VCH, 2001. ISBN 3-527-297778-2.
HINCHLIFFE, A. Molecular modelling for beginners. 2nd ed. Hoboken, NJ: Wiley, 2008. ISBN 978-0470513149 .

Advised literature

SMIT, B. and D. FRENKEL. Understanding molecular simulation: from algorithms to applications. 2nd ed. San Diego: Academic Press, 2002. ISBN 978-0122673511 .