9360-0141/02 – Molecular modeling and nanomaterials design (MOLMOD)

Gurantor departmentCNT - Nanotechnology CentreCredits5
Subject guarantordoc. Ing. Jonáš Tokarský, Ph.D.Subject version guarantordoc. Ing. Jonáš Tokarský, Ph.D.
Study levelundergraduate or graduate
Study languageEnglish
Year of introduction2010/2011Year of cancellation2019/2020
Intended for the facultiesUSPIntended for study typesFollow-up Master
Instruction secured by
LoginNameTuitorTeacher giving lectures
CAP01 prof. RNDr. Pavla Čapková, DrSc.
HLA321 Ing. Dominik Hlaváč
SIM75 doc. Ing. Gražyna Simha Martynková, Ph.D.
TOK006 doc. Ing. Jonáš Tokarský, Ph.D.
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Credit and Examination 2+2

Subject aims expressed by acquired skills and competences

Student will be able to: discuss the differences between quantum and molecular mechanics, classify and characterize the force fields, classify and characterize algorithms used in molecular mechanics and dynamics, discuss and interpret the results of molecular simulations, compare simulation and experimental results, and draw conclusions about properties of nanomaterial, apply molecular modeling in the development of nanomaterials.

Teaching methods

Individual consultations


Students get acquainted with an important tool in current scientific research - the computer molecular modeling. The major part of the course is devoted to the theory of molecular simulations using force fields, i.e., the molecular mechanics and the classical molecular dynamics, but attention is also paid to Monte Carlo methods and mesoscale methods. The next part is devoted to the specific use of molecular mechanics and dynamics in the research and development of nanomaterials, emphasizing the synergy of molecular modeling and experiment to understand the relation between structure and properties. The previous knowledge of students in the field of instrumental analysis is complemented and extended by other possibilities of characterization of nanomaterials. Lectures are supplemented by many examples from the contemporary scientific literature, but also from the scientific practice. The course includes practical exercises in which students apply the acquired knowledge in the field of molecular modeling to solving practical problems.

Compulsory 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.

Recommended literature:

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

Way of continuous check of knowledge in the course of semester


Other requirements

No additional requirements.


Subject has no prerequisities.


Subject has no co-requisities.

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.

Conditions for subject completion

Full-time form (validity from: 2014/2015 Winter semester)
Task nameType of taskMax. number of points
(act. for subtasks)
Min. number of points
Credit and Examination Credit and Examination 100 (100) 51
        Credit Credit 40  20
        Examination Examination 60  40
Mandatory attendence parzicipation:

Show history

Occurrence in study plans

Academic yearProgrammeField of studySpec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2019/2020 (N3942) Nanotechnology (3942T001) Nanotechnology P English Ostrava 1 Compulsory study plan
2018/2019 (N3942) Nanotechnology (3942T001) Nanotechnology P English Ostrava 1 Compulsory study plan
2017/2018 (N3942) Nanotechnology (3942T001) Nanotechnology P English Ostrava 1 Compulsory study plan
2015/2016 (N3942) Nanotechnology (3942T001) Nanotechnology P English Ostrava Compulsory study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner
USP 2018/2019 Full-time English Optional USP - University Study Programmes stu. block
USP 2017/2018 Full-time English Optional USP - University Study Programmes stu. block
USP 2016/2017 Full-time English Optional USP - University Study Programmes stu. block
USP 2015/2016 Full-time English Optional USP - University Study Programmes stu. block