9360-0141/06 – Molecular modeling and nanomaterials design (MOLMOD)

Gurantor departmentCNT - Nanotechnology CentreCredits4
Subject guarantordoc. Ing. Jonáš Tokarský, Ph.D.Subject version guarantordoc. Ing. Jonáš Tokarský, Ph.D.
Study levelundergraduate or graduateRequirementCompulsory
Study languageEnglish
Year of introduction2019/2020Year of cancellation
Intended for the facultiesUSP, FMTIntended for study typesFollow-up Master
Instruction secured by
LoginNameTuitorTeacher giving lectures
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

The study results are verified continuously in the exercises. The results of exercises are processed in the form of five protocols (max. 4 credits per protocol, required minimum 2 credits per protocol). Individual semestral work is elaborated (max. 20 credits, required minimum 10 credits). Semester is completed by summation of credits from protocols and the semestral work (max. 40 credits, required minimum 20 credits). The oral exam follows (max. 60 credits, required minimum 31 credits).


Other requirements

In addition to attendance in exercises, the elaboration of protocol from each exercise and individual semestral work is required during the semester.


Subject has no prerequisities.


Subject has no co-requisities.

Subject syllabus:

1. After introductory information about computer simulations as a theoretical experiment complementing theory and experiment, students are introduced to the history of computational chemistry. The second part of the lecture is devoted to examples of molecular modeling, specific results published in scientific journals are demonstrated. 2. Computational complexity of molecular simulations is discussed, and in connection with this topic also the clusters and parallelization are mentioned. Further, attention is paid to the basic principles of quantum and molecular mechanics and their comparison. 3. Bonding and non-bonding interactions and their empirical description are presented. Members of the potential energy equation are described and the term potential surface is explained. After defining the concept of force field, individual types of force fields are presented, their classification is presented, and students get acquainted with the concept of atomic types within the force fields. 4. The methods of calculating atomic charges are presented, and in relation to the periodic conditions, Ewald summationmethod is explained. Based on the previous topic, the issue of global and local minima of the potential surface is discussed. Basic classification of the optimization algorithms is presented. 5. Attention is paid to the deterministic derivative algorithms. In addition to the general description, each algorithm is demonstrated on example. Students get acquainted with implementation of these algorithms in the Materials Studio modeling environment. 6. Attention is paid to the deterministic non-derivative algorithms. In addition to the general description, each algorithm is demonstrated on example. Further, random and pseudorandom number generators are presented. 7. Attention is paid to the Monte Carlo methods and simulation. Simulated annealing method is presented, and examples of Monte Carlo simulations in the Materials Studio modeling environment are presented. 8. After the introduction of the concept of molecular dynamics, the types of integration algorithms are presented. Students get acquainted with implementation of these algorithms in the Materials Studio modeling environment. Attention is also paid to various types of thermostats and barostats. 9. Students get acquainted with mesoscale simulation methods, with particular attention to the dissipative particle dynamics. Furthere, a multiscale approach to simulations is discussed and examples are presented. 10. Miscibility of polymers is discussed and the Flory-Huggins theory is presented. In connection with this and the previous topic, attention is further paid to the modeling of polymer-based nanostructures. 11. Attention is paid to the molecular structure-properties relationship and to the to the issue of molecular descriptors. Students get acquainted with principle of the QSAR, QSPR, etc. methods. 12. The synergy of computer simulations and experiment is discussed. Students get acquainted with the experimental data as input data for preparation of initial models. Attention is also paid to the verification of modeling results and the creation of modeling strategy based on the experimental data. 13. Based on the previous topic, modeling strategies suitable for selected nanomaterials are presented. Attention is paid in particular to intercalation chemistry and surface-modified nanostructures. 14. The test.

Conditions for subject completion

Full-time form (validity from: 2019/2020 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  21
        Examination Examination 60  31
Mandatory attendence parzicipation: Attendance in lectures is not compulsory. Attendance in exercises is compulsory.

Show history

Occurrence in study plans

Academic yearProgrammeField of studySpec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2022/2023 (N0719A270003) Nanotechnology P English Ostrava 2 Compulsory study plan
2021/2022 (N0719A270003) Nanotechnology P English Ostrava 2 Compulsory study plan
2020/2021 (N0719A270003) Nanotechnology P English Ostrava 2 Compulsory study plan
2019/2020 (N0719A270003) Nanotechnology P English Ostrava 2 Compulsory study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner