| Course Unit Code | 9360-0141/05 |
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| Number of ECTS Credits Allocated | 5 ECTS credits |
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| Type of Course Unit * | Choice-compulsory type A |
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| Level of Course Unit * | Second Cycle |
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| Year of Study * | Second Year |
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| Semester when the Course Unit is delivered | Winter Semester |
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| Mode of Delivery | Face-to-face |
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| Language of Instruction | Czech |
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| Prerequisites and Co-Requisites | Course succeeds to compulsory courses of previous semester |
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| Name of Lecturer(s) | Personal ID | Name |
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| TOK006 | doc. Ing. Jonáš Tokarský, Ph.D. |
| Summary |
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| 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. |
| Learning Outcomes of the Course Unit |
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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.
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| Course Contents |
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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. |
| Recommended or Required Reading |
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| Required Reading: |
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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. |
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 Reading: |
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SMIT, B. and D. FRENKEL. Understanding molecular simulation: from algorithms to applications. 2nd ed. San Diego: Academic Press, 2002. ISBN 978-0122673511.
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SMIT, B. and D. FRENKEL. Understanding molecular simulation: from algorithms to applications. 2nd ed. San Diego: Academic Press, 2002. ISBN 978-0122673511.
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| Planned learning activities and teaching methods |
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| Lectures, Individual consultations, Tutorials |
| Assesment methods and criteria |
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| Task Title | Task Type | Maximum Number of Points
(Act. for Subtasks) | Minimum Number of Points for Task Passing |
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| Credit and Examination | Credit and Examination | 100 (100) | 51 |
| Credit | Credit | 40 | 21 |
| Examination | Examination | 60 | 31 |