9360-0239/01 – Molecular modeling using force fields (MMSP)
| Gurantor department | CNT - Nanotechnology Centre | Credits | 10 |
| Subject guarantor | doc. Ing. Jonáš Tokarský, Ph.D. | Subject version guarantor | doc. Ing. Jonáš Tokarský, Ph.D. |
| Study level | postgraduate | Requirement | Choice-compulsory type B |
| Year | | Semester | winter + summer |
| | Study language | Czech |
| Year of introduction | 2020/2021 | Year of cancellation | |
| Intended for the faculties | FMT | Intended for study types | Doctoral |
Subject aims expressed by acquired skills and competences
Student will be able to identify a problem solvable by molecular modeling, identify relevant data needed to build the initial model, apply a suitable molecular modeling strategy, discuss and interpret the results of molecular simulations
Teaching methods
Lectures
Individual consultations
Tutorials
Summary
The aim of the course is to deepen the student's ability to recognize a problem solvable by molecular modeling methods. In the course of the subject will be discussed especially the questions of input experimental data, selection of appropriate modeling strategy, and interpretation results obtained by molecular modeling. Since the molecular modeling using force fields is used, the course is not focused on the electron properties of materials, but on their structure and behavior under given conditions. Practical exercises, which are the main content of the course, are focused on surface modification, intercalation, sorption, miscibility, but also on X-ray diffraction or infrared spectra simulation. The course will also provide students with examples of successful applications of molecular modeling methods in material research.
Compulsory literature:
Recommended literature:
POSPÍŠIL, M. and M. VETEŠKA. Computational procedures in molecular dynamics. Materials Structure. 2012, vol. 19, no. 2, pp. 71-74
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).
E-learning
Other requirements
Written protocols from practical exercises.
Prerequisities
Subject has no prerequisities.
Co-requisities
Subject has no co-requisities.
Subject syllabus:
Identification of problem solvable by molecular modeling using force fields.
Identification, interpretation, and utilization of data from instrumental analytical methods for the needs of initial model preparation.
Basic chemical calculations for initial model preparation.
Choosing a modeling strategy for given problem.
Interpretation of molecular modeling results and comparison with experimental data.
Molecular modeling of intercalates (practical exercise).
Molecular modeling of miscibility of selected substances (practical exercise).
Molecular modeling of small molecule sorption (practical exercise).
Molecular modeling of nanoparticles on inorganic substrate (practical exercise).
Simulation of X-ray diffraction of inorganic and organic structures (practical exercises).
Simulation of infrared spectra of selected substances (practical exercise).
Conditions for subject completion
Occurrence in study plans
Occurrence in special blocks
Assessment of instruction
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