9360-0141/04 – Molecular modeling and nanomaterials design (MOLMOD)
| Gurantor department | CNT - Nanotechnology Centre | Credits | 4 |
| Subject guarantor | doc. Ing. Jonáš Tokarský, Ph.D. | Subject version guarantor | doc. Ing. Jonáš Tokarský, Ph.D. |
| Study level | undergraduate or graduate | Requirement | Choice-compulsory |
| Year | 2 | Semester | winter |
| | Study language | English |
| Year of introduction | 2016/2017 | Year of cancellation | 2019/2020 |
| Intended for the faculties | USP | Intended for study types | Follow-up Master |
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
Lectures
Individual consultations
Tutorials
Summary
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:
Recommended literature:
Way of continuous check of knowledge in the course of semester
E-learning
Other requirements
No additional requirements.
Prerequisities
Subject has no prerequisities.
Co-requisities
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
Conditions for completion are defined only for particular subject version and form of study
Occurrence in study plans
Occurrence in special blocks
Assessment of instruction
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