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Course, academic year 2023/2024
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Molecular Simulations - NUFY068
Title: Molekulární simulace
Guaranteed by: Department of Physics Education (32-KDF)
Faculty: Faculty of Mathematics and Physics
Actual: from 2021
Semester: both
E-Credits: 3
Hours per week, examination: 1/1, Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Note: you can enroll for the course in winter and in summer semester
Guarantor: doc. RNDr. Miroslav Pospíšil, Ph.D.
Classification: Physics > Teaching
Annotation -
Last update: POSPISIL/MFF.CUNI.CZ (04.04.2008)
Lecture is based on knowledge of solid physics. The aim is to show new trends in structure analysis and describe properties in design of new perspective materials. Theoretical basis of molecular simulations with empirical potentials i.e. molecular mechanics and molecular dynamics is presented. Practical exercises are done in the Cerius2 and Material Studio modelling environment.
Aim of the course -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (27.04.2023)

Acquaintance of the students with the latest methods and procedures in the development of new materials with the required properties by molecular simulation methods.

Course completion requirements -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (27.04.2023)

Gaining credit is a condition for taking the exam.

The credit is tied to the credit calculation task, it is assumed that there will be corrective terms for obtaining the credit and the exam.

Literature -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (27.04.2023)

P. Comba, T.W. Hambley: Molecular Modeling of Inorganic Compouds, VCH, 1995, Weinheim.

C.R.A. Catlow, A.M. Stoneham and Sir J. M. Thomas eds.: New methods for modelling processes within solids and at their surfaces, Oxford science publications, 1993, Cambridge

Vassilios Galiatsatos ed.: Molecular simulation methods for predicting polymer properties, Wiley, 2005, New Jersey.

K.I.Ramachadran, G. Deepa, K. Namboori: Computational Chemistry and Molecular Modeling, Springer-Verlag, 2008, Berlin Heidelberg.

C.V. Ciobanu, C.-Z. Wang, K.M. Ho: Atomic Structure Prediction of Nanostructures, Clusters and Surfaces, Wiley-VCH, 2013, Singapore.

Teaching methods -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (27.04.2023)

Lecture (1h) and exercise (1h).

Requirements to the exam -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (27.04.2023)

The exam consists of written preparation and an oral part. Written preparation precedes the oral part. The student receives three questions, each question is evaluated with a mark and the final mark is the average mark of the marks for each question. If one of the questions is not sufficiently answered, it means that the exam has not been passed. Failure to pass the exam means that three various questions will be asked again at the next deadline.

The requirements for the oral part of the exam correspond to the syllabus of the subject to the extent that was presented at the lecture.

It is probable that a significant part of exams or credits can take place in a distance form. It depends on the development of the current situation and you will be informed about any changes in time.

Syllabus -
Last update: doc. RNDr. Miroslav Pospíšil, Ph.D. (27.04.2023)

Molecular simulations describing structure-properties relationship and including molecular mechanics and molecular dynamics. Various branches of molecular simulations can be applied in physics, chemistry and material design. Crystal structures are visualized in Materials Studio modelling environment.

Molecular mechanics: molecular systems and crystal energy description on the base of empirical force fields. Bond energy in harmonic approximation. Inharmonic potential. Angles bond, torsion, inversion terms. Nonbond interactions: van der Walls, Coulomb, Hydrogen bond. Ewald summation.

Modeling strategy: Building of initial models, suitable energy approximation, choice of empirical force field, minimization strategy. The role of experiments in creation of modeling strategy and results verification. Infrared spectroscopy, X-ray diffraction as complementary methods in the complex structure analysis. The molecular simulation results interpretation. Practical examples of molecular modeling are applied on various structures and bond geometries.

Molecular dynamics: Deterministic molecular dynamics, Newton equation integration, stochastic methods (Monte Carlo) in molecular dynamics, statistic ensembles, temperature and pressure control, dynamics strategies.

Study of dynamic processes: sorption, diffusion, absorption, intercalation, phase transition.

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