470-8749/01 – Introduction to molecular simulations (UMS)

Gurantor departmentDepartment of Applied MathematicsCredits4
Subject guarantorprof. RNDr. René Kalus, Ph.D.Subject version guarantorprof. RNDr. René Kalus, Ph.D.
Study levelundergraduate or graduateRequirementChoice-compulsory type A
Year2Semestersummer
Study languageCzech
Year of introduction2022/2023Year of cancellation
Intended for the facultiesFMTIntended for study typesFollow-up Master
Instruction secured by
LoginNameTuitorTeacher giving lectures
KAL0063 prof. RNDr. René Kalus, Ph.D.
Extent of instruction for forms of study
Form of studyWay of compl.Extent
Full-time Credit and Examination 2+1
Part-time Credit and Examination 10+5

Subject aims expressed by acquired skills and competences

Upon the successful completion of the course, students will be able to: - actively use basic concepts in the field of molecular simulations using Monte Carlo and Molecular Dynamics methods, - implement simple models, - perform computer simulations and analyse their results, - independently extend the acquired knowledge in the field of study.

Teaching methods

Lectures
Tutorials

Summary

Students will learn the theoretical foundations of molecular modelling and will be introduced to the fields of Molecular Dynamics and Monte Carlo methods.

Compulsory literature:

1.Nezbeda, I., Kolafa J., Kotrla M. Úvod do počítačových simulací. Metody Monte Carlo a molekulární dynamiky, Karolinum, Praha 2003, ISBN 80-246-0649-6. 2.Allen, M.P., Tildesley, D.J. Computer Simulations of Liquids. Oxford Science Publications, Oxford 1989, ISBN 0-19-855645-4.

Recommended literature:

1.Hinchliffe, A., Molecular modelling for beginners, Second edition, John Wiley & Sons Ltd, Chichester 2008, ISBN 978-0-470-51313-2.

Way of continuous check of knowledge in the course of semester

Project elaboration and its presentation, oral exam.

E-learning

Other requirements

No further requirements.

Prerequisities

Subject has no prerequisities.

Co-requisities

Subject has no co-requisities.

Subject syllabus:

1. Summary of Classical Statistical Thermodynamics, Statistical Ensembles. 2. Summary of Classical Mechanics, Equations of Motion. 3. Intramolecular and Intermolecular Interactions, Force Fields. 4. Molecular Dynamics Methods for the NVE Ensemble. 5. Molecular Dynamics Methods for other Statistical Ensembles. 6. Numerical Solvers for Equations of Motion. 7. Markov Chains, Transition Matrices, Metropolis Algorithm. 8. Pseudorandom Number Generators. 9. Monte Carlo Methods for the NVT Ensemble. 10. Monte Carlo Methods for other statistical Ensembles. 11. Convergence Accelerating Approaches (parallel tempering). 12. Summary of Quantum Mechanics and Quantum Statistical Thermodynamics. 13. Quantum Monte Carlo methods.

Conditions for subject completion

Full-time form (validity from: 2022/2023 Winter semester)
Task nameType of taskMax. number of points
(act. for subtasks)		Min. number of pointsMax. počet pokusů
Credit and Examination Credit and Examination 100 (100) 51
        Credit Credit 40  10
        Examination Examination 60  20 3
Mandatory attendence participation: Solutions of assigned tasks and their presentation, oral exam.

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Conditions for subject completion and attendance at the exercises within ISP: Completion of all mandatory tasks within individually agreed deadlines.

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Occurrence in study plans

Academic yearProgrammeBranch/spec.Spec.ZaměřeníFormStudy language Tut. centreYearWSType of duty
2024/2025 (N0719A270002) Nanotechnology MM1 P Czech Ostrava 2 Choice-compulsory type A study plan
2023/2024 (N0719A270002) Nanotechnology MM1 P Czech Ostrava 2 Choice-compulsory type A study plan
2022/2023 (N0719A270002) Nanotechnology MM1 P Czech Ostrava 2 Choice-compulsory type A study plan

Occurrence in special blocks

Block nameAcademic yearForm of studyStudy language YearWSType of blockBlock owner

Assessment of instruction

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