C5845 Advanced Biophysical Chemistry - theoretical methods

Faculty of Science
Autumn 2016
Extent and Intensity
2/1/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
doc. RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
Mgr. Jan Novotný, Ph.D. (seminar tutor)
RNDr. Mgr. Iveta Třísková, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry – Chemistry Section – Faculty of Science
Supplier department: Department of Chemistry – Chemistry Section – Faculty of Science
Prerequisites
Successful passing the courses: C5850 - Principles of Biophysical Chemistry (lecture) C5855 - Methods of Biophysical Chemistry (lecture) C5856 - Methods of Biophysical Chemistry (seminar)
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The aim of this subject is to gain deeper knowledge in biophysical chemistry applicable in biomolecular research. The theoretical description of biomolecular systems in solutions by means of physical-statistical and computational methods.
Syllabus
  • 1.Probability theory (How do molecules “know” they should reach equilibrium?) 2.Equilibrium statistical mechanics (ergodic theory, fluctuations) 3.Biomolecular force-fields parameters and molecular dynamics 4.Enhanced sampling computational simulations (replica exchange molecular dynamics - REMD) 5.Free energy calculations 6.Calculations of potential of mean force (PMF) 7.Solubility and hydrophobicity 8.Binding affinity 9.Conformational and allosteric changes 10.Kinetics of conformational changes 11.Protein folding 12.Phase transitions of proteins (molten-globule state) Literature: [1] Peter R. Bergethon: The Physical Basis of Biochemistry [2] Finkelstein and Pittsyn: Protein Physics [3] Cantor & Schimmel: Biophysical Chemistry, Part I [4] Zuckerman D.M.: Statistical Physics of Biomolecules
Literature
    recommended literature
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. New York: W.H. Freeman and Company, 1980, s. i-xxix. ISBN 0716711907. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. New York: W.H. Freeman and Company, 1980, xxvii, 341. ISBN 0716711885. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. New York: W.H. Freeman and Company, 1980, s. i-xxix. ISBN 0716711923. info
Teaching methods
lecture (2 hours) and seminar (1 hour)
Assessment methods
oral examination and credit test
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2016, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2016/C5845