F8510 Physics of biopolymers

Faculty of Science
Spring 2025
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Robert Vácha, PhD. (lecturer), Ing. Ondřej Kroutil, Ph.D. (deputy)
Mgr. Peter Pajtinka (lecturer)
Guaranteed by
prof. RNDr. Robert Vácha, PhD.
Department of Condensed Matter Physics – Physics Section – Faculty of Science
Contact Person: doc. Mgr. Karel Kubíček, PhD.
Supplier department: Department of Condensed Matter Physics – Physics Section – Faculty of Science
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 course is focused on basics of interatomic and intermolecular interactions in biopolymers. It is aimed on description of fundamental forces in biomolecules, influence of solvent, and molecular modeling approach.

The main objective of the course is to provide the students with the ability to
- describe and explain fundamental interactions in biomolecules
- apply the obtained knowledge to practical problems
- understand current trends
Learning outcomes
Student will be able to:
- identify existing biopolymers;
- evaluate individual molecular interactions;
- Identify the dominant interaction;
- describe the basic theory and approximation of biopolymers;
Syllabus
  • 1. electrostatic interactions in vacuum: Coulomb law, superposition principle, interactions of charges, dipoles, rotating dipoles, and induced dipoles, van der Waals interaction
  • 2. electrostatic interactions in aqueous solutions: Poisson-Boltzmann equation, Debye-Hückel theory, Debye screening length, Gouy-Chapman theory, fluctuating charges
  • 3. interactions of big uncharged particles: Hamaker constant, Derjaguin approximation, solution for particles with different geometries
  • 4. entropic interactions: directional entropic forces, ideal chain and its deformations, membrane fluctuations
  • 5. depletion interaction, hydrophobic interaction, DLVO theory, hydrogen bond, salt bridge, π-interaction
  • 6. polymers in aqueous solutions: Flory-Huggins theory, polymer mixtures
  • 7. protein folding: native contacts, funneling, helix-coil transition, swelling, crowding
  • 8. biopolymer models: ab initio, all-atom description, molecular mechanics, coarse-grained simulations
  • 9. radial distribution function, matter arrangement, structure factor
  • 10. solvation of molecules and ions: water – structure and properties, cavitation energy, Born solvation energy
Literature
    recommended literature
  • ISRAELACHVILI, Jacob N. Intermolecular and surface forces. 3rd ed. Amsterdam: Elsevier, 2011, xxx, 674. ISBN 9780123751829. info
  • DILL, Ken A. and Sarina BROMBERG. Molecular driving forces : statistical thermodynamics in biology, chemistry, physics, and nanoscience. 2nd ed. New York: Garland Science, 2011, xx, 756. ISBN 9780815344308. info
Teaching methods
Lectures + class discussion
Assessment methods
A test on computer. Each question has several possible answers with various number of correct answers. Each correct answer results in +1 point, the bad answer is -0.5 point. 40% of the correct answers are required for successful completion.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024.
  • Enrolment Statistics (recent)
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