Graduate School

Selected topics in biophysics

This course is part of the programme:
Physics (Third Level)

Objectives and competences

This course will give an overview of selected topics in biophysics (the science addressing physical processes taking place in biological systems), going in detail on conformational transitions in Biopolymers.

The objective is to provide students with a physical background with a range of biological issues that require quantitative and mathematical approaches.

Prerequisites

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Content (Syllabus outline)

  • Intro: Monomers, oligomers, polymers. Polymers topologies. Conformation vs. configuration. Methods of description of polymer conformations. Coarse-graining. Conformational transitions.
  • Helix-coil transition in polypeptides: Definition of the problem. Phenomenological definition of Zimm-Bragg model. Hamiltonian formulation. Transfer-matrix approach. Correlation length and cooperativity.
  • Protein folding problem: Definition of the problem. Analytical and computational approaches. Go-like modelling and Random Energy Model. Coil-globule transition and glass formation.
  • DNA melting: Definition of the problem. Poland-Sheraga model. Loop factor and the order of phase transition. Zipper model as the single-sequence approximation of Zimm-Bragg model.
  • Modelling water: Biopolymers in water; phase diagrams. Origins of reentrant behavior, cold denaturation.

Intended learning outcomes

Knowledge and understanding:

By the end of the course the students will have specifically addressed the models used to describe changes of biopolymer conformations and the physical foundations behind these phenomena.

Readings

1. M. Rubinstein, Ralph H. Colby. Polymer Physics. Oxford: Oxford University Press, 2003.

2. GROSBERG A . Yu . and KHOKHLOV A . R . , Statistical Physics of Macromolecules. New York: American Insitute of Physics, 1994.

3. Alberts B. Molecular biology of the cell. Sixth edition. New York, NY: Garland Science, Taylor and Francis Group, 2015.

4. C. Cantor, T. Shimmel. Biophysical Chemistry. San-Francisco: Freeman and Co., 1980.

Assessment

Oral exam and seminar presentation. 60/40

Lecturer's references

Assistant professor of Physics at the University of Nova Gorica.

1. BADASYAN, Artem, MAVRIČ, Andraž, KRALJ CIGIĆ, Irena, BENCIK, Tim, VALANT, Matjaž. Polymer nanoparticle sizes from dynamic light scattering and size exclusion chromatography : the case study of polysilanes. Soft matter. 2018, vol. 14, issue 23, str. 4735-4740, ilustr. ISSN 1744-6848.

2. BADASYAN, Artem, TONOYAN, Sh. A., GIACOMETTI, Achille, PODGORNIK, Rudolf, PARSEGIAN, Vozken Adrian, MAMASAKHLISOV, Yevgeni S., MOROZOV, Vladimir. Unified description of solvent effects in the helix-coil transition. Physical review. E, Statistical, nonlinear, and soft matter physics, ISSN 1539-3755, 2014, vol. 89, iss. 2, str. 022723-1-022723-10

3. BADASYAN, Artem, MAMASAKHLISOV, Yevgeni S., PODGORNIK, Rudolf, PARSEGIAN, Vozken Adrian. Solvent effects in the helix-coil transition model can explain the unusual biophysics of intrinsically disordered proteins. The Journal of chemical physics. 2015, vol. 143, iss. 1, str. 014102-1-014102-7

4. BADASYAN, Artem, GIACOMETTI, Achille, PODGORNIK, Rudolf, MAMASAKHLISOV, Yevgeni S., MOROZOV, Vladimir. Helix-coil transition in terms of Potts-like spins. The European physical journal. E, Soft matter, ISSN 1292-8941, 2013, issue 5, art.no. 46, 9 str.

5. BADASYAN, Artem, TONOYAN, Sh. A., GIACOMETTI, Achille, PODGORNIK, Rudolf, PARSEGIAN, Vozken Adrian, MAMASAKHLISOV, Yevgeni S., MOROZOV, Vladimir. Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition. Physical review letters, ISSN 0031-9007. [Print ed.], 2012, vol. 109, iss. 6, str. 068101-1-068101-5.

6. BADASYAN, Artem, TONOYAN, Sh. A., MAMASAKHLISOV, Yevgeni S., GIACOMETTI, Achille, BENIGHT, A. S., MOROZOV, Vladimir. Competition for hydrogen-bond formation in the helix-coil transition and protein folding. Physical review. E, Statistical, nonlinear, and soft matter physics, ISSN 1539-3755, 2011, vol. 83, no. 5, str. 051903-1-051903-9.

University course code: 3FIi23

Year of study: 1

Lecturer:

ECTS: 6

Workload:

  • Lectures: 30 hours
  • Seminar: 30 hours
  • Individual work: 120 hours

Course type: elective

Languages: english

Learning and teaching methods:
teacher frontal lectures and seminars presented by the students and prepared under teacher supervision.