Biophysics

Biophysics as a Physics of biological systems. Introduction to the Physics of Macromolecules.

Enrollment into the current study year. For the exchange students, meeting of the course prerequisites will be checked by the Study committee of the school

1. INTRODUCTION
   Living Organisms. Cell as a minimal living system. Structure of cells. Biophysics as the Physics of Biological Systems. Peculiarities of biological systems.

2. BIOPOLYMERS
   Role of biopolymers in cells and related conformational transitions. Primary, secondary, tertiary and quaternary levels of structural organisation. Importance of biopolymer models:
   experimental and theoretical approaches.

3. BASIC POLYMER PHYSICS
   Structure and classification of polymers. Parameters, relevant for the description of polymer systems. Importance of coarse-graining. Polymer molecule as a statistical system. Size distributions. Balls-on-a-string, free flight, free rotation and other polymer models. Ideal chains. Intramolecular interactions and Flory theory.
   Coil-globule transition.

4. HELIX-COIL TRANSITION IN POLYPEPTIDES
   Experimental observations. Theoretical description with spin models. Zimm-Bragg, Lifson-Roig and Potts-like models. Account of solvent. Conformational transitions in 1D systems: phase transitions or not?

5. DNA MELTING
   Melting experiments. Theory of DNA melting and importance of loop factor. Structural heterogeneity and algebra of non-commutative operators.

6. PROTEIN FOLDING
   Importance of folding. Folding experiments and phase diagram. Native structures, Protein Data Bank and Go-like approach. Spin-based vs Lennard-Jones description and folding simulations. Coarse-grained vs all-atom approach.

Understanding of the structure and the peculiarity of living systems and the limit of applicability of physical approaches. Knowledge of most relevant processes in
cells and their description.

• M. Rubinstein, Ralph H. Colby, Polymer Physics, Oxford University Press (2003). Catalogue
• C.R. Schimmel, P.R. Cantor, Biophysical chemistry - part I and III, W. H. Freeman and Company, San Francisco (1980). Catalogue1 Catalogue3 E-version
• B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter, Molecular Biology of the Cell, 4th edition New York: Garland Science (2002). Catalogue

• oral exam

Dr. Artem Badasyan je izredni profesor za področje fizike na Univerzi v Novi Gorici. Artem Badasyan is associate professor of physics at the University of Nova Gorica.

Izbrane publikacije / selected publications:

1. PEZHUMKATTIL PALAKKAL, Jasnamol, VALANT, Matjaž, BADASYAN, Artem, et al. Unusual magnetodielectric effects in La2CuMnO6 induced by a dynamic crossover in dielectric relaxation at TC. Materials research bulletin, ISSN 0025-5408., Apr. 2018, vol. 100, str. 226-233, doi: 10.1016/j.materresbull.2017.12.027. [COBISS.SI-ID 4979195].

2. 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, ISSN 1744-6848, 2018, vol. 14, issue 23, str. 4735-4740, doi: 10.1039/C8SM00780B. [COBISS.SI-ID 5150715].

3. MAVRIČ, Andraž, BADASYAN, Artem, MALI, Gregor, VALANT, Matjaž. Growth mechanism and structure of electrochemically synthesized dendritic polymethylsilane molecules. European Polymer Journal, ISSN 0014-3057. 2017, vol. 90, str. 162-170, doi: 10.1016/j.eurpolymj.2017.03.018.
4. MAVRIČ, Andraž, BADASYAN, Artem, FANETTI, Mattia, VALANT, Matjaž. Molecular size and solubility conditions of polysilane macromolecules with different topology. Scientific reports, ISSN 2045-2322, 2016, vol. 6, str. 1-8, doi: 10.1038/srep35450. [COBISS.SI-ID 4549883].
5. ŠKRBIĆ, Tatjana, BADASYAN, Artem, HOANG, Trinh Xuan, PODGORNIK, Rudolf, GIACOMETTI, Achille. From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang-Landau approach. Soft matter, ISSN 1744-683X, 2016, vol. 12, iss. 21, str. 4783-4793, ilustr., doi: 10.1039/C6SM00542J.
   [COBISS.SI-ID 2954852].