Biophysics of membranes and cells

Enrollment into the program.
Homework assignment should be completed before taking the oral examination.

Introduction. Structure of biological cells, organelles and other building blocks of cells, cell wall.
Polymer networks. Intracellular network structures. Rigid and soft biological filaments. Planar (two-dimensional) networks: theory of elasticity; membrane networks, cytoskeleton. Spatial (three-dimensional) networks: elastic moduli, entropic elasticity, percolation. Concentrated solutions of semiflexible polymers as networks: elastic and rheological properties. Microtubules.
Membranes. Self-organization of amphiphiles in water, lipid bilayer. Elastic theory of bilayers: bending, stretching deformation. Thermal undulations, persistence length of bilayer. Vesicles. Intracellular membrane structures: mitochondria, endoplasmic reticulum, Golgi apparatus.
Intermembrane interaction. Electrostatic and van der Waals force, entropic repulsion of membranes and polymers, adhesion forces.
Cell. Simple cells: red blood cell, shapes; bacteria.
Dynamics of filaments. Cell structures in motion. Polymerization of actin and tubulin. Molecular motors: translational and rotational motion.
Transmembrane transport. Review of transport mechanisms. Diffusion, solvent transport, osmosis. Passive and active ion transport. Electroosmosis, Nernst potential, Donnan equilibrium. Mitochondria.
Nerve impulses. Cell membrane as electric network, axons, action potential, propagation of nerve impulse, Hodgkin-Huxley mechanism, generation of impulse, synapses.
Homeostasis. Regulation of cell volume, mechanisms of homeostasis, homeostasis in simple models of cells.

T. F. Weiss, Cellular Biophysics, MIT Press, Cambridge, 1996,
D. Boal, Mechanics of the Cell, Cambridge University Press, Cambridge, 2002,
P. Nelson, Biological Physics, W. H. Freeman, New York, 2004,
J. Howard, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer Associates, Sunderland, 2001,
R. Glaser, Biophysics, Springer, Berlin, 2005.

To introduce the mesoscopic theoretical physical basis of the structure and the workings of the biological cell. Describe i) the membrane as the entity that separates the cell from the environment, ii) the network structures providing support and cell shape, and iii) the transmembrane transport as the basic mechanism of exchange of matter and signals at the cell level.

Knowledge and understanding
Understanding of the physical aspects of i) the structure of the building blocks of cells as self-organized molecular structures and ii) the main transport processes in cells.

Application
Students learn to apply a range of physical theories (especially the methods of elasticity, electrostatics and statistical physics as well as soft-matter physics) to describe the mesoscopic and the microscopic structures and processes in biology. In addition, they learn to recognize the physical basis of cell-level biological processes.

Reflection
The course provides an insight into the meaning and the scope of the mesoscopic description of biological systems in terms of physical models. This helps the students to appreciate that both a detailed understanding of the phenomenology of the structure or the process at hand as well as the ability to identify the main and the subdominant mechanisms are needed to construct a model that works well.

Transferable skills
The students learn to carry out an interdisciplinary analysis of a complex system and to apply coarse-grained physical models characterized by a range of time, length, and energy scales.

lectures, tutorials, seminars, homework assignments, consultations

Completed homework assignment (written report, presentation) counts as problem-solving examination
Oral examination
grading: 5 (fail), 6-10 (pass) (according to the Statute of UL)

1. ZIHERL, Primož, SVETINA, Saša. Flat and sigmoidally curved contact zones in vesicle-vesicle adhesion. Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2007, letn. 104, št. 3, str. 761-765. [COBISS-SI-ID 22325721].
2. HOČEVAR BREZAVŠČEK, Ana, ZIHERL, Primož. Degenerate polygonal tilings in simple animal tissues. Physical review. E, Statistical, nonlinear, and soft matter physics, ISSN 1539-3755, 2009, vol. 80, no. 1, str. 011904-1-011904-7. [COBISS-SI-ID 22730279].
3. SAKASHITA, Ai, URAKAMI, Naohito, ZIHERL, Primož, IMAI, Masayuki. Three-dimensional analysis of lipid vesicle transformations. Soft matter, ISSN 1744-683X, 2012, vol. 8, no. 33, str. 8569-8581, doi: 10.1039/C2SM25759A. [COBISS-SI-ID 26017319].

4. HOČEVAR BREZAVŠČEK, Ana, RAUZI, Matteo, LEPTIN, Maria, ZIHERL, Primož. A model of epithelial invagination driven by collective mechanics of identical cells. Biophysical journal, ISSN 0006-3495, 2012, vol. 103, no. 5, str. 1069-1077, doi: 10.1016/j.bpj.2012.07.018. [COBISS-SI-ID 26113063].

5. KRAJNC, Matej, ŠTORGEL, N., HOČEVAR BREZAVŠČEK, Ana, ZIHERL, Primož. A tension-based model of flat and corrugated simple epithelia. Soft matter, ISSN 1744-683X, 2013, vol. 9, no. 34, str. 8368-8377, doi: 10.1039/c3sm51588e. [COBISS-SI-ID 26927143].