Molceular biophysics

Physics, Second Cycle
1. year
Hours per week – 2. semester:

Enrollment into the program.
Written exam (midterm and final) and completed seminar.

Content (Syllabus outline)

X-ray and light scattering: description of the basic experiments with light scattering. Scattered intensity in X-ray and optical light scattering. Equations of von Laue and Bragg. Cochran-Crick-Vand theory of scattering on helices and the Franklin-Gosling experiment. X-ray scattering on DNA and collagen. Light scattering on DNA solutions and the DNA persistence length.
Structure of DNA: The basic properties of DNA molecular structure. Double helix: nitrogen bases and the phosphate backbone. Structural principles of the double helix of Watson-Crick. Deformations of DNA and macroscopic theory of elasticity. Limits of validity of the continuum description.
Filamentous proteins: Structure of collagen. Description of the basic structural properties of filamentous proteins. Triple helix. Gelation of collagen in aqueous solutions.
Globular proteins: Structural principles of globular proteins and X-ray scattering from globular proteins. Principles of protein structure determination.
Statistical mechanics of polymer chains: Eastic energy and the statistical integral. Analogy with quantum mechanics. The Kratky-Porod worm-like chain. Entropy and enthalpy elasticity. The scattering function fo the worm-like chain and the Peterlin approximation. Macroscopic elasticity of polymeric chains. Siggia-Marko interpolation formula and the elastic equation of state. Experiments with atomic force spectroscopy and the persistence length of DNA.
Macromolecular interactions: The phenomenology of interactions between macromolecules. The attraction and repulsion within the DLVO theory. Mean-field theory of electrostatic interactions. The Poisson-Boltzmann equation. Debye screening, the weak and the strong coupling theory of electrostatic interactions. The Netz strong coupling theory of electrostatic interactions. The Lifshitz theory of van der Waals interactions.
DNA and protein aqueous solutions: Osmotic pressure and the Van't Hoff law. Osmotic pressure and macromolecular interactions. The Rand- Parsegian experiment. Osmotic stress in DNA and protein solutions. Equation of state of DNA in aqueous solutions and its phase diagram. Properties of high density DNA mesophases and their relation to the packing of DNA in viruses, bacteria and higher organisms.

  • M. Rubinstein & R.H. Colby, Polymer Physics (Oxford, 2003, 1-96, 137-196, 253-294)
  • C.R. Cantor in P.R. Schimmel: Biophysical Chemistry (Freeman and Comp. 1980, 687-842).
  • V. Bloomfield, D.M. Crothers, I. Tinoco: Nucleic acids (University Science Books, 2000, 1-31, 79-103)
  • M. D. Frank Kamenetskii : Unraveling DNA (1997)
  • H. Schiessel Biophysics for Beginners: A Journey through the Cell Nucleus (2013)
  • R. Podgornik, Physics of DNA (book manuscript, 2008)
Objectives and competences

Introduction to the basic properties of biological macromolecules, DNA and proteins as well as to the general concepts and methods in biophysical research.

Intended learning outcomes

Knowledge and understanding:
Understadning of the structure of fundamental biological macromolecules. Understanding of the basic principles of experimental techniques of macromolecular research. Statistical mechanics of macromolecular interctions.
The acquired knowledge enables the basic understanding of biomaterial properties – DNA and proteins
An example of the application of statmech, elastomechanics and electrodynamics to the structure and interactions of biomolecules.
Transferable skills:
A transition from the fundamental principles of theoretical structural biophysics to the understanding of the basic properties of molecular building blocks of biological systems.

Learning and teaching methods

Lectures, seminars, homeworks and consultations


Midterm written exam
Final written exam
A delivered seminar and a handed in homework
grading: 5 (fail), 6-10 (pass) (according to the Statute of UL)

Lecturer's references

prof. dr. R. Podgornik:
1. Roger H. French, V. Adrian Parsegian, Rudolf Podgornik et al., Long Range Interactions in Nanoscale Science, REVIEWS OF MODERN PHYSICS, 82, 1887 2010.
2. Rudolf Podgornik, D. Harries, J. DeRouchey, H. H. Strey, and V. A. Parsegian, Interactions in Macromolecular Complexes Used as Nonviral Vectors for Gene Delivery, in Gene Therapy: Therapeutic Mechanisms and Strategies, N. Smyth – Templeton, Marcel Dekker, New York (2008), Third Edition.
3. Antonio Siber, Anze Losdorfer Bozic and Rudolf Podgornik, Energies and pressures in viruses: contribution of nonspecific electrostatic interactions, Phys. Chem. Chem. Phys., 2012, 14, 3746–3765.
4. Ali Naji, Matej Kanduč, Roland R. Netz and Rudolf Podgornik: Exotic Electrostatics: Unusual Features of Electrostatic Interactions between Macroions, Understanding Soft Condensed Matter via Modeling and Computation Eds. W.-B. Hu & A.-C. Shi, Series in Soft Condensed Matter Edited by David Andelman and Günter Reiter, World Scientific, Singapore (2010).
5. Anže Lošdorfer Božic, Antonio Šiber and Rudolf Podgornik, Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties, Journal of Biological Physics March 2013, Volume 39, Issue 2, pp 215-228 (2013).
prof. dr. M. Praprotnik:
1. Matej Praprotnik, Luigi Delle Site, Kurt Kremer. Multiscale simulation of soft matter: From scale bridging to adaptive resolution. Annu. Rev. Phys. Chem. 59, 545-571, 2008.
2. Staš Bevc, Christoph Junghans, Kurt Kremer, Matej Praprotnik. Adaptive resolution simulation of salt solutions. New J. Phys. 15, 105007, 2013.
3. Julija Zavadlav, Manuel N. Melo, Siewert J. Marrink, Matej Praprotnik. Adaptive resolution simulation of an atomistic protein in MARTINI water. J. Chem. Phys. 140, 054114, 2014.
4. Julija Zavadlav, Manuel N. Melo, Ana V. Cunha, Alex H. de Vries, Siewert J. Marrink, Matej Praprotnik. Adaptive resolution simulation of MARTINI solvents. J. Chem. Theory Comput. 10, 2591-2598, 2014.
5. Aleksandar Popadić, Jens H. Walther, Petros Koumoutsakos, Matej Praprotnik. Continuum simulations of water flow in carbon nanotube membranes. New J. Phys. 16, 082001, 2014.