Biophysics II

course ID





14 Weeks

Semester DD


Course details

Primary structure: protein sequences, protein alignment codes and dynamic programming. Sequences statistical analysis (Dot-Plot; Needlman-Wunsch; etc.). Evolution and similarity matrices: PAM matrices. Divergent and convergent evolution. The immune system, molecular mimicry and autoimmune diseases: a convergent evolution example. The evolution and the biological constants: four basis; 20 amino acids (a.a.); all a.a. are levorotary; all a.a. are alpha. Secondary structure: alpha-helix and beta-sheet; secondary structure stability: hydropathicity and DeltaG; hydropathicity profiles and amphiphilicity; the Kauzmann model. Tertiary structure: forces that drive protein folding. Numerical simulations: Molecular Dynamics (MD), Langevin dynamics, Monte Carlo (MC) and hybrid MC, ab initio MD (Car-Parrinello). Misfolding and aggregation: the role of metals. Cell membranes: lipids; micelles; Langmuir-Blodgett; lipid rafts. Membrane proteins. Spectroscopic techniques in biology: perturbation theory and cross section. X-ray absorption spectroscopy: the experimental apparatus; data analysis and structural information.


Teching is based on frontal lectures and exercises, aiming at developing a basic knowledge of biophysics concept, makind use of both dedicated mathematical methods and physics analysis.

Teaching rests on frontal lectures and exercises based on general knowledge acquired both
collectively as well as autonomously. Students will be asked to develop the learning skills
needed to continue their studies with a high degree of independence.

Students will be provided with adequate conceptual tools that would allow them to communicate information and suggest problems as well as solutions beyond their strict University context to scholars belonging to both their own strict disciplinary area and in nearby research areas like Chemistry, Biology and Medicine.

Students must be able to acquire the ability of correctly collecting and interpreting experimental data so as to be able to judge their scientific value. Special attention will be paid to the problem of handling the gigantic biological data Banks today available.

The main goal of exercises and tutorials is to check that students are able to exchange information, ideas, problems and solutions to experts as well as non-experts.
The work done during tutorials should allow the students to properly present in public their own research as well as the results of a bibliographic analysis. To this end it is necessary that the students acquire an adequate knowledge of English sufficient to understand today’s scientific literature, exploiting the English courses offered by the Faculty.

Tests will be periodically performed to check the student ability to critically evaluate general textbooks and specialized scientific papers.

Students should also be prepared and trained to be ready for their possible future PhD studies.