Scheda programma d'esame
Anno accademico2019/20
PeriodoPrimo semestre

Programma non disponibile nella lingua selezionata
Learning outcomes

Students are expected to acquire knowledge in molecular biophysics, molecular biology and "nano-medicine". Experimental and modeling techniques to analyze the living matter at the cellular and sub-cellular level are illustrated. Basic concepts of Biochemistry and biology are introduced at the beginning of the course, and a survey of "classical macroscopic biophysics" is given. At the end of the course, some of the most recent biomedical and nano-medicine applications are illustrated.

Assessment criteria of knowledge

The student is tested on his/her ability of exposing a topic, first. His/her capability of going through the topic, of understanding the details and the basic physics underlying given phenomena is also ascertained, beyond the knowledge of the topic itself. His/her capability of making connections with other topics treated in the course or with topics considered to be in the background of a student at this stage of his studies, is also checked. The student must demonstrate his/her capability of rationally deducing consequences from given facts, and of critically addressing the topics. Finally, the capability of making his/her own bibliographic research is also appreciated.


Fundamentals of matter physics. Math: analysis, vector and matrix calcolus

Teaching methods

Lectures, with the aid of slides. The teacher can show tutorials found on the web;

elearning/teams website: download of ppts and communications between teacher-student;

type of interaction between student and teacher: meeting, email, skype, teams;

language: English

  • Introduction to biochemistry
    1. Nature of forces within biomolecules; 
    2. Structure and functions of carbohydrates  
    3. Structure and function of nucleic acids, transcription and translation
    4. Structure and function of proteins, their classification.
    5. Structure and function of lipid membranes, and membrane proteins
    6. Structure of prokaryote and eukaryote cells
    7. Viruses, structure and replication
  • Physical chemistry of the cell
    1. Recall of equilibrium thermodynamics; 
    2. Contribution of intramolecular forces to biomolecular stability  
    3. Protein folding, stereospecific recognition
    4. Equilibrium states: protein-ligand binding
    5. Cooperativity, allostery
    6. Molecular crowding
    7. Non-equilibrium thermodynamics: the linear range
    8. Diffusion, Smoluchowski equation and Fick equation
    9. Membrane and diffusion
    10. Electrokinetic potential, Nerst-Planck equation and ion flow
    11. Ion channels and their structure
    12. Goldman-Hodgkin-Katz description of membrane potential
    13. Modeling membrane as a circuit
    14. Action potential
    15. Voltage-gated ion channels
    16. Voltage clamp and Goldman equation
    17. Cable equation and myelination
    18. Ligand-gated ion channels and synapses
    19. Neuron as integrating units
    20. Non-equilibrium thermodynamics
    21. Instability of steady-states and dissipative structures
    22. reaction-diffusion description, linearized systems
    23. Enzymes, allostery and metabolic regulation
    24. Oscillations in glycolysis
  • Molecular optical spectroscopy
    1. Electronic absorption
    2. Electronic structure and molecular orbitals
    3. UV absorption of proteins and nucleic acids
    4. π-conjugated systems
    5. Rhodopsin, retinal and vision
    6. Linear and circular dichroism
    7. Spontaneous emission and fluorescence
    8. Non-radiative decay
    9. Intersystem crossing and phosphorescence
    10. Fluorescent Proteins: structure and spectroscopic properties
    11. Absorption and scattering in tissues: near-infrared window
    12. Non linear processes: two photons adsorption and second harmonic generation (SHG) 
  • Vibrational spectroscopy
    1. Molecular vibrations
    2. IR spectroscopy (FTIR)
    3. Raman vibrational spectroscopy
    4. Vibrational spectra of proteins
    5. Pre-resonant and resonant Raman spectroscopy
    6. Imaging by Coherent Anti-Stokes Raman Scattering (CARS)
  • Structural spectroscopy of biomolecules
    1. Protein Data Bank (PDB)
    2. Protein crystals
    3. X-ray diffraction
    4. Protein models from the electronic density map
    5. Principles of Nuclear Magnetic Resonance
    6. Brief illustration of 2D NMR
    7. Browsing the PDB: visualisation of biomolecules
  • Computational modeling of biomolecules
    1. Overview of QM methods
    2. Molecular mechanics
    3. Molecular dynamics: time discretization and integrators of the Newton equation
    4. Applications: protein dynamics and receptor-ligand interactions, protein folding
    5. Overview of methods for protein-structure prediction
  • Multi-scale simulations of bio-systems
    1. low-resolution models and multi-scale combinations
    2. Go and network models of biomolecules
    3. Continuum and mechanistic models of biopolymers and membranes
    4. implicit solvent models and surface representations, docking.
  • Microscopy
    1. Recall of optics
    2. Bright field microscope
    3. Numeric aperture and resolution
    4. Contrast and sources of contrast
    5. Fluorescence microscope: wide-field
    6. Confocal microscope
Non-attending students info

Use consultation hours to fill any gap

Assessment methods

The final exam is oral. Students have two options 1. they are interviewed directly on the whole program of the course or 2. Students are suggested to focus on a specific topic, by (autonomously or with the teacher help) searching bibliography on it and writing a very short report. The exam starts with the oral presentation of the topic (5-7 mins), and then the candidate is interviewed on other topics of the course. The student is completely free to choose among the two options, although up to now everyone has chosen option 2. In any case, the knowledge of the whole program is tested and the written report is not considered in the final evaluation.

Ultimo aggiornamento 13/05/2020 12:21