Biophysics

A.Y. 2021/2022
6
Max ECTS
42
Overall hours
SSD
FIS/03 FIS/07
Language
Italian
Learning objectives
The aim of the course is to provide an overview of cellular biophysics by illustrating how physical principles underlying mechanics, thermodynamics, hydrodynamics and kinetics influence cell behaviour.
Expected learning outcomes
The student at the end of the course will have acquired the following skills:
1) He/she will know the basics of the functioning and structure of a cell.
2) He/she will know the genetic code and its function.
3) He/she will be able to provide quantitative estimates for objects and processes relevant to the cell.
4) He/she will know how to apply elasticity theory methods to the study of biological filaments and membranes.
5) He/she will be able to interpret simple cellular processes through the use of statistical mechanics (e.g.: opening of ion channels, ligand receptor kinetics, variation of protein conformation).
6) He/she will know the basic models for the statistical study of biological filaments.
7) He/she will know how to apply hydrodynamics in the cellular context.
8) He/she will be familiar with some dynamic and kinetic processes relevant to cellular functioning, such as polymerization, diffusion and molecular transport.
Course syllabus and organization

Single session

Responsible
Lesson period
First semester
Classes will take place on Zoom. Breakout rooms will be used for group exercises. The lessons will be carried out in synchronous mode and recorded. The recordings will be available on Ariel. Whenever possible, platforms for online exercises and surveys will be used.
Course syllabus
1. Introduction to biophysics
Biophysics and quantitative biology
Cell size and organization
Time scales of cellular processes
Biological models: e. coli, yeast, drosophila
Cell Energetics

2. Thermodynamics and statistical mechanics of cellular processes
Entropy and statistical mechanics: introductory notes
Rna polymerase
Osmotic balance
Two-state systems
Random walk and macromolecules
DNA, force-extension

3. Cell mechanics
Introduction to elasticity
Filaments: tensile, bending, torsion
Polymers: "worm-like chain"
Cytoskeleton mechanics
Membranes: elasticity, shape, vesicles
Active membranes

4. Cellular dynamics and kinetics
Hydrodynamics
Dissemination
Dynamics in crowded environments
Cellular kinetics
Actin polymerization
Microtubules and dynamic instability
Molecular motors
Cellular Division
Prerequisites for admission
To follow the course it is necessary to know the basics of classical mechanics and thermodynamics, as taught in the first and second year of the three-year degree in physics.
Teaching methods
The course includes a series of theoretical lessons also with the use of multimedia material. The student will have at his disposal a series of didactic materials (videos and slides, both produced by the teacher and found online). The materials can be consulted before each lesson and the classroom lessons will allow a more in-depth discussion of the teaching materials and will also include short exercises necessary to fix the learning.
Teaching Resources
Rob Phillips, Jane Kondev, Julie Theriot Herman Garcia, Physical Biology of the Cell (2nd edition). Garland Science, 2012. ISBN-13: 978-0815344506
Assessment methods and Criteria
The examination consists of an oral discussion of the topics covered in the course.
FIS/03 - PHYSICS OF MATTER - University credits: 0
FIS/07 - APPLIED PHYSICS - University credits: 0
Lessons: 42 hours
Professor: Zapperi Stefano
Educational website(s)
Professor(s)
Reception:
11-12 Wednesday
office at the physics department or zoom (send email for an appointment)