Biophysics
A.Y. 2024/2025
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.
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.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
1. Eukaryotic and prokaryotic cells. The structure of the cell.
2. Cell membranes. Thermodynamic phases of fatty acids.
3. Elastic properties of the lipid membrane.
4. Trans-membrane proteins. Electrophoresis. Osmotic pressure.
5. Ionic channels. Mechanosensitive channels.
6. Transcription and translation. The central dogma.
7. DNA and transcription. DNA phases. Promoters.
8. Control of transcription. Thermodynamic models.
9. The case of the Lac repressor
10. Dynamics of transcription regulation
11. Dynamics of protein translation. Gillespie algorithm.
12. Genetic switches.
13. Delayed response and oscillations. Transcriptional networks.
14. Motifs in transcriptional networks. ATP.
15. Kinetic proofreading.
16. Theoretical neuroscience. The neuron.
17. Spike statistics. Reverse correlation.
18. Visual system: retina and primary visual cortex.
19. Decoding. Neural networks.
20. Feedfoward and recurrent networks
21. Associative memory. Plasticity and learning
2. Cell membranes. Thermodynamic phases of fatty acids.
3. Elastic properties of the lipid membrane.
4. Trans-membrane proteins. Electrophoresis. Osmotic pressure.
5. Ionic channels. Mechanosensitive channels.
6. Transcription and translation. The central dogma.
7. DNA and transcription. DNA phases. Promoters.
8. Control of transcription. Thermodynamic models.
9. The case of the Lac repressor
10. Dynamics of transcription regulation
11. Dynamics of protein translation. Gillespie algorithm.
12. Genetic switches.
13. Delayed response and oscillations. Transcriptional networks.
14. Motifs in transcriptional networks. ATP.
15. Kinetic proofreading.
16. Theoretical neuroscience. The neuron.
17. Spike statistics. Reverse correlation.
18. Visual system: retina and primary visual cortex.
19. Decoding. Neural networks.
20. Feedfoward and recurrent networks
21. Associative memory. Plasticity and learning
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
Lectures
Teaching Resources
Philips et al., Physical Biology of the Cell, Garland Science
Boal, Mechanics of the Cell, Cambridge University Press
Alon, An introduction to system biology, Chapman & Hall
Dayan & Abbott, Theoretical neuroscience, MIT Press
Boal, Mechanics of the Cell, Cambridge University Press
Alon, An introduction to system biology, Chapman & Hall
Dayan & Abbott, Theoretical neuroscience, MIT Press
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: 3
FIS/07 - APPLIED PHYSICS - University credits: 3
FIS/07 - APPLIED PHYSICS - University credits: 3
Lessons: 42 hours
Professor:
Tiana Guido
Professor(s)