Physics Protein 1
A.Y. 2024/2025
Learning objectives
In the course we shall discuss the physical principles that control the kinetic and the equilibrium properties of proteins from the perspective of statistical mechanics.
Expected learning outcomes
The student at the end of the course will have the following abilities:
1. To know the tools of statistical mechanics (equilibrium and out-of-equilibrium) to study biomolecules
2. To know the interactions that stabilise proteins
3. To kown the thermodynamic and kinetic properties of proteins
4. To develop little models to describe the properties of biomolecules based on statistical mechanics
1. To know the tools of statistical mechanics (equilibrium and out-of-equilibrium) to study biomolecules
2. To know the interactions that stabilise proteins
3. To kown the thermodynamic and kinetic properties of proteins
4. To develop little models to describe the properties of biomolecules based on statistical mechanics
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
- What proteins are; the thermodynamic hypothesis.
- Review of the main experimental results on proteins
- Phase transitions in proteins
- The beta-hairpin transition
- The protein folding phase transition
- The helix-coil transition
- Interactions among amino acids
- The hydrophobic force
- Polymer theory: the ideal chain, freely-rotating chain, torsional energy
- Interacting polymer: the Virial expansion, coil, theta point, globules, coil-globule transition
- Disordered interactions; the random energy model
- The energy landscape: replica calculations
- Proteins as result of evolution
- Dynamics: Langevin equations, stochastic differential equations and Brownian motion
- The Rouse chain
- The Fokker-Planck equation
- Jumping energy barriers: Kramers equation
- Stochastic processes, detailed balance, kinetics models for proteins
- Dimensional reduction
- Protein aggregation
- Review of the main experimental results on proteins
- Phase transitions in proteins
- The beta-hairpin transition
- The protein folding phase transition
- The helix-coil transition
- Interactions among amino acids
- The hydrophobic force
- Polymer theory: the ideal chain, freely-rotating chain, torsional energy
- Interacting polymer: the Virial expansion, coil, theta point, globules, coil-globule transition
- Disordered interactions; the random energy model
- The energy landscape: replica calculations
- Proteins as result of evolution
- Dynamics: Langevin equations, stochastic differential equations and Brownian motion
- The Rouse chain
- The Fokker-Planck equation
- Jumping energy barriers: Kramers equation
- Stochastic processes, detailed balance, kinetics models for proteins
- Dimensional reduction
- Protein aggregation
Prerequisites for admission
Basic statistical mechanics
Teaching methods
Lectures
Teaching Resources
Notes that can be downloaded from the Ariel site
Assessment methods and Criteria
Oral exams of approximately 1/2 hour to assess the degree of comprehension of the theoretical aspects of protein physics, of the ability to reproduce the calculations discussed during the lectures, of critical thinking and to connect to the subjects learn in other courses.
Professor(s)