Molecular biophysics
A.A. 2020/2021
Obiettivi formativi
The course aims to provide students with a general understanding of the biophysical principles, the experimental techniques and the theoretical models enabling a quantitative description of intra- and inter-molecular interactions of biomolecules, with a main focus on nucleic acids and polypeptides. Primary objectives of the course are the understanding of the thermodynamic basis of equilibrium and kinetic phenomena related to biomolecular binding and conformational dynamics, the knowledge of advanced experimental techniques to quantitatively address the relevant parameters describing these phenomena, and, through practical training on computer programming, the use of computational tools to test the agreement of theoretical models with experimental data. The course also aims to convey the methodological process of physics, as the basis of a quantitative description of bimolecular behaviour.
Risultati apprendimento attesi
At the end of the course the student will be able to:
- apply the concepts of thermodynamic and kinetic modelling to describe the intra- and inter-molecular interactions of proteins and DNA;
- describe the principles of fluorescence-based methods and biosensors to investigate biomolecular conformations and interactions at the nanoscale and correctly interpret and communicate results obtained with these methods;
- design and apply quantitative models to interpret the behaviour of biomolecular systems.
On successful completion of this course, students will gain:
- a critical ability to quantitatively address the behaviour of biomolecules and complex biomolecular systems;
- the capacity to access a wider scientific literature, addressing biological problems with biophysical tools and concepts, typically not included in a standard curriculum in biology.
- apply the concepts of thermodynamic and kinetic modelling to describe the intra- and inter-molecular interactions of proteins and DNA;
- describe the principles of fluorescence-based methods and biosensors to investigate biomolecular conformations and interactions at the nanoscale and correctly interpret and communicate results obtained with these methods;
- design and apply quantitative models to interpret the behaviour of biomolecular systems.
On successful completion of this course, students will gain:
- a critical ability to quantitatively address the behaviour of biomolecules and complex biomolecular systems;
- the capacity to access a wider scientific literature, addressing biological problems with biophysical tools and concepts, typically not included in a standard curriculum in biology.
Periodo: Secondo semestre
Modalità di valutazione: Esame
Giudizio di valutazione: voto verbalizzato in trentesimi
Corso singolo
Questo insegnamento non può essere seguito come corso singolo. Puoi trovare gli insegnamenti disponibili consultando il catalogo corsi singoli.
Programma e organizzazione didattica
Edizione unica
Responsabile
Periodo
Secondo semestre
The lectures and practical experiences will be delivered through the Microsoft Teams platform and can be followed mainly synchronously at set times). Some lessons or parts of lessons or exercises on specific topics will be made available only asynchronously. In compliance with the indications in force, there may be activities in presence in the classroom, of which the students will be suitably informed through notices on the Ariel website. In any case, the recordings of the lessons will be available on the Ariel page of the teaching. The exercises require the use of a computer.
The program and the reference material of the lectures will not change. All the didactic material will be made available through the Ariel platform.
Learning assessment methods and criteria will be maintained, provided that the written and oral tests will take place in person or electronically according to the directives in force at the time of the exam. In electronic mode, both the written and oral exams will take place through Microsoft Teams or similar platform.
The program and the reference material of the lectures will not change. All the didactic material will be made available through the Ariel platform.
Learning assessment methods and criteria will be maintained, provided that the written and oral tests will take place in person or electronically according to the directives in force at the time of the exam. In electronic mode, both the written and oral exams will take place through Microsoft Teams or similar platform.
Programma
The topics are:
- Description of the dynamics of biomolecules in terms of fundamental interactions and diffusive motion.
- Thermodynamic equilibrium of the biomolecular conformations and interactions.
- Thermodynamics of DNA hybridization, protein folding and biomolecular recognition processes.
- Models for the description of the kinetics of intra- and inter-molecular interactions in proteins and nucleic acids.
- Phase separation of biomolecular compounds and spontaneous order at high concentration.
- Physical polymer models for the description of the conformation and intra-chain dynamics of polypeptides and nucleic acids.
- Supramolecular structures of nucleic acids.
- Experimental methods and models for the study of protein folding.
- Protein aggregation and formation of supramolecular structures of polypeptides.
- Protein-DNA interactions and gene regulation.
- Experimental methods based on fluorescence for the study of conformations and binding of biomolecules.
- Time-resolved fluorescence methods and single molecule fluorescence.
- Optical surface biosensors and models for analyzing results.
- Experimental methods based on the scattering of light.
- Molecular tools based on DNA nanotechnology.
- Use of software for symbolic and numerical calculation of thermodynamic and kinetic parameters.
- Writing of Python programs for complex curve fitting based on models, simulation of simple polymeric and multi-particle models, quantitative analysis of results from fluorescence quenching and FRET experiments, numerical resolution of kinetic models, analysis of binding curves obtained from biosensors.
- Description of the dynamics of biomolecules in terms of fundamental interactions and diffusive motion.
- Thermodynamic equilibrium of the biomolecular conformations and interactions.
- Thermodynamics of DNA hybridization, protein folding and biomolecular recognition processes.
- Models for the description of the kinetics of intra- and inter-molecular interactions in proteins and nucleic acids.
- Phase separation of biomolecular compounds and spontaneous order at high concentration.
- Physical polymer models for the description of the conformation and intra-chain dynamics of polypeptides and nucleic acids.
- Supramolecular structures of nucleic acids.
- Experimental methods and models for the study of protein folding.
- Protein aggregation and formation of supramolecular structures of polypeptides.
- Protein-DNA interactions and gene regulation.
- Experimental methods based on fluorescence for the study of conformations and binding of biomolecules.
- Time-resolved fluorescence methods and single molecule fluorescence.
- Optical surface biosensors and models for analyzing results.
- Experimental methods based on the scattering of light.
- Molecular tools based on DNA nanotechnology.
- Use of software for symbolic and numerical calculation of thermodynamic and kinetic parameters.
- Writing of Python programs for complex curve fitting based on models, simulation of simple polymeric and multi-particle models, quantitative analysis of results from fluorescence quenching and FRET experiments, numerical resolution of kinetic models, analysis of binding curves obtained from biosensors.
Prerequisiti
General physics, molecular biology and biochemistry at bachelor level.
Metodi didattici
The course is divided into classroom lectures, in which the topics are illustrated both with slides and on the blackboard. Exercises will be devoted to the development of case studies by computer-based calculation.
Materiale di riferimento
- Ken Dill, Sarina Bromberg, "Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience", Garland Science, 2010
- Michał Kurzyński, Jack Tuszyńsk, "Introduction to Molecular Biophysics", CRC Press, 2003
- Slides of the lessons available on the website of the course
- Michał Kurzyński, Jack Tuszyńsk, "Introduction to Molecular Biophysics", CRC Press, 2003
- Slides of the lessons available on the website of the course
Modalità di verifica dell’apprendimento e criteri di valutazione
Learning assessment will be through written and oral exam at the end of the course. The written exam requires both the solution of problems with the description of the main steps and answering multiple choices tests. The written exam is aimed to broadly verify the understanding of concepts and definitions taught during the course. The oral exam will focus on the discussion of an individual homework report prepared by the student on a case study addressed during the computer-based exercises.
Examples of problems and questions and their evaluation will be provided during the course.
Examples of problems and questions and their evaluation will be provided during the course.
FIS/07 - FISICA APPLICATA (A BENI CULTURALI, AMBIENTALI, BIOLOGIA E MEDICINA) - CFU: 6
Esercitazioni: 16 ore
Lezioni: 40 ore
Lezioni: 40 ore
Docente/i
Ricevimento:
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