Measurement of Nanoscale Interactions in Biological Systems and Data Analysis
A.Y. 2024/2025
Learning objectives
The course aims at providing the students with knowledge of theoretical models and experimental techniques to understand relevant interactions taking place at the nanoscale in biological systems. In particular, the course will focus on modern approaches for the quantitative measurements of nanoscale forces at biomolecular and cellular level. High-resolution imaging and force spectroscopy techniques will be presented and discussed. These methodological and experimental approaches represent a valuable nanobiotechnological tool for the quantitative understanding of basic mechanisms in complex biological processes.
The students will also learn how to extract quantitative information from the experimental data. To this purpose, the basic principles of statistical data analysis, data fitting, estimation of uncertainties and assessment of the statistical significance of differences between measured values will be presented.
The course will include practical demonstrations of the scanning probe techniques in the laboratory and data analysis sessions, based on experimental data from the experiments discussed in the classroom. The course may include topical seminars by experts in the field.
The students will also learn how to extract quantitative information from the experimental data. To this purpose, the basic principles of statistical data analysis, data fitting, estimation of uncertainties and assessment of the statistical significance of differences between measured values will be presented.
The course will include practical demonstrations of the scanning probe techniques in the laboratory and data analysis sessions, based on experimental data from the experiments discussed in the classroom. The course may include topical seminars by experts in the field.
Expected learning outcomes
After the successful completion of the course, the students will possess a robust fundamental knowledge of some basic physical interactions taking place in biological systems at the biomolecular and cellular level. The students will know the basic principles of the experimental techniques for the quantitative characterisation of nanoscale phenomena, in particular based on scanning probe microscopy, and will be able to design experiments to investigate fundamental biological processes.
The students will also acquire practical skills (including basic programming ability) to analyse the experimental data, by fitting suitable analytical or numerical model to them data fitting, estimate uncertainties and assess the statistical significance of the results.
Moreover, the students will acquire the ability to perform literature searches and to critically evaluate the collected information in relation to the specificic problem they are addressing.
The students will also acquire practical skills (including basic programming ability) to analyse the experimental data, by fitting suitable analytical or numerical model to them data fitting, estimate uncertainties and assess the statistical significance of the results.
Moreover, the students will acquire the ability to perform literature searches and to critically evaluate the collected information in relation to the specificic problem they are addressing.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
Part I. Measurement of nanoscale interactions in biological systems (4 CFU)
For all topics covered, there will be a presentation of the underlying basic concepts and theory and of the main experimental techniques, and a discussion of reference papers from the scientific literature.
- Measuring nanoscale forces and imaging nanoscale systems with single molecule, single particle sensitivitivity. Scanning probe and atomic force microscopy. Other experimental techniques for the quantitative investigation of biological interfaces at the nanoscale.
- Interactions between nanocolloids and nanocolloids and surfaces: electrostatic double layer and van der Waals interactions (DLVO). Mention to non DLVO forces (hydrophobic, solvation, steric forces).
- Probing elasticity and spatial configuration of DNA and fibrillar structures. Basic models for the elasticity of semi-rigid polymers (freely-jointed chain, worm-like chain). (persistence length, end-to-end distance,...).
- Single-molecule force spectroscopy. Breaking molecular bonds: energetics and kinetics (the Bell model). Nanoscale affinity mapping and protein unfolding.
- Adhesion force spectroscopy using functionalised probes to test cell adhesion mechanisms and the onset of mechanotransduction. Includes discussion of mechanosensing and the interaction of cells with the microenvironment.
- Testing the nanomechanical properties of biomembranes, cells and tissues. Introduction to basic elasticity concepts, contact mechanics models, and the discussion of the applicability of these models to biological systems.
Part II. Analysis of biological data (2 CFU)
- Basic principles of statistical data and error analysis: averaging (mean and median), weighting of data, estimation of errors and assessment of the significance of differences.
- Presentation of experimental data: plots, data binning and histograms, box plots, etc.
- Fitting analytical and numerical models to the experimental data: linear, polynomial and non-linear regressions, constraints on parameters, estimation of the uncertainties of the fitting parameters (analytical and Monte-Carlo methods).
During practical hands-on data analysis sessions, the students will write custom routines (Matlab/Python ) for analyzing real data from the experiments described in the first part of the course.
For all topics covered, there will be a presentation of the underlying basic concepts and theory and of the main experimental techniques, and a discussion of reference papers from the scientific literature.
- Measuring nanoscale forces and imaging nanoscale systems with single molecule, single particle sensitivitivity. Scanning probe and atomic force microscopy. Other experimental techniques for the quantitative investigation of biological interfaces at the nanoscale.
- Interactions between nanocolloids and nanocolloids and surfaces: electrostatic double layer and van der Waals interactions (DLVO). Mention to non DLVO forces (hydrophobic, solvation, steric forces).
- Probing elasticity and spatial configuration of DNA and fibrillar structures. Basic models for the elasticity of semi-rigid polymers (freely-jointed chain, worm-like chain). (persistence length, end-to-end distance,...).
- Single-molecule force spectroscopy. Breaking molecular bonds: energetics and kinetics (the Bell model). Nanoscale affinity mapping and protein unfolding.
- Adhesion force spectroscopy using functionalised probes to test cell adhesion mechanisms and the onset of mechanotransduction. Includes discussion of mechanosensing and the interaction of cells with the microenvironment.
- Testing the nanomechanical properties of biomembranes, cells and tissues. Introduction to basic elasticity concepts, contact mechanics models, and the discussion of the applicability of these models to biological systems.
Part II. Analysis of biological data (2 CFU)
- Basic principles of statistical data and error analysis: averaging (mean and median), weighting of data, estimation of errors and assessment of the significance of differences.
- Presentation of experimental data: plots, data binning and histograms, box plots, etc.
- Fitting analytical and numerical models to the experimental data: linear, polynomial and non-linear regressions, constraints on parameters, estimation of the uncertainties of the fitting parameters (analytical and Monte-Carlo methods).
During practical hands-on data analysis sessions, the students will write custom routines (Matlab/Python ) for analyzing real data from the experiments described in the first part of the course.
Prerequisites for admission
The students must possess good knowledge of general physics and mathematics, as well as of molecular and cellular biology.
Teaching methods
Frontal lectures, using graphical tablet and slides. The lectures will also include open discussion of selected topical papers, previously distributed to the students.
During the first part of the course, the students will visit research laboratories for practical demonstrations of experimental techniques. Students can also attend topical seminars, led by an expert in the field. Lab demonstrations and seminars accounts for 1 CFU.
During the second part of the course, the students will attend practical hand-on sessions of Python-based data analysis, during which they will write codes and analyse experimental data. Computer work accounts for 1 CFU.
During the first part of the course, the students will visit research laboratories for practical demonstrations of experimental techniques. Students can also attend topical seminars, led by an expert in the field. Lab demonstrations and seminars accounts for 1 CFU.
During the second part of the course, the students will attend practical hand-on sessions of Python-based data analysis, during which they will write codes and analyse experimental data. Computer work accounts for 1 CFU.
Teaching Resources
There is no single textbook covering all the topics. Materials for study will be provided through lecture slides and addressing to specific textbooks, web sites and scientific review papers.
Assessment methods and Criteria
Learning assessment will be carried out through a written exam and an oral exam, at the end of the course, either taken separately or merged into a single exam.
The written exam aims at verifying the understanding of concepts and definitions taught during the course. The oral exam also aims at verifying the student's ability to critically discuss the results of an experiment and to put them into relation to the topics presented during the course.
The written exam will be based on both parts of the course; it includes a practical hands on session in Jupyter Notebook environment focused on data analysis task using Python language, and could also include open questions on all topics covered during the course, including lab demonstrations and topical seminars.
The oral exam will be based on the critical discussion of a selected paper covering arguments that have been presented during the first part of the course. The students will be asked to discuss also the methodological and data analysis details reported in the Materials and Methods section. The paper discussion could stimulate questions on all topics treated during the course.
The written exam aims at verifying the understanding of concepts and definitions taught during the course. The oral exam also aims at verifying the student's ability to critically discuss the results of an experiment and to put them into relation to the topics presented during the course.
The written exam will be based on both parts of the course; it includes a practical hands on session in Jupyter Notebook environment focused on data analysis task using Python language, and could also include open questions on all topics covered during the course, including lab demonstrations and topical seminars.
The oral exam will be based on the critical discussion of a selected paper covering arguments that have been presented during the first part of the course. The students will be asked to discuss also the methodological and data analysis details reported in the Materials and Methods section. The paper discussion could stimulate questions on all topics treated during the course.
FIS/01 - EXPERIMENTAL PHYSICS - University credits: 1
FIS/02 - THEORETICAL PHYSICS, MATHEMATICAL MODELS AND METHODS - University credits: 1
FIS/03 - PHYSICS OF MATTER - University credits: 4
FIS/02 - THEORETICAL PHYSICS, MATHEMATICAL MODELS AND METHODS - University credits: 1
FIS/03 - PHYSICS OF MATTER - University credits: 4
Practicals: 32 hours
Lessons: 32 hours
Lessons: 32 hours
Professor:
Podesta' Alessandro Mario Giacomo
Professor(s)
Reception:
by appointment
Teacher's office, at the Dept. of Physics, via Celoria 16, 20133 Milano