Felix Ritort Group
Small Biosystems Lab
Teaching
I am currently teaching a course on Statistical physics during the second semester of the last year of the undergraduate physics studies and onme part of the course Molecular Biophysics for the Master in Biophysics at the University of Barcelona. I am also coordinating the course Experimental Techniques in Biophysics for the Master in Biophysics at the University of Barcelona.
CURRENT TEACHINGS:
Experimental techniques in biophysics (Master in Biophysics at the University of Barcelona)
Place:Classroom V12M, ground floor, Facultat de Fisica (Old Building)
20/09/11 Introduction (Dr. F. Ritort)
23/09/11 Nuclear magnetic resonance. (Dr. M. Macias) Download further reading PDF download
27/09/11 X ray diffraction. (Dr. I. Fita) Download further reading (1) Download further reading (2) PDF download
30/09/11 Calorimetry. (Dr. R. Prohens) Download further reading PDF download
04/10/11 Nuclear magnetic resonance and X ray diffraction. Lab visit. (Dr. I. Fita and M. Macias, Parc cientific, UB)
07/10/11 Electron microscopy. (Dr. C. Lopez) Download further reading PDF download
11/10/11 Electron microscopy and Calorimetry. Lab visit. (Dr. C. Lopez and R. Prohens, Parc cientific, UB)
14/10/11 Optical tweezers. (Dr. F. Ritort) Download further reading (I) Download further reading (II) Download further reading (III) PDF download
18/10/11 Optical tweezers. Lab visit. (Dr. F. Ritort, Small biosystems lab, Planta 3, Facultat de Fisica)
21/10/11 Magnetic tweezers. (Dr. M. Maņosas) Download further reading PDF download
25/10/11 Magnetic tweezers. Lab visit. (Dr. M. Maņosas, Small biosystems lab, Planta 3, Facultat de Fisica)
28/10/11 Special topic: DNA and RNA in biophysics (Dr. R. Eritja) PDF download
01/11/11 Public holiday
04/11/11 Nanoscale dielectric microscopy (Dr. G. Gomila) PDF download
08/11/11 Single molecule fluorescence. (Dr. M. Garcia-Parajo) Download further reading PDF download
11/11/11 Single molecule fluorescence. Lab visit. (Dr. M. Garcia-Parajo, ICFO, Castelldefels)
15/11/11 Atomic force microscopy. (Dr. D. Navajas) PDF download
18/11/11 Atomic force microscopy. Lab visit. (Dr. J. Alcaraz, Hospital Clinic, UB)
22/11/11 Engineered neural networks. (Dr. J. Soriano) PDF download and what you should have learned from the course Doc download
25/11/11 Engineered neural networks. Lab visit. (Dr. J. Soriano, Planta 6, Facultat Fisica, UB)
29/11/11 Special topic: Inmunodetection of xenobiotics (Dr. P. Marco) PDF download
02/12/11 Special topic: Regulation of bacterial genomes (Dr. M. Pons) PDF download
06/12/11 Public holiday
09/12/11 Public holiday
13/12/11 Molecular synthesis of nucleic acids (J. Camuņas) Download further reading PDF download
16/12/11 . Molecular synthesis of proteins (Dr. S. Frutos) PDF download
20/12/11 Talk on R&D. by Dr. M. Princep, Directora d'Innovaciķ Biocat, BioRegiķ de Catalunya PDF download
23/12/11 Molecular synthesis of nucleic acids and proteins. Lab practical. (J. Camuņas and S. Frutos)
Exercises: Analysis of experimental data obtained with laser tweezers. Deadline for delivering a report: 15th January. Length of report: between 3 and 6 pages.
First exercise: Elastic response of dsDNA and ssDNA. The goal of this exercise is to fit experimental data obtained for the elastic response of two biological polymers (dsDNA and ssDNA) using the extensible Worm-like chain (WLC) and inextensible freely-jointed chain (FJC) models to extract the relevant parameters: persistence length (nanometer units), stretch modulus (pN units), Kuhn length (nanometer units) for two molecules of dsDNA and ssDNA that are fragments of 48kb lambda-phage. The dsDNA has 24508bp and interphosphate distance equal to 0.34nm. Measurements cover the force range 0-47pN. The ssDNA has 13872 bases and interphosphate distance equal to 0.59nm. Measurements cover the force range 3-23pN. Data was collected at 1kHz acquisition rate and a running average of a10Hz was applied. Temperature was set to 25 Celsius in all measurements. Files contain: 1st column (molecular extension in nanometers), 2nd column (force in piconewtons). Download: File download (dsDNA data) , File download (ssDNA data)
Second exercise: Thermodynamics and kinetics of folding/unfolding of a DNA molecule. The goal of this exercise is to analyze a hopping force trace recorded in passive mode where a DNA hairpin of 20 base pairs ending in a pentaloop (GAAAA) hops between the folded and the unfolded conformations. In the experiment the hairpin is mechanically stretched using optical tweezers until a force approximately 14pN is reached. In this condition the hairpin hops between a folded (higher force, lower extension) state and an unfolded (lower force, higher extension) state. From the raw data (1kHz acquistiona frequency) you must extract: 1) the force-dwell distributions, fit them to a sum of two Gaussians and obtain the free energy difference between the folded and unfolded states (express it kT units). Which state (folded or unfolded) is thermodynamically more stable? and; 2) the residence time or lifetime distributions of the folded and unfolded states, the average lifetime (in seconds) and the kinetic rates of folding and unfolding (in units of inverse of seconds). How the ratio of these two rates is related to the previous free energy difference? Measurements were taken at a temperature of 25 Celsius. Files contain: 1st column (time in seconds), 2nd column (force in piconewtons). Download: Download DNA hairpin structure , File download (hopping data)
Oral exam: End of January 2012
Statistical physics
Place:Facultat de Fisica. Starting date: February 2012
Molecular biophysics (Part II)
Place:Facultat de Fisica. Starting date: February 2012
