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Biophysics of Macromolecules – Lecture Notes

Reader for the class ("Skript")

Schedule and Lecture notes "Biophysics of Macromolecules"

  • The schedule is preliminary, it will be refined as the semester proceeds. 
  • We will try to upload PDF files of the lecture slides (typically relatively shortly) before the lectures.
  •  If you need the password for the files, send me an email.

Mo 13.4.  Introduction to biological macromolecules: (JL and DB)
               - Course overview & motivation
               - Fundamentals of molecular biology: Life, cells, evolution
               - Types molecules: DNA/RNA/proteins 
               - The central dogma: transcription and translation
               -  Physical interactions of biological macromolecules  

               Slides: [Part 1 PDF, with password] [Part 2 PDF, with password]
               Movies (probably best to download the file(s) and play them locally):
               [MD simulaton of proten folding 1]
               [MD simulaton of proten folding 2]
               ["Steered" MD simulaton of force-induced protein unfolding

Mo 20.4.  Protein folding and hydrophobic collapse (DB)
               Protein-ligand interactions, binding equilibria, and cooperativity (JL)
               
Slides: [Part 1, with password] [Part 2, with password]
               

Mo 27.4.  Modeling binding kinetics with ODEs and Matlab (DB)
               Nucleic Acids: RNA in the central dogma and beyond (DB)
               
Slides: [PDF, with password]
                 Matlab Code for Simple Binding Kinetics and Binding Curve
               Classic papers on binding cooperativity
               by Monod, Wyman, and Changeux [PDF]
               and by Koshland, Némethy, and Filmer [PDF]  

Mo 4.5.    Small angle X-ray scattering & nucleic acid electrostatics (JL)
               Slides: [PDF, with password]
                 Matlab Code for the ABC Binding System
               Review article about nucleic acid-ion interactions
               by Lipfert et al. (2014) [PDF, with password

Mo 11.5.  Single molecule force spectroscopy & polymer physics (JL)
             
 Slides: [PDF, with password] 

Mo 18.5.  Force spectroscopy and polymer physics, continued (JL)
               Applications to DNA mechanics (JL)
               Single-molecule torque measurements using magnetic tweezers (JL) 

               Slides: [PDF, with password]

Mo 25.5.  No class - Public holiday (Pentecost/Pfingsten)

Mo 1.6.    Force-spectroscopy of ligand-receptor bonds; Bell-Evans theory (JL)
             Enzymes kinetics (Michaelis-Menten) (JL) 
           
 Slides: [PDF, with password]

Mo 8.6.    Cytoskeleton filaments and Actin polymerization (DB)
             Thermal ratchets, treatmilling & ATP hydrolysis (DB)

Mo 15.6.  Molecular Motors: Applications and experiments (by Prof. Claudia Veigel)
               
Slides: [PDF, with password]
               Pointers on giving talks (JL)
               The architecture of the genome - chromatin (JL)
               Slides: [PDF, with password]

Mo 22.6.  Student talks

Mo 29.6.  Life at low Reynolds NumbersLife at low Reynolds Numbers (DB)
             Crowded and disordered environments, Diffusion (DB)

Mo 6.7.   Thermophoresis: Models and detction of binding (DB)
              Viscoelasticity/Polymer Dynamics (DB)

Mo 13.7.  Q&A session

Thursday 23.7. 10.15 - 11.45 Written Exam
Room S 003, Schellingstr. 3
[across the street, south of physics main building]