Symmetry and Conservation in the Cell
BIO-692
17 February - 21 February
The lectures are at 13.15 - 3 pm on Wednesday in CM1 113.
If you are online, here is the link:
https://epfl.zoom.us/j/6568052986?pwd=aFBlMlA2SzNpSU80WmFhTHVuZld0QT09
See meeting invitation for the ID and passcode.
The first lecture on 19th February will give an overview of the topics that will be covered in later lectures. There is a forum page to which everyone can post comments, questions, discussions, etc.
The required reading for this week is the paper on "What is Biophysics." Please read it before the lecture.
We will discuss four themes in this course:
1) Random walks as a mathematical model of physical phenomena
2) Lipid membranes as two-dimensional self-assembled structures
3) How a cell uses the thermodynamics of liquid-liquid phase separation to create membraneless organelles
4) Using computational models to explore cellular dynamics
The marking scheme and required semester project will also be introduced today.
- Mediaspace link to videos (URL)
- Biophysics of the cell (External tool)
- Lecture 1 slides (File)
- Required reading for today - What is Biophysics? (URL)
- Oldfield and Dunker paper on IDPs 2014 (File)
- github repo for the DPD simulation codebase (URL)
- Exercise 1 Pure water DPD input file (File)
- DPD User Guide (File)
- Mac executable osprey-dpd (File)
- Linux executable osprey-dpd (File)
- Windows 10 executable osprey-dpd (File)
- DPD files for helvetios (Folder)
- Possible homework exercises to choose (File)
- Sample semester project reports (Folder)
24 February - 28 February
- Lecture 2 slides (File)
- Required reading for today - History of Brownian Motion - Haw (File)
- Free polymer input file (File)
- Entropic spring input file (File)
- Sticky spring input file (File)
- Zipfile of scripts to convert povray files to vmd format (File)
- init file for VMD visualisation of DPD simulations (File)
- Einstein's derivation of Brownian motion (File)
3 March - 7 March
No lecture this week, but here are the slides. I will go through them at the start of the fourth lecture.
- Lecture 3 slides (File)
- Required reading for today - Molecular force spectroscopy - Reif (File)
- Optional paper on the mathematics of Brownian motion by Gillespie (File)
10 March - 14 March
- Lecture 4 slides (File)
- Required reading - Alberts and Bray, pp 41-47 (File)
- Input files for membrane without GFP (File)
- Input files for membrane with GFP (File)
- Input file for polymer in good/bad solvent (File)
- Lipid pulling input file (File)
- Input file for ring micelle (File)
17 March - 21 March
- Lecture 5 slides (File)
- Interfacial tension input file (File)
- Solution to 1D random walk derivation (File)
- Required reading - Brangwynne - Polymer physics of LLPS (File)
- Entropic spring exercise input file (File)
- Sticky spring exercise input file (File)
- Computational papers on IDP phase separation - Dignon (File)
- Computational papers on IDP phase separation - Dignon, Supplementary Material (File)
- Computational papers on IDP phase separation - Statt (File)
- Computational papers on IDP phase separation - Statt, Supplementary Material (File)
24 March - 28 March
31 March - 4 April
- Lecture 7 slides (File)
- Link to Gong et al who claim to have found perpetual motion in an MD simulation (URL)
- Perpetual motion rebuttal paper by Wong-Ekkabut et al. (File)
7 April - 11 April
14 April - 18 April
21 April - 25 April
No lecture this week dues to Easter break.