Symmetry and Conservation in the Cell
BIO-692
20 February - 24 February
This course is at 12.15 - 3 pm on Monday in CM011.
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 20th February, gives an overview of the topics that will be covered in detail in later lectures. There is a forum page to which everyone can post comments, questions, discussions, etc.
Don't forget to read the required paper 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.
- Lecture 1 slides (File)
- Required reading for today - What is Biophysics? (URL)
- github repo for the DPD simulation codebase (URL)
- Mediaspace link to videos (URL)
- DPD User Guide (File)
- Exercise 1 Pure water DPD input file (File)
- Input file for Exercise 9 - radius of gyration calculation (File)
- Mac executable with work done/distance moved streaming (File)
- Linux executable with work done/distance moved streaming (File)
- Windows 10 executable with work/distance streaming (File)
- Project tips (File)
- Project example 1 (File)
- Project example 2 (File)
- Project example 3 (File)
- Project Example 4 (File)
- More possible projet ideas (File)
- Possible homework exercises to choose (File)
- Windows 10 executable osprey-dpd (File)
- Mac executable osprey-dpd (File)
- Linux executable osprey-dpd (File)
- DPD executable for hevetios (File)
- New dpd executable for helvetios (File)
- Slurm submission script for helvetios 24 hours (File)
- Slurm submission script for helvetios 7 days (File)
- Review of associative polymers (File)
- Soft Matter IDP paper (Folder)
27 February - 3 March
- 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)
- Recent survey of modelling of IDP phase separation (URL)
6 March - 10 March
- Lecture 3 slides (File)
- Required reading for today - Molecular force spectroscopy - Reif (File)
- Optional paper on the mathematics of Brownian motion by Gillespie (File)
- Lipid pulling input file (File)
13 March - 17 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)
- Computational papers on IDP phase separation - Dignon (File)
- Input file for polymer in good/bad solvent (File)
- Input file for lipid pulling experiment (File)
- Input file for ring micelle (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)
20 March - 24 March
27 March - 31 March
3 April - 7 April
- Lecture 7 slides (File)
- Link to Gong et al who seem to have found perpetual motion in an MD simulation (URL)
- Perpetual motion rebuttal paper by Wong-Ekkabut et al. (File)
- Nonlinear equations in 1D (External tool)
10 April - 14 April
No lecture this week due to Easter Monday
17 April - 21 April
24 April - 28 April
1 May - 5 May
8 May - 12 May
15 May - 19 May
22 May - 26 May
Project presentations today.
29 May - 2 June
Holiday