Computational cell biology
BIOENG-455
Media
Media
- Announcements (Forum)
- Link to mediaspace for lecture videos (URL)
- Potential Journal Club papers (Folder)
- Zip file of scripts to convert povray snapshots to VMD format (File)
- Example project reports (Folder)
- Files needed to run DPD code on the helvetios machine (Folder)
- Cluster introduction from Scitas (File)
- Possible homework exercises (File)
- More is Different paper by Phil Anderson (URL)
- Input files for the exercises (Folder)
9 September - 13 September
The course takes place from 12.15 - 16:00 pm on Wednesdays in BC 04 at the EPFL beginning on the 11th September.
NOTE There is a Quiz at the beginning of lecture 1 so you should be in the room promptly.
Background reading is provided on some topics: unless the word "optional" is in the title or description, this is required reading to prepare for the following week's lecture and will be part of the tests.
You must bring a laptop to the lectures as it is needed for the exercises each week.
You can download the DPD simulation code that is required for the exercises and project here. Executables are provided for Linux, Mac OS X and Windows, and there is a User Guide that you can consult to understand how to set up and run a simulation. The "pure water' sample input file should be downloaded for use in the first exercise period.Alternatively, you can get the source code from github and compile it yourself:
https://github.com/Osprey-DPD/osprey-dpd
- Lecture 1 slides (File)
- Alberts and Bray, Ch 2, pp 41-47 (File)
- Optional reading on cellular life as a machine (Folder)
- Optional reading on the next 25 Years of Cell Biology (URL)
- DPD Windows 2K executable (File)
- Windows executable with spherical stress profile (File)
- Windows 10 executable (File)
- DPD executable for linux (File)
- DPD executable for mac (File)
- Pure water DPD input file (File)
- Cheat sheet for executing DPD (URL)
- DPD simulation user guide (File)
16 September - 20 September
- Lecture 2 slides (File)
- Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions (URL)
- Classification of intrinsically disordered regions and proteins (URL)
23 September - 27 September
- Lecture 3 slides (File)
- Molecular Dynamics, J. M. Haile, Ch. 1 (File)
- Entropic spring DPD input file (File)
- Entropic spring under tension input file (File)
- Practise Test 1 (File)
- Answers to Practise test 1 (File)
30 September - 4 October
In-class Test 1 during the first hour of the lecture period.
- Lecture 4 slides (File)
- Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulations (URL)
- Molecular Dynamics, J. M Haile, Ch. 4 (File)
- Optional reading of a paper by Graeter et al. on molecular force spectroscopy if you choose that homework exercise (File)
- Entropic spring input file (File)
- Answers to Test 1 (File)
7 October - 11 October
Journal club this week during the exercise period.
In 10 - 15 minutes with slides, describe the paper you have chosen, especially the computational aspects and why it is interesting.
- Lecture 7 slides (File)
- Insight or Illusion: Seeing inside the cell with mesoscopic simulations (File)
- Force spectroscopy simulations (URL)
- Equilibrium lipid bilayer run (Folder)
14 October - 18 October
Homework 1 is due today.
Distribute Take-home Test 2.
- Lecture 5 slides (File)
- Pitfalls of coarse-graining in molecular simulations (URL)
- Lipid bilayer input file (File)
21 October - 25 October
No lecture or exercises this week.
28 October - 1 November
Take-home test 2 due today.
- Lecture 6 slides (File)
- Colloidal suspensions, Brownian motion, molecular reality: a short history (URL)
- Mathematics of Brownian Motion and Johnson Noise (URL)
- Correlated randomness paper (File)
- FRAP in membrane input file (File)
4 November - 8 November
11 November - 15 November
18 November - 22 November
In-class Test 3 during the first hour of the lecture period.
25 November - 29 November
Homework 2 due next week, 2nd December due to helvetios being down.
2 December - 6 December
- Lecture 12 slides (File)
- Liquid-liquid phase separation in cellular signaling (File)
- Intrinsically-disordered proteins and intrinsically disordered protein regions (URL)
- Are aberrant phase transitions a driver of cellular ageing? (File)
- Critical analysis of blindly assuming disordered proteins phase separate in cells (File)
- Project report tips (File)
9 December - 13 December
16 December - 20 December
Project presentations today.