Computational cell biology
BIOENG-455
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)
8 September - 12 September
The course takes place from 12.15 - 16:00 pm on Wednesdays in BC 04 at the EPFL beginning on the 10th 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 simulation User Guide (File)
- Cheat sheet for executing DPD (URL)
- DPD executable for linux (File)
- DPD executable for mac (File)
- Windows 10 executable (File)
- DPD Windows 2K executable (File)
15 September - 19 September
- Pure water DPD input file (File)
- Entropic spring DPD input file (File)
- Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions (URL)
- Classification of intrinsically disordered regions and proteins (URL)
- Lecture 2 slides (File)
22 September - 26 September
- Lecture 3 slides (File)
- Molecular Dynamics, J. M. Haile, Ch. 1 (File)
- Entropic spring under tension input file (File)
- Practise test 1 (File)
- Answers to practise test 1 (File)
29 September - 3 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)
- Test 1 answers (File)
6 October - 10 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 5 slides (File)
- Insight or Illusion: Seeing inside the cell with mesoscopic simulations (File)
- Force spectroscopy simulations (URL)
- Equilibrium lipid bilayer run (Folder)
13 October - 17 October
Homework 1 is due today - extended to next week.
Distribute Take-home Test 2.
- Lecture 6 slides (File)
- FRAP in membrane input file (File)
- Colloidal suspensions, Brownian motion, molecular reality: a short history (URL)
- Mathematics of Brownian Motion and Johnson Noise (URL)
- Pitfalls of coarse-graining in molecular simulations (URL)
20 October - 24 October
No lecture or exercises this week.
27 October - 31 October
3 November - 7 November
Take home test due today
- Lecture 8 slides and free books (File)
- Alberts and Bray, Ch. 6, pp 280-284 (File)
- Collapse transition of an entropic spring derivation (File)
10 November - 14 November
17 November - 21 November
24 November - 28 November
Test in first hour of the lecture
1 December - 5 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)
8 December - 12 December
15 December - 19 December
Project presentations today.