A simulation of the stepping pattern of the molecular motor Dynein using Brownian mechanics.

• Research

  • Try to get bb-mc.py actually working, which probably means finding a suspected bug in onebound.cpp.
  • Look through how onebound.cpp is working internally.
  • Create figures (rinse and repeat)
  • Create movie data (and movies)?
  • Generate time simulation (i.e. string together probabilities in MC sequence)

• Write latex description of method and figures (eventually thesis)

• Read dynein papers & summarize in the thesis

  • Annotated bibliography
  • Bibtex file
  • Google scholar

• Obtain data from papers

  • Email authors
  • Use gimp or similar? :(

• Read code

  • onebound.cpp
  • dynein_onebound_struct.cpp
  • add more later

• Check linear algebra from Mathematica for the onebound solution.

  • backward may be easier
  • forward may give a nicer result
  • consider using different set of angles (e.g. relative angles)

• Reimplement onebound (in rust?)

  • Note that this may be a way to track down a bug in the C++ code.

• Implement toy dynamics/toy MC for learning

To build this project you will need fac, inkscape, texlive, (specifically, bibtex and pdflatex), python3 with matplotlib, and a C++ compiler such as g++. On a Debian-derived system you can install all of these but fac with:

apt-get install inkscape texlive texlive-xetex texlive-latex-extra build-essential python3-matplotlib