Amyloids

Combinatorial analysis of fluorescence in amyloids composed of split-YFP, Sup35p, and CFP using generating functions.

Paper

main.tex — the main LaTeX document. Compile with:

./build.sh

Requires pdflatex and bibtex.

Simulation scripts

Each script computes the expected percentage of proteins involved in fluorescence, R(n), for increasing amyloid length n:

Script	Section	System	Asymptote
split_yfp_simulation.py	2	Split-YFP only	2/3
sup35_simulation.py	3	Split-YFP + Sup35p	1/3
fret_sup35_simulation.py	4	FRET YFP/CFP + Sup35p	TBD

Plot scripts

Each generates the corresponding figure included in the paper:

Script	Output
plot_split_yfp.py	SplitYFPamyloids.png
plot_sup35.py	splityfpandsup35.png
plot_fret_sup35.py	FretandSup35.png

Requires matplotlib:

python3 -m venv .venv
source .venv/bin/activate
pip install matplotlib

Then run any plot script, e.g. python plot_split_yfp.py.