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.

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

Each generates the corresponding figure included in the paper:

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.

Name		Name	Last commit message	Last commit date
Latest commit History 50 Commits
arxiv_submission		arxiv_submission
.gitignore		.gitignore
FretOnly.png		FretOnly.png
FretandSup35.png		FretandSup35.png
README.md		README.md
SplitYFPamyloids.png		SplitYFPamyloids.png
arxiv_submission.tar.gz		arxiv_submission.tar.gz
build.sh		build.sh
fret_sup35_simulation.py		fret_sup35_simulation.py
main.pdf		main.pdf
main.tex		main.tex
plot_fret_sup35.py		plot_fret_sup35.py
plot_split_yfp.py		plot_split_yfp.py
plot_sup35.py		plot_sup35.py
references.bib		references.bib
split_yfp_simulation.py		split_yfp_simulation.py
split_yfp_unequal_simulation.py		split_yfp_unequal_simulation.py
splityfpandsup35.png		splityfpandsup35.png
sup35_simulation.py		sup35_simulation.py
universe.jpg		universe.jpg
verify_algebra.py		verify_algebra.py
verify_section2.py		verify_section2.py
verify_section2_markov.py		verify_section2_markov.py
verify_section3.py		verify_section3.py
verify_section3_gf.py		verify_section3_gf.py
verify_section5.py		verify_section5.py
verify_section5_gf.py		verify_section5_gf.py
verify_variance.py		verify_variance.py