This code implements a cellular-automaton model for influenza viral fusion. The algorithm and its results are described in: Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell–Cell and Virus–Cell Fusion by Katarzyna Zawada, Kenta Okamoto, and Peter Kasson Journal of Molecular Biology, Volume 430, Issue 5, 2 March 2018, Pages 594-601. https://doi.org/10.1016/j.jmb.2018.01.006
Additional code in ca_globalfit.m implements parameter fitting as described in: Detecting and controlling dye effects in single-virus fusion experiments by Robert Rawle, Ana Villamil Giraldo, Steven Boxer, and Peter Kasson Biophysical Journal, 2019.
The algorithm is based on the work of Tijana Ivanovic and Stephen Harrison: Influenza-virus membrane fusion: cooperative fold-back of stochastically induced hemaggutinin intermediates https://doi.org/10.7554/eLife.00333