This is a project that started independently as my work with permeability trhough lipid membranes and the work in Poolman's lab done by Jacopo Frallicciardi.
They have developed an accurate technique to measure permeability of small polar compounds and now they are interested in understanding how such compounds, especially weak acids and water, permeate through lipid membranes in the context of yeast lipids and yeast plasma membrane.
My simulations are instrumental in understanding what are the driving forces in the process and what happens on the molecular level.
This repository contains the files required to run the simulations described in the associated publication. Many workflows and analysis scripts and notebooks need to be adapted to a specific use in the target context (computer, operating system, file system..). As is, it readily provides the actual settings used in the above described work along with some analysis tools.