Investigating the Structure-Function Relationships of Fluorinated polymeric interfaces for PFAS Capture and Release

This repository contains the Python code used to generate the calculations and the figures in the manuscript.

MD simulation data

Simulations were conducted for 9 systems : 1CF_copol_TFA, 1CF_copol_PFBA, 1CF_copol_PFOA, 3CF_copol_TFA, 3CF_copol_PFBA, 3CF_copol_PFOA, 7CF_copol_TFA, 7CF_copol_PFBA, 7CF_copol_PFOA. All the MD trajectory files with descriptions for the file structure can be found at https://uofi.box.com/s/frus9cjl93m3fcn1drcgx0npkbq2thcp .

Annealing Script

Annealing.py : OpenMM script for a seven-step compression-relaxation equilibriation process for fabrication of the polymer matrix.

Preferential Interaction coefficient calculation:

• PFAS_water_count.py is used to extract the time evolution of PFAS and water counts as a function of z-coordinate the MD trajectories
• PIC_vs_Z.ipynb contains example code used to generate the plots for PIC(z) at a constant time .
• PIC_vs_time.ipynb contains example code used to generate the plots for PIC(t) at a fixed z.

PFAS agglomeration and penetration depth

• PFAS_density.py is used to extract the time evolution of the number of PFAS at discrete z intervals from the MD trajectories.
• AgglomerationPlots.ipynb contains code to generate the plots for discrete PFAS number density and Cumulative PFAS density