Description

The scripts and notebook provided here provide a systematic way to directly calculate neutron reflectivity profiles from molecular dynamics simulations for bilayer systems

Dependences

Refnx python package

How to use

Obtain the SLD for a bilayer using the provided script sld_multiple_deutration_amber.py. Please recenter the output of the script such that the electron density is symmetric around 0.

We assume you have 4 experimental reflectivity profiles for your systems (i) reflectivity profile from silica-D₂O system, from a supported bilayer in (ii) D₂O (iii) H₂O (iv) Contrast-matched silicon (CMSi) contrast (~38% D₂O).

The notebook uses silica reflectivity to obtain the Substrate SLD. The obtained silica substrate SLD is merged into the system SLD at a given position automatically determined by the script.

Using the experimental reflectivity in the three solvent contrast, the script varies $\alpha$, the water fraction at the silica-bilayer interface, and $\gamma$, the fraction of area covered by water patches.

Example files

The example-data has typical neutron scattering length density profiles for the MC3H-DOPC system (refer to the reference) and example reflectivity profiles.

References

Please find the details at https://pubs.rsc.org/en/content/articlelanding/2023/nr/d3nr00987d and cite the reference: Nanoscale, 2023,15, 11647-11656