4. The lipid bilayer

4. The lipid bilayer

Experiments and simulations use DPhPC (1,2-diphytanoyl-sn-glycero-3-phosphocholine), a branched-chain lipid chosen for stable, low-noise planar bilayers. Modelling parameters:

Property	Value	Where
Thickness	2.8 nm	ePNP-NS model (knowledge/01-physics-epnpns/02-governing-equations.md#24-domains-and-boundaries); consistent with FraC's 3.5 nm TMD helices spanning it
Relative permittivity	3.2 (Gramse 2013)	ePNP-NS
— in the APBS work	2	electrostatics.tex tab:pdb2pqr_apbs_parameters
APBS slab thickness	27 Å, with a conical hole	draw_membrane2

Electrostatically the bilayer is an uncharged, ion-impermeable, low-permittivity dielectric slab — very different from the surrounding eps_r ≈ 78 electrolyte, and it measurably reshapes the potential. APBS does not support membranes natively; the external draw_membrane2 tool patches them into the permittivity, ion-accessibility and charge grids at a large I/O cost (5 grids >2 GiB per run; 20 → 200 min). The thesis therefore included the bilayer only for the ~20 pore-only potential maps and omitted it for the >500 energy calculations, having checked it does not change the qualitative conclusions.