three-dimensional finite difference time domain simulation fdtd rsoft 9.0 fullwave  (Rsoft Inc)

Journal: bioRxiv

Article Title: Intracellular photonic crystals in photosynthetic sea slugs form via a kidney-mediated biomineralisation pathway

doi: 10.64898/2026.05.07.723475

Figure Lengend Snippet: a) Bright-field upright optical microscope (Zeiss axioscope, 63X WI objective) of calcophores on the dorsal surface of E. viridis , showing both homogenous ‘glassy’ colour (right), and striped, opalescent ‘crystalline’ optical texture (left). Exposure time for ‘glassy’ images is 2.5X that of ‘crystalline’ ones. Scale bar, 20 µ m. b) Reciprocal space (K-space) images for calcophores showing both ‘glassy’ (bottom) and ‘crystalline’ (top) type optical appearance corresponding to real space images in a , glassy K-space images show homogenous colouring, with a very slight blue shift at high angles. Crystalline K-space images show a strong blue shift at higher scattering angles, and a highly textured, hexagonal colour distribution corresponding to the angular response of the photonic crystals. The edge of the circle in the K-space images corresponds to NA = 0.9 (scattering at 42 ° ). Images taken with Zeiss axioscope, 63X WI objective. c) Dark-field upright optical microscope images of a cluster of calcophores before and after 20 minutes exposure to air. Dark orange carotenoid volumes (top and bottom left) can be used as markers to correlate the calcophores in the two images. Of the 7 calcophores in the cluster 4 of them show a blue-shift. Scale bar, 50 µ m. FDTD simulations of 5 µ m diameter spherical photonic structures found in E. viridis . A gaussian beam of radius 1.25 µ m was used for all simulations. The particles have been simplified to perfect spheres. d) Simulated spectra for a correlated structure (photonic glass), with particle sizes varying from 140 - 200 nm. e) Simulated spectra for expanded FCC photonic crystal with particle-to-particle distances varying from 1 d to 2 d (where d is the diameter of one particle, in this case 160 ± 5 nm). The (111) plane is perpendicular to the detector for simulations. f) Simulated spectra for close packed spheres with polycrystallinity i.e. the simulated structure is composed of multiple crystallographic volumes for d = 140 - 200 nm. g) Experimental bright field spectra (Zeiss axioscope, 63X WI objective, 50 µ m fibre) spectra of E. viridis photonic calcophores, showing photonic glass-like response. Spectra are normalised to a silver mirror. h) Experimental bright field spectra (Zeiss axioscope, 63X WI objective, 50 µ m fibre) spectra of E. viridis photonic calcophores, showing photonic crystal-like response. Spectra are normalised to a silver mirror.

Article Snippet: To match the optical properties of the photonic structures described here to those observed by electron microscopy and to demonstrate an expanded-FCC lattice that captures the measured optical response, we used finite-difference time-domain (FDTD) calculations on structures generated by molecular dynamics ( ).

Techniques: Microscopy