Index – Optical Biomimetics

Index

A

absorption, 108
Ancyluris meliboeus, 157
anti-counterfeiting patterns, 100–4
colour change, 102–3
calculated reflectivity of a succession of multilayered planes, 104
calculated spectra of different elements, 103
chromaticity coordinates a motif, 104
coloured effect linked to polarisation, 102
luminosity change, 103–4
chromaticity coordinates of a motif, 104
same colour presentation without a polariser, 105
anti-reflection devices, 108–46
anti-reflection, 110–13
anti-reflective coatings, 110–11
reflectance as a function of wavelength for AR coatings, 112
single, double and multi-layer coatings, 112–13
single thin film anti-reflection coating schematic, 111
biomimetic non-silicon structures for anti-reflection, 133–6
diamond based, 134–5
Group III-V based, 135–6
metal based, 135
non-linear optical compound based, 136
polymer based, 134
silicon oxide based, 134
biomimetic photonic and anti- reflecting nanostructures, 119–36
corneal nipple arrays in one facet lens, 124
Cryptympana atrata Fabricius photograph, 125
iridescent wings of a Morpho butterfly, 123
representative reflectance spectra of intact wing of Cephonodes hylas, 126
surface relief pattern for an equivalent quintic on a substrate with RI, 122
TEM image of corneal nipple arrays in the nymphalids, 120–1
biomimetic silicon nanotips for anti- reflection, 125–33
geometry-dependent reflectance data for SiNTs, 132–3
hemispherical and specular reflectances, 128
refractive-index profile of SiNT surface, 130
SiNTs cross-section SEM image, 127
specular reflectance from planar silicon and 16 μm-long SiNTs surfaces, 129
future trends, 137–41
low refractive index (RI) bulk materials on RI scale, 140
optimal gradient index AR structure schematic, 139
reflectance as a function of length and spacing of AR nanostructures, 138
representative broad-band applicability of AR structures, 137
glossary of terms, 146
gradient refractive index structures, 113–19
gradient refractive index profiles, 115–16
porous layers, 116–17
rough surface and moth eye structures, 117–19
stereoscan picture of photo-fabricated array, 118
strong and reduced optical reflection schematic, 114–15
anti-reflective coatings, 110–11
anti-reflectors, 5–6
fly-eye and moth-eye antireflector, 6
artificial retinas, 42
associative memories, 33–6
relative holographic efficiency plot, 35

B

bacteriorhodopsin, 20–1, 22–7
applications, 31–43
associative memories, 33–6
chemical sensors, 42–3
photosensors and artificial retinas, 40–2
photovoltaics, 38–40
technologies derived from the bacteriorhodopsin photocycle, 32
volumetric memories, 36–8
branched photocycle, 26–7
enhancement for device applications, 43–53
chemical manipulation, 43, 45–8
genetic engineering, 51–3
synthetic retinal analogs, 49–51
three stages involved in the preparation bacteriorhodopsin, 44–5
main and branched photocycle, 22
main photocycle, 23–6
Biochrome, 21
biomimetic nanostructures
anti-reflection devices, 108–46
anti-reflection, 110–13
biomimetic photonic and anti-reflecting nanostructures, 119–36
future trends, 137–41
glossary of terms, 146
gradient refractive index structures, 113–19
natural designs for various special functions, 109
biomimetic non-silicon structures, 133–6
biomimetic silicon nanotips, 125–33
biomimetics, 20–1, 119
biomolecules
bacteriorhodopsin applications, 31–43
biomimetics and biotechnology, 20–1
enhanced bacteriorhodopsin for device applications, 43–53
future trends, 53–5
optical applications, 20–55
retinylidene proteins for optical devices, 21–31
biopolymers, 173
bioresorbable electronics, 191
biotechnology, 20–1
blue iridescence, 150–1
Bombyx mori, 175
Bosch process, 133
Bragg scattering phenomena, 181
branched photocycle, 26–7
accessing methods, 27
Brewster angle, 90
Brillouin Zone (BZ), 155

C

Cabbage Whites, 162
Callophrys rubi, 161
Calothyrza margaritifera, 164
cell culture techniques, 8
channelrhodopsin-2, 30–1
chemical manipulation, 43, 45–8
chemical sensors, 42–3
chirality, 161
chromoproteins, 204–5
Cicindela, 91, 93
circular polarisation, 84–7, 96–100
cholesteric stage, 100
cholesteric structure of the elytra of Plusiotis chrysargirea., 101
dextrorotatory wave, 86
relations of dispersion in a cholesteric medium, 102
coccolithophores, 10–14, 16
coherent scattering structures, 154
collagen, 191
coral bleaching, 209
corals, 208–9
Cychochilus, 163

D

de-gumming process, 175
deionized membranes, 48
diamond, 134
diatoms, 10–14
frustule contains pores, C. granii iridescence and frustule, 11
natural photonic devices modification, 12–13
diffraction polarisation, 93–4
ground scale of Morpho rhetenor cassica, 96
Discosoma sp., 201
domain averaging, 160
dyesensitised solar cells (DSSCs), 215–17

E

edge detection, 41
effective medium theory (EMT), 113
electroluminescence, 220
electromagnetic metamaterials, silk-based, 187–9
electromagnetic wave, 80–1
electric field and magnetic induction, 81
ellipsometry
angle variation of ultraviolet, visible and near infrared, 89
principle, 87–8
representation of an ellipsometer, 88
EosFP, 206
eubacterial proteorhodopsins, 27–9
photocycle of green proteorhodopsin, 29
excited state proton transport (ESPT), 210–11
experimental pH, 46–8
bacteriorhodopsin photocycle modulation via alteration, 47
exponential-sine (ES) index profile, 115

F

finite-difference time-domain (FDTD) methods, 157
Förster resonance energy transfer (FRET), 213
coral GFPs and other cellular probes, 214–15

G

GaN nanotips, 134
GaSb SWG, 136
genetic engineering, 51–3
six stages of directed evolution of bacteriorhodopsin, 55
timeline through mutagenesis, 52
glancing angle deposition (GLAD) technique, 116
globular-2 (G2F), 202
gold nanoparticles (Au-NPs), 192
graded refractive index, 116
gradient refractive index theory, 113
Gratzel cell, 216
green fluorescent protein (GFP)
control in natural photonic structures, 199–223
photoactive fluorescent proteins, 206–23
structure and diversity, 202–5
formation of the A. victoria wtGFP chromophore, 202
GFP-like proteins, 200
reversible photoswitching of green and red forms of IrisFP in crystals, 204

H

halorhodopsin, 29–30

I

insects
polarisation structure, 90–100
circular, 96–100
linear, 90–6
iridescence
control in natural photonic structures, 147–66
iridescent devices, 7–8
Morpho butterfly wing, blue reflector, FIB-CVD, Ideopsis similes and ZnO replica, 9
iridoviruses, 14–15
K
Kaede, 206
kindling fluorescent proteins, 206, 207

L

lamellar grating theory, 157
Lepidoptera, 148
light-emitting diodes, 220–3
linear polarisation, 82–4, 90–6
electric field of a non-polarised wave, 85
lipid environment, 43, 45–6
M
main photocycle, 23–6
photointermediates, 24
proton transport, 25
quadrupole geometry of the active site, 23
microfluidics, silk-based, 185
microstructures, 165
Mie scattering, 153
Morpho rhetenor, 165
‘moth eye’ AR surface, 117
motion detection, 41
Mueller matrix representation, 82
16 elements, 83
nanoimprinting, 179–80
nanoparticle-doped silk, 192
nanostructure
fabrication using natural synthesis, 173–93
natural photonic structures
control of iridescence, 147–66
nature, 2–5
types of optical reflectors found in nature, 4
optical biomimetic devices, 5–15
optical biomimetic devices fabrication, 15–16
overview, 1–17
polarisation effect and their applications, 79–105
anti-counterfeiting patterns, 100–4
experimental techniques, 87–9
principles, 79–87
structure in insects, 90–100
natural synthesis
nanostructures fabrication, 173–93
non-linear optical materials, 136

O

oligomerisation, 205
one-dimensional multilayer reflectors, 3
optical biomimetic devices, 5–15
anti-reflectors engineering, 5–6
cell culture techniques, 8, 10
diatoms and coccolithophores, 10–14
fabrication, 15–16
iridescent devices engineering, 7–8
iridoviruses, 14–15
optical devices
retinylidene proteins, 21–31
bacteriorhodopsin photocycle, 22–7
potential application, 27–31
optical fibres, silk-based, 183–4
optofluidics, silk-based, 185
organic field effect transistor, silk-based, 186
organic field effect transistor (OFET), 187
organic thin film transistors (OTFT), 186

P

Papilio, 91
dorsal side of Papilio ulysses, 92
Papilio palinurus, 152
Parides sesostris, 158
photoactive fluorescent proteins, 206–23
biological functions of GFP-like proteins, 207–12
coral GFPs as improved FRET and other cellular probes, 214–15
GFP-based solar energy materials and solar cells, 215–20
solid state semiconductors to produce hole-electron pairs and Gratzel cell, 219
GFP-like proteins as solar energy transfer arrays, 212–14
light-emitting diodes, optoelectronic and photochromic materials, 220–3
photointermediates, 25
photonic band gap, 154
photonic crystal fibres (PCF), 7, 8
photonic crystals, 154
photonic structures
control of fluorescence, 199–223
GFP structure and diversity, 202–5
photoactive fluorescent proteins, 206–23
structure of GFP-like proteins, 200
photosensors, 40–1
photostates, 24, 34
photovoltaics, 38–40
fast electrical response produced by flash photolysis, 38
photovoltage produced by a bacteriorhodopsin film, 39
physical vapour deposition technique, 116
Pieris rapae, 162
pigmentry colour, 147
plant chlorophylls, 215–16
plasmonics, silk-integrated, 189–91
polarimetric imaging, 88–90
polarimetric measurement installation, 90
polarisation
anti-counterfeiting patterns, 100–4
effects and applications in natural photonic structures, 79–105
experimental techniques, 87–9
ellipsometry, 87–8
polarimetric imaging, 88–90
principles, 79–87
circular, 84–7
electromagnetic wave, 80–1
linear, 82–4
stokes vector and Mueller matrix representation, 82
structure in insects, 90–100
circular, 96–100
linear, 90–6
polycrystalline diamond, 134
poly(glycolic acid) (PGA), 191
poly(lactic acid) (PLA), 191
porous silicon (PSi), 117
protein aggregation, 205

R

rainforest of the ocean see corals Raleigh scattering scales, 152
random scattering, 2
Rayleigh scattering, 153
reactive ion etching (RIE), 131
reddening, 210
reflection, 108, 127
refractive index, 109
relation of dispersion, 84–7
continuous medium with refractive index n, 86
retinylidene proteins
optical devices, 21–31
bacteriorhodopsin photocycle, 22–7
potential application, 27–31

S

self-masked dry etching (SMDE) technique, 131
sericin, 175
silica deposition vesicle (SDV), 15–16
silicon nanotip (SiNTs), 125–7
silk
electronics and optoelectronics, 185–92
bioresorbable electronics, 191
electrode array on a dissolvable silk film, 189
electronic material, 186–7
nanoparticle-doped silk, 192
shadow masking patterned micro split ring resonators on silk substrates, 188
silk-based electromagnetic metamaterials, 187–9
silk-based organic field effect transistor, 186
silk-integrated plasmonics, 189–91
mechanical properties of spider and silkworm silks and other materials, 175
nanostructures fabrication using natural synthesis, 173–93
optics and photonics, 177–85
aperiodic lattice of nanoholes imprinted in silk, 183
control of thickness of spin-coated silk film, 178
fabrication strategies for silk devices using silk solution, 178
fluorescent silk with localised emission enhancement, 184–5
haemoglobin-doped silk grating acting as bio-active oxygen sensor, 182
rapid nanoimprinting in silk, 180
silk-based microfluidics and optofluidics, 185
silk-based optical and photonic
elements and devices, 179
silk-based optical fibres, 183–4
silk photonic lattices, 181–3
various silk-based materials formats and devices, 176
silk fibroin, 175, 178, 192
silk photonic lattices, 181–3
soft-lithography, 179
spectral analysis, 94, 96
Bidirectional Reflectivity Distribution Function, 99
chromatic variations of the wings of Morpho zephyri, 97
coefficient of reflection of the wing of Morpho menelaus, 98
split ring resonator (SRR), 187
stokes vector, 82
structural black, 165
structural colour, 147–66
control of iridescence, 155–65
control of iridescence in three- dimensional photonic crystals, 158–62
chirality, 161–2
compound structures, 160–1
cross-section through a complete scale of P. sesostris, 159
3D photonic crystal found M. gryneus, 159
honeycomb on P. sesostris, 160
randomness, 158–60
reconstruction of the gyroid structure found in C. Rubi, 162
control of iridescence in two-dimensional structures, 156–8
exaggerating iridescence, 157–8
reducing iridescence, 156–7
tilted ridge lamellae structure, 157
perspectives on butterfly biomimetics, 165–6
structural black and white, 162–5
structural whiteness in the scarab beetle, Cychochilus, 163
types in butterflies, 148–55
butterfly scales structures that produce structural colour, 151
butterfly wing scales, 149
generic butterfly scale schematic, 149
images of type 2 butterfly structure in Papilio palinurus, 153
SEM images of type 1 butterfly structural colours, 152
SEM images of type 3 structural colours, 153
structures associated with particular lattice structures, 154
type 2 body lamellae, 152, 153
type 3 body scattering, 152–5
type 1 ridge lamellae, 150–2
structural white, 165–6
sub-wavelength gratings (SWG), 136
sub-wavelength structures (SWS), 113
Suneve coronata
multi-scaled polarisation, 93
cover scale cross-section, 95
hemispherical reflectivity, 94
synthetic retinal analogs, 49–51
preparation of bacteriorhodopsin
analogs, 50
structure, 51

T

three-dimensional liquid crystals, 3
three-dimensional photonic crystals, 3, 16
time-multiplexed etching process, 133
transmission, 108
Troides magellanus, 157
two-dimensional diffraction gratings, 2
two-dimensional photonic crystals, 3
Tyndall scattering, 153, 156
Tyndall scattering scales, 152

V

volumetric memories, 36–8
branching reaction of bacteriorhodopsin., 37
sequential two-photon version, 36

Z

zinc germanium phosphide (ZGP), 136
zooxanthellae, 208