SUPPLEMENTARY INFORMATION

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1 Supplementary Information for Biocompatible and Functionalized Silk Opals Sunghwan Kim, Alexander N. Mitropoulos, Joshua D. Spitzberg, Hu Tao, David L. Kaplan, and Fiorenzo G. Omenetto (*) (*) To whom correspondence should be addressed. NATURE PHOTONICS 1

2 Figure S1 - Steps in the manufacturing of the Silk-opal (SIO) structure. a, SEM image of PMMA opal structure. To observe the vertical profile, a small portion of the sample was sectioned by razor blade. b, Silk film before (left) and after (right) dissolving PMMA spheres in acetone. Left film is almost transparent due to small refractive index contrast between PMMA spheres (n PMMA = 1.49) and silk (n silk = 1.54). After dissolving the PMMA spheres, green structural color appears due to the diffraction by the SIO. The bottom SEM images confirm that the SIO does not contain PMMA spheres. 2 NATURE PHOTONICS

3 SUPPLEMENTARY INFORMATION Diffraction theory for the SIO We calculate the pseudo photonic band-gap (ppbg) by applying previously established theories, 1, 2 - the phenomenon has been analyzed using the Bragg-Snell formula, as follows: "#$$ = 2 "" "#, (1) where m is the diffraction order, D is the inter-planar spacing in the (111) direction which is perpendicular to the film, θ is the incidence angle from the normal, and n eff is the effective refractive index. This parameter can be theoretically calculated with the Lorentz-Lorentz formula for the effective medium: "" "" = "" + (1 ) "#$, (2) "" "#$ where n sphere and n void are the refractive index of the materials of the sphere and the void, respectively, and f is the filling factor of the spheres in the structure. The ppbg theory and the Bragg-Snell formula can provide the same interpretation only for the determination of reflectance peaks. Further information for the diffraction in the opal structure such as angles, intensities, and bandwidths, can be analyzed and understood using dynamical diffraction theory 3. NATURE PHOTONICS 3

Calculation of the filling factor in FCC structure Figure 2S describes the unit cell of FCC crystal. The volume of the unit cell ( ) is 2 2Λ, where Λ is the lattice constant.

4 Calculation of the filling factor in FCC structure Figure 2S describes the unit cell of FCC crystal. The volume of the unit cell ( ) is 2 2Λ, where Λ is the lattice constant. In a close-packed system, we can consider that there are four spheres with a diameter of Λ inside the unit cell. So total volume of the spheres ( ) is Λ. The filling factor of the spheres in FCC can be defined as / Because the SIO has air-spheres, the filling factor of silk is Figure 2S - Calculation of the filling factor - The schematic of the unit cell in FCC crystal structure. Λ is a lattice constant. Absorption-enhancement at the photonic band-edge Photonic crystals control the propagation of photons due to their periodicity. The photons, for example, can be trapped within a small cavity at frequencies that fall within the PBG, or propagated through the medium with extremely slow group velocity at the photonic band-edge, (e.g. the point with zero slope in the photonic band-structure). When 4 NATURE PHOTONICS

5 SUPPLEMENTARY INFORMATION the photonic crystals contain quantum elements, such as metal nanoparticles, quantum dots, or quantum wells, the nanostructure controls their emission or absorption characteristics by matching the PBG or band-edge. In Fig. 3, 4, we investigated the enhancement of absorption of the Au-NPs shown at the photonic band-edges, two ends that define the L-point pseudo-pbg. To support the experimentally observed enhancement, a finite-differential time-domain (FDTD) simulation was conducted using the open-source FDTD software distributed by MIT 4. For simplicity we assume that the medium has uniform loss (imaginary dielectric constant) instead of modeling the EM response of the Au-NPs. The structure was modeled by assuming that a plane-wave with TE polarization (with the electric field parallel to the inverse opal film) was incident from bottom of the structure, its calculated flux is monitored both at the top and bottom to collect data for the reflected and transmitted electromagnetic field distribution. Figure 3S shows the calculated absorptionspectrum. Consistent with previous work 5, the absorption was strongly enhanced at the band-edge location for the pseudo-pbg in the photonic structure. Though idealized circumstances such as polarized plane-wave, uniform loss, and infinite lateral structure were considered in the simulation, the simulation support the phenomena of absorptionenhancement, as observed experimentally. NATURE PHOTONICS 5

6 Figure 3S - Absorption-enhancement at the band-edge - Absorption spectrum simulated for the inverse opal with uniform loss (ε silk = i). 6 NATURE PHOTONICS

7 SUPPLEMENTARY INFORMATION Water-insoluble SIO by water-annealing When using silk nanostructures in biological environments, silk must be postprocessed to become water-insoluble. Self-assembled silk fibroin films, when partially crystallized, have water-soluble characteristics because water molecules disrupt intermolecular cohesive forces between silk fibroin proteins and enhance chain mobility of noncrystalline domains in proteins 5. In order to make water-insoluble silk opals, β- sheet crystallinity in silk fibroin films should be increased. Some solvents (acetone and IPA), used to remove the PMMA spheres, can ultimately increase the crystallinity by causing β-sheet bonds to occur, but the degree of chemical bonds induced in this way is insufficient to reach high crystallinity for water-insolubility of the SIO. Such crystallinity is imparted by temperature-controlled water vapor annealing (TCWVA) as described in Ref. 6 to obtain water-insoluble SIOs. Figure 4S(a) shows the spectral response of a blue SIO in air and when immersed in water. The reflectance peak of the blue SIO in air is shown at the wavelength of 402 nm. The peak shifted to a wavelength of 546 nm when the sample was immersed in water. Note that the peak of the SIO in water was found to be more red-shifted than our estimation (490 nm) from the pseudo PBG calculation shown in Fig. 4S(a). This implies that the SIO could undergo some physical swelling from immersion in water, (even for high crystallinity samples). Through the measured shift and known parameters, we estimate the SIO to undergo a uniform 11% volume expansion. Microscope images, shown in Fig. 4S(b), were taken to corroborate the volume expansion. The comparison of NATURE PHOTONICS 7

8 the position and size of the grains from the left-top corner, in which there is overlap, suggests that the SIO was swollen by water immersion. Figure 4S Measurements of SIO under water immersion and associated structure swelling. a, Normalized reflectance of the blue SIO when in air (blue solid) and water (green solid). To compare with the calculated estimation, duplicated spectrum with the calculated reflectance peak (blue dash) is shown. b, Sequential microscopic images of the blue SIO in air (red grain) and in water (green grain) are taken and overlapped to compare feature swelling in the structure. Scale bar represent 1 cm. 8 NATURE PHOTONICS

9 SUPPLEMENTARY INFORMATION Angular dependence We measured the transmission of the SIO with Λ= 300 nm as a function of incident angle of light. As expected from Eq. 1, there is a finite angle dependency for observation of spectral selectivity as illustrated below. Figure 5S Angular dependence of SIO Λ=300nm transmission NATURE PHOTONICS 9

10 References 1 Vos, W. L., Sprik, R., Blaaderen, A., Imhof, A., Lagendijk, A. & Wegdam, G. H. Strong effects of photonic band structures on the diffraction of colloidal crystals. Phys. Rev. B 53, (1996). 2 Morandi, C., Marabelli, F., Amendola, V., Meneghetti, M. & Comoretto, D. Light localization effect on the optical properties of opals doped gold nanoparticles. J. Phys. Chem. C 112, (2008). 3 Pan, G., Sood, A. K. & Asher, S. A. Polarization dependence of crystalline colloidal array diffraction. J. Appl. Phys. 84, (1998). 4 Oskooi, A. F., Roundy D., Ibanescu M., Bermel P., Joannopoulos J. D., Johnson S. G., Comp. Phys. Commun. 181, (2010). 5 Florescu, M., Lee, H., Stimpson, A. J. & Dowling, J. Thermal emission and absorption of radiation in finite inverted-opal photonic crystals. Phys. Rev. A 72, (2005). 6 Hu, X., Shmelev, K., Sun, L., Gil, E.-S., Park, S.-H., Cebe, P. & Kaplan. D. L. Regulation of silk material structure by temperature-controlled water vapor annealing. Biomacromolecules 12, (2011). 10 NATURE PHOTONICS

II.2 Photonic Crystals of Core-Shell Colloidal Particles

II.2 Photonic Crystals of Core-Shell Colloidal Particles We report on the fabrication and optical transmission studies of thin three-dimensional photonic crystals of high-dielectric ZnS-core and low-dielectric