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11 protocols using dimension 3100

1

Characterization of Coated Optical Fibers

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The images of coated and uncoated fiber surfaces were obtained by a SEM (JSM-6700F, JEOL) and an AFM (Dimension 3100, Digital Instruments). The cross-sections were prepared by a FIB following a standard preparation method38 (details in Supplementary Method B), before characterization by a TEM (JEM-100CXII, JEOL). The cross-sections were also characterized and confirmed by a 3D surface optical profilometer (Wyko NT 3300, Veeco). The TiO2 layer masses (mTiO2) on the optical fibers were measured gravimetrically by the weight of the optical fibers before and after the dip-coating/drying cycles. The porosity of the TiO2 coating layers, which is defined as the fraction of the total pore volume over the volume of the TiO2 layer, was calculated using Eq. (9). Porosity=1mTiO2ρTiO2LπdD where ρTiO2 is the true density of the TiO2 particles (4.26 g/mL at 25 °C obtained from Sigma-Aldrich), L is the TiO2 coating length, d is the diameter of optical fibers, and D is the thickness of the TiO2 coating layers, which was determined by the cross-sectional profiles of TiO2-QOFs from SEM images. The TiO2 patchiness was calculated by dividing the optical fiber surface in direct contact with TiO2 nanoparticles by the total surface of the optical fiber determining from TEM cross-section images.
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2

Atomic Force Microscopy Imaging of Nanoparticles

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A dispersion of NP (10 µL) was drop cast on freshly cleaned mica substrates and air-dried. To image the blank and loaded NPs obtained from EDE, Cyrene or PEG 400 method, a Dimension 3100 (Digital Instruments, Veeco, Santa Barbara, CA) equipped with a Nanoscope IV controller as well as a JPK-Nanowizard (JPK BioAFM, Bruker Nano, Berlin, Germany) was used. Standard tapping mode silicon cantilevers from Bruker (model RTESPA 300, Bruker, Santa Barbara, CA) with a resonance frequency around 300 kHz in air, a spring constant in the range of 20 to 80 N/m, and a tip radius of less than 10 nm (typically 7 nm) were used for height imaging.
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3

Mechanical Exfoliation of 2H-MoS2 and 3R Crystals

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Bulk 3R and 2H-MoS2 crystals were grown using chemical-vapor transport technique with Cl2 and I2 as the carrier gas, respectively31 . Crystals (3R and 2H-MoS2) were mechanically exfoliated onto a fused quartz substrate. Layer number assignment was determined using a combination of photoluminescence imaging, Raman spectroscopy (Horiba LabRAM HR Evolution, Edison, NJ, USA)31 , 32 (link) and AFM (Dimension 3100, Digital Instruments, Santa Barbara, CA, USA) (Supplementary Fig. S3).
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4

Optical and Atomic Force Microscopy of Organic Films

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Optical microscope images
have been acquired by a Nikon Labophot 2A microscope in combination
with a Nikon type 115 digital camera. Scanning force microscopy (SFM)
studies of the deposited organic films were performed using a Digital
Instruments Dimension 3100 in the tapping mode. The 10 × 10 μm2 images have been acquired at scan speeds of 4–6 μm/s
using SiC tips (μmasch, HQ:NSC15/Al BS) exhibiting a cone angle
of 40°. Nominal values for resonance frequency and tip radius
are 325 kHz and 10 nm, respectively.
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5

Characterization of TiO2 Thin Films

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We used infrared spectroscopy to monitor water and NH3 removal in annealed films. Infrared transmission spectra of the films were measured with a Perkin-Elmer Spectrum 100 series spectrometer with a Universal diamond ATR attachment. The TiO2 thin film thickness and refractive index at 1550 nm were calculated from the transmittance recorded by a Perkin-Elmer 1050 UV-Vis spectrophotometer. The index also matched well with the dispersion diagram fitted from the ellipsometry data collected at an angle of incidence of 70° in the range of 300–1600 nm (Horiba Jobin Yvon UVISEL NIR ellipsometer). The surface and cross-section images of the TiO2 thin film were taken on a JSM-7400 F (JEOL, Inc.) scanning electron microscope (SEM). Surface roughness was also measured through atomic force microscopy (AFM) on a Dimension 3100 (Digital Instruments, Inc.) microscope. Silicon AFM probes (Tap 150-G from Budget Sensors, Inc) with a force constant of 5 N/m and a resonant frequency of 150 KHz were used.
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6

Atomic Force Microscopy of Wing Scales

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A Digital Instruments Dimension 3100 scanning probe microscope (SPM) was used in atomic force microscopy (AFM) tapping mode, together with either a Nanoscope® IIIa or IV controller. AFM data were taken using standard tapping mode tips (Bruker) with a resonance near 320 kHz, lowered down on either the centre or the edge of a single undamaged wing scale in the sample. The data were subsequently flattened and analysed, to produce two-dimensional surface topography height images (with height represented as a colour scale) and rendered three-dimensional surfaces using the software Gwyddion and ImageSXM. Fourier analysis was performed on the scale SPM scans and the ridge spacing extracted from the integrated Fourier transform to give an image-averaged ridge spacing over the 10 µm square image.
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7

AFM Characterization of Coated Glass Slides

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Glass slides coated with BSA and PEO were characterised with an AFM microscope (Dimension 3100, Digital Instruments/Veeco) equipped with a scanner capable of scanning areas of 100 × 100 μm2. Measurements were carried out in air at room temperature. Commercially available tapping mode tips were used on the cantilevers with a resonance frequency ranging from 350–400 kHz. The flat substrates were scanned at various resolutions, ranging from 50 × 50 μm2 to 2 × 2 μm2. The scans show overall similar patterns, however, the topographic features, root mean square (rms) roughness, height profile and average height, were measured in the highest resolution scan. The Digital Instruments Nanoscope IIIa v4.42 software was used for data acquisition and the WSxM 3.0 v8.3 software was used for image analysis [29 (link)].
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8

Microscopy and Spectroscopy Characterization

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Transmission electron microscopy image was carried out with a FEI Tecnai G2 TF20 UT instrument operated at 200 kV. Scanning electron microscopy (SEM) images were recorded on a Philips XL30 FEG SEM microscope. The film samples were cut to small pieces and adhere by Cu tape to the substrates. All samples were sputter-coated with a thin layer of Pt under argon in a sputter coater (Leica EM SCD 500). X-ray photoelectron spectroscopy (XPS) spectra data were collected on a Kratos Axis Ultra DLD instrument. AFM image was carried out using a Digital Instruments Dimension 3100 atomic force microscope.
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9

Atomic Force Microscopy Analysis of Surface Roughness

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AFM was used to characterize surface roughness and morphology (Dimension 3100,Digital Instruments, Veeco, Woodbury, NY, USA). It was performed in tapping mode with an etched silicon tip (OTESPA, tip radius <10 nm) at a rate of 1Hz at room temperature. The roughness average parameter (Ra) obtained from 20 × 20 μm 2 topographical images was used to determine surface roughness. The images were then analyzed using WSxM software. Three measurements per sample on three different samples were carried out to ascertain the homogeneity of the surface modification.
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10

Characterization of Metal Nanostructures

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Transmission electron microscopy (TEM) measurements were carried out using a JEOL JSM2100-F microscope operated at 10 kV. UV-vis absorption spectra were recorded on a Varian Technologies Cary 5000 with diffuse reflectance accessories (DRA). The metal nanostructures were observed using a JEOL JSM6700-F scanning electron microscope (SEM). Atomic force microscopy (AFM) studies on the surface morphologies of the metal nanostructure on the PDMS substrate were performed with a Digital Instruments Dimension 3100 scanning force microscope in tapping mode. Raman spectra were obtained with a Raman Spectrometer from HORIBA Jobin Yvon at an excitation wavelength of 633 nm and a Nikon microscope with a ×50 objective lens and a numerical aperture (NA) of 0.75. The acquisition and accumulation time of each spectrum were 10 s and 5 s, respectively. The scan range was 200 to 2000 cm -1 . SERS substrates were cut into 3 × 3 cm 2 pieces and incubated in 1 mM p-aminothiolpheol (p-ATP) solutions and washed with ethanol, prior to measurements. p-ATP was used as the SERS probe with two critical Raman peaks at 1076 and 1140 cm -1 .
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