The polycrystalline structure on the sample substrate was created by photolithography. We adopt the algorithm in ref. 29 (link) to generate the GB packing geometry. This geometry is transferred to a photo mask, the lattice points on which are opaque circular disks. After exposing the negative photoresist SU8 2000.5 (~500 nm in thickness coated on a glass surface) under the mask, the unexposed disk regions on the photoresist dissolve away in photoresist developers, resulting in circular wells of depths ~500 nm on the photoresist, arranged in a polycrystalline packing. We scanned the SU8 structure under an atomic force microscope with a Bruker OTESPA-R3 tip (tip curvature radius ~7 nm). The scans (Supplementary Fig. 1 ) show that, for the b = 4.60 μm substrate, the diameter of the wells is about 3.6 μm and the depth of the wells is about 550 nm. The values (3.6 μm and 550 nm) can vary slightly (±10%) in experiments from sample to sample.
Otespa r3 tip
Manufactured by Bruker
The OTESPA-R3 tip is a laboratory equipment component designed for use with Bruker's atomic force microscopy (AFM) systems. It functions as a probe that interacts with the sample surface during AFM measurements, enabling high-resolution topographical and material property data acquisition.
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Lab products found in correlation
2 protocols using otespa r3 tip
1
Fabrication of Polycrystalline Substrate
2
Peptide Fibrils on Silicon Wafers
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Silicon wafers (G3390, Plano, Wetzlar, Germany) were used as substrates to measure peptide fibrils. The wafers were cleaned in ethanol (99.8%, Carl Roth, Karlsruhe, Germany), gently shaken and dried under a stream of nitrogen gas prior to use.
Aβ40 samples were deposited onto the substrates by dropping 5 µL sample solution on the silicon wafers for five minutes before the wafers were gently rinsed with 1 mL ultrapure water and dried under a stream of nitrogen gas. Aβ40 samples (1 mg/mL, 50 µL DMSO per 1 mL solution) without and with AuNP-5 or AuNP-20 present (20 µg/mL) were incubated at 25°C in HEPES buffer (0.1 M, pH 7.4). Samples were shaken every 5 min for 4 s (200 rpm), similar to the ThT fluorescence assay, and 1:9 v/v diluted samples (100 µL sample, 900 µL HEPES buffer) were measured at multiple time points. AFM measurements were performed on a Dimension Icon instrument (Bruker, Billerica, MA) with an OTESPA R3 tip (Bruker, Billerica, MA) in tapping mode at room temperature in air. The nominal spring constant of the cantilevers was 26 N/m and the nominal frequency 300 kHz. AFM images were processed using Nanoscope 8.15r3 and Gwyddion 2.51
(http://gwyddion.net/). 61 (link) For processing, rows on the images were aligned, the base flattened and the background levelled using a polynomial fit, if needed.
Aβ40 samples were deposited onto the substrates by dropping 5 µL sample solution on the silicon wafers for five minutes before the wafers were gently rinsed with 1 mL ultrapure water and dried under a stream of nitrogen gas. Aβ40 samples (1 mg/mL, 50 µL DMSO per 1 mL solution) without and with AuNP-5 or AuNP-20 present (20 µg/mL) were incubated at 25°C in HEPES buffer (0.1 M, pH 7.4). Samples were shaken every 5 min for 4 s (200 rpm), similar to the ThT fluorescence assay, and 1:9 v/v diluted samples (100 µL sample, 900 µL HEPES buffer) were measured at multiple time points. AFM measurements were performed on a Dimension Icon instrument (Bruker, Billerica, MA) with an OTESPA R3 tip (Bruker, Billerica, MA) in tapping mode at room temperature in air. The nominal spring constant of the cantilevers was 26 N/m and the nominal frequency 300 kHz. AFM images were processed using Nanoscope 8.15r3 and Gwyddion 2.51
(http://gwyddion.net/). 61 (link) For processing, rows on the images were aligned, the base flattened and the background levelled using a polynomial fit, if needed.
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