DOI: 10.7910/dvn/p91yz8
title: Replication Data for: Natural Spider Silk Nanofibrils Produced by Assembling Molecules or Disassembling Fibers

description: &lt;p&gt;Raw data of optical microscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), and diameter measurements of the exfoliated and self-assembled nanofibrils for our manuscript.&lt;/p&gt;
&lt;h1&gt;File Formats&lt;/h1&gt;
&lt;ul&gt;
&lt;li&gt;&lt;em&gt;AFM raw data&lt;/em&gt; is provided in Gwyddion format, which can be viewed using the Gwyddion AFM viewer, which has been released under the GNU public software licence GPLv3 and can be downloaded free of charge at &lt;a href="http://gwyddion.net/"&gt;http://gwyddion.net/&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Optical microscopy&lt;/em&gt; data is provided in JPEG format&lt;/li&gt;
&lt;li&gt;&lt;em&gt;SEM raw data&lt;/em&gt; is provided in TIFF format&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Data analysis codes&lt;/em&gt; were written in MATLAB (&lt;a href="https://www.mathworks.com/products/matlab"&gt;https://www.mathworks.com/products/matlab&lt;/a&gt;) and stored as *.m files&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Data analysis results&lt;/em&gt; were stored as MATLAB multidimensional arrays (MATLAB “struct” data format, *.mat files)&lt;/li&gt;
&lt;/ul&gt;
&lt;h1&gt;Data (Folder Structure)&lt;/h1&gt;
The data in the dataverse is best viewed in "Tree" mode.
&lt;h2&gt;ReadMe.md&lt;/h2&gt;
&lt;ul&gt;&lt;li&gt;This description in Markdown format.&lt;/li&gt;&lt;/ul&gt;
&lt;h2&gt;Figure 2 - Microscopy Raw Data&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;&lt;em&gt;Figure 2 - panel a.jpg&lt;/em&gt; (7.2 MB) Optical micrograph (JPEG format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Figure 2 - panel b.jpg&lt;/em&gt; (6.1 MB) Optical micrograph (JPEG format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Figure 2 - panel c &amp; f.tif&lt;/em&gt; (1.2 MB) SEM raw data (TIFF format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Figure 2 - panel d.tif&lt;/em&gt; (1.2 MB) SEM raw data (TIFF format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Figure 2 - panel e - Exfoliated Fibrils.gwy&lt;/em&gt; (32.0 MB) AFM raw data (Gwyddion format)&lt;/li&gt;
&lt;/ul&gt;
&lt;h2&gt;Figure 3 - AFM Raw Data&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;&lt;em&gt;Figure 3 - Panel a - Exfoliated fibrils.gwy&lt;/em&gt; (81.5 MB) AFM raw data (Gwyddion format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Figure 3 - Panel c - Self-assembled fibrils.gwy&lt;/em&gt; (24.0 MB) AFM raw data (Gwyddion format)&lt;/li&gt;
&lt;/ul&gt;
&lt;h2&gt;Figure 3 - Diameter Measurements&lt;/h2&gt;
&lt;p&gt;Figure 3a and Figure 3c show the AFM images of exfoliated and self-assembled nanofibrils, respectively. However, due to the AFM tip-induced broadening of lateral dimensions of small features (such as nanofibrils), the diameters of nanofibrils are generally overestimated in AFM images. Hence, the diameters of the nanofibrils were estimated as the full width at half maximum (FWHM) value of line scans taken over nanofibrils perpendicular to their axial direction.&lt;/p&gt;
&lt;p&gt;Line profiles were taken at multiple locations using Gwyddion, and the raw data were stored in MATLAB struct files (&lt;em&gt;lineProfileData_Exfoliated.mat&lt;/em&gt; and &lt;em&gt;lineProfileData_Self-Assembled.mat&lt;/em&gt;). These data files can be directly imported into MATLAB and will appear as “DataExf” and “DataSA” in MATLAB workspace. For instance, “DataExf.x{i}” contains the x-axis data of i-th line profile, and “DataExf.y{i}” contains the y-axis data of i-th line profile.&lt;/p&gt;
&lt;p&gt;The MATLAB codes &lt;em&gt;MainCode_Exf.m&lt;/em&gt; and &lt;em&gt;MainCode_SA.m&lt;/em&gt; are used to fit Gaussian curves for each line profile and calculate the FWHM. The *.m files for functions &lt;em&gt;gaussian.m&lt;/em&gt; and &lt;em&gt;createFit.m&lt;/em&gt; must be in the same folder as the file for the main code. The main code generates figures for each line profile containing raw line profile, related Gaussian fit, and FWHM. These FWHM values are considered as the diameters of the fibrils and stored in variables called “Exf_Dia” and “SA_Dia”. Finally, these values are plotted in a histogram and calculate the statistics such as the mean and the standard deviation.&lt;/p&gt;
&lt;h3&gt;Exfoliated&lt;/h3&gt;
&lt;ul&gt;
&lt;li&gt;&lt;em&gt;createFit.m&lt;/em&gt; (1.1 KB) MATLAB code file (see above)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;gaussian.m&lt;/em&gt; (134 B) MATLAB code file (see above)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;lineProfileData_Exfoliated.mat&lt;/em&gt; (11.7 KB) Line profiles for exfoliated nanofibrils (MATLAB struct format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;MainCode_Exf.m&lt;/em&gt; (1.8 KB) MATLAB code file (see above)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Line profile raw data - Exfoliated&lt;/em&gt; Folder with all corresponding cross section raw data in ASCII format&lt;/li&gt;
&lt;/ul&gt;
&lt;h3&gt;Self Assembled&lt;/h3&gt;
&lt;ul&gt;
&lt;li&gt;&lt;em&gt;createFit.m&lt;/em&gt; (1.1 KB) MATLAB code file (see above)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;gaussian.m&lt;/em&gt; (134 B) MATLAB code file (see above)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;lineProfileData_Self-Assembled.mat&lt;/em&gt; (9.9 KB) Line profiles for self-assembled nanofibrils (MATLAB struct format)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;MainCode_SA.m&lt;/em&gt; (1.8 KB) MATLAB code file (see above)&lt;/li&gt;
&lt;li&gt;&lt;em&gt;Line profile raw data - SelfAssembled&lt;/em&gt; Folder with all corresponding cross section raw data in ASCII format&lt;/li&gt;
&lt;/ul&gt;
&lt;h2&gt;Figure 4 - AFM Raw Data&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Figure 4 - Panal a.gwy (73.4 MB) AFM raw data (Gwyddion format)&lt;/li&gt;
&lt;li&gt;Figure 4 - Panel e.gwy (42.0 MB) AFM raw data (Gwyddion format)&lt;/li&gt;
&lt;/ul&gt;