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1. Replication Data for: Natural Spider Silk Nanofibrils Produced by Assembling Molecules or Disassembling Fibers

   https://doi.org/10.7910/DVN/P91YZ8  

   Perera, Dinidu; Li, Linxuan; Walsh, Chloe; Wang, Qijue; Schniepp, Hannes (January 2022, Harvard Dataverse)

   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. File Formats AFM raw data 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 http://gwyddion.net/ Optical microscopy data is provided in JPEG format SEM raw data is provided in TIFF format Data analysis codes were written in MATLAB (https://www.mathworks.com/products/matlab) and stored as *.m files Data analysis results were stored as MATLAB multidimensional arrays (MATLAB “struct” data format, *.mat files) Data (Folder Structure) The data in the dataverse is best viewed in Tree mode. ReadMe.md This description in Markdown format. Figure 2 - Microscopy Raw Data Figure 2 - panel a.jpg (7.2 MB) Optical micrograph (JPEG format) Figure 2 - panel b.jpg (6.1 MB) Optical micrograph (JPEG format) Figure 2 - panel c f.tif (1.2 MB) SEM raw data (TIFF format) Figure 2 - panel d.tif (1.2 MB) SEM raw data (TIFF format) Figure 2 - panel e - Exfoliated Fibrils.gwy (32.0 MB) AFM raw data (Gwyddion format) Figure 3 - AFM Raw Data Figure 3 - Panel a - Exfoliated fibrils.gwy (81.5 MB) AFM raw data (Gwyddion format) Figure 3 - Panel c - Self-assembled fibrils.gwy (24.0 MB) AFM raw data (Gwyddion format) Figure 3 - Diameter Measurements 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. Line profiles were taken at multiple locations using Gwyddion, and the raw data were stored in MATLAB struct files (lineProfileData_Exfoliated.mat and lineProfileData_Self-Assembled.mat). 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. The MATLAB codes MainCode_Exf.m and MainCode_SA.m are used to fit Gaussian curves for each line profile and calculate the FWHM. The *.m files for functions gaussian.m and createFit.m 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. Exfoliated createFit.m (1.1 KB) MATLAB code file (see above) gaussian.m (134 B) MATLAB code file (see above) lineProfileData_Exfoliated.mat (11.7 KB) Line profiles for exfoliated nanofibrils (MATLAB struct format) MainCode_Exf.m (1.8 KB) MATLAB code file (see above) Line profile raw data - Exfoliated Folder with all corresponding cross section raw data in ASCII format Self Assembled createFit.m (1.1 KB) MATLAB code file (see above) gaussian.m (134 B) MATLAB code file (see above) lineProfileData_Self-Assembled.mat (9.9 KB) Line profiles for self-assembled nanofibrils (MATLAB struct format) MainCode_SA.m (1.8 KB) MATLAB code file (see above) Line profile raw data - SelfAssembled Folder with all corresponding cross section raw data in ASCII format Figure 4 - AFM Raw Data Figure 4 - Panal a.gwy (73.4 MB) AFM raw data (Gwyddion format) Figure 4 - Panel e.gwy (42.0 MB) AFM raw data (Gwyddion format) 

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2. Replication Data for: Long-Range Attraction between Graphene and Water/Oil Interfaces

   https://doi.org/10.7910/DVN/MEBRW1  

   Abeywickrama, Avishi; Adamson, Douglas H; Schniepp, Hannes C; Schniepp, Hannes C (January 2023, Harvard Dataverse)

   Atomic force microscopy (AFM) image raw data, force spectroscopy raw data, data analysis/data plotting, and force modeling. File Formats The raw files of the AFM imaging scans of the colloidal probe surface are provided in NT-MDTs proprietary .mdt file format, which can be opened using the Gwyddion software package. Gwyddion has been released under the GNU public software license GPLv3 and can be downloaded free of charge at http://gwyddion.net/. The processed image files are included in Gwyddions .gwy file format. Force spectroscopy raw files are also provided in .mdt file format, which can be opened using NT-MDTs NOVA Px software (we used 3.2.5 rev. 10881). All the force data were converted to ASCII files (*.txt) using the NOVA Px software to also provide them in human readable form with this data set. The MATLAB codes used for force curve processing and data analysis are given as *.m files and can be opened by MATLAB (https://www.mathworks.com/products/matlab) or by a text editor. The raw and processed force curve data and other values used for data processing are stored in binary form in *.mat MATLAB data files, which can be opened by MATLAB. Organized by figure, all the raw and processed force curve data are given in Excel worksheets (*.xlsx), one per probe/substrate combination. Data (Folder Structure) The data in the dataverse is best viewed in Tree mode. Codes for Force Curve Processing The three MATLAB codes used for force curve processing are contained in this folder. The text file Read me.txt provides all the instructions to process raw force data using these three MATLAB codes. Figure 3B, 3C – AFM images The raw (.mdt) and processed (.gwy) AFM images of the colloidal probe before and after coating with graphene oxide (GO) are contained in this folder. Figure 4 – Force Curve GO The raw data of the force curve shown in Figure 4 and the substrate force curve data (used to find inverse optical lever sensitivity) are given as .mdt files and were exported as ASCII files given in the same folder. The raw and processed force curve data are also given in the variables_GO_Tip 18.mat and GO_Tip 18.xlsx files. The force curve processing codes and instructions can be found in the Codes for Force Curve Processing folder, as mentioned above. Figure 5A – Force–Displacement Curves GO, rGO1, rGO10 All the raw data of the force curves (GO, rGO1, rGO10) shown in Figure 5A and the corresponding substrate force curve data (used to find inverse optical lever sensitivity) are given as .mdt files and were exported as ASCII files given in the same folder. The raw and processed force curve data are also given in *.mat and *.xlsx files. Figure 5B, 5C – Averages of Force and Displacement for Snap-On and Pull-Off Events All the raw data of the force curves (GO, rGO1, rGO10) for all the probes and corresponding substrate force curve data are given as .mdt files and were exported as ASCII files given in this folder. The raw and processed force curve data are also provided in *.mat and *.xlsx files. The snap-on force, snap-on displacement, and pull-off displacement values were obtained from each force curve and averaged as in Code_Figure5B_5C.m. The same code was used for plotting the average values. Figure 6A – Force–Distance Curves GO, rGO1, rGO10 The raw data provided in Figure 5A – Force Displacement Curves GO, rGO1, rGO10 folder were processed into force-vs-distance curves. The raw and processed force curve data are also given in *.mat and *.xlsx files. Figure 6B – Average Snap-On and Pull-Off Distances The same raw data provided in Figure 5B, 5C – Average Snap on Force, Displacement, Pull off Displacement folder were processed into force-vs-distance curves. The raw and processed force curve data of GO, rGO1, rGO10 of all the probes are also given in *.mat and *.xlsx files. The snap-on distance and pull-off distance values were obtained from each force curve and averaged as in Code_Figure6B.m. The code used for plotting is also given in the same text file. Figure 6C – Contact Angles Advancing and receding contact angles were calculated using each processed force-vs-distance curve and averaged according to the reduction time. The obtained values and the code used to plot is given in Code_Figure6C.m. Figure 9A – Force Curve Repetition The raw data of all five force curves and the substrate force curve data are given as .mdt files and were exported as ASCII files given in the same folder. The raw and processed force curve data are also given in *.mat and *.xlsx files. Figure 9B – Repulsive Force Comparison The data of the zoomed-in region of Figure 9A was plotted as Experimental curve. Initial baseline correction was done using the MATLAB code bc.m, and the procedure is given in the Read Me.txt text file. All the raw and processed data are given in rGO10_Tip19_Trial1.xlsx and variables_rGO10_Tip 19.mat files. The MATLAB code used to model other forces and plot all the curves in Figure 9B is given in Exp_vdW_EDL.m. 

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3. Replication Data for: High-Throughput Optical Thickness and Size Characterization of 2D Materials

   https://doi.org/10.7910/DVN/AAKHGV  

   Schniepp, Hannes; Dickinson, W. W. (January 2021, Harvard Dataverse)

   This is the optical microscopy raw data and processed data to our published manuscript. Our code used for analysis has been published in the supporting information of the manuscript, but can also be found here. The data here can be used to test the code and reproduce the published results. The dataset is best viewed in tree mode, because it contains 1000 files, which are organized in folders. The following items are in the root folder: GO, GOe, GOw folders: data from three different samples as discussed in the manuscript ParticleAnalysis-Histograms_and_Data.qti: analyzed histograms and derived plots, as used in the manuscript (QtiPlot format) Each of the three folders with sample data has subfolders Raw images (PNG format) and Processed images (TIFF and ASCII formats). The latter folder contains files of different stages of the processing process: Averaged: Average of raw images EmptySubstrateDivided: Image after division by empty substrate EmptySubstrateDivided-GwyddionExport: Same as previous, but in Gwyddion text (ASCII) image format ExtractedBackground: Fitted plane in Gwyddion text (ASCII) format Final: Image after division by fitted plan Final-Inverted: Final image after inversion (may not be present if inversion not required) 

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4. Expedition 391 Scientific Prospectus Addendum: Walvis Ridge Hotspot

   https://doi.org/10.14379/iodp.sp.391add.2021  

   Sager, W.; Hoernle, K.; Petronotis, K. (February 2021, Scientific prospectus)

   null (Ed.)

   This addendum to the International Ocean Discovery Program Expedition 391 Scientific Prospectus (Walvis Ridge Hotspot; Sager et al., 2020) incorporates minor coordinate changes to Proposed Sites CT-5A, CT-6A, TT-3A, TT-4A, TT-5A, VB-7A, VB-8A, VB-10A, VB-11A, VB-13A, and VB-14A. The revised site coordinates are documented in Proposal 890-Add2, which is available at http://iodp.tamu.edu/​scienceops/​expeditions/​walvis_ridge_hotspot.html. In addition, because of adjustments to the R/V JOIDES Resolution operations schedule caused by the COVID-19 pandemic, the expedition was postponed by a year. At the time of publication of this addendum, the expedition is scheduled to start in Cape Town, South Africa, on 6 December 2021 and end in Cape Town, South Africa, on 5 February 2022. For a detailed description of the geologic background, scientific objectives, drilling and coring strategy, logging strategy, sample and data sharing strategy, and proposed sites, see Tables T1 and T2 in this report and the Expedition 391 Scientific Prospectus (Sager et al., 2020). 

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5. Replication Data for: Protein Secondary Structure in Spider Silk Nanofibrils

   https://doi.org/10.7910/DVN/GMEEYL  

   Schniepp, Hannes C.; Wang, Qijue; McArdle, Patrick; Wang, Stephanie L.; Wilmington, Ryan L.; Xing, Zhen; Greenwood, Alexander; Cotten, Myrian L.; Qazilbash, M. Mumtaz (January 2022, Harvard Dataverse)

   This dataset contains raw data, processed data, and the codes used for data processing in our manuscript from our Fourier-transform infrared (FTIR) spectroscopy, Nuclear magnetic resonance (NMR), Raman spectroscopy, and X-ray diffraction (XRD) experiments. The data and codes for the fits of our unpolarized Raman spectra to polypeptide spectra is also included. The following explains the folder structure of the data provided in this dataset, which is also explained in the file ReadMe.txt. Browsing the data in Tree view is recommended. Folder contents Codes Raman Data Processing: The MATLAB script file RamanDecomposition.m contains the code to decompose the sub-peaks across different polarized Raman spectra (XX, XZ, ZX, ZZ, and YY), considering a set of pre-determined restrictions. The helper functions used in RamanDecomposition.m are included in the Helpers folder. RamanDecomposition.pdf is a PDF printout of the MATLAB code and output. P Value Simulation: 31_helix.ipynb and a_helix.ipynb: These two Jupyter Notebook files contain the intrinsic P value simulation for the 31-helix and alpha-helix structures. The simulation results were used to prepare Supplementary Table 4. See more details in the comments contained. Vector.py, Atom.py, Amino.py, and Helpers.py: These python files contains the class definitions used in 31_helix.ipynb and a_helix.ipynb. See more details in the comments contained. FTIR FTIR Raw Transmission.opj: This Origin data file contains the raw transmission data measured on single silk strand and used for FTIR spectra analysis. FTIR Deconvoluted Oscillators.opj: This Origin data file was generated from the data contained in the previous file using W-VASE software from J. A. Woollam, Inc. FTIR Unpolarized MultiStrand Raw Transmission.opj: This Origin data file contains the raw transmission data measured on multiple silk strands. The datasets contained in the first two files above were used to plot Figure 2a-b and the FTIR data points in Figure 4a, and Supplementary Figure 6. The datasets contained in the third file above were used to plot Supplementary Figure 3a. The datasets contained in the first two files above were used to plot Figure 2a-b, FTIR data points in Figure 4a, and Supplementary Figure 6. NMR Raw data files of the 13C MAS NMR spectra: ascii-spec_CP.txt: cross-polarized spectrum ascii-spec_DP.txt: direct-polarized spectrum Data is in ASCII format (comma separated values) using the following columns: Data point number Intensity Frequency [Hz] Frequency [ppm] Polypeptide Spectrum Fits MATLAB scripts (.m files) and Helpers: The MATLAB script file Raman_Fitting_Process_Part_1.m and Raman_Fitting_Process_Part_2.m contains the step-by-step instructions to perform the fitting process of our calculated unpolarized Raman spectrum, using digitized model polypeptide Raman spectra. The Helper folder contains two helper functions used by the above scripts. See the scripts for further instruction and information. Data aPA.csv, bPA.csv, GlyI.csv, GlyII.csv files: These csv files contain the digitized Raman spectra of poly-alanine, beta-alanine, poly-glycine-I, and poly-glycine-II. Raman_Exp_Data.mat: This MATLAB data file contains the processed, polarized Raman spectra obtained from our experiments. Variable freq is the wavenumber information of each collected spectrum. The variables xx, yy, zz, xz, zx represent the polarized Raman spectra collected. These variables are used to calculate the unpolarized Raman spectrum in Raman_Fitting_Process_Part_2.m. See the scripts for further instruction and information. Raman Raman Raw Data.mat: This MATLAB data file contains all the raw data used for Raman spectra analysis. All variables are of MATLAB structure data type. Each variable has fields called Freq and Raw, with Freq contains the wavenumber information of the measured spectra and Raw contains 5 measured Raman signal strengths. Variable XX, XZ, ZX, ZZ, and YY were used to plot and sub-peak analysis for Figure 2c-d, Raman data points in Figure 4a, Figure 5b, Supplementary Figure 2, and Supplementary Figure 7. Variable WideRange was used to plot and identify the peaks for Supplementary Figure 3b. X-Ray X-Ray.mat: This MATLAB data file contains the raw X-ray data used for the diffraction analysis in Supplementary Figure 5. 

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