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Nanofibrils play a pivotal role in spider silk and are responsible for many of the impressive properties of this unique natural material. However, little is known about the internal structure of these protein fibrils. We carry out polarized Raman and polarized Fourier-transform infrared spectroscopies on native spider silk nanofibrils and determine the concentrations of six distinct protein secondary structures, including β-sheets, and two types of helical structures, for which we also determine orientation distributions. Our advancements in peak assignments are in full agreement with the published silk vibrational spectroscopy literature. We further corroborate our findings with X-ray diffraction and magic-angle spinning nuclear magnetic resonance experiments. Based on the latter and on polypeptide Raman spectra, we assess the role of key amino acids in different secondary structures. For the recluse spider we develop a highly detailed structural model, featuring seven levels of structural hierarchy. The approaches we develop are directly applicable to other proteinaceous materials.

 

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. 

We study the ultrafast time resolved response of 30 nm films of VO₂on a TiO₂substrate when 3.1 eV (400 nm wavelength) pump pulses were used to excite the insulator to metal transition (IMT). We found that the IMT threshold for these samples (≤30µJ/cm²) is more than 3 orders of magnitude lower than that generally reported for a more traditional 1.55 eV (800 nm wavelength) excitation. The samples also exhibited unusual reflectivity dynamics at near-threshold values of pump fluence where their fractional relative reflectivity ΔR/R initially increased before becoming negative after several hundreds of picoseconds, in stark contrast with uniformly negative ΔR/R observed for both higher 400 nm pump fluences and for 800 nm pump pulses. We explain the observed behavior by the interference of the reflected probe beam from the inhomogeneous layers formed inside the film by different phases of VO₂and use a simple diffusion model of the VO₂phase transition to support qualitatively this hypothesis. We also compare the characteristics of the VO₂films grown on undoped TiO₂and on doped TiO₂:Nb substrates and observe more pronounced reflectivity variation during IMT and faster relaxation to the insulating state for the VO₂/TiO₂:Nb sample.