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Title: Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

Abstract

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.

Authors:
 [1];  [1];  [2];  [1];  [1];  [1]
  1. Northeastern Univ., Boston, MA (United States)
  2. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1335575
Report Number(s):
NREL/JA-2700-67564
Journal ID: ISSN 1600-5767; JACGAR
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Applied Crystallography (Online)
Additional Journal Information:
Journal Name: Journal of Applied Crystallography (Online); Journal Volume: 49; Journal Issue: 6; Journal ID: ISSN 1600-5767
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; diffraction pattern simulation; cellulose fibrils; pair-distance quantization; biomass fuels; algorithms

Citation Formats

Zhang, Yan, Inouye, Hideyo, Crowley, Michael, Yu, Leiming, Kaeli, David, and Makowski, Lee. Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances. United States: N. p., 2016. Web. doi:10.1107/S1600576716013297.
Zhang, Yan, Inouye, Hideyo, Crowley, Michael, Yu, Leiming, Kaeli, David, & Makowski, Lee. Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances. United States. doi:10.1107/S1600576716013297.
Zhang, Yan, Inouye, Hideyo, Crowley, Michael, Yu, Leiming, Kaeli, David, and Makowski, Lee. Fri . "Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances". United States. doi:10.1107/S1600576716013297. https://www.osti.gov/servlets/purl/1335575.
@article{osti_1335575,
title = {Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances},
author = {Zhang, Yan and Inouye, Hideyo and Crowley, Michael and Yu, Leiming and Kaeli, David and Makowski, Lee},
abstractNote = {Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.},
doi = {10.1107/S1600576716013297},
journal = {Journal of Applied Crystallography (Online)},
number = 6,
volume = 49,
place = {United States},
year = {Fri Oct 14 00:00:00 EDT 2016},
month = {Fri Oct 14 00:00:00 EDT 2016}
}

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Works referenced in this record:

Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production
journal, February 2007

  • Himmel, M. E.; Ding, S.-Y.; Johnson, D. K.
  • Science, Vol. 315, Issue 5813, p. 804-807
  • DOI: 10.1126/science.1137016