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Title: Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

Abstract

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithm to reconstruct structural information from singleparticle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.

Authors:
 [1];  [2];  [3]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Applied Mathematics; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Center for Advanced Mathematics for Energy Research Applications
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Applied Mathematics; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Center for Advanced Mathematics for Energy Research Applications; Univ. of California, Berkeley, CA (United States). Dept. of Mathematics
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Center for Advanced Mathematics for Energy Research Applications; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21); National Institutes of Health (NIH)
OSTI Identifier:
1366768
Alternate Identifier(s):
OSTI ID: 1379908
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 28; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; structure determination; multitiered iterative phasing; single-particle imaging

Citation Formats

Donatelli, Jeffrey J., Sethian, James A., and Zwart, Peter H. Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase. United States: N. p., 2017. Web. doi:10.1073/pnas.1708217114.
Donatelli, Jeffrey J., Sethian, James A., & Zwart, Peter H. Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase. United States. doi:10.1073/pnas.1708217114.
Donatelli, Jeffrey J., Sethian, James A., and Zwart, Peter H. Mon . "Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase". United States. doi:10.1073/pnas.1708217114.
@article{osti_1366768,
title = {Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase},
author = {Donatelli, Jeffrey J. and Sethian, James A. and Zwart, Peter H.},
abstractNote = {Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithm to reconstruct structural information from singleparticle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.},
doi = {10.1073/pnas.1708217114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 28,
volume = 114,
place = {United States},
year = {Mon Jun 26 00:00:00 EDT 2017},
month = {Mon Jun 26 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1073/pnas.1708217114

Citation Metrics:
Cited by: 4 works
Citation information provided by
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Works referenced in this record:

Reconstruction of an object from the modulus of its Fourier transform
journal, January 1978


Gas dynamic virtual nozzle for generation of microscopic droplet streams
journal, September 2008

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