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Title: Quasielastic neutron scattering in biology: Theory and applications

Abstract

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.

Authors:
 [1];  [2];  [1];  [2];  [3];  [1];  [2];  [1];  [2];  [1];  [2];  [3];  [3];  [1];  [2]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. (United States)
  3. Shanghai Jiao Tong Univ. (China)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1350924
Alternate Identifier(s):
OSTI ID: 1396463
Grant/Contract Number:  
AC05-00OR22725; ERKP752
Resource Type:
Accepted Manuscript
Journal Name:
Biochimica et Biophysica Acta - General Subjects
Additional Journal Information:
Journal Volume: 1861; Journal Issue: PB; Journal ID: ISSN 0304-4165
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; dynamics; biomolecules; neutron scattering; MD simulation

Citation Formats

Vural, Derya, Univ. of Tennessee, Knoxville, TN, Hu, Xiaohu, Univ. of Tennessee, Knoxville, TN, Lindner, Benjamin, Jain, Nitin, Univ. of Tennessee, Knoxville, TN, Miao, Yinglong, Univ. of Tennessee, Knoxville, TN, Cheng, Xiaolin, Univ. of Tennessee, Knoxville, TN, Liu, Zhuo, Hong, Liang, Smith, Jeremy C., and Univ. of Tennessee, Knoxville, TN. Quasielastic neutron scattering in biology: Theory and applications. United States: N. p., 2016. Web. https://doi.org/10.1016/j.bbagen.2016.06.015.
Vural, Derya, Univ. of Tennessee, Knoxville, TN, Hu, Xiaohu, Univ. of Tennessee, Knoxville, TN, Lindner, Benjamin, Jain, Nitin, Univ. of Tennessee, Knoxville, TN, Miao, Yinglong, Univ. of Tennessee, Knoxville, TN, Cheng, Xiaolin, Univ. of Tennessee, Knoxville, TN, Liu, Zhuo, Hong, Liang, Smith, Jeremy C., & Univ. of Tennessee, Knoxville, TN. Quasielastic neutron scattering in biology: Theory and applications. United States. https://doi.org/10.1016/j.bbagen.2016.06.015
Vural, Derya, Univ. of Tennessee, Knoxville, TN, Hu, Xiaohu, Univ. of Tennessee, Knoxville, TN, Lindner, Benjamin, Jain, Nitin, Univ. of Tennessee, Knoxville, TN, Miao, Yinglong, Univ. of Tennessee, Knoxville, TN, Cheng, Xiaolin, Univ. of Tennessee, Knoxville, TN, Liu, Zhuo, Hong, Liang, Smith, Jeremy C., and Univ. of Tennessee, Knoxville, TN. Wed . "Quasielastic neutron scattering in biology: Theory and applications". United States. https://doi.org/10.1016/j.bbagen.2016.06.015. https://www.osti.gov/servlets/purl/1350924.
@article{osti_1350924,
title = {Quasielastic neutron scattering in biology: Theory and applications},
author = {Vural, Derya and Univ. of Tennessee, Knoxville, TN and Hu, Xiaohu and Univ. of Tennessee, Knoxville, TN and Lindner, Benjamin and Jain, Nitin and Univ. of Tennessee, Knoxville, TN and Miao, Yinglong and Univ. of Tennessee, Knoxville, TN and Cheng, Xiaolin and Univ. of Tennessee, Knoxville, TN and Liu, Zhuo and Hong, Liang and Smith, Jeremy C. and Univ. of Tennessee, Knoxville, TN},
abstractNote = {Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.},
doi = {10.1016/j.bbagen.2016.06.015},
journal = {Biochimica et Biophysica Acta - General Subjects},
number = PB,
volume = 1861,
place = {United States},
year = {2016},
month = {6}
}

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