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Title: An automated analysis workflow for optimization of force-field parameters using neutron scattering data

Abstract

Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflowmore » to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.« less

Authors:
;  [1];  [2]; ;  [3];  [4];  [1];  [3];  [4]
  1. Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)
  2. Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)
  3. Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)
  4. (United States)
Publication Date:
OSTI Identifier:
22622299
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Computational Physics; Journal Volume: 340; Other Information: Copyright (c) 2017 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; COMPARATIVE EVALUATIONS; COMPUTERIZED SIMULATION; DATA ANALYSIS; HEAVY WATER; MOLECULAR DYNAMICS METHOD; NANOSTRUCTURES; NEUTRON DIFFRACTION; NEUTRONS; OPTIMIZATION; PROBES; QUASI-ELASTIC SCATTERING; SPECTROSCOPY; SPIN ECHO

Citation Formats

Lynch, Vickie E., Borreguero, Jose M., Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby G., Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, Proffen, Thomas E., Goswami, Monojoy, E-mail: goswamim@ornl.gov, and Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831. An automated analysis workflow for optimization of force-field parameters using neutron scattering data. United States: N. p., 2017. Web. doi:10.1016/J.JCP.2017.03.045.
Lynch, Vickie E., Borreguero, Jose M., Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby G., Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, Proffen, Thomas E., Goswami, Monojoy, E-mail: goswamim@ornl.gov, & Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831. An automated analysis workflow for optimization of force-field parameters using neutron scattering data. United States. doi:10.1016/J.JCP.2017.03.045.
Lynch, Vickie E., Borreguero, Jose M., Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby G., Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, Proffen, Thomas E., Goswami, Monojoy, E-mail: goswamim@ornl.gov, and Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831. Sat . "An automated analysis workflow for optimization of force-field parameters using neutron scattering data". United States. doi:10.1016/J.JCP.2017.03.045.
@article{osti_22622299,
title = {An automated analysis workflow for optimization of force-field parameters using neutron scattering data},
author = {Lynch, Vickie E. and Borreguero, Jose M. and Bhowmik, Debsindhu and Ganesh, Panchapakesan and Sumpter, Bobby G. and Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 and Proffen, Thomas E. and Goswami, Monojoy, E-mail: goswamim@ornl.gov and Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831},
abstractNote = {Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.},
doi = {10.1016/J.JCP.2017.03.045},
journal = {Journal of Computational Physics},
number = ,
volume = 340,
place = {United States},
year = {Sat Jul 01 00:00:00 EDT 2017},
month = {Sat Jul 01 00:00:00 EDT 2017}
}