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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. 2017. "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 = 2017,
month = 7
}
  • 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. In order 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. Here, we describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in amore » deuterated water (D 2O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. In order 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.« less
  • Neutron inelastic scattering (NIS), IR and Raman spectra of the RNA constituents: bases, nucleosides and nucleotides have been analyzed. The complementary aspects of these different experimental techniques makes them especially powerful for assigning the vibrational modes of the molecules of interest. Geometry optimization and harmonic force field calculations of these molecules have been undertaken by quantum mechanical calculations at several theoretical levels: Hartree-Fock (HF), Moller-plesset second-order perturbation (MP2) and Density Functional Theory (DFT). In all cases, it has been shown that HF calculations lead to insufficient results for assigning accurately the intramolecular vibrational modes. In the case of the nucleicmore » bases, these discrepancies could be satisfactorily removed by introducing the correlation effects at MP2 level. However, the application of the MP2 procedure to the large size molecules such as nucleosides and nucleotides is absolutely impossible, taking into account the prohibitive computational time needed. On the basis of our results, the calculations at DFT levels using B3LYP exchange and correlation functional appear to be a cost-effective alternative in obtaining a reliable force field for the whole set of nucleic acid constituents.« less
  • Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less
  • Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors "against QENS data probing the diffusive dynamics of the system. Here, we showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in themore » simulation due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Furthermore, our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. Finally, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less