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Assessing molecular simulation for the analysis of lipid monolayer reflectometry

McCluskey, A. R. ; Grant, J. LU ; Smith, A. J. LU ; Rawle, J. L. ; Barlow, D. J. ; Lawrence, M. J. ; Parker, S. C. and Edler, K. J. LU orcid (2019) In Journal of Physics Communications 3(7).
Abstract

Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This work presents the first direct comparison between the reflectometry profiles obtained from different all-atom and coarse-grained molecular dynamics simulations. These are compared with a traditional model layer structure analysis method to determine the minimum simulation resolution required to accurately reproduce experimental data. We find that systematic limits reduce the efficacy of the MARTINI potential model, while the Berger united-atom and Slipids all-atom potential models agree similarly well... (More)

Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This work presents the first direct comparison between the reflectometry profiles obtained from different all-atom and coarse-grained molecular dynamics simulations. These are compared with a traditional model layer structure analysis method to determine the minimum simulation resolution required to accurately reproduce experimental data. We find that systematic limits reduce the efficacy of the MARTINI potential model, while the Berger united-atom and Slipids all-atom potential models agree similarly well with the experimental data. The model layer structure gives the best agreement, however, the higher resolution simulation-dependent methods produce an agreement that is comparable. Finally, we use the atomistic simulation to advise on possible improvements that may be offered to the model layer structures, creating a more realistic monolayer model. Usage: Electronic Supplementary Information (ESI) including all analysis/plotting scripts and figure files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at https://github.com/arm61/sim_vs_trad (DOI: 10.5281/zenodo.3254719) under a CC BY-SA 4.0 license. Reduced experimental datasets are available at DOI: 10.15125/BATH-00586, under a CC-BY 4.0 license.

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author
; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Coarse graining, Molecular dynamics, Multi modal analysis, Neutron reflectometry
in
Journal of Physics Communications
volume
3
issue
7
article number
075001
publisher
IOP Publishing
external identifiers
  • scopus:85078237929
ISSN
2399-6528
DOI
10.1088/2399-6528/ab12a9
language
English
LU publication?
no
additional info
Publisher Copyright: © 2019 The Author(s).
id
5f669400-3af7-4fd0-aca3-462ad9de1287
date added to LUP
2023-01-18 09:04:31
date last changed
2023-02-06 16:33:13
@article{5f669400-3af7-4fd0-aca3-462ad9de1287,
  abstract     = {{<p>Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This work presents the first direct comparison between the reflectometry profiles obtained from different all-atom and coarse-grained molecular dynamics simulations. These are compared with a traditional model layer structure analysis method to determine the minimum simulation resolution required to accurately reproduce experimental data. We find that systematic limits reduce the efficacy of the MARTINI potential model, while the Berger united-atom and Slipids all-atom potential models agree similarly well with the experimental data. The model layer structure gives the best agreement, however, the higher resolution simulation-dependent methods produce an agreement that is comparable. Finally, we use the atomistic simulation to advise on possible improvements that may be offered to the model layer structures, creating a more realistic monolayer model. Usage: Electronic Supplementary Information (ESI) including all analysis/plotting scripts and figure files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at https://github.com/arm61/sim_vs_trad (DOI: 10.5281/zenodo.3254719) under a CC BY-SA 4.0 license. Reduced experimental datasets are available at DOI: 10.15125/BATH-00586, under a CC-BY 4.0 license.</p>}},
  author       = {{McCluskey, A. R. and Grant, J. and Smith, A. J. and Rawle, J. L. and Barlow, D. J. and Lawrence, M. J. and Parker, S. C. and Edler, K. J.}},
  issn         = {{2399-6528}},
  keywords     = {{Coarse graining; Molecular dynamics; Multi modal analysis; Neutron reflectometry}},
  language     = {{eng}},
  number       = {{7}},
  publisher    = {{IOP Publishing}},
  series       = {{Journal of Physics Communications}},
  title        = {{Assessing molecular simulation for the analysis of lipid monolayer reflectometry}},
  url          = {{http://dx.doi.org/10.1088/2399-6528/ab12a9}},
  doi          = {{10.1088/2399-6528/ab12a9}},
  volume       = {{3}},
  year         = {{2019}},
}