Assessing molecular simulation for the analysis of lipid monolayer reflectometry

A. R. McCluskey*, J. Grant, A. J. Smith, J. L. Rawle, D. J. Barlow, M. J. Lawrence, S. C. Parker, K. J. Edler

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

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 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.

Original languageEnglish
Article number075001
JournalJournal of Physics Communications
Volume3
Issue number7
DOIs
Publication statusPublished - 1 Jul 2019

Keywords

  • Coarse graining
  • Molecular dynamics
  • Multi modal analysis
  • Neutron reflectometry

Fingerprint

Dive into the research topics of 'Assessing molecular simulation for the analysis of lipid monolayer reflectometry'. Together they form a unique fingerprint.

Cite this