Assessing molecular simulation for the analysis of lipid monolayer reflectometry

McCluskey, Andrew R.; Grant, James; Smith, Andrew J.; Rawle, Jonathan; Barlow, David J.; Lawrence, M. Jayne; Parker, Stephen C.; Edler, Karen J.

doi:10.1088/2399-6528/ab12a9

Cited by 13 publications

(14 citation statements)

References 54 publications

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“…To become more quantitative in comparing the simulations with experiments, we have calculated the neutron reflectivity curves emerging from the simulated structures. Indeed, the reflectivity and scattering curves of neutrons or X-rays provide a demanding test for membrane simulation 12,13,65 . Since our substrate model of layers and the coating beads were adjusted for the bare hydrated substrate (see Fig.…”

Section: Neutron Reflectivity Curves Of Dppc Slbsmentioning

confidence: 99%

Coarse-Grain Simulations of Solid Supported Lipid Bilayers with Varying Hydration Levels

Benedetti

Thalmann

et al. 2020

J. Phys. Chem. B

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Supported lipid bilayers (SLBs) are a very popular system for the study of biomimetic membranes. Understanding of the interactions between the solid substrate and the lipid membrane opens pathways to the design of new materials with fine-tunable properties. While it is possible to study SLBs via Molecular Dynamics (MD) simulations, difficulties still remain for these strategies; in particular, the confined water layer thickness and structure are difficult to reproduce in simulations. We have explored different coarse-grained (CG) models for the membrane/support interaction, and their impact on the substrate hydration level. Our results highlight the relevance of including long-range interactions in CG-MD simulations of fluid SLBs. Modeled neutron reflectivity curves are deduced from the structures obtained by molecular simulations, and substrate parameters are optimized to match the experimental and modeled reflectivity curves. We expect our coarse-grained approach to open new perspectives for the simulations of SLBs of increasing complexity, including lipid layers of complex compositions, or adsorbed lipidic layers on patterned surfaces.

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Section: Neutron Reflectivity Curves Of Dppc Slbsmentioning

confidence: 99%

Coarse-Grain Simulations of Solid Supported Lipid Bilayers with Varying Hydration Levels

Benedetti

Thalmann

et al. 2020

J. Phys. Chem. B

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“…In a more recent work, McCluskey et al [46] investigated whether the use of atomistic simulations are necessary to reproduce accurately experimental reflectometry data or whether coarse-grained representations are sufficient. By the comparison between the results obtained using different MD potential models and those originated from a traditional slab description of a monolayer sample, the authors concluded that discrepancy between simulations and experimental data are likely to be observed if the coarse-grained representation is too simplified.…”

Section: Simulation-based Methodsmentioning

confidence: 99%

Applications of neutron reflectometry in biology

Gerelli

2020

EPJ Web Conf.

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Over the last 10 years, neutron reflectometry (NR) has emerged as a powerful technique for the investigation of biologically relevant thin films. The great advantage of NR with respect to many other surface-sensitive techniques is its sub-nanometer resolution that enables structural characterizations at the molecular level. In the case of bio-relevant samples, NR is non-destructive and can be used to probe thin films at buried interfaces or enclosed in bulky sample environment equipment. Moreover, recent advances in biomolecular deutera-tion enabled new labeling strategies to highlight certain structural features and to resolve with better accuracy the location of chemically similar molecules within a thin film. In this chapter I will describe some applications of NR to bio-relevant samples and discuss some of the data analysis approaches available for biological thin films. In particular, examples on the structural characterization of biomembranes, protein films and protein-lipid interactions will be described.

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“…Similarly, simulation or theory can generate continuous VF profiles. Examples include models derived from scaling theories (Field, Toprakcioglu, Dai et al, 1992;de Gennes, 1980), directly from molecular structure (McCluskey et al, 2019;Politsch et al, 2001;Politsch, 2001), from self-consistent field theory calculations (de de Vos & Leermakers, 2009) or from local cavity density functional theory calculations (Reinhardt et al, 2013). However, translation of these theoretical models to experiments is difficult because of the inherent variability of experimental systems (McCluskey et al, 2019).…”

Section: Parameterization Of Reflectometry Modelsmentioning

confidence: 99%

Quantifying the robustness of the neutron reflectometry technique for structural characterization of polymer brushes

et al. 2021

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Neutron reflectometry is the foremost technique for in situ determination of the volume fraction profiles of polymer brushes at planar interfaces. However, the subtle features in the reflectometry data produced by these diffuse interfaces challenge data interpretation. Historically, data analyses have used least-squares approaches that do not adequately quantify the uncertainty of the modeled profile and ignore the possibility of other structures that also match the collected data (multimodality). Here, a Bayesian statistical approach is used that permits the structural uncertainty and multimodality to be quantified for polymer brush systems. A free-form model is used to describe the volume fraction profile, minimizing assumptions regarding brush structure, while only allowing physically reasonable profiles to be produced. The model allows the total volume of polymer and the profile monotonicity to be constrained. The rigor of the approach is demonstrated via a round-trip analysis of a simulated system, before it is applied to real data examining the well characterized collapse of a thermoresponsive brush. It is shown that, while failure to constrain the interfacial volume and consider multimodality may result in erroneous structures being derived, carefully constraining the model allows for robust determination of polymer brush compositional profiles. This work highlights that an appropriate combination of flexibility and constraint must be used with polymer brush systems to ensure the veracity of the analysis. The code used in this analysis is provided, enabling the reproduction of the results and the application of the method to similar problems.

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Assessing molecular simulation for the analysis of lipid monolayer reflectometry

Cited by 13 publications

References 54 publications

Coarse-Grain Simulations of Solid Supported Lipid Bilayers with Varying Hydration Levels

Coarse-Grain Simulations of Solid Supported Lipid Bilayers with Varying Hydration Levels

Applications of neutron reflectometry in biology

Quantifying the robustness of the neutron reflectometry technique for structural characterization of polymer brushes

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