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Cezar HM, Cascella M. SANS Spectra with PLUMED: Implementation and Application to Metainference. J Chem Inf Model 2023; 63:4979-4985. [PMID: 37552250 PMCID: PMC10466380 DOI: 10.1021/acs.jcim.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 08/09/2023]
Abstract
Using small-angle scattering with either X-ray or neutron sources has become common in the investigation of soft-matter systems. These experiments provide information about the coarse shape of the scattered objects, but obtaining more-detailed information can usually only be achieved with the aid of molecular simulations. In this Application Note, we report the implementation of an extension in PLUMED to compute the small-angle neutron scattering (SANS), which can be used for data processing as well for enhanced sampling, in particular with the metainference method to bias simulations and sample structures with a resulting spectrum in agreement with an experimental reference. Our implementation includes a resolution function that can be used to smear the SANS intensities according to beamline error sources and is compatible with both all-atom and coarse-grained simulations. Scripts to aid in the calculation of the scattering lengths when the system is coarse-grained and to aid in preparing the inputs are provided. We illustrate the use of the implementation with metainference by performing coarse-grained simulations of beta-octylglucoside and dodecylphosphocholine micelles in water. With different software and different Hamiltonians, we show that the metainference SANS bias can drive micelles to be split and to change shapes to achieve a better agreement with the experimental reference.
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Affiliation(s)
- Henrique M. Cezar
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033
Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Hylleraas Centre for Quantum Molecular
Sciences and Department of Chemistry, University
of Oslo, PO Box 1033
Blindern, 0315 Oslo, Norway
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Ankner JF, Ashkar R, Browning JF, Charlton TR, Doucet M, Halbert CE, Islam F, Karim A, Kharlampieva E, Kilbey SM, Lin JYY, Phan MD, Smith GS, Sukhishvili SA, Thermer R, Veith GM, Watkins EB, Wilson D. Cinematic reflectometry using QIKR, the quite intense kinetics reflectometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:013302. [PMID: 36725568 DOI: 10.1063/5.0122279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/14/2022] [Indexed: 06/18/2023]
Abstract
The Quite Intense Kinetics Reflectometer (QIKR) will be a general-purpose, horizontal-sample-surface neutron reflectometer. Reflectometers measure the proportion of an incident probe beam reflected from a surface as a function of wavevector (momentum) transfer to infer the distribution and composition of matter near an interface. The unique scattering properties of neutrons make this technique especially useful in the study of soft matter, biomaterials, and materials used in energy storage. Exploiting the increased brilliance of the Spallation Neutron Source Second Target Station, QIKR will collect specular and off-specular reflectivity data faster than the best existing such machines. It will often be possible to collect complete specular reflectivity curves using a single instrument setting, enabling "cinematic" operation, wherein the user turns on the instrument and "films" the sample. Samples in time-dependent environments (e.g., temperature, electrochemical, or undergoing chemical alteration) will be observed in real time, in favorable cases with frame rates as fast as 1 Hz. Cinematic data acquisition promises to make time-dependent measurements routine, with time resolution specified during post-experiment data analysis. This capability will be deployed to observe such processes as in situ polymer diffusion, battery electrode charge-discharge cycles, hysteresis loops, and membrane protein insertion into lipid layers.
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Affiliation(s)
- J F Ankner
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - J F Browning
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - T R Charlton
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Doucet
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - C E Halbert
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - F Islam
- Neutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - A Karim
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| | - E Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - S M Kilbey
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - J Y Y Lin
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M D Phan
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - G S Smith
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S A Sukhishvili
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - R Thermer
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - G M Veith
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E B Watkins
- Neutron Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D Wilson
- Second Target Station Project, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Abstract
Cell membranes - primarily composed of lipids, sterols, and proteins - form a dynamic interface between living cells and their environment. They act as a mechanical barrier around the cell while selectively facilitating material transport, signal transduction, and various other functions necessary for the cell viability. The complex functionality of cell membranes and the hierarchical motions and responses they exhibit demand a thorough understanding of the origin of different membrane dynamics and how they are influenced by molecular additives and environmental cues. These dynamic modes include single-molecule diffusion, thermal fluctuations, and large-scale membrane deformations, to name a few. This review highlights advances in investigating structure-driven dynamics associated with model cell membranes, with a particular focus on insights gained from neutron scattering and spectroscopy experiments. We discuss the uniqueness of neutron contrast variation and its remarkable potential in probing selective membrane structure and dynamics on spatial and temporal scales over which key biological functions occur. We also present a summary of current and future opportunities in synergistic combinations of neutron scattering with molecular dynamics (MD) simulations to gain further understanding of the molecular mechanisms underlying complex membrane functions.
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Affiliation(s)
- Sudipta Gupta
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, VA 24061, USA. and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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Dorrell MW, Beaven AH, Sodt AJ. A combined molecular/continuum-modeling approach to predict the small-angle neutron scattering of curved membranes. Chem Phys Lipids 2020; 233:104983. [PMID: 33035544 DOI: 10.1016/j.chemphyslip.2020.104983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022]
Abstract
This paper develops a framework to compute the small-angle neutron scattering (SANS) from highly curved, dynamically fluctuating, and potentially inhomogeneous membranes. This method is needed to compute the scattering from nanometer-scale membrane domains that couple to curvature, as predicted by molecular modeling. The detailed neutron scattering length density of a small planar bilayer patch is readily available via molecular dynamics simulation. A mathematical, mechanical transformation of the planar scattering length density is developed to predict the scattering from curved bilayers. By simulating a fluctuating, curved, surface-continuum model, long time- and length-scales can be reached while, with the aid of the planar-to-curved transformation, the molecular features of the scattering length density can be retained. A test case for the method is developed by constructing a coarse-grained lipid vesicle following a protocol designed to relieve both the osmotic stress inside the vesicle and the lipid-number stress between the leaflets. A question was whether the hybrid model would be able to replicate the scattering from the highly deformed inner and outer leaflets of the small vesicle. Matching the scattering of the full (molecular vesicle) and hybrid (continuum vesicle) models indicated that the inner and outer leaflets of the full vesicle were expanded laterally, consistent with previous simulations of the Martini forcefield that showed thinning in small vesicles. The vesicle structure is inconsistent with a zero-tension leaflet deformed by a single set of elastic parameters, and the results show that this is evident in the scattering. The method can be applied to translate observations of any molecular model's neutron scattering length densities from small patches to large length and timescales.
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Affiliation(s)
- Mitchell W Dorrell
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, USA; Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Andrew H Beaven
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, USA
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institutes of Child Health and Human Development, National Institutes of Health, USA.
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