Coarse-grained empirical potential structure refinement : Application to a reverse aqueous micelle
Soper, A. K. and Edler, K. J. LU
(2017)
In Biochimica et Biophysica Acta - General Subjects
1861(6).
p.1652-1660
- Abstract
Conventional atomistic computer simulations, involving perhaps up to 106 atoms, can achieve length-scales on the order of a few 10s of nm. Yet many heterogeneous systems, such as colloids, nano-structured materials, or biological systems, can involve correlations over distances up 100s of nm, perhaps even 1 μm in some instances. For such systems it is necessary to invoke coarse-graining, where single atoms are replaced by agglomerations of atoms, usually represented as spheres, in order for the simulation to be performed within a practical computer memory and time scale. Small angle scattering and reflectivity measurements, both X-ray and neutron, are routinely used to investigate structure in these systems, and traditionally... (More)
Conventional atomistic computer simulations, involving perhaps up to 106 atoms, can achieve length-scales on the order of a few 10s of nm. Yet many heterogeneous systems, such as colloids, nano-structured materials, or biological systems, can involve correlations over distances up 100s of nm, perhaps even 1 μm in some instances. For such systems it is necessary to invoke coarse-graining, where single atoms are replaced by agglomerations of atoms, usually represented as spheres, in order for the simulation to be performed within a practical computer memory and time scale. Small angle scattering and reflectivity measurements, both X-ray and neutron, are routinely used to investigate structure in these systems, and traditionally the data have been interpreted in terms of discrete objects, such as spheres, sheets, and cylinders, and combinations thereof. Here we combine the coarse-grained computer simulation approach with neutron small angle scattering to refine the structure of a heterogeneous system, in the present case a reverse aqueous micelle of sodium-dioctyl sulfosuccinate (AOT) and iso-octane. The method closely follows empirical potential structure refinement and involves deriving an empirical interaction potential from the scattering data. As in traditional coarse-grained methods, individual atoms are replaced by spherical density profiles, which, unlike real atoms, can inter-penetrate to a significant extent. The method works over an arbitrary range of length-scales, but is limited to around 2 orders of magnitude in distance above a specified dimension. The smallest value for this dimension is of order 1 nm, but the largest dimension is arbitrary. This article is part of a Special Issue entitled “Recent Advances in Bionanomaterials” Guest Editor: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.
(Less)
- author
- Soper, A. K.
and Edler, K. J.
LU
- publishing date
- 2017-06
- type
- Contribution to journal
- publication status
- published
- keywords
- Coarse-graining, Computer simulation, Empirical potential structure refinement, EPSR, Neutron scattering, X-ray scattering
- in
- Biochimica et Biophysica Acta - General Subjects
- volume
- 1861
- issue
- 6
- pages
- 9 pages
- publisher
- Elsevier
- external identifiers
-
- pmid:28259740
- scopus:85015607782
- ISSN
- 0304-4165
- DOI
- 10.1016/j.bbagen.2017.02.028
- language
- English
- LU publication?
- no
- additional info
- Publisher Copyright: © 2017 Elsevier B.V.
- id
- 5d597e05-e552-47e4-875f-3eaa56ce9bc9
- date added to LUP
- 2023-01-18 09:15:34
- date last changed
- 2024-05-30 13:55:53
@article{5d597e05-e552-47e4-875f-3eaa56ce9bc9,
abstract = {{<p>Conventional atomistic computer simulations, involving perhaps up to 10<sup>6</sup> atoms, can achieve length-scales on the order of a few 10s of nm. Yet many heterogeneous systems, such as colloids, nano-structured materials, or biological systems, can involve correlations over distances up 100s of nm, perhaps even 1 μm in some instances. For such systems it is necessary to invoke coarse-graining, where single atoms are replaced by agglomerations of atoms, usually represented as spheres, in order for the simulation to be performed within a practical computer memory and time scale. Small angle scattering and reflectivity measurements, both X-ray and neutron, are routinely used to investigate structure in these systems, and traditionally the data have been interpreted in terms of discrete objects, such as spheres, sheets, and cylinders, and combinations thereof. Here we combine the coarse-grained computer simulation approach with neutron small angle scattering to refine the structure of a heterogeneous system, in the present case a reverse aqueous micelle of sodium-dioctyl sulfosuccinate (AOT) and iso-octane. The method closely follows empirical potential structure refinement and involves deriving an empirical interaction potential from the scattering data. As in traditional coarse-grained methods, individual atoms are replaced by spherical density profiles, which, unlike real atoms, can inter-penetrate to a significant extent. The method works over an arbitrary range of length-scales, but is limited to around 2 orders of magnitude in distance above a specified dimension. The smallest value for this dimension is of order 1 nm, but the largest dimension is arbitrary. This article is part of a Special Issue entitled “Recent Advances in Bionanomaterials” Guest Editor: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.</p>}},
author = {{Soper, A. K. and Edler, K. J.}},
issn = {{0304-4165}},
keywords = {{Coarse-graining; Computer simulation; Empirical potential structure refinement; EPSR; Neutron scattering; X-ray scattering}},
language = {{eng}},
number = {{6}},
pages = {{1652--1660}},
publisher = {{Elsevier}},
series = {{Biochimica et Biophysica Acta - General Subjects}},
title = {{Coarse-grained empirical potential structure refinement : Application to a reverse aqueous micelle}},
url = {{http://dx.doi.org/10.1016/j.bbagen.2017.02.028}},
doi = {{10.1016/j.bbagen.2017.02.028}},
volume = {{1861}},
year = {{2017}},
}