Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

Nano Reviews & Experiments

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Title Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application
 
Creator Boldon, Lauren; Rensselaer Polytechnic Institute
Laliberte, Fallon; Rensselaer Polytechnic Institute
Liu, Li; Rensselaer Polytechnic Institute
 
Subject small angle X-ray scattering; molecular dynamics; protein folding; nanoparticles; MD-SAXS; atomistic simulation; ab initio; radius of gyration; pair distribution function; Newtonian equations of motion
 
Description In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.Keywords: small angle X-ray scattering; molecular dynamics; protein folding; nanoparticles; MD-SAXS; atomistic simulation; ab initio; radius of gyration; pair distribution function; Newtonian equations of motion(Published: 25 February 2015)Citation: Nano Reviews 2015, 6: 25661 - http://dx.doi.org/10.3402/nano.v6.25661
 
Publisher Co-Action Publishing
 
Contributor
 
Date 2015-02-25
 
Type info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion

 
Format application/pdf
text/html
application/epub+zip
application/xml
 
Identifier http://www.nanoreviewsexperiments.net/index.php/nano/article/view/25661
10.3402/nr.v6.25661
 
Source Nano Reviews & Experiments; Vol 6 (2015) incl Supplements
2002-2727
 
Language eng
 
Relation http://www.nanoreviewsexperiments.net/index.php/nano/article/view/25661/38690
http://www.nanoreviewsexperiments.net/index.php/nano/article/view/25661/38691
http://www.nanoreviewsexperiments.net/index.php/nano/article/view/25661/38692
http://www.nanoreviewsexperiments.net/index.php/nano/article/view/25661/38693
http://www.nanoreviewsexperiments.net/index.php/nano/article/downloadSuppFile/25661/17870
http://www.nanoreviewsexperiments.net/index.php/nano/article/downloadSuppFile/25661/17887
 

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