title: Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.
abstract: 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.
authors.affiliation: Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA; boldol@rpi.edu.
authors.forename: Lauren
authors.initials: L
authors.lastname: Boldon
authors.affiliation: Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
authors.forename: Fallon
authors.initials: F
authors.lastname: Laliberte
authors.affiliation: Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA; liue@rpi.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Liu
keywords: MD-SAXS; Newtonian equations of motion; ab initio; atomistic simulation; molecular dynamics; nanoparticles; pair distribution function; protein folding; radius of gyration; small angle X-ray scattering