Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software
- 21 April 2010
- journal article
- research article
- Published by Springer Science and Business Media LLC in The Journal of Membrane Biology
- Vol. 235 (1), 43-50
- https://doi.org/10.1007/s00232-010-9254-5
Abstract
SIMtoEXP is a software package designed to facilitate the comparison of biomembrane simulations with experimental X-ray and neutron scattering data. It has the following features: (1) Accepts number density profiles from simulations in a standard but flexible format. (2) Calculates the electron density ε(z) and neutron scattering length density ν(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., F ε [q z ] and F ν [q z ]). The resultant four functions are then displayed graphically. (3) Accepts experimental F ε (q z ) and F ν (q z ) data for graphical comparison with simulations. (4) Allows for lipids and other large molecules to be parsed into component groups by the user and calculates the component volumes following Petrache et al. (Biophys J 72:2237–2242, 1997). The software then calculates and displays the contributions of each component group as volume probability profiles, ρ(z), as well as the contributions of each component to ε(z) and ν(z).Keywords
This publication has 13 references indexed in Scilit:
- The Effect of Cholesterol on Short- and Long-Chain Monounsaturated Lipid Bilayers as Determined by Molecular Dynamics Simulations and X-Ray ScatteringBiophysical Journal, 2008
- Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering DataBiophysical Journal, 2008
- Cholesterol Packing around Lipids with Saturated and Unsaturated Chains: A Simulation StudyLangmuir, 2008
- Curvature Effect on the Structure of Phospholipid BilayersLangmuir, 2006
- Simulation-Based Methods for Interpreting X-Ray Data from Lipid BilayersBiophysical Journal, 2006
- Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar VesiclesBiophysical Journal, 2005
- Determination of component volumes of lipid bilayers from simulationsBiophysical Journal, 1997
- Neutron scattering lengths and cross sectionsNeutron News, 1992
- Structure of the fully hydrated gel phase of dipalmitoylphosphatidylcholineBiophysical Journal, 1989
- X-ray scattering factors computed from numerical Hartree–Fock wave functionsActa Crystallographica Section A, 1968