Comparing membrane simulations to scattering experiments : Introducing the SIMtoEXP software

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DOIResolve DOI: http://doi.org/10.1007/s00232-010-9254-5
AuthorSearch for: ; Search for: ; Search for:
TypeArticle
Journal titleJournal of Membrane Biology
Volume235
Issue1
Pages4350; # of pages: 8
SubjectMD simulation; X-ray scattering; Neutron scattering; Computer software
AbstractSIMtoEXP 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 e(z) and neutron scattering length density m(z) profiles along the z direction (i.e., normal to the membrane) and their respective Fourier transforms (i.e., Fe[qz] and Fm[qz]). The resultant four functions are then displayed graphically. (3) Accepts experimental Fe(qz) and Fm(qz) 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, q(z), as well as the contributions of each component to e(z) and m(z).
Publication date
LanguageEnglish
AffiliationNRC Canadian Neutron Beam Centre; National Research Council Canada
Peer reviewedYes
NPARC number16985133
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Record identifierbf30fd6a-005e-454e-b9d0-3f77fd1c4db3
Record created2011-03-08
Record modified2016-05-09
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