Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software |
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| Authors: | Norbert Kučerka John Katsaras John F Nagle |
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| Institution: | (1) Canadian Neutron Beam Centre, National Research Council, Chalk River, ON, K0J 1J0, Canada;(2) Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 832 32 Bratislava, Slovakia;(3) Guelph-Waterloo Physics Institute and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada;(4) Department of Physics, Brock University, 500 Glenridge Avenue, St, Catharines, ON, L2S 3A1, Canada;(5) Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA;(6) Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA; |
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| 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). |
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