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Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software

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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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Acknowledgements

We thank Scott Feller, Jonathan Sachs, Jason Perlmutter and Jeffery Klauda for providing us with simulation data, and Olle Edholm and Frank Heinrich for valuable feedback. N. K. acknowledges partial funding from the Advanced Foods and Materials Network (AFMNet), a Network of Centres of Excellence of Canada. J. F. N. was supported by the U.S. National Institutes of Health, Institute of General Medicine (grant GM44976).

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Authors and Affiliations

  1. Canadian Neutron Beam Centre, National Research Council, Chalk River, ON, K0J 1J0, Canada

    Norbert Kučerka & John Katsaras

  2. Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 832 32, Bratislava, Slovakia

    Norbert Kučerka

  3. Guelph-Waterloo Physics Institute and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada

    John Katsaras

  4. Department of Physics, Brock University, 500 Glenridge Avenue, St, Catharines, ON, L2S 3A1, Canada

    John Katsaras

  5. Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA

    John F. Nagle

  6. Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA

    John F. Nagle

Authors
  1. Norbert Kučerka
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  2. John Katsaras
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  3. John F. Nagle
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Correspondence to John F. Nagle.

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Kučerka, N., Katsaras, J. & Nagle, J.F. Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software. J Membrane Biol 235, 43–50 (2010). https://doi.org/10.1007/s00232-010-9254-5

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  • DOI: https://doi.org/10.1007/s00232-010-9254-5

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