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Molecular Modeling of Biomembranes: A How-to Approach

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Biomedical Applications of Biophysics

Part of the book series: Handbook of Modern Biophysics ((HBBT,volume 3))

Abstract

Computer Simulations have become an important complementary technique to experiment and analytical theory for scientific discoveries. Molecular Dynamics (MD) is one of the most abundant techniques of computer modeling, and is frequently used simulation methods in biomolecular applications. Its popularity may stem from its simplicity and versatile applicability. The fundamental underlying assumption of MD is that the system consists of particles that interact via the classical equations of motion, i.e., both quantum mechanical and relativistic effects are neglected. The exclusion of these effects, however, does not generally have a significant impact on the biomolecular questions being studied.

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  1. Allison N. Dickey

    Present address: Chemical and Biological Engineering Department, Northwestern University, Evanston, IL, 60208, USA

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  1. Department of Chemical Engineering and Materials Science, University of California Davis, Bainer Hall, One Shields Avenue, Davis, CA, 95616, USA

    Allison N. Dickey & Roland Faller

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Correspondence to Roland Faller .

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Editors and Affiliations

  1. Department of Biochemistry and Molecular Medicine, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA

    Thomas Jue Ph.D.

2.1 Electronic Supplementary material

Figure 2.1.

Visualization of a POPA lipid bilayer [32]. Left: The system contains 128 lipids with 5443 water molecules. Middle: The POPA lipids without the water molecules. Right: Only the POPA headgroups are shown. Please visit http://extras.springer.com/ to view a high-resolution full-color version of this illustration. (PDF 2,842 KB)

Figure 2.2.

Electron density profiles of the POPA lipid bilayer from Figure 2.1. The bilayer center corresponds to a value of z = 0 nm. Please visit http://extras.springer.com/ to view a high-resolution full-color version of this illustration. (PDF 2,762 KB)

Figure 2.3.

An example of how the lipid acyl chains are numbered in calculating the order parameter. The POPA lipid shown here differs from the more commonly studied DPPC lipid in that the DPPC choline group is replaced with a hydrogen atom and the sn-2 tail contains a double bond and 18 atoms. Please visit http://extras.springer.com/ to view a high-resolution full-color version of this illustration. (PDF 2,772 KB)

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Dickey, A.N., Faller, R. (2010). Molecular Modeling of Biomembranes: A How-to Approach. In: Jue, T. (eds) Biomedical Applications of Biophysics. Handbook of Modern Biophysics, vol 3. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-233-9_2

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