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Atomistic Monte Carlo Simulation of Lipid Membranes
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
Theoretical Biophysics Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, Berlin D-13125, Germany
* Author to whom correspondence should be addressed.
Received: 28 August 2013; in revised form: 6 December 2013 / Accepted: 9 January 2014 / Published: 24 January 2014
Abstract: Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.
Keywords: Monte Carlo; phospholipid bilayer; cholesterol; diffusion; coordinate transformation; entropy; sampling
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MDPI and ACS Style
Wüstner, D.; Sklenar, H. Atomistic Monte Carlo Simulation of Lipid Membranes. Int. J. Mol. Sci. 2014, 15, 1767-1803.
Wüstner D, Sklenar H. Atomistic Monte Carlo Simulation of Lipid Membranes. International Journal of Molecular Sciences. 2014; 15(2):1767-1803.
Wüstner, Daniel; Sklenar, Heinz. 2014. "Atomistic Monte Carlo Simulation of Lipid Membranes." Int. J. Mol. Sci. 15, no. 2: 1767-1803.