ABSTRACT
Since its inception, the eld of lipid bilayer simulation has contributed a great deal to our understanding of the structure and dynamics of lipid bilayers, and by extension cell membranes. In many ways, the line between simulation and experiment has been blurry for many years, with experimental and simulation data often acting as two halves of a whole, rather than separate disciplines. The situation is somewhat analogous to the case of protein structure determination, where models and calculations are quite often essential to the determination of structures from NMR (nuclear magnetic resonance) or diffraction data. Bilayer simulations differ signicantly from protein simulations in several key ways that we discuss in the next paragraph. We then
4.1 Introduction ............................................................................................................................69 4.2 A Selective History of Lipid Simulation................................................................................. 70
4.2.1 Early Days ................................................................................................................... 70 4.2.2 New Millennium ......................................................................................................... 71
4.3 Membrane Simulations: The Present Day .............................................................................. 71 4.3.1 So You Want to Simulate a Membrane? ..................................................................... 72 4.3.2 Timescales and Lengthscales ..................................................................................... 72 4.3.3 Library of Lipid Models ............................................................................................. 74
4.3.3.1 Sterols .......................................................................................................... 74 4.3.3.2 Others ........................................................................................................... 75
4.3.4 State of the Art (and What Is to Come) ...................................................................... 76 4.3.4.1 Diffusion and Finite-Size Effects ................................................................ 76 4.3.4.2 Undulations and Curvature ..........................................................................77 4.3.4.3 Lipid Mixtures and Immiscibility ............................................................... 78 4.3.4.4 Polarizable Force Fields ............................................................................... 79 4.3.4.5 Transfer of Charged and Polar Side Chains ................................................. 81 4.3.4.6 Helix Tilt ...................................................................................................... 81 4.3.4.7 G-Protein-Coupled Receptors ...................................................................... 82 4.3.4.8 Membrane Curvature and Amphipathic Peptides ....................................... 83
4.3.5 Coarse-Grained Modeling .......................................................................................... 83 4.4 Summary ................................................................................................................................85 References ........................................................................................................................................85
