trunk/mdRipple/mdripple.bib

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@string{acp = {Adv. Chem. Phys.}}

@string{bj = {Biophys. J.}}

@string{cp = {Chem. Phys.}}

@string{cpc = {Comp. Phys. Comm.}}

@string{cpl = {Chem. Phys. Lett.}}

@string{jacs = {J. Am. Chem. Soc.}}

@string{jcc = {J. Comp. Chem.}}

@string{jcp = {J. Chem. Phys.}}

@string{jml = {J. Mol. Liq.}}

@string{jpc = {J. Phys. Chem.}}

@string{jpca = {J. Phys. Chem. A}}

@string{jpcb = {J. Phys. Chem. B}}

@string{mp = {Mol. Phys.}}

@string{pccp = {Phys. Chem. Chem. Phys.}}

@string{pnas = {Proc. Natl. Acad. Sci. USA}}

@string{pra = {Phys. Rev. A}}

@string{prb = {Phys. Rev. B}}

@string{pre = {Phys. Rev. E}}

@string{prl = {Phys. Rev. Lett.}}

@string{rmp = {Rev. Mod. Phys.}}


@article{Benninger:2005qy,
        Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. },
        Annote = {10.1529/biophysj.104.050096},
        Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
        Date-Added = {2007-10-30 11:44:02 -0400},
        Date-Modified = {2007-10-30 11:44:02 -0400},
        Journal = {Biophysical Journal},
        Journal1 = {Biophys. J.},
        Number = {1},
        Pages = {609--622},
        Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
        Ty = {JOUR},
        Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
        Volume = {88},
        Year = {2005}}

@article{NorbertKucerka06012006,
        Abstract = {X-ray data are presented for the benchmark dipalmitoylphosphatidylcholine lipid bilayer in the most biologically relevant state in which the bilayers are fully hydrated and in the fluid (liquid-crystalline) phase. Form factors F(qz) are obtained from a combination of two sample preparations, oriented stacks of bilayers for qz extending to 0.85 A-1 and unilamellar vesicles for smaller qz. Modeling obtains the electron density profile and values for the area per molecule, for the locations of the component groups, and for the different types of thicknesses of the bilayer, such as the hydrocarbon thickness and the steric thickness.
},
        Author = {Kucerka, Norbert and Tristram-Nagle, Stephanie and Nagle, John F.},
        Date-Added = {2007-08-02 15:07:04 -0400},
        Date-Modified = {2007-08-02 15:07:04 -0400},
        Doi = {10.1529/biophysj.106.086017},
        Eprint = {http://www.biophysj.org/cgi/reprint/90/11/L83.pdf},
        Journal = {Biophys. J.},
        Number = {11},
        Pages = {L83-85},
        Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}},
        Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83},
        Volume = {90},
        Year = {2006}}

@article{NorbertKucerka04012005,
        Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
},
        Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
        Date-Added = {2007-08-02 15:04:34 -0400},
        Date-Modified = {2007-08-02 15:04:34 -0400},
        Doi = {10.1529/biophysj.104.056606},
        Eprint = {http://www.biophysj.org/cgi/reprint/88/4/2626.pdf},
        Journal = {Biophys. J.},
        Number = {4},
        Pages = {2626-2637},
        Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
        Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
        Volume = {88},
        Year = {2005}}

@article{Ayton95,
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        Volume = 85,
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@article{Goldstein88,
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@article{Sengupta03,
        Author = {Kheya Sengupta and V. A. Raghunathan and John Katsaras},
        Journal = pre,
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        Pages = {1-12},
        Title = {Structure of the Ripple Phase of Phospholipid Multibilayers},
        Volume = 68,
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@article{Mason01,
        Author = {P. C. Mason and J. F. Nagle and R. M. Epand and J. Katsaras},
        Journal = pre,
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        Pages = {1-4},
        Title = {Anomalous Swelling in Phospholipid bilayers is not coupled to the formation of a ripple phase},
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@article{Tieleman96,
        Author = {D. P. Tieleman and H. J. C. Berendsen},
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        Author = {Krystian Kubica},
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