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Bilayer Systems (bilayer + system)
Selected AbstractsA meso-scale analysis of lipid bilayers with the dissipative particle dynamics method: Thermally fluctuating interfacesINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 6-8 2007Taisuke Sugii Abstract We present a meso-scale simulation of lipid bilayers with the dissipative particle dynamics (DPD) method. The spectrums of the thermal undulation are analysed and the bending rigidity of the lipid bilayers is calculated. In order to define the position of the membrane, we apply a definition of the interface which has been newly proposed by Kikugawa et al. (Comput. Fluids 2007; 36:69,76). We show the applicability of this method to the lipid bilayer system. By means of this definition, the roughness of the extracted interface can be varied and this effect is investigated. The spectral intensity is shown as a function of the undulatory wavenumber q. The spectral intensity in large- q regions is affected by the roughness of the interface. However, we find that the spectral intensity in small- q regions, where the bending rigidity can be calculated, is hardly affected. Moreover, the undulation spectrums show q,4 behaviour in small- q regions, which agrees with the theoretical prediction. The effects of the size of the computational cell are also investigated. All spectrums obtained in the differently sized cells agree well, although the observable range of the wavenumber depends on the cell size. The bending rigidity calculated by spectral intensity from the largest cell is in good agreement with experiments and molecular dynamics simulations in the literature. Copyright © 2007 John Wiley & Sons, Ltd. [source] Chemically selective soft X-ray patterning of polymersJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2007Jian Wang The chemically selective modification of polymer mixtures by monochromated soft X-rays has been explored using the high-brightness fine-focused 50,nm beam of a scanning transmission X-ray microscope. Four different polymer systems were examined: a polymethylmethacrylate (PMMA) polyacrylonitrile (PAN) bilayer film; a PMMA- blend -PAN microphase-separated film; a poly(MMA- co -AN) copolymer film; and a poly(ethyl cyanoacrylate) homopolymer film. A high level of chemically selective modification was achieved for the PMMA/PAN bilayer; in particular, irradiation at 288.45,eV selectively removed the carbonyl group from PMMA while irradiation at 286.80,eV selectively reduced the nitrile group of PAN, even when these irradiations were carried out at the same (x,y) position of the sample. In the last two homogenous polymer systems, similar amounts of damage to the nitrile and carbonyl groups occurred during irradiation at either 286.80 or 288.45,eV. This is attributed to damage transfer between the C[triple-bond]N and C=O groups mediated by primary electrons, secondary electrons or radical/ionic processes, aided by their close spatial proximity. Although the overall thickness of the bilayer sample at 70,nm is smaller than the lateral line spreading of 100,nm, the interface between the layers appears to effectively block the transport of energy, and hence damage, between the two layers. The origins of the line spreading in homogeneous phases and possible origins of the damage blocking effect of the interface are discussed. To demonstrate chemically selective patterning, high-resolution multi-wavelength patterns were created in the PMMA/PAN bilayer system. [source] Structural model for an AxxxG-mediated dimer of surfactant-associated protein CFEBS JOURNAL, Issue 11 2004Visvaldas Kairys The pulmonary surfactant prevents alveolar collapse and is required for normal pulmonary function. One of the important components of the surfactant besides phospholipids is surfactant-associated protein C (SP-C). SP-C shows complex oligomerization behavior and a transition to ,-amyloid-like fibril structures, which are not yet fully understood. Besides this nonspecific oligomerization, MS and chemical cross-linking data combined with CD spectra provide evidence of a specific, mainly ,-helical, dimer at low to neutral pH. Furthermore, resistance to CNBr cleavage and dual NMR resonances of porcine and human recombinant SP-C with Met32 replaced by isoleucine point to a dimerization site located at the C-terminus of the hydrophobic ,-helix of SP-C, where a strictly conserved heptapeptide sequence is found. Computational docking of two SP-C helices, described here, reveals a dimer with a helix,helix interface that strikingly resembles that of glycophorin A and is mediated by an AxxxG motif similar to the experimentally determined GxxxG pattern of glycophorin A. It is highly likely that mature SP-C adopts such a dimeric structure in the lamellar bilayer systems found in the surfactant. Dimerization has been shown in previous studies to have a role in sorting and trafficking of SP-C and may also be important to the surfactant function of this protein. [source] Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiencyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2003Wataru Shinoda Abstract We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 920,930, 2003 [source] Stabilization of Polymer Bilayers by Introducing Crosslinking at the Interface,MACROMOLECULAR RAPID COMMUNICATIONS, Issue 12 2006Narong An Abstract Summary: Bisphenol A solid epoxy serves as an effective reaction compatibilizer to the bisphenol A polycarbonate (PC)/PMMA bilayer systems. Addition of epoxy to the bottom PMMA layer can retard or even prevent the dewetting of PC films by introducing crosslinking between both components at the interface. This is the first investigation of polymer bilayers stabilized by chemical reactions. AFM topographic image of a representative dewetting hole. [source] | ||||||||||