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Sample records for fluid bilayer structure

  1. Fluid bilayer structure determination: Joint refinement in composition space using X-ray and neutron diffraction data

    SciTech Connect

    White, S.H.; Wiener, M.C.

    1994-12-31

    Experimentally-determined structural models of fluid lipid bilayers are essential for verifying molecular dynamics simulations of bilayers and for understanding the structural consequences of peptide interactions. The extreme thermal motion of bilayers precludes the possibility of atomic-level structural models. Defining {open_quote}the structure{close_quote} of a bilayer as the time-averaged transbilayer distribution of the water and the principal lipid structural groups such as the carbonyls and double-bonds (quasimolecular fragments), one can represent the bilayer structure as a sum of Gaussian functions referred to collectively as the quasimolecular structure. One method of determining the structure is by neutron diffraction combined with exhaustive specific deuteration. This method is impractical because of the expense of the chemical syntheses and the limited amount of neutron beam time currently available. We have therefore developed the composition space refinement method for combining X-ray and minimal neutron diffraction data to arrive at remarkably detailed and accurate structures of fluid bilayers. The composition space representation of the bilayer describes the probability of occupancy per unit length across the width of the bilayer of each quasimolecular component and permits the joint refinement of X-ray and neutron lamellar diffraction data by means of a single quasimolecular structure that is fitted simultaneously to both data sets. Scaling of each component by the appropriate neutron or X-ray scattering length maps the composition-space profile to the appropriate scattering length space for comparison to experimental data. The difficulty with the method is that fluid bilayer structures are generally only marginally determined by the experimental data. This means that the space of possible solutions must be extensively explored in conjunction with a thorough analysis of errors.

  2. Molecular Structures of Fluid Phosphatidylethanolamine Bilayers Obtained from Simulation-to-Experiment Comparisons and Experimental Scattering Density Profiles

    DOE PAGES

    Kučerka, Norbert; van Oosten, Brad; Pan, Jianjun; ...

    2014-12-01

    In this paper, following our previous efforts in determining the structures of commonly used PC, PG, and PS bilayers, we continue our studies of fully hydrated, fluid phase PE bilayers. The newly designed parsing scheme for PE bilayers was based on extensive MD simulations, and is utilized in the SDP analysis of both X-ray and neutron (contrast varied) scattering measurements. Obtained experimental scattering form factors are directly compared to our simulation results, and can serve as a benchmark for future developed force fields. Among the evaluated structural parameters, namely, area per lipid A, overall bilayer thickness DB, and hydrocarbon regionmore » thickness 2DC, the PE bilayer response to changing temperature is similar to previously studied bilayers with different headgroups. On the other hand, the reduced hydration of PE headgroups, as well as the strong hydrogen bonding between PE headgroups, dramatically affects lateral packing within the bilayer. Despite sharing the same glycerol backbone, a markedly smaller area per lipid distinguishes PE from other bilayers (i.e., PC, PG, and PS) studied to date. Finally and overall, our data are consistent with the notion that lipid headgroups govern bilayer packing, while hydrocarbon chains dominate the bilayer’s response to temperature changes.« less

  3. Molecular Structures of Fluid Phosphatidylethanolamine Bilayers Obtained from Simulation-to-Experiment Comparisons and Experimental Scattering Density Profiles

    SciTech Connect

    Kučerka, Norbert; van Oosten, Brad; Pan, Jianjun; Heberle, Frederick A.; Harroun, Thad A.; Katsaras, John

    2014-12-01

    In this paper, following our previous efforts in determining the structures of commonly used PC, PG, and PS bilayers, we continue our studies of fully hydrated, fluid phase PE bilayers. The newly designed parsing scheme for PE bilayers was based on extensive MD simulations, and is utilized in the SDP analysis of both X-ray and neutron (contrast varied) scattering measurements. Obtained experimental scattering form factors are directly compared to our simulation results, and can serve as a benchmark for future developed force fields. Among the evaluated structural parameters, namely, area per lipid A, overall bilayer thickness DB, and hydrocarbon region thickness 2DC, the PE bilayer response to changing temperature is similar to previously studied bilayers with different headgroups. On the other hand, the reduced hydration of PE headgroups, as well as the strong hydrogen bonding between PE headgroups, dramatically affects lateral packing within the bilayer. Despite sharing the same glycerol backbone, a markedly smaller area per lipid distinguishes PE from other bilayers (i.e., PC, PG, and PS) studied to date. Finally and overall, our data are consistent with the notion that lipid headgroups govern bilayer packing, while hydrocarbon chains dominate the bilayer’s response to temperature changes.

  4. Nanometric Gap Structure with a Fluid Lipid Bilayer for the Selective Transport and Detection of Biological Molecules.

    PubMed

    Ando, Koji; Tanabe, Masashi; Morigaki, Kenichi

    2016-08-09

    The biological membrane is a natural biosensing platform that can detect specific molecules with extremely high sensitivity. We developed a biosensing methodology by combining a model biological membrane and a nanometer-sized gap structure on a glass substrate. The model membrane comprised lithographically patterned polymeric and fluid lipid bilayers. The polymeric bilayer was bonded to a poly(dimethylsiloxane) (PDMS) sheet by using an adhesion layer with a defined thickness (lipid vesicles). Extruded lipid vesicles having a biotin moiety on the surface were used as the adhesion layer in conjunction with the biotin-streptavidin linkage. A gap structure was formed between the fluid bilayer and PDMS (nanogap junction). The thickness of the gap structure was several tens of nanometers, as determined by the thickness of the adhesion layer. The nanogap junction acted as a sensitive biosensing platform. From a mixture of proteins (cholera toxin and albumin), the target protein (cholera toxin) was selectively transported into the gap by the specific binding to a glycolipid (GM1) in the fluid bilayer and lateral diffusion. The target protein molecules were then detected with an elevated signal-to-noise ratio due to the reduced background noise in the nanometric gap. The combination of selective transport and reduced background noise drastically enhanced the sensitivity toward the target protein. The nanogap junction should have broad biomedical applications by realizing highly selective and sensitive biosensing in samples having diverse coexisting molecules.

  5. Density functional approach to the description of fluids in contact with bilayers.

    PubMed

    Patrykiejew, A; Sokołowski, S; Ilnyskyi, J; Sokołowska, Z

    2010-06-28

    We discuss an application of a density functional approach to describe a bilayer, or a simplified model of a membrane, that is built of tethered chain molecules. The bilayer integrity is maintained by tethering chain particles to two common sheets. We study the structure of a two-component mixture in contact with the bilayer, as well as the solvation force acting between two bilayers, immersed in a fluid. The fluid is a binary mixture involving the component that can cross freely the bilayer and the second impenetrable component. All the calculations are carried out for athermal system, in which only hard-core interactions are present.

  6. Determination of the hydrocarbon core structure of fluid dioleoylphosphocholine (DOPC) bilayers by x-ray diffraction using specific bromination of the double-bonds: effect of hydration.

    PubMed Central

    Hristova, K; White, S H

    1998-01-01

    Changes in the structure of the hydrocarbon core (HC) of fluid lipid bilayers can reveal how bilayers respond to the partitioning of peptides and other solutes (Jacobs, R. E., and S. H. White. 1989. Biochemistry. 28:3421-3437). The structure of the HC of dioleoylphosphocholine (DOPC) bilayers can be determined from the transbilayer distribution of the double-bonds (Wiener, M. C., and S. H. White. 1992. Biophys. J. 61:434-447). This distribution, representing the time-averaged projection of the double-bond positions onto the bilayer normal (z), can be obtained by means of neutron diffraction and double-bond specific deuteration (Wiener, M. C., G. I. King, and S. H. White. 1991. Biophys. J. 60:568-576). For fully resolved bilayer profiles, a close approximation of the distribution could be obtained by x-ray diffraction and isomorphous bromine labeling at the double-bonds of the DOPC sn-2 acyl chain (Wiener, M. C., and S. H. White. 1991. Biochemistry. 30:6997-7008). We have modified the bromine-labeling approach in a manner that permits determination of the distribution in under-resolved bilayer profiles observed at high water contents. We used this new method to determine the transbilayer distribution of the double-bond bromine labels of DOPC over a hydration range of 5.4 to 16 waters per lipid, which reveals how the HC structure changes with hydration. We found that the transbilayer distributions of the bromines can be described by a pair of Gaussians of 1/e half-width A(Br) located at z = +Z(Br) relative to the bilayer center. For hydrations from 5.4 waters up to 9.4 waters per lipid, Z(Br) decreases from 7.97 +/- 0.27 A to 6.59 +/- 0.15 A, while A(Br) increased from 4.62 +/- 0.62 A to 5.92 +/- 0.37 A, consistent with the expected hydration-induced decrease in HC thickness and increase in area per lipid. After the phosphocholine hydration shell was filled at approximately 12 waters per lipid, we observed a shift in Z(Br) to approximately 7.3 A, indicative of a

  7. Determination of the hydrocarbon core structure of fluid dioleoylphosphocholine (DOPC) bilayers by x-ray diffraction using specific bromination of the double-bonds: effect of hydration.

    PubMed

    Hristova, K; White, S H

    1998-05-01

    Changes in the structure of the hydrocarbon core (HC) of fluid lipid bilayers can reveal how bilayers respond to the partitioning of peptides and other solutes (Jacobs, R. E., and S. H. White. 1989. Biochemistry. 28:3421-3437). The structure of the HC of dioleoylphosphocholine (DOPC) bilayers can be determined from the transbilayer distribution of the double-bonds (Wiener, M. C., and S. H. White. 1992. Biophys. J. 61:434-447). This distribution, representing the time-averaged projection of the double-bond positions onto the bilayer normal (z), can be obtained by means of neutron diffraction and double-bond specific deuteration (Wiener, M. C., G. I. King, and S. H. White. 1991. Biophys. J. 60:568-576). For fully resolved bilayer profiles, a close approximation of the distribution could be obtained by x-ray diffraction and isomorphous bromine labeling at the double-bonds of the DOPC sn-2 acyl chain (Wiener, M. C., and S. H. White. 1991. Biochemistry. 30:6997-7008). We have modified the bromine-labeling approach in a manner that permits determination of the distribution in under-resolved bilayer profiles observed at high water contents. We used this new method to determine the transbilayer distribution of the double-bond bromine labels of DOPC over a hydration range of 5.4 to 16 waters per lipid, which reveals how the HC structure changes with hydration. We found that the transbilayer distributions of the bromines can be described by a pair of Gaussians of 1/e half-width A(Br) located at z = +Z(Br) relative to the bilayer center. For hydrations from 5.4 waters up to 9.4 waters per lipid, Z(Br) decreases from 7.97 +/- 0.27 A to 6.59 +/- 0.15 A, while A(Br) increased from 4.62 +/- 0.62 A to 5.92 +/- 0.37 A, consistent with the expected hydration-induced decrease in HC thickness and increase in area per lipid. After the phosphocholine hydration shell was filled at approximately 12 waters per lipid, we observed a shift in Z(Br) to approximately 7.3 A, indicative of a

  8. Structure and fluctuations of a single floating lipid bilayer.

    PubMed

    Daillant, J; Bellet-Amalric, E; Braslau, A; Charitat, T; Fragneto, G; Graner, F; Mora, S; Rieutord, F; Stidder, B

    2005-08-16

    A single lipid molecular bilayer of 17 or 18 carbon chain phosphocholines, floating in water near a flat wall, is prepared in the bilayer gel phase and then heated to the fluid phase. Its structure (electron density profile) and height fluctuations are determined by using x-ray reflectivity and non-specular scattering. By fitting the off-specular signal to that calculated for a two-dimensional membrane using a Helfrich Hamiltonian, we determine the three main physical quantities that govern the bilayer height fluctuations: The wall attraction potential is unexpectedly low; the surface tension, roughly independent on chain length and temperature, is moderate (approximately 5 x 10(-4) J.m(-2)) but large enough to dominate the intermediate range of the fluctuation spectrum; and the bending modulus abruptly decreases by an order-of-magnitude from 10(-18) J to 10(-19) J at the bilayer gel-to-fluid transition.

  9. Formation of an ordered phase by ceramides and diacylglycerols in a fluid phosphatidylcholine bilayer--Correlation with structure and hydrogen bonding capacity.

    PubMed

    Ekman, Peik; Maula, Terhi; Yamaguchi, Shou; Yamamoto, Tetsuya; Nyholm, Thomas K M; Katsumura, Shigeo; Slotte, J Peter

    2015-10-01

    Ceramides and diacylglycerols are lipids with a large hydrophobic part (acyl chains and long-chain base) whereas their polar function (hydroxyl group) is small. They need colipids with large head groups to coexist in bilayer membranes. In this study, we have determined how saturated and unsaturated ceramides and acyl-chain matched diacylglycerols form ordered domains in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers as a function of bilayer concentration. The formation of ordered domains was determined from lifetime analysis of trans-parinaric acid. Ceramides formed ordered domains with equal average tPA lifetime at lower bilayer concentration when compared to acyl-chain matched diacylglycerols. This was true for both saturated (16:0) and mono-unsaturated (18:1) species. This finding suggested that hydrogen bonding among ceramides contributed to their more efficient ordered phase formation, since diacylglycerols do not form similar hydrogen bonding networks. The role of hydrogen bonding in ordered domain formation was further verified by using palmitoyl ceramide analogs with 2N and 3OH methylated long-chain bases. These analogs do not form hydrogen bonds from the 2NH or the 3OH, respectively. While methylation of the 3OH did not affect ordered phase formation compared to native palmitoyl ceramide, 2NH methylation markedly attenuated ceramide ordered phase formation. We conclude that in addition to acyl chain length, saturation, molecular order, and lack of large head group, also hydrogen bonding involving the 2NH is crucial for efficient formation of ceramide-rich domains in fluid phosphatidylcholine bilayers.

  10. Polyelectrolyte multilayer-cushioned fluid lipid bilayers: a parachute model.

    PubMed

    Shao, Jingxin; Wen, Caixia; Xuan, Mingjun; Zhang, Hongyue; Frueh, Johannes; Wan, Mingwei; Gao, Lianghui; He, Qiang

    2017-01-18

    Lipid bilayer membranes supported on polyelectrolyte multilayers are widely used as a new biomembrane model that connects biological and artificial materials since these ultrathin polyelectrolyte supports may mimic the role of the extracellular matrix and cell skeleton in living systems. Polyelectrolyte multilayers were fabricated by a layer-by-layer self-assembly technique. A quartz crystal microbalance with dissipation was used in real time to monitor the interaction between phospholipids and polyelectrolytes in situ on a planar substrate. The surface properties of polyelectrolyte films were investigated by the measurement of contact angles and zeta potential. Phospholipid charge, buffer pH and substrate hydrophilicity were proved to be essential for vesicle adsorption, rupture, fusion and formation of continuous lipid bilayers on the polyelectrolyte multilayers. The results clearly demonstrated that only the mixture of phosphatidylcholine and phosphatidic acid (4 : 1) resulted in fluid bilayers on chitosan and alginate multilayers with chitosan as a top layer at pH 6.5. A coarse-grained molecular simulation study elucidated that the exact mechanism of the formation of fluid lipid bilayers resembles a "parachute" model. As the closest model to the real membrane, polyelectrolyte multilayer-cushioned fluid lipid bilayers can be appropriate candidates for application in biomedical fields.

  11. PI3 kinase enzymology on fluid lipid bilayers.

    PubMed

    Dutta, Debjit; Pulsipher, Abigail; Luo, Wei; Yousaf, Muhammad N

    2014-10-21

    We report the use of fluid lipid bilayer membrane as a model platform to study the influence of the bilayer microenvironment and composition on the enzymology in membrane. As a model system we determined the enzyme kinetics on membranes for the transformation of bilayers containing phosphoinositol(4,5)-bisphosphate (PI(4,5)P2) to phosphoinositol(3,4,5)-trisphosphate (PI(3,4,5)P3) by the enzyme phosphoinositol-3-kinase (PI3K) using radiolabeled ATP. The activity of the enzyme was monitored as a function of the radioactivity incorporated within the bilayer. The transformation of PI(4,5)P2 to PI(3,4,5)P3 was determined using a mass strip assay. The fluidity of the bilayer was confirmed by Fluorescence Recovery After Photobleaching (FRAP) experiments. Kinetic simulations were performed based on Langmuir adsorption and Michaelis-Menton kinetics equations to generate the rate constants for the enzymatic reaction. The effect of cholesterol on the enzyme kinetics was studied by doping the bilayer with 1% cholesterol. This leads to significant reduction in reaction rate due to change in membrane microenvironment. This strategy provides a method to study the enzymology of various kinases and phosphatases occurring at the membrane and also how these reactions are affected by the membrane composition and surface microenvironment.

  12. Controlling the Electronic Structure of Bilayer Graphene

    NASA Astrophysics Data System (ADS)

    Ohta, Taisuke; Bostwick, Aaron; Seyller, Thomas; Horn, Karsten; Rotenberg, Eli

    2006-08-01

    We describe the synthesis of bilayer graphene thin films deposited on insulating silicon carbide and report the characterization of their electronic band structure using angle-resolved photoemission. By selectively adjusting the carrier concentration in each layer, changes in the Coulomb potential led to control of the gap between valence and conduction bands. This control over the band structure suggests the potential application of bilayer graphene to switching functions in atomic-scale electronic devices.

  13. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension.

    PubMed

    Sonne, Jacob; Jensen, Morten Ø; Hansen, Flemming Y; Hemmingsen, Lars; Peters, Günther H

    2007-06-15

    Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.

  14. Fluid Phase Lipid Areas and Bilayer Thicknesses of Commonly Used Phosphatidylcholines as a Function of Temperature

    SciTech Connect

    Kucerka, Norbert; Nieh, Mu-Ping; Katsaras, John

    2011-01-01

    The structural parameters of fluid phase bilayers composed of phosphatidylcholines with fully saturated, mixed, and branched fatty acid chains, at several temperatures, have been determined by simultaneously analyzing small-angle neutron and X-ray scattering data. Bilayer parameters, such as area per lipid and overall bilayer thickness have been obtained in conjunction with intrabilayer structural parameters (e.g. hydrocarbon region thickness). The results have allowed us to assess the effect of temperature and hydrocarbon chain composition on bilayer structure. For example, we found that for all lipids there is, not surprisingly, an increase in fatty acid chain trans-gauche isomerization with increasing temperature. Moreover, this increase in trans-gauche isomerization scales with fatty acid chain length in mixed chain lipids. However, in the case of lipids with saturated fatty acid chains, trans-gauche isomerization is increasingly tempered by attractive chain-chain van der Waals interactions with increasing chain length. Finally, our results confirm a strong dependence of lipid chain dynamics as a function of double bond position along fatty acid chains.

  15. Membrane fusion promoters and inhibitors have contrasting effects on lipid bilayer structure and undulations.

    PubMed Central

    McIntosh, T J; Kulkarni, K G; Simon, S A

    1999-01-01

    It has been established that the fusion of both biological membranes and phospholipid bilayers can be modulated by altering their lipid composition (Chernomordik et al., 1995 .J. Membr. Biol. 146:3). In particular, when added exogenously between apposing membranes, monomyristoylphosphatidylcholine (MMPC) inhibits membrane fusion, whereas glycerol monoleate (GMO), oleic acid (OA), and arachidonic acid (AA) promote fusion. This present study uses x-ray diffraction to investigate the effects of MMPC, GMO, OA, and AA on the bending and stability of lipid bilayers when bilayers are forced together with applied osmotic pressure. The addition of 10 and 30 mol% MMPC to egg phosphatidylcholine (EPC) bilayers maintains the bilayer structure, even when the interbilayer fluid spacing is reduced to approximately 3 A, and increases the repulsive pressure between bilayers so that the fluid spacing in excess water increases by 5 and 15 A, respectively. Thus MMPC increases the undulation pressure, implying that the addition of MMPC promotes out-of-plane bending and decreases the adhesion energy between bilayers. In contrast, the addition of GMO has minor effects on the undulation pressure; 10 and 50 mol% GMO increase the fluid spacing of EPC in excess water by 0 and 2 A, respectively. However, x-ray diffraction indicates that, at small interbilayer separations, GMO, OA, or AA converts the bilayer to a structure containing hexagonally packed scattering units approximately 50 A in diameter. Thus GMO, OA, or AA destabilizes bilayer structure as apposing bilayers are brought into contact, which could contribute to their role in promoting membrane fusion. PMID:10096904

  16. Structure of twisted and buckled bilayer graphene

    NASA Astrophysics Data System (ADS)

    Jain, Sandeep K.; Juričić, Vladimir; Barkema, Gerard T.

    2017-03-01

    We study the atomic structure of twisted bilayer graphene, with very small mismatch angles (θ ∼ {0.28}0), a topic of intense recent interest. We use simulations, in which we combine a recently presented semi-empirical potential for single-layer graphene, with a new term for out-of-plane deformations, (Jain et al 2015 J. Phys. Chem. C 119 9646) and an often-used interlayer potential (Kolmogorov et al 2005 Phys. Rev. B 71 235415). This combination of potentials is computationally cheap but accurate and precise at the same time, allowing us to study very large samples, which is necessary to reach very small mismatch angles in periodic samples. By performing large scale atomistic simulations, we show that the vortices appearing in the Moiré pattern in the twisted bilayer graphene samples converge to a constant size in the thermodynamic limit. Furthermore, the well known sinusoidal behavior of energy no longer persists once the misorientation angle becomes very small (θ \\lt {1}0). We also show that there is a significant buckling after the relaxation in the samples, with the buckling height proportional to the system size. These structural properties have direct consequences on the electronic and optical properties of bilayer graphene.

  17. The effect of bilayer composition on calcium ion transport facilitated by fluid shear stress.

    PubMed

    Giorgio, T D; Yek, S H

    1995-10-04

    Passive calcium ion permeability across liposome bilayers is increased during exposure to fluid shear forces attainable in the mammalian vasculature. In this study, liposomes prepared from three different lipid mixtures (phosphatidylcholine alone; phosphatidylcholine and cholesterol; a mixture of anionic and cationic phospholipids plus cholesterol) are exposed to uniform shear stress in a rotational viscometer. Liposome permeability to calcium ion is estimated from continuous measurement of free intraliposome calcium ion concentration using a fluorescence technique. Calcium ion permeability in the absence of fluid force and susceptibility to shear-induced permeability modulation are positively correlated with estimated bilayer compressibility. Fluid shear forces are presumed to influence bilayer packing and modulate defect formation in proportion to bilayer compressibility. Bilayer defects produced by fluid forces may increase liposome permeability.

  18. Relaxation dynamics of a compressible bilayer vesicle containing highly viscous fluid.

    PubMed

    Sachin Krishnan, T V; Okamoto, Ryuichi; Komura, Shigeyuki

    2016-12-01

    We study the relaxation dynamics of a compressible bilayer vesicle with an asymmetry in the viscosity of the inner and outer fluid medium. First we explore the stability of the vesicle free energy which includes a coupling between the membrane curvature and the local density difference between the two monolayers. Two types of instabilities are identified: a small wavelength instability and a larger wavelength instability. Considering the bulk fluid viscosity and the inter-monolayer friction as the dissipation sources, we next employ Onsager's variational principle to derive the coupled equations both for the membrane and the bulk fluid. The three relaxation modes are coupled to each other due to the bilayer and the spherical structure of the vesicle. Most importantly, a higher fluid viscosity inside the vesicle shifts the crossover mode between the bending and the slipping to a larger value. As the vesicle parameters approach the unstable regions, the relaxation dynamics is dramatically slowed down, and the corresponding mode structure changes significantly. In some limiting cases, our general result reduces to the previously obtained relaxation rates.

  19. Relaxation dynamics of a compressible bilayer vesicle containing highly viscous fluid

    NASA Astrophysics Data System (ADS)

    Sachin Krishnan, T. V.; Okamoto, Ryuichi; Komura, Shigeyuki

    2016-12-01

    We study the relaxation dynamics of a compressible bilayer vesicle with an asymmetry in the viscosity of the inner and outer fluid medium. First we explore the stability of the vesicle free energy which includes a coupling between the membrane curvature and the local density difference between the two monolayers. Two types of instabilities are identified: a small wavelength instability and a larger wavelength instability. Considering the bulk fluid viscosity and the inter-monolayer friction as the dissipation sources, we next employ Onsager's variational principle to derive the coupled equations both for the membrane and the bulk fluid. The three relaxation modes are coupled to each other due to the bilayer and the spherical structure of the vesicle. Most importantly, a higher fluid viscosity inside the vesicle shifts the crossover mode between the bending and the slipping to a larger value. As the vesicle parameters approach the unstable regions, the relaxation dynamics is dramatically slowed down, and the corresponding mode structure changes significantly. In some limiting cases, our general result reduces to the previously obtained relaxation rates.

  20. Controlling the Electronic Structure of Bilayer Graphene

    NASA Astrophysics Data System (ADS)

    Ohta, Taisuke; Bostwick, Aaron; McChesney, Jessica; Seyller, Thomas; Horn, Karsten; Rotenberg, Eli

    2007-03-01

    Carbon-based materials such as carbon nanotubes, graphite intercalation compounds, fullerenes, and ultrathin graphite films exhibit many exotic phenomena such as superconductivity and an anomalous quantum Hall effect. These findings have caused renewed interest in the electronic structure of ultrathin layers of graphene: a single honeycomb carbon layer that is the building block for these materials. There is a strong motivation to incorporate graphene multilayers into atomic-scale devices, spurred on by rapid progress in their fabrication and manipulation. We have synthesized bilayer graphene thin films deposited on insulating silicon carbide and characterized their electronic band structure using angle-resolved photoemission. By selectively adjusting the carrier concentration in each layer, changes in the Coulomb potential led to control of the gap between valence and conduction bands [1]. This control over the band structure suggests the potential application of bilayer graphene to switching functions in atomic scale electronic devices. [1] T. Ohta, A. Bostwick, T. Seyller, K. Horn, E. Rotenberg, Science, 313, 951 (2006).

  1. Acyl chain composition and coexisting fluid phases in lipid bilayers

    NASA Astrophysics Data System (ADS)

    Gu, Yongwen; Bradley, Miranda; Mitchell, Drake

    2011-10-01

    At room temperature phospholipid bilayers enriched in sphingolipids and cholesterol may form a solid phase as well as two coexisting fluid phases. These are the standard fluid phase, or the liquid-disordered phase, ld, and the liquid-ordered phase, lo, which is commonly associated with lipid rafts. Ternary mixtures of palmitoyl-oleoyl-phosphocholine (POPC; 16:0,18:1 PC), sphingomyelin (SPM), and cholesterol (Chol) form coexisting lo, ld and solid phases over a wide range of molar ratios. We are examining the ability of two fluorescent probes to detect these 2 phases: NBD linked to di-16:0 PE which partitions strongly into the lo phase and NBD linked to di-18:1 PE which partitions strongly into the ld phase. We are also examining the effect of the highly polyunsaturated phospholipid stearoyl-docosahexanoyl-phosphocholine (SDPC; 18:0, 22:6 PC) on the ternary phase diagram of POPC/SPM/Chol with particular focus on the functionally important lo/ld coexistence region. We report on the fluorescence lifetime and anisotropy decay dynamics of these two fluorescent probes.

  2. Structure of Sphingomyelin Bilayers: A Simulation Study

    PubMed Central

    Chiu, S. W.; Vasudevan, S.; Jakobsson, Eric; Mashl, R. Jay; Scott, H. Larry

    2003-01-01

    We have carried out a molecular dynamics simulation of a hydrated 18:0 sphingomyelin lipid bilayer. The bilayer contained 1600 sphingomyelin (SM) molecules, and 50,592 water molecules. After construction and initial equilibration, the simulation was run for 3.8 ns at a constant temperature of 50°C and a constant pressure of 1 atm. We present properties of the bilayer calculated from the simulation, and compare with experimental data and with properties of dipalmitoyl phosphatidylcholine (DPPC) bilayers. The SM bilayers are significantly more ordered and compact than DPPC bilayers at the same temperature. SM bilayers also exhibit significant intramolecular hydrogen bonding between phosphate ester oxygen and hydroxyl hydrogen atoms. This results in a decreased hydration in the polar region of the SM bilayer compared with DPPC. Since our simulation system is very large we have calculated the power spectrum of bilayer undulation and peristaltic modes, and we compare these data with similar calculations for DPPC bilayers. We find that the SM bilayer has significantly larger bending modulus and area compressibility compared to DPPC. PMID:14645055

  3. Structure of sphingomyelin bilayers and complexes with cholesterol forming membrane rafts.

    PubMed

    Quinn, Peter J

    2013-07-30

    Sphingomyelin and cholesterol are of interest to biologists because they interact to form condensed structures said to be responsible for a variety of functions that membranes perform. Synchrotron X-ray diffraction methods have been used to investigate the structure of bilayers of D-erythro palmitoyl-sphingomyelin and complexes formed by palmitoyl- and egg-sphingomyelin with cholesterol in aqueous multibilayer dispersions. D-erythro palmitoyl sphingomyelin bilayers exist in two conformers that are distinguished by their lamellar repeat spacing, bilayer thickness, and polar group hydration. The distinction is attributed to hydrogen bonding to water or to intermolecular hydrogen bonds that are disrupted by the formation of ripple structure. The coexisting bilayer structures of pure palmitoyl sphingomyelin are observed in the presence of cholesterol-rich bilayers that are characterized by different bilayer parameters. The presence of cholesterol preferentially affects the conformer of D-erythro sphingomyelin with thicker, more hydrated bilayers. Coexisting bilayers of sphingomyelin and complexes with cholesterol are in register and remain coupled at temperatures at least up to 50 °C. Cholesterol forms a complex of 1.8 mols of sphingomyelin per cholesterol at 37 °C that coexists with bilayers of pure sphingomyelin up to 50 °C. Redistribution of the two lipids takes place on cooling below the fluid- to gel-phase transition temperature, resulting in the withdrawal of sphingomyelin into gel phase and the formation of coexisting bilayers of equimolar proportions of the two lipids. Cholesterol-rich bilayers fit a stripe model at temperatures less than 37 °C characterized by alternating rows of sphingomyelin and cholesterol molecules. A quasicrystalline array models the arrangement at higher temperatures in which each cholesterol molecule is surrounded by seven hydrocarbon chains, each of which is in contact with two cholesterol molecules. The thickness of bilayer

  4. Polyoxometalate (POM) Nanocluster-Induced Phase Transition and Structural Disruption in Lipid Bilayers.

    NASA Astrophysics Data System (ADS)

    Jing, Benxin; Zhu, Y. Elaine; Hutin, Marie; Cronin, Leroy

    2012-02-01

    Polyoxometalate (POM) nanoclusters that are transition metal oxygen clusters with well defined atomic coordination structures have recently emerged as new and functional nanocolloidal materials used as catalysts, anti-cancer medicines, and building blocks for novel functional materials. However, their implications to human health and environment remain poorly investigated. In this work, we examine the interaction of highly charged anionic POM nanocluters with lipid bilayers as a model cell membrane system. It is observed that upon the adsorption of anionic POMs, lipid dynamics is significantly suppressed and lipid bilayers are disrupted with resultant pore and budding-like structural formation. Direct calorimetric experiment of POM interaction with lipid bilayers of varied lipid compositions confirms the POM-induced fluid-to-gel phase transition in lipid bilayers, due to strong electrostatic interaction between POM nanocluster and lipid head groups.

  5. Structural studies of mixed lipid bilayers on solid substrates using x-ray reflectivity

    NASA Astrophysics Data System (ADS)

    Chen, Gang; Mukhopadhyay, Mrinmay; Ma, Yicong; Sinha, Sunil; Jiang, Zhang; Decaro, Curt; Berry, Justin; Lurio, Laurence; Brozell, Adrian; Parikh, Atul

    2009-03-01

    The lipid bilayers of natural membranes generally exist in a fluid state which occurs above the gel to liquid crystalline phase transition temperature. Knowledge of the structure of such bilayers is important for understanding fundamental biological processes mediated by or occurring within membranes. We have performed systematic measurements on bilayers of 1,2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine (DPPE) and its mixture with 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) and cholesterol (CH) on silicon substrates with x-ray reflectivity both below and above their phase transition temperatures. Structural variations as a function of temperature are demonstrated by fitting the reflectivity data with both a model dependent and a model independent routine. Studies of Au nanoparticle labeled DOPC and DOPC + DPPE + CH mixture are also performed and the location of Au nanoparticles in these bilayers is established by analyzing the x-ray reflectivity data.

  6. The effect of temperature on supported dipalmitoylphosphatidylcholine (DPPC) bilayers: structure and lubrication performance.

    PubMed

    Wang, Min; Zander, Thomas; Liu, Xiaoyan; Liu, Chao; Raj, Akanksha; Wieland, D C Florian; Garamus, Vasil M; Willumeit-Römer, Regine; Claesson, Per Martin; Dėdinaitė, Andra

    2015-05-01

    Phospholipids fulfill an important role in joint lubrication. They, together with hyaluronan and glycoproteins, are the biolubricants that sustain low friction between cartilage surfaces bathed in synovial fluid. In this work we have investigated how the friction force and load bearing capacity of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers on silica surfaces are affected by temperature, covering the temperature range 25-52°C. Friction forces have been determined utilizing the AFM colloidal probe technique, which showed that DPPC bilayers are able to provide low friction forces over the whole temperature interval. However, the load bearing capacity is improved at higher temperatures. We interpret this finding as being a consequence of lower rigidity and higher self-healing capacity of the DPPC bilayer in the liquid disordered state compared to the gel state. The corresponding structure of solid supported DPPC bilayers at the silica-liquid interface has been followed using X-ray reflectivity measurements, which suggests that the DPPC bilayer is in the gel phase at 25°C and 39°C and in the liquid disordered state at 55°C. Well-defined bilayer structures were observed for both phases. The deposited DPPC bilayers were also imaged using AFM PeakForce Tapping mode, and these measurements indicated a less homogeneous layer at temperatures below 37°C.

  7. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  8. Band structure mapping of bilayer graphene via quasiparticle scattering

    NASA Astrophysics Data System (ADS)

    Yankowitz, Matthew; Wang, Joel I.-Jan; Li, Suchun; Birdwell, A. Glen; Chen, Yu-An; Watanabe, Kenji; Taniguchi, Takashi; Quek, Su Ying; Jarillo-Herrero, Pablo; LeRoy, Brian J.

    2014-09-01

    A perpendicular electric field breaks the layer symmetry of Bernal-stacked bilayer graphene, resulting in the opening of a band gap and a modification of the effective mass of the charge carriers. Using scanning tunneling microscopy and spectroscopy, we examine standing waves in the local density of states of bilayer graphene formed by scattering from a bilayer/trilayer boundary. The quasiparticle interference properties are controlled by the bilayer graphene band structure, allowing a direct local probe of the evolution of the band structure of bilayer graphene as a function of electric field. We extract the Slonczewski-Weiss-McClure model tight binding parameters as γ0 = 3.1 eV, γ1 = 0.39 eV, and γ4 = 0.22 eV.

  9. Ethanol effects on binary and ternary supported lipid bilayers with gel/fluid domains and lipid rafts.

    PubMed

    Marquês, Joaquim T; Viana, Ana S; De Almeida, Rodrigo F M

    2011-01-01

    Ethanol-lipid bilayer interactions have been a recurrent theme in membrane biophysics, due to their contribution to the understanding of membrane structure and dynamics. The main purpose of this study was to assess the interplay between membrane lateral heterogeneity and ethanol effects. This was achieved by in situ atomic force microscopy, following the changes induced by sequential ethanol additions on supported lipid bilayers formed in the absence of alcohol. Binary phospholipid mixtures with a single gel phase, dipalmitoylphosphatidylcholine (DPPC)/cholesterol, gel/fluid phase coexistence DPPC/dioleoylphosphatidylcholine (DOPC), and ternary lipid mixtures containing cholesterol, mimicking lipid rafts (DOPC/DPPC/cholesterol and DOPC/sphingomyelin/cholesterol), i.e., with liquid ordered/liquid disordered (ld/lo) phase separation, were investigated. For all compositions studied, and in two different solid supports, mica and silicon, domain formation or rearrangement accompanied by lipid bilayer thinning and expansion was observed. In the case of gel/fluid coexistence, low ethanol concentrations lead to a marked thinning of the fluid but not of the gel domains. In the case of ld/lo all the bilayer thins simultaneously by a similar extent. In both cases, only the more disordered phase expanded significantly, indicating that ethanol increases the proportion of disordered domains. Water/bilayer interfacial tension variation and freezing point depression, inducing acyl chain disordering (including opening and looping), tilting, and interdigitation, are probably the main cause for the observed changes. The results presented herein demonstrate that ethanol influences the bilayer properties according to membrane lateral organization.

  10. Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics.

    PubMed

    Boughter, Christopher T; Monje-Galvan, Viviana; Im, Wonpil; Klauda, Jeffery B

    2016-11-17

    In this study, the influence of cholesterol on lipid bilayers is investigated by changing phospholipid headgroup, cholesterol concentration, chain saturation, and temperature. Molecular dynamics (MD) simulations were used to characterize bilayers containing phosphatidylcholine (PC) head groups with either fully saturated dimyristoyl (DM) or monounsaturated dioleoyl (DO) acyl chains and cholesterol concentrations ranging from 5 to 50%. To further explore the effects of cholesterol on bilayers with different head groups, we also performed MD simulations of bilayer systems having 15% cholesterol with phosphatidic acid (PA), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidylserine (PS), each having DM chains and at a temperature above the solid gel phase transition. Additionally, bilayers of DMPA, DMPE, and DMPS with 15% cholesterol were simulated at temperatures below the solid gel phase transition temperatures. Compared to membranes without cholesterol, cholesterol in the model bilayers increases chain order in bilayers with the highest order in the liquid ordered and solid gel phases. Head group properties and acyl chain saturation are also found to critically impact bilayer dynamics, largely through the formation of hydrogen bonds between membrane components. These results provide a better understanding of the basic characteristics on structure and dynamics of cholesterol-containing membranes by revealing molecular details of interactions between cholesterol and phospholipids as well as add to the library of simulation data necessary for the MD community to accurately represent relevant models of atomic-scale systems.

  11. Cyclic and Linear Monoterpenes in Phospholipid Membranes: Phase Behavior, Bilayer Structure, and Molecular Dynamics.

    PubMed

    Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

    2015-10-13

    Monoterpenes are abundant in essential oils extracted from plants. These relatively small and hydrophobic molecules have shown important biological functions, including antimicrobial activity and membrane penetration enhancement. The interaction between the monoterpenes and lipid bilayers is considered important to the understanding of the biological functions of monoterpenes. In this study, we investigated the effect of cyclic and linear monoterpenes on the structure and dynamics of lipids in model membranes. We have studied the ternary system 1,2-dimyristoyl-sn-glycero-3-phosphocholine-monoterpene-water as a model with a focus on dehydrated conditions. By combining complementary techniques, including differential scanning calorimetry, solid-state nuclear magnetic resonance, and small- and wide-angle X-ray scattering, bilayer structure, phase transitions, and lipid molecular dynamics were investigated at different water contents. Monoterpenes cause pronounced melting point depression and phase segregation in lipid bilayers, and the extent of these effects depends on the hydration conditions. The addition of a small amount of thymol to the fluid bilayer (volume fraction of 0.03 in the bilayer) leads to an increased order in the acyl chain close to the bilayer interface. The findings are discussed in relation to biological systems and lipid formulations.

  12. Structural and electronic properties of bilayer and trilayer graphdiyne

    NASA Astrophysics Data System (ADS)

    Zheng, Qiye; Luo, Guangfu; Liu, Qihang; Quhe, Ruge; Zheng, Jiaxin; Tang, Kechao; Gao, Zhengxiang; Nagase, Shigeru; Lu, Jing

    2012-06-01

    Stimulated by the recent experimental synthesis of a new layered carbon allotrope-graphdiyne film, we provide the first systematic ab initio investigation of the structural and electronic properties of bilayer and trilayer graphdiyne and explore the possibility of tuning the energy gap via a homogeneous perpendicular electric field. Our results show that the most stable bilayer and trilayer graphdiyne both have their hexagonal carbon rings stacked in a Bernal way (AB and ABA style configuration, respectively). Bilayer graphdiyne with the most and the second most stable stacking arrangements have direct bandgaps of 0.35 eV and 0.14 eV, respectively; trilayer graphdiyne with stable stacking styles have bandgaps of 0.18-0.33 eV. The bandgaps of the semiconducting bilayer and trilayer graphdiyne generally decrease with increasing external vertical electric field, irrespective of the stacking style. Therefore, the possibility of tuning the electronic structure and optical absorption of bilayer and trilayer graphdiyne with an external electric field is suggested.Stimulated by the recent experimental synthesis of a new layered carbon allotrope-graphdiyne film, we provide the first systematic ab initio investigation of the structural and electronic properties of bilayer and trilayer graphdiyne and explore the possibility of tuning the energy gap via a homogeneous perpendicular electric field. Our results show that the most stable bilayer and trilayer graphdiyne both have their hexagonal carbon rings stacked in a Bernal way (AB and ABA style configuration, respectively). Bilayer graphdiyne with the most and the second most stable stacking arrangements have direct bandgaps of 0.35 eV and 0.14 eV, respectively; trilayer graphdiyne with stable stacking styles have bandgaps of 0.18-0.33 eV. The bandgaps of the semiconducting bilayer and trilayer graphdiyne generally decrease with increasing external vertical electric field, irrespective of the stacking style. Therefore, the

  13. Effect of intra-membrane C60 fullerenes on the modulus of elasticity and the mechanical resistance of gel and fluid lipid bilayers

    NASA Astrophysics Data System (ADS)

    Zhou, Jihan; Liang, Dehai; Contera, Sonia

    2015-10-01

    Penetration and partition of C60 to the lipid bilayer core are both relevant to C60 toxicity, and useful to realise C60 biomedical potential. A key aspect is the effect of C60 on bilayer mechanical properties. Here, we present an experimental study on the mechanical effect of the incorporation of C60 into the hydrophobic core of fluid and gel phase zwitterionic phosphatidylcholine (PC) lipid bilayers. We demonstrate its incorporation inside the hydrophobic lipid core and the effect on the packing of the lipids and the vesicle size using a combination of infrared (IR) spectroscopy, atomic force microscopy (AFM) and laser light scattering. Using AFM we measured the Young's modulus of elasticity (E) of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in the absence (presence) of intra-membranous C60 at 24.5 °C. E of fluid phase supported bilayers is not altered by C60, but E increases with incorporation of C60 in gel phase bilayers. The increase is higher for longer hydrocarbon chains: 1.6 times for DPPC and 2 times for DSPC. However the mechanical resistance of gel phase bilayers of curved bilayered structures decreases with the incorporation of C60. Our combined results indicate that C60 causes a decrease in gel phase lipid mobility, i.e. an increase in membrane viscosity.

  14. Tethered and Polymer Supported Bilayer Lipid Membranes: Structure and Function

    PubMed Central

    Andersson, Jakob; Köper, Ingo

    2016-01-01

    Solid supported bilayer lipid membranes are model systems to mimic natural cell membranes in order to understand structural and functional properties of such systems. The use of a model system allows for the use of a wide variety of analytical tools including atomic force microscopy, impedance spectroscopy, neutron reflectometry, and surface plasmon resonance spectroscopy. Among the large number of different types of model membranes polymer-supported and tethered lipid bilayers have been shown to be versatile and useful systems. Both systems consist of a lipid bilayer, which is de-coupled from an underlying support by a spacer cushion. Both systems will be reviewed, with an emphasis on the effect that the spacer moiety has on the bilayer properties. PMID:27249006

  15. Structure and Thermotropic phase Behavior of Fluorinated Phospholipid Bilayers: A combined Attenuated Total Reflection FTIR Spectroscopy and Imaging Ellipsometry Study

    PubMed Central

    Schuy, Steffen; Faiss, Simon; Yoder, Nicholas C.; Kalsani, Venkateshwarlu; Kumar, Krishna; Janshoff, Andreas; Vogel, Reiner

    2008-01-01

    Lipid bilayers consisting of lipids with terminally perfluoroalkylated chains have remarkable properties. They exhibit increased stability and phase-separated nanoscale patterns in mixtures with nonfluorinated lipids. In order to understand the bilayer properties that are responsible for this behavior, we have analyzed the structure of solid-supported bilayers composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and of a DPPC analogue with 6 terminal perfluorinated methylene units (F6-DPPC). Polarized attenuated total reflection Fourier-transform infrared spectroscopy indicates that for F6-DPPC, the tilt of the lipid acyl chains to the bilayer normal is increased to 39° as compared to 21° for native DPPC, for both lipids in the gel phase. This substantial increase of the tilt angle is responsible for a decrease of the bilayer thickness from 5.4 nm for DPPC to 4.5 nm for F6-DPPC, as revealed by temperature-controlled imaging ellipsometry on microstructured lipid bilayers and solution atomic force microscopy. During the main phase transition from the gel to the fluid phase, both the relative bilayer thickness change and the relative area change are substantially smaller for F6-DPPC than for DPPC. In light of these structural and thermotropic data, we propose a model in which the higher acyl-chain tilt angle in F6-DPPC is the result of a conformational rearrangement to minimize unfavorable fluorocarbon–hydrocarbon interactions in the center of the bilayer due to chain staggering. PMID:18563929

  16. Fluid structure interaction

    NASA Astrophysics Data System (ADS)

    Komatsu, K.

    A few nonflow field problems are considered, taking into account mainly fluid-shell dynamic interaction and fluid-solid impact. Fluid-shell systems are used as models for sloshing and POGO (structure-propulsion coupling oscillation) in liquid rockets, floating lids of oil tanks, large tanks containing fluid, nuclear containment vessels, and head injury studies in biomechanics. The study of structure-water impact finds applications in the problems associated with water landings of reentry vehicles, water entry of torpedoes, and slamming of ships in heavy seas. At least three different methods can be used in handling wet structures. Attention is given to the method which treats fluid by boundary elements and structure by finite elements.

  17. Hierarchically structured porous cadmium selenide polycrystals using polystyrene bilayer templates.

    PubMed

    Park, Jin Young; Hendricks, Nicholas R; Carter, Kenneth R

    2012-09-18

    In this study, a novel approach is demonstrated to fabricate hierarchically structured cadmium selenide (CdSe) layers with size-tunable nano/microporous morphologies achieved using polystyrene (PS) bilayered templates (top layer: colloidal template) via potentiostatic electrochemical deposition. The PS bilayer template is made in two steps. First, various PS patterns (stripes, ellipsoids, and circles) are prepared as the bottom layers through imprint lithography. In a second step, a top template is deposited that consists of a self-assembled layer of colloidal 2D packed PS particles. Electrochemical growth of CdSe crystals in the voids and selective removal of the PS bilayered templates give rise to hierarchically patterned 2D hexagonal porous CdSe structures. This simple and facile technique provides various unconventional porous CdSe films, arising from the effect of the PS bottom templates.

  18. Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations.

    PubMed

    Prates Ramalho, J P; Gkeka, P; Sarkisov, L

    2011-04-05

    In this article, we investigate fluid-gel transformations of a DPPC lipid bilayer in the presence of nanoparticles, using coarse-grained molecular dynamics. Two types of nanoparticles are considered, specifically a 3 nm hydrophobic nanoparticle located in the core of the bilayer and a 6 nm charged nanoparticle located at the interface between the bilayer and water phase. Both negatively and positively charged nanoparticles at the bilayer interface are investigated. We demonstrate that the presence of all types of nanoparticles induces disorder effects in the structure of the lipid bilayer. These effects are characterized using computer visualization of the gel phase in the presence of nanoparticles, radial distribution functions, and order parameters. The 3 nm hydrophobic nanoparticle immersed in the bilayer core and the positively charged nanoparticle at the bilayer surface have no effect on the temperature of the fluid-gel transformation, compared to the bulk case. Interestingly, a negatively charged hydrophobic nanoparticle located at the surface of the bilayer causes slight shift of the fluid-gel transformation to a lower temperature, compared to the bulk bilayer case.

  19. Electronic band structure of magnetic bilayer graphene superlattices

    SciTech Connect

    Pham, C. Huy; Nguyen, T. Thuong

    2014-09-28

    Electronic band structure of the bilayer graphene superlattices with δ-function magnetic barriers and zero average magnetic flux is studied within the four-band continuum model, using the transfer matrix method. The periodic magnetic potential effects on the zero-energy touching point between the lowest conduction and the highest valence minibands of pristine bilayer graphene are exactly analyzed. Magnetic potential is shown also to generate the finite-energy touching points between higher minibands at the edges of Brillouin zone. The positions of these points and the related dispersions are determined in the case of symmetric potentials.

  20. Exchange bias training effect in coupled all ferromagnetic bilayer structures.

    PubMed

    Binek, Ch; Polisetty, S; He, Xi; Berger, A

    2006-02-17

    Exchange coupled bilayers of soft and hard ferromagnetic thin films show remarkable analogies to conventional antiferromagnetic/ferromagnetic exchange bias heterostructures. Not only do all these ferromagnetic bilayers exhibit a tunable exchange bias effect, they also show a distinct training behavior upon cycling the soft layer through consecutive hysteresis loops. In contrast with conventional exchange bias systems, such all ferromagnetic bilayer structures allow the observation of training induced changes in the bias-setting hardmagnetic layer by means of simple magnetometry. Our experiments show unambiguously that the exchange bias training effect is driven by deviations from equilibrium in the pinning layer. A comparison of our experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  1. Exchange Bias Training Effect in Coupled All Ferromagnetic Bilayer Structures

    NASA Astrophysics Data System (ADS)

    Binek, Ch.; Polisetty, S.; He, Xi; Berger, A.

    2006-02-01

    Exchange coupled bilayers of soft and hard ferromagnetic thin films show remarkable analogies to conventional antiferromagnetic/ferromagnetic exchange bias heterostructures. Not only do all these ferromagnetic bilayers exhibit a tunable exchange bias effect, they also show a distinct training behavior upon cycling the soft layer through consecutive hysteresis loops. In contrast with conventional exchange bias systems, such all ferromagnetic bilayer structures allow the observation of training induced changes in the bias-setting hardmagnetic layer by means of simple magnetometry. Our experiments show unambiguously that the exchange bias training effect is driven by deviations from equilibrium in the pinning layer. A comparison of our experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  2. The Effects of Polyunsaturated Lipid Components on bilayer Structure

    NASA Astrophysics Data System (ADS)

    Pramudya, Y.; Kiss, A.; Nguyen, Lam T.; Yuan, J.; Hirst, Linda S.

    2007-03-01

    Polyunsaturated fatty acids (PUFAs), such as DHA (Docosahexanoic Acid) and AA (Alphalinoleic Acid) have been the focus of much research attention in recent years, due to their apparent health benefits and effects on cell physiology. They are found in a variety of biological membranes and have been implicated with lipid raft formation and possible function, particularly in the retinal rod cells and the central nervous system. In this work lipid bilayer structure has been investigated in lipid mixtures, incorporating polyunsaturated fatty acid moieties. The structural effects of increasing concentrations of both symmetric and asymmetric PUFA materials on the bilayer structure are investigated via synchrotron x-ray diffraction on solution samples. We observe bilayer spacings to increase with the percentage of unsaturated fatty acid lipid in the membrane, whilst the degree of ordering significantly decreases. In fact above 20% of fatty acid, well defined bilayers are no longer observed to form. Evidence of phase separation can be clearly seen from these x-ray results and in combination with AFM measurements.

  3. Structure and energetics of interlayer dislocations in bilayer graphene

    NASA Astrophysics Data System (ADS)

    Dai, Shuyang; Xiang, Yang; Srolovitz, David J.

    2016-02-01

    We present a general hybrid model based upon the continuum generalized Peierls-Nabarro model (with density functional theory parametrization) to describe interlayer dislocations in bilayer systems. In this model, the bilayer system is divided into two linear elastic 2D sheets. The strains in each sheet can be relaxed by both elastic in-plane deformation and out-of-plane buckling; this deformation is described via classical linear elastic thin plate theory. The interlayer bonding between these two sheets is described by a three-dimensional generalized stacking-fault energy (GSFE) determined from first principle calculations and based upon the relative displacement between the sheets. The structure and energetics of various interlayer dislocations in bilayer graphene was determined by minimizing the elastic and bonding energy with respect to all displacements. The dislocations break into partials, and pronounced buckling is observed at the partial dislocation locations to relax the strain induced by their edge components. The partial dislocation core width is reduced by buckling. An analytical model is also developed based upon the results obtained in numerical simulation. We develop an analytical model for the bilayer structure and energy and show that these predictions are in excellent agreement with the numerical results.

  4. Stacking-dependent electronic structure of bilayer silicene

    SciTech Connect

    Fu, Huixia; Zhang, Jin; Ding, Zijing; Li, Hui E-mail: smeng@iphy.ac.cn; Meng, Sheng E-mail: smeng@iphy.ac.cn

    2014-03-31

    Bilayer silicene (BLS) is a class of material that possibly holds both topological and superconducting properties; however, its structure is not fully understood. By scanning stacking modes and lattice constants using first principles calculations, several meta-stable configurations are identified, including a slightly faulted-AA packing structure, named slide-2AA. Different from the metallic properties of conventional AA and AB stacking forms, band structure of slide-2AA bilayer presents a sizeable indirect energy gap of ∼1.16 eV. A metal-semiconductor phase transition along the sliding pathway with a small energy barrier is also observed, indicating its electronic properties can be easily tuned by applying small shear force along the BLS surface plane. Such unique quantitative relationship of structure and electronic properties has profound implications in nanoelectronics and electromechanical devices.

  5. Stacking-dependent electronic structure of bilayer silicene

    NASA Astrophysics Data System (ADS)

    Fu, Huixia; Zhang, Jin; Ding, Zijing; Li, Hui; Meng, Sheng

    2014-03-01

    Bilayer silicene (BLS) is a class of material that possibly holds both topological and superconducting properties; however, its structure is not fully understood. By scanning stacking modes and lattice constants using first principles calculations, several meta-stable configurations are identified, including a slightly faulted-AA packing structure, named slide-2AA. Different from the metallic properties of conventional AA and AB stacking forms, band structure of slide-2AA bilayer presents a sizeable indirect energy gap of ˜1.16 eV. A metal-semiconductor phase transition along the sliding pathway with a small energy barrier is also observed, indicating its electronic properties can be easily tuned by applying small shear force along the BLS surface plane. Such unique quantitative relationship of structure and electronic properties has profound implications in nanoelectronics and electromechanical devices.

  6. Diffusive dynamics of vesicles tethered to a fluid supported bilayer by single-particle tracking.

    PubMed

    Yoshina-Ishii, Chiaki; Chan, Yee-Hung M; Johnson, Joseph M; Kung, Li A; Lenz, Peter; Boxer, Steven G

    2006-06-20

    We recently introduced a method to tether intact phospholipid vesicles onto a fluid supported lipid bilayer using DNA hybridization (Yoshina-Ishii, C.; Miller, G. P.; Kraft, M. L; Kool, E. T.; Boxer, S. G. J. Am. Chem. Soc. 2005, 127, 1356-1357). Once tethered, the vesicles can diffuse in two dimensions parallel to the supported membrane surface. The average diffusion coefficient, D, is typically 0.2 microm(2)/s; this is 3-5 times smaller than for individual lipid or DNA-lipid conjugate diffusion in supported bilayers. In this article, we investigate the origin of this difference in the diffusive dynamics of tethered vesicles by single-particle tracking under collision-free conditions. D is insensitive to tethered vesicle size from 30 to 200 nm, as well as a 3-fold change in the viscosity of the bulk medium. The addition of macromolecules such as poly(ethylene glycol) reversibly stops the motion of tethered vesicles without causing the exchange of lipids between the tethered vesicle and supported bilayer. This is explained as a depletion effect at the interface between tethered vesicles and the supported bilayer. Ca ions lead to transient vesicle-vesicle interactions when tethered vesicles contain negatively charged lipids, and vesicle diffusion is greatly reduced upon Ca ion addition when negatively charged lipids are present both in the supported bilayer and tethered vesicles. Both effects are interesting in their own right, and they also suggest that tethered vesicle-supported bilayer interactions are possible; this may be the origin of the reduction in D for tethered vesicles. In addition, the effects of surface defects that reversibly trap diffusing vesicles are modeled by Monte Carlo simulations. This shows that a significant reduction in D can be observed while maintaining normal diffusion behavior on the time scale of our experiments.

  7. The component group structure of DPPC bilayers obtained by specular neutron reflectometry.

    PubMed

    Belička, Michal; Gerelli, Yuri; Kučerka, Norbert; Fragneto, Giovanna

    2015-08-21

    Specular neutron reflectometry was measured on a floating bilayer system consisting of 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine deposited over a 1,2-dibehenoyl-sn-glycero-3-phosphocholine bilayer at 25 and 55 °C. The internal structure of lipid bilayers was described by a one-dimensional neutron scattering length density profile model, originally developed for the evaluation of small-angle scattering data. The reflectivity data from the supported bilayer were evaluated separately and used further as constraints in modeling the floating bilayer reflectivity curves. The model reflectivity curves successfully describe the experimental reflectivities of the supported bilayer in the gel phase and the floating bilayer system in the liquid-crystalline phase. The results yield an internal structure of a deposited bilayer and a floating bilayer on the level of component groups of lipid molecules. The obtained structure of the floating d62-diC16:0PC bilayer displays high resemblance of the bilayer structure in the form of unilamellar vesicles. At the same time, however, the results show differences in comparison to unilamellar vesicle bilayers, most likely due to the undulations of supported bilayers.

  8. Exchange bias training effect in coupled all ferromagnetic bilayer structures

    NASA Astrophysics Data System (ADS)

    Polisetty, Srinivas; He, Xi; Binek, Christian; Berger, Andreas

    2006-03-01

    We study exchange coupled bilayers of soft and hard ferromagnetic (FM) thin films by means of Alternating Gradient Force Magnetometry. A CoCr thin film realizes the magnetically soft layer (SL) which is exchange coupled via a Ru-interlayer with a hard CoPtCrB pinning layer (HL). This new class of all FM bilayers shows remarkable analogies to conventional antiferromagnetic (AF)/FM exchange bias (EB) heterostructures. Not only do these all FM bilayers exhibit a tunable EB effect, they also show a distinct training behavior upon cycling the SL through consecutive hysteresis loops. Training resembles the cycle dependent evolution of the bias field and is to a large extend analogous to the gradual degradation of the EB field observed upon cycling the FM top layer of a AF/FM EB heterostructure through consecutive hysteresis loops. However, in contrast to these conventional EB systems, our all FM bilayer structures allow the observation of training induced changes in the bias-setting HL by means of simple magnetometry. Our experiments show unambiguously that the training effect is driven by deviations from equilibrium in the pinning layer. A comparison of the experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  9. NMR Structures of Membrane Proteins in Phospholipid Bilayers

    PubMed Central

    Radoicic, Jasmina; Lu, George J.; Opella, Stanley J.

    2014-01-01

    Membrane proteins have always presented technical challenges for structural studies because of their requirement for a lipid environment. Multiple approaches exist including X-ray crystallography and electron microscopy that can give significant insights into their structure and function. However, nuclear magnetic resonance (NMR) is unique in that it offers the possibility of determining the structures of unmodified membrane proteins in their native environment of phospholipid bilayers under physiological conditions. Furthermore, NMR enables the characterization of the structure and dynamics of backbone and side chain sites of the proteins alone and in complexes with both small molecules and other biopolymers. The learning curve has been steep for the field as most initial studies were performed under non-native environments using modified proteins until ultimately progress in both techniques and instrumentation led to the possibility of examining unmodified membrane proteins in phospholipid bilayers under physiological conditions. This review aims to provide an overview of the development and application of NMR to membrane proteins. It highlights some of the most significant structural milestones that have been reached by NMR spectroscopy of membrane proteins; especially those accomplished with the proteins in phospholipid bilayer environments where they function. PMID:25032938

  10. Interaction of long-chain n-alcohols with fluid DOPC bilayers: a neutron diffraction study.

    PubMed

    Petrenko, Viktor I; Klacsova, Maria; Beskrovnyy, Anatoly I; Uhrikova, Daniela; Balgavy, Pavol

    2010-12-01

    Lamellar phases composed of fluid dioleoylphosphatidylcholine (DOPC) bilayers containing alkan-1-ols (CnOH, n = 8, 10, 14, 16, 18 is the number of carbon atoms) at CnOH : DOPC = 0.3 molar ratio and hydrated with heavy water at 20.2 ≥ D2O : DOPC ≥ 14.4 molar ratio were studied by neutron diffraction. The bilayer thickness d(L) and the bilayer surface area A(L) per DOPC at the bilayer-water interface were obtained from the lamellar repeat period d using molecular volumes of DOPC, CnOH and D2O, and the Luzatti's method. Both the d(L) and A(L) increase with the CnOH chain length n at CnOH : DOPC = 0.3 molar ratio: d(L) = (3.888 ± 0.066) + (0.016 ± 0.005)·n (in nm), A(L) = (0.6711 ± 0.0107) + (0.0012 ± 0.0008)·n (in nm²).

  11. 1H NMR Shows Slow Phospholipid Flip-Flop in Gel and Fluid Bilayers

    DOE PAGES

    Marquardt, Drew; Heberle, Frederick A.; Miti, Tatiana; ...

    2017-01-20

    We measured the transbilayer diffusion of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in large unilamellar vesicles, in both the gel (Lβ') and fluid (Lα) phases. The choline resonance of headgroup-protiated DPPC exchanged into the outer leaflet of headgroup-deuterated DPPC-d13 vesicles was monitored using 1H NMR spectroscopy, coupled with the addition of a paramagnetic shift reagent. This allowed us to distinguish between the inner and outer bilayer leaflet of DPPC, to determine the flip-flop rate as a function of temperature. Flip-flop of fluid-phase DPPC exhibited Arrhenius kinetics, from which we determined an activation energy of 122 kJ mol–1. In gel-phase DPPC vesicles, flip-flop was notmore » observed over the course of 250 h. Here, our findings are in contrast to previous studies of solid-supported bilayers, where the reported DPPC translocation rates are at least several orders of magnitude faster than those in vesicles at corresponding temperatures. Finally, we reconcile these differences by proposing a defect-mediated acceleration of lipid translocation in supported bilayers, where long-lived, submicron-sized holes resulting from incomplete surface coverage are the sites of rapid transbilayer movement.« less

  12. Superlattice structures in twisted bilayers of folded graphene

    NASA Astrophysics Data System (ADS)

    Schmidt, Hennrik; Rode, Johannes C.; Smirnov, Dmitri; Haug, Rolf J.

    2014-12-01

    The electronic properties of bilayer graphene strongly depend on relative orientation of the two atomic lattices. Whereas Bernal-stacked graphene is most commonly studied, a rotational mismatch between layers opens up a whole new field of rich physics, especially at small interlayer twist. Here we report on magnetotransport measurements on twisted graphene bilayers, prepared by folding of single layers. These reveal a strong dependence on the twist angle, which can be estimated by means of sample geometry. At small rotation, superlattices with a wavelength in the order of 10 nm arise and are observed by friction atomic force microscopy. Magnetotransport measurements in this small-angle regime show the formation of satellite Landau fans. These are attributed to additional Dirac singularities in the band structure and discussed with respect to the wide range of interlayer coupling models.

  13. Metastability and polymorphism in the gel and fluid bilayer phases of dilauroylphosphatidylethanolamine. Two crystalline forms in excess water.

    PubMed

    Seddon, J M; Harlos, K; Marsh, D

    1983-03-25

    The phase behavior of 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) in excess water has been studied by differential scanning calorimetry and x-ray diffraction. In addition to the usual gel phase L beta of lamellar periodicity 5.07 nm and the fluid bilayer phase L alpha of periodicity 4.5 nm, two distinct crystalline forms may also be spontaneously adopted. The L beta phase is only produced by cooling from L alpha and is metastable, relaxing to one of the crystalline forms on incubation. One crystalline polymorph, designated beta 2, has a lamellar periodicity of 4.55 nm and corresponds to the structure of DLPE crystallized from a variety of organic solvents. The other crystalline polymorph, designated beta 1, has a lamellar periodicity of 3.78 nm, which implies that in this form the hydrocarbon chains are tilted at approximately 40 degrees to the bilayer normal. The beta 2 polymorph is obtained on dispersing crystalline DLPE directly in water at T less than 43 degrees C, on incubation in the L alpha phase at 30 degrees C less than T less than 43 degrees C, or on heating the beta 1 form slowly to T greater than 35 degrees C. The beta 1 polymorph is obtained on incubating the L beta phase at T less than 30 degrees C. By calorimetry, the L beta phase undergoes an endothermic transition (delta H = 15.5 kJ X mol-1 (3.7 kcal X mol-1)) at 30.6 degrees C to the fluid bilayer phase L alpha. The beta 1 phase undergoes an endothermic transition (delta H congruent to 50 kJ X mol-1 (12 kcal X mol-1)) to L alpha at 35 degrees C. The beta 2 phase undergoes an endothermic transition (delta H = 57 kJ X mol-1 (13.7 kcal X mol-1)) to L alpha at 43 degrees C.

  14. Reparameterized United Atom Model for Molecular Dynamics Simulations of Gel and Fluid Phosphatidylcholine Bilayers.

    PubMed

    Tjörnhammar, Richard; Edholm, Olle

    2014-12-09

    A new united atom parametrization of diacyl lipids like dipalmitoylphosphatidylcholine (DPPC) and the dimyristoylphosphatidylcholine (DMPC) has been constructed based on ab initio calculations to obtain fractional charges and the dihedral potential of the hydrocarbon chains, while the Lennard-Jones parameters of the acyl chains were fitted to reproduce the properties of liquid hydrocarbons. The results have been validated against published experimental X-ray and neutron scattering data for fluid and gel phase DPPC. The derived charges of the lipid phosphatidylcholine (PC) headgroup are shown to yield dipole components in the range suggested by experiments. The aim has been to construct a new force field that retains and improves the good agreement for the fluid phase and at the same time produces a gel phase at low temperatures, with properties coherent with experimental findings. The gel phase of diacyl-PC lipids forms a regular triangular lattice in the hydrocarbon region. The global bilayer tilt obtains an azimuthal value of 31° and is aligned between lattice vectors in the bilayer plane. We also show that the model yields a correct heat of melting as well as decent heat capacities in the fluid and gel phase of DPPC.

  15. Direct detection of the gel-fluid phase transition of a single supported phospholipid bilayer using quartz crystal microbalance with dissipation monitoring.

    PubMed

    Wargenau, Andreas; Tufenkji, Nathalie

    2014-08-19

    Supported phospholipid bilayers (SPBs) are valuable models for fundamental studies of biological membranes and their interaction with biologically relevant solutes or particles. Herein, we demonstrate the capability of the quartz crystal microbalance with dissipation monitoring (QCM-D) to directly detect the gel-fluid phase transition of a SPB. The approach involves comparison of the frequency response of a bare and a bilayer-coated QCM-D crystal during linear temperature variation. Phase transition results in a change of the resonance frequency that coincides directly with the accompanied change in bilayer thickness detected by ellipsometry. Experiments performed at different heating rates further demonstrate the use of dissipation monitoring to determine the phase transition temperature based on the temperature-induced viscosity changes of the ambient medium in the immediate environment of the bilayer. Unlike other methods, the proposed approach enables precise determination of the phase transition of a SPB without the need for thermal equilibration of the measurement chamber and, thus, has great potential for sensitive detection of structural and/or compositional changes of the bilayer.

  16. Periodic barrier structure in AA-stacked bilayer graphene

    NASA Astrophysics Data System (ADS)

    Redouani, Ilham; Jellal, Ahmed

    2016-06-01

    We study the charge carriers transport in an AA-stacked bilayer graphene modulated by a lateral one-dimensional multibarrier structure. We investigate the band structures of our system, that is made up of two shifted Dirac cones, for finite and zero gap. We use the boundary conditions to explicitly determine the transmission probability of each individual cone (τ =+/- 1) for single, double and finite periodic barrier structure. We find that the Klein tunneling is only possible when the band structure is gapless and can occur at normal incidence as a result of the Dirac nature of the quasiparticles. We observe that the band structure of the barriers can have more than one Dirac points for finite periodic barrier. The resonance peaks appear in the transmission probability, which correspond to the positions of new cones index like associated with τ =+/- 1. Two conductance channels through different cones (τ =+/- 1) are found where the total conductance has been studied and compared to the cases of single layer and AB-stacked bilayer graphene.

  17. Assessment of pseudo-bilayer structures in the heterogate germanium electron-hole bilayer tunnel field-effect transistor

    SciTech Connect

    Padilla, J. L. Alper, C.; Ionescu, A. M.; Medina-Bailón, C.; Gámiz, F.

    2015-06-29

    We investigate the effect of pseudo-bilayer configurations at low operating voltages (≤0.5 V) in the heterogate germanium electron-hole bilayer tunnel field-effect transistor (HG-EHBTFET) compared to the traditional bilayer structures of EHBTFETs arising from semiclassical simulations where the inversion layers for electrons and holes featured very symmetric profiles with similar concentration levels at the ON-state. Pseudo-bilayer layouts are attained by inducing a certain asymmetry between the top and the bottom gates so that even though the hole inversion layer is formed at the bottom of the channel, the top gate voltage remains below the required value to trigger the formation of the inversion layer for electrons. Resulting benefits from this setup are improved electrostatic control on the channel, enhanced gate-to-gate efficiency, and higher I{sub ON} levels. Furthermore, pseudo-bilayer configurations alleviate the difficulties derived from confining very high opposite carrier concentrations in very thin structures.

  18. Reconstitution of rhodopsin into polymerizable planar supported lipid bilayers: influence of dienoyl monomer structure on photoactivation.

    PubMed

    Subramaniam, Varuni; D'Ambruoso, Gemma D; Hall, H K; Wysocki, Ronald J; Brown, Michael F; Saavedra, S Scott

    2008-10-07

    G-protein-coupled receptors (GPCRs) play key roles in cellular signal transduction and many are pharmacologically important targets for drug discovery. GPCRs can be reconstituted in planar supported lipid bilayers (PSLBs) with retention of activity, which has led to development of GPCR-based biosensors and biochips. However, PSLBs composed of natural lipids lack the high stability desired for many technological applications. One strategy is to use synthetic lipid monomers that can be polymerized to form robust bilayers. A key question is how lipid polymerization affects GPCR structure and activity. Here we have investigated the photochemical activity of bovine rhodopsin (Rho), a model GPCR, reconstituted into PSLBs composed of lipids having one or two polymerizable dienoyl moieties located in different regions of the acyl chains. Plasmon waveguide resonance spectroscopy was used to compare the degree of Rho photoactivation in fluid and poly(lipid) PSLBs. The position of the dienoyl moiety was found to have a significant effect: polymerization near the glycerol backbone significantly attenuates Rho activity whereas polymerization near the acyl chain termini does not. Differences in cross-link density near the acyl chain termini also do not affect Rho activity. In unpolymerized PSLBs, an equimolar mixture of phosphatidylethanolamine and phosphatidylcholine (PC) lipids enhances activity relative to pure PC; however after polymerization, the enhancement is eliminated which is attributed to stabilization of the membrane lamellar phase. These results should provide guidance for the design of robust lipid bilayers functionalized with transmembrane proteins for use in membrane-based biochips and biosensors.

  19. Band Structure Asymmetry of Bilayer Graphene Revealed by Infrared Spectroscopy

    SciTech Connect

    Li, Z.Q.; Henriksen, E.A.; Jiang, Z.; Hao, Zhao; Martin, Michael C.; Kim, P.; Stormer, H.L.; Basov, Dimitri N.

    2008-12-10

    We report on infrared spectroscopy of bilayer graphene integrated in gated structures. We observe a significant asymmetry in the optical conductivity upon electrostatic doping of electrons and holes. We show that this finding arises from a marked asymmetry between the valence and conduction bands, which is mainly due to the inequivalence of the two sublattices within the graphene layer and the next-nearest-neighbor interlayer coupling. From the conductivity data, the energy difference of the two sublattices and the interlayer coupling energy are directly determined.

  20. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    PubMed Central

    Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Huang, Jian-Ming; Juwita, Ratna

    2013-01-01

    Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC), lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC) lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications. PMID:23571494

  1. Simulation studies of structure and edge tension of lipid bilayer edges: effects of tail structure and force-field.

    PubMed

    West, Ana; Ma, Kevin; Chung, Jonathan L; Kindt, James T

    2013-08-15

    Molecular dynamics simulations of lipid bilayer ribbons have been performed to investigate the structures and line tensions associated with free bilayer edges. Simulations carried out for dioleoyl phosphatidylcholine with three different force-field parameter sets yielded edge line tensions of 45 ± 2 pN, over 50% greater than the most recently reported experimentally determined value for this lipid. Edge tensions obtained from simulations of a series of phosphatidylcholine lipid bilayer ribbons with saturated acyl tails of length 12-16 carbons and with monounsaturated acyl tails of length 14-18 carbons could be correlated with the excess area associated with forming the edge, through a two-parameter fit. Saturated-tail lipids underwent local thickening near the edge, producing denser packing that correlated with lower line tensions, while unsaturated-tail lipids showed little or no local thickening. In a dipalmitoyl phosphatidylcholine ribbon initiated in a tilted gel-phase structure, lipid headgroups tended to tilt toward the nearer edge producing a herringbone pattern, an accommodation that may account for the reported edge-induced stabilization of an ordered structure at temperatures near a lipid gel-fluid phase transition.

  2. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes.

    PubMed

    Rønnest, A K; Peters, G H; Hansen, F Y; Taub, H; Miskowiec, A

    2016-04-14

    Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic potential within phospholipid membranes imply an enormous electric field of 10(8)-10(9) V m(-1), which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential for DMPG bilayers and found ∼1 V (∼2 ⋅ 10(8) V m(-1)) when in the fluid phase with a monovalent counter-ion and ∼1.4 V (∼2.8 ⋅ 10(8) V m(-1)) when in the gel phase with a divalent counter-ion. The number of water molecules for a fully hydrated DMPG membrane has been estimated to be 9.7 molecules per lipid in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3

  3. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    NASA Astrophysics Data System (ADS)

    Rønnest, A. K.; Peters, G. H.; Hansen, F. Y.; Taub, H.; Miskowiec, A.

    2016-04-01

    Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic potential within phospholipid membranes imply an enormous electric field of 108-109 V m-1, which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential for DMPG bilayers and found ˜1 V (˜2 ṡ 108 V m-1) when in the fluid phase with a monovalent counter-ion and ˜1.4 V (˜2.8 ṡ 108 V m-1) when in the gel phase with a divalent counter-ion. The number of water molecules for a fully hydrated DMPG membrane has been estimated to be 9.7 molecules per lipid in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC

  4. Structural Investigation of Bilayers Formed by 1-Palmitoyl-2-Oleoylphosphatidylnucleosides

    PubMed Central

    Milani, Silvia; Baldelli Bombelli, Francesca; Berti, Debora; Hauß, Thomas; Dante, Silvia; Baglioni, Piero

    2006-01-01

    Bilayers of palmitoyl-oleoylphosphatidylnucleoside derivatives (1-palmitoyl-2-oleoyl-phosphatidyl-adenosine and 1-palmitoyl-2-oleoyl-phosphatidyl-uridine) were synthesized and investigated in the low-water content regime by a combination of neutron diffraction and Fourier transform infrared linear dichroism (LD-FTIR). Attention was focused on the modulation of structural properties operated by the presence of nucleic acid bases (either adenosine or uridine, a purine and a pyrimidine that are complementary in RNA). Base substitution causes major differences in phase behavior of the phospholipids, i.e., water sorption from a controlled humidity atmosphere and smectic periodicity. The profile of scattering length density can be inferred from five diffraction orders for 1-palmitoyl-2-oleoyl-phosphatidyl-uridine lamellar phase. 1-Palmitoyl-2-oleoyl-phosphatidyl-adenosine is characterized by lower and less ready hydration, giving rise to a powder-like sample. A linear dichroism FTIR investigation on the same lamellar phases was undertaken with the purpose of gathering details at the submolecular level on different portions of the molecule. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers were also investigated with the same technique for the sake of comparison. Besides a confirmation of the diffraction data interpretation, FTIR has provided evidence that the same chemical groups at the bilayer interface (namely the sugar-phosphate) have a different orientation depending on whether the base is a purine or a pyrimidine. A very simple geometrical optimization agrees with this observation. This indicates that a different pattern of base interaction is operating in the two cases and that base substitution acts as a modulator of the phase properties. PMID:16326904

  5. Structure of the DMPC lipid bilayer ripple phase†

    PubMed Central

    Akabori, Kiyotaka; Nagle, John F.

    2014-01-01

    High resolution structure is presented for the ripple (Pβ′) phase of the phospholipid dimyristoylphosphatidylcholine. Low angle X-ray scattering from oriented samples yielded 57 orders, more than twice as many as recorded previously. The determined electron density map has a sawtooth profile similar to the result from lower resolution data, but the features are sharper allowing better estimates for the modulated bilayer profile and the distribution of headgroups along the aqueous interface. Analysis of high resolution wide angle X-ray data shows that the hydrocarbon chains in the longer, major side of the asymmetric sawtooth are packed similarly to the LβF gel phase, with chains in both monolayers coupled and tilted by 18° in the same direction. The absence of Bragg rods that could be associated with the minor side is consistent with disordered chains, as often suggested in the literature. However, the new high resolution bilayer profile strongly suggests that the chains in the two monolayers in the minor side and the curved region are not in registry. This staggered monolayer modulated melting suggests a direction for improving theories of the ripple phase. PMID:25503248

  6. Irregular bilayer structure in vesicles prepared from Halobacterium cutirubrum lipids

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1974-01-01

    Fluorescent probes were used to study the structure of the cell envelope of Halobacterium cutirubrum, and, in particular, to explore the effect of the heterogeneity of the lipids in this organism on the structure of the bilayers. The fluorescence polarization of perylene was followed in vesicles of unfractionated lipids and polar lipids as a function of temperature in 3.4 M solutions of NaCl, NaNO3, and KSCN, and it was found that vesicles of unfractionated lipids were more perturbed by chaotropic agents than polar lipids. The dependence of the relaxation times of perylene on temperature was studied in cell envelopes and in vesicles prepared from polar lipids, unfractionated lipids, and mixtures of polar and neutral lipids.

  7. Temperature-Controlled Structure and Kinetics of Ripple Phases in One- and Two-Component Supported Lipid Bilayers

    PubMed Central

    Kaasgaard, Thomas; Leidy, Chad; Crowe, John H.; Mouritsen, Ole G.; Jørgensen, Kent

    2003-01-01

    Temperature-controlled atomic force microscopy (AFM) has been used to visualize and study the structure and kinetics of ripple phases in one-component dipalmitoylphosphatidylcholine (DPPC) and two-component dimyristoylphosphatidylcholine-distearoylphosphatidylcholine (DMPC-DSPC) lipid bilayers. The lipid bilayers are mica-supported double bilayers in which ripple-phase formation occurs in the top bilayer. In one-component DPPC lipid bilayers, the stable and metastable ripple phases were observed. In addition, a third ripple structure with approximately twice the wavelength of the metastable ripples was seen. From height profiles of the AFM images, estimates of the amplitudes of the different ripple phases are reported. To elucidate the processes of ripple formation and disappearance, a ripple-phase DPPC lipid bilayer was taken through the pretransition in the cooling and the heating direction and the disappearance and formation of ripples was visualized. It was found that both the disappearance and formation of ripples take place virtually one ripple at a time, thereby demonstrating the highly anisotropic nature of the ripple phase. Furthermore, when a two-component DMPC-DSPC mixture was heated from the ripple phase and into the ripple-phase/fluid-phase coexistence temperature region, the AFM images revealed that several dynamic properties of the ripple phase are important for the melting behavior of the lipid mixture. Onset of melting is observed at grain boundaries between different ripple types and different ripple orientations, and the longer-wavelength metastable ripple phase melts before the shorter-wavelength stable ripple phase. Moreover, it was observed that the ripple phase favors domain growth along the ripple direction and is responsible for creating straight-edged domains with 60° and 120° angles, as reported previously. PMID:12829489

  8. Excitonic gap formation and condensation in the bilayer graphene structure

    NASA Astrophysics Data System (ADS)

    Apinyan, V.; Kopeć, T. K.

    2016-09-01

    We have studied the excitonic gap formation in the Bernal Stacked, bilayer graphene (BLG) structures at half-filling. Considering the local Coulomb interaction between the layers, we calculate the excitonic gap parameter and we discuss the role of the interlayer and intralayer Coulomb interactions and the interlayer hopping on the excitonic pair formation in the BLG. Particularly, we predict the origin of excitonic gap formation and condensation, in relation to the furthermost interband optical transition spectrum. The general diagram of excitonic phase transition is given, explaining different interlayer correlation regimes. The temperature dependence of the excitonic gap parameter is shown and the role of the chemical potential, in the BLG, is discussed in details.

  9. Layer-stacking effect on electronic structures of bilayer arsenene

    NASA Astrophysics Data System (ADS)

    Mi, Kui; Xie, Jiafeng; Si, M. S.; Gao, C. X.

    2017-01-01

    A monolayer of orthorhombic arsenic (arsenene) is a promising candidate for nano-electronic devices due to the uniquely electronic properties. To further extend its practical applications, an additional layer is introduced to tune the electronic structures. Four layer-stacking manners, namely AA-, AB-, AB‧-, and AC-stacking, are constructed and studied through using first-principles calculations. Compared with monolayer, an indirect-direct gap transition is realized in AB-stacking. More importantly, a semimetal feature appears in the AC- and AB‧-stacked bilayers, leaving the electronic structure of AA-stacking trivial. In addition, the energy dispersion around Γ is largely tuned from the layer-stacking effect. To understand the underlying physics, the \\textbf{k}\\cdot\\textbf{p} approximation is taken to address this issue. Our results show that the level repulsion from the additional layer domaintes the anisotropy of energy dispersion around Γ. The works like ours would shed new light on the tunability of the electronic structure in layered arsenene.

  10. Model-based Approaches for the Determination of Lipid Bilayer Structure from Small-Angle Neutron and X-ray Scattering Data

    SciTech Connect

    Heberle, Frederick A; Pan, Jianjun; Standaert, Robert F; Drazba, Paul; Kucerka, Norbert; Katsaras, John

    2012-01-01

    Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Ku erka et al. (Ku erka et al. 2012; Ku erka et al. 2008). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent in these models. In particular, it is recognized that standalone data do not contain enough information to fully resolve the structure of inherently disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structural parameters, including the much sought after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data sets, as well as the implementation of local volume conservation in the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.

  11. Computation of mixed phosphatidylcholine-cholesterol bilayer structures by energy minimization.

    PubMed Central

    Vanderkooi, G

    1994-01-01

    The energetically preferred structures of dimyristoylphosphatidylcholine (DMPC)-cholesterol bilayers were determined at a 1:1 mole ratio. Crystallographic symmetry operations were used to generate planar bilayers of cholesterol and DMPC. Energy minimization was carried out with respect to bond rotations, rigid body motions, and the two-dimensional lattice constants. The lowest energy structures had a hydrogen bond between the cholesterol hydroxyl and the carbonyl oxygen of the sn-2 acyl chain, but the largest contribution to the intermolecular energy was from the nonbonded interactions between the flat alpha surface of cholesterol and the acyl chains of DMPC. Two modes of packing in the bilayer were found; in structure A (the global minimum), unlike molecules are nearest neighbors, whereas in structure B (second lowest energy) like-like intermolecular interactions predominate. Crystallographic close packing of the molecules in the bilayer was achieved, as judged from the molecular areas and the bilayer thickness. These energy-minimized structures are consistent with the available experimental data on mixed bilayers of lecithin and cholesterol, and may be used as starting points for molecular dynamics or other calculations on bilayers. PMID:8061195

  12. Effect of monoglyceride structure and cholesterol content on water permeability of the droplet bilayer.

    PubMed

    Michalak, Zuzanna; Muzzio, Michelle; Milianta, Peter J; Giacomini, Rosario; Lee, Sunghee

    2013-12-23

    The process of water permeation across lipid membranes has significant implications for cellular physiology and homeostasis, and its study may lead to a greater understanding of the relationship between the structure of lipid bilayer and the role that lipid structure plays in water permeation. In this study, we formed a droplet interface bilayer (DIB) by contacting two aqueous droplets together in an immiscible solvent (squalane) containing bilayer-forming surfactant (monoglycerides). Using the DIB model, we present our results on osmotic water permeabilities and activation energy for water permeation of an associated series of unsaturated monoglycerides as the principal component of droplet bilayers, each having the same chain length but differing in the position and number of double bonds, in the absence and presence of a varying concentration of cholesterol. Our findings suggest that the tailgroup structure in a series of monoglyceride bilayers is seen to affect the permeability and activation energy for the water permeation process. Moreover, we have also established the insertion of cholesterol into the droplet bilayer, and have detected its presence via its effect on water permeability. The effect of cholesterol differs depending on the type of monoglyceride. We demonstrate that the DIB can be employed as a convenient model membrane to rapidly explore subtle structural effects on bilayer water permeability.

  13. Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers

    PubMed Central

    Kim, Taehoon; Lee, Kyu Il; Morris, Phillip; Pastor, Richard W.; Andersen, Olaf S.; Im, Wonpil

    2012-01-01

    Gramicidin A (gA) is a 15-amino-acid antibiotic peptide with an alternating L-D sequence, which forms (dimeric) bilayer-spanning, monovalent cation channels in biological membranes and synthetic bilayers. We performed molecular dynamics simulations of gA dimers and monomers in all-atom, explicit dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), dioleoylphosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayers. The variation in acyl chain length among these different phospholipids provides a way to alter gA-bilayer interactions by varying the bilayer hydrophobic thickness, and to determine the influence of hydrophobic mismatch on the structure and dynamics of both gA channels (and monomeric subunits) and the host bilayers. The simulations show that the channel structure varied little with changes in hydrophobic mismatch, and that the lipid bilayer adapts to the bilayer-spanning channel to minimize the exposure of hydrophobic residues. The bilayer thickness, however, did not vary monotonically as a function of radial distance from the channel. In all simulations, there was an initial decrease in thickness within 4–5 Å from the channel, which was followed by an increase in DOPC and POPC or a further decrease in DLPC and DMPC bilayers. The bilayer thickness varied little in the monomer simulations—except one of three independent simulations for DMPC and all three DLPC simulations, where the bilayer thinned to allow a single subunit to form a bilayer-spanning water-permeable pore. The radial dependence of local lipid area and bilayer compressibility is also nonmonotonic in the first shell around gA dimers due to gA-phospholipid interactions and the hydrophobic mismatch. Order parameters, acyl chain dynamics, and diffusion constants also differ between the lipids in the first shell and the bulk. The lipid behaviors in the first shell around gA dimers are more complex than predicted from a simple mismatch

  14. Evidence for Leaflet-Dependent Redistribution of Charged Molecules in Fluid Supported Phospholipid Bilayers

    PubMed Central

    Shreve, Andrew P.; Howland, Michael C.; Sapuri-Butti, Annapoorna R.; Allen, Toby W.; Parikh, Atul N.

    2009-01-01

    The asymmetric distribution of charged molecules between the leaflets of solid-substrate-supported phospholipid bilayers is studied using imaging ellipsometry, fluorescence microscopy, and numerical solutions of the Poisson-Boltzmann equation. Experiments are facilitated by the use of patterned substrates that allow for side-by-side comparison of lipid monolayers and supported bilayers. On silica surfaces, negatively charged lipid components are shown to be enriched in the outer leaflet of a supported bilayer system at modest salt concentrations. The approaches developed provide a general means for determining asymmetries of charged components in supported lipid bilayers. PMID:19007257

  15. Lipid Bilayers in the Gel Phase Become Saturated by Triton X-100 at Lower Surfactant Concentrations Than Those in the Fluid Phase

    PubMed Central

    Ahyayauch, Hasna; Collado, M. Isabel; Alonso, Alicia; Goñi, Felix M.

    2012-01-01

    It has been repeatedly observed that lipid bilayers in the gel phase are solubilized by lower concentrations of Triton X-100, at least within certain temperature ranges, or other nonionic detergents than bilayers in the fluid phase. In a previous study, we showed that detergent partition coefficients into the lipid bilayer were the same for the gel and the fluid phases. In this contribution, turbidity, calorimetry, and 31P-NMR concur in showing that bilayers in the gel state (at least down to 13–20°C below the gel-fluid transition temperature) become saturated with detergent at lower detergent concentrations than those in the fluid state, irrespective of temperature. The different saturation may explain the observed differences in solubilization. PMID:22713566

  16. Electronic structure of charged bilayer and trilayer phosphorene

    NASA Astrophysics Data System (ADS)

    Jhun, Bukyoung; Park, Cheol-Hwan

    2017-08-01

    We have investigated the electronic structure of charged bilayer and trilayer phoshporene using first-principles density functional theory calculations. We find that the effective dielectric constant for an external electric field applied perpendicular to phosphorene layers increases with the charge density and is twice as large as in an undoped system if the electron density is around 5 ×1013 cm-2. It is known that if few-layer phosphorene is placed under such an electric field, the electron band gap decreases, and if the strength of the electric field is further increased, the band gap closes. We show that the electronic screening due to added charge carriers reduces the amount of this reduction in the band gap and increases the critical strength of the electric field for gap closure. If the electron density is around 4 ×1013 cm-2, for example, this critical field for trilayer phosphorene is 40% higher than that for a charge-neutral system. The results are directly relevant to experiments on few-layer phosphorene with top and bottom electrical gates and/or with chemical dopants.

  17. Structural restraints and heterogeneous orientation of the gramicidin A channel closed state in lipid bilayers.

    PubMed

    Mo, Y; Cross, T A; Nerdal, W

    2004-05-01

    Although there have been several decades of literature illustrating the opening and closing of the monovalent cation selective gramicidin A channel through single channel conductance, the closed conformation has remained poorly characterized. In sharp contrast, the open-state dimer is one of the highest resolution structures yet characterized in a lipid environment. To shift the open/closed equilibrium dramatically toward the closed state, a lower peptide/lipid molar ratio and, most importantly, long-chain lipids have been used. For the first time, structural evidence for a monomeric state has been observed for the native gramicidin A peptide. Solid-state NMR spectroscopy of single-site (15)N-labeled gramicidin in uniformly aligned bilayers in the L(alpha) phase have been observed. The results suggest a kinked structure with considerable orientational heterogeneity. The C-terminal domain is well structured, has a well-defined orientation in the bilayer, and appears to be in the bilayer interfacial region. On the other hand, the N-terminal domain, although appearing to be well structured and in the hydrophobic core of the bilayer, has a broad range of orientations relative to the bilayer normal. The structure is not just half of the open-state dimer, and neither is the structure restricted to the surface of the bilayer. Consequently, the monomeric or closed state appears to be a hybrid of these two models from the literature.

  18. Order Parameters of a Transmembrane Helix in a Fluid Bilayer: Case Study of a WALP Peptide

    PubMed Central

    Holt, Andrea; Rougier, Léa; Réat, Valérie; Jolibois, Franck; Saurel, Olivier; Czaplicki, Jerzy; Killian, J. Antoinette; Milon, Alain

    2010-01-01

    Abstract A new solid-state NMR-based strategy is established for the precise and efficient analysis of orientation and dynamics of transmembrane peptides in fluid bilayers. For this purpose, several dynamically averaged anisotropic constraints, including 13C and 15N chemical shift anisotropies and 13C-15N dipolar couplings, were determined from two different triple-isotope-labeled WALP23 peptides (2H, 13C, and 15N) and combined with previously published quadrupolar splittings of the same peptide. Chemical shift anisotropy tensor orientations were determined with quantum chemistry. The complete set of experimental constraints was analyzed using a generalized, four-parameter dynamic model of the peptide motion, including tilt and rotation angle and two associated order parameters. A tilt angle of 21° was determined for WALP23 in dimyristoylphosphatidylcholine, which is much larger than the tilt angle of 5.5° previously determined from 2H NMR experiments. This approach provided a realistic value for the tilt angle of WALP23 peptide in the presence of hydrophobic mismatch, and can be applied to any transmembrane helical peptide. The influence of the experimental data set on the solution space is discussed, as are potential sources of error. PMID:20441750

  19. Microparticles as biomarkers of lung disease: enumeration in biological fluids using lipid bilayer microspheres.

    PubMed

    McVey, Mark J; Spring, Christopher M; Semple, John W; Maishan, Mazharul; Kuebler, Wolfgang M

    2016-05-01

    Extracellular vesicles, specifically microparticles (MPs), are rapidly gaining attention for their capacity to act as biomarkers for diagnosis, prognosis, or responsiveness to therapy in lung disease, in keeping with the concept of precision medicine. However, MP analysis by high-sensitivity flow cytometry (FCM) is complicated by a lack of accurate means for MP enumeration. To address this gap, we report here an enhanced FCM MP gating and enumeration technique based on the use of novel engineered lipid bilayer microspheres (LBMs). By comparison of LBM-based MP enumeration with conventional bead- or fluorescent-based FCM enumeration techniques and a gravimetric consumption gold standard, we found LBMs to be superior to commercial bead preparations, showing the smallest fixed bias and limits of agreement in Bland Altman analyses. LBMs had simultaneous capacity to aid FCM enumeration of MPs in plasma, BAL, and cell culture supernatants. LBM enumeration detected differences in MP counts in mice exposed to intraperitoneal lipopolysaccharide or saline. LBMs provided for 1) higher sensitivity for gating MPs populations, 2) reduced background within MP gates, 3) more appropriate size, and 4) an inexpensive alternative amenable to different fluorescent tags. LBM-based MP enumeration was useful for a series of different FCM systems assessed, whereas LBM gating benefited high- but not low-sensitivity FCM systems compared with fluorescence gating. By offering exclusive advantages over current means of gating and enumerating MPs, LBMs are uniquely suited to realizing the potential of MPs as biomarkers in biological lung fluids and facilitating precision medicine in lung disease.

  20. Electronic structure of bilayer graphene physisorbed on metal substrates

    NASA Astrophysics Data System (ADS)

    Khan, Emroz; Rahman, Tahmid Sami; Subrina, Samia

    2016-11-01

    Graphene-metal interfaces have recently become popular for graphene growth and for making contacts in numerous thermal and photo-electronic devices. A number of studies have already been made to investigate the interfacial properties when single layer graphene is grown on metal substrates. In this study, we consider the physisorption of bilayer graphene on metals and find a significant bandgap opening which is otherwise absent in the single layer case. This gap arises from the asymmetry in the bilayer due to the charge transfer process at the interface. This charge transfer also causes doping in the bilayer graphene and a corresponding shift in the Fermi level. In this work, we present a thorough investigation into the induced bandgap and Fermi level shift when bilayer graphene is adsorbed on Cu, Al, Ag, Pt, and Au(111) surfaces first by reporting their values from Density Functional Theory (DFT) studies with Local Density Approximation functional used for exchange-correlation energy. Next, to obtain an enhanced picture of the surface physics at play (which is usually obscured by the complexities of DFT), we provide an analytical model to relate the induced bandgap and Fermi level shift to the metal work function and interface separation distance. The values predicted from the model shows a high degree of correlation with the values obtained from the DFT simulation. The results are expected to greatly facilitate the understanding of bilayer graphene adsorption on metals, which in turn may aid the study of graphene electronic devices.

  1. Adsorption of alpha-synuclein on lipid bilayers: modulating the structure and stability of protein assemblies.

    PubMed

    Haque, Farzin; Pandey, Anjan P; Cambrea, Lee R; Rochet, Jean-Christophe; Hovis, Jennifer S

    2010-03-25

    The interaction of alpha-synuclein with phospholipid membranes has been examined using supported lipid bilayers and epi-fluorescence microscopy. The membranes contained phosphatidylcholine (PC) and phosphatidic acid (PA), which mix at physiological pH. Upon protein adsorption, the lipids undergo fluid-fluid phase separation into PC-rich and PA-rich regions. The protein preferentially adsorbs to the PA-rich regions. The adsorption and subsequent aggregation of alpha-synuclein was probed by tuning several parameters: the charge on the lipids, the charge on the protein, and the screening environment. Conditions which promoted the greatest extent of adsorption resulted in structurally heterogeneous aggregates, while comparatively homogeneous aggregates were observed under conditions whereby adsorption did not occur as readily. Our observation that different alterations to the system lead to different degrees of aggregation and different aggregate structures poses a challenge for drug discovery. Namely, therapies aimed at neutralizing alpha-synuclein must target a broad range of potentially toxic, membrane-bound assemblies.

  2. Refined dynamic structure factor of a lipid bilayer on scales comparable to its thickness

    NASA Astrophysics Data System (ADS)

    Zakhvataev, V. E.

    2017-07-01

    The structural inhomogeneity of a lipid bilayer is an obstacle to applying the classical Canham-Helfrich model to describe its dynamics on nanometer length scales. In this paper, a refined expression for the free energy of a single-component lipid bilayer is used to describe the dynamics of lipid density fluctuations. In particular, the expression with a term involving the gradient of the area per lipid [8] is used for the free energy per lipid. A refined expression has been derived for the dynamic structure factor of a free lipid bilayer in the hydrodynamic region. It leads to differences in the interpretation and values of the bilayer parameters in comparison with the standard model.

  3. Structure, composition, and peptide binding properties of detergent soluble bilayers and detergent resistant rafts.

    PubMed Central

    Gandhavadi, M; Allende, D; Vidal, A; Simon, S A; McIntosh, T J

    2002-01-01

    Lipid bilayers composed of unsaturated phosphatidylcholine (PC), sphingomyelin (SM), and cholesterol are thought to contain microdomains that have similar detergent insolubility characteristics as rafts isolated from cell plasma membranes. We chemically characterized the fractions corresponding to detergent soluble membranes (DSMs) and detergent resistant membranes (DRMs) from 1:1:1 PC:SM:cholesterol, compared the binding properties of selected peptides to bilayers with the compositions of DSMs and DRMs, used differential scanning calorimetry to identify phase transitions, and determined the structure of DRMs with x-ray diffraction. Compared with the equimolar starting material, DRMs were enriched in both SM and cholesterol. Both transmembrane and interfacial peptides bound to a greater extent to DSM bilayers than to DRM bilayers, likely because of differences in the mechanical properties of the two bilayers. Thermograms from 1:1:1 PC:SM:cholesterol from 3 to 70 degrees C showed no evidence for a liquid-ordered to liquid-disordered phase transition. Over a wide range of osmotic stresses, each x-ray pattern from equimolar PC:SM:cholesterol or DRMs contained a broad wide-angle band at 4.5 A, indicating that the bilayers were in a liquid-crystalline phase, and several sharp low-angle reflections that indexed as orders of a single lamellar repeat period. Electron density profiles showed that the total bilayer thickness was 57 A for DRMs, which was approximately 5 A greater than that of 1:1:1 PC:SM:cholesterol and 10 A greater than the thickness of bilayers with the composition of DSMs. These x-ray data provide accurate values for the widths of raft and nonraft bilayers that should be important in understanding mechanisms of protein sorting by rafts. PMID:11867462

  4. Structural Degradation and Swelling of Lipid Bilayer under the Action of Benzene.

    PubMed

    Odinokov, Alexey; Ostroumov, Denis

    2015-12-03

    Benzene and other nonpolar organic solvents can accumulate in the lipid bilayer of cellular membranes. Their effect on the membrane structure and fluidity determines their toxic properties and antibiotic action of the organic solvents on the bacteria. We performed molecular dynamics simulations of the interaction of benzene with the dimyristoylphosphatidylcholine (DMPC) bilayer. An increase in the membrane surface area and fluidity was clearly detected. Changes in the acyl chain ordering, tilt angle, and overall bilayer thickness were, however, much less marked. The dependence of all computed quantities on the benzene content showed two regimes separated by the solubility limit of benzene in water. When the amount of benzene exceeded this point, a layer of almost pure benzene started to grow between the membrane leaflets. This process corresponds to the nucleation of a new phase and provides a molecular mechanism for the mechanical rupture of the bilayer under the action of nonpolar compounds.

  5. DFT Calculations of the Electronic Structure and Interlayer Interaction in the Li-INTERCALATED Graphene Bilayer

    NASA Astrophysics Data System (ADS)

    Petrova, N. V.; Yakovkin, I. N.

    The electronic band structure, density of states (DOS) and interlayer interaction in Li-intercalated graphene bilayers are studied by means of density functional theory (DFT) calculations. It has been found that for a pristine bilayer, the relative shift of graphene layers from AB stacking configuration, pertinent to a bulk graphite, to AA configuration results in the opening of the bandgap at Fermi level, so that the bilayer becomes a semiconductor. The Li intercalation of the graphene bilayer significantly increases the density of states at Fermi level, which can be considered as an increased metallicity. The electronic density in the space between graphene layers also substantially increases and leads to related increase of the interlayer interaction. We hope that the obtained results of calculations will be useful for various applications of Li-intercalated graphene layers in nanoelectronics.

  6. Crystalline domain structure and cholesterol crystal nucleation in single hydrated DPPC:cholesterol:POPC bilayers.

    PubMed

    Ziblat, Roy; Leiserowitz, Leslie; Addadi, Lia

    2010-07-21

    Grazing incidence X-ray diffraction measurements were performed on single hydrated bilayers and monolayers of DPPC:Cholesterol:POPC at varying concentrations. There are substantial differences in the phase and structure behavior of the crystalline domains formed within the bilayers relative to the corresponding monolayers, due to interactions between the opposing leaflets. Depending on the lipid composition, these interactions led to phase separation, changes in molecular tilt angle, or formation of cholesterol crystals. In monolayers, DPPC and cholesterol form a single crystalline phase at all compositions studied. In bilayers, a second crystalline phase appears when cholesterol levels are increased: domains of cholesterol and DPPC form monolayer thick crystals where each of the lipid leaflets diffracts independently, whereas excess cholesterol forms cholesterol bilayer thick crystals at a DPPC:Chol ratio < 46:54 +/- 2 mol %. The nucleation of the cholesterol crystals occurs at concentrations relevant to the actual cell plasma membrane composition.

  7. Landau levels in biased graphene structures with monolayer-bilayer interfaces

    NASA Astrophysics Data System (ADS)

    Mirzakhani, M.; Zarenia, M.; Vasilopoulos, P.; Ketabi, S. A.; Peeters, F. M.

    2017-09-01

    The electron energy spectrum in monolayer-bilayer-monolayer and in bilayer-monolayer-bilayer graphene structures is investigated and the effects of a perpendicular magnetic field and electric bias are studied. Different types of monolayer-bilayer interfaces are considered as zigzag (ZZ) or armchair (AC) junctions which modify considerably the bulk Landau levels (LLs) when the spectra are plotted as a function of the center coordinate of the cyclotron orbit. Far away from the two interfaces, one obtains the well-known LLs for extended monolayer or bilayer graphene. The LL structure changes significantly at the two interfaces or junctions where the valley degeneracy is lifted for both types of junctions, especially when the distance between them is approximately equal to the magnetic length. Varying the nonuniform bias and the width of this junction-to-junction region in either structure strongly influence the resulting spectra. Significant differences exist between ZZ and AC junctions in both structures. The densities of states (DOSs) for unbiased structures are symmetric in energy whereas those for biased structures are asymmetric. An external bias creates interface LLs in the gaps between the LLs of the unbiased system in which the DOS can be quite small. Such a pattern of LLs can be probed by scanning tunneling microscopy.

  8. Molecular Organization and Dynamics of Cholesterol Nanodomains in Fluid Lipid Bilayers

    NASA Astrophysics Data System (ADS)

    Cheng, Kwan; Cannon, Brian; Zhu, Qing; Vaughn, Mark; Huang, Juyang

    2007-03-01

    The molecular organization and dynamics of cholesterol nanodomains in lipid bilayers containing phospholipid (PL) and cholesterol (CHOL) were examined using FTIR, time-resolved fluorescence and surface-acting cholesterol oxidase enzyme (COD). In binary PL/CHOL system, abrupt changes in the PL C=O frequency, fluorescence lifetime and rotation rate of chain labeled PL, and the rate of cholesterol oxidation by COD were observed at ˜ 40 mole% of CHO. For ternary PL1/PL2/CHOL system composed of two dissimilar PL's of different chain lengths or headgroup sizes, abrupt changes at PL1/PL2˜ 2 were found. The above critical lipid compositions agree favorably with the theoretical compositions predicted by the lipid superlattice model, suggesting that PL of different structures and CHOL can form regularly distributed, or superlattice-like, nanodomains at the polar headgroup and the acyl chain levels, respectively. The feasibility of the coexistence of headgroup and acyl chain nanodomains was demonstrated by a spacing filling model and MD simulations. We speculate that lipid superlattice domains may play an important role in the regulation of protein/lipid interaction in cells.

  9. Bilayer structure and physical dynamics of the cytochrome b5 dimyristoylphosphatidylcholine interaction.

    PubMed Central

    Chester, D W; Skita, V; Young, H S; Mavromoustakos, T; Strittmatter, P

    1992-01-01

    Cytochrome b5 is a microsomal membrane protein which provides reducing potential to delta 5-, delta 6-, and delta 9-fatty acid desaturases through its interaction with cytochrome b5 reductase. Low angle x-ray diffraction has been used to determine the structure of an asymmetrically reconstituted cytochrome b5:DMPC model membrane system. Differential scanning calorimetry and fluorescence anisotropy studies were performed to examine the bilayer physical dynamics of this reconstituted system. These latter studies allow us to constrain structural models to those which are consistent with physical dynamics data. Additionally, because the nonpolar peptide secondary structure remains unclear, we tested the sensitivity of our model to different nonpolar peptide domain configurations. In this modeling approach, the nonpolar peptide moiety was arranged in the membrane to meet such chemically determined criteria as protease susceptibility of carboxyl- and amino-termini, tyrosine availability for pH titration and tryptophan 109 location, et cetera. In these studies, we have obtained a reconstituted cytochrome b5:DMPC bilayer structure at approximately 6.3 A resolution and conclude that the nonpolar peptide does not penetrate beyond the bilayer midplane. Structural correlations with calorimetry, fluorescence anisotropy and acyl chain packing data suggest that asymmetric cytochrome b5 incorporation into the bilayer increases acyl chain order. Additionally, we suggest that the heme peptide:bilayer interaction facilitates a discreet heme peptide orientation which would be dependent upon phospholipid headgroup composition. Images FIGURE 1 FIGURE 2 FIGURE 7 PMID:1600082

  10. First-principles study of structural properties of SiO2 bilayers

    NASA Astrophysics Data System (ADS)

    Malashevich, Andrei; Ismail-Beigi, Sohrab; Altman, Eric I.

    Two dimensional (2D) materials draw a tremendous amount of interest because they exhibit unique physical properties due to reduced dimensionality. Recently, SiO2 2D bilayer systems were discovered. The structure of these bilayers is formed by two mirror-image planes of corner-sharing SiO4 tetrahedra and does not have a direct relation to bulk SiO2 systems. SiO2 bilayers may be obtained in crystalline or amorphous forms. In the crystalline form, the bilayers are constructed from six-membered rings of corner-sharing SiO4 tetrahedra. The amorphous form has rings of various sizes typically in the range from four to nine Si atoms in the ring. These structures may be of practical interest as atomically thin membranes and molecular sieves. In our work, we study the effect of strain and doping on the crystalline structure of SiO2 bilayers using density functional theory. We analyze the stability of structures depending on the ring size and establish strain and doping conditions that may render the structures with large ring sizes stable. This work is supported by the National Science Foundation through Grants MRSEC NSF DMR-1119826 and NSF DMR-1506800.

  11. Effects of diacylglycerols and Ca2+ on structure of phosphatidylcholine/phosphatidylserine bilayers.

    PubMed Central

    Goldberg, E M; Lester, D S; Borchardt, D B; Zidovetzki, R

    1994-01-01

    The combined effects of the diacylglycerols (DAGs) with the various acyl chains and Ca2+ on the structure of phosphatidylcholine/phosphatidylserine (4:1 mole/mole) bilayers were studied using 2H- and 31P NMR. The following DAG- and Ca(2+)-induced bilayer perturbations were identified. 1) Increased tendency to form nonbilayer lipid phases was induced by diolein or stearoylarachidonoylglycerol, and was synergistically enhanced by the addition of Ca2+. 2) "Transverse" bilayer perturbation was induced by dioctanoylglycerol. The addition of this DAG caused increased ordering of the phospholipid acyl side chains in the region adjacent to the headgroup, with the concomitant decrease of the order toward the bilayer interior. 3) Separation of the phosphatidylcholine and phosphatidylserine bilayer components was induced by combinations of relatively high (1:5 mole/mole to phosphatidylserine) Ca2+ and 25 mol% (to the phospholipids) of diolein, stearoylarachidonoylglycerol, or oleoylacetylglycerol. 4) Lateral phase separation of the bilayers on the regions of different fluidities was induced by dipalmitin. These physicochemical effects were correlated with the effects of these DAGs and Ca2+ on the activity of protein kinase C. The increased tendency to form nonbilayer lipid phases and the transverse bilayer perturbations correlated with the increased protein kinase C activity, whereas the actual presence of the nonbilayer lipid phases, as well as the separation of the phosphatidylcholine and phosphatidylserine components, was associated with the decrease in the protein kinase C activity. The lateral phase separation of the bilayer on gel-like and liquid crystalline regions did not have an effect on the activity of the enzyme. These results demonstrate the importance of the physicochemical properties of the membranes in the process of activation of protein kinase C. PMID:8161692

  12. Theoretical investigation of structural and optical properties of semi-fluorinated bilayer graphene

    NASA Astrophysics Data System (ADS)

    Xiao-Jiao, San; Bai, Han; Jing-Geng, Zhao

    2016-03-01

    We have studied the structural and optical properties of semi-fluorinated bilayer graphene using density functional theory. When the interlayer distance is 1.62 Å, the two graphene layers in AA stacking can form strong chemical bonds. Under an in-plane stress of 6.8 GPa, this semi-fluorinated bilayer graphene becomes the energy minimum. Our calculations indicate that the semi-fluorinated bilayer graphene with the AA stacking sequence and rectangular fluorinated configuration is a nonmagnetic semiconductor (direct gap of 3.46 eV). The electronic behavior at the vicinity of the Fermi level is mainly contributed by the p electrons of carbon atoms forming C=C double bonds. We compare the optical properties of the semi-fluorinated bilayer graphene with those of bilayer graphene stacked in the AA sequence and find that the semi-fluorinated bilayer graphene is anisotropic for the polarization vector on the basal plane of graphene and a red shift occurs in the [010] polarization, which makes the peak at the low-frequency region located within visible light. This investigation is useful to design polarization-dependence optoelectronic devices. Project supported by the Program of Educational Commission of Heilongjiang Province, China (Grant No. 12541131).

  13. Monolayer to Bilayer Structural Transition in Confined Pyrrolidinium-Based Ionic Liquids.

    PubMed

    Smith, Alexander M; Lovelock, Kevin R J; Gosvami, Nitya Nand; Licence, Peter; Dolan, Andrew; Welton, Tom; Perkin, Susan

    2013-02-07

    Ionic liquids can be intricately nanostructured in the bulk and at interfaces resulting from a delicate interplay between interionic and surface forces. Here we report the structuring of a series of dialkylpyrrolidinium-based ionic liquids induced by confinement. The ionic liquids containing cations with shorter alkyl chain substituents form alternating cation-anion monolayer structures on confinement to a thin film, whereas a cation with a longer alkyl chain substituent leads to bilayer formation. The crossover from monolayer to bilayer structure occurs between chain lengths of n = 8 and 10 for these pyrrolidinium-based ionic liquids. The bilayer structure for n = 10 involves full interdigitation of the alkyl chains; this is in contrast with previous observations for imidazolium-based ionic liquids. The results are pertinent to these liquids' application as electrolytes, where the electrolyte is confined inside the pores of a nanoporous electrode, for example, in devices such as supercapacitors or batteries.

  14. Monolayer and bilayer structures in ionic liquids and their mixtures confined to nano-films.

    PubMed

    Smith, Alexander M; Lovelock, Kevin R J; Perkin, Susan

    2013-01-01

    The confinement of liquids to thin films can lead to dramatic changes in their structural arrangement and dynamic properties. Ionic liquids display nano-structures in the bulk of the liquid, consisting of polar and non-polar domains, whereas a solid surface can induce layered structures in the near-surface liquid. Here we compare and contrast the layer structures in a series of imidazolium and pyrrolidinium-based ionic liquids upon confinement of the liquids to films of approximately 0-20 nm between two negatively charged mica surfaces. Using a surface force balance (SFB) we measured the force between the two atomically smooth mica surfaces with ionic liquid between, directly revealing the ion packing and dimensions of layered structures for each liquid. The ionic liquids with shorter alkyl chain substituents form alternating cation-anion monolayer structures on confinement, whilst a longer alkyl chain leads to alignment of the cations in bilayer formation. The crossover from monolayers to bilayers, however, occurs at different alkyl chain lengths for imidazolium- and pyrrolidinium-based ionic liquids with a common anion. In addition, we find that imidazolium cation bilayers are arranged in toe-to-toe orientation, whereas pyrrolidinium cations form bilayers consisting of fully interdigitated alkyl chains. Results for a mixture of monolayer-preferring (i.e. short alkyl chain) and bilayer-preferring (i.e. long alkyl chain) liquids indicate alkyl chain segregation and bilayer-like structures. We discuss the driving forces for these self-assembly effects, and the contrasting behaviour of the imidazolium and pyrrolidinium-type ionic liquids.

  15. Structure and dynamics of a hydrated phospholipid bilayer in the presence of a silica substrate

    NASA Astrophysics Data System (ADS)

    McCune, Matthew; Kosztin, Ioan

    We study the structure and dynamics of a hydrated diyristoyl-phosphatidycholine (DMPC) lipid bilayer supported on a silica substrate using all-atom molecular dynamics (MD) simulation. A similar MD simulation of a freestanding DMPC bilayer is used as a reference to determine changes to both lipid and hydration water properties due to the introduction of the substrate. Long time (0.1 microsecond) MD trajectories were used to investigate the effect of the substrate on the structure and dynamics of the lipid bilayer by determining (i) the spatial distribution of water molecules and selected lipid atoms; (ii) the out of plane fluctuations of the lipid molecules; (iii) the dipole moment orientation of hydration waters; and (iv) the lateral mean-square-displacement of both lipid and water molecules. The obtained results suggest that (i) at equilibrium the space between the substrate and lipid bilayer is filled by only hydration water; (ii) the presence of the substrate has no major influence on the structure of hydration water layers and on the out-of-plane fluctuations of the lipids; and (iii) the silica substrate alters considerably the lateral diffusion of the lipids in the closest bilayer leaflet and the hydration waters between the substrate and DMPC membrane. The reported results appear to be consistent with previous MD and neutron scattering studies. Work supported by National Science Foundation Integrative Graduate Education and Research Traineeship (DGE-1069091). The computations were performed on the HPC resources at the University of Missouri Bioinformatics Consortium (UMBC).

  16. Electron density analysis of the effects of sugars on the structure of lipid bilayers at low hydration - a preliminary study

    SciTech Connect

    Lenné, T.; Kent, B.; Koster, K.L.; Garvey, C.J.; Bryant, G.

    2012-02-06

    Small angle X-ray scattering is used to study the effects of sugars on membranes during dehydration. Previous work has shown that the bilayer and chain-chain repeat spacings of DPPC bilayers are relatively unaffected by the presence of sugars. In this work we present a preliminary analysis of the electron density profiles of DPPC in the presence of sugars at low hydration. The difficulties of determining the correct phasing are discussed. Sugars and other small solutes have been shown to have an important role in improving the tolerance of a range of species to desiccation and freezing. In particular it has been shown that sugars can stabilize membranes in the fluid membrane phase during dehydration, and in the fully dehydrated state. Equivalently, at a particular hydration, the presence of sugars lowers the transition temperature between the fluid and gel phases. There are two competing models for explaining the effects of sugars on membrane phase transition temperatures. One, designated the water replacement hypothesis (WRH) states that sugars hydrogen bond to phospholipid headgroups, thus hindering the fluid-gel phase transition. One version of this model suggests that certain sugars (such as trehalose) achieve the measured effects by inserting between the phospholipid head groups. An alternative model explains the observed effects of sugars in terms of the sugars effect on the hydration repulsion that develops between opposing membranes during dehydration. The hydration repulsion leads to a lateral compressive stress in the bilayer which squeezes adjacent lipids more closely together, resulting in a transition to the gel phase. When sugars are present, their osmotic and volumetric effects reduce the hydration repulsion, reduce the compressive stress in the membranes, and therefore tend to maintain the average lateral separation between lipids. This model is called the hydration forces explanation (HFE). We recently showed that neither mono- nor di

  17. Inverse Proximity Effect in Superconductor-ferromagnet Bilayer Structures

    SciTech Connect

    Xia, Jing

    2010-04-05

    Measurements of the polar Kerr effect using a zero-area-loop Sagnac magnetometer on Pb/Ni and Al/(Co-Pd) proximity-effect bilayers show unambiguous evidence for the 'inverse proximity effect,' in which the ferromagnet (F) induces a finite magnetization in the superconducting (S) layer. To avoid probing the magnetic effects in the ferromagnet, the superconducting layer was prepared much thicker than the light's optical penetration depth. The sign and size of the effect, as well as its temperature dependence agree with recent predictions by Bergeret et al.[1].

  18. Structure of an adsorbed dimyristoylphosphatidylcholine bilayer measured with specular reflection of neutrons.

    PubMed Central

    Johnson, S J; Bayerl, T M; McDermott, D C; Adam, G W; Rennie, A R; Thomas, R K; Sackmann, E

    1991-01-01

    Using specular reflection of neutrons, we investigate for the first time the structure of a single dimyristoylphosphatidylcholine bilayer adsorbed to a planar quartz surface in an aqueous environment. We demonstrate that the bilayer is strongly adsorbed to the quartz surface and is stable to phase state changes as well as exchange of the bulk aqueous phase. Our results show that the main phase transition is between the L alpha phase and the metastable L beta'* phase, with formation of the P beta' ripple phase prevented by lateral stress on the adsorbed bilayer. By performing contrast variation experiments, we are able to elucidate substantial detail in the interfacial structure. We measure a bilayer thickness of 43.0 +/- 1.5 A in the L alpha phase (T = 31 degrees C) and 46.0 +/- 1.5 A in the L beta'* phase (T = 20 degrees C). The polar head group is 8.0 +/- 1.5 A thick in the L alpha phase. The water layer between the quartz and bilayer is 30 +/- 10 A for the lipid in both the L alpha and L'* phase. Our results agree well with those previously reported from experiments using lipid vesicles and monolayers, thus establishing the feasibility of our experimental methods. PMID:2009353

  19. Bi-layered calcium phosphate cement-based composite scaffold mimicking natural bone structure

    PubMed Central

    He, Fupo; Ye, Jiandong

    2013-01-01

    In this study, a core/shell bi-layered calcium phosphate cement (CPC)-based composite scaffold with adjustable compressive strength, which mimicked the structure of natural cortical/cancellous bone, was fabricated. The dense tubular CPC shell was prepared by isostatic pressing CPC powder with a specially designed mould. A porous CPC core with unidirectional lamellar pore structure was fabricated inside the cavity of dense tubular CPC shell by unidirectional freeze casting, followed by infiltration of poly(lactic-co-glycolic acid) and immobilization of collagen. The compressive strength of bi-layered CPC-based composite scaffold can be controlled by varying thickness ratio of dense layer to porous layer. Compared to the scaffold without dense shell, the pore interconnection of bi-layered scaffold was not obviously compromised because of its high unidirectional interconnectivity but poor three dimensional interconnectivity. The in vitro results showed that the rat bone marrow stromal cells attached and proliferated well on the bi-layered CPC-based composite scaffold. This novel bi-layered CPC-based composite scaffold is promising for bone repair. PMID:27877603

  20. Electronic band structure effects in monolayer, bilayer, and hybrid graphene structures

    NASA Astrophysics Data System (ADS)

    Puls, Conor

    Since its discovery in 2005, graphene has been the focus of intense theoretical and experimental study owing to its unique two-dimensional band structure and related electronic properties. In this thesis, we explore the electronic properties of graphene structures from several perspectives including the magnetoelectrical transport properties of monolayer graphene, gap engineering and measurements in bilayer graphene, and anomalous quantum oscillation in the monolayer-bilayer graphene hybrids. We also explored the device implications of our findings, and the application of some experimental techniques developed for the graphene work to the study of a complex oxide, Ca3Ru2O7, exhibiting properties of strongly correlated electrons. Graphene's high mobility and ballistic transport over device length scales, make it suitable for numerous applications. However, two big challenges remain in the way: maintaining high mobility in fabricated devices, and engineering a band gap to make graphene compatible with logical electronics and various optical devices. We address the first challenge by experimentally evaluating mobilities in scalable monolayer graphene-based field effect transistors (FETs) and dielectric-covered Hall bars. We find that the mobility is limited in these devices, and is roughly inversely proportional to doping. By considering interaction of graphene's Dirac fermions with local charged impurities at the interface between graphene and the top-gate dielectric, we find that Coulomb scattering is responsible for degraded mobility. Even in the cleanest devices, a band gap is still desirable for electronic applications of graphene. We address this challenge by probing the band structure of bilayer graphene, in which a field-tunable energy band gap has been theoretically proposed. We use planar tunneling spectroscopy of exfoliated bilayer graphene flakes demonstrate both measurement and control of the energy band gap. We find that both the Fermi level and

  1. Molecular structure and dynamical properties of niosome bilayers with and without cholesterol incorporation: A molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Ritwiset, Aksornnarong; Krongsuk, Sriprajak; Johns, Jeffrey Roy

    2016-09-01

    Niosomes are non-ionic surfactant vesicles having a bilayer structure formed by self-assembly of hydrated surfactants, usually with cholesterol incorporation. Stability and mechanical properties of niosomes strongly depend on type of non-ionic surfactants and compositions used. In this study we present the structural and dynamical properties of niosome bilayers composed of sorbitan monostearate (Span60) with 0% and 50% cholesterol compositions which are investigated by using molecular dynamics simulations. The simulations reveal that niosome bilayer without cholesterol prefer to form in the gel phase with a higher order structure, while in the presence of cholesterol the bilayer exhibits more fluidity having a less ordered structure. The niosome bilayer with 50% cholesterol inclusion shows an increase of area per lipid (∼11%) and thickness (∼39%) compared with the niosome bilayer without cholesterol. The Span60 tailgroup orientation of the niosome bilayers without cholesterol exhibits more tilt (34.5o ± 0.5) than that of the bilayer with 50% cholesterol (15.4o ± 0.8). Additionally, our results show that the addition of cholesterol to the bilayer causes the higher in lateral and transverse diffusion, as well as an increase in the hydrogen bond number between Span60 and water. Such characteristics not only enhance the niosome stability but also increase the fluidity, which are necessary for the niosomal drug delivery.

  2. Lysophosphatidylcholine-arbutin complexes form bilayer-like structures.

    PubMed

    Frías, M A; Winik, B; Franzoni, M B; Levstein, P R; Nicastro, A; Gennaro, A M; Diaz, S B; Disalvo, E A

    2008-05-01

    Arbutin is known to suppress melanin production in murine B16 melanoma cells and inhibit phospholipase action. This encourages the possibility to stabilize it in lipid aggregates for its administration in medical applications. Thus, it was of interest to demonstrate that monomyristoylphosphatidylcholine (14:0 lysoPC) and arbutin may form association complexes. This was studied by Electron Microscopy (EM), 31P Nuclear Magnetic Resonance (31P NMR), Electronic Paramagnetic Resonance (EPR) and Fourier Transform Infrared Spectroscopy (FTIR). EM images show the formation of particles of c.a. 6 nm in diameter. For a 1:1 lysoPC-arbutin molar ratio 31P NMR shows a spectrum with a shoulder that resembles the axially symmetric spectrum characteristic of vesicles. The addition of La3+ ions to the arbutin-lysoPC complex allows one to distinguish two phosphorous populations. These results suggest that arbutin-lysoPC forms vesicles with bilayers stabilized in an interdigitated array. FTIR spectroscopy shows that arbutin interacts with the hydrated population of the carbonyl groups and with the phosphates through the formation of hydrogen bonds. It is interpreted that hydrophobic interactions among the phenol group of arbutin and the acyl chain of lysoPC are responsible for the decrease in acyl chain mobility observed at the 5th C level by EPR. A model proposing the formation of interdigitated bilayers of arbutin-lysoPC could explain the experimental results.

  3. Structure and dynamics of POPC bilayers in water solutions of room temperature ionic liquids

    NASA Astrophysics Data System (ADS)

    Benedetto, Antonio; Bingham, Richard J.; Ballone, Pietro

    2015-03-01

    Molecular dynamics simulations in the NPT ensemble have been carried out to investigate the effect of two room temperature ionic liquids (RTILs), on stacks of phospholipid bilayers in water. We consider RTIL compounds consisting of chloride ([bmim][Cl]) and hexafluorophosphate ([bmim][PF6]) salts of the 1-buthyl-3-methylimidazolium ([bmim]+) cation, while the phospholipid bilayer is made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our investigations focus on structural and dynamical properties of phospholipid and water molecules that could be probed by inelastic and quasi-elastic neutron scattering measurements. The results confirm the fast incorporation of [bmim]+ into the lipid phase already observed in previous simulations, driven by the Coulomb attraction of the cation for the most electronegative oxygens in the POPC head group and by sizeable dispersion forces binding the neutral hydrocarbon tails of [bmim]+ and of POPC. The [bmim]+ absorption into the bilayer favours the penetration of water into POPC, causes a slight but systematic thinning of the bilayer, and further stabilises hydrogen bonds at the lipid/water interface that already in pure samples (no RTIL) display a lifetime much longer than in bulk water. On the other hand, the effect of RTILs on the diffusion constant of POPC (DPOPC) does not reveal a clearly identifiable trend, since DPOPC increases upon addition of [bmim][Cl] and decreases in the [bmim][PF6] case. Moreover, because of screening, the electrostatic signature of each bilayer is only moderately affected by the addition of RTIL ions in solution. The analysis of long wavelength fluctuations of the bilayers shows that RTIL sorption causes a general decrease of the lipid/water interfacial tension and bending rigidity, pointing to the destabilizing effect of RTILs on lipid bilayers.

  4. Structure and dynamics of POPC bilayers in water solutions of room temperature ionic liquids

    SciTech Connect

    Benedetto, Antonio; Bingham, Richard J.; Ballone, Pietro

    2015-03-28

    Molecular dynamics simulations in the NPT ensemble have been carried out to investigate the effect of two room temperature ionic liquids (RTILs), on stacks of phospholipid bilayers in water. We consider RTIL compounds consisting of chloride ([bmim][Cl]) and hexafluorophosphate ([bmim][PF{sub 6}]) salts of the 1-buthyl-3-methylimidazolium ([bmim]{sup +}) cation, while the phospholipid bilayer is made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our investigations focus on structural and dynamical properties of phospholipid and water molecules that could be probed by inelastic and quasi-elastic neutron scattering measurements. The results confirm the fast incorporation of [bmim]{sup +} into the lipid phase already observed in previous simulations, driven by the Coulomb attraction of the cation for the most electronegative oxygens in the POPC head group and by sizeable dispersion forces binding the neutral hydrocarbon tails of [bmim]{sup +} and of POPC. The [bmim]{sup +} absorption into the bilayer favours the penetration of water into POPC, causes a slight but systematic thinning of the bilayer, and further stabilises hydrogen bonds at the lipid/water interface that already in pure samples (no RTIL) display a lifetime much longer than in bulk water. On the other hand, the effect of RTILs on the diffusion constant of POPC (D{sub POPC}) does not reveal a clearly identifiable trend, since D{sub POPC} increases upon addition of [bmim][Cl] and decreases in the [bmim][PF{sub 6}] case. Moreover, because of screening, the electrostatic signature of each bilayer is only moderately affected by the addition of RTIL ions in solution. The analysis of long wavelength fluctuations of the bilayers shows that RTIL sorption causes a general decrease of the lipid/water interfacial tension and bending rigidity, pointing to the destabilizing effect of RTILs on lipid bilayers.

  5. General model of phospholipid bilayers in fluid phase within the single chain mean field theory

    NASA Astrophysics Data System (ADS)

    Guo, Yachong; Pogodin, Sergey; Baulin, Vladimir A.

    2014-05-01

    Coarse-grained model for saturated phospholipids: 1,2-didecanoyl-sn-glycero-3-phosphocholine (DCPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and unsaturated phospholipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2- dioleoyl-sn-glycero-3-phosphocholine (DOPC) is introduced within the single chain mean field theory. A single set of parameters adjusted for DMPC bilayers gives an adequate description of equilibrium and mechanical properties of a range of saturated lipid molecules that differ only in length of their hydrophobic tails and unsaturated (POPC, DOPC) phospholipids which have double bonds in the tails. A double bond is modeled with a fixed angle of 120°, while the rest of the parameters are kept the same as saturated lipids. The thickness of the bilayer and its hydrophobic core, the compressibility, and the equilibrium area per lipid correspond to experimentally measured values for each lipid, changing linearly with the length of the tail. The model for unsaturated phospholipids also fetches main thermodynamical properties of the bilayers. This model is used for an accurate estimation of the free energies of the compressed or stretched bilayers in stacks or multilayers and gives reasonable estimates for free energies. The proposed model may further be used for studies of mixtures of lipids, small molecule inclusions, interactions of bilayers with embedded proteins.

  6. General model of phospholipid bilayers in fluid phase within the single chain mean field theory

    SciTech Connect

    Guo, Yachong; Baulin, Vladimir A.; Pogodin, Sergey

    2014-05-07

    Coarse-grained model for saturated phospholipids: 1,2-didecanoyl-sn-glycero-3-phosphocholine (DCPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and unsaturated phospholipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2- dioleoyl-sn-glycero-3-phosphocholine (DOPC) is introduced within the single chain mean field theory. A single set of parameters adjusted for DMPC bilayers gives an adequate description of equilibrium and mechanical properties of a range of saturated lipid molecules that differ only in length of their hydrophobic tails and unsaturated (POPC, DOPC) phospholipids which have double bonds in the tails. A double bond is modeled with a fixed angle of 120°, while the rest of the parameters are kept the same as saturated lipids. The thickness of the bilayer and its hydrophobic core, the compressibility, and the equilibrium area per lipid correspond to experimentally measured values for each lipid, changing linearly with the length of the tail. The model for unsaturated phospholipids also fetches main thermodynamical properties of the bilayers. This model is used for an accurate estimation of the free energies of the compressed or stretched bilayers in stacks or multilayers and gives reasonable estimates for free energies. The proposed model may further be used for studies of mixtures of lipids, small molecule inclusions, interactions of bilayers with embedded proteins.

  7. General model of phospholipid bilayers in fluid phase within the single chain mean field theory.

    PubMed

    Guo, Yachong; Pogodin, Sergey; Baulin, Vladimir A

    2014-05-07

    Coarse-grained model for saturated phospholipids: 1,2-didecanoyl-sn-glycero-3-phosphocholine (DCPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and unsaturated phospholipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2- dioleoyl-sn-glycero-3-phosphocholine (DOPC) is introduced within the single chain mean field theory. A single set of parameters adjusted for DMPC bilayers gives an adequate description of equilibrium and mechanical properties of a range of saturated lipid molecules that differ only in length of their hydrophobic tails and unsaturated (POPC, DOPC) phospholipids which have double bonds in the tails. A double bond is modeled with a fixed angle of 120°, while the rest of the parameters are kept the same as saturated lipids. The thickness of the bilayer and its hydrophobic core, the compressibility, and the equilibrium area per lipid correspond to experimentally measured values for each lipid, changing linearly with the length of the tail. The model for unsaturated phospholipids also fetches main thermodynamical properties of the bilayers. This model is used for an accurate estimation of the free energies of the compressed or stretched bilayers in stacks or multilayers and gives reasonable estimates for free energies. The proposed model may further be used for studies of mixtures of lipids, small molecule inclusions, interactions of bilayers with embedded proteins.

  8. Particle-based simulations of bilayer membranes: self-assembly, structural analysis, and shock-wave damage

    NASA Astrophysics Data System (ADS)

    Steinhauser, Martin O.; Schindler, Tanja

    2017-01-01

    We report on the results of particle-based, coarse-grained molecular dynamics simulations of amphiphilic lipid molecules in aqueous environment where the membrane structures at equilibrium are subsequently exposed to strong shock waves, and their damage is analyzed. The lipid molecules self-assemble from unbiased random initial configurations to form stable bilayer membranes, including closed vesicles. During self-assembly of lipid molecules, we observe several stages of clustering, starting with many small clusters of lipids, gradually merging together to finally form one single bilayer membrane. We find that the clustering of lipids sensitively depends on the hydrophobic interaction h_c of the lipid tails in our model and on temperature T of the system. The self-assembled bilayer membranes are quantitatively analyzed at equilibrium with respect to their degree of order and their local structure. We also show that—by analyzing the membrane fluctuations and using a linearized theory— we obtain area compression moduli K_A and bending stiffnesses κ _B for our bilayer membranes which are within the experimental range of in vivo and in vitro measurements of biological membranes. We also discuss the density profile and the pair correlation function of our model membranes at equilibrium which has not been done in previous studies of particle-based membrane models. Furthermore, we present a detailed phase diagram of our lipid model that exhibits a sol-gel transition between quasi-solid and fluid domains, and domains where no self-assembly of lipids occurs. In addition, we present in the phase diagram the conditions for temperature T and hydrophobicity h_c of the lipid tails of our model to form closed vesicles. The stable bilayer membranes obtained at equilibrium are then subjected to strong shock waves in a shock tube setup, and we investigate the damage in the membranes due to their interaction with shock waves. Here, we find a transition from self

  9. Light scattering on the structural characterization of DMPG vesicles along the bilayer anomalous phase transition.

    PubMed

    Enoki, Thais A; Henriques, Vera B; Lamy, M Teresa

    2012-12-01

    Highly charged vesicles of the saturated anionic lipid dimyristoyl phosphatidylglycerol (DMPG) in low ionic strength medium exhibit a very peculiar thermo-structural behavior. Along a wide gel-fluid transition region, DMPG dispersions display several anomalous characteristics, like low turbidity, high electrical conductivity and viscosity. Here, static and dynamic light scattering (SLS and DLS) were used to characterize DMPG vesicles at different temperatures. Similar experiments were performed with the largely studied zwitterionic lipid dimyristoyl phosphatidylcholine (DMPC). SLS and DLS data yielded similar dimensions for DMPC vesicles at all studied temperatures. However, for DMPG, along the gel-fluid transition region, SLS indicated a threefold increase in the vesicle radius of gyration, whereas the hydrodynamic radius, as obtained from DLS, increased 30% only. Despite the anomalous increase in the radius of gyration, DMPG lipid vesicles maintain isotropy, since no light depolarization was detected. Hence, SLS data are interpreted regarding the presence of isotropic vesicles within the DMPG anomalous transition, but highly perforated vesicles, with large holes. DLS/SLS discrepancy along the DMPG transition region is discussed in terms of the interpretation of the Einstein-Stokes relation for porous vesicles. Therefore, SLS data are shown to be much more appropriate for measuring porous vesicle dimensions than the vesicle diffusion coefficient. The underlying nanoscopic process which leads to the opening of pores in charged DMPG bilayer is very intriguing and deserves further investigation. One could envisage biotechnological applications, with vesicles being produced to enlarge and perforate in a chosen temperature and/or pH value. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  10. Molecular dynamics simulation of the structure of dimyristoylphosphatidylcholine bilayers with cholesterol, ergosterol, and lanosterol.

    PubMed Central

    Smondyrev, A M; Berkowitz, M L

    2001-01-01

    Five molecular dynamics computer simulations were performed on different phospholipid:sterol membrane systems in order to study the influence of sterol structure on membrane properties. Three of these simulated bilayer systems were composed of a 1:8 sterol:phospholipid ratio, each of which employed one of the sterol molecules: cholesterol, ergosterol, and lanosterol. The two other simulations were of a bilayer with a 1:1 sterol:phospholipid ratio. These simulations employed cholesterol and lanosterol, respectively, as their sterol components. The observed differences in simulations with cholesterol and lanosterol may have their implication on the form of the phospholipid/sterol phase diagram. PMID:11259280

  11. Transient cavitation in fluid-structure interactions

    SciTech Connect

    Kot, C.A.; Hsieh, B.J.; Youngdahl, C.K.; Valentin, R.A.

    1981-11-01

    A generalized column separation model is extended to predict transient cavitation associated with fluid-structure interactions. The essential feature of the combined fluid-structure interaction calculations is the coupling between the fluid transient, which is computed one dimensionally, and the structural response which can be multidimensional. Proper coupling is achieved by defining an average, one-dimensional, structural velocity and by assuming a spatially uniform pressure loading of the structure. This procedure is found to be effective even for complex finite element structural models for which the required computational time step is orders of magnitude smaller than that for the fluid transient. Computational examples and comparison with experimental data show that neglecting cavitation and setting the fluid velocity at all times equal to that of the structural boundary leads to unreal negative pressure predictions. A properly coupled column separation model reproduces the important features of fluid-structure interactions, converges rapidly, and gives reasonable fluid and structural response predictions. 9 refs.

  12. Dependency of {gamma}-secretase complex activity on the structural integrity of the bilayer

    SciTech Connect

    Zhou, Hua; Zhou, Shuxia; Walian, Peter J.; Jap, Bing K.

    2010-11-12

    Research highlights: {yields} Partial solubilization of membranes with CHAPSO can increase {gamma}-secretase activity. {yields} Completely solubilized {gamma}-secretase is inactive. {yields} Purified {gamma}-secretase regains activity after reconstitution into lipid bilayers. {yields} A broad range of detergents can be used to successfully reconstitute {gamma}-secretase. -- Abstract: {gamma}-secretase is a membrane protein complex associated with the production of A{beta} peptides that are pathogenic in Alzheimer's disease. We have characterized the activity of {gamma}-secretase complexes under a variety of detergent solubilization and reconstitution conditions, and the structural state of proteoliposomes by electron microscopy. We found that {gamma}-secretase activity is highly dependent on the physical state or integrity of the membrane bilayer - partial solubilization may increase activity while complete solubilization will abolish it. The activity of well-solubilized {gamma}-secretase can be restored to near native levels when properly reconstituted into a lipid bilayer environment.

  13. Determination of the electronic structure of bilayer graphene from infrared spectroscopy results

    SciTech Connect

    Zhang, L. M.; Li, Z. Q.; Basov, D. N.; Fogler, M. M.; Hao, Z.; Martin, Michael C.

    2008-11-12

    We present an experimental study of the infrared conductivity, transmission, and reflection of a gated bilayer graphene and their theoretical analysis within the Slonczewski-Weiss-McClure (SWMc) model. The infrared response is shown to be governed by the interplay of the interband and the intraband transitions among the four bands of the bilayer. The position of the main conductivity peak at thecharge-neutrality point is determined by the interlayer tunneling frequency. The shift of this peak as a function of the gate voltage gives information about less known parameters of the SWMc model such as those responsible for the electron-hole and sublattice asymmetries. These parameter values are shown to be consistent with recent electronic structure calculations for the bilayer graphene and the SWMc parameters commonly used for the bulk graphite.

  14. Monolayer-to-bilayer transformation of silicenes and their structural analysis

    NASA Astrophysics Data System (ADS)

    Yaokawa, Ritsuko; Ohsuna, Tetsu; Morishita, Tetsuya; Hayasaka, Yuichiro; Spencer, Michelle J. S.; Nakano, Hideyuki

    2016-02-01

    Silicene, a two-dimensional honeycomb network of silicon atoms like graphene, holds great potential as a key material in the next generation of electronics; however, its use in more demanding applications is prevented because of its instability under ambient conditions. Here we report three types of bilayer silicenes that form after treating calcium-intercalated monolayer silicene (CaSi2) with a BF4- -based ionic liquid. The bilayer silicenes that are obtained are sandwiched between planar crystals of CaF2 and/or CaSi2, with one of the bilayer silicenes being a new allotrope of silicon, containing four-, five- and six-membered sp3 silicon rings. The number of unsaturated silicon bonds in the structure is reduced compared with monolayer silicene. Additionally, the bandgap opens to 1.08 eV and is indirect; this is in contrast to monolayer silicene which is a zero-gap semiconductor.

  15. Monolayer-to-bilayer transformation of silicenes and their structural analysis

    PubMed Central

    Yaokawa, Ritsuko; Ohsuna, Tetsu; Morishita, Tetsuya; Hayasaka, Yuichiro; Spencer, Michelle J. S.; Nakano, Hideyuki

    2016-01-01

    Silicene, a two-dimensional honeycomb network of silicon atoms like graphene, holds great potential as a key material in the next generation of electronics; however, its use in more demanding applications is prevented because of its instability under ambient conditions. Here we report three types of bilayer silicenes that form after treating calcium-intercalated monolayer silicene (CaSi2) with a BF4− -based ionic liquid. The bilayer silicenes that are obtained are sandwiched between planar crystals of CaF2 and/or CaSi2, with one of the bilayer silicenes being a new allotrope of silicon, containing four-, five- and six-membered sp3 silicon rings. The number of unsaturated silicon bonds in the structure is reduced compared with monolayer silicene. Additionally, the bandgap opens to 1.08 eV and is indirect; this is in contrast to monolayer silicene which is a zero-gap semiconductor. PMID:26847858

  16. Structure of exciton condensates in imbalanced electron-hole bilayers

    NASA Astrophysics Data System (ADS)

    Varley, J. R.; Lee, D. K. K.

    2016-11-01

    We investigate the possibility of excitonic superfluidity in electron-hole bilayers. We calculate the phase diagram of the system for the whole range of electron-hole density imbalance and for different degrees of electrostatic screening, using mean-field theory and a Ginzburg-Landau expansion. We are able to resolve differences on previous work in the literature which concentrated on restricted regions of the parameter space. We also give detailed descriptions of the pairing wave function in the Fulde-Ferrell-Larkin-Ovchinnikov paired state. The Ginzburg-Landau treatment allows us to investigate the energy scales involved in the pairing state and discuss the possible spontaneous breaking of two-dimensional translation symmetry in the ground state.

  17. An unconventional bilayer ice structure on a NaCl(001) film.

    PubMed

    Chen, Ji; Guo, Jing; Meng, Xiangzhi; Peng, Jinbo; Sheng, Jiming; Xu, Limei; Jiang, Ying; Li, Xin-Zheng; Wang, En-Ge

    2014-05-30

    Water-solid interactions are of broad importance both in nature and technology. The hexagonal bilayer model based on the Bernal-Fowler-Pauling ice rules has been widely adopted to describe water structuring at interfaces. Using a cryogenic scanning tunnelling microscope, here we report a new type of two-dimensional ice-like bilayer structure built from cyclic water tetramers on an insulating NaCl(001) film, which is completely beyond this conventional bilayer picture. A novel bridging mechanism allows the interconnection of water tetramers to form chains, flakes and eventually a two-dimensional extended ice bilayer containing a regular array of Bjerrum D-type defects. Ab initio density functional theory calculations substantiate this bridging growth mode and reveal a striking proton-disordered ice structure. The formation of the periodic Bjerrum defects with unusually high density may have a crucial role as H donor sites in directing multilayer ice growth and in catalysing heterogeneous chemical reactions on water-coated salt surfaces.

  18. Scanning tunneling spectroscopy of inhomogeneous electronic structure in monolayer and bilayer graphene on SiC

    NASA Astrophysics Data System (ADS)

    Brar, Victor W.; Zhang, Yuanbo; Yayon, Yossi; Ohta, Taisuke; McChesney, Jessica L.; Bostwick, Aaron; Rotenberg, Eli; Horn, Karsten; Crommie, Michael F.

    2007-09-01

    The authors present a scanning tunneling spectroscopy (STS) study of the local electronic structure of single and bilayer graphene grown epitaxially on a SiC(0001) surface. Low voltage topographic images reveal fine, atomic-scale carbon networks, whereas higher bias images are dominated by emergent spatially inhomogeneous large-scale structure similar to a carbon-rich reconstruction of SiC(0001). STS spectroscopy shows an ˜100meV gaplike feature around zero bias for both monolayer and bilayer graphene/SiC, as well as significant spatial inhomogeneity in electronic structure above the gap edge. Nanoscale structure at the SiC/graphene interface is seen to correlate with observed electronic spatial inhomogeneity. These results are relevant for potential devices involving electronic transport or tunneling in graphene/SiC.

  19. Structural and electro-optical properties of bilayer graphyne like BN sheet

    NASA Astrophysics Data System (ADS)

    Behzad, Somayeh

    2016-12-01

    The structural, electronic and optical properties of bilayer graphyne like BN sheet (BNyne) with different stacking manners have been explored by the first-principles calculations. The stabilities of α-BNyne bilayers with different stacking manners are compared. The α-BNyne Bilayers have wide band gaps. Compared to the single α-BNyne, the numbers of energy bands are doubled due to the interlayer interactions and the band gap is reduced. The AB-I configuration has a direct band gap while the band gap becomes indirect for AA-II. The calculated ε2 (ω) of bilayer α-BNyne for (Eǁx) is similar to that of the monolayer α-BNyne, except for the small changes of peak positions and increasing of peak intensities. For (Eǁz), the first absorption peak occures at 3.86 eV, and the prominant peak of monolayer at 9.17 eV becomes broadened. These changes are related to the new transitions resulting from the band splitting.

  20. D IR Line Shapes for Determining the Structure of a Peptide in a Bilayer

    NASA Astrophysics Data System (ADS)

    Woys, Ann Marie; Lin, Y. S.; Skinner, J. S.; Zanni, M. T.; Reddy, A. S.; de Pablo, J. J.

    2010-06-01

    Structure of the antimicrobial peptide, ovispirin, on a lipid bilayer was determined using 2D IR spectroscopy and spectra calculated from molecular dynamics simulations. Ovispirin is an 18 residue amphipathic peptide that binds parallel to the membrane in a mostly alpha helical conformation. 15 of the 18 residues were ^1^3C^1^8O isotopically labeled on the backbone to isolate the amide I vibration at each position. 2D IR spectra were collected for each labeled peptide in 3:1 POPC/POPG vesicles, and peak width along the diagonal was measured. The diagonal line width is sensitive to the vibrator's electrostatic environment, which varies through the bilayer. We observe an oscillatory line width spanning 10 to 24 cm-1 and with a period of nearly 3.6 residues. To further investigate the position of ovispirin in a bilayer, molecular dynamics simulations determined the peptide depth to be just below the lipid headgroups. The trajectory of ovispirin at this depth was used to calculate 2D IR spectra, from which the diagonal line width is measured. Both experimental and simulated line widths are similar in periodicity and suggest a kink in the peptide backbone and the tilt in the bilayer. A. Woys, Y. S. Lin, A. S. Reddy, W. Xiong, J. J. de Pablo, J. S. Skinner, and M. T. Zanni, JACS 132, 2832-2838 (2010).

  1. A Bilayered Structure Comprised of Functionalized Carbon Nanotubes for Desalination by Membrane Distillation.

    PubMed

    Bhadra, Madhuleena; Roy, Sagar; Mitra, Somenath

    2016-08-03

    The development of a novel carbon nanotube (CNT) immobilized membrane comprised of a double-layer structure is presented for water desalination by membrane distillation. The bilayered structure is comprised of CNTs functionalized with a hydrophobic octadecyl amine group on the feed side and carboxylated CNTs on the permeate side. The latter is more hydrophilic. The hydrophobic CNTs provide higher water vapor permeation, while the hydrophilic CNTs facilitate the condensation of water vapor. Together, these led to superior performance, and flux in a direct contact membrane distillation mode was found to be as high as 121 kg/m(2)h at 80 °C. The bilayered membrane represented an enhancement of 70% over the unmodified membrane and 37% over a membrane which had a monolayered structure where only the feed side was CNT-modified.

  2. Self-Organization of a Stable Pore Structure in a Phospholipid Bilayer

    NASA Astrophysics Data System (ADS)

    Koshiyama, Kenichiro; Yano, Takeru; Kodama, Tetsuya

    2010-07-01

    We demonstrate the self-organization process of a stable pore structure in a phospholipid bilayer by unsteady and nonequilibrium molecular dynamics simulations. The simulation is started from an initial state including some amount of water molecules in its hydrophobic region, which is a model of a cell membrane stimulated by ultrasound radiation for the membrane permeabilization (sonoporation). We show that, in several nanoseconds, the bilayer-water system can spontaneously develop into a water-filled pore structure without any mechanical and electrical forcing from outside, when the initial number of water molecules in the hydrophobic region exceeds a critical value. The increase in the initial number of water molecules enhances the probability of pore formation, and sometimes induces the formation of transient micellelike structures of phospholipid molecules.

  3. Self-organization of a stable pore structure in a phospholipid bilayer.

    PubMed

    Koshiyama, Kenichiro; Yano, Takeru; Kodama, Tetsuya

    2010-07-02

    We demonstrate the self-organization process of a stable pore structure in a phospholipid bilayer by unsteady and nonequilibrium molecular dynamics simulations. The simulation is started from an initial state including some amount of water molecules in its hydrophobic region, which is a model of a cell membrane stimulated by ultrasound radiation for the membrane permeabilization (sonoporation). We show that, in several nanoseconds, the bilayer-water system can spontaneously develop into a water-filled pore structure without any mechanical and electrical forcing from outside, when the initial number of water molecules in the hydrophobic region exceeds a critical value. The increase in the initial number of water molecules enhances the probability of pore formation, and sometimes induces the formation of transient micellelike structures of phospholipid molecules.

  4. Partitioning into Colloidal Structures of Fasted State Intestinal Fluid Studied by Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    We performed molecular dynamics (MD) simulations to obtain insights into the structure and molecular interactions of colloidal structures present in fasted state intestinal fluid. Drug partitioning and interaction were studied with a mixed system of the bile salt taurocholate (TCH) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLiPC). Spontaneous aggregation of TCH and DLiPC from unconstrained MD simulations at the united-atom level using the Berger/Gromos54A7 force fields demonstrated that intermolecular hydrogen bonding between TCH molecules was an important factor in determining the overall TCH and DLiPC configuration. In bilayered systems, these intermolecular hydrogen bonds resulted in embedded transmembrane TCH clusters. Free energy simulations using the umbrella sampling technique revealed that the stability of these transmembrane TCH clusters was superior when they consisted of 3 or 4 TCH per bilayer leaflet. All-atom simulations using the Slipids/GAFF force fields showed that the TCH embedded in the bilayer decreased the energy barrier to penetrate the bilayer (ΔGpen) for water, ethanol, and carbamazepine, but not for the more lipophilic felodipine and danazol. This suggests that diffusion of hydrophilic to moderately lipophilic molecules through the bilayer is facilitated by the embedded TCH molecules. However, the effect of embedded TCH on the overall lipid/water partitioning was significant for danazol, indicating that the incorporation of TCH plays a crucial role for the partitioning of lipophilic solutes into e.g. lipidic vesicles existing in fasted state intestinal fluids. To conclude, the MD simulations revealed important intermolecular interactions in lipidic bilayers, both between the bile components themselves and with the drug molecules. PMID:27934534

  5. Graphane/fluorographene bilayer: considerable C-H···F-C hydrogen bonding and effective band structure engineering.

    PubMed

    Li, Yafei; Li, Fengyu; Chen, Zhongfang

    2012-07-11

    Systematic density functional theory (DFT) computations revealed the existence of considerable C-H···F-C bonding between the experimentally realized graphane and fluorographene layers. The unique C-H···F-C bonds define the conformation of graphane/fluorographene (G/FG) bilayer and contribute to its stability. Interestingly, G/FG bilayer has an energy gap (0.5 eV) much lower than those of individual graphane and fluorographene. The binding strength of G/FG bilayer can be significantly enhanced by applying appropriate external electric field (E-field). Especially, changing the direction and strength of E-field can effectively modulate the energy gap of G/FG bilayer, and correspondingly causes a semiconductor-metal transition. These findings open new opportunities in fabricating new electronics and opto-electronics devices based on G/FG bilayer, and call for more efforts in using weak interactions for band structure engineering.

  6. Fluid control structures in microfluidic devices

    NASA Technical Reports Server (NTRS)

    Mathies, Richard A. (Inventor); Grover, William H. (Inventor); Skelley, Alison (Inventor); Lagally, Eric (Inventor); Liu, Chung N. (Inventor)

    2008-01-01

    Methods and apparatus for implementing microfluidic analysis devices are provided. A monolithic elastomer membrane associated with an integrated pneumatic manifold allows the placement and actuation of a variety of fluid control structures, such as structures for pumping, isolating, mixing, routing, merging, splitting, preparing, and storing volumes of fluid. The fluid control structures can be used to implement a variety of sample introduction, preparation, processing, and storage techniques.

  7. Fluid control structures in microfluidic devices

    DOEpatents

    Mathies, Richard A.; Grover, William H.; Skelley, Alison; Lagally, Eric; Liu, Chung N.

    2017-05-09

    Methods and apparatus for implementing microfluidic analysis devices are provided. A monolithic elastomer membrane associated with an integrated pneumatic manifold allows the placement and actuation of a variety of fluid control structures, such as structures for pumping, isolating, mixing, routing, merging, splitting, preparing, and storing volumes of fluid. The fluid control structures can be used to implement a variety of sample introduction, preparation, processing, and storage techniques.

  8. Fluid control structures in microfluidic devices

    DOEpatents

    Mathies, Richard A.; Grover, William H.; Skelley, Alison; Lagally, Eric; Liu, Chung N.

    2008-11-04

    Methods and apparatus for implementing microfluidic analysis devices are provided. A monolithic elastomer membrane associated with an integrated pneumatic manifold allows the placement and actuation of a variety of fluid control structures, such as structures for pumping, isolating, mixing, routing, merging, splitting, preparing, and storing volumes of fluid. The fluid control structures can be used to implement a variety of sample introduction, preparation, processing, and storage techniques.

  9. Structure and location of amiodarone in a membrane bilayer as determined by molecular mechanics and quantitative x-ray diffraction.

    PubMed

    Trumbore, M; Chester, D W; Moring, J; Rhodes, D; Herbette, L G

    1988-09-01

    Amiodarone is a drug used in the treatment of cardiac arrhythmias and is believed to have a persistent interaction with cellular membranes. This study sought to examine the structure and location of amiodarone in a membrane bilayer. Amiodarone has a high membrane partition coefficient on the order of 10(6). Small angle x-ray diffraction was used to determine the position of the iodine atoms of amiodarone in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under conditions of low temperature and hydration where the DPPC bilayer is in the gel state. The time-averaged position of the iodine atoms was determined to be approximately 6 A from the center (terminal methyl region) of the lipid bilayer. A dielectric constant of kappa = 2, which approximates that of the bilayer hydrocarbon core region, was used in calculating a minimum energy structure for membrane-bound amiodarone. This calculated structure when compared with the crystal structure of amiodarone demonstrated that amiodarone could assume a conformation in the bilayer significantly different from that in the crystal. The results reported here are an attempt to correlate the position of a membrane-active drug in a lipid bilayer with its time-averaged conformation. This type of analysis promises to be of great use in the design of drugs with greater potency and higher specificity.

  10. Structure and location of amiodarone in a membrane bilayer as determined by molecular mechanics and quantitative x-ray diffraction.

    PubMed Central

    Trumbore, M; Chester, D W; Moring, J; Rhodes, D; Herbette, L G

    1988-01-01

    Amiodarone is a drug used in the treatment of cardiac arrhythmias and is believed to have a persistent interaction with cellular membranes. This study sought to examine the structure and location of amiodarone in a membrane bilayer. Amiodarone has a high membrane partition coefficient on the order of 10(6). Small angle x-ray diffraction was used to determine the position of the iodine atoms of amiodarone in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under conditions of low temperature and hydration where the DPPC bilayer is in the gel state. The time-averaged position of the iodine atoms was determined to be approximately 6 A from the center (terminal methyl region) of the lipid bilayer. A dielectric constant of kappa = 2, which approximates that of the bilayer hydrocarbon core region, was used in calculating a minimum energy structure for membrane-bound amiodarone. This calculated structure when compared with the crystal structure of amiodarone demonstrated that amiodarone could assume a conformation in the bilayer significantly different from that in the crystal. The results reported here are an attempt to correlate the position of a membrane-active drug in a lipid bilayer with its time-averaged conformation. This type of analysis promises to be of great use in the design of drugs with greater potency and higher specificity. PMID:3207838

  11. Superhard behaviour, low residual stress, and unique structure in diamond-like carbon films by simple bilayer approach

    SciTech Connect

    Dwivedi, Neeraj; Kumar, Sushil; Malik, Hitendra K.

    2012-07-15

    Simple bilayer approach is proposed for synthesizing hard and superhard diamond-like carbon (DLC) coatings with reduced residual stress. For this, M/DLC bilayer (M = Ti and Cu) structures are grown using hybrid system involving radio frequency (RF)-sputtering and RF-plasma enhanced chemical vapor deposition techniques. Ti/DLC bilayer deposited at negative self bias of 100 V shows superhard behaviour with hardness (H) as 49 GPa. Cu/DLC bilayer grown at self bias of 100 V exhibits hard behaviour with H as 22.8 GPa. The hardness of Ti/DLC (Cu/DLC) bilayer gets changed from superhard (hard) to hard (moderate hard) regime, when the self bias is raised to 300 V. Residual stress in Ti/DLC (Cu/DLC) bilayer is found to be significantly low that varies in the range of 1 GPa-1.65 GPa (0.8 GPa-1.6 GPa). The microstructure and morphology are studied by Raman spectroscopy, scanning electron microscopy (SEM), and atomic force microscopy (AFM). SEM and AFM pictures reveal the creation of nanostructured features in the deposited bilayers. Raman, SEM, and AFM analyses are correlated with the nano-mechanical properties. Owing to excellent nano-mechanical properties, these bilayers can find their direct industrial applications as hard and protective coatings.

  12. Laurdan spectrum decomposition as a tool for the analysis of surface bilayer structure and polarity: a study with DMPG, peptides and cholesterol.

    PubMed

    Lúcio, Aline D; Vequi-Suplicy, Cíntia C; Fernandez, Roberto M; Lamy, M Teresa

    2010-03-01

    The highly hydrophobic fluorophore Laurdan (6-dodecanoyl-2-(dimethylaminonaphthalene)) has been widely used as a fluorescent probe to monitor lipid membranes. Actually, it monitors the structure and polarity of the bilayer surface, where its fluorescent moiety is supposed to reside. The present paper discusses the high sensitivity of Laurdan fluorescence through the decomposition of its emission spectrum into two Gaussian bands, which correspond to emissions from two different excited states, one more solvent relaxed than the other. It will be shown that the analysis of the area fraction of each band is more sensitive to bilayer structural changes than the largely used parameter called Generalized Polarization, possibly because the latter does not completely separate the fluorescence emission from the two different excited states of Laurdan. Moreover, it will be shown that this decomposition should be done with the spectrum as a function of energy, and not wavelength. Due to the presence of the two emission bands in Laurdan spectrum, fluorescence anisotropy should be measured around 480 nm, to be able to monitor the fluorescence emission from one excited state only, the solvent relaxed state. Laurdan will be used to monitor the complex structure of the anionic phospholipid DMPG (dimyristoyl phosphatidylglycerol) at different ionic strengths, and the alterations caused on gel and fluid membranes due to the interaction of cationic peptides and cholesterol. Analyzing both the emission spectrum decomposition and anisotropy it was possible to distinguish between effects on the packing and on the hydration of the lipid membrane surface. It could be clearly detected that a more potent analog of the melanotropic hormone alpha-MSH (Ac-Ser(1)-Tyr(2)-Ser(3)-Met(4)-Glu(5)-His(6)-Phe(7)-Arg(8)-Trp(9)-Gly(10)-Lys(11)-Pro(12)-Val(13)-NH(2)) was more effective in rigidifying the bilayer surface of fluid membranes than the hormone, though the hormone significantly decreases the

  13. The influence of hyaluronan on the structure of a DPPC-bilayer under high pressures.

    PubMed

    Zander, Thomas; Wieland, D C Florian; Raj, Akanksha; Wang, Min; Nowak, Benedikt; Krywka, Christina; Dėdinaitė, Andra; Claesson, Per Martin; Garamus, Vasil M; Schreyer, Andreas; Willumeit-Römer, Regine

    2016-06-01

    The superior lubrication properties of synovial joints have inspired many studies aiming at uncovering the molecular mechanisms which give rise to low friction and wear. However, the mechanisms are not fully understood yet, and, in particular, it has not been elucidated how the biolubricants present at the interface of cartilage respond to high pressures, which arise during high loads of joints. In this study we utilize a simple model system composed of two biomolecules that have been implied as being important for joint lubrication. It consists of a solid supported dipalmitoylphosphatidylcholin (DPPC) bilayer, which was formed via vesicles fusion on a flat Si wafer, and the anionic polysaccharide hyaluronan (HA). We first characterized the structure of the HA layer that adsorbed to the DPPC bilayers at ambient pressure and different temperatures using X-ray reflectivity (XRR) measurements. Next, XRR was utilized to evaluate the response of the system to high hydrostatic pressures, up to 2kbar (200MPa), at three different temperatures. By means of fluorescence microscopy images the distribution of DPPC and HA on the surface was visualized. Our data suggest that HA adsorbs to the headgroup region that is oriented towards the water side of the supported bilayer. Phase transitions of the bilayer in response to temperature and pressure changes were also observed in presence and absence of HA. Our results reveal a higher stability against high hydrostatic pressures for DPPC/HA composite layers compared to that of the DPPC bilayer in absence of HA. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Molecular characterization of gel and liquid-crystalline structures of fully hydrated POPC and POPE bilayers.

    PubMed

    Leekumjorn, Sukit; Sum, Amadeu K

    2007-05-31

    Molecular dynamics simulations were used for a comprehensive study of the structural properties of monounsaturated POPC and POPE bilayers in the gel and liquid-crystalline state at a number of temperatures, ranging from 250 to 330 K. Though the chemical structures of POPC and POPE are largely similar (choline versus ethanolamine headgroup), their transformation processes from a gel to a liquid-crystalline state are contrasting. In the similarities, the lipid tails for both systems are tilted below the phase transition and become more random above the phase transition temperature. The average area per lipid and bilayer thickness were found less sensitive to phase transition changes as the unsaturated tails are able to buffer reordering of the bilayer structure, as observed from hysteresis loops in annealing simulations. For POPC, changes in the structural properties such as the lipid tail order parameter, hydrocarbon trans-gauche isomerization, lipid tail tilt-angle, and level of interdigitation identified a phase transition at about 270 K. For POPE, three temperature ranges were identified, in which the lower one (270-280 K) was associated with a pre-transition state and the higher (290-300 K) with the post-transition state. In the pre-transition state, there was a significant increase in the number of gauche arrangements formed along the lipid tails. Near the main transition (280-290 K), there was a lowering of the lipid order parameters and a disappearance of the tilted lipid arrangement. In the post-transition state, the carbon atoms along the lipid tails became less hindered as their density profiles showed uniform distributions. This study also demonstrates that atomistic simulations of current lipid force fields are capable of capturing the phase transition behavior of lipid bilayers, providing a rich set of molecular and structural information at and near the main transition state.

  15. Direct Measurement of the Tunable Electronic Structure of Bilayer MoS 2 by Interlayer Twist

    DOE PAGES

    Yeh, Po-Chun; Jin, Wencan; Zaki, Nader; ...

    2016-01-13

    We measure the interlayer twist angle-dependent electronic band structure of bilayer molybdenum-disulfide (MoS2), using angle-resolved photoemission on micrometer-scale sample areas. Our measurements, performed on arbitrarily stacked bilayer MoS2 flakes prepared by chemical vapor deposition, provide direct evidence for a downshift of the quasiparticle energy of the valence band at the Brillouin zone center (more » $$\\bar{Γ}$$ point) with the interlayer twist angle, up to a maximum of 120 meV at a twist angle of ~40°. Our direct measurements of the valence band structure enable the extraction of the hole effective mass as a function of the interlayer twist angle. While our results at $$\\bar{Γ}$$ agree with recently published photoluminescence data, our measurements of the quasiparticle spectrum over the full 2D Brillouin zone reveal a richer and more complicated change in the electronic structure than previously theoretically predicted. Furthermore, the electronic structure measurements reported here, including the evolution of the effective mass with twist-angle, provide new insight into the physics of twisted transition-metal dichalcogenide bilayers and serve as a guide for the practical design of MoS2 optoelectronic and spin-/valley-tronic devices.« less

  16. Improve the operational stability of the inverted organic solar cells using bilayer metal oxide structure.

    PubMed

    Chang, Jingjing; Lin, Zhenhua; Jiang, Changyun; Zhang, Jie; Zhu, Chunxiang; Wu, Jishan

    2014-11-12

    Operational stability is a big obstacle for the application of inverted organic solar cells (OSCs), however, less talked about in the research reports. Due to photoinduced degradation of the metal oxide interlayer, which can cause shunts generation and degeneration in ZnO interlayer, a significant degradation of open circuit voltage (Voc) and fill factor (FF) has been observed by in situ periodic measurements of the device current density-voltage (J-V) curves with light illumination. By combining TiOx and ZnO to form bilayer structures on ITO, the photovoltaic performance is improved and the photoinduced degradation is reduced. It was found that the device based on ZnO/TiOx bilayer structure achieved better operational stability as compared to that with ZnO or TiOx interlayer.

  17. Voltage-impulse-induced nonvolatile tunable magnetoelectric inductor based on multiferroic bilayer structure

    NASA Astrophysics Data System (ADS)

    Su, Hua; Tang, Xiaoli; Zhang, Huaiwu; Sun, Nian X.

    2016-07-01

    In this study, we developed a voltage-impulse-induced nonvolatile tunable magnetoelectric inductor, which used an amorphous magnetic ribbon/lead zirconate titanate (PZT) multiferroic bilayer structure as a magnetic core. The PZT substrate, which contained defect dipoles through acceptor doping, was used in the bilayer structure to obtain an asymmetric strain-E “butterfly” curve. Different and stable voltage-impulse-induced in-plane residual stain states could be obtained by applying specific voltage impulse excitation modes. These residual strain states induced a nonvolatile inductance variation in the inductor through strain-mediated magnetoelectric coupling. This method provided a promising approach to realize nonvolatile tunable inductors for miniaturized circuits and systems.

  18. Effect of ZrOx/HfOx bilayer structure on switching uniformity and reliability in nonvolatile memory applications

    NASA Astrophysics Data System (ADS)

    Lee, Joonmyoung; Bourim, El Mostafa; Lee, Wootae; Park, Jubong; Jo, Minseok; Jung, Seungjae; Shin, Jungho; Hwang, Hyunsang

    2010-10-01

    We have investigated the bilayer structure of binary oxides such as HfOx and ZrOx for applications to resistance memory. The ZrOx/HfOx bilayer structure shows a lower reset current and operating voltage than an HfOx monolayer under dc sweep voltage. Furthermore, the bilayer structure exhibits a tight distribution of switching parameters, good switching endurance up to 105 cycles, and good data retention at 85 °C. The resistive switching mechanism of memory devices incorporating the ZrOx/HfOx bilayer structure can be attributed to the control of multiple conducting filaments through the occurrence of redox reactions at the tip of the localized filament.

  19. Spherical Nanoparticle Supported Lipid Bilayers for the Structural Study of Membrane Geometry-Sensitive Molecules

    PubMed Central

    Kim, Edward Y.; Briley, Nicole E.; Tyndall, Erin R.; Xu, Jie; Li, Conggang; Ramamurthi, Kumaran S.; Flanagan, John M.; Tian, Fang

    2015-01-01

    Many essential cellular processes including endocytosis and vesicle trafficking require alteration of membrane geometry. These changes are usually mediated by proteins that can sense and/or induce membrane curvature. Using spherical nanoparticle supported lipid bilayers (SSLBs), we characterize how SpoVM, a bacterial development factor, interacts with differently curved membranes by magic angle spinning solid-state NMR. Our results demonstrate that SSLBs are an effective system for structural and topological studies of membrane geometry-sensitive molecules. PMID:26488086

  20. Thickness dependencies of structural and magnetic properties of cubic and tetragonal Heusler alloy bilayer films

    NASA Astrophysics Data System (ADS)

    Ranjbar, R.; Suzuki, K. Z.; Sugihara, A.; Ando, Y.; Miyazaki, T.; Mizukami, S.

    2017-07-01

    The thickness dependencies of the structural and magnetic properties for bilayers of cubic Co-based Heusler alloys (CCHAs: Co2FeAl (CFA), Co2FeSi (CFS), Co2MnAl (CMA), and Co2MnSi (CMS)) and D022-MnGa were investigated. Epitaxy of the B2 structure of CCHAs on a MnGa film was achieved; the smallest thickness with the B2 structure was found for 3-nm-thick CMS and CFS. The interfacial exchange coupling (Jex) was antiferromagnetic (AFM) for all of the CCHAs/MnGa bilayers except for unannealed CFA/MnGa samples. A critical thickness (tcrit) at which perpendicular magnetization appears of approximately 4-10 nm for the CMA/MnGa and CMS/MnGa bilayers was observed, whereas this thickness was 1-3 nm for the CFA/MnGa and CFS/MnGa films. The critical thickness for different CCHAs materials is discussed in terms of saturation magnetization (Ms) and the Jex .

  1. Structure and magnetic property of the FePt/CrPt bilayer.

    PubMed

    Wang, Xiaoyu; Wang, Hai; Jiang, Hongwei; Wang, Peijie; Wang, Jinliang

    2012-02-01

    In this work we have studied the growth sequence of L10-CrPt antiferromagnetic layer effects on the microstructure and magnetic properties of the FePt/CrPt bilayer. The microstructure characteristics were investigated by means of X-ray diffraction and the magnetic properties were measured at room temperature by using a vibrating sample magnetometer. Structural analysis showed that the low-temperature ordering and the in-plane orientation of the FePt layer with the CrPt underlayer were promoted due to lattice mismatch optimized after annealing at 350 degrees. Meanwhile, magnetic analysis also revealed that the FePt/CrPt bilayer had much larger exchange bias (H(E)) and higher coercivity (Hc) when the CrPt layer was as the underlayer after annealing at 350 degrees.

  2. The effect of spin-orbit coupling in band structure and edge states of bilayer graphene

    SciTech Connect

    Sahdan, Muhammad Fauzi; Darma, Yudi

    2015-04-16

    Topological insulators are predicted to be useful ranging from spintronics to quantum computation. Graphene was first predicted to be the precursor of topological insulator by Kane-Mele. They developed a Hamiltonian model to describe the gap opening in graphene. In this work, we investigate the band structure of bilayer grapheme and also its edge states by using this model with analytical approach. The results of our calculation show that the gap opening occurs at K and K’ point in bilayer graphene.In addition, a pair of gapless edge modes occurs both in the zigzag and arm-chair configurations are no longer exist. There are gap created at the edge even though thery are very small.

  3. Organic photovoltaic devices with the bilayer cathode interfacial structure of pyromellitic dianhydride and lithium fluoride

    NASA Astrophysics Data System (ADS)

    Nam, Eunkyoung; Oh, Seungsik; Jung, Donggeun; Kim, Hyoungsub; Chae, Heeyeop; Yi, Junsin

    2012-10-01

    In this study, we fabricated and characterized an organic photovoltaic (OPV) device with a pyromellitic dianhydride (PMDA)/lithium fluoride (LiF) cathode interfacial layer between poly(3-hexylthiophene-2,5-diyl)(P3HT)+[6,6]-phenyl C61 butyric acid methyl ester (PCBM) and Al. Compared to the OPV device with a LiF-only cathode interfacial layer having a power conversion efficiency (PCE) of 2.7%, the OPV device with the bilayer cathode interfacial structure [PMDA (0.3 nm)/LiF (0.7 nm)] exhibited a reduced resistance and a PCE value enhanced to 3.9% under an illumination condition of 100 mW cm-2 (AM1.5). The observed improvement of the OPV characteristics was attributed to the reduced leakage current of the device by the bilayer cathode interfacial layer.

  4. Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

    SciTech Connect

    Sumino, Ayumi; Dewa, Takehisa; Takeuchi, Toshikazu; Sugiura, Ryuta; Sasaki, Nobuaki; Misawa, Nobuo; Tero, Ryugo; Urisu, Tsuneo; Gardiner, Alastair T.; Cogdell, Richard J.; Hashimoto, Hideki; Nango, Mamoru

    2011-07-11

    The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAY), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.

  5. Interlayer coupling in commensurate and incommensurate bilayer structures of transition-metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Wang, Zhan; Yao, Wang; Liu, Gui-Bin; Yu, Hongyi

    2017-03-01

    The interlayer couplings in commensurate and incommensurate bilayer structures of transition-metal dichalcogenides are investigated with perturbative treatment. The interlayer coupling in ±K valleys can be decomposed into a series of hopping terms with distinct phase factors. In H-type and R-type commensurate bilayers, the interference between the three main hopping terms leads to a sensitive dependence of the interlayer coupling strength on the translation that can explain the position dependent local band gap modulation in a heterobilayer moiré superlattice. The interlayer couplings in the Γ valley of valence band and Q valley of conduction band are also studied, where the strong coupling strengths of several hundred meV can play important roles in mediating the ultrafast interlayer charge transfer in heterobilayers of transition-metal dichalcogenides.

  6. Biopolymer-Lipid Bilayer Interaction Modulates the Physical Properties of Liposomes: Mechanism and Structure.

    PubMed

    Tan, Chen; Zhang, Yating; Abbas, Shabbar; Feng, Biao; Zhang, Xiaoming; Xia, Wenshui; Xia, Shuqin

    2015-08-19

    This study was conducted to elucidate the conformational dependence of the modulating ability of chitosan, a positively charged biopolymer, on a new type of liposome composed of mixed lipids including egg yolk phosphatidylcholine (EYPC) and nonionic surfactant (Tween 80). Analysis of the dynamic and structure of bilayer membrane upon interaction with chitosan by fluorescence and electron paramagnetic resonance techniques demonstrated that, in addition to providing a physical barrier for the membrane surface, the adsorption of chitosan extended and crimped chains rigidified the lipid membrane. However, the decrease in relative microviscosity and order parameter suggested that the presence of chitosan coils disturbed the membrane organization. It was also noted that the increase of fluidity in the lipid bilayer center was not pronounced, indicating the shallow penetration of coils into the hydrophobic interior of bilayer. Microscopic observations revealed that chitosan adsorption not only affected the morphology of liposomes but also modulated the particle aggregation and fusion. Especially, a number of very heterogeneous particles were visualized, which tended to confirm the role of chitosan coils as a "polymeric surfactant". In addition to particle deformation, the membrane permeability was also tuned. These findings may provide a new perspective to understand the physiological functionality of biopolymer and design biopolymer-liposome composite structures as delivery systems for bioactive components.

  7. Bilayer splitting in the electronic structure of heavily overdoped Bi(2)Sr(2)CaCu(2)O(8+delta).

    PubMed

    Feng, D L; Armitage, N P; Lu, D H; Damascelli, A; Hu, J P; Bogdanov, P; Lanzara, A; Ronning, F; Shen, K M; Eisaki, H; Kim, C; Shen, Z X; Shimoyama, J; Kishio, K

    2001-06-11

    The electronic structure of heavily overdoped Bi(2)Sr(2)CaCu(2)O(8+delta) is investigated by angle-resolved photoemission spectroscopy. The long-sought bilayer band splitting in this two-plane system is observed in both normal and superconducting states, which qualitatively agrees with the bilayer Hubbard model calculations. The maximum bilayer energy splitting is about 88 meV for the normal state feature, while it is only about 20 meV for the superconducting peak.

  8. Evanescent-wave amplification studied using a bilayer periodic circuit structure and its effective medium model

    NASA Astrophysics Data System (ADS)

    Liu, Ruopeng; Zhao, Bo; Lin, Xian Qi; Cheng, Qiang; Cui, Tie Jun

    2007-03-01

    In this paper, we present both theoretical analysis and experimental verification of evanescent-wave amplification by using a bilayer periodic circuit structure and its effective medium model. We propose a series-shunt capacitor (C-C) structure to simulate a magnetic plasma, whose permittivity is positive and permeability is negative, and a series-shunt inductor (L-L) structure to simulate an electric plasma, whose permittivity is negative and permeability is positive, in which the structure cells are not required to be electrically small. In addition, we derive and define an effective permittivity and permeability for the C-C and L-L structures in closed forms, which are completely different from the published ones. When the two structures are cascaded together to form a bilayer structure, we show that evanescent waves which exist in two single layers independently can be amplified exponentially if a certain resonant condition is satisfied. Such a resonant condition is equivalent to the antimatching condition for the permittivity and permeability of the effectively electric and magnetic plasmas. To show the accuracy of this equivalent medium model, we compare both circuit-simulation results for the C-C and L-L structures and theoretical-prediction results for the effective magnetic and electric plasmas, which have excellent agreement. Finally, we design an experiment using lumped capacitors and inductors mounted on a printed circuit board to verify the amplification of evanescent waves sufficiently. The measurement results have good agreement with the simulation results.

  9. Investigation of the effect of bilayer membrane structures and fluctuation amplitudes on SANS/SAXS profile for short membrane wavelength

    SciTech Connect

    Lee, Victor; Hawa, Takumi

    2013-09-28

    The effect of bilayer membrane structures and fluctuation amplitudes on small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) profile is investigated based on harmonic motions of the surfactant bilayers with bending as well as thickness fluctuation motions. In this study we consider the case in which the wavelength of the bilayer membrane is shorter than the thickness of the membrane. We find that the thickness of the surfactant bilayer membrane, d{sub m}, affects both q{sub dip} and q{sub peak} of I(q,0) profile, and that the fluctuation amplitude, a, of the membrane changes the peak of I(q,0). A simple formula is derived to estimate the thickness of the bilayer based on the q{sub dip} of the profile obtained from the simulation. The resulting estimates of the thickness of the bilayer with harmonic motion showed accuracy within 1%. Moreover, the bilayer thicknesses estimated from the proposed formula show an excellent agreement with the SANS and SAXS experimental results available in the literatures. We also propose a curve fit model, which describes the relationship between the fluctuation amplitude and the normalized q{sub peak} ratio. The present results show the feasibility of the simple formula to estimate the fluctuation amplitude based on the SANS and SAXS profiles.

  10. Investigation of the effect of bilayer membrane structures and fluctuation amplitudes on SANS/SAXS profile for short membrane wavelength

    NASA Astrophysics Data System (ADS)

    Lee, Victor; Hawa, Takumi

    2013-09-01

    The effect of bilayer membrane structures and fluctuation amplitudes on small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) profile is investigated based on harmonic motions of the surfactant bilayers with bending as well as thickness fluctuation motions. In this study we consider the case in which the wavelength of the bilayer membrane is shorter than the thickness of the membrane. We find that the thickness of the surfactant bilayer membrane, dm, affects both qdip and qpeak of I(q,0) profile, and that the fluctuation amplitude, a, of the membrane changes the peak of I(q,0). A simple formula is derived to estimate the thickness of the bilayer based on the qdip of the profile obtained from the simulation. The resulting estimates of the thickness of the bilayer with harmonic motion showed accuracy within 1%. Moreover, the bilayer thicknesses estimated from the proposed formula show an excellent agreement with the SANS and SAXS experimental results available in the literatures. We also propose a curve fit model, which describes the relationship between the fluctuation amplitude and the normalized qpeak ratio. The present results show the feasibility of the simple formula to estimate the fluctuation amplitude based on the SANS and SAXS profiles.

  11. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.

    PubMed

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations.

    PubMed Central

    Saiz, L; Klein, M L

    2001-01-01

    The structure of a fully hydrated mixed (saturated/polyunsaturated) chain lipid bilayer in the biologically relevant liquid crystalline phase has been examined by performing a molecular dynamics study. The model membrane, a 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC, 18:0/22:6 PC) lipid bilayer, was investigated at constant (room) temperature and (ambient) pressure, and the results obtained in the nanosecond time scale reproduced quite well the available experimental data. Polyunsaturated fatty acids are found in high concentrations in neuronal and retinal tissues and are essential for the development of human brain function. The docosahexaenoic fatty acid, in particular, is fundamental for the proper function of the visual receptor rhodopsin. The lipid bilayer order has been investigated through the orientational order parameters. The water-lipid interface has been explored thoroughly in terms of its dimensions and the organization of the different components. Several types of interactions occurring in the system have been analyzed, specifically, the water-hydrocarbon chain, lipid-lipid and lipid-water interactions. The distribution of dihedral angles along the chains and the molecular conformations of the polyunsaturated chain of the lipids have also been studied. Special attention has been focused on the microscopic (molecular) origin of the effects of polyunsaturations on the different physical properties of membranes. PMID:11423407

  13. Structure of (KIAGKIA)3 aggregates in phospholipid bilayers by solid-state NMR.

    PubMed

    Toke, Orsolya; O'Connor, R D; Weldeghiorghis, Thomas K; Maloy, W Lee; Glaser, Ralf W; Ulrich, Anne S; Schaefer, Jacob

    2004-07-01

    The interchain (13)C-(19)F dipolar coupling measured in a rotational-echo double-resonance (REDOR) experiment performed on mixtures of differently labeled KIAGKIA-KIAGKIA-KIAGKIA (K3) peptides (one specifically (13)C labeled, and the other specifically (19)F labeled) in multilamellar vesicles of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol (1:1) shows that K3 forms close-packed clusters, primarily dimers, in bilayers at a lipid/peptide molar ratio (L/P) of 20. Dipolar coupling to additional peptides is weaker than that within the dimers, consistent with aggregates of monomers and dimers. Analysis of the sideband dephasing rates indicates a preferred orientation between the peptide chains of the dimers. The combination of the distance and orientation information from REDOR is consistent with a parallel (N-N) dimer structure in which two K3 helices intersect at a cross-angle of approximately 20 degrees. Static (19)F NMR experiments performed on K3 in oriented lipid bilayers show that between L/P = 200 and L/P = 20, K3 chains change their absolute orientation with respect to the membrane normal. This result suggests that the K3 dimers detected by REDOR at L/P = 20 are not on the surface of the bilayer but are in a membrane pore.

  14. Water replacement hypothesis in atomic detail--factors determining the structure of dehydrated bilayer stacks.

    PubMed

    Golovina, Elena A; Golovin, Andrey V; Hoekstra, Folkert A; Faller, Roland

    2009-07-22

    According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (<1:1, 1:1, and >1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar "stacks" through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis.

  15. Water Replacement Hypothesis in Atomic Detail—Factors Determining the Structure of Dehydrated Bilayer Stacks

    PubMed Central

    Golovina, Elena A.; Golovin, Andrey V.; Hoekstra, Folkert A.; Faller, Roland

    2009-01-01

    Abstract According to the water replacement hypothesis, trehalose stabilizes dry membranes by preventing the decrease of spacing between membrane lipids under dehydration. In this study, we use molecular-dynamics simulations to investigate the influence of trehalose on the area per lipid (APL) and related structural properties of dehydrated bilayers in atomic detail. The starting conformation of a palmitoyloleolylphosphatidylcholine lipid bilayer in excess water was been obtained by self-assembly. A series of molecular-dynamics simulations of palmitoyloleolylphosphatidylcholine with different degrees of dehydration (28.5, 11.7, and 5.4 waters per lipid) and different molar trehalose/lipid ratios (<1:1, 1:1, and >1:1) were carried out in the NPT ensemble. Water removal causes the formation of multilamellar “stacks” through periodic boundary conditions. The headgroups reorient from pointing outward to inward with dehydration. This causes changes in the electrostatic interactions between interfaces, resulting in interface interpenetration. Interpenetration creates self-spacing of the bilayers and prevents gel-phase formation. At lower concentrations, trehalose does not separate the interfaces, and acting together with self-spacing, it causes a considerable increase of APL. APL decreases at higher trehalose concentrations when the layer of sugar physically separates the interfaces. When interfaces are separated, the model confirms the water replacement hypothesis. PMID:19619463

  16. Mosaic Interdigitated Structure in Nanoparticle-Templated Phospholipid Bilayer Supports Partial Lipidation of Apolipoprotein A-I.

    PubMed

    Sun, Wangqiang; Wu, Weiqiang; McMahon, Kaylin M; Rink, Jonathan S; Thaxton, C Shad

    2016-06-01

    Using gold nanoparticle-templated high-density lipoprotein-like particles as a model, the nanoparticle-templated phospholipid bilayer is studied from the bottom-up. Data support the phospholipids have a mosaic interdigitated structure. The discontinuous lipid milieu supports partial lipidation of apolipoprotein A-I, different from an ordinary phospholipid bilayer, suggesting that synergy between nanoparticle templates and bound phospholipid layers can modulate amphiphilic proteins for desired functions.

  17. An ab initio study of the electronic structure of indium and gallium chalcogenide bilayers.

    PubMed

    Ayadi, T; Debbichi, L; Said, M; Lebègue, S

    2017-09-21

    Using first principle calculations, we have studied the structural and electronic properties of two dimensional bilayers of indium and gallium chalcogenides. With density functional theory corrected for van der Waals interactions, the different modes of stacking were investigated in a systematic way, and several of them were found to compete in energy. Then, their band structures were obtained with the GW approximation and found to correspond to indirect bandgap semiconductors with a small dependency on the mode of stacking. Finally, by analysing the electron density, it appeared that GaSe-InS is a promising system for electron-hole separation.

  18. An ab initio study of the electronic structure of indium and gallium chalcogenide bilayers

    NASA Astrophysics Data System (ADS)

    Ayadi, T.; Debbichi, L.; Said, M.; Lebègue, S.

    2017-09-01

    Using first principle calculations, we have studied the structural and electronic properties of two dimensional bilayers of indium and gallium chalcogenides. With density functional theory corrected for van der Waals interactions, the different modes of stacking were investigated in a systematic way, and several of them were found to compete in energy. Then, their band structures were obtained with the GW approximation and found to correspond to indirect bandgap semiconductors with a small dependency on the mode of stacking. Finally, by analysing the electron density, it appeared that GaSe-InS is a promising system for electron-hole separation.

  19. Structural and elastic properties of hybrid bilayer graphene/h-BN with different interlayer distances using DFT

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Malakpour, S.; Ajori, S.

    2014-08-01

    Importance of synthesizing graphene-substrate hybrid structure to open a band gap in graphene and apply them in novel nanoelectronic devices is undeniable. Graphene/hexagonal boron-nitride (h-BN) hybrid bilayer is an important type of these structures. The synthesized h-BN/graphene is found to have interesting electrical properties which is very sensitive to the change of the interlayer distance. This has encourages researchers to tune the energy and band gap of such structures. A change in the interlayer distance can also alter the mechanical properties, considerably, due to the variation of interaction energies. The current study is aimed to characterize the mechanical properties variation with interlayer distance change for h-BN/graphene hybrid bilayer structure. To this end, density functional theory calculations are employed within the generalized gradient approximation (GGA) framework. The results demonstrate that there are different possible equilibrium interlayer distances between layers related to two types of layer configuration, i.e. AA and AB. It is found that increasing the interlayer distance causes reduction of Young's modulus. Also, Young's modulus of hybrid structure is approximately between those of graphene/graphene and h-BN/h-BN bilayer structures and also lower than pristine monolayer graphene and graphite. Unlike the pure bilayer structures, Poisson's ratio of hybrid bilayer structure is found to be higher than those of pristine monolayer graphene and h-BN nanosheets.

  20. Ceramides modulate protein kinase C activity and perturb the structure of Phosphatidylcholine/Phosphatidylserine bilayers.

    PubMed Central

    Huang, H W; Goldberg, E M; Zidovetzki, R

    1999-01-01

    We studied the effects of natural ceramide and a series of ceramide analogs with different acyl chain lengths on the activity of rat brain protein kinase C (PKC) and on the structure of bovine liver phosphatidylcholine (BLPC)/dipalmitoylphosphatidylcholine (DPPC)/dipalmitoylphosphatidylserine (DPPS) (3:1:1 molar ratio) bilayers using (2)H-NMR and specific enzymatic assays in the absence or presence of 7.5 mol % diolein (DO). Only a slight activation of PKC was observed upon addition of the short-chain ceramide analogs (C(2)-, C(6)-, or C(8)-ceramide); natural ceramide or C(16)-ceramide had no effect. In the presence of 7.5 mol % DO, natural ceramide and C(16)-ceramide analog slightly attenuated DO-enhanced PKC activity. (2)H-NMR results demonstrated that natural ceramide and C(16)-ceramide induced lateral phase separation of gel-like and liquid crystalline domains in the bilayers; however, this type of membrane perturbation has no direct effect on PKC activity. The addition of both short-chain ceramide analogs and DO had a synergistic effect in activating PKC, with maximum activity observed with 20 mol % C(6)-ceramide and 15 mol % DO. Further increases in C(6)-ceramide and/or DO concentrations led to decreased PKC activity. A detailed (2)H-NMR investigation of the combined effects of C(6)-ceramide and DO on lipid bilayer structure showed a synergistic effect of these two reagents to increase membrane tendency to adopt nonbilayer structures, resulting in the actual presence of such structures in samples exceeding 20 mol % ceramide and 15 mol % DO. Thus, the increased tendency to form nonbilayer lipid phases correlates with increased PKC activity, whereas the actual presence of such phases reduced the activity of the enzyme. Moreover, the results show that short-chain ceramide analogs, widely used to study cellular effects of ceramide, have biological effects that are not exhibited by natural ceramide. PMID:10465759

  1. Electronic structure of twisted bilayer graphene with doping and under electric fields

    NASA Astrophysics Data System (ADS)

    Xian, Lede; Barraza-Lopez, Salvador; Chou, Mei-Yin

    2011-03-01

    Rotational stacking faults of graphene layers in epitaxial graphene are believed to electronically decouple adjacent layers, thus single-layer graphene-like behavior can be observed. In addition, the layers close to the SiC substrate are known to be electron doped. Using density functional theory and a pi-electron, highly tuned tight-binding model, we study the modifications of the band structure in rotational stack-faulted bilayer graphene induced by doping and by external electric fields. In particular, the interlayer coupling, the magnitude of the Fermi velocity, and the possible impact on charge transport will be discussed.

  2. Nanoporous Au structures by dealloying Au/Ag thermal- or laser-dewetted bilayers on surfaces

    NASA Astrophysics Data System (ADS)

    Ruffino, F.; Torrisi, V.; Grillo, R.; Cacciato, G.; Zimbone, M.; Piccitto, G.; Grimaldi, M. G.

    2017-03-01

    Nanoporous Au attracts great technological interest and it is a promising candidate for optical and electrochemical sensors. In addition to nanoporous Au leafs and films, recently, interest was focused on nanoporous Au micro- and nano-structures on surfaces. In this work we report on the study of the characteristics of nanoporous Au structures produced on surfaces. We developed the following procedures to fabricate the nanoporous Au structures: we deposited thin Au/Ag bilayers on SiO2 or FTO (fluorine-doped tin oxide) substrates with thickness xAu and xAg of the Au and Ag layers; we induced the alloying and dewetting processes of the bilayers by furnace annealing processes of the bilayers deposited on SiO2 and by laser irradiations of the bilayers deposited on FTO; the alloying and dewetting processes result in the formation of AuxAgy alloy sub-micron particles being x and y tunable by xAu and xAg. These particles are dealloyed in HNO3 solution to remove the Ag atoms. We obtain, so, nanoporous sub-micron Au particles on the substrates. Analyzing the characteristics of these particles we find that: a) the size and shape of the particles depend on the nature of the dewetting process (solid-state dewetting on SiO2, molten-state dewetting on FTO); b) the porosity fraction of the particles depends on how the alloying process is reached: about 32% of porosity for the particles fabricated by the furnace annealing at 900 °C, about 45% of porosity for the particles fabricated by the laser irradiation at 0.5 J/cm2, in both cases independently on the Ag concentration in the alloy; c) After the dealloying process the mean volume of the Au particles shrinks of about 39%; d) After an annealing at 400 °C the nanoporous Au particles reprise their initial volume while the porosity fraction is reduced. Arguments to justify these behaviors are presented.

  3. Valley and band structure engineering of folded MoS2 bilayers

    NASA Astrophysics Data System (ADS)

    Jiang, Tao; Liu, Hengrui; Huang, Di; Zhang, Shuai; Li, Yingguo; Gong, Xingao; Shen, Yuen-Ron; Liu, Wei-Tao; Wu, Shiwei

    2014-10-01

    Artificial structures made of stacked two-dimensional crystals have recently been the focus of intense research activity. As in twisted or stacked graphene layers, these structures can show unusual behaviours and new phenomena. Among the various layered compounds that can be exfoliated, transition-metal dichalcogenides exhibit interesting properties governed by their structural symmetry and interlayer coupling, which are highly susceptible to stacking. Here, we obtain—by folding exfoliated MoS2 monolayers—MoS2 bilayers with different stacking orders, as monitored by second harmonic generation and photoluminescence. Appropriate folding can break the inversion symmetry and suppress interlayer hopping, evoking strong valley and spin polarizations that are not achieved in natural MoS2 bilayers of Bernal stacking. It can also enlarge the indirect bandgap by more than 100 meV through a decrease in the interlayer coupling. Our work provides an effective and versatile means to engineer transition-metal dichalcogenide materials with desirable electronic and optical properties.

  4. Origin of Structural Transformation in Mono- and Bi-Layered Molybdenum Disulfide

    NASA Astrophysics Data System (ADS)

    Sun, Xiaoli; Wang, Zhiguo; Li, Zhijie; Fu, Y. Q.

    2016-05-01

    Mono- and multi-layered molybdenum disulfide (MoS2) is considered to be one of the next generation anode materials for rechargeable ion batteries. Structural transformation from trigonal prismatic (2H) to octahedral (1T) upon lithium or sodium intercalation has been in-situ observed experimentally using transmission electron microscope during studies of their electrochemical dynamics processes. In this work, we explored the fundamental mechanisms of this structural transformation in both mono- and bi-layered MoS2 using density functional theory. For the intercalated MoS2, the Li and Na donate their electrons to the MoS2. Based on the theoretical analysis, we confirmed that, for the first time, electron transfer is dominant in initiating this structural transformation, and the results provide an in-depth understanding of the transformation mechanism induced by the electron doping. The critical values of electron concentrations for this structural transformation are decreased with increasing the layer thickness.

  5. Linking lipid architecture to bilayer structure and mechanics using self-consistent field modelling

    SciTech Connect

    Pera, H.; Kleijn, J. M.; Leermakers, F. A. M.

    2014-02-14

    To understand how lipid architecture determines the lipid bilayer structure and its mechanics, we implement a molecularly detailed model that uses the self-consistent field theory. This numerical model accurately predicts parameters such as Helfrichs mean and Gaussian bending modulus k{sub c} and k{sup ¯} and the preferred monolayer curvature J{sub 0}{sup m}, and also delivers structural membrane properties like the core thickness, and head group position and orientation. We studied how these mechanical parameters vary with system variations, such as lipid tail length, membrane composition, and those parameters that control the lipid tail and head group solvent quality. For the membrane composition, negatively charged phosphatidylglycerol (PG) or zwitterionic, phosphatidylcholine (PC), and -ethanolamine (PE) lipids were used. In line with experimental findings, we find that the values of k{sub c} and the area compression modulus k{sub A} are always positive. They respond similarly to parameters that affect the core thickness, but differently to parameters that affect the head group properties. We found that the trends for k{sup ¯} and J{sub 0}{sup m} can be rationalised by the concept of Israelachivili's surfactant packing parameter, and that both k{sup ¯} and J{sub 0}{sup m} change sign with relevant parameter changes. Although typically k{sup ¯}<0, membranes can form stable cubic phases when the Gaussian bending modulus becomes positive, which occurs with membranes composed of PC lipids with long tails. Similarly, negative monolayer curvatures appear when a small head group such as PE is combined with long lipid tails, which hints towards the stability of inverse hexagonal phases at the cost of the bilayer topology. To prevent the destabilisation of bilayers, PG lipids can be mixed into these PC or PE lipid membranes. Progressive loading of bilayers with PG lipids lead to highly charged membranes, resulting in J{sub 0}{sup m}≫0, especially at low ionic

  6. Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer nanodiscs.

    PubMed

    Raschle, Thomas; Hiller, Sebastian; Yu, Tsyr-Yan; Rice, Amanda J; Walz, Thomas; Wagner, Gerhard

    2009-12-16

    Biophysical studies of membrane proteins are often impeded by the requirement for a membrane mimicking environment. Detergent micelles are the most common choice, but the denaturing properties make them unsatisfactory for studies of many membrane proteins and their interactions. In the present work, we explore phospholipid bilayer nanodiscs as membrane mimics and employ electron microscopy and solution NMR spectroscopy to characterize the structure and function of the human voltage dependent anion channel (VDAC-1) as an example of a polytopic integral membrane protein. Electron microscopy reveals the formation of VDAC-1 multimers, an observation that is consistent with results obtained in native mitochondrial outer membranes. High-resolution NMR spectroscopy demonstrates a well folded VDAC-1 protein and native NADH binding functionality. The observed chemical shift changes upon addition of the native ligand NADH to nanodisc-embedded VDAC-1 resemble those of micelle-embedded VDAC-1, indicating a similar structure and function in the two membrane-mimicking environments. Overall, the ability to study integral membrane proteins at atomic resolution with solution NMR in phospholipid bilayers, rather than in detergent micelles, offers exciting novel possibilities to approach the biophysical properties of membrane proteins under nondenaturing conditions, which makes this technology particular suitable for protein-protein interactions and other functional studies.

  7. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer.

    PubMed Central

    Tu, K; Tobias, D J; Blasie, J K; Klein, M L

    1996-01-01

    We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with nw = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffraction results. The area per lipid and the details of the in-plane hydrocarbon chain structure were in excellent agreement with wide-angle x-ray diffraction results. The only significant deviation is that the chains met in a pleated arrangement at the bilayer center, although they should be parallel. Novel discoveries made in the present work include the observation of a bimodal headgroup orientational distribution. Furthermore, we found that there are a significant number of gauche conformations near the ends of the hydrocarbon chains and, in addition to verifying a previous suggestion that there is partial rotational ordering in the hydrocarbon chains, that the two chains in a given molecule are inequivalent with respect to rotations. Finally, we have investigated the lipid/water interface and found that the water penetrates beneath the headgroups, but not as far as the carbonyl groups, that the phosphates are strongly hydrated almost exclusively at the nonesterified oxygen atoms, and that the hydration of the ammonium groups is more diffuse, with some water molecules concentrated in the grooves between the methyl groups. Images FIGURE 2 FIGURE 7 FIGURE 8 FIGURE 12 FIGURE 16 PMID:8789079

  8. Electronic miniband structure, heat capacity and magnetic susceptibility of monolayer and bilayer silicene in TI, VSPM and BI regimes

    NASA Astrophysics Data System (ADS)

    Yarmohammadi, Mohsen

    2017-04-01

    In the current work, we theoretically study the electronic band structure (EBS), electronic heat capacity (EHC) and magnetic susceptibility (MS) of three structures including monolayer, AA-stacked and AB-stacked bilayer silicene based on the Kane-Mele Hamiltonian model and Green's function method. The particular attention of this study is paid to the effect of external electric field on the aforementioned physical properties. By variation of the electric field, three phases are found: Topological insulator (TI), valley-spin polarized metal (VSPM) and band insulator (BI). Marvellously, its electronic minibands show that the spin-up contribution of charge carriers with lowest energy bands behaves like relativistic Dirac fermions with linear (parabolic) energy dispersions in monolayer (bilayer) case near the Dirac points. An insightful analysis shows that the maximum and minimum value of EHC peak appear for (AA) AB-stacked bilayer and monolayer silicene in TI (BI) regime while in MS curves appear for (AB) AA-stacked bilayer and monolayer lattices in TI (BI) regime, respectively. Moreover, we have observed a phase transition from antiferromagnetic to ferromagnetic and paramagnetic in the monolayer and bilayer structures in the VSPM regime based on the MS findings, respectively.

  9. Bilayer graphene formed by passage of current through graphite: evidence for a three-dimensional structure.

    PubMed

    Harris, Peter J F; Slater, Thomas J A; Haigh, Sarah J; Hage, Fredrik S; Kepaptsoglou, Despoina M; Ramasse, Quentin M; Brydson, Rik

    2014-11-21

    The passage of an electric current through graphite or few-layer graphene can result in a striking structural transformation, but there is disagreement about the precise nature of this process. Some workers have interpreted the phenomenon in terms of the sublimation and edge reconstruction of essentially flat graphitic structures. An alternative explanation is that the transformation actually involves a change from a flat to a three-dimensional structure. Here we describe detailed studies of carbon produced by the passage of a current through graphite which provide strong evidence that the transformed carbon is indeed three-dimensional. The evidence comes primarily from images obtained in the scanning transmission electron microscope using the technique of high-angle annular dark-field imaging, and from a detailed analysis of electron energy loss spectra. We discuss the possible mechanism of the transformation, and consider potential applications of 'three-dimensional bilayer graphene'.

  10. Structure of Functional Staphylococcus aureus α-Hemolysin Channels in Tethered Bilayer Lipid Membranes.

    NASA Astrophysics Data System (ADS)

    Heinrich, Frank; Valincius, Gintaras; McGillivray, Duncan J.; Robertson, Joseph W. F.; Ignatjev, Ilja; Kasianowicz, John J.; Loesche, Mathias

    2008-03-01

    We demonstrate the functional reconstitution of the Staphylococcus aureus α-hemolysin channel in membranes tethered to gold. Electrical impedance spectroscopy measurements show that the pores have essentially the same properties as those formed in free-standing bilayer lipid membranes. Neutron reflectometry (NR) provides high-resolution structural information on the interaction between the channel and the disordered membrane, and validates predictions based on the channel x-ray crystal structure. NR also shows that the proximity of the solid interface does not affect the molecular architecture of the protein-membrane complex. The results suggest that this technique could be used to elucidate molecular details about the association of other proteins with membranes. It also may provide structural information on domain organization and stimuli-responsive reorganization for transmembrane proteins in membrane mimics.

  11. New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers.

    PubMed

    Singh, Moirangthem Kiran; Shweta, Him; Khan, Mohammad Firoz; Sen, Sobhan

    2016-09-21

    Environment polarity and hydration at lipid/water interfaces play important roles in membrane biology, which are investigated here using a new homologous series of 4-aminophthalimide-based fluorescent molecules (4AP-Cn; n = 2-10, 12) having different lipophilicities (octanol/water partition coefficient - log P). We show that 4AP-Cn molecules probe a peculiar stepwise polarity (E) profile at the lipid/water interface of the gel-phase (Lβ') DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) bilayer at room temperature, which was not anticipated in earlier studies. However, the same molecules probe only a subtle but continuous polarity change at the interface of water and the fluid-phase (Lα) DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayer at room temperature. Fluorescence quenching experiments indicate that solutes with different log P values adsorb at different depths across DPPC/water and DOPC/water interfaces, which correlate with the polarity profiles observed at the interfaces. Molecular dynamics simulations performed on eight probe-lipid systems (four in each of the DPPC and DOPC bilayers - a total run of 2.6 μs) support experimental results, providing further information on the relative position and angle distributions as well as hydration of probes at the interfaces. Simulation results indicate that besides positions, probe orientations also play an important role in defining the local dielectric environment by controlling the probes' exposure to water at the interfaces especially of the gel-phase DPPC bilayer. The results suggest that 4AP-Cn probes are well suited for studying solvation properties at lipid/water interfaces of gel- and fluid-phases simultaneously.

  12. Computational criterion for application of the characteristic effective medium approximation to ultrathin Co Au multi-bilayer structures

    NASA Astrophysics Data System (ADS)

    Haija, A. J.; Larry Freeman, W.; DeNinno, Matthew

    2008-11-01

    The basic optical properties, reflectivity and transmissivity, of three sets of Co-Au bilayer structures are calculated for normal incidence in the wavelength range 300-700 nm. Each set consists of a total number of bilayer identity periods m=1, 2, 3, 4, 5, 6. The thickness of the bilayer in each set is 5, 7, and 9 nm. The composition of the bilayer is kept fixed: 40% Co and 60% Au. The calculations are done for ideal layered Co-Au stacks using the characteristic matrix technique. Calculations for each stack based on the thicknesses of the two composite layers and their optical constants are contrasted against calculations using the characteristic effective medium approximation, CEMA. A third calculation of the optical properties for each stack is performed, again using the CEMA, but when the whole stack, called the effective stack, ES, is treated as one uniform medium of effective optical constants. The comparison of the three sets of calculations for all sets is intended to shed more light onto the validity of the CEMA approximation that has been established for thin bilayer structures whose constituents have thicknesses much less than the wavelength of the incident radiation. The study establishes a limit based on the product of the number of layers m and the identity period of the stack h, beyond which the CEMA approximation cannot be applied. This limit is consistent with a previous study carried out on Ag-SiO ultrathin stacks.

  13. Effects of Synthetic Amphiphilic alpha-Helical Peptides on the Electrochemical and Structural Properties of Supported Hybrid Bilayers on Gold

    SciTech Connect

    Smith,M.; Tong, J.; Genzer, J.; Fischer, D.; Kilpatrick, P.

    2006-01-01

    Amphiphilic {alpha}-helices were formed from designed synthetic peptides comprising alanine, phenylalanine, and lysine residues. The insertion of the -helical peptides into hybrid bilayers assembled on gold was studied by a variety of methods to assess the resulting structural characteristics, such as electrical resistance and molecular orientation. Self-assembled monolayers (SAMs) of dodecanethiol (DDT); octadecanethiol (ODT); and 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE) were formed on gold substrates with and without incorporated peptide. Supported hybrid bilayers and multilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were formed on SAMs by the 'paint-freeze' method of bilayer formation. Modeling of electrochemical impedance spectroscopy data using equivalent electrochemical circuits revealed that the addition of peptide decreased dramatically the resistive element of the bilayer films while maintaining the value of the capacitive element, indicating successful incorporation of peptide into a well-formed bilayer. Near-edge X-ray absorption fine structure spectroscopy data provided evidence that the molecules in the SAMs and hybrid multilayers were ordered even in the presence of peptide. The peptide insertion into the SAM was confirmed by observing the {pi}* resonance peak correlating with phenylalanine and a peak in the nitrogen K-edge regime attributable to the peptide bond.

  14. Structural characterization on the gel to liquid-crystal phase transition of fully hydrated DSPC and DSPE bilayers.

    PubMed

    Qin, Shan-Shan; Yu, Zhi-Wu; Yu, Yang-Xin

    2009-06-11

    The structural properties of fully hydrated distearoylphosphatidylcholine (DSPC) and distearoylphosphatidylethanolamine (DSPE) bilayers near the main phase transition were investigated using molecular dynamics simulations on the basis of a united-atom model. Although largely similar in their molecular structures, the two lipids were found with different molecular packing modes at temperatures below the phase transition. For DSPC, three packing modes, namely, cross-tilt, partially interdigitated, and "mixed" gel phases, were observed, while, for DSPE, the lipid tails were almost perpendicular to the lipid surface. Above the main transition temperature, both lipid bilayers transformed into a disordered liquid-crystal phase with marked greater area per lipid and gauche % of the acyl chains and smaller bilayer thickness and order parameter, in comparison with the gel phase. The transformation process of liquid-crystal to gel phase was proved to experience the nucleation and growth stages in a hexagonal manner. The electron density profiles of some major components of both lipid bilayers at various temperatures have been calculated, and the results reveal that both lipid bilayers have less interdigitation around the main transition temperature.

  15. Engineering Electronic Structure of a Two-Dimensional Topological Insulator Bi(111) Bilayer on Sb Nanofilms by Quantum Confinement Effect.

    PubMed

    Bian, Guang; Wang, Zhengfei; Wang, Xiao-Xiong; Xu, Caizhi; Xu, SuYang; Miller, Thomas; Hasan, M Zahid; Liu, Feng; Chiang, Tai-Chang

    2016-03-22

    We report on the fabrication of a two-dimensional topological insulator Bi(111) bilayer on Sb nanofilms via a sequential molecular beam epitaxy growth technique. Our angle-resolved photoemission measurements demonstrate the evolution of the electronic band structure of the heterostructure as a function of the film thickness and reveal the existence of a two-dimensional spinful massless electron gas within the top Bi bilayer. Interestingly, our first-principles calculation extrapolating the observed band structure shows that, by tuning down the thickness of the supporting Sb films into the quantum dimension regime, a pair of isolated topological edge states emerges in a partial energy gap at 0.32 eV above the Fermi level as a consequence of quantum confinement effect. Our results and methodology of fabricating nanoscale heterostructures establish the Bi bilayer/Sb heterostructure as a platform of great potential for both ultra-low-energy-cost electronics and surface-based spintronics.

  16. Bilayer structure and lipid dynamics in a model stratum corneum with oleic acid.

    PubMed

    Hoopes, Matthew I; Noro, Massimo G; Longo, Marjorie L; Faller, Roland

    2011-03-31

    The stratum corneum is the uppermost layer of the skin and acts as a barrier to keep out contaminants and retain moisture. Understanding the molecular structure and behavior of this layer will provide guidance for optimizing its biological function. In this study we use a model mixture comprised of equimolar portions of ceramide NS (24:0), lignoceric acid, and cholesterol to model the effect of the addition of small amounts of oleic acid to the bilayer at 300 and 340 K. Five systems at each temperature have been simulated with concentrations between 0 and 0.1 mol % oleic acid. Our major finding is that subdiffusive behavior over the 200 ns time scale is evident in systems at 340 K, with cholesterol diffusion being enhanced with increased oleic acid. Importantly, cholesterol and other species diffuse faster when radial densities indicate nearest neighbors include more cholesterol. We also find that, with the addition of oleic acid, the bilayer midplane and interfacial densities are reduced and there is a 3% decrease in total thickness occurring mostly near the hydrophilic interface at 300 K with reduced overall density at 340 K. Increased interdigitation occurs independent of oleic acid with a temperature increase. Slight ordering of the long non-hydroxy fatty acid of the ceramide occurs near the hydrophilic interface as a function of the oleic acid concentration, but no significant impact on hydrogen bonding is seen in the chosen oleic acid concentrations.

  17. Control over band structure and tunneling in bilayer graphene induced by velocity engineering.

    PubMed

    Cheraghchi, Hosein; Adinehvand, Fatemeh

    2014-01-08

    The band structure and transport properties of massive Dirac fermions in bilayer graphene with velocity modulation in space are investigated in the presence of a previously created band gap. It is pointed out that velocity engineering may be considered as a factor to control the band gap of symmetry-broken bilayer graphene. The band gap is direct and independent of velocity value if the velocity modulated in two layers is set up equally. Otherwise, in the case of interlayer asymmetric velocity, not only is the band gap indirect, but also the electron-hole symmetry fails. This band gap is controllable by the ratio of the velocity modulated in the upper layer to the velocity modulated in the lower layer. In more detail, the shift of momentum from the conduction band edge to the valence band edge can be engineered by the gate bias and velocity ratio. A transfer matrix method is also elaborated to calculate the four-band coherent conductance through a velocity barrier possibly subjected to a gate bias. Electronic transport depends on the ratio of velocity modulated inside the barrier to that for surrounding regions. As a result, a quantum version of total internal reflection is observed for thick enough velocity barriers. Moreover, a transport gap originating from the applied gate bias is engineered by modulating the velocities of the carriers in the upper and lower layers.

  18. Formation and structural analysis of twisted bilayer graphene on Ni(111) thin films

    NASA Astrophysics Data System (ADS)

    Iwasaki, Takayuki; Zakharov, Alexei A.; Eelbo, Thomas; Waśniowska, Marta; Wiesendanger, Roland; Smet, Jurgen H.; Starke, Ulrich

    2014-07-01

    We synthesized twisted bilayer graphene on single crystalline Ni(111) thin films to analyze the statistical twist angle distribution on a large scale. The twisted bilayer graphene was formed by combining two growth methods, namely the catalytic surface reaction of hydrocarbons and carbon segregation from Ni. Low energy electron diffraction (LEED) investigations directly revealed dominant twist angles of 13°, 22°, 38°, and 47°. We show that the angle distribution is closely related to the sizes of Moiré superlattices which form at commensurate rotation angles. In addition to the commensurate angles, quasi-periodic Moiré structures were also formed in the vicinity of the dominant angles, confirmed by microscopic observations with low energy electron microscopy and scanning tunneling microscopy (STM). The quasi-periodic Moiré patterns are presumably caused by insufficient mobility of carbon atoms during the segregation growth while cooling. Micro-LEED studies reveal that the size of single twisted domains is below 400 nm. Atomic-scale characterization by STM indicates that the twisted layer grown by segregation is located underneath the layer grown by surface reaction, i.e. between the Ni surface and the top single-crystal graphene layer.

  19. Bilayer Structure and Lipid Dynamics in a Model Stratum Corneum with Oleic Acid

    SciTech Connect

    Hoopes, Matthew I.; Noro, Massimo G.; Longo, Marjorie L.; Faller, Roland

    2011-03-31

    The stratum corneum is the uppermost layer of the skin and acts as a barrier to keep out contaminants and retain moisture. Understanding the molecular structure and behavior of this layer will provide guidance for optimizing its biological function. In this study we use a model mixture comprised of equimolar portions of ceramide NS (24:0), lignoceric acid, and cholesterol to model the effect of the addition of small amounts of oleic acid to the bilayer at 300 and 340 K. Five systems at each temperature have been simulated with concentrations between 0 and 0.1 mol % oleic acid. Our major finding is that subdiffusive behavior over the 200 ns time scale is evident in systems at 340 K, with cholesterol diffusion being enhanced with increased oleic acid. Importantly, cholesterol and other species diffuse faster when radial densities indicate nearest neighbors include more cholesterol. We also find that, with the addition of oleic acid, the bilayer midplane and interfacial densities are reduced and there is a 3% decrease in total thickness occurring mostly near the hydrophilic interface at 300 K with reduced overall density at 340 K. Increased interdigitation occurs independent of oleic acid with a temperature increase. Slight ordering of the long non-hydroxy fatty acid of the ceramide occurs near the hydrophilic interface as a function of the oleic acid concentration, but no significant impact on hydrogen bonding is seen in the chosen oleic acid concentrations.

  20. Atomic structure and bonding of the interfacial bilayer between Au nanoparticles and epitaxially regrown MgAl{sub 2}O{sub 4} substrates

    SciTech Connect

    Zhu, Guo-zhen; Majdi, Tahereh; Preston, John S.; Shao, Yang; Bugnet, Matthieu; Botton, Gianluigi A.

    2014-12-08

    A unique metal/oxide interfacial bilayer formed between Au nanoparticles and MgAl{sub 2}O{sub 4} substrates following thermal treatment is reported. Associated with the formation of the bilayer was the onset of an abnormal epitaxial growth of the substrate under the nanoparticle. According to the redistribution of atoms and the changes of their electronic structure probed across the interface by a transmission electron microscopy, we suggest two possible atomic models of the interfacial bilayer.

  1. Topography-guided buckling of swollen polymer bilayer films into three-dimensional structures.

    PubMed

    Jeong, Joonwoo; Cho, Yigil; Lee, Su Yeon; Gong, Xingting; Kamien, Randall D; Yang, Shu; Yodh, A G

    2017-02-07

    Thin films that exhibit spatially heterogeneous swelling often buckle into the third dimension to minimize stress. These effects, in turn, offer a promising strategy to fabricate complex three-dimensional structures from two-dimensional sheets. Here we employ surface topography as a new means to guide buckling of swollen polymer bilayer films and thereby control the morphology of resulting three-dimensional objects. Topographic patterns are created on poly(dimethylsiloxane) (PDMS) films selectively coated with a thin layer of non-swelling parylene on different sides of the patterned films. After swelling in an organic solvent, various structures are formed, including half-pipes, helical tubules, and ribbons. We demonstrate these effects and introduce a simple geometric model that qualitatively captures the relationship between surface topography and the resulting swollen film morphologies. The model's limitations are also examined.

  2. Electronic structure of sodium cobalt oxide: Comparing mono- and bilayer hydrate

    NASA Astrophysics Data System (ADS)

    Arita, Ryotaro

    2005-04-01

    To shed light on the mechanism of superconductivity in sodium cobalt oxide bilayer-hydrate (BLH), we perform a density functional calculation with full structure optimization for BLH and its related nonsuperconducting phase, monolayer hydrate (MLH). We find that these hydrates have similar band structures, but a notable difference can be seen in the a1g band around the Fermi level. While its dispersion in the z direction is negligibly small for BLH, it is of the order of 0.1eV for MLH. This result implies that the three-dimensional feature of the a1g band may be the origin for the absence of superconductivity in MLH.

  3. Transport in bilayer and trilayer graphene: band gap engineering and band structure tuning

    NASA Astrophysics Data System (ADS)

    Zhu, Jun

    2014-03-01

    Controlling the stacking order of atomically thin 2D materials offers a powerful tool to control their properties. Linearly dispersed bands become hyperbolic in Bernal (AB) stacked bilayer graphene (BLG). Both Bernal (ABA) and rhombohedral (ABC) stacking occur in trilayer graphene (TLG), producing distinct band structures and electronic properties. A symmetry-breaking electric field perpendicular to the sample plane can further modify the band structures of BLG and TLG. In this talk, I will describe our experimental effort in these directions using dual-gated devices. Using thin HfO2 film deposited by ALD as gate dielectric, we are able to apply large displacement fields D > 6 V/nm and observe the opening and saturation of the field-induced band gap Eg in bilayer and ABC-stacked trilayer graphene, where the conduction in the mid gap changes by more than six decades. Its field and temperature dependence highlights the crucial role played by Coulomb disorder in facilitating hopping conduction and suppressing the effect of Eg in the tens of meV regime. In contrast, mid-gap conduction decreases with increasing D much more rapidly in clean h-BN dual-gated devices. Our studies also show the evolution of the band structure in ABA-stacked TLG, in particular the splitting of the Dirac-like bands in large D field and the signatures of two-band transport at high carrier densities. Comparison to theory reveals the need for more sophisticated treatment of electronic screening beyond self-consistent Hartree calculations to accurately predict the band structures of trilayer graphene and graphenic materials in general.

  4. Effect of Ion-Binding and Chemical Phospholipid Structure on the Nanomechanics of Lipid Bilayers Studied by Force Spectroscopy

    PubMed Central

    Garcia-Manyes, Sergi; Oncins, Gerard; Sanz, Fausto

    2005-01-01

    The nanomechanical response of supported lipid bilayers has been studied by force spectroscopy with atomic force microscopy. We have experimentally proved that the amount of ions present in the measuring system has a strong effect on the force needed to puncture a 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer with an atomic force microscope tip, thus highlighting the role that monovalent cations (so far underestimated, e.g., Na+) play upon membrane stability. The increase in the yield threshold force has been related to the increase in lateral interactions (higher phospholipid-phospholipid interaction, decrease in area per lipid) promoted by ions bound into the membrane. The same tendency has also been observed for other phosphatidylcholine bilayers, namely, 2-dilauroyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, and 1,2-dioleoyl-sn-3-phosphocholine, and also for phosphatidylethanolamine bilayers such as 1-palmitoyl-2-oleoyl-sn-3-phosphoethanolamine. Finally, this effect has been also tested on a natural lipid bilayer (Escherichia coli lipid extract), showing the same overall tendency. The kinetics of the process has also been studied, together with the role of water upon membrane stability and its effect on membrane nanomechanics. Finally, the effect of the chemical structure of the phospholipid molecule on the nanomechanical response of the membrane has also been discussed. PMID:15980180

  5. Rational Design of ZnO:H/ZnO Bilayer Structure for High-Performance Thin-Film Transistors.

    PubMed

    Abliz, Ablat; Huang, Chun-Wei; Wang, Jingli; Xu, Lei; Liao, Lei; Xiao, Xiangheng; Wu, Wen-Wei; Fan, Zhiyong; Jiang, Changzhong; Li, Jinchai; Guo, Shishang; Liu, Chuansheng; Guo, Tailiang

    2016-03-01

    The intriguing properties of zinc oxide-based semiconductors are being extensively studied as they are attractive alternatives to current silicon-based semiconductors for applications in transparent and flexible electronics. Although they have promising properties, significant improvements on performance and electrical reliability of ZnO-based thin film transistors (TFTs) should be achieved before they can be applied widely in practical applications. This work demonstrates a rational and elegant design of TFT, composed of poly crystalline ZnO:H/ZnO bilayer structure without using other metal elements for doping. The field-effect mobility and gate bias stability of the bilayer structured devices have been improved. In this device structure, the hydrogenated ultrathin ZnO:H active layer (∼3 nm) could provide suitable carrier concentration and decrease the interface trap density, while thick pure-ZnO layer could control channel conductance. Based on this novel structure, a high field-effect mobility of 42.6 cm(2) V(-1) s(-1), a high on/off current ratio of 10(8) and a small subthreshold swing of 0.13 V dec(-1) have been achieved. Additionally, the bias stress stability of the bilayer structured devices is enhanced compared to the simple single channel layer ZnO device. These results suggest that the bilayer ZnO:H/ZnO TFTs have a great potential for low-cost thin-film electronics.

  6. Thermal and structural properties of ionic fluids.

    PubMed

    Bartsch, Hendrik; Dannenmann, Oliver; Bier, Markus

    2015-04-01

    The electrostatic interaction in ionic fluids is well known to give rise to a characteristic phase behavior and structure. Sometimes its long range is proposed to single out the electrostatic potential over other interactions with shorter ranges. Here the importance of the range for the phase behavior and the structure of ionic fluids is investigated by means of grandcanonical Monte Carlo simulations of the lattice restricted primitive model (LRPM). The long-ranged electrostatic interaction is compared to various types of short-ranged potentials obtained by sharp and/or smooth cutoff schemes. Sharply cutoff electrostatic potentials are found to lead to a strong dependence of the phase behavior and the structure on the cutoff radius. However, when combined with a suitable additional smooth cutoff, the short-ranged LRPM is found to exhibit quantitatively the same phase behavior and structure as the conventional long-ranged LRPM. Moreover, the Stillinger-Lovett perfect screening property, which is well known to be generated by the long-ranged electrostatic potential, is also fulfilled by short-ranged LRPMs with smooth cutoffs. By showing that the characteristic phase behavior and structure of ionic fluids can also be found in systems with short-ranged potentials, one can conclude that the decisive property of the electrostatic potential in ionic fluids is not the long range but rather the valency dependence.

  7. Structure-Based Prediction of Drug Distribution Across the Headgroup and Core Strata of a Phospholipid Bilayer Using Surrogate Phases

    PubMed Central

    2015-01-01

    locations for 27 compounds. The resulting structure-based prediction system for intrabilayer distribution will facilitate more realistic modeling of passive transport and drug interactions with those integral membrane proteins, which have the binding sites located in the bilayer, such as some enzymes, influx and efflux transporters, and receptors. If only overall bilayer accumulation is of interest, the 1-octanol/W P values suffice to model the studied set. PMID:25179490

  8. Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases.

    PubMed

    Natesan, Senthil; Lukacova, Viera; Peng, Ming; Subramaniam, Rajesh; Lynch, Sandra; Wang, Zhanbin; Tandlich, Roman; Balaz, Stefan

    2014-10-06

    locations for 27 compounds. The resulting structure-based prediction system for intrabilayer distribution will facilitate more realistic modeling of passive transport and drug interactions with those integral membrane proteins, which have the binding sites located in the bilayer, such as some enzymes, influx and efflux transporters, and receptors. If only overall bilayer accumulation is of interest, the 1-octanol/W P values suffice to model the studied set.

  9. Importance of the sphingosine base double-bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers.

    PubMed

    Janosi, Lorant; Gorfe, Alemayehu

    2010-11-03

    The precise role of the sphingosine base trans double bond for the unique properties of sphingomyelins (SMs), one of the main lipid components in raftlike structures of biological membranes, has not been fully explored. Several reports comparing the hydration, lipid packing, and hydrogen-bonding behaviors of SM and glycerophospholipid bilayers found remarkable differences overall. However, the atomic interactions linking the double-bond geometry with these thermodynamic and structural changes remained elusive. A recent report on ceramides, which differ from SMs only by their hydroxyl headgroup, has shown that replacing the trans double bond of the sphingosine base by cis weakens the hydrogen-bonding potential of these lipids and thereby alters their biological activity. Based on data from extensive (a total 0.75 μs) atomistic molecular dynamics simulations of bilayers composed of all-trans, all-cis, and a trans/cis (4:1 ratio) racemic mixture of sphingomyelin lipids, here we show that the trans configuration allows for the formation of significantly more hydrogen bonds than the cis. The extra hydrogen bonds enabled tighter packing of lipids in the all-trans and trans/cis bilayers, thus reducing the average area per lipid while increasing the chain order and the bilayer thickness. Moreover, fewer water molecules access the lipid-water interface of the all-trans bilayer than of the all-cis bilayer. These results provide the atomic basis for the importance of the natural sphingomyelin trans double-bond conformation for the formation of ordered membrane domains.

  10. Preservation of bilayer structure in human erythrocytes and erythrocyte ghosts after phospholipase treatment. A 31P-NMR study.

    PubMed

    van Meer, G; de Kruijff, B; op den Kamp, J A; van Deenen, L L

    1980-02-15

    1. Fresh human erythrocytes were treated with lytic and non-lytic combinations of phospholipases A2, C and sphingomyelinase. The 31P-NMR spectra of ghosts derived from such erythrocytes show that, in all cases, the residual phospholipids and lysophospholipids remain organized in a bilayer configuration. 2. A bilayer configuration of the (lyso)phospholipids was also observed after treatment of erythrocyte ghosts with various phospholipases even in the case that 98% of the phospholipid was converted into lysophospholipid (72%) and ceramides (26%). 3. A slightly decreased order of the phosphate group of phospholipid molecules, seen as reduced effective chemical shift anisotropy in the 31P-NMR spectra, was found following the formation of diacyglycerols and ceramides in the membrane of intact erythrocytes. Treatment of ghosts always resulted in an extensive decrease in the order of the phosphate groups. 4. The results allow the following conclusions to made: a. Hydrolysis of phospholipids in intact red cells and ghosts does not result in the formation of non-bilayer configuration of residual phospholipids and lysophospholipids. b. Haemolysis, which is obtained by subsequent treatment of intact cells with sphingomyelinase and phospholipase A2, or with phospholipase C, cannot be ascribed to the formation of non-bilayer configuration of phosphate-containing lipids. c. Preservation of bilayer structure, even after hydrolysis of all phospholipid, shows that other membrane constitutents, e.g. cholesterol and/or membrane proteins play an important role in stabilizing the structure of the erythrocyte membrane. d. A major prerequisite for the application of phospholipases in lipid localization studies, the preservation of a bilayer configuration during phospholipid hydrolysis, is met for the erythrocyte membrane.

  11. Local spectroscopy of moiré-induced electronic structure in gate-tunable twisted bilayer graphene

    NASA Astrophysics Data System (ADS)

    Wong, Dillon; Wang, Yang; Jung, Jeil; Pezzini, Sergio; DaSilva, Ashley M.; Tsai, Hsin-Zon; Jung, Han Sae; Khajeh, Ramin; Kim, Youngkyou; Lee, Juwon; Kahn, Salman; Tollabimazraehno, Sajjad; Rasool, Haider; Watanabe, Kenji; Taniguchi, Takashi; Zettl, Alex; Adam, Shaffique; MacDonald, Allan H.; Crommie, Michael F.

    2015-10-01

    Twisted bilayer graphene (tBLG) forms a quasicrystal whose structural and electronic properties depend on the angle of rotation between its layers. Here, we present a scanning tunneling microscopy study of gate-tunable tBLG devices supported by atomically smooth and chemically inert hexagonal boron nitride (BN). The high quality of these tBLG devices allows identification of coexisting moiré patterns and moiré super-superlattices produced by graphene-graphene and graphene-BN interlayer interactions. Furthermore, we examine additional tBLG spectroscopic features in the local density of states beyond the first van Hove singularity. Our experimental data are explained by a theory of moiré bands that incorporates ab initio calculations and confirms the strongly nonperturbative character of tBLG interlayer coupling in the small twist-angle regime.

  12. The Influence of Short-Chain Alcohols on Interfacial Tension, Mechanical Properties, Area/Molecule, and Permeability of Fluid Lipid Bilayers

    PubMed Central

    Ly, Hung V.; Longo, Marjorie L.

    2004-01-01

    We used micropipette aspiration to directly measure the area compressibility modulus, bending modulus, lysis tension, lysis strain, and area expansion of fluid phase 1-stearoyl, 2-oleoyl phosphatidylcholine (SOPC) lipid bilayers exposed to aqueous solutions of short-chain alcohols at alcohol concentrations ranging from 0.1 to 9.8 M. The order of effectiveness in decreasing mechanical properties and increasing area per molecule was butanol>propanol>ethanol>methanol, although the lysis strain was invariant to alcohol chain-length. Quantitatively, the trend in area compressibility modulus follows Traube's rule of interfacial tension reduction, i.e., for each additional alcohol CH2 group, the concentration required to reach the same area compressibility modulus was reduced roughly by a factor of 3. We convert our area compressibility data into interfacial tension values to: confirm that Traube's rule is followed for bilayers; show that alcohols decrease the interfacial tension of bilayer-water interfaces less effectively than oil-water interfaces; determine the partition coefficients and standard Gibbs adsorption energy per CH2 group for adsorption of alcohol into the lipid headgroup region; and predict the increase in area per headgroup as well as the critical radius and line tension of a membrane pore for each concentration and chain-length of alcohol. The area expansion predictions were confirmed by direct measurements of the area expansion of vesicles exposed to flowing alcohol solutions. These measurements were fitted to a membrane kinetic model to find membrane permeability coefficients of short-chain alcohols. Taken together, the evidence presented here supports a view that alcohol partitioning into the bilayer headgroup region, with enhanced partitioning as the chain-length of the alcohol increases, results in chain-length-dependent interfacial tension reduction with concomitant chain-length-dependent reduction in mechanical moduli and membrane thickness. PMID

  13. Structure determination of membrane proteins in their native phospholipid bilayer environment by rotationally aligned solid-state NMR spectroscopy.

    PubMed

    Opella, Stanley J

    2013-09-17

    One of the most important topics in experimental structural biology is determining the structures of membrane proteins. These structures represent one-third of all of the information expressed from a genome, distinguished by their locations within the phospholipid bilayer of cells, organelles, or enveloped viruses. Their highly hydrophobic nature and insolubility in aqueous media means that they require an amphipathic environment. They have unique functions in transport, catalysis, channel formation, and signaling. Researchers are particularly interested in G-protein coupled receptors (GPCRs) because they modulate many biological processes, and about half of the approximately 800 of these proteins within the human genome are or can be turned into drug receptors that affect a wide range of diseases. Because of experimental difficulties, researchers have studied membrane proteins using a wide variety of artificial media that mimic membranes, such as mixed organic solvents or detergents. More sophisticated mimics include bilayer discs (bicelles) and the lipid cubic phase (LCP), but both of these contain a very large detergent component, which can disrupt the stability and function of membrane proteins. To have confidence in the resulting structures and their biological functions and to avoid disrupting these delicate proteins, the structures of membrane proteins should be determined in their native environment of liquid crystalline phospholipid bilayers under physiological conditions. This Account describes a recently developed general method for determining the structures of unmodified membrane proteins in phospholipid bilayers by solid-state NMR spectroscopy. Because it relies on the natural, rapid rotational diffusion of these proteins about the bilayer normal, this method is referred to as rotationally aligned (RA) solid-state NMR. This technique elaborates on oriented sample (OS) solid-state NMR, its complementary predecessor. These methods exploit the power of

  14. Long-range surface plasmons supported by a bilayer metallic structure for sensing applications.

    PubMed

    Zekriti, M; Nesterenko, Dmitry V; Sekkat, Z

    2015-03-10

    We show, both theoretically and experimentally, that long-range surface plasmons (LRSPs) are supported by asymmetric structure, consisting of a thin silver/gold bilayer metallic film sandwiched between a magnesium fluoride (i.e., MgF2) buffer layer and a sensing medium (water). The geometrical parameters of the structure are optimized to yield efficient excitation of LRSPs by using transfer matrix method based on Fresnel reflection. The excitation of LRSPs was performed by using a custom-made automated optical setup based on angular interrogation with the precision of 0.01°. We demonstrate that the bimetallic asymmetric structure achieves better minimum reflectivity resolution than monometallic (gold) asymmetric structure. Finally, figures of merit are compared for bimetallic, monometallic, and conventional SPR structures, and we found that the bimetallic asymmetric structure provides a higher figure of merit; e.g., more than double for monometallic LRSP configuration and 8 times as compared to the conventional surface plasmon resonance sensor.

  15. Influence of bilayer resist processing on p-i-n OLEDs: towards multicolor photolithographic structuring of organic displays

    NASA Astrophysics Data System (ADS)

    Krotkus, Simonas; Nehm, Frederik; Janneck, Robby; Kalkura, Shrujan; Zakhidov, Alex A.; Schober, Matthias; Hild, Olaf R.; Kasemann, Daniel; Hofmann, Simone; Leo, Karl; Reineke, Sebastian

    2015-03-01

    Recently, bilayer resist processing combined with development in hydrofluoroether (HFE) solvents has been shown to enable single color structuring of vacuum-deposited state-of-the-art organic light-emitting diodes (OLED). In this work, we focus on further steps required to achieve multicolor structuring of p-i-n OLEDs using a bilayer resist approach. We show that the green phosphorescent OLED stack is undamaged after lift-off in HFEs, which is a necessary step in order to achieve RGB pixel array structured by means of photolithography. Furthermore, we investigate the influence of both, double resist processing on red OLEDs and exposure of the devices to ambient conditions, on the basis of the electrical, optical and lifetime parameters of the devices. Additionally, water vapor transmission rates of single and bilayer system are evaluated with thin Ca film conductance test. We conclude that diffusion of propylene glycol methyl ether acetate (PGMEA) through the fluoropolymer film is the main mechanism behind OLED degradation observed after bilayer processing.

  16. Calcein release behavior from liposomal bilayer; influence of physicochemical/mechanical/structural properties of lipids.

    PubMed

    Maherani, Behnoush; Arab-Tehrany, Elmira; Kheirolomoom, Azadeh; Geny, David; Linder, Michel

    2013-11-01

    The design of the drug delivery depends upon different parameters. One of the most noticeable factors in design of the drug delivery is drug-release profile which determines the site of action, the concentration of the drug at the time of administration, the period of time that the drug must remain at a therapeutic concentration. To get a better understanding of drug release, large unilamellar liposomes containing calcein were prepared using 1,2-dioleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1,2-palmitoyl-sn-glycero-3-phosphocholine, and a mixture of them; calcein was chosen as a model of hydrophilic drug. The calcein permeability across liposomal membrane (with different compositions) was evaluated on the basis of the first-order kinetic by spectrofluorometer. Also, the effects of liposome composition/fluidity as well as the incubation temperature/pH were investigated. Furthermore, we simulated the digestion condition in the gastrointestinal tract in humans, to mimic human gastro-duodenal digestion to monitor calcein release during the course of the digestion process. In vitro digestion model ''pH stat'' was used to systematically examine the influence of pH/enzyme on phospholipid liposomes digestion under simulated gastro-duodenal digestion. The results revealed that calcein permeates across liposomal membrane without membrane disruption. The release rate of calcein from the liposomes depends on the number and fluidity of bilayers and its mechanical/physical properties such as permeability, bending elasticity. Chemo-structural properties of drugs like as partition coefficient (Log P), H-bonding, polar surface area (PSA) are also determinative parameter in release behavior. Finally, stimulated emission depletion (STED) microscopy was used to study calcein translocation through liposomal bilayers.

  17. Structural characterization of Fe/Ag bilayers by RBS and AFM

    NASA Astrophysics Data System (ADS)

    Tunyogi, A.; Tanczikó, F.; Osváth, Z.; Pászti, F.

    2008-11-01

    Fe/Ag thin films are intensively investigated due to their special magnetic properties. Recently a deposition-order dependent asymmetric interface has been found. When iron is grown on silver, the interface is sharp, while the growth of Ag on Fe results in a long, low-energy tail of the Ag peak in the Rutherford backscattering spectrometry (RBS) spectra. The main purpose of this paper is to show that the low-energy Ag tail is caused by grain boundary diffusion, and that, when elevating the growing temperature of the Ag layer this effect becomes more significant. Two sets of polycrystalline and epitaxial Fe/Ag bilayers were prepared simultaneously onto Si(1 1 1) and MgO(1 0 0), respectively. The iron layers were grown at 250 °C and annealed at 450 °C in both sets, while the Ag layer was grown in the first set at room temperature (RT) and in the second set at 250 °C (HT). The sample composition, the interface sharpness and the quality of the epitaxy were studied by Rutherford backscattering spectrometry (RBS) combined with channeling effect. The surface morphology was determined by atomic force microscopy (AFM). RBS spectra show that in the case of RT samples the epitaxial MgO/Fe/Ag bilayer has sharp, well-defined interface, while for the polycrystalline Si/Fe/Ag sample the silver peak has a low-energy tail. Both the Fe and Ag peaks smeared out in the case of HT samples. AFM-images show that the RT samples have a continuous Ag layer, while the HT samples have fragmented surfaces. The RBS spectra taken on the HT samples were successfully simulated by the RBS-MAST code taking into account their fragmented structures.

  18. Coherent structures for front propagation in fluids

    NASA Astrophysics Data System (ADS)

    Mitchell, Kevin; Mahoney, John

    2014-03-01

    Our goal is to characterize the nature of reacting flows by identifying important ``coherent'' structures. We follow the recent work by Haller, Beron-Vera, and Farazmand which formalized the notion of lagrangian coherent structures (LCSs) in fluid flows. In this theory, LCSs were derived from the Cauchy-Green strain tensor. We adapt this perspective to analogously define coherent structures in reacting flows. By this we mean a fluid flow with a reaction front propagating through it such that the propagation does not affect the underlying flow. A reaction front might be chemical (Belousov-Zhabotinsky, flame front, etc.) or some other type of front (electromagnetic, acoustic, etc.). While the recently developed theory of burning invariant manifolds (BIMs) describes barriers to front propagation in time-periodic flows, this current work provides an important complement by extending to the aperiodic setting. Funded by NSF Grant CMMI-1201236.

  19. High coverage fluid-phase floating lipid bilayers supported by ω-thiolipid self-assembled monolayers

    PubMed Central

    Hughes, Arwel V.; Holt, Stephen A.; Daulton, Emma; Soliakov, Andrei; Charlton, Timothy R.; Roser, Steven J.; Lakey, Jeremy H.

    2014-01-01

    Large area lipid bilayers, on solid surfaces, are useful in physical studies of biological membranes. It is advantageous to minimize the interactions of these bilayers with the substrate and this can be achieved via the formation of a floating supported bilayer (FSB) upon either a surface bound phospholipid bilayer or monolayer. The FSB's independence is enabled by the continuous water layer (greater than 15 Å) that remains between the two. However, previous FSBs have had limited stability and low density. Here, we demonstrate by surface plasmon resonance and neutron reflectivity, the formation of a complete self-assembled monolayer (SAM) on gold surfaces by a synthetic phosphatidylcholine bearing a thiol group at the end of one fatty acyl chain. Furthermore, a very dense FSB (more than 96%) of saturated phosphatidylcholine can be formed on this SAM by sequential Langmuir–Blodgett and Langmuir–Schaefer procedures. Neutron reflectivity used both isotopic and magnetic contrast to enhance the accuracy of the data fits. This system offers the means to study transmembrane proteins, membrane potential effects (using the gold as an electrode) and even model bacterial outer membranes. Using unsaturated phosphatidylcholines, which have previously failed to form stable FSBs, we achieved a coverage of 73%. PMID:25030385

  20. Structural Dynamics Of The S4 Voltage-Sensor Helix In Lipid Bilayers Lacking Lipid Phosphates

    PubMed Central

    Andersson, Magnus; Freites, J. Alfredo; Tobias, Douglas J.; White, Stephen H.

    2011-01-01

    Voltage-dependent K+ (Kv) channels require lipid phosphates for functioning. The S4 helix, which carries the gating charges in the voltage-sensing domain (VSD), inserts into membranes while being stabilized by a protein-lipid interface in which lipid phosphates play an essential role. To examine the physical basis of the protein-lipid interface in the absence of lipid phosphates, we performed molecular dynamics (MD) simulations of a KvAP S4 variant (S4mut) in bilayers with and without lipid phosphates. We find that in dioleoyltrimethylammoniumpropane (DOTAP) bilayers lacking lipid phosphates, the gating charges are solvated by anionic counterions and, hence, lack the bilayer support provided by phosphate-containing palmitoyloleoylglycerophosphocholine (POPC) bilayers. The result is a water-permeable bilayer with a significantly smaller deformations around the peptide. Together, these results provide an explanation for the non-functionality of VSDs in terms of a destabilizing protein-lipid interface. PMID:21692541

  1. Dynamical structure factors and excitation modes of the bilayer Heisenberg model

    NASA Astrophysics Data System (ADS)

    Lohöfer, M.; Coletta, T.; Joshi, D. G.; Assaad, F. F.; Vojta, M.; Wessel, S.; Mila, F.

    2015-12-01

    Using quantum Monte Carlo simulations along with higher-order spin-wave theory, bond-operator and strong-coupling expansions, we analyze the dynamical spin structure factor of the spin-half Heisenberg model on the square-lattice bilayer. We identify distinct contributions from the low-energy Goldstone modes in the magnetically ordered phase and the gapped triplon modes in the quantum disordered phase. In the antisymmetric (with respect to layer inversion) channel, the dynamical spin structure factor exhibits a continuous evolution of spectral features across the quantum phase transition, connecting the two types of modes. Instead, in the symmetric channel, we find a depletion of the spectral weight when moving from the ordered to the disordered phase. While the dynamical spin structure factor does not exhibit a well-defined distinct contribution from the amplitude (or Higgs) mode in the ordered phase, we identify an only marginally damped amplitude mode in the dynamical singlet structure factor, obtained from interlayer bond correlations, in the vicinity of the quantum critical point. These findings provide quantitative information in direct relation to possible neutron or light scattering experiments in a fundamental two-dimensional quantum-critical spin system.

  2. Origin of Structural Transformation in Mono- and Bi-Layered Molybdenum Disulfide

    PubMed Central

    Sun, Xiaoli; Wang, Zhiguo; Li, Zhijie; Fu, Y. Q.

    2016-01-01

    Mono- and multi-layered molybdenum disulfide (MoS2) is considered to be one of the next generation anode materials for rechargeable ion batteries. Structural transformation from trigonal prismatic (2H) to octahedral (1T) upon lithium or sodium intercalation has been in-situ observed experimentally using transmission electron microscope during studies of their electrochemical dynamics processes. In this work, we explored the fundamental mechanisms of this structural transformation in both mono- and bi-layered MoS2 using density functional theory. For the intercalated MoS2, the Li and Na donate their electrons to the MoS2. Based on the theoretical analysis, we confirmed that, for the first time, electron transfer is dominant in initiating this structural transformation, and the results provide an in-depth understanding of the transformation mechanism induced by the electron doping. The critical values of electron concentrations for this structural transformation are decreased with increasing the layer thickness. PMID:27225416

  3. Structural Dynamics of the Magnesium-bound Conformation of CorA in a lipid bilayer

    PubMed Central

    Dalmas, Olivier; Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien; Roux, Benoit; Perozo, Eduardo

    2010-01-01

    Summary The transmembrane conformation of Thermotoga maritima CorA, a Magnesium transport system, has been studied in it’s Mg2+-bound form by site-directed spin labeling and electron paramagnetic resonance spectroscopy. Probe mobility together with accessibility data were used to evaluate the overall dynamics and relative arrangement of individual transmembrane segments TM1 and TM2. TM1 extends toward the cytoplasmic side creating a water filled cavity, while TM2 is located in the periphery of the oligomer, contacting the lipid bilayer. A structural model for the conserved extracellular loop was generated based on EPR data and MD simulations, in which residue E316 is located towards the fivefold symmetry axis in position to electrostatically influence divalent ion translocation. Electrostatic analyses of our model suggest that, in agreement with the crystal structure, Mg2+ -bound CorA is in a close conformation. The present results suggest that long-range structural rearrangements are necessary to allow Mg2+ translocation. PMID:20637423

  4. Helicity and singular structures in fluid dynamics

    PubMed Central

    Moffatt, H. Keith

    2014-01-01

    Helicity is, like energy, a quadratic invariant of the Euler equations of ideal fluid flow, although, unlike energy, it is not sign definite. In physical terms, it represents the degree of linkage of the vortex lines of a flow, conserved when conditions are such that these vortex lines are frozen in the fluid. Some basic properties of helicity are reviewed, with particular reference to (i) its crucial role in the dynamo excitation of magnetic fields in cosmic systems; (ii) its bearing on the existence of Euler flows of arbitrarily complex streamline topology; (iii) the constraining role of the analogous magnetic helicity in the determination of stable knotted minimum-energy magnetostatic structures; and (iv) its role in depleting nonlinearity in the Navier-Stokes equations, with implications for the coherent structures and energy cascade of turbulence. In a final section, some singular phenomena in low Reynolds number flows are briefly described. PMID:24520175

  5. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study [Atomic-level structure of carbon nanotube porins in lipid bilayers: an in-situ small-angle x-ray scattering (SAXS) study

    DOE PAGES

    Tran, Ich C.; Tunuguntla, Ramya H.; Kim, Kyunghoon; ...

    2016-06-20

    Carbon nanotube porins (CNTPs), small segments of carbon nanotubes capable of forming defined pores in lipid membranes, are important future components for bionanoelectronic devices as they could provide a robust analog of biological membrane channels. Furthermore, in order to control the incorporation of these CNT channels into lipid bilayers, it is important to understand the structure of the CNTPs before and after insertion into the lipid bilayer as well as the impact of such insertion on the bilayer structure. Here we employed a noninvasive in situ probe, small-angle X-ray scattering, to study the integration of CNT porins into dioleoylphosphatidylcholine bilayers.more » These results show that CNTPs in solution are stabilized by a monolayer of lipid molecules wrapped around their outer surface. We also demonstrate that insertion of CNTPs into the lipid bilayer results in decreased bilayer thickness with the magnitude of this effect increasing with the concentration of CNTPs.« less

  6. Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study [Atomic-level structure of carbon nanotube porins in lipid bilayers: an in-situ small-angle x-ray scattering (SAXS) study

    SciTech Connect

    Tran, Ich C.; Tunuguntla, Ramya H.; Kim, Kyunghoon; Lee, Jonathan R. I.; Willey, Trevor M.; Weiss, Thomas M.; Noy, Aleksandr; van Buuren, Tony

    2016-06-20

    Carbon nanotube porins (CNTPs), small segments of carbon nanotubes capable of forming defined pores in lipid membranes, are important future components for bionanoelectronic devices as they could provide a robust analog of biological membrane channels. Furthermore, in order to control the incorporation of these CNT channels into lipid bilayers, it is important to understand the structure of the CNTPs before and after insertion into the lipid bilayer as well as the impact of such insertion on the bilayer structure. Here we employed a noninvasive in situ probe, small-angle X-ray scattering, to study the integration of CNT porins into dioleoylphosphatidylcholine bilayers. These results show that CNTPs in solution are stabilized by a monolayer of lipid molecules wrapped around their outer surface. We also demonstrate that insertion of CNTPs into the lipid bilayer results in decreased bilayer thickness with the magnitude of this effect increasing with the concentration of CNTPs.

  7. Assessment of hydrocarbon fluid structures from microelements

    SciTech Connect

    Punanova, S.A.

    1993-12-31

    Determination of features of the microelemental composition of hydrocarbon fluid structures of different phase states (oil and condensate) has been carried out along with an investigation of the distribution of microelements in fractions and components of crude oils and also a study of the direction of change in the composition of naphthides during catagenetic processes. The microelemental composition of oils and condensates from Turkmeniya, East Ciscaucasia and West Siberia has been studied.

  8. Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins.

    PubMed

    Hagn, Franz; Etzkorn, Manuel; Raschle, Thomas; Wagner, Gerhard

    2013-02-06

    Structural studies of membrane proteins are still hampered by difficulties of finding appropriate membrane-mimicking media that maintain protein structure and function. Phospholipid nanodiscs seem promising to overcome the intrinsic problems of detergent-containing environments. While nanodiscs can offer a near-native environment, the large particle size complicates their routine use in the structural analysis of membrane proteins by solution NMR. Here, we introduce nanodiscs assembled from shorter ApoA-I protein variants that are of markedly smaller diameter and show that the resulting discs provide critical improvements for the structure determination of membrane proteins by NMR. Using the bacterial outer-membrane protein OmpX as an example, we demonstrate that the combination of small nanodisc size, high deuteration levels of protein and lipids, and the use of advanced non-uniform NMR sampling methods enable the NMR resonance assignment as well as the high-resolution structure determination of polytopic membrane proteins in a detergent-free, near-native lipid bilayer setting. By applying this method to bacteriorhodopsin, we show that our smaller nanodiscs can also be beneficial for the structural characterization of the important class of seven-transmembrane helical proteins. Our set of engineered nanodiscs of subsequently smaller diameters can be used to screen for optimal NMR spectral quality for small to medium-sized membrane proteins while still providing a functional environment. In addition to their key improvements for de novo structure determination, due to their smaller size these nanodiscs enable the investigation of interactions between membrane proteins and their (soluble) partner proteins, unbiased by the presence of detergents that might disrupt biologically relevant interactions.

  9. Probe-location dependent resonance energy transfer at lipid/water interfaces: comparison between the gel- and fluid-phase of lipid bilayer.

    PubMed

    Singh, Moirangthem Kiran; Khan, Mohammad Firoz; Shweta, Him; Sen, Sobhan

    2017-07-20

    Despite significant interest in understanding the role of the local dielectric environment and lipid-bilayer fluidity/rigidity in resonance energy transfer between chromophores at lipid/water interfaces, a comprehensive approach to quantify such environmental dependence on energy transfer is missing - primarily because of the scarcity of suitable probes. Here we present the results on multi-chromophoric Förster resonance energy transfer (FRET) from a series of 4-aminophthalimide-based molecules (4AP-Cn; n = 2-10, 12) of different lipophilicity (donors), which reside at different depths across the lipid/water interfaces, to rhodamine-6G (Rh6G; acceptor) molecules that stay in a water-rich region near the lipid headgroups. We apply steady-state and time-resolved fluorescence spectroscopy, and find that multi-chromophoric FRET from the series of 4AP-Cn donors to the Rh6G acceptor occurs in a peculiar stepwise fashion at the lipid/water interface of a gel-phase (Lβ') DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) bilayer at room temperature. However, the same donor-acceptor pairs show only subtle but continuous donor-depth-dependent FRET at the lipid/water interface of a fluid-phase (Lα) DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayer. These features were found to correlate with the lipid-phase dependent local environmental polarity sensed by 4AP-Cn donors at the interfaces. Molecular dynamics (MD) simulations, combined with experimental results, show that relative depth (and angle) variation of the 4AP-Cn donors and Rh6G acceptor directly controls the FRET efficiencies through fine tuning of the emission and absorption spectra of the donors and acceptor, respectively. The results indicate that the 4AP-Cn probes are well-suited as donors for FRET studies, which allow the FRET parameters at lipid/water interfaces of gel- and fluid-phases of lipid-bilayers to be quantified and compared simultaneously.

  10. Structures, dynamics, and water permeation free energy across bilayers of Lipid A and its analog studied with molecular dynamics simulation.

    PubMed

    Wei, Tao; Huang, Tiefan; Qiao, Baofu; Zhang, Mo; Ma, Heng; Zhang, Lin

    2014-11-20

    Fundamental studies of the supramolecular layer structures, dynamics and water permeation free energy of hexa-acyl-chain Lipid A and its analogue of tetra-acyl chains would be useful for polymer membranes design for endotoxin removal in water treatment, drug delivery and other biotechnologies. In this work, we studied their supramolecular bilayer by using molecular dynamics simulations and efficient free energy computations. Our simulation accuracy was verified by the agreement between the bilayer structural properties (structure factor, bilayer thickness, and the area per lipid) and lateral diffusion coefficient in our simulation and experimental measurements. More importantly, our simulation for the first time illustrated hexagonal compact packing of the hydrocarbon acyl chains within a leaflet of Lipid A membrane (at 298 K and water content of 40 wt %), which is consistent with experiments. In contrast, Lipid A analogue is found with less ordered ripple structures at the same condition. Our study also demonstrated slower dynamics and larger and broader free energy barrier (∼23 kJ/mol) for water permeation for Lipid A, compared with that of Lipid A analogue. Moreover, the analysis of dynamics showed that highly hydrated hydrophilic diglucosamine backbone is structurally stable, whereas the interdigitated hydrophobic acyl chain tails inside the membrane with faster dynamics screen the aqueous environment from the lipid interior and also reinforce the membrane's structural stability.

  11. Direct growth of graphene-dielectric bi-layer structure on device substrates from Si-based polymer

    NASA Astrophysics Data System (ADS)

    Seo, Hong-Kyu; Kim, Kyunghun; Min, Sung-Yong; Lee, Yeongjun; Eon Park, Chan; Raj, Rishi; Lee, Tae-Woo

    2017-06-01

    To facilitate the utilization of graphene films in conventional semiconducting devices (e.g. transistors and memories) which includes an insulating layer such as gate dielectric, facile synthesis of bi-layers composed of a graphene film and an insulating layer by one-step thermal conversion will be very important. We demonstrate a simple, inexpensive, scalable and patternable process to synthesize graphene-dielectric bi-layer films from solution-processed polydimethylsiloxane (PDMS) under a Ni capping layer. This method fabricates graphene-dielectric bi-layer structure simultaneously directly on substrate by thermal conversion of PDMS without using additional graphene transfer and patterning process or formation of an expensive dielectric layer, which makes the device fabrication process much easier. The graphene-dielectric bi-layer on a conducting substrate was used in bottom-contact pentacene field-effect transistors that showed ohmic contact and small hysteresis. Our new method will provide a way to fabricate flexible electronic devices simply and inexpensively.

  12. Peptide-induced bilayer thinning structure of unilamellar vesicles and the related binding behavior as revealed by X-ray scattering.

    PubMed

    Su, Chun-Jen; Wu, Shiuan-Shiaou; Jeng, U-Ser; Lee, Ming-Tao; Su, An-Chung; Liao, Kuei-Fen; Lin, Wei-Yu; Huang, Yu-Shan; Chen, Chun-Yu

    2013-02-01

    We have studied the bilayer thinning structure of unilamellar vesicles (ULV) of a phospholipid 1,2-dierucoyl-sn-glycero-3-phosphocholine (di22:1PC) upon binding of melittin, a water-soluble amphipathic peptide. Successive thinning of the ULV bilayers with increasing peptide concentration was monitored via small-angle X-ray scattering (SAXS). Results suggest that the two leaflets of the ULV of closed bilayers are perturbed and thinned asymmetrically upon free peptide binding, in contrast to the centro-symmetric bilayer thinning of the substrate-oriented multilamellar membranes (MLM) with premixed melittin. Moreover, thinning of the melittin-ULV bilayer associates closely with peptide concentration in solution and saturates at ~4%, compared to the ~8% maximum thinning observed for the correspondingly premixed peptide-MLM bilayers. Linearly scaling the thinning of peptide-ULV bilayers to that of the corresponding peptide-MLM of a calibrated peptide-to-lipid ratio, we have deduced the number of bound peptides on the ULV bilayers as a function of free peptide concentration in solution. The hence derived X-ray-based binding isotherm allows extraction of a low binding constant of melittin to the ULV bilayers, on the basis of surface partition equilibrium and the Gouy-Chapman theory. Moreover, we show that the ULV and MLM bilayers of di22:1PC share a same thinning constant upon binding of a hydrophobic peptide alamethicin; this result supports the linear scaling approach used in the melittin-ULV bilayer thinning for thermodynamic binding parameters of water-soluble peptides. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Lipid Bilayers Covalently Anchored to Carbon Nanotubes

    PubMed Central

    Dayani, Yasaman; Malmstadt, Noah

    2012-01-01

    The unique physical and electrical properties of carbon nanotubes make them an exciting material for applications in various fields such as bioelectronics and biosensing. Due to the poor water solubility of carbon nanotubes, functionalization for such applications has been a challenge. Of particular need are functionalization methods for integrating carbon nanotubes with biomolecules and constructing novel hybrid nanostructures for bionanoelectronic applications. We present a novel method for the fabrication of dispersible, biocompatible carbon nanotube-based materials. Multi-walled carbon nanotubes (MWCNTs) are covalently modified with primary amine-bearing phospholipids in a carbodiimide-activated reaction. These modified carbon nanotubes have good dispersibility in nonpolar solvents. Fourier transform infrared (FTIR) spectroscopy shows peaks attributable to the formation of amide bonds between lipids and the nanotube surface. Simple sonication of lipid-modified nanotubes with other lipid molecules leads to the formation of a uniform lipid bilayer coating the nanotubes. These bilayer-coated nanotubes are highly dispersible and stable in aqueous solution. Confocal fluorescence microscopy shows labeled lipids on the surface of bilayer-modified nanotubes. Transmission electron microscopy (TEM) shows the morphology of dispersed bilayer-coated MWCNTs. Fluorescence quenching of lipid-coated MWCNTs confirms the bilayer configuration of the lipids on the nanotube surface and fluorescence anisotropy measurements show that the bilayer is fluid above the gel-to-liquid transition temperature. The membrane protein α-hemolysin spontaneously inserts into the MWCNT-supported bilayer, confirming the biomimetic membrane structure. These biomimetic nanostructures are a promising platform for the integration of carbon nanotube-based materials with biomolecules. PMID:22568448

  14. Lipid bilayers covalently anchored to carbon nanotubes.

    PubMed

    Dayani, Yasaman; Malmstadt, Noah

    2012-05-29

    The unique physical and electrical properties of carbon nanotubes make them an exciting material for applications in various fields such as bioelectronics and biosensing. Due to the poor water solubility of carbon nanotubes, functionalization for such applications has been a challenge. Of particular need are functionalization methods for integrating carbon nanotubes with biomolecules and constructing novel hybrid nanostructures for bionanoelectronic applications. We present a novel method for the fabrication of dispersible, biocompatible carbon nanotube-based materials. Multiwalled carbon nanotubes (MWCNTs) are covalently modified with primary amine-bearing phospholipids in a carbodiimide-activated reaction. These modified carbon nanotubes have good dispersibility in nonpolar solvents. Fourier transform infrared (FTIR) spectroscopy shows peaks attributable to the formation of amide bonds between lipids and the nanotube surface. Simple sonication of lipid-modified nanotubes with other lipid molecules leads to the formation of a uniform lipid bilayer coating the nanotubes. These bilayer-coated nanotubes are highly dispersible and stable in aqueous solution. Confocal fluorescence microscopy shows labeled lipids on the surface of bilayer-modified nanotubes. Transmission electron microscopy (TEM) shows the morphology of dispersed bilayer-coated MWCNTs. Fluorescence quenching of lipid-coated MWCNTs confirms the bilayer configuration of the lipids on the nanotube surface, and fluorescence anisotropy measurements show that the bilayer is fluid above the gel-to-liquid transition temperature. The membrane protein α-hemolysin spontaneously inserts into the MWCNT-supported bilayer, confirming the biomimetic membrane structure. These biomimetic nanostructures are a promising platform for the integration of carbon nanotube-based materials with biomolecules.

  15. Pair structure and the pairing interaction in a bilayer Hubbard model for unconventional superconductivity

    SciTech Connect

    Maier, Thomas A

    2011-01-01

    The bilayer Hubbard model with an intralayer hopping t and an interlayer hopping t{sub {lambda}} provides an interesting testing ground for several aspects of what has been called unconventional superconductivity. One can study the type of pair structures which arise when there are multiple Fermi surfaces. One can also examine the pairing for a system in which the structure of the spin-fluctuation spectral weight can be changed. Using a dynamic cluster quantum Monte Carlo approximation, we find that near half filling, if the splitting between the bonding and antibonding bands t{sub {lambda}}/t is small, the gap has B{sub 1g} (d{sub x{sup 2}-y{sup 2}}-wave) symmetry, but when the splitting becomes larger, A{sub 1g} (s{sup {+-}}-wave) pairing is favored. We also find that in the s{sup {+-}} pairing region, the pairing is driven by interlayer spin fluctuations and that T{sub c} is enhanced.

  16. Capturing suboptical dynamic structures in lipid bilayer patches formed from free-standing giant unilamellar vesicles.

    PubMed

    Bhatia, Tripta; Cornelius, Flemming; Ipsen, John H

    2017-08-01

    There is accumulating evidence that the small-scale lateral organization of biological membranes has a crucial role in signaling and trafficking in cells. However, it has been difficult to characterize these features with existing methods for preparing and analyzing freestanding membranes, because the dynamics occurs below the optical resolution possible with these protocols. We have developed a protocol that permits the imaging of lipid nanodomains and lateral protein organization in membranes of giant unilamellar vesicles (GUVs). Freestanding GUVs are transferred onto a mica support, and after treatment with magnesium chloride, they collapse to form planar lipid bilayer (PLB) patches. Rapid GUV collapse onto the mica preserves the lateral organization of freestanding membranes and thus makes it possible to image 'snapshots' of GUVs up to nanometer resolution by high-resolution microscopy. The method has been applied to classical lipid raft mixtures in which suboptical domain fluctuations have been imaged in both the liquid-ordered and liquid-disordered membrane phases. High-resolution scanning by atomic force microscopy (AFM) of membranes composed of binary and ternary lipid mixtures reconstituted with Na(+)/K(+)-ATPase (NKA) has revealed the spatial distribution and orientations of individual proteins, as well as details of membrane lateral structure. Immunolabeling followed by confocal microscopy can also provide information about the spatial distribution of proteins. The protocol opens up a new avenue for quantitative biophysical studies of suboptical dynamic structures in biomembranes, which are local and short-lived. Preparation of GUVs, PLB patches and their imaging takes <24 h.

  17. Structural characterization of a C-terminally truncated E5 oncoprotein from papillomavirus in lipid bilayers.

    PubMed

    Windisch, Dirk; Ziegler, Colin; Bürck, Jochen; Ulrich, Anne S

    2014-12-01

    E5 is the major transforming oncoprotein of bovine papillomavirus, which activates the platelet-derived growth factor receptor β in a highly specific manner. The short transmembrane protein E5 with only 44 residues interacts directly with the transmembrane segments of the receptor, but structural details are not available. Biophysical investigations are challenging, because the hydrophobic E5 protein tends to aggregate and get cross-linked non-specifically via two Cys residues near its C-terminus. Here, we demonstrate that a truncation by 10 amino acids creates a more manageable protein that can be conveniently used for structure analysis. Synchrotron radiation circular dichroism and solid-state (15)N- and (31)P-nuclear magnetic resonance spectroscopy show that this E5 variant serves as a representative model for the wild-type protein. The helical conformation of the transmembrane segment, its orientation in the lipid bilayer, and the ability to form homodimers in the membrane are not affected by the C-terminal truncation.

  18. Covalent attachment of lipid vesicles to a fluid supported bilayer allows observation of DNA-mediated vesicle interactions

    PubMed Central

    van Lengerich, Bettina; Rawle, Robert J.; Boxer, Steven G.

    2010-01-01

    Specific membrane interactions such as lipid vesicle docking and fusion can be mediated by synthetic DNA-lipid conjugates as a model for the protein-driven processes that are ubiquitous in biological systems. Here we present a method of tethering vesicles to a supported lipid bilayer that allows simultaneous deposition of cognate vesicle partners displaying complementary DNA, resulting in well-mixed populations of tethered vesicles that are laterally mobile. Vesicles are covalently attached to a supporting lipid bilayer using a DNA-templated click reaction; then DNA-mediated interactions between tethered vesicles are triggered by spiking the salt concentration. These interactions, such as docking and fusion, can then be observed for individual vesicles as they collide on the surface. The architecture of this new system also permits control over the number of lipid anchors that tether the vesicle to the supporting bilayer. The diffusion coefficient of tethered vesicles anchored by two lipids is approximately 1.6-fold slower than that of vesicles anchored only with a single lipid, consistent with a simple physical model. PMID:20180548

  19. Covalent attachment of lipid vesicles to a fluid-supported bilayer allows observation of DNA-mediated vesicle interactions.

    PubMed

    van Lengerich, Bettina; Rawle, Robert J; Boxer, Steven G

    2010-06-01

    Specific membrane interactions such as lipid vesicle docking and fusion can be mediated by synthetic DNA-lipid conjugates as a model for the protein-driven processes that are ubiquitous in biological systems. Here we present a method of tethering vesicles to a supported lipid bilayer that allows the simultaneous deposition of cognate vesicle partners displaying complementary DNA, resulting in well-mixed populations of tethered vesicles that are laterally mobile. Vesicles are covalently attached to a supporting lipid bilayer using a DNA-templated click reaction; then DNA-mediated interactions between tethered vesicles are triggered by spiking the salt concentration. These interactions, such as docking and fusion, can then be observed for individual vesicles as they collide on the surface. The architecture of this new system also permits control over the number of lipid anchors that tether the vesicle to the supporting bilayer. The diffusion coefficient of tethered vesicles anchored by two lipids is approximately 1.6-fold slower than that of vesicles anchored only with a single lipid, consistent with a simple physical model.

  20. Direct Measurement of the Tunable Electronic Structure of Bilayer MoS 2 by Interlayer Twist

    SciTech Connect

    Yeh, Po-Chun; Jin, Wencan; Zaki, Nader; Kunstmann, Jens; Chenet, Daniel; Arefe, Ghidewon; Sadowski, Jerzy T.; Dadap, Jerry I.; Sutter, Peter; Hone, James; Osgood, Richard M.

    2016-01-13

    We measure the interlayer twist angle-dependent electronic band structure of bilayer molybdenum-disulfide (MoS2), using angle-resolved photoemission on micrometer-scale sample areas. Our measurements, performed on arbitrarily stacked bilayer MoS2 flakes prepared by chemical vapor deposition, provide direct evidence for a downshift of the quasiparticle energy of the valence band at the Brillouin zone center ($\\bar{Γ}$ point) with the interlayer twist angle, up to a maximum of 120 meV at a twist angle of ~40°. Our direct measurements of the valence band structure enable the extraction of the hole effective mass as a function of the interlayer twist angle. While our results at $\\bar{Γ}$ agree with recently published photoluminescence data, our measurements of the quasiparticle spectrum over the full 2D Brillouin zone reveal a richer and more complicated change in the electronic structure than previously theoretically predicted. Furthermore, the electronic structure measurements reported here, including the evolution of the effective mass with twist-angle, provide new insight into the physics of twisted transition-metal dichalcogenide bilayers and serve as a guide for the practical design of MoS2 optoelectronic and spin-/valley-tronic devices.

  1. Bilayered graphene/h-BN with folded holes as new nanoelectronic materials: modeling of structures and electronic properties

    PubMed Central

    Chernozatonskii, Leonid A.; Demin, Viсtor A.; Bellucci, Stefano

    2016-01-01

    The latest achievements in 2-dimensional (2D) material research have shown the perspective use of sandwich structures in nanodevices. We demonstrate the following generation of bilayer materials for electronics and optoelectronics. The atomic structures, the stability and electronic properties of Moiré graphene (G)/h-BN bilayers with folded nanoholes have been investigated theoretically by ab-initio DFT method. These perforated bilayers with folded hole edges may present electronic properties different from the properties of both graphene and monolayer nanomesh structures. The closing of the edges is realized by C-B(N) bonds that form after folding the borders of the holes. Stable ≪round≫ and ≪triangle≫ holes organization are studied and compared with similar hole forms in single layer graphene. The electronic band structures of the considered G/BN nanomeshes reveal semiconducting or metallic characteristics depending on the sizes and edge terminations of the created holes. This investigation of the new types of G/BN nanostructures with folded edges might provide a directional guide for the future of this emerging area. PMID:27897237

  2. Bilayered graphene/h-BN with folded holes as new nanoelectronic materials: modeling of structures and electronic properties

    NASA Astrophysics Data System (ADS)

    Chernozatonskii, Leonid A.; Demin сtor A., Vi; Bellucci, Stefano

    2016-11-01

    The latest achievements in 2-dimensional (2D) material research have shown the perspective use of sandwich structures in nanodevices. We demonstrate the following generation of bilayer materials for electronics and optoelectronics. The atomic structures, the stability and electronic properties of Moiré graphene (G)/h-BN bilayers with folded nanoholes have been investigated theoretically by ab-initio DFT method. These perforated bilayers with folded hole edges may present electronic properties different from the properties of both graphene and monolayer nanomesh structures. The closing of the edges is realized by C-B(N) bonds that form after folding the borders of the holes. Stable ≪round≫ and ≪triangle≫ holes organization are studied and compared with similar hole forms in single layer graphene. The electronic band structures of the considered G/BN nanomeshes reveal semiconducting or metallic characteristics depending on the sizes and edge terminations of the created holes. This investigation of the new types of G/BN nanostructures with folded edges might provide a directional guide for the future of this emerging area.

  3. Structure and dynamics of Penetratin's association and translocation to a lipid bilayer

    NASA Astrophysics Data System (ADS)

    Ignacio J., General; Asciutto, Eliana K.

    2017-03-01

    Penetratin belongs to the important class of small and positively charged peptides, capable of entering cells. The determination of the optimal peptidic structure for translocation is challenging; results obtained so far are varied and dependent on several factors. In this work, we review the dynamics of association of Penetratin with a modeled dioleoyl-phosphatidylcholine (DOPC) lipid membrane using molecular dynamics simulations with last generation force fields. Penetratin's structural preferences are determined using a Markov state model. It is observed that the peptide retains a helical form in the membrane associated state, just as in water, with the exception of both termini which lose helicity, facilitating the interaction of terminal residues with the phosphate groups on the membrane's outer layer. The optimal orientation for insertion is found to be with the peptide's axis forming a small angle with the interface, and with R1 stretching toward the bilayer. The interaction between arginine side-chains and phosphate groups is found to be greater than the corresponding to lysine, mainly due to a higher number of hydrogen bonds between them. The free energy profile of translocation is qualitatively studied using Umbrella Sampling. It is found that there are different paths of penetration, that greatly differ in size of free energy barrier. The lowest path is compatible with residues R10 to K13 leading the way through the membrane and pulling the rest of the peptide. When the other side is reached, the C-terminus overtakes those residues, and finally breaks out of the membrane. The peptide's secondary structure during this traversal suffers some changes with respect to the association structure but, overall, conserves its helicity, with both termini in a more disordered state.

  4. Direct observation of asymmetric band structure of bilayer graphene through quantum capacitance measurements

    NASA Astrophysics Data System (ADS)

    Kanayama, Kaoru; Nagashio, Kosuke; Nishimura, Tomonori; Toriumi, Akira

    2014-03-01

    Although upper conduction and valence sub-bands in bilayer graphene are known to be asymmetric, a detailed analysis based on the electrical measurements is very limited due to the infirm quality of gate insulator. In this study, the electrical quality of the top-gate Y2O3 insulator is drastically improved by the high-pressure O2 post-deposition annealing at 100 atm and the carrier density of ~8*1013 cm-2 is achieved. In quantum capacitance measurements, the drastic increase of the density of states is observed in addition to the van Hove singularity, suggesting that the Fermi energy reaches upper sub-band. At the same carrier density, the sudden reduction of the conductivity is observed, indicating that the inter-band scattering occurs. The estimated carrier density required to fill the upper sub-bands is different between electron and hole sides, i.e., asymmetric band structure between upper conduction and valence bands is revealed by the electrical measurements.

  5. Structural Dynamics of an Isolated-Voltage Sensor Domain in Lipid Bilayer

    PubMed Central

    Chakrapani, Sudha; Cuello, Luis G.; Cortes, Marien D.; Perozo, Eduardo

    2009-01-01

    Summary A strong interplay between the voltage-sensor domain (VSD) and the pore domain (PD) underlies voltage-gated channel functions. In a few voltage-sensitive proteins, the VSD has been shown to function without a canonical PD, although its structure and oligomeric state remain unknown. Here using EPR spectroscopy we show that the isolated-VSD of KvAP can remain monomeric in reconstituted bilayer and retain a transmembrane conformation. We find that water-filled crevices extend deep into the membrane around S3, a scaffold conducive to transport of proton/cations is intrinsic to the VSD. Differences in solvent accessibility in comparison to the full-length KvAP, allowed us to define an interacting footprint of the PD on the VSD. This interaction is centered around S1 and S2 and shows a rotation of 70–100° relative to Kv1.2-Kv2.1 chimera. Sequence-conservation patterns in Kv channels, Hv channels and voltage-sensitive phosphatases reveal several near-universal features suggesting a common molecular architecture for all VSDs. PMID:18334215

  6. Effect of Bilayer Structure on the Long-Term Stability of Nanocrystalline Porous Silicon Ultrasonic Emitter

    NASA Astrophysics Data System (ADS)

    Watabe, Yoshifumi; Honda, Yoshiaki; Koshida, Nobuyoshi

    2007-09-01

    Due to a strong quantum confinement effect, both the thermal conductivity α and heat capacity per unit volume C of nanocrystalline porous silicon (nc-PS) are extremely lowered in comparison to those of single-crystalline silicon (c-Si). This high contrast between the thermal properties of nc-PS and c-Si makes it possible to produce an efficient ultrasound emitter device based on interfacial thermoacoustic transfer with no mechanical surface vibrations. The most important parameter of this device is the thermal effusivity (α C)1/2 of the nc-PS layer, since the theoretical acoustic output is in inversely proportional to (α C)1/2. To stabilize the acoustic output by suppressing possible change in (α C)1/2 during a long-term operation, a bilayer structure is introduced into the nc-PS layer in this work. Due to the increased stability against oxidation, the device operates for a long time without any significant degradation. The observed long-term stability ensures the applicability of this emitter in functional acoustic devices such as sensors, speakers, and actuators.

  7. Asymmetric Structural Features in Single Supported Lipid Bilayers Containing Cholesterol and GM1 Resolved with Synchrotron X-Ray Reflectivity

    PubMed Central

    Reich, Christian; Horton, Margaret R.; Krause, Bärbel; Gast, Alice P.; Rädler, Joachim O.; Nickel, Bert

    2008-01-01

    The cell membrane comprises numerous protein and lipid molecules capable of asymmetric organization between leaflets and liquid-liquid phase separation. We use single supported lipid bilayers (SLBs) to model cell membranes, and study how cholesterol and asymmetrically oriented ganglioside receptor GM1 affect membrane structure using synchrotron x-ray reflectivity. Using mixtures of cholesterol, sphingomyelin, and 1,2-dioleoyl-sn-glycero-3-phosphocholine, we characterize the structure of liquid-ordered and liquid-disordered SLBs in terms of acyl-chain density, headgroup size, and leaflet thickness. SLBs modeling the liquid-ordered phase are 10 Å thicker and have a higher acyl-chain electron density (〈ρchain〉 = 0.33 e−/Å3) compared to SLBs modeling the liquid-disordered phase, or pure phosphatidylcholine SLBs (〈ρchain〉 = 0.28 e−/Å3). Incorporating GM1 into the distal bilayer leaflet results in membrane asymmetry and thickening of the leaflet of 4–9 Å. The structural effect of GM1 is more complex in SLBs of cholesterol/sphingomyelin/1,2-dioleoyl-sn-glycero-3-phosphocholine, where the distal chains show a high electron density (〈ρchain〉 = 0.33 e−/Å3) and the lipid diffusion constant is reduced by ∼50%, as measured by fluorescence microscopy. These results give quantitative information about the leaflet asymmetry and electron density changes induced by receptor molecules that penetrate a single lipid bilayer. PMID:18375517

  8. Elliptical structure of phospholipid bilayer nanodiscs encapsulated by scaffold proteins: casting the roles of the lipids and the protein.

    PubMed

    Skar-Gislinge, Nicholas; Simonsen, Jens Bæk; Mortensen, Kell; Feidenhans'l, Robert; Sligar, Stephen G; Lindberg Møller, Birger; Bjørnholm, Thomas; Arleth, Lise

    2010-10-06

    Phospholipid bilayers host and support the function of membrane proteins and may be stabilized in disc-like nanostructures, allowing for unprecedented solution studies of the assembly, structure, and function of membrane proteins (Bayburt et al. Nano Lett. 2002, 2, 853-856). Based on small-angle neutron scattering in combination with variable-temperature studies of synchrotron small-angle X-ray scattering on nanodiscs in solution, we show that the fundamental nanodisc unit, consisting of a lipid bilayer surrounded by amphiphilic scaffold proteins, possesses intrinsically an elliptical shape. The temperature dependence of the curvature of the nanodiscs prepared with two different phospholipid types (DLPC and POPC) shows that it is the scaffold protein that determines the overall elliptical shape and that the nanodiscs become more circular with increasing temperature. Our data also show that the hydrophobic bilayer thickness is, to a large extent, dictated by the scaffolding protein and adjusted to minimize the hydrophobic mismatch between protein and phospholipid. Our conclusions result from a new comprehensive and molecular-based model of the nanodisc structure and the use of this to analyze the experimental scattering profile from nanodiscs. The model paves the way for future detailed structural studies of functional membrane proteins encapsulated in nanodiscs.

  9. Fluid Structure Interaction in a Turbine Blade

    NASA Technical Reports Server (NTRS)

    Gorla, Rama S. R.

    2004-01-01

    An unsteady, three dimensional Navier-Stokes solution in rotating frame formulation for turbomachinery applications is presented. Casting the governing equations in a rotating frame enabled the freezing of grid motion and resulted in substantial savings in computer time. The turbine blade was computationally simulated and probabilistically evaluated in view of several uncertainties in the aerodynamic, structural, material and thermal variables that govern the turbine blade. The interconnection between the computational fluid dynamics code and finite element structural analysis code was necessary to couple the thermal profiles with the structural design. The stresses and their variations were evaluated at critical points on the Turbine blade. Cumulative distribution functions and sensitivity factors were computed for stress responses due to aerodynamic, geometric, mechanical and thermal random variables.

  10. Tethered bilayer membranes as a complementary tool for functional and structural studies: The pyolysin case.

    PubMed

    Preta, Giulio; Jankunec, Marija; Heinrich, Frank; Griffin, Sholeem; Sheldon, Iain Martin; Valincius, Gintaras

    2016-09-01

    We demonstrate the use of tethered bilayer lipid membranes (tBLMs) as an experimental platform for functional and structural studies of membrane associated proteins by electrochemical techniques. The reconstitution of the cholesterol-dependent cytolysin (CDC) pyolysin (PLO) from Trueperella pyogenes into tBLMs was followed in real-time by electrochemical impedance spectroscopy (EIS). Changes of the EIS parameters of the tBLMs upon exposure to PLO solutions were consistent with the dielectric barrier damage occurring through the formation of water-filled pores in membranes. Parallel experiments involving a mutant version of PLO, which is able to bind to the membranes but does not form oligomer pores, strengthen the reliability of this methodology, since no change in the electrochemical impedance was observed. Complementary atomic force microscopy (AFM) and neutron reflectometry (NR) measurements revealed structural details of the membrane bound PLO, consistent with the structural transformations of the membrane bound toxins found for other cholesterol dependent cytolysins. In this work, using the tBLMs platform we also observed a protective effect of the dynamin inhibitor Dynasore against pyolysin as well as pneumolysin. An effect of Dynasore in tBLMs, which was earlier observed in experiments with live cells, confirms the biological relevance of the tBLMs models, as well as demonstrates the potential of the electrochemical impedance spectroscopy to quantify membrane damage by the pore forming toxins. In conclusion, tBLMs are a reliable and complementary method to explore the activity of CDCs in eukaryotic cells and to develop strategies to limit the toxic effects of CDCs.

  11. Fluid Structure Interaction Effect on Sandwich Composite Structures

    DTIC Science & Technology

    2011-09-01

    14. SUBJECT TERMS Fluid Structure Interaction, FSI, composite, balsa, low velocity impact, sandwich composites, VARTM , Vacuum Assisted Resin Transfer...11 1. Vacuum Assisted Resin Transfer Molding ( VARTM ) ...................11 2. Procedure...required equipment for VARTM composite production. ..............10 Figure 4. VARTM Lay-up (From [8

  12. Complex fluid-fluid interfaces: rheology and structure.

    PubMed

    Fuller, Gerald G; Vermant, Jan

    2012-01-01

    Complex fluid-fluid interfaces are common to living systems, foods, personal products, and the environment. They occur wherever surface-active molecules and particles collect at fluid interfaces and render them nonlinear in their response to flow and deformation. When this occurs, the interfaces acquire a complex microstructure that must be interrogated. Interfacial rheological material properties must be measured to appreciate their role in such varied processes as lung function, cell division, and foam and emulsion stability. This review presents the methods that have been devised to determine the microstructure of complex fluid-fluid interfaces. Complex interfacial microstructure leads to rheological complexity. This behavior is often responsible for stabilizing interfacial systems such as foams and emulsions, and it can also have a profound influence on wetting/dewetting dynamics. Interfacial rheological characterization relies on the development of tools with the sensitivity to respond to small surface stresses in a way that isolates them from bulk stresses. This development is relatively recent, and reviews of methods for both shear and dilatational measurements are offered here.

  13. Influence of material parameters on acoustic wave propagation modes in ZnO/Si bi-layered structures.

    PubMed

    Gao, Hui-dong; Zhang, Shu-Yi; Qi, Xue; Wasa, Kiyotaka; Wu, Hao-Dong

    2005-12-01

    The influences of material properties on acoustic wave propagation modes in ZnO/Si bi-layered structures are studied. The transfer matrix method is used to calculate dispersion relations, wave field distributions, and electromechanical coupling coefficients of acoustic wave propagation modes in ZnO/Si bi-layered systems, in which the thickness of the substrate is of the same order of magnitude as the wavelength of the propagating wave modes. The influences of the thin film parameters on the acoustic wave propagation modes and their electromechanical coupling coefficients of the wave modes also are obtained. In addition, some experimental results for characterizing the wave propagation modes and their frequencies have also been obtained, which agree well with the theoretical predictions.

  14. Graphene‐Based Polymer Bilayers with Superior Light‐Driven Properties for Remote Construction of 3D Structures

    PubMed Central

    Tang, Zhenhua; Gao, Ziwei; Wang, Fei; Wang, Yonglin

    2017-01-01

    3D structure assembly in advanced functional materials is important for many areas of technology. Here, a new strategy exploits IR light‐driven bilayer polymeric composites for autonomic origami assembly of 3D structures. The bilayer sheet comprises a passive layer of poly(dimethylsiloxane) (PDMS) and an active layer comprising reduced graphene oxides (RGOs), thermally expanding microspheres (TEMs), and PDMS. The corresponding fabrication method is versatile and simple. Owing to the large volume expansion of the TEMs, the two layers exhibit large differences in their coefficients of thermal expansion. The RGO‐TEM‐PDMS/PDMS bilayers can deflect toward the PDMS side upon IR irradiation via the cooperative effect of the photothermal effect of the RGOs and the expansion of the TEMs, and exhibit excellent light‐driven, a large bending deformation, and rapid responsive properties. The proposed RGO‐TEM‐PDMS/PDMS composites with excellent light‐driven bending properties are demonstrated as active hinges for building 3D geometries such as bidirectionally folded columns, boxes, pyramids, and cars. The folding angle (ranging from 0° to 180°) is well‐controlled by tuning the active hinge length. Furthermore, the folded 3D architectures can permanently preserve the deformed shape without energy supply. The presented approach has potential in biomedical devices, aerospace applications, microfluidic devices, and 4D printing. PMID:28546911

  15. Gel-to-fluid phase transformations in solid-supported phospholipid bilayers assembled by the Langmuir-Blodgett technique: effect of the Langmuir monolayer phase state and molecular density.

    PubMed

    Ramkaran, Mohini; Badia, Antonella

    2014-08-14

    Planar-supported phospholipid bilayers are increasingly used as synthetic membranes for scientific and practical applications. The thermotropic phase properties of supported bilayers are important for recreating biologically relevant situations. Unlike free-standing lipid membranes that undergo one gel-to-fluid or main phase transition, mica-supported single bilayers have been found to undergo two separate leaflet transitions. Although the distinctive nature of the main transition in mica-supported bilayers has been attributed to different effects, determining their relevance has been problematic because vesicle fusion, the technique most widely used to prepare solid-supported bilayer membranes, does not allow one to readily control the lipid surface coverage and molecular density. To circumvent the limitations of the vesicle fusion method and systematically investigate the effects on the individual leaflet transitions of the lipid phase state and molecular density before deposition on the substrate, mica-supported single bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) were prepared using the Langmuir-Blodgett technique. The gel-to-fluid transitions of the bilayer leaflets were tracked by controlled-temperature atomic force microscopy to determine the relative fractions of the gel and fluid phases as a function of temperature. The fraction of solid versus temperature data was fit to the van't Hoff equation to determine the leaflet melting temperatures and transition enthalpies. The phase state and molecular density of the Langmuir monolayer precursor at the transfer pressure of 35 mN m(-1) was found to have a greater effect on the main transition temperature and width of the distal (upper) leaflet than that of the proximal (lower) one. The contributions of substrate-mediated condensation, asymmetric lipid densities, and surface area available for thermal expansion of the bilayer are addressed

  16. Compositional and structural characterization of monolayers and bilayers composed of native pulmonary surfactant from wild type mice.

    PubMed

    Bernardino de la Serna, Jorge; Hansen, Soren; Berzina, Zane; Simonsen, Adam C; Hannibal-Bach, Hans K; Knudsen, Jens; Ejsing, Christer S; Bagatolli, Luis A

    2013-11-01

    This work comprises a structural and dynamical study of monolayers and bilayers composed of native pulmonary surfactant from mice. Spatially resolved information was obtained using fluorescence (confocal, wide field and two photon excitation) and atomic force microscopy methods. Lipid mass spectrometry experiments were also performed in order to obtain relevant information on the lipid composition of this material. Bilayers composed of mice pulmonary surfactant showed coexistence of distinct domains at room temperature, with morphologies and lateral packing resembling the coexistence of liquid ordered (lo)/liquid disordered (ld)-like phases reported previously in porcine lung surfactant. Interestingly, the molar ratio of saturated (mostly DPPC)/non-saturated phospholipid species and cholesterol measured in the innate material corresponds with that of a DOPC/DPPC/cholesterol mixture showing lo/ld phase coexistence at a similar temperature. This suggests that at quasi-equilibrium conditions, key lipid classes in this complex biological material are still able to produce the same scaffold observed in relevant but simpler model lipid mixtures. Also, robust structural and dynamical similarities between mono- and bi-layers composed of mice pulmonary surfactant were observed when the monolayers reach a surface pressure of 30mN/m. This value is in line with theoretically predicted and recently measured surface pressures, where the monolayer-bilayer equivalence occurs in samples composed of single phospholipids. Finally, squeezed out material attached to pulmonary surfactant monolayers was observed at surface pressures near the beginning of the monolayer reversible exclusion plateau (~40mN/m). Under these conditions this material adopts elongated tubular shapes and displays ordered lateral packing as indicated by spatially resolved LAURDAN GP measurements. © 2013.

  17. Dynamics and Emergent Structures in Active Fluids

    NASA Astrophysics Data System (ADS)

    Baskaran, Aparna

    2014-03-01

    In this talk, we consider an active fluid of colloidal sized particles, with the primary manifestation of activity being a self-replenishing velocity along one body axis of the particle. This is a minimal model for varied systems such as bacterial colonies, cytoskeletal filament motility assays vibrated granular particles and self propelled diffusophoretic colloids, depending on the nature of interaction among the particles. Using microscopic Brownian dynamics simulations, coarse-graining using the tools of non-equilibrium statistical mechanics and analysis of macroscopic hydrodynamic theories, we characterize emergent structures seen in these systems, which are determined by the symmetry of the interactions among the active units, such as propagating density waves, dense stationary bands, asters and phase separated isotropic clusters. We identify a universal mechanism, termed ``self-regulation,'' as the underlying physics that leads to these structures in diverse systems. Support from NSF through DMR-1149266 and DMR-0820492.

  18. Fluid transients in fluid-structure interaction - 1985

    SciTech Connect

    Dodge, F.T.; Moody, F.J.

    1985-01-01

    This book presents the papers given at a conference which considered fluid flow in reactor cooling systems. Topics covered at the conference included computerized simulation, pressure surges, transient flow in piping, steam condensation in water, BWR type reactors, PWR type reactors, relief valves, shock waves, control elements, zero gravity in spacecraft, two-phase flow, steam turbines, and turbulent flow.

  19. Dependence of antimicrobial selectivity and potency on oligomer structure investigated using substrate supported lipid bilayers and sum frequency generation vibrational spectroscopy.

    PubMed

    Avery, Christopher W; Som, Abhigyan; Xu, Yongjiang; Tew, Gregory N; Chen, Zhan

    2009-10-15

    Sum frequency generation (SFG) vibrational spectroscopy was used to study interactions between solid-supported lipid bilayers mimicking microbial and erythrocyte cellular membranes and synthetic antimicrobial arylamide oligomers named 2, 3, and 4, designed with the facial amphiphilicity common to naturally occurring antimicrobial peptides. The three compounds have the same backbone structure but varied side chains. The inherent interfacial sensitivity of SFG allowed for simultaneous monitoring of lipid ordering in the individual bilayer leaflets and orientation of 2, 3, and 4 upon interaction with the bilayer. Critical concentrations at which the inner leaflet is disrupted were determined for each oligomer. Spectral evidence of the oligomers' interaction with the bilayer below the critical concentrations was also found. Oligomers 2 and 3 tilted toward the bilayer surface normal, in agreement with previous experimental and simulation results. These oligomers selectively interact with microbial membrane models over erythrocyte membrane models, correlating well to previously published SFG studies on antimicrobial oligomer 1. It was shown that the oligomers interact with the lipid bilayers differently, indicating their different activity and selectivity. This research further shows that SFG is a particularly useful technique for the investigation of interaction mechanisms between cell membranes and membrane-active molecules. Additionally, SFG provides details of the specific interactions between these novel antimicrobials and lipid bilayers.

  20. Creation of quasi-Dirac points in the Floquet band structure of bilayer graphene.

    PubMed

    Cheung, W M; Chan, K S

    2017-06-01

    We study the Floquet quasi-energy band structure of bilayer graphene when it is illuminated by two laser lights with frequencies [Formula: see text] and [Formula: see text] using Floquet theory. We focus on the dynamical gap formed by the conduction band with Floquet index  =  -1 and the valence band with Floquet index  =  +1 to understand how Dirac points can be formed. It is found that the dynamical gap does not have rotation symmetry in the momentum space, and quasi-Dirac points, where the conduction and valence bands almost touch, can be created when the dynamical gap closes along some directions with suitably chosen radiation parameters. We derive analytical expressions for the direction dependence of the dynamical gaps using Lowdin perturbation theory to gain a better understanding of the formation of quasi-Dirac points. When both radiations are circularly polarized, the gap can be exactly zero along some directions, when only the first and second order perturbations are considered. Higher order perturbations can open a very small gap in this case. When both radiations are linearly polarized, the gap can be exactly zero up to the fourth order perturbation and more than one quasi-Dirac point is formed. We also study the electron velocity around a dynamical gap and show that the magnitude of the velocity drops to values close to zero when the k vector is near to the gap minimum. The direction of the velocity also changes around the gap minimum, and when the gap is larger in value the change in the velocity direction is more gradual. The warping effect does not affect the formation of a Dirac point along the k x axis, while it prevents its formation when there is phase shift between the two radiations.

  1. Creation of quasi-Dirac points in the Floquet band structure of bilayer graphene

    NASA Astrophysics Data System (ADS)

    Cheung, W. M.; Chan, K. S.

    2017-06-01

    We study the Floquet quasi-energy band structure of bilayer graphene when it is illuminated by two laser lights with frequencies ω and 2ω using Floquet theory. We focus on the dynamical gap formed by the conduction band with Floquet index  =  -1 and the valence band with Floquet index  =  +1 to understand how Dirac points can be formed. It is found that the dynamical gap does not have rotation symmetry in the momentum space, and quasi-Dirac points, where the conduction and valence bands almost touch, can be created when the dynamical gap closes along some directions with suitably chosen radiation parameters. We derive analytical expressions for the direction dependence of the dynamical gaps using Lowdin perturbation theory to gain a better understanding of the formation of quasi-Dirac points. When both radiations are circularly polarized, the gap can be exactly zero along some directions, when only the first and second order perturbations are considered. Higher order perturbations can open a very small gap in this case. When both radiations are linearly polarized, the gap can be exactly zero up to the fourth order perturbation and more than one quasi-Dirac point is formed. We also study the electron velocity around a dynamical gap and show that the magnitude of the velocity drops to values close to zero when the k vector is near to the gap minimum. The direction of the velocity also changes around the gap minimum, and when the gap is larger in value the change in the velocity direction is more gradual. The warping effect does not affect the formation of a Dirac point along the k x axis, while it prevents its formation when there is phase shift between the two radiations.

  2. Structural impact of cations on lipid bilayer models: nanomechanical properties by AFM-force spectroscopy.

    PubMed

    Redondo-Morata, Lorena; Giannotti, Marina I; Sanz, Fausto

    2014-02-01

    Atomic Force Microscopy (AFM) has become an invaluable tool for studying the micro- and nanoworlds. As a stand-alone, high-resolution imaging technique and force transducer, it defies most other surface instrumentation in ease of use, sensitivity and versatility. The main strength of AFM relies on the possibility to operate in an aqueous environment on a wide variety of biological samples, from single molecules - DNA or proteins - to macromolecular assemblies like biological membranes. Understanding the effect of mechanical stress on membranes is of primary importance in biophysics, since cells are known to perform their function under a complex combination of forces. In the later years, AFM-based Force-Spectroscopy (AFM-FS) has provided a new vista on membrane mechanics in a confined area within the nanometer realm, where most of the specific molecular interactions take place. Lipid membranes are electrostatically charged entities that physiologically coexist with electrolyte solutions. Thus, specific interactions with ions are a matter of considerable interest. The distribution of ions in the solution and their interaction with the membranes are factors that substantially modify the structure and dynamics of the cell membranes. Furthermore, signaling processes are modified by the membrane capability of retaining ions. Supported Lipid Bilayers (SLBs) are a versatile tool to investigate phospholipid membranes mimicking biological surfaces. In the present contribution, we review selected experiments on the mechanical stability of SLBs as models of lipid membranes by means of AFM-FS, with special focus on the effect of cations and ionic strength in the overall nanomechanical stability.

  3. Hydration, structure, and molecular interactions in the headgroup region of dioleoylphosphatidylcholine bilayers: an electron spin resonance study.

    PubMed

    Ge, Mingtao; Freed, Jack H

    2003-12-01

    The relationship between bilayer hydration and the dynamic structure of headgroups and interbilayer water in multilamellar vesicles is investigated by electron spin resonance methods. Temperature variations of the order parameter of a headgroup spin label DPP-Tempo in DOPC in excess water and partially dehydrated (10 wt % water) show a cusp-like pattern around the main phase transition, Tc. This pattern is similar to those of temperature variations of the quadrupolar splitting of interbilayer D2O in PC and PE bilayers previously measured by 2H NMR, indicating that the ordering of the headgroup and the interbilayer water are correlated. The cusp-like pattern of these and other physical properties around Tc are suggestive of quasicritical fluctuations. Also, an increase (a decrease) in ordering of DPP-Tempo is correlated with water moving out of (into) interbilayer region into (from) the bulk water phase near the freezing point, Tf. Addition of cholesterol lowers Tf, which remains the point of increasing headgroup ordering. Using the small water-soluble spin probe 4-PT, it is shown that the ordering of interbilayer water increases with bilayer dehydration. It is suggested that increased ordering in the interbilayer region, implying a lowering of entropy, will itself lead to further dehydration of the interbilayer region until its lowered pressure resists further flow, i.e., an osmotic phenomenon.

  4. Hydration, Structure, and Molecular Interactions in the Headgroup Region of Dioleoylphosphatidylcholine Bilayers: An Electron Spin Resonance Study

    PubMed Central

    Ge, Mingtao; Freed, Jack H.

    2003-01-01

    The relationship between bilayer hydration and the dynamic structure of headgroups and interbilayer water in multilamellar vesicles is investigated by electron spin resonance methods. Temperature variations of the order parameter of a headgroup spin label DPP-Tempo in DOPC in excess water and partially dehydrated (10 wt % water) show a cusp-like pattern around the main phase transition, Tc. This pattern is similar to those of temperature variations of the quadrupolar splitting of interbilayer D2O in PC and PE bilayers previously measured by 2H NMR, indicating that the ordering of the headgroup and the interbilayer water are correlated. The cusp-like pattern of these and other physical properties around Tc are suggestive of quasicritical fluctuations. Also, an increase (a decrease) in ordering of DPP-Tempo is correlated with water moving out of (into) interbilayer region into (from) the bulk water phase near the freezing point, Tf. Addition of cholesterol lowers Tf, which remains the point of increasing headgroup ordering. Using the small water-soluble spin probe 4-PT, it is shown that the ordering of interbilayer water increases with bilayer dehydration. It is suggested that increased ordering in the interbilayer region, implying a lowering of entropy, will itself lead to further dehydration of the interbilayer region until its lowered pressure resists further flow, i.e., an osmotic phenomenon. PMID:14645091

  5. Influence of temperature on structure and magnetic properties of exchange coupled TbCo/FeNi bilayers.

    PubMed

    Svalov, A V; Balymov, K G; Fernández, A; Orue, I; Larrañaga, A; Vas'kovsky, V O; Gutiérrez, J; Kurlyandskaya, G V

    2012-09-01

    Among amorphous films of rare earth-transition metal (RE-TM) alloys as exchange-biasing layers in magnetoresistive heads and spin-valve sensors, the amorphous Tb-Co films have most high practical potential. In the present work the influence of the temperature and the heat treatment parameters on the structure and magnetic properties was studied for exchange bias FeNi/Tb35Co65 bilayers annealed in vacuum or a nitrogen flow. A simple explanation of the dependence of the magnetic properties on the temperature and the heat treatment parameters connected with structural changes in each one of the layers was proposed.

  6. Flow and structure of fluids in functionalized nanopores

    NASA Astrophysics Data System (ADS)

    Bordin, José Rafael; Barbosa, Marcia C.

    2017-02-01

    We investigate through non-equilibrium molecular dynamics simulations the structure and flow of fluids in functionalized nanopores. The nanopores are modeled as cylindrical structures with solvophilic and solvophobic sites. Two fluids are modeled. The first is a standard Lennard Jones fluid. The second one is modeled with an isotropic two-length scale potential, which exhibits in bulk water-like anomalies. Our results indicate distinct dependence of the overall mass flux for each species of fluid with the number of solvophilic sites for different nanotubes' radii. Also, the density and fluid structure are dependent on the nanotube radius and the solvophilic properties of the nanotube. This indicates that the presence of a second length scale in the fluid-fluid interaction will lead to distinct behavior. Also, our results show that chemically functionalized nanotubes with different radii will have distinct nanofluidic features. Our results are explained on the basis of the characteristic scale fluid properties and the effects of nanoconfinement.

  7. Simplified Aeroelastic Model for Fluid Structure Interaction between Microcantilever Sensors and Fluid Surroundings

    PubMed Central

    Wang, Fei; Zhao, Liang; Zhang, Yanling; Qiao, Zhi

    2015-01-01

    Fluid-structural coupling occurs when microcantilever sensors vibrate in a fluid. Due to the complexity of the mechanical characteristics of microcantilevers and lack of high-precision microscopic mechanical testing instruments, effective methods for studying the fluid-structural coupling of microcantilevers are lacking, especially for non-rectangular microcantilevers. Here, we report fluid-structure interactions (FSI) of the cable-membrane structure via a macroscopic study. The simplified aeroelastic model was introduced into the microscopic field to establish a fluid-structure coupling vibration model for microcantilever sensors. We used the finite element method to solve the coupled FSI system. Based on the simplified aeroelastic model, simulation analysis of the effects of the air environment on the vibration of the commonly used rectangular microcantilever was also performed. The obtained results are consistent with the literature. The proposed model can also be applied to the auxiliary design of rectangular and non-rectangular sensors used in fluid environments. PMID:25898213

  8. Simplified Aeroelastic Model for Fluid Structure Interaction between Microcantilever Sensors and Fluid Surroundings.

    PubMed

    Wang, Fei; Zhao, Liang; Zhang, Yanling; Qiao, Zhi

    2015-01-01

    Fluid-structural coupling occurs when microcantilever sensors vibrate in a fluid. Due to the complexity of the mechanical characteristics of microcantilevers and lack of high-precision microscopic mechanical testing instruments, effective methods for studying the fluid-structural coupling of microcantilevers are lacking, especially for non-rectangular microcantilevers. Here, we report fluid-structure interactions (FSI) of the cable-membrane structure via a macroscopic study. The simplified aeroelastic model was introduced into the microscopic field to establish a fluid-structure coupling vibration model for microcantilever sensors. We used the finite element method to solve the coupled FSI system. Based on the simplified aeroelastic model, simulation analysis of the effects of the air environment on the vibration of the commonly used rectangular microcantilever was also performed. The obtained results are consistent with the literature. The proposed model can also be applied to the auxiliary design of rectangular and non-rectangular sensors used in fluid environments.

  9. Coupling analysis of fluid-structure interaction in fluid-filled elbow pipe

    NASA Astrophysics Data System (ADS)

    Xu, W. W.; Wu, D. Z.; Wang, L. Q.

    2012-11-01

    Fluid in the ship pipeline, due to power equipment components (such as impellers, plungers, etc.) and valves, will induce turbulence, cavitations, which generate high-frequency vibration excitation lines. The measurements results show that fluid-induced vibration of the pipeline is not only confined to the pipeline, but also have an impact on the hull structure. Pipe vibration due to transient flow is very common in marine pipe system Thus fluid-structure interaction problems in shipping lines is being paid more and more attention. In this paper, the fluid-filled elbow pipe is simulated considering fluid-structure interaction (FSI) by the software ADINA. And the simulation results are validated through comparison with results obtained by other numerical solution. The results show that FSI affects the pipe-filled-water modal frequencies seriously, but have little effects on pipe vibration shapes, and the free vibration frequency of the fluid-filled pipe is lower than that of empty pipe. The pipe vibration amplitude and effective stress caused by fluid increase as the fluid velocity increase. Pipe continues vibrating after fluid velocity is steady, and the vibration is dispersing as time increase. The protection against vibration near the elbow is important because the maximum pipe deformation caused by fluid near the elbow. The maximum effective stress increases from 0 to 1.4MPa due to the fluid velocity increases from 0 to 20m/s in 5 seconds. So it is necessary to consider the FSI for fluid-filled pipe.

  10. Human cannabinoid 1 GPCR C-terminal domain interacts with bilayer phospholipids to modulate the structure of its membrane environment.

    PubMed

    Tiburu, Elvis K; Tyukhtenko, Sergiy; Zhou, Han; Janero, David R; Struppe, Jochem; Makriyannis, Alexandros

    2011-03-01

    G protein-coupled receptors (GPCRs) play critical physiological and therapeutic roles. The human cannabinoid 1 GPCR (hCB1) is a prime pharmacotherapeutic target for addiction and cardiometabolic disease. Our prior biophysical studies on the structural biology of a synthetic peptide representing the functionally significant hCB1 transmembrane helix 7 (TMH7) and its cytoplasmic extension, helix 8 (H8), [hCB1(TMH7/H8)] demonstrated that the helices are oriented virtually perpendicular to each other in membrane-mimetic environments. We identified several hCB1(TMH7/H8) structure-function determinants, including multiple electrostatic amino-acid interactions and a proline kink involving the highly conserved NPXXY motif. In phospholipid bicelles, TMH7 structure, orientation, and topology relative to H8 are dynamically modulated by the surrounding membrane phospholipid bilayer. These data provide a contextual basis for the present solid-state NMR study to investigate whether intermolecular interactions between hCB1(TMH7/H8) and its phospholipid environment may affect membrane-bilayer structure. For this purpose, we measured (1)H-(13)C heteronuclear dipolar couplings for the choline, glycerol, and acyl-chain regions of dimyristoylphosphocholine in a magnetically aligned hCB1(TMH7/H8) bicelle sample. The results identify discrete regional interactions between hCB1(TMH7/H8) and membrane lipid molecules that increase phospholipid motion and decrease phospholipid order, indicating that the peptide's partial traversal of the bilayer alters membrane structure. These data offer new insight into hCB1(TMH7/H8) properties and support the concept that the membrane bilayer itself may serve as a mechanochemical mediator of hCB1/GPCR signal transduction. Since interaction with its membrane environment has been implicated in hCB1 function and its modulation by small-molecule therapeutics, our work should help inform hCB1 pharmacology and the design of hCB1-targeted drugs.

  11. Finite element modeling of lipid bilayer membranes

    NASA Astrophysics Data System (ADS)

    Feng, Feng; Klug, William S.

    2006-12-01

    A numerical simulation framework is presented for the study of biological membranes composed of lipid bilayers based on the finite element method. The classic model for these membranes employs a two-dimensional-fluid-like elastic constitutive law which is sensitive to curvature, and subjects vesicles to physically imposed constraints on surface area and volume. This model is implemented numerically via the use of C1-conforming triangular Loop subdivision finite elements. The validity of the framework is tested by computing equilibrium shapes from previously-determined axisymmetric shape-phase diagram of lipid bilayer vesicles with homogeneous material properties. Some of the benefits and challenges of finite element modeling of lipid bilayer systems are discussed, and it is indicated how this framework is natural for future investigation of biologically realistic bilayer structures involving nonaxisymmetric geometries, binding and adhesive interactions, heterogeneous mechanical properties, cytoskeletal interactions, and complex loading arrangements. These biologically relevant features have important consequences for the shape mechanics of nonidealized vesicles and cells, and their study requires not simply advances in theory, but also advances in numerical simulation techniques, such as those presented here.

  12. Gelled Complex Fluids: Combining Unique Structures with Mechanical Stability.

    PubMed

    Stubenrauch, Cosima; Gießelmann, Frank

    2016-03-01

    Gelled complex fluids are soft materials in which the microstructure of the complex fluid is combined with the mechanical stability of a gel. To obtain a gelled complex fluid one either adds a gelator to a complex fluid or replaces the solvent in a gel by a complex fluid. The most prominent example of a "natural" gelled complex fluid is the cell. There are various strategies by which one can form a gelled complex fluid; one such strategy is orthogonal self-assembly, that is, the independent but simultaneous formation of two coexisting self-assembled structures within one system. The aim of this Review is to describe the structure and potential applications of various man-made gelled complex fluids and to clarify whether or not the respective system is formed by orthogonal self-assembly.

  13. Ripples and the formation of anisotropic lipid domains: imaging two-component supported double bilayers by atomic force microscopy.

    PubMed Central

    Leidy, Chad; Kaasgaard, Thomas; Crowe, John H; Mouritsen, Ole G; Jørgensen, Kent

    2002-01-01

    Direct visualization of the fluid-phase/ordered-phase domain structure in mica-supported bilayers composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine/1,2-distearoyl-sn-glycero-3-phosphocholine mixtures is performed with atomic force microscopy. The system studied is a double bilayer supported on a mica surface in which the top bilayer (which is not in direct contact with the mica) is visualized as a function of temperature. Because the top bilayer is not as restricted by the interactions with the surface as single supported bilayers, its behavior is more similar to a free-standing bilayer. Intriguing straight-edged anisotropic fluid-phase domains were observed in the fluid-phase/ordered-phase coexistence temperature range, which resemble the fluid-phase/ordered-phase domain patterns observed in giant unilamellar vesicles composed of such phospholipid mixtures. With the high resolution provided by atomic force microscopy, we investigated the origin of these anisotropic lipid domain patterns, and found that ripple phase formation is directly responsible for the anisotropic nature of these domains. The nucleation and growth of fluid-phase domains are found to be directed by the presence of ripples. In particular, the fluid-phase domains elongate parallel to the ripples. The results show that ripple phase formation may have implications for domain formation in biological systems. PMID:12414696

  14. Microwave Surface Impedance Investigation of the Superconducting Proximity Effect in Superconductor/normal - Bilayer Structures

    NASA Astrophysics Data System (ADS)

    Pambianchi, Michael Scott

    1995-01-01

    This thesis seeks to develop a clearer understanding of the microwave-frequency electrodynamics of thin normal metal films which are superconducting by virtue of intimate contact with a superconducting film. It is found in superconductar/normal -metal (S/N) bilayer thin films of Nb/Cu and Nb/Al that the effective penetration depth and the surface resistance decrease precipitously as the temperature is lowered toward zero, unlike the exponentially slow variation of these quantities with temperature in a bare superconducting film. This behavior is associated with the temperature dependence of the characteristic penetration length scale of the superconducting order parameter in the normal metal film, which diverges as T to 0. However, theory predicts that the normal metal films under study in this thesis, having thicknesses in the range 100-800A, are much thinner than this decay length and hence should not show strong temperature dependence as this length scale diverges. We conclude that this theory is not adequate for describing the spatial dependence of the induced order parameter very near the S/N interface, and develop an improved model of the electrodynamics of proximity-coupled systems with very thin normal metal layers which reproduces the observed data. We demonstrate that a much shorter effective decay length for the order parameter in the normal layer can correctly describe the extent of proximity coupling in these structures. The advantages of the parallel-plate resonator technique in exploring these effects are presented. The distinctive ability of the technique to simultaneously gather data on the properties of the induced superconducting condensate (penetration depth data) and the properties of the spectrum of excitations above it (surface resistance data) in the proximity-coupled normal metal set the technique apart from previous methods, and allow it to study the very thin normal metal layers on which data are presented here. In addition to the much

  15. SSME LOX post flow analysis/fluid structure interaction. Volume 2: Fluid structure interaction

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The progress made in resolving the computational issues associated with modeling high temperature and pressure viscous flows in advanced propulsion systems is documented. An overview of adaptive computational methods for various classes of fluid-structure interaction problems is presented. The key features associated with several approaches are outlined and the advantages/disadvantages of each are summarized. A mathematical formulation is presented for general fluid-structure interaction problems with a moving domain. The two adaptive approaches are discussed used in solving the benchmark problems. The first scheme is a user interactive scheme which is quite versatile and easy to implement but requires an excessive amount of monitoring by the operator and is computationally inefficient. The second method is a new, local remeshing method for handling a general class of fluid-structure interaction problems. This method couples many of the attractive features of other approaches into a computationally efficient and versatile method. The results obtained for two test cases are presented. Results from both the user interactive and local remeshing procedure are described. The current status of the project and future goals to be completed are summarized.

  16. Highly efficient manipulation of Laplace fields in film system with structured bilayer composite.

    PubMed

    Lan, Chuwen; Lei, Ming; Bi, Ke; Li, Bo; Zhou, Ji

    2016-12-26

    Using metamaterials or transformation optics to manipulate Laplace fields, such as magnetic, electric and thermal fields, has become a research highlight. These studies, however, are usually limited to a bulk material system and to single field manipulation. In this paper, we focus on a film system and propose a general practical method applicable for such a system. In this method, the background film is covered with another one to construct a so-called "bilayer composite" to achieve required physical parameters. On the basis of the bilayer composite, a multi-physics cloak and a multi-physics concentrator for electric current and thermal flux are designed, fabricated, and demonstrated. This work provides an efficient way to control and manipulate single/ multi-physics Laplace fields like a dc electric field and a thermal field in a film system, which may find potential applications in IC technology, MEMS, and so on.

  17. Effect of interface roughness on exchange coupling in polycrystalline Co/CoO bilayer structure: An in-situ investigation

    NASA Astrophysics Data System (ADS)

    Kumar, Dileep; Singh, Sadhana; Gupta, Ajay

    2016-08-01

    The effect of interface roughness on exchange-bias (EB) properties of polycrystalline Co/CoO bilayer structure has been studied in-situ. Isothermal annealing of a 135 Å thick Co layer under the partial pressure of pure oxygen at 573 K results in the formation of a 35 Å thick CoO layer, the surface roughness of which increases with the increasing annealing time. Bilayers were characterized in-situ using magneto-optic Kerr effect, reflection high energy electron diffraction, and x-ray reflectivity for their magnetic and structural properties during each stage of bilayer growth. Combined analysis revealed that the increase in the roughness from 7 ±0.5 Å to 13 ±Å causes the exchange bias field (HEB) to decrease from 171 Oe to 81 Oe, whereas coercivity (HC) increases up to 616 Oe. In contrast to some earlier studies on polycrystalline films, where HEB increased with roughness due to the increase in the uncompensated spins at ferromagnetic-antiferromagnetic (AFM) layer interface, in the present case, dependence of HEB and HC on the roughness is attributed to the disorder at the interface of AFM layer, which leads to a decrease in HEB due to weakening of the effective spin coupling at the interface. Present in-situ experiments make it possible to study the variations in EB properties with the interface roughness in a single sample, and thus avoiding the possibility of the sample to sample variation in the morphological properties along with the change in the interface roughness.

  18. New group-V elemental bilayers: A tunable structure model with four-, six-, and eight-atom rings

    NASA Astrophysics Data System (ADS)

    Kong, Xiangru; Li, Linyang; Leenaerts, Ortwin; Liu, Xiong-Jun; Peeters, François M.

    2017-07-01

    Two-dimensional group-V elemental materials have attracted widespread attention due to their nonzero band gap while displaying high electron mobility. Using first-principles calculations, we propose a series of new elemental bilayers with group-V elements (Bi, Sb, As). Our study reveals the dynamical stability of four-, six-, and eight-atom ring structures, demonstrating their possible coexistence in such bilayer systems. The proposed structures for Sb and As are large-gap semiconductors that are potentially interesting for applications in future nanodevices. The Bi structures have nontrivial topological properties with a direct nontrivial band gap. The nontrivial gap is shown to arise from a band inversion at the Brillouin zone center due to the strong intrinsic spin-orbit coupling in Bi atoms. Moreover, we demonstrate the possibility of tuning the properties of these materials by enhancing the ratio of six-atom rings to four- and eight-atom rings, which results in wider nontrivial band gaps and lower formation energies.

  19. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES: Novel Bilayer Structures for Short Wavelength High Density Magneto-Optical Data Storage

    NASA Astrophysics Data System (ADS)

    Wang, Xian-Ying; Wang, Jing; Wang, Zhan-Yong; Yang, Jun-He

    2008-06-01

    We report a novel bi-layer thin film structure for high density magneto-optical (MO) data storage, which combines the advantages of blue wavelength and magnetically induced superresolution (MSR) recording. A double-layer system of exchange-coupled light rare-earth (LRE) element doped NdGdFeCo and traditional TbFeCo is used as the recording medium. The experimental results demonstrate that this NdGdFeCo/TbFeCo double layer has large Kerr rotation under blue wavelength. Centre aperture detection (CAD) MSR effect with temperature rising is also observed. Theoretical calculation is also carried out to verify the experimental results. These results collectively suggest that the new bilayer structure is very promising in next generation high density MO data storage.

  20. Oxidation of Membrane Curvature-Regulating Phosphatidylethanolamine Lipid Results in Formation of Bilayer and Cubic Structures.

    PubMed

    Sankhagowit, Shalene; Lee, Ernest Y; Wong, Gerard C L; Malmstadt, Noah

    2016-03-15

    Oxidation is associated with conditions related to chronic inflammations and aging. Cubic structures have been observed in the smooth endoplasmic reticulum and mitochondrial membranes of cells under oxidative stress (e.g., tumor cells and virus-infected cells). It has been previously suspected that oxidation can result in the rearrangement of lipids from a fluid lamellar phase to a cubic structure in organelles containing membranes enriched with amphiphiles that have nonzero intrinsic curvature, such as phosphatidylethanolamine (PE) and cardiolipin. This study focuses on the oxidation of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), a lipid that natively forms an inverted hexagonal phase at physiological conditions. The oxidized samples contain an approximately 3:2 molar ratio of nonoxidized to oxidized DOPE. Optical microscopy images collected during the hydration of this mixture from a dried film suggest that the system evolves into a coexistence of a stable fluid lamellar phase and transient square lattice structures with unit cell sizes of 500-600 nm. Small-angle X-ray scattering of the same lipid mixture yielded a body-centered Im3m cubic phase with the lattice parameter of 14.04 nm. On average, the effective packing parameter of the oxidized DOPE species was estimated to be 0.657 ± 0.069 (standard deviation). This suggests that the oxidation of PE leads to a group of species with inverted molecular intrinsic curvature. Oxidation can create amphiphilic subpopulations that potently impact the integrity of the membrane, since negative Gaussian curvature intrinsic to cubic phases can enable membrane destabilization processes.

  1. Molecular Dynamics of a Water-Lipid Bilayer Interface

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  2. Molecular Dynamics of a Water-Lipid Bilayer Interface

    NASA Technical Reports Server (NTRS)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  3. Lipid bilayer deposition and patterning via air bubble collapse.

    PubMed

    Mager, Morgan D; Melosh, Nicholas A

    2007-08-28

    We report a new method for forming patterned lipid bilayers on solid substrates. In bubble collapse deposition (BCD), an air bubble is first "inked" with a monolayer of phospholipid molecules and then touched to the surface of a thermally oxidized silicon wafer and the air is slowly withdrawn. As the bubble shrinks, the lipid monolayer pressure increases. Once the monolayer exceeds the collapse pressure, it folds back on itself, depositing a stable lipid bilayer on the surface. These bilayer disks have lateral diffusion coefficients consistent with high quality supported bilayers. By sequentially depositing bilayers in overlapping areas, fluid connections between bilayers of different compositions are formed. Performing vesicle rupture on the open substrate surrounding this bilayer patch results in a fluid but spatially isolated bilayer. Very little intermixing was observed between the vesicle rupture and bubble-deposited bilayers.

  4. Characterization of fluid transport in microscale structures

    SciTech Connect

    Paul, P.H.

    1998-01-01

    A new tool for imaging both scalar transport and velocity fields in liquid flows through microscale structures is described. The technique employs an ultraviolet laser pulse to write a pattern into the flow by uncaging a fluorescent dye. This is followed, at selected time delays, by flood illumination with a pulse of visible light which excites the uncaged dye. The resulting fluorescence image collected onto a sensitive CCD camera. The instrument is designed as an oil immersion microscope to minimize the beam steering effects. The caged fluorescent dye is seeded in trace quantities throughout the active fluid, thus images with high contrast and minimal distortion due to any molecular diffusion history can be obtained at any point within the microchannel by selectivity activating the dye in the immediate region of interest. The author reports images of pressure- and electrokinetically-driven steady flow within round cross section capillaries having micron scale inner diameters. The author also demonstrates the ability to recover the velocity profile from a time sequence of these scalar images by direct inversion of the conserved scalar advection-convection equation.

  5. Off-easy-plane antiferromagnetic spin canting in coupled FePt/NiO bilayer structure with perpendicular exchange bias

    NASA Astrophysics Data System (ADS)

    Gao, Tenghua; Itokawa, Nobuhide; Wang, Jian; Yu, Youxing; Harumoto, Takashi; Nakamura, Yoshio; Shi, Ji

    2016-08-01

    We report on the investigation of perpendicular exchange bias in FePt (001 ) /NiO (1 ¯1 ¯1 ) orthogonal exchange couple with FePt partially L 10 ordered. From initial magnetization curve measurement and magnetic domain imaging, we find that, for the as-grown bilayer structure, the FePt layer experiences a small-angle magnetization rotation when it is magnetized near to saturation in film normal direction. After field cooling, the bilayer structure shows a significant enhancement of perpendicular magnetic anisotropy, indicating the field mediated coupling between the spins across the FePt/NiO interface. According to Koon's theoretical calculation on the basis of lowest energy ferromagnetic/antiferromagnetic coupling configuration for compensated spins at antiferromagnetic side, we consider slightly slanted Ni spins at the interface off the (1 ¯1 ¯1 ) easy plane can stabilize the spin coupling between FePt and NiO and result in the observed exchange bias in this paper. This consideration was further confirmed by stripe domain width calculation.

  6. NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes.

    PubMed

    Mahalakshmi, Radhakrishnan; Franzin, Carla M; Choi, Jungyuen; Marassi, Francesca M

    2007-12-01

    The beta-barrels found in the outer membranes of prokaryotic and eukaryotic organisms constitute an important functional class of proteins. Here we present solid-state NMR spectra of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. We show that OmpX is folded in both glass-supported oriented lipid bilayers and in lipid bicelles that can be magnetically oriented with the membrane plane parallel or perpendicular to the direction of the magnetic field. The presence of resolved peaks in these spectra demonstrates that OmpX undergoes rotational diffusion around an axis perpendicular to the membrane surface. A tightly hydrogen-bonded domain of OmpX resists exchange with D2O for days and is assigned to the transmembrane beta-barrel, while peaks at isotropic resonance frequencies that disappear rapidly in D2O are assigned to the extracellular and periplasmic loops. The two-dimensional 1H/15N separated local field spectra of OmpX have several resolved peaks, and agree well with the spectra calculated from the crystal structure of OmpX rotated with the barrel axis nearly parallel (5 degrees tilt) to the direction of the magnetic field. The data indicate that it will be possible to obtain site-specific resonance assignments and to determine the structure, tilt, and rotation of OmpX in membranes using the solid-state NMR methods that are currently being applied to alpha-helical membrane proteins.

  7. Coupling neutron reflectivity with cell-free protein synthesis to probe membrane protein structure in supported bilayers

    DOE PAGES

    Soranzo, Thomas; Martin, Donald K.; Lenormand, Jean -Luc; ...

    2017-06-13

    Here, the structure of the p7 viroporin, an oligomeric membrane protein ion channel involved in the assembly and release of the hepatitis C virus, was determined from proteins expressed and inserted directly into supported model lipid membranes using cell-free protein expression. Cell-free protein expression allowed (i) high protein concentration in the membrane, (ii) control of the protein’s isotopic constitution, and (iii) control over the lipid environment available to the protein. Here, we used cell-free protein synthesis to directly incorporate the hepatitis C virus (HCV) p7 protein into supported lipid bilayers formed from physiologically relevant lipids (POPC or asolectin) for bothmore » direct structural measurements using neutron reflectivity (NR) and conductance measurements using electrical impedance spectroscopy (EIS). We report that HCV p7 from genotype 1a strain H77 adopts a conical shape within lipid bilayers and forms a viroporin upon oligomerization, confirmed by EIS conductance measurements. This combination of techniques represents a novel approach to the study of membrane proteins and, through the use of selective deuteration of particular amino acids to enhance neutron scattering contrast, has the promise to become a powerful tool for characterizing the protein conformation in physiologically relevant environments and for the development of biosensor applications.« less

  8. Simulation study of the structure and phase behavior of ceramide bilayers and the role of lipid head group chemistry

    PubMed Central

    Guo, Shan; Moore, Timothy C.; Iacovella, Christopher R.; Strickland, L. Anderson; McCabe, Clare

    2014-01-01

    Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field of Berger (Biophys. J. 1997, 72); while both force fields are shown to closely match experiment from a structural standpoint at the physiological temperature of skin, the modified CHARMM force field is better able to capture the thermotropic phase transitions observed in experiment. The role of ceramide chemistry and its impact on structural ordering is examined by comparing ceramide NS to NP, using the validated CHARMM-based force field. These simulations demonstrate that changing from ceramide NS to NP results in changes to the orientation of the OH groups in the lipid headgroups. The arrangement of OH groups perpendicular to the bilayer normal for ceramide NP, verse parallel for NS, results in the formation of a distinct hydrogen bonding network, that is ultimately responsible for shifting the gel-to-liquid phase transition to higher temperature, in direct agreement with experiment. PMID:24501589

  9. TiB 2/TiSi 2 bilayer fabrication by various techniques: Structure and contact properties

    NASA Astrophysics Data System (ADS)

    Pelleg, Joshua; Sade, G.

    2006-01-01

    TiB 2/TiSi 2 films were produced by several techniques in an attempt to evaluate the most appropriate method to fabricate this system. Analysis by X-ray diffraction, Auger electron spectroscopy, transmission and high-resolution transmission electron microscopy indicate that the best method to obtain the above system is by sequential cosputtering of the layers without exposure to air between the two cosputtering sequences. Post-deposition annealing was performed to obtain a low resistive bilayer. Schottky diodes fabricated by this method provided an average barrier height of ∼0.68 V with an ideality factor in the range of 1.0-1.04 (excluding the as-deposited specimen). In specimens fabricated by silicidation of TiB 2/Ti films formation of TiSi 2 was Ti thickness dependent [G. Sade, Ph.D. Thesis, Ben Gurion University of the Negev, Beer Sheva, Israel, 1999]. Small amounts of Ti 5Si 3 were observed at 1123 K. The attempts to obtain a TiB 2/TiSi 2 bilayer from (Ti+B) enriched with Ti at 1073 K resulted in the formation of small amounts of Ti 5Si 3, and some crystallization of the amorphous TiB 2 also occurred. Diodes fabricated by this technique showed Ohmic rather than rectifying character. The shift from rectifying to Ohmic behavior is the result of B out-diffusion to the Si and the consequent change of the substrate from an n- to a p-type Si. The results place the Fermi level of TiB 2 about 0.9 eV below the silicon conduction band. A remedy to this problem could result in a challenging method of fabricating a TiB 2/TiSi 2 bilayer structure in a one-step process.

  10. sup 31 P and sup 2 H NMR studies of structure and motion in bilayers of phosphatidylcholine and phosphatidylethanolamine

    SciTech Connect

    Ghosh, R. )

    1988-10-04

    The structural and motional properties of mixed bilayers of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) have been examined by using wide-line {sup 31}P, {sup 14}N, and {sup 2H} NMR. {sup 2}H and {sup 14}N NMR data showed that in mixed bilayers containing both PC and PE the conformations of the head-group moieties are essentially identical with those observed for bilayers containing a single phospholipid species. Equimolar amounts of cholesterol induce also only a small change in head-group conformation. For all phospholipid mixtures studied, the {sup 31}P T{sub 1} relaxation was homogeneous over the whole powder spectrum and could be fitted to a single-exponential decay. The {sup 31}P vs temperature profiles were analyzed by a simple correlation model. The presence of equimolar amounts of PE containing either the same (POPE) or a different (Escherichia coli PE) fatty acid composition had essentially no effect on the rate of rotational diffusion of the phosphate groups, with the correlation time being found to be 0.68 ns at 20{degree}C. The presence of equimolar amounts of cholesterol decreased the correlation time to 0.65 ns, and also the activation energy was reduced to 22.6 kJ mol{sup {minus}1}. The authors interpret the decrease in activation energy as being due to the spacing effect of cholesterol which reduces the H-bonding interactions between head-groups, allowing them to rotate more freely. For all cases examined, the rotational diffusion of the phosphate moieties was slower than that observed for the rigid glycerol backbone of the molecule, the latter probably corresponding to overall phospholipid rotation.

  11. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  12. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

    PubMed

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  13. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    NASA Astrophysics Data System (ADS)

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  14. A Method of Simulating Fluid Structure Interactions for Deformable Decelerators

    NASA Astrophysics Data System (ADS)

    Gidzak, Vladimyr Mykhalo

    A method is developed for performing simulations that contain fluid-structure interactions between deployable decelerators and a high speed compressible flow. The problem of coupling together multiple physical systems is examined with discussion of the strength of coupling for various methods. A non-monolithic strongly coupled option is presented for fluid-structure systems based on grid deformation. A class of algebraic grid deformation methods is then presented with examples of increasing complexity. The strength of the fluid-structure coupling is validated against two analytic problems, chosen to test the time dependent behavior of structure on fluid interactions, and of fluid on structure interruptions. A one-dimentional material heating model is also validated against experimental data. Results are provided for simulations of a wind tunnel scale disk-gap-band parachute with comparison to experimental data. Finally, a simulation is performed on a flight scale tension cone decelerator, with examination of time-dependent material stress, and heating.

  15. Structure, Topology and Tilt of Cell-Signaling Peptides Containing Nuclear Localization Sequences in Membrane Bilayers Determined by Solid-State NMR and Molecular Dynamics Simulation Studies

    PubMed Central

    Ramamoorthy, Ayyalusamy; Kandasamy, Senthil K.; Lee, Dong-Kuk; Kidambi, Srikanth; Larson, Ronald G.

    2008-01-01

    Cell-signaling peptides have been extensively used to transport functional molecules across the plasma membrane into living cells. These peptides consist of a hydrophobic sequence and a cationic nuclear localization sequence (NLS). It has been assumed that the hydrophobic region penetrates through the hydrophobic lipid bilayer and delivers the NLS inside the cell. To better understand the transport mechanism of these peptides, in this study, we investigated the structure, orientation, tilt of the peptide relative to the bilayer normal, and the membraneinteraction of two cell-signaling peptides, SA and SKP. Results from CD and solid-state NMR experiments combined with molecular dynamics simulations suggest that the hydrophobic region is helical and has a transmembrane orientation with the helical axis tilted away from the bilayer normal. The influence of the hydrophobic mismatch, between the hydrophobic length of the peptide and the hydrophobic thickness of the bilayer, on the tilt angle of the peptides was investigated using thicker POPC and thinner DMPC bilayers. NMR experiments showed that the hydrophobic domain of each peptide has a tilt angle of 15±3° in POPC, while in DMPC 25±3° and 30±3° tilts were observed for SA and SKP peptides respectively. These results are in good agreement with molecular dynamics simulations, which predicts a tilt angle of 13.3° (SA in POPC), 16.4° (SKP in POPC), 22.3° (SA in DMPC) and 31.7° (SKP in POPC). These results and simulations on the hydrophobic fragment of SA or SKP suggest that the tilt of helices increases with a decrease in the bilayer thickness without changing the phase, order, and structure of the lipid bilayers. PMID:17240980

  16. Lattice Boltzmann Methods for Fluid Structure Interaction

    DTIC Science & Technology

    2012-09-01

    THIS PAGE INTENTIONALLY LEFT BLANK xvi LIST OF TABLES Table 1. Geometry and fluid parameters for Poiseuille flow test case. . . . . . 32 Table 2...The first test case is a two-dimensional flow case between parallel plates. The flow condition is depicted in Figure 12. 31 Figure 12: Poiseuille flow ...Geometry and fluid parameters for Poiseuille flow test case. The solution to this problem is known to be a function of y only and is given in Equation 42

  17. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

    DOE PAGES

    Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

    2014-10-29

    We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

  18. Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; Ho, Chian-Sing; Khadka, Nawal; Katsaras, John

    2014-10-29

    We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

  19. Structure and Topology of a Peptide Segment of the 6th Transmembrane Domain of the Saccharomyces cerevisae α-Factor Receptor in Phospholipid Bilayers

    PubMed Central

    Valentine, Kathleen G.; Liu, Shi-Feng; Marassi, Francesca M.; Veglia, Gianluigi; Opella, Stanley J.; Ding, Fa-Xiang; Wang, Shu-Hua; Arshava, Boris; Becker, Jeffrey M.

    2012-01-01

    A detailed analysis of the structure of an 18-residue peptide AQSLLVPSIIFILAYSLK [M6(252–269, C252A)] in 1,2-dimyristoyl-sn-glycero-phosphocholine bilayers was carried out using solid state NMR and attenuated total reflection Fourier transform infrared spectroscopy. The peptide corresponds to a portion of the 6th transmembrane domain of the α-factor receptor of Saccharomyces cerevisiae. Ten homologs of M6(252–269, C252A) were synthesized in which individual residues were labeled with 15N. One- and two-dimensional solid state NMR experiments were used to determine the chemical shifts and 1H–15N dipolar coupling constants for the 15N-labeled peptides in oriented dimyristoylphosphatidylcholine bilayers on stacked glass plates. These parameters were used to calculate the structure and orientation of M6(252–269, C252A) in the bilayers. The results indicate that the carboxyl terminal residues (9–14) are α-helical and oriented with an angle of about 8° with respect to the bilayer normal. Independently, an attenuated total reflection Fourier transform infrared spectroscopy analysis on M6(252–269, C252A) in a 1,2-dimyristoyl-sn-glycero-phosphocholine bilayer concluded that the helix tilt angle was about 12.5°. The results on the structure of M6(252–269, C252A) in bilayers are in good agreement with the structure determined in trifluoroethanol/water solutions (B. Arshava et al. Biopolymers, 1998, Vol. 46, pp. 343–357) . The present study shows that solid state NMR spectroscopy can provide high resolution information on the structure of transmembrane domains of a G protein-coupled receptor. PMID:11473349

  20. Structure and dehydration of layered perovskite niobate with bilayer hydrates prepared by exfoliation/self-assembly process

    SciTech Connect

    Chen Yufeng; Zhao Xinhua; Ma Hui; Ma Shulan; Huang Gailing; Makita, Yoji; Bai Xuedong; Yang Xiaojing

    2008-07-15

    The crystals of an H-form niobate of HCa{sub 2}Nb{sub 3}O{sub 10}.xH{sub 2}O (x=0.5) being tetragonal symmetry (space group P4/mbm) with unit cell parameters a=5.4521(6) and c=14.414(2) A were exfoliated into nanosheets with the triple-layered perovskite structure. The colloid suspension of the nanosheets was put into dialysis membrane tubing and allowed self-assembly in a dilute KCl solution. By this method, a novel layered K-form niobate KCa{sub 2}Nb{sub 3}O{sub 10}.xH{sub 2}O (x=1.3, typically) with bilayer hydrates in the interlayer was produced. The Rieveld refinement and transmission electron microscope (TEM)/selected-area electron diffraction (SAED) observation indicated that the orientations of the a-/b-axis of each nanosheet as well as the c-axis are uniform, and the self-assembled compound had the same symmetry, tetragonal (P4/mbm) with a=5.453(2) and c=16.876(5) A, as the H-form precursor; the exfoliation/self-assembly process does not markedly affect the two-dimensional lattice of the layer. The large basal spacing resulted from the interlayer K{sup +} ions solvated by two layers of water molecules. The interlayer bilayers-water was gradually changed to monolayer when the temperatures higher than 100 deg. C, and all the water molecules lost when over 600 deg. C. Accompanying the dehydration, the crystal structure transformed from tetragonal to orthorhombic symmetry. Water molecules may take an important role for the layer layered compound to adjust the unit cell to tetragonal symmetry. - Graphical abstract: The structure of layered perovskite niobate KCa{sub 2}Nb{sub 3}O{sub 10}.xH{sub 2}O (x=1.3) having a bilayers-hydrates interlayer, obtained via the exfoliation of an H-form precursor and the self-assembly of Ca{sub 2}Nb{sub 3}O{sub 10}{sup -} nanosheets, was first discussed in detail and determined to be tetragonal symmetry (P4/mbm). The dehydration resulted in the structural transformation to orthorhombic structure.

  1. Solving Fluid Structure Interaction Problems with an Immersed Boundary Method

    NASA Technical Reports Server (NTRS)

    Barad, Michael F.; Brehm, Christoph; Kiris, Cetin C.

    2016-01-01

    An immersed boundary method for the compressible Navier-Stokes equations can be used for moving boundary problems as well as fully coupled fluid-structure interaction is presented. The underlying Cartesian immersed boundary method of the Launch Ascent and Vehicle Aerodynamics (LAVA) framework, based on the locally stabilized immersed boundary method previously presented by the authors, is extended to account for unsteady boundary motion and coupled to linear and geometrically nonlinear structural finite element solvers. The approach is validated for moving boundary problems with prescribed body motion and fully coupled fluid structure interaction problems. Keywords: Immersed Boundary Method, Higher-Order Finite Difference Method, Fluid Structure Interaction.

  2. Direct Probing of the Electronic Structures of Single-Layer and Bilayer Graphene with a Hexagonal Boron Nitride Tunneling Barrier.

    PubMed

    Jung, Suyong; Myoung, Nojoon; Park, Jaesung; Jeong, Tae Young; Kim, Hakseong; Watanabe, Kenji; Taniguchi, Takashi; Ha, Dong Han; Hwang, Chanyong; Park, Hee Chul

    2017-01-11

    The chemical and mechanical stability of hexagonal boron nitride (h-BN) thin films and their compatibility with other free-standing two-dimensional (2D) crystals to form van der Waals heterostructures make the h-BN-2D tunnel junction an intriguing experimental platform not only for the engineering of specific device functionalities but also for the promotion of quantum measurement capabilities. Here, we exploit the h-BN-graphene tunnel junction to directly probe the electronic structures of single-layer and bilayer graphene in the presence and the absence of external magnetic fields with unprecedented high signal-to-noise ratios. At a zero magnetic field, we identify the tunneling spectra related to the charge neutrality point and the opening of the electric-field-induced bilayer energy gap. In the quantum Hall regime, the quantization of 2D electron gas into Landau levels (LL) is seen as early as 0.2 T, and as many as 30 well-separated LL tunneling conductance oscillations are observed for both electron- and hole-doped regions. Our device simulations successfully reproduce the experimental observations. Additionally, we extract the relative permittivity of three-to-five layer h-BN and find that the screening capability of thin h-BN films is as much as 60% weaker than bulk h-BN.

  3. The ring structure and organization of light harvesting 2 complexes in a reconstituted lipid bilayer, resolved by atomic force microscopy.

    PubMed

    Stamouli, Amalia; Kafi, Sidig; Klein, Dionne C G; Oosterkamp, Tjerk H; Frenken, Joost W M; Cogdell, Richard J; Aartsma, Thijs J

    2003-04-01

    The main function of the transmembrane light-harvesting complexes in photosynthetic organisms is the absorption of a light quantum and its subsequent rapid transfer to a reaction center where a charge separation occurs. A combination of freeze-thaw and dialysis methods were used to reconstitute the detergent-solubilized Light Harvesting 2 complex (LH2) of the purple bacterium Rhodopseudomonas acidophila strain 10050 into preformed egg phosphatidylcholine liposomes, without the need for extra chemical agents. The LH2-containing liposomes opened up to a flat bilayer, which were imaged with tapping and contact mode atomic force microscopy under ambient and physiological conditions, respectively. The LH2 complexes were packed in quasicrystalline domains. The endoplasmic and periplasmic sides of the LH2 complexes could be distinguished by the difference in height of the protrusions from the lipid bilayer. The results indicate that the complexes entered in intact liposomes. In addition, it was observed that the most hydrophilic side, the periplasmic, enters first in the membrane. In contact mode the molecular structure of the periplasmic side of the transmembrane pigment-protein complex was observed. Using Föster's theory for describing the distance dependent energy transfer, we estimate the dipole strength for energy transfer between two neighboring LH2s, based on the architecture of the imaged unit cell.

  4. Polymer bulk heterojunction solar cells with PEDOT:PSS bilayer structure as hole extraction layer.

    PubMed

    Kim, Wanjung; Kim, Namhun; Kim, Jung Kyu; Park, Insun; Choi, Yeong Suk; Wang, Dong Hwan; Chae, Heeyeop; Park, Jong Hyeok

    2013-06-01

    A high current density obtained in a limited, nanometer-thick region is important for high efficiency polymer solar cells (PSCs). The conversion of incident photons to charge carriers only occurs in confined active layers; therefore, charge-carrier extraction from the active layer within the device by using solar light has an important impact on the current density and the related to power conversion efficiency. In this study, we observed a surprising result, that is, extracting the charge carrier generated in the active layer of a PSC device, with a thickness-controlled PEDOT:PSS bilayer that acted as a hole extraction layer (HEL), yielded a dramatically improved power conversion efficiency in two different model systems (P3HT:PC₆₀BM and PCDTBT:PC₇₀BM). To understand this phenomenon, we conducted optical strength simulation, photocurrent-voltage measurements, incident photon to charge carrier efficiency measurements, ultraviolet photoelectron spectroscopy, and AFM studies. The results revealed that approximately 60 nm was the optimum PEDOT:PSS bilayer HEL thickness in PSCs for producing the maximum power conversion efficiency.

  5. Pre-resonance-stimulated Raman scattering for water bilayer structure on laser-induced plasma bubble surface.

    PubMed

    Li, Zhanlong; Li, Hongdong; Fang, Wenhui; Wang, Shenghan; Sun, Chenglin; Li, Zuowei; Men, Zhiwei

    2015-07-15

    Pre-resonance-stimulated Raman scattering (PSRS) from water molecules in the air/water interfacial regions was studied when the laser-induced plasma bubble was generated at the interfaces. A characteristically lower Raman shift of OH-stretching vibrational modes of water molecules at around 3000  cm(-1) (370 meV) was observed, in which the mechanisms were possibly attributed to the strong hydrogen bond in a well-ordered water bilayer structure that was formed on a laser-induced plasma bubble surface. Simultaneously, the PSRS of ice Ih at about 3100  cm(-1) was obtained, which also belonged to the strong hydrogen bond effect in ice Ih structure.

  6. [Highly Efficient Bilayer-Structure Yellow-Green OLED with MADN Hole-Transport Layer and the Impedance Spectroscopy Analysis].

    PubMed

    Zhang, Xiao-wen; Mo, Bing-jie; Liu, Li-ming; Wang, Hong-hang; Chen, Er-wei; Xu, Ji-wen; Wang, Hua

    2015-12-01

    Abstract Highly efficient bilayer-structure yellow-green organic light-emitting device (OLED) has been demonstrated based on MADN as hole-transport layer (HTL) and host-guest coped system of [Alq₃: 0.7 Wt% rubrene] as emitting and electron-trans- port layer. The device gives yellow-green emission through incomplete energy transfer from the host of Alq₃ to the guest of ru- brene. An electroluminescent peak of 560 nm, 1931 CIE color coordinates of (0.46, 0.52) and a maximum current efficiency of 7.63 cd · A⁻¹ (which has been enhanced by 30% in comparison with the counterpart having conventional NPB HTL) are ob- served. The hole-transporting characteristics of MADN and NPB have been systematically investigated by constructing hole-only devices and employing impedance spectroscopy analysis. Our results indicate that MADN can be served as an effective hole-trans- port material and its hole-transporting ability is slightly inferior to NPB. This overcomes the shortcoming of hole transporting more quickly than electron in OLED and improves carrier balance in the emitting layer. Consequently, the device current efficien- cy is promoted. In addition, the current efficiency of bilayer-structure OLED with MADN as HTL is comparable to that of conv- entinol trilayer-structure device with MADN as HTL and Alq₃ as electron-transport layer. This indicates that the simplified bi- layer-structure device can be achieved without sacrificing current efficiency. The emitting layer of [Alq: 0.7 Wt% rubrene possesses superior elecron-transporting ability.

  7. Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation.

    PubMed

    Nagao, Takashi; Mishima, Daisuke; Javkhlantugs, Namsrai; Wang, Jun; Ishioka, Daisuke; Yokota, Kiyonobu; Norisada, Kazushi; Kawamura, Izuru; Ueda, Kazuyoshi; Naito, Akira

    2015-11-01

    The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region. The chemical shift anisotropy of the carbonyl carbon of isotopically labeled alamethicin was also analyzed with the assumption that alamethicin molecules rotate rapidly about the bilayer normal of the phospholipid bilayers. It is considered that the adjacent peptide planes form an angle of 100° or 120° when it forms α-helix or 310-helix, respectively. These properties lead to an oscillation of the chemical shift anisotropy with respect to the phase angle of the peptide plane. Anisotropic data were acquired for the 4 and 7 sites of the N- and C-termini, respectively. The results indicated that the helical axes for the N- and C-termini were tilted 17° and 32° to the bilayer normal, respectively. The chemical shift oscillation curves indicate that the N- and C-termini form the α-helix and 310-helix, respectively. The C-terminal 310-helix of alamethicin in the bilayer was experimentally observed and the unique bending structure of alamethicin was further confirmed by measuring the internuclear distances of [1-(13)C] and [(15)N] doubly-labeled alamethicin. Molecular dynamics simulation of alamethicin embedded into dimyristoyl phophatidylcholine (DMPC) bilayers indicates that the helical axes for α-helical N- and 310-helical C-termini are tilted 12° and 32° to the bilayer normal, respectively, which is in good agreement with the solid state NMR results. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

    PubMed Central

    Cheng, Sara Y.; Chou, George; Buie, Creighton; Vaughn, Mark W.; Compton, Campbell; Cheng, Kwan H.

    2016-01-01

    This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface” [1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes. PMID:27054174

  9. Electrical and structural characterization of plasma polymerized polyaniline/TiO2 heterostructure diode: a comparative study of single and bilayer TiO2 thin film electrode.

    PubMed

    Ameen, Sadia; Akhtar, M Shaheer; Kimi, Young Soon; Yang, O-Bong; Shin, Hyung-Shik

    2011-04-01

    A heterostructure was fabricated using p-type plasma polymerized polyaniline (PANI) and n-type (single and bilayer) titanium dioxide (TiO2) thin film on FTO glass. The deposition of single and bilayer TiO2 thin film on FTO substrate was achieved through doctor blade followed by dip coating technique before subjected to plasma enhanced polymerization. To fabricate p-n heterostructure, a plasma polymerization of aniline was conducted using RF plasma at 13.5 MHz and at the power of 120 W on the single and bilayer TiO2 thin film electrodes. The morphological, optical and the structural characterizations revealed the formation of p-n heterostructures between PANI and TiO2 thin film. The PANI/bilayer TiO2 heterostructure showed the improved current-voltage (I-V) characteristics due to the substantial deposition of PANI molecules into the bilayer TiO2 thin film which provided good conducting pathway and reduced the degree of excitons recombination. The change of linear I-V behavior of PANI/TiO2 heterostructure to non linear behavior with top Pt contact layer confirmed the formation of Schottky contact at the interfaces of Pt layer and PANI/TiO2 thin film layers.

  10. Reference Map Technique for Incompressible Fluid-Structure Interaction Problems

    NASA Astrophysics Data System (ADS)

    Rycroft, Chris; Wu, Chen-Hung; Yu, Yue; Kamrin, Ken

    2016-11-01

    We present a fully Eulerian approach to simulate soft structures immersed in an incompressible fluid. The flow is simulated on a fixed grid using a second order projection method to solve the incompressible Navier-Stokes equations, and the fluid-structure interfaces are modeled using the level set method. By introducing a reference map variable to model finite-deformation constitutive relations in the structure on the same grid as the fluid, the interfacial coupling is highly simplified. This fully Eulerian approach provides a computationally efficient alternative to moving mesh approaches. Example simulations featuring many-body contacts and flexible swimmers will be presented.

  11. Bilayer surface association of the pHLIP peptide promotes extensive backbone desolvation and helically-constrained structures.

    PubMed

    Brown, Mia C; Yakubu, Rauta A; Taylor, Jay; Halsey, Christopher M; Xiong, Jian; Jiji, Renee D; Cooley, Jason W

    2014-01-01

    Despite their presence in many aspects of biology, the study of membrane proteins lags behind that of their soluble counterparts. Improving structural analysis of membrane proteins is essential. Deep-UV resonance Raman (DUVRR) spectroscopy is an emerging technique in this area and has demonstrated sensitivity to subtle structural transitions and changes in protein environment. The pH low insertion peptide (pHLIP) has three distinct structural states: disordered in an aqueous environment, partially folded and associated with a lipid membrane, and inserted into a lipid bilayer as a transmembrane helix. While the soluble and membrane-inserted forms are well characterized, the partially folded membrane-associated state has not yet been clearly described. The amide I mode, known to be sensitive to protein environment, is the same in spectra of membrane-associated and membrane-inserted pHLIP, indicating comparable levels of backbone dehydration. The amide S mode, sensitive to helical structure, indicates less helical character in the membrane-associated form compared to the membrane-inserted state, consistent with previous findings. However, the structurally sensitive amide III region is very similar in both membrane-associated and membrane-inserted pHLIP, suggesting that the membrane-associated form has a large amount of ordered structure. Where before the membrane-associated state was thought to contain mostly unordered structure and reside in a predominantly aqueous environment, we have shown that it contains a significant amount of ordered structure and rests deeper within the lipid membrane.

  12. Multiferroic properties of CoFe2O4/Bi3.4La0.6Ti3O12 bilayer structure at room temperature

    NASA Astrophysics Data System (ADS)

    Charris-Hernández, A.; Melgarejo, R.; Barrionuevo, D.; Kumar, A.; Tomar, M. S.

    2013-07-01

    Bi3.4La0.6Ti3O12/CoFe2O4 bilayer films were synthesized by chemical solution method and deposited by spin coating on Pt (Pt/TiO2/SiO2/Si) substrate. X-ray diffraction of the bilayer system revealed the composite-like structure. The leakage current is less than 10-7 A at electric field below100 kV/cm, and it shows the ohmic behavior. Dielectric constant decreases with increasing frequency and reaches to 140 at 10-6 Hz. Bi3.4La0.6Ti3O12/CoFe2O4 system shows the co-existence of ferroelectric polarization (Pr) = 51 μC/cm2 and magnetization (Mr) = 206 emu/cm3 at room temperature. Observed ferromagnetic and ferroelectric responses in bilayer system may be useful for bi-functional devices.

  13. A new fluid-solid interface algorithm for simulating fluid structure problems in FGM plates

    NASA Astrophysics Data System (ADS)

    Eghtesad, A.; Shafiei, A. R.; Mahzoon, M.

    2012-04-01

    The capability to track material interfaces, especially in fluid structure problems, is among the advantages of meshless methods. In the present paper, the Smoothed Particle Hydrodynamics (SPH) method is used to investigate elastic-plastic deformation of AL and ceramic-metal FGM (Functionally Graded Materials) plates under the impact of water in a fluid-solid interface. Instead of using an accidental repulsive force which is not stable at higher pressures, a new scheme is proposed to improve the interface contact behavior between fluid and solid structure. This treatment not only prevents the interpenetration of fluid and solid particles significantly, but also maintains the gap distance between fluid and solid boundary particles in a reasonable range. A new scheme called corrected smooth particle method (CSPM) is applied to both fluid and solid particles to improve the free surface behavior. In order to have a more realistic free surface behavior in fluid, a technique is used to detect the free surface boundary particles during the solution process. The results indicate that using the proposed interface algorithm together with CSPM correction, one can predict the dynamic behavior of FGM plates under the impact of fluid very promisingly.

  14. Bilayered vascular graft derived from human induced pluripotent stem cells with biomimetic structure and function

    PubMed Central

    Nakayama, Karina H; Joshi, Prajakta A; Lai, Edwina S; Gujar, Prachi; Joubert, Lydia-M; Chen, Bertha; Huang, Ngan F

    2015-01-01

    Background: We developed an aligned bi-layered vascular graft derived from human induced pluripotent stem cells (iPSCs) that recapitulates the cellular composition, orientation, and anti-inflammatory function of blood vessels. Materials & methods: The luminal layer consisted of longitudinal-aligned nanofibrillar collagen containing primary endothelial cells (ECs) or iPSC-derived ECs (iPSC-ECs). The outer layer contained circumferentially oriented nanofibrillar collagen with primary smooth muscle cells (SMCs) or iPSC-derived SMCs(iPSC-SMCs). Results: On the aligned scaffolds, cells organized F-actin assembly within 8º from the direction of nanofibrils. When compared to randomly-oriented scaffolds, EC-seeded aligned scaffolds had significant reduced inflammatory response, based on adhesivity to monocytes. Conclusion: This study highlights the importance of anisotropic scaffolds in directing cell form and function, and has therapeutic significance as physiologically relevant blood vessels. PMID:26440211

  15. The Molecular Structure of the Liquid Ordered Phase of Lipid Bilayers

    PubMed Central

    Sodt, Alexander J.; Sandar, Michael Logan; Gawrisch, Klaus; Pastor, Richard W.; Lyman, Edward

    2014-01-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld), are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways. PMID:24345334

  16. Magnetic structure in Fe/Sm-Co exchange spring bilayers with intermixed interfaces.

    SciTech Connect

    Liu, Y.; te Velthuis, S. G. E.; Jiang, J. S.; Choi, Y.; Bader, S. D.; Parizzi, A. A.; Ambaye, H.; Lauter, V.

    2011-05-06

    The depth profile of the intrinsic magnetic properties in an Fe/Sm-Co bilayer fabricated under nearly optimal spring-magnet conditions was determined by complementary studies of polarized neutron reflectometry and micromagnetic simulations. We found that at the Fe/Sm-Co interface, the magnetic properties change gradually at the length scale of 8 nm. In this intermixed interfacial region, the saturation magnetization and magnetic anisotropy are lower and the exchange stiffness is higher than values estimated from the model based on a mixture of Fe and Sm-Co phases. Therefore, the intermixed interface yields superior exchange coupling between the Fe and Sm-Co layers, but at the cost of average magnetization.

  17. Acoustic responses of coupled fluid-structure system by acoustic-structural analogy

    NASA Technical Reports Server (NTRS)

    Shin, Y. S.; Chargin, M. K.

    1983-01-01

    The use of an analogy between structural mechanics and acoustics makes it possible to solve fluid-structural interaction (FSI) problems using an existing structural analysis computer program. This method was implemented in MSC/NASTRAN program and the FSI analysis was performed using two dimensional coupled fluid beam model to assess and evaluate the adequacy of this approach. The coupled modal analysis of 3-D model is also briefly discussed. The normal mode, modal frequency response and transient response analysis of 2-D coupled fluid beam system is presented. The significant reduction of the acoustic pressure response at the fluid structure interface is observed as a result of fluid structure interaction.

  18. Tetra- and Penta-Cyclic Triterpenes Interaction with Lipid Bilayer Membrane: A Structural Comparative Study.

    PubMed

    Abboud, Rola; Charcosset, Catherine; Greige-Gerges, Hélène

    2016-06-01

    The effect of tetracyclic (cortisol, prednisolone, and 9-fluorocortisol acetate) and pentacyclic (uvaol and erythrodiol) triterpenes (TTPs) on the fluidity of dipalmitoyl phosphatidyl choline (DPPC) liposome membrane was investigated by differential scanning calorimetry, Raman spectroscopy, and fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH). Liposomes were prepared in the absence and presence of TTPs at molar ratios DPPC:TTP 100:1, 100:2.5, and 100:10. All the studied TTPs abolished the pre-transition and modified the intensity of the Raman peak at 715 cm(-1) proving the interaction of TTP molecules with the choline head group of phospholipids. An increase in the Raman height intensity ratios of the peaks I 2935/2880, I 2844/2880, and I 1090/1130, giving information about the ratio disorder/order of the alkyl chains, and a decrease of the main transition temperature demonstrated the interaction of TTPs with the alkyl chains. The tetracyclic TTPs produced broadening of the phase transition profile. Besides, a scarcely splitting of the main transition peak was obtained with prednisolone and 9-fluorocortisol acetate. The results of fluorescence depolarization of DPH showed that the studied molecules fluidized the liposomal membrane at 25, 41, and 50 °C. Pentacyclic TTPs, being more hydrophobic than tetracyclic ones, demonstrated higher fluidizing effect than tetracyclic TTPs in the liquid crystalline phase suggesting a deeper incorporation in the lipid bilayer. The presence of a free polar head group at the ring D seems to control the TTP incorporation in the bilayer and consequently its effect on the membrane fluidity.

  19. Molecular mechanics and structure of the fluid-solid interface in simple fluids

    NASA Astrophysics Data System (ADS)

    Wang, Gerald J.; Hadjiconstantinou, Nicolas G.

    2017-09-01

    Near a fluid-solid interface, the fluid spatial density profile is highly nonuniform at the molecular scale. This nonuniformity can have profound effects on the dynamical behavior of the fluid and has been shown to play an especially important role when modeling a wide variety of nanoscale heat and momentum transfer phenomena. We use molecular-mechanics arguments and molecular-dynamics (MD) simulations to develop a better understanding of the structure of the first fluid layer directly adjacent to the solid in the layering regime, as delineated by a nondimensional number that compares the effects of wall-fluid interaction to thermal energy. Using asymptotic analysis of the Nernst-Planck equation, we show that features of the fluid density profile close to the wall, such as the areal density of the first layer ΣFL (defined as the number of atoms in this layer per unit of fluid-solid interfacial area), can be expressed as polynomial functions of the fluid average density ρave. This is found to be in agreement with MD simulations, which also show that the width of the first layer hFL is a linear function of the average density and only a weak function of the temperature T . These results can be combined to show that, for system average densities corresponding to a dense fluid (ρave≥0.7 ), the ratio C ≡ΣFLρavehFL, representing a density enhancement with respect to the bulk fluid, depends only weakly on temperature and is essentially independent of density. Further MD simulations suggest that the above results, nominally valid for large systems (solid in contact with semi-infinite fluid), also describe fluid-solid interfaces under considerable nanoconfinement, provided ρave is appropriately defined.

  20. Enhanced resistive switching and multilevel behavior in bilayered HfAlO/HfAlO{sub x} structures for non-volatile memory applications

    SciTech Connect

    Faita, F. L.; Silva, J. P. B.; Pereira, M.; Gomes, M. J. M.

    2015-12-14

    In this work, hafnium aluminum oxide (HfAlO) thin films were deposited by ion beam sputtering deposition technique on Si substrate. The presence of oxygen vacancies in the HfAlO{sub x} layer deposited in oxygen deficient environment is evidenced from the photoluminescence spectra. Furthermore, HfAlO(oxygen rich)/HfAlO{sub x}(oxygen poor) bilayer structures exhibit multilevel resistive switching (RS), and the switching ratio becomes more prominent with increasing the HfAlO layer thickness. The bilayer structure with HfAlO/HfAlO{sub x} thickness of 30/40 nm displays the enhanced multilevel resistive switching characteristics, where the high resistance state/intermediate resistance state (IRS) and IRS/low resistance state resistance ratios are ≈10{sup 2} and ≈5 × 10{sup 5}, respectively. The switching mechanisms in the bilayer structures were investigated by the temperature dependence of the three resistance states. This study revealed that the multilevel RS is attributed to the coupling of ionic conduction and the metallic conduction, being the first associated to the formation and rupture of conductive filaments related to oxygen vacancies and the second with the formation of a metallic filament. Moreover, the bilayer structures exhibit good endurance and stability in time.

  1. Interleaflet mixing and coupling in liquid-disordered phospholipid bilayers.

    PubMed

    Capponi, Sara; Freites, J Alfredo; Tobias, Douglas J; White, Stephen H

    2016-02-01

    Organized as bilayers, phospholipids are the fundamental building blocks of cellular membranes and determine many of their biological functions. Interactions between the two leaflets of the bilayer (interleaflet coupling) have been implicated in the passage of information through membranes. However, physically, the meaning of interleaflet coupling is ill defined and lacks a structural basis. Using all-atom molecular dynamics simulations of fluid phospholipid bilayers of five different lipids with differing degrees of acyl-chain asymmetry, we have examined interleaflet mixing to gain insights into coupling. Reasoning that the transbilayer distribution of terminal methyl groups is an appropriate measure of interleaflet mixing, we calculated the transbilayer distributions of the acyl chain terminal methyl groups for five lipids: dioleoylphosphatidylcholine (DOPC), palmitoyloleoylphosphatidylcholine (POPC), stearoyloleoylphosphatidylcholine (SOPC), oleoylmyristoylphosphatidylcholine (OMPC), and dimyristoylphosphatidylcholine (DMPC). We observed in all cases very strong mixing across the bilayer midplane that diminished somewhat with increasing acyl-chain ordering defined by methylene order parameters. A hallmark of the interleaflet coupling idea is complementarity, which postulates that lipids with short alkyl chains in one leaflet will preferentially associate with lipids with long alkyl chains in the other leaflet. Our results suggest a much more complicated picture for thermally disordered bilayers that we call distributed complementarity, as measured by the difference in the peak positions of the sn-1 and sn-2 methyl distributions in the same leaflet. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Characteristic length scale of the magnon accumulation in Fe3O4/Pt bilayer structures by incoherent thermal excitation

    NASA Astrophysics Data System (ADS)

    Anadón, A.; Ramos, R.; Lucas, I.; Algarabel, P. A.; Morellón, L.; Ibarra, M. R.; Aguirre, M. H.

    2016-07-01

    The dependence of Spin Seebeck effect (SSE) with the thickness of the magnetic materials is studied by means of incoherent thermal excitation. The SSE voltage signal in Fe3O4/Pt bilayer structure increases with the magnetic material thickness up to 100 nm, approximately, showing signs of saturation for larger thickness. This dependence is well described in terms of a spin current pumped in the platinum film by the magnon accumulation in the magnetic material. The spin current is generated by a gradient of temperature in the system and detected by the Pt top contact by means of inverse spin Hall effect. Calculations in the frame of the linear response theory adjust with a high degree of accuracy the experimental data, giving a thermal length scale of the magnon accumulation (Λ) of 17 ± 3 nm at 300 K and Λ = 40 ± 10 nm at 70 K.

  3. Suppression of photo-bias induced instability for amorphous indium tungsten oxide thin film transistors with bi-layer structure

    SciTech Connect

    Liu, Po-Tsun Chang, Chih-Hsiang; Chang, Chih-Jui

    2016-06-27

    This study investigates the instability induced by bias temperature illumination stress (NBTIS) for an amorphous indium-tungsten-oxide thin film transistor (a-IWO TFT) with SiO{sub 2} backchannel passivation layer (BPL). It is found that this electrical degradation phenomenon can be attributed to the generation of defect states during the BPL process, which deteriorates the photo-bias stability of a-IWO TFTs. A method proposed by adding an oxygen-rich a-IWO thin film upon the a-IWO active channel layer could effectively suppress the plasma damage to channel layer during BPL deposition process. The bi-layer a-IWO TFT structure with an oxygen-rich back channel exhibits superior electrical reliability of device under NBTIS.

  4. Blue--green to near-IR switching electroluminescence from Si-rich silicon oxide/nitride bilayer structures

    NASA Astrophysics Data System (ADS)

    Berencén, Y.; Jambois, O.; Ramírez, J. M.; Rebled, J. M.; Estradé, S.; Peiró, F.; Domínguez, C.; Rodríguez, J. A.; Garrido, B.

    2011-07-01

    Blue--green to near-IR switching electroluminescence (EL) has been achieved in a metal-oxide-semiconductor light emitting device, where the dielectric has been replaced by a Si-rich silicon oxide/nitride bilayer structure. To form Si nanostructures, the layers were implanted with Si ions at high energy, resulting in a Si excess of 19%, and subsequently annealed at 1000°C. Transmission electron microscopy and EL studies allowed ascribing the blue--green emission to the Si nitride related defects and the near-IR band with the emission of the Si-nanoclusters embedded into the SiO2 layer. Charge transport analysis is reported and allows for identifying the origin of this two-wavelength switching effect.

  5. Interaction of n-octyl β,D-glucopyranoside with giant magnetic-fluid-loaded phosphatidylcholine vesicles: direct visualization of membrane curvature fluctuations as a function of surfactant partitioning between water and lipid bilayer.

    PubMed

    Ménager, Christine; Guemghar, Dihya; Cabuil, Valérie; Lesieur, Sylviane

    2010-10-05

    The present study deals with the morphological modifications of giant dioleoyl phosphatidylcholine vesicles (DOPC GUVs) induced by the nonionic surfactant n-octyl β,D-glucopyranoside at sublytic levels, i.e., in the first steps of the vesicle-to-micelle transition process, when surfactant inserts into the vesicle bilayer without disruption. Experimental conditions were perfected to exactly control the surfactant bilayer composition of the vesicles, in line with former work focused on the mechanical properties of the membrane of magnetic-fluid-loaded DOPC GUVs submitted to a magnetic field. The purpose here was to systematically examine, in the absence of any external mechanical constraint, the dynamics of giant vesicle shape and membrane deformations as a function of surfactant partitioning between the aqueous phase and the lipid membrane, beforehand established by turbidity measurements from small unilamellar vesicles.

  6. The structure of fluid trifluoromethane and methylfluoride

    NASA Astrophysics Data System (ADS)

    Neuefeind, J.; Fischer, H. E.; Schröer, W.

    2000-10-01

    We present hard x-ray and neutron diffraction measurements on the polar fluorocarbons HCF3 and H3CF under supercritical conditions and for a range of molecular densities spanning about a factor of ten. The Levesque-Weiss-Reatto inversion scheme has been used to deduce the site-site potentials underlying the measured partial pair distribution functions. The orientational correlations between adjacent fluorocarbon molecules - which are characterized by quite large dipole moments but no tendency to form hydrogen bonds - are small compared to a highly polar system like fluid hydrogen chloride. In fact, the orientational correlations in HCF3 and H3CF are found to be nearly as small as those of fluid CF4, a fluorocarbon with no dipole moment.

  7. Structures of High Density Molecular Fluids

    SciTech Connect

    Baer, B; Cynn, H; Iota, V; Yoo, C-S

    2002-02-01

    The goal of this proposal is to develop an in-situ probe for high density molecular fluids. We will, therefore, use Coherent Anti-Stokes Raman Spectroscopy (CARS) applied to laser heated samples in a diamond-anvil cell (DAC) to investigate molecular fluids at simultaneous conditions of high temperatures (T > 2000K) and high pressures (P > 10 GPa.) Temperatures sufficient to populate vibrational levels above the ground state will allow the vibrational potential to be mapped by CARS. A system capable of heating and probing these samples will be constructed. Furthermore, the techniques that enable a sample to be sufficiently heated and probed while held at static high pressure in a diamond-anvil-cell will be developed. This will be an in-situ investigation of simple molecules under conditions relevant to the study of detonation chemistry and the Jovain planet interiors using state of the art non-linear spectroscopy, diamond-anvil-cells, and laser heating technology.

  8. Supersonic Parachute Aerodynamic Testing and Fluid Structure Interaction Simulation

    NASA Astrophysics Data System (ADS)

    Lingard, J. S.; Underwood, J. C.; Darley, M. G.; Marraffa, L.; Ferracina, L.

    2014-06-01

    The ESA Supersonic Parachute program expands the knowledge of parachute inflation and flying characteristics in supersonic flows using wind tunnel testing and fluid structure interaction to develop new inflation algorithms and aerodynamic databases.

  9. Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies

    SciTech Connect

    Tian, Jianhui; Nickels, Jonathan; Katsaras, John; Cheng, Xiaolin

    2016-04-27

    Spatial organization within lipid bilayers is an important feature for a range of biological processes. Leaflet compositional asymmetry and lateral lipid organization are just two of the ways in which membrane structure appears to be more complex than initially postulated by the fluid mosaic model. This raises the question of how the phase behavior in one bilayer leaflet may affect the apposing leaflet and how one begins to construct asymmetric model systems to investigate these interleaflet interactions. In this paper, we report on all-atom molecular dynamics simulations (a total of 4.1 μs) of symmetric and asymmetric bilayer systems composed of liquid-ordered (Lo) or liquid-disordered (Ld) leaflets, based on the nanodomain-forming POPC/DSPC/cholesterol system. We begin by analyzing an asymmetric bilayer with leaflets derived from simulations of symmetric Lo and Ld bilayers. In this system, we observe that the properties of the Lo and Ld leaflets are similar to those of the Lo and Ld leaflets in corresponding symmetric systems. However, it is not obvious that mixing the equilibrium structures of their symmetric counterparts is the most appropriate way to construct asymmetric bilayers nor that these structures will manifest interleaflet couplings that lead to domain registry/antiregistry. We therefore constructed and simulated four additional asymmetric bilayer systems by systematically adding or removing lipids in the Ld leaflet to mimic potential density fluctuations. We find that the number of lipids in the Ld leaflet affects its own properties, as well as those of the apposing Lo leaflet. Collectively, the simulations reveal the presence of weak acyl chain interdigitation across bilayer leaflets, suggesting that interdigitation alone does not contribute significantly to the interleaflet coupling in nonphase-separated bilayers of this chemical composition. Finally, however, the properties of both leaflets appear to be sensitive to changes in in-plane lipid

  10. Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies

    SciTech Connect

    Tian, Jianhui; Nickels, Jonathan; Katsaras, John; Cheng, Xiaolin

    2016-04-27

    Spatial organization within lipid bilayers is an important feature for a range of biological processes. Leaflet compositional asymmetry and lateral lipid organization are just two of the ways in which membrane structure appears to be more complex than initially postulated by the fluid mosaic model. This raises the question of how the phase behavior in one bilayer leaflet may affect the apposing leaflet and how one begins to construct asymmetric model systems to investigate these interleaflet interactions. In this paper, we report on all-atom molecular dynamics simulations (a total of 4.1 μs) of symmetric and asymmetric bilayer systems composed of liquid-ordered (Lo) or liquid-disordered (Ld) leaflets, based on the nanodomain-forming POPC/DSPC/cholesterol system. We begin by analyzing an asymmetric bilayer with leaflets derived from simulations of symmetric Lo and Ld bilayers. In this system, we observe that the properties of the Lo and Ld leaflets are similar to those of the Lo and Ld leaflets in corresponding symmetric systems. However, it is not obvious that mixing the equilibrium structures of their symmetric counterparts is the most appropriate way to construct asymmetric bilayers nor that these structures will manifest interleaflet couplings that lead to domain registry/antiregistry. We therefore constructed and simulated four additional asymmetric bilayer systems by systematically adding or removing lipids in the Ld leaflet to mimic potential density fluctuations. We find that the number of lipids in the Ld leaflet affects its own properties, as well as those of the apposing Lo leaflet. Collectively, the simulations reveal the presence of weak acyl chain interdigitation across bilayer leaflets, suggesting that interdigitation alone does not contribute significantly to the interleaflet coupling in nonphase-separated bilayers of this chemical composition. Finally, however, the properties of both leaflets appear to be sensitive to changes in in-plane lipid

  11. Fluid-Structure Interactions with Flexible and Rigid Bodies

    NASA Astrophysics Data System (ADS)

    Daily, David Jesse

    Fluid structure interactions occur to some extent in nearly every type of fluid flow. Understanding how structures interact with fluids and visa-versa is of vital importance in many engineering applications. The purpose of this research is to explore how fluids interact with flexible and rigid structures. A computational model was used to model the fluid structure interactions of vibrating synthetic vocal folds. The model simulated the coupling of the fluid and solid domains using a fluid-structure interface boundary condition. The fluid domain used a slightly compressible flow solver to allow for the possibility of acoustic coupling with the subglottal geometry and vibration of the vocal fold model. As the subglottis lengthened, the frequency of vibration decreased until a new acoustic mode could form in the subglottis. Synthetic aperture particle image velocimetry (SAPIV) is a three-dimensional particle tracking technique. SAPIV was used to image the jet of air that emerges from vibrating human vocal folds (glottal jet) during phonation. The three-dimensional reconstruction of the glottal jet found faint evidence of flow characteristics seen in previous research, such as axis-switching, but did not have sufficient resolution to detect small features. SAPIV was further applied to reconstruct the smaller flow characteristics of the glottal jet of vibrating synthetic vocal folds. Two- and four-layer synthetic vocal fold models were used to determine how the glottal jet from the synthetic models compared to the glottal jet from excised human vocal folds. The two- and four-layer models clearly exhibited axis-switching which has been seen in other 3D analyses of the glottal jet. Cavitation in a quiescent fluid can break a rigid structure such as a glass bottle. A new cavitation number was derived to include acceleration and pressure head at cavitation onset. A cavitation stick was used to validate the cavitation number by filling it with different depths and hitting

  12. AN INCOMPRESSIBLE ALE METHOD FOR FLUID-STRUCTURE INTERACTION

    SciTech Connect

    Dunn, T A

    2004-12-01

    Multi-disciplinary analysis is becoming more and more important to tackle todays complex engineering problems. Therefore, computational tools must be able to handle the complex multi-physics requirements of these problems. A computer code may need to handle the physics associated with fluid dynamics, structural mechanics, heat transfer, chemistry, electro-magnetics, or a variety of other disciplines--all coupled in a highly non-linear system. The objective of this project was to couple an incompressible fluid dynamics package to a solid mechanics code. The code uses finite-element methods and is useful for three-dimensional transient problems with fluid-structure interaction. The code is designed for efficient performance on large multi-processor machines. An ALE finite element method was developed to investigate fluid-structure interaction. The write-up contains information about the method, the problem formulation, and some results from example test problems.

  13. Solvent effect on phosphatidylcholine headgroup dynamics as revealed by the energetics and dynamics of two gel-state bilayer headgroup structures at subzero temperatures.

    PubMed Central

    Hsieh, C. H.; Wu, W. G.

    1995-01-01

    The packing and dynamics of lipid bilayers at the phosphocholine headgroup region within the temperature range of -40 to -110 degrees C have been investigated by solid-state nuclear magnetic resonance (NMR) measurements of selectively deuterium-labeled H2O/dimyristoylphosphatidylcholine (DMPC) bilayers. Two coexisting signals with 2H NMR quadrupolar, splittings of 36.1 and 9.3 (or smaller) kHz were detected from the -CD3 of choline methyl group. These two signals have been assigned to two coexisting gel-state headgroup structures with fast rotational motion of -CD3 and -N(CD3)3 group, respectively, with a threefold symmetry. The largest quadrupolar splitting of the NMR signal detected from the -CD2 of C alpha and C beta methylene segment was found to be 115.2 kHz, which is 10% lower than its static value of 128.2 kHz. Thus, there are extensive motions of the entire choline group of gel-state phosphatidylcholine bilayers even at a subzero temperature of -110 degrees C. These results strongly support the previous suggestion (E. J. Dufourc, C. Mayer, J. Stohrer, G. Althoff, and G. Kothe, 1992, Biophys. J. 61:42-57) that 31P chemical shift tensor elements of DMPC determined under similar conditions are not the rigid static values. The free energy difference between the two gel-state headgroup structures was determined to be 26.3 +/- 0.9 kJ/mol for fully hydrated bilayers. Furthermore, two structures with similar free energy difference were also detected for "frozen" phosphorylcholine chloride solution in a control experiment, leading to the conclusion that the two structures may be governed solely by the energetics of fully hydrated phosphocholine headgroup. The intermolecular interactions among lipids, however, stabilize the static headgroup structure as evidenced by the apparently lower free energy difference between the two structures for partially hydrated lipid bilayers. Evidence is also presented to suggest that one of the headgroup structures with

  14. From lanosterol to cholesterol: structural evolution and differential effects on lipid bilayers.

    PubMed Central

    Miao, Ling; Nielsen, Morten; Thewalt, Jenifer; Ipsen, John H; Bloom, Myer; Zuckermann, Martin J; Mouritsen, Ole G

    2002-01-01

    Cholesterol is an important molecular component of the plasma membranes of mammalian cells. Its precursor in the sterol biosynthetic pathway, lanosterol, has been argued by Konrad Bloch (Bloch, K. 1965. Science. 150:19-28; 1983. CRC Crit. Rev. Biochem. 14:47-92; 1994. Blonds in Venetian Paintings, the Nine-Banded Armadillo, and Other Essays in Biochemistry. Yale University Press, New Haven, CT.) to also be a precursor in the molecular evolution of cholesterol. We present a comparative study of the effects of cholesterol and lanosterol on molecular conformational order and phase equilibria of lipid-bilayer membranes. By using deuterium NMR spectroscopy on multilamellar lipid-sterol systems in combination with Monte Carlo simulations of microscopic models of lipid-sterol interactions, we demonstrate that the evolution in the molecular chemistry from lanosterol to cholesterol is manifested in the model lipid-sterol membranes by an increase in the ability of the sterols to promote and stabilize a particular membrane phase, the liquid-ordered phase, and to induce collective order in the acyl-chain conformations of lipid molecules. We also discuss the biological relevance of our results, in particular in the context of membrane domains and rafts. PMID:11867458

  15. Ultrasensitive organic phototransistors with multispectral response based on thin-film/single-crystal bilayer structures

    SciTech Connect

    Pinto, R. M.; Gouveia, W.; Neves, A. I. S.; Alves, H.

    2015-11-30

    We report on highly efficient organic phototransistors (OPTs) based on thin-film/single-crystal planar bilayer junctions between 5,6,11,12-tetraphenyltetracene (rubrene) and [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PC{sub 61}BM). The OPTs show good field-effect characteristics in the dark, with high hole-mobility (4–5 cm{sup 2} V{sup −1} s{sup −1}), low-contact resistance (20 kΩ cm), and low-operating voltage (≤5 V). Excellent sensing capabilities allow for light detection in the 400–750 nm range, with photocurrent/dark current ratio as high as 4 × 10{sup 4}, responsivity on the order of 20 AW{sup −1} at 27 μW cm{sup −2}, and an external quantum efficiency of 52 000%. Photocurrent generation is attributed to enhanced electron and hole transfer at the interface between rubrene and PC{sub 61}BM, and fast response times are observed as a consequence of the high-mobility of the interfaces. The optoelectronic properties exhibited in these OPTs outperform those typically provided by a-Si based devices, enabling future applications where multifunctionality in a single-device is sought.

  16. Ultrasensitive organic phototransistors with multispectral response based on thin-film/single-crystal bilayer structures

    NASA Astrophysics Data System (ADS)

    Pinto, R. M.; Gouveia, W.; Neves, A. I. S.; Alves, H.

    2015-11-01

    We report on highly efficient organic phototransistors (OPTs) based on thin-film/single-crystal planar bilayer junctions between 5,6,11,12-tetraphenyltetracene (rubrene) and [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM). The OPTs show good field-effect characteristics in the dark, with high hole-mobility (4-5 cm2 V-1 s-1), low-contact resistance (20 kΩ cm), and low-operating voltage (≤5 V). Excellent sensing capabilities allow for light detection in the 400-750 nm range, with photocurrent/dark current ratio as high as 4 × 104, responsivity on the order of 20 AW-1 at 27 μW cm-2, and an external quantum efficiency of 52 000%. Photocurrent generation is attributed to enhanced electron and hole transfer at the interface between rubrene and PC61BM, and fast response times are observed as a consequence of the high-mobility of the interfaces. The optoelectronic properties exhibited in these OPTs outperform those typically provided by a-Si based devices, enabling future applications where multifunctionality in a single-device is sought.

  17. Changes in lipid bilayer structure caused by the helix-to-sheet transition of an HIV-1 gp41 fusion peptide derivative

    DOE PAGES

    Heller, William T.; Rai, Durgesh K.

    2017-01-16

    HIV-1, like other enveloped viruses, undergoes fusion with the cell membrane to infect it. Viral coat proteins are thought to bind the virus to the membrane and actively fuse the viral and cellular membranes together. The actual molecular mechanism of fusion is challenging to visualize, resulting in the use of model systems. In this paper, the bilayer curvature modifying properties of a synthetic variant of the HIV-1 gp41 fusion peptide with lipid bilayer vesicles composed of a mixture of dimyristoyl phosphatidylcholine (DMPC) and dimyristoyl phosphatidylserine (DMPS) were studied. In 7:3 DMPC:DMPS vesicles made with deuterium-labeled DMPC, the peptide was observedmore » to undergo a concentration-dependent conformational transition between an α-helix and an antiparallel β-sheet. Through the use of small-angle neutron scattering (SANS) and selective deuterium labeling, it was revealed that conformational transition of the peptide is also accompanied by a transition in the structure of the lipid bilayer. In addition to changes in the distribution of the lipid between the leaflets of the vesicle, the SANS data are consistent with two regions having different thicknesses. Finally, of the two different bilayer structures, the one corresponding to the smaller area fraction, being ~8% of the vesicle area, is much thicker than the remainder of the vesicle, which suggests that there are regions of localized negative curvature similar to what takes place at the point of contact between two membranes immediately preceding fusion.« less

  18. Intercalation of bovine serum albumin coated gold clusters between phospholipid bilayers: temperature-dependent behavior of lipid-AuQC@BSA assemblies with red emission and superlattice structure.

    PubMed

    Söptei, Balázs; Mihály, Judith; Visy, Júlia; Wacha, András; Bóta, Attila

    2014-04-10

    A method has been developed to encapsulate bovine serum albumin (BSA)-coated gold quantum clusters (AuQC@BSA) in a multilamellar system of dipalmitoylphosphatidylcholine (DPPC). Results have shown that intercalation of AuQC@BSA particles into lipid bilayers occurs in the presence of CaCl2. Intense red photoluminescence emission was observed after encapsulation of the clusters. A well-defined structure was found with periodic distances drastically larger than that in the pure DPPC/water system. Although Ca(2+) ions can change the dipole characteristics of the lipid bilayer surface, leading to unbinding between the bilayers of multilamellar DPPC/water system, the repulsion is shielded in the presence of AuQC@BSA particles. A coherent superlattice structure evolves due to mixed Ca(2+)-DPPC and Ca(2+)-AuQC@BSA interactions. Studies at different temperatures have suggested a correlation between the luminescence properties of the clusters and phase transition of the lipid layers. The temperature-dependent behavior assumes the connection between the coating and the lipid bilayer surface. Temperature-dependent features of lipid intercalated Au clusters provide new opportunities in their application.

  19. Changes in lipid bilayer structure caused by the helix-to-sheet transition of an HIV-1 gp41 fusion peptide derivative.

    PubMed

    Heller, William T; Rai, Durgesh K

    2017-03-01

    HIV-1, like other enveloped viruses, undergoes fusion with the cell membrane to infect it. Viral coat proteins are thought to bind the virus to the membrane and actively fuse the viral and cellular membranes together. The actual molecular mechanism of fusion is challenging to visualize, resulting in the use of model systems. Here, the bilayer curvature modifying properties of a synthetic variant of the HIV-1 gp41 fusion peptide with lipid bilayer vesicles composed of a mixture of dimyristoyl phosphatidylcholine (DMPC) and dimyristoyl phosphatidylserine (DMPS) were studied. In 7:3 DMPC:DMPS vesicles made with deuterium-labeled DMPC, the peptide was observed to undergo a concentration-dependent conformational transition between an α-helix and an antiparallel β-sheet. Through the use of small-angle neutron scattering (SANS) and selective deuterium labeling, it was revealed that conformational transition of the peptide is also accompanied by a transition in the structure of the lipid bilayer. In addition to changes in the distribution of the lipid between the leaflets of the vesicle, the SANS data are consistent with two regions having different thicknesses. Of the two different bilayer structures, the one corresponding to the smaller area fraction, being ∼8% of the vesicle area, is much thicker than the remainder of the vesicle, which suggests that there are regions of localized negative curvature similar to what takes place at the point of contact between two membranes immediately preceding fusion. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Electronic structures and elastic properties of monolayer and bilayer transition metal dichalcogenides MX2 (M = Mo, W; X = O, S, Se, Te): A comparative first-principles study

    NASA Astrophysics Data System (ADS)

    Zeng, Fan; Zhang, Wei-Bing; Tang, Bi-Yu

    2015-09-01

    First-principle calculations with different exchange-correlation functionals, including LDA, PBE, and vdW-DF functional in the form of optB88-vdW, have been performed to investigate the electronic and elastic properties of two-dimensional transition metal dichalcogenides (TMDCs) with the formula of MX2(M = Mo, W; X = O, S, Se, Te) in both monolayer and bilayer structures. The calculated band structures show a direct band gap for monolayer TMDCs at the K point except for MoO2 and WO2. When the monolayers are stacked into a bilayer, the reduced indirect band gaps are found except for bilayer WTe2, in which the direct gap is still present at the K point. The calculated in-plane Young moduli are comparable to that of graphene, which promises possible application of TMDCs in future flexible and stretchable electronic devices. We also evaluated the performance of different functionals including LDA, PBE, and optB88-vdW in describing elastic moduli of TMDCs and found that LDA seems to be the most qualified method. Moreover, our calculations suggest that the Young moduli for bilayers are insensitive to stacking orders and the mechanical coupling between monolayers seems to be negligible. Project supported by the Construct Program of the Key Discipline in Hunan Province, China and Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province, China.

  1. Irradiated bilayer graphene

    NASA Astrophysics Data System (ADS)

    Abergel, D. S. L.; Chakraborty, Tapash

    2011-01-01

    We describe the gated bilayer graphene system when it is subjected to intense terahertz frequency electromagnetic radiation. We examine the electron band structure and density of states via exact diagonalization methods within Floquet theory. We find that dynamical states are induced which lead to modification of the band structure. We first examine the situation where there is no external magnetic field. In the unbiased case, dynamical gaps appear in the spectrum which manifest as dips in the density of states. For finite inter-layer bias (where a static gap is present in the band structure of unirradiated bilayer graphene), dynamical states may be induced in the static gap. These states can show a high degree of valley polarization. When the system is placed in a strong magnetic field, the radiation induces coupling between the Landau levels which allows dynamical levels to exist. For strong fields, this means the Landau levels are smeared to form a near-continuum of states.

  2. Fluid-structure interaction in compliant insect wings.

    PubMed

    Eberle, A L; Reinhall, P G; Daniel, T L

    2014-06-01

    Insect wings deform significantly during flight. As a result, wings act as aeroelastic structures wherein both the driving motion of the structure and the aerodynamic loading of the surrounding fluid potentially interact to modify wing shape. We explore two key issues associated with the design of compliant wings: over a range of driving frequencies and phases of pitch-heave actuation, how does wing stiffness influence (1) the lift and thrust generated and (2) the relative importance of fluid loading on the shape of the wing? In order to examine a wide range of parameters relevant to insect flight, we develop a computationally efficient, two-dimensional model that couples point vortex methods for fluid force computations with structural finite element methods to model the fluid-structure interaction of a wing in air. We vary the actuation frequency, phase of actuation, and flexural stiffness over a range that encompasses values measured for a number of insect taxa (10-90 Hz; 0-π rad; 10(-7)-10(-5) N m(2)). We show that the coefficients of lift and thrust are maximized at the first and second structural resonant frequencies of the system. We also show that even in regions of structural resonance, fluid loading never contributes more than 20% to the development of flight forces.

  3. Evaluation of dentinal fluid flow behaviours: a fluid-structure interaction simulation.

    PubMed

    Su, Kuo-Chih; Chuang, Shu-Fen; Ng, Eddie Yin-Kwee; Chang, Chih-Han

    2014-11-01

    This study uses the fluid-structure interaction (FSI) method to investigate the fluid flow in dental pulp. First, the FSI method is used for the biomechanical simulation of dental intrapulpal responses during force loading (50, 100 and 150 N) on a tooth. The results are validated by comparison with experimental outcomes. Second, the FSI method is used to investigate an intact tooth subjected to a mechanical stimulus during loading at various loading rates. Force loading (0-100 N) is applied gradually to an intact tooth surface with loading rates of 125, 62.5, 25 and 12.5 N/s, respectively, and the fluid flow changes in the pulp are evaluated. FSI analysis is found to be suitable for examining intrapulpal biomechanics. An external force applied to a tooth with a low loading rate leads to a low fluid flow velocity in the pulp chamber, thus avoiding tooth pain.

  4. Doping-driven structural distortion in the bilayer iridate (Sr1-xLax) 3Ir2O7

    NASA Astrophysics Data System (ADS)

    Hogan, Tom; Wang, Xiaoping; Chu, H.; Hsieh, David; Wilson, Stephen D.

    2017-05-01

    Neutron single-crystal diffraction and rotational anisotropy optical second harmonic generation data are presented resolving the nature of the structural distortion realized in electron-doped (Sr1 -xLax )3Ir2O7 with x =0.035 and x =0.071 . Once electrons are introduced into the bilayer spin-orbit assisted Mott insulator Sr3Ir2O7 , previous studies have identified the appearance of a low-temperature structural distortion and have suggested the presence of a competing electronic instability in the phase diagram of this material. Our measurements resolve a lowering of the structural symmetry from monoclinic C 2 /c to monoclinic P 21/c and the creation of two unique Ir sites within the chemical unit cell as the lattice distorts below a critical temperature TS. Details regarding the modifications to oxygen octahedral rotations and tilting through the transition are discussed as well as the evolution of the low-temperature distorted lattice as a function of carrier substitution.

  5. Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning.

    PubMed

    Dong, Xuewei; Sun, Yunxiang; Wei, Guanghong; Nussinov, Ruth; Ma, Buyong

    2017-10-05

    Alzheimer's disease, a common neurodegenerative disease, is characterized by the aggregation of amyloid-β (Aβ) peptides. The interactions of Aβ with membranes cause changes in membrane morphology and ion permeation, which are responsible for its neurotoxicity and can accelerate fibril growth. However, the Aβ-lipid interactions and how these induce membrane perturbation and disruption at the atomic level and the consequences for the Aβ organization are not entirely understood. Here, we perform multiple atomistic molecular dynamics simulations on three protofibrillar Aβ9-40 trimers. Our simulations show that, regardless of the morphologies and the initial orientations of the three different protofibrillar Aβ9-40 trimers, the N-terminal β-sheet of all trimers preferentially binds to the membrane surface. The POPG lipid bilayers enhance the structural stability of protofibrillar Aβ trimers by stabilizing inter-peptide β-sheets and D23-K28 salt-bridges. The interaction causes local membrane thinning. We found that the trimer structure related to Alzheimer's disease brain tissue () is the most stable both in water solution and at membrane surface, and displays slightly stronger membrane perturbation capability. These results provide mechanistic insights into the membrane-enhanced structural stability of protofibrillar Aβ oligomers and the first step of Aβ-induced membrane disruption at the atomic level.

  6. SPAR improved structure/fluid dynamic analysis capability

    NASA Technical Reports Server (NTRS)

    Oden, J. T.; Pearson, M. L.

    1983-01-01

    The capability of analyzing a coupled dynamic system of flowing fluid and elastic structure was added to the SPAR computer code. A method, developed and adopted for use in SPAR utilizes the existing assumed stress hybrid plan element in SPAR. An operational mode was incorporated in SPAR which provides the capability for analyzing the flaw of a two dimensional, incompressible, viscous fluid within rigid boundaries. Equations were developed to provide for the eventual analysis of the interaction of such fluids with an elastic solid.

  7. Small data global existence for a fluid-structure model

    NASA Astrophysics Data System (ADS)

    Ignatova, Mihaela; Kukavica, Igor; Lasiecka, Irena; Tuffaha, Amjad

    2017-02-01

    We address the system of partial differential equations modeling motion of an elastic body inside an incompressible fluid. The fluid is modeled by the incompressible Navier-Stokes equations while the structure is represented by the damped wave equation with interior damping. The additional boundary stabilization γ, considered in our previous paper, is no longer necessary. We prove the global existence and exponential decay of solutions for small initial data in a suitable Sobolev space.

  8. SPAR improved structure-fluid dynamic analysis capability, phase 2

    NASA Technical Reports Server (NTRS)

    Pearson, M. L.

    1984-01-01

    An efficient and general method of analyzing a coupled dynamic system of fluid flow and elastic structures is investigated. The improvement of Structural Performance Analysis and Redesign (SPAR) code is summarized. All error codes are documented and the SPAR processor/subroutine cross reference is included.

  9. Viscoelastic fluid-structure interaction between a non-Newtonian fluid flow and flexible cylinder

    NASA Astrophysics Data System (ADS)

    Dey, Anita; Modarres-Sadeghi, Yahya; Rothstein, Jonathan

    2016-11-01

    It is well known that when a flexible or flexibly-mounted structure is placed perpendicular to the flow of a Newtonian fluid, it can oscillate due to the shedding of separated vortices at high Reynolds numbers. If the same flexible object is placed in non-Newtonian flows, however, the structure's response is still unknown. Unlike Newtonian fluids, the flow of viscoelastic fluids can become unstable at infinitesimal Reynolds numbers due to a purely elastic flow instability. In this talk, we will present a series of experiments investigating the response of a flexible cylinder placed in the cross flow of a viscoelastic fluid. The elastic flow instabilities occurring at high Weissenberg numbers can exert fluctuating forces on the flexible cylinder thus leading to nonlinear periodic oscillations of the flexible structure. These oscillations are found to be coupled to the time-dependent state of viscoelastic stresses in the wake of the flexible cylinder. The static and dynamic responses of the flexible cylinder will be presented over a range of flow velocities, along with measurements of velocity profiles and flow-induced birefringence, in order to quantify the time variation of the flow field and the state of stress in the fluid.

  10. Dye-sensitized solar cells consisting of dye-bilayer structure stained with two dyes for harvesting light of wide range of wavelength

    NASA Astrophysics Data System (ADS)

    Inakazu, Fumi; Noma, Yusuke; Ogomi, Yuhei; Hayase, Shuzi

    2008-09-01

    Dye-sensitized solar cells (DSCs) containing dye-bilayer structure of black dye and NK3705 (3-carboxymethyl-5-[3-(4-sulfobutyl)-2(3H)-bezothiazolylidene]-2-thioxo-4-thiazolidinone, sodium salt) in one TiO2 layer (2-TiO-BD-NK) are reported. The 2-TiO-BD-NK structure was fabricated by staining one TiO2 layer with these two dyes, step by step, under a pressurized CO2 condition. The dye-bilayer structure was observed by using a confocal laser scanning microscope. The short circuit current (Jsc) and the incident photon to current efficiency of the cell (DSC-2-TiO-BD-NK) was almost the sum of those of DSC stained with black dye only (DSC-1-TiO-BD) and DSC stained with NK3705 only (DSC-1-TiO-NK).

  11. Fluid-structure interaction of reticulated porous wings

    NASA Astrophysics Data System (ADS)

    Strong, Elizabeth; Jawed, Mohammad; Reis, Pedro

    Insects of the orders Neuroptera and Hymenoptera locomote via flapping flight with reticulated wings that have porous structures that confers them with remarkable lightweight characteristics. Yet these porous wings still perform as contiguous plates to provide the necessary aerodynamic lift and drag required for flight. Even though the fluid flow past the bulk of these insects may be in high Reynolds conditions, viscosity can dominate over inertia in the flow through the porous sub-features. Further considering the flexibility of these reticulated wings yields a highly nonlinear fluid-structure interaction problem. We perform a series of dynamically-scaled precision model experiments to gain physical insight into this system. Our experiments are complemented with computer simulations that combine the Discrete Elastic Rods method and a model for the fluid loading that takes into account the `leakiness' through the porous structure. Our results are anticipated to find applications in micro-air vehicle aerodynamics.

  12. Order-disorder structural transition in a confined fluid

    NASA Astrophysics Data System (ADS)

    de la Calleja-Mora, E. M.; Krott, Leandro B.; Barbosa, M. C.

    2016-05-01

    In this paper we analyze the amorphous/solid to disordered liquid structural phase transitions of an anomalous confined fluid in terms of their fractal dimensions. The model studied is composed by particles interaction through a two-length scales potential confined by two infinite plates. This fluid that in the bulk exhibits water-like anomalies under confinement forms layers of particles. We show that the fluid at the contact layer forms at high densities structures and transitions that can be mapped into fractal dimensions. The multi-fractal singularity spectrum is obtained in all these cases and it is used as the order parameter to quantify the structural transitions for each stage on the confined liquid. This mapping shows that the fractal dimension increases with the density and with the temperature.

  13. Interfacial patterns in magnetorheological fluids: Azimuthal field-induced structures

    NASA Astrophysics Data System (ADS)

    Dias, Eduardo O.; Lira, Sérgio A.; Miranda, José A.

    2015-08-01

    Despite their practical and academic relevance, studies of interfacial pattern formation in confined magnetorheological (MR) fluids have been largely overlooked in the literature. In this work, we present a contribution to this soft matter research topic and investigate the emergence of interfacial instabilities when an inviscid, initially circular bubble of a Newtonian fluid is surrounded by a MR fluid in a Hele-Shaw cell apparatus. An externally applied, in-plane azimuthal magnetic field produced by a current-carrying wire induces interfacial disturbances at the two-fluid interface, and pattern-forming structures arise. Linear stability analysis, weakly nonlinear theory, and a vortex sheet approach are used to access early linear and intermediate nonlinear time regimes, as well as to determine stationary interfacial shapes at fully nonlinear stages.

  14. Study of the influence of semiconductor material parameters on acoustic wave propagation modes in GaSb/AlSb bi-layered structures by Legendre polynomial method

    NASA Astrophysics Data System (ADS)

    Othmani, Cherif; Takali, Farid; Njeh, Anouar; Ben Ghozlen, Mohamed Hédi

    2016-09-01

    The propagation of Rayleigh-Lamb waves in bi-layered structures is studied. For this purpose, an extension of the Legendre polynomial (LP) method is proposed to formulate the acoustic wave equation in the bi-layered structures induced by thin film Gallium Antimonide (GaSb) and with Aluminum Antimonide (AlSb) substrate in moderate thickness. Acoustic modes propagating along a bi-layer plate are shown to be quite different than classical Lamb modes, contrary to most of the multilayered structures. The validation of the LP method is illustrated by a comparison between the associated numerical results and those obtained using the ordinary differential equation (ODE) method. The convergency of the LP method is discussed through a numerical example. Moreover, the influences of thin film GaSb parameters on the characteristics Rayleigh-Lamb waves propagation has been studied in detail. Finally, the advantages of the Legendre polynomial (LP) method to analyze the multilayered structures are described. All the developments performed in this work were implemented in Matlab software.

  15. Structural and electronic properties of AB- and AA-stacking bilayer-graphene intercalated by Li, Na, Ca, B, Al, Si, Ge, Ag, and Au atoms

    NASA Astrophysics Data System (ADS)

    Tayran, Ceren; Aydin, Sezgin; Çakmak, Mehmet; Ellialtıoğlu, Şinasi

    2016-04-01

    The structural and electronic properties of X (=Li, Na, Ca, B, Al, Si, Ge, Ag, and Au)-intercalated AB- and AA-stacking bilayer-graphene have been investigated by using ab initio density functional theory. It is shown that Boron (Lithium)-intercalated system is energetically more stable than the others for the AB (AA) stacking bilayer-graphene systems. The structural parameters, electronic band structures, and orbital nature of actual interactions are studied for the relaxed stable geometries. It is seen that the higher the binding energy, the smaller is the distance between the layers, in these systems. The electronic band structures for these systems show that different intercalated atoms can change the properties of bilayer-graphene differently. For qualitative description of the electronic properties, the metallicities of the systems are also calculated and compared with each other. The Mulliken analysis and electron density maps clearly indicate that the interactions inside a single layer (intralayer interactions) are strong and highly covalent, while the interactions between the two layers (interlayer interactions) are much weaker.

  16. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization

    NASA Astrophysics Data System (ADS)

    Abou Najm, M. R.; Atallah, N. M.; Selker, J. S.; Roques, C.; Stewart, R. D.; Rupp, D. E.; Saad, G.; El-Fadel, M.

    2015-12-01

    Classic porous media characterization relies on typical infiltration experiments with Newtonian fluids (i.e., water) to estimate hydraulic conductivity. However, such experiments are generally not able to discern important characteristics such as pore size distribution or pore structure. We show that introducing non-Newtonian fluids provides additional unique flow signatures that can be used for improved pore structure characterization while still representing the functional hydraulic behavior of real porous media. We present a new method for experimentally estimating the pore structure of porous media using a combination of Newtonian and non-Newtonian fluids. The proposed method transforms results of N infiltration experiments using water and N-1 non-Newtonian solutions into a system of equations that yields N representative radii (Ri) and their corresponding percent contribution to flow (wi). This method allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation comparing the functional flow behavior of different soils to their modeled flow with N representative radii revealed the ability of the proposed method to represent the water retention and infiltration behavior of real soils. The experimental results showed the ability of such fluids to outsmart Newtonian fluids and infer pore size distribution and unsaturated behavior using simple saturated experiments. Specifically, we demonstrate using synthetic porous media that the use of different non-Newtonian fluids enables the definition of the radii and corresponding percent contribution to flow of multiple representative pores, thus improving the ability of pore-scale models to mimic the functional behavior of real porous media in terms of flow and porosity. The results advance the knowledge towards conceptualizing the complexity of porous media and can potentially impact applications in fields like irrigation efficiencies, vadose zone hydrology, soil

  17. Stomatosomes, blastula vesicles and bilayer disks: morphological richness of structures formed in dilute aqueous mixtures of a cationic and an anionic surfactant.

    PubMed

    Kakehashi, Rie; Karlsson, Göran; Almgren, Mats

    2009-03-15

    Cryogenic transmission electron microscopy (cryoTEM) was used to study the structures formed in mixtures of sodium dodecylsulfate (SDS) and dodecyltrimethylammonium bromide (DTAB) in dilute aqueous solutions with 0-300 mM NaBr. The DTAB mole fraction, X, was in the range 0.2-0.4, limited at 25 degrees C by precipitation of solid DTA-DS at X=0.38 without salt to X=0.25 at 300 mM NaBr. At a total surfactant concentration of 100 mM the samples separated into two liquid phases (the bottom phase birefringent) within a narrow (+/-0.01 mole fraction units) composition range. At the mid-point X varied from 0.32 without salt to 0.22 at 300 mM NaBr. Elemental analysis of C, S, O, and N in the separated phases of a sample with 100 mM NaBr and X=0.26 showed the top phase to contain almost only SDS at a low concentration, 14 mM, and the bottom phase 175 mM total surfactant, with X=0.27. Elemental analysis on samples without added salt gave erratic results, indicating problems in the physical separation of the phases. The cryoTEM survey of the separated phases revealed similar problems. Without salt both phases showed similar structures, whereas the top phase in the sample with added salt was void of structures larger than small micelles. The cryoTEM survey revealed a variety of structures being simultaneously present in most samples. A general trend with increasing X was an evolution from globular micelles, over disks, bands, branched bands transforming into sparse webs, perforated bilayer structures, and finally smooth bilayers. Increasing salt and total surfactant concentrations resulted in the emergence of structures with smaller mean curvature at lower X. Perforated bilayers were found in samples with 100 mM or less of added salt, and usually persisted to DTAB contents where precipitates appeared. The porous bilayers seemed to derive from sparse webs of band-like structures, and the hole size decreased with increasing X and salt concentration. Two types of recurrent

  18. Magnetism and electronic structure of (001)- and (111)-oriented LaTiO{sub 3} bilayers sandwiched in LaScO{sub 3} barriers

    SciTech Connect

    Weng, Yakui; Dong, Shuai

    2015-05-07

    In this study, the magnetism and electronic structure of LaTiO{sub 3} bilayers along both the (001) and (111) orientations are calculated using the density functional theory. The band insulator LaScO{sub 3} is chosen as the barrier layer and substrate to obtain the isolating LaTiO{sub 3} bilayer. For both the (001)- and (111)-oriented cases, LaTiO{sub 3} demonstrates the G-type antiferromagnetism as the ground state, similar to the bulk material. However, the electronic structure is significantly changed. The occupied bands of Ti are much narrower in the (111) case, giving a nearly flat band. As a result, the exchange coupling between nearest-neighbor Ti ions is reformed in these superlattices, which will affect the Néel temperature significantly.

  19. High extinction ratio and low transmission loss thin-film terahertz polarizer with a tunable bilayer metal wire-grid structure.

    PubMed

    Huang, Zhe; Parrott, Edward P J; Park, Hongkyu; Chan, Hau Ping; Pickwell-MacPherson, Emma

    2014-02-15

    A thin-film terahertz polarizer is proposed and realized via a tunable bilayer metal wire-grid structure to achieve high extinction ratios and good transmission. The polarizer is fabricated on top of a thin silica layer by standard micro-fabrication techniques to eliminate the multireflection effects. The tunable alignment of the bilayer aluminum-wire grid structure enables tailoring of the extinction ratio and transmission characteristics. Using terahertz time-domain spectroscopy (THz-TDS), a fabricated polarizer is characterized, with extinction ratios greater than 50 dB and transmission losses below 1 dB reported in the 0.2-1.1 THz frequency range. These characteristics can be improved by further tuning the polarizer parameters such as the pitch, metal film thickness, and lateral displacement.

  20. Amphiphilic lipids in solution: a simulational study of lipid bilayer formation

    NASA Astrophysics Data System (ADS)

    Vogel, Thomas; Landau, David P.; Gai, Lili; Maerzke, Katie A.; Iacovella, Christopher R.; McCabe, Clare M.; Cummings, Peter T.

    2013-03-01

    Amphiphilic molecules consisting of hydrophilic head and hydrophobic tail groups self-assemble into a wide variety of structures, such as bilayers (membranes), micelles, or vesicles (liposomes) when mixed with a suitable solvent. The understanding of this lipid self-assembly is essential for industrial, biological, or medical applications, but computer simulations are generally challenging due to the complex structure of the energy landscape. We show results for the lipid bilayer formation process obtained by newly developed parallel Wang-Landau Monte Carlo and statistical temperature molecular dynamics simulations. By applying those methods to a generic coarse-grained model for amphiphilic molecules in solution, we were able to obtain the thermodynamical data over the whole relevant temperature and energy range and to unravel the membrane formation process including all structural sub-transitions between different fluid and gel-phase bilayers. Research supported by NSF

  1. Structural damping using encapsulated shear thickening fluids

    NASA Astrophysics Data System (ADS)

    Soutrenon, Mathieu; Michaud, Véronique

    2012-04-01

    Smart structures with tunable damping and stiffness characteristics are of high interest to aerospace applications, but often require an external power source to be activated. This can be avoided by using highly concentrated silica suspensions, which exhibit a shear-thickening behavior, linked to a dramatic increase in viscous dissipation. These materials are however liquid at rest, and sensitive to humidity, so they are difficult to implement as such into structural applications. In the present work, highly concentrated solutions of monodisperse silica particles in PEG were selected for their strong thickening effect at rather low critical shear strain. Damping properties were characterized by measuring the energy dissipated per cycle at low frequency (<2Hz) during oscillatory tests using a rheometer. STF were impregnated in an open-cell foam scaffold and encapsulated into a RTV-silicone to produce patches that can be handled easily. Silicone also protects the STF against outgassing or humidity pickup. Experimental results show a simultaneous increase of stiffness and damping properties for theses patches at low frequencies and large strains. Damping is thus getting closer to the range of elastomeric commercial damping materials, possibly overtaking them in specific conditions.

  2. Fluid-structure Interaction Simulations of Deformable Soft Tissue

    NASA Astrophysics Data System (ADS)

    Borazjani, Iman

    2011-11-01

    Soft tissue interacts with the surrounding fluid environment in many biological and biomedical applications. Simulating such an interaction is quite challenging due to the large non-linear deformations of tissue, flow pulsatility, transition to turbulence, and non-linear fluid-structure interaction. We have extended our previous three-dimensional fluid-structure interaction (FSI) framework for rigid bodies (Borazjani, Ge, and Sotiropoulos, Journal of Computational Physics, 2008) to deformable soft tissue by coupling our incompressible Navier-Stokes solver for fluids with a non-linear large deformation finite element method for soft tissue. We use Fung-type constitutive law for the soft tissue that can capture the stress-strain behavior of the tissue. The FSI solver adopts a strongly-coupled partitioned approach that is stabilized with under-relaxation and Aitken acceleration technique. We validate our solvers against the experimental data for tissue valves and elastic tubes. We show the capabilities of our solver by simulating the fluid-structure interaction of tissue valves implanted in the aortic positions and elastic collapsible tubes. This work was partly supported by the Center for Computational Research at the University at Buffalo.

  3. Structural features of glycosyltransferases synthesizing major bilayer and nonbilayer-prone membrane lipids in Acholeplasma laidlawii and Streptococcus pneumoniae.

    PubMed

    Edman, Maria; Berg, Stefan; Storm, Patrik; Wikström, Malin; Vikström, Susanne; Ohman, Anders; Wieslander, Ake

    2003-03-07

    In membranes of Acholeplasma laidlawii two consecutively acting glucosyltransferases, the (i) alpha-monoglucosyldiacylglycerol (MGlcDAG) synthase (alMGS) (EC ) and the (ii) alpha-diglucosyl-DAG (DGlcDAG) synthase (alDGS) (EC ), are involved in maintaining (i) a certain anionic lipid surface charge density and (ii) constant nonbilayer/bilayer conditions (curvature packing stress), respectively. Cloning of the alDGS gene revealed related uncharacterized sequence analogs especially in several Gram-positive pathogens, thermophiles and archaea, where the encoded enzyme function of a potential Streptococcus pneumoniae DGS gene (cpoA) was verified. A strong stimulation of alDGS by phosphatidylglycerol (PG), cardiolipin, or nonbilayer-prone 1,3-DAG was observed, while only PG stimulated CpoA. Several secondary structure prediction and fold recognition methods were used together with SWISS-MODEL to build three-dimensional model structures for three MGS and two DGS lipid glycosyltransferases. Two Escherichia coli proteins with known structures were identified as the best templates, the membrane surface-associated two-domain glycosyltransferase MurG and the soluble GlcNAc epimerase. Differences in electrostatic surface potential between the different models and their individual domains suggest that electrostatic interactions play a role for the association to membranes. Further support for this was obtained when hybrids of the N- and C-domain, and full size alMGS with green fluorescent protein were localized to different regions of the E. coli inner membrane and cytoplasm in vivo. In conclusion, it is proposed that the varying abilities to bind, and sense lipid charge and curvature stress, are governed by typical differences in charge (pI values), amphiphilicity, and hydrophobicity for the N- and (catalytic) C-domains of these structurally similar membrane-associated enzymes.

  4. Mitral valve dynamics in structural and fluid-structure interaction models.

    PubMed

    Lau, K D; Diaz, V; Scambler, P; Burriesci, G

    2010-11-01

    Modelling and simulation of heart valves is a challenging biomechanical problem due to anatomical variability, pulsatile physiological pressure loads and 3D anisotropic material behaviour. Current valvular models based on the finite element method can be divided into: those that do model the interaction between the blood and the valve (fluid-structure interaction or 'wet' models) and those that do not (structural models or 'dry' models). Here an anatomically sized model of the mitral valve has been used to compare the difference between structural and fluid-structure interaction techniques in two separately simulated scenarios: valve closure and a cardiac cycle. Using fluid-structure interaction, the valve has been modelled separately in a straight tubular volume and in a U-shaped ventricular volume, in order to analyse the difference in the coupled fluid and structural dynamics between the two geometries. The results of the structural and fluid-structure interaction models have shown that the stress distribution in the closure simulation is similar in all the models, but the magnitude and closed configuration differ. In the cardiac cycle simulation significant differences in the valvular dynamics were found between the structural and fluid-structure interaction models due to difference in applied pressure loads. Comparison of the fluid domains of the fluid-structure interaction models have shown that the ventricular geometry generates slower fluid velocity with increased vorticity compared to the tubular geometry. In conclusion, structural heart valve models are suitable for simulation of static configurations (opened or closed valves), but in order to simulate full dynamic behaviour fluid-structure interaction models are required.

  5. CO2-Selective Absorbents in Air: Reverse Lipid Bilayer Structure Forming Neutral Carbamic Acid in Water without Hydration.

    PubMed

    Inagaki, Fuyuhiko; Matsumoto, Chiaki; Iwata, Takashi; Mukai, Chisato

    2017-04-05

    Emission gas and air contain not only CO2 but also plentiful moisture, making it difficult to achieve selective CO2 absorption without hydration. To generate absorbed CO2 (wet CO2) under heating, the need for external energy to release the absorbed water has been among the most serious problems in the fields of carbon dioxide capture and storage (CCS) and direct air capture (DAC). We found that the introduction of the hydrophobic phenyl group into alkylamines of CO2 absorbents improved the absorption selectivity between CO2 and water. Furthermore, ortho-, meta-, and para-xylylenediamines (OXDA, MXDA, PXDA, respectively) absorbed only CO2 in air without any hydration. Notably, MXDA·CO2 was formed as an anhydrous carbamic acid even in water, presumably because it was covered with hydrophobic phenyl groups, which induces a reverse lipid bilayer structure. Dry CO2 was obtained from heating MXDA·CO2 at 103-120 °C, which was revealed to involve chemically the Grignard reaction to form the resulting carboxylic acids in high yields.

  6. Improved fluid-structure coupling. [BWR

    SciTech Connect

    McMaster, W.H.; Gong, E.Y.; Landram, C.S.

    1981-01-01

    In the computer code PELE-IC, an incompressible Eulerian hydrodynamic algorithm was coupled to a Lagrangian finite element shell algorithm for the analysis of pressure suppression in boiling water reactors. This effort also required the development of a free surface algorithm capable of handling expanding gas bubbles. These algorithms have been improved to strengthen the coupling and to add the capability for following the more complex free surfaces resulting from steam condensation. These improvements have also permitted more economical 2D calculations and have made it feasible to develop a 3D version. A compressible option using the acoustic approximation has also been added, furthering the usefulness of the code. The coupling improvements were made in three areas which are identified as (1) preferential coupling, (2) merged cell coupling, and (3) free surface-structure coupling, and are described. These algorithms have been additionally implemented in a three dimensional version of the code called PELE3D. This version has a free surface capability to follow expanding and contracting bubbles and is coupled to a curved rigid surface.

  7. Stability and permeability of amphiphile bilayers.

    PubMed

    Exerowa, D; Kashchiev, D; Platikanov, D

    1992-05-30

    investigating short-range forces in biological structures, the interaction between membranes and cell fusion. It is also shown that the foam bilayer is a suitable model for studying the alveolar surface and stability. On that basis a clinical diagnostic method is developed for assessment of the human foetal lung maturity.

  8. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  9. Decay of dipolar vortex structures in a stratified fluid

    NASA Astrophysics Data System (ADS)

    Flór, J. B.; van Heijst, G. J. F.; Delfos, R.

    1995-02-01

    In this paper the viscous decay of dipolar vortex structures in a linearly stratified fluid is investigated experimentally, and a comparison of the experimental results with simple theoretical models is made. The dipoles are generated by a pulsed horizontal injection of fluid. In a related experimental study by Flór and van Heijst [J. Fluid Mech. 279, 101 (1994)], it was shown that, after the emergence of the pancake-shaped vortex structure, the flow is quasi-two-dimensional and decays due to the vertical diffusion of vorticity and entrainment of ambient irrotational fluid. This results in an expansion of the vortex structure. Two decay models with the horizontal flow based on the viscously decaying Lamb-Chaplygin dipole, are presented. In a first model, the thickness and radius of the dipole are assumed constant, and in a second model also the increasing thickness of the vortex structure is taken into account. The models are compared with experimental data obtained from flow visualizations and from digital analysis of particle-streak photographs. Although both models neglect entrainment and the decay is modeled by diffusion only, a reasonable agreement with the experiments is obtained.

  10. Children's Working Memory: Its Structure and Relationship to Fluid Intelligence

    ERIC Educational Resources Information Center

    Hornung, Caroline; Brunner, Martin; Reuter, Robert A. P.; Martin, Romain

    2011-01-01

    Working memory (WM) has been predominantly studied in adults. The insights provided by these studies have led to the development of competing theories on the structure of WM and conflicting conclusions on how strongly WM components are related to higher order thinking skills such as fluid intelligence. However, it remains unclear whether and to…

  11. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization

    NASA Astrophysics Data System (ADS)

    Abou Najm, Majdi; Atallah, Nabil; Selker, John; Roques, Clément; Stewart, Ryan; Rupp, David; Saad, George; El-Fadel, Mutasem

    2016-04-01

    Classic porous media characterization relies on typical infiltration experiments with Newtonian fluids (i.e., water) to estimate hydraulic conductivity. However, such experiments are generally not able to discern important characteristics such as pore size distribution or pore structure. We show that introducing non-Newtonian fluids provides additional unique flow signatures that can be used for improved pore structure characterization. We present a new method that transforms results of N infiltration experiments using water and N-1 non-Newtonian solutions into a system of equations that yields N representative radii (Ri) and their corresponding percent contribution to flow (wi). Those radii and weights are optimized in terms of flow and porosity to represent the functional hydraulic behavior of real porous media. The method also allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation revealed the ability of the proposed method to represent the water retention and functional infiltration behavior of real soils. The experimental results showed the ability of such fluids to outsmart Newtonian fluids and infer pore size distribution and unsaturated behavior using simple saturated experiments. Specifically, we demonstrate using synthetic porous media composed of different combinations of sizes and numbers of capillary tubes that the use of different non-Newtonian fluids enables the prediction of the pore structure. The results advance the knowledge towards conceptualizing the complexity of porous media and can potentially impact applications in fields like irrigation efficiencies, vadose zone hydrology, soil-root-plant continuum, carbon sequestration into geologic formations, soil remediation, petroleum reservoir engineering, oil exploration and groundwater modeling.

  12. How lidocaine influences the bilayer thickness and bending elasticity of biomembranes

    NASA Astrophysics Data System (ADS)

    Yi, Zheng; Nagao, Michihiro; Bossev, Dobrin P.

    2010-11-01

    We have studied how local anesthetics influence the structural and dynamical properties of model bio-membranes. The measurements of small-angle neutron scattering have been performed on 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) unilamellar vesicles with different concentrations of lidocaine in D2O to determine the bilayer thickness as a function of the lidocaine concentration. The neutron-spin echo spectroscopy (NSE) has been used to study the influence of lidocaine on the bending elasticity of DMPC bilayers in fluid crystal phase (Lα) and the ripple gel (Pβ') phase.

  13. Structure and homogeneity of pseudo-physiological phospholipid bilayers and their deposition characteristics on carboxylic acid terminated self-assembled monolayers.

    PubMed

    Mechler, Adam; Praporski, Slavica; Piantavigna, Stefania; Heaton, Steven M; Hall, Kristopher N; Aguilar, Marie-Isabel; Martin, Lisandra L

    2009-02-01

    Supported phospholipid bilayers are frequently used to establish a pseudo-physiological environment required for the study of protein function or the design of enzyme-based biosensors and biocatalytic reactors. These membranes are deposited from bilayer vesicles (liposomes) that rupture and fuse into a planar membrane upon adhesion to a surface. However, the morphology and homogeneity of the resulting layer is affected by the characteristics of the precursor liposome suspension and the substrate. Here we show that two distinct liposome populations contribute to membrane formation--equilibrium liposomes and small unilamellar vesicles. Liposome deposition onto carboxylic acid terminated self-assembled monolayers resulted in planar mono- and multilayer, vesicular and composite membranes, as a function of liposome size and composition. Quartz crystal microbalance data provided estimates for layer thicknesses and sheer moduli and were used for classification of the final structure. Finally, atomic force microscopy data illustrated the inherently inhomogeneous and dynamic nature of these membranes.

  14. Study of structure of the TiO{sub 2}–MoO{sub 3} bilayer films by Raman spectroscopy

    SciTech Connect

    Santos, Elias de Barros; Sigoli, Fernando Aparecido; Mazali, Italo Odone

    2014-12-15

    Highlights: • TiO{sub 2}–MoO{sub 3} bilayer thin films were easily prepared by dip-coating technique. • Ti and Mo metallo-organic compounds were used as source of its respective oxide. • TiO{sub 2} in anatase phase and orthorhombic phase of α-MoO{sub 3} were identified. • The bilayer structure was investigated by Raman spectroscopy. - Abstract: In this work, TiO{sub 2}–MoO{sub 3} films were easily prepared by dip-coating technique and metallo-organic decomposition process (MOD). Raman analyses indicate the formation of TiO{sub 2} in anatase phase and orthorhombic phase of α-MoO{sub 3}. It was observed that the Raman bands intensities attributed to TiO{sub 2} and MoO{sub 3} oxides were dependent on the number of decomposition–deposition cycles (DDC). The different number of DDC generates films with different thicknesses and the Raman signal was sensitive to this variation. Raman analyses provided qualitative information about the bilayer structure of the bi-component TiO{sub 2}–MoO{sub 3} films, which was confirmed by scanning electron microscopy. In this direction, the dip-coating technique and MOD process can be an efficient strategy to facile preparation of many samples to be used in applications.

  15. Structural aspects of magnetic fluid stabilization in aqueous agarose solutions

    NASA Astrophysics Data System (ADS)

    Nagornyi, A. V.; Petrenko, V. I.; Avdeev, M. V.; Yelenich, O. V.; Solopan, S. O.; Belous, A. G.; Gruzinov, A. Yu.; Ivankov, O. I.; Bulavin, L. A.

    2017-06-01

    Structure characterization of magnetic fluids (MFs) synthesized by three different methods in aqueous solutions of agarose was done by means of small-angle neutron (SANS) and synchrotron X-ray scattering (SAXS). The differences in the complex aggregation observed in the studied magnetic fluids were related to different stabilizing procedures of the three kinds of MFs. The results of the analysis of the scattering (mean size of single polydisperse magnetic particles, fractal dimensions of the aggregates) are consistent with the data of transmission electron microscopy (TEM).

  16. Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order.

    PubMed

    Chiantia, Salvatore; London, Erwin

    2012-12-05

    A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholine (PC) in the inner leaflet and sphingomyelin (SM) in the outer leaflet. The coupling of both lateral diffusion and membrane order was monitored as a function of PC and SM acyl chain structure. The presence in the outer leaflet of brain SM, which decreased outer-leaflet lateral diffusion, had little effect upon lateral diffusion in inner leaflets composed of dioleoyl PC (i.e., diffusion was only weakly coupled in the two leaflets) but did greatly reduce lateral diffusion in inner leaflets composed of PC with one saturated and one oleoyl acyl chain (i.e., diffusion was strongly coupled in these cases). In addition, reduced outer-leaflet diffusion upon introduction of outer-leaflet milk SM or a synthetic C24:0 SM, both of which have long interdigitating acyl chains, also greatly reduce diffusion of inner leaflets composed of dioleoyl PC, indicative of strong coupling. Strikingly, several assays showed that the ordering of the outer leaflet induced by the presence of SM was not reflected in increased lipid order in the inner leaflet, i.e., there was no detectable coupling between inner and outer leaflet membrane order. We propose a model for how lateral diffusion can be coupled in opposite leaflets and discuss how this might impact membrane function.

  17. Particle trapping and impedance measurement using bilayer electrodes integrated with microcavity structure

    NASA Astrophysics Data System (ADS)

    Chen, Guan-Ting; Liu, Chia-Feng; Jang, Ling-Sheng; Li, Shun-Lai; Wang, Min-Haw

    2017-03-01

    Traditional planar electrodes for single-particle impedance measurement have difficulty in trapping and positioning particles. This paper proposes a microfluidic device for single-particle trapping and impedance measurement with a microcavity configuration. A carbon dioxide (CO2) laser technique was used to fabricate the microcavity structure, which can capture 15 µm diameter particles without requiring additional trapping structures. The measurement electrodes on both sides of the microcavity were fabricated using electroplating and deposition techniques. The advantages of the microcavity structure and electrodes are discussed. The bottom electrode spreads into the microcavity to increase measurement sensitivity and shrink the exit aperture to around 10 µm for particle trapping. The experimental results show that the device successfully captured particles and distinguished the impedance of a particle from that of phosphate-buffered saline solution.

  18. Finite element solution of transient fluid-structure interaction problems

    NASA Technical Reports Server (NTRS)

    Everstine, Gordon C.; Cheng, Raymond S.; Hambric, Stephen A.

    1991-01-01

    A finite element approach using NASTRAN is developed for solving time-dependent fluid-structure interaction problems, with emphasis on the transient scattering of acoustic waves from submerged elastic structures. Finite elements are used for modeling both structure and fluid domains to facilitate the graphical display of the wave motion through both media. For the liquid, the use of velocity potential as the fundamental unknown results in a symmetric matrix equation. The approach is illustrated for the problem of transient scattering from a submerged elastic spherical shell subjected to an incident tone burst. The use of an analogy between the equations of elasticity and the wave equation of acoustics, a necessary ingredient to the procedure, is summarized.

  19. Fluid-thermal-structural study of aerodynamically heated leading edges

    NASA Technical Reports Server (NTRS)

    Deuchamphai, Pramote; Thornton, Earl A.; Wieting, Allan R.

    1988-01-01

    A finite element approach for integrated fluid-thermal-structural analysis of aerodynamically heated leading edges is presented. The Navier-Stokes equations for high speed compressible flow, the energy equation, and the quasi-static equilibrium equations for the leading edge are solved using a single finite element approach in one integrated, vectorized computer program called LIFTS. The fluid-thermal-structural coupling is studied for Mach 6.47 flow over a 3-in diam cylinder for which the flow behavior and the aerothermal loads are calibrated by experimental data. Issues of the thermal-structural response are studied for hydrogen-cooled, super thermal conducting leading edges subjected to intense aerodynamic heating.

  20. Adaptivity and smart algorithms for fluid-structure interaction

    NASA Technical Reports Server (NTRS)

    Oden, J. Tinsley

    1990-01-01

    This paper reviews new approaches in CFD which have the potential for significantly increasing current capabilities of modeling complex flow phenomena and of treating difficult problems in fluid-structure interaction. These approaches are based on the notions of adaptive methods and smart algorithms, which use instantaneous measures of the quality and other features of the numerical flowfields as a basis for making changes in the structure of the computational grid and of algorithms designed to function on the grid. The application of these new techniques to several problem classes are addressed, including problems with moving boundaries, fluid-structure interaction in high-speed turbine flows, flow in domains with receding boundaries, and related problems.

  1. High frequency flow-structural interaction in dense subsonic fluids

    NASA Technical Reports Server (NTRS)

    Liu, Baw-Lin; Ofarrell, J. M.

    1995-01-01

    Prediction of the detailed dynamic behavior in rocket propellant feed systems and engines and other such high-energy fluid systems requires precise analysis to assure structural performance. Designs sometimes require placement of bluff bodies in a flow passage. Additionally, there are flexibilities in ducts, liners, and piping systems. A design handbook and interactive data base have been developed for assessing flow/structural interactions to be used as a tool in design and development, to evaluate applicable geometries before problems develop, or to eliminate or minimize problems with existing hardware. This is a compilation of analytical/empirical data and techniques to evaluate detailed dynamic characteristics of both the fluid and structures. These techniques have direct applicability to rocket engine internal flow passages, hot gas drive systems, and vehicle propellant feed systems. Organization of the handbook is by basic geometries for estimating Strouhal numbers, added mass effects, mode shapes for various end constraints, critical onset flow conditions, and possible structural response amplitudes. Emphasis is on dense fluids and high structural loading potential for fatigue at low subsonic flow speeds where high-frequency excitations are possible. Avoidance and corrective measure illustrations are presented together with analytical curve fits for predictions compiled from a comprehensive data base.

  2. α-Synuclein interactions with phospholipid model membranes: Key roles for electrostatic interactions and lipid-bilayer structure.

    PubMed

    Pirc, Katja; Ulrih, Nataša Poklar

    2015-10-01

    α-Synuclein is a small presynaptic protein that is critically implicated in the onset of Parkinson's disease and other neurodegenerative disorders. It has been assumed that the pathogenesis of α-synuclein is associated with its aggregation, while for its physiological function, binding of α-synuclein to the synaptic vesicle membrane appears to be most important. The present study investigated the mechanism of α-synuclein binding to the lipid membrane. Upon binding to negatively charged small unilamellar vesicles consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol in the liquid-crystalline state, α-synuclein undergoes conformational transition from its native unfolded form to an α-helical structure. The positively charged N-terminal part of α-synuclein is likely to be involved in interactions with the negatively charged lipid surface. α-Synuclein did not associate with vesicles consisting of the zwitterionic (neutral) lipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. The data obtained by circular dichroism spectroscopy, fluorescence anisotropy measurements, differential scanning calorimetry, and calcein efflux assays indicate that in addition to electrostatic interactions, hydrophobic interactions are important in the association of α-synuclein with membranes. The mechanism of α-synuclein binding to lipid membranes is primarily dependent on the surface charge density of the lipid bilayer and the phase state of the lipids. We propose that α-synuclein has a lipid ordering effect and thermally stabilises vesicles. Copyright © 2015. Published by Elsevier B.V.

  3. Simulating Pediatric Ventricular Assist Device Operation Using Fluid Structure Interaction

    NASA Astrophysics Data System (ADS)

    Long, Chris; Bazilevs, Yuri; Marsden, Alison

    2012-11-01

    Ventricular Assist Devices (VADs) provide mechanical circulatory support to patients in heart failure. They are primarily used to extend life until cardiac transplant, but also show promise as a ``bridge-to-recovery'' device in pediatric patients. Commercially available pediatric pumps are pulsatile displacement pumps, with two distinct chambers for air and blood separated by a thin, flexible membrane. The air chamber pneumatically drives the membrane, which drives blood through the other chamber via displacement. The primary risk factor associated with these devices is stroke or embolism due to thrombogenesis in the blood chamber, occurring in as many as 40% of patients. Our goal is to perform simulations that accurately model the hemodynamics of the device, as well as the non-linear membrane buckling. We apply a finite-element based fluid solver, with an Arbitrary Lagrangian-Eulerian (ALE) framework to account for mesh motion. Isogeometric Analysis with a Kirchhoff-Love shell formulation is used on the membrane, and two distinct fluid subdomains are used for the air and blood chambers. The Fluid Structure Interaction (FSI) problem is solved simultaneously, using a Matrix Free method to model the interactions at the fluid-structure boundary. Methods and results are presented.

  4. Fluid Structure Interaction Simulations of Pediatric Ventricular Assist Device Operation

    NASA Astrophysics Data System (ADS)

    Long, Chris; Marsden, Alison; Bazilevs, Yuri

    2011-11-01

    Pediatric ventricular assist devices (PVADs) are used for mechanical circulatory support in children with failing hearts. They can be used to allow the heart to heal naturally or to extend the life of the patient until transplant. A PVAD has two chambers, blood and air, separated by a flexible membrane. The air chamber is pressurized, which drives the membrane and pumps the blood. The primary risk associated with these devices is stroke or embolism from thrombogenesis. Simulation of these devices is difficult due to a complex coupling of two fluid domains and a thin membrane, requiring fluid-structure interaction modeling. The goal of this work is to accurately simulate the hemodynamics of a PVAD. We perform FSI simulations using an Arbitrary Lagrangian-Eulerian (ALE) finite element framework to account for large motions of the membrane and the fluid domains. The air, blood, and membrane are meshed as distinct subdomains, and a method for non-matched discretizations at the fluid-structure interface is presented. The use of isogeometric analysis to model the membrane mechanics is also discussed, and the results of simulations are presented.

  5. Reduced order modeling of fluid/structure interaction.

    SciTech Connect

    Barone, Matthew Franklin; Kalashnikova, Irina; Segalman, Daniel Joseph; Brake, Matthew Robert

    2009-11-01

    This report describes work performed from October 2007 through September 2009 under the Sandia Laboratory Directed Research and Development project titled 'Reduced Order Modeling of Fluid/Structure Interaction.' This project addresses fundamental aspects of techniques for construction of predictive Reduced Order Models (ROMs). A ROM is defined as a model, derived from a sequence of high-fidelity simulations, that preserves the essential physics and predictive capability of the original simulations but at a much lower computational cost. Techniques are developed for construction of provably stable linear Galerkin projection ROMs for compressible fluid flow, including a method for enforcing boundary conditions that preserves numerical stability. A convergence proof and error estimates are given for this class of ROM, and the method is demonstrated on a series of model problems. A reduced order method, based on the method of quadratic components, for solving the von Karman nonlinear plate equations is developed and tested. This method is applied to the problem of nonlinear limit cycle oscillations encountered when the plate interacts with an adjacent supersonic flow. A stability-preserving method for coupling the linear fluid ROM with the structural dynamics model for the elastic plate is constructed and tested. Methods for constructing efficient ROMs for nonlinear fluid equations are developed and tested on a one-dimensional convection-diffusion-reaction equation. These methods are combined with a symmetrization approach to construct a ROM technique for application to the compressible Navier-Stokes equations.

  6. A symmetric modal formulation of fluid-structure interaction, including a static approximation to higher order fluid modes

    NASA Technical Reports Server (NTRS)

    Macneal, R. H.; Citerley, R.; Chargin, M.

    1980-01-01

    A method of fluid-structure coupling which provides symmetrical matrix equations of standard form solved by existing finite element computer programs is presented. The method postulates that the uncoupled vibration modes of the fluid or the structure be calculated before the coupled analysis. A numerical solution of vibration modes in an axisymmetric container demonstrated that a static approximation to higher order fluid modes can improve the accuracy of dynamic response computations using modal methods.

  7. Application of integrated fluid-thermal-structural analysis methods

    NASA Technical Reports Server (NTRS)

    Wieting, Allan R.; Dechaumphai, Pramote; Bey, Kim S.; Thornton, Earl A.; Morgan, Ken

    1988-01-01

    Hypersonic vehicles operate in a hostile aerothermal environment which has a significant impact on their aerothermostructural performance. Significant coupling occurs between the aerodynamic flow field, structural heat transfer, and structural response creating a multidisciplinary interaction. Interfacing state-of-the-art disciplinary analysis methods is not efficient, hence interdisciplinary analysis methods integrated into a single aerothermostructural analyzer are needed. The NASA Langley Research Center is developing such methods in an analyzer called LIFTS (Langley Integrated Fluid-Thermal-Structural) analyzer. The evolution and status of LIFTS is reviewed and illustrated through applications.

  8. Application of integrated fluid-thermal structural analysis methods

    NASA Technical Reports Server (NTRS)

    Wieting, Allan R.; Dechaumphai, Pramote; Bey, Kim S.; Thornton, Earl A.; Morgan, Ken

    1988-01-01

    Hypersonic vehicles operate in a hostile aerothermal environment which has a significant impact on their aerothermostructural performance. Significant coupling occurs between the aerodynamic flow field, structural heat transfer, and structural response creating a multidisciplinary interaction. Interfacing state-of-the-art disciplinary analysis methods are not efficient, hence interdisciplinary analysis methods integrated into a single aerothermostructural analyzer are needed. The NASA Langley Research Center is developing such methods in an analyzer called LIFTS (Langley Integrated Fluid-Thermal-Structural) analyzer. The evolution and status of LIFTS is reviewed and illustrated through applications.

  9. Parallel adaptive fluid-structure interaction simulation of explosions impacting on building structures

    SciTech Connect

    Deiterding, Ralf; Wood, Stephen L

    2013-01-01

    We pursue a level set approach to couple an Eulerian shock-capturing fluid solver with space-time refinement to an explicit solid dynamics solver for large deformations and fracture. The coupling algorithms considering recursively finer fluid time steps as well as overlapping solver updates are discussed in detail. Our ideas are implemented in the AMROC adaptive fluid solver framework and are used for effective fluid-structure coupling to the general purpose solid dynamics code DYNA3D. Beside simulations verifying the coupled fluid-structure solver and assessing its parallel scalability, the detailed structural analysis of a reinforced concrete column under blast loading and the simulation of a prototypical blast explosion in a realistic multistory building are presented.

  10. Tuning structure and roughness in exchange biased NiO/permalloy bilayers

    NASA Astrophysics Data System (ADS)

    Thomas, Luc; Negulescu, Béatrice; Dumont, Yves; Tessier, Michel; Keller, Niels; Wack, André; Guyot, Marcel

    2003-05-01

    Polycrystalline NiO thin films have been grown by pulsed laser deposition on quartz substrates. These films exhibit a strong texture, which can be tuned by changing deposition parameters such as substrate temperature or oxygen partial pressure. By varying the deposition temperature from room temperature up to 900 °C, (220), (111), and (200) textured films are prepared. In the temperature zones separating these orientations, competition between different growth directions leads to smaller crystallites, characterized by broader diffraction lines. Surface roughness measured by atomic force microscopy is strongly correlated with these structural features. Roughness is minimum for highly textured samples (about 7Å for 500 Å thick films), and it exhibits two peaks in the intermediate zones, with maximum values of about 40 Å. In order to correlate exchange bias with these structural features, 100 Å thick FeNi layers were deposited by rf sputtering on top of the 500 Å thick NiO films. Hysteresis loops were measured at 10 K by superconducting quantum interference device magnetometry after the samples were cooled in a 100 Oe magnetic field. Exchange bias is maximum for (111) oriented samples. No clear correlation between exchange bias and surface roughness is observed at low temperature. Exchange bias temperature dependence strongly depends upon NiO films deposition temperature. The blocking temperature, for which the exchange bias vanishes, varies between 150 K for (220) oriented samples and 250 K for (111) textured samples, and it exceeds room temperature for (200) films.

  11. Bilayer Membrane Modulation of Membrane Type 1 Matrix Metalloproteinase (MT1-MMP) Structure and Proteolytic Activity

    PubMed Central

    Cerofolini, Linda; Amar, Sabrina; Lauer, Janelle L.; Martelli, Tommaso; Fragai, Marco; Luchinat, Claudio; Fields, Gregg B.

    2016-01-01

    Cell surface proteolysis is an integral yet poorly understood physiological process. The present study has examined how the pericellular collagenase membrane-type 1 matrix metalloproteinase (MT1-MMP) and membrane-mimicking environments interplay in substrate binding and processing. NMR derived structural models indicate that MT1-MMP transiently associates with bicelles and cells through distinct residues in blades III and IV of its hemopexin-like domain, while binding of collagen-like triple-helices occurs within blades I and II of this domain. Examination of simultaneous membrane interaction and triple-helix binding revealed a possible regulation of proteolysis due to steric effects of the membrane. At bicelle concentrations of 1%, enzymatic activity towards triple-helices was increased 1.5-fold. A single mutation in the putative membrane interaction region of MT1-MMP (Ser466Pro) resulted in lower enzyme activation by bicelles. An initial structural framework has thus been developed to define the role(s) of cell membranes in modulating proteolysis. PMID:27405411

  12. The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter.

    PubMed

    Zoghbi, Maria E; Cooper, Rebecca S; Altenberg, Guillermo A

    2016-02-26

    ATP-binding cassette exporters use the energy of ATP hydrolysis to transport substrates across membranes by switching between inward- and outward-facing conformations. Essentially all structural studies of these proteins have been performed with the proteins in detergent micelles, locked in specific conformations and/or at low temperature. Here, we used luminescence resonance energy transfer spectroscopy to study the prototypical ATP-binding cassette exporter MsbA reconstituted in nanodiscs at 37 °C while it performs ATP hydrolysis. We found major differences when comparing MsbA in these native-like conditions with double electron-electron resonance data and the crystal structure of MsbA in the open inward-facing conformation. The most striking differences include a significantly smaller separation between the nucleotide-binding domains and a larger fraction of molecules with associated nucleotide-binding domains in the nucleotide-free apo state. These studies stress the importance of studying membrane proteins in an environment that approaches physiological conditions.

  13. Including fluid shear viscosity in a structural acoustic finite element model using a scalar fluid representation

    PubMed Central

    Cheng, Lei; Li, Yizeng; Grosh, Karl

    2013-01-01

    An approximate boundary condition is developed in this paper to model fluid shear viscosity at boundaries of coupled fluid-structure system. The effect of shear viscosity is approximated by a correction term to the inviscid boundary condition, written in terms of second order in-plane derivatives of pressure. Both thin and thick viscous boundary layer approximations are formulated; the latter subsumes the former. These approximations are used to develop a variational formation, upon which a viscous finite element method (FEM) model is based, requiring only minor modifications to the boundary integral contributions of an existing inviscid FEM model. Since this FEM formulation has only one degree of freedom for pressure, it holds a great computational advantage over the conventional viscous FEM formulation which requires discretization of the full set of linearized Navier-Stokes equations. The results from thick viscous boundary layer approximation are found to be in good agreement with the prediction from a Navier-Stokes model. When applicable, thin viscous boundary layer approximation also gives accurate results with computational simplicity compared to the thick boundary layer formulation. Direct comparison of simulation results using the boundary layer approximations and a full, linearized Navier-Stokes model are made and used to evaluate the accuracy of the approximate technique. Guidelines are given for the parameter ranges over which the accurate application of the thick and thin boundary approximations can be used for a fluid-structure interaction problem. PMID:23729844

  14. A fluid-structure interaction solver for the fluid flow through reed type valves

    NASA Astrophysics Data System (ADS)

    González, I.; Naseri, A.; Rigola, J.; Pérez-Segarra, C. D.; Oliva, A.

    2017-08-01

    Suction and discharge processes with self actuated valves have a major influence in efficiency and reliability of hermetic reciprocating compressors. Understanding the operation completely in order to enhance compressor’s design needs precise prediction of the fluid-structure interaction complexities involved in these processes. This paper presents a comprehensive description of a numerical methodology to account for the coupled behaviour of a reed valve and a turbulent flow. The method is based on a partitioned semi-implicit scheme that only strongly couples the fluid pressure term to the structural solver. A three-dimensional CFD analysis with LES turbulence modelling is used for the flow while a combination of plate theory and mode summation method is used for the solid. The dynamically changing domains are tackled by means of lagrangian and arbitrary lagrangian-eulerian approaches for the solid and the fluid, respectively. The whole model is compared with experimental data at Reynolds number 10, 000, showing good agreement in lift amplitude and deformation fluctuations. Finally, as an illustrative case, results regarding lift, pressures, force and effective areas are compared with those of a valve with wider gland.

  15. Effects of annealing time on the structure, morphology, and stress of gold-chromium bilayer film

    NASA Astrophysics Data System (ADS)

    Zhang, Hong; Jin, Yun-Xia; Wang, Hu; Kong, Fang-Yu; Huang, Hao-Peng; Cui, Yun

    2016-10-01

    In this work, a 200-nm-thick gold film with a 10-nm-thick chromium layer used as an adhesive layer is fabricated on fused silica by the electron beam evaporation method. The effects of annealing time at 300 °C on the structure, morphology and stress of the film are studied. We find that chromium could diffuse to the surface of the film by formatting a solid solution with gold during annealing. Meanwhile, chromium is oxidized on the surface and diffused downward along the grain grooves in the gold film. The various operant mechanisms that change the residual stresses of gold films for different annealing times are discussed. Project supported by the National Natural Science Foundation of China (Grant No. 61405225).

  16. Effect of biocompatible polymers on the structural integrity of lipid bilayers under external stimuli

    NASA Astrophysics Data System (ADS)

    Wang, Jia-Yu; Kausik, Ravinath; Chen, Chi-Yuan; Han, Song-I.; Marks, Jeremy; Lee, Ka Yee

    2010-03-01

    Cell membrane dysfunction due to loss of structural integrity is the pathology of tissue death in trauma and common diseases. It is now established that certain biocompatible polymers, such as Poloxamer 188, Poloxamine 1107 and polyethylene glycol (PEG), are effective in sealing of injured cell membranes, and able to prevent acute necrosis. Despite these broad applications of these polymers for human health, the fundamental mechanisms by which these polymers interact with cell membranes are still under debate. Here, the effects of a group of biocompatible polymers on phospholipid membrane integrity under osmotic and oxidative stress were explored using giant unilamellar vesicles as model cell membranes. Our results suggest that the adsorption of the polymers on the membrane surface is responsible for the cell membrane resealing process due to its capability of slowing down the surface hydration dynamics.

  17. Laterally structured ripple and square phases with one and two dimensional thickness modulations in a model bilayer system.

    PubMed

    Debnath, Ananya; Thakkar, Foram M; Maiti, Prabal K; Kumaran, V; Ayappa, K G

    2014-10-14

    Molecular dynamics simulations of bilayers in a surfactant/co-surfactant/water system with explicit solvent molecules show formation of topologically distinct gel phases depending upon the bilayer composition. At low temperatures, the bilayers transform from the tilted gel phase, Lβ', to the one dimensional (1D) rippled, Pβ' phase as the surfactant concentration is increased. More interestingly, we observe a two dimensional (2D) square phase at higher surfactant concentration which, upon heating, transforms to the gel Lβ' phase. The thickness modulations in the 1D rippled and square phases are asymmetric in two surfactant leaflets and the bilayer thickness varies by a factor of ∼2 between maximum and minimum. The 1D ripple consists of a thinner interdigitated region of smaller extent alternating with a thicker non-interdigitated region. The 2D ripple phase is made up of two superimposed square lattices of maximum and minimum thicknesses with molecules of high tilt forming a square lattice translated from the lattice formed with the thickness minima. Using Voronoi diagrams we analyze the intricate interplay between the area-per-head-group, height modulations and chain tilt for the different ripple symmetries. Our simulations indicate that composition plays an important role in controlling the formation of low temperature gel phase symmetries and rippling accommodates the increased area-per-head-group of the surfactant molecules.

  18. The effects of annealing temperature on structure and photoluminescence of SiC/AlN bilayer thin film

    NASA Astrophysics Data System (ADS)

    He, Xiao-xiong; Li, He-qin; Fan, Wen-bin; Do, Zhi

    2010-10-01

    The SiC/AlN bilayer thin films were grown by RF magnetron sputtering on the silicon(100)substrate, then were annealed from 500°C to 1000°C through the nitrogen gas. The optimum synthetic process was obtained, that is, the gas pressure was 0.5Pa, the flux of Ar was 60sccm, the sputtering power of SiC target was 150W for 1.5hr, while the sputtering power of pure Al target was 100W for 1hr, and the ratio of Ar to N2 was 2:1. Next the XRD, AFM and photoluminescence (PL) spectra of these films were measured with D/Max-γB X-ray diffraction and FL-4500 Fluorometric meter. Two PL emission peaks were observed respectively around 381nm and 400nm, and they came from the SiC particles and the carbon clusters respectively. The intensity of PL emission rises with the increasing of annealing temperature. The PL emission intensity of SiC/AlN bilayer thin film at 381nm is superior to SiC monolayer thin film while the that of SiC/AlN bilayer at 400 nm is inferior to SiC monolayer thin film. In addition to, the grain size of SiC/AlN bilayer thin film is finer than that of SiC monolayer thin film resulting from AFM morphology.

  19. Automating the parallel processing of fluid and structural dynamics calculations

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

    The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilties to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

  20. Automating the parallel processing of fluid and structural dynamics calculations

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Cole, Gary L.

    1987-01-01

    The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

  1. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  2. Structural Anisotropy and Orientation-Induced Casimir Repulsion in Fluids

    DTIC Science & Technology

    2011-05-10

    PHYSICAL REVIEW A 83, 052503 (2011) Structural anisotropy and orientation-induced Casimir repulsion in fluids Alexander P. McCauley,1 F. S. S. Rosa...Massachusetts 02139, USA (Received 22 September 2010; published 10 May 2011) In this work we theoretically consider the Casimir force between two...the dependence of the exact Casimir force between the arrays under both lateral translations and rotations. Although typically the force between such

  3. Bilayer Implants

    PubMed Central

    Schagemann, Jan C.; Rudert, Nicola; Taylor, Michelle E.; Sim, Sotcheadt; Quenneville, Eric; Garon, Martin; Klinger, Mathias; Buschmann, Michael D.; Mittelstaedt, Hagen

    2016-01-01

    Objective To compare the regenerative capacity of 2 distinct bilayer implants for the restoration of osteochondral defects in a preliminary sheep model. Methods Critical sized osteochondral defects were treated with a novel biomimetic poly-ε-caprolactone (PCL) implant (Treatment No. 2; n = 6) or a combination of Chondro-Gide and Orthoss (Treatment No. 1; n = 6). At 19 months postoperation, repair tissue (n = 5 each) was analyzed for histology and biochemistry. Electromechanical mappings (Arthro-BST) were performed ex vivo. Results Histological scores, electromechanical quantitative parameter values, dsDNA and sGAG contents measured at the repair sites were statistically lower than those obtained from the contralateral surfaces. Electromechanical mappings and higher dsDNA and sGAG/weight levels indicated better regeneration for Treatment No. 1. However, these differences were not significant. For both treatments, Arthro-BST revealed early signs of degeneration of the cartilage surrounding the repair site. The International Cartilage Repair Society II histological scores of the repair tissue were significantly higher for Treatment No. 1 (10.3 ± 0.38 SE) compared to Treatment No. 2 (8.7 ± 0.45 SE). The parameters cell morphology and vascularization scored highest whereas tidemark formation scored the lowest. Conclusion There was cell infiltration and regeneration of bone and cartilage. However, repair was incomplete and fibrocartilaginous. There were no significant differences in the quality of regeneration between the treatments except in some histological scoring categories. The results from Arthro-BST measurements were comparable to traditional invasive/destructive methods of measuring quality of cartilage repair. PMID:27688843

  4. Effects of Polyhexamethylene Biguanide and Polyquaternium-1 on Phospholipid Bilayer Structure and Dynamics.

    PubMed

    Horner, Ian J; Kraut, Nadine D; Hurst, Jerod J; Rook, Alyssa M; Collado, Crystal M; Atilla-Gokcumen, G Ekin; Maziarz, E Peter; Liu, X Michael; Merchea, Mohinder M; Bright, Frank V

    2015-08-20

    Multipurpose solutions (MPS) are a single solution that functions to simultaneously rinse, disinfect, clean, and store soft contact lenses. Several commercial MPS products contain polyhexamethylene biguanide (PHMB) and/or polyquaternium-1 (PQ-1) as antimicrobial agents. In this paper we have created an in vitro small unilamellar vesicle (SUV) model of the corneal epithelial surface, and we have assessed the interactions of PHMB and PQ-1 with several model biomembranes by using fluorescence spectroscopy, dynamic light scattering (DLS), and liquid chromatography-mass spectrometry (LC-MS). Steady-state and time-resolved fluorescence were used to assess the membrane acyl chain and polar headgroup region local microenvironment as a function of added PHMB or PQ-1. DLS was used to detect and quantify SUV aggregation induced by PHMB and PQ-1. LC-MS was used to determine the liposomal composition from any precipitated materials in comparison to the as-prepared SUVs. The results are consistent with PHMB adsorbing onto and PQ-1 intercalating into the biomembrane structure. The differences between the two interaction mechanisms have substantial impacts on the biomembrane dynamics and stability.

  5. Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails.

    PubMed

    Paloncýová, Markéta; Vávrová, Kateřina; Sovová, Žofie; DeVane, Russell; Otyepka, Michal; Berka, Karel

    2015-07-30

    Ceramides are indispensable constituents of the stratum corneum (SC), the uppermost impermeable layer of human skin. Ceramides with shorter (four- to eight-carbon acyl chains) fatty acid chains increase skin and model membrane permeability, while further shortening of the chain leads to increased resistance to penetration almost as good as that of ceramides from healthy skin (24 carbons long on average). Here we address the extent to which the atomistic CHARMM36 and coarse-grain MARTINI molecular dynamics (MD) simulations reflect the skin permeability data. As a result, we observed the same bell-shaped permeability trend for water that was observed in the skin and multilayer membrane experiments for model compounds. We showed that the enhanced permeability of the short ceramides is mainly caused by the disturbance of their headgroup conformation because of their inability to accommodate the shorter lipid acyl chain into a typical hairpin conformation, which further led to their destabilization and phase separation. As MD simulations described well delicate structural features of SC membranes, they seem to be suitable for further studies of the SC superstructure, including the development of skin penetration enhancers for transdermal drug delivery and skin toxicity risk assessment studies.

  6. Coupling fluid-structure interaction with phase-field fracture

    NASA Astrophysics Data System (ADS)

    Wick, Thomas

    2016-12-01

    In this work, a concept for coupling fluid-structure interaction with brittle fracture in elasticity is proposed. The fluid-structure interaction problem is modeled in terms of the arbitrary Lagrangian-Eulerian technique and couples the isothermal, incompressible Navier-Stokes equations with nonlinear elastodynamics using the Saint-Venant Kirchhoff solid model. The brittle fracture model is based on a phase-field approach for cracks in elasticity and pressurized elastic solids. In order to derive a common framework, the phase-field approach is re-formulated in Lagrangian coordinates to combine it with fluid-structure interaction. A crack irreversibility condition, that is mathematically characterized as an inequality constraint in time, is enforced with the help of an augmented Lagrangian iteration. The resulting problem is highly nonlinear and solved with a modified Newton method (e.g., error-oriented) that specifically allows for a temporary increase of the residuals. The proposed framework is substantiated with several numerical tests. In these examples, computational stability in space and time is shown for several goal functionals, which demonstrates reliability of numerical modeling and algorithmic techniques. But also current limitations such as the necessity of using solid damping are addressed.

  7. Tunable soft structure in charged fluids confined by dielectric interfaces

    PubMed Central

    Zwanikken, Jos W.; Olvera de la Cruz, Monica

    2013-01-01

    Fluids of charged particles act as the supporting medium for chemical reactions and physical, dynamical, and biological processes. The local structure in an electrolytic background is deformed by micro- and nanoscopic polarizable objects. Vice versa, the forces between the objects are regulated by the cohesive properties of the background. We study here the range and strength of these forces and the microscopic origin from which they emerge. We find the forces to be sensitively dependent on the material properties of the charged fluid and the immersed solutes. The induced interactions can be varied over decades, offering high tunability and aided by accurate theory, control in experiments and applications. To distinguish correlational effects from simple ionic screening, we describe electrolyte-induced forces between neutral objects. The interplay of thermal motion, short-range repulsions, and electrostatic forces is responsible for a soft structure in the fluid. This structure changes near polarizable interfaces and causes diverse attractions between confining walls that seem well-exploited by microbiological systems. For parameters that correspond to monovalent electrolytes in biologically and technologically relevant aqueous environments, we find induced forces between nanoscopic areas of the order of piconewtons over a few nanometers. PMID:23487798

  8. Tunable soft structure in charged fluids confined by dielectric interfaces.

    PubMed

    Zwanikken, Jos W; Olvera de la Cruz, Monica

    2013-04-02

    Fluids of charged particles act as the supporting medium for chemical reactions and physical, dynamical, and biological processes. The local structure in an electrolytic background is deformed by micro- and nanoscopic polarizable objects. Vice versa, the forces between the objects are regulated by the cohesive properties of the background. We study here the range and strength of these forces and the microscopic origin from which they emerge. We find the forces to be sensitively dependent on the material properties of the charged fluid and the immersed solutes. The induced interactions can be varied over decades, offering high tunability and aided by accurate theory, control in experiments and applications. To distinguish correlational effects from simple ionic screening, we describe electrolyte-induced forces between neutral objects. The interplay of thermal motion, short-range repulsions, and electrostatic forces is responsible for a soft structure in the fluid. This structure changes near polarizable interfaces and causes diverse attractions between confining walls that seem well-exploited by microbiological systems. For parameters that correspond to monovalent electrolytes in biologically and technologically relevant aqueous environments, we find induced forces between nanoscopic areas of the order of piconewtons over a few nanometers.

  9. Surfactant transport on viscous bilayers

    NASA Astrophysics Data System (ADS)

    Matar, Omar; Craster, Richard; Warner, Mark

    2001-11-01

    We model the external delivery of surfactant to pulmonary airways, an integral part of Surfactant Replacement Therapy (SRT), a method of treatment of Respiratory Distress Syndrome in neonates. We examine the spreading dynamics of insoluble surfactant by Marangoni stresses along the mucus-perciliary liquid bilayers that line the inside of airways. The bilayer is modelled as a thin highly viscous mucus surface film (mucus) overlying a much less viscous perciliary liquid layer (PCL); this is appropriate for small airways. By exploiting this large viscosity constrast, a variant of standard lubrication theory is adopted wherein terms, which would have otherwise been neglected in the lubrication approximation, are promoted in order to model correctly the presence of the mucus. Inclusion of van der Waals forces in the model permit the study of the effect of this mucus 'skin' on the possibility of bilayer rupture, a potential cause of failure of SRT. We find that increasing the viscosity contrast and initial mucus layer thickness delays the onset of rupture, while increasing the relative significance of Marangoni stresses leads to more marked thinning and rapid bilayer rupture [1]. [1] O. K. Matar, R. V. Craster and M. R. Warner, submitted to J. Fluid Mech. (2001).

  10. The structural role of cholesterol in cell membranes: from condensed bilayers to lipid rafts.

    PubMed

    Krause, Martin R; Regen, Steven L

    2014-12-16

    CONSPECTUS: Defining the two-dimensional structure of cell membranes represents one of the most daunting challenges currently facing chemists, biochemists, and biophysicists. In particular, the time-averaged lateral organization of the lipids and proteins that make up these natural enclosures has yet to be established. As the classic Singer-Nicolson model of cell membranes has evolved over the past 40 years, special attention has focused on the structural role played by cholesterol, a key component that represents ca. 30% of the total lipids that are present. Despite extensive studies with model membranes, two fundamental issues have remained a mystery: (i) the mechanism by which cholesterol condenses low-melting lipids by uncoiling their acyl chains and (ii) the thermodynamics of the interaction between cholesterol and high- and low-melting lipids. The latter bears directly on one of the most popular notions in modern cell biology, that is, the lipid raft hypothesis, whereby cholesterol is thought to combine with high-melting lipids to form "lipid rafts" that float in a "sea" of low-melting lipids. In this Account, we first describe a chemical approach that we have developed in our laboratories that has allowed us to quantify the interactions between exchangeable mimics of cholesterol and low- and high-melting lipids in model membranes. In essence, this "nearest-neighbor recognition" (NNR) method involves the synthesis of dimeric forms of these lipids that contain a disulfide moiety as a linker. By means of thiolate-disulfide interchange reactions, equilibrium mixtures of dimers are then formed. These exchange reactions are initiated either by adding dithiothreitol to a liposomal dispersion to generate a small amount of thiol monomer or by including a small amount of thiol monomer in the liposomes at pH 5.0 and then raising the pH to 7.4. We then show how such NNR measurements have allowed us to distinguish between two very different mechanisms that have been

  11. Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

    PubMed

    Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

    2014-09-01

    Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

  12. Thermodynamic and structural properties of confined discrete-potential fluids.

    PubMed

    Benavides, A L; del Pino, L A; Gil-Villegas, A; Sastre, F

    2006-11-28

    The thermodynamic and structural behaviors of confined discrete-potential fluids are analyzed by computer simulations, studying in a systematic way the effects observed by varying the density, temperature, and parameters of the potentials that characterize the molecule-molecule interactions. The Gibbs ensemble simulation technique for confined fluids [A. Z. Panagiotopoulos, Mol. Phys. 62, 701 (1987)] is applied to a fluid confined between two parallel hard walls. Two different systems have been considered, both formed by spherical particles that differ by the interparticle pair potential: a square well plus square shoulder or a square shoulder plus square well interaction. These model interactions can describe in an effective way pair potentials of real molecular and colloidal systems. Results are compared with the simpler reference systems of square-shoulder and square-well fluids, both under confinement. From the adsorption characterization through the use of density profiles, it is possible to obtain specific values of the interparticle potential parameters that result in a positive to negative adsorption transition.

  13. Time-Dependent Thermally-Driven Interfacial Flows in Multilayered Fluid Structures

    NASA Technical Reports Server (NTRS)

    Haj-Hariri, Hossein; Borhan, A.

    1996-01-01

    A computational study of thermally-driven convection in multilayered fluid structures will be performed to examine the effect of interactions among deformable fluid-fluid interfaces on the structure of time-dependent flow in these systems. Multilayered fluid structures in two models configurations will be considered: the differentially heated rectangular cavity with a free surface, and the encapsulated cylindrical liquid bridge. An extension of a numerical method developed as part of our recent NASA Fluid Physics grant will be used to account for finite deformations of fluid-fluid interfaces.

  14. Analysis of fluid-structural instability in water

    SciTech Connect

    Piccirillo, N.

    1997-02-01

    Recent flow testing of stainless steel hardware in a high pressure/high temperature water environment produced an apparent fluid-structural instability. The source of instability was investigated by studying textbook theory and by performing NASTRAN finite element analyses. The modal analyses identified the mode that was being excited, but the flutter instability analysis showed that the design is stable if minimal structural damping is present. Therefore, it was suspected that the test hardware was the root cause of the instability. Further testing confirmed this suspicion.

  15. Fluid transport and coherent structures of translating and flapping wings.

    PubMed

    Eldredge, Jeff D; Chong, Kwitae

    2010-03-01

    The Lagrangian coherent structures (LCSs) of simple wing cross sections in various low Reynolds number motions are extracted from high-fidelity numerical simulation data and examined in detail. The entrainment process in the wake of a translating ellipse is revealed by studying the relationship between attracting structures in the wake and upstream repelling structures, with the help of blocks of tracer particles. It is shown that a series of slender lobes in the repelling LCS project upstream from the front of the ellipse and "pull" fluid into the wake. Each lobe is paired with a corresponding wake vortex, into which the constituent fluid particles are folded. Flexible and rigid foils in flapping motion are studied, and the resulting differences in coherent structures are used to elucidate their differences in force generation. The clarity with which these flow structures are revealed, compared to the vorticity or velocity fields, provides new insight into the vortex shedding mechanisms that play an important role in unsteady aerodynamics.

  16. A thermal stack structure for measurement of fluid flow

    NASA Astrophysics Data System (ADS)

    Zhao, Hao; Mitchell, S. J. N.; Campbell, D. H.; Gamble, Harold S.

    2003-03-01

    A stacked thermal structure for fluid flow sensing has been designed, fabricated, and tested. A double-layer polysilicon process was employed in the fabrication. Flow measurement is based on the transfer of heat from a temperature sensor element to the moving fluid. The undoped or lightly doped polysilicon temperature sensor is located on top of a heavily doped polysilicon heater element. A dielectric layer between the heater and the sensor elements provides both thermal coupling and electrical isolation. In comparison to a hot-wire flow sensor, the heating and sensing functions are separated, allowing the electrical characteristics of each to be optimized. Undoped polysilicon has a large temperature coefficient of resistance (TCR) up to 7 %/K and is thus a preferred material for the sensor. However, heavily doped polysilicon is preferred for the heater due to its lower resistance. The stacked flow sensor structure offers a high thermal sensitivity making it especially suitable for medical applications where the working temperatures are restricted. Flow rates of various fluids can be measured over a wide range. The fabricated flow sensors were used to measure the flow rate of water in the range μl - ml/min and gas (Helium) in the range 10 - 100ml/min.

  17. A reduced order model for fluid-structure interaction of thin shell structures conveying fluid for physiological applications

    NASA Astrophysics Data System (ADS)

    Chang, Gary Han; Modarres-Sadeghi, Yahya

    2015-11-01

    In this work, a reduced-order model (ROM) is constructed to study fluid-structure interaction of thin shell structures conveying fluid. The method of snapshot Proper Orthogonal Decomposition (POD) is used to construct the reduced-order bases based on a series of CFD results, which then are improved using a QR-factorization technique to satisfy the various boundary conditions in physiological flow problems. In the process, two sets of POD modes are extracted: those due to the shell wall's motion and those due to the pulsatile flow. The Modal Assurance Criterion (MAC) technique is used for selecting the final POD modes used in the reduced-order model. The structure model is solved by Galerkin's method and the FSI coupling is done by adapting a coupled momentum method. The results show that the dynamic behavior of thin shells conveying fluid is closely related to the distribution of the shell's Gaussian curvature, the existence of imperfections and the physiological flow conditions. This method can effectively construct a computationally efficient FSI model, which allows us to examine a wide range of parameters which exist in real-life physiological problems.

  18. A model for the nicotinic acetylcholine receptor ion channel: structure of the transmembrane M2 segments as a pentameric assembly in a lipid bilayer

    NASA Astrophysics Data System (ADS)

    Saiz, Leonor; Klein, Michael L.

    2003-03-01

    The nicotinic acetylcholine receptor (nAChR) is the neurotransmitter gated ion channel responsible for the fast propagation of electrical signals between cells at the nerve-muscle synapse and neurons. The current model for the pore region of the nAChR consists of a bundle of five M2 alpha helices, which is supported by recent solution and solid-state NMR spectroscopy experiments on micelle samples and oriented (DMPC) bilayers. In order to investigate the structure and properties of pore forming region of a simple model for the nAChR, we have performed a molecular dynamics simulation study of the homo-pentameric bundle of M2 peptides in a DMPC lipid bilayer at similar conditions to those of the NMR experiments. During the nanosecond time scale investigated, the peptide bundle adopts a left-handed supercoil structure and the calculated average tilt of the helices agrees well with the recent NMR data. The water filled bundle displays a funnel-like structure. We focuss on those aspects of the structure and dynamics relevant to the function of the channel.

  19. Electrostatics of cell membrane recognition: structure and activity of neutral and cationic rigid push-pull rods in isoelectric, anionic, and polarized lipid bilayer membranes.

    PubMed

    Sakai, N; Gerard, D; Matile, S

    2001-03-21

    Design, synthesis, and structural and functional studies of rigid-rod ionophores of different axial electrostatic asymmetry are reported. The employed design strategy emphasized presence of (a) a rigid scaffold to minimize the conformational complexity, (b) a unimolecular ion-conducting pathway to minimize the suprastructural complexity and monitor the function, (c) an extended fluorophore to monitor structure, (d) variable axial rod dipole, and (e) variable terminal charges to create axial asymmetry. Studies in isoelectric, anionic, and polarized bilayer membranes confirmed a general increase in activity of uncharged rigid push-pull rods in polarized bilayers. The similarly increased activity of cationic rigid push-pull rods with an electrostatic asymmetry comparable to that of alpha-helical bee toxin melittin (positive charge near negative axial dipole terminus) is shown by fluorescence-depth quenching experiments to originate from the stabilization of transmembrane rod orientation by the membrane potential. The reduced activity of rigid push-pull rods having an electrostatic asymmetry comparable to that in alpha-helical natural antibiotics (a positive charge near the positive axial dipole terminus) is shown by structural studies to originate from rod "ejection" by membrane potentials comparable to that found in mammalian plasma membranes. This structural evidence for cell membrane recognition by asymmetric rods is unprecedented and of possible practical importance with regard to antibiotic resistance.

  20. Algorithms of Crescent Structure Detection in Human Biological Fluid Facies

    NASA Astrophysics Data System (ADS)

    Krasheninnikov, V. R.; Malenova, O. E.; Yashina, A. S.

    2017-05-01

    One of the effective methods of early medical diagnosis is based on the image analysis of human biological fluids. In the process of fluid crystallization there appear characteristic patterns (markers) in the resulting layer (facies). Each marker is a highly probable sign of some pathology even at an early stage of a disease development. When mass health examination is carried out, it is necessary to analyze a large number of images. That is why, the problem of algorithm and software development for automated processing of images is rather urgent nowadays. This paper presents algorithms to detect a crescent structures in images of blood serum and cervical mucus facies. Such a marker indicates the symptoms of ischemic disease. The algorithm presented detects this marker with high probability when the probability of false alarm is low.

  1. Structural and electronic properties of expanding fluid metals

    NASA Astrophysics Data System (ADS)

    Tamura, K.; Matsuda, K.; Inui, M.

    2008-03-01

    It has been theoretically predicted that interacting electron gas suffers a negative compressibility when the electron density is sufficiently reduced. Dielectric anomaly is another expression of compressional instability in which the static dielectric function of electron gas changes sign from positive to negative. In a medium with a negative dielectric function, like charges can attract. Expanding fluid alkali metals are the ideal system in which such instability of electron gas can be probed via the structural response of ions. We have performed x-ray diffraction and small angle x-ray scattering measurements using synchrotron radiation for expanding fluid rubidium and cesium. On the basis of the experimental results we discuss the existence of compressional instability and dielectric anomaly in three-dimensional electron gas.

  2. Fluid Structure Interaction of Parachutes in Supersonic Planetary Entry

    NASA Technical Reports Server (NTRS)

    Sengupta, Anita

    2011-01-01

    A research program to provide physical insight into disk-gap-band parachute operation in the supersonic regime on Mars was conducted. The program included supersonic wind tunnel tests, computational fluid dynamics and fluid structure interaction simulations. Specifically, the nature and cause of the "area oscillation" phenomenon were investigated to determine the scale, aerodynamic, and aero-elastic dependence of the supersonic parachute collapse and re-inflation event. A variety of non-intrusive, temporally resolved, and high resolution diagnostic techniques were used to interrogate the flow and generate validation datasets. The results of flow visualization, particle image velocimetry, load measurements, and photogrammetric reconstruction will be presented. Implications to parachute design, use, and verification will also be discussed.

  3. Electron holography on HfO2/HfO2-x bilayer structures with multilevel resistive switching properties

    NASA Astrophysics Data System (ADS)

    Niu, G.; Schubert, M. A.; Sharath, S. U.; Zaumseil, P.; Vogel, S.; Wenger, C.; Hildebrandt, E.; Bhupathi, S.; Perez, E.; Alff, L.; Lehmann, M.; Schroeder, T.; Niermann, T.

    2017-05-01

    Unveiling the physical nature of the oxygen-deficient conductive filaments (CFs) that are responsible for the resistive switching of the HfO2-based resistive random access memory (RRAM) devices represents a challenging task due to the oxygen vacancy related defect nature and nanometer size of the CFs. As a first important step to this goal, we demonstrate in this work direct visualization and a study of physico-chemical properties of oxygen-deficient amorphous HfO2-x by carrying out transmission electron microscopy electron holography as well as energy dispersive x-ray spectroscopy on HfO2/HfO2-x bilayer heterostructures, which are realized by reactive molecular beam epitaxy. Furthermore, compared to single layer devices, Pt/HfO2/HfO2-x /TiN bilayer devices show enhanced resistive switching characteristics with multilevel behavior, indicating their potential as electronic synapses in future neuromorphic computing applications.

  4. Developing a cyber-physical fluid dynamics facility for fluid-structure interaction studies

    NASA Astrophysics Data System (ADS)

    Mackowski, Andrew W.; Williamson, Charles H. K.

    2011-07-01

    In fluid-structure interaction studies, such as vortex-induced vibration, one needs to select essential parameters for the system, such as mass, spring stiffness, and damping. Normally, these parameters are set physically by the mechanical arrangement. However, our approach utilizes a combination of a physical system, comprises a fluid and a mechanical actuator, and a cyber system, taking the form of a computer-based force-feedback controller. This arrangement allows us to impose mass-spring-damping parameters in virtual space and in up to six degrees of freedom. [A similar concept, in one degree of freedom, was pioneered by a group at MIT (see Hover et al., 1998), in studies of vortex-induced vibration of cables.] Although the use of a cyber-physical system has clear advantages over using a purely physical experiment, there are serious challenges to overcome in the design of the governing control system. Our controller, based on a discretization of Newton's laws, makes it straightforward to add and modify any kind of nonlinear, time-varying, or directional force: it is virtually specified but imposed on a physical object. We implement this idea in both a first-generation and a second-generation facility. In this paper, we present preliminary applications of this approach in flow-structure interactions.

  5. Structure, dynamics, and hydration of POPC/POPS bilayers suspended in NaCl, KCl, and CsCl solutions.

    PubMed

    Jurkiewicz, Piotr; Cwiklik, Lukasz; Vojtíšková, Alžběta; Jungwirth, Pavel; Hof, Martin

    2012-03-01

    Effects of alkali metal chlorides on the properties of mixed negatively charged lipid bilayers are experimentally measured and numerically simulated. Addition of 20mol% of negatively charged phosphatidylserine to zwitterionic phosphatidylcholine strengthens adsorption of monovalent cations revealing their specificity, in the following order: Cs(+)bilayer where they pair with oxygen atoms of carbonyl groups (with pairing with sn-2 carbonyl being about twice stronger than pairing with the sn-1 one). Moreover, the cations bridge neighboring lipids forming clusters of up to 4 lipid molecules, which decreases the area per lipid, thickens the membrane, causes rising of lipid headgroups, and hinders lipid dynamics. All these effects follow the same Hofmeister ordering as the cationic adsorption to the bilayer.

  6. The Atlastin C-terminal Tail Is an Amphipathic Helix That Perturbs the Bilayer Structure during Endoplasmic Reticulum Homotypic Fusion

    PubMed Central

    Faust, Joseph E.; Desai, Tanvi; Verma, Avani; Ulengin, Idil; Sun, Tzu-Lin; Moss, Tyler J.; Betancourt-Solis, Miguel A.; Huang, Huey W.; Lee, Tina; McNew, James A.

    2015-01-01

    Fusion of tubular membranes is required to form three-way junctions found in reticular subdomains of the endoplasmic reticulum. The large GTPase Atlastin has recently been shown to drive endoplasmic reticulum membrane fusion and three-way junction formation. The mechanism of Atlastin-mediated membrane fusion is distinct from SNARE-mediated membrane fusion, and many details remain unclear. In particular, the role of the amphipathic C-terminal tail of Atlastin is still unknown. We found that a peptide corresponding to the Atlastin C-terminal tail binds to membranes as a parallel α helix, induces bilayer thinning, and increases acyl chain disorder. The function of the C-terminal tail is conserved in human Atlastin. Mutations in the C-terminal tail decrease fusion activity in vitro, but not GTPase activity, and impair Atlastin function in vivo. In the context of unstable lipid bilayers, the requirement for the C-terminal tail is abrogated. These data suggest that the C-terminal tail of Atlastin locally destabilizes bilayers to facilitate membrane fusion. PMID:25555915

  7. Structure and dynamic properties of diunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine lipid bilayer from molecular dynamics simulation.

    PubMed Central

    Hyvönen, M T; Rantala, T T; Ala-Korpela, M

    1997-01-01

    Unsaturated fatty acid chains are known to be an essential structural part of biomembranes, but only monounsaturated chains have been included in the molecular dynamics (MD) simulations of membrane systems. Here we present a 1-ns MD simulation for a diunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC; 16:0/18:2[delta9,12]) bilayer. The structural behavior of the phosphatidylcholine headgroup, the glycerol backbone, and the hydrating water were assessed and found to be consistent with the existing information about similar systems from both experimental and computational studies. Further analysis was focused on the structure of the double bond region and the effects of the diunsaturation on the bilayer interior. The behavior of the diunsaturated sn-2 chains is affected by the tilted beginning of the chain and the four main conformations of the double bond region. The double bonds of the sn-2 chains also influenced the characteristics of the saturated chains in the sn-1 position. Furthermore, extreme conformations of the sn-2 chains existed that are likely to be related to the functional role of the double bonds. The results here point out the importance of polyunsaturation for the biological interpretations deduced from the membrane MD simulations. Images FIGURE 2 FIGURE 6 FIGURE 9 FIGURE 16 PMID:9414205

  8. Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.

    PubMed Central

    Patterson, W. R.; Anderson, D. H.; DeGrado, W. F.; Cascio, D.; Eisenberg, D.

    1999-01-01

    We report the 0.75 A crystal structure of a racemic mixture of the 12-residue designed peptide "Alpha-1" (Acetyl-ELLKKLLEELKG), the L-enantiomer of which is described in the accompanying paper. Equivalent solutions of the centrosymmetric bilayers were determined by two direct phasing programs in space groups P1 and P1bar. The unit cell contains two L-alpha-helices and two D-alpha-helices. The columnar-sheet bilayer motif seen in L-Alpha-1 is maintained in the D,L-Alpha-1 structure except that each sheet of head-to-tail helices is composed of one enantiomer and is related to its neighboring sheets by inversion symmetry. Comparison to the L-Alpha-1 structure provides further insight into peptide design. The high resolution and small asymmetric unit allowed building an intricate model (R = 13.1%, Rfree = 14.5%) that incorporates much of the discrete disorder of peptide and solvent. Ethanolamine and 2-methyl-2,4-pentanediol (MPD) molecules bind near helix termini. Rigid body analysis identifies sites of restricted displacements and torsions. Side-chain discrete disorder propagates into the backbone of one helix but not the other. Although no side chain in Alpha-1 is rigid, the environments in the crystal restrict some of them to no or only one active torsion. PMID:10422829

  9. Optimal Force Generation with Fluid-Structure Interactions

    NASA Astrophysics Data System (ADS)

    Peng, Diing-wen

    Typical computational and experimental methods are unsuitable for studying large scale optimization problems involving complex fluid structure interactions, primarily due to their time-consuming nature. A novel experimental approach is proposed here that provides a high-fidelity and efficient alternative to discover optimal parameters arising from the passive interaction between structural elasticity and fluid dynamic forces. This approach utilizes motors, force transducers, and active controllers to emulate the effects of elasticity, eliminating the physical need to replace structural components in the experiment. A clustering genetic algorithm is then used to tune the structural parameters to achieve desired optimality conditions, resulting in approximated global optimal regions within the search bound. A prototype fluid-structure interaction experiment inspired by the lift generation of flapping wing insects is presented to highlight the capabilities of this approach. The experiment aims to maximize the average lift on a sinusoidally translating plate, by optimizing the damping ratio and natural frequency of the plate's elastic pitching dynamics. Reynolds number, chord length, and stroke length are varied between optimizations to explore their relationships to the optimal structural parameters. The results reveal that only limited ranges of stroke lengths are conducive to lift generation; there also exists consistent trends between optimal stroke length, natural frequency, and damping ratio. The measured lift, pitching angle, and torque on the plate for optimal scenarios exhibit the same frequency as the translation frequency, and the phase angles of the optimal structural parameters at this frequency are found to be independent of the stroke length. This critical phase can be then characterized by a linear function of the chord length and Reynolds number. Particle image velocimetry measurements are acquired for the kinematics generated with optimal and

  10. Fluid-Structure Interaction in a Fluid-Filled Composite Structure Subjected to Low Velocity Impact

    DTIC Science & Technology

    2016-06-01

    2.  Resin and Hardener .......................................................................5  3.  E-Glass / Epoxy Composite ...Figure 16.   Composite Structure Cut to Size for Testing. ............................................19 Figure 17.   Examples of Resin Voids in the...analyzed. In two of these studies, the composite was a sandwich construction and in the third, the composite was E-glass and resin only. The research

  11. Assembly of RNA nanostructures on supported lipid bilayers

    PubMed Central

    Dabkowska, Aleksandra P.; Michanek, Agnes; Jaeger, Luc; Rabe, Michael; Chworos, Arkadiusz; Höök, Fredrik; Nylander, Tommy; Sparr, Emma

    2014-01-01

    The assembly of nucleic acid nanostructures with controlled size and shape has large impact in the fields of nanotechnology, nanomedicine and synthetic biology. The directed arrangement of nanostructures at interfaces is important for many applications. In spite of this, the use of laterally mobile lipid bilayers to control RNA three-dimensional nanostructure formation on surfaces remains largely unexplored. Here, we direct the self-assembly of RNA building blocks into three-dimensional structures of RNA on fluid lipid bilayers composed of cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or mixtures of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) and cationic sphingosine. We demonstrate the stepwise supramolecular assembly of discrete building blocks through specific and selective RNA-RNA interactions, based on results from quartz crystal microbalance with dissipation (QCM-D), ellipsometry, fluorescence recovery after photobleaching (FRAP) and total internal reflection fluorescence microscopy (TIRF) experiments. The assembly can be controlled to give a densely packed single layer of RNA polyhedrons at the fluid lipid bilayer surface. We show that assembly of the 3D structure can be modulated by sequence specific interactions, surface charge and changes in the salt composition and concentration. In addition, the tertiary structure of the RNA polyhedron can be controllably switched from an extended structure to one that is dense and compact. The versatile approach to building up three-dimensional structures of RNA does not require modification of the surface or the RNA molecules, and can be used as a bottom-up means of nanofabrication of functionalized bio-mimicking surfaces. PMID:25417592

  12. Fluid-structure interaction in blood flow capturing non-zero longitudinal structure displacement

    NASA Astrophysics Data System (ADS)

    Bukač, Martina; Čanić, Sunčica; Glowinski, Roland; Tambača, Josip; Quaini, Annalisa

    2013-02-01

    We present a new model and a novel loosely coupled partitioned numerical scheme modeling fluid-structure interaction (FSI) in blood flow allowing non-zero longitudinal displacement. Arterial walls are modeled by a linearly viscoelastic, cylindrical Koiter shell model capturing both radial and longitudinal displacement. Fluid flow is modeled by the Navier-Stokes equations for an incompressible, viscous fluid. The two are fully coupled via kinematic and dynamic coupling conditions. Our numerical scheme is based on a new modified Lie operator splitting that decouples the fluid and structure sub-problems in a way that leads to a loosely coupled scheme which is unconditionally stable. This was achieved by a clever use of the kinematic coupling condition at the fluid and structure sub-problems, leading to an implicit coupling between the fluid and structure velocities. The proposed scheme is a modification of the recently introduced “kinematically coupled scheme” for which the newly proposed modified Lie splitting significantly increases the accuracy. The performance and accuracy of the scheme were studied on a couple of instructive examples including a comparison with a monolithic scheme. It was shown that the accuracy of our scheme was comparable to that of the monolithic scheme, while our scheme retains all the main advantages of partitioned schemes, such as modularity, simple implementation, and low computational costs.

  13. Phosphoinositides alter lipid bilayer properties

    PubMed Central

    Hobart, E. Ashley; Koeppe, Roger E.; Andersen, Olaf S.

    2013-01-01

    Phosphatidylinositol-4,5-bisphosphate (PIP2), which constitutes ∼1% of the plasma membrane phospholipid, plays a key role in membrane-delimited signaling. PIP2 regulates structurally and functionally diverse membrane proteins, including voltage- and ligand-gated ion channels, inwardly rectifying ion channels, transporters, and receptors. In some cases, the regulation is known to involve specific lipid–protein interactions, but the mechanisms by which PIP2 regulates many of its various targets remain to be fully elucidated. Because many PIP2 targets are membrane-spanning proteins, we explored whether the phosphoinositides might alter bilayer physical properties such as curvature and elasticity, which would alter the equilibrium between membrane protein conformational states—and thereby protein function. Taking advantage of the gramicidin A (gA) channels’ sensitivity to changes in lipid bilayer properties, we used gA-based fluorescence quenching and single-channel assays to examine the effects of long-chain PIP2s (brain PIP2, which is predominantly 1-stearyl-2-arachidonyl-PIP2, and dioleoyl-PIP2) on bilayer properties. When premixed with dioleoyl-phosphocholine at 2 mol %, both long-chain PIP2s produced similar changes in gA channel function (bilayer properties); when applied through the aqueous solution, however, brain PIP2 was a more potent modifier than dioleoyl-PIP2. Given the widespread use of short-chain dioctanoyl-phosphoinositides, we also examined the effects of diC8-phosphoinositol (PI), PI(4,5)P2, PI(3,5)P2, PI(3,4)P2, and PI(3,4,5)P3. The diC8 phosphoinositides, except for PI(3,5)P2, altered bilayer properties with potencies that decreased with increasing head group charge. Nonphosphoinositide diC8 phospholipids generally were more potent bilayer modifiers than the polyphosphoinositides. These results show that physiological increases or decreases in plasma membrane PIP2 levels, as a result of activation of PI kinases or phosphatases, are likely

  14. Shock-driven fluid-structure interaction for civil design

    SciTech Connect

    Wood, Stephen L; Deiterding, Ralf

    2011-11-01

    The multiphysics fluid-structure interaction simulation of shock-loaded structures requires the dynamic coupling of a shock-capturing flow solver to a solid mechanics solver for large deformations. The Virtual Test Facility combines a Cartesian embedded boundary approach with dynamic mesh adaptation in a generic software framework of flow solvers using hydrodynamic finite volume upwind schemes that are coupled to various explicit finite element solid dynamics solvers (Deiterding et al., 2006). This paper gives a brief overview of the computational approach and presents first simulations that utilize the general purpose solid dynamics code DYNA3D for complex 3D structures of interest in civil engineering. Results from simulations of a reinforced column, highway bridge, multistory building, and nuclear reactor building are presented.

  15. Structural changes in supercritical fluids at high pressures

    NASA Astrophysics Data System (ADS)

    Santoro, Mario; Gorelli, Federico A.

    2008-06-01

    The structure of an archetypal model simple fluid system as argon has been investigated by x-ray diffraction at high pressures and room and high temperatures. Despite the markedly supercritical conditions (T=2 4Tc,P>102Pc) , the structure factor S(Q) is very similar, close to the melting line, to that observed in the liquid phase, thereby assessing a liquidlike structure with high atomic correlation, as proposed in a recent inelastic experiment. On the other hand, the S(Q) continuously changes upon approaching the extrapolation of the liquid-gas coexistence line in the (P/Pc,T/Tc) plane, ultimately exhibiting low atomic correlation, which reasonably indicates intermediate character between liquid and gas. The analysis of the S(Q) s based on the hard-sphere model shows that the changes are driven by the decrease in the packing fraction and the increase in the nearest-neighbor distance with decreasing pressure.

  16. Prediction of a structural transition in the hard disk fluid.

    PubMed

    Piasecki, Jarosław; Szymczak, Piotr; Kozak, John J

    2010-10-28

    Starting from the second equilibrium equation in the BBGKY hierarchy under the Kirkwood superposition closure, we implement a new method for studying the asymptotic decay of correlations in the hard disk fluid in the high density regime. From our analysis and complementary numerical studies, we find that exponentially damped oscillations can occur only up to a packing fraction η(∗)∼0.718, a value that is in substantial agreement with the packing fraction, η∼0.723, believed to characterize the transition from the ordered solid phase to a dense fluid phase, as inferred from Mak's Monte Carlo simulations [Phys. Rev. E 73, 065104 (2006)]. Next, we show that the same method of analysis predicts that the exponential damping of oscillations in the hard sphere fluid becomes impossible when λ=4nπσ(3)[1+H(1)]≥34.81, where H(1) is the contact value of the correlation function, n is the number density, and σ is the sphere diameter in exact agreement with the condition, λ≥34.8, which is first reported in a numerical study of the Kirkwood equation by Kirkwood et al. [J. Chem. Phys. 18, 1040 (1950)]. Finally, we show that our method confirms the absence of any structural transition in hard rods for the entire range of densities below close packing.

  17. Fluid-Structure interaction modeling in deformable porous arteries

    NASA Astrophysics Data System (ADS)

    Zakerzadeh, Rana; Zunino, Paolo

    2015-11-01

    A computational framework is developed to study the coupling of blood flow in arteries interacting with a poroelastic arterial wall featuring possibly large deformations. Blood is modeled as an incompressible, viscous, Newtonian fluid using the Navier-Stokes equations and the arterial wall consists of a thick material which is modeled as a Biot system that describes the mechanical behavior of a homogeneous and isotropic elastic skeleton, and connecting pores filled with fluid. Discretization via finite element method leads to the system of nonlinear equations and a Newton-Raphson scheme is adopted to solve the resulting nonlinear system through consistent linearization. Moreover, interface conditions are imposed on the discrete level via mortar finite elements or Nitsche's coupling. The discrete linearized coupled FSI system is solved by means of a splitting strategy, which allows solving the Navier-Stokes and Biot equations separately. The numerical results investigate the effects of proroelastic parameters on the pressure wave propagation in arteries, filtration of incompressible fluids through the porous media, and the structure displacement. The fellowship support from the Computational Modeling & Simulation PhD program at University of Pittsburgh for Rana Zakerzadeh is gratefully acknowledged.

  18. Computational modeling of fluid structural interaction in arterial stenosis

    NASA Astrophysics Data System (ADS)

    Bali, Leila; Boukedjane, Mouloud; Bahi, Lakhdar

    2013-12-01

    Atherosclerosis affects the arterial blood vessels causing stenosis because of which the artery hardens resulting in loss of elasticity in the affected region. In this paper, we present: an approach to model the fluid-structure interaction through such an atherosclerosis affected region of the artery, The blood is assumed as an incompressible Newtonian viscous fluid, and the vessel wall was treated as a thick-walled, incompressible and isotropic material with uniform mechanical properties. The numerical simulation has been studied in the context of The Navier-Stokes equations for an interaction with an elastic solid. The study of fluid flow and wall motion was initially carried out separately, Discretized forms of the transformed wall and flow equations, which are coupled through the boundary conditions at their interface, are obtained by control volume method and simultaneously to study the effects of wall deformability, solutions are obtained for both rigid and elastic walls. The results indicate that deformability of the wall causes an increase in the time average of pressure drop, but a decrease in the maximum wall shear stress. Displacement and stress distributions in the wall are presented.

  19. Density and structural anomalies in soft-repulsive dimeric fluids.

    PubMed

    Munaó, Gianmarco; Saija, Franz

    2016-04-14

    We report Monte Carlo results for the fluid structure of a system of dimeric particles interacting via a core-softened potential. More specifically, dimers interact through a repulsive pair potential of an inverse-power form, modified in such a way that the repulsion strength is softened for a given range of distances. The aim of such a study is to investigate how both the elongation of the dimers and the softness of the potential affect some features of the model. Our results show that the dimeric fluid exhibits both density and structural anomalies, even if the interaction is not characterized by two length scales. Upon increasing the aspect ratio of the dimers, such anomalies are progressively hindered, with the structural anomaly surviving even after the disappearance of the density anomaly. These results shed light on the peculiar behaviour of molecular systems of non-spherical shape, showing how geometrical and interaction parameters play a fundamental role in determining the presence of anomalies.

  20. Molecular dynamics simulation of dipalmitoylphosphatidylserine bilayer with Na+ counterions.

    PubMed Central

    Pandit, Sagar A; Berkowitz, Max L

    2002-01-01

    We performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer. PMID:11916841

  1. A self-excited flapper from fluid-structure interaction

    NASA Astrophysics Data System (ADS)

    Curet, Oscar M.; Breuer, Kenneth S.

    2010-11-01

    The flexible nature of lifting and propulsive surfaces is a common characteristic of aquatic and aerial locomotion in animals. These surfaces may not only move actively, but also passively or with a combination of both. What is the nature of this passive movement? What is the role of this passive motion on force generation, efficiency and muscle control? Here, we present results using a simple wing model with two degrees of freedom designed to study passive flapping, and fluid-structure interaction. The wing is composed of a flat plate with a hinged trailing flap. The wing is cantilevered to the main body to enable a flapping motion with a well-defined natural frequency. We test the wing model in a wind tunnel. At low speed the wing is stationary. Above a critical velocity the trailing wing section starts to oscillate, generating an oscillating lift force on the wing. This oscillating lift force results on a self-excited flapping motion of the wing. We measure the kinematics and the forces generated by the wing as a function of flow velocity and stiffness of the cantilever. Comparisons with aeroelasticity theory will be presented as well as details of the fluid-structure interactions.

  2. Modeling fluid-structure interactions in shallow microchannels

    NASA Astrophysics Data System (ADS)

    Shidhore, Tanmay C.; Christov, Ivan C.

    2016-11-01

    Rectangular microfluidic conduits with deformable walls are some of the simplest and most extensively studied microfluidic devices, primarily due to their practical design applications in a variety of fields like biology, medical diagnostics (e.g., lab-on-a-chip), nanotechnology, etc. Experimentally, these devices are found to deform into a non-rectangular cross-section due to fluid-structure interactions occurring at the channel walls. These deformations significantly affect the flow profile, which results in a non-linear relationship between the flow rate and the pressure drop, which cannot be explained by a 'generalised Poiseuille flow solution'. To this end, we perform a numerical study of these fluid-structure interactions and their effect on the flow rate and the pressure drop occurring in microfluidic conduits with a single deformable wall. The behavior of several shallow conduit systems (l >> w >> h) with rigid base and side walls and a soft top wall (e.g., PDMS) is simulated under laminar flow conditions using the commercial software suite ANSYS. Simulation results are compared against experimental pressure drop-flow rate data from the literature and also newly developed analytical expressions for the wall deformation, the pressure and the normalized flow rate.

  3. Fluid Structure Interaction Analysis on Sidewall Aneurysm Models

    NASA Astrophysics Data System (ADS)

    Hao, Qing

    2016-11-01

    Wall shear stress is considered as an important factor for cerebral aneurysm growth and rupture. The objective of present study is to evaluate wall shear stress in aneurysm sac and neck by a fluid-structure-interaction (FSI) model, which was developed and validated against the particle image velocimetry (PIV) data. In this FSI model, the flow characteristics in a straight tube with different asymmetric aneurysm sizes over a range of Reynolds numbers from 200 to 1600 were investigated. The FSI results agreed well with PIV data. It was found that at steady flow conditions, when Reynolds number above 700, one large recirculating vortex would be formed, occupying the entire aneurysm sac. The center of the vortex is located at region near to the distal neck. A pair of counter rotating vortices would however be formed at Reynolds number below 700. Wall shear stresses reached highest level at the distal neck of the aneurysmal sac. The vortex strength, in general, is stronger at higher Reynolds number. Fluid Structure Interaction Analysis on Sidewall Aneurysm Models.

  4. Discrete Data Transfer Technique for Fluid-Structure Interaction

    NASA Technical Reports Server (NTRS)

    Samareh, Jamshid A.

    2007-01-01

    This paper presents a general three-dimensional algorithm for data transfer between dissimilar meshes. The algorithm is suitable for applications of fluid-structure interaction and other high-fidelity multidisciplinary analysis and optimization. Because the algorithm is independent of the mesh topology, we can treat structured and unstructured meshes in the same manner. The algorithm is fast and accurate for transfer of scalar or vector fields between dissimilar surface meshes. The algorithm is also applicable for the integration of a scalar field (e.g., coefficients of pressure) on one mesh and injection of the resulting vectors (e.g., force vectors) onto another mesh. The author has implemented the algorithm in a C++ computer code. This paper contains a complete formulation of the algorithm with a few selected results.

  5. Development of a Fluid Structures Interaction Test Technique for Fabrics

    NASA Technical Reports Server (NTRS)

    Zilliac, Gregory G.; Heineck, James T.; Schairer, Edward T.; Mosher, Robert N.; Garbeff, Theodore Joseph

    2012-01-01

    Application of fluid structures interaction (FSI) computational techniques to configurations of interest to the entry, descent and landing (EDL) community is limited by two factors - limited characterization of the material properties for fabrics of interest and insufficient experimental data to validate the FSI codes. Recently ILC Dover Inc. performed standard tests to characterize the static stress-strain response of four candidate fabrics for use in EDL applications. The objective of the tests described here is to address the need for a FSI dataset for CFD validation purposes. To reach this objective, the structural response of fabrics was measured in a very simple aerodynamic environment with well controlled boundary conditions. Two test series were undertaken. The first series covered a range of tunnel conditions and the second focused on conditions that resulted in fabric panel buckling.

  6. Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies

    DOE PAGES

    Tian, Jianhui; Nickels, Jonathan; Katsaras, John; ...

    2016-04-27

    Spatial organization within lipid bilayers is an important feature for a range of biological processes. Leaflet compositional asymmetry and lateral lipid organization are just two of the ways in which membrane structure appears to be more complex than initially postulated by the fluid mosaic model. This raises the question of how the phase behavior in one bilayer leaflet may affect the apposing leaflet and how one begins to construct asymmetric model systems to investigate these interleaflet interactions. In this paper, we report on all-atom molecular dynamics simulations (a total of 4.1 μs) of symmetric and asymmetric bilayer systems composed ofmore » liquid-ordered (Lo) or liquid-disordered (Ld) leaflets, based on the nanodomain-forming POPC/DSPC/cholesterol system. We begin by analyzing an asymmetric bilayer with leaflets derived from simulations of symmetric Lo and Ld bilayers. In this system, we observe that the properties of the Lo and Ld leaflets are similar to those of the Lo and Ld leaflets in corresponding symmetric systems. However, it is not obvious that mixing the equilibrium structures of their symmetric counterparts is the most appropriate way to construct asymmetric bilayers nor that these structures will manifest interleaflet couplings that lead to domain registry/antiregistry. We therefore constructed and simulated four additional asymmetric bilayer systems by systematically adding or removing lipids in the Ld leaflet to mimic potential density fluctuations. We find that the number of lipids in the Ld leaflet affects its own properties, as well as those of the apposing Lo leaflet. Collectively, the simulations reveal the presence of weak acyl chain interdigitation across bilayer leaflets, suggesting that interdigitation alone does not contribute significantly to the interleaflet coupling in nonphase-separated bilayers of this chemical composition. Finally, however, the properties of both leaflets appear to be sensitive to changes in in

  7. Variation of thermal conductivity of DPPC lipid bilayer membranes around the phase transition temperature

    PubMed Central

    Youssefian, Sina; Lambert, Christopher R.; Van Dessel, Steven

    2017-01-01

    Given their amphiphilic nature and chemical structure, phospholipids exhibit a strong thermotropic and lyotropic phase behaviour in an aqueous environment. Around the phase transition temperature, phospholipids transform from a gel-like state to a fluid crystalline structure. In this transition, many key characteristics of the lipid bilayers such as structure and thermal properties alter. In this study, we employed atomistic simulation techniques to study the structure and underlying mechanisms of heat transfer in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers around the fluid–gel phase transformation. To investigate this phenomenon, we performed non-equilibrium molecular dynamics simulations for a range of different temperature gradients. The results show that the thermal properties of the DPPC bilayer are highly dependent on the temperature gradient. Higher temperature gradients cause an increase in the thermal conductivity of the DPPC lipid bilayer. We also found that the thermal conductivity of DPPC is lowest at the transition temperature whereby one lipid leaflet is in the gel phase and the other is in the liquid crystalline phase. This is essentially related to a growth in thermal resistance between the two leaflets of lipid at the transition temperature. These results provide significant new insights into developing new thermal insulation for engineering applications. PMID:28539484

  8. Unconventional Superconductivity in Bilayer Transition Metal Dichalcogenides.

    PubMed

    Liu, Chao-Xing

    2017-02-24

    Bilayer transition metal dichalcogenides (TMDs) belong to a class of materials with two unique features, the coupled spin-valley-layer degrees of freedom and the crystal structure that is globally centrosymmetric but locally noncentrosymmetric. In this Letter, we will show that the combination of these two features can lead to a rich phase diagram for unconventional superconductivity, including intralayer and interlayer singlet pairings and interlayer triplet pairings, in bilayer superconducting TMDs. In particular, we predict that the inhomogeneous Fulde-Ferrell-Larkin-Ovchinnikov state can exist in bilayer TMDs under an in-plane magnetic field. We also discuss the experimental relevance of our results and possible experimental signatures.

  9. Small-angle and wide-angle X-ray scattering study on the bilayer structure of synthetic and bovine heart cardiolipins

    NASA Astrophysics Data System (ADS)

    Takahashi, Hiroshi; Hayakawa, Tomohiro; Ito, Kazuki; Takata, Masaki; Kobayashi, Toshihide

    2010-10-01

    Cardiolipin (CL) is a membrane phospholipid containing four fatty acid chains. CL plays an important role in energy transformation in mitochondria. The disorder of CL biosynthesis is involved in a genetic disease, Barth syndrome. Alteration of fatty acid composition of CLs has been found in Barth syndrome patients, i.e., the decrease of unsaturated fatty acid chains. In this study, we investigated how the degree of saturation alters the structure of CL bilayers by using X-ray scattering. Bovine heart CL and two synthetic CLs were compared. Fatty acid compositions of these three CLs have different saturation. Small-angle X-ray scattering data showed that the decrease of the number of double bonds in the unsaturated fatty acid chains causes to thicken the CL bilayers. In addition, wide-angle X-ray scattering data suggested that the decrease reduces the degree of disorder of the hydrophobic region in a liquid crystalline phase. These results may be related to the dysfunction of mitochondria in Barth syndrome.

  10. Temperature-dependent in-plane structure formation of an X-shaped bolapolyphile within lipid bilayers.

    PubMed

    Lechner, Bob-Dan; Ebert, Helgard; Prehm, Marko; Werner, Stefan; Meister, Annette; Hause, Gerd; Beerlink, André; Saalwächter, Kay; Bacia, Kirsten; Tschierske, Carsten; Blume, Alfred

    2015-03-10

    Polyphilic compound B12 is an X-shaped molecule with a stiff aromatic core, flexible aliphatic side chains, and hydrophilic end groups. Forming a thermotropic triangular honeycomb phase in the bulk between 177 and 182 °C but no lyotropic phases, it is designed to fit into DPPC or DMPC lipid bilayers, in which it phase separates at room temperature, as observed in giant unilamellar vesicles (GUVs) by fluorescence microscopy. TEM investigations of bilayer aggregates support the incorporation of B12 into intact membranes. The temperature-dependent behavior of the mixed samples was followed by differential scanning calorimetry (DSC), FT-IR spectroscopy, fluorescence spectroscopy, and X-ray scattering. DSC results support in-membrane phase separation, where a reduced main transition and new B12-related transitions indicate the incorporation of lipids into the B12-rich phase. The phase separation was confirmed by X-ray scattering, where two different lamellar repeat distances are visible over a wide temperature range. Polarized ATR-FTIR and fluorescence anisotropy experiments support the transmembrane orientation of B12, and FT-IR spectra further prove a stepwise "melting" of the lipid chains. The data suggest that in the B12-rich domains the DPPC chains are still rigid and the B12 molecules interact with each other via π-π interactions. All results obtained at temperatures above 75 °C confirm the formation of a single, homogeneously mixed phase with freely mobile B12 molecules.

  11. A high performance transparent resistive switching memory made from ZrO{sub 2}/AlON bilayer structure

    SciTech Connect

    Tsai, Tsung-Ling; Chang, Hsiang-Yu; Tseng, Tseung-Yuen; Lou, Jesse Jen-Chung

    2016-04-11

    In this study, the switching properties of an indium tin oxide (ITO)/zirconium oxide (ZrO{sub 2})/ITO single layer device and those of a device with an aluminum oxynitride (AlON) layer were investigated. The devices with highly transparent characteristics were fabricated. Compared with the ITO/ZrO{sub 2}/ITO single layer device, the ITO/ZrO{sub 2}/AlON/ITO bilayer device exhibited a larger ON/OFF ratio, higher endurance performance, and superior retention properties by using a simple two-step forming process. These substantial improvements in the resistive switching properties were attributed to the minimized influence of oxygen migration through the ITO top electrode (TE), which can be realized by forming an asymmetrical conductive filament with the weakest part at the ZrO{sub 2}/AlON interface. Therefore, in the ITO/ZrO{sub 2}/AlON/ITO bilayer device, the regions where conductive filament formation and rupture occur can be effectively moved from the TE interface to the interior of the device.

  12. Combining ligand-induced quantum-confined stark effect with type II heterojunction bilayer structure in CdTe and CdSe nanocrystal-based solar cells.

    PubMed

    Yaacobi-Gross, Nir; Garphunkin, Natalia; Solomeshch, Olga; Vaneski, Aleksandar; Susha, Andrei S; Rogach, Andrey L; Tessler, Nir

    2012-04-24

    We show that it is possible to combine several charge generation strategies in a single device structure, the performance of which benefits from all methods used. Exploiting the inherent type II heterojunction between layered structures of CdSe and CdTe colloidal quantum dots, we systematically study different ways of combining such nanocrystals of different size and surface chemistry and with different linking agents in a bilayer solar cell configuration. We demonstrate the beneficial use of two distinctly different sizes of NCs not only to improve the solar spectrum matching but also to reduce exciton binding energy, allowing their efficient dissociation at the interface. We further make use of the ligand-induced quantum-confined Stark effect in order to enhance charge generation and, hence, overall efficiency of nanocrystal-based solar cells.

  13. Measuring the structure factor of simple fluids under extreme conditions

    NASA Astrophysics Data System (ADS)

    Weck, Gunnar

    2013-06-01

    The structure and dynamics of fluids, although a long standing matter of investigations, is still far from being well established. In particular, with the existence of a first order liquid-liquid phase transition (LLT) discovered in liquid phosphorus at 0.9 GPa and 1300 K it is now recognized that the fluid state could present complex structural changes. At present, very few examples of LLTs have been clearly evidenced, which may mean that a larger range of densities must be probed. First order transitions between a molecular and a polymeric liquid have been recently predicted by first principles calculations in liquid nitrogen at 88 GPa and 2000 K and in liquid CO2 at 45 GPa and 1850 K. The only device capable of reaching these extreme conditions is the diamond anvil cell (DAC), in which, the sample is sandwiched between two diamond anvils of thickness 100 times larger. Consequently, the diffracted signal from the sample is very weak compared to the Compton signal of the anvils, and becomes hardly measurable for pressures above ~20 GPa. A similar problem has been faced by the high pressure community using large volume press so as to drastically reduce the x-ray background from the sample environment. In the angle-dispersive diffraction configuration, it was proposed to use a multichannel collimator (MCC). This solution has been implemented to fit the constraints of the Paris-Edimburg (PE) large volume press and it is now routinely used on beamline ID27 of the European Synchrotron Radiation Facility. In this contribution, we present our adaptation of the MCC device accessible at ID27 for the DAC experiment. Because of the small sample volume a careful alignment procedure between the MCC slits and the DAC had to be implemented. The data analysis procedure initially developed by Eggert et al. has also been completed in order to take into account the complex contribution of the MCC slits. A large reduction of the Compton diffusion from the diamond anvils is obtained

  14. Bicuspid aortic valve hemodynamics: a fluid-structure interaction study

    NASA Astrophysics Data System (ADS)

    Chandra, Santanu; Seaman, Clara; Sucosky, Philippe

    2011-11-01

    The bicuspid aortic valve (BAV) is a congenital defect in which the aortic valve forms with two leaflets instead of three. While calcific aortic valve disease (CAVD) also develops in the normal tricuspid aortic valve (TAV), its progression in the BAV is more rapid. Although studies have suggested a mechano-potential root for the disease, the native BAV hemodynamics remains largely unknown. This study aimed at characterizing BAV hemodynamics and quantifying the degree of wall-shear stress (WSS) abnormality on BAV leaflets. Fluid-structure interaction models validated with particle-image velocimetry were designed to predict the flow and leaflet dynamics in idealized TAV and BAV anatomies. Valvular function was quantified in terms of the effective orifice area. The regional leaflet WSS was characterized in terms of oscillatory shear index, temporal shear magnitude and temporal shear gradient. The predictions indicate the intrinsic degree of stenosis of the BAV anatomy, reveal drastic differences in shear stress magnitude and pulsatility on BAV and TAV leaflets and confirm the side- and site-specificity of the leaflet WSS. Given the ability of abnormal fluid shear stress to trigger valvular inflammation, these results support the existence of a mechano-etiology of CAVD in the BAV.

  15. Fluid Structural Analysis of Urine Flow in a Stented Ureter

    PubMed Central

    Gómez-Blanco, J. Carlos; Martínez-Reina, F. Javier; Cruz, Domingo; Pagador, J. Blas; Sánchez-Margallo, Francisco M.; Soria, Federico

    2016-01-01

    Many urologists are currently studying new designs of ureteral stents to improve the quality of their operations and the subsequent recovery of the patient. In order to help during this design process, many computational models have been developed to simulate the behaviour of different biological tissues and provide a realistic computational environment to evaluate the stents. However, due to the high complexity of the involved tissues, they usually introduce simplifications to make these models less computationally demanding. In this study, the interaction between urine flow and a double-J stented ureter with a simplified geometry has been analysed. The Fluid-Structure Interaction (FSI) of urine and the ureteral wall was studied using three models for the solid domain: Mooney-Rivlin, Yeoh, and Ogden. The ureter was assumed to be quasi-incompressible and isotropic. Data obtained in previous studies from ex vivo and in vivo mechanical characterization of different ureters were used to fit the mentioned models. The results show that the interaction between the stented ureter and urine is negligible. Therefore, we can conclude that this type of models does not need to include the FSI and could be solved quite accurately assuming that the ureter is a rigid body and, thus, using the more simple Computational Fluid Dynamics (CFD) approach. PMID:27127535

  16. The asymptotic structure of a slender coiling fluid thread

    NASA Astrophysics Data System (ADS)

    Blount, Maurice; Lister, John

    2010-11-01

    The buckling of a viscous fluid thread as it falls through air onto a stationary surface is a well-known breakfast-time phenomenon which exhibits a rich variety of dynamical regimes [1]. Since the bending resistance of a slender thread is small, bending motion is largely confined to a short region of coiling near the surface. If the height of fall is large enough, then the thread above the coiling region forms a `tail' that falls nearly vertically under gravity but is deflected slightly due to forces exerted on it by the coil. Although it is possible to use force balances in the coil to estimate scalings for the coiling frequency, we analyse the solution structure of the entire thread in the asymptotic limit of a very slender thread and thereby include the dynamic interaction between the coil and the tail. Quantitative predictions of the coiling frequency are obtained which demonstrate the existence of leading-order corrections to scalings previously derived. In particular, we show that in the regime where the deflection of the tail is governed by a balance between centrifugal acceleration, hoop stress and gravity, the tail behaves as a flexible circular pendulum that is forced by bending stress exerted by the coil. The amplitude of the response is calculated and the previously observed resonance when the coiling frequency coincides with one of the eigenfrequencies of a free flexible pendulum is thereby explained. [1] N.M. Ribe et al., J. Fluid Mech. 555, 275-297.

  17. Fluid Structural Analysis of Urine Flow in a Stented Ureter.

    PubMed

    Gómez-Blanco, J Carlos; Martínez-Reina, F Javier; Cruz, Domingo; Pagador, J Blas; Sánchez-Margallo, Francisco M; Soria, Federico

    2016-01-01

    Many urologists are currently studying new designs of ureteral stents to improve the quality of their operations and the subsequent recovery of the patient. In order to help during this design process, many computational models have been developed to simulate the behaviour of different biological tissues and provide a realistic computational environment to evaluate the stents. However, due to the high complexity of the involved tissues, they usually introduce simplifications to make these models less computationally demanding. In this study, the interaction between urine flow and a double-J stented ureter with a simplified geometry has been analysed. The Fluid-Structure Interaction (FSI) of urine and the ureteral wall was studied using three models for the solid domain: Mooney-Rivlin, Yeoh, and Ogden. The ureter was assumed to be quasi-incompressible and isotropic. Data obtained in previous studies from ex vivo and in vivo mechanical characterization of different ureters were used to fit the mentioned models. The results show that the interaction between the stented ureter and urine is negligible. Therefore, we can conclude that this type of models does not need to include the FSI and could be solved quite accurately assuming that the ureter is a rigid body and, thus, using the more simple Computational Fluid Dynamics (CFD) approach.

  18. Noncollinear Fe spin structure in (Sm-Co)/Fe exchange-spring bilayers: layer-resolved {sup 57}Fe Mssbauer spectroscopy and electronic structure calculations.

    SciTech Connect

    Uzdin, V. M.; Vega, A.; Khrenov, A.; Keune, W.; Kuncser, V. E.; Jiang, J. S.; Bader, S. D.

    2012-01-01

    Magnetization reversal in nanoscale (Sm-Co)/Fe (hard/soft) bilayer exchange-spring magnets with in-plane uniaxial magnetic anisotropy was investigated by magnetometry, conversion-electron Moessbauer spectroscopy (CEMS) and atomistic Fe spin-structure calculations. Magnetization loops along the easy direction exhibit signatures typical of exchange-spring magnets. In-field CEMS at inclined {gamma}-ray incidence onto thin (2 nm) {sup 57}Fe probe layers embedded at various depths in the 20-nm-thick natural (soft) Fe layer provides depth-dependent information (via the line-intensity ratio R{sub 23} as a function of the applied field H) about the in-plane rotation of Fe spins. A minimum in the R{sub 23}-vs-H dependence at (H{sub min}, R{sub min}) determines the field where Fe magnetic moments roughly adopt an average perpendicular orientation during their reversal from positive to negative easy-axis orientation. A monotonic decrease of H{sub min} with distance from the hard/soft interface is observed. Rotation of Fe spins takes place even in the interface region in applied fields far below the field of irreversible switching, H{sub irr}, of the hard phase. Formation of an Fe-Co alloy is detected in the interface region. For comparison, the noncollinear Fe spin structure during reversal and the resulting R{sub 23} ratio were obtained by electronic-structure calculations based on a quantum-mechanical Hamiltonian for itinerant electrons. The coupling at the hard/soft interface is described by the uniaxial exchange-anisotropy field, hint, as a parameter. Our calculated R{sub 23} ratios as a function of the (reduced) applied field h exhibit similar features as observed in the experiment, in particular a minimum at (h{sub min}, R{sub min}). R{sub min} is found to increase with hint, thus providing a measure of the interface coupling. Evidence is provided for the existence of fluctuations of the interface coupling. The calculations also show that the Fe spin spiral formed

  19. Noncollinear Fe spin structure in (Sm-Co)/Fe exchange-spring bilayers: Layer-resolved 57Fe Mössbauer spectroscopy and electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Uzdin, V. M.; Vega, A.; Khrenov, A.; Keune, W.; Kuncser, V. E.; Jiang, J. S.; Bader, S. D.

    2012-01-01

    Magnetization reversal in nanoscale (Sm-Co)/Fe (hard/soft) bilayer exchange-spring magnets with in-plane uniaxial magnetic anisotropy was investigated by magnetometry, conversion-electron Mössbauer spectroscopy (CEMS) and atomistic Fe spin-structure calculations. Magnetization loops along the easy direction exhibit signatures typical of exchange-spring magnets. In-field CEMS at inclined γ-ray incidence onto thin (2 nm) 57Fe probe layers embedded at various depths in the 20-nm-thick natural (soft) Fe layer provides depth-dependent information (via the line-intensity ratio R23 as a function of the applied field H) about the in-plane rotation of Fe spins. A minimum in the R23-vs-H dependence at (Hmin, Rmin) determines the field where Fe magnetic moments roughly adopt an average perpendicular orientation during their reversal from positive to negative easy-axis orientation. A monotonic decrease of Hmin with distance from the hard/soft interface is observed. Rotation of Fe spins takes place even in the interface region in applied fields far below the field of irreversible switching, Hirr, of the hard phase. Formation of an Fe-Co alloy is detected in the interface region. For comparison, the noncollinear Fe spin structure during reversal and the resulting R23 ratio were obtained by electronic-structure calculations based on a quantum-mechanical Hamiltonian for itinerant electrons. The coupling at the hard/soft interface is described by the uniaxial exchange-anisotropy field, hint, as a parameter. Our calculated R23 ratios as a function of the (reduced) applied field h exhibit similar features as observed in the experiment, in particular a minimum at (hmin, Rmin). Rmin is found to increase with hint, thus providing a measure of the interface coupling. Evidence is provided for the existence of fluctuations of the interface coupling. The calculations also show that the Fe spin spiral formed during reversal is highly inhomogeneous. In general, our simulation of the Fe spin

  20. The interaction of polyphenols with bilayers: conditions for increasing bilayer adhesion.

    PubMed Central

    Huh, N W; Porter, N A; McIntosh, T J; Simon, S A

    1996-01-01

    Because proteins and other molecules with a high polyphenol content are commonly involved in adhesion processes, we are investigating the interactions between polyphenols and biological materials. A naturally occurring polyphenol that binds a variety of proteins and lipids is tannic acid (TA), which contains five digallic acid residues covalently linked to a central D-glucose. A previous study has shown that TA increases the adhesion between apposing phosphatidylcholine (PC) bilayers and over a very narrow concentration range collapses the interbilayer fluid space from about 15 A to 5 A. To determine the chemical requirements a polyphenolic molecule must possess to increase bilayer adhesion, we have synthesized several simpler TA analogs that vary in their size, shape, and number of gallic acid and hydroxyl groups. X-ray diffraction, absorbance, binding, and differential scanning calorimetry measurements were used to investigate the interaction of these polyphenolic molecules with egg PC (EPC) and dipalmitoyl PC (DPPC) bilayers. Of these synthetic polyphenols, only penta-O-galloyl-alpha-D-glucose (PGG) was able to completely mimic the effects of TA by collapsing the interbilayer fluid space from 15 A to 5 A, decreasing the dipole potential by about 300 mV, increasing the transition enthalpy of DPPC liposomes, and inducing an interdigitated phase in DPPC. Binding studies indicated that the fluid space was reduced to 5 A at an EPC:PGG mole ratio of 5:1. We conclude that these polyphenols collapse the fluid space of PC bilayers because they 1) are amphipathic and partition into the bilayers interfacial region, 2) are long enough to span the interbilayer space, 3) contain several gallic acids distributed so that they can partition simultaneously into apposing bilayers, and 4) have sufficient gallic acid residues to interact with all lipid headgroups and cover the bilayer surface. Under these conditions we conclude that the polyphenols from interbilayer bridges. We

  1. Visualizing the dynamics of complex spatial networks in structured fluids

    NASA Astrophysics Data System (ADS)

    Scherdel, S.; Schoberth, H. G.; Magerle, R.

    2007-07-01

    We present a data reduction and visualization approach for the microdomain dynamics in block copolymers and similar structured fluids. Microdomains are reduced to thin smooth lines with colored branching points and visualized with a tool for protein visualization. As a result the temporal evolution of large volume data sets can be perceived within seconds. This approach is demonstrated with simulation results based on the dynamic density functional theory of the ordering of microdomains in a thin film of block copolymers. As an example we discuss the dynamics at the cylinder-to-gyroid grain boundary and compare it to the epitaxial cylinder-to-gyroid phase transition predicted by Matsen [Phys. Rev. Lett. 80, 4470 (1998)].

  2. Functional One-Dimensional Lipid Bilayers on Carbon Nanotube Templates

    SciTech Connect

    Artyukhin, A; Shestakov, A; Harper, J; Bakajin, O; Stroeve, P; Noy, A

    2004-07-23

    We present one-dimensional (1-D) lipid bilayer structures that integrate carbon nanotubes with a key biological environment-phospholipid membrane. Our structures consist of lipid bilayers wrapped around carbon nanotubes modified with a hydrophilic polymer cushion layer. Despite high bilayer curvature, the lipid membrane maintains its fluidity and can sustain repeated damage-recovery cycles. We also present the first evidence of spontaneous insertion of pore-forming proteins into 1-D lipid bilayers. These structures could lead to the development of new classes of biosensors and bioelectronic devices.

  3. Structural cooling fluid tube for supporting a turbine component and supplying cooling fluid to transition section

    DOEpatents

    Charron, Richard; Pierce, Daniel

    2015-08-11

    A shaft cover support for a gas turbine engine is disclosed. The shaft cover support not only provides enhanced support to a shaft cover of the gas turbine engine, but also includes a cooling fluid chamber for passing fluids from a rotor air cooling supply conduit to an inner ring cooling manifold. Furthermore, the shaft cover support may include a cooling shield supply extending from the cooling fluid chamber between the radially outward inlet and the radially inward outlet on the radially extending region and in fluid communication with the cooling fluid chamber for providing cooling fluids to a transition section. The shaft cover support may also provide additional stiffness and reduce interference of the flow from the compressor. In addition, the shaft cover support accommodates a transition section extending between compressor and turbine sections of the gas turbine engine.

  4. Structural controls on fluid escape from the subduction interface

    NASA Astrophysics Data System (ADS)

    Reynard, Bruno; Tauzin, Benoit; Bodin, Thomas; Perrillat, Jean-Philippe; Debayle, Eric

    2017-04-01

    Seismic activity and non-volcanic tremors are often associated with fluid circulation resulting from the dehydration of subducting plates. Tremors in the overriding continental crust of several subduction zones suggest fluid circulation at shallower depths, but potential fluid pathways are still poorly documented. Fluids are also released at different depths in hot and cold subduction zones, which may result in different schemes of fluid escape. We document potential fluid pathways in Cascadia, one of the hottest subduction zone, using receiver function analysis. We provide evidence for a seismic discontinuity near 15 km depth in the crust of the overriding North American plate. This interface is segmented, and its interruptions are spatially correlated with conductive regions of the forearc and shallow swarms of seismicity and non-volcanic tremors. The comparison of seismological and electrical conductivity profiles suggests that fluid escape is controlled by fault zones between blocks of accreted terranes in the overriding plate. These zones constitute fluid escape routes that may influence the seismic cycle by releasing fluid pressure from the megathrust. Results on Cascadia are compared to fluid escape routes suggested by former geophysical observations in NE Japan, one of the coldest subduction zones. Links between fluid escape, permeability and fluid-rock reactions at or above the plate interface are discussed.

  5. Parallel Three-Dimensional Computation of Fluid Dynamics and Fluid-Structure Interactions of Ram-Air Parachutes

    NASA Technical Reports Server (NTRS)

    Tezduyar, Tayfun E.

    1998-01-01

    This is a final report as far as our work at University of Minnesota is concerned. The report describes our research progress and accomplishments in development of high performance computing methods and tools for 3D finite element computation of aerodynamic characteristics and fluid-structure interactions (FSI) arising in airdrop systems, namely ram-air parachutes and round parachutes. This class of simulations involves complex geometries, flexible structural components, deforming fluid domains, and unsteady flow patterns. The key components of our simulation toolkit are a stabilized finite element flow solver, a nonlinear structural dynamics solver, an automatic mesh moving scheme, and an interface between the fluid and structural solvers; all of these have been developed within a parallel message-passing paradigm.

  6. Fluid-structure interactions in compressible cavity flows

    SciTech Connect

    Wagner, Justin L.; Casper, Katya Marie; Beresh, Steven J.; Hunter, Patrick S.; Spillers, Russell Wayne; Henfling, John F.; Mayes, Randall L.

    2015-06-08

    Experiments were performed to understand the complex fluid-structure interactions that occur during aircraft internal store carriage. A cylindrical store was installed in a rectangular cavity having a length-to-depth ratio of 3.33 and a length-to-width ratio of 1. The Mach number ranged from 0.6 to 2.5 and the incoming boundary layer was turbulent. Fast-response pressure measurements provided aeroacoustic loading in the cavity, while triaxial accelerometers provided simultaneous store response. Despite occupying only 6% of the cavity volume, the store significantly altered the cavity acoustics. The store responded to the cavity flow at its natural structural frequencies, and it exhibited a directionally dependent response to cavity resonance. Specifically, cavity tones excited the store in the streamwise and wall-normal directions consistently, whereas a spanwise response was observed only occasionally. Also, the streamwise and wall-normal responses were attributed to the longitudinal pressure waves and shear layer vortices known to occur during cavity resonance. Although the spanwise response to cavity tones was limited, broadband pressure fluctuations resulted in significant spanwise accelerations at store natural frequencies. As a result, the largest vibrations occurred when a cavity tone matched a structural natural frequency, although energy was transferred more efficiently to natural frequencies having predominantly streamwise and wall-normal motions.

  7. Fluid-structure interactions in compressible cavity flows

    DOE PAGES

    Wagner, Justin L.; Casper, Katya Marie; Beresh, Steven J.; ...

    2015-06-08

    Experiments were performed to understand the complex fluid-structure interactions that occur during aircraft internal store carriage. A cylindrical store was installed in a rectangular cavity having a length-to-depth ratio of 3.33 and a length-to-width ratio of 1. The Mach number ranged from 0.6 to 2.5 and the incoming boundary layer was turbulent. Fast-response pressure measurements provided aeroacoustic loading in the cavity, while triaxial accelerometers provided simultaneous store response. Despite occupying only 6% of the cavity volume, the store significantly altered the cavity acoustics. The store responded to the cavity flow at its natural structural frequencies, and it exhibited a directionallymore » dependent response to cavity resonance. Specifically, cavity tones excited the store in the streamwise and wall-normal directions consistently, whereas a spanwise response was observed only occasionally. Also, the streamwise and wall-normal responses were attributed to the longitudinal pressure waves and shear layer vortices known to occur during cavity resonance. Although the spanwise response to cavity tones was limited, broadband pressure fluctuations resulted in significant spanwise accelerations at store natural frequencies. As a result, the largest vibrations occurred when a cavity tone matched a structural natural frequency, although energy was transferred more efficiently to natural frequencies having predominantly streamwise and wall-normal motions.« less

  8. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2012-04-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  9. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2011-10-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  10. Dynamic adsorption and structure of interfacial bilayers adsorbed from lipopeptide surfactants at the hydrophilic silicon/water interface: effect of the headgroup length.

    PubMed

    Jia, Donghui; Tao, Kai; Wang, Jiqian; Wang, Chengdong; Zhao, Xiubo; Yaseen, Mohammed; Xu, Hai; Que, Guohe; Webster, John R P; Lu, Jian R

    2011-07-19

    Lipopeptides are an important group of biosurfactants expressed by microorganisms. Because they are well-known for being biocompatible, biodegradable, and highly surface active, they are attractive for a wide range of applications. Natural lipopeptide surfactants are however impure; it is hence difficult to use them for exploring the structure-function relation. In this work, a series of cationic lipopeptide surfactants, C(14)K(n) (n = 1-4), where C denotes the myristic acyl chain and K denotes lysine (Lys), have been synthesized, and their interfacial behavior has been characterized by studying their adsorption at the silicon/water interface (bearing a thin native oxide layer) using spectroscopic ellipsometry and neutron reflection (NR). The dynamic adsorption was marked by an initial fast step within the first 2-3 min followed by a slow molecular relaxation process over the subsequent 20-30 min. The initial rate of time-dependent adsorption and the equilibrated adsorbed amount showed a steady decrease with increasing n, indicating the impact of the molecular size, structure, and charge. NR revealed the formation of sandwiched bilayers from C(14)K(n), similar to conventional surfactants such as nonionic C(12)E(6) and cationic C(16)TAB. However, the electrostatic attraction between K and the silica surface caused confinement of the K groups, forcing the head segments into a predominantly flat-on conformation. This characteristic structural feature was confirmed by the almost constant thickness of the headgroup regions ranging from 8 to 11 Å as determined from NR combined with partial deuterium labeling to the acyl tail. An increase in area per molecular pair with n resulted directly from increasing the footprint. As a result, the hydrophobic back-to-back tail mixing and acyl chain tilting rose with n. The extent of chain-head intermixing became so intensified that the C(14)K(4) bilayer could be approximated to a uniform layer distribution.

  11. Structural and electrical properties of AuPd/Mo bi-layer films for transition edge sensors

    NASA Astrophysics Data System (ADS)

    Boucher, R.; May, T.; Wagner, Th; Zakosarenko, V.; Anders, S.; Mayer, H. G.

    2006-01-01

    We have tuned the transition temperature of the AuPd/Mo bi-layer in the temperature range 100-800 mK and used models derived from the Usadel theory to predict and fit the behaviour of the transition temperature. As expected, the influence of the AuPd on the transition temperature is stronger than that found by others from pure Au, but weaker than that of pure Pd. The extracted coherence length of the Cooper pairs in the metal alloy points to the greatest influence coming from the Pd part of the AuPd. X-ray measurements show the films to be textured, with the Mo(110) and AuPd(111) peaks being dominant in the out-of-plane direction. The transition width is seen to increase with the spread of the orientation of the z direction of the individual grains.

  12. Bathroom greywater recycling using polyelectrolyte-complex bilayer membrane: Advanced study of membrane structure and treatment efficiency.

    PubMed

    Oh, K S; Poh, P E; Chong, M N; Chan, E S; Lau, E V; Saint, C P

    2016-09-05

    Polyelectrolyte-complex bilayer membrane (PCBM) was fabricated using biodegradable chitosan and alginate polymers for subsequent application in the treatment of bathroom greywater. In this study, the properties of PCBMs were studied and it was found that the formation of polyelectrolyte network reduced the molecular weight cut-off (MWCO) from 242kDa in chitosan membrane to 2.71kDa in PCBM. The decrease in MWCO of PCBM results in better greywater treatment efficiency, subsequently demonstrated in a greywater filtration study where treated greywater effluent met the household reclaimed water standard of <2 NTU turbidity and <30ppm total suspended solids (TSS). In addition, a further 20% improvement in chemical oxygen demand (COD) removal was achieved as compared to a single layer chitosan membrane. Results from this study show that the biodegradable PCBM is a potential membrane material in producing clean treated greywater for non-potable applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Experimental and numerical aspects of a thermal fluid-structure phenomenon

    NASA Astrophysics Data System (ADS)

    Gleim, Tobias; Birken, Philipp; Weiland, Matthias; Kuhl, Detlef; Meister, Andreas; Wünsch, Olaf

    2017-07-01

    A fundamental research experiment for thermal fluid-structure-interaction for the verification of a partitioned approach with non-linear material properties is examined. In the following, a specimen is heated as well as cooled within a wind tunnel. The thermal fluid-structure-interaction is first experimentally investigated and subsequently numerically validated. For the numerical simulation, two existing programs (a fluid and a structure code) are coupled using a partitioned approach.

  14. Fluid Analysis and Improved Structure of an ATEG Heat Exchanger Based on Computational Fluid Dynamics

    NASA Astrophysics Data System (ADS)

    Tang, Z. B.; Deng, Y. D.; Su, C. Q.; Yuan, X. H.

    2015-06-01

    In this study, a numerical model has been employed to analyze the internal flow field distribution in a heat exchanger applied for an automotive thermoelectric generator based on computational fluid dynamics. The model simulates the influence of factors relevant to the heat exchanger, including the automotive waste heat mass flow velocity, temperature, internal fins, and back pressure. The result is in good agreement with experimental test data. Sensitivity analysis of the inlet parameters shows that increase of the exhaust velocity, compared with the inlet temperature, makes little contribution (0.1 versus 0.19) to the heat transfer but results in a detrimental back pressure increase (0.69 versus 0.21). A configuration equipped with internal fins is proved to offer better thermal performance compared with that without fins. Finally, based on an attempt to improve the internal flow field, a more rational structure is obtained, offering a more homogeneous temperature distribution, higher average heat transfer coefficient, and lower back pressure.

  15. Influence of ceramide on the internal structure and hydration of the phospholipid bilayer studied by neutron and X-ray scattering

    NASA Astrophysics Data System (ADS)

    Kiselev, M. A.; Zemlyanaya, E. V.; Ryabova, N. Y.; Hauss, T.; Almasy, L.; Funari, S. S.; Zbytovska, J.; Lombardo, D.

    2014-07-01

    Small angle neutron scattering (SANS), neutron diffraction and X-ray powder diffraction were used to investigate influence of N-stearoyl phytosphingosine (CER[NP]) and α-hydroxy- N-stearoyl phytosphingosine (CER[AP]) on the internal structure and hydration of DMPC membrane in fully and partly hydrated states at T = 30 °C. Application of Fourier analysis for diffraction data and model calculations for the SANS data evidence that addition of both CER[NP] and CER[AP] in small concentrations promotes significant changes in the organization of DMPC bilayers, such as the increase of the hydrophobic core region. SANS data evidence a decrease in the average radius and polydispersity of the vesicles that can be ascribed to hydrogen bonds interactions that favor tight lipid packing with a compact, more rigid character.

  16. Stability Test of White LED with Bilayer Structure of Red InP Quantum Dots and Yellow YAG:Ce3+ Phosphor.

    PubMed

    Park, Kwangwon; Deressa, Gemechu; Kim, Daehan; Kim, Jongsu; Kim, Jihoon; Kim, Taehoon

    2016-02-01

    The white-light-emitting diode (white LED), based on the bilayer structure of red InP quantum dots (QDs) with 610 nm peak, and yellow YAG:Ce3+ phosphor with 550 nm peak, were fabricated through a conventional 5050 type LED fabrication process. The white LED exhibited high luminous efficiency of >130 Im/W and high color rendering index of >80 under operating current of 60 mA and color temperature of 5800 K. As an increase of QDs concentrations, the white LED showed higher color rendering index along with lower luminous efficiency, and the energy loss in the reabsorption process between yellow YAG:Ce3+ emission and red QD absorption was observed. As the temperature increases, the x-color coordinates were significantly changed, indicating that the InP QDs still have lower thermal stability. Also our white LED showed about 50% lumen maintenance after 45,000 hours of normal operation.

  17. A non-magnetic spacer layer effect on spin layers (7/2,3) in a bi-layer ferromagnetic dendrimer structure: Monte Carlo study

    NASA Astrophysics Data System (ADS)

    Jabar, A.; Tahiri, N.; Bahmad, L.; Benyoussef, A.

    2016-11-01

    A bi-layer system consisting of layers of spins (7/2, 3) in a ferromagnetic dendrimer structure, separated by a non-magnetic spacer, is studied by Monte Carlo simulations. The effect of the RKKY interactions is investigated and discussed for such system. It is shown that the magnetic properties in the two magnetic layers depend strongly on the thickness of the magnetic and non-magnetic layers. The total magnetizations and susceptibilities are studied as a function of the reduced temperature. The effect of the reduced exchange interactions as well as the reduced crystal field is outlined. On other hand, the critical temperature is discussed as a function of the magnetic layer values. To complete this study we presented and discussed the magnetic hysteresis cycles.

  18. Minimal continuum theories of structure formation in dense active fluids

    NASA Astrophysics Data System (ADS)

    Dunkel, Jörn; Heidenreich, Sebastian; Bär, Markus; Goldstein, Raymond E.

    2013-04-01

    Self-sustained dynamical phases of living matter can exhibit remarkable similarities over a wide range of scales, from mesoscopic vortex structures in microbial suspensions and motility assays of biopolymers to turbulent large-scale instabilities in flocks of birds or schools of fish. Here, we argue that, in many cases, the phenomenology of such active states can be efficiently described in terms of fourth- and higher-order partial differential equations. Structural transitions in these models can be interpreted as Landau-type kinematic transitions in Fourier (wavenumber) space, suggesting that microscopically different biological systems can share universal long-wavelength features. This general idea is illustrated through numerical simulations for two classes of continuum models for incompressible active fluids: a Swift-Hohenberg-type scalar field theory, and a minimal vector model that extends the classical Toner-Tu theory and appears to be a promising candidate for the quantitative description of dense bacterial suspensions. We discuss how microscopic symmetry-breaking mechanisms can enter macroscopic continuum descriptions of collective microbial motion near surfaces, and conclude by outlining future applications.

  19. Lennard-Jones fluids in two-dimensional nano-pores. Multi-phase coexistence and fluid structure

    NASA Astrophysics Data System (ADS)

    Yatsyshin, Petr; Savva, Nikos; Kalliadasis, Serafim

    2014-03-01

    We present a number of fundamental findings on the wetting behaviour of nano-pores. A popular model for fluid confinement is a one-dimensional (1D) slit pore formed by two parallel planar walls and it exhibits capillary condensation (CC): a first-order phase transition from vapour to capillary-liquid (Kelvin shift). Capping such a pore at one end by a third orthogonal wall forms a prototypical two-dimensional (2D) pore. We show that 2D pores possess a wetting temperature such that below this temperature CC remains of first order, above it becomes a continuous phase transition manifested by a slab of capillary-liquid filling the pore from the capping wall. Continuous CC exhibits hysteresis and can be preceded by a first-order capillary prewetting transition. Additionally, liquid drops can form in the corners of the 2D pore (remnant of 2D wedge prewetting). The three fluid phases, vapour, capillary-liquid slab and corner drops, can coexist at the pore triple point. Our model is based on the statistical mechanics of fluids in the density functional formulation. The fluid-fluid and fluid-substrate interactions are dispersive. We analyze in detail the microscopic fluid structure, isotherms and full phase diagrams. Our findings also suggest novel ways to control wetting of nano-pores. We are grateful to the European Research Council via Advanced Grant No. 247031 for support.

  20. Direct differentiation of the quasi-incompressible fluid formulation of fluid-structure interaction using the PFEM

    NASA Astrophysics Data System (ADS)

    Zhu, Minjie; Scott, Michael H.

    2017-07-01

    Accurate and efficient response sensitivities for fluid-structure interaction (FSI) simulations are important for assessing the uncertain response of coastal and off-shore structures to hydrodynamic loading. To compute gradients efficiently via the direct differentiation method (DDM) for the fully incompressible fluid formulation, approximations of the sensitivity equations are necessary, leading to inaccuracies of the computed gradients when the geometry of the fluid mesh changes rapidly between successive time steps or the fluid viscosity is nonzero. To maintain accuracy of the sensitivity computations, a quasi-incompressible fluid is assumed for the response analysis of FSI using the particle finite element method and DDM is applied to this formulation, resulting in linearized equations for the response sensitivity that are consistent with those used to compute the response. Both the response and the response sensitivity can be solved using the same unified fractional step method. FSI simulations show that although the response using the quasi-incompressible and incompressible fluid formulations is similar, only the quasi-incompressible approach gives accurate response sensitivity for viscous, turbulent flows regardless of time step size.

  1. Intercalation of small hydrophobic molecules in lipid bilayers containing cholesterol

    SciTech Connect

    Worcester, D.L.; Hamacher, K.; Kaiser, H.; Kulasekere, R.; Torbet, J.

    1994-12-31

    Partitioning of small hydrophobic molecules into lipid bilayers containing cholesterol has been studied using the 2XC diffractometer at the University of Missouri Research Reactor. Locations of the compounds were determined by Fourier difference methods with data from both deuterated and undeuterated compounds introduced into the bilayers from the vapor phase. Data fitting procedures were developed for determining how well the compounds were localized. The compounds were found to be localized in a narrow region at the center of the hydrophobic layer, between the two halves of the bilayer. The structures are therefore intercalated structures with the long axis of the molecules in the plane of the bilayer.

  2. Effect of variations in the structure of a polyleucine-based alpha-helical transmembrane peptide on its interaction with phosphatidylglycerol bilayers.

    PubMed

    Liu, Feng; Lewis, Ruthven N A H; Hodges, Robert S; McElhaney, Ronald N

    2004-03-30

    High-sensitivity differential scanning calorimetry and Fourier transform infrared spectroscopy were used to study the interaction of a cationic alpha-helical transmembrane peptide, acetyl-Lys(2)-Leu(24)-Lys(2)-amide (L(24)), and members of the homologous series of anionic n-saturated diacyl phosphatidylglycerols (PGs). Analogues of L(24), in which the lysine residues were replaced by 2,3-diaminopropionic acid (L(24)DAP), or in which a leucine residue at each end of the polyleucine sequence was replaced by a tryptophan (WL(22)W), were also studied to investigate the roles of lysine side-chain snorkeling and aromatic side-chain interactions with the interfacial region of phospholipid bilayers. The gel/liquid-crystalline phase transition temperature of the host PG bilayers is altered by these peptides in a hydrophobic mismatch-dependent manner, as previously found with zwitterionic phosphatidylcholine (PC) bilayers. However, all three peptides reduce the phase transition temperature and enthalpy to a greater extent in anionic PG bilayers than in zwitterionic PC bilayers, with WL(22)W having the largest effect. All three peptides form very stable alpha-helices in PG bilayers, but small conformational changes are induced in response to a mismatch between peptide hydrophobic length and gel-state lipid bilayer hydrophobic thickness. Moreover, electrostatic and hydrogen-bonding interactions occur between the terminal lysine residues of L(24) and L(24)DAP and the polar headgroups of PG bilayers. However, such interactions were not observed in PG/WL(22)W bilayers, suggesting that the cation-pi interactions between the tryptophan and lysine residues predominate. These results indicate that the lipid-peptide interactions are affected not only by the hydrophobic mismatch between these peptides and the host lipid bilayer, but also by the tryptophan-modulated electrostatic and hydrogen-bonding interactions between the positively charged lysine residues at the termini of these

  3. Computational Modeling for Fluid-Porous Structure Interaction with Large Structural Deformation

    NASA Astrophysics Data System (ADS)

    Zakerzadeh, Rana; Zunino, Paolo

    2016-11-01

    In this work, we utilize numerical models to investigate the importance of poroelasticity in the interaction of blood flow with a porohyperelastic vessel wall, and to establish a connection between the apparent viscoelastic behavior of the structure part and the intramural filtration flow. The main novelty is in the design of a Nitsche's splitting strategy, which separates the fluid from the structure sub-problems for the Fluid-Porous Structure Interaction system undergoing large deformations. The general idea is to use this model to study the influence of different parameters on energy dissipation in a poroelastic medium. We also study a new benchmark test specifically designed to investigate the effect of poroelasticity on large deformations.

  4. Differences in the physical properties of lipid monolayers and bilayers on a spherical solid support.

    PubMed Central

    Linseisen, F M; Hetzer, M; Brumm, T; Bayerl, T M

    1997-01-01

    A monolayer of 1,2-dipalmitoyl-d62-glycero-3-phosphocholine (DPPC-d62) coated onto silanized silica beads (spherical supported monolayer: SSM) is studied by 2H-NMR and DSC. The results are compared with those obtained from a single bilayer on the same solid support (spherical supported vesicles: SSV) and from multilamellar vesicles (MLV). The phase transition temperature (Tm) of the SSMs is significantly higher than that of the bilayer systems and the extent of this difference depends on the lipid density in the monolayer that is determined during its preparation. 2H-NMR reveals a gel and fluid phase coexistence in the SSM transition region. A comparison of the 2H-NMR line shapes suggests the presence of highly curved structures for the fluid phase of the SSM samples. From a comparison of SSM and SSV transverse relaxation in the fluid phase we can conclude that the lateral diffusion coefficient D1 in supported monolayers is similar to that in bilayers. Images FIGURE 1 PMID:9083669

  5. Temperature-induced changes in optical properties of thin film TiO2-Al2O3 bi-layer structures grown by atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Ali, Rizwan; Saleem, Muhammad Rizwan; Honkanen, Seppo

    2016-02-01

    We investigate the optical properties and corresponding temperature-induced changes in highly uniform thin amorphous films and their bi-layer stacks grown by Atomic Layer Deposition (ALD). The environmentally driven conditions such as temperature, humidity and pressure have a significant influence on optical properties of homogeneous and heterogeneous bi-layer stacked structures of TiO2-Al2O3 and subsequently affect the specific sensitive nature of optical signals from nano-optical devices. Owing to the super hydrophilic behavior and inhibited surface defects in the form of hydrogenated species, the thermo-optic coefficient (TOC) of ~ 100 nm thick ALD-TiO2 films vary significantly with temperature, which can be used for sensing applications. On the other hand, the TOC of ~ 100 nm thick ALD-Al2O3 amorphous films show a differing behavior with temperature. In this work, we report on reduction of surface defects in ALD-TiO2 films by depositing a number of ultra-thin ALD-Al2O3 films to act as impermeable barrier layers. The designed and fabricated heterostructures of ALD-TiO2/Al2O3 films with varying ALD-Al2O3 thicknesses are exploited to stabilize the central resonance peak of Resonant Waveguide Gratings (RWGs) in thermal environments. The temperature-dependent optical constants of ALD-TiO2/Al2O3 bi-layer films are measured by a variable angle spectroscopic ellipsometer (VASE), covering a wide spectral range 380 <= λ <= 1800 nm at a temperature range from 25 to 105 °C. The Cauchy model is used to design and retrieve refractive indices at these temperatures, measured with three angles of incidence (59°, 67°, and 75°). The optical constants of 100 nm thick ALD-TiO2 and various combinational thicknesses of ALD-Al2O3 films are used to predict TOCs using a polynomial fitting algorithm.

  6. Energy effects on the structure and thermodynamic properties of nanoconfined fluids (a density functional theory study).

    PubMed

    Keshavarzi, Ezat; Kamalvand, Mohammad

    2009-04-23

    The structure and properties of fluids confined in nanopores may show a dramatic departure from macroscopic bulk fluids. The main reason for this difference lies in the influence of system walls. In addition to the entropic wall effect, system walls can significantly change the energy of the confined fluid compared to macroscopic bulk fluids. The energy effect of the walls on a nanoconfined fluid appears in two forms. The first effect is the cutting off of the intermolecular interactions by the walls, which appears for example in the integrals for calculation of the thermodynamic properties. The second wall effect involves the wall-molecule interactions. In such confined fluids, the introduction of wall forces and the competition between fluid-wall and fluid-fluid forces could lead to interesting thermodynamic properties, including new kinds of phase transitions not observed in the macroscopic fluid systems. In this article, we use the perturbative fundamental measure density functional theory to study energy effects on the structure and properties of a hard core two-Yukawa fluid confined in a nanoslit. Our results show the changes undergone by the structure and phase transition of the nanoconfined fluids as a result of energy effects.

  7. Fluid-structure interaction simulation of an avian flight model.

    PubMed

    Ruck, Sebastian; Oertel, Herbert

    2010-12-15

    A three-dimensional numerical avian model was developed to investigate the unsteady and turbulent aerodynamic performance of flapping wings for varying wingbeat frequencies and flow velocities (up to 12 Hz and 9 m s(-1)), corresponding to a reduced frequency range of k=0.22 to k=1.0 and a Reynolds number range of Re=16,000 to Re=50,000. The wings of the bird-inspired model consist of an elastic membrane. Simplifying the complicated locomotion kinematics to a sinusoidal wing rotation about two axes, the main features of dynamic avian flight were approximated. Numerical simulation techniques of fluid-structure interaction (FSI) providing a fully resolved flow field were applied to calculate the aerodynamic performance of the flapping elastic wings with the Reynolds averaged Navier-Stokes (RANS) approach. The results were used to characterize and describe the macroscopic flow configurations in terms of starting, stopping, trailing and bound vortices. For high reduced frequencies up to k=0.67 it was shown that the wake does not consist of individual vortex rings known as the discrete vortex ring gait. Rather, the wake is dominated by a chain of elliptical vortex rings on each wing. The structures are interlocked at the starting and stopping vortices, which are shed in pairs at the reversal points of the wingbeat cycle. For decreasing reduced frequency, the results indicate a transition to a continuous vortex gait. The upstroke becomes more aerodynamically active, leading to a consistent circulation of the bound vortex on the wing and a continuous spanwise shedding of small scale vortices. The formation of the vortices shed spanwise in pairs at the reversal points is reduced and the wake is dominated by the tip and root vortices, which form long drawn-out vortex structures.

  8. The effect of variations in phospholipid and sterol structure on the nature of lipid-sterol interactions in lipid bilayer model membranes.

    PubMed

    Mannock, David A; Lewis, Ruthven N A H; McMullen, Todd P W; McElhaney, Ronald N

    2010-06-01

    This review deals with the effect of variations in phospholipid and sterol structure on the nature and magnitude of lipid-sterol interactions in lipid bilayer model membranes. The first portion of the review covers the effect of Chol itself on the thermotropic phase behavior and organization of a variety of different glycero- and sphingolipid membrane lipid classes, varying in the structure and charge of their polar headgroups and in the length and structure of their fatty acyl chains. The second part of this review deals with the effect of variations in sterol structure on the thermotropic phase behavior and organization primarily of the well studied DPPC model membrane system. In the third section, we focus on some of the contributions of sterol functional group chemistry, molecular conformation and dynamics, to sterol-lipid interactions. Using those studies, we re-examine the results of recently published experimental and computer-modeling studies to provide a new more dynamic molecular interpretation of sterol-lipid interactions. We suggest that the established view of the rigid sterol ring system and extended alkyl side-chain obtained from physical studies of cholesterol-phospholipid mixtures may not apply in lipid mixtures differing in their sterol chemical structure. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

  9. Viscoelastic deformation of lipid bilayer vesicles.

    PubMed

    Wu, Shao-Hua; Sankhagowit, Shalene; Biswas, Roshni; Wu, Shuyang; Povinelli, Michelle L; Malmstadt, Noah

    2015-10-07

    Lipid bilayers form the boundaries of the cell and its organelles. Many physiological processes, such as cell movement and division, involve bending and folding of the bilayer at high curvatures. Currently, bending of the bilayer is treated as an elastic deformation, such that its stress-strain response is independent of the rate at which bending strain is applied. We present here the first direct measurement of viscoelastic response in a lipid bilayer vesicle. We used a dual-beam optical trap (DBOT) to stretch 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) giant unilamellar vesicles (GUVs). Upon application of a step optical force, the vesicle membrane deforms in two regimes: a fast, instantaneous area increase, followed by a much slower stretching to an eventual plateau deformation. From measurements of dozens of GUVs, the average time constant of the slower stretching response was 0.225 ± 0.033 s (standard deviation, SD). Increasing the fluid viscosity did not affect the observed time constant. We performed a set of experiments to rule out heating by laser absorption as a cause of the transient behavior. Thus, we demonstrate here that the bending deformation of lipid bilayer membranes should be treated as viscoelastic.

  10. Viscoelastic deformation of lipid bilayer vesicles†

    PubMed Central

    Wu, Shao-Hua; Sankhagowit, Shalene; Biswas, Roshni; Wu, Shuyang; Povinelli, Michelle L.

    2015-01-01

    Lipid bilayers form the boundaries of the cell and its organelles. Many physiological processes, such as cell movement and division, involve bending and folding of the bilayer at high curvatures. Currently, bending of the bilayer is treated as an elastic deformation, such that its stress-strain response is independent of the rate at which bending strain is applied. We present here the first direct measurement of viscoelastic response in a lipid bilayer vesicle. We used a dual-beam optical trap (DBOT) to stretch 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) giant unilamellar vesicles (GUVs). Upon application of a step optical force, the vesicle membrane deforms in two regimes: a fast, instantaneous area increase, followed by a much slower stretching to an eventual plateau deformation. From measurements of dozens of GUVs, the average time constant of the slower stretching response was 0.225 ± 0.033 s (standard deviation, SD). Increasing the fluid viscosity did not affect the observed time constant. We performed a set of experiments to rule out heating by laser absorption as a cause of the transient behavior. Thus, we demonstrate here that the bending deformation of lipid bilayer membranes should be treated as viscoelastic. PMID:26268612

  11. Bias induced modulation of electrical and thermal conductivity and heat capacity of BN and BN/graphene bilayers

    NASA Astrophysics Data System (ADS)

    Chegel, Raad

    2017-04-01

    By using the tight binding approximation and Green function method, the electronic structure, density of state, electrical conductivity, heat capacity of BN and BN/graphene bilayers are investigated. The AA-, AB1- and AB2- BN/graphene bilayers have small gap unlike to BN bilayers which are wide band gap semiconductors. Unlike to BN bilayer, the energy gap of graphene/BN bilayers increases with external field. The magnitude of the change in the band gap of BN bilayers is much higher than the graphene/BN bilayers. Near absolute zero, the σ(T) is zero for BN bilayers and it increases with temperature until reaches maximum value then decreases. The BN/graphene bilayers have larger electrical conductivity larger than BN bilayers. For both bilayers, the specific heat capacity has a Schottky anomaly.

  12. Assembly of RNA nanostructures on supported lipid bilayers

    NASA Astrophysics Data System (ADS)

    Dabkowska, Aleksandra P.; Michanek, Agnes; Jaeger, Luc; Rabe, Michael; Chworos, Arkadiusz; Höök, Fredrik; Nylander, Tommy; Sparr, Emma

    2014-12-01

    The assembly of nucleic acid nanostructures with controlled size and shape has large impact in the fields of nanotechnology, nanomedicine and synthetic biology. The directed arrangement of nano-structures at interfaces is important for many applications. In spite of this, the use of laterally mobile lipid bilayers to control RNA three-dimensional nanostructure formation on surfaces remains largely unexplored. Here, we direct the self-assembly of RNA building blocks into three-dimensional structures of RNA on fluid lipid bilayers composed of cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or mixtures of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) and cationic sphingosine. We demonstrate the stepwise supramolecular assembly of discrete building blocks through specific and selective RNA-RNA interactions, based on results from quartz crystal microbalance with dissipation (QCM-D), ellipsometry, fluorescence recovery after photobleaching (FRAP) and total internal reflection fluorescence microscopy (TIRF) experiments. The assembly can be controlled to give a densely packed single layer of RNA polyhedrons at the fluid lipid bilayer surface. We show that assembly of the 3D structure can be modulated by sequence specific interactions, surface charge and changes in the salt composition and concentration. In addition, the tertiary structure of the RNA polyhedron can be controllably switched from an extended structure to one that is dense and compact. The versatile approach to building up three-dimensional structures of RNA does not require modification of the surface or the RNA molecules, and can be used as a bottom-up means of nanofabrication of functionalized bio-mimicking surfaces.The assembly of nucleic acid nanostructures with controlled size and shape has large impact in the fields of nanotechnology, nanomedicine and synthetic biology. The directed arrangement of nano-structures at interfaces is important for many applications. In spite of

  13. Mobility of water and selected atoms in DMPG lipid bilayer membranes

    NASA Astrophysics Data System (ADS)

    Hansen, F. Y.; Roennest, A.; Peters, G. H.; Taub, H.; Miskowiec, A.

    2013-03-01

    Molecular dynamics simulations have been used to study the structure and mobility of water and selected atoms in dimyristoyl-phosphoglycerol (DMPG) lipids forming a fully hydrated free standing bilayer membrane at 310 K. The effect of the anionic headgroup in DMPG on structure and dynamics has been studied by comparison with simulation[2] and experimental[3] results for bilayer membranes of dimyristoyl-phosphorylcholine (DMPC) lipids, which have a neutral head group and the same aliphatic tails. The membrane is found to be in the fluid phase with monovalent sodium counter ions and in the gel phase with divalent calcium counter ions as evidenced by an area/lipid change and the NMR order parameter. The simulation results are compared with preliminary neutron scattering results. Supported by NSF Grant No. DGE-1069091

  14. Osmotic control of bilayer fusion.

    PubMed Central

    Fisher, L R; Parker, N S

    1984-01-01

    We have used photography and capacitance measurement to monitor the steps in the interaction and eventual fusion of optically black lipid bilayers (BLMs), hydrostatically bulged to approximately hemispherical shape and pushed together mechanically. A necessary first step is drainage of aqueous solution from between the bilayers to allow close contact of the bilayers. The drainage can be controlled by varying the osmotic difference across the bilayers. If the differences are such as to remove water from between the bilayers, fusion occurs after a time that depends on the net osmotic difference and the area of contact. If there is an osmotic flow of water into the space between the bilayers, fusion never occurs. In the fusion process, a single central bilayer forms from the original apposed pair of bilayers. The central bilayer may later burst to allow mixing of the two volumes originally bounded by the separate bilayer; the topological equivalent of exocytosis. Images FIGURE 2 PMID:6541065

  15. Anisotropic dynamic changes in the pore network structure, fluid diffusion and fluid flow in articular cartilage under compression.

    PubMed

    Greene, George W; Zappone, Bruno; Söderman, Olle; Topgaard, Daniel; Rata, Gabriel; Zeng, Hongbo; Israelachvili, Jacob N

    2010-04-01

    A compression cell designed to fit inside an NMR spectrometer was used to investigate the in situ mechanical strain response, structural changes to the internal pore structure, and the diffusion and flow of interstitial water in full-thickness cartilage samples as it was deforming dynamically under a constant compressive load (pressure). We distinguish between the hydrostatic pressure acting on the interstitial fluid and the pore pressure acting on the cartilage fibril network. Our results show that properties related to the pore matrix microstructure such as diffusion and hydraulic conductivity are strongly influenced by the hydrostatic pressure in the interstitial fluid of the dynamically deforming cartilage which differ significantly from the properties measured under static i.e. equilibrium loading conditions (when the hydrostatic pressure has relaxed back to zero). The magnitude of the hydrostatic fluid pressure also appears to affect the way cartilage's pore matrix changes during deformation with implications for the diffusion and flow-driven fluid transport through the deforming pore matrix. We also show strong evidence for a highly anisotropic pore structure and deformational dynamics that allows cartilage to deform without significantly altering the axial porosity of the matrix even at very large strains. The insensitivity of the axial porosity to compressive strain may be playing a critical function in directing the flow of pressurized interstitial fluid in the compressed cartilage to the surface, to support the load, and provide a protective interfacial fluid film that 'weeps' out from the deforming tissue and thereby enhances the (elasto)hydrodynamic efficacy of sliding joints. Our results appear to show a close synergy between the structure of cartilage and both the hydrodynamic and boundary lubrication mechanisms. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. Elementary Excitations and Dynamic Structure of Quantum Fluids

    NASA Astrophysics Data System (ADS)

    Saarela, M.

    The equations of motion method for studying excitations and dynamic structure of quantum fluids is reviewed in this series of lectures. The method is based on the least action principle where one minimizes the action integral of the dynamic system. As a result one gets the continuity equations, which connect the density fluctuations and currents to an external driving force. The external force is assumed to infinitesimal and the response of the system to that is linear. The real poles of the linear response function determine the elementary excitation modes and the imaginary part of the self energy defines the continuum limit and gives the finite lifetime of the decaying modes. Our dynamic wave function contains time-dependent one- and two-particle correlation functions, which includes couplings between three modes. Thus one mode can split into two modes if energy and momentum are conserved. We begin with the Feenberg's β-derivative formulation of the optimized ground state and then derive general equations of motion for the dynamic system from the least action principle. We show how the simplest one-body approximation leads to the Feynman theory of excitations. By including the fluctuating two-body correlation function within the uniform limit one recovers the correlated basic function approximation. The fully consistent theory gives a good account of the elementary excitations and we show results on current patterns in the maxon-roton regions and on the precursor of the liquid-solid phase transition. Finally we apply the method to the excitations of the impurity and derive the hydrodynamic effective mass of the 3He impurity in 4He and the 3He dynamic structure function.

  17. Optimization of poly(L-lactic acid)/segmented polyurethane electrospinning process for the production of bilayered small-diameter nanofibrous tubular structures.

    PubMed

    Montini Ballarin, F; Caracciolo, P C; Blotta, E; Ballarin, V L; Abraham, G A

    2014-09-01

    The present study is focused on the electrospinning process as a versatile technique to obtain nanofibrous tubular structures for potential applications in vascular tissue engineering. A bilayered scaffolding structure composed of poly(L-lactic acid) (PLLA)/bioresorbable segmented polyurethane (SPEU) blends for small-diameter (5mm) vascular bypass grafts was obtained by multilayering electrospinning. Polymer blend ratios were chosen to mimic the media and adventitia layers. The influence of the different electrospinning parameters into the fiber formation, fiber morphology and fiber mean diameter for PLLA, SPEU and two PLLA/SPEU blends were studied. Flat and two-parallel plate collectors were used to analyze the effect of the electrostatic field on the PLLA nanofiber alignment in the rotating mandrel. Membrane topography resulted in random or aligned nanofibrous structures depending on the auxiliary collector setup used. Finally, composition, surface hydrophilicity, thermal properties and morphology of nanofibrous scaffolds were characterized and discussed. Since the development of tissue engineered microvascular prostheses is still a challenge, the prepared scaffolding tubular structures are promising candidates for vascular tissue engineering.

  18. Engineering plant membranes using droplet interface bilayers

    PubMed Central

    Barlow, N. E.; Smpokou, E.; Macey, R.; Gould, I. R.; Turnbull, C.; Flemming, A. J.; Brooks, N. J.; Ces, O.; Barter, L. M. C.

    2017-01-01

    Droplet interface bilayers (DIBs) have become widely recognised as a robust platform for constructing model membranes and are emerging as a key technology for the bottom-up assembly of synthetic cell-like and tissue-like structures. DIBs are formed when lipid-monolayer coated water droplets are brought together inside a well of oil, which is excluded from the interface as the DIB forms. The unique features of the system, compared to traditional approaches (e.g., supported lipid bilayers, black lipid membranes, and liposomes), is the ability to engineer multi-layered bilayer networks by connecting multiple droplets together in 3D, and the capability to impart bilayer asymmetry freely within these droplet architectures by supplying droplets with different lipids. Yet despite these achievements, one potential limitation of the technology is that DIBs formed from biologically relevant components have not been well studied. This could limit the reach of the platform to biological systems where bilayer composition and asymmetry are understood to play a key role. Herein, we address this issue by reporting the assembly of asymmetric DIBs designed to replicate the plasma membrane compositions of three different plant species; Arabidopsis thaliana, tobacco, and oats, by engineering vesicles with different amounts of plant phospholipids, sterols and cerebrosides for the first time. We show that vesicles made from our plant lipid formulations are stable and can be used to assemble asymmetric plant DIBs. We verify this using a bilayer permeation assay, from which we extract values for absolute effective bilayer permeation and bilayer stability. Our results confirm that stable DIBs can be assembled from our plant membrane mimics and could lead to new approaches for assembling model systems to study membrane translocation and to screen new agrochemicals in plants. PMID:28396711

  19. Flexible Bilayers with Spontaneous Curvature Lead to Lamellar Gels and Spontaneous Vesicles

    SciTech Connect

    Coldren,B.; Warriner, H.; van Zanten, R.; Zasadzinski, J.; Sirota, E.

    2006-01-01

    Mixtures of cetyltrimethylammonium tosylate (CTAT) and sodium dodecylbenzene sulfonate (SDBS) in water form a fluid lamellar phase at {le}40 wt % water but surprisingly turn into viscous gels at higher water fractions. The gels are characterized by spherulite and other bilayer defects consistent with a low bending elasticity, {kappa} {approx} k{sub B}T, and a nonzero spontaneous curvature. Caill{acute e} analysis of the small-angle x-ray line shape confirms that for 7:3 wt:wt CTAT:SDBS bilayers at 50% water, {kappa} = 0.62 {+-} 0.09 k{sub B}T and {kappa} = -0.9 {+-} 0.2 k{sub B}T. For 13:7 wt:wt CTAT:SDBS bilayers, the measured bending elasticity decreases with increasing water dilution in good agreement with predictions based on renormalization theory, giving {kappa}{sub 0} = 0.28 k{sub B}T. These results show that surfactant mixing is sufficient to make {kappa} {approx} k{sub B}T, which promotes strong, Helfrich-type repulsion between bilayers that can dominate the van der Waals attraction. These are necessary conditions for spontaneous vesicles formed at even higher water fractions to be equilibrium structures.

  20. Quantifying the bending of bilayer temperature-sensitive hydrogels.