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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

    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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles

    PubMed Central

    Kučerka, Norbert; Liu, Yufeng; Chu, Nanjun; Petrache, Horia I.; Tristram-Nagle, Stephanie; Nagle, John F.

    2005-01-01

    Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30°C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 Å−1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 Å provided |F(qz)| for low qz, 0.1 < qz < 0.3 Å−1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2πh/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 ± 0.5 Å2 for DMPC and 63.2 ± 0.5 Å2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles ρ(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values. PMID:15665131

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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).

  17. 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.

  18. 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.

  19. 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.

  20. Modeling liquid crystal bilayer structures with minimal surfaces.

    PubMed

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W

    2004-01-22

    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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).

  18. 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.

  19. 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.

  20. 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).

  1. 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].

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  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. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Capillary electrophoresis with noncovalently bilayer-coated capillaries for stability study of allergenic proteins in simulated gastrointestinal fluids.

    PubMed

    Zheng, Chang; Liu, Youping; Zhou, Qiuhong; Di, Xin

    2010-10-15

    A novel noncovalently bilayer-coated capillary using cationic polymer polybrene (PB) and anionic polymer (sodium 4-styrenesulfonate) (PSS) as coatings was prepared. This PB-PSS coating showed good migration-time reproducibility for proteins and high stability in the range of pH 2-10 and in the presence of 1M NaOH, acetonitrile and methanol. Capillary electrophoresis with PB-PSS coated capillaries was successfully applied to quantitatively investigate the stability of bovine serum albumin, ovomucoid, β-lactoglobulin and lysozyme in simulated gastrointestinal fluids. β-lactoglobulin A and β-lactoglobulin B were both stable in simulated gastric fluid with degradation percentages of 34.3% and 17.2% after 60min of incubation, respectively. Bovine serum albumin, ovomucoid and lysozyme were stable in simulated intestinal fluid with degradation percentages of 17.7%, 23.4% and 22.8% after 60min of incubation, respectively. The superiority of the proposed method over sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and capillary electrophoresis with untreated fused silica capillaries was demonstrated and emphasized.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Domain growth, budding, and fission in phase-separating self-assembled fluid bilayers.

    PubMed

    Laradji, Mohamed; Sunil Kumar, P B

    2005-12-08

    A systematic investigation of the phase-separation dynamics in self-assembled binary fluid vesicles and open membranes is presented. We use large-scale dissipative particle dynamics to explicitly account for solvent, thereby allowing for numerical investigation of the effects of hydrodynamics and area-to-volume constraints. In the case of asymmetric lipid composition, we observed regimes corresponding to coalescence of flat patches, budding, vesiculation, and coalescence of caps. The area-to-volume constraint and hydrodynamics have a strong influence on these regimes and the crossovers between them. In the case of symmetric mixtures, irrespective of the area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The same exponent is also found in the case of open membranes with symmetric composition.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  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. 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.

  2. 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.

  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. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. New Approaches for Microscopic Hydrodynamics for the Study of Fluid-Structure Interactions Subject to Thermal Fluctuations

    NASA Astrophysics Data System (ADS)

    Atzberger, Paul

    2012-02-01

    Many problems in fluid mechanics involve the interaction of a hydrodynamic flow with an elastic structure. Recent advances in biology and engineering further motivate such studies at small length and time scales. At such scales traditional continuum mechanics descriptions must be augmented to take into account microscopic phenomena, such as spontaneous thermal fluctuations. This presents a variety of challenges both in formulating appropriate physical models and in computational simulation. In the context of fluid-structure interactions, additional challenges arise from the often subtle interplay between elastic mechanics, hydrodynamic coupling, and thermal fluctuations. In this talk, we present a set of new approaches which address central mathematical, physical, and computational issues for how to incorporate in the description of such fluid-structure interactions thermal fluctuations. We also address important numerical issues in the approximation of the resulting stochastic partial differential equations. We also discuss results for specific illustrative applications including studies of polymeric fluids, vesicles, gels, and lipid bilayer membranes.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  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. 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.

  4. 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

  5. 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.

  6. 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.

  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. 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.

  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. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  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. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Effects of Fluid-Structure Interaction on Dynamic Response of Composite Structures: Experimental and Numerical Studies

    DTIC Science & Technology

    2013-08-01

    composite structures in water and air to enhance the understanding of the effects of fluid-structure interaction on marine composite structural...naval structures are in continuous contact with a water medium. As a result, proper understanding of fluid-structure interaction is important for a...Fluid-Structure Interaction (FSI) is more critical for the former structures. The objective of this study was to investigate the effect of water on

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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 SiO2 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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).

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  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. 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.

  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. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Structure of electrorheological fluids: a dielectric study of chain formation.

    PubMed

    Horváth, B; Szalai, I

    2012-12-01

    A dielectric measurement method has been proposed to apply to the study of the microstructure of electrorheological (ER) fluids. To test our measurement method the dielectric permittivity increment caused by pair and chain formation was measured in dilute Brownian ER fluids composed of silicone oil and nanosized silica particles. The critical values of the electric field required to induce structure formation were experimentally determined from the electric field dependence of the measured permittivity increment. From the electric field induced time evolution of the relative permittivity of ER fluids, the characteristic times of the pair and chain formation were calculated. Our experimental results for the time constants are in good agreement with the corresponding theoretical data obtained from the Eyring theory.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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).

  6. 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.

  7. 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

  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 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

  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. 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.

  11. 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

  12. Control of Low Reynolds Number Flows with Fluid Structure Interactions

    DTIC Science & Technology

    2014-02-02

    2010, pp. 539- 544. [55] Yilmaz, T.O., and Rockwell, D., "Flow Structure on Finite-Span Wings Due to Pitch - up Motion," Journal of Fluid...flows with large separated regions are also typical for flapping - wing MAVs. Leading-edge vortices are known to enhance lift in unsteady aerodynamics...effective for delta wings [6]; 2) instability of the separation bubble [7]; and 3) wake instability [8,9]. Flow control research on separated flows

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  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. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Structural Anisotropy and Orientation-Induced Casimir Repulsion in Fluids

    DTIC Science & Technology

    2011-05-10

    Physics , Lecture Notes in Physics , edited by D. A. R. Dalvit, P. W. Milonni, D. C. Roberts, and F. S. S. Rosa (Springer, New York) (in press). [53] A... PHYSICAL REVIEW A 83, 052503 (2011) Structural anisotropy and orientation-induced Casimir repulsion in fluids Alexander P. McCauley,1 F. S. S. Rosa...2,3 Alejandro W. Rodriguez,4,5 John D. Joannopoulos,1 D. A. R. Dalvit,3 and Steven G. Johnson4 1Department of Physics , Massachusetts Institute of

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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).

  12. 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).

  13. 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

  14. 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.

  15. 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.

  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. 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.

  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. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. Bilayer Graphene Electromechanical Systems

    NASA Astrophysics Data System (ADS)

    Champagne, Alexandre; Storms, Matthew; Yigen, Serap; Reulet, Bertrand

    Bilayer graphene is an outstanding electromechanical system, and its electronic and mechanical properties, as well as their coupling, are widely tunable. To the best of our knowledge, simultaneous charge transport and mechanical spectroscopy (via RF mixing) has not been realized in bilayer graphene. We present data showing clear electromechanical resonances in three suspended bilayer devices whose length range from 1 to 2 microns. We first describe the low-temperature current annealing of the devices which is crucial to achieve the transconductance, I -VG , necessary to implement a RF mixing detection method. We describe our RF mixing circuit and data. We measure clear mechanical resonances ranging in frequency from 50 to 140 MHz. We show that we can smoothly tune the resonance frequencies of our bilayer resonators with mechanical strain applied via a backgate voltage. We measure quality factors up to 4000. We briefly discuss the effects of the RF driving power on the dispersion of the mechanical resonance. We aim to use these high quality mechanical resonance as a mechanical sensor of the bilayer quantum Hall phase transitions. We show initial data of a bilayer mechanical resonance as a function of magnetic field and quantum Hall phase transitions.

  14. Thermophysical Fluid Dynamics: the Key to the Structures of Fluid Objects

    NASA Astrophysics Data System (ADS)

    Houben, H.

    2013-12-01

    It has become customary to model the hydrodynamics of fluid planets like Jupiter and Saturn by spinning up general circulation models until they reach a statistical steady state. This approach is physically sound, based on the thermodynamic expectation that the system will eventually achieve a state of maximum entropy, but the models have not been specifically designed for this purpose. Over the course of long integrations, numerical artifacts can drive the system to a state that does not correspond to the physically realistic end state. A different formulation of the governing equations promises better results. The equations of motion are recast as scalar conservation laws in which the diabatic and irreversible terms (both entropy-changing) are clearly identified. The balance between these terms defines the steady state of the system analytically, without the need for any temporal integrations. The conservation of mass in this system is trivial. Conservation of angular momentum replaces the zonal momentum equation and determines the zonal wind from a balance between the tidal torque and frictional dissipation. The principle of wave-mean flow non-interaction is preserved. Bernoulli's Theorem replaces the energy equation. The potential temperature structure is determined by the balance between work done against friction and heat transfer by convection and radiation. An equation of state and the traditional momentum equations in the meridional plane are sufficient to complete the model. Based on the assumption that the final state vertical and meridional winds are small compared to the zonal wind (in any case they are impossible to predict ab initio as they are driven by wave flux convergences), these last equations determine the pressure and density (and hence gravity) fields of the basic state. The thermal wind relation (in its most general form with the axial derivative of the zonal wind balancing the baroclinicity) is preserved. The model is not hydrostatic (in

  15. Specifics of freezing of Lennard-Jones fluid confined to molecularly thin layers

    NASA Astrophysics Data System (ADS)

    Vishnyakov, Aleksey; Neimark, Alexander V.

    2003-04-01

    Freezing of a Lennard-Jones fluid between solid surfaces was studied using grand canonical Monte Carlo and molecular dynamics simulations. We explored the formation of frozen phases of hexagonal and orthorhombic symmetry in mono-, bi-, and tri-layer structures. The freezing transition, the type of lattice, and translational and orientational ordering were identified on the basis of orientational order parameters, in-plane two-body and three-body translational correlation functions, orientational correlation functions, and analysis of molecular mobilities. We have found that the freezing temperature is a nonmonotonous function of the pore width: orthorhombic bi-layer freezes at lower temperatures than hexagonal monolayer and hexagonal bi-layer. As the pore width increases, the transition from a hexagonal monolayer to an orthorhombic bi-layer occurred via disordered liquidlike and quasi-long-range four-fold ordered bi-layers. The latter, "quadratic" structure is characterized by an algebraically decaying four-fold orientational correlation function. The transition from crystalline hexagonal bi-layer to orthorhombic tri-layer occurs through a bi-layer structure with two uncoupled hexagonal monolayers. The quadratic phase was observed also as an intermediate structure during freezing of a liquidlike bi-layer into an orthorhombic quasi-crystal. The formation of the quadratic phase was associated with step-wise densification of fluid, a sharp increase of the local orientational order parameter, and a significant reduction of fluid mobility. In the process of solidification, the system passed through a sequence of high-density jammed structures, in which the four-fold symmetry developed progressively, as the temperature decreased.

  16. Multi-dimensional arbitrary Lagrangian-Eulerian method for dynamic fluid-structure interaction. [LMFBR

    SciTech Connect

    Wang, C.Y.; Zeuch, W.R.

    1982-01-01

    This paper describes an arbitrary Lagrangian-Eulerian method for analyzing fluid-structure interactions in fast-reactor containment with complex internal structures. The fluid transient can be calculated either implicitly or explicitly, using a finite-difference mesh with vertices that may be moved with the fluid (Lagrangian), held fixed (Eulerian), or moved in any other prescribed manner (hybrid Lagrangian Eulerian). The structural response is computed explicitly by two nonlinear, elastic-plastic finite-element modules formulated in corotational coordinates. Interaction between fluid and structure is accounted for by enforcing the interface boundary conditions. The method has convincing advantages in treating complicated phenomena such as flow through perforated structures, large material distortions, flow around corners and irregularities, and highly contorted fluid boundaries. Several sample problems are given to illustrate the effectiveness of this arbitrary Lagrangian-Eulerian method.

  17. Fabrication of CuInS2 films from electrodeposited Cu/In bilayers: effects of preheat treatment on their structural, photoelectrochemical and solar cell properties.

    PubMed

    Lee, Sun Min; Ikeda, Shigeru; Yagi, Tetsuro; Harada, Takashi; Ennaoui, Ahmed; Matsumura, Michio

    2011-04-14

    Polycrystalline CuInS(2) films were fabricated by sulfurization of electrodeposited Cu and In metallic precursor films in a Cu-rich composition at 520 °C in H(2)S (5% in Ar). Structural analyses revealed that the adherence of the thus-formed CuInS(2) film to the Mo substrate was strongly dependent on heating profiles of the Cu/In bilayer film: a CuInS(2) film with poor adherence having many crevices was formed when the Cu/In bilayer film was heated monotonously from room temperature to 520 °C in Ar within 25 min followed by sulfurization, whereas CuInS(2) films with good adherence were obtained when the Cu/In films were pretreated at 110 °C in Ar for 10-60 min just before increasing the temperature up to 520 °C for sulfurization. It was also clarified that the CuInS(2) film obtained without 110 °C pretreatment had pinholes inside the film, whereas the CuInS(2) films formed after 110 °C pretreatment showed no notable pinholes. Photoelectrochemical responses of these CuInS(2) films in an electrolyte solution containing Eu(III) indicated that the CuInS(2) films obtained after 110 °C pretreatment had higher external quantum efficiency (EQE) values than those of films obtained without 110 °C pretreatment, mainly due to better adherence of 110 °C pretreated CuInS(2) films to the Mo substrate than the CuInS(2) film obtained without 110 °C pretreatment. The performance of solar cells with an Al:ZnO/Zn(S,O)/CdS/CuInS(2)/Mo structure also depended on the structural characteristics of the CuInS(2) films, i.e., preliminary conversion efficiencies of ca. 5% were obtained for devices based on the CuInS(2) films obtained after 110 °C pretreatment, whereas the device prepared by the CuInS(2) film without 110 °C pretreatment showed the conversion efficiency less than 1.5%.

  18. Effect of variations in the structure of a polyleucine-based alpha-helical transmembrane peptide on its interaction with phosphatidylethanolamine Bilayers.

    PubMed

    Liu, Feng; Lewis, Ruthven N A H; Hodges, Robert S; McElhaney, Ronald N

    2004-10-01

    High-sensitivity differential scanning calorimetry and Fourier transform infrared spectroscopy were used to study the interaction of a cationic alpha-helical transmembrane peptide, acetyl-Lys2-Leu24-Lys2-amide (L24), and members of the homologous series of zwitterionic n-saturated diacyl phosphatidylethanolamines (PEs). Analogs of L24, in which the lysine residues were replaced by 2,3-diaminopropionic acid (acetyl-DAP2-Leu24-DAP2-amide (L24DAP)) or in which a leucine residue at each end of the polyleucine sequence was replaced by a tryptophan (Ac-K2-W-L22-W-K2-amide (WL22W)), 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 PE bilayers is altered by these peptides in a hydrophobic mismatch-independent manner, in contrast to the hydrophobic mismatch-dependent manner observed previously with zwitterionic phosphatidylcholine (PC) and anionic phosphatidylglycerol (PG) bilayers. Moreover, all three peptides reduce the phase transition temperature to a greater extent in PE bilayers than in PC and PG bilayers, indicating a greater disruption of PE gel-phase bilayer organization. Moreover, the lysine-anchored L24 reduces the phase transition temperature, enthalpy, and the cooperativity of PE bilayers to a much greater extent than DAP-anchored L24DAP, whereas replacement of the terminal leucines by tryptophan residues (Ac-K2-W-L22-W-K2-amide) only slightly attenuates the effects of this peptide on the chain-melting phase transition of the host PE bilayers. All three peptides form very stable alpha-helices in PE bilayers, but small conformational changes occur in response to mismatch between peptide hydrophobic length and gel-state lipid bilayer hydrophobic thickness. These results suggest that the lysine snorkeling plays a significant role in the peptide-PE interactions and that cation

  19. Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins.

    PubMed

    Reif, Maria M; Winger, Moritz; Oostenbrink, Chris

    2013-02-12

    The GROMOS 54A8 force field [Reif et al. J. Chem. Theory Comput.2012, 8, 3705-3723] is the first of its kind to contain nonbonded parameters for charged amino acid side chains that are derived in a rigorously thermodynamic fashion, namely a calibration against single-ion hydration free energies. Considering charged moieties in solution, the most decisive signature of the GROMOS 54A8 force field in comparison to its predecessor 54A7 can probably be found in the thermodynamic equilibrium between salt-bridged ion pair formation and hydration. Possible shifts in this equilibrium might crucially affect the properties of electrolyte solutions or/and the stability of (bio)molecules. It is therefore important to investigate the consequences of the altered description of charged oligoatomic species in the GROMOS 54A8 force field. The present study focuses on examining the ability of the GROMOS 54A8 force field to accurately model the structural properties of electrolyte solutions, lipid bilayers, and proteins. It is found that (i) aqueous electrolytes involving oligoatomic species (sodium acetate, methylammonium chloride, guanidinium chloride) reproduce experimental salt activity derivatives for concentrations up to 1.0 m (1.0-molal) very well, and good agreement between simulated and experimental data is also reached for sodium acetate and methylammonium chloride at 2.0 m concentration, while not even qualitative agreement is found for sodium chloride throughout the whole range of examined concentrations, indicating a failure of the GROMOS 54A7 and 54A8 force-field parameter sets to correctly account for the balance between ion-ion and ion-water binding propensities of sodium and chloride ions; (ii) the GROMOS 54A8 force field reproduces the liquid crystalline-like phase of a hydrated DPPC bilayer at a pressure of 1 bar and a temperature of 323 K, the area per lipid being in agreement with experimental data, whereas other structural properties (volume per lipid, bilayer

  20. Extended ALE Method for fluid-structure interaction problems with large structural displacements

    NASA Astrophysics Data System (ADS)

    Basting, Steffen; Quaini, Annalisa; Čanić, Sunčica; Glowinski, Roland

    2017-02-01

    Standard Arbitrary Lagrangian-Eulerian (ALE) methods for the simulation of fluid-structure interaction (FSI) problems fail due to excessive mesh deformations when the structural displacement is large. We propose a method that successfully deals with this problem, keeping the same mesh connectivity while enforcing mesh alignment with the structure. The proposed Extended ALE Method relies on a variational mesh optimization technique, where mesh alignment with the structure is achieved via a constraint. This gives rise to a constrained optimization problem for mesh optimization, which is solved whenever the mesh quality deteriorates. The performance of the proposed Extended ALE Method is demonstrated on a series of numerical examples involving 2D FSI problems with large displacements. Two-way coupling between the fluid and structure is considered in all the examples. The FSI problems are solved using either a Dirichlet-Neumann algorithm, or a Robin-Neumann algorithm. The Dirichlet-Neumann algorithm is enhanced by an adaptive relaxation procedure based on Aitken's acceleration. We show that the proposed method has excellent performance in problems with large displacements, and that it agrees well with a standard ALE method in problems with mild displacement.

  1. ADP ribosylation factor 6 binding to phosphatidylinositol 4,5-bisphosphate-containing vesicles creates defects in the bilayer structure: an electron spin resonance study.

    PubMed Central

    Ge, M; Cohen, J S; Brown, H A; Freed, J H

    2001-01-01

    The effects of binding of myristoylated ADP ribosylation factor 6 (myr-ARF6), an activator of phospholipase D (PLD), to a model membrane were investigated using an electron spin resonance (ESR) labeling technique. Initial studies were conducted in vesicles composed of 1-palmitoyl-2-oleoyl phosphatidylethanolamine, dipalmitoylphosphatidylcholine, phosphatidylinositol 4,5-biphosphate (PIP(2)), and cholesterol. Recombinant ARF6 binding significantly enhances defects in both the headgroup and acyl-chain regions of the membrane, which are revealed by the emergence of sharp components in the spectra from a headgroup label, 1,2-dipalmitoylphosphatidyl-2,2,6,6-tetramethyl-1-piperidinyloxy-choline (DPPTC), and a chain label, 10PC, after myr-ARF6 binding. Binding of non-myristoylated ARF6 (non-ARF6) shows markedly reduced effects. Interestingly, no change in spectra from DPPTC was observed upon myr-ARF6 binding when PIP(2) in the vesicles was replaced by other negatively charged lipids, including phosphatidylinositol, phosphatidylserine, and phosphatidylglycerol, even when normalized for charge. The production of the sharp peak appears to be a specific event, because another GTP binding protein, CDC42, which binds PIP(2) and activates PLD, fails to induce changes in vesicle structure. These results suggest a previously unappreciated role for ARF in mediating a protein/lipid interaction that produces defects in lipid bilayers. This function may serve as an initial event in destabilizing membrane structure for subsequent membrane fusion or biogenesis of vesicles. PMID:11463641

  2. Global Model Reduction for Fluid-Structure Interaction in Flapping Flexible Wings

    NASA Astrophysics Data System (ADS)

    Wei, Mingjun; Yang, Tao

    2009-11-01

    Reduced-order models (ROMs) for fully-coupled fluid-structure interaction problems are desired in many applications (e.g. design of flapping-wing Micro Air Vehicles). Traditional approach is to build ROMs individually for fluid and solid and couple them through the interface. In this work, we suggest an approach to apply model reduction globally on a uniform description of fluid and solid in Eulerian framework. The idea has been made possible by a set of combined fluid-structue equations, where solid properties are presented as extra terms to Navier-Stokes equations. Then, typical Proper Orthogonal Decomposition (POD)/Galerkin projection can be used for model reduction as in most fluid-only problems, with special care of the extra ``solid'' terms. In the example, we show that one can capture most energy by only a few POD modes. More importantly, the leading POD modes show the signatures of both fluid flow and solid structure.

  3. Structural cooling fluid tube for supporting a turbine component and supplying cooling fluid

    SciTech Connect

    Charron, Richard; Pierce, Daniel

    2015-02-24

    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. As such, the shaft cover support accomplishes in a single component what was only partially accomplished in two components in conventional configurations. 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 engine. The shaft cover support has a radially extending region that is offset from the inlet and outlet that enables the shaft cover support to surround the transition, thereby reducing the overall length of this section of the engine.

  4. Bi-layer channel structure-based oxide thin-film transistors consisting of ZnO and Al-doped ZnO with different Al compositions and stacking sequences

    NASA Astrophysics Data System (ADS)

    Cho, Sung Woon; Yun, Myeong Gu; Ahn, Cheol Hyoun; Kim, So Hee; Cho, Hyung Koun

    2015-03-01

    Zinc oxide (ZnO)-based bi-layers, consisting of ZnO and Al-doped ZnO (AZO) layers grown by atomic layer deposition, were utilized as the channels of oxide thin-film transistors (TFTs). Thin AZO layers (5 nm) with different Al compositions (5 and 14 at. %) were deposited on top of and beneath the ZnO layers in a bi-layer channel structure. All of the bi-layer channel TFTs that included the AZO layers showed enhanced stability (Δ V Th ≤ 3.2 V) under a positive bias stress compared to the ZnO single-layer channel TFT (Δ V Th = 4.0 V). However, the AZO/ZnO bi-layer channel TFTs with an AZO interlayer between the gate dielectric and the ZnO showed a degraded field effect mobility (0.3 cm2/V·s for 5 at. % and 1.8 cm2/V·s for 14 at. %) compared to the ZnO single-layer channel TFT (5.5 cm2/V·s) due to increased scattering caused by Al-related impurities near the gate dielectric/channel interface. In contrast, the ZnO/AZO bi-layer channel TFTs with an AZO layer on top of the ZnO layer exhibited an improved field effect mobility (7.8 cm2/V·s for 14 at. %) and better stability. [Figure not available: see fulltext.

  5. Properties of a Hydrated Excess Proton Near the Cholesterol-Containing Phospholipid Bilayer

    NASA Astrophysics Data System (ADS)

    Yamashita, Takefumi

    In order to study effects of cholesterol (Chol) on the interaction between the excess proton and the phospholipid bilayer, reactive molecular dynamics simulations are performed with the multistate empirical valence bond model. Although Chol significantly affects the bilayer structure, the proton affinity of the Chol-containing phospholipid bilayer is as high as that of the pure phospholipid bilayer. It is found that the excess proton is strongly trapped by the carbonyl groups and the phosphate groups of the phospholipids. This structure is quite similar to the structure observed in the pure lipid bilayer systems.

  6. Silicate-COH melt and fluid structure, their physicochemical properties, and partitioning of nominally refractory oxides between melts and fluids

    NASA Astrophysics Data System (ADS)

    Mysen, Bjorn O.

    2012-09-01

    Structural characterization of silicate melts and aqueous fluids equilibrated at pressures and temperatures corresponding to the Earth's interior requires measurements in-situ while the samples are at the pressure and temperature of interest. To this end, structure and structure-property relations of melts and coexisting fluids in silicate-COH systems have been determined at temperatures up to 1000 °C and at pressures to ~ 2.0 GPa. The water component of silicate-H2O systems shows aqueous fluids, supercritical fluids, and hydrous melts to comprise molecular H2O (H2O0) and OH-groups, bonded to Si4+ and likely Al3+. The abundance-ratio, OH/H2O0, is positively correlated with temperature. The extent of hydrogen bonding diminishes with temperature and cannot be detected at above ~ 450 °C and ~ 0.4 GPa. Its ∆H is near 10 kJ/mol for water dissolved in hydrous melt as compared with ≥ 20 kJ/mol for pure H2O. Hydrogen bonding cannot, therefore, be the cause of property behavior in hydrous magmatic systems because the temperature in hydrous magmatic systems exceeds 600 °C. In SiO2-H2O fluid, silicate solute comprises Q0 and Q1 species with a ∆H of the polymerization reaction of ~ 15 kJ/mol assuming no pressure effect. In the Qn-notations, the value of n indicates the number of bridging oxygen in a silicate or aluminosilicate polymeric species. In chemically more complex alkali aluminosilicate systems, the silicate speciation in melts, in aqueous fluid, and in supercritical fluids comprises the same Q-species, but their abundance and proportions differ with the more polymerized species dominant in melt. Silicate-water interaction in the fluids, melts and supercritical fluids is described with the expression, 12Q3 + 13H2O ⇋ 2Q2 + 6Q1 + 4Q0 with ∆H = 400-450 kJ/mol. The solubility of geochemically important trace elements such as, for example, HFSE in silicate-saturated aqueous fluid under deep crustal and upper mantle pressure and temperature conditions is orders

  7. Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation

    PubMed Central

    Toraya, Shuichi; Javkhlantugs, Namsrai; Mishima, Daisuke; Nishimura, Katsuyuki; Ueda, Kazuyoshi; Naito, Akira

    2010-01-01

    Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state 31P and 13C NMR spectroscopy. 31P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (Tc) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the Tc. 13C NMR spectra of site-specifically 13C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers. PMID:21081076

  8. Dependence of inverse-spin Hall effect and spin-rectified voltage on tantalum thickness in Ta/CoFeB bilayer structure

    SciTech Connect

    Kim, Sang-Il; Seo, Min-Su; Park, Seung-Young; Kim, Dong-Jun; Park, Byong-Guk

    2015-01-19

    Ta-layer thickness (t{sub Ta}) dependence of the measured DC voltage V from the inverse-spin Hall effect (ISHE) in Ta/CoFeB bilayer structure is experimentally investigated using the ferromagnetic resonance in the TE{sub 011} resonant cavity. The ISHE signals excluding the spin-rectified effect (SRE) were separated from the fitted curve of V against t{sub Ta}. For t{sub Ta} ≈ λ{sub Ta} (Ta-spin diffusion length = 2.7 nm), the deviation in ISHE voltage V{sub ISH} between the experimental and theoretical values is significantly increased because of the large SRE contribution, which also results in a large deviation in the spin Hall angle θ{sub SH} (from 10% to 40%). However, when t{sub Ta} ≫ λ{sub Ta}, the V{sub ISH} values are consistent with theoretical values because the SRE terms become negligible, which subsequently improves the accuracy of the obtained θ{sub SH} within 4% deviation. The results will provide an outline for an accurate estimation of the θ{sub SH} for materials with small λ value, which would be useful for utilizing the spin Hall effect in a 3-terminal spintronic devices in which magnetization can be controlled by in-plane current.

  9. The influence of oscillating electromagnetic fields on membrane structure and function: Synthetic liposome and natural membrane bilayer systems with direct application to the controlled delivery of chemical agents

    SciTech Connect

    Liburdy, R.P.; de Manincor, D.; Fingado, B.

    1989-09-01

    Investigations have been conducted to determine if an imposed electromagnetic field can influence membrane transport, and ion and drug permeability in both synthetic and natural cell membrane systems. Microwave fields enhance accumulation of sodium in the lymphocyte and induce protein shedding at Tc. Microwaves also trigger membrane permeability of liposome systems under specific field exposure conditions. Sensitivity varies in a defined way in bilayers displaying a membrane structural phase transition temperature, Tc; maximal release was observed at or near Tc. Significantly, liposome systems without a membrane phase transition were also found to experience permeability increases but, in contrast, this response was temperature independent. The above results indicate that field-enhanced drug release occurs in liposome vesicles that possess a Tc as well as non-Tc liposomes. Additional studies extend non-Tc liposome responses to the in vivo case in which microwaves trigger Gentamicin release from a liposome depot'' placed subcutaneously in the rat hind leg. In addition, evidence is provided that cell surface sequestered liposomes can be triggered by microwave fields to release drugs directly into target cells. 24 refs., 6 figs.

  10. Finite-size effects on electronic structure and local properties in passivated AA-stacked bilayer armchair-edge graphene nanoribbons.

    PubMed

    Chen, Xiongwen; Shi, Zhengang; Xiang, Shaohua; Song, Kehui; Zhou, Guanghui

    2017-03-01

    Based on the tight-binding model and dual-probe scanning tunneling microscopy technology, we theoretically investigate the electronic structure and local property in the passivated AA-stacked bilayer armchair-edge graphene nanoribbons (AABLAGNRs). We show that they are highly sensitive to the size of the ribbons, which is evidently different from the single-layer armchair-edge graphene nanoribbons. The '3p' rule only applies to the narrow AABLGNRs. Namely, in the passivated 3p- and (3p  +  1)-AABLGNRs, the narrow ribbons are semiconducting while the medium and wide ribbons are metallic. Although the passivated (3p  +  2)-AABLGNRs are metallic, the '3j' rule only applies to the narrow and medium ribbons. Namely, electrons are in the semiconducting states at sites of line 3j while they are in the metallic states at other sites. This induces a series of parallel and discrete metallic channels, consisting of lines 3j  -  1 and 3j  -  2, for the low-energy electronic transports. In the passivated wide (3p  +  2)-AABLGNRs, all electrons are in the metallic states. Additionally, the '3p' and '3j' rules are controllable to disappear and reappear by applying an external perpendicular electric field. Resultantly, an electric filed-driven current switch can be realized in the passivated narrow and medium (3p  +  2)-AABLGNRs.

  11. Finite-size effects on electronic structure and local properties in passivated AA-stacked bilayer armchair-edge graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Chen, Xiongwen; Shi, Zhengang; Xiang, Shaohua; Song, Kehui; Zhou, Guanghui

    2017-03-01

    Based on the tight-binding model and dual-probe scanning tunneling microscopy technology, we theoretically investigate the electronic structure and local property in the passivated AA-stacked bilayer armchair-edge graphene nanoribbons (AABLAGNRs). We show that they are highly sensitive to the size of the ribbons, which is evidently different from the single-layer armchair-edge graphene nanoribbons. The ‘3p’ rule only applies to the narrow AABLGNRs. Namely, in the passivated 3p- and (3p  +  1)-AABLGNRs, the narrow ribbons are semiconducting while the medium and wide ribbons are metallic. Although the passivated (3p  +  2)-AABLGNRs are metallic, the ‘3j’ rule only applies to the narrow and medium ribbons. Namely, electrons are in the semiconducting states at sites of line 3j while they are in the metallic states at other sites. This induces a series of parallel and discrete metallic channels, consisting of lines 3j  -  1 and 3j  -  2, for the low-energy electronic transports. In the passivated wide (3p  +  2)-AABLGNRs, all electrons are in the metallic states. Additionally, the ‘3p’ and ‘3j’ rules are controllable to disappear and reappear by applying an external perpendicular electric field. Resultantly, an electric filed-driven current switch can be realized in the passivated narrow and medium (3p  +  2)-AABLGNRs.

  12. Structural characterization of hemoglobins from Monilifera and Frenulata tubeworms (Siboglinids): first discovery of giant hexagonal-bilayer hemoglobin in the former "Pogonophora" group.

    PubMed

    Meunier, Cédric; Andersen, Ann C; Bruneaux, Matthieu; Le Guen, Dominique; Terrier, Peran; Leize-Wagner, Emmanuelle; Zal, Franck

    2010-01-01

    Siboglinids are symbiotic polychete annelids having hemoglobins as essential oxygen- and sulfide-carriers for their endosymbiotic bacteria. We analyzed the structure of the hemoglobins from two species of siboglinids: the monilifera Sclerolinum contortum and the frenulata Oligobrachia webbi (i.e. haakonmosbiensis) from Norwegian cold seeps. Measured by Multi-Angle Laser Light Scattering (MALLS), Sclerolinum shows a 3190+/-50 kDa hexagonal bilayer hemoglobin (HBL-Hb) and a 461+/-46 kDa ring-Hb, just as vestimentifera, whereas Oligobrachia has a 409+/-3.7 kDa ring-Hb only. Electrospray Ionization-Mass Spectrometry (ESI-MS) showed Sclerolinum HBL-Hb composed of seven monomeric globins (15-16 kDa), three disulfide-bonded globin heterodimers and three linkers. The heterodimers always contain globin-b (15814.4+/-1.5 Da). Sclerolinum ring-Hb is composed of globins and dimers with identical masses as its HBL-Hb, but lacks linkers. Oligobrachia ring-Hb has three globin monomers (14-15 kDa) only, with no disulfide-bonded dimers. Comparison of Sclerolinum hemoglobins between Storegga and Haakon Mosby Mud Volcano, using the normalized height of deconvoluted ESI-MS peaks, shows differences in globin monomers abundances that could reflect genetic differences or differential gene expression between distinct seep populations. The discovery of HBL-Hb in Sclerolinum is a new element supporting the hypothesis of monilifera being phylogenetically more closely related to vestimentifera, than to frenulata.

  13. Mesoscopic simulation for the structures of magnetic fluids

    NASA Astrophysics Data System (ADS)

    Li, Wuming; Li, Qiang

    2017-02-01

    The microstructures of magnetic fluids are simulated using a dissipative particle dynamics (DPD)-based method and are fundamentally important for controlling the macroscopic properties of magnetic fluids and understanding the corresponding rheological behaviors in diverse engineering applications. The cubic polynomial spline function often used as smoothing function in smoothed particle hydrodynamics (SPH) is employed as the conservative force potential function, which can provide a stronger conservative force weight function than the conventional weight function by choosing properly the cutoff radius between the dissipative particles. By employing the above method, the desired results are obtained for both stronger and weaker magnetic particle-particle interaction under the condition of varying the mass of the dissipative particles. In addition, the influences of the magnetic particle-particle interaction and of the magnetic particle area fraction on the microstructure of magnetic fluids are also investigated, respectively, and the obtained results agree qualitatively well with those in the literature obtained by other numerical approaches and experiments. The numerical solutions of the mean equilibrium velocities of the magnetic and dissipative particles are also calculated and approximate the corresponding theoretical values very well. Therefore the employed DPD-based method is highly effective in the simulation of the microstructure of magnetic fluids.

  14. Stability of Numerical Interface Conditions for Fluid/Structure Interaction

    SciTech Connect

    Banks, J W; Sjogreen, B

    2009-08-13

    In multi physics computations, where a compressible fluid is coupled with a linearly elastic solid, it is standard to enforce continuity of the normal velocities and of the normal stresses at the interface between the fluid and the solid. In a numerical scheme, there are many ways that the velocity- and stress-continuity can be enforced in the discrete approximation. This paper performs a normal mode analysis to investigate the stability of different numerical interface conditions for a model problem approximated by upwind type of finite difference schemes. The analysis shows that depending on the ratio of densities between the solid and the fluid, some numerical interface conditions are stable up to the maximal CFL-limit, while other numerical interface conditions suffer from a severe reduction of the stable CFL-limit. The paper also presents a new interface condition, obtained as a simplified charcteristic boundary condition, that is proved to not suffer from any reduction of the stable CFL-limit. Numerical experiments in one space dimension show that the new interface condition is stable also for computations with the non-linear Euler equations of compressible fluid flow coupled with a linearly elastic solid.

  15. Photon correlation spectroscopy of bilayer lipid membranes.

    PubMed Central

    Crilly, J F; Earnshaw, J C

    1983-01-01

    Light scattering by thermal fluctuations on simple monoglyceride bilayer membranes has been used to investigate the viscoelastic properties of these structures. Spectroscopic analysis of these fluctuations (capillary waves) permits the nonperturbative measurement of the interfacial tension and a shear interfacial viscosity acting normal to the membrane plane. The methods were established by studies of solvent and nonsolvent bilayers of glycerol monooleate (GMO). Changes in the tension of GMO/n-decane membranes induced by altering the composition of the parent solution were detected and quantified. In a test of the reliability of the technique controlled variations of the viscosity of the aqueous bathing solution were accurately monitored. The technique was applied to solvent-free bilayers formed from dispersions of GMO in squalane. The lower tensions observed attested to the comparative absence of solvent in such bilayers. In contrast to the solvent case, the solvent-free membranes exhibited a significant transverse shear viscosity, indicative of the enhanced intermolecular interactions within the bilayer. PMID:6838962

  16. Diffusion coefficients in leaflets of bilayer membranes.

    PubMed

    Seki, Kazuhiko; Mogre, Saurabh; Komura, Shigeyuki

    2014-02-01

    We study diffusion coefficients of liquid domains by explicitly taking into account the two-layered structure called leaflets of the bilayer membrane. In general, the velocity fields associated with each leaflet are different and the layers sliding past each other cause frictional coupling. We obtain analytical results of diffusion coefficients for a circular liquid domain in a leaflet, and quantitatively study their dependence on the interleaflet friction. We also show that the diffusion coefficients diverge in the absence of coupling between the bilayer and solvents, even when the interleaflet friction is taken into account. In order to corroborate our theory, the effect of the interleaflet friction on the correlated diffusion is examined.

  17. In situ Raman spectroscopic investigation of the structure of subduction-zone fluids

    USGS Publications Warehouse

    Mibe, Kenji; Chou, I.-Ming; Bassett, William A.

    2008-01-01

    In situ Raman spectra of synthetic subduction-zone fluids (KAlSi3O8-H2O system) were measured to 900?? and 2.3 GPa using a hydrothermal diamond-anvil cell. The structures of aqueous fluid and hydrous melt become closer when conditions approach the second critical endpoint. Almost no three-dimensional network was observed in the supercritical fluid above 2 GPa although a large amount of silicate component is dissolved, suggesting that the physical and chemical properties of these phases change drastically at around the second critical endpoint. Our experimental results indicate that the fluids released from a subducting slab change from aqueous fluid to supercritical fluid with increasing depth under the volcanic arcs. Copyright 2008 by the American Geophysical Union.

  18. Modelling of fluid-structure interaction with multiphase viscous flows using an immersed-body method

    NASA Astrophysics Data System (ADS)

    Yang, P.; Xiang, J.; Fang, F.; Pavlidis, D.; Latham, J.-P.; Pain, C. C.

    2016-09-01

    An immersed-body method is developed here to model fluid-structure interaction for multiphase viscous flows. It does this by coupling a finite element multiphase fluid model and a combined finite-discrete element solid model. A coupling term containing the fluid stresses is introduced within a thin shell mesh surrounding the solid surface. The thin shell mesh acts as a numerical delta function in order to help apply the solid-fluid boundary conditions. When used with an advanced interface capturing method, the immersed-body method has the capability to solve problems with fluid-solid interfaces in the presence of multiphase fluid-fluid interfaces. Importantly, the solid-fluid coupling terms are treated implicitly to enable larger time steps to be used. This two-way coupling method has been validated by three numerical test cases: a free falling cylinder in a fluid at rest, elastic membrane and a collapsing column of water moving an initially stationary solid square. A fourth simulation example is of a water-air interface with a floating solid square being moved around by complex hydrodynamic flows including wave breaking. The results show that the immersed-body method is an effective approach for two-way solid-fluid coupling in multiphase viscous flows.

  19. Supported lipid bilayer/carbon nanotube hybrids

    NASA Astrophysics Data System (ADS)

    Zhou, Xinjian; Moran-Mirabal, Jose M.; Craighead, Harold G.; McEuen, Paul L.

    2007-03-01

    Carbon nanotube transistors combine molecular-scale dimensions with excellent electronic properties, offering unique opportunities for chemical and biological sensing. Here, we form supported lipid bilayers over single-walled carbon nanotube transistors. We first study the physical properties of the nanotube/supported lipid bilayer structure using fluorescence techniques. Whereas lipid molecules can diffuse freely across the nanotube, a membrane-bound protein (tetanus toxin) sees the nanotube as a barrier. Moreover, the size of the barrier depends on the diameter of the nanotube-with larger nanotubes presenting bigger obstacles to diffusion. We then demonstrate detection of protein binding (streptavidin) to the supported lipid bilayer using the nanotube transistor as a charge sensor. This system can be used as a platform to examine the interactions of single molecules with carbon nanotubes and has many potential applications for the study of molecular recognition and other biological processes occurring at cell membranes.

  20. The function and structure of the cerebrospinal fluid outflow system

    PubMed Central

    2010-01-01

    This review traces the development of our understanding of the anatomy and physiological properties of the two systems responsible for the drainage of cerebrospinal fluid (CSF) into the systemic circulation. The roles of the cranial and spinal arachnoid villi (AV) and the lymphatic outflow systems are evaluated as to the dominance of one over the other in various species and degree of animal maturation. The functional capabilities of the total CSF drainage system are presented, with evidence that the duality of the system is supported by the changes in fluid outflow dynamics in human and sub-human primates in hydrocephalus. The review also reconciles the relative importance and alterations of each of the outflow systems in a variety of clinical pathological conditions. PMID:20565964

  1. Control of the active site structure of giant bilayer hemoglobin from the Annelid Eisenia foetida using hierarchic assemblies

    SciTech Connect

    Girasole, Marco; Arcovito, Alessandro; Marconi, Augusta; Davoli, Camilla; Congiu-Castellano, Agostina; Bellelli, Andrea; Amiconi, Gino

    2005-12-05

    The active site structure of the oxygenated derivative of the main subassemblies (whole protein, dodecamers, and trimers) of the giant haemoglobin from Eisenia foetida has been characterized by x-ray absorption near edge structure spectroscopy. The data revealed a remarkable effect of the hierarchic assemblies on the active site of the subunit. Specifically, the whole protein has the same site structure of the dodecamer, while a sharp conformational transition occurs when the dodecamer is disassembled into trimers (and monomers) revealing that constraints due to the protein matrix determine the active site geometry and, consequently, the protein function in these large complexes.

  2. Light Driven Formation and Rupture of Droplet Bilayers

    PubMed Central

    Dixit, Sanhita S.; Kim, Hanyoup; Vasilyev, Arseny; Eid, Aya; Faris, Gregory W.

    2010-01-01

    We demonstrate optical manipulation of nanoliter aqueous droplets containing surfactant or lipid molecules and immersed in an organic liquid using near infrared light. The resulting emulsion droplets are manipulated using both the thermocapillary effect and convective fluid motion. Droplet pair-interactions induced in the emulsion upon optical initiation and control provide direct observations of the coalescence steps in intricate detail. Droplet-droplet adhesion (bilayer formation) is observed under several conditions. Selective bilayer rupture is also realized using the same infrared laser. The technique provides a novel approach to study thin film drainage and interface stability in emulsion dynamics. The formation of stable lipid bilayers at the adhesion interface between interacting water droplets can provide an optical platform to build droplet-based lipid bilayer assays. The technique also has relevance for understanding and improving microfluidics applications by devising Petri dish based droplet assays requiring no substrate fabrication. PMID:20361732

  3. Bilayer-thickness-mediated interactions between integral membrane proteins.

    PubMed

    Kahraman, Osman; Koch, Peter D; Klug, William S; Haselwandter, Christoph A

    2016-04-01

    Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane

  4. Swimming and pumping of helical structures in viscous fluids

    NASA Astrophysics Data System (ADS)

    Li, Lei; Spagnolie, Saverio

    2014-11-01

    Many flagellated microorganisms including E. coli swim by rotating slender helical flagella, while ciliated organisms like Paramecia swim by passing helical waves along their surfaces. We will discuss a framework for studying such problems where the Stokes equations describing viscous flow are written in helical coordinates. Analytical predictions match well with full numerical simulations, and suggest optimal geometries. This work may also aid designs in microfluidic manipulation, microswimmer engineering, and the mixing of viscous fluids.

  5. Modified Immersed Finite Element Method For Fully-Coupled Fluid-Structure Interations

    PubMed Central

    Wang, Xingshi; Zhang, Lucy T.

    2013-01-01

    In this paper, we develop a “modified” immersed finite element method (mIFEM), a non-boundary-fitted numerical technique, to study fluid-structure interactions. Using this method, we can more precisely capture the solid dynamics by solving the solid governing equation instead of imposing it based on the fluid velocity field as in the original immersed finite element (IFEM). Using the IFEM may lead to severe solid mesh distortion because the solid deformation is been over-estimated, especially for high Reynolds number flows. In the mIFEM, the solid dynamics is solved using appropriate boundary conditions generated from the surrounding fluid, therefore produces more accurate and realistic coupled solutions. We show several 2-D and 3-D testing cases where the mIFEM has a noticeable advantage in handling complicated fluid-structure interactions when the solid behavior dominates the fluid flow. PMID:24223445

  6. Photochemical on-off switching of structural color of a multi-bilayered film consisting of azobenzene-polymer liquid crystal and polyvinylalcohol

    NASA Astrophysics Data System (ADS)

    Kurihara, Seiji; Moritsugu, Masaki; Kuwahara, Yutaka; Ogata, Tomonari

    2011-10-01

    Photo-responsive multi-bilayered film consisting of azobenzene polymer liquid crystals (PAzo) and polyvinylalcohol (PVA) was prepared on a glass substrate by spin coating of the polymer solutions alternately. The reflectivity of the multi-bilayered film disappeared by annealing at 80 °C. The disappearance of the reflection by the annealing was related to the thermal out-of-plane molecular orientation of PAzo even in the multi-bilayered film, leading to a very small difference in refractive indices between PAzo and PVA. The reflectance of the multi-bilayered film was increased again by UV irradiation because of the transformation from the out-of-plane orientation to the in-plane random orientation, resulting in the restoration of difference in the refractive indices. In this way, the on-off switching of the reflection was achieved by combination of the thermally spontaneous out-of-plane molecular orientation and following photoisomerization of PAzo comprising the multi-bilayered film.

  7. Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

    DOEpatents

    Aizenberg, Joanna; Burgess, Ian B.; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

    2016-03-08

    A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

  8. Implementation of Interaction Algorithm to Non-Matching Discrete Interfaces Between Structure and Fluid Mesh

    NASA Technical Reports Server (NTRS)

    Chen, Shu-Po

    1999-01-01

    This paper presents software for solving the non-conforming fluid structure interfaces in aeroelastic simulation. It reviews the algorithm of interpolation and integration, highlights the flexibility and the user-friendly feature that allows the user to select the existing structure and fluid package, like NASTRAN and CLF3D, to perform the simulation. The presented software is validated by computing the High Speed Civil Transport model.

  9. Fluid transients in fluid-structure interaction - 1987; Proceedings of the Third Symposium, Boston, MA, Dec. 13-18, 1987

    NASA Astrophysics Data System (ADS)

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

    Papers are presented on a three-dimensional analysis of liquid oxygen sloshing in the Space Shuttle external tank, the flow-induced oscillations of a novel double-wing spring-mass system, added mass and damping coefficents for a hexagonal cylinder, and a new hydraulic pressure intensifier using an oil hammer. Other topics include junction losses in pulsating flow, a finite element analysis of a slender fluid-structure system, two-phase blowdown through a short tube, and check valve behavior under transient flow conditions. Also considered are forces in initially empty pipes subject to rapid filling, a modal analysis of vibrations in liquid-filled piping systems, efficient computation of the pipeline break problem, and fluid dynamics associated with ductile pipeline fracture.

  10. Fully-Coupled Fluid/Structure Vibration Analysis Using MSC/NASTRAN

    NASA Technical Reports Server (NTRS)

    Fernholz, Christian M.; Robinson, Jay H.

    1996-01-01

    MSC/NASTRAN's performance in the solution of fully-coupled fluid/structure problems is evaluated. NASTRAN is used to perform normal modes (SOL 103) and forced-response analyses (SOL 108, 111) on cylindrical and cubic fluid/structure models. Bulk data file cards unique to the specification of a fluid element are discussed and analytic partially-coupled solutions are derived for each type of problem. These solutions are used to evaluate NASTRAN's solutions for accuracy. Appendices to this work include NASTRAN data presented in fringe plot form, FORTRAN source code listings written in support of this work, and NASTRAN data file usage requirements for each analysis.

  11. Fluid flow structure around the mixer in a reactor with mechanical mixing

    SciTech Connect

    Lecheva, A.; Zheleva, I.

    2015-10-28

    Fluid flow structure around the mixer in a cylindrical reactor with mechanical mixing is studied and numerical results are presented in this article. The model area is complex because of the presence of convex corners of the mixer in the fluid flow. Proper boundary conditions for the vorticity calculated on the base of the stream function values near solid boundaries of the examined area are presented. The boundary value problem of motion of swirling incompressible viscous fluid in a vertical tank reactor with a mixer is solved numerically. The calculations are made by a computer code, written in MATLAB. The complex structure of the flow around the mixing disk is described and commented.

  12. Immobilized lipid-bilayer materials

    DOEpatents

    Sasaki, Darryl Y.; Loy, Douglas A.; Yamanaka, Stacey A.

    2000-01-01

    A method for preparing encapsulated lipid-bilayer materials in a silica matrix comprising preparing a silica sol, mixing a lipid-bilayer material in the silica sol and allowing the mixture to gel to form the encapsulated lipid-bilayer material. The mild processing conditions allow quantitative entrapment of pre-formed lipid-bilayer materials without modification to the material's spectral characteristics. The method allows for the immobilization of lipid membranes to surfaces. The encapsulated lipid-bilayer materials perform as sensitive optical sensors for the detection of analytes such as heavy metal ions and can be used as drug delivery systems and as separation devices.

  13. Development of an integrated BEM approach for hot fluid structure interaction: BEST-FSI: Boundary Element Solution Technique for Fluid Structure Interaction

    NASA Technical Reports Server (NTRS)

    Dargush, G. F.; Banerjee, P. K.; Shi, Y.

    1992-01-01

    As part of the continuing effort at NASA LeRC to improve both the durability and reliability of hot section Earth-to-orbit engine components, significant enhancements must be made in existing finite element and finite difference methods, and advanced techniques, such as the boundary element method (BEM), must be explored. The BEM was chosen as the basic analysis tool because the critical variables (temperature, flux, displacement, and traction) can be very precisely determined with a boundary-based discretization scheme. Additionally, model preparation is considerably simplified compared to the more familiar domain-based methods. Furthermore, the hyperbolic character of high speed flow is captured through the use of an analytical fundamental solution, eliminating the dependence of the solution on the discretization pattern. The price that must be paid in order to realize these advantages is that any BEM formulation requires a considerable amount of analytical work, which is typically absent in the other numerical methods. All of the research accomplishments of a multi-year program aimed toward the development of a boundary element formulation for the study of hot fluid-structure interaction in Earth-to-orbit engine hot section components are detailed. Most of the effort was directed toward the examination of fluid flow, since BEM's for fluids are at a much less developed state. However, significant strides were made, not only in the analysis of thermoviscous fluids, but also in the solution of the fluid-structure interaction problem.

  14. Landau quantization and Fermi velocity renormalization in twisted graphene bilayers

    NASA Astrophysics Data System (ADS)

    Yin, Long-Jing; Qiao, Jia-Bin; Wang, Wen-Xiao; Zuo, Wei-Jie; Yan, Wei; Xu, Rui; Dou, Rui-Fen; Nie, Jia-Cai; He, Lin

    2015-11-01

    Currently there is a lively discussion concerning Fermi velocity renormalization in twisted bilayers and several contradicted experimental results are reported. Here we study electronic structures of the twisted bilayers by scanning tunneling microscopy (STM) and spectroscopy (STS). The interlayer coupling strengths between the adjacent bilayers are measured according to energy separations of two pronounced low-energy van Hove singularities (VHSs) in the STS spectra. We demonstrate that there is a large range of values for the interlayer interaction not only in different twisted bilayers, but also in twisted bilayers with the same rotation angle. Below the VHSs, the observed Landau quantization in the twisted bilayers is identical to that of massless Dirac fermions in graphene monolayer, which allows us to measure the Fermi velocity directly. Our result indicates that the Fermi velocity of the twisted bilayers depends remarkably on both the twisted angles and the interlayer coupling strengths. This removes the discrepancy about the Fermi velocity renormalization in the twisted bilayers and provides a consistent interpretation of all current data.

  15. Hormonal composition of follicular fluid from abnormal follicular structures in mares.

    PubMed

    Beltman, M E; Walsh, S W; Canty, M J; Duffy, P; Crowe, M A

    2014-12-01

    The objective was to characterise the hormonal composition of follicular fluid from mares with distinct anovulatory-cystic follicles. Follicular fluid was aspirated from six mares that presented with cystic follicles and from pre-ovulatory follicles of five normal mares (controls). Differences in progesterone, oestradiol, testosterone, IGF-I and IGF binding were analysed using Fisher's exact test. There were greater (P < 0.03) follicular fluid oestradiol concentrations in normal follicles and the testosterone concentration of the cystic fluid was greater (P < 0.05) than that of the normal fluid. There also was a greater (P < 0.03) percentage of IGF-I binding and lower (P < 0.02) IGF-I concentrations in the fluid collected from the cystic structures compared with the fluid from normal follicles. Despite the limited number of animals, the fact that fluid aspirated from cystic follicles had higher testosterone and lower oestradiol concentrations could be of diagnostic value when a practitioner wants to distinguish between a cystic and non-cystic persistent follicle. The research reported here also indicates a likely role for the IGF system in the pathogenesis of the development and maintenance of anovulatory follicular structures in mare ovaries.

  16. Strongly coupled partitioned approach for fluid structure interaction in free surface flows

    NASA Astrophysics Data System (ADS)

    Facci, Andrea Luigi; Ubertini, Stefano

    2016-06-01

    In this paper we describe and validate a methodology for the numerical simulation of the fluid structure interaction in free surface flows. Specifically, this study concentrates on the vertical impact of a rigid body on the water surface, (i.e. on the hull slamming problem). The fluid flow is modeled through the volume of fluid methodology, and the structure dynamics is described by the Newton's second law. An iterative algorithm guarantees the tight coupling between the fluid and solid solvers, allowing the simulations of lightweight (i.e. buoyant) structures. The methodology is validated comparing numerical results to experimental data on the free fall of different rigid wedges. The correspondence between numerical results and independent experimental findings from literature evidences the reliability and the accuracy of the proposed approach.

  17. A Finite Element Procedure for Calculating Fluid-Structure Interaction Using MSC/NASTRAN

    NASA Technical Reports Server (NTRS)

    Chargin, Mladen; Gartmeier, Otto

    1990-01-01

    This report is intended to serve two purposes. The first is to present a survey of the theoretical background of the dynamic interaction between a non-viscid, compressible fluid and an elastic structure is presented. Section one presents a short survey of the application of the finite element method (FEM) to the area of fluid-structure-interaction (FSI). Section two describes the mathematical foundation of the structure and fluid with special emphasis on the fluid. The main steps in establishing the finite element (FE) equations for the fluid structure coupling are discussed in section three. The second purpose is to demonstrate the application of MSC/NASTRAN to the solution of FSI problems. Some specific topics, such as fluid structure analogy, acoustic absorption, and acoustic contribution analysis are described in section four. Section five deals with the organization of the acoustic procedure flowchart. Section six includes the most important information that a user needs for applying the acoustic procedure to practical FSI problems. Beginning with some rules concerning the FE modeling of the coupled system, the NASTRAN USER DECKs for the different steps are described. The goal of section seven is to demonstrate the use of the acoustic procedure with some examples. This demonstration includes an analytic verification of selected FE results. The analytical description considers only some aspects of FSI and is not intended to be mathematically complete. Finally, section 8 presents an application of the acoustic procedure to vehicle interior acoustic analysis with selected results.

  18. Exact coherent structures: from fluid turbulence to cardiac arrhythmias

    NASA Astrophysics Data System (ADS)

    Grigoriev, Roman; Marcotte, Christopher; Byrne, Gregory

    2014-03-01

    Ventricular fibrillation, a life threatening cardiac arrhythmia, is an example of spatiotemporally chaotic state dominated by multiple interacting spiral waves. Recent studies of weak fluid turbulence suggest that spatiotemporal chaos in general can be understood as a walk among exact unstable regular solutions (exact coherent states, ECS) of nonlinear evolution equations. Several classes of ECS are believed to play a dominant role; most typically these are equilibria and periodic orbits or relative equilibria and relative periodic orbits for systems with global continuous symmetries. Numerical methods originally developed in the context of fluid turbulence can also be applied to models of cardiac dynamics which possess translational and rotational symmetries and, indeed, allowed us to identify relative equilibria and periodic orbits describing isolated spirals with, respectively, fixed and drifting cores. In order to find regular solutions featuring multiple interacting spirals a new approach is required that takes into consideration the dynamics of slowly drifting cores associated with local, rather than global, symmetries. We describe how local symmetries can be reduced and more general types of ECS computed that dominate spiral wave chaos in models of cardiac tissue.

  19. Three Dimensional Viscous Finite Element Formulation For Acoustic Fluid Structure Interaction

    PubMed Central

    Cheng, Lei; White, Robert D.; Grosh, Karl

    2010-01-01

    A three dimensional viscous finite element model is presented in this paper for the analysis of the acoustic fluid structure interaction systems including, but not limited to, the cochlear-based transducers. The model consists of a three dimensional viscous acoustic fluid medium interacting with a two dimensional flat structure domain. The fluid field is governed by the linearized Navier-Stokes equation with the fluid displacements and the pressure chosen as independent variables. The mixed displacement/pressure based formulation is used in the fluid field in order to alleviate the locking in the nearly incompressible fluid. The structure is modeled as a Mindlin plate with or without residual stress. The Hinton-Huang’s 9-noded Lagrangian plate element is chosen in order to be compatible with 27/4 u/p fluid elements. The results from the full 3d FEM model are in good agreement with experimental results and other FEM results including Beltman’s thin film viscoacoustic element [2] and two and half dimensional inviscid elements [21]. Although it is computationally expensive, it provides a benchmark solution for other numerical models or approximations to compare to besides experiments and it is capable of modeling any irregular geometries and material properties while other numerical models may not be applicable. PMID:20174602

  20. Fluid-structure interaction and structural analyses using a comprehensive mitral valve model with 3D chordal structure.

    PubMed

    Toma, Milan; Einstein, Daniel R; Bloodworth, Charles H; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

    2016-06-25

    Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be 'invisible' to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Spin-resolved band structure of heterojunction Bi-bilayer/3D topological insulator in the quantum dimension regime in annealed Bi2Te2.4Se0.6

    PubMed Central

    Klimovskikh, I. I.; Sostina, D.; Petukhov, A.; Rybkin, A. G.; Eremeev, S. V.; Chulkov, E. V.; Tereshchenko, O. E.; Kokh, K. A.; Shikin, A. M.

    2017-01-01

    Two- and three-dimensional topological insulators are the key materials for the future nanoelectronic and spintronic devices and quantum computers. By means of angle- and spin-resolved photoemission spectroscopy we study the electronic and spin structure of the Bi-bilayer/3D topological insulator in quantum tunneling regime formed under the short annealing of Bi2Te2.4Se0.6. Owing to the temperature-induced restructuring of the topological insulator’s surface quintuple layers, the hole-like spin-split Bi-bilayer bands and the parabolic electronic-like state are observed instead of the Dirac cone. Scanning Tunneling Microscopy and X-ray Photoemission Spectroscopy measurements reveal the appearance of the Bi2 terraces at the surface under the annealing. The experimental results are supported by density functional theory calculations, predicting the spin-polarized Bi-bilayer bands interacting with the quintuple-layers-derived states. Such an easily formed heterostructure promises exciting applications in spin transport devices and low-energy electronics. PMID:28378826

  2. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters.

    PubMed

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia; Skotland, Tore; Sylvänne, Tuulia; Kauhanen, Dimple; Ekroos, Kim; Sandvig, Kirsten; Vattulainen, Ilpo

    2016-06-01

    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers׳ compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids׳ topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3].

  3. "Nanocrystal bilayer for tandem catalysis"

    SciTech Connect

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong

    2011-01-24

    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  4. Soft particles at fluid interfaces: wetting, structure, and rheology

    NASA Astrophysics Data System (ADS)

    Isa, Lucio

    Most of our current knowledge concerning the behavior of colloidal particles at fluid interfaces is limited to model spherical, hard and uniform objects. Introducing additional complexity, in terms of shape, composition or surface chemistry or by introducing particle softness, opens up a vast range of possibilities to address new fundamental and applied questions in soft matter systems at fluid interfaces. In this talk I will focus on the role of particle softness, taking the case of core-shell microgels as a paradigmatic example. Microgels are highly swollen and cross-linked hydrogel particles that, in parallel with their practical applications, e.g. for emulsion stabilization and surface patterning, are increasingly used as model systems to capture fundamental properties of bulk materials. Most microgel particles develop a core-shell morphology during synthesis, with a more cross-linked core surrounded by a corona of loosely linked and dangling polymer chains. I will first discuss the difference between the wetting of a hard spherical colloid and a core-shell microgel at an oil-water interface, pinpointing the interplay between adsorption at the interface and particle deformation. I will then move on to discuss the interplay between particle morphology and the microstructure and rheological properties of the interface. In particular, I will demonstrate that synchronizing the compression of a core-shell microgel-laden fluid interface with the deposition of the interfacial monolayer makes it possible to transfer the 2D phase diagram of the particles onto a solid substrate, where different positions correspond to different values of the surface pressure and the specific area. Using atomic force microscopy, we analyzed the microstructure of the monolayer and discovered a phase transition between two crystalline phases with the same hexagonal symmetry, but with two different lattice constants. The two phases correspond to shell-shell or core-core inter

  5. Sterically stabilized water based magnetic fluids: Synthesis, structure and properties

    NASA Astrophysics Data System (ADS)

    Bica, Doina; Vékás, Ladislau; Avdeev, Mikhail V.; Marinică, Oana; Socoliuc, Vlad; Bălăsoiu, Maria; Garamus, Vasil M.

    2007-04-01

    Magnetic fluids (MFs), prepared by chemical co-precipitation followed by double layer steric and electrostatic (combined) stabilization of magnetite nanoparticles dispersed in water, are presented. Several combinations of surfactants with different chain lengths (lauric acid (LA), myristic acid (MA), oleic acid (OA) and dodecyl-benzene-sulphonic acid (DBS)) were used, such as LA+LA, MA+MA, LA+DBS, MA+DBS, OA+DBS, OA+OA and DBS+DBS. Static light scattering, transmission electron microscopy, small angle neutron scattering, magnetic and magneto-rheological measurements revealed that MFs with MA+MA or LA+LA biocompatible double layer covered magnetite nanoparticles are the most stable colloidal systems among the investigated samples, and thus suitable for biomedical applications.

  6. Fluid-Structure Interaction Modeling of High-Aspect Ratio Nuclear Fuel Plates Using COMSOL

    SciTech Connect

    Curtis, Franklin G; Ekici, Kivanc; Freels, James D

    2013-01-01

    The High Flux Isotope Reactor at the Oak Ridge National Lab is in the research stage of converting its fuel from high-enriched uranium to low-enriched uranium. Due to different physical properties of the new fuel and changes to the internal fuel plate design, the current safety basis must be re-evaluated through rigorous computational analyses. One of the areas being explored is the fluid-structure interaction phenomenon due to the interaction of thin fuel plates (50 mils thickness) and the cooling fluid (water). Detailed computational fluid dynamics and fluid-structure interaction simulations have only recently become feasible due to improved numerical algorithms and advancements in computing technology. For many reasons including the already built-in fluid-structure interaction module, COMSOL has been chosen for this complex problem. COMSOL's ability to solve multiphysics problems using a fully-coupled and implicit solution algorithm is crucial in obtaining a stable and accurate solution. Our initial findings show that COMSOL can accurately model such problems due to its ability to closely couple the fluid dynamics and the structural dynamics problems.

  7. Development of an integrated BEM approach for hot fluid structure interaction

    NASA Technical Reports Server (NTRS)

    Dargush, Gary F.; Banerjee, Prasanta K.; Honkala, Keith A.

    1991-01-01

    The development of a boundary element formulation for the study of hot fluid-structure interaction in earth-to-orbit engine hot section components is described. The initial primary thrust of the program to date was directed quite naturally toward the examination of fluid flow, since boundary element methods for fluids are at a much less developed state. This required the development of integral formulations for both the solid and fluid, and some preliminary infrastructural enhancements to a boundary element code to permit coupling of the fluid-structure problem. Boundary element formulations are implemented in two dimensions for both the solid and the fluid. The solid is modeled as an uncoupled thermoelastic medium under plane strain conditions, while several formulations are investigated for the fluid. For example, both vorticity and primitive variable approaches are implemented for viscous, incompressible flow, and a compressible version is developed. All of the above boundary element implementations are incorporated in a general purpose two-dimensional code. Thus, problems involving intricate geometry, multiple generic modeling regions, and arbitrary boundary conditions are all supported.

  8. Structure of Amantadine-Bound M2 Transmembrane Peptide of Influenza A in Lipid Bilayers from Magic-Angle-Spinning Solid-State NMR: the Role of Ser31 in Amantadine Binding

    PubMed Central

    Cady, Sarah D.; Mishanina, Tatiana V.; Hong, Mei

    2014-01-01

    The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine, whose effectiveness has been abolished by a single-site mutation of Ser31 to Asn in the transmembrane domain of the protein. Recent high-resolution structures of the M2 transmembrane domain obtained from detergent-solubilized protein in solution and crystal environments gave conflicting drug binding sites. We present magic-angle-spinning solid-state NMR results of Ser31 and a number of other residues in the M2 transmembrane peptide (M2TMP) bound to lipid bilayers. Comparison of the spectra of the membrane-bound apo and complexed M2TMP indicates that Ser31 is the site of the largest chemical shift perturbation by amantadine. The chemical shift constraints lead to a monomer structure with a small kink of the helical axis at Gly34. A tetramer model is then constructed using the helix tilt angle and several interhelical distances previously measured on unoriented bilayer samples. This tetramer model differs from the solution and crystal structures in terms of the openness of the N-terminus of the channel, the constriction at Ser31, and the sidechain conformations of Trp41, a residue important for channel gating. Moreover, the tetramer model suggests that Ser31 may interact with amantadine amine via hydrogen bonding. While the apo and drug-bound M2TMP have similar average structures, the complexed peptide has much narrower linewidths at physiological temperature, indicating drug-induced changes of the protein dynamics in the membrane. Further, at low temperature, several residues show narrower lines in the complexed peptide than the apo peptide, indicating that amantadine binding reduces the conformational heterogeneity of specific residues. The differences of the current solid-state NMR structure of the bilayer-bound M2TMP from the detergent-based M2 structures suggest that the M2 conformation is sensitive to the environment, and care must be taken when interpreting

  9. An actuated elastic sheet interacting with passive and active structures in a viscoelastic fluid

    NASA Astrophysics Data System (ADS)

    Chrispell, J. C.; Fauci, L. J.; Shelley, M.

    2013-01-01

    We adapt the classic Taylor swimming sheet set-up to investigate both the transient and long-time dynamics of an actuated elastic sheet immersed in a viscoelastic fluid as it interacts with neighboring structures. While the preferred kinematics of the sheet are specified, the flexible sheet interacts with the surrounding fluid and other structures, and its realized kinematics emerges from this coupling. We use an immersed boundary framework to evolve the Oldroyd-B/Navier-Stokes equations and capture the spatial and temporal development of viscoelastic stresses and sheet shape. We compare the dynamics when the actuated sheet swims next to a free elastic membrane, with and without bending rigidity, and next to a fixed wall. We demonstrate that the sheets can exploit the neighboring structures to enhance their swimming speed and efficiency, and also examine how this depends upon fluid viscoelasticity. When the neighboring structure is likewise an actuated elastic sheet, we investigate the viscoelastic dynamics of phase-locking.

  10. A gridless technique for fluid/structural dynamic coupling on flexible membranes

    SciTech Connect

    Wolfe, W.P.; Nelsen, J.M.; Baty, R.S.; Laguna, G.A.; Mello, F.J.; Hailey, C.E.; Snyder, N.T.

    1996-01-01

    A gridless method has been developed for the simulation of coupled fluid/structural interactions over arbitrary bodies. This method uses Eulerian-based points arbitrarily distributed over the computational domain with no formal connectivity as typically required for a traditional grid. Comparisons are made with known exact solutions for simple two-dimensional model problems. Methods of improving the accuracy of the current implementation by using higher order approximations have been implemented. Accuracy improvement by using point adaption has been investigated. Plane strain and axisymmetric shells have been added to the code structural code PRONTO2D for future fluid/structural calculations. To date, coupled fluid/structure calculations have not been made.

  11. A fictitious domain/mortar element method for fluid-structure interaction

    NASA Astrophysics Data System (ADS)

    Baaijens, Frank P. T.

    2001-04-01

    A new method for the computational analysis of fluid-structure interaction of a Newtonian fluid with slender bodies is developed. It combines ideas of the fictitious domain and the mortar element method by imposing continuity of the velocity field along an interface by means of Lagrange multipliers. The key advantage of the method is that it circumvents the need for complicated mesh movement strategies common in arbitrary Lagrangian-Eulerian (ALE) methods, usually used for this purpose. Copyright

  12. Vortex methods for fluid-structure interaction problems with deforming geometries and their application to swimming

    NASA Astrophysics Data System (ADS)

    Gazzola, Mattia; Chatelain, Philippe; Koumoutsakos, Petros

    2010-11-01

    We present a vortex particle-mesh method for fluid-structure interaction problems. The proposed methodology combines implicit interface capturing, Brinkmann penalization techniques, and the self-consistent computation of momentum transfer between the fluid and the structure. In addition, our scheme is able to handle immersed bodies characterized by non-solenoidal deformations, allowing the study of arbitrary deforming geometries. This attractively simple algorithm is shown to accurately reproduce reference simulations for rigid and deforming structures. Its suitability for biological locomotion problems is then demonstrated with the simulation of self-propelled anguilliform swimmers.

  13. Profile structures of the voltage-sensor domain and the voltage-gated K+-channel vectorially oriented in a single phospholipid bilayer membrane at the solid-vapor and solid-liquid interfaces determined by x-ray interferometry

    NASA Astrophysics Data System (ADS)

    Gupta, S.; Liu, J.; Strzalka, J.; Blasie, J. K.

    2011-09-01

    One subunit of the prokaryotic voltage-gated potassium ion channel from Aeropyrum pernix (KvAP) is comprised of six transmembrane α helices, of which S1-S4 form the voltage-sensor domain (VSD) and S5 and S6 contribute to the pore domain (PD) of the functional homotetramer. However, the mechanism of electromechanical coupling interconverting the closed-to-open (i.e., nonconducting-to-K+-conducting) states remains undetermined. Here, we have vectorially oriented the detergent (OG)-solubilized VSD in single monolayers by two independent approaches, namely “directed-assembly” and “self-assembly,” to achieve a high in-plane density. Both utilize Ni coordination chemistry to tether the protein to an alkylated inorganic surface via its C-terminal His6 tag. Subsequently, the detergent is replaced by phospholipid (POPC) via exchange, intended to reconstitute a phospholipid bilayer environment for the protein. X-ray interferometry, in which interference with a multilayer reference structure is used to both enhance and phase the specular x-ray reflectivity from the tethered single membrane, was used to determine directly the electron density profile structures of the VSD protein solvated by detergent versus phospholipid, and with either a moist He (moderate hydration) or bulk aqueous buffer (high hydration) environment to preserve a native structure conformation. Difference electron density profiles, with respect to the multilayer substrate itself, for the VSD-OG monolayer and VSD-POPC membranes at both the solid-vapor and solid-liquid interfaces, reveal the profile structures of the VSD protein dominating these profiles and further indicate a successful reconstitution of a lipid bilayer environment. The self-assembly approach was similarly extended to the intact full-length KvAP channel for comparison. The spatial extent and asymmetry in the profile structures of both proteins confirm their unidirectional vectorial orientation within the reconstituted membrane and

  14. An Immersed Boundary Method for Solving the Compressible Navier-Stokes Equations with Fluid Structure Interaction

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

    An immersed boundary method for the compressible Navier-Stokes equation and the additional infrastructure that is needed to solve moving boundary problems and fully coupled fluid-structure interaction is described. All the methods described in this paper were implemented in NASA's LAVA solver framework. The underlying immersed boundary method is based on the locally stabilized immersed boundary method that was previously introduced by the authors. In the present paper this method is extended to account for all aspects that are involved for fluid structure interaction simulations, such as fast geometry queries and stencil computations, the treatment of freshly cleared cells, and the coupling of the computational fluid dynamics solver with a linear structural finite element method. The current approach is validated for moving boundary problems with prescribed body motion and fully coupled fluid structure interaction problems in 2D and 3D. As part of the validation procedure, results from the second AIAA aeroelastic prediction workshop are also presented. The current paper is regarded as a proof of concept study, while more advanced methods for fluid structure interaction are currently being investigated, such as geometric and material nonlinearities, and advanced coupling approaches.

  15. Colloidal binary mixtures at fluid-fluid interfaces under steady shear: structural, dynamical and mechanical response†

    PubMed Central

    Zell, Zachary A.; Squires, Todd M.; Isa, Lucio

    2015-01-01

    We experimentally study the link between structure, dynamics and mechanical response of two-dimensional (2D) binary mixtures of colloidal microparticles spread at water/oil interfaces. The particles are driven into steady shear by a microdisk forced to rotate at a controlled angular velocity. The flow causes particles to layer into alternating concentric rings of small and big colloids. The formation of such layers is linked to the local, position-dependent shear rate, which triggers two distinct dynamical regimes: particles either move continuously (“Flowing”) close to the microdisk, or exhibit intermittent “Hopping” between local energy minima farther away. The shear-rate-dependent surface viscosity of the monolayers can be extracted from a local interfacial stress balance, giving “macroscopic” flow curves whose behavior corresponds to the distinct microscopic regimes of particle motion. Hopping Regions reveal a higher resistance to flow compared to the Flowing Regions, where spatial organization into layers reduces dissipation. PMID:26347409

  16. A circuit model for defective bilayer graphene transistors

    NASA Astrophysics Data System (ADS)

    Umoh, Ime J.; Moktadir, Zakaria; Hang, Shuojin; Kazmierski, Tom J.; Mizuta, Hiroshi

    2016-05-01

    This paper investigates the behaviour of a defective single-gate bilayer graphene transistor. Point defects were introduced into pristine graphene crystal structure using a tightly focused helium ion beam. The transfer characteristics of the exposed transistors were measured ex-situ for different defect concentrations. The channel peak resistance increased with increasing defect concentration whilst the on-off ratio showed a decreasing trend for both electrons and holes. To understand the electrical behaviour of the transistors, a circuit model for bilayer graphene is developed which shows a very good agreement when validated against experimental data. The model allowed parameter extraction of bilayer transistor and can be implemented in circuit level simulators.

  17. Numerical simulation of the fluid-structure interaction between air blast waves and soil structure

    NASA Astrophysics Data System (ADS)

    Umar, S.; Risby, M. S.; Albert, A. Luthfi; Norazman, M.; Ariffin, I.; Alias, Y. Muhamad

    2014-03-01

    Normally, an explosion threat on free field especially from high explosives is very dangerous due to the ground shocks generated that have high impulsive load. Nowadays, explosion threats do not only occur in the battlefield, but also in industries and urban areas. In industries such as oil and gas, explosion threats may occur on logistic transportation, maintenance, production, and distribution pipeline that are located underground to supply crude oil. Therefore, the appropriate blast resistances are a priority requirement that can be obtained through an assessment on the structural response, material strength and impact pattern of material due to ground shock. A highly impulsive load from ground shocks is a dynamic load due to its loading time which is faster than ground response time. Of late, almost all blast studies consider and analyze the ground shock in the fluid-structure interaction (FSI) because of its influence on the propagation and interaction of ground shock. Furthermore, analysis in the FSI integrates action of ground shock and reaction of ground on calculations of velocity, pressure and force. Therefore, this integration of the FSI has the capability to deliver the ground shock analysis on simulation to be closer to experimental investigation results. In this study, the FSI was implemented on AUTODYN computer code by using Euler-Godunov and the arbitrary Lagrangian-Eulerian (ALE). Euler-Godunov has the capability to deliver a structural computation on a 3D analysis, while ALE delivers an arbitrary calculation that is appropriate for a FSI analysis. In addition, ALE scheme delivers fine approach on little deformation analysis with an arbitrary motion, while the Euler-Godunov scheme delivers fine approach on a large deformation analysis. An integrated scheme based on Euler-Godunov and the arbitrary Lagrangian-Eulerian allows us to analyze the blast propagation waves and structural interaction simultaneously.

  18. Fluid-structure interaction in abdominal aortic aneurysms: Structural and geometrical considerations

    NASA Astrophysics Data System (ADS)

    Mesri, Yaser; Niazmand, Hamid; Deyranlou, Amin; Sadeghi, Mahmood Reza

    2015-08-01

    Rupture of the abdominal aortic aneurysm (AAA) is the result of the relatively complex interaction of blood hemodynamics and material behavior of arterial walls. In the present study, the cumulative effects of physiological parameters such as the directional growth, arterial wall properties (isotropy and anisotropy), iliac bifurcation and arterial wall thickness on prediction of wall stress in fully coupled fluid-structure interaction (FSI) analysis of five idealized AAA models have been investigated. In particular, the numerical model considers the heterogeneity of arterial wall and the iliac bifurcation, which allows the study of the geometric asymmetry due to the growth of the aneurysm into different directions. Results demonstrate that the blood pulsatile nature is responsible for emerging a time-dependent recirculation zone inside the aneurysm, which directly affects the stress distribution in aneurismal wall. Therefore, aneurysm deviation from the arterial axis, especially, in the lateral direction increases the wall stress in a relatively nonlinear fashion. Among the models analyzed in this investigation, the anisotropic material model that considers the wall thickness variations, greatly affects the wall stress values, while the stress distributions are less affected as compared to the uniform wall thickness models. In this regard, it is confirmed that wall stress predictions are more influenced by the appropriate structural model than the geometrical considerations such as the level of asymmetry and its curvature, growth direction and its extent.

  19. Simulation Studies of Alamethicin-Bilayer Interactions

    PubMed Central

    Biggin, P. C.; Breed, J.; Son, H. S.; Sansom, M. S. P.

    1997-01-01

    Alamethicin is an α-helical peptide that forms voltage-activated ion channels. Experimental data suggest that channel formation occurs via voltage-dependent insertion of alamethicin helices into lipid bilayers, followed by self-assembly of inserted helices to form a parallel helix bundle. Changes in the kink angle of the alamethicin helix about its central proline residue have also been suggested to play a role in channel gating. Alamethicin helices generated by simulated annealing and restrained molecular dynamics adopt a kink angle similar to that in the x-ray crystal structure, even if such simulations start with an idealized unkinked helix. This suggests that the kinked helix represents a stable conformation of the molecule. Molecular dynamics simulations in the presence of a simple bilayer model and a transbilayer voltage difference are used to explore possible mechanisms of helix insertion. The bilayer is represented by a hydrophobicity potential. An alamethicin helix inserts spontaneously in the absence of a transbilayer voltage. Application of a cis positive voltage decreases the time to insertion. The helix kink angle fluctuates during the simulations. Insertion of the helix is associated with a decrease in the mean kink angle, thus helping the alamethicin molecule to span the bilayer. The simulation results are discussed in terms of models of alamethicin channel gating. ImagesFIGURE 1FIGURE 6 PMID:9017192

  20. Stability analysis of the pulmonary liquid bilayer.

    NASA Astrophysics Data System (ADS)

    Halpern, David; Grotberg, James

    2010-11-01

    The lung consists of liquid-lined compliant airways that convey air to and from the alveoli where gas exchange takes place. Because the airways are coated with a bilayer consisting of a mucus layer on top of a periciliary fluid layer, a surface tension instability can generate flows within the bilayer and induce the formation of liquid plugs that block the passage of air. This is a problem for example with premature neonates whose lungs do not produce sufficient quantities of surfactant and suffer from respiratory distress syndrome. To study this instability a system of coupled nonlinear evolution equations are derived using lubrication theory for the thicknesses of the two liquid layers which are assumed to be Newtonian. A normal mode analysis is used to investigate the initial growth of the disturbances, and reveals how the grow rate is affected by the ratio of viscosities λ, film thicknesses η and surface tensions δ of the two layers which can change by disease. Numerical solutions of the evolution equations show that there is a critical bilayer thickness ɛc above which closure occurs, and that a more viscous and thicker layer compared to the periciliary layer closes more slowly. However, ɛcis weakly dependent on λ, η and δ. We also examine the potential impact of wall shear stress and normal stress on cell damage. This work is funded by NIH HL85156.

  1. Bilayer Edges Catalyze Supported Lipid Bilayer Formation

    PubMed Central

    Weirich, Kimberly L.; Israelachvili, Jacob N.; Fygenson, D. Kuchnir

    2010-01-01

    Abstract Supported lipid bilayers (SLB) are important for the study of membrane-based phenomena and as coatings for biosensors. Nevertheless, there is a fundamental lack of understanding of the process by which they form from vesicles in solution. We report insights into the mechanism of SLB formation by vesicle adsorption using temperature-controlled time-resolved fluorescence microscopy at low vesicle concentrations. First, lipid accumulates on the surface at a constant rate up to ∼0.8 of SLB coverage. Then, as patches of SLB nucleate and spread, the rate of accumulation increases. At a coverage of ∼1.5 × SLB, excess vesicles desorb as SLB patches rapidly coalesce into a continuous SLB. Variable surface fluorescence immediately before SLB patch formation argues against the existence of a critical vesicle density necessary for rupture. The accelerating rate of accumulation and the widespread, abrupt loss of vesicles coincide with the emergence and disappearance of patch edges. We conclude that SLB edges enhance vesicle adhesion to the surface and induce vesicle rupture, thus playing a key role in the formation of continuous SLB. PMID:20085721

  2. Confinement Effects on the Structure of Complex Fluids

    NASA Astrophysics Data System (ADS)

    Kim, Mahn

    2009-03-01

    Actin is a key component of the protein complex responsible for producing contractile force in skeletal muscle. Filamentous actin, called F-actin, is a two-stranded helical protofilament with a diameter of ˜8nm and a contour length of ˜10m. The experimental results show that the persistence length of the F-actin is 4 -20 m. One of interesting problems is to find the structure of a semiflexible filament in a confined space [1], such as a channel width less than the persistence length. The other interesting problem is to find the surface treatment effect on the liquid crystal structure in a confined space. The boundary conditions imposed by the walls of the microchannel generate the spatial patterning of defect domains in a smectic liquid crystal [2] and the formation of a large-area ordered structure [3] by using the structure of smectic liquid in the microchannels. We found that the F-actin undergoes a transition from a 2D randomly oriented regime to a 1D biaxially confined regime with the effective persistence length. We were able to generate defect domains that are nearly uniformly arranged in 2D ordered patterns by controlling the surface hydrophobicity. Furthermore, the formation of a large-area ordered structure of toric focal conic domains was generated. This work was done with C. R. Safinya's group at UCSB and Hee-Tae Jung's group at KAIST. [4pt] [1] M.C Choi at. al, Macromolecules 2005,38, 9882-9884[0pt] [2] M. C. Choi at. al, PNAS 2004, 101, 17340-17344[0pt] [3] D. K. Yoon at. al, Nature Materials, 2007, 6, 866-870

  3. Partitioned semi-implicit methods for simulation of biomechanical fluid-structure interaction problems

    NASA Astrophysics Data System (ADS)

    Naseri, A.; Lehmkuhl, O.; Gonzalez, I.; Oliva, A.

    2016-09-01

    This paper represents numerical simulation of fluid-structure interaction (FSI) system involving an incompressible viscous fluid and a lightweight elastic structure. We follow a semi-implicit approach in which we implicitly couple the added-mass term (pressure stress) of the fluid to the structure, while other terms are coupled explicitly. This significantly reduces the computational cost of the simulations while showing adequate stability. Several coupling schemes are tested including fixed-point method with different static and dynamic relaxation, as well as Newton-Krylov method with approximated Jacobian. Numerical tests are conducted in the context of a biomechanical problem. Results indicate that the Newton-Krylov solver outperforms fixed point ones while introducing more complexity to the problem due to the evaluation of the Jacobian. Fixed-point solver with Aitken's relaxation method also proved to be a simple, yet efficient method for FSI simulations.

  4. Structure, biomimetics, and fluid dynamics of fish skin surfaces*

    NASA Astrophysics Data System (ADS)

    Lauder, George V.; Wainwright, Dylan K.; Domel, August G.; Weaver, James C.; Wen, Li; Bertoldi, Katia

    2016-10-01

    The interface between the fluid environment and the surface of the body in swimming fishes is critical for both physiological and hydrodynamic functions. The skin surface in most species of fishes is covered with bony scales or toothlike denticles (in sharks). Despite the apparent importance of fish surfaces for understanding aquatic locomotion and near-surface boundary layer flows, relatively little attention has been paid to either the nature of surface textures in fishes or possible hydrodynamic effects of variation in roughness around the body surface within an individual and among species. Fish surfaces are remarkably diverse and in many bony fishes scales can have an intricate surface texture with projections, ridges, and comblike extensions. Shark denticles (or scales) are toothlike and project out of the skin to form a complexly textured surface that interacts with free-stream flow. Manufacturing biomimetic foils with fishlike surfaces allows hydrodynamic testing and we emphasize here the importance of dynamic test conditions where the effect of surface textures is assessed under conditions of self-propulsion. We show that simple two-dimensional foils with patterned cuts do not perform as well as a smooth control surface, but that biomimetic shark skin foils can swim at higher self-propelled speeds than smooth controls. When the arrangement of denticles on the foil surface is altered, we find that a staggered-overlapped pattern outperforms other arrangements. Flexible foils made of real shark skin outperform sanded controls when foils are moved with a biologically realistic motion program. We suggest that focus on the mechanisms of drag reduction by fish surfaces has been too limiting and an additional role of fish surface textures may be to alter leading edge vortices and flow patterns on moving surfaces in a way that enhances thrust. Analysis of water flow over an artificial shark skin foil under both static and dynamic conditions shows that a shear layer

  5. Two way fluid structure interaction analysis of a valveless micropump by CFD

    NASA Astrophysics Data System (ADS)

    Cǎlimǎnescu, Ioan; Dumitrache, Constantin L.; Grigorescu, Lucian

    2015-02-01

    In the microfluid control system, a valve-less micropump is a necessary component. It has the ability to pump a wide variety of fluids automatically and accurately on a micro scale. The dynamic characteristics of a valve-less micropump influence the performance of the microfluid control system. Consequently, it is of great importance to be able to accurately predict the dynamic characteristics of micropumps for appropriate design and usage of the microfluid control system. In this paper, we describe a corrugated diaphragm valveless micropump approached from the Computational Fluid Dynamics point of view in which the Fluid Structure Interaction is based on the Two Way principle, meaning that the diaphragm is moving and the fluid (water like fluid) is sucked from the inlet and pushed back to the outlet using the nozzle effect. The technical solution of micropumps without valves is a very clever idea to replace the custom valves with nozzles, with the same effect but virtually without any components beside the inlet and the outlet nozzles. The paperwork is demonstrating via a complex simulation involving the structural-fluid interaction the nozzle effects and the functioning of this kind of micropumps.

  6. In vitro flow assessment: from PC-MRI to computational fluid dynamics including fluid-structure interaction

    NASA Astrophysics Data System (ADS)

    Kratzke, Jonas; Rengier, Fabian; Weis, Christian; Beller, Carsten J.; Heuveline, Vincent

    2016-04-01

    Initiation and development of cardiovascular diseases can be highly correlated to specific biomechanical parameters. To examine and assess biomechanical parameters, numerical simulation of cardiovascular dynamics has the potential to complement and enhance medical measurement and imaging techniques. As such, computational fluid dynamics (CFD) have shown to be suitable to evaluate blood velocity and pressure in scenarios, where vessel wall deformation plays a minor role. However, there is a need for further validation studies and the inclusion of vessel wall elasticity for morphologies being subject to large displacement. In this work, we consider a fluid-structure interaction (FSI) model including the full elasticity equation to take the deformability of aortic wall soft tissue into account. We present a numerical framework, in which either a CFD study can be performed for less deformable aortic segments or an FSI simulation for regions of large displacement such as the aortic root and arch. Both of the methods are validated by means of an aortic phantom experiment. The computational results are in good agreement with 2D phase-contrast magnetic resonance imaging (PC-MRI) velocity measurements as well as catheter-based pressure measurements. The FSI simulation shows a characteristic vessel compliance effect on the flow field induced by the elasticity of the vessel wall, which the CFD model is not capable of. The in vitro validated FSI simulation framework can enable the computation of complementary biomechanical parameters such as the stress distribution within the vessel wall.

  7. Three-dimensional structure of fluid conduits sustaining an active deep marine cold seep

    USGS Publications Warehouse

    Hornbach, M.J.; Ruppel, C.; Van Dover, C.L.

    2007-01-01

    Cold seeps in deep marine settings emit fluids to the overlying ocean and are often associated with such seafloor flux indicators as chemosynthetic biota, pockmarks, and authigenic carbonate rocks. Despite evidence for spatiotemporal variability in the rate, locus, and composition of cold seep fluid emissions, the shallow subseafloor plumbing systems have never been clearly imaged in three dimensions. Using a novel, high-resolution approach, we produce the first three-dimensional image of possible fluid conduits beneath a cold seep at a study site within the Blake Ridge gas hydrate province. Complex, dendritic features diverge upward toward the seafloor from feeder conduits at depth and could potentially draw flow laterally by up to 103 m from the known seafloor seep, a pattern similar to that suggested for some hydrothermal vents. The biodiversity, community structure, and succession dynamics of chemosynthetic communities at cold seeps may largely reflect these complexities of subseafloor fluid flow.

  8. The immiscible cholesterol bilayer domain exists as an integral part of phospholipid bilayer membranes.

    PubMed

    Raguz, Marija; Mainali, Laxman; Widomska, Justyna; Subczynski, Witold K

    2011-04-01

    Electron paramagnetic resonance (EPR) spin-labeling methods were used to study the organization of cholesterol and phospholipids in membranes formed from Chol/POPS (cholesterol/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine) mixtures, with mixing ratios from 0 to 3. It was confirmed using the discrimination by oxygen transport and polar relaxation agent accessibility methods that the immiscible cholesterol bilayer domain (CBD) was present in all of the suspensions when the mixing ratio exceeded the cholesterol solubility threshold (CST) in the POPS membrane. The behavior of phospholipid molecules was monitored with phospholipid analogue spin labels (n-PCs), and the behavior of cholesterol was monitored with the cholesterol analogue spin labels CSL and ASL. Results indicated that phospholipid and cholesterol mixtures can form a membrane suspension up to a mixing ratio of ~2. Additionally, EPR spectra for n-PC, ASL, and CSL indicated that both phospholipids and cholesterol exist in these suspensions in the lipid-bilayer-like structures. EPR spectral characteristics of n-PCs (spin labels located in the phospholipid cholesterol bilayer, outside the CBD) change with increase in the cholesterol content up to and beyond the CST. These results present strong evidence that the CBD forms an integral part of the phospholipid bilayer when formed from a Chol/POPS mixture up to a mixing ratio of ~2. Interestingly, CSL in cholesterol alone (without phospholipids) when suspended in buffer does not detect formation of bilayer-like structures. A broad, single-line EPR signal is given, similar to that obtained for the dry film of cholesterol before addition of the buffer. This broad, single-line signal is also observed in suspensions formed for Chol/POPS mixtures (as a background signal) when the Chol/POPS ratio is much greater than 3. It is suggested that the EPR spin-labeling approach can discriminate and characterize the fraction of cholesterol that forms the CBD within the

  9. Structure and electrical properties of sputtered TiO2/ZrO2 bilayer composite dielectrics upon annealing in nitrogen

    PubMed Central

    2012-01-01

    The high-k dielectric TiO2/ZrO2 bilayer composite film was prepared on a Si substrate by radio frequency magnetron sputtering and post annealing in N2 at various temperatures in the range of 573 K to 973 K. Transmission electron microscopy observation revealed that the bilayer film fully mixed together and had good interfacial property at 773 K. Metal-oxide-semiconductor capacitors with high-k gate dielectric TiO2/ZrO2/p-Si were fabricated using Pt as the top gate electrode and as the bottom side electrode. The largest property permittivity of 46.1 and a very low leakage current density of 3.35 × 10-5 A/cm2 were achieved for the sample of TiO2/ZrO2/Si after annealing at 773 K. PMID:22221384

  10. Isogeometric Fluid structure Interaction Analysis with Applications to Arterial Blood Flow

    NASA Astrophysics Data System (ADS)

    Bazilevs, Y.; Calo, V. M.; Zhang, Y.; Hughes, T. J. R.

    2006-09-01

    A NURBS (non-uniform rational B-splines)-based isogeometric fluid structure interaction formulation, coupling incompressible fluids with non-linear elastic solids, and allowing for large structural displacements, is developed. This methodology, encompassing a very general class of applications, is applied to problems of arterial blood flow modeling and simulation. In addition, a set of procedures enabling the construction of analysis-suitable NURBS geometries directly from patient-specific imaging data is outlined. The approach is compared with representative benchmark problems, yielding very good results. Computation of a patient-specific abdominal aorta is also performed, giving qualitative agreement with computations by other researchers using similar models.

  11. Structure of a fluid interface near the critical point

    NASA Technical Reports Server (NTRS)

    Schmidt, James W.

    1988-01-01

    The structure of the liquid-liquid interface of three very different mixtures (carbon disulfide + methanol, methanol + cyclohexane + deuterated cyclohexane, and nitrobenzene + n-decane) has been studied using ellipsometry in the reduced temperature range between 0.0009 and 0.042. Although the elliptical thickness varies by an order of magnitude between these mixtures, the data from all three mixtures can be scaled to the same universal constant by a combined mean-field plus capillary-wave model of the interface. The universal constant determined experimentally is significantly less than the theoretical value.

  12. Nanoparticle-lipid bilayer interactions studied with lipid bilayer arrays

    NASA Astrophysics Data System (ADS)

    Lu, Bin; Smith, Tyler; Schmidt, Jacob J.

    2015-04-01

    The widespread environmental presence and commercial use of nanoparticles have raised significant health concerns as a result of many in vitro and in vivo assays indicating toxicity of a wide range of nanoparticle species. Many of these assays have identified the ability of nanoparticles to damage cell membranes. These interactions can be studied in detail using artificial lipid bilayers, which can provide insight into the nature of the particle-membrane interaction through variation of membrane and solution properties not possible with cell-based assays. However, the scope of these studies can be limited because of the low throughput characteristic of lipid bilayer platforms. We have recently described an easy to use, parallel lipid bilayer platform which we have used to electrically investigate the activity of 60 nm diameter amine and carboxyl modified polystyrene nanoparticles (NH2-NP and COOH-NP) with over 1000 lipid bilayers while varying lipid composition, bilayer charge, ionic strength, pH, voltage, serum, particle concentration, and particle charge. Our results confirm recent studies finding activity of NH2-NP but not COOH-NP. Detailed analysis shows that NH2-NP formed pores 0.3-2.3 nm in radius, dependent on bilayer and solution composition. These interactions appear to be electrostatic, as they are regulated by NH2-NP surface charge, solution ionic strength, and bilayer charge. The ability to rapidly measure a large number of nanoparticle and membrane parameters indicates strong potential of this bilayer array platform for additional nanoparticle bilayer studies.The widespread environmental presence and commercial use of nanoparticles have raised significant health concerns as a result of many in vitro and in vivo assays indicating toxicity of a wide range of nanoparticle species. Many of these assays have identified the ability of nanoparticles to damage cell membranes. These interactions can be studied in detail using artificial lipid bilayers, which

  13. Ceramide acyl chain length markedly influences miscibility with palmitoyl sphingomyelin in bilayer membranes.

    PubMed

    Westerlund, Bodil; Grandell, Pia-Maria; Isaksson, Y Jenny E; Slotte, J Peter

    2010-07-01

    Ceramides are precursors of major sphingolipids and can be important cellular effectors. The biological effects of ceramides have been suggested to stem from their biophysical effects on membrane structure affecting the lateral and transbilayer organization of other membrane components. In this study we investigated the effect of acyl chain composition in ceramides (C4-C24:1) on their miscibility with N-palmitoyl-sphingomyelin (PSM) using differential scanning calorimetry. We found that short-chain (C4 and C8) ceramides induced phase separation and lowered the T (m) and enthalpy of the PSM endotherm. We conclude that short-chain ceramides were more miscible in the fluid-phase than in the gel-phase PSM bilayers. Long-chain ceramides induced apparent heterogeneity in the bilayers. The main PSM endotherm decreased in cooperativity and enthalpy with increasing ceramide concentration. New ceramide-enriched components could be seen in the thermograms at all ceramide concentrations above X (Cer) = 0.05. These broad components had higher T (m) values than pure PSM. C24:1 ceramide exhibited complex behavior in the PSM bilayers. The miscibility of C24:1 ceramide with PSM at low (X (Cer) = 0.05-0.10) concentrations was exceptionally good according to the cooperativity of the transition. At higher concentrations, multiple components were detected, which might have arisen from interdigitated gel-phases formed by this very asymmetric ceramide. The results of this study indicate that short-chain and long-chain ceramides have very different effects on the sphingomyelin bilayers. There also seems to be a correlation between their miscibility in binary systems and the effect of ceramides of different hydrophobic length on sphingomyelin-rich domains in multicomponent membranes.

  14. Boron doped Si rich oxide/SiO{sub 2} and silicon rich nitride/SiN{sub x} bilayers on molybdenum-fused silica substrates for vertically structured Si quantum dot solar cells

    SciTech Connect

    Lin, Ziyun Wu, Lingfeng; Jia, Xuguang; Zhang, Tian; Puthen-Veettil, Binesh; Yang, Terry Chien-Jen; Conibeer, Gavin; Perez-Wurfl, Ivan

    2015-07-28

    Vertically structured Si quantum dots (QDs) solar cells with molybdenum (Mo) interlayer on quartz substrates would overcome current crowding effects found in mesa-structured cells. This study investigates the compatibility between boron (B) doped Si QDs bilayers and Mo-fused silica substrate. Both Si/SiO{sub 2} and Si/SiN{sub x} based QDs bilayers were studied. The material compatibility under high temperature treatment was assessed by examining Si crystallinity, microstress, thin film adhesion, and Mo oxidation. It was observed that the presence of Mo interlayer enhanced the Si QDs size confinement, crystalline fraction, and QDs size uniformity. The use of B doping was preferred compared to phosphine (PH{sub 3}) doping studied previously in terms of better surface and interface properties by reducing oxidized spots on the film. Though crack formation due to thermal mismatch after annealing remained, methods to overcome this problem were proposed in this paper. Schematic diagram to fabricate full vertical structured Si QDs solar cells was also suggested.

  15. Existence of a Steady Flow of Stokes Fluid Past a Linear Elastic Structure Using Fictitious Domain

    NASA Astrophysics Data System (ADS)

    Halanay, Andrei; Murea, Cornel Marius; Tiba, Dan

    2016-06-01

    We use fictitious domain method with penalization for the Stokes equation in order to obtain approximate solutions in a fixed larger domain including the domain occupied by the structure. The coefficients of the fluid problem, excepting the penalizing term, are independent of the deformation of the structure. It is easy to check the inf-sup condition and the coercivity of the Stokes problem in the fixed domain. Subtracting the structure equations from the fictitious fluid equations in the structure domain, we obtain a weak formulation in a fixed domain, where the continuity of the stress at the interface does not appear explicitly. Existence of a solution is proved when the structure displacement is generated by a finite number of modes.

  16. Fluid-Structure Interaction Study on a Pre-Buckled Deformable Flat Ribbon

    NASA Astrophysics Data System (ADS)

    Fovargue, Lauren; Shams, Ehsan; Watterson, Amy; Corson, Dave; Filardo, Benjamin; Zimmerman, Daniel; Shan, Bob; Oberai, Assad

    2015-11-01

    A Fluid-Structure Interaction study is conducted for the flow over a deformable flat ribbon. This mechanism, which is called ribbon frond, maybe used as a device for pumping water and/or harvesting energy in rivers. We use a lower dimensional mathematical model, which represents the ribbon as a pre-buckled structure. The surface forces from the fluid flow, dictate the deformation of the ribbon, and the ribbon in turn imposes boundary conditions for the incompressible Navier-Stokes equations. The mesh motion is handled using an Arbitrary Lagrangian-Eulerian (ALE) scheme and the fluid-structure coupling is handled by iterating over the staggered governing equations for the structure, the fluid and the mesh. Simulations are conducted at three different free stream velocities. The results, including the frequency of oscillations, show agreement with experimental data. The vortical structures near the surface of the ribbon and its deformation are highly correlated. It is observed that the ribbon motion exhibits deviation from a harmonic motion, especially at lower free stream velocities. The behavior of the ribbon is compared to swimming animals, such as eels, in order to better understand its performance. The authors acknowledge support from ONR SBIR Phase II, contract No. N0001412C0604 and USDA, NIFA SBIR Phase I, contract No. 2013-33610-20836 and NYSERDA PON 2569, contract No. 30364.

  17. Random bilayer phases of dilute surfactant solutions

    NASA Astrophysics Data System (ADS)

    Cates, M. E.; Roux, D.

    1990-12-01

    Surfactant molecules in dilute solution may aggregate reversibly into extended structures. For suitably chosen molecules, the preferred packing involves a locally flat bilayer which tends to wander entropically at large distances. At low temperatures (and/or high concentrations) the system forms a stack of flat sheets with one-dimensional quasi-long range order (a smectic liquid crystal), but at high temperatures or low concentrations, the stack can melt into a random surface structure that resembles a multiply connected labyrinth or 'sponge' of bilayer in a sea of solvent. Recent theoretical and experimental progress in understanding the properties of the sponge is reviewed. The authors argue that the sponge phase may provide a good system for the study of various liquid-state critical phenomena.

  18. FE Modelling of the Fluid-Structure-Acoustic Interaction for the Vocal Folds Self-Oscillation

    NASA Astrophysics Data System (ADS)

    Švancara, Pavel; Horáček, J.; Hrůza, V.

    The flow induced self-oscillation of the human vocal folds in interaction with acoustic processes in the simplified vocal tract model was explored by three-dimensional (3D) finite element (FE) model. Developed FE model includes vocal folds pretension before phonation, large deformations of the vocal fold tissue, vocal folds contact, fluid-structure interaction, morphing the fluid mesh according the vocal folds motion (Arbitrary Lagrangian-Eulerian approach), unsteady viscous compressible airflow described by the Navier-Stokes equations and airflow separation during the glottis closure. Iterative partitioned approach is used for modelling the fluid-structure interaction. Computed results prove that the developed model can be used for simulation of the vocal folds self-oscillation and resulting acoustic waves. The developed model enables to numerically simulate an influence of some pathological changes in the vocal fold tissue on the voice production.

  19. Structural Transition in a Fluid of Spheroids: A Low-Density Vestige of Jamming

    NASA Astrophysics Data System (ADS)

    Cohen, A. P.; Dorosz, S.; Schofield, A. B.; Schilling, T.; Sloutskin, E.

    2016-03-01

    A thermodynamically equilibrated fluid of hard spheroids is a simple model of liquid matter. In this model, the coupling between the rotational degrees of freedom of the constituent particles and their translations may be switched off by a continuous deformation of a spheroid of aspect ratio t into a sphere (t =1 ). We demonstrate, by experiments, theory, and computer simulations, that dramatic nonanalytic changes in structure and thermodynamics of the fluids take place, as the coupling between rotations and translations is made to vanish. This nonanalyticity, reminiscent of a second-order liquid-liquid phase transition, is not a trivial consequence of the shape of an individual particle. Rather, free volume considerations relate the observed transition to a similar nonanalyticity at t =1 in structural properties of jammed granular ellipsoids. This observation suggests a deep connection to exist between the physics of jamming and the thermodynamics of simple fluids.

  20. Sensitivity and Approximation of Coupled Fluid-Structure Equations by Virtual Control Method

    SciTech Connect

    Murea, Cornel Marius Vazquez, Carlos

    2005-08-15

    The formulation of a particular fluid-structure interaction as an optimal control problem is the departure point of this work. The control is the vertical component of the force acting on the interface and the observation is the vertical component of the velocity of the fluid on the interface. This approach permits us to solve the coupled fluid-structure problem by partitioned procedures. The analytic expression for the gradient of the cost function is obtained in order to devise accurate numerical methods for the minimization problem. Numerical results arising from blood flow in arteries are presented. To solve the optimal control problem numerically, we use a quasi-Newton method which employs the analytic gradient of the cost function and the approximation of the inverse Hessian is updated by the Broyden, Fletcher, Goldforb, Shano (BFGS) scheme. This algorithm is faster than fixed point with relaxation or block Newton methods.

  1. Polarization-phase tomography of biological fluids polycrystalline structure

    NASA Astrophysics Data System (ADS)

    Dubolazov, A. V.; Vanchuliak, O. Ya.; Garazdiuk, M.; Sidor, M. I.; Motrich, A. V.; Kostiuk, S. V.

    2013-12-01

    Our research is aimed at designing an experimental method of Fourier's laser polarization phasometry of the layers of human effusion for an express diagnostics during surgery and a differentiation of the degree of severity (acute - gangrenous) appendectomy by means of statistical, correlation and fractal analysis of the coherent scattered field. A model of generalized optical anisotropy of polycrystal networks of albumin and globulin of the effusion of appendicitis has been suggested and the method of Fourier's phasometry of linear (a phase shift between the orthogonal components of the laser wave amplitude) and circular (the angle of rotation of the polarization plane) birefringence with a spatial-frequency selection of the coordinate distributions for the differentiation of acute and gangrenous conditions have been analytically substantiated. Comparative studies of the efficacy of the methods of direct mapping of phase distributions and Fourier's phasometry of a laser radiation field transformed by the dendritic and spherolitic networks of albumin and globulin of the layers of effusion of appendicitis on the basis of complex statistical, correlation and fractal analysis of the structure of phase maps.

  2. Renormalizing a viscous fluid model for large scale structure formation

    SciTech Connect

    Führer, Florian; Rigopoulos, Gerasimos E-mail: gerasimos.rigopoulos@ncl.ac.uk

    2016-02-01

    Using the Stochastic Adhesion Model (SAM) as a simple toy model for cosmic structure formation, we study renormalization and the removal of the cutoff dependence from loop integrals in perturbative calculations. SAM shares the same symmetry with the full system of continuity+Euler equations and includes a viscosity term and a stochastic noise term, similar to the effective theories recently put forward to model CDM clustering. We show in this context that if the viscosity and noise terms are treated as perturbative corrections to the standard eulerian perturbation theory, they are necessarily non-local in time. To ensure Galilean Invariance higher order vertices related to the viscosity and the noise must then be added and we explicitly show at one-loop that these terms act as counter terms for vertex diagrams. The Ward Identities ensure that the non-local-in-time theory can be renormalized consistently. Another possibility is to include the viscosity in the linear propagator, resulting in exponential damping at high wavenumber. The resulting local-in-time theory is then renormalizable to one loop, requiring less free parameters for its renormalization.

  3. Determining an Effective Shear Modulus in Tubular Organs for Fluid-Structure Interaction

    NASA Astrophysics Data System (ADS)

    Chisena, Robert; Brasseur, James; Costanzo, Francesco; Gregersen, Hans; Zhao, Jingbo

    2014-11-01

    Fluid-structure interaction (FSI) is central to the mechanics of fluid-filled tubular organs such as the intestine and esophagus. The motions of fluid chyme are driven by a muscularis wall layer of circular and longitudinal muscle fibers. The coupled motions of the fluid and elastic solid phases result from a local balance between active and passive muscle stress components, fluid pressure, and fluid viscous stresses. Model predictions depend on the passive elastic response of the muscularis layer, which is typically parameterized with an average isotropic elastic modulus (EM), currently measured in vivo and in vitro with estimates for total hoop stress within a distension experiment. We have shown that this approach contains serious error due to the overwhelming influence of incompressibility on the hydrostatic component. We present a new approach in which an effective shear modulus, containing only deviatoric contributions, is measured to overcome this serious error. Using in vitro measurements from pig intestines, we compare our new approach to the current method, showing vastly different predictions. We will also report on our current analysis which aims to determine the influence of residual stress on the EM measurements and comment on it use in FSI simulations.

  4. Full-Eulerian fluid-structure coupling simulation of hyperelastic channel flow

    NASA Astrophysics Data System (ADS)

    Nagano, Naohiro; Sugiyama, Kazuyasu; Takeuchi, Shintaro; Satoshi, II; Takagi, Shu; Matsumoto, Yoichiro

    2010-11-01

    A full-Eulerian simulation for coupling a Newtonian fluid and hyperelastic material is conducted. The system involves an interaction problem between the fluid and hyperelastic walls and is driven by pressure difference, mimicking a blood flow in a blood vessel. A single set of the governing equations for the fluid and solid is employed, and a volume-of-fluid idea is employed to describe a multi-component geometry. The solid stress is defined in Eulerian frame by using a left Cauchy-Green deformation tensor, and the temporal change in the solid deformation is described by updating the tensor. The method employs a uniform fixed grid system for both fluid and solid and it does not require any mesh generation or reconstruction, aiming at facilitating the practical bio-mechanical fluid-structure analysis based on a medical image. The validity of the simulation results is established through comparison with a theoretical prediction. As an application of the present method, pulsating flows are simulated to demonstrate a nonlinear behavior of the flow rate on the pulsating amplitude, and an effect of employing an anisotropic hyperelastic material is discussed.

  5. Tunneling Plasmonics in Bilayer Graphene.

    PubMed

    Fei, Z; Iwinski, E G; Ni, G X; Zhang, L M; Bao, W; Rodin, A S; Lee, Y; Wagner, M; Liu, M K; Dai, S; Goldflam, M D; Thiemens, M; Keilmann, F; Lau, C N; Castro-Neto, A H; Fogler, M M; Basov, D N

    2015-08-12

    We report experimental signatures of plasmonic effects due to electron tunneling between adjacent graphene layers. At subnanometer separation, such layers can form either a strongly coupled bilayer graphene with a Bernal stacking or a weakly coupled double-layer graphene with a random stacking order. Effects due to interlayer tunneling dominate in the former case but are negligible in the latter. We found through infrared nanoimaging that bilayer graphene supports plasmons with a higher degree of confinement compared to single- and double-layer graphene, a direct consequence of interlayer tunneling. Moreover, we were able to shut off plasmons in bilayer graphene through gating within a wide voltage range. Theoretical modeling indicates that such a plasmon-off region is directly linked to a gapped insulating state of bilayer graphene, yet another implication of interlayer tunneling. Our work uncovers essential plasmonic properties in bilayer graphene and suggests a possibility to achieve novel plasmonic functionalities in graphene few-layers.

  6. Tunneling Plasmonics in Bilayer Graphene

    NASA Astrophysics Data System (ADS)

    Fei, Z.; Iwinski, E. G.; Ni, G. X.; Zhang, L. M.; Bao, W.; Rodin, A. S.; Lee, Y.; Wagner, M.; Liu, M. K.; Dai, S.; Goldflam, M. D.; Thiemens, M.; Keilmann, F.; Lau, C. N.; Castro-Neto, A. H.; Fogler, M. M.; Basov, D. N.

    2015-08-01

    We report experimental signatures of plasmonic effects due to electron tunneling between adjacent graphene layers. At sub-nanometer separation, such layers can form either a strongly coupled bilayer graphene with a Bernal stacking or a weakly coupled double-layer graphene with a random stacking order. Effects due to interlayer tunneling dominate in the former case but are negligible in the latter. We found through infrared nano-imaging that bilayer graphene supports plasmons with a higher degree of confinement compared to single- and double-layer graphene, a direct consequence of interlayer tunneling. Moreover, we were able to shut off plasmons in bilayer graphene through gating within a wide voltage range. Theoretical modeling indicates that such a plasmon-off region is directly linked to a gapped insulating state of bilayer graphene: yet another implication of interlayer tunneling. Our work uncovers essential plasmonic properties in bilayer graphene and suggests a possibility to achieve novel plasmonic functionalities in graphene few-layers.

  7. A Parallel Monolithic Approach for Fluid-Structure Interaction in a Cerebral Aneurysm

    NASA Astrophysics Data System (ADS)

    Sahin, Mehmet; Eken, Ali

    2014-11-01

    A parallel fully-coupled approach has been developed for the fluid-structure interaction problem in a cerebral artery with aneurysm. An Arbitrary Lagrangian-Eulerian formulation based on the side-centered unstructured finite volume method is employed for the governing incompressible Navier-Stokes equations and the classical Galerkin finite element formulation is used to discretize the constitutive law for the Saint Venant-Kirchhoff material in a Lagrangian frame for the solid domain. The time integration method for the structure domain is based on the energy conserving mid-point method while the second-order backward difference is used within the fluid domain. The resulting large-scale algebraic linear equations are solved using a one-level restricted additive Schwarz preconditioner with a block-incomplete factorization within each partitioned sub-domains. The parallel implementation of the present fully coupled unstructured fluid-structure solver is based on the PETSc library. The proposed numerical algorithm is initially validated for several classical benchmark problems and then applied to a more complicated problem involving unsteady pulsatile blood flow in a cerebral artery with aneurysm as a realistic fluid-structure interaction problem encountered in biomechanics. The authors acknowledge financial support from Turkish National Scientific and Technical Research Council through Project Number 112M107.

  8. A mixed time integration method for large scale acoustic fluid-structure interaction

    SciTech Connect

    Christon, M.A.; Wineman, S.J.; Goudreau, G.L.; Foch, J.D.

    1994-07-18

    The transient, coupled, interaction of sound with structures is a process in which an acoustic fluid surrounding an elastic body contributes to the effective inertia and elasticity of the body. Conversely, the presence of an elastic body in an acoustic medium influences the behavior of propagating disturbances. This paper details the application of a mixed explicit-implicit time integration algorithm to the fully coupled acoustic fluidstructure interaction problem. Based upon a dispersion analysis of the semi-discrete wave equation a second-order, explicit scheme for solving the wave equation is developed. The combination of a highly vectorized, explicit, acoustic fluid solver with an implicit structural code for linear elastodynamics has resulted in a simulation tool, PING, for acoustic fluid-structure interaction. PING`s execution rates range from 1{mu}s/Element/{delta}t for rigid scattering to 10{mu}s/Element/{delta}t for fully coupled problems. Several examples of PING`s application to 3-D problems serve in part to validate the code, and also to demonstrate the capability to treat complex geometry, acoustic fluid-structure problems which require high resolution meshes.

  9. Development of an integrated BEM approach for hot fluid structure interaction

    NASA Technical Reports Server (NTRS)

    Dargush, G. F.; Banerjee, P. K.

    1989-01-01

    The progress made toward the development of a boundary element formulation for the study of hot fluid-structure interaction in Earth-to-Orbit engine hot section components is reported. The convective viscous integral formulation was derived and implemented in the general purpose computer program GP-BEST. The new convective kernel functions, in turn, necessitated the development of refined integration techniques. As a result, however, since the physics of the problem is embedded in these kernels, boundary element solutions can now be obtained at very high Reynolds number. Flow around obstacles can be solved approximately with an efficient linearized boundary-only analysis or, more exactly, by including all of the nonlinearities present in the neighborhood of the obstacle. The other major accomplishment was the development of a comprehensive fluid-structure interaction capability within GP-BEST. This new facility is implemented in a completely general manner, so that quite arbitrary geometry, material properties and boundary conditions may be specified. Thus, a single analysis code (GP-BEST) can be used to run structures-only problems, fluids-only problems, or the combined fluid-structure problem. In all three cases, steady or transient conditions can be selected, with or without thermal effects. Nonlinear analyses can be solved via direct iteration or by employing a modified Newton-Raphson approach.

  10. Development of an integrated BEM approach for hot fluid structure interaction

    NASA Technical Reports Server (NTRS)

    Dargush, G. F.; Banerjee, P. K.; Shi, Y.

    1991-01-01

    The development of a comprehensive fluid-structure interaction capability within a boundary element computer code is described. This new capability is implemented in a completely general manner, so that quite arbitrary geometry, material properties and boundary conditions may be specified. Thus, a single analysis code can be used to run structures-only problems, fluids-only problems, or the combined fluid-structure problem. In all three cases, steady or transient conditions can be selected, with or without thermal effects. Nonlinear analyses can be solved via direct iteration or by employing a modified Newton-Raphson approach. A number of detailed numerical examples are included at the end of these two sections to validate the formulations and to emphasize both the accuracy and generality of the computer code. A brief review of the recent applicable boundary element literature is included for completeness. The fluid-structure interaction facility is discussed. Once again, several examples are provided to highlight this unique capability. A collection of potential boundary element applications that have been uncovered as a result of work related to the present grant is given. For most of those problems, satisfactory analysis techniques do not currently exist.

  11. Immersogeometric cardiovascular fluid-structure interaction analysis with divergence-conforming B-splines.

    PubMed

    Kamensky, David; Hsu, Ming-Chen; Yu, Yue; Evans, John A; Sacks, Michael S; Hughes, Thomas J R

    2017-02-01

    This paper uses a divergence-conforming B-spline fluid discretization to address the long-standing issue of poor mass conservation in immersed methods for computational fluid-structure interaction (FSI) that represent the influence of the structure as a forcing term in the fluid subproblem. We focus, in particular, on the immersogeometric method developed in our earlier work, analyze its convergence for linear model problems, then apply it to FSI analysis of heart valves, using divergence-conforming B-splines to discretize the fluid subproblem. Poor mass conservation can manifest as effective leakage of fluid through thin solid barriers. This leakage disrupts the qualitative behavior of FSI systems such as heart valves, which exist specifically to block flow. Divergence-conforming discretizations can enforce mass conservation exactly, avoiding this problem. To demonstrate the practical utility of immersogeometric FSI analysis with divergence-conforming B-splines, we use the methods described in this paper to construct and evaluate a computational model of an in vitro experiment that pumps water through an artificial valve.

  12. Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system.

    PubMed

    Anderson, Rika E; Beltrán, Mónica Torres; Hallam, Steven J; Baross, John A

    2013-02-01

    Physical and chemical gradients are dominant factors in shaping hydrothermal vent microbial ecology, where archaeal and bacterial habitats encompass a range between hot, reduced hydrothermal fluid and cold, oxidized seawater. To determine the impact of these fluid gradients on microbial communities inhabiting these systems, we surveyed bacterial and archaeal community structure among and between hydrothermal plumes, diffuse flow fluids, and background seawater in several hydrothermal vent sites on the Juan de Fuca Ridge using 16S rRNA gene diversity screening (clone libraries and terminal restriction length polymorphisms) and quantitative polymerase chain reaction methods. Community structure was similar between hydrothermal plumes and background seawater, where a number of taxa usually associated with low-oxygen zones were observed, whereas high-temperature diffuse fluids exhibited a distinct phylogenetic profile. SUP05 and Arctic96BD-19 sulfur-oxidizing bacteria were prevalent in all three mixing regimes where they exhibited overlapping but not identical abundance patterns. Taken together, these results indicate conserved patterns of redox-driven niche partitioning between hydrothermal mixing regimes and microbial communities associated with sinking particles and oxygen-deficient waters. Moreover, the prevalence of SUP05 and Arctic96BD-19 in plume and diffuse flow fluids indicates a more cosmopolitan role for these groups in the ecology and biogeochemistry of the dark ocean.

  13. Lipid bilayers suspended on microfabricated supports

    NASA Astrophysics Data System (ADS)

    Ogier, Simon D.; Bushby, Richard J.; Cheng, Yaling; Cox, Tim I.; Evans, Stephen D.; Knowles, Peter F.; Miles, Robert E.; Pattison, Ian

    2001-03-01

    The plasma membrane, that exists as part of many animal and plant cells, is a regulator for the transport of ions and small molecules across cell boundaries. Two main components involved are the phospholipid bilayer and the transport proteins. This paper details the construction of a micromachined support for bilayers (MSB) as a first step towards the development of highly selective and highly sensitive ion-channel based biosensors. The device consists of a ~100 micrometer hole in a polymeric support above a cavity that can hold ~25 nL of electrolyte. Electrodes attached to the structure allow the resistance of the membranes to be measured using d.c. conductivity. The MSB is made in two halves, using SU8 ultra-thick resist, which are subsequently bonded together to make the final structure. A layer of gold, surrounding the aperture, enables self-assembled monolayers of alkanethiols to be used to make the polymeric structure biocompatible. Lipid membranes have been formed over these holes with resistances comparable with those of natural membranes >10 MOhmcm^2. The ion-channel gramicidin has successfully been incorporated into the bilayer and its activity monitored. It is proposed that this type of device could be used not only for studying membrane transport phenomena but also as part of an ion-channel based biosensor.

  14. Electronic properties of asymmetrically doped twisted graphene bilayers

    NASA Astrophysics Data System (ADS)

    Trambly de Laissardière, Guy; Namarvar, Omid Faizy; Mayou, Didier; Magaud, Laurence

    2016-06-01

    Rotated graphene bilayers form an exotic class of nanomaterials with fascinating electronic properties governed by the rotation angle θ . For large rotation angles, the electron eigenstates are restricted to one layer and the bilayer behaves like two decoupled graphene layers. At intermediate angles, Dirac cones are preserved but with a lower velocity and van Hove singularities are induced at energies where the two Dirac cones intersect. At very small angles, eigenstates become localized in peculiar moiré zones. We analyze here the effect of an asymmetric doping for a series of commensurate rotated bilayers on the basis of tight-binding calculations of their band dispersions, density of states, participation ratio, and diffusive properties. While a small doping level preserves the θ dependence of the rotated bilayer electronic structure, larger doping induces a further reduction of the band velocity in the same way as a further reduction of the rotation angle.

  15. Enhanced electrocaloric effect in composition gradient bilayer thick films

    NASA Astrophysics Data System (ADS)

    Hou, Ying; Yang, Lu; Qian, Xiaoshi; Zhang, Tian; Zhang, Q. M.

    2016-03-01

    We report the enhanced electrocaloric (EC) response over a broad temperature range in composition gradient Ba(ZrTi)O3 based bilayer thick films. A large EC temperature change of -4.9 K under an electric field of 10 MV/m around room temperature, large electrocaloric coefficient ΔT/ΔE = 0.49 × 10-6 K m V-1 were observed in the BaZr0.17Ti0.83O3/BaZr0.20Ti0.80O3 bilayer thick films, which are improved compared with BaZr0.20Ti0.80O3 and BaZr0.17Ti0.83O3 homogeneous bilayer films. The result reveals the potential of the composition gradient bilayer structure in improving the electrocaloric effect, which may provide an effective route to achieve large EC temperature change under a low electric field.

  16. Biophysical changes induced by xenon on phospholipid bilayers.

    PubMed

    Booker, Ryan D; Sum, Amadeu K

    2013-05-01

    Structural and dynamic changes in cell membrane properties induced by xenon, a volatile anesthetic molecule, may affect the function of membrane-mediated proteins, providing a hypothesis for the mechanism of general anesthetic action. Here, we use molecular dynamics simulation and differential scanning calorimetry to examine the biophysical and thermodynamic effects of xenon on model lipid membranes. Our results indicate that xenon atoms preferentially localize in the hydrophobic core of the lipid bilayer, inducing substantial increases in the area per lipid and bilayer thickness. Xenon depresses the membrane gel-liquid crystalline phase transition temperature, increasing membrane fluidity and lipid head group spacing, while inducing net local ordering effects in a small region of the lipid carbon tails and modulating the bilayer lateral pressure profile. Our results are consistent with a role for nonspecific, lipid bilayer-mediated mechanisms in producing xenon's general anesthetic action.

  17. Small angle x-ray scattering study of the interaction of poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) triblock copolymers with lipid bilayers.

    SciTech Connect

    Firestone, M. A.; Wolf, A. C.; Seifert, S.; Univ. Chicago

    2003-11-01

    The relationship between molecular architecture and the nature of interactions with lipid bilayers has been studied for a series of poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers using small-angle X-ray scattering (SAXS) and thermal analysis (differential scanning calorimetry, DSC). The number of molecular repeat units in the hydrophobic poly(propylene oxide), PPO, block has been found to be a critical determinant of the nature of triblock copolymer-lipid bilayer association. For dimyristoyl-sn-glycero-3-phosphocholine (DMPC)-based biomembrane structures, polymers possessing a PPO chain length commensurate with the acyl chain dimensions of the lipid bilayer yield highly ordered, swollen lamellar structures consistent with well-integrated (into the lipid bilayer) PPO blocks. Triblock copolymers of lesser PPO chain length yield materials with structural characteristics similar to a simple dispersion of DMPC in water. Increasing the concentration (from 4 to 12 mol %) of well-integrated triblock copolymers enhances the structural ordering of the lamellar phase, while concentrations exceeding 16 mol % result in the formation of a hexagonal phase. Examination of temperature-induced changes in the structure of these mesophases (complex fluids) reveals that if the temperature is reduced sufficiently, all compositions exclude polymer and thus exhibit the characteristic SAXS pattern for hydrated DMPC bilayers. Increasing the temperature promotes better insertion of the polymers possessing PPO chain lengths sufficient for membrane insertion. No temperature-induced structural changes are observed in compositions prepared with PEO-PPO-PEO polymers that feature PPO length insufficient to permit full incorporation into the lipid bilayer.

  18. Linearized formulation for fluid-structure interaction: Application to the linear dynamic response of a pressurized elastic structure containing a fluid with a free surface

    NASA Astrophysics Data System (ADS)

    Schotté, J.-S.; Ohayon, R.

    2013-05-01

    To control the linear vibrations of structures partially filled with liquids is of prime importance in various industries such as aerospace, naval, civil and nuclear engineering. It is proposed here to investigate a linearized formulation adapted to a rational computation of the vibrations of such coupled systems. Its particularity is to be fully Lagrangian since it considers the fluid displacement field with respect to a static equilibrium configuration as the natural variable describing the fluid motion, as classically done in structural dynamics. As the coupled system considered here is weakly damped in the low frequency domain (low modal density), the analysis of the vibrations of the associated undamped conservative system constitutes the main objective of this paper. One originality of the present formulation is to take into account the effect of the pressurization of the tank on the dynamics of the system, particularly in the case of a compressible liquid. We propose here a new way of deriving the linearized equations of the coupled problem involving a deformable structure and an inner inviscid liquid with a free surface. A review of the classical case considering a heavy incompressible liquid is followed by an application to the new case involving a light compressible liquid. A solution procedure in the frequency domain is proposed and a numerical discretization using the finite element method is discussed. In order to reduce the computational costs, an appropriate reduced order matrix model using modal synthesis approach is also presented.

  19. Mechanism of unassisted ion transport across membrane bilayers

    NASA Technical Reports Server (NTRS)

    Wilson, M. A.; Pohorille, A.

    1996-01-01

    To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

  20. Robustly Engineering Thermal Conductivity of Bilayer Graphene by Interlayer Bonding

    PubMed Central

    Zhang, Xiaoliang; Gao, Yufei; Chen, Yuli; Hu, Ming

    2016-01-01

    Graphene and its bilayer structure are the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. Their realistic applications in emerging nanoelectronics usually call for thermal transport manipulation in a controllable and precise manner. In this paper we systematically studied the effect of interlayer covalent bonding, in particular different interlay bonding arrangement, on the thermal conductivity of bilayer graphene using equilibrium molecular dynamics simulations. It is revealed that, the thermal conductivity of randomly bonded bilayer graphene decreases monotonically with the increase of interlayer bonding density, however, for the regularly bonded bilayer graphene structure the thermal conductivity possesses unexpectedly non-monotonic dependence on the interlayer bonding density. The results suggest that the thermal conductivity of bilayer graphene depends not only on the interlayer bonding density, but also on the detailed topological configuration of the interlayer bonding. The underlying mechanism for this abnormal phenomenon is identified by means of phonon spectral energy density, participation ratio and mode weight factor analysis. The large tunability of thermal conductivity of bilayer graphene through rational interlayer bonding arrangement paves the way to achieve other desired properties for potential nanoelectronics applications involving graphene layers. PMID:26911859

  1. Robustly Engineering Thermal Conductivity of Bilayer Graphene by Interlayer Bonding.

    PubMed

    Zhang, Xiaoliang; Gao, Yufei; Chen, Yuli; Hu, Ming

    2016-02-25

    Graphene and its bilayer structure are the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. Their realistic applications in emerging nanoelectronics usually call for thermal transport manipulation in a controllable and precise manner. In this paper we systematically studied the effect of interlayer covalent bonding, in particular different interlay bonding arrangement, on the thermal conductivity of bilayer graphene using equilibrium molecular dynamics simulations. It is revealed that, the thermal conductivity of randomly bonded bilayer graphene decreases monotonically with the increase of interlayer bonding density, however, for the regularly bonded bilayer graphene structure the thermal conductivity possesses unexpectedly non-monotonic dependence on the interlayer bonding density. The results suggest that the thermal conductivity of bilayer graphene depends not only on the interlayer bonding density, but also on the detailed topological configuration of the interlayer bonding. The underlying mechanism for this abnormal phenomenon is identified by means of phonon spectral energy density, participation ratio and mode weight factor analysis. The large tunability of thermal conductivity of bilayer graphene through rational interlayer bonding arrangement paves the way to achieve other desired properties for potential nanoelectronics applications involving graphene layers.

  2. Simulation of a pulsatile total artificial heart: Development of a partitioned Fluid Structure Interaction model

    NASA Astrophysics Data System (ADS)

    Sonntag, Simon J.; Kaufmann, Tim A. S.; Büsen, Martin R.; Laumen, Marco; Linde, Torsten; Schmitz-Rode, Thomas; Steinseifer, Ulrich

    2013-04-01

    Heart disease is one of the leading causes of death in the world. Due to a shortage in donor organs artificial hearts can be a bridge to transplantation or even serve as a destination therapy for patients with terminal heart insufficiency. A pusher plate driven pulsatile membrane pump, the Total Artificial Heart (TAH) ReinHeart, is currently under development at the Institute of Applied Medical Engineering of RWTH Aachen University.This paper presents the methodology of a fully coupled three-dimensional time-dependent Fluid Structure Interaction (FSI) simulation of the TAH using a commercial partitioned block-Gauss-Seidel coupling package. Partitioned coupling of the incompressible fluid with the slender flexible membrane as well as a high fluid/structure density ratio of about unity led inherently to a deterioration of the stability (‘artificial added mass instability’). The objective was to conduct a stable simulation with high accuracy of the pumping process. In order to achieve stability, a combined resistance and pressure outlet boundary condition as well as the interface artificial compressibility method was applied. An analysis of the contact algorithm and turbulence condition is presented. Independence tests are performed for the structural and the fluid mesh, the time step size and the number of pulse cycles. Because of the large deformation of the fluid domain, a variable mesh stiffness depending on certain mesh properties was specified for the fluid elements. Adaptive remeshing was avoided. Different approaches for the mesh stiffness function are compared with respect to convergence, preservation of mesh topology and mesh quality. The resulting mesh aspect ratios, mesh expansion factors and mesh orthogonalities are evaluated in detail. The membrane motion and flow distribution of the coupled simulations are compared with a top-view recording and stereo Particle Image Velocimetry (PIV) measurements, respectively, of the actual pump.

  3. Comparative computer simulation study of cholesterol in hydrated unary and binary lipid bilayers and in an anhydrous crystal.

    PubMed

    Plesnar, Elzbieta; Subczynski, Witold K; Pasenkiewicz-Gierula, Marta

    2013-07-25

    Models created with molecular dynamics simulations are used to compare the organization and dynamics of cholesterol (Chol) molecules in three different environments: (1) a hydrated pure Chol bilayer that models the Chol bilayer domain, which is a pure Chol domain embedded in the bulk membrane; (2) a 2-palmitoyl-3-oleoyl-d-glycerol-1-phosphorylcholine bilayer saturated with cholesterol (POPC-Chol50) that models the bulk membrane; (3) a Chol crystal. The computer model of the hydrated pure Chol bilayer is stable on the microsecond time scale. Some structural characteristics of Chol molecules in the Chol bilayer are similar to those in the POPC-Chol50 bilayer (e.g., tilt of Chol rings and chains), while others are similar to those in Chol crystals (e.g., surface area per Chol, bilayer thickness). The key result of this study is that the Chol bilayer has, unexpectedly, a dynamic structure, with Chol mobility similar to that in the POPC-Chol50 bilayer though slower. This is the major difference compared to Chol crystals, where Chol molecules are immobile. Also, water accessibility to Chol-OH groups in the Chol bilayer is not limited. On average, each Chol molecule makes 2.3 hydrogen bonds with water in the Chol bilayer, compared with 1.7 hydrogen bonds in the POPC-Col50 bilayer.

  4. Fluid Flow through Porous Sandstone with Overprinting and Intersecting Geological Structures of Various Types

    NASA Astrophysics Data System (ADS)

    Zhou, X.; Karimi-Fard, M.; Durlofsky, L.; Aydin, A.

    2010-12-01

    Impact of a wide variety of structural heterogeneities on fluid flow in an aeolian sandstone in the Valley of Fire State Park (NV), such as (1) dilatant fractures (joints), (2) shear fractures (faults), and (3) contraction/compaction structures (compaction bands), are considered. Each type of these structures has its own geometry, spacing, distribution, connectivity, and hydraulic properties, which either enhance or impede subsurface fluid flow. Permeability of these structures may, on average, be a few orders of magnitude higher or lower than those of the corresponding matrix rocks. In recent years, the influence of a single type of these heterogeneities on fluid flow has been studied individually, such as joints, compaction bands or faults. However, as different types of geological structures are commonly present together in the same rock volume, their combined effect requires a more detailed assessment. In this study, fluid flow simulations are performed using a special finite-volume discretization technique that was developed by Karimi-Fard et al. (2004; 2006). Using this approach, thin features such as fractures and compaction bands are represented as linear elements in unstructured 2D models and as planar elements in 3D models, which significantly reduces the total number of cells and simplifies grid generation. The cell geometric information and the cell-to-cell transmissibility obtained from this discretization technique are input to Stanford’s General Purpose Research Simulator (GPRS) for fluid flow simulation. To account for the effects of the various geological structures on subsurface flow, we perform permeability upscaling over regions corresponding to large-scale simulation grid blocks in order to obtain equivalent permeability components in two principal directions. We will focus on the following problems: (1) compaction bands of multisets; (2) compartmentalization of compaction bands of high-angle, low-angle and horizontal; (3) joints overprinting

  5. Four fluid model and numerical simulations of magnetic structures in the heliosheath

    NASA Astrophysics Data System (ADS)

    Avinash, K.; Cox, S. M.; Shaikh, D.; Zank, G. P.

    2007-12-01

    A magnetic hole/hump is a stable structure with small scale minima/maxima of the mean magnetic field in the centre. Such structure has been observed in inter-planetary magnetic field, planetary magneto sheath, cometary's plasma, and very recently in the heliosheath, as revealed by Voyager I observations. Recently, we have proposed a realistic three fluid model that comprises of three fluids in the model are electrons, heliosheath ions, and neutrals. Stationary, time independent solutions of this model consisting of holes, humps, trains of holes and humps etc. were found to be consistent with Voyager observations e.g. a few tens of ion gyro-radii width, large magnetic maxima/minima, oblique angles of propagation and well approximated by Gaussians. In the first part of the present work, we extend the three fluid model to a four fluid model consisting of electrons, pick up ions (PUI), solar wind ions (SWI), and neutrals. The PUIs are generated by neutrals via charge exchange with SWI. The kinetic pressure of PUI is nearly three to four times the pressure of SWI. Hence these are more suited to mediate small scale structures in heliosheath like shocks, magnetic holes/humps etc. We show that the constant energy exchange between these two fluid drives them non adiabatic. The modified adiabatic index, is calculated by solving the corresponding enthalpy equation. The PUI are found to be isothermal ( = 1) while SWI have 1.25. In the four fluid model, these effects are captured by including a modified equation of state for PUIs and SWIs. The phase space of time independent solutions in terms of the Mach numbers of PUI and SWI is constructed to delineate the parameter space which allows structure formation. In the second part of the present work, we examine the stability of our time independent solution by evolving them via a full set of modified Hall-MHD equations. The evolutions are examined using two codes e.g. a pseudo spectral code and a code based on finite difference

  6. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES: The phenomenon of even bulk mode variance in a ferromagnetic A-A bilayer system

    NASA Astrophysics Data System (ADS)

    Zhou, Wen-Ping; Yun, Guo-Hong; Liang, Xi-Xia

    2009-12-01

    The eigenproblems of spin waves in a symmetrical ferromagnetic bilayered system with periodic boundary conditions are solved using the interface-rescaling approach (IRA). The results show that interface coupling between two sublayers would not change the excitation energy of odd bulk modes, but change excitation energy of even bulk modes. We call this peculiar phenomenon the phenomenon of even bulk mode variance (PEBMV). There are two kinds of mechanisms which cause PEBMV: phase reversal and phase translation of the magnon at the interface, corresponding, respectively, to the antiferromagnetic and ferromagnetic interface coupling cases. PEBMV embodies the selective effect of the interface on different bulk magnons.

  7. Bursting Bubbles and Bilayers

    PubMed Central

    Wrenn, Steven P.; Dicker, Stephen M.; Small, Eleanor F.; Dan, Nily R.; Mleczko, Michał; Schmitz, Georg; Lewin, Peter A.

    2012-01-01

    This paper discusses various interactions between ultrasound, phospholipid monolayer-coated gas bubbles, phospholipid bilayer vesicles, and cells. The paper begins with a review of microbubble physics models, developed to describe microbubble dynamic behavior in the presence of ultrasound, and follows this with a discussion of how such models can be used to predict inertial cavitation profiles. Predicted sensitivities of inertial cavitation to changes in the values of membrane properties, including surface tension, surface dilatational viscosity, and area expansion modulus, indicate that area expansion modulus exerts the greatest relative influence on inertial cavitation. Accordingly, the theoretical dependence of area expansion modulus on chemical composition - in particular, poly (ethylene glyclol) (PEG) - is reviewed, and predictions of inertial cavitation for different PEG molecular weights and compositions are compared with experiment. Noteworthy is the predicted dependence, or lack thereof, of inertial cavitation on PEG molecular weight and mole fraction. Specifically, inertial cavitation is predicted to be independent of PEG molecular weight and mole fraction in the so-called mushroom regime. In the “brush” regime, however, inertial cavitation is predicted to increase with PEG mole fraction but to decrease (to the inverse 3/5 power) with PEG molecular weight. While excellent agreement between experiment and theory can be achieved, it is shown that the calculated inertial cavitation profiles depend strongly on the criterion used to predict inertial cavitation. This is followed by a discussion of nesting microbubbles inside the aqueous core of microcapsules and how this significantly increases the inertial cavitation threshold. Nesting thus offers a means for avoiding unwanted inertial cavitation and cell death during imaging and other applications such as sonoporation. A review of putative sonoporation mechanisms is then presented, including those

  8. General hydrophobic interaction potential for surfactant/lipid bilayers from direct force measurements between light-modulated bilayers

    PubMed Central

    Donaldson, Stephen H.; Lee, C. Ted; Chmelka, Bradley F.; Israelachvili, Jacob N.

    2011-01-01

    We establish and quantify correlations among the molecular structures, interaction forces, and physical processes associated with light-responsive self-assembled surfactant monolayers or bilayers at interfaces. Using the surface forces apparatus (SFA), the interaction forces between adsorbed monolayers and bilayers of an azobenzene-functionalized surfactant can be drastically and controllably altered by light-induced conversion of trans and cis molecular conformations. These reversible conformation changes affect significantly the shape of the molecules, especially in the hydrophobic region, which induces dramatic transformations of molecular packing in self-assembled structures, causing corresponding modulation of electrostatic double layer, steric hydration, and hydrophobic interactions. For bilayers, the isomerization from trans to cis exposes more hydrophobic groups, making the cis bilayers more hydrophobic, which lowers the activation energy barrier for (hemi)fusion. A quantitative and general model is derived for the interaction potential of charged bilayers that includes the electrostatic double-layer force of the Derjaguin–Landau–Verwey–Overbeek theory, attractive hydrophobic interactions, and repulsive steric-hydration forces. The model quantitatively accounts for the elastic strains, deformations, long-range forces, energy maxima, adhesion minima, as well as the instability (when it exists) as two bilayers breakthrough and (hemi)fuse. These results have several important implications, including quantitative and qualitative understanding of the hydrophobic interaction, which is furthermore shown to be a nonadditive interaction. PMID:21896718

  9. Impurities and electronic localization in graphene bilayers

    NASA Astrophysics Data System (ADS)

    Ojeda Collado, H. P.; Usaj, Gonzalo; Balseiro, C. A.

    2015-01-01

    We analyze the electronic properties of bilayer graphene with Bernal stacking and a low concentration of adatoms. Assuming that the host bilayer lies on top of a substrate, we consider the case where impurities are adsorbed only on the upper layer. We describe nonmagnetic impurities as a single orbital hybridized with carbon's pz states. The effect of impurity doping on the local density of states with and without a gated electric field perpendicular to the layers is analyzed. We look for Anderson localization in the different regimes and estimate the localization length. In the biased system, the field-induced gap is partially filled by strongly localized impurity states. Interestingly, the structure, distribution, and localization length of these states depend on the field polarization.

  10. Phase Behavior of Lipid Bilayers under Tension

    PubMed Central

    Uline, Mark J.; Schick, M.; Szleifer, Igal

    2012-01-01

    Given the proposed importance of membrane tension in regulating cellular functions, we explore the effects of a finite surface tension on phase equilibrium using a molecular theory that captures the quantitative structure of the phase diagram of the tensionless DPPC/DOPC/Cholesterol lipid bilayer. We find that an increase in the surface tension decreases the temperature of the transition from liquid to gel in a pure DPPC system by ∼1.0 K/(mN/m), and decreases the liquid-disordered to liquid-ordered transition at constant chemical potentials by approximately the same amount. Our results quantitatively isolate the role of tension in comparison to other thermodynamic factors, such as pressure, in determining the phase behavior of lipid bilayers. PMID:22325274

  11. Review of bilayer tablet technology.

    PubMed

    Abebe, Admassu; Akseli, Ilgaz; Sprockel, Omar; Kottala, Niranjan; Cuitiño, Alberto M

    2014-01-30

    Therapeutic strategies based on oral delivery of bilayer (and multilayer) tablets are gaining more acceptance among brand and generic products due to a confluence of factors including advanced delivery strategies, patient compliance and combination therapy. Successful manufacturing of these ever more complex systems needs to overcome a series of challenges from formulation design to tablet press monitoring and control. This article provides an overview of the state-of-the-art of bilayer tablet technology, highlighting the main benefits of this type of oral dosage forms while providing a description of current challenges and advances toward improving manufacturing practices and product quality. Several aspects relevant to bilayer tablet manufacturing are addressed including material properties, lubrication, layer ordering, layer thickness, layer weight control, as well as first and final compression forces. A section is also devoted to bilayer tablet characterization that present additional complexities associated with interfaces between layers. The available features of the manufacturing equipment for bilayer tablet production are also described indicating the different strategies for sensing and controls offered by bilayer tablet press manufacturers. Finally, a roadmap for bilayer tablet manufacturing is advanced as a guideline to formulation design and selection of process parameters and equipment.

  12. Physics of the cigarette filter: fluid flow through structures with randomly-placed obstacles

    NASA Astrophysics Data System (ADS)

    Stanley, H. Eugene; Andrade, José S.

    2001-06-01

    This talk briefly reviews the subject of fluid flow through disordered media. In particular, we focus on the sorts of considerations that may be necessary to move statistical physics from the description of idealized flows in the limit of zero Reynolds number to more realistic flows of real fluids moving at a nonzero velocity, where inertia effects mean that dangling ends are explored and the backbone is not entirely explored by the fluid. We discuss several intriguing features, such as the surprisingly sharp change in behavior from a localized to delocalized flow structure (distribution of flow velocities) that seems to occur at a critical value of Re which is orders of magnitude smaller than the critical value of Re where turbulence sets in.

  13. Experiment for validation of fluid-structure interaction models and algorithms.

    PubMed

    Hessenthaler, A; Gaddum, N R; Holub, O; Sinkus, R; Röhrle, O; Nordsletten, D

    2016-11-04

    In this paper a fluid-structure interaction (FSI) experiment is presented. The aim of this experiment is to provide a challenging yet easy-to-setup FSI test case that addresses the need for rigorous testing of FSI algorithms and modeling frameworks. Steady-state and periodic steady-state test cases with constant and periodic inflow were established. Focus of the experiment is on biomedical engineering applications with flow being in the laminar regime with Reynolds numbers 1283 and 651. Flow and solid domains were defined using computer-aided design (CAD) tools. The experimental design aimed at providing a straightforward boundary condition definition. Material parameters and mechanical response of a moderately viscous Newtonian fluid and a nonlinear incompressible solid were experimentally determined. A comprehensive data set was acquired by using magnetic resonance imaging to record the interaction between the fluid and the solid, quantifying flow and solid motion.

  14. A Unified Numerical Method for Fluid-Structure Interaction Applied to Human Cochlear Mechanics

    NASA Astrophysics Data System (ADS)

    Böhnke, Frank; Köster, Daniel

    2011-11-01

    A main problem with the numerical simulation of mechanical wave propagation in the cochlea is the coupling of the orthotropic elastic solid (cochlear partition and further structures) and the fluid (perilymph). We developed a unified approach employing velocity and pressure in the entire domain. The numerical approach consists in a finite-volume solver for the coupled solution of equations of motion for fluid and solid working on a single three-dimensional continuum domain. We represent the perilymph as a compressible and viscous fluid with the mechanical properties of water. The cochlear partition is modelled as a 2D membrane whose orthotropicity is represented by a shear modulus. Numerical results of a 3D uncoiled box model show a frequency dependent locus of maximum displacement along the cochlear partition, representing traveling waves.

  15. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

    PubMed Central

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  16. An investigation of the fluid-structure interaction of piston/cylinder interface

    NASA Astrophysics Data System (ADS)

    Pelosi, Matteo

    The piston/cylinder lubricating interface represents one of the most critical design elements of axial piston machines. Being a pure hydrodynamic bearing, the piston/cylinder interface fulfills simultaneously a bearing and sealing function under oscillating load conditions. Operating in an elastohydrodynamic lubrication regime, it also represents one of the main sources of power loss due to viscous friction and leakage flow. An accurate prediction of the time changing tribological interface characteristics in terms of fluid film thickness, dynamic pressure field, load carrying ability and energy dissipation is necessary to create more efficient interface designs. The aim of this work is to deepen the understanding of the main physical phenomena defining the piston/cylinder fluid film and to discover the impact of surface elastic deformations and heat transfer on the interface behavior. For this purpose, a unique fully coupled multi-body dynamics model has been developed to capture the complex fluid-structure interaction phenomena affecting the non-isothermal fluid film conditions. The model considers the squeeze film effect due to the piston micro-motion and the change in fluid film thickness due to the solid boundaries elastic deformations caused by the fluid film pressure and by the thermal strain. The model has been verified comparing the numerical results with measurements taken on special designed test pumps. The fluid film calculated dynamic pressure and temperature fields have been compared. Further validation has been accomplished comparing piston/cylinder axial viscous friction forces with measured data. The model has been used to study the piston/cylinder interface behavior of an existing axial piston unit operating at high load conditions. Numerical results are presented in this thesis.

  17. Self-assembled lipid bilayer materials

    DOEpatents

    Sasaki, Darryl Y.; Waggoner, Tina A.; Last, Julie A.

    2005-11-08

    The present invention is a self-assembling material comprised of stacks of lipid bilayers formed in a columnar structure, where the assembly process is mediated and regulated by chemical recognition events. The material, through the chemical recognition interactions, has a self-regulating system that corrects the radial size of the assembly creating a uniform diameter throughout most of the structure. The materials form and are stable in aqueous solution. These materials are useful as structural elements for the architecture of materials and components in nanotechnology, efficient light harvesting systems for optical sensing, chemical processing centers, and drug delivery vehicles.

  18. Numerical Analysis of Constrained Dynamical Systems, with Applications to Dynamic Contact of Solids, Nonlinear Elastodynamics and Fluid-Structure Interactions

    DTIC Science & Technology

    2000-12-01

    NUMERICAL ANALYSIS OF CONSTRAINED DYNAMICAL SYSTEMS, WITH APPLICATIONS TO DYNAMIC CONTACT OF SOLIDS, NONLINEAR ELASTODYNAMICS AND FLUID-STRUCTURE...2000 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Numerical Analysis of Constrained Dynamical Systems, with 5b. GRANT NUMBER Applications to Dynamic...This extension allows the analysis of fluid-structure interfaces through the Lagrangian contact logic previously developed. Similarly, we have developed

  19. Methods for simulation-based analysis of fluid-structure interaction.

    SciTech Connect

    Barone, Matthew Franklin; Payne, Jeffrey L.

    2005-10-01

    Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonal decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.

  20. Large-Scale Numerical Simulation of Fluid Structure Interactions in Low Reynolds Number Flows

    NASA Astrophysics Data System (ADS)

    Eken, Ali; Sahin, Mehmet

    2011-11-01

    A fully coupled numerical algorithm has been developed for the numerical simulation of large-scale fluid structure interaction problems. The incompressible Navier-Stokes equations are discretized using an Arbitrary Lagrangian-Eulerian (ALE) formulation based on the side-centered unstructured finite volume method. A special attention is given to satisfy the discrete continuity equation within each element at discrete level as well as the Geometric Conservation Law (GCL). The linear elasticity equations are discretized within the structure domain using the Galerkin finite element method. The resulting algebraic linear equations are solved in a fully coupled form using a monolitic multigrid method. The implementation of the fully coupled iterative solvers is based on the PETSc library for improving the efficiency of the parallel code. The present numerical algorithm is initially validated for a beam in cross flow and then it is used to simulate the fluid structure interaction of a membrane-wing micro aerial vehicle (MAV).

  1. Static characteristics design of hydrostatic guide-ways based on fluid-structure interactions

    NASA Astrophysics Data System (ADS)

    Lin, Shuo; Yin, YueHong

    2016-10-01

    With the raising requirements in micro optical systems, the available machines become hard to achieve the process dynamic and accuracy in all aspects. This makes compact design based on fluid/structure interactions (FSI) important. However, there is a difficulty in studying FSI with oil film as fluid domain. This paper aims at static characteristic design of a hydrostatic guide-way with capillary restrictors based on FSI. The pressure distribution of the oil film land is calculated by solving the Reynolds-equation with Galerkin technique. The deformation of structure is calculated by commercial FEM software, MSC. Nastran. A matlab program is designed to realize the coupling progress by modifying the load boundary in the submitting file and reading the deformation result. It's obvious that the stiffness of the hydrostatic bearing decreases with the weakening of the bearing structure. This program is proposed to make more precise prediction of bearing stiffness.

  2. Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

    SciTech Connect

    R. James Kirkpatrick; Andrey G. Kalinichev

    2008-11-25

    Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for

  3. Coupled BE/FE/BE approach for scattering from fluid-filled structures

    NASA Technical Reports Server (NTRS)

    Everstine, Gordon C.; Cheng, Raymond S.

    1990-01-01

    NASHUA is a coupled finite element/boundary element capability built around NASTRAN for calculating the low frequency far-field acoustic pressure field radiated or scattered by an arbitrary, submerged, three-dimensional, elastic structure subjected to either internal time-harmonic mechanical loads or external time-harmonic incident loadings. Described here are the formulation and use of NASHUA for solving such structural acoustics problems when the structure is fluid-filled. NASTRAN is used to generate the structural finite element model and to perform most of the required matrix operations. Both fluid domains are modeled using the boundary element capability in NASHUA, whose matrix formulation (and the associated NASTRAN DMAP) for evacuated structures can be used with suitable interpretation of the matrix definitions. After computing surface pressures and normal velocities, far-field pressures are evaluated using an asymptotic form of the Helmholtz exterior integral equation. The proposed numerical approach is validated by comparing the acoustic field scattered from a submerged fluid-filled spherical thin shell to that obtained with a series solution, which is also derived here.

  4. A Coupled Fluid-Structure Interaction Analysis of Solid Rocket Motor with Flexible Inhibitors

    NASA Technical Reports Server (NTRS)

    Yang, H. Q.; West, Jeff

    2014-01-01

    A capability to couple NASA production CFD code, Loci/CHEM, with CFDRC's structural finite element code, CoBi, has been developed. This paper summarizes the efforts in applying the installed coupling software to demonstrate/investigate fluid-structure interaction (FSI) between pressure wave and flexible inhibitor inside reusable solid rocket motor (RSRM). First a unified governing equation for both fluid and structure is presented, then an Eulerian-Lagrangian framework is described to satisfy the interfacial continuity requirements. The features of fluid solver, Loci/CHEM and structural solver, CoBi, are discussed before the coupling methodology of the solvers is described. The simulation uses production level CFD LES turbulence model with a grid resolution of 80 million cells. The flexible inhibitor is modeled with full 3D shell elements. Verifications against analytical solutions of structural model under steady uniform pressure condition and under dynamic condition of modal analysis show excellent agreements in terms of displacement distribution and eigen modal frequencies. The preliminary coupled result shows that due to acoustic coupling, the dynamics of one of the more flexible inhibitors shift from its first modal frequency to the first acoustic frequency of the solid rocket motor.

  5. FaCSI: A block parallel preconditioner for fluid-structure interaction in hemodynamics

    NASA Astrophysics Data System (ADS)

    Deparis, Simone; Forti, Davide; Grandperrin, Gwenol; Quarteroni, Alfio

    2016-12-01

    Modeling Fluid-Structure Interaction (FSI) in the vascular system is mandatory to reliably compute mechanical indicators in vessels undergoing large deformations. In order to cope with the computational complexity of the coupled 3D FSI problem after discretizations in space and time, a parallel solution is often mandatory. In this paper we propose a new block parallel preconditioner for the coupled linearized FSI system obtained after space and time discretization. We name it FaCSI to indicate that it exploits the Factorized form of the linearized FSI matrix, the use of static Condensation to formally eliminate the interface degrees of freedom of the fluid equations, and the use of a SIMPLE preconditioner for saddle-point problems. FaCSI is built upon a block Gauss-Seidel factorization of the FSI Jacobian matrix and it uses ad-hoc preconditioners for each physical component of the coupled problem, namely the fluid, the structure and the geometry. In the fluid subproblem, after operating static condensation of the interface fluid variables, we use a SIMPLE preconditioner on the reduced fluid matrix. Moreover, to efficiently deal with a large number of processes, FaCSI exploits efficient single field preconditioners, e.g., based on domain decomposition or the multigrid method. We measure the parallel performances of FaCSI on a benchmark cylindrical geometry and on a problem of physiological interest, namely the blood flow through a patient-specific femoropopliteal bypass. We analyze the dependence of the number of linear solver iterations on the cores count (scalability of the preconditioner) and on the mesh size (optimality).

  6. Structural consequences of cohesion in gravitational instabilities triggered by fluid overpressure: Analytical derivation and experimental testing

    NASA Astrophysics Data System (ADS)

    Mourgues, R.; Costa, A. C. G.; Marques, F. O.; Lacoste, A.; Hildenbrand, A.

    2016-06-01

    The critical taper theory of Coulomb wedges has been classically applied to compressive regimes (accretionary prisms/fold-and-thrust belts), and more recently to gravitational instabilities. Following the initial hypothesis of the theory, we provide an alternative expression of the exact solution for a non-cohesive wedge by considering the balance of forces applied to the external surfaces. Then, we use this approach to derive a solution for the case of cohesive wedges. We show that cohesion has conspicuous structural effects, including a minimum length required for sliding and the formation of listric faults. The stabilizing effect of cohesion is accentuated in the foremost thin domain of the wedge, defining a required Minimum Failure Length (MFL), and producing sliding of a rigid mass above the detachment. This MFL decreases with less cohesion, a smaller coefficient of internal friction, larger fluid overpressure ratio, and steeper upper and basal surfaces for the wedge. Listricity of the normal faults depends on the fluid overpressure magnitude within the wedge. For moderate fluid overpressure, normal faults are curved close to the surface, and become straight at depth. In contrast, where fluid overpressure exceeds a critical value corresponding to the fluid pressure required to destabilize the surface of a noncohesive wedge, the state of stress changes and rotates at depth. The faults are straight close to the surface and listric at depth, becoming parallel to the upper surface if the wedge is thick enough. We tested some of these structural effects of a cohesive wedge on gravitational instabilities using analogue models where cohesive material was subjected to pore-fluid pressure. The shape of the faults obtained in the models is consistent with the predictions of the theory.

  7. A computational DFT study of structural transitions in textured solid-fluid interfaces

    NASA Astrophysics Data System (ADS)

    Yatsyshin, Petr; Parry, Andrew O.; Kalliadasis, Serafim

    2015-11-01

    Fluids adsorbed at walls, in capillary pores and slits, and in more exotic, sculpted geometries such as grooves and wedges can exhibit many new phase transitions, including wetting, pre-wetting, capillary-condensation and filling, compared to their bulk counterparts. As well as being of fundamental interest to the modern statistical mechanical theory of inhomogeneous fluids, these are also relevant to nanofluidics, chemical- and bioengineering. In this talk we will show using a microscopic Density Functional Theory (DFT) for fluids how novel, continuous, interfacial transitions associated with the first-order prewetting line, can occur on steps, in grooves and in wedges, that are sensitive to both the range of the intermolecular forces and interfacial fluctuation effects. These transitions compete with wetting, filling and condensation producing very rich phase diagrams even for relatively simple geometries. We will also discuss practical aspects of DFT calculations, and demonstrate how this statistical-mechanical framework is capable of yielding complex fluid structure, interfacial tensions, and regions of thermodynamic stability of various fluid configurations. As a side note, this demonstrates that DFT is an excellent tool for the investigations of complex multiphase systems. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031.

  8. FOUR-FLUID MODEL AND NUMERICAL SIMULATIONS OF MAGNETIC STRUCTURES IN THE HELIOSHEATH

    SciTech Connect

    Avinash, K.; Cox, Sean M.; Shaikh, Dastgeer; Zank, G. P.

    2009-04-10

    The first part of this paper extends the three-fluid model of Avinash and Zank for magnetic structures in the heliosheath to a four-fluid model consisting of electrons, pick-up ions (PUIs), solar wind ions (SWIs), and neutral hydrogen. The PUIs are generated by neutrals via charge exchange with SWI. Since the kinetic pressure of PUI is nearly three to four times the pressure of SWI, these are more suited to mediate small-scale structures in the heliosheath such as magnetic holes (MH)/humps etc. The constant energy exchange between these two fluids drives them nonadiabatic. The PUIs are isothermal ({gamma} = 1) while SWIs are nonadiabatic with an index {gamma} {approx} 1.25. The four-fluid model captures these effects via a modified equation of state for PUI and SWI. The phase space of time-independent solutions in terms of the Mach numbers of PUI and SWI is constructed to delineate the parameter space which allows structure formation in the heliosheath. The second part of the paper examines the stability of the time-independent solutions computed in the first part by evolving them via a full system of Hall-MHD equations. The simulation results show that these solutions are not quite stable. As the structure propagates it develops growing oscillations in the wings. Concomitantly, there are changes in the amplitude and width of the structure. This instability could be due to local changes in the velocity of the structure and reflects an exchange between the kinetic and magnetic parts of the total energy. Our results about the presence of growing oscillations in the wings of solitary wave solutions are consistent with the recent analysis of MHs in the heliosheth by Burlaga et al. Their analysis also shows evidence for the presence of oscillations and instabilities in the wings of MHs in the heliosheath.

  9. Aeroacoustical coupling in a ducted shallow cavity and fluid/structure effects on a steam line

    NASA Astrophysics Data System (ADS)

    Lafon, P.; Caillaud, S.; Devos, J. P.; Lambert, C.

    2003-11-01

    A pure tone phenomenon has been observed at 460Hz in a piping steam line. The acoustical energy has been identified to be generated in an open gate valve and to be of cavity noise type. This energy is then transmitted to the main pipe by fluid/structure coupling. The objectives here are to display the mechanism of the flow acoustic coupling in the cavity and in the duct through an aeroacoustical analysis and to understand the way of energy transfer from the fluid to the main pipe through a vibroacoustical analysis. Concerning the first objective, an experimental study by means of 2/7 scale models in air is analysed by means of numerical flow simulation. The flow acoustic phenomena are modelled by computing the Euler equations. Two different computations are carried out: in the first one, a pure Euler modelling is used, in the second one, a boundary layer obtained from experimental data is introduced in the computation in order to have a realistic flow profile upstream the cavity. The boundary layer flow profile appears to be essential to recover the experimentally observed coupling between the shear-layer instability and the acoustical transverse mode of the pipe. The numerical results confirm that the second aerodynamic mode is responsible for the oscillation. While the predicted frequency agrees about 1% with the scale model experiments, the predicted amplitude is approximately 15dB too low. For the second objective, fluid/structure coupling in the main pipe is studied using two fully coupled methods. The first method consists in a modal analysis of the line using a fluid-structure finite element model. The second one is based on the analysis of dispersion diagrams derived from the local equations of cylindrical shells filled with fluid. The way of energy transfer in transverse acoustical waves coupled with flexion-ovalization deformations of the pipe is highlighted using both methods. The dispersion diagrams allow a fast and accurate analysis. The modal analysis

  10. Predicting proton titration in cationic micelle and bilayer environments

    NASA Astrophysics Data System (ADS)

    Morrow, Brian H.; Eike, David M.; Murch, Bruce P.; Koenig, Peter H.; Shen, Jana K.

    2014-08-01

    Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pKa's in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pKa of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pKa of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.

  11. Predicting proton titration in cationic micelle and bilayer environments

    SciTech Connect

    Morrow, Brian H.; Shen, Jana K.; Eike, David M.; Murch, Bruce P.; Koenig, Peter H.

    2014-08-28

    Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pK{sub a}’s in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pK{sub a} of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pK{sub a} of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.

  12. Lipid domains in supported lipid bilayer for atomic force microscopy.

    PubMed

    Lin, Wan-Chen; Blanchette, Craig D; Ratto, Timothy V; Longo, Marjorie L

    2007-01-01

    Phase-separated supported lipid bilayers have been widely used to study the phase behavior of multicomponent lipid mixtures. One of the primary advantages of using supported lipid bilayers is that the two-dimensional platform of this model membrane system readily allows lipid-phase separation to be characterized by high-resolution imaging techniques such as atomic force microscopy (AFM). In addition, when supported lipid bilayers have been functionalized with a specific ligand, protein-membrane interactions can also be imaged and characterized through AFM. It has been recently demonstrated that when the technique of vesicle fusion is used to prepare supported lipid bilayers, the thermal history of the vesicles before deposition and the supported lipid bilayers after formation will have significant effects on the final phase-separated domain structures. In this chapter, three methods of vesicle preparations as well as three deposition conditions will be presented. Also, the techniques and strategies of using AFM to image multicomponent phase-separated supported lipid bilayers and protein binding will be discussed.

  13. Minimal Bending Energies of Bilayer Polyhedra

    NASA Astrophysics Data System (ADS)

    Haselwandter, Christoph A.; Phillips, Rob

    2010-11-01

    Motivated by recent experiments on bilayer polyhedra composed of amphiphilic molecules, we study the elastic bending energies of bilayer vesicles forming polyhedral shapes. Allowing for segregation of excess amphiphiles along the ridges of polyhedra, we find that bilayer polyhedra can indeed have lower bending energies than spherical bilayer vesicles. However, our analysis also implies that, contrary to what has been suggested on the basis of experiments, the snub dodecahedron, rather than the icosahedron, generally represents the energetically favorable shape of bilayer polyhedra.

  14. Lipid bilayers on nano-templates

    DOEpatents

    Noy, Aleksandr; Artyukhin, Alexander B.; Bakajin, Olgica; Stoeve, Pieter

    2009-08-04

    A lipid bilayer on a nano-template comprising a nanotube or nanowire and a lipid bilayer around the nanotube or nanowire. One embodiment provides a method of fabricating a lipid bilayer on a nano-template comprising the steps of providing a nanotube or nanowire and forming a lipid bilayer around the polymer cushion. One embodiment provides a protein pore in the lipid bilayer. In one embodiment the protein pore is sensitive to specific agents

  15. An immersed boundary method for fluid-structure interactions in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Spagnolie, Saverio

    2015-11-01

    The nematic phase of a liquid crystal is characterized by a spontaneous local molecular alignment leading to an anisotropic (direction-dependent) response to deformations. A body moving through such a phase can induce complex viscous and elastic structures in the flow, and the fluid's anisotropic response can generate surprising forces on the immersed body. Bacteria swimming in a liquid crystal, for instance, have been observed to align with the orientation of the underlying director field. The complexity of such problems generally makes mathematical analysis intractable, and the computation of solutions can still be very challenging. In this talk an immersed boundary method for computing fluid-structure interactions in a nematic liquid crystal will be discussed. The Ericksen-Leslie equations, or a more general Landau-de Gennes model, are solved on a fixed, regular grid. Immersed boundaries communicate forces onto the fluid as in Peskin's original method, but now also torques on the nematic director field through molecular anchoring boundary conditions. Sample applications will also be discussed, including the locomotion of undulatory bodies in anisotropic fluids.

  16. Growth of rectangular hollow tube single crystals with rutile-type structure in supercritical fluids

    NASA Astrophysics Data System (ADS)

    Niwa, Ken; Tokunaga, Tomoharu; Hasegawa, Masashi

    2013-06-01

    Super critical fluid is known as a suitable solvent in the dissolution and extraction process, due to its extreme high solubility and reactivity. On the other hand, further experimental approaches using supercritical fluid would offer new insights, especially in the field of novel material synthesis and crystal growth. We here report on the successful growth of single crystals with the rutile-type structure (MO2; M = Ti, Si, Ge and Sn) in the supercritical fluids (water or oxygen) by using laser heated diamond-anvil cell at above 5 GPa. The resultant product showed the rectangular hollow tube with several tens of microns in length and the wall thickness of less than 500 nm. TEM analyses demonstrated that this rectangular hollow tube single crystal is surrounded by the (110) face and grown along the [001] direction. The preferential growth of (110) face is consistent with the lowest surface energy of (110) in the rutile-type structure. In addition, the rapid cooling rate of LHDAC and the high-solubility of oxides into the supercritical fluids also play an important role for the formation of the rectangular hollow tube. The details of the experiments will be discussed in the presentation.

  17. Characterization of hydrofoil damping due to fluid-structure interaction using piezocomposite actuators

    NASA Astrophysics Data System (ADS)

    Seeley, Charles; Coutu, André; Monette, Christine; Nennemann, Bernd; Marmont, Hugues

    2012-03-01

    Hydroelectric power generation is an important non-fossil fuel power source to help meet the world’s energy needs. Fluid-structure interaction (FSI), in the form of mass loading and damping, governs the dynamic response of water turbines, such as Francis turbines. Although the effects of fluid mass loading are well documented, fluid damping is also a critical quantity that may limit vibration amplitudes during service, and therefore help to avoid premature failure of the turbines. However, fluid damping has received less attention in the literature. This paper presents an experimental investigation of damping due to FSI. Three hydrofoils were designed and built to investigate damping due to FSI. Piezoelectric actuation using macrofiber composites (MFCs) provided excitation to the hydrofoil test structure, independent of the flow conditions, to overcome the noisy environment. Natural frequency and damping estimates were experimentally obtained from sine sweep frequency response functions measured with a laser vibrometer through a window in the test section. The results indicate that, although the natural frequencies were not substantially affected by the flow, the damping ratios were observed to increase in a linear manner with respect to flow velocity.

  18. Phase equilibria, fluid structure, and diffusivity of a discotic liquid crystal.

    PubMed

    Cienega-Cacerez, Octavio; Moreno-Razo, José Antonio; Díaz-Herrera, Enrique; Sambriski, Edward John

    2014-05-14

    Molecular Dynamics simulations were performed for the Gay-Berne discotic fluid parameterized by GB(0.345, 0.2, 1.0, 2.0). The volumetric phase diagram exhibits isotropic (IL), nematic (ND), and two columnar phases characterized by radial distribution functions: the transversal fluid structure varies between a hexagonal columnar (CD) phase (at higher temperatures and pressures) and a rectangular columnar (CO) phase (at lower temperatures and pressures). The slab-wise analysis of fluid dynamics suggests the formation of grain-boundary defects in the CO phase. Longitudinal fluid structure is highly periodic with narrow peaks for the CO phase, suggestive of a near-crystalline (yet diffusive) system, but is only short-ranged for the CD phase. The IL phase does not exhibit anisotropic diffusion. Transversal diffusion is more favorable in the ND phase at all times, but only favorable at short times for the columnar phases. In the columnar phases, a crossover occurs where longitudinal diffusion is favored over transversal diffusion at intermediate-to-long timescales. The anomalous diffusivity is pronounced in both columnar phases, with three identifiable contributions: (a) the rattling of discogens within a transient "interdigitation" cage, (b) the hopping of discogens across columns, and (c) the drifting motion of discogens along the orientation of the director.

  19. Fluid-Structure Interaction Effects on Mass Flow Rates in Solid Rocket Motors

    DTIC Science & Technology

    2015-09-02

    Thesis 3. DATES COVERED (From - To) 12 August 2015 – 02 September 2015 4. TITLE AND SUBTITLE Fluid- Structure Interaction Effects on Mass Flow Rates... structure interaction (FSI) effects between the combusting gases and propellant alter the motor chamber pressure and mass flow rate. To account for the...Rev. 8-98) Prescribed by ANSI Std. 239.18 Approved for public release; distribution is unlimited. PA#    FLUID‐ STRUCTURE  INTERACTION EFFECTS ON

  20. Emergent Structures in an Active Polar Fluid: Dynamics of Shape, Scattering, and Merger

    NASA Astrophysics Data System (ADS)

    Husain, Kabir; Rao, Madan

    2017-02-01

    Spatially localized defect structures emerge spontaneously in a hydrodynamic description of an active polar fluid comprising polar "actin" filaments and "myosin" motor proteins that (un)bind to filaments and exert active contractile stresses. These emergent defect structures are characterized by distinct textures and can be either static or mobile—we derive effective equations of motion for these "extended particles" and analyze their shape, kinetics, interactions, and scattering. Depending on the impact parameter and propulsion speed, these active defects undergo elastic scattering or merger. Our results are relevant for the dynamics of actomyosin-dense structures at the cell cortex, reconstituted actomyosin complexes, and 2D active colloidal gels.

  1. Nonequilibrium phenomena in the phase separation of a two-component lipid bilayer.

    PubMed Central

    de Almeida, Rodrigo F M; Loura, Luís M S; Fedorov, Aleksandre; Prieto, Manuel

    2002-01-01

    Lipid bilayers composed of two phospholipids with significant acyl-chain mismatch behave as nonideal mixtures. Although many of these systems are well characterized from the equilibrium point of view, studies concerning their nonequilibrium dynamics are still rare. The kinetics of lipid demixing (phase separation) was studied in model membranes (large unilamellar vesicles of 1:1 dilauroylphosphatidylcholine (C(12) acyl chain) and distearoylphosphatidylcholine (C(18) acyl chain)). For this purpose, photophysical techniques (fluorescence intensity, anisotropy, and fluorescence resonance energy transfer) were applied using suitable probes (gel phase probe trans-parinaric acid and fluid phase probe N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-dilauroylphosphatidylethanolamine). The nonequilibrium situation was induced by a sudden thermal quench from a one-fluid phase equilibrium situation (higher temperature) to the gel/fluid coexistence range (lower temperature). We verified that the attainment of equilibrium is a very slow process (occurs in a time scale of hours), leading to large domains at infinite time. The nonequilibrium structure stabilization is due essentially to temporarily rigidified C(12) chains in the interface between gel/fluid domains, which decrease the interfacial tension by acting as surfactants. The relaxation process becomes faster with the increase of the temperature drop. In addition, heterogeneity is already present in the supposed homogeneous fluid mixture at the higher temperature. PMID:11806924

  2. Structure and thermodynamics of discrete potential fluids in the OZ HMSA formalism

    NASA Astrophysics Data System (ADS)

    Guillén-Escamilla, I.; Chávez-Páez, M.; Castañeda-Priego, R.

    2007-02-01

    We study the structural and thermodynamic properties of three discrete potential fluids: the square well (SW), the square well-barrier (SWB), and the square well-barrier-well (SWBW) fluids by means of the Ornstein-Zernike (OZ) integral equation and the HMSA (hybrid mean spherical approximation) closure relation. The radial distribution functions, structure factors, and pressure of the systems are calculated as a function of the strength of the attractive and repulsive parts of the potential in an extended range of densities, mainly covering the range 0.1 <= ρ* <= 0.9. We find that far away from the liquid-vapour coexistence region the HMSA theory is an accurate approach that compares well with Monte Carlo simulations. We also find that when the attractive parts of the potential dominate over the repulsive part the structure factor at low q values shows a considerable increase, which suggests the formation of large-scale domains that locally exhibit fluid-like structure.

  3. Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

    DOE PAGES

    Smith, Jeremy C.; Cheng, Xiaolin; Nickels, Jonathan D.

    2015-07-29

    Understanding of cell membrane organization has evolved significantly from the classic fluid mosaic model. It is now recognized that biological membranes are highly organized structures, with differences in lipid compositions between inner and outer leaflets and in lateral structures within the bilayer plane, known as lipid rafts. These organizing principles are important for protein localization and function as well as cellular signaling. However, the mechanisms and biophysical basis of lipid raft formation, structure, dynamics and function are not clearly understood. One key question, which we focus on in this review, is how lateral organization and leaflet compositional asymmetry are coupled.more » Detailed information elucidating this question has been sparse because of the small size and transient nature of rafts and the experimental challenges in constructing asymmetric bilayers. Resolving this mystery will require advances in both experimentation and modeling. We discuss here the preparation of model systems along with experimental and computational approaches that have been applied in efforts to address this key question in membrane biology. Furthermore, we seek to place recent and future advances in experimental and computational techniques in context, providing insight into in-plane and transverse organization of biological membranes.« less

  4. Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

    SciTech Connect

    Smith, Jeremy C.; Cheng, Xiaolin; Nickels, Jonathan D.

    2015-07-29

    Understanding of cell membrane organization has evolved significantly from the classic fluid mosaic model. It is now recognized that biological membranes are highly organized structures, with differences in lipid compositions between inner and outer leaflets and in lateral structures within the bilayer plane, known as lipid rafts. These organizing principles are important for protein localization and function as well as cellular signaling. However, the mechanisms and biophysical basis of lipid raft formation, structure, dynamics and function are not clearly understood. One key question, which we focus on in this review, is how lateral organization and leaflet compositional asymmetry are coupled. Detailed information elucidating this question has been sparse because of the small size and transient nature of rafts and the experimental challenges in constructing asymmetric bilayers. Resolving this mystery will require advances in both experimentation and modeling. We discuss here the preparation of model systems along with experimental and computational approaches that have been applied in efforts to address this key question in membrane biology. Furthermore, we seek to place recent and future advances in experimental and computational techniques in context, providing insight into in-plane and transverse organization of biological membranes.

  5. Cholesterol's location in lipid bilayers

    SciTech Connect

    Marquardt, Drew; Kučerka, Norbert; Wassall, Stephen R.; Harroun, Thad A.; Katsaras, John

    2016-04-04

    It is well known that cholesterol modifies the physical properties of lipid bilayers. For example, the much studied liquid-ordered Lo phase contains rapidly diffusing lipids with their acyl chains in the all trans configuration, similar to gel phase bilayers. Moreover, the Lo phase is commonly associated with cholesterol-enriched lipid rafts, which are thought to serve as platforms for signaling proteins in the plasma membrane. Cholesterol's location in lipid bilayers has been studied extensively, and it has been shown – at least in some bilayers – to align differently from its canonical upright orientation, where its hydroxyl group is in the vicinity of the lipid–water interface. In this study we review recent works describing cholesterol's location in different model membrane systems with emphasis on results obtained from scattering, spectroscopic and molecular dynamics studies.

  6. Cholesterol's location in lipid bilayers

    DOE PAGES

    Marquardt, Drew; Kučerka, Norbert; Wassall, Stephen R.; ...

    2016-04-04

    It is well known that cholesterol modifies the physical properties of lipid bilayers. For example, the much studied liquid-ordered Lo phase contains rapidly diffusing lipids with their acyl chains in the all trans configuration, similar to gel phase bilayers. Moreover, the Lo phase is commonly associated with cholesterol-enriched lipid rafts, which are thought to serve as platforms for signaling proteins in the plasma membrane. Cholesterol's location in lipid bilayers has been studied extensively, and it has been shown – at least in some bilayers – to align differently from its canonical upright orientation, where its hydroxyl group is in themore » vicinity of the lipid–water interface. In this study we review recent works describing cholesterol's location in different model membrane systems with emphasis on results obtained from scattering, spectroscopic and molecular dynamics studies.« less

  7. Metamorphic fluids and uplift-erosion history of a portion of the Kapuskasing structural zone, Ontario, as deduced from fluid inclusions

    NASA Technical Reports Server (NTRS)

    Rudnick, R. L.; Ashwal, L. D.; Henry, D. J.

    1983-01-01

    Fluid inclusions can be used to determine the compositional evolution of fluids present in high grade metamorphic rocks (Touret, 1979) along with the general P-T path followed by the rocks during uplift and erosion (Hollister et al., 1979). In this context, samples of high grade gneisses from the Kapuskasing structural zone (KSZ, Fig. 1) of eastern Ontario were studied in an attempt to define the composition of syn- and post-metamorphic fluids and help constrain the uplift and erosion history of the KSZ. Recent work by Percival (1980), Percival and Card (1983) and Percival and Krogh (1983) shows that the KSZ represents lower crustal granulites that form the lower portion of an oblique cross section through the Archean crust, which was up faulted along a northeast striking thrust fault. The present fluid inclusion study places constraints upon the P-T path which the KSZ followed during uplift and erosion.

  8. Bilayer membrane interactions with nanofabricated scaffolds

    DOE PAGES

    Collier, C. Patrick

    2015-07-29

    Membrane function is facilitated by lateral organization within the lipid bilayer, including phase-separation of lipids into more ordered domains (lipid rafts) and anchoring of the membrane to a cytoskeleton. These features have proven difficult to reproduce in model membrane systems such as black lipid membranes, unilamellar vesicles and supported bilayers. However, advances in micro/nanofabrication have resulted in more realistic synthetic models of membrane-cytoskeleton interactions that can help uncover the design rules responsible for biological membrane formation and organization. This review will focus on describing micro-/nanostructured scaffolds that can emulate the connections of a cellular membrane to an underlying “cytoskeleton”. Thismore » includes molecular-based scaffolds anchored to a solid substrate through surface chemistry, solid-state supports modified by material deposition, lithography and etching, the creation of micro/nanoporous arrays, integration with microfluidics, and droplet-based bilayers at interfaces. Lastly, model systems such as these are increasing our understanding of structure and organization in cell membranes, and how they result in the emergence of functionality at the nanoscale.« less

  9. Bilayer membrane interactions with nanofabricated scaffolds

    SciTech Connect

    Collier, C. Patrick

    2015-07-29

    Membrane function is facilitated by lateral organization within the lipid bilayer, including phase-separation of lipids into more ordered domains (lipid rafts) and anchoring of the membrane to a cytoskeleton. These features have proven difficult to reproduce in model membrane systems such as black lipid membranes, unilamellar vesicles and supported bilayers. However, advances in micro/nanofabrication have resulted in more realistic synthetic models of membrane-cytoskeleton interactions that can help uncover the design rules responsible for biological membrane formation and organization. This review will focus on describing micro-/nanostructured scaffolds that can emulate the connections of a cellular membrane to an underlying “cytoskeleton”. This includes molecular-based scaffolds anchored to a solid substrate through surface chemistry, solid-state supports modified by material deposition, lithography and etching, the creation of micro/nanoporous arrays, integration with microfluidics, and droplet-based bilayers at interfaces. Lastly, model systems such as these are increasing our understanding of structure and organization in cell membranes, and how they result in the emergence of functionality at the nanoscale.

  10. Self-folding graphene-polymer bilayers

    SciTech Connect

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  11. Diffusion in Single Supported Lipid Bilayers

    NASA Astrophysics Data System (ADS)

    Armstrong, C. L.; Trapp, M.; Rheinstädter, M. C.

    2011-03-01

    Despite their potential relevance for the development of functionalized surfaces and biosensors, the study of single supported membranes using neutron scattering has been limited by the challenge of obtaining relevant dynamic information from a sample with minimal material. Using state of the art neutron instrumentation we have, for the first time, modeled lipid diffusion in single supported lipid bilayers. While we find that the diffusion coefficient for the single bilayer system is comparable to a multi-lamellar lipid system, the molecular mechanism for lipid motion in the single bilayer is a continuous diffusion process with no sign of the flow-like ballistic motion reported in the stacked membrane system. In the future, these membranes will be used to hold and align proteins, mimicking physiological conditions enabling the study of protein structure, function and interactions in relevant and highly topical membrane/protein systems with minimal sample material. C.L. Armstrong, M.D. Kaye, M. Zamponi, E. Mamontov, M. Tyagi, T. Jenkins and M.C. Rheinstädter, Soft Matter Communication, 2010, Advance Article, DOI: 10.1039/C0SM00637H

  12. Resonant frequency of the silicon micro-structure of MEMS vector hydrophone in fluid-structure interaction

    NASA Astrophysics Data System (ADS)

    Zhang, Guojun; Zhao, Peng; Zhang, Wendong

    2015-04-01

    The MEMS vector hydrophone developed by the North University of China has advantages of high Signal to Noise Ratio, ease of array integration, etc. However, the resonance frequency of the MEMS device in the liquid is different from that in the air due to the fluid-structure interaction (FSI). Based on the theory of Fluid-Solid Coupling, a generalized distributed mass attached on the micro-structure has been found, which results in the resonance frequency of the microstructure in the liquid being lower than that in the air. Then, an FSI simulation was conducted by ANSYS software. Finally, the hydrophone was measured by using a shaking table and a vector hydrophone calibration system respectively. Results show that, due to the FSI, the resonance frequency of the MEMS devices of the bionic vector hydrophone in the liquid declines approximately 30% compared to the case in the air.

  13. A fully-coupled fluid-structure interaction simulation of cerebral aneurysms

    NASA Astrophysics Data System (ADS)

    Bazilevs, Y.; Hsu, M.-C.; Zhang, Y.; Wang, W.; Liang, X.; Kvamsdal, T.; Brekken, R.; Isaksen, J. G.

    2009-10-01

    This paper presents a computational vascular fluid-structure interaction (FSI) methodology and its application to patient-specific aneurysm models of the middle cerebral artery bifurcation. A fully coupled fluid-structural simulation approach is reviewed, and main aspects of mesh generation in support of patient-specific vascular FSI analyses are presented. Quantities of hemodynamic interest such as wall shear stress and wall tension are studied to examine the relevance of FSI modeling as compared to the rigid arterial wall assumption. We demonstrate the importance of including the flexible wall modeling in vascular blood flow simulations by performing a comparison study that involves four patient-specific models of cerebral aneurysms varying in shape and size.

  14. Thermodynamic properties and static structure factor for a Yukawa fluid in the mean spherical approximation.

    PubMed

    Montes-Perez, J; Cruz-Vera, A; Herrera, J N

    2011-12-01

    This work presents the full analytic expressions for the thermodynamic properties and the static structure factor for a hard sphere plus 1-Yukawa fluid within the mean spherical approximation. To obtain these properties of the fluid type Yukawa analytically it was necessary to solve an equation of fourth order for the scaling parameter on a large scale. The physical root of this equation was determined by imposing physical conditions. The results of this work are obtained from seminal papers of Blum and Høye. We show that is not necessary the use the series expansion to solve the equation for the scaling parameter. We applied our theoretical result to find the thermodynamic and the static structure factor for krypton. Our results are in good agreement with those obtained in an experimental form or by simulation using the Monte Carlo method.

  15. Scalar-fluid theories: cosmological perturbations and large-scale structure

    SciTech Connect

    Koivisto, Tomi S.; Saridakis, Emmanuel N.; Tamanini, Nicola E-mail: Emmanuel_Saridakis@baylor.edu

    2015-09-01

    Recently a new Lagrangian framework was introduced to describe interactions between scalar fields and relativistic perfect fluids. This allows two consistent generalizations of coupled quintessence models: non-vanishing pressures and a new type of derivative interaction. The implications of these to the formation of cosmological large-scale structure are uncovered here at the linear order. The full perturbation equations in the two cases are derived in a unified formalism and their Newtonian, quasi-static limit is studied analytically. Requiring the absence of an effective sound speed term in the coupled dark matter fluid restricts the Lagrangian to be a linear function of the matter number density. This leaves new potentially viable classes of both algebraically and derivatively interacting models wherein the coupling may impact the background expansion dynamics and imprint new signatures into the large-scale structure.

  16. Advanced optical measuring systems for measuring the properties of fluids and structures

    NASA Technical Reports Server (NTRS)

    Decker, A. J.

    1986-01-01

    Four advanced optical models are reviewed for the measurement of visualization of flow and structural properties. Double-exposure, diffuse-illumination, holographic interferometry can be used for three-dimensional flow visualization. When this method is combined with optical heterodyning, precise measurements of structural displacements or fluid density are possible. Time-average holography is well known as a method for displaying vibrational mode shapes, but it also can be used for flow visualization and flow measurements. Deflectometry is used to measure or visualize the deflection of light rays from collimation. Said deflection occurs because of refraction in a fluid or because of reflection from a tilted surface. The moire technique for deflectometry, when combined with optical heterodyning, permits very precise measurements of these quantities. The rainbow schlieren method of deflectometry allows varying deflection angles to be encoded with colors for visualization.

  17. Optimal design of a new multipole bilayer magnetorheological brake

    NASA Astrophysics Data System (ADS)

    Shiao, Yaojung; Ngoc, Nguyen Anh; Lai, Chien-Hung

    2016-11-01

    This article presents a new high-torque multipole bilayer magneto-rheological brake (MRB). This MRB has a unique structural design with multiple electromagnetic poles and multiple media layers of magnetorheological fluid (MRF). The MRB has two rotors located on the outer and inner sides of a six-pole stator, and therefore, it can provide higher torque and a larger torque-to-volume ratio (TVR) than conventional single- or multipole single-layer MRBs can. Moreover, the problem of potential MRF leakage is solved by using cylindrical separator rings around the stator. In this study, first, the structure of the proposed MRB is introduced. An analog magnetic circuit was built for the MRB to investigate the effects of the MRB parameters on the magnetic field intensity of the MRF layers. In addition, a 3D electromagnetic model of the MRB was developed to simulate and examine the magnetic flux intensity and corresponding braking torque. An approximate optimization method was then applied to obtain the optimal geometric dimensions for the major dimensional parameters of the MRB. The MRB was manufactured and tested to validate its torque and dynamic characteristics. The results showed that the proposed MRB exhibited great enhancement of the braking torque and TVR.

  18. Convergence acceleration for partitioned simulations of the fluid-structure interaction in arteries

    NASA Astrophysics Data System (ADS)

    Radtke, Lars; Larena-Avellaneda, Axel; Debus, Eike Sebastian; Düster, Alexander

    2016-06-01

    We present a partitioned approach to fluid-structure interaction problems arising in analyses of blood flow in arteries. Several strategies to accelerate the convergence of the fixed-point iteration resulting from the coupling of the fluid and the structural sub-problem are investigated. The Aitken relaxation and variants of the interface quasi-Newton -least-squares method are applied to different test cases. A hybrid variant of two well-known variants of the interface quasi-Newton-least-squares method is found to perform best. The test cases cover the typical boundary value problem faced when simulating the fluid-structure interaction in arteries, including a strong added mass effect and a wet surface which accounts for a large part of the overall surface of each sub-problem. A rubber-like Neo Hookean material model and a soft-tissue-like Holzapfel-Gasser-Ogden material model are used to describe the artery wall and are compared in terms of stability and computational expenses. To avoid any kind of locking, high-order finite elements are used to discretize the structural sub-problem. The finite volume method is employed to discretize the fluid sub-problem. We investigate the influence of mass-proportional damping and the material model chosen for the artery on the performance and stability of the acceleration strategies as well as on the simulation results. To show the applicability of the partitioned approach to clinical relevant studies, the hemodynamics in a pathologically deformed artery are investigated, taking the findings of the test case simulations into account.

  19. Active noise control - Piezoceramic actuators in fluid/structure interaction models

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Fang, W.; Smith, R. C.

    1991-01-01

    A model for a 2-D acoustic cavity with a flexible boundary (a beam) controlled via piezoceramic patches producing bending moments in the beam is considered. The associated control problem for this fluid/structure interaction system to reduce the acoustic pressure in the cavity involves unbounded control inputs. Approximation methods in the context of an LQR state space formulation are discussed, and numerical results are presented to demonstrate the effectiveness of this approach in computing feedback controls for noise reduction.

  20. Superlubricity in quasicrystalline twisted bilayer graphene

    NASA Astrophysics Data System (ADS)

    Koren, Elad; Duerig, Urs

    2016-05-01

    The unique atomic positions in quasicrystals lead to peculiar self-similarity and fractal-like structural morphology. Accordingly, many of the material properties are supposed to manifest exceptional characteristics. In this Rapid Communication, we explain through numerical simulations the fundamental and peculiar aspects of quasicrystals wearless friction manifested in a 30° twisted bilayer graphene system. In particular, the sliding force exhibits a fractal structure with distinct area correlations due to the natural mixture between both periodic and aperiodic lateral modulations. In addition, zero power scaling of the sliding force with respect to the contact area is demonstrated for a geometric sequence of dodecagonal elements.

  1. Polyunsaturated Fatty Acids in Lipid Bilayers and Tubules

    NASA Astrophysics Data System (ADS)

    Hirst, Linda S.; Yuan, Jing; Pramudya, Yohannes; Nguyen, Lam T.

    2007-03-01

    Omega-3 polyunsaturated fatty acids (PUFAs) are found in a variety of biological membranes and have been implicated with lipid raft formation and possible function, typical molecules include DHA (Docosahexanoic Acid) and AA (Alphalinoleic Acid) which have been the focus of considerable attention in recent years. We are interested in the phase behavior of these molecules in the lipid bilayer. The addition of lipid molecules with polyunsaturated chains has a clear effect on the fluidity and curvature of the membrane and we investigate the effects the addition of polyunsaturated lipids on bilayer structure and tubule formation. Self-assembled cylindrical lipid tubules have attracted considerable attention because of their interesting structures and potential technological applications. Using x-ray diffraction techniques, Atomic Force Microscopy and confocal fluorescence imaging, both symmetric and mixed chain lipids were incorporated into model membranes and the effects on bilayer structure and tubule formation investigated.

  2. Formation of droplet interface bilayers in a Teflon tube

    PubMed Central

    Walsh, Edmond; Feuerborn, Alexander; Cook, Peter R.

    2016-01-01

    Droplet-interface bilayers (DIBs) have applications in disciplines ranging from biology to computing. We present a method for forming them manually using a Teflon tube attached to a syringe pump; this method is simple enough it should be accessible to those without expertise in microfluidics. It exploits the properties of interfaces between three immiscible liquids, and uses fluid flow through the tube to pack together drops coated with lipid monolayers to create bilayers at points of contact. It is used to create functional nanopores in DIBs composed of phosphocholine using the protein α-hemolysin (αHL), to demonstrate osmotically-driven mass transfer of fluid across surfactant-based DIBs, and to create arrays of DIBs. The approach is scalable, and thousands of DIBs can be prepared using a robot in one hour; therefore, it is feasible to use it for high throughput applications. PMID:27681313

  3. Formation of droplet interface bilayers in a Teflon tube

    NASA Astrophysics Data System (ADS)

    Walsh, Edmond; Feuerborn, Alexander; Cook, Peter R.

    2016-09-01

    Droplet-interface bilayers (DIBs) have applications in disciplines ranging from biology to computing. We present a method for forming them manually using a Teflon tube attached to a syringe pump; this method is simple enough it should be accessible to those without expertise in microfluidics. It exploits the properties of interfaces between three immiscible liquids, and uses fluid flow through the tube to pack together drops coated with lipid monolayers to create bilayers at points of contact. It is used to create functional nanopores in DIBs composed of phosphocholine using the protein α-hemolysin (αHL), to demonstrate osmotically-driven mass transfer of fluid across surfactant-based DIBs, and to create arrays of DIBs. The approach is scalable, and thousands of DIBs can be prepared using a robot in one hour; therefore, it is feasible to use it for high throughput applications.

  4. Formation of droplet interface bilayers in a Teflon tube.

    PubMed

    Walsh, Edmond; Feuerborn, Alex