Spatially Resolved Dust, Gas, and Star Formation in the Dwarf Magellanic Irregular NGC 4449

NASA Astrophysics Data System (ADS)

Calzetti, D.; Wilson, G. W.; Draine, B. T.; Roussel, H.; Johnson, K. E.; Heyer, M. H.; Wall, W. F.; Grasha, K.; Battisti, A.; Andrews, J. E.; Kirkpatrick, A.; Rosa González, D.; Vega, O.; Puschnig, J.; Yun, M.; Östlin, G.; Evans, A. S.; Tang, Y.; Lowenthal, J.; Sánchez-Arguelles, D.

2018-01-01

We investigate the relation between gas and star formation in subgalactic regions, ∼360 pc to ∼1.5 kpc in size, within the nearby starburst dwarf NGC 4449, in order to separate the underlying relation from the effects of sampling at varying spatial scales. Dust and gas mass surface densities are derived by combining new observations at 1.1 mm, obtained with the AzTEC instrument on the Large Millimeter Telescope, with archival infrared images in the range 8–500 μm from the Spitzer Space Telescope and the Herschel Space Observatory. We extend the dynamic range of our millimeter (and dust) maps at the faint end, using a correlation between the far-infrared/millimeter colors F(70)/F(1100) (and F(160)/F(1100)) and the mid-infrared color F(8)/F(24) that we establish for the first time for this and other galaxies. Supplementing our data with maps of the extinction-corrected star formation rate (SFR) surface density, we measure both the SFR–molecular gas and the SFR–total gas relations in NGC 4449. We find that the SFR–molecular gas relation is described by a power law with an exponent that decreases from ∼1.5 to ∼1.2 for increasing region size, while the exponent of the SFR–total gas relation remains constant with a value of ∼1.5 independent of region size. We attribute the molecular law behavior to the increasingly better sampling of the molecular cloud mass function at larger region sizes; conversely, the total gas law behavior likely results from the balance between the atomic and molecular gas phases achieved in regions of active star formation. Our results indicate a nonlinear relation between SFR and gas surface density in NGC 4449, similar to what is observed for galaxy samples. Based on observations obtained with the Large Millimeter Telescope Alfonso Serrano—a binational collaboration between INAOE (Mexico) and the University of Massachusetts–Amherst (USA).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine

The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and themore » LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.« less

Mechanisms of plastic deformation in highly cross-linked UHMWPE for total hip components--the molecular physics viewpoint.

PubMed

Takahashi, Yasuhito; Shishido, Takaaki; Yamamoto, Kengo; Masaoka, Toshinori; Kubo, Kosuke; Tateiwa, Toshiyuki; Pezzotti, Giuseppe

2015-02-01

Plastic deformation is an unavoidable event in biomedical polymeric implants for load-bearing application during long-term in-vivo service life, which involves a mass transfer process, irreversible chain motion, and molecular reorganization. Deformation-induced microstructural alterations greatly affect mechanical properties and durability of implant devices. The present research focused on evaluating, from a molecular physics viewpoint, the impact of externally applied strain (or stress) in ultra-high molecular weight polyethylene (UHMWPE) prostheses, subjected to radiation cross-linking and subsequent remelting for application in total hip arthroplasty (THA). Two different types of commercial acetabular liners, which belong to the first-generation highly cross-linked UHMWPE (HXLPE), were investigated by means of confocal/polarized Raman microprobe spectroscopy. The amount of crystalline region and the spatial distribution of molecular chain orientation were quantitatively analyzed according to a combined theory including Raman selection rules for the polyethylene orthorhombic structure and the orientation distribution function (ODF) statistical approach. The structurally important finding was that pronounced recrystallization and molecular reorientation increasingly appeared in the near-surface regions of HXLPE liners with increasing the amount of plastic (compressive) deformation stored in the microstructure. Such molecular rearrangements, occurred in response to external strains, locally increase surface cross-shear (CS) stresses, which in turn trigger microscopic wear processes in HXLPE acetabular liners. Thus, on the basis of the results obtained at the molecular scale, we emphasize here the importance of minimizing the development of irrecoverable deformation strain in order to retain the pristine and intrinsically high wear performance of HXLPE components. Copyright © 2014 Elsevier Ltd. All rights reserved.

Infrared analysis of polyethylene wear specimens using attenuated total reflection spectroscopy. [effects of radiation on the surface properties of materials for total joint protheses

NASA Technical Reports Server (NTRS)

Jones, W. R.; Lauer, J. L.

1979-01-01

Attenuated total reflection infrared spectroscopy was used to analyze ultrahigh molecular weight polyethylene wear test specimens. Three different specimens were analyzed. One specimen was gamma irradiated to a dose of 5.0 MRad, another to a dose of 2.5 MRad, and the final specimen was unirradiated. There was no conclusive evidence of chemical changes (i.e., unsaturation or oxidation) in the surface regions of any of the polyethylene samples. Therefore, it was concluded that the gamma irradiation sterilization procedure shoud not alter the boundary lubricating properties of the polyethylene.

Molecular docking of superantigens with class II major histocompatibility complex proteins.

PubMed

Olson, M A; Cuff, L

1997-01-01

The molecular recognition of two superantigens with class II major histocompatibility complex molecules was simulated by using protein-protein docking. Superantigens studied were staphylococcal enterotoxin B (SEB) and toxic shock syndrome toxin-1 (TSST-1) in their crystallographic assemblies with HLA-DR1. Rigid-body docking was performed sampling configurational space of the interfacial surfaces by employing a strategy of partitioning the contact regions on HLA-DR1 into separate molecular recognition units. Scoring of docked conformations was based on an electrostatic continuum model evaluated with the finite-difference Poisson-Boltzmann method. Estimates of nonpolar contributions were derived from the buried molecular surface areas. We found for both superantigens that docking the HLA-DR1 surface complementary with the SEB and TSST-1 contact regions containing a homologous hydrophobic surface loop provided sufficient recognition for the reconstitution of native-like conformers exhibiting the highest-scoring free energies. For the SEB complex, the calculations were successful in reproducing the total association free energy. A comparison of the free-energy determinants of the conserved hydrophobic contact residue indicates functional similarity between the two proteins for this interface. Though both superantigens share a common global association mode, differences in binding topology distinguish the conformational specificities underlying recognition.

Surface accommodation of molecular contaminants

NASA Technical Reports Server (NTRS)

Chen, Philip T.; Hedgeland, Randy J.; Thomson, Shaun R.

1990-01-01

Theoretical consideration and supporting data are presented regarding the nature of the transport mechanisms which cause the adsorption of gases on spacecraft surfaces. Particular attention is given to the concept of a sticking coefficient which is the ratio of the thermally accommodated mass to the total incident mass. Existing molecular accommodation data are examined in terms of spacecraft applications and recent contamination-control data are introduced. Two distinct yet linked concepts emerge which are the accommodation and sticking coefficients, and surface roughness contributes significantly to both coefficients. A general equation regarding the coefficients is developed, and the data are found to fit the equation basically. It is concluded that a more precise characterization of the coefficients can be obtained through experimentation under simulated spacecraft conditions.

Poly(styrene-co-butadiene) random copolymer thin films and nanostructures on a mica surface: morphology and contact angles of nanodroplets.

PubMed

McClements, Jake; Buffone, Cosimo; Shaver, Michael P; Sefiane, Khellil; Koutsos, Vasileios

2017-09-20

The self-assembly of poly(styrene-co-butadiene) random copolymers on mica surfaces was studied by varying solution concentrations and polymer molecular weights. Toluene solutions of the poly(styrene-co-butadiene) samples were spin coated onto a mica surface and the resulting polymer morphology was investigated by atomic force microscopy. At higher concentrations, thin films formed with varying thicknesses; some dewetting was observed which depended on the molecular weight. Total dewetting did not occur despite the polymer's low glass transition temperature. Instead, partial dewetting was observed suggesting that the polymer was in a metastable equilibrium state. At lower concentrations, spherical cap shaped nanodroplets formed with varying sizes from single polymer chains to aggregates containing millions of chains. As the molecular weight was increased, fewer aggregates were observed on the surface, albeit with larger sizes resulting from increased solution viscosities and more chain entanglements at higher molecular weights. The contact angles of the nanodroplets were shown to be size dependent. A minimum contact angle occurs for droplets with radii of 100-250 nm at each molecular weight. Droplets smaller than 100 nm showed a sharp increase in contact angle; attributed to an increase in the elastic modulus of the droplets, in addition, to a positive line tension value. Droplets larger than 250 nm also showed an increased contact angle due to surface heterogeneities which cannot be avoided for larger droplets. This increase in contact angle plateaus as the droplet size reaches the macroscopic scale.

Surface chemistry of PH 3, PF 3 and PCl 3 on Ru(0001)

NASA Astrophysics Data System (ADS)

Tao, H.-S.; Diebold, U.; Shinn, N. D.; Madey, T. E.

1994-06-01

The adsorption, desorption and decomposition of PH 3, PF 3 and PCl 3 on Ru(0001) have been studied by soft X-ray photoelectron spectroscopy (SXPS) using synchrotron radiation. Due to large chemical shifts in the P 2p core levels, different phosphorus containing surface species can be identified. We find that PF 3 adsorbs molecularly on Ru(0001) at 80 and 300 K. At 80 K, PH 3 saturates the surface with one layer of atomic hydrogen, elemental phosphorus, subhydride (i.e., PHx (0 < x < 3)) and PH 3, with a total phosphorus coverage of 0.4 ML. At 300 K, PH 3 decomposes into atomic hydrogen and elemental phosphorus with a phosphorus coverage of 0.8 ML. At 80 K, PCl 3 adsorbs dissociatively into atomic chlorine, elemental phosphorus, PCl and possibly PCl 2 and PCl 3 in the first monolayer. Formation of multilayers of PCl 3 is observed at 80 K. At 300 K, PCl 3 adsorbs dissociatively as atomic chlorine and elemental phosphorus with a saturation phosphorus coverage of 0.1 ML. The variation in total phosphorus uptake at 300 K from PX3 ( X = H, FandCl) adsorption is a result of competition between site blocking by dissociation fragments and displacement reactions. Annealing surfaces with adsorbed phosphorus to 1000 K results in formation of RuzP ( z = 1 or 2), which is manifested by the chemical shifts in the P2p core level, as well as the P LVV Auger transition. The recombination of adsorbed phosphorus and adsorbed X ( = H, FandCl) from decomposition is also observed, but is a minor reaction channel on the surface. Thermochemical data are used to analyze the different stabilities of PX 3 at 300 K, namely, PF 3 adsorbs molecularly and PH 3 and PCl 3 dissociate completely. First, we compare the heat of molecular adsorption and the heat of dissociative adsorption of PX 3 on Ru(0001), using an enthalpy approach, and find results consistent with experimental observations. Second, we compare the total bond energy difference between molecular adsorption and complete dissociation of PX 3 on Ru(0001). In particular, we apply Shustorovich's bond-order conservation-Morse potential (BOC-MP) method to estimate the heat of adsorption for PH 3 and PCl 3 and the bond energies of the relaxed P-X bonds of the adsorbed PX 3 on the surface. The bond strength difference among the relaxed P-X bonds (i.e., the relaxed P-F bond ( 475 {kJ}/{mol}) is much stronger than either the relaxed P-H bond ( 287 {kJ}/{mol}) or the relaxed P-Cl bond ( 288 {kJ}/{mol})) suggests that PF 3 is more stable than PH 3 and PCl 3 on Ru(0001) at 300 K. These values are used to evaluate the total bond energy differences between molecular adsorption and complete dissociation for each of the PX 3, and the results agree with the experimental trends.

A theoretical study for mechanical contact between carbon nanotubes

NASA Astrophysics Data System (ADS)

Takagi, Yoshiteru; Uda, Tsuyoshi; Ohno, Takahisa

2005-03-01

We have theoretically investigated motions of single-walled carbon nanotubes (SWNTs) which are mounted on a flat substrate layer of SWNTs by tight-binding molecular dynamics simulations. One of the most interesting motions is the conversion of force and torque, where the force and torque acting initially on the mounted tube finally results in the lateral motion and rolling of the supporting tubes in the substrate. This motion is well understood in terms of the total energy surface of the SWNT/SWNT system. It is suggested that an undulation of the total energy surface plays a role as an atomic-scale gear tooth in the field of nanomechanics, in spite of the atomically smooth surface of SWNT.

The effect of grain size and surface area on organic matter, lignin and carbohydrate concentration, and molecular compositions in Peru Margin sediments

USGS Publications Warehouse

Bergamaschi, B.A.; Tsamakis, E.; Keil, R.G.; Eglinton, T.I.; Montlucon, D.B.; Hedges, J.I.

1997-01-01

A C-rich sediment sample from the Peru Margin was sorted into nine hydrodynamically-determined grain size fractions to explore the effect of grain size distribution and sediment surface area on organic matter content and composition. The neutral monomeric carbohydrate composition, lignin oxidation product yields, total organic carbon, and total nitrogen contents were determined independently for each size fraction, in addition to sediment surface area and abundance of biogenic opal. The percent organic carbon and percent total nitrogen were strongly related to surface area in these sediments. In turn, the distribution of surface area closely followed mass distribution among the textural size classes, suggesting hydrodynamic controls on grain size also control organic carbon content. Nevertheless, organic compositional distinctions were observed between textural size classes. Total neutral carbohydrate yields in the Peru Margin sediments were found to closely parallel trends in total organic carbon, increasing in abundance among grain size fractions in proportion to sediment surface area. Coincident with the increases in absolute abundance, rhamnose and mannose increased as a fraction of the total carbohydrate yield in concert with surface area, indicating these monomers were preferentially represented in carbohydrates associated with surfaces. Lignin oxidation product yields varied with surface area when normalized to organic carbon, suggesting that the terrestrially-derived component may be diluted by sorption of marine derived material. Lignin-based parameters suggest a separate source for terrestrially derived material associated with sand-size material as opposed to that associated with silts and clays. Copyright ?? 1997 Elsevier Science Ltd.

The effect of grain size and surface area on organic matter, lignin and carbohydrate concentration, and molecular compositions in Peru Margin sediments

NASA Astrophysics Data System (ADS)

Bergamaschi, Brian A.; Tsamakis, Elizabeth; Keil, Richard G.; Eglinton, Timothy I.; Montluçon, Daniel B.; Hedges, John I.

1997-03-01

A C-rich sediment sample from the Peru Margin was sorted into nine hydrodynamically-determined grain size fractions to explore the effect of grain size distribution and sediment surface area on organic matter content and composition. The neutral monomeric carbohydrate composition, lignin oxidation product yields, total organic carbon, and total nitrogen contents were determined independently for each size fraction, in addition to sediment surface area and abundance of biogenic opal. The percent organic carbon and percent total nitrogen were strongly related to surface area in these sediments. In turn, the distribution of surface area closely followed mass distribution among the textural size classes, suggesting hydrodynamic controls on grain size also control organic carbon content. Nevertheless, organic compositional distinctions were observed between textural size classes. Total neutral carbohydrate yields in the Peru Margin sediments were found to closely parallel trends in total organic carbon, increasing in abundance among grain size fractions in proportion to sediment surface area. Coincident with the increases in absolute abundance, rhamnose and mannose increased as a fraction of the total carbohydrate yield in concert with surface area, indicating these monomers were preferentially represented in carbohydrates associated with surfaces. Lignin oxidation product yields varied with surface area when normalized to organic carbon, suggesting that the terrestrially-derived component may be diluted by sorption of marine derived material. Lignin-based parameters suggest a separate source for terrestrially derived material associated with sand-size material as opposed to that associated with silts and clays.

A NASBA on microgel-tethered molecular-beacon microarray for real-time microbial molecular diagnostics.

PubMed

Ma, Y; Dai, X; Hong, T; Munk, G B; Libera, M

2016-12-19

Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions. Here we extend this approach to include both real-time detection together with integrated NASBA amplification. We fabricate small (∼250 μm × 250 μm) simplex, duplex, and five-plex assays with microarray spots of controllable size (∼20 μm diameter), position, and shape to detect bacteria and fungi in a bloodstream-infection model. The targets, primers, and microgel-tethered probes can be combined in a single isothermal reaction chamber with no post-amplification labelling. We extract total RNA from clinical blood samples and differentiate between Gram-positive and Gram-negative bloodstream infection in a duplex assay to detect RNA- amplicons. The sensitivity based on our current protocols in a simplex assay to detect specific ribosomal RNA sequences within total RNA extracted from S. aureus and E. coli cultures corresponds to tens of bacteria per ml. We furthermore show that the platform can detect RNA- amplicons from synthetic target DNA with 1 fM sensitivity in sample volumes that contain about 12 000 DNA molecules. These experiments demonstrate an alternative approach that can enable rapid and real-time microarray-based molecular diagnostics.

Contamination of agricultural lands by polycyclic aromatic hydrocarbons (Tver region, Russia)

NASA Astrophysics Data System (ADS)

Zhidkin, Andrey; Koshovskii, Timur; Gennadiev, Alexander

2016-04-01

It is important to study sources and concentrations of polycyclic aromatic hydrocarbons (PAHs) in the agriculture soils within areas without intensive contaminations. Our studied object was soil and snow cover in the taiga zone (Tver region, Russia). A total of 52 surface (0-30 cm) and 31 subsurface (30-50 cm) soil samples, and 13 snow samples were collected in 35 soil pits, located in forest, crop and layland soils. Studied concentrations of the following 11 individual compounds: two-ring compounds (diphenyl and naphthalene homologues); three-ring compounds (fluorene, phenanthrene, anthracene); four-ring compounds (chrysene, pyrene, tetraphene); five-ring compounds (perylene, benzo[a]pyrene); and six-ring compounds (benzo[ghi]perylene). Analyses made by specrtofluorometry method at the temperature of liquid nitrogen. The total concentrations of all PAHs in soil samples ranged from 9 to 770 ng*g-1 with a median of 96 ng*g-1. The sum of high molecular weight PAHs was significantly lower than the sum of low molecular weight PAHs in the studied soils. The phenanthrene concentration was highest and ranged from 1.2 to 720 ng*g-1 (medium 72 ng*g-1). Compared PAHs reserves in snow cover (μg*m-2) with the reserves in topsoil layer (μg*m-2 in the upper 30 cm). Low molecular weight PAHs (fluorene, phenanthrene, diphenyl, naphthalene) reserves in snow was less than 20% from the reserves in the soil surface layer. High molecular weight PAHs (benzo[a]pyrene, chrysene, perylene, pyrene and tetraphene) reserves in snow was about 50-70% from the reserves in soil surface layer. High molecular weight PAHs (benzo[ghi]perylene and anthracene) reserves in snow was more than in topsoil. PAHs vertical distribution in soil profiles was statistically examined. The total concentration of all PAHs decreased with depth in all studied forest soils. In the arable soils was no significant trend in domination of PAHs total concentrations in the plowing and subsoil layers. The ratio of topsoil to subsoil concentrations of PAHs is different for differ congeners. Contents of phenanthrene and fluorene predominantly increase with the depth. Content of high molecular weight PAHs (benzo[a]pyrene, anthracene, tetraphene, perylene and pyrene) predominantly decreased with the depth. Other PAHs congeners have indistinct profile distributions in studied pits. Based on studied results PAHs divided to associations with different concentrations, sources and vertical distribution in soils: a) phenanthrene and fluorine; b) naphthalene, diphenyl; c) pyrene, benzo(a)pyrene, tetraphene, perylene, chrysene; d) anthracene and benzo(ghi)perylene. Research is funded by Russian Science Foundation (Project 14-27-00083).

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Molecular dynamics simulation of temperature effects on low energy near-surface cascades and surface damage in Cu

NASA Astrophysics Data System (ADS)

Zhu, Guo; Sun, Jiangping; Guo, Xiongxiong; Zou, Xixi; Zhang, Libin; Gan, Zhiyin

2017-06-01

The temperature effects on near-surface cascades and surface damage in Cu(0 0 1) surface under 500 eV argon ion bombardment were studied using molecular dynamics (MD) method. In present MD model, substrate system was fully relaxed for 1 ns and a read-restart scheme was introduced to save total computation time. The temperature dependence of damage production was calculated. The evolution of near-surface cascades and spatial distribution of adatoms at varying temperature were analyzed and compared. It was found that near-surface vacancies increased with temperature, which was mainly due to the fact that more atoms initially located in top two layers became adatoms with the decrease of surface binding energy. Moreover, with the increase of temperature, displacement cascades altered from channeling-like structure to branching structure, and the length of collision sequence decreased gradually, because a larger portion of energy of primary knock-on atom (PKA) was scattered out of focused chain. Furthermore, increasing temperature reduced the anisotropy of distribution of adatoms, which can be ascribed to that regular registry of surface lattice atoms was changed with the increase of thermal vibration amplitude of surface atoms.

Polycyclic aromatic hydrocarbons in ambient air, surface soil and wheat grain near a large steel-smelting manufacturer in northern China.

PubMed

Liu, Weijian; Wang, Yilong; Chen, Yuanchen; Tao, Shu; Liu, Wenxin

2017-07-01

The total concentrations and component profiles of polycyclic aromatic hydrocarbons (PAHs) in ambient air, surface soil and wheat grain collected from wheat fields near a large steel-smelting manufacturer in Northern China were determined. Based on the specific isomeric ratios of paired species in ambient air, principle component analysis and multivariate linear regression, the main emission source of local PAHs was identified as a mixture of industrial and domestic coal combustion, biomass burning and traffic exhaust. The total organic carbon (TOC) fraction was considerably correlated with the total and individual PAH concentrations in surface soil. The total concentrations of PAHs in wheat grain were relatively low, with dominant low molecular weight constituents, and the compositional profile was more similar to that in ambient air than in topsoil. Combined with more significant results from partial correlation and linear regression models, the contribution from air PAHs to grain PAHs may be greater than that from soil PAHs. Copyright © 2016. Published by Elsevier B.V.

Surface accumulation of low molecular weight dissolved organic matter in surface waters and horizontal off-shelf spreading of nutrients and humic-like fluorescence in the Chukchi Sea of the Arctic Ocean.

PubMed

Chen, Meilian; Jung, Jinyoung; Lee, Yun Kyung; Hur, Jin

2018-05-23

Polar regions play unique roles in global overturning circulation, carbon cycling, and climate change. In this study, seawater dissolved organic matter (DOM) was characterized for the Chukchi Sea in the Arctic Ocean in the summer season. The seawater generally contains high concentrations of dissolved organic carbon (DOC, up to 92 μM C) and tyrosine-like fluorescence (up to 0.21 RU), and it was enriched with heteroatomic molecular formula with nitrogen-containing and sulfur-containing formulas counting 2246 (~41% of total identified molecular formula) and 1838 (~34%), respectively. Significant correlations were observed between salinity and the absorption coefficient at 254 nm, between chlorophyll-a and DOC as well as the tyrosine-like component, C 270/302 (C ex/em maxima), and between biological index and two protein-like components, C 275/338 and C 305/344 . A comparison between surface waters and close-to-seafloor deep waters suggested a trend of the accumulation of low molecular weight (LMW) fraction (~54-74%, nominal average molecular weight M n  < ~350 Da) in the surface waters. Another interesting finding from spatial data was an obvious horizontal off-shelf spreading of nutrients and humic-like fluorescence. This study sheds novel insights of DOM characteristics and dynamics in the highly productive polar sea. Copyright © 2018 Elsevier B.V. All rights reserved.

Air-water interface-induced smectic bilayer

NASA Astrophysics Data System (ADS)

El Abed, A.; Pouzet, E.; Fauré, M.-C.; Sanière, M.; Abillon, O.

2000-11-01

We show, using surface pressure versus molecular area isotherms measurements and x-ray reflectivity, that the long diblock semifluorinated n-hexaeicosane molecules, F(CF2)8-(CH2)18H, form a stable smectic bilayer phase, noted M1, with a total thickness of 3.3 nm, at an apparent molecular area about 0.3 nm2, though in the bulk the used molecules do not form smectic phases at any temperature. We discuss different molecular packing models according to our experimental data and deduce that molecules are antiparallel with fluorinated chains outwards and interleaved hydrocarbon chains inwards.

Molecular chirality and domain shapes in lipid monolayers on aqueous surfaces

NASA Astrophysics Data System (ADS)

Krüger, Peter; Lösche, Mathias

2000-11-01

The shapes of domain boundaries in the mesoscopic phase separation of phospholipids in aqueous surface monolayers are analyzed with particular attention to the influence of molecular chirality. We have calculated equilibrium shapes of such boundaries, and show that the concept of spontaneous curvature-derived from an effective pair potential between the chiral molecules-yields an adequate description of the contribution of chirality to the total energy of the system. For enantiomeric dipalmitoylphosphatidylcholine in pure monolayers, and in mixtures with impurities that adsorb preferentially at the (one-dimensional) boundary line between the isotropic and anisotropic fluid phases, such as cyanobiphenyl (5CB), a total energy term that includes line tension, electrostatic dipole-dipole interaction, and spontaneous curvature is sufficient to describe the shapes of well-separated domain boundaries in full detail. As soon as interdomain distances fall below the domain sizes upon compression of a monolayer, fluctuations take over in determining its detailed structural morphology. Using Minkowski measures for the well-studied dimyristoyl phosphatidic acid (DMPA)/cholesterol system, we show that calculations accounting for line tension, electrostatic repulsion, and molecular chirality yield boundary shapes that are of the same topology as the experimentally observed structures. At a fixed molecular area in the phase coexistence region, the DMPA/cholesterol system undergoes an exponential decay of the line tension λ with decreasing subphase temperature T.

Electronic structure of uracil-like nucleobases adsorbed on Si(001): uracil, thymine and 5-fluorouracil

NASA Astrophysics Data System (ADS)

Molteni, Elena; Onida, Giovanni; Cappellini, Giancarlo

2016-04-01

We study the electronic properties of the Si(001):Uracil, Si(001):Thymine, and Si(001):5-Fluorouracil systems, focusing on the Si dimer-bridging configuration with adsorption governed by carbonyl groups. While the overall structural and electronic properties are similar, with small differences due to chemical substitutions, much larger effects on the surface band dispersion and bandgap show up as a function of the molecular orientation with respect to the surface. An off-normal orientation of the molecular planes is favored, showing larger bandgap and lower total energy than the upright position. We also analyze the localization of gap-edge occupied and unoccupied surface states. Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjb/e2016-70011-1

Effect of lubricant composition on the fatigue properties of ultra-high molecular weight polyethylene for total knee replacement.

PubMed

Aurora, A; DesJardins, J D; Joseph, P F; LaBerge, M

2006-05-01

Ultrahigh molecular weight polyethylene (UHMWPE) fatigue is a critical factor affecting the longevity of total knee replacement (TKR) bearings. With the increased need for laboratory studies to mimic near in vivo conditions for accurate characterization of material performance, the present study investigated the role of hyaluronic acid (HA) in testing lubricant on the crack growth response of UHMWPE. It was hypothesized that the change in lubricant viscosity as a result of HA would affect the fatigue life of the polymer. A fracture mechanics approach as per ASTM E 647 was adopted for this study. Surface micrograph and surface chemistry analyses were employed to study the micromechanisms of fatigue failure and protein adsorption of the specimen surfaces. Rheological analysis indicated that the addition of HA to diluted bovine serum increased testing lubricant viscosity. HA concentrations of 2.22, 0.55, and 1.5 g/l closely matched the viscosity ranges reported for osteoarthritis, rheumatoid arthritic diseased joint fluid, and periprosthetic fluids respectively. Results showed that the addition of HA to standard diluted bovine serum lubricants, in concentrations similar to that of periprosthetic fluid, delayed crack initiation and crack growth during fatigue testing.

Diffusion dynamics of the Li+ ion on a model surface of amorphous carbon: a direct molecular orbital dynamics study.

PubMed

Tachikawa, Hiroto; Shimizu, Akira

2005-07-14

Diffusion processes of the Li+ ion on a model surface of amorphous carbon (Li+C96H24 system) have been investigated by means of the direct molecular orbital (MO) dynamics method at the semiempirical AM1 level. The total energy and energy gradient on the full-dimensional AM1 potential energy surface were calculated at each time step in the dynamics calculation. The optimized structure, where Li+ is located in the center of the cluster, was used as the initial structure at time zero. The dynamics calculation was carried out in the temperature range 100-1000 K. The calculations showed that the Li+ ion vibrates around the equilibrium point below 200 K, while the Li+ ion moves on the surface above 250 K. At intermediate temperatures (300 K < T < 400 K), the ion moves on the surface and falls in the edge regions of the cluster. At higher temperatures (600 K < T), the Li+ ion transfers freely on the surface and edge regions. The diffusion pathway of the Li+ ion was discussed on the basis of theoretical results.

Radiation cross-linking in ultra-high molecular weight polyethylene for orthopaedic applications

NASA Astrophysics Data System (ADS)

Oral, Ebru; Muratoglu, Orhun K.

2007-12-01

The motivation for radiation cross-linking of ultra-high molecular weight polyethylene (UHMWPE) is to increase its wear resistance to be used as bearing surfaces for total joint arthroplasty. However, radiation also leaves behind long-lived residual free radicals in this polymer, the reactions of which can detrimentally affect mechanical properties. In this review, we focus on the radiation cross-linking and oxidative stability of first and second generation highly cross-linked UHMWPEs developed in our laboratory.

DOE Office of Scientific and Technical Information (OSTI.GOV)

He Liang; Xiu Faxian; Huang Guan

In this paper, we report the epitaxial growth of Bi{sub 2}Se{sub 3} thin films on Si (111) substrate, using molecular beam epitaxy (MBE). We show that the as-grown samples have good crystalline quality, and their surfaces exhibit terracelike quintuple layers. Angel-resolved photoemission experiments demonstrate single-Dirac-conelike surface states. These results combined with the temperature- and thickness-dependent magneto-transport measurements, suggest the presence of a shallow impurity band. Below a critical temperature of {approx}100K, the surface states of a 7 nm thick film contribute up to 50% of the total conduction.

Molecular-Scale Investigation of Heavy Metal Ions at a Charged Langmuir Monolayer

NASA Astrophysics Data System (ADS)

Rock, William; Qiao, Baofu; Uysal, Ahmet; Bu, Wei; Lin, Binhua

Solvent extraction - the surfactant-aided preferential transfer of a species from an aqueous to an organic phase - is an important technique used in heavy and precious metal refining and reprocessing. Solvent extraction requires transfer through an oil/water interface, and interfacial interactions are expected to control transfer kinetics and phase stability, yet these key interactions are poorly understood. Langmuir monolayers with charged headgroups atop concentrated salt solutions containing heavy metal ions act as a model of solvent extraction interfaces; studies of ions at a charged surface are also fundamentally important to many other phenomena including protein solvation, mineral surface chemistry, and electrochemistry. We probe these charged interfaces using a variety of surface-sensitive techniques - vibrational sum frequency generation (VSFG) spectroscopy, x-ray reflectivity (XRR), x-ray fluorescence near total reflection (XFNTR), and grazing incidence diffraction (GID). We integrate experiments with Molecular Dynamics (MD) simulations to uncover the molecular-level interfacial structure. This work is supported by the U.S. DOE, BES, Contract DE-AC02-06CH11357. ChemMatCARS is supported by NSF/CHE-1346572.

A high-dispersion molecular gas component in nearby galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caldú-Primo, Anahi; Walter, Fabian; Sandstrom, Karin

2013-12-01

We present a comprehensive study of the velocity dispersion of the atomic (H I) and molecular (H{sub 2}) gas components in the disks (R ≲ R {sub 25}) of a sample of 12 nearby spiral galaxies with moderate inclinations. Our analysis is based on sensitive high-resolution data from the THINGS (atomic gas) and HERACLES (molecular gas) surveys. To obtain reliable measurements of the velocity dispersion, we stack regions several kiloparsecs in size, after accounting for intrinsic velocity shifts due to galactic rotation and large-scale motions. We stack using various parameters: the galactocentric distance, star formation rate surface density, H Imore » surface density, H{sub 2} surface density, and total gas surface density. We fit single Gaussian components to the stacked spectra and measure median velocity dispersions for H I of 11.9 ± 3.1 km s{sup –1} and for CO of 12.0 ± 3.9 km s{sup –1}. The CO velocity dispersions are thus, surprisingly, very similar to the corresponding ones of H I, with an average ratio of σ{sub HI}/σ{sub CO}= 1.0 ± 0.2 irrespective of the stacking parameter. The measured CO velocity dispersions are significantly higher (factor of ∼2) than the traditional picture of a cold molecular gas disk associated with star formation. The high dispersion implies an additional thick molecular gas disk (possibly as thick as the H I disk). Our finding is in agreement with recent sensitive measurements in individual edge-on and face-on galaxies and points toward the general existence of a thick disk of molecular gas, in addition to the well-known thin disk in nearby spiral galaxies.« less

The influence of the cluster environment on the star formation efficiency of 12 Virgo spiral galaxies

NASA Astrophysics Data System (ADS)

Vollmer, B.; Wong, O. I.; Braine, J.; Chung, A.; Kenney, J. D. P.

2012-07-01

The influence of the environment on gas surface density and star formation efficiency of cluster spiral galaxies is investigated. We extend previous work on radial profiles by a pixel-to pixel analysis looking for asymmetries due to environmental interactions. The star formation rate is derived from GALEX UV and Spitzer total infrared data based on the 8, 24, 70, and 160 μm data. As in field galaxies, the star formation rate for most Virgo galaxies is approximately proportional to the molecular gas mass. Except for NGC 4438, the cluster environment does not affect the star formation efficiency with respect to the molecular gas. Gas truncation is not associated with major changes in the total gas surface density distribution of the inner disk of Virgo spiral galaxies. In three galaxies (NGC 4430, NGC 4501, and NGC 4522), possible increases in the molecular fraction and the star formation efficiency with respect to the total gas, of factors of 1.5 to 2, are observed on the windward side of the galactic disk. A significant increase of the star formation efficiency with respect to the molecular gas content on the windward side of ram pressure-stripped galaxies is not observed. The ram-pressure stripped extraplanar gas of 3 highly inclined spiral galaxies (NGC 4330, NGC 4438, and NGC 4522) shows a depressed star formation efficiency with respect to the total gas, and one of them (NGC 4438) shows a depressed rate even with respect to the molecular gas. The interpretation is that stripped gas loses the gravitational confinement and associated pressure of the galactic disk, and the gas flow is diverging, so the gas density decreases and the star formation rate drops. We found two such regions of low star formation efficiency in the more face-on galaxies NGC 4501 and NGC 4654 which are both undergoing ram pressure stripping. These regions show low radio continuum emission or unusually steep radio spectral index. However, the stripped extraplanar gas in one highly inclined galaxy (NGC 4569) shows a normal star formation efficiency with respect to the total gas. We propose this galaxy is different because it is observed long after peak pressure, and its extraplanar gas is now in a converging flow as it resettles back into the disk. Appendices are available in electronic form http://www.aanda.org

Enhancement of the natural organic matter removal from drinking water by nanofiltration.

PubMed

Matilainen, A; Liikanen, R; Nyström, M; Lindqvist, N; Tuhkanen, T

2004-03-01

Finnish surface waters are abundant in natural organic matter. Natural organic matter can be removed from drinking water in a water treatment process by coagulation and filtration. The standard treatment operations are not able to remove the smallest molar mass fraction of organic matter and the intermediate molar mass matter is only partly removed. The removal of residual natural organic matter from drinking water by nanofiltration was evalueted in this study. Three different nanofiltration membranes were compared in filtering six pre-treated surface waters. The total organic carbon content of the feed waters varied from 2.0 to 4.2 mg l(-1). Other water quality parameters measured were conductivity, alkalinity, hardness, UV-absorbance, SUVA, E2/E3 value and molecular size distribution by high-performance size-exclusion chromatography. The natural organic matter removal efficiencies of the membranes were good and varied between 100% and 49%, and between 85% and 47% according to molecular size distribution and total organic carbon measurements, respectively. Removal of different molecular size fractions varied from 100% to 56%, 100% to 54% and 88% to 19%, regarding high molar mass, intermediate molar mass and low molar mass organic matter, respectively. The Desal-5 DL membrane produced the highest natural organic matter removals.

Spin-symmetry conversion and internal rotation in high J molecular systems

NASA Astrophysics Data System (ADS)

Mitchell, Justin; Harter, William

2006-05-01

Dynamics and spectra of molecules with internal rotation or rovibrational coupling is approximately modeled by rigid or semi-rigid rotors with attached gyroscopes. Using Rotational Energy (RE)^1 surfaces, high resolution molecular spectra for high angular momentum show two distinct but related phenomena; spin-symmetry conversion and internal rotation. For both cases the high total angular momentum allows for transitions that would otherwise be forbidden. Molecular body-frame J-localization effects associated with tight energy level-clusters dominate the rovibronic spectra of high symmetry molecules, particularly spherical tops at J>10. ^2 The effects include large and widespread spin-symmetry mixing contrary to conventional wisdom^3 about weak nuclear moments. Such effects are discussed showing how RE surface plots may predict them even at low J. Classical dynamics of axially constrained rotors are approximated by intersecting rotational-energy-surfaces (RES) that have (J-S).B.(J-S) forms in the limit of constraints that do no work. Semi-classical eigensolutions are compared to those found by direct diagonalization. ^1 W.G Hater, in Handbook of Atomic, Molecular and Optical Physics, edited by G.W.F Drake (Springer, Germany 2006) ^2 W. G. Harter, Phys. Rev. A24,192-262(1981). ^3 G. Herzberg, Infrared and Raman Spectra (VanNostrand 1945) pp. 458,463.

Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: I. Construction of an affinity binding model.

PubMed

Zhang, Lin; Sun, Yan

2014-04-29

Platelet adhesion on a collagen surface through integrin α2β1 has been proven to be significant for the formation of arterial thrombus. However, the molecular determinants mediating the integrin-collagen complex remain unclear. In the present study, the dynamics of integrin-collagen binding and molecular interactions were investigated using molecular dynamics (MD) simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis. Hydrophobic interaction is identified as the major driving force for the formation of the integrin-collagen complex. On the basis of the MD simulation and MM-PBSA results, an affinity binding model (ABM) of integrin for collagen is constructed; it is composed of five residues, including Y157, N154, S155, R288, and L220. The ABM has been proven to capture the major binding motif contributing 84.8% of the total binding free energy. On the basis of the ABM, we expect to establish a biomimetic design strategy of platelet adhesion inhibitors, which would be beneficial for the development of potent peptide-based drugs for thrombotic diseases.

Peptides for functionalization of InP semiconductors.

PubMed

Estephan, Elias; Saab, Marie-belle; Larroque, Christian; Martin, Marta; Olsson, Fredrik; Lourdudoss, Sebastian; Gergely, Csilla

2009-09-15

The challenge is to achieve high specificity in molecular sensing by proper functionalization of micro/nano-structured semiconductors by peptides that reveal specific recognition for these structures. Here we report on surface modification of the InP semiconductors by adhesion peptides produced by the phage display technique. An M13 bacteriophage library has been used to screen 10(10) different peptides against the InP(001) and the InP(111) surfaces to finally isolate specific peptides for each orientation of the InP. MALDI-TOF/TOF mass spectrometry has been employed to study real affinity of the peptide towards the InP surfaces. The peptides serve for controlled placement of biotin onto InP to bind then streptavidin. Our Atomic Force Microscopy study revealed a total surface coverage of molecules when the InP surface was functionalized by its specific biotinylated peptide (YAIKGPSHFRPS). Finally, fluorescence microscopy has been employed to demonstrate the preferential attachment of the peptide onto a micro-patterned InP surface. Use of substrate specific peptides could present an alternative solution for the problems encountered in the actually existing sensing methods and molecular self-assembly due to the unwanted unspecific interactions.

Molecular collision processes in the presence of picosecond laser pulses

NASA Technical Reports Server (NTRS)

Lee, H. W.; George, T. F.

1979-01-01

Radiative transitions in molecular collision processes taking place in the presence of picosecond pulses are studied within a semiclassical formalism. An expression for adiabatic potential surfaces in the electronic-field representation is obtained, which directly leads to the evaluation of transition probabilities. Calculations with a Landau-Zener-type model indicate that picosecond pulses can be much more effective in inducing transitions than a single long pulse of the same intensity and the same total energy, if the intensity is sufficiently high that the perturbation treatment is not valid.

Effect of the biota diversity on the composition of low-molecular-weight water-soluble organic compounds in southern tundra soils

NASA Astrophysics Data System (ADS)

Shamrikova, E. V.; Kubik, O. S.; Punegov, V. V.; Gruzdev, I. V.

2014-03-01

Water extracts from the organic horizons of southern-tundra loamy permafrost-affected soils (a surface-gleyed tundra soil, a surface-gleyed soddy tundra soil (Haplic Stagnosols (Gelic)), and a peaty tundra soil (Histic Cryosol (Reductaquic)) and their undecomposed moss layers have been analyzed. The total weight concentration of the cations (Ca2+, Mg2+, K+, and Na+) determined by the atomic absorption method reaches 20 mg/dm3 in the organic horizons and 40-90 mg/dm3 in the undecomposed moss layers. Potassium and calcium ions dominate in all the organic horizons (80-90% of the total weight); potassium ions prevail in the mosses (about 70%). The weight concentration of carbon in the water-soluble organic compounds is 0.04-0.07 g/dm3 in the organic horizons and 0.20-0.40 g/dm3 in the undecomposed moss layers. The content of low-molecular-weight organic compounds (alcohols, carbohydrates, and acids) identified by gas chromatography and chromatomass spectrometry is 1-30 mg/dm3 in the organic horizons of the soils and 80-180 mg/dm3 in the mosses, which does not exceed 26% of the total organic carbon in the extracts.

Changes in Soil Organic Matter Abundance, Molecular Composition, and Diversity in an Arid Ecosystem in Response to Long-term Elevated CO2 Manipulation.

NASA Astrophysics Data System (ADS)

Hess, N. J.; Tfaily, M.; Evans, R. D.; Koyama, A.

2017-12-01

Little is known about how soils in arid ecosystems will respond to rising atmospheric CO2 concentration yet arid and semi-arid ecosystems cover more than 40% of Earth's land surface. Previous work in the Mojave Desert (Evans et al., 2014 Nature Climate Change) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric CO2 at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and stabilization using high resolution mass spectrometry at the NDFF site. Samples were collected from soil profiles to 1 m in depth with a 0.2 m a increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of soil organic matter (SOM) were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient CO2. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated CO2 compared to ambient plots suggested that elevated CO2 altered microbial carbon (C) use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated CO2 and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated CO2, give the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.

Chemical activation of bituminous coal for hampering oligomerization of organic contaminants.

PubMed

Yan, Liang; Sorial, George A

2011-12-15

Activated carbons prepared by KOH activation of bituminous coal were studied for hampering oligomerization of phenolic compounds on its surface. A total of 24 activated carbons with different microporosity and BET surface area were created. The effect of the different variables of the activation process (KOH/bituminous coal ratio, heating temperature, activation time, and flow rate of nitrogen gas) on critical carbon parameters was analyzed. The impact of activated carbon on oligomerization was examined by conducting isotherm experiments at a neutral pH on Carbon(exp) produced with optimal characteristics and granular activated carbon (GAC) F400 for phenol, 2-methylphenol and 2-ethylphenol. These isotherms were collected under anoxic (absence of molecular oxygen) and oxic (presence of molecular oxygen) conditions. The single solute adsorption of phenol, 2-methylphenol and 2-ethylphenol on Carbon(exp) showed no obvious differences between oxic and anoxic environment, which indicated that the Carbon(exp) sample is very effective in hampering the oligomerization of phenolic compounds under oxic conditions. On the other hand, F400, which have lower micropore percentage and BET surface area, significant increases in the adsorptive capacity had been observed when molecular oxygen was present. Copyright © 2011 Elsevier B.V. All rights reserved.

C+/H2 gas in star-forming clouds and galaxies

NASA Astrophysics Data System (ADS)

Nordon, Raanan; Sternberg, Amiel

2016-11-01

We present analytic theory for the total column density of singly ionized carbon (C+) in the optically thick photon dominated regions (PDRs) of far-UV irradiated (star-forming) molecular clouds. We derive a simple formula for the C+ column as a function of the cloud (hydrogen) density, the far-UV field intensity, and metallicity, encompassing the wide range of galaxy conditions. When assuming the typical relation between UV and density in the cold neutral medium, the C+ column becomes a function of the metallicity alone. We verify our analysis with detailed numerical PDR models. For optically thick gas, most of the C+ column is mixed with hydrogen that is primarily molecular (H2), and this `C+/H2' gas layer accounts for almost all of the `CO-dark' molecular gas in PDRs. The C+/H2 column density is limited by dust shielding and is inversely proportional to the metallicity down to ˜0.1 solar. At lower metallicities, H2 line blocking dominates and the C+/H2 column saturates. Applying our theory to CO surveys in low-redshift spirals, we estimate the fraction of C+/H2 gas out of the total molecular gas to be typically ˜0.4. At redshifts 1 < z < 3 in massive disc galaxies the C+/H2 gas represents a very small fraction of the total molecular gas (≲ 0.16). This small fraction at high redshifts is due to the high gas surface densities when compared to local galaxies.

Biocompatibility of modified ultra-high-molecular-weight polyethylene

NASA Astrophysics Data System (ADS)

Novotná, Z.; Lacmanová, V.; Rimpelová, S.; Juřik, P.; Polívková, M.; Å vorčik, V.

2016-09-01

Ultra-high-molecular-weight polyethylene (UHMWPE, PE) is a synthetic polymer used for biomedical applications because of its high impact resistance, ductility and stability in contact with physiological fluids. Therefore this material is being used in human orthopedic implants such as total joint replacements. Surface modification of this material relates to changes of its surface hydrophilicity, energy, microstructure, roughness, and morphology, all influencing its biological response. In our recent work, PE was treated by an Ar+ plasma discharge and then grafted with biologically active polyethylene glycol in order to enhance adhesion and proliferation of mouse fibroblast (L929). The surface properties of pristine PE and its grafted counterparts were studied by goniometry (surface wettability). Furthermore, Atomic Force Microscopy was used to determine the surface morphology and roughness. The biological response of the L929 cell lines seeded on untreated and plasma treated PE matrices was quantified in terms of the cell adhesion, density, and metabolic activity. Plasma treatment leads to the ablation of the polymer surface layers. Plasma treatment and subsequent poly(ethylene glycol) grafting lead to dramatic changes in the polymer surface morphology and roughness. Biological tests, performed in vitro, show increased adhesion and proliferation of cells on modified polymers. Grafting with poly(ethylene glycol) increases cell proliferation compared to plasma treatment.

Image method for induced surface charge from many-body system of dielectric spheres

NASA Astrophysics Data System (ADS)

Qin, Jian; de Pablo, Juan J.; Freed, Karl F.

2016-09-01

Charged dielectric spheres embedded in a dielectric medium provide the simplest model for many-body systems of polarizable ions and charged colloidal particles. We provide a multiple scattering formulation for the total electrostatic energy for such systems and demonstrate that the polarization energy can be rapidly evaluated by an image method that generalizes the image methods for conducting spheres. Individual contributions to the total electrostatic energy are ordered according to the number of polarized surfaces involved, and each additional surface polarization reduces the energy by a factor of (a/R)3ɛ, where a is the sphere radius, R the average inter-sphere separation, and ɛ the relevant dielectric mismatch at the interface. Explicit expressions are provided for both the energy and the forces acting on individual spheres, which can be readily implemented in Monte Carlo and molecular dynamics simulations of polarizable charged spheres, thereby avoiding costly computational techniques that introduce a surface charge distribution that requires numerical solution.

IImage method for induced surface charge from many-body system of dielectric spheres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Jian; de Pablo, Juan J.; Freed, Karl F.

2016-09-28

Charged dielectric spheres embedded in a dielectric medium provide the simplest model for many-body systems of polarizable ions and charged colloidal particles. We provide a multiple scattering formulation for the total electrostatic energy for such systems and demonstrate that the polarization energy can be rapidly evaluated by an image method that generalizes the image methods for conducting spheres. Individual contributions to the total electrostatic energy are ordered according to the number of polarized surfaces involved, and each additional surface polarization reduces the energy by a factor of (a/R)(3) epsilon, where a is the sphere radius, R the average inter-sphere separation,more » and. the relevant dielectric mismatch at the interface. Explicit expressions are provided for both the energy and the forces acting on individual spheres, which can be readily implemented in Monte Carlo and molecular dynamics simulations of polarizable charged spheres, thereby avoiding costly computational techniques that introduce a surface charge distribution that requires numerical solution.« less

Determination of Protein Surface Hydration by Systematic Charge Mutations

NASA Astrophysics Data System (ADS)

Yang, Jin; Jia, Menghui; Qin, Yangzhong; Wang, Dihao; Pan, Haifeng; Wang, Lijuan; Xu, Jianhua; Zhong, Dongping; Dongping Zhong Collaboration; Jianhua Xu Collaboration

Protein surface hydration is critical to its structural stability, flexibility, dynamics and function. Recent observations of surface solvation on picosecond time scales have evoked debate on the origin of such relatively slow motions, from hydration water or protein charged sidechains, especially with molecular dynamics simulations. Here, we used a unique nuclease with a single tryptophan as a local probe and systematically mutated neighboring three charged residues to differentiate the contributions from hydration water and charged sidechains. By mutations of alternative one and two and all three charged residues, we observed slight increases in the total tryptophan Stokes shifts with less neighboring charged residue(s) and found insensitivity of charged sidechains to the relaxation patterns. The dynamics is correlated with hydration water relaxation with the slowest time in a dense charged environment and the fastest time at a hydrophobic site. On such picosecond time scales, the protein surface motion is restricted. The total Stokes shifts are dominantly from hydration water relaxation and the slow dynamics is from water-driven relaxation, coupled with local protein fluctuations.

Detection of creatinine enriched on a surface imprinted polystyrene film using FT-ATR-IR.

PubMed

Sreenivasan, K

2006-01-01

The surface of polystyrene (PS) was chemically modified by coating a thin layer of polyaniline (PANI) by oxidizing aniline using ammonium persulfate. Affinity sites for creatinine, a clinically relevant molecule, were created in the coated layer by adding creatinine as print molecules during the oxidation. The imprinted layer adsorbed creatinine was compared to non-imprinted surface reflecting the creation of creatinine-specific sites on the surface. The equilibrium was attained rapidly, indicating that a material of this kind is suitable for sensing applications. The adsorbed creatinine on the surface was detected using the technique of Fourier transform attenuated total internal reflection infra red spectroscopy (FT-ATR-IR). The results show that molecularly imprinted surface can enrich molecules of interest and the enriched molecules can be detected using FT-IR.

Simulation on Melting Process of Water Using Molecular Dynamics Method

NASA Astrophysics Data System (ADS)

Okawa, Seiji; Saito, Akio; Kang, Chaedong

Simulation on phase change from ice to water was presented using molecular dynamics method. 576molecules were placed in a cell at ice forming arrangement. The volume of the cell was fixed so that the density of ice was kept at 923 kg/m3. Periodic boundary condition was used. According to the phase diagram of water, melting point of ice at the density of 923 kg/m3 is about 400 K. In order to perform melting process from surface, only the molecules near the boundary were scaled at each time step to keep its average temperature at 420 K, and the average temperature of other molecules were set to 350 K as initial condition. By observing time variation of the change in molecular arrangement, it was found that the hydrogen bond network near the boundary surface started to break its configuration and the melting surface moved towards the center until no more ice forming configuration was observed. This phenomenon was also discussed in a form of temperature and energy variation. The total energy increased and reached to a steady state at the time around 6.5 ps. This increment was due to the energy supplied from the boundary at a constant temperature. The temperature in the cell kept almost constant at 380 K during the period between 0.6 and 5.5 ps. This period coincides with melting process observed in molecular arrangement. Hence, it can be said that 380 K corresponds to the melting point. The total energy stored in the cell consisted of sensible and latent heat. Specific heat of water and ice were calculated, and they were found to be 5.6 kJ/kg·K and 3.7 kJ/kg·K, respectively. Hence, latent heat was found to be 316kJ/kg. These values agreed quite well to the physical properties of water.

Development and Evaluation of EPA Method 1615 for Detection of Enterovirus and Norovirus in Water

PubMed Central

Brinkman, Nichole E.; Griffin, Shannon M.; McMinn, Brian R.; Rhodes, Eric R.; Varughese, Eunice A.; Grimm, Ann C.; Parshionikar, Sandhya U.; Wymer, Larry; Fout, G. Shay

2013-01-01

The U.S. EPA developed a sample concentration and preparation assay in conjunction with the total culturable virus assay for concentrating and measuring culturable viruses in source and drinking waters as part of the Information Collection Rule (ICR) promulgated in 1996. In an effort to improve upon this method, the U.S. EPA recently developed Method 1615: Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Method 1615 uses a culturable virus assay with reduced equipment and labor costs compared to the costs associated with the ICR virus method and introduces a new molecular assay for the detection of enteroviruses and noroviruses by reverse transcription-quantitative PCR. In this study, we describe the optimization of several new components of the molecular assay and examine virus recovery from ground, reagent-grade, and surface water samples seeded with poliovirus type 3 and murine norovirus. For the culturable virus and molecular assays, mean poliovirus recovery using the complete method was 58% and 20% in groundwater samples, 122% and 39% using low-titer spikes in reagent-grade water, 42% and 48% using high-titer spikes in reagent-grade water, and 11% and 10% in surface water with high turbidity, respectively. Murine norovirus recovery by the molecular assay was 30% in groundwater samples, less than 8% in both low- and high-titer spikes in reagent-grade water, and 6% in surface water with high turbidity. This study demonstrates the effectiveness of Method 1615 for use with groundwater samples and highlights the need for further research into its effectiveness with surface water. PMID:23087037

ESI-FTICR-MS Molecular Characterization of DOM Degradation under Warming in Tundra Soils from Barrow, Alaska

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hongmei Chen; Ziming Yang; Rosalie Chu

This dataset provides the results of warming incubation of Arctic soils from trough areas of a high-center polygon at the Barrow Environmental Observatory (BEO) in northern Alaska, United States. The organic-rich soil (8-20 cm below ground surface) and the mineral-rich soil (22-45 cm below surface) were separated, and the thawed and homogenized subsamples from each soil were incubated at -2 degrees C or 8 degrees C for 122 days under anoxic conditions (headspace filled with N2). The extracted DOM from soil samples were analyzed by Fourier transform ion cyclotron resonance mass spectrometry coupled with electrospray ionization (ESI-FTICR-MS). Reported analytes includemore » soil water content, dissolved organic carbon, total organic carbon, MS peaks' m/z and intensities, and elemental composition of identified molecular formulas.« less

Protein Corona Composition Does Not Accurately Predict Hematocompatibility of Colloidal Gold Nanoparticles

PubMed Central

Dobrovolskaia, Marina A.; Neun, Barry W.; Man, Sonny; Ye, Xiaoying; Hansen, Matthew; Patri, Anil K.; Crist, Rachael M.; McNeil, Scott E.

2014-01-01

Proteins bound to nanoparticle surfaces are known to affect particle clearance by influencing immune cell uptake and distribution to the organs of the mononuclear phagocytic system. The composition of the protein corona has been described for several types of nanomaterials, but the role of the corona in nanoparticle biocompatibility is not well established. In this study we investigate the role of nanoparticle surface properties (PEGylation) and incubation times on the protein coronas of colloidal gold nanoparticles. While neither incubation time nor PEG molecular weight affected the specific proteins in the protein corona, the total amount of protein binding was governed by the molecular weight of PEG coating. Furthermore, the composition of the protein corona did not correlate with nanoparticle hematocompatibility. Specialized hematological tests should be used to deduce nanoparticle hematotoxicity. PMID:24512761

Influence of Molecular Orientation on Charge-Transfer Processes at Phthalocyanine/Metal Oxide Interfaces and Relationship to Organic Photovoltaic Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Hsiao-Chu; MacDonald, Gordon A.; Shi, Yanrong

2015-05-04

The effect of the molecular orientation distribution of the first monolayer of donor molecules at the hole-harvesting contact in an organic photovoltaic (OPV) on device efficiency was investigated. Two zinc phthalocyanine (ZnPc) phosphonic acids (PA) deposited on indium tin oxide (ITO) electrodes are compared: ZnPc(PA)4 contains PA linkers in all four quadrants, and ZnPcPA contains a PA linker in one quadrant. ZnPcPA monolayers exhibited a broad distribution of molecular orientations whereas ZnPc(PA)4 adsorption produced a monolayer with a narrower orientation distribution with the molecular plane more parallel to the ITO surface. We used potential-modulated attenuated total reflectance spectroelectrochemistry (PM-ATR) tomore » characterize the charge-transfer kinetics of these films and show that the highest rate constants correspond to ZnPc subpopulations that are oriented more parallel to the ITO surface plane. For ZnPc(PA)4, rate constants exceeded 104 s–1 and are among the highest ever reported for a surface-confined redox couple, which is attributable to both its orientation and the small ZnPc–electrode separation distance. The performance of OPVs with ITO hole-harvesting contacts modified with ZnPc(PA)4 was comparable to that achieved with highly activated bare ITO contacts, whereas for ZnPcPA-modified contacts, the OPV performance was similar to that observed with (hole-blocking) alkyl-PA modifiers. These results demonstrate the synergism between molecular structure, energetics, and dynamics at interfaces in OPVs.« less

Structure of high-index GaAs surfaces - the discovery of the stable GaAs(2511) surface

NASA Astrophysics Data System (ADS)

Jacobi, K.; Geelhaar, L.; Márquez, J.

We present a brief overview of surface structures of high-index GaAs surfaces, putting emphasis on recent progress in our own laboratory. By adapting a commercial scanning tunneling microscope (STM) to our molecular beam epitaxy and ultra high vacuum analysis chamber system, we have been able to atomically resolve the GaAs( {1} {1} {3})B(8 ×1), (114)Aα2(2×1), (137), (3715), and (2511) surface structures. In cooperation with P. Kratzer and M. Scheffler from the Theory Department of the Fritz-Haber Institute we determined the structure of some of these surfaces by comparing total-energy calculations and STM image simulations with the atomically resolved STM images. We present the results for the {112}, {113}, and {114} surfaces. Then we describe what led us to proceed into the inner parts of the stereographic triangle and to discover the hitherto unknown stable GaAs(2511) surface.

Chemical and physical analyses of wax ester properties

PubMed Central

Patel, Sejal; Nelson, Dennis R.; Gibbs, Allen G.

2001-01-01

Wax esters are major constituents of the surface lipids in many terrestrial arthropods, but their study is complicated by their diversity. We developed a procedure for quantifying isomers in mixtures of straight-chain saturated and unsaturated wax esters having the same molecular weights, using single-ion monitoring of the total ion current data from gas chromatography-mass spectrometry. We examined the biological consequences of structural differences by measuring the melting temperatures, Tm, of >60 synthetic wax esters, containing 26–48 carbon atoms. Compounds containing saturated alcohol and acid moieties melted at 38–73°C. The main factor affecting Tm was the total chain length of the wax ester, but the placement of the ester bond also affected Tm. Insertion of a double bond into either the alcohol or acid moiety decreased Tm by ∼30°C. Simple mixtures of wax esters with n-alkanes melted several °C lower than predicted from the melting points of the component lipids. Our results indicate that the wax esters of primary alcohols that are most typically found on the cuticle of terrestrial arthropods occur in a solid state under physiological conditions, thereby conferring greater waterproofing. Wax esters of secondary alcohols, which occur on melanopline grasshoppers, melted >60°C below primary esters of the same molecular weight and reduced Tm of the total surface lipids to environmental values. PMID:15455064

Multi-scale modelling to relate beryllium surface temperature, deuterium concentration and erosion in fusion reactor environment

DOE PAGES

Safi, E.; Valles, G.; Lasa, A.; ...

2017-03-27

Beryllium (Be) has been chosen as the plasma-facing material for the main wall of ITER, the next generation fusion reactor. Identifying the key parameters that determine Be erosion under reactor relevant conditions is vital to predict the ITER plasma-facing component lifetime and viability. To date, a certain prediction of Be erosion, focusing on the effect of two such parameters, surface temperature and D surface content, has not been achieved. In this paper, we develop the first multi-scale KMC-MD modeling approach for Be to provide a more accurate database for its erosion, as well as investigating parameters that affect erosion. First,more » we calculate the complex relationship between surface temperature and D concentration precisely by simulating the time evolution of the system using an object kinetic Monte Carlo (OKMC) technique. These simulations provide a D surface concentration profile for any surface temperature and incoming D energy. We then describe how this profile can be implemented as a starting configuration in molecular dynamics (MD) simulations. We finally use MD simulations to investigate the effect of temperature (300–800 K) and impact energy (10–200 eV) on the erosion of Be due to D plasma irradiations. The results reveal a strong dependency of the D surface content on temperature. Increasing the surface temperature leads to a lower D concentration at the surface, because of the tendency of D atoms to avoid being accommodated in a vacancy, and de-trapping from impurity sites diffuse fast toward bulk. At the next step, total and molecular Be erosion yields due to D irradiations are analyzed using MD simulations. The results show a strong dependency of erosion yields on surface temperature and incoming ion energy. The total Be erosion yield increases with temperature for impact energies up to 100 eV. However, increasing temperature and impact energy results in a lower fraction of Be atoms being sputtered as BeD molecules due to the lower D surface concentrations at higher temperatures. Finally, these findings correlate well with different experiments performed at JET and PISCES-B devices.« less

Multi-scale modelling to relate beryllium surface temperature, deuterium concentration and erosion in fusion reactor environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safi, E.; Valles, G.; Lasa, A.

Beryllium (Be) has been chosen as the plasma-facing material for the main wall of ITER, the next generation fusion reactor. Identifying the key parameters that determine Be erosion under reactor relevant conditions is vital to predict the ITER plasma-facing component lifetime and viability. To date, a certain prediction of Be erosion, focusing on the effect of two such parameters, surface temperature and D surface content, has not been achieved. In this paper, we develop the first multi-scale KMC-MD modeling approach for Be to provide a more accurate database for its erosion, as well as investigating parameters that affect erosion. First,more » we calculate the complex relationship between surface temperature and D concentration precisely by simulating the time evolution of the system using an object kinetic Monte Carlo (OKMC) technique. These simulations provide a D surface concentration profile for any surface temperature and incoming D energy. We then describe how this profile can be implemented as a starting configuration in molecular dynamics (MD) simulations. We finally use MD simulations to investigate the effect of temperature (300–800 K) and impact energy (10–200 eV) on the erosion of Be due to D plasma irradiations. The results reveal a strong dependency of the D surface content on temperature. Increasing the surface temperature leads to a lower D concentration at the surface, because of the tendency of D atoms to avoid being accommodated in a vacancy, and de-trapping from impurity sites diffuse fast toward bulk. At the next step, total and molecular Be erosion yields due to D irradiations are analyzed using MD simulations. The results show a strong dependency of erosion yields on surface temperature and incoming ion energy. The total Be erosion yield increases with temperature for impact energies up to 100 eV. However, increasing temperature and impact energy results in a lower fraction of Be atoms being sputtered as BeD molecules due to the lower D surface concentrations at higher temperatures. Finally, these findings correlate well with different experiments performed at JET and PISCES-B devices.« less

Multi-scale modelling to relate beryllium surface temperature, deuterium concentration and erosion in fusion reactor environment

NASA Astrophysics Data System (ADS)

Safi, E.; Valles, G.; Lasa, A.; Nordlund, K.

2017-05-01

Beryllium (Be) has been chosen as the plasma-facing material for the main wall of ITER, the next generation fusion reactor. Identifying the key parameters that determine Be erosion under reactor relevant conditions is vital to predict the ITER plasma-facing component lifetime and viability. To date, a certain prediction of Be erosion, focusing on the effect of two such parameters, surface temperature and D surface content, has not been achieved. In this work, we develop the first multi-scale KMC-MD modeling approach for Be to provide a more accurate database for its erosion, as well as investigating parameters that affect erosion. First, we calculate the complex relationship between surface temperature and D concentration precisely by simulating the time evolution of the system using an object kinetic Monte Carlo (OKMC) technique. These simulations provide a D surface concentration profile for any surface temperature and incoming D energy. We then describe how this profile can be implemented as a starting configuration in molecular dynamics (MD) simulations. We finally use MD simulations to investigate the effect of temperature (300-800 K) and impact energy (10-200 eV) on the erosion of Be due to D plasma irradiations. The results reveal a strong dependency of the D surface content on temperature. Increasing the surface temperature leads to a lower D concentration at the surface, because of the tendency of D atoms to avoid being accommodated in a vacancy, and de-trapping from impurity sites diffuse fast toward bulk. At the next step, total and molecular Be erosion yields due to D irradiations are analyzed using MD simulations. The results show a strong dependency of erosion yields on surface temperature and incoming ion energy. The total Be erosion yield increases with temperature for impact energies up to 100 eV. However, increasing temperature and impact energy results in a lower fraction of Be atoms being sputtered as BeD molecules due to the lower D surface concentrations at higher temperatures. These findings correlate well with different experiments performed at JET and PISCES-B devices.

Electrical properties of surface and interface layers of the N- and In-polar undoped and Mg-doped InN layers grown by PA MBE

NASA Astrophysics Data System (ADS)

Komissarova, T. A.; Kampert, E.; Law, J.; Jmerik, V. N.; Paturi, P.; Wang, X.; Yoshikawa, A.; Ivanov, S. V.

2018-01-01

Electrical properties of N-polar undoped and Mg-doped InN layers and In-polar undoped InN layers grown by plasma-assisted molecular beam epitaxy (PA MBE) were studied. Transport parameters of the surface and interface layers were determined from the measurements of the Hall coefficient and resistivity as well as the Shubnikov-de Haas oscillations at magnetic fields up to 60 T. Contributions of the 2D surface, 3D near-interface, and 2D interface layers to the total conductivity of the InN films were defined and discussed to be dependent on InN surface polarity, Mg doping, and PA MBE growth conditions.

Enhancement of Water Evaporation on Solid Surfaces with Nanoscale Hydrophobic-Hydrophilic Patterns.

PubMed

Wan, Rongzheng; Wang, Chunlei; Lei, Xiaoling; Zhou, Guoquan; Fang, Haiping

2015-11-06

Using molecular dynamics simulations, we show that the evaporation of nanoscale water on hydrophobic-hydrophilic patterned surfaces is unexpectedly faster than that on any surfaces with uniform wettability. The key to this phenomenon is that, on the patterned surface, the evaporation rate from the hydrophilic region only slightly decreases due to the correspondingly increased water thickness; meanwhile, a considerable number of water molecules evaporate from the hydrophobic region despite the lack of water film. Most of the evaporated water from the hydrophobic region originates from the hydrophilic region by diffusing across the contact lines. Further analysis shows that the evaporation rate from the hydrophobic region is approximately proportional to the total length of the contact lines.

Interpreting the sub-linear Kennicutt-Schmidt relationship: the case for diffuse molecular gas

NASA Astrophysics Data System (ADS)

Shetty, Rahul; Clark, Paul C.; Klessen, Ralf S.

2014-08-01

Recent statistical analysis of two extragalactic observational surveys strongly indicate a sub-linear Kennicutt-Schmidt (KS) relationship between the star formation rate (ΣSFR) and molecular gas surface density (Σmol). Here, we consider the consequences of these results in the context of common assumptions, as well as observational support for a linear relationship between ΣSFR and the surface density of dense gas. If the CO traced gas depletion time (τ_dep^CO) is constant, and if CO only traces star-forming giant molecular clouds (GMCs), then the physical properties of each GMC must vary, such as the volume densities or star formation rates. Another possibility is that the conversion between CO luminosity and Σmol, the XCO factor, differs from cloud-to-cloud. A more straightforward explanation is that CO permeates the hierarchical interstellar medium, including the filaments and lower density regions within which GMCs are embedded. A number of independent observational results support this description, with the diffuse gas comprising at least 30 per cent of the total molecular content. The CO bright diffuse gas can explain the sub-linear KS relationship, and consequently leads to an increasing τ_dep^CO with Σmol. If ΣSFR linearly correlates with the dense gas surface density, a sub-linear KS relationship indicates that the fraction of diffuse gas fdiff grows with Σmol. In galaxies where Σmol falls towards the outer disc, this description suggests that fdiff also decreases radially.

Oxidation of Cyclohexene Catalyzed by Nanoporous Au(Ag) in Liquid Phase

DOE PAGES

Dou, Jian; Tang, Yu; Nguyen, Luan; ...

2016-12-22

Nanoporous gold with minor silver content has been identified as a new type of gold based catalyst for selective oxidation of cyclohexene with molecular oxygen in liquid. By oxidation of the leached nanoporous gold foils in ozone, the minor silver content was oxidized in this paper to form silver oxide nanoclusters on the surface of nanoporous gold. With further treatment in methanol, the surface silver oxide was reduced and surface alloy was formed on gold ligaments. Both nanoporous gold treated with ozone only and the one with ozone and then methanol are very active for selective oxidation of cyclohexene withmore » molecular oxygen in liquid of cyclohexene with a turn-over-frequency (TOF) of 0.55–0.99 molecules per surface Au atom per second under a solvent-free and initiator- free condition. The total selectivity for production of 2-cyclohexene-1-one, 2-cyclohexene-1-ol, and cyclohexene oxide was increased from 57.5 % to 80.8 % by an additional treatment of nanoporous gold in methanol after activation in zone. Finally, the correlation of catalytic selectivity for the production of the three products and corresponding surface chemistry of ligament suggests that (1) the formed Au–Ag alloy surface is favorable for the formation of 2-cyclohexen-1-one, 2-cyclohexene-1-ol, and cyclohexene oxide and (2) the surface silver oxide is favorable for the production of cyclohexenyl hydroperoxide.« less

Oxidation of Cyclohexene Catalyzed by Nanoporous Au(Ag) in Liquid Phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dou, Jian; Tang, Yu; Nguyen, Luan

Nanoporous gold with minor silver content has been identified as a new type of gold based catalyst for selective oxidation of cyclohexene with molecular oxygen in liquid. By oxidation of the leached nanoporous gold foils in ozone, the minor silver content was oxidized in this paper to form silver oxide nanoclusters on the surface of nanoporous gold. With further treatment in methanol, the surface silver oxide was reduced and surface alloy was formed on gold ligaments. Both nanoporous gold treated with ozone only and the one with ozone and then methanol are very active for selective oxidation of cyclohexene withmore » molecular oxygen in liquid of cyclohexene with a turn-over-frequency (TOF) of 0.55–0.99 molecules per surface Au atom per second under a solvent-free and initiator- free condition. The total selectivity for production of 2-cyclohexene-1-one, 2-cyclohexene-1-ol, and cyclohexene oxide was increased from 57.5 % to 80.8 % by an additional treatment of nanoporous gold in methanol after activation in zone. Finally, the correlation of catalytic selectivity for the production of the three products and corresponding surface chemistry of ligament suggests that (1) the formed Au–Ag alloy surface is favorable for the formation of 2-cyclohexen-1-one, 2-cyclohexene-1-ol, and cyclohexene oxide and (2) the surface silver oxide is favorable for the production of cyclohexenyl hydroperoxide.« less

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.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces and surface-based properties. Retrieval performance, applications in structure-activity modeling of complex biological properties, and comparisons with existing research and commercial methods demonstrate the validity and effectiveness of the approach. PMID:17634096

Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display

PubMed Central

Desvaux, Mickaël; Candela, Thomas; Serror, Pascale

2018-01-01

The cell envelope of parietal monoderm bacteria (archetypal Gram-positive bacteria) is formed of a cytoplasmic membrane (CM) and a cell wall (CW). While the CM is composed of phospholipids, the CW is composed at least of peptidoglycan (PG) covalently linked to other biopolymers, such as teichoic acids, polysaccharides, and/or polyglutamate. Considering the CW is a porous structure with low selective permeability contrary to the CM, the bacterial cell surface hugs the molecular figure of the CW components as a well of the external side of the CM. While the surfaceome corresponds to the totality of the molecules found at the bacterial cell surface, the proteinaceous complement of the surfaceome is the proteosurfaceome. Once translocated across the CM, secreted proteins can either be released in the extracellular milieu or exposed at the cell surface by associating to the CM or the CW. Following the gene ontology (GO) for cellular components, cell-surface proteins at the CM can either be integral (GO: 0031226), i.e., the integral membrane proteins, or anchored to the membrane (GO: 0046658), i.e., the lipoproteins. At the CW (GO: 0009275), cell-surface proteins can be covalently bound, i.e., the LPXTG-proteins, or bound through weak interactions to the PG or wall polysaccharides, i.e., the cell wall binding proteins. Besides monopolypeptides, some proteins can associate to each other to form supramolecular protein structures of high molecular weight, namely the S-layer, pili, flagella, and cellulosomes. After reviewing the cell envelope components and the different molecular mechanisms involved in protein attachment to the cell envelope, perspectives in investigating the proteosurfaceome in parietal monoderm bacteria are further discussed. PMID:29491848

A MOLECULAR STAR FORMATION LAW IN THE ATOMIC-GAS-DOMINATED REGIME IN NEARBY GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schruba, Andreas; Walter, Fabian; Dumas, Gaelle

2011-08-15

We use the IRAM HERACLES survey to study CO emission from 33 nearby spiral galaxies down to very low intensities. Using 21 cm line atomic hydrogen (H I) data, mostly from THINGS, we predict the local mean CO velocity based on the mean H I velocity. By re-normalizing the CO velocity axis so that zero corresponds to the local mean H I velocity we are able to stack spectra coherently over large regions. This enables us to measure CO intensities with high significance as low as I{sub CO} {approx} 0.3 K km s{sup -1} ({Sigma}{sub H{sub 2}}{approx}1 M{sub sun} pc{supmore » -2}), an improvement of about one order of magnitude over previous studies. We detect CO out to galactocentric radii r{sub gal} {approx} r{sub 25} and find the CO radial profile to follow a remarkably uniform exponential decline with a scale length of {approx}0.2 r{sub 25}. Here we focus on stacking as a function of radius, comparing our sensitive CO profiles to matched profiles of H I, H{alpha}, far-UV (FUV), and Infrared (IR) emission at 24 {mu}m and 70 {mu}m. We observe a tight, roughly linear relationship between CO and IR intensity that does not show any notable break between regions that are dominated by molecular gas ({Sigma}{sub H{sub 2}}>{Sigma}{sub H{sub i}}) and those dominated by atomic gas ({Sigma}{sub H{sub 2}}<{Sigma}{sub H{sub i}}). We use combinations of FUV+24 {mu}m and H{alpha}+24 {mu}m to estimate the recent star formation rate (SFR) surface density, {Sigma}{sub SFR}, and find approximately linear relations between {Sigma}{sub SFR} and {Sigma}{sub H{sub 2}}. We interpret this as evidence of stars forming in molecular gas with little dependence on the local total gas surface density. While galaxies display small internal variations in the SFR-to-H{sub 2} ratio, we do observe systematic galaxy-to-galaxy variations. These galaxy-to-galaxy variations dominate the scatter in relationships between CO and SFR tracers measured at large scales. The variations have the sense that less massive galaxies exhibit larger ratios of SFR-to-CO than massive galaxies. Unlike the SFR-to-CO ratio, the balance between atomic and molecular gas depends strongly on the total gas surface density and galactocentric radius. It must also depend on additional parameters. Our results reinforce and extend to lower surface densities, a picture in which star formation in galaxies can be separated into two processes: the assembly of star-forming molecular clouds and the formation of stars from H{sub 2}. The interplay between these processes yields a total gas-SFR relation with a changing slope, which has previously been observed and identified as a star formation threshold.« less

Chemical composition and cycling of dissolved organic matter in the Mid-Atlantic Bight

NASA Astrophysics Data System (ADS)

Aluwihare, Lihini I.; Repeta, Daniel J.; Chen, Robert F.

This study focuses on the chemical characterization of high molecular-weight dissolved organic matter (HMW DOM) isolated from the Middle Atlantic Bight in April 1994 and March 1996. Using proton nuclear magnetic resonance spectroscopy ( 1HNMR) and monosaccharide analysis we compared both spatial and temporal variations in the chemical structure of HMW DOM across this region. Our analyses support the presence of at least two compositionally distinct components to HMW DOM. The major component is acyl polysaccharide (APS), a biopolymer rich in carbohydrates, acetate and lipid, accounting for between 50% and 80% of the total high molecular-weight dissolved organic carbon (HMW DOC) in surface samples. APS is most abundant in fully marine, surface-water samples, and is a product of autochthonous production. Organic matter with spectral properties characteristic of humic substances is the second major component of HMW DOM. Humic substances are most abundant (up to 49% of the total carbon) in samples collected from estuaries, near the coast, and in deep water, suggesting both marine and perhaps terrestrial sources. Radiocarbon analyses of neutral monosaccharides released by the hydrolysis of APS have similar and modern (average 71‰) Δ 14C values. Radiocarbon data support our suggestion that these sugars occur as part of a common macromolecule, with an origin via recent biosynthesis. Preliminary radiocarbon data for total neutral monosaccharides isolated from APS at 300 and 750 m show this fraction to be substantially enriched relative to total HMW DOC and DOC. The relatively enriched radiocarbon values of APS at depth suggest APS is rapidly transported into the deep ocean.

Influence of growth conditions and surface reaction byproducts on GaN grown via metal organic molecular beam epitaxy: Toward an understanding of surface reaction chemistry

NASA Astrophysics Data System (ADS)

Pritchett, David; Henderson, Walter; Burnham, Shawn D.; Doolittle, W. Alan

2006-04-01

The surface reaction byproducts during the growth of GaN films via metal organic molecular beam epitaxy (MOMBE) were investigated as a means to optimize material properties. Ethylene and ethane were identified as the dominant surface reaction hydrocarbon byproducts, averaging 27.63% and 7.15% of the total gas content present during growth. Intense ultraviolet (UV) photoexcitation during growth was found to significantly increase the abundance of ethylene and ethane while reducing the presence of H2 and N2. At 920°C, UV excitation was shown to enhance growth rate and crystalline quality while reducing carbon incorporation. Over a limited growth condition range, a 4.5×1019-3.4×1020 cm-3 variation in carbon incorporation was achieved at constant high vacuum. Coupled with growth rate gains, UV excitation yielded films with ˜58% less integrated carbon content. Structural material property variations are reported for various ammonia flows and growth temperatures. The results suggest that high carbon incorporation can be achieved and regulated during MOMBE growth and that in-situ optimization through hydrocarbon analysis may provide further enhancement in the allowable carbon concentration range.

Gallium arsenide based surface plasmon resonance for glucose monitoring

NASA Astrophysics Data System (ADS)

Patil, Harshada; Sane, Vani; Sriram, G.; Indumathi, T. S; Sharan, Preeta

2015-07-01

The recent trends in the semiconductor and microwave industries has enabled the development of scalable microfabrication technology which produces a superior set of performance as against its counterparts. Surface Plasmon Resonance (SPR) based biosensors are a special class of optical sensors that become affected by electromagnetic waves. It is found that bio-molecular recognition element immobilized on the SPR sensor surface layer reveals a characteristic interaction with various sample solutions during the passage of light. The present work revolves around developing painless glucose monitoring systems using fluids containing glucose like saliva, urine, sweat or tears instead of blood samples. Non-invasive glucose monitoring has long been simulated using label free detection mechanisms and the same concept is adapted. In label-free detection, target molecules are not labeled or altered, and are detected in their natural forms. Label-free detection mechanisms involves the measurement of refractive index (RI) change induced by molecular interactions. These interactions relates the sample concentration or surface density, instead of total sample mass. After simulation it has been observed that the result obtained is highly accurate and sensitive. The structure used here is SPR sensor based on channel waveguide. The tools used for simulation are RSOFT FULLWAVE, MEEP and MATLAB etc.

Electrochemical oxygen reduction behavior of selectively deposited platinum atoms on gold nanoparticles.

PubMed

Sarkar, A; Kerr, J B; Cairns, E J

2013-07-22

Carbon-supported Pt@Au "core-shell" nanoparticles with varying surface concentration of platinum atoms have been synthesized using a novel redox-mediated synthesis approach. The synthesis technique allows for a selective deposition of platinum atoms on the surface of prefabricated gold nanoparticles. Energy dispersive spectroscopic analyses in a scanning electron microscope reveal that the platinum to gold atomic ratios are close to the nominal values, validating the synthesis scheme. X-ray diffraction data indicate an un-alloyed structure. The platinum to gold surface atomic ratio determined from cyclic voltammetry and copper under-potential deposition experiments reveal good agreement with the calculated values at low platinum concentration. However, there is an increase in non-uniformity in the deposition process upon increasing the platinum concentration. Koutecky-Levich analysis of the samples indicates a transition of the total number of electrons transferred (n) in the electrochemical oxygen reduction reaction from two to four electrons upon increasing the surface concentration of platinum atoms. Furthermore, the data indicate that isolated platinum atoms can reduce molecular oxygen but via a two-electron route. Moreover, successful four-electron reduction of molecular oxygen requires clusters of platinum atoms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Establishment of a Molecular Serotyping Scheme and a Multiplexed Luminex-Based Array for Enterobacter aerogenes

PubMed Central

Guo, Xi; Wang, Min; Wang, Lu; Wang, Yao; Chen, Tingting; Wu, Pan; Chen, Min; Liu, Bin; Feng, Lu

2018-01-01

Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes. A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results. Further, a multiplex Luminex-based array was developed, and a double-blind test was conducted with 97 clinical specimens from Shanghai, China, to validate our array. The results of these analyses indicated that strains containing PSgc4 and PSgc7 comprised the predominant groups. We then examined 86 publicly available E. aerogenes strain genomes and identified an additional seven novel PSgc types, with PSgc10 being the most abundant type. In total, our study identified 15 PSgc types in E. aerogenes, providing the basis for a molecular serotyping scheme. From these results, differing epidemic patterns were identified between strains that were predominant in different regions. Our study highlights the feasibility and reliability of a serotyping system based on PSgc diversity, and for the first time, presents a molecular serotyping system, as well as an antigenic scheme for E. aerogenes, providing the basis for molecular diagnostics and epidemiological surveillance of this important emerging pathogen. PMID:29616012

Establishment of a Molecular Serotyping Scheme and a Multiplexed Luminex-Based Array for Enterobacter aerogenes.

PubMed

Guo, Xi; Wang, Min; Wang, Lu; Wang, Yao; Chen, Tingting; Wu, Pan; Chen, Min; Liu, Bin; Feng, Lu

2018-01-01

Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes . A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results. Further, a multiplex Luminex-based array was developed, and a double-blind test was conducted with 97 clinical specimens from Shanghai, China, to validate our array. The results of these analyses indicated that strains containing PSgc4 and PSgc7 comprised the predominant groups. We then examined 86 publicly available E. aerogenes strain genomes and identified an additional seven novel PSgc types, with PSgc10 being the most abundant type. In total, our study identified 15 PSgc types in E. aerogenes , providing the basis for a molecular serotyping scheme. From these results, differing epidemic patterns were identified between strains that were predominant in different regions. Our study highlights the feasibility and reliability of a serotyping system based on PSgc diversity, and for the first time, presents a molecular serotyping system, as well as an antigenic scheme for E. aerogenes , providing the basis for molecular diagnostics and epidemiological surveillance of this important emerging pathogen.

Molecular clouds without detectable CO

NASA Technical Reports Server (NTRS)

Blitz, Leo; Bazell, David; Desert, F. Xavier

1990-01-01

The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to ben an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is then only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase

Molecular clouds without detectable CO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blitz, L.; Bazell, D.; Desert, F.X.

1990-03-01

The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to be an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is thenmore » only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase 18 refs.« less

A combined experimental and DFT investigation of disazo dye having pyrazole skeleton

NASA Astrophysics Data System (ADS)

Şener, Nesrin; Bayrakdar, Alpaslan; Kart, Hasan Hüseyin; Şener, İzzet

2017-02-01

Disazo dye containing pyrazole skeleton has been synthesized. The structure of the dye has been confirmed by using FT-IR, 1H NMR, 13C NMR, HRMS spectral technique and elemental analysis. The molecular geometry and infrared spectrum are also calculated by the Density Functional Theory (DFT) employing B3LYP level with 6-311G (d,p) basis set. The chemical shifts calculation for 1H NMR of the title molecule is done by using by Gauge-Invariant Atomic Orbital (GIAO) method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via Gauss Sum 3.0 program. Frontier molecular orbitals such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and molecular electrostatic potential surface on the title molecule are predicted for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical values have been compared.

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Aerosol Optical Depth Retrievals From High-Resolution Commercial Satellite Imagery Over Areas of High Surface Reflectance

NASA Astrophysics Data System (ADS)

Vincent, D. A.; Nielsen, K. E.; Durkee, P. A.; Reid, J. S.

2005-12-01

The advancement and proliferation of high-resolution commercial imaging satellites presents a new opportunity for overland aerosol characterization. Current aerosol optical depth retrieval methods typically fail over areas with high surface reflectance, such as urban areas and deserts, since the upwelling radiance due to scattering by aerosols is small compared to the radiance resulting from surface reflection. The method proposed here uses shadows cast on the surface to exploit the differences between radiance from the adjacent shaded and unshaded areas of the scene. Shaded areas of the scene are primarily illuminated by diffuse irradiance that is scattered downward from the atmosphere, while unshaded areas are illuminated by both diffuse and direct solar irradiance. The first-order difference between the shaded and unshaded areas is the direct component. Given uniform surface reflectance for the shaded and unshaded areas, the difference in reflected radiance measured by a satellite sensor is related to the direct transmission of solar radiation and inversely proportional to total optical depth. Using an iterative approach, surface reflectance and mean aerosol reflectance can be partitioned to refine the retrieved total optical depth. Aerosol optical depth can then be determined from its contribution to the total atmospheric optical depth (following correction for molecular Rayleigh scattering). Intitial results based on QuickBird imagery and AERONET data collected during the United Arab Emirates Unified Aerosol Experiment (UAE2) indicate that aerosol optical depth retrievals are possible in the visible and near-infrared region with an accuracy of ~0.04.

Surface-induced dissociation of methanol cations: A non-ergodic process

DOE PAGES

Shukla, Anil K.

2017-09-01

Here, dissociation of methanol molecular cations, CH 3OH +, to CH 2OH + on collision with a self-assembled monolayer surface of fluorinated alkyl thiol on gold 111 crystal has been studied at 12.5 eV collision energy. Two energetically and spatially distinct processes contribute to the dissociation process: one involving loss of very large amount of energy approaching the initial kinetic energy of the primary ions with scattering of fragment ions over a broad angular range between surface normal and surface parallel while the second process results from small amount of energy loss with fragment ions scattered over a narrow angularmore » range close to the surface parallel. There is a third process with relatively small contribution to total dissociation whose characteristics are very similar to the low energy loss process. Finally, these results demonstrate that surface-induced dissociation of methanol cations via hydrogen loss is non-ergodic.« less

Analysis of fluid film lubrication in artificial hip joint replacements with surfaces of high elastic modulus.

PubMed

Jin, Z M; Dowson, D; Fisher, J

1997-01-01

Lubrication mechanisms and contact mechanics have been analysed for total hip joint replacements made from hard bearing surfaces such as metal-on-metal and ceramic-on-ceramic. A similar analysis for ultra-high molecular weight polyethylene (UHMWPE) against a hard bearing surface has also been carried out and used as a reference. The most important factor influencing the predicted lubrication film thickness has been found to be the radial clearance between the ball and the socket. Full fluid film lubrication may be achieved in these hard/hard bearings provided that the surface finish of the bearing surface and the radial clearance are chosen correctly and maintained. Furthermore, there is a close relation between the predicted contact half width and the predicted lubrication film thickness. Therefore, it is important to analyse the contact mechanics in artificial hip joint replacements. Practical considerations of manufacturing these bearing surfaces have also been discussed.

Surface-induced dissociation of methanol cations: A non-ergodic process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shukla, Anil K.

Here, dissociation of methanol molecular cations, CH 3OH +, to CH 2OH + on collision with a self-assembled monolayer surface of fluorinated alkyl thiol on gold 111 crystal has been studied at 12.5 eV collision energy. Two energetically and spatially distinct processes contribute to the dissociation process: one involving loss of very large amount of energy approaching the initial kinetic energy of the primary ions with scattering of fragment ions over a broad angular range between surface normal and surface parallel while the second process results from small amount of energy loss with fragment ions scattered over a narrow angularmore » range close to the surface parallel. There is a third process with relatively small contribution to total dissociation whose characteristics are very similar to the low energy loss process. Finally, these results demonstrate that surface-induced dissociation of methanol cations via hydrogen loss is non-ergodic.« less

Palladium nanoparticles formed on titanium silicate ETS-10.

PubMed

Lin, Christopher C H; Danaie, Mohsen; Mitlin, David; Kuznicki, Steven M

2011-03-01

We report that surface templated and supported palladium nanoparticles self assemble on ETS-10 type molecular sieve surfaces by simple exchange and activation procedures in the absence of a reductant. This procedure is similar to the one previously reported for silver nanoparticle self assembly on ETS-10. We observed a bimodal distribution with particle sizes ranging from 2-5 and 15-30 nm. This simple, economical method generates high concentrations (approximately 12 wt% of total composite) of uniform, metallic palladium nanoparticles that are multiply twinned and thermally stable making them potentially unique for advanced catalytic and electronic applications.

Separation techniques: Chromatography

PubMed Central

Coskun, Ozlem

2016-01-01

Chromatography is an important biophysical technique that enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis. Proteins can be purified based on characteristics such as size and shape, total charge, hydrophobic groups present on the surface, and binding capacity with the stationary phase. Four separation techniques based on molecular characteristics and interaction type use mechanisms of ion exchange, surface adsorption, partition, and size exclusion. Other chromatography techniques are based on the stationary bed, including column, thin layer, and paper chromatography. Column chromatography is one of the most common methods of protein purification. PMID:28058406

Microeukaryotic diversity in marine environments, an analysis of surface layer sediments from the East Sea.

PubMed

Park, Soo-Je; Park, Byoung-Joon; Pham, Vinh Hoa; Yoon, Dae-No; Kim, Si-Kwan; Rhee, Sung-Keun

2008-06-01

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.

A Ratio of Spore to Viable Organisms: A Case Study of the JPL-SAF Cleanroom

NASA Technical Reports Server (NTRS)

Hendrickson, Ryan; Urbaniak, Camilla; Malli Mohan, Ganesh Babu; Aronson, Heidi; Venkateswaran, Kasthuri

2017-01-01

Spacecraft surfaces that are destined to land on potential life-harboring celestial bodies are required to be rigorously cleaned and continuously monitored for spore bioburden as a proxy for spacecraft cleanliness. The NASA standard assay (NSA), used for spacecraft bioburden estimates, specifically measures spores that are cultivable, aerobic, resistant to heat shock, and grow at 30 C in a nutrient-rich medium. Since the vast majority of microorganisms cannot be cultivated using the NSA, it is necessary to utilize state-of-the art molecular techniques to better understand the presence of all viable microorganisms, not just those measured with the NSA. In this study, the nutrient-deprived low biomass cleanrooms, where spacecraft are assembled, were used as a surrogate for spacecraft surfaces to measure the ratio of NSA spores in relation to the total viable microorganism population in order to make comparisons with the 2006 Space Studies Board (SSB) estimate of 1 spore per approximately 50,000 viable organisms. Ninety-eight surface wipe samples were collected from the Spacecraft Assembly Facility (SAF) cleanroom at the Jet Propulsion Laboratory (JPL) over a 6-month period. The samples were processed and analyzed using classical microbiology along with molecular methodology. Traditional microbiology plating methods were used to determine the cultivable bacterial, fungal, and spore populations. Molecular assays were used to determine the total organisms (TO, dead and live) and the viable organisms (VO, live). The TO was measured using adenosine triphosphate (ATP) and quantitative polymerase chain reaction (qPCR) assays. The VO was measured using internal ATP, propidium monoazide (PMA)-qPCR, and flow cytometry (after staining for viable microorganisms) assays. Based on the results, it was possible to establish a ratio between spore counts and VO for each viability assay. The ATP-based spore to VO ratio ranged from 149-746, and the bacterial PMA-qPCR assay-based ratio ranged from 314-1,491 VO, per spore. The most conservative estimate came from fluorescent-assisted cell sorting (FACS), which estimated the ratio to be 12,091 VO per 1 NSA spore. Since archaeal (less than 1%) and fungal (approximately 2%) populations were negligible, the spore to VO ratios were based on bacterial population estimates. The most conservative ratio from this study can be used as a replacement for the SSB estimate on nutrient-deprived (oligotrophic) desiccated spacecraft surfaces, to estimate the VO from NSA measurements without utilizing state-of-the art molecular methods that are costly and require more biomass than is typically found on spacecraft surfaces.

Optical differential reflectance spectroscopy for photochromic molecules on solid surfaces

NASA Astrophysics Data System (ADS)

Nickel, Fabian; Bernien, Matthias; Lipowski, Uwe; Kuch, Wolfgang

2018-03-01

Optical reflectance of thin adsorbates on solid surfaces is able to reveal fundamental changes of molecular properties compared to bulk systems. The detection of very small changes in the optical reflectance required several technical improvements in the past decades. We present an experimental setup that is capable of high-quality measurements of submonolayers and ultrathin layers of photochromic molecules on surfaces as well as quantifying their isomerization kinetics. By using photomultipliers as detectors, an enhancement of the signal-to-noise ratio by a factor of three with a total reduction of light exposure on the sample by at least four orders of magnitude is achieved. The potential of the experimental setup is demonstrated by a characterization of the photoswitching and thermal switching of a spirooxazine derivate on a bismuth surface.

Diffusion on Cu surfaces

NASA Technical Reports Server (NTRS)

Karimi, Majid

1993-01-01

Understanding surface diffusion is essential in understanding surface phenomena, such as crystal growth, thin film growth, corrosion, physisorption, and chemisorption. Because of its importance, various experimental and theoretical efforts have been directed to understand this phenomena. The Field Ion Microscope (FIM) has been the major experimental tool for studying surface diffusion. FIM have been employed by various research groups to study surface diffusion of adatoms. Because of limitations of the FIM, such studies are only limited to a few surfaces: nickel, platinum, aluminum, iridium, tungsten, and rhodium. From the theoretical standpoint, various atomistic simulations are performed to study surface diffusion. In most of these calculations the Embedded Atom Method (EAM) along with the molecular static (MS) simulation are utilized. The EAM is a semi-empirical approach for modeling the interatomic interactions. The MS simulation is a technique for minimizing the total energy of a system of particles with respect to the positions of its particles. One of the objectives of this work is to develop the EAM functions for Cu and use them in conjunction with the molecular static (MS) simulation to study diffusion of a Cu atom on a perfect as well as stepped Cu(100) surfaces. This will provide a test of the validity of the EAM functions on Cu(100) surface and near the stepped environments. In particular, we construct a terrace-ledge-kink (TLK) model and calculate the migration energies of an atom on a terrace, near a ledge site, near a kink site, and going over a descending step. We have also calculated formation energies of an atom on the bare surface, a vacancy in the surface, a stepped surface, and a stepped-kink surface. Our results are compared with the available experimental and theoretical results.

The chemical evolution of molecular clouds

NASA Technical Reports Server (NTRS)

Iglesias, E.

1977-01-01

The nonequilibrium chemistry of dense molecular clouds (10,000 to 1 million hydrogen molecules per cu cm) is studied in the framework of a model that includes the latest published chemical data and most of the recent theoretical advances. In this model the only important external source of ionization is assumed to be high-energy cosmic-ray bombardment; standard charge-transfer reactions are taken into account as well as reactions that transfer charge from molecular ions to trace-metal atoms. Schemes are proposed for the synthesis of such species as NCO, HNCO, and CN. The role played by adsorption and condensation of molecules on the surface of dust grains is investigated, and effects on the chemical evolution of a dense molecular cloud are considered which result from varying the total density or the elemental abundances and from assuming negligible or severe condensation of gaseous species on dust grains. It is shown that the chemical-equilibrium time scale is given approximately by the depletion times of oxygen and nitrogen when the condensation efficiency is negligible; that this time scale is probably in the range from 1 to 4 million years, depending on the elemental composition and initial conditions in the cloud; and that this time scale is insensitive to variations in the total density.

Drug-polymer interactions at water-crystal interfaces and implications for crystallization inhibition: molecular dynamics simulations of amphiphilic block copolymer interactions with tolazamide crystals.

PubMed

Gao, Yi; Olsen, Kenneth W

2015-07-01

A diblock copolymer, poly(ethylene glycol)-block-poly(lactic acid) (PEG-b-PLA), modulates the crystal growth of tolazamide (TLZ), resulting in a crystal morphology change from needles to plates in aqueous media. To understand this crystal surface drug-polymer interaction, we conducted molecular dynamics simulations on crystal surfaces of TLZ in water containing PEG-b-PLA. A 130-ns simulation of the polymer in a large water box was run before initiating 50 ns simulations with each of the crystal surfaces. The simulations demonstrated differentiated drug-polymer interactions that are consistent with experimental studies. Interaction of PEG-b-PLA with the (001) face occurred more rapidly (≤10 ns) and strongly (total interaction energy of -121.1 kJ/mol/monomer) than that with the (010) face (∼35 ns, -85.4 kJ/mol/monomer). There was little interaction with the (100) face. Hydrophobic and van der Waals (VDW) interactions were the dominant forces, accounting for more than 90% of total interaction energies. It suggests that polymers capable of forming strong hydrophobic and VDW interactions might be more effective in inhibiting crystallization of poorly water-soluble and hydrophobic drugs in aqueous media (such as gastrointestinal fluid) than those with hydrogen-bonding capacities. Such in-depth analysis and understanding facilitate the rational selection of polymers in designing supersaturation-based enabling formulations. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Adsorption of molecular additive onto lead halide perovskite surfaces: A computational study on Lewis base thiophene additive passivation

NASA Astrophysics Data System (ADS)

Zhang, Lei; Yu, Fengxi; Chen, Lihong; Li, Jingfa

2018-06-01

Organic additives, such as the Lewis base thiophene, have been successfully applied to passivate halide perovskite surfaces, improving the stability and properties of perovskite devices based on CH3NH3PbI3. Yet, the detailed nanostructure of the perovskite surface passivated by additives and the mechanisms of such passivation are not well understood. This study presents a nanoscopic view on the interfacial structure of an additive/perovskite interface, consisting of a Lewis base thiophene molecular additive and a lead halide perovskite surface substrate, providing insights on the mechanisms that molecular additives can passivate the halide perovskite surfaces and enhance the perovskite-based device performance. Molecular dynamics study on the interactions between water molecules and the perovskite surfaces passivated by the investigated additive reveal the effectiveness of employing the molecular additives to improve the stability of the halide perovskite materials. The additive/perovskite surface system is further probed via molecular engineering the perovskite surfaces. This study reveals the nanoscopic structure-property relationships of the halide perovskite surface passivated by molecular additives, which helps the fundamental understanding of the surface/interface engineering strategies for the development of halide perovskite based devices.

Thermodynamics of GaN(s)-NH3(v)+N2(v)+H2(v) system - Electronic aspects of the processes at GaN(0001) surface

NASA Astrophysics Data System (ADS)

Kempisty, Pawel; Strak, Pawel; Sakowski, Konrad; Krukowski, Stanislaw

2017-08-01

Comprehensive analysis of GaN(0001) surface in equilibrium with ammonia/hydrogen mixture was undertaken using results of ab initio calculations. Adsorption energies of the species derived from ammonia and molecular hydrogen and their stable sites were obtained. It was shown that the adsorption process type and energy depend on the position of Fermi level at the surface. Hydrogen decomposes into two separate H atoms, always adsorbed in the positions on top of the surface Ga atoms (On-top). Ammonia adsorption at GaN(0001) surface proceeds molecularly to ammonia in the On-top position or dissociatively into NH2 radicals in bridge (NH2-bridge) or On-top positions or into NH radicals in H3 (NH-H3) site. Presence of these species affects Fermi level pinning at the surface due to creation of new surface states. The Fermi level pinning in function of the surface attached species concentration was determined using extended electron counting rule (EECR). Results of ab initio calculations fully proved validity of the EECR predictions. Thermodynamic analysis of the surface in equilibrium with molecular hydrogen and ammonia vapor mixture is made giving the range of ammonia and hydrogen pressures, corresponding to Fermi level pinned at Ga-broken bond state for NH-H3&H and NH3&H and NH2-bridge&H coverage and at VBM for NH3 & H coverage. As the region of Fermi level pinned at Ga broken bond state corresponds to very low pressures, at pressures close to normal, GaN(0001) surface is almost totally covered by H, NH3 and NH2 located in On-top positions. It is also shown however that dominant portion of the hydrogen and ammonia pressures corresponds to Fermi level not pinned. Among them are these corresponding to MOVPE and HVPE growth conditions in which the surface is almost fully covered by NH3, NH2 and H species in On-top positions.

Proton transfer to charged platinum electrodes. A molecular dynamics trajectory study.

PubMed

Wilhelm, Florian; Schmickler, Wolfgang; Spohr, Eckhard

2010-05-05

A recently developed empirical valence bond (EVB) model for proton transfer on Pt(111) electrodes (Wilhelm et al 2008 J. Phys. Chem. C 112 10814) has been applied in molecular dynamics (MD) simulations of a water film in contact with a charged Pt surface. A total of seven negative surface charge densities σ between -7.5 and -18.9 µC cm(-2) were investigated. For each value of σ, between 30 and 84 initial conditions of a solvated proton within a water slab were sampled, and the trajectories were integrated until discharge of a proton occurred on the charged surfaces. We have calculated the mean rates for discharge and for adsorption of solvated protons within the adsorbed water layer in contact with the metal electrode as a function of surface charge density. For the less negative values of σ we observe a Tafel-like exponential increase of discharge rate with decreasing σ. At the more negative values this exponential increase levels off and the discharge process is apparently transport limited. Mechanistically, the Tafel regime corresponds to a stepwise proton transfer: first, a proton is transferred from the bulk into the contact water layer, which is followed by transfer of a proton to the charged surface and concomitant discharge. At the more negative surface charge densities the proton transfer into the contact water layer and the transfer of another proton to the surface and its discharge occur almost simultaneously.

Molecular mobility in the monolayers of foam films stabilized by porcine lung surfactant.

PubMed Central

Lalchev, Z I; Todorov, R K; Christova, Y T; Wilde, P J; Mackie, A R; Clark, D C

1996-01-01

Certain physical properties of a range of foam film types that are believed to exist in vivo in the lung have been investigated. The contribution of different lung surfactant components found in porcine lung surfactant to molecular surface diffusion in the plane of foam films has been investigated for the first time. The influence of the type and thickness of black foam films, temperature, electrolyte concentration, and extract composition on surface diffusion has been studied using the fluorescence recovery after photobleaching technique. Fluorescent phospholipid probe molecules in foam films stabilized by porcine lung surfactant samples or their hydrophobic extracts consisting of surfactant lipids and hydrophobic lung surfactant proteins, SP-B and SP-C, exhibited more rapid diffusion than observed in films of its principal lipid component alone, L-alpha-phosphatidylcholine dipalmitoyl. This effect appears to be due to contributions from minor lipid components present in the total surfactant lipid extracts. The minor lipid components influence the surface diffusion in foam films both by their negative charge and by lowering the phase transition temperature of lung surfactant samples. In contrast, the presence of high concentrations of the hydrophillic surfactant protein A (SP-A) and non-lung-surfactant proteins in the sample reduced the diffusion coefficient (D) of the lipid analog in the adsorbed layer of the films. Hysteresis behavior of D was observed during temperature cycling, with the cooling curve lying above the heating curve. However, in cases where some surface molecular aggregation and surface heterogeneity were observed during cooling, the films became more rigid and molecules at the interfaces became immobilized. The thickness, size, capillary pressure, configuration, and composition of foam films of lung surfactant prepared in vitro support their investigation as realistic structural analogs of the surface films that exist in vivo in the lung. Compared to other models currently in use, foam films provide new opportunities for studying the properties and function of physiologically important alveolar surface films. Images FIGURE 1 FIGURE 2 PMID:8913597

Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single-wall carbon nanotubes.

PubMed

Torres, Ana M; Scheiner, Steve; Roy, Ajit K; Garay-Tapia, Andrés M; Bustamante, John; Kar, Tapas

2016-08-05

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single-walled carbon nanotubes with large molecules, such as polymers and biomolecules, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C18 H32 O2 ), a fatty acid, at the surface of a (10,0) zigzag nanotube is considered for test purposes. Three smaller segmented models have been created from the full (10,0)-LA system and interaction energies were calculated for these models and compared with the full system at different levels of theory, namely ωB97XD, LDA. The success of this SAA is confirmed as the sum of the interaction energies is in very good agreement with the total interaction energy. Besides reducing computational cost, another merit of SAA is an estimation of the contributions from different sections of the large system to the total interaction energy which can be studied in-depth using a higher level of theory to estimate several properties of each segment. On the negative side, bulk properties, such as HOMO-LUMO (highest occupied molecular orbital - lowest occupied molecular orbital) gap, of the entire system cannot be estimated by adding results from segment models. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Atomic to Molecular Transition in the Interstellar Medium

NASA Technical Reports Server (NTRS)

Goldsmith, Paul F.

2012-01-01

Study of H2 in UV and IR continues to surprise us with complexity of excitation state, OPR, and role in astrochemistry. Atomic H in molecular clouds is a very powerful tool suggesting that they are not "young" but that it takes millions of years to convert primarily atomic hydrogen clouds to 99.9% molecular form. Laboratory data suggests that H2 formation is efficient over broader range of temperatures than thought to be the case a few years ago, but range is still limited. Issues of complex grain morphology and surface structure make this a very difficult field in which to obtain definitively meaningful results. Ongoing and future observations of CI and CII will improve our understanding of the structure of clouds, their total mass, and how they have evolved and will continue to do so.

Ions in water: Free energies, surface effects, and geometrical constraints

NASA Astrophysics Data System (ADS)

Herce, Henry David

In this work, we present our results for ion solvation in finite and infinite water clusters. Molecular Dynamic simulations are used to connect the fundamental macroscopic quantities such as free energy, internal energy and entropy with the underlying microscopic description. Molecular dynamics studies complement experimental results and lead to a deeper insight into the solvation and diffusion of ionic species. Beyond its intrinsic interest, the ion solvation problem has practical relevance because of its role as ideal model system with which to construct and test ion-water interaction potentials. The ionic charging free energy is a very sensitive probe for the treatment of electrostatics in any given simulation setting. In this work, we present methods to compute the ionic charging free energy in systems characterized by atomic charges, and higher-order multipoles, mainly dipoles and quadrupoles. The results of these methods under periodic boundary conditions and spherical boundary conditions are then compared. For the treatment of spherical boundary conditions, we introduce a generalization of Gauss' law that links the microscopic variables to the relevant thermodynamic quantities. Ionic solvation in finite clusters is a problem relevant for many areas of chemistry and biology, such as the gas-liquid interface of tropospheric aerosol particles, or the interphase between water and proteins, membranes, etc. Careful evaluations of the free energy, internal energy and entropy are used to address controversial or unresolved issues, related to the underlying physical cause of surface solvation, and the basic assumptions that go with it. Our main conclusions are the following: (i) The main cause of surface solvation of a single ion in a water cluster is both water and ion polarization, coupled to the charge and size of the ion. Interestingly, the total energy of the ion increases near the cluster surface, while the total energy of water decreases. Also, our analysis clearly shows that the cause of surface solvation is not the size of the total water dipole (unless this is too small). (ii) The entropic contribution is the same order of magnitude as the energetic contribution, and therefore cannot be neglected for quantitative results. (iii) A pure energetic analysis can give a qualitative description of the ion position at room temperature. (iv) We have observed surface solvation of a large positive iodine-like ion in a polarizable water cluster, but not in a non-polarizable water cluster.

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis.

PubMed

Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas; Mostofian, Barmak; Smith, Jeremy C

2017-11-03

Deconstruction of cellulose is crucial for the chemical conversion of lignocellulose into fuel/bioproduct precursors. Recently, a water-organosolv cosolvent system (THF-water) has been shown to both phase-separate on cellulose surfaces and partially deconstruct Avicel  (cellulose) in the absence of acid. Here we employ molecular dynamics simulations to determine whether other common water-organosolv cosolvent systems (acetone, ethanol, and γ-valerolactone) exhibit phase separation at cellulose surface and whether this alters a purely physical cellulose dissociation pathway. Despite finding varied degrees of phase-separation of organosolv on cellulose surfaces, physical dissociation is not enhanced. Interestingly, however, the total amount the median water-cellulose contact lifetimes increases for the cosolvent systems in the order of THF > acetone > ethanol > γ-valerolactone. Together our results indicate two points: a purely physical process for deconstruction of cellulose is unlikely for these cosolvents, and in THF-water, unlike γ-valerolactone- (and some concentrations of acetone and ethanol) water cosolvents, a significant fraction of surface water is slowed. This slowing may be of importance in enhancing chemical deconstruction of cellulose, as it permits an increase in potential THF-water-cellulose reactions, even while the amount of water near cellulose is decreased.

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas

Deconstruction of cellulose is crucial for the chemical conversion of lignocellulose into fuel/bioproduct precursors. Recently, a water-organosolv cosolvent system (THF-water) has been shown to both phase-separate on cellulose surfaces and partially deconstruct Avicel (cellulose) in the absence of acid. Here we employ molecular dynamics simulations to determine whether other common water-organosolv cosolvent systems (acetone, ethanol, and γ-valerolactone) exhibit phase separation at cellulose surface and whether this alters a purely physical cellulose dissociation pathway. Despite finding varied degrees of phase-separation of organosolv on cellulose surfaces, physical dissociation is not enhanced. Interestingly, however, the total amount the median water-cellulose contact lifetimes increasesmore » for the cosolvent systems in the order of THF > acetone > ethanol > γ-valerolactone. Together our results indicate two points: a purely physical process for deconstruction of cellulose is unlikely for these cosolvents, and in THF-water, unlike γ-valerolactone- (and some concentrations of acetone and ethanol) water cosolvents, a significant fraction of surface water is slowed. As a result, this slowing may be of importance in enhancing chemical deconstruction of cellulose, as it permits an increase in potential THF-water-cellulose reactions, even while the amount of water near cellulose is decreased.« less

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis

DOE PAGES

Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas; ...

2017-11-03

Deconstruction of cellulose is crucial for the chemical conversion of lignocellulose into fuel/bioproduct precursors. Recently, a water-organosolv cosolvent system (THF-water) has been shown to both phase-separate on cellulose surfaces and partially deconstruct Avicel (cellulose) in the absence of acid. Here we employ molecular dynamics simulations to determine whether other common water-organosolv cosolvent systems (acetone, ethanol, and γ-valerolactone) exhibit phase separation at cellulose surface and whether this alters a purely physical cellulose dissociation pathway. Despite finding varied degrees of phase-separation of organosolv on cellulose surfaces, physical dissociation is not enhanced. Interestingly, however, the total amount the median water-cellulose contact lifetimes increasesmore » for the cosolvent systems in the order of THF > acetone > ethanol > γ-valerolactone. Together our results indicate two points: a purely physical process for deconstruction of cellulose is unlikely for these cosolvents, and in THF-water, unlike γ-valerolactone- (and some concentrations of acetone and ethanol) water cosolvents, a significant fraction of surface water is slowed. As a result, this slowing may be of importance in enhancing chemical deconstruction of cellulose, as it permits an increase in potential THF-water-cellulose reactions, even while the amount of water near cellulose is decreased.« less

Simultaneous multicolor detection system of the single-molecular microbial antigen by total internal reflection fluorescence microscopy with fluorescent nanocrystal quantum dots

NASA Astrophysics Data System (ADS)

Hoshino, Akiyoshi; Fujioka, Kouki; Yamamoto, Mayu; Manabe, Noriyoshi; Yasuhara, Masato; Suzuki, Kazuo; Yamamoto, Kenji

2005-11-01

Immunological diagnostic methods have been widely performed and showed high performance in molecular and cellular biology, molecular imaging, and medical diagnostics. We have developed novel methods for the fluorescent labeling of several antibodies coupled with fluorescent nanocrystals QDs. In this study we demonstrated that two bacterial toxins, diphtheria toxin and tetanus toxin, were detected simultaneously in the same view field of a cover slip by using directly QD-conjugated antibodies. We have succeeded in detecting bacterial toxins by counting luminescent spots on the evanescent field with using primary antibody conjugated to QDs. In addition, each bacterial toxin in the mixture can be separately detected by single excitation laser with emission band pass filters, and simultaneously in situ pathogen quantification was performed by calculating the luminescent density on the surface of the cover slip. Our results demonstrate that total internal reflection fluorescence microscopy (TIRFM) enables us to distinguish each antigen from mixed samples and can simultaneously quantitate multiple antigens by QD-conjugated antibodies. Bioconjugated QDs could have great potentialities for in practical biomedical applications to develop various high-sensitivity detection systems.

Multiscale geometric modeling of macromolecules I: Cartesian representation

NASA Astrophysics Data System (ADS)

Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei

2014-01-01

This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace-Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the polarized curvature, for the prediction of protein binding sites.

Parallel, stochastic measurement of molecular surface area.

PubMed

Juba, Derek; Varshney, Amitabh

2008-08-01

Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface area computation that maps well to the emerging multi-core architectures. Our algorithm is also progressive, providing a rough estimate of surface area immediately and refining this estimate as time goes on. Furthermore, the algorithm generates points on the molecular surface which can be used for point-based rendering. We demonstrate a GPU implementation of our algorithm and show that it compares favorably with several existing molecular surface computation programs, giving fast estimates of the molecular surface area with good accuracy.

Periodic subsystem density-functional theory

NASA Astrophysics Data System (ADS)

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2014-11-01

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn-Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dual approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn-Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.

Periodic subsystem density-functional theory.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2014-11-07

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn-Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dual approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn-Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.

Preparation and evaluation of a macroporous molecularly imprinted hybrid silica monolithic column for recognition of proteins by high performance liquid chromatography.

PubMed

Lin, Zian; Yang, Fan; He, Xiwen; Zhao, Xiaomiao; Zhang, Yukui

2009-12-04

A novel type of macroporous molecularly imprinted hybrid silica monolithic column was first developed for recognition of proteins. The macroporous silica-based monolithic skeleton was synthesized in a 4.6mm i.d. stainless steel column by a mild sol-gel process with methyltrimethoxysilane (MTMS) as a sole precursor, and then vinyl groups were introduced onto the surface of the silica skeleton by chemical modification of gamma-methacryloxypropyltrimethoxysilane (gamma-MAPS). Subsequently, the molecularly imprinted polymer (MIP) coating was copolymerized and anchored onto the surface of the silica monolith. Bovine serum albumin (BSA) and lysozyme (Lyz), which differ greatly in molecular size, isoelectric point, and charge, were representatively selected for imprinted templates to evaluate recognition property of the hybrid silica-based MIP monolith. Some important factors, such as template-monomer molar ratio, total monomer concentration and crosslinking density, were systematically investigated. Under the optimum conditions, the obtained hybrid silica-based MIP monolith showed higher binding affinity for template than its corresponding non-imprinted (NIP) monolith. The imprinted factor (IF) for BSA and Lyz reached 9.07 and 6.52, respectively. Moreover, the hybrid silica-based MIP monolith displayed favorable binding characteristics for template over competitive protein. Compared with the imprinted silica beads for stationary phase and in situ organic polymer-based hydrogel MIP monolith, the hybrid silica MIP monolith exhibited higher recognition, stability and lifetime.

Periodic subsystem density-functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genova, Alessandro; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide

2014-11-07

By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn–Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dualmore » approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn–Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.« less

Remote Sensing of Surface Propagation Parameters: Application of Imagery Simulation Model Results.

DTIC Science & Technology

1982-10-31

total at * 10.6um, while that for water vapor continuum ab- sorption is 75%. While visible radiance data may * xi be useful in predicting visible range...data. In a subsequent study undertaken to investigate the relative wavelength depen- dent effects of atmospheric particulates and water vapor con...humidity dependent variations in non- 2-2 aerosol atmospheric transmission due to molecular absorption by water vapor, and (5) radiative transfer

Translations on Eastern Europe Scientific Affairs No. 549

DTIC Science & Technology

1977-06-21

of gauges for measuring pressure, dimension and special parameters, and may be used at all types of industrial enterprises in any country...occurring in the arteries considerably narrow their lumen up to its complete occlusion obstructing completely the inflow of blood to the tissues of the...years 12 new buildings with a total surface of about 100,000 m should be built for molecular biology, for the sum of 1.4 million zlotys. 36 In

Application of 252Cf plasma desorption mass spectrometry in dental research

NASA Astrophysics Data System (ADS)

Fritsch, Hans-Walter; Schmidt, Lothar; Köhl, Peter; Jungclas, Hartmut; Duschner, Heins

1993-07-01

Topically applied fluorides introduced in dental hygiene products elevate the concentration levels of fluoride in oral fluids and thus also affect chemical reactions of enamel de- and remineralisation. The chemical reactions on the surface of tooth enamel still are a subject of controversy. Here 252Cf-plasma desorption mass spectrometry and argon ion etching are used to analyse the molecular structure of the upper layes of enamel. The mass spectrum of untreated enamel is characterised by a series of cluster ions containing phosphate. It is evident that under certain conditions the molecular structure of the surface enamel is completely transformed by treatment with fluorides. The result of the degradation and precipitation processes is reflected by a total replacement of the phosphate by fluoride in the measured cluster ion distribution. Stepwise etching of the upper layers by Ar+ ions reveals the transition from a nearly pure CaF2 structure to the unchanged composition of the enamel mineral.

Hindered rotation and nuclear spin isomers separation of molecularly chemisorbed H2 on Pd(210)

NASA Astrophysics Data System (ADS)

Arguelles, Elvis F.; Kasai, Hideaki

2018-03-01

We investigated the hindered rotation and nuclear spin isomer separation of H2 on Pd(210) for various pre-adsorbed atomic hydrogen coverages (Θ), by total energy calculations based on density functional theory. Our results revealed that H2 is in the molecularly chemisorbed state and the adsorption is characterized by a highly anisotropic potential energy surface. Further, we found that J = 1 degenerate level splitting is insensitive to the increase in Θ from 1 to 2 ML. This is due to the comparable potential strengths hindering/restricting the polar rotations in both coverages. On a fully H passivated (3 ML) Pd(210), H2 is in a weakly physisorbed state with a negligible potential anisotropy. Our findings suggest that the activation barrier for polar rotational motion does not strongly depend on the adsorption energy but rather on the surface-molecule bond. The estimated rotational state desorption energies show a separation of ortho and para isomers by around 7.0 meV.

Gadolinium-modulated 19F signals from Perfluorocarbon Nanoparticles as a New Strategy for Molecular Imaging

PubMed Central

Neubauer, Anne M.; Myerson, Jacob; Caruthers, Shelton D.; Hockett, Franklin D.; Winter, Patrick M.; Chen, Junjie; Gaffney, Patrick J.; Robertson, J. David; Lanza, Gregory M.; Wickline, Samuel A.

2008-01-01

Recent advances in the design of fluorinated nanoparticles for magnetic resonance molecular imaging have enabled specific detection of 19F nuclei, providing unique and quantifiable spectral signatures. However, a pressing need for signal enhancement exists because the total 19F in imaging voxels is often limited. By directly incorporating a relaxation agent (gadolinium) into the lipid monolayer that surrounds the perfluorocarbon, a marked augmentation of the 19F signal from 200nm nanoparticles was achieved. This design increases the magnetic relaxation rate of the 19F nuclei 4-fold at 1.5 T and effects a 125% increase in signal, an effect which is maintained when they are targeted to human plasma clots. By varying the surface concentration of gadolinium, the relaxation effect can be quantitatively modulated to tailor particle properties. This novel strategy dramatically improves the sensitivity and range of 19F MRI/MRS and forms the basis for designing contrast agents capable of sensing their surface chemistry. PMID:18956457

Substituent influence on the structural, vibrational and electronic properties of 2,5-dihydrothiophene-1,1-dioxide by experimental and DFT methods.

PubMed

Arjunan, V; Thirunarayanan, S; Durga Devi, G; Mohan, S

2015-11-05

Spectroscopic and theoretical quantum chemical studies of 2,5-dihydrothiophene-1,1-dioxide and 3-methyl-2,5-dihydrothiophene-1,1-dioxide have been carried out by FTIR and FT-Raman spectral techniques along with B3LYP methods. The geometry of the compounds have been optimised by B3LYP method with 6-311++G(∗∗) and cc-pVTZ basis sets. The geometrical parameters obtained at B3LYP levels have been compared with the experimental values. Molecular electrostatic potential surface, total electron density distribution and frontier molecular orbital are constructed at B3LYP/cc-pVTZ level to understand the electronic properties. The charge density distribution and sites of chemical reactivity of the molecules have been obtained by mapping electron density isosurface with electrostatic potential surfaces. Natural bond orbital analysis of the molecules are carried out and the occupancies and the atomic hybrid contributions are calculated. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular-dynamics study on characteristics of energy and tangential momentum accommodation coefficients

NASA Astrophysics Data System (ADS)

Yamaguchi, Hiroki; Matsuda, Yu; Niimi, Tomohide

2017-07-01

Gas-surface interaction is studied by the molecular dynamics method to investigate qualitatively characteristics of accommodation coefficients. A large number of trajectories of gas molecules colliding to and scattering from a surface are statistically analyzed to calculate the energy (thermal) accommodation coefficient (EAC) and the tangential momentum accommodation coefficient (TMAC). Considering experimental measurements of the accommodation coefficients, the incident velocities are stochastically sampled to represent a bulk condition. The accommodation coefficients for noble gases show qualitative coincidence with experimental values. To investigate characteristics of these accommodation coefficients in detail, the gas-surface interaction is parametrically studied by varying the molecular mass of gas, the gas-surface interaction strength, and the molecular size of gas, one by one. EAC increases with increasing every parameter, while TMAC increases with increasing the interaction strength, but decreases with increasing the molecular mass and the molecular size. Thus, contradictory results in experimentally measured TMAC for noble gases could result from the difference between the surface conditions employed in the measurements in the balance among the effective parameters of molecular mass, interaction strength, and molecular size, due to surface roughness and/or adsorbed molecules. The accommodation coefficients for a thermo-fluid dynamics field with a temperature difference between gas and surface and a bulk flow at the same time are also investigated.

Prediction of Mass Spectral Response Factors from Predicted Chemometric Data for Druglike Molecules

NASA Astrophysics Data System (ADS)

Cramer, Christopher J.; Johnson, Joshua L.; Kamel, Amin M.

2017-02-01

A method is developed for the prediction of mass spectral ion counts of drug-like molecules using in silico calculated chemometric data. Various chemometric data, including polar and molecular surface areas, aqueous solvation free energies, and gas-phase and aqueous proton affinities were computed, and a statistically significant relationship between measured mass spectral ion counts and the combination of aqueous proton affinity and total molecular surface area was identified. In particular, through multilinear regression of ion counts on predicted chemometric data, we find that log10(MS ion counts) = -4.824 + c 1•PA + c 2•SA, where PA is the aqueous proton affinity of the molecule computed at the SMD(aq)/M06-L/MIDI!//M06-L/MIDI! level of electronic structure theory, SA is the total surface area of the molecule in its conjugate base form, and c 1 and c 2 have values of -3.912 × 10-2 mol kcal-1 and 3.682 × 10-3 Å-2. On a 66-molecule training set, this regression exhibits a multiple R value of 0.791 with p values for the intercept, c 1, and c 2 of 1.4 × 10-3, 4.3 × 10-10, and 2.5 × 10-6, respectively. Application of this regression to an 11-molecule test set provides a good correlation of prediction with experiment ( R = 0.905) albeit with a systematic underestimation of about 0.2 log units. This method may prove useful for semiquantitative analysis of drug metabolites for which MS response factors or authentic standards are not readily available.

Surface functionalization of solid state ultra-high molecular weight polyethylene through chemical grafting

NASA Astrophysics Data System (ADS)

Sherazi, Tauqir A.; Rehman, Tayyiba; Naqvi, Syed Ali Raza; Shaikh, Ahson Jabbar; Shahzad, Sohail Anjum; Abbas, Ghazanfar; Raza, Rizwan; Waseem, Amir

2015-12-01

The surface of ultra-high molecular weight polyethylene (UHMWPE) powder was functionalized with styrene using chemical grafting technique. The grafting process was initiated through radical generation on base polymer matrix in the solid state by sodium thiosulfate, while peroxides formed at radical sites during this process were dissociated by ceric ammonium nitrate. Various factors were optimized and reasonably high level of monomer grafting was achieved, i.e., 15.6%. The effect of different acids as additive and divinyl benzene (DVB) as a cross-linking agent was also studied. Post-grafting sulfonation was conducted to introduce the ionic moieties to the grafted polymer. Ion-exchange capacity (IEC) was measured experimentally and is found to be 1.04 meq g-1, which is in close agreement with the theoretical IEC values. The chemical structure of grafted and functionalized polymer was characterized by attenuated total reflection infrared spectroscopy (ATR-FTIR) and thermal properties were investigated by thermo gravimetric analysis (TGA) and differential scanning calorimetry (DSC). Thermal analysis depicts that the presence of radicals on the polymer chain accelerates the thermal decomposition process. The results signify that the chemical grafting is an effective tool for substantial surface modification and subsequent functionalization of polyethylene.

Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo.

PubMed

Parsons, Neal; Levin, Deborah A; van Duin, Adri C T; Zhu, Tong

2014-12-21

The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(Σg+1)-N2(Σg+1) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

Surface structures of L10-MnGa (001) by scanning tunneling microscopy and first-principles theory

NASA Astrophysics Data System (ADS)

Corbett, J. P.; Guerrero-Sanchez, J.; Richard, A. L.; Ingram, D. C.; Takeuchi, N.; Smith, A. R.

2017-11-01

We report on the surface reconstructions of L10-ordered MnGa (001) thin films grown by molecular beam epitaxy on a 50 nm Mn3N2 (001) layer freshly grown on a magnesium oxide (001) substrate. Scanning tunneling microscopy, Auger electron spectroscopy, and reflection high energy electron diffraction are combined with first-principles density functional theory calculations to determine the reconstructions of the L10-ordered MnGa (001) surface. We find two lowest energy reconstructions of the MnGa (001) face: a 1 × 1 Ga-terminated structure and a 1 × 2 structure with a Mn replacing a Ga in the 1 × 1 Ga-terminated surface. The 1 × 2 reconstruction forms a row structure along [100]. The manganese:gallium stoichiometry within the surface based on theoretical modeling is in good agreement with experiment. Magnetic moment calculations for the two lowest energy structures reveal important surface and bulk effects leading to oscillatory total magnetization for ultra-thin MnGa (001) films.

Molecular effective coverage surface area of optical clearing agents for predicting optical clearing potential

NASA Astrophysics Data System (ADS)

Feng, Wei; Ma, Ning; Zhu, Dan

2015-03-01

The improvement of methods for optical clearing agent prediction exerts an important impact on tissue optical clearing technique. The molecular dynamic simulation is one of the most convincing and simplest approaches to predict the optical clearing potential of agents by analyzing the hydrogen bonds, hydrogen bridges and hydrogen bridges type forming between agents and collagen. However, the above analysis methods still suffer from some problem such as analysis of cyclic molecule by reason of molecular conformation. In this study, a molecular effective coverage surface area based on the molecular dynamic simulation was proposed to predict the potential of optical clearing agents. Several typical cyclic molecules, fructose, glucose and chain molecules, sorbitol, xylitol were analyzed by calculating their molecular effective coverage surface area, hydrogen bonds, hydrogen bridges and hydrogen bridges type, respectively. In order to verify this analysis methods, in vitro skin samples optical clearing efficacy were measured after 25 min immersing in the solutions, fructose, glucose, sorbitol and xylitol at concentration of 3.5 M using 1951 USAF resolution test target. The experimental results show accordance with prediction of molecular effective coverage surface area. Further to compare molecular effective coverage surface area with other parameters, it can show that molecular effective coverage surface area has a better performance in predicting OCP of agents.

Surface Electrostatic Potential and Water Orientation in the presence of Sodium Octanoate Dilute Monolayers Studied by Means of Molecular Dynamics Simulations.

PubMed

Bernardino, Kalil; de Moura, André F

2015-10-13

A series of atomistic molecular dynamics simulations were performed in the present investigation to assess the spontaneous formation of surfactant monolayers of sodium octanoate at the water-vacuum interface. The surfactant surface coverage increased until a saturation threshold was achieved, after which any further surfactant addition led to the formation of micellar aggregates within the solution. The saturated films were not densely packed, as might be expected for short-chained surfactants, and all films regardless of the surface coverage presented surfactant molecules with the same ordering pattern, namely, with the ionic heads toward the aqueous solution and the tails lying nearly parallel to the interface. The major contributions to the electrostatic surface potential came from the charged heads and the counterion distribution, which nearly canceled out each other. The balance between the oppositely charged ions rendered the electrostatic contributions from water meaningful, amounting to ca. 10% of the contributions arising from the ionic species. And even the aliphatic tails, whose atoms bear relatively small partial atomic charges as compared to the polar molecules and molecular fragments, contributed with ca. 20% of the total electrostatic surface potential of the systems under investigation. Although the aliphatic tails were not so orderly arranged as in a compact film, the C-H bonds assumed a preferential orientation, leading to an increased contribution to the electrostatic properties of the interface. The most prominent feature arising from the partitioning of the electrostatic potential into individual contributions was the long-range ordering of the water molecules. This ordering of the water molecules produced a repulsive dipole-dipole interaction between the two interfaces, which increased with the surface coverage. Only for a water layer wider than 10 nm was true bulk behavior observed, and the repulsive dipole-dipole interaction faded away.

Quantum chemical calculations, molecular dynamic (MD) simulations and experimental studies of using some azo dyes as corrosion inhibitors for iron. Part 2: Bis-azo dye derivatives

NASA Astrophysics Data System (ADS)

Madkour, Loutfy H.; Kaya, Savaş; Guo, Lei; Kaya, Cemal

2018-07-01

The adsorption behavior and inhibition mechanism of five synthesized bis-azo dye (BAD) derivatives on the corrosion of iron in aerated HNO3 and NaOH were investigated by performing potentiostatic polarization, weight loss (WL), thermometric and UV-visible spectra measurements. DFT calculations is applied to study the correlation between corrosion inhibition and global reactivity descriptors such as: EHOMO, ELUMO, molecular gap (ΔE), the dipole moment (μ), the global hardness (η), softness(S), electronegativity (χ), proton affinity (PA), electrophilicity (ω), nucleophilicity (ɛ), electrons transferred from inhibitors to metal surface (ΔN), initial molecule-metal interaction energy (Δψ), total electronic energy (E) and the energy change during electronic back-donation process (ΔEb-d). To mimic the real environment of corrosion inhibition, molecular dynamic (MD) simulations in aqueous phase have also been modelled consisting of all concerned species (inhibitor molecule, H2O, H3O+ ion, NO3- ion, OH- and Fe surface). The results confirmed that BAD molecules inhibit iron by adsorption behavior through donating and accepting electrons together with the formation of [Fe (II) and Fe (III)-BAD] chelate complex compounds. BAD's behavior is mainly chemisorption with some physisorption obeyed Frumkin and that of El-Awady adsorption isotherm. Kinetic parameters such as: (Kb, 1/y, Kads, f, ΔG°ads) have been determined and discussed. Binding energies of BAD molecules on Fe (110) surface followed the order: BAD_ 2 > BAD_ 1 > BAD_ 3 > BAD_ 4 > BAD_ 5. Theoretical results were found to be consistent with the experimental data reported. Our results provide important atomic/molecular insights into the anticorrosive mechanism of inhibitor molecules, which could help in understanding the organic-metal interface and designing more appropriate organic corrosion inhibitors.

Single-Molecule Light-Sheet Imaging of Suspended T Cells.

PubMed

Ponjavic, Aleks; McColl, James; Carr, Alexander R; Santos, Ana Mafalda; Kulenkampff, Klara; Lippert, Anna; Davis, Simon J; Klenerman, David; Lee, Steven F

2018-05-08

Adaptive immune responses are initiated by triggering of the T cell receptor. Single-molecule imaging based on total internal reflection fluorescence microscopy at coverslip/basal cell interfaces is commonly used to study this process. These experiments have suggested, unexpectedly, that the diffusional behavior and organization of signaling proteins and receptors may be constrained before activation. However, it is unclear to what extent the molecular behavior and cell state is affected by the imaging conditions, i.e., by the presence of a supporting surface. In this study, we implemented single-molecule light-sheet microscopy, which enables single receptors to be directly visualized at any plane in a cell to study protein dynamics and organization in live, resting T cells. The light sheet enabled the acquisition of high-quality single-molecule fluorescence images that were comparable to those of total internal reflection fluorescence microscopy. By comparing the apical and basal surfaces of surface-contacting T cells using single-molecule light-sheet microscopy, we found that most coated-glass surfaces and supported lipid bilayers profoundly affected the diffusion of membrane proteins (T cell receptor and CD45) and that all the surfaces induced calcium influx to various degrees. Our results suggest that, when studying resting T cells, surfaces are best avoided, which we achieve here by suspending cells in agarose. Copyright © 2018. Published by Elsevier Inc.

Transient variation of martian ground-atmosphere thermal boundary layer structure.

NASA Technical Reports Server (NTRS)

Pallmann, A. J.; Dannevik, W. P.

1972-01-01

Results of a numerical simulation of the diurnal redistribution of temperature by radiative and molecular-conductive processes in the Martian soil-atmosphere system. An attempt is made to assess the importance of atmospheric molecular conduction near the surface and to estimate the characteristic depth of the diurnal temperature wave. The computational results are found to indicate a dual structure in the diurnal temperature wave propagation pattern, with a diffusive-type wave in the lowest 150 m superimposed on a radiatively induced disturbance with a characteristic scale of 1.8 km. Atmospheric molecular thermal conduction typically accounts for about 15% of the total heating/cooling in the lowest 25 m. Thermal conduction in both the soil and atmosphere appears to be an important factor in the thermal coupling of these subsystems. A free-convection regime in the conduction layer is predicted by the model for about five hours of the Martian day.

Synthesis, tautomeric stability, spectroscopy and computational study of a potential molecular switch of (Z)-4-(phenylamino)pent-3-en-2-one

NASA Astrophysics Data System (ADS)

Fahid, Farzaneh; Kanaani, Ayoub; Pourmousavi, Seied Ali; Ajloo, Davood

2017-04-01

The (Z)-4-(phenylamino) pent-3-en-2-one (PAPO) was synthesised applying carbon-based solid acid and described by experimental techniques. Calculated results reveal that its keto-amine form is more stable than its enol-imine form. A relaxed potential energy surface scan has been accomplished based on the optimised geometry of NH tautomeric form to depict the potential energy barrier related to intramolecular proton transfer. The spectroscopic results and theoretical calculations demonstrate that the intramolecular hydrogen bonding strength of PAPO is stronger than that in 4-amino-3-penten-2-one)APO(. In addition, molecular electrostatic potential, total and partial density of stats (TDOS, PDOS) and non-linear optical properties of the compound were studied using same theoretical calculations. Our calculations show that the title molecule has the potential to be used as molecular switch.

Segregation formation, thermal and electronic properties of ternary cubic CdZnTe clusters: MD simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Kurban, Mustafa; Erkoç, Şakir

2017-04-01

Surface and core formation, thermal and electronic properties of ternary cubic CdZnTe clusters are investigated by using classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations. In this work, MD simulations of the CdZnTe clusters are performed by means of LAMMPS by using bond order potential (BOP). MD simulations are carried out at different temperatures to study the segregation phenomena of Cd, Zn and Te atoms, and deviation of clusters and heat capacity. After that, using optimized geometries obtained, excess charge on atoms, dipole moments, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, HOMO-LUMO gaps (Eg) , total energies, spin density and the density of states (DOS) have been calculated with DFT. Simulation results such as heat capacity and segregation formation are compared with experimental bulk and theoretical results.

Distribution and sources of aliphatic hydrocarbons and fatty acids in surface sediments of a tropical estuary south west coast of India (Cochin estuary).

PubMed

Gireeshkumar, T R; Deepulal, P M; Chandramohanakumar, N

2015-03-01

Surface sediments samples from the Cochin estuary were measured for elemental, stable isotopic and molecular biomarkers (aliphatic hydrocarbons and fatty acids) to study the sources and distribution of sedimentary organic matter. Concentrations of total organic carbon (TOC), total nitrogen (TN) and stable isotopic ratios of carbon (δ(13)C) ranged from 0.62 to 2.74 %, 0.09 to 0.25 % and -27.5 to 21.7 ‰, respectively. Sedimentary n-alkanes ranged from 6.03 to 43.23 μg g(-1) with an average of 16.79 μg g(-1), while total fatty acids varied from 22.55 to 440.69 μg g(-1). The TOC/TN ratios and δ(13)C suggest a mixture of marine- and terrestrial-derived organic matter in the surface sediments with increasing contributions from marine-derived organic matter towards the seaward side. Long-chain n-alkanes derived from higher plants predominated the inner part of the estuary, while short-chain n-alkanes derived from planktonic sources predominated the bar mouth region. The even carbon preference of the C12-C22 n-alkanes may refer to the direct biogenic contribution from bacteria, fungi and yeast species and to the potential direct petroleum inputs. The presence of odd mid-chain n-alkanes in the sediments indicates the organic matter inputs from submerged and floating macrophytes (water hyacinth). Various molecular indices such as carbon preference index, terrestrial to aquatic ratio, average chain length and the ratios of mid-chain n-alkanes support the aforementioned inferences. The high contribution of odd and branched chain fatty acids along with very low contribution of polyunsaturated fatty acids, suggest the effective utilisation of algae-derived organic matter by bacteria and the effective recycling of labile organic matter in whole settling and deposition processes. The distributional variability of n-alkanes and fatty acids reveals the preferential utilisation of marine-derived organic matter and the selective preservation of terrestrial-derived organic matter in surface sediments of the Cochin estuary.

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

PubMed

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Molecular surface mesh generation by filtering electron density map.

PubMed

Giard, Joachim; Macq, Benoît

2010-01-01

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

Molecular switches and motors on surfaces.

PubMed

Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

2013-01-01

Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds.

PubMed

Yu, Li; Sun, Jian; Wang, Qian; Guan, Yan; Zhou, Le; Zhang, Jingxuan; Zhang, Lanying; Yang, Huai

2017-06-01

Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re-encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as "computer hardware", where molecular motors can be reformatted and reprogramed as geometric information. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective scanning tunnelling microscope electron-induced reactions of single biphenyl molecules on a Si(100) surface.

PubMed

Riedel, Damien; Bocquet, Marie-Laure; Lesnard, Hervé; Lastapis, Mathieu; Lorente, Nicolas; Sonnet, Philippe; Dujardin, Gérald

2009-06-03

Selective electron-induced reactions of individual biphenyl molecules adsorbed in their weakly chemisorbed configuration on a Si(100) surface are investigated by using the tip of a low-temperature (5 K) scanning tunnelling microscope (STM) as an atomic size source of electrons. Selected types of molecular reactions are produced, depending on the polarity of the surface voltage during STM excitation. At negative surface voltages, the biphenyl molecule diffuses across the surface in its weakly chemisorbed configuration. At positive surface voltages, different types of molecular reactions are activated, which involve the change of adsorption configuration from the weakly chemisorbed to the strongly chemisorbed bistable and quadristable configurations. Calculated reaction pathways of the molecular reactions on the silicon surface, using the nudge elastic band method, provide evidence that the observed selectivity as a function of the surface voltage polarity cannot be ascribed to different activation energies. These results, together with the measured threshold surface voltages and the calculated molecular electronic structures via density functional theory, suggest that the electron-induced molecular reactions are driven by selective electron detachment (oxidation) or attachment (reduction) processes.

Parallel Decomposition of the Fictitious Lagrangian Algorithm and its Accuracy for Molecular Dynamics Simulations of Semiconductors.

NASA Astrophysics Data System (ADS)

Yeh, Mei-Ling

We have performed a parallel decomposition of the fictitious Lagrangian method for molecular dynamics with tight-binding total energy expression into the hypercube computer. This is the first time in literature that the dynamical simulation of semiconducting systems containing more than 512 silicon atoms has become possible with the electrons treated as quantum particles. With the utilization of the Intel Paragon system, our timing analysis predicts that our code is expected to perform realistic simulations on very large systems consisting of thousands of atoms with time requirements of the order of tens of hours. Timing results and performance analysis of our parallel code are presented in terms of calculation time, communication time, and setup time. The accuracy of the fictitious Lagrangian method in molecular dynamics simulation is also investigated, especially the energy conservation of the total energy of ions. We find that the accuracy of the fictitious Lagrangian scheme in small silicon cluster and very large silicon system simulations is good for as long as the simulations proceed, even though we quench the electronic coordinates to the Born-Oppenheimer surface only in the beginning of the run. The kinetic energy of electrons does not increase as time goes on, and the energy conservation of the ionic subsystem remains very good. This means that, as far as the ionic subsystem is concerned, the electrons are on the average in the true quantum ground states. We also tie up some odds and ends regarding a few remaining questions about the fictitious Lagrangian method, such as the difference between the results obtained from the Gram-Schmidt and SHAKE method of orthonormalization, and differences between simulations where the electrons are quenched to the Born -Oppenheimer surface only once compared with periodic quenching.

Immunochemical Investigations of Cell Surface Antigens of Anaerobic Bacteria

DTIC Science & Technology

1977-01-15

sterile cecal contents were included in all inocula, our data indicates * that cecal contents from germ free rats can be used in place of sterile cecal...The void volume of the column was estimated with blue dextran. Molecular size of the un- digested Pool 1 material was estimated using a PM-30 membrane...51) using bovine serum albumin as a standard. Total sugars were measured by the phenol-sulfuric acid method (52) using glucose as a standards

Young Investigator Program: Tribology of Nanostructured Silicon Carbide for MEMS and NEMS Applications in Extreme Environments

DTIC Science & Technology

2011-02-01

was calculated as the difference between the lowest point of the rigid indenter and the initial position of the sample’s free surface. The total...SiC A high pressure structural phase transformation (HPPT) was previously reported for silicon, gallium arsenide, and silicon nitride and indirect...molecular dynamics (MD) simulations with thermodynamic analysis to settle this debate whether silicon carbide (SiC) can undergo a high pressure phase

Supersonic molecular beam experiments on surface chemical reactions.

PubMed

Okada, Michio

2014-10-01

The interaction of a molecule and a surface is important in various fields, and in particular in complex systems like biomaterials and their related chemistry. However, the detailed understanding of the elementary steps in the surface chemistry, for example, stereodynamics, is still insufficient even for simple model systems. In this Personal Account, I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams demonstrate a significant role of the translational energy of the incident molecules. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths specific for the hyperthermal energy region, and to develop new methods for the fabrication of thin films. On the other hand, oriented molecular beams also demonstrate the possibility of understanding surface chemical reactions in detail by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for finely monitoring the elementary step of the surface chemical reactions and creating new materials on surfaces. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Surface Immobilization of Molecular Electrocatalysts for Energy Conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bullock, R. Morris; Das, Atanu K.; Appel, Aaron M.

2017-03-22

Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical energy and chemical energy. Molecular catalysts offer precise control of their structure, and the ability to modify the substituents to understand structure-reactivity relationships that are more difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. Copper-catalyzed click reactions are often used to form covalent bonds to surfaces, and pi-pi stacking of pyrenemore » substituents appended to the ligand of a molecular complex is a frequently used method to achieve non-covalent surface immobilization. This mini-review highlights surface confinement of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.« less

Electron-stimulated reactions in nanoscale water films adsorbed on (alpha)-Al2O3(0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Nikolay G.; Kimmel, Gregory A.

2018-05-11

The radiation-induced decomposition and desorption of nanoscale amorphous solid water (D2O) films adsorbed on -Al2O3(0001) surface was studied at low temperature in ultrahigh vacuum using temperature programmed desorption (TPD) and electron stimulated desorption (ESD) with a mono-energetic, low energy electron source. ESD yields of molecular products ( D2, O2 and D¬2O) and the total sputtering yield increased with increasing D2O coverage up to ~15 water monolayers (i.e. ~15 1015 cm-2) to a coverage-independent level for thicker water films. Experiments with isotopically-layered water films (D2O and H2O) demonstrated that the highest water decomposition yields occurred at the interfaces of the nanoscalemore » water films with the alumina substrate and vacuum. However, the increased reactivity of the water/alumina interface is relatively small compared to the enhancements in the non-thermal reactions previously observed at the water/Pt(111) and water/TiO2(110) interfaces. We propose that the relatively low activity of Al2O3(0001) for the radiation-induced production of molecular hydrogen is associated with lower reactivity of this surface with hydrogen atoms, which are likely precursors for the molecular hydrogen.« less

Electron-stimulated reactions in nanoscale water films adsorbed on α-Al 2 O 3 (0001)

DOE PAGES

Petrik, Nikolay G.; Kimmel, Greg A.

2018-04-11

The radiation-induced decomposition and desorption of nanoscale amorphous solid water (D 2O) films adsorbed on an α-Al 2O 3(0001) surface was studied at low temperature in ultrahigh vacuum using temperature programmed desorption (TPD) and electron stimulated desorption (ESD) with a mono-energetic, low energy electron source. ESD yields of molecular products (D 2, O 2 and D 2O) and the total sputtering yield increased with increasing D 2O coverage up to ~15 water monolayers (i.e. ~15 x 10 15 cm -2) to a coverage-independent level for thicker water films. Experiments with isotopically-layered water films (D 2O and H 2O) demonstrated thatmore » the highest water decomposition yields occurred at the interfaces of the nanoscale water films with the alumina substrate and vacuum. However, the increased reactivity of the water/alumina interface is relatively small compared to the enhancements in the non-thermal reactions previously observed at the water/Pt(111) and water/TiO 2(110) interfaces. Here, we propose that the relatively low activity of Al 2O 3(0001) for the radiation-induced production of molecular hydrogen is associated with lower reactivity of this surface with hydrogen atoms, which are likely precursors for the formation of molecular hydrogen.« less

Electron-stimulated reactions in nanoscale water films adsorbed on α-Al 2 O 3 (0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Nikolay G.; Kimmel, Greg A.

The radiation-induced decomposition and desorption of nanoscale amorphous solid water (D 2O) films adsorbed on an α-Al 2O 3(0001) surface was studied at low temperature in ultrahigh vacuum using temperature programmed desorption (TPD) and electron stimulated desorption (ESD) with a mono-energetic, low energy electron source. ESD yields of molecular products (D 2, O 2 and D 2O) and the total sputtering yield increased with increasing D 2O coverage up to ~15 water monolayers (i.e. ~15 x 10 15 cm -2) to a coverage-independent level for thicker water films. Experiments with isotopically-layered water films (D 2O and H 2O) demonstrated thatmore » the highest water decomposition yields occurred at the interfaces of the nanoscale water films with the alumina substrate and vacuum. However, the increased reactivity of the water/alumina interface is relatively small compared to the enhancements in the non-thermal reactions previously observed at the water/Pt(111) and water/TiO 2(110) interfaces. Here, we propose that the relatively low activity of Al 2O 3(0001) for the radiation-induced production of molecular hydrogen is associated with lower reactivity of this surface with hydrogen atoms, which are likely precursors for the formation of molecular hydrogen.« less

Interfacial structure of soft matter probed by SFG spectroscopy.

PubMed

Ye, Shen; Tong, Yujin; Ge, Aimin; Qiao, Lin; Davies, Paul B

2014-10-01

Sum frequency generation (SFG) vibrational spectroscopy, an interface-specific technique in contrast to, for example, attenuated total reflectance spectroscopy, which is only interface sensitive, has been employed to investigate the surface and interface structure of soft matter on a molecular scale. The experimental arrangement required to carry out SFG spectroscopy, with particular reference to soft matter, and the analytical methods developed to interpret the spectra are described. The elucidation of the interfacial structure of soft matter systems is an essential prerequisite in order to understand and eventually control the surface properties of these important functional materials. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface hopping trajectory simulations with spin-orbit and dynamical couplings

NASA Astrophysics Data System (ADS)

Granucci, Giovanni; Persico, Maurizio; Spighi, Gloria

2012-12-01

In this paper we consider the inclusion of the spin-orbit interaction in surface hopping molecular dynamics simulations to take into account spin forbidden transitions. Two alternative approaches are examined. The spin-diabatic one makes use of eigenstates of the spin-free electronic Hamiltonian and of hat{S}^2 and is commonly applied when the spin-orbit coupling is weak. We point out some inconsistencies of this approach, especially important when more than two spin multiplets are coupled. The spin-adiabatic approach is based on the eigenstates of the total electronic Hamiltonian including the spin-orbit coupling. Advantages and drawbacks of both strategies are discussed and illustrated with the help of two model systems.

Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

PubMed

Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

2017-06-12

Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Libing; Fu, Li; Wang, Hong-fei

2017-03-14

Significant questions remain with respect to the structure and polymorphs of cellulose. These include the cellulose surface layers and the bulk crystalline core as well as the conformational differences. The Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with the conventional SFG-VS (non-TIR) can help to resolve these questions by selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous; while the surface layers of Iβ cellulose are crystalline but with different structuralmore » and spectroscopic signatures than that of its crystalline core. This work demonstrates the capacity of TIR and Non-TIR SFG-VS tools in selectively studying the structures and polymorphs of cellulose. In addition, these results also suggest that the assignments of major vibrational peaks for cellulose need to be further determined.« less

Texturing of UHMWPE surface via NIL for low friction and wear properties

NASA Astrophysics Data System (ADS)

Suryadi Kustandi, Tanu; Choo, Jian Huei; Low, Hong Yee; Sinha, Sujeet K.

2010-01-01

Wear is a major obstacle limiting the useful life of implanted ultra-high molecular weight polyethylene (UHMWPE) components in total joint arthroplasty. It has been a continuous effort in the implant industry to reduce the frictional wear problem of UHMWPE by improving the structure, morphology and mechanical properties of the polymer. In this paper, a new paradigm that utilizes nanoimprint lithography (NIL) in producing textures on the surface of UHMWPE is proposed to efficiently improve the tribological properties of the polymer. Friction and wear experiments were conducted on patterned and controlled (non-patterned) UHMWPE surfaces using a commercial tribometer, mounted with a silicon nitride ball, under a dry-sliding condition with normal loads ranging from 60 to 200 mN. It has been shown that the patterned UHMWPE surface showed a reduction in the coefficient of friction between 8% and 35% as compared with the controlled (non-patterned) surface, depending on the magnitude of the normal load. Reciprocating wear experiments also showed that the presence of surface textures on the polymer resulted in lower wear depth and width, with minimal material transfer to the sliding surface.

Defining Protein Electrostatic Recognition Processes

DTIC Science & Technology

1989-11-30

of the electrostatic potentiai on the molecular surface of negatively charged Asp-101 in the fifth residue of JH1. the hapten and the V regions of...making and aligning expanded molecular dot surfaces for each molecule and checking these surfaces for interpenetration. The program TURNIP used these...the molecular surfaces are separated by 6 and 12A. All orientations have the exposed heme edge of cytochrome c facing the acidic patch of plastocyanin

ON THE STAR FORMATION LAW FOR SPIRAL AND IRREGULAR GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elmegreen, Bruce G., E-mail: bge@us.ibm.com

2015-12-01

A dynamical model for star formation on a galactic scale is proposed in which the interstellar medium is constantly condensing to star-forming clouds on the dynamical time of the average midplane density, and the clouds are constantly being disrupted on the dynamical timescale appropriate for their higher density. In this model, the areal star formation rate scales with the 1.5 power of the total gas column density throughout the main regions of spiral galaxies, and with a steeper power, 2, in the far outer regions and in dwarf irregular galaxies because of the flaring disks. At the same time, theremore » is a molecular star formation law that is linear in the main and outer parts of disks and in dIrrs because the duration of individual structures in the molecular phase is also the dynamical timescale, canceling the additional 0.5 power of surface density. The total gas consumption time scales directly with the midplane dynamical time, quenching star formation in the inner regions if there is no accretion, and sustaining star formation for ∼100 Gyr or more in the outer regions with no qualitative change in gas stability or molecular cloud properties. The ULIRG track follows from high densities in galaxy collisions.« less

xGASS: total cold gas scaling relations and molecular-to-atomic gas ratios of galaxies in the local Universe

NASA Astrophysics Data System (ADS)

Catinella, Barbara; Saintonge, Amélie; Janowiecki, Steven; Cortese, Luca; Davé, Romeel; Lemonias, Jenna J.; Cooper, Andrew P.; Schiminovich, David; Hummels, Cameron B.; Fabello, Silvia; Geréb, Katinka; Kilborn, Virginia; Wang, Jing

2018-05-01

We present the extended GALEX Arecibo SDSS Survey (xGASS), a gas fraction-limited census of the atomic hydrogen (H I) gas content of 1179 galaxies selected only by stellar mass (M⋆ = 109-1011.5 M⊙) and redshift (0.01 < z < 0.05). This includes new Arecibo observations of 208 galaxies, for which we release catalogues and H I spectra. In addition to extending the GASS H I scaling relations by one decade in stellar mass, we quantify total (atomic+molecular) cold gas fractions and molecular-to-atomic gas mass ratios, Rmol, for the subset of 477 galaxies observed with the IRAM 30 m telescope. We find that atomic gas fractions keep increasing with decreasing stellar mass, with no sign of a plateau down to log M⋆/M⊙ = 9. Total gas reservoirs remain H I-dominated across our full stellar mass range, hence total gas fraction scaling relations closely resemble atomic ones, but with a scatter that strongly correlates with Rmol, especially at fixed specific star formation rate. On average, Rmol weakly increases with stellar mass and stellar surface density μ⋆, but individual values vary by almost two orders of magnitude at fixed M⋆ or μ⋆. We show that, for galaxies on the star-forming sequence, variations of Rmol are mostly driven by changes of the H I reservoirs, with a clear dependence on μ⋆. Establishing if galaxy mass or structure plays the most important role in regulating the cold gas content of galaxies requires an accurate separation of bulge and disc components for the study of gas scaling relations.

Hydrogen retention in lithium and lithium oxide films

NASA Astrophysics Data System (ADS)

Buzi, L.; Yang, Y.; Domínguez-Gutiérrez, F. J.; Nelson, A. O.; Hofman, M.; Krstić, P. S.; Kaita, R.; Koel, B. E.

2018-04-01

Pure lithium (Li) surfaces are difficult to maintain in fusion devices due to rapid oxide formation, therefore, parameterizing and understanding the mechanisms of hydrogen (H, D) retention in lithium oxide (Li2O) in addition to pure Li is crucial for Li plasma-facing material applications. To compare H retention in Li and Li2O films, measurements were made as a function of surface temperature (90-520 K) under ultrahigh vacuum (UHV) conditions using temperature programmed desorption (TPD). In both cases, the total retention dropped with surface temperature, from 95% at 90 K to 35% at 520 K Li2O films retained H in similar amounts as pure Li. Molecular Dynamics (MD) modeling was used to elucidate the mechanisms of H retention, and results were consistent with experiments in terms of both retention fraction and the drop of retention with temperature.

Adsorption and Dissociation of Water on the (0001) Surface of DHCP Americium

NASA Astrophysics Data System (ADS)

Dholabhai, Pratik; Ray, Asok

2009-03-01

Ab initio total energy calculations within the framework of density functional theory have been performed for water molecule adsorption on the (0001) surface of double hexagonal closed packed americium. Subsequent partial dissociation (OH+H) and complete dissociation (H+O+H) of the water molecule have been examined. The completely dissociated configuration exhibits the strongest binding with the surface followed by partially dissociated species, with all molecular H2O configurations showing weak physisorption. The change in work functions and net magnetic moments before and after adsorption will be presented for all the cases studied. The adsorbate-substrate interactions will be elaborated using the difference charge density distributions and the local density of states. The effects of adsorption on Am 5f electron localization-delocalization in the vicinity of the Fermi level will be discussed.

Composition of the atmosphere at the surface of Mars - Detection of argon-36 and preliminary analysis

NASA Technical Reports Server (NTRS)

Owen, T.; Biemann, K.

1976-01-01

The composition of the Martian atmosphere was determined by the mass spectrometer in the molecular analysis experiment. The presence of argon and nitrogen was confirmed and a value of 1 to 2750 plus or minus 500 for the ratio of argon-36 to argon-40 was established. A preliminary interpretation of these results suggests that Mars had a slightly more massive atmosphere in the past, but that much less total outgassing has occurred on Mars than on earth.

High-field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Schmitt-Kopplin, P.

2013-03-01

High-performance, non-target, high-resolution organic structural spectroscopy was applied to solid phase extracted marine dissolved organic matter (SPE-DOM) isolated from four different depths in the open South Atlantic Ocean off the Angola coast (3° E, 18° S; Angola Basin) and provided molecular level information with extraordinary coverage and resolution. Sampling was performed at depths of 5 m (Angola Current; near-surface photic zone), 48 m (Angola Current; fluorescence maximum), 200 m (still above Antarctic Intermediate Water, AAIW; upper mesopelagic zone) and 5446 m (North Atlantic Deep Water, NADW; abyssopelagic, ~30 m above seafloor) and produced SPE-DOM with near 40% carbon yield and beneficial nuclear magnetic resonance (NMR) relaxation properties, a crucial prerequisite for the acquisition of NMR spectra with excellent resolution. 1H and 13C NMR spectra of all four marine SPE-DOM showed smooth bulk envelopes, reflecting intrinsic averaging from massive signal overlap, with a few percent of visibly resolved signatures and variable abundances for all major chemical environments. The abundance of singly oxygenated aliphatics and acetate derivatives in 1H NMR spectra declined from surface to deep marine SPE-DOM, whereas C-based aliphatics and carboxyl-rich alicyclic molecules (CRAM) increased in abundance. Surface SPE-DOM contained fewer methyl esters than all other samples, likely a consequence of direct exposure to sunlight. Integration of 13C NMR spectra revealed continual increase of carboxylic acids and ketones from surface to depth, reflecting a progressive oxygenation, with concomitant decline of carbohydrate-related substructures. Aliphatic branching increased with depth, whereas the fraction of oxygenated aliphatics declined for methine, methylene and methyl carbon. Lipids in the oldest SPE-DOM at 5446 m showed a larger share of ethyl groups and methylene carbon than observed in the other samples. Two-dimensional NMR spectra showed exceptional resolution and depicted resolved molecular signatures in excess of a certain minimum abundance. Classical methyl groups terminating aliphatic chains represented ~15% of total methyl in all samples investigated. A noticeable fraction of methyl (~2%) was bound to olefinic carbon. Methyl ethers were abundant in surface marine SPE-DOM, and the chemical diversity of carbohydrates was larger than that of freshwater and soil DOM. In all samples, we identified sp2-hybridized carbon chemical environments with discrimination of isolated and conjugated olefins and α,β-unsaturated double bonds. Olefinic proton and carbon atoms were more abundant than aromatic ones; olefinic unsaturation in marine SPE-DOM will be more directly traceable to ultimate biogenic precursors than aromatic unsaturation. The abundance of furan, pyrrol and thiophene derivatives was marginal, whereas benzene derivatives, phenols and six-membered nitrogen heterocycles were prominent; a yet unassigned set of six-membered N-heterocycles with likely more than one single nitrogen occurred in all samples. Various key polycyclic aromatic hydrocarbon substructures suggested the presence of thermogenic organic matter at all water depths. Progressive NMR cross-peak attenuation from surface to deep marine SPE-DOM was particularly strong in COSY NMR spectra and indicated a continual disappearance of biosignatures as well as entropy gain from an ever increased molecular diversity. Nevertheless, a specific near-seafloor SPE-DOM signature of unsaturated molecules recognized in both NMR and Fourier transform ion cyclotron mass spectrometry (FTICR/MS) possibly originated from sediment leaching. The conformity of key NMR and FTICR/MS signatures suggested the presence of a large set of identical molecules throughout the entire ocean column even though the investigated water masses belonged to different oceanic regimes and currents. FTICR/MS showed abundant CHO, CHNO, CHOS and CHNOS molecular series with slightly increasing numbers of mass peaks and average mass from surface to bottom SPE-DOM. The proportion of CHO and CHNO negative ions increased from surface to depth, whereas CHOS and especially CHNOS molecular series markedly declined. While certain rather aliphatic CHOS and CHNOS ions were observed solely in the surface, deep marine SPE-DOM was enriched in unique unsaturated and rather oxygenated CHO and CHNO molecular series. With the exception of abyssopelagic SPE-DOM at 5446 m, which showed a peculiar CHOS chemistry of unsaturated carbon and reduced sulphur (black sulphur), CHO and CHNO molecular series contributed ~87% to total positive electrospray ionization FTICR mass peak integral, with a near constant ratio of CHNO / CHO molecular compositions near 1.13 ± 0.05. In case of all four marine SPE-DOM, remarkably disparate average elemental compositions as determined from either MS and NMR spectra were observed, caused by a pronounced ionization selectivity in electrospray ionization FTICR/MS. The study demonstrates that the exhaustive characterization of complex unknowns in marine DOM will enable a meaningful classification of individual marine biogeosignatures. Future in-depth functional biodiversity studies with a clear understanding of DOM structure and function might eventually lead to a novel, unified perception of biodiversity and biogeochemistry.

Molecular simulation insights on the in vacuo adsorption of amino acids on graphene oxide surfaces with varying surface oxygen densities

NASA Astrophysics Data System (ADS)

Rahmani, Farzin; Nouranian, Sasan; Mahdavi, Mina; Al-Ostaz, Ahmed

2016-11-01

In this fundamental study, a series of molecular dynamics simulations were performed in vacuo to investigate the energetics and select geometries of 20 standard amino acids (AAs) on pristine graphene (PG) and graphene oxide (GO) surfaces as a function of graphene surface oxygen density. These interactions are of key interest to graphene/biomolecular systems. Our results indicate that aromatic AAs exhibit the strongest total interactions with the PG surfaces due to π-π stacking. Tryptophan (Trp) has the highest aromaticity due to its indole side chain and, hence, has the strongest interaction among all AAs (-16.66 kcal/mol). Aliphatic, polar, and charged AAs show various levels of affinity to the PG sheets depending on the strength of their side chain hydrophobic interactions. For example, arginine (Arg) with its guanidinium side chain exhibits the strongest interaction with the PG sheets (-13.81 kcal/mol) following aromatic AAs. Also, glycine (Gly; a polar AA) has the weakest interaction with the PG sheets (-7.29 kcal/mol). When oxygen-containing functional groups are added to the graphene sheets, the π-π stacking in aromatic AAs becomes disrupted and perfect parallelism of the aromatic rings is lost. Moreover, hydrogen bonding and/or electrostatic interactions become more pronounced. Charged AAs exhibit the strongest interactions with the GO surfaces. In general, the AA-GO interactions increase with increasing surface oxygen density, and the effect is more pronounced at higher O/C ratios. This study provides a quantitative measure of AA-graphene interactions for the design and tuning of biomolecular systems suitable for biosensing, drug delivery, and gene delivery applications.

Antarctic snow: metals bound to high molecular weight dissolved organic matter.

PubMed

Calace, Nicoletta; Nardi, Elisa; Pietroletti, Marco; Bartolucci, Eugenia; Pietrantonio, Massimiliana; Cremisini, Carlo

2017-05-01

In this paper we studied some heavy metals (Cu, Zn, Cd, Pb, As, U) probably associated to high molecular weight organic compounds present in the Antarctic snow. Snow-pit samples were collected and analysed for high molecular weight fraction and heavy metals bound to them by means of ultrafiltration treatment. High molecular weight dissolved organic matter (HMW-DOM) recovered by ultrafiltration showed a dissolved organic carbon concentration (HMW-DOC) of about 18-83% of the total dissolved organic carbon measured in Antarctic snow. The characterisation of HMW-DOM fraction evidenced an ageing of organic compounds going from surface layers to the deepest ones with a shift from aliphatic compounds and proteins/amino sugars to more high unsaturated character and less nitrogen content. The heavy metals associated to HMW-DOM fraction follows the order: Zn > Cu > Pb > Cd ∼ As ∼ U. The percentage fraction of metals bound to HMW-DOM respect to total metal content follows the order: Cu > Pb > Zn, Cd in agreement with humic substance binding ability (Irwing-William series). Going down to depth of trench, all metals except arsenic, showed a high concentration peak corresponding to 2.0-2.5 m layer. This result was attributed to particular structural characteristic of organic matter able to form different type of complexes (1:1, 1:2, 1:n) with metals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular clumps in the W51 giant molecular cloud

NASA Astrophysics Data System (ADS)

Parsons, H.; Thompson, M. A.; Clark, J. S.; Chrysostomou, A.

2012-08-01

In this paper, we present a catalogue of dense molecular clumps located within the W51 giant molecular cloud (GMC). This work is based on Heterodyne Array Receiver Programme 13CO J = 3-2 observations of the W51 GMC and uses the automated CLUMPFIND algorithm to decompose the region into a total of 1575 clumps of which 1130 are associated with the W51 GMC. We clearly see the distinct structures of the W51 complex and the high-velocity stream previously reported. We find the clumps have characteristic diameters of 1.4 pc, excitation temperatures of 12 K, densities of 5.6 × 1021 cm-2, surface densities 0.02 g cm-2 and masses of 90 M⊙. We find a total mass of dense clumps within the GMC of 1.5 × 105 M⊙, with only 1 per cent of the clumps detected by number and 4 per cent by mass found to be supercritical. We find a clump-forming efficiency of 14 ± 1 per cent for the W51 GMC and a supercritical clump-forming efficiency of 0.5-0.5+2.3 per cent. Looking at the clump mass distribution, we find it is described by a single power law with a slope of α=2.4-0.1+0.2 above ˜100 M⊙. By comparing locations of supercritical clumps and young clusters, we see that any future star formation is likely to be located away from the currently active W51A region.

Bidirectional Reflectance Function Measurement of Molecular Contaminant Scattering in the Vacuum Ultraviolet

NASA Technical Reports Server (NTRS)

Herren, Kenneth A.; Gregory, Don A.

2006-01-01

Bi-directional reflectance distribution function (BRDF) measurements of optical surfaces both before and after molecular contamination were done using UV, VUV and visible light. Molecular contamination of optical surfaces from outgassed material has been shown in many cases to proceed from acclimation centers, and to produce many roughly hemispherical "islands" of contamination on the surface. Vacuum Ultraviolet (VW) wavelengths are used here to measure angularly scattered light from optical surfaces.

First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface

NASA Astrophysics Data System (ADS)

Yang, Yu; Zhang, Ping

2015-05-01

Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.

Surface segregation and surface tension of polydisperse polymer melts.

PubMed

Minnikanti, Venkatachala S; Qian, Zhenyu; Archer, Lynden A

2007-04-14

The effect of polydispersity on surface segregation of a lower molecular weight polymer component in a higher molecular weight linear polymer melt host is investigated theoretically. We show that the integrated surface excess zM of a polymer component of molecular weight M satisfies a simple relation zM=2Ue(M/Mw-1)phiM, where Mw is the weight averaged molecular weight, phiM is the polymer volume fraction, and Ue is the attraction of polymer chain ends to the surface. Ue is principally of entropic origin, but also reflects any energetic preference of chain ends to the surface. We further show that the surface tension gammaM of a polydisperse melt of high molar mass components depends on the number average degree of polymerization Mn as, gammaM=gammainfinity+2UerhobRT/Mn. The parameter gammainfinity is the asymptotic surface tension of an infinitely long polymer of the same chemistry, rhob is the bulk density of the polymer, R is the universal gas constant, and T is the temperature. The predicted gammaM compare favorably with surface tension values obtained from self-consistent field theory simulations that include equation of state effects, which account for changes in polymer density with molecular weight. We also compare the predicted surface tension with available experimental data.

Integrated approach to characterize fouling on a flat sheet membrane gravity driven submerged membrane bioreactor.

PubMed

Fortunato, Luca; Jeong, Sanghyun; Wang, Yiran; Behzad, Ali R; Leiknes, TorOve

2016-12-01

Fouling in membrane bioreactors (MBR) is acknowledged to be complex and unclear. An integrated characterization methodology was employed in this study to understand the fouling on a gravity-driven submerged MBR (GD-SMBR). It involved the use of different analytical tools, including optical coherence tomography (OCT), liquid chromatography with organic carbon detection (LC-OCD), total organic carbon (TOC), flow cytometer (FCM), adenosine triphosphate analysis (ATP) and scanning electron microscopy (SEM). The three-dimensional (3D) biomass morphology was acquired in a real-time through non-destructive and in situ OCT scanning of 75% of the total membrane surface directly in the tank. Results showed that the biomass layer was homogeneously distributed on the membrane surface. The amount of biomass was selectively linked with final destructive autopsy techniques. The LC-OCD analysis indicated the abundance of low molecular weight (LMW) organics in the fouling composition. Three different SEM techniques were applied to investigate the detailed fouling morphology on the membrane. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oxygen dynamics and transport in the Mediterranean sponge Aplysina aerophoba.

PubMed

Hoffmann, Friederike; Røy, Hans; Bayer, Kristina; Hentschel, Ute; Pfannkuchen, Martin; Brümmer, Franz; de Beer, Dirk

2008-01-01

The Mediterranean sponge Aplysina aerophoba kept in aquaria or cultivation tanks can stop pumping for several hours or even days. To investigate changes in the chemical microenvironments, we measured oxygen profiles over the surface and into the tissue of pumping and non-pumping A. aerophoba specimens with Clark-type oxygen microelectrodes (tip diameters 18-30 μm). Total oxygen consumption rates of whole sponges were measured in closed chambers. These rates were used to back-calculate the oxygen distribution in a finite-element model. Combining direct measurements with calculations of diffusive flux and modeling revealed that the tissue of non-pumping sponges turns anoxic within 15 min, with the exception of a 1 mm surface layer where oxygen intrudes due to molecular diffusion over the sponge surface. Molecular diffusion is the only transport mechanism for oxygen into non-pumping sponges, which allows total oxygen consumption rates of 6-12 μmol cm -3  sponge day -1 . Sponges of different sizes had similar diffusional uptake rates, which is explained by their similar surface/volume ratios. In pumping sponges, oxygen consumption rates were between 22 and 37 μmol cm -3  sponge day -1 , and the entire tissue was oxygenated. Combining different approaches of direct oxygen measurement in living sponges with a dynamic model, we can show that tissue anoxia is a direct function of the pumping behavior. The sponge-microbe system of A. aerophoba thus has the possibility to switch actively between aerobic and anaerobic metabolism by stopping the water flow for more than 15 min. These periods of anoxia will greatly influence physiological variety and activity of the sponge microbes. Detailed knowledge about the varying chemical microenvironments in sponges will help to develop protocols to cultivate sponge-associated microbial lineages and improve our understanding of the sponge-microbe-system.

Photoresponsive surface molecularly imprinted polymer on ZnO nanorods for uric acid detection in physiological fluids.

PubMed

Tang, Qian; Li, Zai-Yong; Wei, Yu-Bo; Yang, Xia; Liu, Lan-Tao; Gong, Cheng-Bin; Ma, Xue-Bing; Lam, Michael Hon-Wah; Chow, Cheuk-Fai

2016-09-01

A photoresponsive surface molecularly imprinted polymer for uric acid in physiological fluids was fabricated through a facile and effective method using bio-safe and biocompatible ZnO nanorods as a support. The strategy was carried out by introducing double bonds on the surface of the ZnO nanorods with 3-methacryloxypropyltrimethoxysilane. The surface molecularly imprinted polymer on ZnO nanorods was then prepared by surface polymerization using uric acid as template, water-soluble 5-[(4-(methacryloyloxy)phenyl)diazenyl]isophthalic acid as functional monomer, and triethanolamine trimethacryl ester as cross-linker. The surface molecularly imprinted polymer on ZnO nanorods showed good photoresponsive properties, high recognition ability, and fast binding kinetics toward uric acid, with a dissociation constant of 3.22×10(-5)M in aqueous NaH2PO4 buffer at pH=7.0 and a maximal adsorption capacity of 1.45μmolg(-1). Upon alternate irradiation at 365 and 440nm, the surface molecularly imprinted polymer on ZnO nanorods can quantitatively uptake and release uric acid. Copyright © 2016 Elsevier B.V. All rights reserved.

Cold plasma: A new technology to modify wheat flour functionality

PubMed Central

Bahrami, Niloufar; Bayliss, Danny; Chope, Gemma; Penson, Simon; Perehinec, Tania; Fisk, Ian D.

2016-01-01

Atmospheric pressure cold plasma has the potential to modify biological chemistry and modulate physical surface properties. Wheat flour was treated by low levels of cold plasma (air, 15 V and 20 V) for 60 or 120 s. There was no change in the total aerobic bacterial count or total mould count as a result of treatment. Treatment did not impact the concentration of total non-starch lipids, or non-polar and glycolipids. However, treatment did reduce total free fatty acids and phospholipids and was dose dependent. Oxidation markers (hydroperoxide value and head space n-hexanal) increased with treatment time and voltage, which confirmed the acceleration of lipid oxidation. Total proteins were not significantly influenced by treatment although there was a trend towards higher molecular weight fractions which indicated protein oxidation and treated flour did produce a stronger dough. This study confirms the potential of cold plasma as a tool to modify flour functionality. PMID:26920291

En route to surface-bound electric field-driven molecular motors.

PubMed

Jian, Huahua; Tour, James M

2003-06-27

Four caltrop-shaped molecules that might be useful as surface-bound electric field-driven molecular motors have been synthesized. The caltrops are comprised of a pair of electron donor-acceptor arms and a tripod base. The molecular arms are based on a carbazole or oligo(phenylene ethynylene) core with a strong net dipole. The tripod base uses a silicon atom as its core. The legs of the tripod bear sulfur-tipped bonding units, as acetyl-protected benzylic thiols, for bonding to a gold surface. The geometry of the tripod base allows the caltrop to project upward from a metallic surface after self-assembly. Ellipsometric studies show that self-assembled monolayers of the caltrops are formed on Au surfaces with molecular thicknesses consistent with the desired upright-shaft arrangement. As a result, the zwitterionic molecular arms might be controllable when electric fields are applied around the caltrops, thereby constituting field-driven motors.

A molecular model for ice nucleation and growth, attachment 1

NASA Technical Reports Server (NTRS)

Plummer, P. L. M.

1981-01-01

The quantum mechanical technique is used to study ionic, configurational, and impurity defects in the ice surface. In addition to static calculations of the energetics of the water monomer-ice surface interactions, molecular dynamics studies were initiated. The calculations of the monomer-ice surface interaction, molecular dynamics studies were initiated. The calculations of monomer-ice surface interactions indicate that many adsorption sites exist on the ice surfaces and that the barriers between bonding sites are relatively low. Bonding on the prism face of ice is preferentially above lattice sites.

A comparative study on vibrational, conformational and electronic structure of 2-chloro-4-methyl-3-nitropyridine and 2-chloro-6-methylpyridine

NASA Astrophysics Data System (ADS)

Arjunan, V.; Saravanan, I.; Marchewka, Mariusz K.; Mohan, S.

Experimental FTIR and FT-Raman spectroscopic analysis of 2-chloro-4-methyl-3-nitropyridine (2C4M3NP) and 2-chloro-6-methylpyridine (2C6MP) have been performed. A detailed quantum chemical calculations have been carried out using B3LYP and B3PW91 methods with 6-311++G** and cc-pVTZ basis sets. Conformation analysis was carried for 2C4M3NP and 2C6MP. The temperature dependence of thermodynamic properties has been analysed. The atomic charges, electronic exchange interaction and charge delocalisation of the molecule have been performed by natural bond orbital (NBO) analysis. Molecular electrostatic surface potential (MESP), total electron density distribution and frontier molecular orbitals (FMOs) are constructed at B3LYP/6-311++G** level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecules have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach.

Molecular Characterization of Streptococcus agalactiae Isolates From Pregnant and Non-Pregnant Women at Yazd University Hospital, Iran.

PubMed

Sadeh, Maryam; Firouzi, Roya; Derakhshandeh, Abdollah; Bagher Khalili, Mohammad; Kong, Fanrong; Kudinha, Timothy

2016-02-01

Streptococcus agalactiae (Group B streptococcus, GBS) that colonize the vaginas of pregnant women may occasionally cause neonatal infections. It is one of the most common causes of sepsis and meningitis in neonates and of invasive diseases in pregnant women. It can also cause infectious disease among immunocompromised individuals. The distribution of capsular serotypes and genotypes varies over time and by geographic era. The serotyping and genotyping data of GBS in Iranian pregnant and non-pregnant women seems very limited. The aim of this study was to investigate the GBS ‎molecular capsular serotype ‎and genotype distribution of pregnant and non-pregnant carrier ‎women at Yazd university hospital, in Iran.‎. In this cross-sectional study, a total of 100 GBS strains isolated from 237 pregnant and 413 non-pregnant women were investigated for molecular capsular serotypes and surface protein genes using the multiplex PCR assay. The Chi-square method was used for statistical analysis. Out of 650 samples, 100 (15.4%) were identified as GBS, with a predominance of capsular serotypes III (50%) [III-1 (49), III-3 (1)], followed by II (25%), Ia (12%), V (11%), and Ib (2%), which was similar with another study conducted in Tehran, Iran, but they had no serotype Ia in their report. The surface protein antigen genes distribution was rib (53%), epsilon (38%), alp2/3 (6%), and alpha-c (3%). The determination of serotype and surface proteins of GBS strains distribution would ‎be ‎relevant ‎for the future possible formulation of a GBS vaccine.

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

PubMed Central

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

DOE PAGES

Tringe, J. W.; Ileri, N.; Levie, H. W.; ...

2015-08-01

We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more » Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less

Spectroscopic investigation, hirshfeld surface analysis and molecular docking studies on anti-viral drug entecavir

NASA Astrophysics Data System (ADS)

Fathima Rizwana, B.; Prasana, Johanan Christian; Abraham, Christina Susan; Muthu, S.

2018-07-01

Entecavir, a new deoxyguanine nucleoside analogue, is a selective inhibitor of the replication of the hepatitis B virus. In the present study, Quantum mechanical approach was carried out on the title compound to study the vibrational spectrum, the stability of the compound, the intermolecular and intramolecular interactions by using Density Functional Theory (DFT) with B3LYP 6-311++G(d,p) basis set. The B3LYP/DFT method was chosen because diverse studies have shown that the results obtained with it are in good agreement with those determined by other costly computational methods. The computational methods were aided by the experimental spectroscopic techniques, namely FTIR and FT Raman spectroscopies. The optimized molecular geometry, vibrational wavenumbers, infrared intensities and Raman scattering activities were calculated. The calculated HOMO and LUMO energies were found to be -6.397 eV and -1.504 eV which indicate the charge transfer within the molecule. The maximum absorption wavelength and the band gap energy of the title compound were obtained from the UV absorption spectrum computed theoretically. Natural Bond Orbital analysis has been carried out to explain the charge transfer (or) delocalization of charge due to the intra molecular interactions. The molecule orbital contributions are studied by using the total (TDOS), partial (PDOS), and overlap population (OPDOS) density of states. Molecular electrostatic potential (MEP), First order hyperpolarizability, Hirshfield surface analysis and Fukui functions calculation were also performed. From the calculations the first order hyperpolarizability was found to be 2.3854 × 10-30 esu. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures have been calculated. Molecular docking studies were made on the title compound to study the hydrogen bond interactions and the minimum binding energy was calculated.

The effect of processing on the surface physical stability of amorphous solid dispersions.

PubMed

Yang, Ziyi; Nollenberger, Kathrin; Albers, Jessica; Moffat, Jonathan; Craig, Duncan; Qi, Sheng

2014-11-01

The focus of this study was to investigate the effect of processing on the surface crystallization of amorphous molecular dispersions and gain insight into the mechanisms underpinning this effect. The model systems, amorphous molecular dispersions of felodipine-EUDRAGIT® E PO, were processed both using spin coating (an ultra-fast solvent evaporation based method) and hot melt extrusion (HME) (a melting based method). Amorphous solid dispersions with drug loadings of 10-90% (w/w) were obtained by both processing methods. Samples were stored under 75% RH/room temperatures for up to 10months. Surface crystallization was observed shortly after preparation for the HME samples with high drug loadings (50-90%). Surface crystallization was characterized by powder X-ray diffraction (PXRD), ATR-FTIR spectroscopy and imaging techniques (SEM, AFM and localized thermal analysis). Spin coated molecular dispersions showed significantly higher surface physical stability than hot melt extruded samples. For both systems, the progress of the surface crystal growth followed zero order kinetics on aging. Drug enrichment at the surfaces of HME samples on aging was observed, which may contribute to surface crystallization of amorphous molecular dispersions. In conclusion it was found the amorphous molecular dispersions prepared by spin coating had a significantly higher surface physical stability than the corresponding HME samples, which may be attributed to the increased process-related apparent drug-polymer solubility and reduced molecular mobility due to the quenching effect caused by the rapid solvent evaporation in spin coating. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling Bacteria Surface Acid-Base Properties: The Overprint Of Biology

NASA Astrophysics Data System (ADS)

Amores, D. R.; Smith, S.; Warren, L. A.

2009-05-01

Bacteria are ubiquitous in the environment and are important repositories for metals as well as nucleation templates for a myriad of secondary minerals due to an abundance of reactive surface binding sites. Model elucidation of whole cell surface reactivity simplifies bacteria as viable but static, i.e., no metabolic activity, to enable fits of microbial data sets from models derived from mineral surfaces. Here we investigate the surface proton charging behavior of live and dead whole cell cyanobacteria (Synechococcus sp.) harvested from a single parent culture by acid-base titration using a Fully Optimized ContinUouS (FOCUS) pKa spectrum method. Viability of live cells was verified by successful recultivation post experimentation, whereas dead cells were consistently non-recultivable. Surface site identities derived from binding constants determined for both the live and dead cells are consistent with molecular analogs for organic functional groups known to occur on microbial surfaces: carboxylic (pKa = 2.87-3.11), phosphoryl (pKa = 6.01-6.92) and amine/hydroxyl groups (pKa = 9.56-9.99). However, variability in total ligand concentration among the live cells is greater than those between the live and dead. The total ligand concentrations (LT, mol- mg-1 dry solid) derived from the live cell titrations (n=12) clustered into two sub-populations: high (LT = 24.4) and low (LT = 5.8), compared to the single concentration for the dead cell titrations (LT = 18.8; n=5). We infer from these results that metabolic activity can substantively impact surface reactivity of morphologically identical cells. These results and their modeling implications for bacteria surface reactivities will be discussed.

Water-soluble low-molecular-weight organic acids in automorphic loamy soils of the tundra and taiga zones

NASA Astrophysics Data System (ADS)

Shamrikova, E. V.; Gruzdev, I. V.; Punegov, V. V.; Khabibullina, F. M.; Kubik, O. S.

2013-06-01

The formation features of water-soluble low-molecular-weight organic acids (LMWOAs) in a zonal series of automorphic soils on loose silicate rocks from the middle taiga to the southern tundra (typical podzolic, gley-podzolic, and surface-gley tundra soils) were first revealed by gas chromatography mass spectrometry and gas-liquid chromatography. The content of LMWOAs varies within the range of 1-14 mg/dm3, which corresponds to 1-5% of the total carbon of the water-soluble soil organic matter. It has been shown that a subzonal feature of gley-podzolic soils in the northern taiga is the high content of LMWOAs, including primarily the strongest aliphatic hydroxyl acids. Possible mechanisms of their formation and accumulation in soils have been considered.

Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

PubMed

Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

2014-04-28

Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

Understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates

NASA Technical Reports Server (NTRS)

Etters, R. D.

1985-01-01

Work directed toward understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates is reported. The motivation, apart from expanding our basic knowledge about these systems, was to understand and predict the properties of new materials synthesized at high pressure, including pressure induced metallic and superconducting states. As a consequence, information about the states of matter of the Jovian planets and their satellites, which are natural high pressure laboratories was also provided. The work on molecular surfaces and finite two and three dimensional clusters of atoms and molecules was connected with the composition and behavior of planetary atmospheres and on the processes involved in forming surface layers, which is vital to the development of composite materials and microcircuitry.

Application of a self-organizing map and positive matrix factorization to investigate the spatial distributions and sources of polycyclic aromatic hydrocarbons in soils from Xiangfen County, northern China.

PubMed

Tao, Shi-Yang; Zhong, Bu-Qing; Lin, Yan; Ma, Jin; Zhou, Yongzhang; Hou, Hong; Zhao, Long; Sun, Zaijin; Qin, Xiaopeng; Shi, Huading

2017-07-01

The concentrations of 16 priority polycyclic aromatic hydrocarbons (PAHs) were measured in 128 surface soil samples from Xiangfen County, northern China. The total mass concentration of these PAHs ranged from 52 to 10,524ng/g, with a mean of 723ng/g. Four-ring PAHs contributed almost 50% of the total PAH burden. A self-organizing map and positive matrix factorization were applied to investigate the spatial distribution and source apportionment of PAHs. Three emission sources of PAHs were identified, namely, coking ovens (21.9%), coal/biomass combustion (60.1%), and anthracene oil (18.0%). High concentrations of low-molecular-weight PAHs were particularly apparent in the coking plant zone in the region around Gucheng Town. High-molecular-weight PAHs mainly originated from coal/biomass combustion around Gucheng Town, Xincheng Town, and Taosi Town. PAHs in the soil of Xiangfen County are unlikely to pose a significant cancer risk for the population. Copyright © 2017 Elsevier Inc. All rights reserved.

State-of-the-art molecular approaches to elucidate the genetic inventory of spacecraft surfaces and associated environments

NASA Astrophysics Data System (ADS)

Venkateswaran, Kasthuri; La Duc, Myron; James; Osman, Shariff; Andersen, Gary; Huber, Julie; Sogin, Mitchell

The scientific literature teems with reports of microbial diversity from seemingly every niche imaginable, from deep within Antarctic ice to ocean-floor hydrothermal systems. The fields of applied microbiology and molecular biology have made enormous technological advancements over the past two decades, from the development of PCR-amplification of DNA to the forensic detection of what many consider to be "miniscule" amounts of blood and other such biomatter. Despite advances in the specificity and sensitivity of molecular biological technologies, the abilities to efficiently sample and extract nucleic acids from low-biomass matrices, and accurately describe the true microbial diversity housed in such samples, remain significant challenges. To minimize the likelihood of forward contamination of Mars, Europa, or any other extraterrestrial environment, significant effort is invested to ensure that environments in which spacecraft are assembled are maintained appropriately and kept as free of microbial contamination as possible. To this end, routine analyses, largely based on spore-counts and cultivation-based approaches, are carried out to validate the cleanliness of such surfaces. However, only by applying the most efficient and accurate molecular means of analysis can conclusions be drawn on the actual bioburden and microbial diversity associated with these environments. For any measure of sample-derived bioburden, a large portion is inevitably lost in sampling. Furthermore, a 90 Since the surface area of a spacecraft is fixed, it is not possible to simply increase sample size to improve yield. It is therefore critical to assure that current methods of purification of biomolecules sampled from this limited resource are 1) optimal for achieving total yield of biota present and 2) conserving of the true microbial diversity of the sampled environment. This project focuses on the development of capabilities to effectively and efficiently generate a genetic inventory of microbes present about the surfaces of spacecraft and associated clean-room facilities. This entails the evaluation and optimization of molecular-based strategies designed to assess microbial burden and diversity arising from samples of low biomass. Such strategies include conventional clone library analysis, DNA microarray screening, and V6-Tag Sequencing. The capabilities resulting from this work will enable NASA to establish genetic inventories of spacecraft, as recommended by the National Research Council, to better understand the risk of forward contamination.

Driving and controlling molecular surface rotors with a terahertz electric field.

PubMed

Neumann, Jan; Gottschalk, Kay E; Astumian, R Dean

2012-06-26

Great progress has been made in the design and synthesis of molecular motors and rotors. Loosely inspired by biomolecular machines such as kinesin and the FoF1 ATPsynthase, these molecules are hoped to provide elements for construction of more elaborate structures that can carry out tasks at the nanoscale corresponding to the tasks accomplished by elementary machines in the macroscopic world. Most of the molecular motors synthesized to date suffer from the drawback that they operate relatively slowly (less than kHz). Here we show by molecular dynamics studies of a diethyl sulfide rotor on a gold(111) surface that a high-frequency oscillating electric field normal to the surface can drive directed rotation at GHz frequencies. The maximum directed rotation rate is 10(10) rotations per second, significantly faster than the rotation of previously reported directional molecular rotors. Understanding the fundamental basis of directed motion of surface rotors is essential for the further development of efficient externally driven artificial rotors. Our results represent a step toward the design of a surface-bound molecular rotary motor with a tunable rotation frequency and direction.

The effect of cesium carbonate on 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C{sub 61} aggregation in films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindemann, William R.; Wang, Wenjie; Shinar, Joseph

2014-11-10

Surface-pressure versus molecular area isotherms, X-ray reflectivity, and X-ray near-total reflection fluorescence were used to study the properties of 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C{sub 61} (PCBM) that was pre-mixed with cesium carbonate and spread as a film at the air-water interface. The pre-mixed PCBM with cesium carbonate demonstrated a strikingly strong effect on the organization of the film. Whereas films formed from pure PCBM solution were rough due to strong inter-molecular interactions, the films formed from the mixture were much smoother. This indicates that the cesium carbonate moderates the inter-molecular interactions among PCBM molecules, hinting that the cesium diffusion observed in inverted organic photovoltaicmore » structures and the likely ensuing ionic Cs-PCBM interaction decrease aggregation tendency of PCBM. This implies that the use of cesium salts affects the morphology of the organic layer and consequently improves the efficiency of these devices.« less

Development of self-assembled molecular structures on polymeric surfaces and their applications as ultrasonically responsive barrier coatings for on-demand, pulsatile drug delivery

NASA Astrophysics Data System (ADS)

Kwok, Connie Sau-Kuen

Nature in the form of DNA, proteins, and cells has the remarkable ability to interact with its environment by processing biological information through specific molecular recognition at the interface. As such, materials that are capable of triggering an appropriate biological response need to be engineered at the biomaterial surface. Chemically and structurally well-defined self-assembled monolayers (SAMs), biomimetics of the lipid bilayer in cell membranes, have been created and studied mostly on rigid metallic surfaces. This dissertation is motivated by the lack of methods to generate a molecularly designed surface for biomedical polymers and thus provides an enabling technology to engineer a polymeric surface precisely at a molecular and cellular level. To take this innovation one step further, we demonstrated that such self-assembled molecular structure coated on drug-containing polymeric devices could act as a stimulus-responsive barrier for controlled drug delivery. A simple, one-step procedure for generating ordered, crystalline methylene chains on polymeric surfaces via urethane linkages was successfully developed. The self-assemblies and molecular structures of these crystalline methylene chains are comparable to the SAM model surfaces, as evidenced by various surface characterization techniques (XPS, TOF-SIMS, and FTIR-ATR). For the first time, these self-assembled molecular structures are shown to function collectively as an ultrasound-responsive barrier membrane for pulsatile drug delivery, including delivery of low-molecular-weight ciprofloxacin and high-molecular-weight insulin. Encouraging results, based on the insulin-activated deoxyglucose uptakes in adipocytes, indicate that the released insulin remained biologically active. Both chemical and acoustic analyses suggest that the ultrasound-assisted release mechanism is primarily induced by transient cavitation, which causes temporary disruption of the self-assembled overlayer, and thus allows temporal release of the encapsulated drugs. In addition to acoustic energy, self-assembled surfaces experience order-disorder transition and have a transition temperature higher than body temperature if longer alkyl chains (C18) are used. The C18-assembled surface barrier membrane exhibits a relatively superior impermeable coating than the shorter C12 chains. The versatility of derivatizing the terminal groups of the self-assembled molecular structures is illustrated by attaching poly (ethyleneoxide) oligomers to the alkyl chains to minimize nonspecific protein adsorption. This study lays an important foundation for future work in conjugating other biomolecules to develop surface-based diagnostics and biomaterials. With much success, this original research work of forming self-assembled crystalline structures on synthetic materials still allows for numerous opportunities for new applications and possibly even more new discoveries.

Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

NASA Astrophysics Data System (ADS)

López-Moreno, S.; Romero, A. H.

2015-04-01

Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni.

PubMed

López-Moreno, S; Romero, A H

2015-04-21

Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

Genome Wide assessment of Early Osseointegration in Implant-Adherent Cells

NASA Astrophysics Data System (ADS)

Thalji, Ghadeer N.

Objectives: To determine the molecular processes involved in osseointegration. Materials and methods: A structured literature review concerning in vitro and in vivo molecular assessment of osseointegration was performed. A rat and a human model were then used to identify the early molecular processes involved in osseointegration associated with a micro roughened and nanosurface superimposed featured implants. In the rat model, 32 titanium implants with surface topographies exhibiting a micro roughened (AT-II) and nanosurface superimposed featured implants (AT-I) were placed in the tibiae of 8 rats and subsequently harvested at 2 and 4 days after placement. Whereas in the human model, four titanium mini-implants with either a moderately roughened surface (TiOblast) or super-imposed nanoscale topography (Osseospeed) were placed in edentulous sites of eleven systemically healthy subjects and subsequently removed after 3 and 7 days. Total RNA was isolated from cells adherent to retrieved implants. A whole genome microarray using the Affymetrix 1.1 ST Array platform was used to describe the gene expression profiles that were differentially regulated by the implant surfaces. Results: The literature review provided evidence that particular topographic cues can be specifically integrated among the many extracellular signals received by the cell in its signal transduction network. In the rat model, functionally relevant categories related to ossification, skeletal system development, osteoblast differentiation, bone development and biomineral tissue development were upregulated and more prominent at AT-I compared to AT-II. In the human model, there were no significant differences when comparing the two-implant surfaces at each time point. However, the microarray identified several genes that were differentially regulated at day 7 vs. day 3 for both implant surfaces. Functionally relevant categories related to the extracellular matrix, collagen fibril organization and angiogenesis were upregulated at both surfaces. Abundant upregulation of several differential markers of alternative activated macrophages was also observed. The biological processes involved with the inflammatory/immune response gene expression were concomitantly downregulated. Conclusions: The presence of micro-roughened and nanosurface features modulated in vivo bone response. This work confirms previous evaluations and further implicates modulation of the inflammatory/immune responses as a factor affecting the accrual of bone mass shortly after implant placement.

Atomic force microscopy – looking at mechanosensors on the cell surface

PubMed Central

Heinisch, Jürgen J.; Lipke, Peter N.; Beaussart, Audrey; El Kirat Chatel, Sofiane; Dupres, Vincent; Alsteens, David; Dufrêne, Yves F.

2012-01-01

Summary Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment. However, the way in which these proteins respond to mechanical stimuli and assemble into large complexes remains poorly understood at the molecular level. In the past years, atomic force microscopy (AFM) has revolutionized the way in which biologists analyze cell surface proteins to molecular resolution. In this Commentary, we discuss how the powerful set of advanced AFM techniques (e.g. live-cell imaging and single-molecule manipulation) can be integrated with the modern tools of molecular genetics (i.e. protein design) to study the localization and molecular elasticity of individual mechanosensors on the surface of living cells. Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells. PMID:23077172

Accurate double many-body expansion potential energy surface of HS2A2A‧) by scaling the external correlation

NASA Astrophysics Data System (ADS)

Lu-Lu, Zhang; Yu-Zhi, Song; Shou-Bao, Gao; Yuan, Zhang; Qing-Tian, Meng

2016-05-01

A globally accurate single-sheeted double many-body expansion potential energy surface is reported for the first excited state of HS2 by fitting the accurate ab initio energies, which are calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set. By using the double many-body expansion-scaled external correlation method, such calculated ab initio energies are then slightly corrected by scaling their dynamical correlation. A grid of 2767 ab initio energies is used in the least-square fitting procedure with the total root-mean square deviation being 1.406 kcal·mol-1. The topographical features of the HS2(A2A‧) global potential energy surface are examined in detail. The attributes of the stationary points are presented and compared with the corresponding ab initio results as well as experimental and other theoretical data, showing good agreement. The resulting potential energy surface of HS2(A2A‧) can be used as a building block for constructing the global potential energy surfaces of larger S/H molecular systems and recommended for dynamic studies on the title molecular system. Project supported by the National Natural Science Foundation of China (Grant No. 11304185), the Taishan Scholar Project of Shandong Province, China, the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014AM022), the Shandong Province Higher Educational Science and Technology Program, China (Grant No. J15LJ03), the China Postdoctoral Science Foundation (Grant No. 2014M561957), and the Post-doctoral Innovation Project of Shandong Province, China (Grant No. 201402013).

Surface induced molecular dynamics of thin lipid films confined to submicron cavities: A 1H multiple-quantum NMR study

NASA Astrophysics Data System (ADS)

Jagadeesh, B.; Prabhakar, A.; Demco, D. E.; Buda, A.; Blümich, B.

2005-03-01

The dynamics and molecular order of thin lipid (lecithin) films confined to 200, 100 and 20 nm cylindrical pores with varying surface coverage, were investigated by 1H multiple-quantum NMR. The results show that the molecular dynamics in the surface controlled layers are less hindered compared to those in the bulk. Dynamic heterogeneity among terminal CH 3 groups is evident. Enhanced dynamic freedom is observed for films with area per molecule, ˜ 128 Å 2. The results are discussed in terms of changes in the lipid molecular organization with respect to surface concentration, its plausible motional modes and dynamic heterogeneity.

Hydrogen retention in lithium and lithium oxide films

DOE PAGES

Buzi, L.; Yang, Y.; Dominguez-Gutierrez, F. J.; ...

2018-02-09

Pure lithium (Li) surfaces are difficult to maintain in fusion devices due to rapid oxide formation, therefore, parameterizing and understanding the mechanisms of hydrogen (H, D) retention in lithium oxide (Li 2O) in addition to pure Li is crucial for Li plasma-facing material applications. To compare H retention in Li and Li 2O films, measurements were made as a function of surface temperature (90–520 K) under ultrahigh vacuum (UHV) conditions using temperature programmed desorption (TPD). In both cases, the total retention dropped with surface temperature, from 95% at 90 K to 35% at 520 K Li 2O films retained Hmore » in similar amounts as pure Li. Finally, Molecular Dynamics (MD) modeling was used to elucidate the mechanisms of H retention, and results were consistent with experiments in terms of both retention fraction and the drop of retention with temperature.« less

Hydrogen retention in lithium and lithium oxide films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buzi, L.; Yang, Y.; Dominguez-Gutierrez, F. J.

Pure lithium (Li) surfaces are difficult to maintain in fusion devices due to rapid oxide formation, therefore, parameterizing and understanding the mechanisms of hydrogen (H, D) retention in lithium oxide (Li 2O) in addition to pure Li is crucial for Li plasma-facing material applications. To compare H retention in Li and Li 2O films, measurements were made as a function of surface temperature (90–520 K) under ultrahigh vacuum (UHV) conditions using temperature programmed desorption (TPD). In both cases, the total retention dropped with surface temperature, from 95% at 90 K to 35% at 520 K Li 2O films retained Hmore » in similar amounts as pure Li. Finally, Molecular Dynamics (MD) modeling was used to elucidate the mechanisms of H retention, and results were consistent with experiments in terms of both retention fraction and the drop of retention with temperature.« less

Evaporation and condensation at a liquid surface. I. Argon

NASA Astrophysics Data System (ADS)

Yasuoka, Kenji; Matsumoto, Mitsuhiro; Kataoka, Yosuke

1994-11-01

Molecular dynamics computer simulations were carried out to investigate the dynamics of evaporation and condensation for argon at the temperature of 80 and 100 K. From the decrease of the survival probability of vapor molecules, the ratio of self reflection to collision is estimated to be 12%-15%, only weakly dependent on the temperature. This suggests that argon vapor molecules are in the condition of almost complete capture, and the condensation is considered to be a barrierless process. The total ratio of reflection which is evaluated with the flux correlation of condensation and evaporation is 20% at both temperature. The difference between these two ratios of reflection is ascribed to a phenomenon that vapor molecules colliding with the surface drive out other liquid molecules. This molecule exchange at the surface is as important as the self-reflection, and the conventional picture of condensation as a unimolecular chemical reaction is not appropriate.

Fluorescence excitation and imaging of single molecules near dielectric-coated and bare surfaces: a theoretical study.

PubMed

Axelrod, Daniel

2012-08-01

Microscopic fluorescent samples of interest to cell and molecular biology are commonly embedded in an aqueous medium near a solid surface that is coated with a thin film such as a lipid multilayer, collagen, acrylamide, or a cell wall. Both excitation and emission of fluorescent single molecules near film-coated surfaces are strongly affected by the proximity of the coated surface, the film thickness, its refractive index and the fluorophore's orientation. For total internal reflection excitation, multiple reflections in the film can lead to resonance peaks in the evanescent intensity versus incidence angle curve. For emission, multiple reflections arising from the fluorophore's near field emission can create a distinct intensity pattern in both the back focal plane and the image plane of a high aperture objective. This theoretical analysis discusses how these features can be used to report film thickness and refractive index, and fluorophore axial position and orientation. © 2012 The Author Journal of Microscopy © 2012 Royal Microscopical Society.

Floating stacking faults on the (111) surface of FCC metals: a finite-temperature first-principles study

NASA Astrophysics Data System (ADS)

Rechtsman, Mikael; de Gironcoli, Stefano; Ceder, Gerbrand; Marzari, Nicola

2003-03-01

The (111) surfaces of FCC metals can develop anomalous thermal expansion properties at high temperatures (e.g. for the case of Ag(111)), and display floating stacking faults during homoepitaxial growth in the presence of surfactants. Inspired by the results of high-temperature ensemble-DFT molecular dynamics simulations, we investigate here the relative stability of FCC and HCP stacking in simple and transition metals (Al, Ag, Zn), searching for a structural phase transition taking place at the surface layer in the high-temperature regime. We use a combination of total-energy structural relaxations and linear-response perturbation theory to determine the surface phonon dispersions, and then the relative free energies in the quasi-harmonic approximation. Our results in Al show that the vibrational entropy strongly favors HCP stacking, substantially offsetting the energetic cost of the stacking fault that becomes favored close to the melting temperature. Besides its fundamental interest, HCP phonon softening is relevant in determining the relative stability of small islands during homoeptiaxial growth.

The RMS survey: galactic distribution of massive star formation

NASA Astrophysics Data System (ADS)

Urquhart, J. S.; Figura, C. C.; Moore, T. J. T.; Hoare, M. G.; Lumsden, S. L.; Mottram, J. C.; Thompson, M. A.; Oudmaijer, R. D.

2014-01-01

We have used the well-selected sample of ˜1750 embedded, young, massive stars identified by the Red MSX Source (RMS) survey to investigate the Galactic distribution of recent massive star formation. We present molecular line observations for ˜800 sources without existing radial velocities. We describe the various methods used to assign distances extracted from the literature and solve the distance ambiguities towards approximately 200 sources located within the solar circle using archival H I data. These distances are used to calculate bolometric luminosities and estimate the survey completeness (˜2 × 104 L⊙). In total, we calculate the distance and luminosity of ˜1650 sources, one third of which are above the survey's completeness threshold. Examination of the sample's longitude, latitude, radial velocities and mid-infrared images has identified ˜120 small groups of sources, many of which are associated with well-known star formation complexes, such as G305, G333, W31, W43, W49 and W51. We compare the positional distribution of the sample with the expected locations of the spiral arms, assuming a model of the Galaxy consisting of four gaseous arms. The distribution of young massive stars in the Milky Way is spatially correlated with the spiral arms, with strong peaks in the source position and luminosity distributions at the arms' Galactocentric radii. The overall source and luminosity surface densities are both well correlated with the surface density of the molecular gas, which suggests that the massive star formation rate per unit molecular mass is approximately constant across the Galaxy. A comparison of the distribution of molecular gas and the young massive stars to that in other nearby spiral galaxies shows similar radial dependences. We estimate the total luminosity of the embedded massive star population to be ˜0.76 × 108 L⊙, 30 per cent of which is associated with the 10 most active star-forming complexes. We measure the scaleheight as a function of the Galactocentric distance and find that it increases only modestly from ˜20-30 pc between 4 and 8 kpc, but much more rapidly at larger distances.

Coupling molecular catalysts with nanostructured surfaces for efficient solar fuel production

NASA Astrophysics Data System (ADS)

Jin, Tong

Solar fuel generation via carbon dioxide (CO2) reduction is a promising approach to meet the increasing global demand for energy and to minimize the impact of energy consumption on climate change. However, CO2 is thermodynamically stable; its activation often requires the use of appropriate catalysts. In particular, molecular catalysts with well-defined structures and tunability have shown excellent activity in photochemical CO2 reduction. These homogenous catalysts, however, suffer from poor stability under photochemical conditions and difficulty in recycling from the reaction media. Heterogenized molecular catalysts, particularly those prepared by coupling molecular catalysts with solid-state surfaces, have attracted more attention in recent years as potential solutions to address the issues associated with molecular catalysts. In this work, solar CO2 reduction is investigated using systems coupling molecular catalysts with robust nanostructured surfaces. In Chapter 2, heterogenization of macrocyclic cobalt(III) and nickel (II) complexes on mesoporous silica surface was achieved by different methods. Direct ligand derivatization significantly lowered the catalytic activity of Co(III) complex, while grafting the Co(III) complex onto silica surface through Si-O-Co linkage resulted in hybrid catalysts with excellent activity in CO2 reduction in the presence of p-terphenyl as a molecular photosensitizer. An interesting loading effect was observed, in which the optimal activity was achieved at a medium Co(III) surface density. Heterogenization of the Ni(II) complex on silica surface has also been implemented, the poor photocatalytic activity of the hybrid catalyst can be attributed to the intrinsic nature of the homogeneous analogue. This study highlighted the importance of appropriate linking strategies in preparing functional heterogenized molecular catalysts. Coupling molecular complexes with light-harvesting surfaces could avoid the use of expensive molecular photosensitizers. In Chapter 3, effective coupling of the macrocyclic Co(III) complex with titanium dioxide (TiO¬2) nanoparticles was achieved by two deposition methods. The synthesized hybrid photocatalysts were thoroughly characterized with a variety of techniques. Upon UV light irradiation, photoexcited electrons in TiO2 nanoparticles were transferred to the surface Co(III) catalyst for CO2 reduction. Production of carbon monoxide (CO) from CO2 was confirmed by isotope labeling combined with infrared spectroscopy. Deposition of the Co(III) catalyst through Ti-O-Co linkages was essential for the photo-induced electron transfer and CO2-reduction activity using the hybrid photocatalysts. In Chapter 4, molecular Re(I) and Co(II) catalysts were coupled with silicon-based photoelectrodes, including a silicon nanowire (SiNW) photoelectrode, to achieve photoelectrochemical CO2 reduction. Photovoltages between 300-600 mV were obtained using the molecular catalysts on the silicon photoelectrodes. SiNWs exhibited enhanced properties, including significantly higher photovoltages than a planar silicon photoelectrode, the ability to protect one of the molecular catalysts from photo-induced decomposition, and excellent selectivity towards CO production in CO2 reduction. Recent theoretical and experimental work have demonstrated low-energy, binuclear pathways for CO2-to-CO conversion using several molecular catalysts. In such binuclear pathways, two metal centers work cooperatively to achieve two-electron CO2 reduction. Chapter 5 describes our effort to promote the binuclear pathway by grafting the molecular Co(III) catalyst onto silica surfaces. Different linking strategies were attempted to achieve this goal by planting the surface Co(III) sites in close proximity.

Physical re-examination of parameters on a molecular collisions-based diffusion model for diffusivity prediction in polymers.

PubMed

Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

2011-12-29

Molecular collisions, which are the microscopic origin of molecular diffusive motion, are affected by both the molecular surface area and the distance between molecules. Their product can be regarded as the free space around a penetrant molecule defined as the "shell-like free volume" and can be taken as a characteristic of molecular collisions. On the basis of this notion, a new diffusion theory has been developed. The model can predict molecular diffusivity in polymeric systems using only well-defined single-component parameters of molecular volume, molecular surface area, free volume, and pre-exponential factors. By consideration of the physical description of the model, the actual body moved and which neighbor molecules are collided with are the volume and the surface area of the penetrant molecular core. In the present study, a semiempirical quantum chemical calculation was used to calculate both of these parameters. The model and the newly developed parameters offer fairly good predictive ability. © 2011 American Chemical Society

Prediction of Sliding Friction Coefficient Based on a Novel Hybrid Molecular-Mechanical Model.

PubMed

Zhang, Xiaogang; Zhang, Yali; Wang, Jianmei; Sheng, Chenxing; Li, Zhixiong

2018-08-01

Sliding friction is a complex phenomenon which arises from the mechanical and molecular interactions of asperities when examined in a microscale. To reveal and further understand the effects of micro scaled mechanical and molecular components of friction coefficient on overall frictional behavior, a hybrid molecular-mechanical model is developed to investigate the effects of main factors, including different loads and surface roughness values, on the sliding friction coefficient in a boundary lubrication condition. Numerical modelling was conducted using a deterministic contact model and based on the molecular-mechanical theory of friction. In the contact model, with given external loads and surface topographies, the pressure distribution, real contact area, and elastic/plastic deformation of each single asperity contact were calculated. Then asperity friction coefficient was predicted by the sum of mechanical and molecular components of friction coefficient. The mechanical component was mainly determined by the contact width and elastic/plastic deformation, and the molecular component was estimated as a function of the contact area and interfacial shear stress. Numerical results were compared with experimental results and a good agreement was obtained. The model was then used to predict friction coefficients in different operating and surface conditions. Numerical results explain why applied load has a minimum effect on the friction coefficients. They also provide insight into the effect of surface roughness on the mechanical and molecular components of friction coefficients. It is revealed that the mechanical component dominates the friction coefficient when the surface roughness is large (Rq > 0.2 μm), while the friction coefficient is mainly determined by the molecular component when the surface is relatively smooth (Rq < 0.2 μm). Furthermore, optimal roughness values for minimizing the friction coefficient are recommended.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L-cystine surfaces. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal step sites, thereby articulating a strategy for stone prevention based on molecular design. The second part of this thesis describes the crystal growth and inhibition of a P2X3 receptor antagonist, denoted as DAPSA, recently reported as a non-opioid treatment of chronic pain. The low solubility of this compound results in the formation of drug-induced renal calculi (a.k.a. xenostones). in situ AFM of the morphologically significant (011) DAPSA surface revealed dislocation-actuated growth spirals with an anisotropic morphology, behavior that can be attributed to the non-uniform rate of solute attachment to eight crystallographically unique steps of the spiral, a direct consequence of the dissymmetry of this crystal surface. Eighteen molecular imposters were selected from the screening library to systematically investigate the roles of imposter substitute position, size, and functionality on the step velocities along the eight unique crystallographic directions. A non-uniform reduction in step velocities was observed, signaling site discrimination of imposter binding that can be attributed to stereochemical recognition of the imposters at specific crystal sites. The anisotropy of growth inhibition observed in the presence of the various imposters is consistent with binding energies calculated for the thirty-two crystallographically unique kink sites on steps advancing along predominant growth directions. These results provide insight to the design of growth inhibitors for molecular crystalline solids with complex and dissymmetric surfaces, while also suggesting a strategy for formulations containing congeners that can prevent harmful crystal growth in human renal structures. The last two crystalline systems discussed in this thesis are two isomorphous crystal systems that are ideal for the study of impurity incorporation at dissymmetric surfaces because their morphology is dominated by dissymmetric {101} growth faces. Growth processes on the dissymmetric (101) surfaces of these crystalline systems were investigated using metadynamics simulations to determine the free energy of adsorption for solute and impurity attachment to different flat, stepped, and kinked (101) surface terminations. Results suggest that growth occurs via a non-Kossel crystal growth mechanism, and highlights the need for dissymmetric surface structures (i.e. steps and kinks) for a higher fidelity in the orientation of adsorbed molecules. Overall, the results presented in this thesis suggest that growth of molecular crystals, particularly at dissymmetric surfaces, is complex and requires the combination of several experimental and computational techniques to decipher the mechanisms responsible for growth phenomena. The use of molecular imposters to inhibit growth can be useful for the development of therapeutics for pathological crystals, but can also inform processes by which crystal growth occurs at complex surfaces as a result of their site selectivity.

Adsorption equilibrium and thermodynamics of CO2 and CH4 on carbon molecular sieves

NASA Astrophysics Data System (ADS)

Song, Xue; Wang, Li'ao; Ma, Xu; Zeng, Yunmin

2017-02-01

Carbon molecular sieves (CMS) are widely used in the separation of dioxide carbon and methane. In this research, three commercial CMS were utilized to analyze the pore structure and chemical properties. The adsorption isotherms of CO2 and CH4 were studied at 298 K, 308 K and 318 K over the pressure range of 0-1 MPa by an Intelligent Gravimetric analysis (IGA-100B, UK). Langmuir model was adopted to fit the experimental data. The working capacity and selectivity were employed to evaluate the adsorbents. The adsorption thermodynamics were discussed. The adsorbed amounts of both CO2 and CH4 are found to be highly related with the BET specific surface area and the volume of micropores, and also are interrelated with the total pore volume and micropore surface area. The standard enthalpy change (ΔHΘ), standard Gibbs free energy (ΔGΘ) and standard entropy change (ΔSΘ) at zero surface loading are negative, manifesting the adsorption process is exothermic and spontaneous, and the system tends to be ordered. With the increasing surface coverage, the absolute values of Gibbs free energy (ΔG) decrease whereas the absolute values of enthalpy change (ΔH) and entropy change(ΔS) increase. This indicates that as the adsorbed amount increases, the degree of the spontaneity reduces, the intermolecular forces among the adsorbate molecules increase, the orderliness of the system improves and the adsorbed amount approaches the maximum adsorbed capacity.

Sensing (un)binding events via surface plasmons: effects of resonator geometry

NASA Astrophysics Data System (ADS)

Antosiewicz, Tomasz J.; Claudio, Virginia; Käll, Mikael

2016-04-01

The resonance conditions of localized surface plasmon resonances (LSPRs) can be perturbed in any number ways making plasmon nanoresonators viable tools in detection of e.g. phase changes, pH, gasses, and single molecules. Precise measurement via LSPR of molecular concentrations hinge on the ability to confidently count the number of molecules attached to a metal resonator and ideally to track binding and unbinding events in real-time. These two requirements make it necessary to rigorously quantify relations between the number of bound molecules and response of plasmonic sensors. This endeavor is hindered on the one hand by a spatially varying response of a given plasmonic nanosensor. On the other hand movement of molecules is determined by stochastic effects (Brownian motion) as well as deterministic flow, if present, in microfluidic channels. The combination of molecular dynamics and the electromagnetic response of the LSPR yield an uncertainty which is little understood and whose effect is often disregarded in quantitative sensing experiments. Using a combination of electromagnetic finite-difference time-domain (FDTD) calculations of the plasmon resonance peak shift of various metal nanosensors (disk, cone, rod, dimer) and stochastic diffusion-reaction simulations of biomolecular interactions on a sensor surface we clarify the interplay between position dependent binding probability and inhomogeneous sensitivity distribution. We show, how the statistical characteristics of the total signal upon molecular binding are determined. The proposed methodology is, in general, applicable to any sensor and any transduction mechanism, although the specifics of implementation will vary depending on circumstances. In this work we focus on elucidating how the interplay between electromagnetic and stochastic effects impacts the feasibility of employing particular shapes of plasmonic sensors for real-time monitoring of individual binding reactions or sensing low concentrations - which characteristics make a given sensor optimal for a given task. We also address the issue of how particular illumination conditions affect the level of uncertainty of the measured signal upon molecular binding.

Surface enhanced Raman scattering on Tardigrada--towards monitoring and imaging molecular structures in live cryptobiotic organisms.

PubMed

Kneipp, Harald; Møbjerg, Nadja; Jørgensen, Aslak; Bohr, Henrik G; Hélix-Nielsen, Claus; Kneipp, Janina; Kneipp, Katrin

2013-10-01

Tardigrades are microscopic metazoans which are able to survive extreme physical and chemical conditions by entering a stress tolerant state called cryptobiosis. At present, the molecular mechanisms behind cryptobiosis are still poorly understood. We show that surface enhanced Raman scattering supported by plasmonic gold nanoparticles can measure molecular constituents and their local distribution in live tardigrades. Surface enhanced Raman signatures allow to differentiate between two species and indicate molecular structural differences between tardigrades in water and in a dry state. This opens new avenues for exploring cryptobiosis by studying molecular changes in live cryptobiotic organisms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A molecular catalyst for water oxidation that binds to metal oxide surfaces

PubMed Central

Sheehan, Stafford W.; Thomsen, Julianne M.; Hintermair, Ulrich; Crabtree, Robert H.; Brudvig, Gary W.; Schmuttenmaer, Charles A.

2015-01-01

Molecular catalysts are known for their high activity and tunability, but their solubility and limited stability often restrict their use in practical applications. Here we describe how a molecular iridium catalyst for water oxidation directly and robustly binds to oxide surfaces without the need for any external stimulus or additional linking groups. On conductive electrode surfaces, this heterogenized molecular catalyst oxidizes water with low overpotential, high turnover frequency and minimal degradation. Spectroscopic and electrochemical studies show that it does not decompose into iridium oxide, thus preserving its molecular identity, and that it is capable of sustaining high activity towards water oxidation with stability comparable to state-of-the-art bulk metal oxide catalysts. PMID:25757425

Autonomous molecular cascades for evaluation of cell surfaces

NASA Astrophysics Data System (ADS)

Rudchenko, Maria; Taylor, Steven; Pallavi, Payal; Dechkovskaia, Alesia; Khan, Safana; Butler, Vincent P., Jr.; Rudchenko, Sergei; Stojanovic, Milan N.

2013-08-01

Molecular automata are mixtures of molecules that undergo precisely defined structural changes in response to sequential interactions with inputs. Previously studied nucleic acid-based automata include game-playing molecular devices (MAYA automata) and finite-state automata for the analysis of nucleic acids, with the latter inspiring circuits for the analysis of RNA species inside cells. Here, we describe automata based on strand-displacement cascades directed by antibodies that can analyse cells by using their surface markers as inputs. The final output of a molecular automaton that successfully completes its analysis is the presence of a unique molecular tag on the cell surface of a specific subpopulation of lymphocytes within human blood cells.

PEEK-OPTIMA™ as an alternative to cobalt chrome in the femoral component of total knee replacement: A preliminary study

PubMed Central

Cowie, Raelene M; Briscoe, Adam; Fisher, John; Jennings, Louise M

2016-01-01

PEEK-OPTIMA™ (Invibio Ltd, UK) has been considered as an alternative joint arthroplasty bearing material due to its favourable mechanical properties and the biocompatibility of its wear debris. In this study, the potential to use injection moulded PEEK-OPTIMA™ as an alternative to cobalt chrome in the femoral component of a total knee replacement was investigated in terms of its wear performance. Experimental wear simulation of three cobalt chrome and three PEEK-OPTIMA™ femoral components articulating against all-polyethylene tibial components was carried out under two kinematic conditions: 3 million cycles under intermediate kinematics (maximum anterior-posterior displacement of 5 mm) followed by 3 million cycles under high kinematic conditions (anterior-posterior displacement 10 mm). The wear of the GUR1020 ultra-high-molecular-weight polyethylene tibial components was assessed by gravimetric analysis; for both material combinations under each kinematic condition, the mean wear rates were low, that is, below 5 mm3/million cycles. Specifically, under intermediate kinematic conditions, the wear rate of the ultra-high-molecular-weight polyethylene tibial components was 0.96 ± 2.26 mm3/million cycles and 2.44 ± 0.78 mm3/million cycle against cobalt chrome and PEEK-OPTIMA™ implants, respectively (p = 0.06); under high kinematic conditions, the wear rates were 2.23 ± 1.85 mm3/million cycles and 4.44 ± 2.35 mm3/million cycles, respectively (p = 0.03). Following wear simulation, scratches were apparent on the surface of the PEEK-OPTIMA™ femoral components. The surface topography of the femoral components was assessed using contacting profilometry and showed a statistically significant increase in measured surface roughness of the PEEK-OPTIMA™ femoral components compared to the cobalt chrome implants. However, this did not appear to influence the wear rate, which remained linear over the duration of the study. These preliminary findings showed that PEEK-OPTIMA™ gives promise as an alternative bearing material to cobalt chrome alloy in the femoral component of a total knee replacement with respect to wear performance. PMID:27637723

The Effect of Ag and Ag+N Ion Implantation on Cell Attachment Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urkac, Emel Sokullu; Oztarhan, Ahmet; Gurhan, Ismet Deliloglu

2009-03-10

Implanted biomedical prosthetic devices are intended to perform safely, reliably and effectively in the human body thus the materials used for orthopedic devices should have good biocompatibility. Ultra High Molecular Weight Poly Ethylene (UHMWPE) has been commonly used for total hip joint replacement because of its very good properties. In this work, UHMWPE samples were Ag and Ag+N ion implanted by using the Metal-Vapor Vacuum Arc (MEVVA) ion implantation technique. Samples were implanted with a fluency of 1017 ion/cm2 and extraction voltage of 30 kV. Rutherford Backscattering Spectrometry (RBS) was used for surface studies. RBS showed the presence of Agmore » and N on the surface. Cell attachment properties investigated with model cell lines (L929 mouse fibroblasts) to demonstrate that the effect of Ag and Ag+N ion implantation can favorably influence the surface of UHMWPE for biomedical applications. Scanning electron microscopy (SEM) was used to demonstrate the cell attachment on the surface. Study has shown that Ag+N ion implantation represents more effective cell attachment properties on the UHMWPE surfaces.« less

The primary solar-type atmosphere surrounding the accreting Earth: H2O-induced high surface temperature.

NASA Astrophysics Data System (ADS)

Sasaki, S.

In the solar nebula, a growing planet attracts ambient gas to form a solar-type atmosphere. The structure of this H2-He atmosphere is calculated assuming the Earth was formed in the nebula. The blanketing effect of the atmosphere renders the planetary surface molten when the planetary mass exceeds 0.2 ME (ME being the present Earth's mass). Reduction of the surface melt by atmospheric H2 should add a large amount of H2O to the atmosphere: under the quartz-iron-fayalite oxygen buffer, partial pressure ratio P(H2O)/P(H2) becomes higher than 0.1. Enhancing opacity and gas mean molecular weight, the excess H2O raises the temperature and renders the atmosphere in convective equilibrium, while the dissociation of H2 suppresses the adiabatic temperature gradient. The surface temperature of the proto-Earth can be as high as 4700K when its mass is 1 ME. Such a high temperature may accelerate the evaporation of surface materials. A deep totally-molten magma ocean should exist in the accretion Earth.

Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding.

PubMed

Goldman, Nir; Aradi, Bálint; Lindsey, Rebecca K; Fried, Laurence E

2018-05-08

We detail the creation of a multicenter density functional tight binding (DFTB) model for hydrogen on δ-plutonium, using a framework of new Slater-Koster interaction parameters and a repulsive energy based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES), where two- and three-center atomic interactions are represented by linear combinations of Chebyshev polynomials. We find that our DFTB/ChIMES model yields a total electron density of states for bulk δ-Pu that compares well to that from Density Functional Theory, as well as to a grid of energy calculations representing approximate H 2 dissociation paths on the δ-Pu (100) surface. We then perform molecular dynamics simulations and minimum energy pathway calculations to determine the energetics of surface dissociation and subsurface diffusion on the (100) and (111) surfaces. Our approach allows for the efficient creation of multicenter repulsive energies with a relatively small investment in initial DFT calculations. Our efforts are particularly pertinent to studies that rely on quantum calculations for interpretation and validation, such as experimental determination of chemical reactivity both on surfaces and in condensed phases.

Colloidal gold-modified optical fiber for chemical and biochemical sensing.

PubMed

Cheng, Shu-Fang; Chau, Lai-Kwan

2003-01-01

A novel class of fiber-optic evanescent-wave sensor was constructed on the basis of modification of the unclad portion of an optical fiber with self-assembled gold colloids. The optical properties and, hence, the attenuated total reflection spectrum of self-assembled gold colloids on the optical fiber changes with different refractive index of the environment near the colloidal gold surface. With sucrose solutions of increasing refractive index, the sensor response decreases linearly. The colloidal gold surface was also functionalized with glycine, succinic acid, or biotin to enhance the selectivity of the sensor. Results show that the sensor response decreases linearly with increasing concentration of each analyte. When the colloidal gold surface was functionalized with biotin, the detection limit of the sensor for streptavidin was 9.8 x 10(-11) M. Using this approach, we demonstrate proof-of-concept of a class of refractive index sensor that is sensitive to the refractive index of the environment near the colloidal gold surface and, hence, is suitable for label-free detection of molecular or biomolecular binding at the surface of gold colloids.

Next generation extended Lagrangian first principles molecular dynamics

NASA Astrophysics Data System (ADS)

Niklasson, Anders M. N.

2017-08-01

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Next generation extended Lagrangian first principles molecular dynamics.

PubMed

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

The conformation of the monomethyl ethers of methyl beta-lactoside in D2O and Me2SO-d6 solutions.

PubMed

Fernández, P; Jiménez-Barbero, J

1993-10-04

The solution conformations of all the possible monomethyl ethers of methyl beta-lactoside have been analysed using molecular mechanics and dynamics calculations and nuclear magnetic resonance data (variable temperature and NOE experiments). The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low-energy region with phi = -100 +/- 40 degrees and psi = -135 +/- 35 degrees, which is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides.

Effect of dielectric discontinuity on a spherical polyelectrolyte brush

NASA Astrophysics Data System (ADS)

Tergolina, Vinicius B.; dos Santos, Alexandre P.

2017-09-01

In this paper we perform molecular dynamics simulations of a spherical polyelectrolyte brush and counterions in a salt-free medium. The dielectric discontinuity on the grafted nanoparticle surface is taken into account by the method of image charges. Properties of the polyelectrolyte brush are obtained for different parameters, including valency of the counterions, radius of the nanoparticle, and the brush total charge. The monovalent counterions density profiles are obtained and compared with a simple mean-field theoretical approach. The theory allows us to obtain osmotic properties of the system.

Electrostatically self-assembled polyoxometalates on molecular-dye-functionalized diamond.

PubMed

Zhong, Yu Lin; Ng, Wibowo; Yang, Jia-Xiang; Loh, Kian Ping

2009-12-30

We have successfully immobilized phosphotungstic acid (PTA), a polyoxometalate, on the surface of boron-doped diamond (BDD) surface through electrostatic self-assembly of PTA on pyridinium dye-functionalized-BDD. The inorganic/organic bilayer structure on BDD is found to exhibit fast surface-confined reversible electron transfer. The molecular dye-grafted BDD can undergo controllable electrical stripping and regeneration of PTA which can be useful for electronics or sensing applications. Furthermore, we have demonstrated the use of PTA as a molecular switch in which the direction of photocurrent from diamond to methyl viologen is reversed by the surface bound PTA. Robust photocurrent converter based on such molecular system-diamond platform can operate in corrosive medium which is not tolerated by indium tin oxide electrodes.

MODELING THE INTERACTION OF AGROCHEMICALS WITH ENVIRONMENTAL SURFACES: PESTICIDES ON RUTILE AND ORGANO-RUTILE SURFACES

EPA Science Inventory

Non-bonded interactions between model pesticides and organo-mineral surfaces have been studied using molecular mechanical conformational calculations and molecular dynamics simulations. The minimum energy conformations and relative binding energies for the interaction of atrazine...

Wetting of crystalline polymer surfaces: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Fan, Cun Feng; Caǧin, Tahir

1995-11-01

Molecular dynamics has been used to study the wetting of model polymer surfaces, the crystal surfaces of polyethylene (PE), poly(tetrafluoroethylene) (PTFE), and poly(ethylene terephthalate) (PET) by water and methylene iodide. In the simulation a liquid droplet is placed on a model surface and constant temperature, rigid body molecular dynamics is carried out while the model surface is kept fixed. A generally defined microscopic contact angle between a liquid droplet and a solid surface is quantitatively calculated from the volume of the droplet and the interfacial area between the droplet and the surface. The simulation results agree with the trend in experimental data for both water and methylene iodide. The shape of the droplets on the surface is analyzed and no obvious anisotropy of the droplets is seen in the surface plane, even though the crystal surfaces are highly oriented. The surface free energies of the model polymer surfaces are estimated from their contact angles with the two different liquid droplets.

An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

PubMed

Sahihi, M; Ghayeb, Y

2014-08-01

Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Selective vibrational pumping of molecular hydrogen via gas phase atomic recombination.

PubMed

Esposito, Fabrizio; Capitelli, Mario

2009-12-31

Formation of rovibrational excited molecular hydrogen from atomic recombination has been computationally studied using three body dynamics and orbiting resonance theory. Each of the two methods in the frame of classical mechanics, that has been used for all of the calculations, appear complementary rather than complete, with similar values in the low temperature region, and predominance of three body dynamics for temperatures higher than about 1000 K. The sum of the two contributions appears in fairly good agreement with available data from the literature. Dependence of total recombination on the temperature over pressure ratio is stressed. Detailed recombination toward rovibrational states is presented, with large evidence of importance of rotation in final products. Comparison with gas-surface recombination implying only physiadsorbed molecules shows approximate similarities at T = 5000 K, being on the contrary different at lower temperature.

DFT STUDY OF CO AND NO ADSORPTION ON BORON NITRIDE (BN)n = 3 - 5 NANOCLUSTERS

NASA Astrophysics Data System (ADS)

Zahedi, Ehsan; Pangh, Abdolhakim; Ghorbanpour, Hamed

2015-11-01

Interaction of CO and NO molecules by different orientations on (BN)n=3-5 clusters have been studied at the B3LYP/6-311+G* level of theory. Total electronic energies have been corrected for geometrical counterpoise (gCP) and dispersion (D3) energies at the B3LYP/6-31G* level. Formation of a new sigma bond between the gas and (BN)3 cluster, atom in molecules (AIM) results, density of states spectrums (DOS), molecular electrostatic potential (MEP) surfaces, and visualization of wave function of molecular orbitals in the nearest bonding regions to the Fermi level have confirmed that adsorption of CO by carbon end atom, and NO by nitrogen end atom is covalent in nature, so that the charge transfer is occurred from gas molecule to the cluster.

Saturn Magnetospheric Impact on Surface Molecular Chemistry and Astrobiological Potential of Enceladus

NASA Technical Reports Server (NTRS)

Cooper, Paul D.; Cooper, John F.; Sittler, Edward C.; Burger, Matthew H.; Sturner, Steven J.; Rymer, Abigail M.

2008-01-01

The active south polar surface of Enceladus is exposed to strong chemical processing by direct interaction with charged plasma and energetic particles in the local magnetospheric environment of this icy moon. Chemical oxidation activity is suggested by detection of H202 at the surface in this region and less directly by substantial presence of C02, CO, and N2 in the plume gases. Molecular composition of the uppermost surface, including ejecta from plume activity, is radiolytically transformed mostly by penetrating energetic electrons with lesser effects from more depleted populations of energetic protons. The main sources of molecular plasma ions and E-ring dust grains in the magnetospheric environment are the cryovolcanic plume emissions from Enceladus. These molecular ions and the dust grains are chemically processed by magnetospheric interactions that further impact surface chemistry on return to Enceladus. For example, H20 neutrals dominating the emitted plume gas return to the surface mostly as H30+ ions after magnetospheric processing. Surface oxidant loading is further increased by return of radiolytically processed ice grains from the E-ring. Plume frost deposition and micrometeoroid gardening protect some fraction of newly produced molecular species from destruction by further irradiation. The evident horizontal and vertical mobility of surface ices in the south polar region drive mixing of these processed materials into the moon interior with potential impacts on deep ice molecular chemistry and plume gas production. Similarly as suggested previously for Europa, the externally driven source of radiolytic oxidants could affect evolution of life in any subsurface liquid water environments of Enceladus.

Degradation of organic pollutants in/on snow and ice by singlet molecular oxygen (¹O₂*) and an organic triplet excited state.

PubMed

Bower, Jonathan P; Anastasio, Cort

2014-04-01

Singlet molecular oxygen (¹O₂*) can be a significant sink for a variety of electron-rich pollutants in surface waters and atmospheric drops. We recently found that ¹O₂* concentrations are enhanced by up to a factor of 10(4) on illuminated ice compared to in the equivalent liquid solution, suggesting that ¹O₂* could be an important oxidant for pollutants in snow. To examine this, here we study the degradation of three model organic pollutants: furfuryl alcohol (to represent furans), tryptophan (for aromatic amino acids), and bisphenol A (for phenols). Each compound was studied in illuminated aqueous solution and ice containing Rose Bengal (RB, a sensitizer for ¹O₂*) and sodium chloride (to adjust the concentration of total solutes). The RB-mediated loss of each organic compound is enhanced on illuminated ice compared to in solution, by factors of 6400 for furfuryl alcohol, 8300 for tryptophan, and 50 for bisphenol A for ice containing 0.065 mM total solutes. Rates of loss of furfuryl alcohol and tryptophan decrease at a higher total solute concentration, in qualitative agreement with predictions from freezing-point depression. In contrast, the loss of bisphenol A on ice is independent of total solute concentration. Relative to liquid tests, the enhanced loss of tryptophan on ice during control experiments made with deoxygenated solutions and solutions in D₂O show that the triplet excited state of Rose Bengal may also contribute to loss of pollutants on ice.

Thermodynamic Control of Two-Dimensional Molecular Ionic Nanostructures on Metal Surfaces

DOE PAGES

Jeon, Seokmin; Doak, Peter W.; Sumpter, Bobby G.; ...

2016-07-26

Bulk molecular ionic solids exhibit fascinating electronic properties, including electron correlations, phase transitions and superconducting ground states. In contrast, few of these phenomena have so far been observed in low-dimensional molecular structures, including thin films, nanoparticles and molecular blends, not in the least because most of such structures have so far been composed of nearly closed-shell molecules. It is therefore desirable to develop low-dimensional molecular structures of ionic molecules toward fundamental studies and potential applications. Here we present detailed analysis of monolayer-thick structures of the canonical TTF-TCNQ (tetrathiafulvalene 7,7,8,8-tetracyanoquinodimethane) system grown on low-index gold and silver surfaces. The most distinctivemore » property of the epitaxial growth is the wide abundance of stable TTF/TCNQ ratios, in sharp contrast to the predominance of 1:1 ratio in the bulk. We propose the existence of the surface phase-diagram that controls the structures of TTF-TCNQ on the surfaces, and demonstrate phase-transitions that occur upon progressively increasing the density of TCNQ while keeping the surface coverage of TTF fixed. Based on direct observations, we propose the binding motif behind the stable phases and infer the dominant interactions that enable the existence of the rich spectrum of surface structures. Finally, we also show that the surface phase diagram will control the epitaxy beyond monolayer coverage. Multiplicity of stable surface structures, the corollary rich phase diagram and the corresponding phase-transitions present an interesting opportunity for low-dimensional molecular systems, particularly if some of the electronic properties of the bulk can be preserved or modified in the surface phases.« less

Effect of electrostatic interaction on the location of molecular probe in polymer-surfactant supramolecular assembly: a solvent relaxation study.

PubMed

Singh, Prabhat K; Kumbhakar, Manoj; Pal, Haridas; Nath, Sukhendu

2008-07-03

Effect of electrostatic interaction on the location of a solubilized molecular probe with ionic character in a supramolecular assembly composed of a triblock copolymer, P123 ((ethylene oxide) 20-(propylene oxide) 70-(ethylene oxide) 20) and a cosurfactant cetyltrimethylammonium chloride (CTAC) in aqueous medium has been studied using steady-state and time-resolved fluorescence measurements. Coumarin-343 dye in its anionic form has been used as the molecular probe. In the absence of the surfactant, CTAC, the probe C343 prefers to reside at the surface region of the P123 micelle, showing a relatively less dynamic Stokes' shift, as a large part of the Stokes' shift is missed in the present measurements due to faster solvent relaxation at micellar surface region. As the concentration of CTAC is increased in the solution, the percentage of the total dynamic Stokes' shift observed from time-resolved measurements gradually increases until it reaches a saturation value. Observed results have been rationalized on the basis of the mixed micellar structure of the supramolecular assembly, where the hydrocarbon chain of the CTAC surfactant dissolves into the nonpolar poly(propylene oxide) (PPO) core of the P123 micelle and the positively charged headgroup of CTAC resides at the interfacial region between the central PPO core and the surrounding hydrated poly(ethylene oxide) (PEO) shell or the corona region. The electrostatic attraction between the anionic probe molecule and the positively charged surface of the PPO core developed by the presence of CTAC results in a gradual shift of the probe in the deeper region of the micellar corona region with an increase in the CTAC concentration, as clearly manifested from the solvation dynamics results.

Molecular recognition at methyl methacrylate/n-butyl acrylate (MMA/nBA) monomer unit boundaries of phospholipids at p-MMA/nBA copolymer surfaces.

PubMed

Yu, Min; Urban, Marek W; Sheng, Yinghong; Leszczynski, Jerzy

2008-09-16

Lipid structural features and their interactions with proteins provide a useful vehicle for further advances in membrane proteins research. To mimic one of potential lipid-protein interactions we synthesized poly(methyl methacrylate/ n-butyl acrylate) (p-MMA/nBA) colloidal particles that were stabilized by phospholipid (PLs). Upon the particle coalescence, PL stratification resulted in the formation of surface localized ionic clusters (SLICs). These entities are capable of recognizing MMA/nBA monomer interfaces along the p-MMA/nBA copolymer backbone and form crystalline SLICs at the monomer interface. By utilizing attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and selected area electron diffraction (SAD) combined with ab initio calculations, studies were conducted that identified the origin of SLICs as well as their structural features formed on the surface of p-MMA/nBA copolymer films stabilized by 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) PL. Specific entities responsible for SLIC formation are selective noncovalent bonds of anionic phosphate and cationic quaternary ammonium segments of DLPC that interact with two neighboring carbonyl groups of nBA and MMA monomers of the p-MMA/nBA polymer backbone. To the best of our knowledge this is the first example of molecular recognition facilitated by coalescence of copolymer colloidal particles and the ability of PLs to form SLICs at the boundaries of the neighboring MMA and nBA monomer units of the p-MMA/nBA chain. The dominating noncovalent bonds responsible for the molecular recognition is a combination of H-bonding and electrostatic interactions.

High-speed collision of copper nanoparticle with aluminum surface: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Pogorelko, Victor V.; Mayer, Alexander E.; Krasnikov, Vasiliy S.

2016-12-01

We investigate the effect of the high-speed collision of copper nanoparticles with aluminum surface by means of molecular dynamic simulations. Studied diameter of nanoparticles is varied within the range 7.2-22 nm and the velocity of impact is equal to 500 or 1000 m/s. Dislocation analysis shows that a large quantity of dislocations is formed within the impact area. Overall length of dislocations is determined, first of all, by the impact velocity and by the size of incident copper nanoparticle, in other words, by the kinetic energy of the nanoparticle. Dislocations occupy the total volume of the impacted aluminum single crystal layer (40.5 nm in thickness) in the form of intertwined structure in the case of large kinetic energy of the incident nanoparticle. Decrease in the initial kinetic energy or increase in the layer thickness lead to restriction of the penetration depth of the dislocation net; formation of separate dislocation loops is observed in this case. Increase in the initial system temperature slightly raises the dislocation density inside the bombarded layer and considerably decreases the dislocation density inside the nanoparticle. The temperature increase also leads to a deeper penetration of the copper atoms inside the aluminum. Additional molecular dynamic simulations show that the deposited particles demonstrate a very good adhesion even in the case of the considered relatively large nanoparticles. Medium energy of the nanoparticles corresponding to velocity of about 500 m/s and elevated temperature of the system about 700-900 K are optimal parameters for production of high-quality layers of copper on the aluminum surface. These conditions provide both a good adhesion and a less degree of the plastic deformation. At the same time, higher impact velocities can be used for combined treatment consisting of both the plastic deformation and the coating.

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE PAGES

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.; ...

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Analysis of surface damage in retrieved carbon fiber-reinforced and plain polyethylene tibial components from posterior stabilized total knee replacements.

PubMed

Wright, T M; Rimnac, C M; Faris, P M; Bansal, M

1988-10-01

The performance of carbon fiber-reinforced ultra-high molecular weight polyethylene was compared with that of plain (non-reinforced) polyethylene on the basis of the damage that was observed on the articulating surfaces of retrieved tibial components of total knee prostheses. Established microscopy techniques for subjectively grading the presence and extent of surface damage and the histological structure of the surrounding tissues were used to evaluate twenty-six carbon fiber-reinforced and twenty plain polyethylene components that had been retrieved after an average of twenty-one months of implantation. All of the tibial components were from the same design of total knee replacement. The two groups of patients from whom the components were retrieved did not differ with regard to weight, the length of time that the component had been implanted, the radiographic position and angular alignment of the component, the original diagnosis, or the reason for removal of the component. The amounts and types of damage that were observed did not differ for the two materials. For both materials, the amount of damage was directly related to the length of time that the component had been implanted. The histological appearance of tissues from the area around the component did not differ for the two materials, except for the presence of fragments of carbon fiber in many of the samples from the areas around carbon fiber-reinforced components.

Electrochemical immobilization of Fluorescent labelled probe molecules on a FTO surface for affinity detection based on photo-excited current

NASA Astrophysics Data System (ADS)

Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro

2011-10-01

Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.

Investigating the Counteracting Effect of Trehalose on Urea-Induced Protein Denaturation Using Molecular Dynamics Simulation.

PubMed

Paul, Subrata; Paul, Sandip

2015-08-27

Molecular dynamics simulations are performed to investigate the counteracting effect of trehalose against urea-induced denaturation of S-peptide analogue. The calculations of Cα root-mean-square deviation, radius of gyration, and solvent-accessible surface area reveal that the peptide loses its native structure in aqueous 8 M urea solution at 310 K and that this unfolding process is prevented in the presence of trehalose. Interestingly, the native structure of the peptide in ternary mixed urea/trehalose solution is similar to that in the pure water system. The estimation of helical percentage of peptide residues as well as peptide-peptide intramolecular hydrogen bond number for different systems also support the above findings. Decomposition of protein-urea total interaction energy into electrostatic and van der Waals contributions shows that the presence of trehalose molecules makes the latter contribution unfavorable without affecting the former. These observations are further supported by preferential interaction calculations. Furthermore, the hydrogen bond analyses show that with the addition of urea molecules to the peptide-water system, the formation of peptide-urea hydrogen bonds takes place at the expense of peptide-water hydrogen bonds. In ternary mixed osmolytes system, because of formation of a considerable amount of peptide-trehalose hydrogen bonds, some urea molecules are excluded from the peptide surface. This essentially reduces the interaction between peptide and urea molecules, and because of this, we notice a reduction in the number of peptide-urea hydrogen bonds. Interestingly, the total number of peptide-solution species hydrogen bonds in the pure water system is very similar to that for the mixed osmolytes system. From these observations we infer that in the ternary solution, peptide-solution species hydrogen bonds are shared by water, urea, and trehalose molecules. The presence of trehalose in the mixed osmolyte system causes a significant reduction in the translational dynamics of water molecules. We discuss these results to understand the molecular explanation of trehalose's counteracting ability on urea-induced protein denaturation.

Hailstones: a window into the microbial and chemical inventory of a storm cloud.

PubMed

Šantl-Temkiv, Tina; Finster, Kai; Dittmar, Thorsten; Hansen, Bjarne Munk; Thyrhaug, Runar; Nielsen, Niels Woetmann; Karlson, Ulrich Gosewinkel

2013-01-01

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are among the most extreme habitats on Earth, where microbial life exists.

Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud

PubMed Central

Šantl-Temkiv, Tina; Finster, Kai; Dittmar, Thorsten; Hansen, Bjarne Munk; Nielsen, Niels Woetmann; Karlson, Ulrich Gosewinkel

2013-01-01

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are among the most extreme habitats on Earth, where microbial life exists. PMID:23372660

Chemistry and temperature-assisted dehydrogenation of C60H30 molecules on TiO2(110) surfaces

NASA Astrophysics Data System (ADS)

Sánchez-Sánchez, Carlos; Martínez, José Ignacio; Lanzilotto, Valeria; Biddau, Giulio; Gómez-Lor, Berta; Pérez, Rubén; Floreano, Luca; López, María Francisca; Martín-Gago, José Ángel

2013-10-01

The thermal induced on-surface chemistry of large polycyclic aromatic hydrocarbons (PAHs) deposited on dielectric substrates is very rich and complex. We evidence temperature-assisted (cyclo)dehydrogenation reactions for C60H30 molecules and the subsequent bottom-up formation of assembled nanostructures, such as nanodomes, on the TiO2(110) surface. To this aim we have deposited, under ultra-high vacuum, a submonolayer coverage of C60H30 and studied, by a combination of experimental techniques (STM, XPS and NEXAFS) and theoretical methods, the different chemical on-surface interaction stages induced by the increasing temperature. We show that room temperature adsorbed molecules exhibit a weak interaction and freely diffuse on the surface, as previously reported for other aromatics. Nevertheless, a slight annealing induces a transition from this (meta)stable configuration into chemisorbed molecules. This adsorbate-surface interaction deforms the C60H30 molecular structure and quenches surface diffusion. Higher annealing temperatures lead to partial dehydrogenation, in which the molecule loses some of the hydrogen atoms and LUMO levels spread in the gap inducing a net total energy gain. Further annealing, up to around 750 K, leads to complete dehydrogenation. At these temperatures the fully dehydrogenated molecules link between them in a bottom-up coupling, forming nanodomes or fullerene-like monodisperse species readily on the dielectric surface. This work opens the door to the use of on-surface chemistry to generate new bottom-up tailored structures directly on high-K dielectric surfaces.The thermal induced on-surface chemistry of large polycyclic aromatic hydrocarbons (PAHs) deposited on dielectric substrates is very rich and complex. We evidence temperature-assisted (cyclo)dehydrogenation reactions for C60H30 molecules and the subsequent bottom-up formation of assembled nanostructures, such as nanodomes, on the TiO2(110) surface. To this aim we have deposited, under ultra-high vacuum, a submonolayer coverage of C60H30 and studied, by a combination of experimental techniques (STM, XPS and NEXAFS) and theoretical methods, the different chemical on-surface interaction stages induced by the increasing temperature. We show that room temperature adsorbed molecules exhibit a weak interaction and freely diffuse on the surface, as previously reported for other aromatics. Nevertheless, a slight annealing induces a transition from this (meta)stable configuration into chemisorbed molecules. This adsorbate-surface interaction deforms the C60H30 molecular structure and quenches surface diffusion. Higher annealing temperatures lead to partial dehydrogenation, in which the molecule loses some of the hydrogen atoms and LUMO levels spread in the gap inducing a net total energy gain. Further annealing, up to around 750 K, leads to complete dehydrogenation. At these temperatures the fully dehydrogenated molecules link between them in a bottom-up coupling, forming nanodomes or fullerene-like monodisperse species readily on the dielectric surface. This work opens the door to the use of on-surface chemistry to generate new bottom-up tailored structures directly on high-K dielectric surfaces. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03706a

The contour-buildup algorithm to calculate the analytical molecular surface.

PubMed

Totrov, M; Abagyan, R

1996-01-01

A new algorithm is presented to calculate the analytical molecular surface defined as a smooth envelope traced out by the surface of a probe sphere rolled over the molecule. The core of the algorithm is the sequential build up of multi-arc contours on the van der Waals spheres. This algorithm yields substantial reduction in both memory and time requirements of surface calculations. Further, the contour-buildup principle is intrinsically "local", which makes calculations of the partial molecular surfaces even more efficient. Additionally, the algorithm is equally applicable not only to convex patches, but also to concave triangular patches which may have complex multiple intersections. The algorithm permits the rigorous calculation of the full analytical molecular surface for a 100-residue protein in about 2 seconds on an SGI indigo with R4400++ processor at 150 Mhz, with the performance scaling almost linearly with the protein size. The contour-buildup algorithm is faster than the original Connolly algorithm an order of magnitude.

Adsorption, dissociation and diffusion of hydrogen on the ZrCo surface and subsurface: A comprehensive study using first principles approach

NASA Astrophysics Data System (ADS)

Chattaraj, D.; Kumar, Nandha; Ghosh, Prasenjit; Majumder, C.; Dash, Smruti

2017-11-01

With increasing demand for hydrogen economy driven world, the fundamental research of hydrogen-metal interactions has gained momentum. In this work we report a systematic theoretical study of the stability of different surfaces of intermetallic ZrCo that is a possible candidate as a getter bed for tritium. Our first principles ab initio thermodynamic calculations predict that amongst the (100), (110) and (111) surfaces, the stoichiometric (110) surface is the most stable one over a wide range of Co chemical potential. We have also studied adsorption, dissociation and diffusion of hydrogen on the (110) surface. On the basis of total energy, it is seen that adsorption of molecular hydrogen (H2) on the surface is much weaker than atomic hydrogen. The H2 decomposition on ZrCo surface can easily take place and the dissociation barrier is calculated to be 0.70 eV. The strength of binding of H atom on the surface is more or less independent of surface coverage till 1.0 ML of H. The thermodynamic stability of atomic H adsorbed on the surface, in subsurface and bulk decreases from surface to bulk to subsurface. Though the H atoms are mobile on the surface, their diffusion to the subsurface involves a barrier of about 0.79 eV.

Exploring the Surface Sensitivity of ToF-SIMS by Measuring the Implantation and Sampling Depths of Bin and C60 Ions in Organic Films

PubMed Central

Muramoto, Shin; Brison, Jeremy; Castner, David G.

2011-01-01

The surface sensitivity of Binq+ (n = 1, 3, 5, q = 1, 2) and C60q+ (q = 1, 2) primary ions in static time-of-flight secondary ion mass spectrometry (ToF-SIMS) experiments were investigated for molecular trehalose and polymeric tetraglyme organic films. Parameters related to surface sensitivity (impact crater depth, implantation depth, and molecular escape depths) were measured. Under static ToF-SIMS conditions (primary ion doses of 1 × 1012 ions/cm2), the 25 keV Bi1+ primary ions were the most surface sensitive with a molecular escape depth of 1.8 nm for protein films with tetraglyme overlayers, but they had the deepest implantation depth (~18 and 26 nm in trehalose and tetraglyme films, respectively). The 20 keV C60++ primary ions were the second most surface sensitive with a slightly larger molecular escape depth of 2.3 nm. The most important factor that determined the surface sensitivity of the primary ion was its impact crater depth, or the amount of surface erosion. The most surface sensitive primary ions, Bi1+ and C60++, created impact craters with depths of 0.3 and 1.0 nm, respectively, in tetraglyme films. In contrast, Bi5++ primary ions created impact craters with a depth of 1.8 nm in tetraglyme films and were the least surface sensitive with a molecular escape depth of 4.7 nm. PMID:22084828

Wetting properties of molecularly rough surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Svoboda, Martin; Lísal, Martin, E-mail: lisal@icpf.cas.cz; Department of Physics, Institute of Science, J. E. Purkinje University, 400 96 Ústí n. Lab.

2015-09-14

We employ molecular dynamics simulations to study the wettability of nanoscale rough surfaces in systems governed by Lennard-Jones (LJ) interactions. We consider both smooth and molecularly rough planar surfaces. Solid substrates are modeled as a static collection of LJ particles arranged in a face-centered cubic lattice with the (100) surface exposed to the LJ fluid. Molecularly rough solid surfaces are prepared by removing several strips of LJ atoms from the external layers of the substrate, i.e., forming parallel nanogrooves on the surface. We vary the solid-fluid interactions to investigate strongly and weakly wettable surfaces. We determine the wetting properties bymore » measuring the equilibrium droplet profiles that are in turn used to evaluate the contact angles. Macroscopic arguments, such as those leading to Wenzel’s law, suggest that surface roughness always amplifies the wetting properties of a lyophilic surface. However, our results indicate the opposite effect from roughness for microscopically corrugated surfaces, i.e., surface roughness deteriorates the substrate wettability. Adding the roughness to a strongly wettable surface shrinks the surface area wet with the liquid, and it either increases or only marginally affects the contact angle, depending on the degree of liquid adsorption into the nanogrooves. For a weakly wettable surface, the roughness changes the surface character from lyophilic to lyophobic due to a weakening of the solid-fluid interactions by the presence of the nanogrooves and the weaker adsorption of the liquid into the nanogrooves.« less

Fluorescence-correlation spectroscopy study of molecular transport within reversed-phase chromatographic particles compared to planar model surfaces.

PubMed

Cooper, Justin; Harris, Joel M

2014-12-02

Reversed-phase liquid chromatography (RPLC) is a widely used technique for molecular separations. Stationary-phase materials for RPLC generally consist of porous silica-gel particles functionalized with n-alkane ligands. Understanding motions of molecules within the interior of these particles is important for developing efficient chromatographic materials and separations. To characterize these dynamics, time-resolved spectroscopic methods (photobleach recovery, fluorescence correlation, single-molecule imaging) have been adapted to measure molecular diffusion rates, typically at n-alkane-modified planar silica surfaces, which serve as models of chromatographic interfaces. A question arising from these studies is how dynamics of molecules on a planar surface relate to motions of molecules within the interior of a porous chromatographic particle. In this paper, imaging-fluorescence-correlation spectroscopy is used to measure diffusion rates of a fluorescent probe molecule 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) within authentic RPLC porous silica particles and compared with its diffusion at a planar C18-modified surface. The results show that surface diffusion on the planar C18 substrate is much faster than the diffusion rate of the probe molecule through a chromatographic particle. Surface diffusion within porous particles, however, is governed by molecular trajectories along the tortuous contours of the interior surface of the particles. By accounting for the greater surface area that a molecule must explore to diffuse macroscopic distances through the particle, the molecular-scale diffusion rates on the two surfaces can be compared, and they are virtually identical. These results provide support for the relevance of surface-diffusion measurements made on planar model surfaces to the dynamic behavior of molecules on the internal surfaces of porous chromatographic particles.

Polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs in the coastal seawater, surface sediment and oyster from Dalian, Northeast China.

PubMed

Hong, Wen-Jun; Jia, Hongliang; Li, Yi-Fan; Sun, Yeqing; Liu, Xianjie; Wang, Luo

2016-06-01

A total of 46 polycyclic aromatic hydrocarbons (PAHs, 21 parent and 25 alkylated) were determined in seawater, surface sediment and oyster from coastal area of Dalian, North China. The concentration of Σ46PAHs in seawater, sediment, and oyster were 136-621 ng/L, 172-4700 ng/g dry weight (dw) and 60.0-129 ng/g wet weight (ww) in winter, and 65.0-1130 ng/L, 71.1-1090 ng/g dw and 72.8-216 ng/g ww in summer, respectively. High PAH levels were found in industrial area both in winter and summer. Selected PAH levels in sediments were compared with Sediments Quality Guidelines (ERM-ERL, TEL-PEL indexes) for evaluation probable toxic effects on marine organism and the results indicate that surface sediment from all sampling sites have a low to medium ecotoxicological risk. Daily intake of PAHs via oyster as seafood by humans were estimated and the results indicated that oyster intake would not pose a health risk to humans even 30 days after a oil spill accident near by. Water-sediment exchange analysis showed that, both in winter and summer, the fluxes for most high molecular weight PAHs were from seawater to sediment, while for low molecular weight PAHs, an equilibrium was reached between seawater and sediment. Copyright © 2016 Elsevier Inc. All rights reserved.

Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding

NASA Astrophysics Data System (ADS)

Bush, Derek B.; Knotts, Thomas A.

2017-04-01

Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces. To overcome this limitation, this study uses molecular simulation and an advanced, experimentally validated, coarse-grain, protein-surface model to compare fab-lysozyme binding in bulk solution and when the fab is tethered to hydrophobic and hydrophilic surfaces. The results show that the tether site in the fab, as well as the surface hydrophobicity, significantly impacts the binding process and suggests that the optimal design involves tethering fabs upright on a hydrophilic surface. The results offer an unprecedented, molecular-level picture of the binding process and give hope that the rational design of protein-microarrays is possible.

Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

NASA Astrophysics Data System (ADS)

Sinha, Sumona; Wang, C.-H.; Mukherjee, M.

2017-07-01

This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation as well as orientation and surface morphology of deposited rubrene thin film at rubrene/Ag interfaces and are beneficial for the improvement of the device performance.

H(D) → D(H) + Cu(111) collision system: Molecular dynamics study of surface temperature effects

PubMed Central

Vurdu, Can D.; Güvenç, Ziya B.

2011-01-01

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. PMID:21528959

H(D) → D(H) + Cu(111) collision system: molecular dynamics study of surface temperature effects.

PubMed

Vurdu, Can D; Güvenç, Ziya B

2011-04-28

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

Optimization of ultrasound assisted extraction of bioactive components from brown seaweed Ascophyllum nodosum using response surface methodology.

PubMed

Kadam, Shekhar U; Tiwari, Brijesh K; Smyth, Thomas J; O'Donnell, Colm P

2015-03-01

The objective of this study was to investigate the effect of key extraction parameters of extraction time (5-25 min), acid concentration (0-0.06 M HCl) and ultrasound amplitude (22.8-114 μm) on yields of bioactive compounds (total phenolics, fucose and uronic acid) from Ascophyllumnodosum. Response surface methodology was employed to optimize the extraction variables for bioactive compounds' yield. A second order polynomial model was fitted well to the extraction experimental data with (R(2)>0.79). Extraction yields of 143.12 mgGAE/gdb, 87.06 mg/gdb and 128.54 mg/gdb were obtained for total phenolics, fucose and uronic acid respectively at optimized extraction conditions of extraction time (25 min), acid concentration (0.03 M HCl) and ultrasonic amplitude (114 μm). Mass spectroscopy analysis of extracts show that ultrasound enhances the extraction of high molecular weight phenolic compounds from A. nodosum. This study demonstrates that ultrasound assisted extraction (UAE) can be employed to enhance extraction of bioactive compounds from seaweed. Copyright © 2014 Elsevier B.V. All rights reserved.

Diamond-coated ATR prism for infrared absorption spectroscopy of surface-modified diamond nanoparticles

NASA Astrophysics Data System (ADS)

Remes, Z.; Kozak, H.; Rezek, B.; Ukraintsev, E.; Babchenko, O.; Kromka, A.; Girard, H. A.; Arnault, J.-C.; Bergonzo, P.

2013-04-01

Linear antenna microwave chemical vapor deposition process was used to homogeneously coat a 7 cm long silicon prism by 85 nm thin nanocrystalline diamond (NCD) layer. To show the advantages of the NCD-coated prism for attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) of nanoparticles, we apply diamond nanoparticles (DNPs) of 5 nm nominal size with various surface modifications by a drop-casting of their methanol dispersions. ATR-FTIR spectra of as-received, air-annealed, plasma-oxidized, and plasma-hydrogenated DNPs were measured in the 4000-1500 cm-1 spectral range. The spectra show high spectral resolution, high sensitivity to specific DNP surface moieties, and repeatability. The NCD coating provides mechanical protection against scratching and chemical stability of the surface. Moreover, unlike on bare Si surface, NCD hydrophilic properties enable optically homogeneous coverage by DNPs with some aggregation on submicron scale as evidenced by scanning electron microscopy and atomic force microscopy. Compared to transmission FTIR regime with KBr pellets, direct and uniform deposition of DNPs on NCD-ATR prism significantly simplifies and speeds up the analysis (from days to minutes). We discuss prospects for in situ monitoring of surface modifications and molecular grafting.

Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tanping, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu; Kumar, Revati, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu

2015-11-07

We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaksmore » down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.« less

Pore-scale lattice Boltzmann simulation of micro-gaseous flow considering surface diffusion effect

DOE PAGES

Wang, Junjian; Kang, Qinjun; Chen, Li; ...

2016-11-21

Some recent studies have shown that adsorbed gas and its surface diffusion have profound influence on micro-gaseous flow through organic pores in shale gas reservoirs. Here, a multiple-relaxation-time (MRT) LB model is adopted to estimate the apparent permeability of organic shale and a new boundary condition, which combines Langmuir adsorption theory with Maxwellian diffusive reflection boundary condition, is proposed to capture gas slip and surface diffusion of adsorbed gas. The simulation results match well with previous studies carried out using Molecular Dynamics (MD) and show that Maxwell slip boundary condition fails to characterize gas transport in the near wall regionmore » under the influence of the adsorbed gas. The total molar flux can be either enhanced or reduced depending on variations in adsorbed gas coverage and surface diffusion velocity. The effects of pore width, pressure as well as Langmuir properties on apparent permeability of methane transport in organic pores are further studied. It is found that the surface transport plays a significant role in determining the apparent permeability, and the variation of apparent permeability with pore size and pressure is affected by the adsorption and surface diffusion.« less

Effect of polar surfaces on organic molecular crystals

NASA Astrophysics Data System (ADS)

Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

Joint L1 and Total Variation Regularization for Fluorescence Molecular Tomography

PubMed Central

Dutta, Joyita; Ahn, Sangtae; Li, Changqing; Cherry, Simon R.; Leahy, Richard M.

2012-01-01

Fluorescence molecular tomography (FMT) is an imaging modality that exploits the specificity of fluorescent biomarkers to enable 3D visualization of molecular targets and pathways in vivo in small animals. Owing to the high degree of absorption and scattering of light through tissue, the FMT inverse problem is inherently illconditioned making image reconstruction highly susceptible to the effects of noise and numerical errors. Appropriate priors or penalties are needed to facilitate reconstruction and to restrict the search space to a specific solution set. Typically, fluorescent probes are locally concentrated within specific areas of interest (e.g., inside tumors). The commonly used L2 norm penalty generates the minimum energy solution, which tends to be spread out in space. Instead, we present here an approach involving a combination of the L1 and total variation norm penalties, the former to suppress spurious background signals and enforce sparsity and the latter to preserve local smoothness and piecewise constancy in the reconstructed images. We have developed a surrogate-based optimization method for minimizing the joint penalties. The method was validated using both simulated and experimental data obtained from a mouse-shaped phantom mimicking tissue optical properties and containing two embedded fluorescent sources. Fluorescence data was collected using a 3D FMT setup that uses an EMCCD camera for image acquisition and a conical mirror for full-surface viewing. A range of performance metrics were utilized to evaluate our simulation results and to compare our method with the L1, L2, and total variation norm penalty based approaches. The experimental results were assessed using Dice similarity coefficients computed after co-registration with a CT image of the phantom. PMID:22390906

Impact of surface chemistry

PubMed Central

Somorjai, Gabor A.; Li, Yimin

2011-01-01

The applications of molecular surface chemistry in heterogeneous catalyst technology, semiconductor-based technology, medical technology, anticorrosion and lubricant technology, and nanotechnology are highlighted in this perspective. The evolution of surface chemistry at the molecular level is reviewed, and the key roles of surface instrumentation developments for in situ studies of the gas–solid, liquid–solid, and solid–solid interfaces under reaction conditions are emphasized. PMID:20880833

Ejection of nanoclusters from gold nanoislet layers by 38 keV Au ions in the elastic stopping mode.

PubMed

Baranov, I A; Della-Negra, S; Domaratsky, V P; Chemezov, A V; Kirillov, S N; Novikov, A C; Obnorsky, V V; Pautrat, M; Urbassek, H M; Wien, K; Yarmiychuk, S V; Zhurkin, E E

2009-07-01

Total absolute yields of the ejected gold were obtained regardless of the type of the particles are--atoms, clusters, nanoclusters,--as well as absolute yields of gold nanoclusters, from nanoislet gold targets under bombardment by monoatomic gold ions at 45 degrees to the target surface with the energy 38 keV, i.e., in the "purely" elastic stopping mode -6 keV/nm up to the fluence of 4 x 10(12) cm2. Three targets had gold nanoislets on the substrate surface: 2-12 nm; -18 nm; -35 nm, the most probable sizes being 7.1; 9.4; 17.5 nm respectively. The part of the surface area covered with gold was known. Total transfer of gold was determined by means of the neutron-activation analysis and decreased from 450 to 20 at/ion. The number of the ejected gold nanoclusters was determined using TEM and decreased from approximately 0.06 to < 0.01 per one 38 keV Au ion with the increase of the most probable sizes of the nanoislets on the target from 7.1 to 17.5 nm. The yields appeared to be surprisingly high, which is of scientific and practical importance. Tentative estimations were made using molecular dynamics simulations.

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Surface diffusion of Si, Ge and C adatoms on Si (001) substrate studied by the molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Chen, Zhi-Hui; Yu, Zhong-Yuan; Lu, Peng-Fei; Liu, Yu-Min

2009-10-01

Depositions of Si, Ge and C atoms onto a preliminary Si (001) substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.

Reaction of hydrogen with Ag(111): binding states, minimum energy paths, and kinetics.

PubMed

Montoya, Alejandro; Schlunke, Anna; Haynes, Brian S

2006-08-31

The interaction of atomic and molecular hydrogen with the Ag(111) surface is studied using periodic density functional total-energy calculations. This paper focuses on the site preference for adsorption, ordered structures, and energy barriers for H diffusion and H recombination. Chemisorbed H atoms are unstable with respect to the H(2) molecule in all adsorption sites below monolayer coverage. The three-hollow sites are energetically the most favorable for H chemisorption. The binding energy of H to the surface decreases slightly up to one monolayer, suggesting a small repulsive H-H interaction on nonadjacent sites. Subsurface and vacancy sites are energetically less favorable for H adsorption than on-top sites. Recombination of chemisorbed H atoms leads to the formation of gas-phase H(2) with no molecular chemisorbed state. Recombination is an exothermic process and occurs on the bridge site with a pronounced energy barrier. This energy barrier is significantly higher than that inferred from experimental temperature-programmed desorption (TPD) studies. However, there is significant permeability of H atoms through the recombination energy barrier at low temperatures, thus increasing the rate constant for H(2) desorption due to quantum tunneling effects, and improving the agreement between experiment and theory.

Surface characterization of modern resin composites: a multitechnique approach.

PubMed

Silikas, Nick; Kavvadia, Katerina; Eliades, George; Watts, David

2005-04-01

To characterize the surface properties of some modern resin composites employing a series of physicochemical methods. Specimens from three microhybrid (Palfique Estellite-PE, Z250 Filtek-ZF, Tetric Ceram-TC) and one nanofilled (Supreme Filtek-SF) conventionally photo-cured resin composites polished with Soflex disks were studied for the following properties: Surface chemical composition and degree of C=C conversion (FTIR), surface energetics (contact angles), surface texture (AFM), surface roughness (AFM, stylus profilometry) and gloss (60 degrees-, 20 degrees-angle specular gloss). Polar and non polar molecular groups were identified in all products including NH and CONH (SF, ZF, TC). SF and ZF demonstrated higher conversion than PE and TC (P< 0.05). No significant differences (P> 0.05) were found in critical surface tension, total work of adhesion and its polar and dispersion components, the latter being the highest in all products. AFM showed the smoothest surface texture in PE. The ranking of Sa, Sq, Ra and Rz roughness parameters was PEZF>TC, P< 0.05) were more sensitive than 60 degree-angle measurements (PE, SF>TC, P< 0.05) in revealing gloss differences. A positive correlation was found between Sa and Ra and a negative one between Sa and 20 degree-angle gloss.

EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

NASA Astrophysics Data System (ADS)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on metal surfaces, focusing on electronic and vibrational spectroscopy in one case and scanning tunneling microscopy studies in the other. Original research articles describe results in many aspects of the field, including: Self-assembly, self-organization, and controlled growth of molecular layers on various substrates. Highly-ordered arrays provide model systems with extraordinary structural properties, allowing one to adjust interactions between molecules and between molecule and substrate, and can be robustly prepared from solution, an essential prerequisite for applications. Conformational or electronic switching of molecules adsorbed at metal and semiconductor surfaces. These studies highlight the elementary processes governing molecular switching at surfaces as well as the wide range of possible stimuli. Carbon-based substrates such as graphene or carbon nanotubes. These substrates are attractive due to their effective two-dimensionality which implies that switching of adsorbed molecules can effect a significant back-action on the substrate. Mechanisms of conformational switching. Several contributions study the role of electron-vibron coupling and heating in current-induced conformational switching. We hope that the collection of articles presented here will stimulate and encourage researchers in surface physics and interfacial chemistry to contribute to the still emerging field of molecular switches at surfaces. We wish to acknowledge the support and input from many colleagues in preparing this special section. A significant part of this work has been conducted in the framework of the Sonderforschungsbereich 658 Elementary Processes in Molecular Switches at Surfaces of the Deutsche Forschungsgemeinschaft, to which we are grateful for financial support. Molecular surfaces at switches contents Molecular switches at surfacesMartin Weinelt and Felix von Oppen Optically and thermally induced molecular switching processes at metal surfacesPetra Tegeder Effects of electron-vibration coupling in transport through single moleculesKatharina J Franke and Jose Ignacio Pascual Vibrational heating in single-molecule switches: an energy-dependent density-of-states approachT Brumme, R Gutierrez and G Cuniberti Reversible switching of single tin phthalocyanine molecules on the InAs(111)A surfaceC Nacci, K Kanisawa and S Fölsch Tuning the interaction between carbon nanotubes and dipole switches: the influence of the change of the nanotube-spiropyran distanceP Bluemmel, A Setaro, C Maity, S Hecht and S Reich Carbon nanotubes as substrates for molecular spiropyran-based switchesE Malic, A Setaro, P Bluemmel, Carlos F Sanz-Navarro, Pablo Ordejón, S Reich and A Knorr Ultrafast dynamics of dithienylethenes differently linked to the surface of TiO2 nanoparticlesLars Dworak, Marc Zastrow, Gehad Zeyat, Karola Rück-Braun and Josef Wachtveitl Switching the electronic properties of Co-octaethylporphyrin molecules on oxygen-covered Ni films by NO adsorptionC F Hermanns, M Bernien, A Krüger, J Miguel and W Kuch STM-switching of organic molecules on semiconductor surfaces: an above threshold density matrix model for 1,5 cyclooctadiene on Si(100)K Zenichowski, Ch Nacci, S Fölsch, J Dokić, T Klamroth and P Saalfrank A switch based on self-assembled thymineFatih Kalkan, Michael Mehlhorn and Karina Morgenstern The growth and electronic structure of azobenzene-based functional molecules on layered crystalsJ Iwicki, E Ludwig, J Buck, M Kalläne, F Köhler, R Herges, L Kipp and K Rossnagel Voltage-dependent conductance states of a single-molecule junctionY F Wang, N Néel, J Kröger, H Vázquez, M Brandbyge, B Wang and R Berndt Molecules with multiple switching units on a Au(111) surface: self-organization and single-molecule manipulationJohannes Mielke, Sofia Selvanathan, Maike Peters, Jutta Schwarz, Stefan Hecht and Leonhard Grill Preparing and regulating a bi-stable molecular switch by atomic manipulationS Sakulsermsuk, R E Palmer and P A Sloan Mixed self-assembled monolayers of azobenzene photoswitches with trifluoromethyl and cyano end groupsDaniel Brete, Daniel Przyrembel, Christian Eickhoff, Robert Carley, Wolfgang Freyer, Karsten Reuter, Cornelius Gahl and Martin Weinelt Reversible electron-induced cis-trans isomerization mediated by intermolecular interactionsCh Lotze, Y Luo, M Corso, K J Franke, R Haag and J I Pascual Transport properties of graphene functionalized with molecular switchesNiels Bode, Eros Mariani and Felix von Oppen

Fibronectin and bovine serum albumin adsorption and conformational dynamics on inherently conducting polymers: a QCM-D study.

PubMed

Molino, Paul J; Higgins, Michael J; Innis, Peter C; Kapsa, Robert M I; Wallace, Gordon G

2012-06-05

Quartz crystal microbalance with dissipation monitoring (QCM-D) was employed to characterize the adsorption of the model proteins, bovine serum albumin (BSA) and fibronectin (FN), to polypyrrole doped with dextran sulfate (PPy-DS) as a function of DS loading and surface roughness. BSA adsorption was greater on surfaces of increased roughness and was above what could be explained by the increase in surface area alone. Furthermore, the additional mass adsorbed on the rough films was concomitant with an increase in the rigidity of the protein layer. Analysis of the dynamic viscoelastic properties of the protein adlayer reveal BSA adsorption on the rough films occurs in two phases: (1) arrival and initial adsorption of protein to the polymer surface and (2) postadsorption molecular rearrangement to a more dehydrated and compact conformation that facilitates further recruitment of protein to the polymer interface, likely forming a multilayer. In contrast, FN adsorption was independent of surface roughness. However, films prepared from solutions containing the highest concentration of DS (20 mg/mL) demonstrated both an increase in adsorbed mass and adlayer viscoelasticity. This is attributed to the higher DS loading in the conducting polymer film resulting in presentation of a more hydrated molecular structure indicative of a more unfolded and bioactive conformation. Modulating the redox state of the PPy-DS polymers was shown to modify both the adsorbed mass and viscoelastic nature of FN adlayers. An oxidizing potential increased both the total adsorbed mass and the adlayer viscoelasticity. Our findings demonstrate that modification of polymer physicochemical and redox condition alters the nature of protein-polymer interaction, a process that may be exploited to tailor the bioactivity of protein through which interactions with cells and tissues may be controlled.

Tuning the deposition of molecular graphene nanoribbons by surface functionalization.

PubMed

Konnerth, R; Cervetti, C; Narita, A; Feng, X; Müllen, K; Hoyer, A; Burghard, M; Kern, K; Dressel, M; Bogani, L

2015-08-14

We show that individual, isolated graphene nanoribbons, created with a molecular synthetic approach, can be assembled on functionalised wafer surfaces treated with silanes. The use of surface groups with different hydrophobicities allows tuning the density of the ribbons and assessing the products of the polymerisation process.

Tuning the deposition of molecular graphene nanoribbons by surface functionalization

NASA Astrophysics Data System (ADS)

Konnerth, R.; Cervetti, C.; Narita, A.; Feng, X.; Müllen, K.; Hoyer, A.; Burghard, M.; Kern, K.; Dressel, M.; Bogani, L.

2015-07-01

We show that individual, isolated graphene nanoribbons, created with a molecular synthetic approach, can be assembled on functionalised wafer surfaces treated with silanes. The use of surface groups with different hydrophobicities allows tuning the density of the ribbons and assessing the products of the polymerisation process.

Preparation of a silicon surface for subsequent growth of dilute nitride alloys by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Lazarenko, A. A.; Berezovskaya, T. N.; Denisov, D. V.; Sobolev, M. S.; Pirogov, E. V.; Nikitina, E. V.

2017-11-01

This article discusses the process of preparation of a silicon surface for subsequent growth of dilute nitride alloys by molecular-beam epitaxy. The method of preparation of Si (100) and Si (111) substrates was developed. This method provides reproducible high-quality silicon surface for molecular-beam epitaxy of Si-GaP heterostructures. As a result, it managed to reduce the eviction oxide temperature below 800 °C, which is an important parameter for the MBE technology.

On the Appearance of Thresholds in the Dynamical Model of Star Formation

NASA Astrophysics Data System (ADS)

Elmegreen, Bruce G.

2018-02-01

The Kennicutt–Schmidt (KS) relationship between the surface density of the star formation rate (SFR) and the gas surface density has three distinct power laws that may result from one model in which gas collapses at a fixed fraction of the dynamical rate. The power-law slope is 1 when the observed gas has a characteristic density for detection, 1.5 for total gas when the thickness is about constant as in the main disks of galaxies, and 2 for total gas when the thickness is regulated by self-gravity and the velocity dispersion is about constant, as in the outer parts of spirals, dwarf irregulars, and giant molecular clouds. The observed scaling of the star formation efficiency (SFR per unit CO) with the dense gas fraction (HCN/CO) is derived from the KS relationship when one tracer (HCN) is on the linear part and the other (CO) is on the 1.5 part. Observations of a threshold density or column density with a constant SFR per unit gas mass above the threshold are proposed to be selection effects, as are observations of star formation in only the dense parts of clouds. The model allows a derivation of all three KS relations using the probability distribution function of density with no thresholds for star formation. Failed galaxies and systems with sub-KS SFRs are predicted to have gas that is dominated by an equilibrium warm phase where the thermal Jeans length exceeds the Toomre length. A squared relation is predicted for molecular gas-dominated young galaxies.

Importance of molecular Rayleigh scattering in the enhancement of clear sky reflectance in the vicinity of boundary layer cumulus clouds

NASA Astrophysics Data System (ADS)

Wen, Guoyong; Marshak, Alexander; Cahalan, Robert F.

2008-12-01

Clouds increase the complexity of atmospheric radiative transfer processes, particularly for aerosol retrievals in clear regions in the vicinity of clouds. This study focuses on identifying mechanisms responsible for the enhancement of nadir reflectance in clear regions in the vicinity of cumulus clouds and quantifies the relative importance of each mechanism. Using cloud optical properties and surface albedo derived from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) and Moderate Resolution Imaging Spectroradiometer (MODIS), we performed extensive Monte Carlo simulations of radiative transfer in two cumulus scenes in a biomass burning region in Brazil. The results show that the scattering of radiation by clouds, followed by upward Rayleigh scattering by molecules above cloud top over clear gaps, is the dominant mechanism for the enhancement of visible reflectance in clear regions in boundary layer cumulus field over dark surfaces with aerosols trapped in the boundary layer. The Rayleigh scattering contributes ˜80% and ˜50% to the total enhancement for wavelengths 0.47 μm (with aerosol optical thickness 0.2) and 0.66 μm (with aerosol optical thickness 0.1), respectively. Out of the total contribution of molecular scattering, ˜90% arises from the clear atmosphere above cloud top height. The mechanism is valid for a large range of aerosol optical thicknesses (up to 1 in this study) for 0.47 μm, and for aerosol optical thickness up to 0.2 for 0.66 μm. Our results provide a basis to develop simplifications for future aerosol remote sensing from satellite.

Modeling adsorption: Investigating adsorbate and adsorbent properties

NASA Astrophysics Data System (ADS)

Webster, Charles Edwin

1999-12-01

Surface catalyzed reactions play a major role in current chemical production technology. Currently, 90% of all chemicals are produced by heterogeneously catalyzed reactions. Most of these catalyzed reactions involve adsorption, concentrating the substrate(s) (the adsorbate) on the surface of the solid (the adsorbent). Pore volumes, accessible surface areas, and the thermodynamics of adsorption are essential in the understanding of solid surface characteristics fundamental to catalyst and adsorbent screening and selection. Molecular properties such as molecular volumes and projected molecular areas are needed in order to convert moles adsorbed to surface volumes and areas. Generally, these molecular properties have been estimated from bulk properties, but many assumptions are required. As a result, different literature values are employed for these essential molecular properties. Calculated molar volumes and excluded molecular areas are determined and tabulated for a variety of molecules. Molecular dimensions of molecules are important in the understanding of molecular exclusion as well as size and shape selectivity, diffusion, and adsorbent selection. Molecular dimensions can also be used in the determination of the effective catalytic pore size of a catalyst. Adsorption isotherms, on zeolites, (crystalline mineral oxides) and amorphous solids, can be analyzed with the Multiple Equilibrium Analysis (MEA) description of adsorption. The MEA produces equilibrium constants (Ki), capacities (ni), and thermodynamic parameters (enthalpies, ΔHi, and entropies, ΔSi) of adsorption for each process. Pore volumes and accessible surface areas are calculated from the process capacities. Adsorption isotherms can also be predicted for existing and new adsorbate-adsorbent systems with the MEA. The results show that MEA has the potential of becoming a standard characterization method for microporous solids that will lead to an increased understanding of their behavior in gas adsorption and catalysis. These studies are also applicable to environmental cleanup applications, such as waste stream purification and separation procedures as well as decontamination of chemical warfare agents.

Analysis of structural changes in active site of luciferase adsorbed on nanofabricated hydrophilic Si surface by molecular-dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishiyama, Katsuhiko; Hoshino, Tadatsugu; Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522

2007-05-21

Interactions between luciferase and a nanofabricated hydrophilic Si surface were explored by molecular-dynamics simulations. The structural changes in the active-site residues, the residues affecting the luciferin binding, and the residues affecting the bioluminescence color were smaller on the nanofabricated hydrophilic Si surface than on both a hydrophobic Si surface and a hydrophilic Si surface. The nanofabrication and wet-treatment techniques are expected to prevent the decrease in activity of luciferase on the Si surface.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Natural solar photolysis of total organic chlorine, bromine and iodine in water.

PubMed

Abusallout, Ibrahim; Hua, Guanghui

2016-04-01

Municipal wastewater has been increasingly used to augment drinking water supplies due to the growing water scarcity. Wastewater-derived disinfection byproducts (DBPs) may negatively affect the aquatic ecosystems and human health of downstream communities during water reuse. The objective of this research was to determine the degradation kinetics of total organic chlorine (TOCl), bromine (TOBr) and iodine (TOI) in water by natural sunlight irradiation. Outdoor solar photolysis experiments were performed to investigate photolytic degradation of the total organic halogen (TOX) formed by fulvic acid and real water and wastewater samples. The results showed that TOX degradation by sunlight irradiation followed the first-order kinetics with half-lives in the range of 2.6-10.7 h for different TOX compounds produced by fulvic acid. The TOX degradation rates were generally in the order of TOI > TOBr ≅ TOCl(NH2Cl) > TOCl(Cl2). High molecular weight TOX was more susceptible to solar photolysis than corresponding low molecular weight halogenated compounds. The nitrate and sulfite induced indirect TOX photolysis rates were less than 50% of the direct photolysis rates under the conditions of this study. Fulvic acid and turbidity in water reduced TOX photodegradation. These results contribute to a better understanding of the fate of chlorinated, brominated and iodinated DBPs in surface waters. Published by Elsevier Ltd.

Prioritization of anti-malarial hits from nature: chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs.

PubMed

Egieyeh, Samuel Ayodele; Syce, James; Malan, Sarel F; Christoffels, Alan

2016-01-29

A large number of natural products have shown in vitro antiplasmodial activities. Early identification and prioritization of these natural products with potential for novel mechanism of action, desirable pharmacokinetics and likelihood for development into drugs is advantageous. Chemo-informatic profiling of these natural products were conducted and compared to currently registered anti-malarial drugs (CRAD). Natural products with in vitro antiplasmodial activities (NAA) were compiled from various sources. These natural products were sub-divided into four groups based on inhibitory concentration (IC50). Key molecular descriptors and physicochemical properties were computed for these compounds and analysis of variance used to assess statistical significance amongst the sets of compounds. Molecular similarity analysis, estimation of drug-likeness, in silico pharmacokinetic profiling, and exploration of structure-activity landscape were also carried out on these sets of compounds. A total of 1040 natural products were selected and a total of 13 molecular descriptors were analysed. Significant differences were observed among the sub-groups of NAA and CRAD for at least 11 of the molecular descriptors, including number of hydrogen bond donors and acceptors, molecular weight, polar and hydrophobic surface areas, chiral centres, oxygen and nitrogen atoms, and shape index. The remaining molecular descriptors, including clogP, number of rotatable bonds and number of aromatic rings, did not show any significant difference when comparing the two compound sets. Molecular similarity and chemical space analysis identified natural products that were structurally diverse from CRAD. Prediction of the pharmacokinetic properties and drug-likeness of these natural products identified over 50% with desirable drug-like properties. Nearly 70% of all natural products were identified as potentially promiscuous compounds. Structure-activity landscape analysis highlighted compound pairs that form 'activity cliffs'. In all, prioritization strategies for the NAA were proposed. Chemo-informatic profiling of NAA and CRAD have produced a wealth of information that may guide decisions and facilitate anti-malarial drug development from natural products. Articulation of the information provided within an interactive data-mining environment led to a prioritized list of NAA.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

PubMed

Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

2007-04-01

The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

Solid surface vs. liquid surface: nanoarchitectonics, molecular machines, and DNA origami.

PubMed

Ariga, Katsuhiko; Mori, Taizo; Nakanishi, Waka; Hill, Jonathan P

2017-09-13

The investigation of molecules and materials at interfaces is critical for the accumulation of new scientific insights and technological advances in the chemical and physical sciences. Immobilization on solid surfaces permits the investigation of different properties of functional molecules or materials with high sensitivity and high spatial resolution. Liquid surfaces also present important media for physicochemical innovation and insight based on their great flexibility and dynamicity, rapid diffusion of molecular components for mixing and rearrangements, as well as drastic spatial variation in the prevailing dielectric environment. Therefore, a comparative discussion of the relative merits of the properties of materials when positioned at solid or liquid surfaces would be informative regarding present-to-future developments of surface-based technologies. In this perspective article, recent research examples of nanoarchitectonics, molecular machines, DNA nanotechnology, and DNA origami are compared with respect to the type of surface used, i.e. solid surfaces vs. liquid surfaces, for future perspectives of interfacial physics and chemistry.

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

PubMed Central

Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael

2001-01-01

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861

From 20 cm - 1 micron: Measuring the Gas and Dust in Massive Low Surface Brightness Galaxies

NASA Astrophysics Data System (ADS)

Kearsley, E.; O'Neil, K.

2005-12-01

Archival data from the IRAS, 2MASS, NVSS, and FIRST catalogs, supplemented with new measurements of HI, are used to analyze the relationship between the relative mass of the various components of galaxies (stars, atomic hydrogen, dust, and molecular gas) using a small sample of nearby (z<0.1), massive low surface brightness galaxies. The sample is compared to three sets of published data: a large collection of radio sources from the UGC having a radio continuum intensity >2.5 mJy (Condon, Cotton, & Broderick 2002 AJ 124, 675) ; a smaller sample of low surface brightness galaxies (Galaz, et al 2002 2002 AJ 124, 1360); and a collection of NIR low surface brightness galaxies (Monnier-Ragaigne, et al 2002 Ap&SS 281, 145). Overall, our sample properties are similar to the comparison samples in regard to NIR color, gas, stellar, and dynamic mass ratios, etc. Based off the galaxies' q-value (determined from the FIR/1.4 GHz ratio), it appears likely that at least two of the 28 galaxies studied harbor AGN. Notably, we also find that if we naively assume the ratio of the dust and molecular gas mass relative to the mass of HI is a constant we are unable to predict the observed ratio of stellar mass to HI mass, indicating that the HI mass ratio is a poor indicator of the total baryonic mass in the studied galaxies. HI measurements obtained during this study using the Green Bank Telescope also provide a correction to the velocity of UGC 11068.

Self assembled molecular monolayers on high surface area materials as molecular getters

DOEpatents

King, David E.; Herdt, Gregory C.; Czanderna, Alvin W.

1997-01-01

The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium.

Self assembled molecular monolayers on high surface area materials as molecular getters

DOEpatents

King, D.E.; Herdt, G.C.; Czanderna, A.W.

1997-01-07

The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium. 9 figs.

Covalent Immobilization of Microtubules on Glass Surfaces for Molecular Motor Force Measurements and Other Single-Molecule Assays

PubMed Central

Nicholas, Matthew P.; Rao, Lu; Gennerich, Arne

2014-01-01

Rigid attachment of microtubules (MTs) to glass cover slip surfaces is a prerequisite for a variety of microscopy experiments in which MTs are used as substrates for MT-associated proteins, such as the molecular motors kinesin and cytoplasmic dynein. We present an MT-surface coupling protocol in which aminosilanized glass is formylated using the cross-linker glutaraldehyde, fluorescence-labeled MTs are covalently attached, and the surface is passivated with highly pure beta-casein. The technique presented here yields rigid MT immobilization while simultaneously blocking the remaining glass surface against nonspecific binding by polystyrene optical trapping microspheres. This surface chemistry is straightforward and relatively cheap and uses a minimum of specialized equipment or hazardous reagents. These methods provide a foundation for a variety of optical tweezers experiments with MT-associated molecular motors and may also be useful in other assays requiring surface-immobilized proteins. PMID:24633798

An advanced molecule-surface scattering instrument for study of vibrational energy transfer in gas-solid collisions.

PubMed

Ran, Qin; Matsiev, Daniel; Wodtke, Alec M; Auerbach, Daniel J

2007-10-01

We describe an advanced and highly sensitive instrument for quantum state-resolved molecule-surface energy transfer studies under ultrahigh vacuum (UHV) conditions. The apparatus includes a beam source chamber, two differential pumping chambers, and a UHV chamber for surface preparation, surface characterization, and molecular beam scattering. Pulsed and collimated supersonic molecular beams are generated by expanding target molecule mixtures through a home-built pulsed nozzle, and excited quantum state-selected molecules were prepared via tunable, narrow-band laser overtone pumping. Detection systems have been designed to measure specific vibrational-rotational state, time-of-flight, angular and velocity distributions of molecular beams coming to and scattered off the surface. Facilities are provided to clean and characterize the surface under UHV conditions. Initial experiments on the scattering of HCl(v = 0) from Au(111) show many advantages of this new instrument for fundamental studies of the energy transfer at the gas-surface interface.

ALMA Observations of Molecular Clouds in Three Group-centered Elliptical Galaxies: NGC 5846, NGC 4636, and NGC 5044

NASA Astrophysics Data System (ADS)

Temi, Pasquale; Amblard, Alexandre; Gitti, Myriam; Brighenti, Fabrizio; Gaspari, Massimo; Mathews, William G.; David, Laurence

2018-05-01

We present new ALMA CO(2–1) observations of two well-studied group-centered elliptical galaxies: NGC 4636 and NGC 5846. In addition, we include a revised analysis of Cycle 0 ALMA observations of the central galaxy in the NGC 5044 group. We find evidence that molecular gas is a common presence in bright group-centered galaxies (BGG). CO line widths are broader than Galactic molecular clouds, and using the reference Milky Way X CO, the total molecular mass ranges from 2.6 × 105 M ⊙ in NGC 4636 to 6.1 × 107 M ⊙ in NGC 5044. Complementary observations using the ALMA Compact Array do not exhibit any detection of a CO diffuse component at the sensitivity level achieved by current exposures. The origin of the detected molecular features is still uncertain, but these ALMA observations suggest that they are the end product of the hot gas cooling process and not the result of merger events. Some of the molecular clouds are associated with dust features as revealed by HST dust extinction maps, suggesting that these clouds formed from dust-enhanced cooling. The global nonlinear condensation may be triggered via the chaotic turbulent field or buoyant uplift. The large virial parameter of the molecular structures and correlation with the warm ({10}3{--}{10}5 {{K}})/hot (≥106) phase velocity dispersion provide evidence that they are unbound giant molecular associations drifting in the turbulent field, consistent with numerical predictions of the chaotic cold accretion process. Alternatively, the observed large CO line widths may be generated by molecular gas flowing out from cloud surfaces due to heating by the local hot gas atmosphere.

On the chemical dynamics of extracellular polysaccharides in the high Arctic surface microlayer

NASA Astrophysics Data System (ADS)

Gao, Q.; Leck, C.; Rauschenberg, C.; Matrai, P. A.

2012-07-01

The surface microlayer (SML) represents a unique system of which the physicochemical characteristics may differ from those of the underlying subsurface seawater (SSW). Within the Arctic pack ice area, the SML has been characterized as enriched in small colloids of biological origin, resulting from extracellular polymeric secretions (EPS). During the Arctic Summer Cloud Ocean Study (ASCOS) in August 2008, particulate organic matter (POM, with size range > 0.22 μm) and dissolved organic matter (DOM, < 0.22 μm, obtained after filtration) samples were collected and chemically characterized from the SML and the corresponding SSW at an open lead centered at 87.5° N and 5° E. Total organic carbon was persistently enriched in the SML with a mean enrichment factor (EF) of 1.45 ± 0.41, whereas sporadic depletions of dissolved carbohydrates and amino acids were observed. Monosaccharide compositional analysis reveals that EPS in the Arctic lead was formed mainly of distinctive heteropolysaccharides, enriched in xylose, fucose and glucose. The mean concentrations of total hydrolysable neutral sugars in SSW were 94.9 ± 37.5 nM in high molecular weight (HMW) DOM (> 5 kDa) and 64.4 ± 14.5 nM in POM. The enrichment of polysaccharides in the SML appeared to be a common feature, with EFs ranging from 1.7 to 7.0 for particulate polysaccharides and 3.5 to 12.1 for polysaccharides in the HMW DOM fraction. A calculated monosaccharide yield suggests that polymers in the HMW DOM fraction were scavenged, without substantial degradation, into the SML. Bubble scavenging experiments showed that newly aggregated particles could be formed abiotically by coagulation of low molecular weight nanometer-sized gels. Aerosol particles, artificially generated by bubbling experiments, were enriched in polysaccharides by factors of 22-70, relative to the source seawater. We propose that bubble scavenging of surface-active polysaccharides could be one of the possible mechanisms for the enrichment of polysaccharides in the high Arctic open lead SML.

On the chemical dynamics of extracellular polysaccharides in the high Arctic surface microlayer

NASA Astrophysics Data System (ADS)

Gao, Q.; Leck, C.; Rauschenberg, C.; Matrai, P. A.

2012-01-01

The surface microlayer (SML) represents a unique system of which the physicochemical characteristics may differ from those of the underlying subsurface seawater (SSW). Within the Arctic pack ice area, the SML has been characterized as enriched in small colloids of biological origin, resulting from extracellular polymeric secretions (EPS). During the Arctic Summer Cloud-Ocean Study (ASCOS) in August 2008, particulate and dissolved organic matter (POM, DOM) samples were collected and chemically characterized from the SML and the corresponding SSW at an open lead centered at 87.5° N and 5° E. Total organic carbon was persistently enriched in the SML with a mean enrichment factor (EF) of 1.45 ± 0.41, whereas sporadic depletions of dissolved carbohydrates and amino acids were observed. Monosaccharide compositional analysis reveals that EPS in the Arctic lead was formed mainly of distinctive heteropolysaccharides, enriched in xylose, fucose and glucose. The mean concentrations of total hydrolysable neutral sugars in SSW were 94.9 ± 37.5 nM in high molecular weight (HMW) DOM and 64.4 ± 14.5 nM in POM. The enrichment of polysaccharides in the SML appeared to be a common feature, with EFs ranging from 1.7 to 7.0 for particulate polysaccharides and 3.5 to 12.1 for polysaccharides in the HMW DOM fraction. A calculated monosaccharide yield suggests that polymers in the HMW DOM fraction were scavenged, without substantial degradation, into the SML. Bubble scavenging experiments showed that newly aggregated particles could be formed abiotically by coagulation of low molecular weight nanometer-sized gels. Experimentally-generated aerosol particles were enriched in polysaccharides by factors of 22-70, relative to the source seawater. We propose that bubble scavenging of surface-active polysaccharides was one of the possible mechanisms for the enrichment of polysaccharides in the SML.

Environmental carcinogenic polycyclic aromatic hydrocarbons in soil from Himalayas, India: Implications for spatial distribution, sources apportionment and risk assessment.

PubMed

Devi, Ningombam Linthoingambi; Yadav, Ishwar Chandra; Shihua, Qi; Dan, Yang; Zhang, Gan; Raha, Priyankar

2016-02-01

The Indian Himalayan Region (IHR) is one of the important mountain ecosystems among the global mountain system which support wide variety of flora, fauna, human communities and cultural diversities. Surface soil samples (n = 69) collected from IHR were analysed for 16 priority polycyclic aromatic hydrocarbons (PAH) listed by USEPA. The ∑16PAH concentration in surface soil ranged from 15.3 to 4762 ngg(-1) (mean 458 ngg(-1)). The sum total of low molecular weight PAH (∑LMW-PAHs) (mean 74.0 ngg(-1)) were relatively lower than the high molecular weight PAH (∑HMW-PAHs) (mean 384 ngg(-1)). The concentration of eight carcinogenic PAHs (BaA, CHR, BbF, BkF, BaP, DahA, IcdP, BghiP) were detected high in mountain soil from IHR and ranged from 0.73 to 2729 ngg(-1) (mean 272 ngg(-1)). Based on spatial distribution map, high concentration of HMW- and LMW-PAHs were detected at GS1 site in Guwahati (615 and 4071 ngg(-1)), and lowest concentration of HMW-PAHs were found at IS6 in Itanagar (5.80 ngg(-1)) and LMW-PAHs at DS2 (17.3 ngg(-1)) in Dibrugarh. Total organic carbon (TOC) in mountain soil was poorly connected with ∑PAHs (r(2) = 0.072) and Car-PAHs (r(2) = 0.048), suggesting the little role of TOC in adsorption of PAHs. Isomeric ratio of PAHs showed the source of PAH contamination in IHR is mixed of petrogenic and pyrogenic origin and was affirmed by PAHs composition profile. These source apportionment results were further confirmed by principal component analysis (PCA). Eco-toxicological analysis showed the calculated TEQ for most carcinogenic PAH were 2-4 times more than the Dutch allowed limit, while TEQ of BaP was 25 times high, suggesting increasing trend of carcinogenicity of surface soil. Copyright © 2015 Elsevier Ltd. All rights reserved.

Relaxation times and modes of disturbed aggregate distribution in micellar solutions with fusion and fission of micelles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakharov, Anatoly I.; Adzhemyan, Loran Ts.; Shchekin, Alexander K., E-mail: akshch@list.ru

2015-09-28

We have performed direct numerical calculations of the kinetics of relaxation in the system of surfactant spherical micelles under joint action of the molecular mechanism with capture and emission of individual surfactant molecules by molecular aggregates and the mechanism of fusion and fission of the aggregates. As a basis, we have taken the difference equations of aggregation and fragmentation in the form of the generalized kinetic Smoluchowski equations for aggregate concentrations. The calculations have been made with using the droplet model of molecular surfactant aggregates and two modified Smoluchowski models for the coefficients of aggregate-monomer and aggregate-aggregate fusions which takemore » into account the effects of the aggregate size and presence of hydrophobic spots on the aggregate surface. A full set of relaxation times and corresponding relaxation modes for nonequilibrium aggregate distribution in the aggregation number has been found. The dependencies of these relaxation times and modes on the total concentration of surfactant in the solution and the special parameter controlling the probability of fusion in collisions of micelles with other micelles have been studied.« less

Assembly and Characterization ofWell-DefinedHigh-Molecular-Weight Poly(p-phenylene) Polymer Brushes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jihua; Dadmun, Mark D; Mays, Jimmy

2011-01-01

The assembly and characterization of well-de ned, end-tethered poly- (p-phenylene) (PPP) brushes having high molecular weight, low polydispersity and high 1,4-stereoregularity are presented. The PPP brushes are formed using a precursor route that relies on either self-assembly or spin coating of high molecular weight (degrees of poly- merizations 54, 146, and 238) end-functionalized poly(1,3-cyclohexadiene) (PCHD) chains from benzene solutions onto silicon or quartz substrates, followed by aromatization of the end-attached PCHD chains on the surface. The approach allows the thickness (grafting density) of the brushes to be easily varied. The dry brushes before and after aromatization are characterized by ellipsometry,more » atomic force microscopy, grazing angle attenuated total re ectance Fourier transform infrared spectroscopy, and UV-Vis spectros- copy. The properties of the PPP brushes are compared with those of lms made using oligo- paraphenylenes and with ab initio density functional theory simulations of optical proper- ties. Our results suggest conversion to fully aromatized, end-tetheredPPPpolymerbrusheshaving eective conjugation lengths of 5 phenyl units.« less

Assembly and Characterization of Well Defined High Molecular Weight Poly(p-phenylene) Polymer Brushes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alonzo Calderon, Jose E; Kilbey, II, S Michael; Ankner, John Francis

2011-01-01

The assembly and characterization of well-defined, end-tethered poly(p-phenylene) (PPP) brushes having high molecular weight, low polydispersity and high 1,4-stereoregularity are presented. The PPP brushes are formed using a precursor route that relies on either self-assembly or spin coating of high molecular weight (degrees of polymerizations 54, 146, and 238) end-functionalized poly(1,3-cyclohexadiene) (PCHD) chains from benzene solutions onto silicon or quartz substrates, followed by aromatization of the end-attached PCHD chains on the surface. The approach allows the thickness (grafting density) of the brushes to be easily varied. The dry brushes before and after aromatization are characterized by ellipsometry, atomic force microscopy,more » grazing angle attenuated total reflectance Fourier transform infrared spectroscopy, and UV-Vis spectroscopy. The properties of the PPP brushes are compared with those of films made using oligo-paraphenylenes and with ab initio density functional theory simulations of optical properties. Our results suggest conversion to fully aromatized, end-tethered PPP polymer brushes having effective conjugation lengths of 5 phenyl units.« less

Specific binding of large aggregates of amphiphilic molecules to the respective antibodies.

PubMed

Nabok, Alexei; Tsargorodskaya, Anna; Holloway, Alan; Starodub, Nikolay F; Demchenko, Anna

2007-07-31

The Binding of nonylphenol to respective antibodies immobilized on solid substrates was studied with the methods of total internal reflection ellipsometry (TIRE) and QCM (quartz crystal microbalance) impedance spectroscopy. The binding reaction was proved to be highly specific having an association constant of KA=1.6x10(6) mol(-1) L and resulted in an increase in both the adsorbed layer thickness of 23 nm and the added mass of 18.3 microg/cm2 at saturation. The obtained responses of both TIRE and QCM methods are substantially higher than anticipated for the immune binding of single molecules of nonylphenol. The mechanism of binding of large aggregates of nonylphenol was suggested instead. Modeling of the micelle of amphiphilic nonylphenol molecules in aqueous solutions yielded a micelle size of about 38 nm. The mechanism of binding of large molecular aggregates to respective antibodies can be extended to other hydrophobic low-molecular-weight toxins such as T-2 mycotoxin. The formation of large molecular aggregates of nonylphenol and T-2 mycotoxin molecules on the surface was proved by the AFM study.

A direct evidence of vibrationally delocalized response at ice surface.

PubMed

Ishiyama, Tatsuya; Morita, Akihiro

2014-11-14

Surface-specific vibrational spectroscopic responses at isotope diluted ice and amorphous ice are investigated by molecular dynamics (MD) simulations combined with quantum mechanics/molecular mechanics calculations. The intense response specific to the ordinary crystal ice surface is predicted to be significantly suppressed in the isotopically diluted and amorphous ices, demonstrating the vibrational delocalization at the ordinary ice surface. The collective vibration at the ice surface is also analyzed with varying temperature by the MD simulation.

InP and GaAs characterization with variable stoichiometry obtained by molecular spray

NASA Technical Reports Server (NTRS)

Massies, J.; Linh, N. T.; Olivier, J.; Faulconnier, P.; Poirier, R.

1979-01-01

Both InP and GaAs surfaces were studied in parallel. A molecular spray technique was used to obtain two semiconductor surfaces with different superficial compositions. The structures of these surfaces were examined by electron diffraction. Electron energy loss was measured spectroscopically in order to determine surface electrical characteristics. The results are used to support conclusions relative to the role of surface composition in establishing a Schottky barrier effect in semiconductor devices.

Surface chemistry and moisture sorption properties of wood coated with multifunctional alkoxysilanes by sol-gel process

Treesearch

Mandla A. Tshabalala; Peter Kingshott; Mark R. VanLandingham; David Plackett

2003-01-01

Sol-gel surface deposition of a hydrophobic polysiloxane coating on wood was accomplished by using a mixture of a low molecular weight multifunctional alkoxysilane, methyltrimethoxysilane (MTMOS), and a high molecular weight multifunctional alkoxysilane, hexadecyltrimethoxysilane (HDTMOS). Investigation of the surface chemistry and morphology of the wood specimens by...

Reactivity of etoricoxib based on computational study of molecular orbitals, molecular electrostatic potential surface and Mulliken charge analysis

NASA Astrophysics Data System (ADS)

Sachdeva, Ritika; Soni, Abhinav; Singh, V. P.; Saini, G. S. S.

2018-05-01

Etoricoxib is one of the selective cyclooxygenase inhibitor drug which plays a significant role in the pharmacological management of arthritis and pain. The theoretical investigation of its reactivity is done using Density Functional Theory calculations. Molecular Electrostatic Potential Surface of etoricoxib and its Mulliken atomic charge distribution are used for the prediction of its electrophilic and nucleophilic sites. The detailed analysis of its frontier molecular orbitals is also done.

Metastability of isoformyl ions in collisions with helium and hydrogen. [in interstellar molecular clouds

NASA Technical Reports Server (NTRS)

Green, S.

1984-01-01

The stability of HOC(+) ions under conditions in interstellar molecular clouds is considered. In particular, the possibility that collisions with helium or hydrogen will induce isomerization to the stable HCO(+) form is examined theoretically. Portions of the electronic potential energy surfaces for interaction with He and H atoms are obtained from standard quantum mechanical calculations. Collisions with He atoms are found to be totally ineffective for inducing isomerization. Collisions with H atoms are found to be ineffective at low interstellar temperatures owing to a small (about 500 K) barrier in the entrance channel; at higher temperatures where this barrier can be overcome, however, collisions with hydrogen atoms do result in conversion to the stable HCO(+) form. Although detailed calculations are not presented, it is argued that low-energy collisions with H2 molecules are also ineffective in destroying the metastable ion.

The greenhouse of Titan.

NASA Technical Reports Server (NTRS)

Sagan, C.

1973-01-01

Analysis of non-gray radiative equilibrium and gray convective equilibrium on Titan suggests that a massive molecular-hydrogen greenhouse effect may be responsible for the disagreement between the observed IR temperatures and the equilibrium temperature of an atmosphereless Titan. Calculations of convection indicate a probable minimum optical depth of 14 which corresponds to a molecular hydrogen shell of substantial thickness with total pressures of about 0.1 bar. It is suggested that there is an equilibrium between outgassing and blow-off on the one hand and accretion from the protons trapped in a hypothetical Saturnian magnetic field on the other, in the present atmosphere of Titan. It is believed that an outgassing equivalent to the volatilization of a few kilometers of subsurface ice is required to maintain the present blow-off rate without compensation for all geological time. The presence of an extensive hydrogen corona around Titan is postulated, with surface temperatures up to 200 K.

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

NASA Astrophysics Data System (ADS)

Wang, Hong-Fei

2016-12-01

Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there have been many progresses in the development of methodology and instrumentation in the SFG-VS toolbox that have significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

A parametric study of surface roughness and bonding mechanisms of aluminum alloys with epoxies: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Timilsina, Rajendra; Termaath, Stephanie

The marine environment is highly aggressive towards most materials. However, aluminium-magnesium alloys (Al-Mg, specifically, 5xxx series) have exceptionally long service life in such aggressive marine environments. For instance, an Al-Mg alloy, AA5083, is extensively used in naval structures because of its good mechanical strength, formability, seawater corrosion resistance and weldability. However, bonding mechanisms of these alloys with epoxies in a rough surface environment are not fully understood yet. It requires a rigorous investigation at molecular or atomic levels. We performed a molecular dynamics simulation to study an adherend surface preparation and surface bonding mechanisms of Al-Mg alloy (AA5083) with different epoxies by developing several computer models. Various distributions of surface roughness are introduced in the models and performed molecular dynamics simulations. Formation of a beta phase (Al3Mg2) , microstructures, bonding energies at the interface, bonding strengths and durability are investigated. Office of Naval Research.

A review of molecular phase separation in binary self-assembled monolayers of thiols on gold surfaces

NASA Astrophysics Data System (ADS)

Ong, Quy; Nianias, Nikolaos; Stellacci, Francesco

2017-09-01

Binary self-assembled monolayers (SAMs) on gold surfaces have been known to undergo molecular phase separation to various degrees and have been subject to both experimental and theoretical studies. On gold nanoparticles in particular, binary SAMs ligand shells display intriguing morphologies. Consequently, unexpected behaviors of the nanoparticles with respect to their biological, chemical, and interfacial properties have been observed. It is critical that the phase separation of binary SAMs be understood at both molecular and macroscopic level to create, and then manipulate, the useful properties of the functionalized surfaces. We look into the current understanding of molecular phase separation of binary SAMs on gold surfaces, represented by Au(111) flat surfaces and Au nanoparticles, from both theoretical and experimental aspects. We point out shortcomings and describe several research strategies that will address them in the future. Contribution to the Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Pule Pileni.

Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hong-Fei

Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there has been significant progress in the development of methodology and instrumentation in the SFG-VS toolbox that has significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, somemore » of the controversial issues that have been puzzling the community are to be discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.« less

Molecular level studies on interfacial hydration of zwitterionic and other antifouling polymers in situ.

PubMed

Leng, Chuan; Sun, Shuwen; Zhang, Kexin; Jiang, Shaoyi; Chen, Zhan

2016-08-01

Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. Zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this review, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. Using SFG spectroscopy, we have measured the hydration layers of antifouling materials and found that strong hydrogen bonds are key to the formation of strong hydration layers preventing protein fouling at the polymer interfaces. Antifouling polymers have wide applications in biomedical engineering and marine industry. Recently, zwitterionic materials have been reported as promising candidates for antifouling applications, while strong hydration is believed to be the key antifouling mechanism. However, zwitterionic materials can be designed with various molecular structures, which affect their hydration and antifouling performance. Moreover, although strong hydration has been proposed to occur at the material surfaces, probing the solid material/water interfaces is challenging with traditional analytical techniques. Here in this manuscript, we will review our studies on surface hydration of zwitterionic materials and other antifouling materials by using sum frequency generation (SFG) vibrational spectroscopy, which provides molecular understanding of the water structures at various material surfaces. The materials studied include zwitterionic polymer brushes with different molecular structures, amphiphilic polymers with zwitterionic groups, uncharged hydrophilic polymer brushes, amphiphilic polypeptoids, and widely used antifouling material poly(ethylene glycol). We will compare the differences among zwitterionic materials with various molecular structures as well as the differences between antifouling materials and fouling surfaces of control samples. We will also discuss the effects of pH and biological molecules like proteins on the surface hydration of the zwitterionic materials. All the SFG results indicate that strongly hydrogen-bonded water at the materials' surfaces (strong surface hydration) is closely correlated to the good antifouling properties of the materials. This review will be widely interested by readers of Acta Biomaterialia and will impact many different research fields in chemistry, materials, engineering, and beyond. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Mechanisms of Surface-Mediated DNA Hybridization

PubMed Central

2015-01-01

Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100 000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state. PMID:24708278

FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins

PubMed Central

Vorobjev, Yury N.; Vila, Jorge A.

2009-01-01

A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford–Schellman integral if the proteins contain more than ∼20–25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pKa's of the ionizable groups of these proteins within an average absolute value of 0.4 pK units and a maximum error of 1.2 pK units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford–Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics, as a function of pH. PMID:18683966

Ordered adsorption of coagulation factor XII on negatively charged polymer surfaces probed by sum frequency generation vibrational spectroscopy.

PubMed

Chen, Xiaoyun; Wang, Jie; Paszti, Zoltan; Wang, Fulin; Schrauben, Joel N; Tarabara, Volodymyr V; Schmaier, Alvin H; Chen, Zhan

2007-05-01

Electrostatic interactions between negatively charged polymer surfaces and factor XII (FXII), a blood coagulation factor, were investigated by sum frequency generation (SFG) vibrational spectroscopy, supplemented by several analytical techniques including attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), quartz crystal microbalance (QCM), zeta-potential measurement, and chromogenic assay. A series of sulfonated polystyrenes (sPS) with different sulfonation levels were synthesized as model surfaces with different surface charge densities. SFG spectra collected from FXII adsorbed onto PS and sPS surfaces with different surface charge densities showed remarkable differences in spectral features and especially in spectral intensity. Chromogenic assay experiments showed that highly charged sPS surfaces induced FXII autoactivation. ATR-FTIR and QCM results indicated that adsorption amounts on the PS and sPS surfaces were similar even though the surface charge densities were different. No significant conformational change was observed from FXII adsorbed onto surfaces studied. Using theoretical calculations, the possible contribution from the third-order nonlinear optical effect induced by the surface electric field was evaluated, and it was found to be unable to yield the SFG signal enhancement observed. Therefore it was concluded that the adsorbed FXII orientation and ordering were the main reasons for the remarkable SFG amide I signal increase on sPS surfaces. These investigations indicate that negatively charged surfaces facilitate or induce FXII autoactivation on the molecular level by imposing specific orientation and ordering on the adsorbed protein molecules.

HIGH STAR FORMATION RATES IN TURBULENT ATOMIC-DOMINATED GAS IN THE INTERACTING GALAXIES IC 2163 AND NGC 2207

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elmegreen, Bruce G.; Kaufman, Michele; Bournaud, Frédéric

CO observations of the interacting galaxies IC 2163 and NGC 2207 are combined with HI, H α , and 24 μ m observations to study the star formation rate (SFR) surface density as a function of the gas surface density. More than half of the high-SFR regions are HI dominated. When compared to other galaxies, these HI-dominated regions have excess SFRs relative to their molecular gas surface densities but normal SFRs relative to their total gas surface densities. The HI-dominated regions are mostly located in the outer part of NGC 2207 where the HI velocity dispersion is high, 40–50 kmmore » s{sup −1}. We suggest that the star-forming clouds in these regions have envelopes at lower densities than normal, making them predominantly atomic, and cores at higher densities than normal because of the high turbulent Mach numbers. This is consistent with theoretical predictions of a flattening in the density probability distribution function for compressive, high Mach number turbulence.« less

Effect of different drying methods on chemical composition and bioactivity of tea polysaccharides.

PubMed

Wang, Yuanfeng; Liu, Yangyang; Huo, Jianglei; Zhaoa, Xintong; Zhao, Tingtong; Zheng, Jian; Ren, Jian; Wei, Xinlin

2013-11-01

Four polysaccharides (TPS-F, TPS-V, TPS-S and TPS-M) were obtained from tea (Camellia sinensis) leaves by freeze-drying, vacuum-drying, spray-drying and microwave-vacuum drying, respectively. Their chemical composition and biological properties were comparatively studied. The results showed these TPS were similar in IR, UV absorption and distribution of molecular weight. However, they showed significant differences (P<0.05) in yields of crude polysaccharides and contents of protein and total polyphenols. Furthermore, morphological analysis showed their surface differed from each other in size and shape when viewed by SEM, from which surface of TPS-F was rough and porous, surface of TPS-S was evenly particles, and surfaces of the other two were similar to anomalistic bricks. In addition, the bioactivity of them was also evaluated. It was found TPS-F exhibited relatively better ability on metal chelating and superoxide radicals scavenging assays than others, and TPS-V exhibited higher ability on α-glycosidase and α-amylase inhibition assays than others with inhibitory percentages of 82.75% and 92.8%. Copyright © 2013 Elsevier B.V. All rights reserved.

In vitro determination of HT oxidation activity and tritium concentration in soil and vegetation during the chronic HT release experiment at Chalk River

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ichimasa, Y.; Ichimasa, M.; Jiang, H.

1995-10-01

The oxidation activity of molecular tritium (HT) in soils and vegetation collected in experimental plots during the 1994 chronic HT release experiment at Chalk River was determined in vitro laboratory experiments after the release. HT oxidation activity was highest in surface soils in the natural plot, about 3-4 times that in soils in the cultivated plots. HT oxidation activity in weeds and Komatsuna leaves was about 2 and 0.4% of that in the cultivated soil, respectively. The number of HT-oxidizing bacteria isolated from soils was highest in the surface soil (0-5 cm) in the natural plot. The viable cell numbersmore » in surface soils in the cultivated and natural plots were almost the same. The total occurrence rates of HT-oxidizing bacteria in the surface soils were 22% in the natural plot, and 7.5% in the cultivated plot. The occurrence rates of HT-oxidizing airborne bacteria during the release on two culture media were 4.2 and 1.9%. 16 refs., 3 figs., 3 tabs.« less

Fabrication of precision high quality facets on molecular beam epitaxy material

DOEpatents

Petersen, Holly E.; Goward, William D.; Dijaili, Sol P.

2001-01-01

Fabricating mirrored vertical surfaces on semiconductor layered material grown by molecular beam epitaxy (MBE). Low energy chemically assisted ion beam etching (CAIBE) is employed to prepare mirrored vertical surfaces on MBE-grown III-V materials under unusually low concentrations of oxygen in evacuated etching atmospheres of chlorine and xenon ion beams. UV-stabilized smooth-surfaced photoresist materials contribute to highly vertical, high quality mirrored surfaces during the etching.

High- and low-molecular-mass microbial surfactants.

PubMed

Rosenberg, E; Ron, E Z

1999-08-01

Microorganisms synthesize a wide variety of high- and low-molecular-mass bioemulsifiers. The low-molecular-mass bioemulsifiers are generally glycolipids, such as trehalose lipids, sophorolipids and rhamnolipids, or lipopeptides, such as surfactin, gramicidin S and polymyxin. The high-molecular-mass bioemulsifiers are amphipathic polysaccharides, proteins, lipopolysaccharides, lipoproteins or complex mixtures of these biopolymers. The low-molecular-mass bioemulsifiers lower surface and interfacial tensions, whereas the higher-molecular-mass bioemulsifiers are more effective at stabilizing oil-in-water emulsions. Three natural roles for bioemulsifiers have been proposed: (i) increasing the surface area of hydrophobic water-insoluble growth substrates; (ii) increasing the bioavailability of hydrophobic substrates by increasing their apparent solubility or desorbing them from surfaces; (iii) regulating the attachment and detachment of microorganisms to and from surfaces. Bioemulsifiers have several important advantages over chemical surfactants, which should allow them to become prominent in industrial and environmental applications. The potential commercial applications of bioemulsifiers include bioremediation of oil-polluted soil and water, enhanced oil recovery, replacement of chlorinated solvents used in cleaning-up oil-contaminated pipes, vessels and machinery, use in the detergent industry, formulations of herbicides and pesticides and formation of stable oil-in-water emulsions for the food and cosmetic industries.

Anisotropic Nanomechanics of Boron Nitride Nanotubes: Nanostructured "Skin" Effect

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu; Cho, KyeongJae

2000-01-01

The stiffness and plasticity of boron nitride nanotubes are investigated using generalized tight-binding molecular dynamics and ab-initio total energy methods. Due to boron-nitride BN bond buckling effects, compressed zigzag BN nanotubes are found to undergo novel anisotropic strain release followed by anisotropic plastic buckling. The strain is preferentially released towards N atoms in the rotated BN bonds. The tubes buckle anisotropically towards only one end when uniaxially compressed from both. A "skin-effect" model of smart nanocomposite materials is proposed which will localize the structural damage towards the 'skin' or surface side of the material.

Mutual influence of molecular diffusion in gas and surface phases

NASA Astrophysics Data System (ADS)

Hori, Takuma; Kamino, Takafumi; Yoshimoto, Yuta; Takagi, Shu; Kinefuchi, Ikuya

2018-01-01

We develop molecular transport simulation methods that simultaneously deal with gas- and surface-phase diffusions to determine the effect of surface diffusion on the overall diffusion coefficients. The phenomenon of surface diffusion is incorporated into the test particle method and the mean square displacement method, which are typically employed only for gas-phase transport. It is found that for a simple cylindrical pore, the diffusion coefficients in the presence of surface diffusion calculated by these two methods show good agreement. We also confirm that both methods reproduce the analytical solution. Then, the diffusion coefficients for ink-bottle-shaped pores are calculated using the developed method. Our results show that surface diffusion assists molecular transport in the gas phase. Moreover, the surface tortuosity factor, which is known to be uniquely determined by physical structure, is influenced by the presence of gas-phase diffusion. This mutual influence of gas-phase diffusion and surface diffusion indicates that their simultaneous calculation is necessary for an accurate evaluation of the diffusion coefficients.

H2 emission as a tracer of molecular hydrogen: Large-scale observations of Orion

NASA Technical Reports Server (NTRS)

Luhman, M. L.; Jaffe, D. T.; Keller, L. D.; Pak, Soojong

1994-01-01

We have detected extremely extended (greater than 1.5 deg, or 12 pc) near-infrared H2 line emission from the Orion A molecular cloud. We have mapped emission in the 1.601 micrometer(s) upsilon = 6 - 4 Q(1) and 2.121 micrometer(s) upsilon = 1 - 0 S(1) lines of H2 along a approx. 2 deg R.A. cut and from a 6' x 6' region near theta(sup 1) Ori C. The surface brightness of the extended H2 line emission is 10(exp -6) to 10(exp -5) ergs/s/sq. cm/sr. Based on the distribution and relative strengths of the H2 lines, we conclude that UV fluorescene is most likely the dominant H2 emission mechanism in the outer parts of the Orion cloud. Shock-heated gas does not make a major contribution to the H2 emission in this region. The fluorescent component of the total H2 upsilon = 1 - 0 S(1) luminosity from Orion is 30-40 solar luminosity. Molecular hydrogen excited by UV radiation from nearby OB stars contributes 98%-99% of the global H2 line emission from the Orion molecular cloud, even though this cloud has a powerful shock-excited H2 source in its core. The ability to detect large-scale H2 directly opens up new possibilities for the study of molecular clouds.

Characterization of GaN microstructures grown by plasma-assisted molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lo, Ikai; Pang, Wen-Yuan; Hsu, Yu-Chi

2013-06-15

The characterization of GaN microstructures grown by plasma-assisted molecular beam epitaxy on LiAlO{sub 2} substrate was studied by cathodoluminescence and photoluminescence measurements. We demonstrated that the cathodoluminescence from oblique semi-polar surfaces of mushroom-shaped GaN was much brighter than that from top polar surface due to the reduction of polarization field on the oblique semi-polar surfaces. It implies that the oblique semi-polar surface is superior for the light-emitting surface of wurtzite nano-devices.

Structural Characterization of Vapor-deposited Organic Glasses

NASA Astrophysics Data System (ADS)

Gujral, Ankit

Physical vapor deposition, a common route of thin film fabrication for organic electronic devices, has recently been shown to produce organic glassy films with enhanced kinetic stability and anisotropic structure. Anisotropic structures are of interest in the organic electronics community as it has been shown that certain structures lead to enhanced device performance, such as higher carrier mobility and better light outcoupling. A mechanism proposed to explain the origin of the stability and anisotropy of vapor-deposited glasses relies on two parameters: 1) enhanced molecular mobility at the free surface (vacuum interface) of a glass, and 2) anisotropic molecular packing at the free surface of the supercooled liquid of the glass-forming system. By vapor-depositing onto a substrate maintained at Tsubstrate < Tg (where Tg is the glass transition temperature), the enhanced molecular mobility at the free surface allows every molecule that lands on the surface to at least partially equilibrate to the preferred anisotropic molecular packing motifs before being buried by further deposition. The extent of equilibration depends on the mobility at the surface, controlled by Tsubstrate, and the residence time on the free surface, controlled by the rate of deposition. This body of work deals with the optimization of deposition conditions and system chemistry to prepare and characterize films with functional anisotropic structures. Here, we show that structural anisotropy can be attained for a variety of molecular systems including a rod-shaped non-mesogen, TPD, a rod-shaped smectic mesogen, itraconazole, two discotic mesogens, phenanthroperylene-ester and triphenylene-ester, and a disc-shaped non-mesogen, m-MTDATA. Experimental evidence is also provided of the anisotropic molecular packing at the free surface (vacuum interface) for the disc-shaped systems that are consistent with the expectations of the proposed mechanism and the final bulk state of the vapor-deposited glasses.

Evolution of genetic polymorphisms of Plasmodium falciparum merozoite surface protein (PfMSP) in Thailand.

PubMed

Kuesap, Jiraporn; Chaijaroenkul, Wanna; Ketprathum, Kanchanok; Tattiyapong, Puntanat; Na-Bangchang, Kesara

2014-02-01

Plasmodium falciparum malaria is a major public health problem in Thailand due to the emergence of multidrug resistance. The understanding of genetic diversity of malaria parasites is essential for developing effective drugs and vaccines. The genetic diversity of the merozoite surface protein-1 (PfMSP-1) and merozoite surface protein-2 (PfMSP-2) genes was investigated in a total of 145 P. falciparum isolates collected from Mae Sot District, Tak Province, Thailand during 3 different periods (1997-1999, 2005-2007, and 2009-2010). Analysis of genetic polymorphisms was performed to track the evolution of genetic change of P. falciparum using PCR. Both individual genes and their combination patterns showed marked genetic diversity during the 3 study periods. The results strongly support that P. falciparum isolates in Thailand are markedly diverse and patterns changed with time. These 2 polymorphic genes could be used as molecular markers to detect multiple clone infections and differentiate recrudescence from reinfection in P. falciparum isolates in Thailand.

Rational engineering of a mesohalophilic carbonic anhydrase to an extreme halotolerant biocatalyst

PubMed Central

Warden, Andrew C.; Williams, Michelle; Peat, Thomas S.; Seabrook, Shane A.; Newman, Janet; Dojchinov, Greg; Haritos, Victoria S.

2015-01-01

Enzymes expressed by highly salt-tolerant organisms show many modifications compared with salt-affected counterparts including biased amino acid and lower α-helix content, lower solvent accessibility and negative surface charge. Here, we show that halotolerance can be generated in an enzyme solely by modifying surface residues. Rational design of carbonic anhydrase II is undertaken in three stages replacing 18 residues in total, crystal structures confirm changes are confined to surface residues. Catalytic activities and thermal unfolding temperatures of the designed enzymes increase at high salt concentrations demonstrating their shift to halotolerance, whereas the opposite response is found in the wild-type enzyme. Molecular dynamics calculations reveal a key role for sodium ions in increasing halotolerant enzyme stability largely through interactions with the highly ordered first Na+ hydration shell. For the first time, an approach to generate extreme halotolerance, a trait with broad application in industrial biocatalysis, in a wild-type enzyme is demonstrated. PMID:26687908

Weak competing interactions control assembly of strongly bonded TCNQ ionic acceptor molecules on silver surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Changwon; Rojas, Geoffrey A.; Jeon, Seokmin

2014-09-19

The energy scales of interactions that control molecular adsorption and assembly on surfaces can vary by several orders of magnitude, yet the importance of each contributing interaction is not apparent a priori. Tetracyanoquinodimethane (TCNQ) is an archetypal electron acceptor molecule and it is a key component of organic metals. On metal surfaces, this molecule also acts as an electron acceptor, producing negatively charged adsorbates. It is therefore rather intriguing to observe attractive molecular interactions in this system that were reported previously for copper and silver surfaces. In this paper, our experiments compared TCNQ adsorption on noble metal surfaces of Ag(100)more » and Ag(111). In both cases we found net attractive interactions down to the lowest coverage. However, the morphology of the assemblies was strikingly different, with two-dimensional islands on Ag(100) and one-dimensional chains on Ag(111) surfaces. This observation suggests that the registry effect governed by the molecular interaction with the underlying lattice potential is critical in determining the dimensionality of the molecular assembly. Using first-principles density functional calculations with a van der Waals correction scheme, we revealed that the strengths of major interactions (i.e., lattice potential corrugation, intermolecular attraction, and charge-transfer-induced repulsion) are all similar in energy. The van der Waals interactions, in particular, almost double the strength of attractive interactions, making the intermolecular potential comparable in strength to the diffusion potential and promoting self-assembly. However, it is the anisotropy of local intermolecular interactions that is primarily responsible for the difference in the topology of the molecular islands on Ag(100) and Ag(111) surfaces. Finally, we anticipate that the intermolecular potential will become more attractive and dominant over the diffusion potential with increasing molecular size, providing new design strategies for the structure and charge transfer within molecular layers.« less

MODELING THE INTERACTION OF AGROCHEMICALS WITH ENVIRONMENTAL SURFACES

EPA Science Inventory

The interactions between agrochemicals and organo-mineral surfaces were studied using molecular mechanical conformational calculations and molecular dynamics simulations. Atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine), 2,4-D (1, 2-dichlorophenoxyacetic acid), and DD...

Supramolecular assembly of (Z)-ethyl 2-cyano-3-((4-fluorophenyl)amino) acrylate, crystal structure, Hirshfeld surface analysis and DFT studies

NASA Astrophysics Data System (ADS)

Matos, Catiúcia R. M. O.; Vitorino, Letícia S.; de Oliveira, Pedro H. R.; de Souza, Maria Cecília B. V.; Cunha, Anna C.; Boechat, Fernanda da C. S.; Resende, Jackson A. L. C.; Carneiro, José Walkimar de M.; Ronconi, Célia M.

2016-09-01

A mixture of the E and Z isomers of ethyl 2-cyano-3-((4-fluorophenyl)amino) acrylate was synthesized and characterized by elemental analysis, attenuated total reflectance-Fourier transform infrared spectroscopy, 1H and 13C nuclear magnetic resonance spectroscopy. The structure of the Z isomer was determined by single crystal X-ray diffraction, which revealed a three-dimensional supramolecular network governed by Csbnd H⋯N, Csbnd H⋯O, and Csbnd H⋯F hydrogen bonds and π⋯π stacking interactions. The combination of these interactions plays an important role in stabilizing the self-assembly process and the molecular conformation. Hirshfeld surface analysis indicated the roles of the noncovalent interactions in the crystal packing, which were quantified by fingerprint plots and DFT calculations.

Quantitative RHEED Studies of MBE Growth of 3-5 Compounds

DTIC Science & Technology

1991-06-03

Vertical - Cavity Surface - Emitting Laser Using Molecular Beam Epitaxial ...Growth of Vertical Cavity Surface - emitting Lasers Our work under this ARO contract on the control of MBE growth has enhanced our ability to grow...pattern about the surface structure of nearly perfect crystals prepared by Molecular Beam Epitaxy ( MBE ) and to use these techniques

Molecular recognition in gas sensing: Results from acoustic wave and in-situ FTIR measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hierlemann, A.; Ricco, A.J.; Bodenhoefer, K.

Surface acoustic wave (SAW) measurements were combined with direct, in-situ molecular spectroscopy to understand the interactions of surface-confined sensing films with gas-phase analytes. This was accomplished by collecting Fourier-transform infrared external-reflectance spectra (FTIR-ERS) on operating SAW devices during dosing of their specifically coated surfaces with key analytes.

Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets.

PubMed

Bacle, Amélie; Gautier, Romain; Jackson, Catherine L; Fuchs, Patrick F J; Vanni, Stefano

2017-04-11

Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

L-Tryptophan on Cu(111): engineering a molecular labyrinth driven by indole groups

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yitamben, E. N.; Clayborne, A.; Darling, Seth B.

2015-05-21

The present article investigates the adsorption and molecular orientation of L-Tryptophan, which is both an essential amino acid important for protein synthesis and of particular interest for the development of chiral molecular electronics and biocompatible processes and devices, on Cu(111) using scanning tunneling microscopy and spectroscopy at 55 K and at room temperature. The arrangement of chemisorbed L-Tryptophan on the copper surface varies with both temperature and surface coverage. At low coverage, small clusters form on the surface irrespective of temperature, while at high coverage an ordered chain structure emerges at room temperature, and a tightly packed structure forms amore » molecular labyrinth at low temperature. The dominating superstructure of the adsorbates arises from intermolecular hydrogen bonding, and pi-bonding interactions between the indole groups of neighboring molecules and the Cu surface.« less

Engineering On-Surface Spin Crossover: Spin-State Switching in a Self-Assembled Film of Vacuum-Sublimable Functional Molecule.

PubMed

Kumar, Kuppusamy Senthil; Studniarek, Michał; Heinrich, Benoît; Arabski, Jacek; Schmerber, Guy; Bowen, Martin; Boukari, Samy; Beaurepaire, Eric; Dreiser, Jan; Ruben, Mario

2018-03-01

The realization of spin-crossover (SCO)-based applications requires study of the spin-state switching characteristics of SCO complex molecules within nanostructured environments, especially on surfaces. Except for a very few cases, the SCO of a surface-bound thin molecular film is either quenched or heavily altered due to: (i) molecule-surface interactions and (ii) differing intermolecular interactions in films relative to the bulk. By fabricating SCO complexes on a weakly interacting surface, the interfacial quenching problem is tackled. However, engineering intermolecular interactions in thin SCO active films is rather difficult. Here, a molecular self-assembly strategy is proposed to fabricate thin spin-switchable surface-bound films with programmable intermolecular interactions. Molecular engineering of the parent complex system [Fe(H 2 B(pz) 2 ) 2 (bpy)] (pz = pyrazole, bpy = 2,2'-bipyridine) with a dodecyl (C 12 ) alkyl chain yields a classical amphiphile-like functional and vacuum-sublimable charge-neutral Fe II complex, [Fe(H 2 B(pz) 2 ) 2 (C 12 -bpy)] (C 12 -bpy = dodecyl[2,2'-bipyridine]-5-carboxylate). Both the bulk powder and 10 nm thin films sublimed onto either quartz glass or SiO x surfaces of the complex show comparable spin-state switching characteristics mediated by similar lamellar bilayer like self-assembly/molecular interactions. This unprecedented observation augurs well for the development of SCO-based applications, especially in molecular spintronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping

NASA Astrophysics Data System (ADS)

Lu, Jianfeng; Zhou, Zhennan

2018-02-01

To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.

Exploring Surface Analysis Techniques for the Detection of Molecular Contaminants on Spacecraft

NASA Technical Reports Server (NTRS)

Rutherford, Gugu N.; Seasly, Elaine; Thornblom, Mark; Baughman, James

2016-01-01

Molecular contamination is a known area of concern for spacecraft. To mitigate this risk, projects involving space flight hardware set requirements in a contamination control plan that establishes an allocation budget for the exposure of non-volatile residues (NVR) onto critical surfaces. The purpose of this work will focus on non-contact surface analysis and in situ monitoring to mitigate molecular contamination on space flight hardware. By using Scanning Electron Microscopy and Energy Dispersive Spectroscopy (SEM-EDS) with Raman Spectroscopy, an unlikely contaminant was identified on space flight hardware. Using traditional and surface analysis methods provided the broader view of the contamination sources allowing for best fit solutions to prevent any future exposure.

Predictive Finite Rate Model for Oxygen-Carbon Interactions at High Temperature

NASA Astrophysics Data System (ADS)

Poovathingal, Savio

An oxidation model for carbon surfaces is developed to predict ablation rates for carbon heat shields used in hypersonic vehicles. Unlike existing empirical models, the approach used here was to probe gas-surface interactions individually and then based on an understanding of the relevant fundamental processes, build a predictive model that would be accurate over a wide range of pressures and temperatures, and even microstructures. Initially, molecular dynamics was used to understand the oxidation processes on the surface. The molecular dynamics simulations were compared to molecular beam experiments and good qualitative agreement was observed. The simulations reproduced cylindrical pitting observed in the experiments where oxidation was rapid and primarily occurred around a defect. However, the studies were limited to small systems at low temperatures and could simulate time scales only of the order of nanoseconds. Molecular beam experiments at high surface temperature indicated that a majority of surface reaction products were produced through thermal mechanisms. Since the reactions were thermal, they occurred over long time scales which were computationally prohibitive for molecular dynamics to simulate. The experiments provided detailed dynamical data on the scattering of O, O2, CO, and CO2 and it was found that the data from molecular beam experiments could be used directly to build a model. The data was initially used to deduce surface reaction probabilities at 800 K. The reaction probabilities were then incorporated into the direct simulation Monte Carlo (DSMC) method. Simulations were performed where the microstructure was resolved and dissociated oxygen convected and diffused towards it. For a gas-surface temperature of 800 K, it was found that despite CO being the dominant surface reaction product, a gas-phase reaction forms significant CO2 within the microstructure region. It was also found that surface area did not play any role in concentration of reaction products because the reaction probabilities were in the diffusion dominant regime. The molecular beam data at different surface temperatures was then used to build a finite rate model. Each reaction mechanism and all rate parameters of the new model were determined individually based on the molecular beam data. Despite the experiments being performed at near vacuum conditions, the finite rate model developed using the data could be used at pressures and temperatures relevant to hypersonic conditions. The new model was implemented in a computational fluid dynamics (CFD) solver and flow over a hypersonic vehicle was simulated. The new model predicted similar overall mass loss rates compared to existing models, however, the individual species production rates were completely different. The most notable difference was that the new model (based on molecular beam data) predicts CO as the oxidation reaction product with virtually no CO2 production, whereas existing models predict the exact opposite trend. CO being the dominant oxidation product is consistent with recent high enthalpy wind tunnel experiments. The discovery that measurements taken in molecular beam facilities are able to determine individual reaction mechanisms, including dependence on surface coverage, opens up an entirely new way of constructing ablation models.

Measurement of surface stay times for physical adsorption of gases. Ph.D. Thesis - Va. Univ.; [using molecular beam time of flight technique

NASA Technical Reports Server (NTRS)

Wilmoth, R. G.

1973-01-01

A molecular beam time-of-flight technique is studied as a means of determining surface stay times for physical adsorption. The experimental approach consists of pulsing a molecular beam, allowing the pulse to strike an adsorbing surface and detecting the molecular pulse after it has subsequently desorbed. The technique is also found to be useful for general studies of adsorption under nonequilibrium conditions including the study of adsorbate-adsorbate interactions. The shape of the detected pulse is analyzed in detail for a first-order desorption process. For mean stay times, tau, less than the mean molecular transit times involved, the peak of the detected pulse is delayed by an amount approximately equal to tau. For tau much greater than these transit times, the detected pulse should decay as exp(-t/tau). However, for stay times of the order of the transit times, both the molecular speed distributions and the incident pulse duration time must be taken into account.

On the computation of molecular surface correlations for protein docking using fourier techniques.

PubMed

Sakk, Eric

2007-08-01

The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.

Molecular Insight into the Slipperiness of Ice.

PubMed

Weber, Bart; Nagata, Yuki; Ketzetzi, Stefania; Tang, Fujie; Smit, Wilbert J; Bakker, Huib J; Backus, Ellen H G; Bonn, Mischa; Bonn, Daniel

2018-05-16

Measurements of the friction coefficient of steel-on-ice over a large temperature range reveal very high friction at low temperatures (-100 °C) and a steep decrease in the friction coefficient with increasing temperature. Very low friction is only found over the limited temperature range typical for ice skating. The strong decrease in the friction coefficient with increasing temperature exhibits Arrhenius behavior with an activation energy of E a ≈ 11.5 kJ mol -1 . Remarkably, molecular dynamics simulations of the ice-air interface reveal a very similar activation energy for the mobility of surface molecules. Weakly hydrogen-bonded surface molecules diffuse over the surface in a rolling motion, their number and mobility increasing with increasing temperature. This correlation between macroscopic friction and microscopic molecular mobility indicates that slippery ice arises from the high mobility of its surface molecules, making the ice surface smooth and the shearing of the weakly bonded surface molecules easy.

CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE*

PubMed Central

MIKUCKI, MICHAEL; ZHOU, Y. C.

2017-01-01

This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization. PMID:29056778

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

PubMed

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

Influence of Natural Organic Matter (NOM) Character on the Distribution of Chlorinated and Chloraminated Disinfection By-Products (DBPs) at Rand Water

NASA Astrophysics Data System (ADS)

Marais, Savia S.; Ncube, Esper J.; Haarhoff, Johannes; Msagati, Titus AM; Mamba, Bhekie B.; Nkambule, Thabo I.

2016-04-01

Certain disinfection by-products (DBPs) are likely human carcinogens or present mutagenic effects while many DBPs are unidentified. Considering the possibility of DBPs being harmful to human health and the fact that trihalomethanes (THMs) are the only regulated DBP in the South African National Standard (SANS:241) for drinking water, special interest in the precursors to these DBPs' formation is created. It is essential to understand the reactivity and character of the precursors responsible for the formation of DBPs in order to enhance precursor removal strategies during the treatment of drinking water. In this study the character of NOM within surface water and the subsequent distribution of THMs formed in the drinking water from Rand Waters' full scale treatment plant were investigated. Molecular size distribution (MSD) of NOM within the surface water was determined by high performance size exclusion chromatography (HPSEC). Specific ultraviolet absorbance (SUVA) and UV254 measurements formed part of the NOM character study as they provide an indication of the aromaticity of organic matter. The four THMs; bromoform, chloroform, dibromochloromethane (DBCM) and bromodichloromethane (BDCM)were measured by gas chromatography. The sum of these four THMs was expressed as total trihalomethane (TTHM). On average the chloroform constituted 76.2% of the total TTHM, BDCM 22.5% while DBCM and bromoform measured below the detection limit. THM speciation after chlorination and chloramination concentrations increased in the sequence bromoform < DBCM < BDCM < chloroform. Results of the MSD showed a significant correlation between NOM of high molecular size (peak I) and TTHM formation specifically during the summer months (R2= 0.971, p < 0.05). High molecular weight (HMW) NOM also related well to chloroform formation (R2 = 0.963, p < 0.05) however, the formation of BDCM was not due to HWM fraction as indicated by weak regression coefficient. A positive correlation existed between SUVA and UV254 removal percentage (R2 = 0.937, p < 0.05). Seasonal variability in NOM character was evident in the source water in summer when high temperatures and rainfall occurred. The results displayed are an indication that aromatic NOM were the main precursor to TTHM formation, more prominently during summer. Keywords: disinfection by-products, molecular size distribution, natural organic matter, UV254

Catalysis beyond frontier molecular orbitals: Selectivity in partial hydrogenation of multi-unsaturated hydrocarbons on metal catalysts

PubMed Central

Liu, Wei; Jiang, Yingda; Dostert, Karl-Heinz; O’Brien, Casey P.; Riedel, Wiebke; Savara, Aditya; Schauermann, Swetlana; Tkatchenko, Alexandre

2017-01-01

The mechanistic understanding and control over transformations of multi-unsaturated hydrocarbons on transition metal surfaces remains one of the major challenges of hydrogenation catalysis. To reveal the microscopic origins of hydrogenation chemoselectivity, we performed a comprehensive theoretical investigation on the reactivity of two α,β-unsaturated carbonyls—isophorone and acrolein—on seven (111) metal surfaces: Pd, Pt, Rh, Ir, Cu, Ag, and Au. In doing so, we uncover a general mechanism that goes beyond the celebrated frontier molecular orbital theory, rationalizing the C═C bond activation in isophorone and acrolein as a result of significant surface-induced broadening of high-energy inner molecular orbitals. By extending our calculations to hydrogen-precovered surface and higher adsorbate surface coverage, we further confirm the validity of the “inner orbital broadening mechanism” under realistic catalytic conditions. The proposed mechanism is fully supported by our experimental reaction studies for isophorone and acrolein over Pd nanoparticles terminated with (111) facets. Although the position of the frontier molecular orbitals in these molecules, which are commonly considered to be responsible for chemical interactions, suggests preferential hydrogenation of the C═O double bond, experiments show that hydrogenation occurs at the C═C bond on Pd catalysts. The extent of broadening of inner molecular orbitals might be used as a guiding principle to predict the chemoselectivity for a wide class of catalytic reactions at metal surfaces. PMID:28782033

21 CFR 172.820 - Polyethylene glycol (mean molecular weight 200-9,500).

Code of Federal Regulations, 2010 CFR

2010-04-01

... ethylene oxide and water with a mean molecular weight of 200 to 9,500. (2) It contains no more than 0.2 percent total by weight of ethylene and diethylene glycols when tested by the analytical methods... the total ethylene and diethylene glycol content of polyethylene glycols having mean molecular weights...

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

Ionic strength independence of charge distributions in solvation of biomolecules

NASA Astrophysics Data System (ADS)

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

2014-12-01

Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.

Molecular Gibbs Surface Excess and CO2-Hydrate Density Determine the Strong Temperature- and Pressure-Dependent Supercritical CO2-Brine Interfacial Tension.

PubMed

Ji, Jiayuan; Zhao, Lingling; Tao, Lu; Lin, Shangchao

2017-06-29

In CO 2 geological storage, the interfacial tension (IFT) between supercritical CO 2 and brine is critical for the storage capacitance design to prevent CO 2 leakage. IFT relies not only on the interfacial molecule properties but also on the environmental conditions at different storage sites. In this paper, supercritical CO 2 -NaCl solution systems are modeled at 343-373 K and 6-35 MPa under the salinity of 1.89 mol/L using molecular dynamics simulations. After computing and comparing the molecular density profile across the interface, the atomic radial distribution function, the molecular orientation distribution, the molecular Gibbs surface excess (derived from the molecular density profile), and the CO 2 -hydrate number density under the above environmental conditions, we confirm that only the molecular Gibbs surface excess of CO 2 molecules and the CO 2 -hydrate number density correlate strongly with the temperature- and pressure-dependent IFTs. We also compute the populations of two distinct CO 2 -hydrate structures (T-type and H-type) and attribute the observed dependence of IFTs to the dominance of the more stable, surfactant-like T-type CO 2 -hydrates at the interface. On the basis of these new molecular mechanisms behind IFT variations, this study could guide the rational design of suitable injecting environmental pressure and temperature conditions. We believe that the above two molecular-level metrics (Gibbs surface excess and hydrate number density) are of great fundamental importance for understanding the supercritical CO 2 -water interface and engineering applications in geological CO 2 storage.

Development and Testing of Molecular Adsorber Coatings

NASA Technical Reports Server (NTRS)

Abraham, Nithin; Hasegawa, Mark; Straka, Sharon

2012-01-01

The effect of on-orbit molecular contamination has the potential to degrade the performance of spaceflight hardware and diminish the lifetime of the spacecraft. For example, sensitive surfaces, such as optical surfaces, electronics, detectors, and thermal control surfaces, are vulnerable to the damaging effects of contamination from outgassed materials. The current solution to protect these surfaces is through the use of zeolite coated ceramic adsorber pucks. However, these pucks and its additional complex mounting hardware requirements result in several disadvantages, such as size, weight, and cost related concerns, that impact the spacecraft design and the integration and test schedule. As a result, a new innovative molecular adsorber coating was developed as a sprayable alternative to mitigate the risk of on-orbit molecular contamination. In this study, the formulation for molecular adsorber coatings was optimized using various binders, pigment treatment methods, binder to pigment ratios, thicknesses, and spray application techniques. The formulations that passed coating adhesion and vacuum thermal cycling tests were further tested for its adsorptive capacity. Accelerated molecular capacitance tests were performed in an innovatively designed multi-unit system containing idealized contaminant sources. This novel system significantly increased the productivity of the testing phase for the various formulations that were developed. Work performed during the development and testing phases has demonstrated successful application of molecular adsorber coatings onto metallic substrates, as well as, very promising results for the adhesion performance and the molecular capacitance of the coating. Continued testing will assist in the qualification of molecular adsorber coatings for use on future contamination sensitive spaceflight missions.

Engineered Aptamers to Probe Molecular Interactions on the Cell Surface

PubMed Central

Batool, Sana; Bhandari, Sanam; George, Shanell; Okeoma, Precious; Van, Nabeela; Zümrüt, Hazan E.; Mallikaratchy, Prabodhika

2017-01-01

Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics. PMID:28850067

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martinez, Andre P.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.

The molecular weight and polydispersity of the chains in a polymer brush are critical parameters determining the brush properties. However, the characterization of polymer brushes is hindered by the vanishingly small mass of polymer present in brush layers. In this study, in order to obtain sufficient quantities of polymer for analysis, polymer brushes were grown from high surface area fibrous nylon membranes by ATRP. We synthesized the brushes with varying surface initiator densities, polymerization times, and amounts of sacrificial initiator, then cleaved from the substrate, and analyzed by GPC and NMR. Characterization showed that the surface-grown polymer chains were moremore » polydisperse and had lower average molecular weight compared to solution-grown polymers synthesized concurrently. Furthermore, the molecular weight distribution of the polymer brushes was observed to be bimodal, with a low molecular weight population of chains representing a significant mass fraction of the polymer chains at high surface initiator densities. Moreover, the origin of this low MW polymer fraction is proposed to be the termination of growing chains by recombination during the early stages of polymerization, a mechanism confirmed by molecular dynamics simulations of brush polymerization.« less

Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

NASA Astrophysics Data System (ADS)

Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

2017-08-01

The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

Formulation and characterization of poly(ethylene glycol)-based, 5-aminolevulinic acid-loaded solid-dosage forms intended for photodynamic and photodiagnostic methodologies in the colorectal region.

PubMed

McCarron, Paul A; Andrews, Gavin P; Morrow, Desmond I J; Woolfson, A David; Donnelly, Ryan F

2007-01-01

Aminolevulinic acid-loaded, poly(ethylene glycol) disks prepared using three molecular weights (1000, 6000, and 10,000) were shown to be of potential for rectal administration as part of photodynamic and photodiagnostic colorectal procedures. The disk-shaped delivery system was mechanically robust, as judged by friability measurements. Calorimetric analysis confirmed that low concentrations of ALA (1% w/w) were dispersed completely throughout the PEG matrix, but higher concentrations (5% w/w and 10% w/w) formed crystalline suspensions. The molecular weight of the PEG determined the melting temperature, with PEG 1000 being suitable for melting around body temperature. The drug release kinetics were shown to be a function of both molecular weight and drug loading. Although the higher molecular weight PEG disks were resistant to surface erosion arising from an aqueous receptor phase, this effect was counterbalanced by more rapid and complete release when the ALA loading was increased. The lowest loading used (1% w/w) produced incomplete release, often not exceeding 30% of the total amount of drug. Results suggest that this simple formulation containing ALA can be administered directly to the colorectal area and is a feasible alternative to peroral dosing of ALA.

Water Adsorption on Clean and Defective Anatase TiO2 (001) Nanotube Surfaces: A Surface Science Approach.

PubMed

Kenmoe, Stephane; Lisovski, Oleg; Piskunov, Sergei; Bocharov, Dmitry; Zhukovskii, Yuri F; Spohr, Eckhard

2018-05-31

We use ab initio molecular dynamics simulations to study the adsorption of thin water films with 1 and 2 ML coverage on anatase TiO 2 (001) nanotubes. The nanotubes are modeled as 2D slabs, which consist of partially constrained and partially relaxed structural motifs from nanotubes. The effect of anion doping on the adsorption is investigated by substituting O atoms with N and S impurities on the nanotube slab surface. Due to strain-induced curvature effects, water adsorbs molecularly on defect-free surfaces via weak bonds on Ti sites and H bonds to surface oxygens. While the introduction of an S atom weakens the interaction of the surface with water, which adsorbs molecularly, the presence of an N impurity renders the surface more reactive to water, with a proton transfer from the water film and the formation of an NH group at the N site. At 2 ML coverage, a further surface-assisted proton transfer takes place in the water film, resulting in the formation of an OH - group and an NH 2 + cationic site on the surface.

The Spatially Resolved Star Formation Law From Integral Field Spectroscopy: VIRUS-P Observations of NGC 5194

NASA Astrophysics Data System (ADS)

Blanc, Guillermo A.; Heiderman, Amanda; Gebhardt, Karl; Evans, Neal J., II; Adams, Joshua

2009-10-01

We investigate the relation between the star formation rate (SFR) surface density (ΣSFR) and the mass surface density of gas (Σgas) in NGC 5194 (a.k.a. M51a, Whirlpool Galaxy). Visible Integral field Replicable Unit Spectrograph Prototype (VIRUS-P) integral field spectroscopy of the central 4.1 × 4.1 kpc2 of the galaxy is used to measure Hα, Hβ, [O III]λ5007, [N II]λλ6548,6584, and [S II]λλ6717,6731 emission line fluxes for 735 regions ~170 pc in diameter. We use the Balmer decrement to calculate nebular dust extinctions, and correct the observed fluxes in order to accurately measure ΣSFR in each region. Archival H I 21 cm and CO maps with spatial resolution similar to that of VIRUS-P are used to measure the atomic and molecular gas surface density for each region. We present a new method for fitting the star formation law (SFL), which includes the intrinsic scatter in the relation as a free parameter, allows the inclusion of non-detections in both Σgas and ΣSFR, and is free of the systematics involved in performing linear regressions over incomplete data in logarithmic space. After rejecting regions whose nebular spectrum is affected by the central active galactic nucleus in NGC 5194, we use the [S II]/Hα ratio to separate spectroscopically the contribution from the diffuse ionized gas (DIG) in the galaxy, which has a different temperature and ionization state from those of H II regions in the disk. The DIG only accounts for 11% of the total Hα luminosity integrated over the whole central region, but on local scales it can account for up to a 100% of the Hα emission, especially in the inter-arm regions. After removing the DIG contribution from the Hα fluxes, we measure a slope N = 0.82 ± 0.05, and an intrinsic scatter epsilon = 0.43 ± 0.02 dex for the molecular gas SFL. We also measure a typical depletion timescale \\tau =\\Sigma _H\\,{\\mathsc{i}+H_2}/\\Sigma _{SFR} \\approx 2 Gyr, in good agreement with recent measurements by Bigiel et al. The atomic gas density shows no correlation with the SFR, and the total gas SFL in the sampled density range closely follows the molecular gas SFL. Integral field spectroscopy allows a much cleaner measurement of Hα emission line fluxes than narrow-band imaging, since it is free of the systematics introduced by continuum subtraction, underlying photospheric absorption, and contamination by the [N II] doublet. We assess the validity of different corrections usually applied in narrow-band measurements to overcome these issues and find that while systematics are introduced by these corrections, they are only dominant in the low surface brightness regime. The disagreement with the previous measurement of a super-linear molecular SFL by Kennicutt et al. is most likely due to differences in the fitting method. Our results support the recent evidence for a low, and close to constant, star formation efficiency (SFE =τ-1) in the molecular component of the interstellar medium. The data show an excellent agreement with the recently proposed model of the SFL by Krumholz et al. The large intrinsic scatter observed may imply the existence of other parameters, beyond the availability of gas, which are important in setting the SFR.

Quantitative structure-cytotoxicity relationship of phenylpropanoid amides.

PubMed

Shimada, Chiyako; Uesawa, Yoshihiro; Ishihara, Mariko; Kagaya, Hajime; Kanamoto, Taisei; Terakubo, Shigemi; Nakashima, Hideki; Takao, Koichi; Saito, Takayuki; Sugita, Yoshiaki; Sakagami, Hiroshi

2014-07-01

A total of 12 phenylpropanoid amides were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity, tumor selectivity and anti-HIV activity, in order to investigate on their biological activities. Cytotoxicity against four human oral squamous cell carcinoma (OSCC) cell lines and three human oral normal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor selectivity was evaluated by the ratio of the mean CC50 (50% cytotoxic concentration) against normal oral cells to that against OSCC cell lines. Anti-HIV activity was evaluated by the ratio of CC50 to EC50 (50% cytoprotective concentration from HIV infection). Physicochemical, structural, and quantum-chemical parameters were calculated based on the conformations optimized by the LowModeMD method followed by density functional theory (DFT) method. Twelve phenylpropanoid amides showed moderate cytotoxicity against both normal and OSCC cell lines. N-Caffeoyl derivatives coupled with vanillylamine and tyramine exhibited relatively higher tumor selectivity. Cytotoxicity against normal cells was correlated with descriptors related to electrostatic interaction such as polar surface area and chemical hardness, whereas cytotoxicity against tumor cells correlated with free energy, surface area and ellipticity. The tumor-selective cytotoxicity correlated with molecular size (surface area) and electrostatic interaction (the maximum electrostatic potential). The molecular size, shape and ability for electrostatic interaction are useful parameters for estimating the tumor selectivity of phenylpropanoid amides. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Fatigue crack propagation resistance of virgin and highly crosslinked, thermally treated ultra-high molecular weight polyethylene.

PubMed

Gencur, Sara J; Rimnac, Clare M; Kurtz, Steven M

2006-03-01

To prolong the life of total joint replacements, highly crosslinked ultra-high molecular weight polyethylenes (UHMWPEs) have been introduced to improve the wear resistance of the articulating surfaces. However, there are concerns regarding the loss of ductility and potential loss in fatigue crack propagation (FCP) resistance. The objective of this study was to evaluate the effects of gamma radiation-induced crosslinking with two different post-irradiation thermal treatments on the FCP resistance of UHMWPE. Two highly crosslinked and one virgin UHMWPE treatment groups (ram-extruded, orthopedic grade, GUR 1050) were examined. For the two highly crosslinked treatment groups, UHMWPE rods were exposed to 100 kGy and then underwent post-irradiation thermal processing either above the melt temperature or below the melt temperature (2 h-150 degrees C, 110 degrees C). Compact tension specimens were cyclically loaded to failure and the fatigue crack growth rate, da/dN, vs. cyclic stress intensity factor, DeltaK, behavior was determined and compared between groups. Scanning electron microscopy was used to examine fracture surface characteristics. Crosslinking was found to decrease the ability of UHMWPE to resist crack inception and propagation under cyclic loading. The findings also suggested that annealing as a post-irradiation treatment may be somewhat less detrimental to FCP resistance of UHMWPE than remelting. Scanning electron microscopy examination of the fracture surfaces demonstrated that the virgin treatment group failed in a more ductile manner than the two highly crosslinked treatment groups.

Extensive Bone Reaction From Catastrophic Oxidized Zirconium Wear.

PubMed

Cassar-Gheiti, Adrian J; Collins, Dennis; McCarthy, Tom

2016-01-01

The use of alternative bearing surfaces for total hip arthroplasty has become popular to minimize wear and increase longevity, especially in young patients. Oxidized zirconium (Oxinium; Smith & Nephew, Memphis, Tennessee) femoral heads were introduced in the past decade for use in total hip arthroplasty. The advantages of oxidized zirconium include less risk of fracture compared with traditional ceramic heads. This case report describes a patient with a history of bilateral avascular necrosis of the femoral head after chemotherapy for acute lymphoblastic leukemia. Nonoperative management of avascular necrosis failed, and the patient was treated with bilateral total hip arthroplasty. The patient was followed at regular intervals and had slow eccentric polyethylene wear during a 10-year period. After 10 years, the patient had accelerated wear, with femoral and acetabular bone changes as a result of Oxinium and ultrahigh-molecular-weight polyethylene wear during a 6-month period. This article highlights the unusual accelerated bone changes that occurred as a result of Oxinium wear particles. Copyright 2016, SLACK Incorporated.

[Preparation and evaluation of novel mesoporous molecular sieve of baicalin surface molecularly imprinted polymers].

PubMed

Gu, Xia-li; He, Hong-liang; Shi, Li-ying; Gao, Yan-kun; Chen, Li-na

2015-05-01

Taking mesoporous molecular sieve MCM-41 as a substrate, baicalin (BA) as template, acrylamide (AM) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as a cross-linking agent, ethanol as solvent, under thermal polymerization initiator of azobis isobutyronitrilo (AIBN) , a kind of selective recognition of baicalin surface molecularly imprinted polymer was synthesized. The surface morphologies and characteristics of the MIPs were characterized by infrared spectroscopy (IR) and transmission electron microscope (TEM). The adsorption properties of polymer microsphere for the template were tested by the dynamic adsorption equilibrium experiments and static adsorption equilibrium experiments. The experiment showed that the imprinting process was successfully and the well-ordered one-dimensional pore structure of MCM-41 was still preserved. Furthermore, molecularly imprinted polymers had higher selective ability for BA, then provided a new method for the efficient separation and enrichment of baicalin active ingredients from medicinal plants Scutellaria baicalensis.

A Molecular Simulation Study of Antibody-Antigen Interactions on Surfaces for the Rational Design of Next-Generation Antibody Microarrays

NASA Astrophysics Data System (ADS)

Bush, Derek B.

Antibody microarrays constitute a next-generation sensing platform that has the potential to revolutionize the way that molecular detection is conducted in many scientific fields. Unfortunately, current technologies have not found mainstream use because of reliability problems that undermine trust in their results. Although several factors are involved, it is believed that undesirable protein interactions with the array surface are a fundamental source of problems where little detail about the molecular-level biophysics are known. A better understanding of antibody stability and antibody-antigen binding on the array surface is needed to improve microarray technology. Despite the availability of many laboratory methods for studying protein stability and binding, these methods either do not work when the protein is attached to a surface or they do not provide the atomistic structural information that is needed to better understand protein behavior on the surface. As a result, molecular simulation has emerged as the primary method for studying proteins on surfaces because it can provide metrics and views of atomistic structures and molecular motion. Using an advanced, coarse-grain, protein-surface model this study investigated how antibodies react to and function on different types of surfaces. Three topics were addressed: (1) the stability of individual antibodies on surfaces, (2) antibody binding to small antigens while on a surface, and (3) antibody binding to large antigens while on a surface. The results indicate that immobilizing antibodies or antibody fragments in an upright orientation on a hydrophilic surface can provide the molecules with thermal stability similar to their native aqueous stability, enhance antigen binding strength, and minimize the entropic cost of binding. Furthermore, the results indicate that it is more difficult for large antigens to approach the surface than small antigens, that multiple binding sites can aid antigen binding, and that antigen flexiblity simultaneously helps and hinders the binding process as it approaches the surface. The results provide hope that next-generation microarrays and other devices decorated with proteins can be improved through rational design.

Mechanisms and energetics of hydride dissociation reactions on surfaces of plasma-deposited silicon thin films

NASA Astrophysics Data System (ADS)

Singh, Tejinder; Valipa, Mayur S.; Mountziaris, T. J.; Maroudas, Dimitrios

2007-11-01

We report results from a detailed analysis of the fundamental silicon hydride dissociation processes on silicon surfaces and discuss their implications for the surface chemical composition of plasma-deposited hydrogenated amorphous silicon (a-Si:H) thin films. The analysis is based on a synergistic combination of first-principles density functional theory (DFT) calculations of hydride dissociation on the hydrogen-terminated Si(001)-(2×1) surface and molecular-dynamics (MD) simulations of adsorbed SiH3 radical precursor dissociation on surfaces of MD-grown a-Si :H films. Our DFT calculations reveal that, in the presence of fivefold coordinated surface Si atoms, surface trihydride species dissociate sequentially to form surface dihydrides and surface monohydrides via thermally activated pathways with reaction barriers of 0.40-0.55eV. The presence of dangling bonds (DBs) results in lowering the activation barrier for hydride dissociation to 0.15-0.20eV, but such DB-mediated reactions are infrequent. Our MD simulations on a-Si :H film growth surfaces indicate that surface hydride dissociation reactions are predominantly mediated by fivefold coordinated surface Si atoms, with resulting activation barriers of 0.35-0.50eV. The results are consistent with experimental measurements of a-Si :H film surface composition using in situ attenuated total reflection Fourier transform infrared spectroscopy, which indicate that the a-Si :H surface is predominantly covered with the higher hydrides at low temperatures, while the surface monohydride, SiH(s ), becomes increasingly more dominant as the temperature is increased.

Surface Modification Enhanced Reflection Intensity of Quartz Crystal Microbalance Sensors upon Molecular Adsorption.

PubMed

Kojima, Taisuke

2018-01-01

Molecular adsorption on a sensing surface involves molecule-substrate and molecule-molecule interactions. Combining optical systems and a quartz crystal microbalance (QCM) on the same sensing surface allows the quantification of such interactions and reveals the physicochemical properties of the adsorbed molecules. However, low sensitivity of the current reflection-based techniques compared to the QCM technique hinders the quantitative analysis of the adsorption events. Here, a layer-by-layer surface modification of a QCM sensor is studied to increase the optical sensitivity. The intermediate layers of organic-inorganic molecules and metal-metal oxide were explored on a gold (Au) surface of a QCM sensor. First, polyhedral oligomeric silsesquioxane-derivatives that served as the organic-inorganic intermediate layer were synthesized and modified on the Au-QCM surface. Meanwhile, titanium oxide, fabricated by anodic oxidation of titanium, was used as a metal-metal oxide intermediate layer on a titanium-coated QCM surface. The developed technique enabled interrogation of the molecular adsorption owing to the enhanced optical sensitivity.

Photo-responsive surface topology in chiral nematic media

NASA Astrophysics Data System (ADS)

Liu, Danqing; Bastiaansen, Cees W. M.; Toonder, Jaap. M. J.; Broer, Dirk J.

2012-03-01

We report on the design and fabrication of 'smart surfaces' that exhibit dynamic changes in their surface topology in response to exposure to light. The principle is based on anisotropic geometric changes of a liquid crystal network upon a change of the molecular order parameter. The photomechanical property of the coating is induced by incorporating an azobenzene moiety into the liquid crystal network. The responsive surface topology consists of regions with two different types of molecular order: planar chiral-nematic areas and homeotropic. Under flood exposure with 365 nm light the surfaces deform from flat to one with a surface relief. The height of the relief structures is of the order of 1 um corresponding to strain difference of around 20%. Furthermore, we demonstrate surface reliefs can form either convex or concave structures upon exposure to UV light corresponding to the decrease or increase molecular order parameter, respectively, related to the isomeric state of the azobenzene crosslinker. The reversible deformation to the initial flat state occurs rapidly after removing the light source.

Magnetic memory of a single-molecule quantum magnet wired to a gold surface.

PubMed

Mannini, Matteo; Pineider, Francesco; Sainctavit, Philippe; Danieli, Chiara; Otero, Edwige; Sciancalepore, Corrado; Talarico, Anna Maria; Arrio, Marie-Anne; Cornia, Andrea; Gatteschi, Dante; Sessoli, Roberta

2009-03-01

In the field of molecular spintronics, the use of magnetic molecules for information technology is a main target and the observation of magnetic hysteresis on individual molecules organized on surfaces is a necessary step to develop molecular memory arrays. Although simple paramagnetic molecules can show surface-induced magnetic ordering and hysteresis when deposited on ferromagnetic surfaces, information storage at the molecular level requires molecules exhibiting an intrinsic remnant magnetization, like the so-called single-molecule magnets (SMMs). These have been intensively investigated for their rich quantum behaviour but no magnetic hysteresis has been so far reported for monolayers of SMMs on various non-magnetic substrates, most probably owing to the chemical instability of clusters on surfaces. Using X-ray absorption spectroscopy and X-ray magnetic circular dichroism synchrotron-based techniques, pushed to the limits in sensitivity and operated at sub-kelvin temperatures, we have now found that robust, tailor-made Fe(4) complexes retain magnetic hysteresis at gold surfaces. Our results demonstrate that isolated SMMs can be used for storing information. The road is now open to address individual molecules wired to a conducting surface in their blocked magnetization state, thereby enabling investigation of the elementary interactions between electron transport and magnetism degrees of freedom at the molecular scale.

Role of molecular properties of ulvans on their ability to elaborate antiadhesive surfaces.

PubMed

Gadenne, Virginie; Lebrun, Laurent; Jouenne, Thierry; Thebault, Pascal

2015-03-01

Antiadhesive properties of polysaccharides (such ulvans) once immobilized on a surface are described in the literature but the parameters governing their antifouling properties are not yet well identified. In the present study, the relationship between molecular parameters of ulvans and the inhibition of bacterial adhesion was investigated. To this aim, various ulvans were grafted on silicon wafers under two different experimental immobilization conditions. Results showed that the experimental immobilization conditions and the polysaccharides molecular weight led to specific layer conformations which exhibited a key role in the surface antiadhesive properties. © 2014 Wiley Periodicals, Inc.

Spectroscopic identification of binary and ternary surface complexes of Np(V) on gibbsite.

PubMed

Gückel, Katharina; Rossberg, André; Müller, Katharina; Brendler, Vinzenz; Bernhard, Gert; Foerstendorf, Harald

2013-12-17

For the first time, detailed molecular information on the Np(V) sorption species on amorphous Al(OH)3 and crystalline gibbsite was obtained by in situ time-resolved Attenuated Total Reflection Fourier-Transform Infrared (ATR FT-IR) and Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. The results consistently demonstrate the formation of mononuclear inner sphere complexes of the NpO2(+) ion irrespective of the prevailing atmospheric condition. The impact of the presence of atmospheric equivalent added carbonate on the speciation in solution and on the surfaces becomes evident from vibrational data. While the 1:1 aqueous carbonato species (NpO2CO3(-)) was found to become predominant in the circumneutral pH range, it is most likely that this species is sorbed onto the gibbsite surface as a ternary inner sphere surface complex where the NpO2(+) moiety is directly coordinated to the functional groups of the gibbsite's surface. These findings are corroborated by results obtained from EXAFS spectroscopy providing further evidence for a bidentate coordination of the Np(V) ion on amorphous Al(OH)3. The identification of the Np(V) surface species on gibbsite constitutes a basic finding for a comprehensive description of the dissemination of neptunium in groundwater systems.

Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Dai, L.; Sorkin, V.; Zhang, Y. W.

2017-04-01

We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

Internal Energy Dependence of Molecular Condensation Coefficients Determined from Molecular Beam Surface Scattering Experiments

DOE R&D Accomplishments Database

Sibener, S. J.; Lee, Y. T.

1978-05-01

An experiment was performed which confirms the existence of an internal mode dependence of molecular sticking probabilities for collisions of molecules with a cold surface. The scattering of a velocity selected effusive beam of CCl{sub 4} from a 90 K CC1{sub 4} ice surface has been studied at five translational velocities and for two different internal temperatures. At a surface temperature of 90 K (approx. 99% sticking probability) a four fold increase in reflected intensity was observed for the internally excited (560 K) CC1{sub 4} relative to the room temperature (298 K) CC1{sub 4} at a translational velocity of 2.5 X 10{sup 4} cm/sec. For a surface temperature of 90 K all angular distributions were found to peak 15{sup 0} superspecularly independent of incident velocity.

Surface density: a new parameter in the fundamental metallicity relation of star-forming galaxies

NASA Astrophysics Data System (ADS)

Hashimoto, Tetsuya; Goto, Tomotsugu; Momose, Rieko

2018-04-01

Star-forming galaxies display a close relation among stellar mass, metallicity, and star formation rate (or molecular-gas mass). This is known as the fundamental metallicity relation (FMR) (or molecular-gas FMR), and it has a profound implication on models of galaxy evolution. However, there still remains a significant residual scatter around the FMR. We show here that a fourth parameter, the surface density of stellar mass, reduces the dispersion around the molecular-gas FMR. In a principal component analysis of 29 physical parameters of 41 338 star-forming galaxies, the surface density of stellar mass is found to be the fourth most important parameter. The new 4D fundamental relation forms a tighter hypersurface that reduces the metallicity dispersion to 50 per cent of that of the molecular-gas FMR. We suggest that future analyses and models of galaxy evolution should consider the FMR in a 4D space that includes surface density. The dilution time-scale of gas inflow and the star-formation efficiency could explain the observational dependence on surface density of stellar mass.

Method of Stamping Surface-Enhance Raman Spectroscopy for Label-Free, Multiplexed, Molecular Sensing and Imaging

NASA Technical Reports Server (NTRS)

Shih, Wei-Chuan (Inventor)

2017-01-01

The present disclosure relates the use of a stamping surface enhanced Raman scattering (S-SERS) technique with nanoporous gold disk (NPGD) plasmonic substrates to produce a label-free, multiplexed molecular sensing and imaging technique. A NPGD SERS substrate is stamped onto a surface containing one or more target molecules, followed by SERS measurement of the target molecules located between the surface and SERS substrate. The target molecules may be deposited on the surface, which may be a carrier substrate such as polydimethylsiloxane (PDMS).

Molecular self-assembly on surfaces

NASA Astrophysics Data System (ADS)

Mateo-Marti, E.; Pradier, C. M.

2012-09-01

The aim of the present research is to study the interaction of biomolecules, among them single amino acids, on metallic and mineral surfaces, and their chemical reactivity by means of powerful surface science techniques. Therefore, the use of simple biomolecules gives fundamental and significant information, including an adequate control of biomolecule-surface interactions, which will be unattainable to develop with more complex molecules. Furthermore, these studies are focussed on the catalytic properties of different surfaces that could be involved in molecular self-organization processes and the formation of prebiotic organic compounds.

JSEP Fellowship

DTIC Science & Technology

1993-06-28

entitled "MBE Grown Microcavities for Optoelectronic Devices." In the dissertation work,1 the precision of molecular - beam epitaxy (MBE) is taken...Layers For Surface Normal Optoelectronic Devices," North American Conference on Molecular Beam Epitaxy , Ottawa, Canada, October 12-14, 1992, to be...8. C. Lei, T. J. Rogers, D. G. Deppe, and B. G. Streetman, "InGaAs-GaAs Quantum Well Vertical-Cavity Surface-Emitting Laser Using Molecular Beam

Insulin adsorption on crystalline SiO2: Comparison between polar and nonpolar surfaces using accelerated molecular-dynamics simulations

NASA Astrophysics Data System (ADS)

Nejad, Marjan A.; Mücksch, Christian; Urbassek, Herbert M.

2017-02-01

Adsorption of insulin on polar and nonpolar surfaces of crystalline SiO2 (cristobalite and α -quartz) is studied using molecular dynamics simulation. Acceleration techniques are used in order to sample adsorption phase space efficiently and to identify realistic adsorption conformations. We find major differences between the polar and nonpolar surfaces. Electrostatic interactions govern the adsorption on polar surfaces and can be described by the alignment of the protein dipole with the surface dipole; hence spreading of the protein on the surface is irrelevant. On nonpolar surfaces, on the other hand, van-der-Waals interaction dominates, inducing surface spreading of the protein.

SFG analysis of the molecular structures at the surfaces and buried interfaces of PECVD ultralow-dielectric constant pSiCOH: Reactive ion etching and dielectric recovery

NASA Astrophysics Data System (ADS)

Myers, John N.; Zhang, Xiaoxian; Huang, Huai; Shobha, Hosadurga; Grill, Alfred; Chen, Zhan

2017-05-01

Molecular structures at the surface and buried interface of an amorphous ultralow-k pSiCOH dielectric film were quantitatively characterized before and after reactive ion etching (RIE) and subsequent dielectric repair using sum frequency generation (SFG) vibrational spectroscopy and Auger electron spectroscopy. SFG results indicated that RIE treatment of the pSiCOH film resulted in a depletion of ˜66% of the surface methyl groups and changed the orientation of surface methyl groups from ˜47° to ˜40°. After a dielectric recovery process that followed the RIE treatment, the surface molecular structure was dominated by methyl groups with an orientation of ˜55° and the methyl surface coverage at the repaired surface was 271% relative to the pristine surface. Auger depth profiling indicated that the RIE treatment altered the top ˜25 nm of the film and that the dielectric recovery treatment repaired the top ˜9 nm of the film. Both SFG and Auger profiling results indicated that the buried SiCNH/pSiCOH interface was not affected by the RIE or the dielectric recovery process. Beyond characterizing low-k materials, the developed methodology is general and can be used to distinguish and characterize different molecular structures and elemental compositions at the surface, in the bulk, and at the buried interface of many different polymer or organic thin films.

A study of internal energy relaxation in shocks using molecular dynamics based models

NASA Astrophysics Data System (ADS)

Li, Zheng; Parsons, Neal; Levin, Deborah A.

2015-10-01

Recent potential energy surfaces (PESs) for the N2 + N and N2 + N2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N2 + N2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available.

Influence of the molecular architecture on the adsorption onto solid surfaces: comb-like polymers.

PubMed

Guzmán, Eduardo; Ortega, Francisco; Prolongo, Margarita G; Starov, Victor M; Rubio, Ramón G

2011-09-28

The processes of adsorption of grafted copolymers onto negatively charged surfaces were studied using a dissipative quartz crystal microbalance (D-QCM) and ellipsometry. The control parameters in the study of the adsorption are the existence or absence on the molecular architecture of grafted polyethyleneglycol (PEG) chains with different lengths and the chemical nature of the main chain, poly(allylamine) (PAH) or poly(L-lysine) (PLL). It was found out that the adsorption kinetics of the polymers showed a complex behavior. The total adsorbed amount depends on the architecture of the polymer chains (length of the PEG chains), on the polymer concentration and on the chemical nature of the main chain. The comparison of the thicknesses of the adsorbed layers obtained from D-QCM and from ellipsometry allowed calculation of the water content of the layers that is intimately related to the grafting length. The analysis of D-QCM results also provides information about the shear modulus of the layers, whose values have been found to be typical of a rubber-like polymer system. It is shown that the adsorption of polymers with a charged backbone is not driven exclusively by the electrostatic interactions, but the entropic contributions as a result of the trapping of water in the layer structure are of fundamental importance.

Concentration and density changes at an electrode surface and the principle of unchanging total concentration

DOE PAGES

Stephen W. Feldberg; Lewis, Ernie R.

2016-02-17

In this study, the principle of unchanging total concentration as described by Oldham and Feldberg [J. Phys. Chem. B, 103, 1699 (1999)] is invoked to analyze systems comprising a redox pair (X z1 1 and X z2 2) plus one or more non-electroactive species (X z3 3,X z4 4...X zjmax jmax) where X zj j is the j th species with charge z j and concentration; c j. The principle states that if the diffusion coefficients for all species are identical and mass transport is governed by the Nernst-Planck expression, the total concentration does not change during any electrochemical perturbation,more » i.e.: Σ jmax j=1[X zj j]=Σ jmax j=1 c j = S P With this principle we deduce the electrochemically induced difference between the surface and bulk concentrations for each species. Those concentration differences are translated into density differences which are a function of the density of the solvent and of the concentration differences, molecular masses and the standard partial molar volumes of all species. Those density differences in turn can induce convection that will ultimately modify the observed current. However, we did not attempt to quantify details of the natural convection and current modification produced by those density differences.« less

Spatial and temporal distribution and sources of polycyclic aromatic hydrocarbons in sediments of Taihu Lake, eastern China.

PubMed

Tang, Zhi; Guo, Jianyang; Liao, Haiqing; Zhao, Xiaoli; Wu, Fengchang; Zhu, Yuanrong; Zhang, Liang; Giesy, John P

2015-04-01

Spatial and temporal distributions of concentrations of polycyclic aromatic hydrocarbons (PAHs) in surface sediments and dated sediment core from Taihu Lake in eastern China were determined. The sum of concentrations of PAHs (sum of total 16 USEPA priority PAH (∑PAHs)) of the entire Taihu Lake ranged from 2.9 × 10(2) to 8.4 × 10(2) ng/g dry mass (dm). Concentrations of ∑PAHs in surface sediments near more urbanized regions of the lake shore were greater than those in areas more remote from the urban centers. Temporal trends in concentrations of ∑PAHs ranged from 5.1 × 10(2) to 1.5 × 10(3) ng/g dm, increasing from deeper layers to surface sediments with some fluctuations, especially in the past three decades after the inception of China's Reform and Opening Up Policy, in which China's economy and urbanization underwent rapid development. Forensic analysis of surface sediments indicates that PAHs originated primarily from combustion of grass/wood/coal except for the special function water area, which was most likely influenced by petroleum products of traveling vessels. Vertical profiles of relative concentrations of PAHs suggested that the contribution of lesser-molecular-weight PAHs was gradually decreasing, while due to the heavier consumption of petroleum products, the proportion of greater-molecular-weight PAHs was increasing. When assessed by use of the rather conservative, apparent effect threshold method, concentrations of ∑PAHs in sediments from most locations in Taihu Lake are predicted to pose little risk of harm to benthic invertebrates.

Molecular receptors in metal oxide sol-gel materials prepared via molecular imprinting

DOEpatents

Sasaki, Darryl Y.; Brinker, C. Jeffrey; Ashley, Carol S.; Daitch, Charles E.; Shea, Kenneth J.; Rush, Daniel J.

2000-01-01

A method is provided for molecularly imprinting the surface of a sol-gel material, by forming a solution comprised of a sol-gel material, a solvent, an imprinting molecule, and a functionalizing siloxane monomer of the form Si(OR).sub.3-n X.sub.n, wherein n is an integer between zero and three and X is a functional group capable of reacting with the imprinting molecule, evaporating the solvent, and removing the imprinting molecule to form the molecularly imprinted metal oxide sol-gel material. The use of metal oxide sol-gels allows the material porosity, pore size, density, surface area, hardness, electrostatic charge, polarity, optical density, and surface hydrophobicity to be tailored and be employed as sensors and in catalytic and separations operations.

Methods and apparatuses for preparing a surface to have catalytic activity

DOEpatents

Cooks, Robert G [West Lafayette, IN; Peng, Wen-Ping [West Lafayette, IN; Ouyang, Zheng [West Lafayette, IN; Goodwin, Michael P [West Lafayette, IN

2011-03-22

The invention provides methods and apparatuses that utilize mass spectrometry for preparation of a surface to have catalytic activity through molecular soft-landing of mass selected ions. Mass spectrometry is used to generate combinations of atoms in a particular geometrical arrangement, and ion soft-landing selects this molecular entity or combination of entities and gently deposits the entity or combination intact onto a surface.

Molecular Dynamics Simulations of Surface Processes: Oxygen Recombination on Silica Surfaces at High Temperature

DTIC Science & Technology

2007-07-01

SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18 . NUMBER OF PAGES 22 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT...unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39- 18 Molecular Dynamics Simulations of Surface...phase. O + Oad + silica -------> O2(v,j) + silica ( 18 ) The first step is

A kainate receptor subunit promotes the recycling of the neuron-specific K+-Cl- co-transporter KCC2 in hippocampal neurons.

PubMed

Pressey, Jessica C; Mahadevan, Vivek; Khademullah, C Sahara; Dargaei, Zahra; Chevrier, Jonah; Ye, Wenqing; Huang, Michelle; Chauhan, Alamjeet K; Meas, Steven J; Uvarov, Pavel; Airaksinen, Matti S; Woodin, Melanie A

2017-04-14

Synaptic inhibition depends on a transmembrane gradient of chloride, which is set by the neuron-specific K + -Cl - co-transporter KCC2. Reduced KCC2 levels in the neuronal membrane contribute to the generation of epilepsy, neuropathic pain, and autism spectrum disorders; thus, it is important to characterize the mechanisms regulating KCC2 expression. In the present study, we determined the role of KCC2-protein interactions in regulating total and surface membrane KCC2 expression. Using quantitative immunofluorescence in cultured mouse hippocampal neurons, we discovered that the kainate receptor subunit GluK2 and the auxiliary subunit Neto2 significantly increase the total KCC2 abundance in neurons but that GluK2 exclusively increases the abundance of KCC2 in the surface membrane. Using a live cell imaging assay, we further determined that KCC2 recycling primarily occurs within 1-2 h and that GluK2 produces an ∼40% increase in the amount of KCC2 recycled to the membrane during this time period. This GluK2-mediated increase in surface recycling translated to a significant increase in KCC2 expression in the surface membrane. Moreover, we found that KCC2 recycling is enhanced by protein kinase C-mediated phosphorylation of the GluK2 C-terminal residues Ser-846 and Ser-868. Lastly, using gramicidin-perforated patch clamp recordings, we found that the GluK2-mediated increase in KCC2 recycling to the surface membrane translates to a hyperpolarization of the reversal potential for GABA (E GABA ). In conclusion, our results have revealed a mechanism by which kainate receptors regulate KCC2 expression in the hippocampus. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Current Progress of Nanomaterials in Molecularly Imprinted Electrochemical Sensing.

PubMed

Zhong, Chunju; Yang, Bin; Jiang, Xinxin; Li, Jianping

2018-01-02

Nanomaterials have received much attention during the past decade because of their excellent optical, electronic, and catalytic properties. Nanomaterials possess high chemical reactivity, also high surface energy. Thus, provide a stable immobilization platform for biomolecules, while preserving their reactivity. Due to the conductive and catalytic properties, nanomaterials can also enhance the sensitivity of molecularly imprinted electrochemical sensors by amplifying the electrode surface, increasing the electron transfer, and catalyzing the electrochemical reactions. Molecularly imprinted polymers that contain specific molecular recognition sites can be designed for a particular target analyte. Incorporating nanomaterials into molecularly imprinted polymers is important because nanomaterials can improve the response signal, increase the sensitivity, and decrease the detection limit of the sensors. This study describes the classification of nanomaterials in molecularly imprinted polymers, their analytical properties, and their applications in the electrochemical sensors. The progress of the research on nanomaterials in molecularly imprinted polymers and the application of nanomaterials in molecularly imprinted polymers is also reviewed.

Electron-stimulated reactions in nanoscale water films adsorbed on α-Al 2O 3 (0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrik, Nikolay G.; Kimmel, Gregory A.

The radiation-induced decomposition and desorption of nanoscale amorphous solid water (D2O) films adsorbed on -Al2O3(0001) surface was studied at low temperature in ultrahigh vacuum using temperature programmed desorption (TPD) and electron stimulated desorption (ESD) with a mono-energetic, low energy electron source. ESD yields of molecular products ( D2, O2 and D¬2O) and the total sputtering yield increased with increasing D2O coverage up to ~15 water monolayers (i.e. ~15 1015 cm-2) to a coverage-independent level for thicker water films. Experiments with isotopically-layered water films (D2O and H2O) demonstrated that the highest water decomposition yields occurred at the interfaces of the nanoscalemore » water films with the alumina substrate and vacuum. However, the increased reactivity of the water/alumina interface is relatively small compared to the enhancements in the non-thermal reactions previously observed at the water/Pt(111) and water/TiO2(110) interfaces. We propose that the relatively low activity of Al2O3(0001) for the radiation-induced production of molecular hydrogen is associated with lower reactivity of this surface with hydrogen atoms, which are likely precursors for the molecular hydrogen.100 eV electrons are stopped in the H 2O portion of the isotopically-layered nanoscale film on α-Al 2O 3(0001) but D 2is produced at the D 2O/alumina interface by mobile electronic excitations and/or hydronium ions.« less

Understanding gas-surface interactions from direct force measurements using a specialized torsion balance

NASA Technical Reports Server (NTRS)

Cook, S. R.; Hoffbauer, M. A.

1996-01-01

The first comprehensive measurements of the magnitude and direction of the forces exerted on surfaces by molecular beams are discussed and used to obtain information about the microscopic properties of the gas-surface interactions. This unique approach is not based on microscopic measurements of the scattered molecules. The reduced force coefficients are introduced as a new set of parameters that completely describe the macroscopic average momentum transfer to a surface by an incident molecular beam. By using a specialized torsion balance and molecular beams of N2, CO, CO2, and H2, the reduced force coefficients are determined from direct measurements of the force components exerted on surface of a solar panel array material, Kapton, SiO2-coated Kapton, and Z-93 as a function of the angle of incidence ranging from 0 degrees to 85 degrees. The absolute flux densities of the molecular beams were measured using a different torsion balance with a beam-stop that nullified the force of the scattered molecules. Standard time-of-flight techniques were used to determine the flux-weighted average velocities of the various molecular beams ranging from 1600 m/s to 4600 m/s. The reduced force coefficients can be used to directly obtain macroscopic average properties of the scattered molecules, such as the flux-weighted average velocity and translational energy, that can then be used to determine microscopic details concerning gas-surface interactions without the complications associated with averaging microscopic measurements.

Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

NASA Technical Reports Server (NTRS)

Menon, Madhu

1998-01-01

In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

Probing equilibrium of molecular and deprotonated water on TiO 2 (110)

DOE PAGES

Wang, Zhi-Tao; Wang, Yang-Gang; Mu, Rentao; ...

2017-02-06

Understanding water structure and its deprotonation dynamics on oxide surfaces is key to understanding many physical and chemical processes. In this study, we directly measure the energy barriers associated with the protonation equilibrium of water on the prototypical oxide surface, rutile-TiO2(110) by a combination of a supersonic molecular beam, scanning tunneling microscopy, and ab initio molecular dynamics simulations. We show that long-range electrostatic fields emanating from the oxide lead to steering and reorientation of the molecules approaching the surface, activating the O-H bonds and inducing deprotonation. The incident energy dependent studies allow for a direct determination of the dissociation barrier.more » Temperature dependent imaging yields the reverse barrier and the equilibrium constant. Molecularly bound water is preferred by 0.035 eV over the surface-bound hydroxyls. The techniques developed in this work are readily extended to other systems where the understanding of bond-activation processes is critical.« less

Capillary waves' dynamics at the nanoscale

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Chacón, Enrique; Tarazona, Pedro

2008-12-01

We study the dynamics of thermally excited capillary waves (CW) at molecular scales, using molecular dynamics simulations of simple liquid slabs. The analysis is based on the Fourier modes of the liquid surface, constructed via the intrinsic sampling method (Chacón and Tarazona 2003 Phys. Rev. Lett. 91 166103). We obtain the time autocorrelation of the Fourier modes to get the frequency and damping rate Γd(q) of each mode, with wavenumber q. Continuum hydrodynamics predicts \\Gamma (q) \\propto q\\gamma (q) and thus provides a dynamic measure of the q-dependent surface tension, γd(q). The dynamical estimation is much more robust than the structural prediction based on the amplitude of the Fourier mode, γs(q). Using the optimal estimation of the intrinsic surface, we obtain quantitative agreement between the structural and dynamic pictures. Quite surprisingly, the hydrodynamic prediction for CW remains valid up to wavelengths of about four molecular diameters. Surface tension hydrodynamics break down at shorter scales, whereby a transition to a molecular diffusion regime is observed.

Outgassing Measurements for Three Materials, Combined with Vacuum Ultraviolet Radiation Illumination of the Volatile Condensable Materials

NASA Technical Reports Server (NTRS)

Albyn, Keith

2005-01-01

The photolysis of three organic materials, by vacuum ultraviolet (VUV) radiation, has been quantified using 15-MHz temperature-controlled quartz microbalances (TQCM's). The rate at which molecular species, released from the individual samples, condensed on two TQCM s was measured for periods of up to 139.9-hours. The individual samples were heated in an effusion cell and the emitted molecular species collected on a pair of TQCM's which were maintained at -40 degrees Celsius. At several points during the deposition measurement, the deposition surface of one TQCM was illuminated by a 30 Watt deuterium lamp, and the loss of material from that surface was observed. V W illumination of the TQCM, concurrent with condensation, reduced the rate that material was lost from the deposition surface. These measurements present a contrasting picture of molecular deposition, in the presence of VUV, to that presented by other investigators who observed an enhanced rate of molecular deposition, when the deposition surface was illuminated by VUV.

Probing equilibrium of molecular and deprotonated water on TiO 2(110)

DOE PAGES

Wang, Zhi -Tao; Wang, Yang -Gang; Mu, Rentao; ...

2017-02-06

Understanding water structure and its deprotonation dynamics on oxide surfaces is key to understanding many physical and chemical processes. In this study, we directly measure the energy barriers associated with the protonation equilibrium of water on the prototypical oxide surface, rutile-TiO 2(110) by a combination of a supersonic molecular beam, scanning tunneling microscopy, and ab initio molecular dynamics simulations. We show that long-range electrostatic fields emanating from the oxide lead to steering and reorientation of the molecules approaching the surface, activating the O-H bonds and inducing deprotonation. The incident energy dependent studies allow for a direct determination of the dissociationmore » barrier. Temperature dependent imaging yields the reverse barrier and the equilibrium constant. Molecularly bound water is preferred by 0.035 eV over the surface-bound hydroxyls. In conclusion, the techniques developed in this work are readily extended to other systems where the understanding of bond-activation processes is critical.« less

A Novel Method to Assess Wear Rates of Retrieved Tibial Inserts Following in-vivo Use

NASA Astrophysics Data System (ADS)

Paniogue, Tanille J.

Ultra-high molecular weight polyethylene (UHMWPE) on cobalt chrome is the bearing couple of choice for total knee arthroplasty. The number of patients undergoing total knee arthroplasty has been steadily growing and is projected to continue increasing rapidly in the near future. Many of these patients are younger and more active and therefore need a longer lasting device. However, many of these devices fail prematurely and often the primary reason for failure and ultimately revision is due to wear related issues. Therefore, examining how wear rates of the UHMWPE tibial insert change during in-vivo use can help elucidate the mechanisms of accelerated wear and hopefully aid in finding solutions to combat wear related failures. Different crosslinking treatments have been employed by manufacturers to improve wear resistance of the polyethylene. While this has been shown to be an effective way to reduce wear, crosslinking has led to other issues such as oxidative instability and a decline in mechanical properties. The purpose of this body of work is to examine how changes in oxidation, after in-vivo use, affect wear resistance. A novel testing method was developed to test the native articular surface from retrieved tibial inserts in a laboratory Pin-on-Disk (POD) simulator. The method was validated using short-duration implant articular surfaces and non-articular control pins. In the absence of high surface oxidation or severe surface damage, the articular surface pins had comparable steady state wear rates to their bulk counterparts. Tests of devices with longer in-vivo service show chemical changes consistent with a free-radical mediated oxidation mechanism. Tribological assessment of the articular surfaces shows increasing wear rates as a function of oxidation. While this relationship has been hypothesized in the literature, these experiments represent the first physical demonstration of the phenomenon. The wear mechanism is further explored through infrared spectroscopy, assessment of the wear scar, and documentation of evolution of the contact surfaces in the articulation.

Adsorption of hydrogen on stable and metastable Ir(100) surfaces

NASA Astrophysics Data System (ADS)

Arman, Mohammad Alif; Klein, Andreas; Ferstl, Pascal; Valookaran, Abhilash; Gustafson, Johan; Schulte, Karina; Lundgren, Edvin; Heinz, Klaus; Schneider, Alexander; Mittendorfer, Florian; Hammer, Lutz; Knudsen, Jan

2017-02-01

Using the combination of high resolution core level spectroscopy and density functional theory we present a detailed spectroscopic study for all clean and hydrogen covered phases of Ir(100). The results are complemented by an investigation of the hydrogen desorption process from various phases using temperature programmed desorption spectroscopy and scanning tunneling microscopy. In total, all experimentally determined core level shifts match very well with those predicted by density functional theory based on established structural models. In particular, we find for the (bridge site) adsorption on the unreconstructed 1×1 phase that the initial core level shift of surface Ir atoms is altered by +0.17 eV for each Ir-H bond formed. In the submonolayer regime we find evidence for island formation at low temperatures. For the H-induced deconstructed 5×1-H phase we identify four different surface core level shifts with two of them being degenerate. Finally, for the reconstructed 5×1-hex phase also four surface components are identified, which undergo a rather rigid core level shift of +0.15 eV upon hydrogen adsorption suggesting a similarly homogeneous charge transfer to all Ir surface atoms. Thermodesorption experiments for the 5×1-H phase reveal two different binding states for hydrogen independent of the total coverage. We conclude that the surface always separates into patches of fully covered deconstructed and uncovered reconstructed phases. We could also show by tunneling microscopy that with the desorption of the last hydrogen atom from the deconstructed unit cell the surface instantaneously reverts into the reconstructed state. Eventually, we could determine the saturation coverage upon molecular adsorption for all phases to be θmax1 × 1 - H = 1.0 ML , θmax5 × 1 - H = 0.8 ML , and θmax5 × 1 - hex - H ≥ 1.0 ML .

Molecular orientation in a dielectric liquid-vapor interphase

NASA Astrophysics Data System (ADS)

Chacón, E.; Mederos, L.; Navascués, G.; Tarazona, P.

1985-04-01

The density functional theory of Chacón et al. is used to study the molecular orientation in an interphase of a weak dipolar fluid. Explicit expressions are obtained using standard perturbation techniques. Molecular orientation, local susceptibility, and the Gibbsean surface susceptibility are evaluated for a Stockmayer model of dipolar fluid. The effect of the surface structure on the bulk ferroelectric transition is discussed in the light of the present theory and the numerical results.

Structure of Solids Surfaces in Wear Situations.

DTIC Science & Technology

1984-10-17

Laser Interference Microscopy." Invited Lecture by J.L. Lauer at the 1982 AFOSR Molecular Dynamics and Surface Chemistry Contractors’ .-. Conference on... molecular and crystalline structure. Preliminary studies of aircraft fuel deposits by FIEMS were reported previously [11 so that the apparatus and its...was probably no more than a few molecular layers thick. It shows strong bands at 820, 960. 1130, 1250, 1380, 1560, 1600 and at 1640 (strong) cm .The

Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

PubMed

Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

2017-11-22

Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

Surface functionalisation with viscosity-sensitive BODIPY molecular rotor

NASA Astrophysics Data System (ADS)

Vyšniauskas, Aurimas; Lopez-Duarte, Ismael; Thompson, Alex J.; Bull, James A.; Kuimova, Marina K.

2018-07-01

Surface functionalisation with viscosity sensitive dyes termed ‘molecular rotors’ can potentially open up new opportunities in sensing, for example for non-invasive biological viscosity imaging, in studying the effect of shear stress on lipid membranes and in cells, and in imaging contacts between surfaces upon applied pressure. We have functionalised microscope slides with BODIPY-based molecular rotor capable of viscosity sensing via its fluorescence lifetime. We have optimised functionalisation conditions and prepared the slides with the BODIPY rotor attached directly to the surface of glass slides and through polymer linkers of 5 kDa and 40 kDa in mass. The slides were characterised for their sensitivity to viscosity, and used to measure viscosity of supported lipid bilayers during photooxidation, and of giant unilamellar vesicles lying on the surface of the slide. We conclude that our functionalised slides show promise for a variety of viscosity sensing applications.

Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makarov, G N; Petin, A N

2016-03-31

We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF{sub 6} and CF{sub 3}I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF{sub 6} molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with amore » surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation. (laser separation of isotopes)« less

Controlled clockwise and anticlockwise rotational switching of a molecular motor.

PubMed

Perera, U G E; Ample, F; Kersell, H; Zhang, Y; Vives, G; Echeverria, J; Grisolia, M; Rapenne, G; Joachim, C; Hla, S-W

2013-01-01

The design of artificial molecular machines often takes inspiration from macroscopic machines. However, the parallels between the two systems are often only superficial, because most molecular machines are governed by quantum processes. Previously, rotary molecular motors powered by light and chemical energy have been developed. In electrically driven motors, tunnelling electrons from the tip of a scanning tunnelling microscope have been used to drive the rotation of a simple rotor in a single direction and to move a four-wheeled molecule across a surface. Here, we show that a stand-alone molecular motor adsorbed on a gold surface can be made to rotate in a clockwise or anticlockwise direction by selective inelastic electron tunnelling through different subunits of the motor. Our motor is composed of a tripodal stator for vertical positioning, a five-arm rotor for controlled rotations, and a ruthenium atomic ball bearing connecting the static and rotational parts. The directional rotation arises from sawtooth-like rotational potentials, which are solely determined by the internal molecular structure and are independent of the surface adsorption site.

Effects of low molecular weight organic acids on (137)Cs release from contaminated soils.

PubMed

Chiang, Po Neng; Wang, Ming Kuang; Huang, Pan Ming; Wang, Jeng Jong

2011-06-01

Radio pollutant removal is one of several priority restoration strategies for the environment. This study assessed the effect of low molecular weight organic acid on the lability and mechanisms for release of (137)Cs from contaminated soils. The amount of (137)Cs radioactivity released from contaminated soils reacting with 0.02 M low molecular weight organic acids (LMWOAs) specifically acetic, succinic, oxalic, tartaric, and citric acid over 48 h were 265, 370, 760, 850, and 1002 Bq kg(-1), respectively. The kinetic results indicate that (137)Cs exhibits a two-step parabolic diffusion equation and a good linear relationship, indicating that the parabolic diffusion equation describes the data quite well, as shown by low p and high r(2) values. The fast stage, which was found to occur within a short period of time (0.083-3 h), corresponds to the interaction of LMWOAs with the surface of clay minerals; meanwhile, during the slow stage, which occurs over a much longer time period (3-24 h), desorption primarily is attributed to inter-particle or intra-particle diffusion. After a fifth renewal of the LMWOAs, the total levels of (137)Cs radioactivity released by acetic, succinic, oxalic, tartaric, and citric acid were equivalent to 390, 520, 3949, 2061, and 4422 Bq kg(-1) soil, respectively. H(+) can protonate the hydroxyl groups and oxygen atoms at the broken edges or surfaces of the minerals, thereby weakening Fe-O and Al-O bonds. After protonation of H(+), organic ligands can attack the OH and OH(2) groups in the minerals easily, to form complexes with surface structure cations, such as Al and Fe. The amounts of (137)Cs released from contaminated soil treated with LMWOAs were substantially increased, indicating that the LMWOAs excreted by the roots of plants play a critical role in (137)Cs release. Copyright © 2011 Elsevier Ltd. All rights reserved.

Molecular- and nm-scale Investigation of the Structure and Compositional Heterogeneity of Naturally Occurring Ferrihydrite

NASA Astrophysics Data System (ADS)

Cismasu, C.; Michel, F. M.; Stebbins, J. F.; Tcaciuc, A. P.; Brown, G. E.

2008-12-01

Ferrihydrite is a hydrated Fe(III) nano-oxide that forms in vast quantities in contaminated acid mine drainage environments. As a result of its high surface area, ferrihydrite is an important environmental sorbent, and plays an essential role in the geochemical cycling of pollutant metal(loid)s in these settings. Despite its environmental relevance, this nanomineral remains one of the least understood environmental solids in terms of its structure (bulk and surface), compositional variations, and the factors affecting its reactivity. Under natural aqueous conditions, ferrihydrite often precipitates in the presence of several inorganic compounds such as aluminum, silica, arsenic, etc., or in the presence of organic matter. These impurities can affect the molecular-level structure of naturally occurring ferrihydrite, thus modifying fundamental properties that are directly correlated with solid-phase stability and surface reactivity. Currently there exists a significant gap in our understanding of the structure of synthetic vs. natural ferrihydrites, due to the inherent difficulties associated to the investigation of these poorly crystalline nanophases. In this study, we combined synchrotron- and laboratory-based techniques to characterize naturally occurring ferrihydrite from an acid mine drainage system situated at the New Idria mercury mine in California. We used high-energy X-ray total scattering and pair distribution function analysis to elucidate quantitative structural details of these samples. We have additionally used scanning transmission X-ray microscopy high resolution imaging (30 nm) to evaluate the spatial relationship of major elements Si, Al, and C within ferrihydrite. Al, Si and C K-edge near- edge X-ray absorption fine structure spectroscopy and 27Al nuclear magnetic resonance spectroscopy were used to obtain short-range structural information. By combining these techniques we attain the highest level of resolution permitted by current analytical methods to study such naturally occurring nanomaterials, both at the molecular- and nm-scale. This work provides structural information at the short-, medium- and long- range, as well as evidence of compositional heterogeneity, and mineral/organic matter associations.

Experimental and theoretical comparison of the O K-edge nonresonant inelastic X-ray scattering and X-ray absorption spectra of NaReO4.

PubMed

Bradley, Joseph A; Yang, Ping; Batista, Enrique R; Boland, Kevin S; Burns, Carol J; Clark, David L; Conradson, Steven D; Kozimor, Stosh A; Martin, Richard L; Seidler, Gerald T; Scott, Brian L; Shuh, David K; Tyliszczak, Tolek; Wilkerson, Marianne P; Wolfsberg, Laura E

2010-10-06

Accurate X-ray absorption spectra (XAS) of first row atoms, e.g., O, are notoriously difficult to obtain due to the extreme sensitivity of the measurement to surface contamination, self-absorption, and saturation affects. Herein, we describe a comprehensive approach for determining reliable O K-edge XAS data for ReO(4)(1-) and provide methodology for obtaining trustworthy and quantitative data on nonconducting molecular systems, even in the presence of surface contamination. This involves comparing spectra measured by nonresonant inelastic X-ray scattering (NRIXS), a bulk-sensitive technique that is not prone to X-ray self-absorption and provides exact peak intensities, with XAS spectra obtained by three different detection modes, namely total electron yield (TEY), fluorescence yield (FY), and scanning transmission X-ray microscopy (STXM). For ReO(4)(1-), TEY measurements were heavily influenced by surface contamination, while the FY and STXM data agree well with the bulk NRIXS analysis. These spectra all showed two intense pre-edge features indicative of the covalent interaction between the Re 5d and O 2p orbitals. Density functional theory calculations were used to assign these two peaks as O 1s excitations to the e and t(2) molecular orbitals that result from Re 5d and O 2p covalent mixing in T(d) symmetry. Electronic structure calculations were used to determine the amount of O 2p character (%) in these molecular orbitals. Time dependent-density functional theory (TD-DFT) was also used to calculate the energies and intensities of the pre-edge transitions. Overall, under these experimental conditions, this analysis suggests that NRIXS, STXM, and FY operate cooperatively, providing a sound basis for validation of bulk-like excitation spectra and, in combination with electronic structure calculations, suggest that NaReO(4) may serve as a well-defined O K-edge energy and intensity standard for future O K-edge XAS studies.

Photonics walking up a human hair

NASA Astrophysics Data System (ADS)

Zeng, Hao; Parmeggiani, Camilla; Martella, Daniele; Wasylczyk, Piotr; Burresi, Matteo; Wiersma, Diederik S.

2016-03-01

While animals have access to sugars as energy source, this option is generally not available to artificial machines and robots. Energy delivery is thus the bottleneck for creating independent robots and machines, especially on micro- and nano- meter length scales. We have found a way to produce polymeric nano-structures with local control over the molecular alignment, which allowed us to solve the above issue. By using a combination of polymers, of which part is optically sensitive, we can create complex functional structures with nanometer accuracy, responsive to light. In particular, this allowed us to realize a structure that can move autonomously over surfaces (it can "walk") using the environmental light as its energy source. The robot is only 60 μm in total length, thereby smaller than any known terrestrial walking species, and it is capable of random, directional walking and rotating on different dry surfaces.

Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

NASA Astrophysics Data System (ADS)

Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

2012-10-01

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ˜40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.

Immunological purification and partial characterization of variant-specific surface antigen messenger RNA of Trypanosoma brucei brucei.

PubMed Central

Lheureux, M; Lheureux, M; Vervoort, T; Van Meirvenne, N; Steinert, M

1979-01-01

Polyadenylated RNA isolated from total polyribosomes of two variable antigen types (VATs) of T. brucei brucei were shown to program the synthesis, in mRNA-dependant reticulocyte lysates, of a wide variety of polypeptides. After immunoprecipitation of these cell-free products with an homologous antiserum raised against purified variant-specific surface antigen (VSSA), a major electrophoretic band was apparent on fluorography. It was confirmed that this band corresponds to the variable antigen since only an excess of purified homologous antigen will provoke competition. The apparent molecular weight of the in vitro synthesized antigen is about 63,000 daltons. The VSSA mRNA has been found in membrane-bound polyribosomes and a 15 fold immunological purification of this mRNA has been obtained, using partially purified anti-VSSA IgG in conjunction with inactivated Staphylococcus aureus. Images PMID:116191

General contamination criteria for optical surfaces. [instrument performance losses in spaceborne conditions

NASA Technical Reports Server (NTRS)

Bremer, J. C.

1982-01-01

Physical models are developed for establishing criteria to decide on the acceptable contamination level of optical devices in space-borne conditions. Optical systems can be degraded in terms of decreased throughput, i.e., transmissivity or reflectivity, or increases in the total integrated scatter (TIS). Performance losses can be caused by particulate accretion, molecular film accretion, and impact cratering. A quantitative relationship is defined for film thickness and loss of throughput. Formulas are also developed for cases where induced surface defects are larger than the desired viewing wavelengths, or smaller or of the same order of the observed wavelengths. The techniques are used to quantify the degradation of a VUV solar coronagraph, a VUV stellar telescope, and a solar cell due to TIS. Applications are projected for estimating the contamination sensitivity of specific instruments, assessing the contamination hazard from known particulates, or to define clean room standards.

Polycyclic Aromatic Hydrocarbons in Coastal Sediment of Klang Strait, Malaysia: Distribution Pattern, Risk Assessment and Sources

PubMed Central

Tavakoly Sany, Seyedeh Belin; Hashim, Rosli; Salleh, Aishah; Rezayi, Majid; Mehdinia, Ali; Safari, Omid

2014-01-01

Concentration, source, and ecological risk of polycyclic aromatic hydrocarbons (PAHs) were investigated in 22 stations from surface sediments in the areas of anthropogenic pollution in the Klang Strait (Malaysia). The total PAH level in the Klang Strait sediment was 994.02±918.1 µg/kg dw. The highest concentration was observed in stations near the coastline and mouth of the Klang River. These locations were dominated by high molecular weight PAHs. The results showed both pyrogenic and petrogenic sources are main sources of PAHs. Further analyses indicated that PAHs primarily originated from pyrogenic sources (coal combustion and vehicular emissions), with significant contribution from petroleum inputs. Regarding ecological risk estimation, only station 13 was moderately polluted, the rest of the stations suffered rare or slight adverse biological effects with PAH exposure in surface sediment, suggesting that PAHs are not considered as contaminants of concern in the Klang Strait. PMID:24747349

Sub-micrometer Geometrically Encoded Fluorescent Barcodes Self-Assembled from DNA

PubMed Central

Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

2012-01-01

The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here we use DNA-origami technology to construct sub-micrometer nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be unambiguously decoded using epifluorescence or total internal reflection fluorescence (TIRF) microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ~40 nm. One species of the barcodes was used to tag yeast surface receptors, suggesting their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments. PMID:23000997

Modeling Adsorption and Reactions of Organic Molecules at Metal Surfaces

PubMed Central

2014-01-01

Conspectus The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdWsurf method that accurately accounts for the collective electronic response effects enables reliable modeling of structure and stability for a broad class of organic molecules adsorbed on metal surfaces. This method was demonstrated to achieve quantitative accuracy for aromatic hydrocarbons (benzene, naphthalene, anthracene, and diindenoperylene), C60, and sulfur/oxygen-containing molecules (thiophene, NTCDA, and PTCDA) on close-packed and stepped metal surfaces, leading to an overall accuracy of 0.1 Å in adsorption heights and 0.1 eV in binding energies with respect to state-of-the-art experiments. An unexpected finding is that vdW interactions contribute more to the binding of strongly bound molecules on transition-metal surfaces than for molecules physisorbed on coinage metals. The accurate inclusion of vdW interactions also significantly improves tilting angles and adsorption heights for all the studied molecules, and can qualitatively change the potential-energy surface for adsorbed molecules with flexible functional groups. Activation barriers for molecular switches and reaction precursors are modified as well. PMID:24915492

Molecular dynamics study of nanodroplet diffusion on smooth solid surfaces

NASA Astrophysics Data System (ADS)

Niu, Zhao-Xia; Huang, Tao; Chen, Yong

2018-10-01

We perform molecular dynamics simulations of Lennard-Jones particles in a canonical ensemble to study the diffusion of nanodroplets on smooth solid surfaces. Using the droplet-surface interaction to realize a hydrophilic or hydrophobic surface and calculating the mean square displacement of the center-of-mass of the nanodroplets, the random motion of nanodroplets could be characterized by shorttime subdiffusion, intermediate-time superdiffusion, and long-time normal diffusion. The short-time subdiffusive exponent increases and almost reaches unity (normal diffusion) with decreasing droplet size or enhancing hydrophobicity. The diffusion coefficient of the droplet on hydrophobic surfaces is larger than that on hydrophilic surfaces.

Structural features of the adsorption layer of pentacene on the graphite surface and the PMMA/graphite hybrid surface

NASA Astrophysics Data System (ADS)

Fadeeva, A. I.; Gorbunov, V. A.; Litunenko, T. A.

2017-08-01

Using the molecular dynamics and the Monte Carlo methods, we have studied the structural features and growth mechanism of the pentacene film on graphite and polymethylmethacrylate /graphite surfaces. Monolayer capacity and molecular area, optimal angles between the pentacene molecules and graphite and PMMA/graphite surfaces as well as the characteristic angles between the neighboring pentacene molecules in the adsorption layer were estimated. It is shown that the orientation of the pentacene molecules in the film is determined by a number of factors, including the surface concentration of the molecules, relief of the surface, presence or absence of the polymer layer and its thickness. The pentacene molecules adsorbed on the graphite surface keep a horizontal position relative to the long axis at any surface coverage/thickness of the film. In the presence of the PMMA layer on the graphite, the increase of the number of pentacene molecules as well as the thickness of the PMMA layer induce the change of molecular orientation from predominantly horizontal to vertical one. The reason for such behavior is supposed to be the roughness of the PMMA surface.

Effect of substrates on the molecular orientation of silicon phthalocyanine dichloride thin films

NASA Astrophysics Data System (ADS)

Deng, Juzhi; Baba, Yuji; Sekiguchi, Tetsuhiro; Hirao, Norie; Honda, Mitsunori

2007-05-01

Molecular orientations of silicon phthalocyanine dichloride (SiPcCl2) thin films deposited on three different substrates have been measured by near-edge x-ray absorption fine structure (NEXAFS) spectroscopy using linearly polarized synchrotron radiation. The substrates investigated were highly oriented pyrolitic graphite (HOPG), polycrystalline gold and indium tin oxide (ITO). For thin films of about five monolayers, the polarization dependences of the Si K-edge NEXAFS spectra showed that the molecular planes of SiPcCl2 on three substrates were nearly parallel to the surface. Quantitative analyses of the polarization dependences revealed that the tilted angle on HOPG was only 2°, which is interpreted by the perfect flatness of the HOPG surface. On the other hand, the tilted angle on ITO was 26°. Atomic force microscopy (AFM) observation of the ITO surface showed that the periodicity of the horizontal roughness is of the order of a few nanometres, which is larger than the molecular size of SiPcCl2. It is concluded that the morphology of the top surface layer of the substrate affects the molecular orientation of SiPcCl2 molecules not only for mono-layered adsorbates but also for multi-layered thin films.

Distribution of Chains in Polymer Brushes Produced by a “Grafting From” Mechanism

DOE PAGES

Martinez, Andre P.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.; ...

2016-01-11

The molecular weight and polydispersity of the chains in a polymer brush are critical parameters determining the brush properties. However, the characterization of polymer brushes is hindered by the vanishingly small mass of polymer present in brush layers. In this study, in order to obtain sufficient quantities of polymer for analysis, polymer brushes were grown from high surface area fibrous nylon membranes by ATRP. We synthesized the brushes with varying surface initiator densities, polymerization times, and amounts of sacrificial initiator, then cleaved from the substrate, and analyzed by GPC and NMR. Characterization showed that the surface-grown polymer chains were moremore » polydisperse and had lower average molecular weight compared to solution-grown polymers synthesized concurrently. Furthermore, the molecular weight distribution of the polymer brushes was observed to be bimodal, with a low molecular weight population of chains representing a significant mass fraction of the polymer chains at high surface initiator densities. Moreover, the origin of this low MW polymer fraction is proposed to be the termination of growing chains by recombination during the early stages of polymerization, a mechanism confirmed by molecular dynamics simulations of brush polymerization.« less

Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins

NASA Astrophysics Data System (ADS)

Petrone, Luigi; Kumar, Akshita; Sutanto, Clarinda N.; Patil, Navinkumar J.; Kannan, Srinivasaraghavan; Palaniappan, Alagappan; Amini, Shahrouz; Zappone, Bruno; Verma, Chandra; Miserez, Ali

2015-10-01

Interfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus' assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives.

A low Earth orbit molecular beam space simulation facility

NASA Technical Reports Server (NTRS)

Cross, J. B.

1984-01-01

A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.

Evaluation of 3M™ Molecular Detection Assay (MDA) Listeria for the Detection of Listeria species in Selected Foods and Environmental Surfaces: Collaborative Study, First Action 2014.06.

PubMed

Bird, Patrick; Flannery, Jonathan; Crowley, Erin; Agin, James; Goins, David; Monteroso, Lisa; Benesh, DeAnn

2015-01-01

The 3M™ Molecular Detection Assay (MDA) Listeria is used with the 3M Molecular Detection System for the detection of Listeria species in food, food-related, and environmental samples after enrichment. The assay utilizes loop-mediated isothermal amplification to rapidly amplify Listeria target DNA with high specificity and sensitivity, combined with bioluminescence to detect the amplification. The 3M MDA Listeria method was evaluated using an unpaired study design in a multilaboratory collaborative study and compared to the AOAC Official Method of AnalysisSM (OMA) 993.12 Listeria monocytogenes in Milk and Dairy Products reference method for the detection of Listeria species in full-fat (4% milk fat) cottage cheese (25 g test portions). A total of 15 laboratories located in the continental United States and Canada participated. Each matrix had three inoculation levels: an uninoculated control level (0 CFU/test portion), and two levels artificially contaminated with Listeria monocytogenes, a low inoculum level (0.2-2 CFU/test portion) and a high inoculum level (2-5 CFU/test portion) using nonheat-stressed cells. In total, 792 unpaired replicate portions were analyzed. Statistical analysis was conducted according to the probability of detection (POD) model. Results obtained for the low inoculum level test portions produced a difference in cross-laboratory POD value of -0.07 with a 95% confidence interval of (-0.19, 0.06). No statistically significant differences were observed in the number of positive samples detected by the 3M MDA Listeria method versus the AOAC OMA method.

High field NMR Spectroscopy and FTICR Mass Spectrometry: Powerful Discovery Tools for the Characterization of Marine Dissolved Organic Matter

NASA Astrophysics Data System (ADS)

Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Grill, P.; Schmitt-Kopplin, P.

2012-04-01

High-field NMR and FTMS of SPE-derived marine dissolved organic matter (SPE-DOM) from the South Atlantic Ocean provided molecular level information of complex unknowns with unprecedented coverage of carbon and resolution. SPE-DOM represented major oceanic regimes of general significance: 5 m (near surface photic zone), 48 m (fluorescence maximum), 200 m (upper mesopelagic zone) and 5446 m (30 m above ground). 1H NMR spectra showed rather smooth bulk NMR envelopes with a few percent of visibly resolved signatures. 1H NMR spectra of SPE-DOM indicated considerable variance in abundance for all major chemical environments. Two-dimensional NMR spectra of SPE-DOM displayed exceptional resolution. JRES (sensitive but limited resolution), COSY (highly resolved) and HMBC NMR (informative but limited S/N ratio) spectra depicted resolved molecular signatures in excess of a certain minimum abundance. COSY cross peaks were most diverse for sample FMAX and conformed to >1,500 molecules present. Classical methyl groups terminating aliphatic chains represented only ~ 15 % of total methyl in all marine DOM investigated; 2 % of methyl was bound to olefinic carbon. Methyl ethers were abundant in surface marine DOM, and the chemical diversity of carbohydrates was larger than that of freshwater and soil DOM. TOCSY and HSQC cross peaks enabled unprecedented depiction of sp2-hybridized carbon chemical environments in marine SPE-DOM with discrimination of isolated and conjugated olefins as well as ?,?-unsaturated double bonds. Olefinic protons were more abundant than aromatic protons; relative HSQC cross peak integrals indicated more abundant olefinic carbon than aromatic carbon in all marine DOM as well. Furan, pyrrol and thiophene derivatives were marginal. Benzene derivatives and phenols as well as six-membered nitrogen heterocycles were prominent. Various key polycyclic aromatic hydrocarbon substructures suggested the presence of thermogenic organic matter (TMOC) in marine DOM at all water depths. Eventually, olefinic unsaturation in marine DOM will be more directly traceable to ultimate biogenic precursors than aromatic unsaturation. The conformity of key NMR signatures suggests the presence of a numerous set of identical molecules throughout the entire ocean column even if the investigated water masses belonged to different oceanic regimes and currents. High field (12 T) negative electrospray ionization FTICR mass spectra showed abundant CHO, CHNO, CHOS and CHNOS molecular series with slightly increasing numbers of mass peaks and average mass from surface to bottom SPE-DOM. The proportion of CHO and CHNO molecular series increased from surface to depth whereas CHOS and especially CHNOS molecular series markedly declined. The exhaustive characterization of complex unknowns in marine DOM will enable a meaningful assessment of individual marine biogeosignatures which carry the holistic memory of the oceanic water masses.

Effect of Coadsorbed Water on the Photodecomposition of Acetone on TiO2(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.

2008-06-10

The influence of coadsorbed water on the photodecomposition of acetone on TiO2 was examined using temperature programmed desorption (TPD) and the rutile TiO2(110) surface as a model photocatalyst. Of the two major influences ascribed to water in the heterogeneous photocatalysis literature (promotion via OH radical supply and inhibition due to site blocking), only the negative influence of water was observed. As long as the total water and acetone coverage was maintained well below the first layer saturation coverage (‘1 ML’), little inhibition of acetone photodecomposition was observed. However, as the total water+acetone coverage exceeded 1 ML, acetone was preferentially displacedmore » from the first layer to physisorbed states by water and the extent of acetone photodecomposition attenuated. The displacement originated from water compressing acetone into high coverage regions where increased acetone-acetone repulsions caused displacement from the first layer. The immediate product of acetone photodecomposition was adsorbed acetate, which occupies twice as many surface sites per molecule as compared to acetone. Since the acetate intermediate was more stable on the TiO2(110) surface than either water or acetone (as gauged by TPD) and since its photodecomposition rate was less than that of acetone, additional surface sites were not opened up during acetone photodecomposition for previously displaced acetone molecules to re-enter the first layer. Results in this study suggest that increased molecular-level repulsions between organic molecules brought about by increased water coverage are as influential in the inhibiting effect of water on photooxidation rates as are water-organic repulsions.« less

The Potential Role Played by the Fullerene-Like Structures of Interstellar Carbon Dust in the Formation of Molecular Hydrogen in Space

NASA Astrophysics Data System (ADS)

Cataldo, Franco; Iglesias-Groth, Susana

After a general introduction to the problem of formation of molecular hydrogen from atomic hydrogen in the interstellar medium and in the dense molecular clouds in particular, and after the explanation of the key role played by the surfaces on this process, it is proposed that the most suitable carbon surface for the formation of molecular hydrogen (from the radiative association process of atomic hydrogen) can be represented by carbon black rather than by graphite. Furthermore, it is proposed that the fullerene-like structures present in the carbon black graphene sheets are the reaction sites where molecular hydrogen may be formed.

AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

PubMed Central

Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

2011-01-01

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

Evaporation and condensation at a liquid surface. II. Methanol

NASA Astrophysics Data System (ADS)

Matsumoto, Mitsuhiro; Yasuoka, Kenji; Kataoka, Yosuke

1994-11-01

The rates of evaporation and condensation of methanol under the vapor-liquid equilibrium condition at the temperature of 300 and 350 K are investigated with a molecular dynamics computer simulation. Compared with the argon system (reported in part I), the ratio of self-reflection is similar (˜10%), but the ratio of molecule exchange is several times larger than the argon, which suggests that the conventional assumption of condensation as a unimolecular process completely fails for associating fluids. The resulting total condensation coefficient is 20%-25%, and has a quantitative agreement with a recent experiment. The temperature dependence of the evaporation-condensation behavior is not significant.

Ultrasonic spray coating polymer and small molecular organic film for organic light-emitting devices.

PubMed

Liu, Shihao; Zhang, Xiang; Zhang, Letian; Xie, Wenfa

2016-11-22

Ultrasonic spray coating process (USCP) with high material -utilization, low manufacture costs and compatibility to streamline production has been attractive in researches on photoelectric devices. However, surface tension exists in the solvent is still a huge obstacle to realize smooth organic film for organic light emitting devices (OLEDs) by USCP. Here, high quality polymer anode buffer layer and small molecular emitting layer are successfully realized through USCP by introducing extra-low surface tension diluent and surface tension control method. The introduction of low surface tension methyl alcohol is beneficial to the formation of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films and brings obvious phase separation and improved conductivity to PEDOT:PSS film. Besides, a surface tension control method, in which new stable tension equilibrium is built at the border of wetting layer, is proposed to eliminate the effect of surface tension during the solvent evaporation stage of ultrasonic spray coating the film consists of 9,9-Spirobifluoren-2-yl-diphenyl-phosphine oxide doped with 10 wt% tris [2-(p -tolyl) pyridine] iridium (III). A smooth and homogenous small molecular emitting layer without wrinkles is successfully realized. The effectiveness of the ultrasonic spray coating polymer anode buffer layer and small molecular emitting layer are also proved by introducing them in OLEDs.

Ultrasonic spray coating polymer and small molecular organic film for organic light-emitting devices

NASA Astrophysics Data System (ADS)

Liu, Shihao; Zhang, Xiang; Zhang, Letian; Xie, Wenfa

2016-11-01

Ultrasonic spray coating process (USCP) with high material -utilization, low manufacture costs and compatibility to streamline production has been attractive in researches on photoelectric devices. However, surface tension exists in the solvent is still a huge obstacle to realize smooth organic film for organic light emitting devices (OLEDs) by USCP. Here, high quality polymer anode buffer layer and small molecular emitting layer are successfully realized through USCP by introducing extra-low surface tension diluent and surface tension control method. The introduction of low surface tension methyl alcohol is beneficial to the formation of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films and brings obvious phase separation and improved conductivity to PEDOT:PSS film. Besides, a surface tension control method, in which new stable tension equilibrium is built at the border of wetting layer, is proposed to eliminate the effect of surface tension during the solvent evaporation stage of ultrasonic spray coating the film consists of 9,9-Spirobifluoren-2-yl-diphenyl-phosphine oxide doped with 10 wt% tris [2-(p -tolyl) pyridine] iridium (III). A smooth and homogenous small molecular emitting layer without wrinkles is successfully realized. The effectiveness of the ultrasonic spray coating polymer anode buffer layer and small molecular emitting layer are also proved by introducing them in OLEDs.

Covalent immobilization of molecularly imprinted polymer nanoparticles using an epoxy silane.

PubMed

Kamra, Tripta; Chaudhary, Shilpi; Xu, Changgang; Johansson, Niclas; Montelius, Lars; Schnadt, Joachim; Ye, Lei

2015-05-01

Molecularly imprinted polymers (MIPs) can be used as antibody mimics to develop robust chemical sensors. One challenging problem in using MIPs for sensor development is the lack of reliable conjugation chemistry that allows MIPs to be fixed on transducer surface. In this work, we study the use of epoxy silane to immobilize MIP nanoparticles on model transducer surfaces without impairing the function of the immobilized nanoparticles. The MIP nanoparticles with a core-shell structure have selective molecular binding sites in the core and multiple amino groups in the shell. The model transducer surface is functionalized with a self-assembled monolayer of epoxy silane, which reacts with the core-shell MIP particles to enable straightforward immobilization. The whole process is characterized by studying the treated surfaces after each preparation step using atomic force microscopy, scanning electron microscopy, fluorescence microscopy, contact angle measurements and X-ray photoelectron spectroscopy. The microscopy results show that the MIP particles are immobilized uniformly on surface. The photoelectron spectroscopy results further confirm the action of each functionalization step. The molecular selectivity of the MIP-functionalized surface is verified by radioligand binding analysis. The particle immobilization approach described here has a general applicability for constructing selective chemical sensors in different formats. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Enhanced the performance of graphene oxide/polyimide hybrid membrane for CO2 separation by surface modification of graphene oxide using polyethylene glycol

NASA Astrophysics Data System (ADS)

Wu, Li-guang; Yang, Cai-hong; Wang, Ting; Zhang, Xue-yang

2018-05-01

Polyethylene glycol (PEG) with different molecular weights was first used to modify graphene oxide (GO) samples. Subsequently, polyimide (PI) hybrid membranes containing modified-GO were fabricated via in situ polymerization. The separation performance of these hybrid membranes was evaluated using permeation experiments for CO2 and N2 gases. The morphology characterization showed that PEG with suitable molecular weight could be successfully grafted on the GO surface. PEG modification altered the surface properties of GO and introduced defective structures onto GO surface. This caused strong surface polarity and high free volume of membranes containing PEG-modified GO, thereby improving the separation performance of membranes. The addition of PEG-GO with low molecular weight effectively increased gas diffusion through hybrid membranes. The hybrid membranes containing PEG-GO with large molecular weight had high solubility performance for CO2 gas due to the introduction of numerous polar groups into polymeric membranes. With the loading content of modified GO, the CO2 gas permeability of hybrid membranes initially increased but eventually decreased. The optimal content of modified GO in membranes reached 3.0 wt%. When too much PEG added (exceeding 30 g), some impurities formed on GO surface and some aggregates appeared in the resulting hybrid membrane, which depressed the membrane performance.

Molecular Machine Powered Surface Programmatic Chain Reaction for Highly Sensitive Electrochemical Detection of Protein.

PubMed

Zhu, Jing; Gan, Haiying; Wu, Jie; Ju, Huangxian

2018-04-17

A bipedal molecular machine powered surface programmatic chain reaction was designed for electrochemical signal amplification and highly sensitive electrochemical detection of protein. The bipedal molecular machine was built through aptamer-target specific recognition for the binding of one target protein with two DNA probes, which hybridized with surface-tethered hairpin DNA 1 (H1) via proximity effect to expose the prelocked toehold domain of H1 for the hybridization of ferrocene-labeled hairpin DNA 2 (H2-Fc). The toehold-mediated strand displacement reaction brought the electrochemical signal molecule Fc close to the electrode and meanwhile released the bipedal molecular machine to traverse the sensing surface by the surface programmatic chain reaction. Eventually, a large number of duplex structures of H1-H2 with ferrocene groups facing to the electrode were formed on the sensor surface to generate an amplified electrochemical signal. Using thrombin as a model target, this method showed a linear detection range from 2 pM to 20 nM with a detection limit of 0.76 pM. The proposed detection strategy was enzyme-free and allowed highly sensitive and selective detection of a variety of protein targets by using corresponding DNA-based affinity probes, showing potential application in bioanalysis.

Ultrasonic spray coating polymer and small molecular organic film for organic light-emitting devices

PubMed Central

Liu, Shihao; Zhang, Xiang; Zhang, Letian; Xie, Wenfa

2016-01-01

Ultrasonic spray coating process (USCP) with high material -utilization, low manufacture costs and compatibility to streamline production has been attractive in researches on photoelectric devices. However, surface tension exists in the solvent is still a huge obstacle to realize smooth organic film for organic light emitting devices (OLEDs) by USCP. Here, high quality polymer anode buffer layer and small molecular emitting layer are successfully realized through USCP by introducing extra-low surface tension diluent and surface tension control method. The introduction of low surface tension methyl alcohol is beneficial to the formation of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films and brings obvious phase separation and improved conductivity to PEDOT:PSS film. Besides, a surface tension control method, in which new stable tension equilibrium is built at the border of wetting layer, is proposed to eliminate the effect of surface tension during the solvent evaporation stage of ultrasonic spray coating the film consists of 9,9-Spirobifluoren-2-yl-diphenyl-phosphine oxide doped with 10 wt% tris [2-(p -tolyl) pyridine] iridium (III). A smooth and homogenous small molecular emitting layer without wrinkles is successfully realized. The effectiveness of the ultrasonic spray coating polymer anode buffer layer and small molecular emitting layer are also proved by introducing them in OLEDs. PMID:27874030

On-surface formation of one-dimensional polyphenylene through Bergman cyclization.

PubMed

Sun, Qiang; Zhang, Chi; Li, Zhiwen; Kong, Huihui; Tan, Qinggang; Hu, Aiguo; Xu, Wei

2013-06-12

On-surface fabrication of covalently interlinked conjugated nanostructures has attracted significant attention, mainly because of the high stability and efficient electron transport ability of these structures. Here, from the interplay of scanning tunneling microscopy imaging and density functional theory calculations, we report for the first time on-surface formation of one-dimensional polyphenylene chains through Bergman cyclization followed by radical polymerization on Cu(110). The formed surface nanostructures were further corroborated by the results for the ex situ-synthesized molecular product after Bergman cyclization. These findings are of particular interest and importance for the construction of molecular electronic nanodevices on surfaces.

Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties.

PubMed

Zhang, Z; Fenter, P; Cheng, L; Sturchio, N C; Bedzyk, M J; Predota, M; Bandura, A; Kubicki, J D; Lvov, S N; Cummings, P T; Chialvo, A A; Ridley, M K; Bénézeth, P; Anovitz, L; Palmer, D A; Machesky, M L; Wesolowski, D J

2004-06-08

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties (structure, diffusivity, dielectric constant), surface protonation and hydrolysis, and the effect of solution ionic strength.

Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

DOEpatents

Brennan, T.M.; Hammons, B.E.; Tsao, J.Y.

1992-12-15

A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth. 3 figs.

Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

DOEpatents

Brennan, Thomas M.; Hammons, B. Eugene; Tsao, Jeffrey Y.

1992-01-01

A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth.

Developments in Molecular Recognition and Sensing at Interfaces

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

2007-01-01

In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

PubMed

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-05

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

NASA Astrophysics Data System (ADS)

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-01

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

High mass resolution isochronous time-of-flight spectrograph for three-dimensional space plasma measurements

NASA Technical Reports Server (NTRS)

Moebius, E.; Bochsler, P.; Ghielmetti, A. G.; Hamilton, D. C.

1990-01-01

By combining a toroidal electrostatic analyzer with a novel cylindrically symmetric isochronous time-of-flight mass spectrometer, an instrument was developed that simultaneously determines the three-dimensional distribution function of ions and differentiates species. The ion mass is determined to high resolution (M/Delta-M greater than 50) from the time of flight within a harmonic field configuration defined by hyperboloid equipotential surfaces. A second conventional time-of-flight channel makes use of particles leaving the thin entrance foil as neutrals. An additional solid state detector in which the neutrals are stopped allows the total energy and thereby the ionic charge of the incident ions to be determined as well. Information from the neutral and the ion channels can be combined to determine the total mass of an incident molecular ion and the mass of one atomic fragment.

Chemometric analysis of attenuated total reflectance infrared spectra of Proteus mirabilis strains with defined structures of LPS.

PubMed

Zarnowiec, Paulina; Mizera, Andrzej; Chrapek, Magdalena; Urbaniak, Mariusz; Kaca, Wieslaw

2016-07-01

Proteus spp. strains are some of the most important pathogens associated with complicated urinary tract infections and bacteremia affecting patients with immunodeficiency and long-term urinary catheterization. For epidemiological purposes, various molecular typing methods have been developed for this pathogen. However, these methods are labor intensive and time consuming. We evaluated a new method of differentiation between strains. A collection of Proteus spp. strains was analyzed by attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy in the mid-infrared region. ATR FT-IR spectroscopy used in conjunction with a diamond ATR accessory directly produced the biochemical profile of the surface chemistry of bacteria. We conclude that a combination of ATR FT-IR spectroscopy and mathematical modeling provides a fast and reliable alternative for discrimination between Proteus isolates, contributing to epidemiological research. © The Author(s) 2016.

Polychlorinated biphenyls (PCBs) in recreational marina sediments of San Diego Bay, southern California.

PubMed

Neira, Carlos; Vales, Melissa; Mendoza, Guillermo; Hoh, Eunha; Levin, Lisa A

2018-01-01

Polychlorinated biphenyl (PCB) concentrations were determined in surface sediments from three recreational marinas in San Diego Bay, California. Total PCB concentrations ranged from 23 to 153, 31-294, and 151-1387ngg -1 for Shelter Island Yacht Basin (SIYB), Harbor Island West (HW) and Harbor Island East (HE), respectively. PCB concentrations were significantly higher in HE and PCB group composition differed relative to HW and SIYB, which were not significantly different from each other in concentration or group composition. In marina sediments there was a predominance (82-85%) of heavier molecular weight PCBs with homologous groups (6CL-7CL) comprising 59% of the total. In HE 75% of the sites exceeded the effect range median (ERM), and toxicity equivalence (TEQ dioxin-like PCBs) values were higher relative to those of HW and SIYB, suggesting a potential ecotoxicological risk. Copyright © 2017 Elsevier Ltd. All rights reserved.

Optical properties monitor: Experiment definition phase

NASA Technical Reports Server (NTRS)

Wilkes, Donald R.; Bennett, Jean M.; Hummer, Leigh L.; Chipman, Russell A.; Hadaway, James B.; Pezzaniti, Larry

1990-01-01

The stability of materials used in the space environment will continue to be a limiting technology for space missions. The Optical Properties Monitor (OPM) Experiment provides a comprehensive space research program to study the effects of the space environment (both natural and induced) on optical, thermal and space power materials. The OPM Experiment was selected for definition under the NASA/OAST In-Space Technology Experiment Program. The results of the OPM Definition Phase are presented. The OPM experiment will expose selected materials to the space environment and measure the effects with in-space optical measurements. In-space measurements include total hemispherical reflectance total integrated scatter and VUV reflectance/transmittance. The in-space measurements will be augmented with extensive pre- and post-flight sample measurements to determine other optical, mechanical, electrical, chemical or surface effects of space exposure. Environmental monitors will provide the amount and time history of the sample exposure to solar irradiation, atomic oxygen and molecular contamination.

Optical properties monitor: Experiment definition phase

NASA Technical Reports Server (NTRS)

Wilkes, Donald R.; Bennett, Jean M.; Hummer, Leigh L.; Chipman, Russell A.; Hadaway, James B.; Pezzaniti, Larry

1989-01-01

The stability of materials used in the space environment will continue to be a limiting technology for space missions. The Optical Properties Monitor (OPM) Experiment provides a comprehensive space research program to study the effects of the space environment-both natural and induced-on optical, thermal and space power materials. The OPM Experiment was selected for definition under the NASA/OAST In-Space Technology Experiment Program. The results of the OPM Definition Phase are presented. The OPM Experiment will expose selected materials to the space environment and measure the effects with in-space optical measurements. In-space measurements include total hemispherical reflectance total integrated scatter and VUV reflectance/transmittance. The in-space measurements will be augmented with extensive pre- and post-flight sample measurements to determine other optical, mechanical, electrical, chemical or surface effects of space exposure. Environmental monitors will provide the amount and time history of the sample exposure to solar irradiation, atomic oxygen and molecular contamination.

Fate of polycyclic aromatic hydrocarbon (PAH) contamination in a mangrove swamp in Hong Kong following an oil spill.

PubMed

Ke, L; Wong, Teresa W Y; Wong, Y S; Tam, Nora F Y

2002-01-01

The fate of polycyclic aromatic hydrocarbon (PAH) contamination in a mangrove swamp (Yi O) in Hong Kong after an oil spill accident was investigated. The concentrations and profiles of PAHs in surface sediments collected from five quadrats (each of 10 m x 10 m) covering different degrees of oil contamination and the most contaminated mangrove leaves were examined in December 2000 (30 days after the accident) and March 2001 (126 days later). The concentrations of total PAHs in surface sediments ranged from 138 to 2,135 ng g(-1), and PAHs concentrations decreased with time. In the most contaminated sediments, total PAHs dropped from 2,135 (30 days) to 1,196 ng g(-1) (120 days), and the decrease was smaller in less contaminated sediments. The percentage reduction in sediment PAHs over three months (44%) was less significant than that in contaminated leaves (85%), indicating PAH in or on leaves disappeared more rapidly. The PAH profiles were very similar in sediments collected from quadrats Q1 and Q2 with benzo[a]anthracene and pyrene being the most abundant PAH compounds, but were different in the other three quadrats. The proportion of the light molecular weight PAHs to total PAHs increased after three months, especially phenanthrene. Results suggest that physical and photo-chemical weathering (tidal washing and photo-oxidation) of crude oil in surface sediments and on plant leaves were important processes in the first few months after the oil spill. The PAH contamination in Yi O swamp came from both petrogenic and pyrolytic sources. The petrogenic characteristic in the most contaminated sediment was confirmed with high values of phenanthrene to anthracene ratio (>10) and low values of fluoranthene to pyrene ratio (0.3-0.4).

Preparation of a Versatile Bifunctional Zeolite for Targeted Imaging Applications

PubMed Central

Ndiege, Nicholas; Raidoo, Renugan; Schultz, Michael K.; Larsen, Sarah

2011-01-01

Bifunctional zeolite Y was prepared for use in targeted in vivo molecular imaging applications. The strategy involved functionalization of the external surface of zeolite Y with chloropropyltriethoxysilane followed by reaction with sodium azide to form azide-functionalized NaY, which is amenable to copper(1) catalyzed click chemistry. In this study, a model alkyne (4-pentyn-1-ol) was attached to the azide-terminated surface via click chemistry to demonstrate feasibility for attachment of molecular targeting vectors (e.g., peptides, aptamers) to the zeolite surface. The modified particle efficiently incorporates the imaging radioisotope gallium-68 (68Ga) into the pores of the azide-functionalized NaY zeolite to form a stable bifunctional molecular targeting vector. The result is a versatile “clickable” zeolite platform that can be tailored for future in vivo molecular targeting and imaging modalities. PMID:21306141

Adsorption and recognition characteristics of surface molecularly imprinted polymethacrylic acid/silica toward genistein.

PubMed

Zhang, Yanyan; Gao, Baojiao; An, Fuqiang; Xu, Zeqing; Zhang, Tingting

2014-09-12

In this paper, on the basis of surface-initiated graft polymerization, a new surface molecular imprinting technique is established by molecular design. And molecularly imprinted polymer MIP-PMAA/SiO2 is successfully prepared with genistein as template. The adsorption and recognition characteristics of MIP-PMAA/SiO2 for genistein are studied in depth by using static method, dynamic method and competitive adsorption experiment. The experimental results show that MIP-PMAA/SiO2 possesses very strong adsorption affinity and specific recognition for genistein. The saturated adsorption capacity could reach to 0.36mmolg(-1). The selectivity coefficients relative to quercetin and rutin are 5.4 and 11.8, respectively. Besides, MIP-PMAA/SiO2 is regenerated easily and exhibits excellent reusability. Copyright © 2014 Elsevier B.V. All rights reserved.

Water interactions with condensed organic phases: a combined experimental and theoretical study of molecular-level processes

NASA Astrophysics Data System (ADS)

Johansson, Sofia M.; Kong, Xiangrui; Thomson, Erik S.; Papagiannakopoulos, Panos; Pettersson, Jan B. C.; Lovrić, Josip; Toubin, Céline

2016-04-01

Water uptake on aerosol particles modifies their chemistry and microphysics with important implications for air quality and climate. A large fraction of the atmospheric aerosol consists of organic aerosol particles or inorganic particles with condensed organic components. Here, we combine laboratory studies using the environmental molecular beam (EMB) method1 with molecular dynamics (MD) simulations to characterize water interactions with organic surfaces in detail. The over-arching aim is to characterize the mechanisms that govern water uptake, in order to guide the development of physics-based models to be used in atmospheric modelling. The EMB method enables molecular level studies of interactions between gases and volatile surfaces at near ambient pressure,1 and the technique may provide information about collision dynamics, surface and bulk accommodation, desorption and diffusion kinetics. Molecular dynamics simulations provide complementary information about the collision dynamics and initial interactions between gas molecules and the condensed phase. Here, we focus on water interactions with condensed alcohol phases that serve as highly simplified proxies for systems in the environment. Gas-surface collisions are in general found to be highly inelastic and result in efficient surface accommodation of water molecules. As a consequence, surface accommodation of water can be safely assumed to be close to unity under typical ambient conditions. Bulk accommodation is inefficient on solid alcohol and the condensed materials appear to produce hydrophobic surface structures, with limited opportunities for adsorbed water to form hydrogen bonds with surface molecules. Accommodation is significantly more efficient on the dynamic liquid alcohol surfaces. The results for n-butanol (BuOH) are particularly intriguing where substantial changes in water accommodation taking place over a 10 K interval below and above the BuOH melting point.2 The governing mechanisms for the observed water accommodation are discussed based on the combined EMB and MD results. The studies illustrate that the detailed surface properties of the condensed organic phase may substantially modify water uptake, with potential implications for the properties and action of aerosols and clouds in the Earth system. References: 1. X.R. Kong, E. S. Thomson, P. Papagiannakopoulos, S.M. Johansson, and J.B.C. Pettersson, Water Accommodation on Ice and Organic Surfaces: Insights from Environmental Molecular Beam Experiments. J. Phys. Chem. B 118 (2014) 13378-13386. 2. P. Papagiannakopoulos, X. Kong, E. S. Thomson, N. Marković, and J. B. C. Pettersson, Surface Transformations and Water Uptake on Liquid and Solid Butanol near the Melting Temperature. J. Phys. Chem. C 117 (2013) 6678-6685.

The Chemistry and Excitation of Water in Molecular Clouds

NASA Technical Reports Server (NTRS)

Hollenbach, David

2003-01-01

We model the chemistry and thermal balance of opaque molecular clouds exposed to an external flux of ultraviolet photons. We include the processes of gas phase and grain surface chemical reactions; in particular we examine closely the freezing of atoms and molecules onto grain surfaces and the desorption of molecules from grain surfaces as a function of depth into a molecular cloud. We find that on the surface of a molecular cloud the gas phase water abundances are low because of photodissociation, and the grain phase water (ice) abundance is low because of photodesorption of water from the grain surfaces. Deeper into the cloud, at A(sub v) less than or approximately 2-8 depending on the strength of the external ultraviolet flux, the gas phase water abundance increases with depth as the photodissociation rates decline due to dust attenuation of the ultraviolet field. However, beyond A(sub v) less than or approximately 2-8 the gas phase water abundance declines because the water freezes as water ice on the grains, and photodesorption is no longer effective in clearing the ice. A peak water abundance of about 10(exp -6) to 10(exp -7) occurs at about A(sub v) approximately 2-8, relatively independent of the gas density and the ultraviolet field. We show that such a model matches very closely the observations of the Submillimeter Wave Astronomical Satellite (SWAS), a NASA Small Explorer Mission. The model elucidates several mechanisms that have been recently invoked to understand gas phase chemistry in clouds, including-the freeze-out of molecules onto grain surface, the desorption of these molecules from the surfaces, and the abundance gradients of molecules as functions of depth into molecular clouds.

Poly(glycidyl ether)-Based Monolayers on Gold Surfaces: Control of Grafting Density and Chain Conformation by Grafting Procedure, Surface Anchor, and Molecular Weight.

PubMed

Heinen, Silke; Weinhart, Marie

2017-03-07

For a meaningful correlation of surface coatings with their respective biological response reproducible coating procedures, well-defined surface coatings, and thorough surface characterization with respect to layer thickness and grafting density are indispensable. The same applies to polymeric monolayer coatings which are intended to be used for, e.g., fundamental studies on the volume phase transition of surface end-tethered thermoresponsive polymer chains. Planar gold surfaces are frequently used as model substrates, since they allow a variety of straightforward surface characterization methods. Herein we present reproducible grafting-to procedures performed with thermoresponsive poly(glycidyl ether) copolymers composed of glycidyl methyl ether (GME) and ethyl glycidyl ether (EGE). The copolymers feature different molecular weights (2 kDa, 9 kDa, 24 kDa) and are equipped with varying sulfur-containing anchor groups in order to achieve adjustable grafting densities on gold surfaces and hence control the tethered polymers' chain conformation. We determined "wet" and "dry" thicknesses of these coatings by QCM-D and ellipsometry measurements and deduced anchor distances and degrees of chain overlap of the polymer chains assembled on gold. Grafting under cloud point conditions allowed for higher degrees of chain overlap compared to grafting from a good solvent like ethanol, independent of the used sulfur-containing anchor group for polymers with low (2 kDa) and medium (9 kDa) molecular weights. By contrast, the achieved grafting densities and thus chain overlaps of surface-tethered polymers with high (24 kDa) molecular weights were identical for both grafting methods. Monolayers prepared from an ethanolic solution of poly(glycidyl ether)s equipped with sterically demanding disulfide-containing anchors revealed the lowest degrees of chain overlap. The ratio of the radius of gyration to the anchor distance (2 R g /l) of the latter coating was found to be lower than 1.4, indicating that the assembly was rather in the mushroom-like than in the brush regime. Polymer chains with thiol-containing anchors of different alkyl chain lengths (C 11 SH vs C 4 SH) formed assemblies with comparable degrees of chain overlap with 2 R g /l values above 1.4 and are thus in the brush regime. Molecular weights influenced the achievable degree of chain overlap on the surface. Coatings prepared with the medium molecular weight polymer (9 kDa) resulted in the highest chain packing density. Control of grafting density and thus chain overlap in different regimes (brush vs mushroom) on planar gold substrates are attainable for monolayer coatings with poly(GME-ran-EGE) by adjusting the polymer's molecular weight and anchor group as well as the conditions for the grafting-to procedure.

THE MOLECULAR GAS DENSITY IN GALAXY CENTERS AND HOW IT CONNECTS TO BULGES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisher, David B.; Bolatto, Alberto; Drory, Niv

2013-02-20

In this paper we present gas density, star formation rate (SFR), stellar masses, and bulge-disk decompositions for a sample of 60 galaxies. Our sample is the combined sample of the BIMA SONG, CARMA STING, and PdBI NUGA surveys. We study the effect of using CO-to-H{sub 2} conversion factors that depend on the CO surface brightness, and also that of correcting SFRs for diffuse emission from old stellar populations. We estimate that SFRs in bulges are typically lower by 20% when correcting for diffuse emission. Using the surface brightness dependent conversion factor, we find that over half of the galaxies inmore » our sample have {Sigma}{sub mol} > 100 M {sub Sun} pc{sup -2}. Though our sample is not complete in any sense, our results are enough to rule out the assumption that bulges are uniformly gas-poor systems. We find a trend between gas density of bulges and bulge Sersic index; bulges with lower Sersic index have higher gas density. Those bulges with low Sersic index (pseudobulges) have gas fractions that are similar to that of disks. Conversely, the typical molecular gas fraction in classical bulges is more similar to that of an elliptical galaxy. We also find that there is a strong correlation between bulges with the highest gas surface density and the galaxy being barred. However, we also find that classical bulges with low gas surface density can be barred as well. Our results suggest that understanding the connection between the central surface density of gas in disk galaxies and the presence of bars should also take into account the total gas content of the galaxy. Finally, we show that when using the corrected SFRs and gas densities, the correlation between SFR surface density and gas surface density of bulges is similar to that of disks. This implies that at the scale of the bulges the timescale for converting gas into stars is comparable to those results found in disks.« less

Ultra-High Aggregate Bandwidth Two-Dimensional Multiple-Wavelength Diode Laser Arrays

DTIC Science & Technology

1994-04-09

surface temperature across the wafer during the growth of the cavity spacer region using the fact that the molecular beam epitaxy (MBE) growth of GaAs...substrate surface temperature across the wafer during the growth of the cavity spacer region. Using the fact that, during an molecular beam epitaxy (MBE...K. Bacher and J.S. Harris, "Periodically Induced Mode Shift in Vertical Cavity Fabry Perot Etalons Grown by Molecular Beam Epitaxy ," to be presented

Molecular ligand modulation of palladium nanocatalysts for highly efficient and robust heterogeneous oxidation of cyclohexenone to phenol

DOE PAGES

Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi; ...

2017-01-06

Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less

Mn induced 1 × 2 reconstruction in the τ-MnAl(0 0 1) surface

NASA Astrophysics Data System (ADS)

Guerrero-Sánchez, J.; Takeuchi, Noboru

2018-05-01

We report on first principles total energy calculations to describe the structural, electronic and magnetic properties of MnAl(0 0 1) surfaces. We have concentrated in structural models having 1 × 1 and 1 × 2 periodicities, since recent experiments of the similar MnGa(0 0 1) surface have found 1 × 1 and 1 × 2 reconstructions. Our calculations show the existence of two stable structures for different ranges of chemical potential. A 1 × 1 surface is stable for Al-rich conditions, whereas a Mn-induced 1 × 2 reconstruction appears after increasing the Mn chemical potential up to Mn-rich conditions. It is important to notice that experimentally, Mn rich conditions are important for improved magnetic properties. The Mn layers in both structures have ferromagnetic arrangements, but they are aligned antiferromagnetically with the almost no magnetic Al atoms. Moreover, the on top Mn atoms, which produce the 1 × 2 reconstruction, align antiferromagnetically with the second layer Mn atoms. These findings are similar to those obtained experimentally in MnGa thin films grown by molecular beam epitaxy. Therefore, this method could also be used to grow the proposed MnAl films.

Characterization of QCM sensor surfaces coated with molecularly imprinted nanoparticles.

PubMed

Reimhult, Kristina; Yoshimatsu, Keiichi; Risveden, Klas; Chen, Si; Ye, Lei; Krozer, Anatol

2008-07-15

Molecularly imprinted polymers (MIPs) are gaining great interest as tailor-made recognition materials for the development of biomimetic sensors. Various approaches have been adopted to interface MIPs with different transducers, including the use of pre-made imprinted particles and the in situ preparation of thin polymer layers directly on transducer surfaces. In this work we functionalized quartz crystal microbalance (QCM) sensor crystals by coating the sensing surfaces with pre-made molecularly imprinted nanoparticles. The nanoparticles were immobilized on the QCM transducers by physical entrapment in a thin poly(ethylene terephthalate) (PET) layer that was spin-coated on the transducer surface. By controlling the deposition conditions, it was possible to gain a high nanoparticle loading in a stable PET layer, allowing the recognition sites in nanoparticles to be easily accessed by the test analytes. In this work, different sensor surfaces were studied by micro-profilometry and atomic force microscopy and the functionality was evaluated using quartz crystal microbalance with dissipation (QCM-D). The molecular recognition capability of the sensors were also confirmed using radioligand binding analysis by testing their response to the presence of the test compounds, (R)- and (S)-propranolol in aqueous buffer.

Molecular-orbital models for the catalytic activity and selectivity of coordinatively unsaturated platinum surfaces and complexes

NASA Astrophysics Data System (ADS)

Balazs, A. C.; Johnson, K. H.

1982-01-01

Electronic structures have been calculated for 5-, 6-, and 10-atom Pt clusters, as well as for a Pt(PH 3) 4 coordination complex, using the self-consistent-field X-alpha scattered-wave (SCF-Xα-SW) molecular-orbital technique. The 10-atom cluster models the local geometry of a flat, unreconstructed Pt(100) surface, while the 5- and 6-atom clusters show features of a stepped Pt surface. Pt(PH 3) 4 resembles the chemically similar homogeneous catalyst Pt(PPh 3) 4. Common to all these coordinatively unsaturated complexes are orbitals lying near or coinciding with the highest occupied molecular orbital ("Fermi level") which show pronounced d lobes pointing directly into the vacuum. Under the hypothesis that these molecular orbitals are mainly responsible for the chemical activities of the above species, one can account for the relative similarities and differences in catalytic activity and selectivity displayed by unreconstructed Pt(100) surfaces, stepped Pt surfaces or particles, and isolated Pt(PPh 3) 4 coordination complexes. The relevance of these findings to catalyst-support interactions is also discussed. Finally, relativistic corrections to the electronic structures are calculated and their implications on catalytic properties discussed.

Production of High Molecular Weight Organic Compounds on the Surfaces of Amorphous Iron Silicate Catalysts: Implications for Organic Synthesis in the Solar Nebula

NASA Technical Reports Server (NTRS)

Gilmour, I.; Hill, H. G. M.; Pearson, V. K.; Sephton, M. A.; Nuth, J. A., III

2002-01-01

The high molecular weight organic products of Fischer-Tropsch/Haber-Bosch syntheses on the surfaces of Fe-silicate catalysts have been studied by GCMS. Additional information is contained in the original extended abstract.

Polyacrylamide Molecular Weight and Phosphogypsum Effects on Infiltration and Erosion in Semi-Arid Soils

USDA-ARS?s Scientific Manuscript database

Seal formation at the surface of semi-arid soils during rainstorms reduces soil infiltration rate (IR) and causes runoff and erosion. Surface application of dry anionic polyacrylamide (PAM) with high molecular weight (MW) has been found to be effective in stabilizing soil aggregates, and decreasing ...

Polyacrylamide molecular weight and phosphogypsum effects on infiltration and erosion in semi-arid soils

USDA-ARS?s Scientific Manuscript database

Seal formation at the surface of semi-arid soils during rainstorms reduces soil infiltration rate (IR) and causes runoff and erosion. Surface application of dry anionic polyacrylamide (PAM) with high molecular weight (MW) has been found to be effective in stabilizing soil aggregates, and decreasing ...

A Pulsed Laser and Molecular Beam Apparatus for Surface Studies

DTIC Science & Technology

1985-03-01

will be carried out are in part described in the proposal A Pulsed Laser and Molecular Beam Apparatus for Surface Studies submitted by Howard ... University in November 1982 for review by AFOSR, under the DOD University Instrumentation Program. This report describes the progress made during the

Aps and Tep Chemical Characterization: Link Between The Dom and Pom Pools

NASA Astrophysics Data System (ADS)

Gogou, A.; Repeta, D. J.

The ocean inventory of dissolved organic carbon (DOC) is approximately 750 GT, comprising one of the Earth's largest carbon reservoirs on Earth. Despite its potential significance, the mechanisms that lead to DOM production and to spatial and temporal variations of DOM concentration in the world ocean are poorly understood. Chemical characterization studies show that up to 50% of HMW DOM is a structurally well-defined class of acylated polysaccharides (APS), which exhibits novel molecular-level characteris tics. Although APS synthesis occurs in the euphotic zone, a large fraction of the marine inventory of APS (appr. 10-30 GT C), resides in the deep ocean, and is approximately equal in mass to the total marine inventory of particulate organic carbon. While radiocarbon dating of deep sea DOC yields very old apparent ages (4000-6000 ybp), radiocarbon measurements made by our group on individual APS sugars shows that APS in the deep ocean has a radiocarbon value of +56 per mil, equivalent to surface water POC and DIC. This is the first clear evidence for the presence of "young" DOC in the deep ocean. One mechanism that could be important for the rapid removal of APS from surface seawater is physical removal by macroaggregates. To investigate the significance of this mechanism, we studied the chemical composition of surface-active POM (TEP) produced naturally on surface waters and in laboratory experiments, after bubbling of HMW DOM isolated from algal cultures. 1H-NMR spectral properties and molecular-level distribution of neutral sugars in natural and artificially produced TEP closely resembled those observed for cultured and oceanic HMW DOM, while they are significantly different from those of suspended particulate matter in the ocean (Gogou and Repeta, 2000). The results of these experiments provide evidence that POM with similar chemical characteristics to HMW DOM can be produced from algal-derived DOM in the surface ocean.

Influence of Substrates on the Surface Characteristics and Membrane Proteome of Fibrobacter succinogenes S85

PubMed Central

Raut, Mahendra P.; Karunakaran, Esther; Mukherjee, Joy; Biggs, Catherine A.; Wright, Phillip C.

2015-01-01

Although Fibrobacter succinogenes S85 is one of the most proficient cellulose degrading bacteria among all mesophilic organisms in the rumen of herbivores, the molecular mechanism behind cellulose degradation by this bacterium is not fully elucidated. Previous studies have indicated that cell surface proteins might play a role in adhesion to and subsequent degradation of cellulose in this bacterium. It has also been suggested that cellulose degradation machinery on the surface may be selectively expressed in response to the presence of cellulose. Based on the genome sequence, several models of cellulose degradation have been suggested. The aim of this study is to evaluate the role of the cell envelope proteins in adhesion to cellulose and to gain a better understanding of the subsequent cellulose degradation mechanism in this bacterium. Comparative analysis of the surface (exposed outer membrane) chemistry of the cells grown in glucose, acid-swollen cellulose and microcrystalline cellulose using physico-chemical characterisation techniques such as electrophoretic mobility analysis, microbial adhesion to hydrocarbons assay and Fourier transform infra-red spectroscopy, suggest that adhesion to cellulose is a consequence of an increase in protein display and a concomitant reduction in the cell surface polysaccharides in the presence of cellulose. In order to gain further understanding of the molecular mechanism of cellulose degradation in this bacterium, the cell envelope-associated proteins were enriched using affinity purification and identified by tandem mass spectrometry. In total, 185 cell envelope-associated proteins were confidently identified. Of these, 25 proteins are predicted to be involved in cellulose adhesion and degradation, and 43 proteins are involved in solute transport and energy generation. Our results supports the model that cellulose degradation in F. succinogenes occurs at the outer membrane with active transport of cellodextrins across for further metabolism of cellodextrins to glucose in the periplasmic space and inner cytoplasmic membrane. PMID:26492413

TMEM2: A missing link in hyaluronan catabolism identified?

PubMed

Yamaguchi, Yu; Yamamoto, Hayato; Tobisawa, Yuki; Irie, Fumitoshi

2018-03-27

Hyaluronan (HA) is a glycosaminoglycan (GAG) composed of repeating disaccharide units of glucuronic acid and N-acetylglucosamine. HA is an extremely long, unbranched polymer, which often exceeds 10 6  Da and sometimes reaches 10 7  Da. A feature that epitomizes HA is its rapid turnover; one-third of the total body HA is turned over daily. The current model of HA catabolism postulates that high-molecular weight HA in the extracellular space is first cleaved into smaller fragments by a hyaluronidase(s) that resides at the cell surface, followed by internalization of fragments and their degradation into monosaccharides in lysosomes. Over the last decade, considerable research has shown that the HYAL family of hyaluronidases plays significant roles in HA catabolism. Nonetheless, the identity of a hyaluronidase responsible for the initial step of HA cleavage on the cell surface remains elusive, as biochemical and enzymological properties of HYAL proteins are not entirely consistent with those expected of cell surface hyaluronidases. Recent identification of transmembrane 2 (TMEM2) as a cell surface protein that possesses potent hyaluronidase activity suggests that it may be the "missing" cell surface hyaluronidase, and that novel models of HA catabolism should include this protein. Copyright © 2017 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Physical vapor deposition as a route to glasses with liquid crystalline order

NASA Astrophysics Data System (ADS)

Gomez, Jaritza

Physical vapor deposition (PVD) is an effective route to prepare glasses with a unique combination of properties. Substrate temperatures near the glass transition (Tg) and slow deposition rates can access enhanced mobility at the surface of the glass allowing molecules at the surface additional time to sample different molecular configurations. The temperature of the substrate can be used to control molecular mobility during deposition and properties in the resulting glasses such as higher density, kinetic stability and preferential molecular orientation. PVD was used to prepare glasses of itraconazole, a smectic A liquid crystal. We characterized molecular orientation using infrared and ellipsometry. Molecular orientation can be controlled by choice of Tsubstrate in a range of temperatures near Tg. Glasses deposited at Tsubstrate = Tg show nearly vertical molecular orientation relative to the substrate; at lower Tsubstrate, molecules are nearly parallel to the substrate. The molecular orientation depends on the temperature of the substrate during preparation and not on the molecular orientation of the underlying layer. This allows preparing samples of layers with differing orientations. We find these glasses are homogeneous solids without evidence of domain boundaries and are molecularly flat. We interpret the combination of properties obtained for vapor-deposited glasses of itraconazole to result from a process where molecular orientation is determined by the structure and dynamics at the free surface of the glass during deposition. We report the thermal and structural properties of glasses prepared using PVD of a rod-like molecule, posaconazole, which does not show equilibrium liquid crystal phases. These glasses show substantial molecular orientation that can be controlled by choice of Tsubstrate during deposition. Ellipsometry and IR indicate that glasses prepared at Tg - 3 K are highly ordered. At these Tsubstrate, molecules show preferential vertical orientation and orientation is similar to that measured in aligned nematic liquid crystal. Our results are consistent with a recently proposed mechanism where molecular orientation in equilibrium liquids can be trapped in PVD glasses and suggest that the orientation at the free surface of posaconazole is nematic-like. In addition, we show posaconazole glasses show high kinetic stability controlled by Tsubstrate.

PAMAM-Based Dendrimers with Different Alkyl Chains Self-Assemble on Silica Surfaces: Controllable Layer Structure and Molecular Aggregation.

PubMed

Zhang, Minghui; Yang, Hui; Wang, Shujuan; Zhang, Wei; Hou, Qingfeng; Guo, Donghong; Liu, Fanghui; Chen, Ting; Wu, Xu; Wang, Jinben

2018-06-20

Amphiphilic poly(amidoamine) (PAMAM) dendrimers are a well-known dendritic family due to their remarkable ability to self-assemble on solid surface. However, the relationship between molecular conformation (or adsorption kinetics) of a self-assembled layer and molecular amphiphilicity of such kind of dendrimer is still lacking, which limits the development of modulating self-assembling structures and surface functionality. With this in mind, we synthesized a series of amphiphilic PAMAM-based dendrimers, denoted as G 1 C n , with different alkyl chains ( n = 8, 12, and 16), and investigated the molecular aggregation on silica surfaces by means of quartz crystal microbalance with dissipation, atomic force microscopy, and contact angle. After rinsing, remaining adsorption amounts of G 1 C 12 were higher than those of G 1 C 8 at high concentrations, suggesting that G 1 C 12 adlayers were more stable due to the stronger intermolecular hydrophobic interactions, whereas it preferred to adopt the intramolecular hydrophobic interactions for G 1 C 16 , with low adsorption amounts and unstable adlayers. Bilayer-like structures were inferred in G 1 C 8 and G 1 C 12 adlayers with loose conformation, whereas monolayer structures were likely to exist in the sparse adsorption film of G 1 C 16 . Our results provided more detailed understanding of the effect of molecular structure on the self-assembled structures of amphiphilic dendrimers on solid surfaces, shedding light on the controlled microstructure and wettability of functional surface by modulating the length of hydrophobic chains of dendrimers and a potential application of dendrimer-substrate combinations.

Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

NASA Astrophysics Data System (ADS)

Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

2015-12-01

Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models makes the system act like a band-stop filter over an infinite frequency range.

Orientation distribution and process modeling of thermotropic liquid crystalline copolyester (TLCP) injection-moldings

NASA Astrophysics Data System (ADS)

Bubeck, Robert; Fang, Jun; Burghardt, Wesley; Burgard, Susan; Fischer, Daniel

2009-03-01

The influence of melt processing conditions upon mechanical properties and degrees of compound molecular orientation have been thoroughly studied for a series of well-defined injection molded samples fabricated from VECTRA (TM) A950 and 4,4'-dihydroxy-a-methylstilbene TLCPs. Fracture and tensile data were correlated with processing conditions, orientation, and molecular weight. Mechanical properties for both TLCPs were found to follow a ``universal'' Anisotropy Factor (AF) associated with the bimodal orientation states in the plaques determined from 2-D WAXS. Surface orientations were globally surveyed using Attenuated Total Reflectance -- Fourier Transform Infrared (ATR-FTIR) spectroscopy and C K edge Near-Edge X-ray Absorption Fine Structure (NEXAFS). The results derived from the two spectroscopy techniques confirmed each other well. These results along with those from 2-D WAXS in transmission were compared with the results of process modeling using a commercial program, MOLDFLOW(TM). The agreement between model predictions and the measured orientation states was gratifyingly good.

Involvement of the glucose moiety in the molecular recognition of methyl beta-lactoside by ricin: synthesis, conformational analysis, and binding studies of different derivatives at the C-3 region.

PubMed

Fernández, P; Jiménez-Barbero, J; Martín-Lomas, M; Solís, D; Díaz-Mauriño, T

1994-04-01

Syntheses of the 3-aminodeoxy (4), 3-deoxy-3-methyl (5), and 3-epi (6) derivatives of methyl beta-lactoside (1) have been achieved from 1 in a straightforward way, and their solution conformations in water and dimethyl sulfoxide analysed through molecular mechanics and dynamics calculations and nuclear magnetic resonance data. The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low energy region with phi = 15 +/- 45 degrees and psi = -25 +/- 30 degrees, that is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides. The binding of the different compounds to ricin, the galactose-specific toxin from Ricinus communis, has been investigated. The results confirm the involvement of the C-3 region in a nonpolar interaction with the protein at the periphery of the combining site.

Application of molecularly imprinted polymers to selective removal of clofibric acid from water.

PubMed

Dai, Chaomeng; Zhang, Juan; Zhang, Yalei; Zhou, Xuefei; Liu, Shuguang

2013-01-01

A new molecularly imprinted polymer (MIP) adsorbent for clofibric acid (CA) was prepared by a non-covalent protocol. Characterization of the obtained MIP was achieved by scanning electron microscopy (SEM) and nitrogen sorption. Sorption experimental results showed that the MIP had excellent binding affinity for CA and the adsorption of CA by MIP was well described by pseudo-second-order model. Scatchard plot analysis revealed that two classes of binding sites were formed in the MIP with dissociation constants of 7.52 ± 0.46 mg L(-1) and 114 ± 4.2 mg L(-1), respectively. The selectivity of MIP demonstrated higher affinity for CA over competitive compound than that of non-imprinted polymers (NIP). The MIP synthesized was used to remove CA from spiked surface water and exhibited significant binding affinity towards CA in the presence of total dissolved solids (TDS). In addition, MIP reusability was demonstrated for at least 12 repeated cycles without significant loss in performance.

Concentration, composition and sources of PAHs in the coastal sediments of the exclusive economic zone (EEZ) of Qatar, Arabian Gulf.

PubMed

Soliman, Y S; Al Ansari, E M S; Wade, T L

2014-08-30

Surface sediments were collected from sixteen locations in order to assess levels and sources of polycyclic aromatic hydrocarbons (PAHs) in sediments of Qatar exclusive economic zone (EEZ). Samples were analyzed for 16 parent PAHs, 18 alkyl homologs and for dibenzothiophenes. Total PAHs concentration (∑PAHs) ranged from 2.6 ng g(-1) to 1025 ng g(-1). The highest PAHs concentrations were in sediments in and adjacent to harbors. Alkylated PAHs predominated most of the sampling locations reaching up to 80% in offshore locations. Parent PAHs and parent high molecular weight PAHs dominated location adjacent to industrial activities and urban areas. The origin of PAHs sources to the sediments was elucidated using ternary plot, indices, and molecular ratios of specific compounds such as (Ant/Phe+Ant), (Flt/Flt+Pyr). PAHs inputs to most coastal sites consisted of mixture of petroleum and combustion derived sources. However, inputs to the offshore sediments were mainly of petroleum origin. Copyright © 2014 Elsevier Ltd. All rights reserved.

The effect of cesium carbonate on 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C 61 aggregation in films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindemann, William R.; Wang, Wenjie; Fungura, Fadzai

2014-11-11

Surface-pressure isotherms, X-ray reflectivity, and X-ray near-total reflection fluorescence were used to study the properties of 1-(3-methoxycarbonyl)propyl-1-phenyl[6,6]C 61 (PCBM) that was pre-mixed with cesium carbonate and spread as a film at the air-water interface. The pre-mixed PCBM with cesium carbonate demonstrated a strikingly strong effect on the organization of the film. Whereas films formed from pure PCBM solution were rough due to strong inter-molecular interactions, the films formed from the mixture were much smoother. This indicates that the cesium carbonate moderates the inter-molecular interactions among PCBM molecules, hinting that the cesium diffusion observed in inverted organic photovoltaics and the likelymore » ensuing ionic Cs-PCBM interaction decrease aggregation tendency of PCBM. As a result, this implies that the use of cesium salts affects the morphology of the organic layer and consequently improves the efficiency of these devices.« less

Application of Molecularly Imprinted Polymers to Selective Removal of Clofibric Acid from Water

PubMed Central

Dai, Chaomeng; Zhang, Juan; Zhang, Yalei; Zhou, Xuefei; Liu, Shuguang

2013-01-01

A new molecularly imprinted polymer (MIP) adsorbent for clofibric acid (CA) was prepared by a non-covalent protocol. Characterization of the obtained MIP was achieved by scanning electron microscopy (SEM) and nitrogen sorption. Sorption experimental results showed that the MIP had excellent binding affinity for CA and the adsorption of CA by MIP was well described by pseudo-second-order model. Scatchard plot analysis revealed that two classes of binding sites were formed in the MIP with dissociation constants of 7.52±0.46 mg L−1 and 114±4.2 mg L−1, respectively. The selectivity of MIP demonstrated higher affinity for CA over competitive compound than that of non-imprinted polymers (NIP). The MIP synthesized was used to remove CA from spiked surface water and exhibited significant binding affinity towards CA in the presence of total dissolved solids (TDS). In addition, MIP reusability was demonstrated for at least 12 repeated cycles without significant loss in performance. PMID:24205143

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

PubMed

Poudel, Lokendra; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Podgornik, Rudolf; Steinmetz, Nicole F; Ching, Wai-Yim

2015-05-18

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In Situ Infrared Spectroscopy of Oligoaniline Intermediates Created under Alkaline Conditions.

PubMed

Šeděnková, Ivana; Stejskal, Jaroslav; Trchová, Miroslava

2014-12-26

The progress of the oxidation of aniline with ammonium peroxydisulfate in an alkaline aqueous medium has been monitored in situ by attenuated total reflection (ATR) Fourier transform infrared spectroscopy. The growth of the microspheres and of the film at the ATR crystal surface, as well as the changes proceeding in the surrounding aqueous medium, are reflected in the spectra. The evolution of the spectra and the changes in the molecular structure occurring during aniline oxidation in alkaline medium are discussed with the help of differential spectra. Several processes connected with the various stages of aniline oxidation were distinguished. The progress of hydrolysis of the aniline in water and further an oxidation of aminophenol to benzoquinone imines in the presence of peroxydisulfate in alkaline medium have been detected in the spectra in real time. The precipitated solid oxidation product was analyzed by mass spectrometry. It is composed of oligomers, mainly trimers to octamers, of various molecular structures incorporating in addition to aniline constitutional units also p-benzoquinone or p-benzoquinoneimine moieties.

Hydration of excess electrons trapped in charge pockets on molecular surfaces

NASA Astrophysics Data System (ADS)

Jalbout, Abraham F.; Del Castillo, R.; Adamowicz, Ludwik

2007-01-01

In this work we strive to design a novel electron trap located on a molecular surface. The process of electron trapping involves hydration of the trapped electron. Previous calculations on surface electron trapping revealed that clusters of OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), while the hydrogen atoms on the opposite side of the surface form pockets of positive charge that can attract extra negative charge. The excess electron density on such surfaces can be further stabilized by interactions with water molecules. Our calculations show that these anionic systems are stable with respect to vertical electron detachment (VDE).

Paralytic shellfish poisoning (PSP) toxin binders for optical biosensor technology: problems and possibilities for the future: a review

PubMed Central

Campbell, K.; Rawn, D.F.K.; Niedzwiadek, B.; Elliott, C.T.

2011-01-01

This review examines the developments in optical biosensor technology, which uses the phenomenon of surface plasmon resonance, for the detection of paralytic shellfish poisoning (PSP) toxins. Optical biosensor technology measures the competitive biomolecular interaction of a specific biological recognition element or binder with a target toxin immobilised onto a sensor chip surface against toxin in a sample. Different binders such as receptors and antibodies previously employed in functional and immunological assays have been assessed. Highlighted are the difficulties in detecting this range of low molecular weight toxins, with analogues differing at four chemical substitution sites, using a single binder. The complications that arise with the toxicity factors of each toxin relative to the parent compound, saxitoxin, for the measurement of total toxicity relative to the mouse bioassay are also considered. For antibodies, the cross-reactivity profile does not always correlate to toxic potency, but rather to the toxin structure to which it was produced. Restrictions and availability of the toxins makes alternative chemical strategies for the synthesis of protein conjugate derivatives for antibody production a difficult task. However, when two antibodies with different cross-reactivity profiles are employed, with a toxin chip surface generic to both antibodies, it was demonstrated that the cross-reactivity profile of each could be combined into a single-assay format. Difficulties with receptors for optical biosensor analysis of low molecular weight compounds are discussed, as are the potential of alternative non-antibody-based binders for future assay development in this area. PMID:21623494

3D ZnO/Ag Surface-Enhanced Raman Scattering on Disposable and Flexible Cardboard Platforms

PubMed Central

Pimentel, Ana; Araújo, Andreia; Águas, Hugo; Martins, Rodrigo; Fortunato, Elvira

2017-01-01

In the present study, zinc oxide (ZnO) nanorods (NRs) with a hexagonal structure have been synthesized via a hydrothermal method assisted by microwave radiation, using specialized cardboard materials as substrates. Cardboard-type substrates are cost-efficient and robust paper-based platforms that can be integrated into several opto-electronic applications for medical diagnostics, analysis and/or quality control devices. This class of substrates also enables highly-sensitive Raman molecular detection, amiable to several different operational environments and target surfaces. The structural characterization of the ZnO NR arrays has been carried out by X-ray diffraction (XRD), scanning electron microscopy (SEM) and optical measurements. The effects of the synthesis time (5–30 min) and temperature (70–130 °C) of the ZnO NR arrays decorated with silver nanoparticles (AgNPs) have been investigated in view of their application for surface-enhanced Raman scattering (SERS) molecular detection. The size and density of the ZnO NRs, as well as those of the AgNPs, are shown to play a central role in the final SERS response. A Raman enhancement factor of 7 × 105 was obtained using rhodamine 6 G (R6G) as the test analyte; a ZnO NR array was produced for only 5 min at 70 °C. This condition presents higher ZnO NR and AgNP densities, thereby increasing the total number of plasmonic “hot-spots”, their volume coverage and the number of analyte molecules that are subject to enhanced sensing.

The development of soil organic matter in restored biodiverse Jarrah forests of South-Western Australia as determined by ASE and GCMS.

PubMed

Lin, Deborah S; Greenwood, Paul F; George, Suman; Somerfield, Paul J; Tibbett, Mark

2011-08-01

Soil organic matter (SOM) is known to increase with time as landscapes recover after a major disturbance; however, little is known about the evolution of the chemistry of SOM in reconstructed ecosystems. In this study, we assessed the development of SOM chemistry in a chronosequence (space for time substitution) of restored Jarrah forest sites in Western Australia. Replicated samples were taken at the surface of the mineral soil as well as deeper in the profile at sites of 1, 3, 6, 9, 12, and 17 years of age. A molecular approach was developed to distinguish and quantify numerous individual compounds in SOM. This used accelerated solvent extraction in conjunction with gas chromatography mass spectrometry. A novel multivariate statistical approach was used to assess changes in accelerated solvent extraction (ASE)-gas chromatography-mass spectrometry (GCMS) spectra. This enabled us to track SOM developmental trajectories with restoration time. Results showed total carbon concentrations approached that of native forests soils by 17 years of restoration. Using the relate protocol in PRIMER, we demonstrated an overall linear relationship with site age at both depths, indicating that changes in SOM chemistry were occurring. The surface soils were seen to approach native molecular compositions while the deeper soil retained a more stable chemical signature, suggesting litter from the developing diverse plant community has altered SOM near the surface. Our new approach for assessing SOM development, combining ASE-GCMS with illuminating multivariate statistical analysis, holds great promise to more fully develop ASE for the characterisation of SOM.

Paralytic shellfish poisoning (PSP) toxin binders for optical biosensor technology: problems and possibilities for the future: a review.

PubMed

Campbell, K; Rawn, D F K; Niedzwiadek, B; Elliott, C T

2011-06-01

This review examines the developments in optical biosensor technology, which uses the phenomenon of surface plasmon resonance, for the detection of paralytic shellfish poisoning (PSP) toxins. Optical biosensor technology measures the competitive biomolecular interaction of a specific biological recognition element or binder with a target toxin immobilised onto a sensor chip surface against toxin in a sample. Different binders such as receptors and antibodies previously employed in functional and immunological assays have been assessed. Highlighted are the difficulties in detecting this range of low molecular weight toxins, with analogues differing at four chemical substitution sites, using a single binder. The complications that arise with the toxicity factors of each toxin relative to the parent compound, saxitoxin, for the measurement of total toxicity relative to the mouse bioassay are also considered. For antibodies, the cross-reactivity profile does not always correlate to toxic potency, but rather to the toxin structure to which it was produced. Restrictions and availability of the toxins makes alternative chemical strategies for the synthesis of protein conjugate derivatives for antibody production a difficult task. However, when two antibodies with different cross-reactivity profiles are employed, with a toxin chip surface generic to both antibodies, it was demonstrated that the cross-reactivity profile of each could be combined into a single-assay format. Difficulties with receptors for optical biosensor analysis of low molecular weight compounds are discussed, as are the potential of alternative non-antibody-based binders for future assay development in this area.

Surface plasmon-assisted microscope.

PubMed

Borejdo, Julian; Gryczynski, Zygmunt; Fudala, Rafal; Joshi, Chaitanya R; Borgmann, Kathleen; Ghorpade, Anuja; Gryczynski, Ignacy

2018-06-01

Total internal reflection microscopy (TIRF) has been a powerful tool in biological research. The most valuable feature of the method has been the ability to image 100- to 200-nm-thick layer of cell features adjacent to a coverslip, such as membrane lipids, membrane receptors, and structures proximal-to-basal membranes. Here, we demonstrate an alternative method of imaging thin-layer proximal-to-basal membranes by placing a sample on a high refractive index coverslip covered by a thin layer of gold. The sample is illuminated using the Kretschmann method (i.e., from the top to an aqueous medium). Fluorophores that are close to the metal surface induce surface plasmons in the metal film. Fluorescence from fluorophores near the metal surface couple with surface plasmons allowing them to penetrate the metal surface and emerge at a surface plasmon coupled emission angle. The thickness of the detection layer is further reduced in comparison with TIRF by metal quenching of fluorophores at a close proximity (below 10 nm) to a surface. Fluorescence is collected by a high NA objective and imaged by EMCCD or converted to a signal by avalanche photodiode fed by a single-mode optical fiber inserted in the conjugate image plane of the objective. The system avoids complications of through-the-objective TIRF associated with shared excitation and emission light path, has thin collection thickness, produces excellent background rejection, and is an effective method to study molecular motion. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Exploiting β-Cyclodextrin in Molecular Imprinting for Achieving Recognition of Benzylparaben in Aqueous Media

PubMed Central

Asman, Saliza; Mohamad, Sharifah; Muhamad Sarih, Norazilawati

2015-01-01

The molecularly imprinted polymer (MIP) based on methacrylic acid functionalized β-cyclodextrin (MAA-β-CD) monomer was synthesized for the purpose of selective recognition of benzylparaben (BzP). The MAA-β-CD monomer was produced by bridging a methacrylic acid (MAA) and β-cyclodextrin (β-CD) using toluene-2,4-diisocyanate (TDI) by reacting the –OH group of MAA and one of the primary –OH groups of β-CD. This monomer comprised of triple interactions that included an inclusion complex, π–π interaction, and hydrogen bonding. To demonstrate β-CD performance in MIPs, two MIPs were prepared; molecularly imprinted polymer-methacrylic acid functionalized β-cyclodextrin, MIP(MAA-β-CD), and molecularly imprinted polymer-methacrylic acid, MIP(MAA); both prepared by a reversible addition fragmentation chain transfer polymerization (RAFT) in the bulk polymerization process. Both MIPs were characterized using the Fourier Transform Infrared Spectroscopy (FTIR), Field Emission Scanning Electron Microscopy (FESEM), and Brunauer-Emmett-Teller (BET). The presence of β-CD not only influenced the morphological structure, it also affected the specific surface area, average pore diameter, and total pore volume of the MIP. The rebinding of the imprinting effect was evaluated in binding experiments, which proved that the β-CD contributed significantly to the enhancement of the recognition affinity and selective adsorption of the MIP. PMID:25667978

Rapid detection of IHNV by molecular padlock recognition and surface-associated isothermal amplification

NASA Astrophysics Data System (ADS)

McCarthy, Erik L.; Egeler, Teressa J.; Bickerstaff, Lee E.; Pereira da Cunha, Mauricio; Millard, Paul J.

2005-11-01

RNA sequences derived from infectious hematopoeitic necrosis virus (IHNV) could be detected using a combination of surface-associated molecular padlock DNA probes (MPP) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV were recognized by MPP. Circularized MPP were then captured on the inner surface of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA gave rise to DNA concatamers, which were in turn bound by the fluorescent reporter SYBR Green II nucleic acid stain, and measured by microfluorimetry. Surface-associated molecular padlock technology, combined with isothermal RCA, exhibited high selectivity and sensitivity without thermal cycling. This technology is applicable to direct RNA and DNA detection, permitting detection of a variety of viral or bacterial pathogens.

Molecular Velcro constructed from polymer loop brushes showing enhanced adhesion force

NASA Astrophysics Data System (ADS)

Zhou, Tian; Han, Biao; Han, Lin; Li, Christopher; Department of Materials Science; Engineering Team; School of Biomedical Engineering, Science; Health Systems Team

2015-03-01

Molecular Velcro is commonly seen in biological systems as the formation of strong physical entanglement at molecular scale could induce strong adhesion, which is crucial to many biological processes. To mimic this structure, we designed, and fabricated polymer loop brushes using polymer single crystals with desired surface functionality and controlled chain folding. Compared with reported loop brushes fabricated using triblock copolymers, the present loop bushes have precise loop sizes, loop grafting density, and well controlled tethering locations on the solid surface. Atomic force microscopy-based force spectroscopy measurements using a polymer chain coated probe reveal that the adhesion force are significantly enhanced on the loop brush surface as compared with its single-strand counterpart. This study directly shows the effect of polymer brush conformation on their properties, and suggests a promising strategy for advanced polymer surface design.

Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

PubMed

Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

2015-10-20

Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces.

Lotus Dust Mitigation Coating and Molecular Adsorber Coating

NASA Technical Reports Server (NTRS)

O'Connor, Kenneth M.; Abraham, Nithin S.

2015-01-01

NASA Goddard Space Flight Center has developed two unique coating formulations that will keep surfaces clean and sanitary and contain contaminants.The Lotus Dust Mitigation Coating, modeled after the self-cleaning, water-repellant lotus leaf, disallows buildup of dust, dirt, water, and more on surfaces. This coating, has been successfully tested on painted, aluminum, glass, silica, and some composite surfaces, could aid in keeping medical assets clean.The Molecular Adsorber Coating is a zeolite-based, sprayable molecular adsorber coating, designed to prevent outgassing in materials in vacuums. The coating works well to adsorb volatiles and contaminates in manufacturing and processing, such as in pharmaceutical production. The addition of a biocide would also aid in controlling bacteria levels.

Energetic ion bombardment of Ag surfaces by C60+ and Ga+ projectiles.

PubMed

Sun, Shixin; Szakal, Christopher; Winograd, Nicholas; Wucher, Andreas

2005-10-01

The ion bombardment-induced release of particles from a metal surface is investigated using energetic fullerene cluster ions as projectiles. The total sputter yield as well as partial yields of neutral and charged monomers and clusters leaving the surface are measured and compared with corresponding data obtained with atomic projectile ions of similar impact kinetic energy. It is found that all yields are enhanced by about one order of magnitude under bombardment with the C60+ cluster projectiles compared with Ga+ ions. In contrast, the electronic excitation processes determining the secondary ion formation probability are unaffected. The kinetic energy spectra of sputtered particles exhibit characteristic differences which reflect the largely different nature of the sputtering process for both types of projectiles. In particular, it is found that under C60+ impact (1) the energy spectrum of sputtered atoms peaks at significantly lower kinetic energies than for Ga+ bombardment and (2) the velocity spectra of monomers and dimers are virtually identical, a finding which is in pronounced contrast to all published data obtained for atomic projectiles. The experimental findings are in reasonable agreement with recent molecular dynamics simulations.

Hydrogen speciation in hydrated layers on nuclear waste glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aines, R.D.; Weed, H.C.; Bates, J.K.

1987-01-15

The hydration of an outer layer on nuclear waste glasses is known to occur during leaching, but the actual speciation of hydrogen (as water or hydroxyl groups) in these layers has not been determined. As part of the Nevada Nuclear Waste Storage Investigations Project, we have used infrared spectroscopy to determine hydrogen speciations in three nuclear waste glass compositions (SRL-131 & 165, and PNL 76-68), which were leached at 90{sup 0}C (all glasses) or hydrated in a vapor-saturated atmosphere at 202{sup 0}C (SRL-131 only). Hydroxyl groups were found in the surface layers of all the glasses. Molecular water was foundmore » in the surface of SRL-131 and PNL 76-68 glasses that had been leached for several months in deionized water, and in the vapor-hydrated sample. The water/hydroxyl ratio increases with increasing reaction time; molecular water makes up most of the hydrogen in the thick reaction layers on vapor-phase hydrated glass while only hydroxyl occurs in the least reacted samples. Using the known molar absorptivities of water and hydroxyl in silica-rich glass the vapor-phase layer contained 4.8 moles/liter of molecular water, and 0.6 moles water in the form hydroxyl. A 15 {mu}m layer on SRL-131 glass formed by leaching at 90{sup 0}C contained a total of 4.9 moles/liter of water, 2/3 of which was as hydroxyl. The unreacted bulk glass contains about 0.018 moles/liter water, all as hydroxyl. The amount of hydrogen added to the SRL-131 glass was about 70% of the original Na + Li content, not the 300% that would result from alkali=hydronium ion interdiffusion. If all the hydrogen is then assumed to be added as the result of alkali-H{sup +} interdiffusion, the molecular water observed may have formed from condensation of the original hydroxyl groups.« less

Blood Accessibility to Fibrin in Venous Thrombosis is Thrombus Age-Dependent and Predicts Fibrinolytic Efficacy: An In Vivo Fibrin Molecular Imaging Study

PubMed Central

Stein-Merlob, Ashley F.; Kessinger, Chase W.; Erdem, S. Sibel; Zelada, Henry; Hilderbrand, Scott A.; Lin, Charles P.; Tearney, Guillermo J.; Jaff, Michael R.; Reed, Guy L.; Henke, Peter K.; McCarthy, Jason R.; Jaffer, Farouc A.

2015-01-01

Fibrinolytic therapy of venous thromboembolism (VTE) is increasingly utilized, yet limited knowledge is available regarding in vivo mechanisms that govern fibrinolytic efficacy. In particular, it is unknown how age-dependent thrombus organization limits direct blood contact with fibrin, the target of blood-based fibrinolytic agents. Utilizing high-resolution in vivo optical molecular imaging with FTP11, a near-infrared fluorescence (NIRF) fibrin-specific reporter, here we investigated the in vivo interrelationships of blood accessibility to fibrin, thrombus age, thrombus neoendothelialization, and fibrinolysis in murine venous thrombosis (VT). In both stasis VT and non-stasis VT, NIRF microscopy showed that FTP11 fibrin binding was thrombus age-dependent. FTP11 localized to the luminal surface of early-stage VT, but only minimally to subacute VT (p<0.001). Transmission electron microscopy of early stage VT revealed direct blood cell contact with luminal fibrin-rich surfaces. In contrast, subacute VT exhibited an encasing CD31+ neoendothelial layer that limited blood cell contact with thrombus fibrin in both VT models. Next we developed a theranostic strategy to predict fibrinolytic efficacy based on the in vivo fibrin accessibility to blood NIRF signal. Mice with variably aged VT underwent FTP11 injection and intravital microscopy (IVM), followed by tissue plasminogen activator infusion to induce VT fibrinolysis. Fibrin molecular IVM revealed that early stage VT, but not subacute VT, bound FTP11 (p<0.05), and experienced higher rates of fibrinolysis and total fibrinolysis (p<0.05 vs. subacute VT). Before fibrinolysis, the baseline FTP11 NIRF signal predicted the net fibrinolysis at 60 minutes (p<0.001). Taken together, these data provide novel insights into the temporal evolution of VT and its susceptibility to therapeutic fibrinolysis. Fibrin molecular imaging may provide a theranostic strategy to identify venous thrombi amenable to fibrinolytic therapies. PMID:26516370

Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

PubMed

Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

2008-08-01

Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

Foraging on the potential energy surface: a swarm intelligence-based optimizer for molecular geometry.

PubMed

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D; Sebastiani, Daniel

2012-11-21

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry

NASA Astrophysics Data System (ADS)

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D.; Sebastiani, Daniel

2012-11-01

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

An engineering assessment of gas/surface interactions in free-molecular aerodynamics

NASA Technical Reports Server (NTRS)

Knox, E. C.; Liver, Peter A.; Collins, Frank G.

1991-01-01

Data available on the gas/surface interaction (GSI) phenomenon, particularly in the rarefied to near-free-molecular flow regime are collected, categorized, and analyzed with a purpose of developing a GSI model that could be used as a guide to spacecraft designers. The study shows that there are not enough useful data for building a high-confidence GSI model. However, sufficient results are obtained to suggest that continued reliance on the diffuse GSI model is inappropriate, particularly in the near-free-molecular regime.

A test of star formation laws in disk galaxies. II. Dependence on dynamical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suwannajak, Chutipong; Tan, Jonathan C.; Leroy, Adam K.

2014-05-20

We use the observed radial profiles of the mass surface densities of total, Σ {sub g}, and molecular, Σ{sub H2}, gas, rotation velocity, and star formation rate (SFR) surface density, Σ{sub sfr}, of the molecular-rich (Σ{sub H2} ≥ Σ{sub HI}/2) regions of 16 nearby disk galaxies to test several star formation (SF) laws: a 'Kennicutt-Schmidt (K-S)' law, Σ{sub sfr}=A{sub g}Σ{sub g,2}{sup 1.5}; a 'Constant Molecular' law, Σ{sub sfr} = A {sub H2}Σ{sub H2,2}; the turbulence-regulated laws of Krumholz and McKee (KM05) and Krumholz, McKee, and Tumlinson (KMT09); a 'Gas-Ω' law, Σ{sub sfr}=B{sub Ω}Σ{sub g}Ω; and a shear-driven 'giant molecular cloudmore » (GMC) Collision' law, Σ{sub sfr} = B {sub CC}Σ {sub g}Ω(1-0.7β), where β ≡ d ln v {sub circ}/d ln r. If allowed one free normalization parameter for each galaxy, these laws predict the SFR with rms errors of factors of 1.4-1.8. If a single normalization parameter is used by each law for the entire galaxy sample, then rms errors range from factors of 1.5-2.1. Although the Constant Molecular law gives the smallest rms errors, the improvement over the KMT, K-S, and GMC Collision laws is not especially significant, particularly given the different observational inputs that the laws utilize and the scope of included physics, which ranges from empirical relations to detailed treatment of interstellar medium processes. We next search for systematic variation of SF law parameters with local and global galactic dynamical properties of disk shear rate (related to β), rotation speed, and presence of a bar. We demonstrate with high significance that higher shear rates enhance SF efficiency per local orbital time. Such a trend is expected if GMC collisions play an important role in SF, while an opposite trend would be expected if the development of disk gravitational instabilities is the controlling physics.« less

Defect controlled magnetism in FeP/graphene/Ni(111)

PubMed Central

Bhandary, Sumanta; Eriksson, Olle; Sanyal, Biplab

2013-01-01

Spin switching of organometallic complexes by ferromagnetic surfaces is an important topic in the area of molecular nanospintronics. Moreover, graphene has been shown as a 2D surface for physisorption of molecular magnets and strain engineering on graphene can tune the spin state of an iron porphyrin (FeP) molecule from S = 1 to S = 2. Our ab initio density functional calculations suggest that a pristine graphene layer placed between a Ni(111) surface and FeP yields an extremely weak exchange interaction between FeP and Ni whereas the introduction of defects in graphene shows a variety of ferromagnetic and antiferromagnetic exchange interactions. Moreover, these defects control the easy axes of magnetization, strengths of magnetic anisotropy energies and spin-dipolar contributions. Our study suggests a new way of manipulating molecular magnetism by defects in graphene and hence has the potential to be explored in designing spin qubits to realize logic operations in molecular nanospintronics. PMID:24296980

Resonant-enhanced spectroscopy of molecular rotations with a scanning tunneling microscope.

PubMed

Natterer, Fabian Donat; Patthey, François; Brune, Harald

2014-07-22

We use rotational excitation spectroscopy with a scanning tunneling microscope to investigate the rotational properties of molecular hydrogen and its isotopes physisorbed on the surfaces of graphene and hexagonal boron nitride (h-BN), grown on Ni(111), Ru(0001), and Rh(111). The rotational excitation energies are in good agreement with ΔJ = 2 transitions of freely spinning p-H2 and o-D2 molecules. The variations of the spectral line shapes for H2 among the different surfaces can be traced back to a molecular resonance-mediated tunneling mechanism. Our data for H2/h-BN/Rh(111) suggest a local intrinsic gating on this surface due to lateral static dipoles. Spectra on a mixed monolayer of H2, HD, and D2 display all three J = 0 → 2 rotational transitions, irrespective of tip position, thus pointing to a multimolecule excitation, or molecular mobility in the physisorbed close-packed layer.

Growth and modelling of spherical crystalline morphologies of molecular materials

NASA Astrophysics Data System (ADS)

Shalev, O.; Biswas, S.; Yang, Y.; Eddir, T.; Lu, W.; Clarke, R.; Shtein, M.

2014-10-01

Crystalline, yet smooth, sphere-like morphologies of small molecular compounds are desirable in a wide range of applications but are very challenging to obtain using common growth techniques, where either amorphous films or faceted crystallites are the norm. Here we show solvent-free, guard flow-assisted organic vapour jet printing of non-faceted, crystalline microspheroids of archetypal small molecular materials used in organic electronic applications. We demonstrate how process parameters control the size distribution of the spheroids and propose an analytical model and a phase diagram predicting the surface morphology evolution of different molecules based on processing conditions, coupled with the thermophysical and mechanical properties of the molecules. This experimental approach opens a path for exciting applications of small molecular organic compounds in optical coatings, textured surfaces with controlled wettability, pharmaceutical and food substance printing and others, where thick organic films and particles with high surface area are needed.

Surfaces of Fluorinated Pyridinium Block Copolymers with Enhanced Antibacterial Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan,S.; Ward, R.; Hexemer, A.

2006-01-01

Polystyrene-b-poly(4-vinylpyridine) copolymers were quaternized with 1-bromohexane and 6-perfluorooctyl-1-bromohexane. Surfaces prepared from these polymers were characterized by contact angle measurements, near-edge X-ray absorption fine structure spectroscopy and X-ray photoelectron spectroscopy. The fluorinated pyridinium surfaces showed enhanced antibacterial activity compared to their nonfluorinated counterparts. Even a polymer with a relatively low molecular weight pyridinium block showed high antimicrobial activity. The bactericidal effect was found to be related to the molecular composition and organization in the top 2-3 nm of the surface and increased with increasing hydrophilicity and pyridinium concentration of the surface.

Polymer adsorption on silica and wettability of graphene oxide surfaces, experiments and simulations

NASA Astrophysics Data System (ADS)

Mortazavian, Hamid

Among the various classifications of polymer composites, studying polymers adsorbed to a surface such as silica is important due to their numerous applications. Adsorbed polymers usually show different properties than their bulk counterparts due to their interactions with the surface. In this study, we observed tightly- and loosely-bound polymer and mobile components in poly(vinyl acetate) (PVAc) on silica both with temperature-modulated differential scanning calorimetry (TMDSC) experiments and computer simulations. The more-mobile component which correlated to the region of low density at the air interface is reported for the first time using TMDSC thermograms. Pore size distribution and pore volume development of adsorbed PMMA samples showed different behavior below and above the tightly-bound amount of the polymer. The amount of tightly-bound polymer was obtained by a linear regression analysis of the ratio of the area under the two glass transitions. The values obtained vary from 0.52 to 0.86 mg PVAc/m2 silica depending upon the molecular mass for the amounts of PVAc and the specific surface area of fumed silica. Direct comparisons of the thermal properties and intermolecular interactions were performed between PVAc and poly(methyl methacrylate) (PMMA) with similar molecular masses and adsorbed amounts on silica. A larger amount of tightly-bound polymer and a greater change in glass transition were observed for adsorbed PMMA compared to adsorbed PVAc. These observations suggested that the interactions between PMMA and silica were stronger than those between PVAc and silica. Molecular modeling of these surface polymers showed that PMMA associates more strongly with silica than does PVAc through additional hydrogen-bonding interactions. Graphene oxide (GO) material surface characteristics make it easy to functionalize, making it a water repellant surface. To test the effect of chemical makeup and size of attached groups on the surface wettability of GO, we performed experimental water contact angle measurements and molecular modeling investigations on functionalized GO surfaces. Experimental and molecular simulation water contact angle measurements showed quantitative agreement for functionalizing groups with the same chain length at a variety of surface coverages.

Switchable host-guest systems on surfaces.

PubMed

Yang, Ying-Wei; Sun, Yu-Long; Song, Nan

2014-07-15

CONSPECTUS: For device miniaturization, nanotechnology follows either the "top-down" approach scaling down existing larger-scale devices or the "bottom-up' approach assembling the smallest possible building blocks to functional nanoscale entities. For synthetic nanodevices, self-assembly on surfaces is a superb method to achieve useful functions and enable their interactions with the surrounding world. Consequently, adaptability and responsiveness to external stimuli are other prerequisites for their successful operation. Mechanically interlocked molecules such as rotaxanes and catenanes, and their precursors, that is, molecular switches and supramolecular switches including pseudorotaxanes, are molecular machines or prototypes of machines capable of mechanical motion induced by chemical signals, biological inputs, light or redox processes as the external stimuli. Switching of these functional host-guest systems on surfaces becomes a fundamental requirement for artificial molecular machines to work, mimicking the molecular machines in nature, such as proteins and their assemblies operating at dynamic interfaces such as the surfaces of cell membranes. Current research endeavors in material science and technology are focused on developing either a new class of materials or materials with novel/multiple functionalities by shifting host-guest chemistry from solution phase to surfaces. In this Account, we present our most recent attempts of building monolayers of rotaxanes/pseudorotaxanes on surfaces, providing stimuli-induced macroscopic effects and further understanding on the switchable host-guest systems at interfaces. Biocompatible versions of molecular machines based on synthetic macrocycles, such as cucurbiturils, pillararenes, calixarenes, and cyclodextrins, have been employed to form self-assembled monolayers of gates on the surfaces of mesoporous silica nanoparticles to regulate the controlled release of cargo/drug molecules under a range of external stimuli, such as light, pH variations, competitive binding, and enzyme. Rotaxanes have also been assembled onto the surfaces of gold nanodisks and microcantilevers to realize active molecular plasmonics and synthetic molecular actuators for device fabrication and function. Pillararenes have been successfully used to control and aid the synthesis of gold nanoparticles, semiconducting quantum dots, and magnetic nanoparticles. The resulting organic-inorganic hydrid nanomaterials have been successfully used for controlled self-assembly, herbicide sensing and detection, pesticide removal, and so forth, taking advantage of the selective binding of pillarenes toward target molecules. Cyclodextrins have also been successfully functionalized onto the surface of gold nanoparticles to serve as recycling extractors for C60. Many interesting prototypes of nanodevices based on synthetic macrocycles and their host-guest chemistry have been constructed and served for different potential applications. This Account will be a summary of the efforts made mainly by us, and others, on the host-guest chemistry of synthetic macrocyclic compounds on the surfaces of different solid supports.

HIGHLY SELECTIVE SENSORS FOR CHEMICAL AND BIOLOGICAL WARFARE AGENTS, INSECTICIDES AND VOCS BASED ON A MOLECULAR SURFACE IMPRINTING TECHNIQUE

EPA Science Inventory

Abstract was given as an oral platform presentation at the Pittsburgh Conference, Orlando FL (March 5-9, 2006). Research described is the development of sensors based on molecular surface imprinting. Applications include the monitoring of chemical and biological agents and inse...

Molecular assemblies as protective barriers and adhesion promotion interlayer

DOEpatents

King, David E.; Czanderna, Alvin W.; Kennedy, Cheryl E.

1996-01-01

A protective diffusion barrier having adhesive qualifies for metalized surfaces is provided by a passivating agent having the formula HS--(CH.sub.2).sub.11 --COOH Which forms a very dense, transparent organized molecular assembly or layer that is impervious to water, alkali, and other impurities and corrosive substances that typically attack metal surfaces.

Cross-Shear Implementation in Sliding-Distance-Coupled Finite Element Analysis of Wear in Metal-on-Polyethylene Total Joint Arthroplasty: Intervertebral Total Disc Replacement as an Illustrative Application

PubMed Central

Goreham-Voss, Curtis M.; Hyde, Philip J.; Hall, Richard M.; Fisher, John; Brown, Thomas D.

2010-01-01

Computational simulations of wear of orthopaedic total joint replacement implants have proven to valuably complement laboratory physical simulators, for pre-clinical estimation of abrasive/adhesive wear propensity. This class of numerical formulations has primarily involved implementation of the Archard/Lancaster relationship, with local wear computed as the product of (finite element) contact stress, sliding speed, and a bearing-couple-dependent wear factor. The present study introduces an augmentation, whereby the influence of interface cross-shearing motion transverse to the prevailing molecular orientation of the polyethylene articular surface is taken into account in assigning the instantaneous local wear factor. The formulation augment is implemented within a widely-utilized commercial finite element software environment (ABAQUS). Using a contemporary metal-on-polyethylene total disc replacement (ProDisc-L) as an illustrative implant, physically validated computational results are presented to document the role of cross-shearing effects in alternative laboratory consensus testing protocols. Going forward, this formulation permits systematically accounting for cross-shear effects in parametric computational wear studies of metal-on-polyethylene joint replacements, heretofore a substantial limitation of such analyses. PMID:20399432

Fundamental data on the desorption of pure interstellar ices

NASA Astrophysics Data System (ADS)

Brown, Wendy A.; Bolina, Amandeep S.

2007-01-01

The desorption of molecular ices from grain surfaces is important in a number of astrophysical environments including dense molecular clouds, cometary nuclei and the surfaces and atmospheres of some planets. With this in mind, we have performed a detailed investigation of the desorption of pure water, pure methanol and pure ammonia ices from a model dust-grain surface. We have used these results to determine the desorption energy, order of desorption and the pre-exponential factor for the desorption of these molecular ices from our model surface. We find good agreement between our desorption energies and those determined previously; however, our values for the desorption orders, and hence also the pre-exponential factors, are different to those reported previously. The kinetic parameters derived from our data have been used to model desorption on time-scales relevant to astrophysical processes and to calculate molecular residence times, given in terms of population half-life as a function of temperature. These results show the importance of laboratory data for the understanding of astronomical situations whereby icy mantles are warmed by nearby stars and by other dynamical events.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iu, Kaikong; Thomas, J.K.

Direct time-resolved studies of singlet molecular oxygen ({sup 1}{Delta}{sub g}O{sub 2}) phosphorescence ({sup 3}{Sigma}{sub g} {sup {minus}}O{sub 2} ({nu} = 0) {l arrow} {sup 1}{Delta}{sub g}O{sub 2} ({nu} = 0); 1,270 nm) in heterogeneous silica gel/cyclohexane systems are presented. Singlet molecular oxygen ({sup 1}{Delta}{sub g}O{sub 2}) is created through a photosensitization process on silica gel surfaces. The experimental results show that the lifetimes of singlet molecular oxygen ({sup 1}{Delta}{sub g}O{sub 2}) in both porous and compressed fumed silica/gel cyclohexane systems are significantly less than that in liquid cyclohexane. The shortened singlet molecular oxygen lifetime is due mainly to quenching bymore » adsorbed water and silanol groups on the silica gel surface. In addition, monoamines coadsorbed on the silica gel surface do not quench singlet molecular oxygen ({sup 1}{Delta}{sub g}O{sub 2}); however, diamines such as DABCO or piperazine maintain their quenching activity, but the quenching kinetics are not of the Stern-Volmer type. The singlet molecular oxygen lifetime increases on loading the porous silica gel/cyclohexane system with monoamine. Coadsorption of piperazine increases quenching of {sup 1}{Delta}{sub g} O{sub 2} by DABCO.« less

Formation of Ordered Arrays of Proteins on Surfaces

NASA Technical Reports Server (NTRS)

Lenhoff, A. M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. While the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models, with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation and crystal growth.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi

Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less

Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

PubMed

Zhao, Lei; Cheng, Jiangtao

2017-09-07

In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

Atomic and molecular layer deposition for surface modification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vähä-Nissi, Mika, E-mail: mika.vaha-nissi@vtt.fi; Sievänen, Jenni; Salo, Erkki

2014-06-01

Atomic and molecular layer deposition (ALD and MLD, respectively) techniques are based on repeated cycles of gas–solid surface reactions. A partial monolayer of atoms or molecules is deposited to the surface during a single deposition cycle, enabling tailored film composition in principle down to molecular resolution on ideal surfaces. Typically ALD/MLD has been used for applications where uniform and pinhole free thin film is a necessity even on 3D surfaces. However, thin – even non-uniform – atomic and molecular deposited layers can also be used to tailor the surface characteristics of different non-ideal substrates. For example, print quality of inkjetmore » printing on polymer films and penetration of water into porous nonwovens can be adjusted with low-temperature deposited metal oxide. In addition, adhesion of extrusion coated biopolymer to inorganic oxides can be improved with a hybrid layer based on lactic acid. - Graphical abstract: Print quality of a polylactide film surface modified with atomic layer deposition prior to inkjet printing (360 dpi) with an aqueous ink. Number of printed dots illustrated as a function of 0, 5, 15 and 25 deposition cycles of trimethylaluminum and water. - Highlights: • ALD/MLD can be used to adjust surface characteristics of films and fiber materials. • Hydrophobicity after few deposition cycles of Al{sub 2}O{sub 3} due to e.g. complex formation. • Same effect on cellulosic fabrics observed with low temperature deposited TiO{sub 2}. • Different film growth and oxidation potential with different precursors. • Hybrid layer on inorganic layer can be used to improve adhesion of polymer melt.« less

Adsorption of Aqueous Crude Oil Components on the Basal Surfaces of Clay Minerals: Molecular Simulations Including Salinity and Temperature Effects

DOE PAGES

Greathouse, J. A.; Cygan, R. T.; Fredrich, J. T.; ...

2017-09-28

Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cationsmore » at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their co-adsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid)—expected to be prevalent at near-neutral pH conditions in petroleum reservoirs—readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.« less

Adsorption of Aqueous Crude Oil Components on the Basal Surfaces of Clay Minerals: Molecular Simulations Including Salinity and Temperature Effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greathouse, J. A.; Cygan, R. T.; Fredrich, J. T.

Molecular simulations of the adsorption of representative organic molecules onto the basal surfaces of various clay minerals were used to assess the mechanisms of enhanced oil recovery associated with salinity changes and water flooding. Simulations at the density functional theory (DFT) and classical levels provide insights into the molecular structure, binding energy, and interfacial behavior of saturate, aromatic, and resin molecules near clay mineral surfaces. Periodic DFT calculations reveal binding geometries and ion pairing mechanisms at mineral surfaces while also providing a basis for validating the classical force field approach. Through classical molecular dynamics simulations, the influence of aqueous cationsmore » at the interface and the role of water solvation are examined to better evaluate the dynamical nature of cation-organic complexes and their co-adsorption onto the clay surfaces. The extent of adsorption is controlled by the hydrophilic nature and layer charge of the clay mineral. All organic species studied showed preferential adsorption on hydrophobic mineral surfaces. However, the anionic form of the resin (decahydro-2-naphthoic acid)—expected to be prevalent at near-neutral pH conditions in petroleum reservoirs—readily adsorbs to the hydrophilic kaolinite surface through a combination of cation pairing and hydrogen bonding with surface hydroxyl groups. Analysis of cation-organic pairing in both the adsorbed and desorbed states reveals a strong preference for organic anions to coordinate with divalent calcium ions rather than monovalent sodium ions, lending support to current theories regarding low-salinity water flooding.« less

Effect of water and alkali modifications on ETS-10 for the cycloaddition of CO2 to propylene oxide.

PubMed

Doskocil, Eric J

2005-02-17

Sodium oxide (NaOx) impregnated Engelhard Titanosilicate-10 (ETS-10) molecular sieve catalysts were prepared to enhance the basicity associated with ETS-10 and subsequently investigated for the cycloaddition of carbon dioxide to propylene oxide to produce propylene carbonate. For dry NaOx-modified ETS-10 catalysts that contained no adsorbed water, a maximum yield of propylene carbonate was achieved at a loading of 2.0 excess NaOx species per unit cell. However, the greatest enhancements in the rate of reaction were observed when small amounts of water were adsorbed onto the unmodified ETS-10 catalyst immediately prior to reaction. Surface-bound water appears to enhance the surface Bronsted acidity of the unmodified ETS-10 catalyst via the formation of surface -OH groups at lower water loadings, producing a surface of better-tuned acid-base bifunctional characteristics for the cycloaddition reaction. At levels of hydration greater than 12.5% by mass, the yield of propylene carbonate was further enhanced, but at a smaller rate than that observed at lower rehydration levels, which is more indicative of an enhanced transport effect. Adsorption microcalorimetry of carbon dioxide indicated that, at loadings less than 2.0 NaOx per unit cell, the total uptake of the CO2 adsorption sites required for the reaction were less than in the parent ETS-10 material. However, at higher levels of NaOx occlusion, where the total uptake and strength of the adsorption sites exceeded those observed for the as-received ETS-10 material, the cycloaddition activity of this catalyst suffered due to the reduced pore volume and surface area. It appears that precise tuning of both the surface acidity and basicity is crucial in creating an effective acid-base bifunctional ETS-10 catalyst for the cycloaddition reaction investigated.

Imaging fluorescence-correlation spectroscopy for measuring fast surface diffusion at liquid/solid interfaces.

PubMed

Cooper, Justin T; Harris, Joel M

2014-08-05

The development of techniques to probe interfacial molecular transport is important for understanding and optimizing surface-based analytical methods including surface-enhanced spectroscopies, biological assays, and chemical separations. Single-molecule-fluorescence imaging and tracking has been used to measure lateral diffusion rates of fluorescent molecules at surfaces, but the technique is limited to the study of slower diffusion, where molecules must remain relatively stationary during acquisition of an image in order to build up sufficient intensity in a spot to detect and localize the molecule. Although faster time resolution can be achieved by fluorescence-correlation spectroscopy (FCS), where intensity fluctuations in a small spot are related to the motions of molecules on the surface, long-lived adsorption events arising from surface inhomogeneity can overwhelm the correlation measurement and mask the surface diffusion of the moving population. Here, we exploit a combination of these two techniques, imaging-FCS, for measurement of fast interfacial transport at a model chromatographic surface. This is accomplished by rapid imaging of the surface using an electron-multiplied-charged-coupled-device (CCD) camera, while limiting the acquisition to a small area on the camera to allow fast framing rates. The total intensity from the sampled region is autocorrelated to determine surface diffusion rates of molecules with millisecond time resolution. The technique allows electronic control over the acquisition region, which can be used to avoid strong adsorption sites and thus minimize their contribution to the measured autocorrelation decay and to vary the acquisition area to resolve surface diffusion from adsorption and desorption kinetics. As proof of concept, imaging-FCS was used to measure surface diffusion rates, interfacial populations, and adsorption-desorption rates of 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine (DiI) on planar C18- and C1-modified surfaces.