Process for making dense thin films

DOEpatents

Jacobson, Craig P.; Visco, Steven J.; DeJonghe, Lutgard C.

2005-07-26

Provided are low-cost, mechanically strong, highly electronically conductive porous substrates and associated structures for solid-state electrochemical devices, techniques for forming these structures, and devices incorporating the structures. The invention provides solid state electrochemical device substrates of novel composition and techniques for forming thin electrode/membrane/electrolyte coatings on the novel or more conventional substrates. In particular, in one embodiment the invention provides techniques for firing of device substrate to form densified electrolyte/membrane films 5 to 20 microns thick. In another embodiment, densified electrolyte/membrane films 5 to 20 microns thick may be formed on a pre-sintered substrate by a constrained sintering process. In some cases, the substrate may be a porous metal, alloy, or non-nickel cermet incorporating one or more of the transition metals Cr, Fe, Cu and Ag, or alloys thereof.

Plasma-electric field controlled growth of oriented graphene for energy storage applications

NASA Astrophysics Data System (ADS)

Ghosh, Subrata; Polaki, S. R.; Kamruddin, M.; Jeong, Sang Mun; (Ken Ostrikov, Kostya

2018-04-01

It is well known that graphene grows as flat sheets aligned with the growth substrate. Oriented graphene structures typically normal to the substrate have recently attracted major attention. Most often, the normal orientation is achieved in a plasma-assisted growth and is believed to be due to the plasma-induced in-built electric field, which is usually oriented normal to the substrate. This work focuses on the effect of an in-built electric field on the growth direction, morphology, interconnectedness, structural properties and also the supercapacitor performance of various configurations of graphene structures and reveals the unique dependence of these features on the electric field orientation. It is shown that tilting of growth substrates from parallel to the normal direction with respect to the direction of in-built plasma electric field leads to the morphological transitions from horizontal graphene layers, to oriented individual graphene sheets and then interconnected 3D networks of oriented graphene sheets. The revealed transition of the growth orientation leads to a change in structural properties, wetting nature, types of defect in graphitic structures and also affects their charge storage capacity when used as supercapacitor electrodes. This simple and versatile approach opens new opportunities for the production of potentially large batches of differently oriented and structured graphene sheets in one production run.

Sapphire substrate-induced effects in VO2 thin films grown by oxygen plasma-assisted pulsed laser deposition

NASA Astrophysics Data System (ADS)

Skuza, J. R.; Scott, D. W.; Pradhan, A. K.

2015-11-01

We investigate the structural and electronic properties of VO2 thin films on c-plane sapphire substrates with three different surface morphologies to control the strain at the substrate-film interface. Only non-annealed substrates with no discernible surface features (terraces) provided a suitable template for VO2 film growth with a semiconductor-metal transition (SMT), which was much lower than the bulk transition temperature. In addition to strain, oxygen vacancy concentration also affects the properties of VO2, which can be controlled through deposition conditions. Oxygen plasma-assisted pulsed laser deposition allows favorable conditions for VO2 film growth with SMTs that can be easily tailored for device applications.

Structures And Fabrication Techniques For Solid State Electrochemical Devices

DOEpatents

Visco, Steven J.; Jacobson, Craig P.; DeJonghe, Lutgard C.

2005-12-27

Provided are low-cost, mechanically strong, highly electronically conductive porous substrates and associated structures for solid-state electrochemical devices, techniques for forming these structures, and devices incorporating the structures. The invention provides solid state electrochemical device substrates of novel composition and techniques for forming thin electrode/membrane/electrolyte coatings on the novel or more conventional substrates. In particular, in one embodiment the invention provides techniques for co-firing of device substrate (often an electrode) with an electrolyte or membrane layer to form densified electrolyte/membrane films 5 to 20 microns thick. In another embodiment, densified electrolyte/membrane films 5 to 20 microns thick may be formed on a pre-sintered substrate by a constrained sintering process. In some cases, the substrate may be a porous metal, alloy, or non-nickel cermet incorporating one or more of the transition metals Cr, Fe, Cu and Ag, or alloys thereof.

Structures and fabrication techniques for solid state electrochemical devices

DOEpatents

Visco, Steven J.; Jacobson, Craig P.; DeJonghe, Lutgard C.

2003-08-12

Provided are low-cost, mechanically strong, highly electronically conductive porous substrates and associated structures for solid-state electrochemical devices, techniques for forming these structures, and devices incorporating the structures. The invention provides solid state electrochemical device substrates of novel composition and techniques for forming thin electrode/membrane/electrolyte coatings on the novel or more conventional substrates. In particular, in one embodiment the invention provides techniques for co-firing of device substrate (often an electrode) with an electrolyte or membrane layer to form densified electrolyte/membrane films 5 to 20 microns thick. In another embodiment, densified electrolyte/membrane films 5 to 20 microns thick may be formed on a pre-sintered substrate by a constrained sintering process. In some cases, the substrate may be a porous metal, alloy, or non-nickel cermet incorporating one or more of the transition metals Cr, Fe, Cu and Ag, or alloys thereof.

Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters.

PubMed

Miyamoto, Naoki; Yoshimura, Miho; Okubo, Yuji; Suzuki-Nagata, Kayo; Tsumuraya, Takeshi; Ito, Nobutoshi; Fujii, Ikuo

2018-05-01

Catalytic antibody 7B9, which was elicited against p-nitrobenzyl phosphonate transition-state analogue (TSA) 1, hydrolyzes a wide range of p-nitrobenzyl monoesters and thus shows broad substrate tolerance. To reveal the molecular basis of this substrate tolerance, the 7B9 Fab fragment complexed with p-nitrobenzyl ethylphosphonate 2 was crystallized and the three-dimensional structure was determined. The crystal structure showed that the strongly antigenic p-nitrobenzyl moiety occupied a relatively shallow antigen-combining site and therefore the alkyl moiety was located outside the pocket. These results support the observed broad substrate tolerance of 7B9 and help rationalize how 7B9 can catalyze various p-nitrobenzyl ester derivatives. The crystal structure also showed that three amino acid residues (Asn H33 , Ser H95 , and Arg L96 ) were placed in key positions to form hydrogen bonds with the phosphonate oxygens of the transitions-state analogue. In addition, the role of these amino acid residues was examined by site-directed mutagenesis to alanine: all mutants (Asn H33 Ala, Ser H95 Ala, and Arg L96 Ala) showed no detectable catalytic activity. Coupling the findings from our structural studies with these mutagenesis results clarified the structural basis of the observed broad substrate tolerance of antibody 7B9-catalyzed hydrolyses. Our findings provide new strategies for the generation of catalytic antibodies that accept a broad range of substrates, aiding their practical application in synthetic organic chemistry. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Catalytic Function of Enzymes.

ERIC Educational Resources Information Center

Splittgerber, Allan G.

1985-01-01

Discusses: structure of the enzyme molecule; active site; reaction mechanism; transition state; factors affecting enzyme reaction rates, concentration of enzyme; concentration of substrate; product concentration; temperature effects and pH effects; factors causing a lowering of activation energy; proximity and orientation effects; substrate strain…

Ab Initio Study of Interfacial Structure Transformation of Amorphous Carbon Catalyzed by Ti, Cr, and W Transition Layers.

PubMed

Li, Xiaowei; Li, Lei; Zhang, Dong; Wang, Aiying

2017-11-29

Amorphous carbon (a-C) films composited with transition layers exhibit the desirable improvement of adhesion strength between films and substrate, but the further understanding on the interfacial structure transformation of a-C structure induced by transition layers is still lacked. In this paper, using ab initio calculations, we comparatively studied the interfacial structure between Ti, Cr, or W transition layers and a-C film from the atomic scale, and demonstrated that the addition of Ti, Cr, or W catalyzed the graphitic transformation of a-C structure at different levels, which provided the theoretical guidance for designing a multilayer nanocomposite film for renewed application.

Effect of strain on structure and charge order transitions in epitaxial Bi0.4Ca0.6MnO3 films on perovskite (001) and (011) substrates

NASA Astrophysics Data System (ADS)

Kim, Dae Ho; Christen, Hans M.; Varela, Maria; Lee, Ho Nyung; Lowndes, Douglas H.

2006-05-01

The effect of epitaxial strain on the charge order (CO) transition in Bi0.4Ca0.6MnO3 films was studied by varying the strain's strength and symmetry via the use of SrTiO3 and LaAlO3 substrates having different crystallographic orientations. The film on pseudocubic (001) LaAlO3, under symmetric compressive strain, exhibits a clear CO transition. In the film on a (001) SrTiO3 substrate, under symmetric tensile strain, highly segregated line-shaped features in the Bi distribution are seen in Z-contrast scanning transmission microscopy, accompanied by a strongly broadened CO transition. The asymmetric tensile stress on (011) SrTiO3 results in an apparent compressive strain state with a deviation from tetragonality (i.e., γ ≠90°), accompanied by the sharpest CO transition. These comparisons illustrate the importance of considering both the strength and symmetry of epitaxial strain.

Metal oxide nanorod arrays on monolithic substrates

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

Gao, Pu-Xian; Guo, Yanbing; Ren, Zheng

A metal oxide nanorod array structure according to embodiments disclosed herein includes a monolithic substrate having a surface and multiple channels, an interface layer bonded to the surface of the substrate, and a metal oxide nanorod array coupled to the substrate surface via the interface layer. The metal oxide can include ceria, zinc oxide, tin oxide, alumina, zirconia, cobalt oxide, and gallium oxide. The substrate can include a glass substrate, a plastic substrate, a silicon substrate, a ceramic monolith, and a stainless steel monolith. The ceramic can include cordierite, alumina, tin oxide, and titania. The nanorod array structure can includemore » a perovskite shell, such as a lanthanum-based transition metal oxide, or a metal oxide shell, such as ceria, zinc oxide, tin oxide, alumina, zirconia, cobalt oxide, and gallium oxide, or a coating of metal particles, such as platinum, gold, palladium, rhodium, and ruthenium, over each metal oxide nanorod. Structures can be bonded to the surface of a substrate and resist erosion if exposed to high velocity flow rates.« less

Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.

PubMed

Hou, Guanhua; Cui, Qiang

2013-07-17

The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.

Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron†

PubMed Central

Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; St Maurice, Martin

2012-01-01

Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg2+-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we solved the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and cupferron, to 2.2-Å resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state/intermediate since its binding affinity to 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, cupferron, and the ground state analogue (S)-atrolacatate reveal that the para-carbon of the substrate phenyl ring moves by 0.8–1.2 Å between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to MR with bound (S)-atrolactate, the intermediate-Mg2+ distance shortens, suggesting a tighter complex with the catalytic Mg2+. In addition, Tyr 54 moves nearer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle. PMID:22264153

Structural and Electromagnetic Properties of Ni-Mn-Ga Thin Films Deposited on Si Substrates

NASA Astrophysics Data System (ADS)

Pereira, M. J.; Lourenço, A. A. C. S.; Amaral, V. S.

2014-07-01

Ni2MnGa thin films raise great interest due to their properties, which provide them with strong potential for technological applications. Ni2MnGa thin films were prepared by r.f. sputtering deposition on Si substrates at low temperature (400 ºC). Film thicknesses in the range 10-120 nm were obtained. A study of the structural, magnetic and electrical properties of the films is presented. We find that the deposited films show some degree of crystallinity, with coexisting cubic and tetragonal structural phases, the first one being preponderant over the latter, particularly in the thinner films. The films possess soft magnetic properties and their coercivity is thickness dependent in the range 15-200 Oe at 300K. Electrical resistivity measurements signal the structural transition and suggest the occurrence of avalanche and return-point memory effects, in temperature cycling through the magnetic/structural transition range.

Molecular dynamics study about the effect of substrate temperature on a-Si:H structure

NASA Astrophysics Data System (ADS)

Luo, Yaorong; Gong, Hongyong; Zhou, Naigen; Huang, Haibin; Zhou, Lang

2018-01-01

Molecular dynamics simulation of the microstructure of hydrogenated amorphous silicon (a-Si:H) thin film with different substrate temperatures has been performed based on the Tersoff potential. The results showed that: the silicon thin film maintained amorphous structure in the substrate temperature range from 200 to 1000 K; high substrate temperature could smooth the surface. The first neighbour Voronoi polyhedron was dominated by the tetrahedron. When the substrate temperature increased, the content of tetrahedrons increased due to the transition from pentahedrons and hexahedrons to tetrahedrons. The change of the second neighbour Voronoi polyhedron could be classified into two cases: one case with low medium coordination number decreased as temperature increased, while the other one with high medium coordination number showed an opposite change tendency. It indicated that the local paracrystalline structure arrangement of the second neighbour atoms had been enhanced as substrate temperature rose.

Self-Assembled Multilayer Structure and Enhanced Thermochromic Performance of Spinodally Decomposed TiO2-VO2 Thin Film.

PubMed

Sun, Guangyao; Zhou, Huaijuan; Cao, Xun; Li, Rong; Tazawa, Masato; Okada, Masahisa; Jin, Ping

2016-03-23

Composite films of VO2-TiO2 were deposited on sapphire (11-20) substrate by cosputtering method. Self-assembled well-ordered multilayer structure with alternating Ti- and V-rich epitaxial thin layer was obtained by thermal annealing via a spinodal decomposition mechanism. The structured thermochromic films demonstrate superior optical modulation upon phase transition, with significantly reduced transition temperature. The results provide a facile and novel approach to fabricate smart structures with excellent performance.

Deacylation transition states of a bacterial DD-peptidase.

PubMed

Adediran, S A; Kumar, I; Pratt, R F

2006-10-31

Beta-lactam antibiotics restrict bacterial growth by inhibiting DD-peptidases. These enzymes catalyze the final transpeptidation step in bacterial cell wall biosynthesis. Although much structural information is now available for these enzymes, the mechanism of the actual transpeptidation reaction has not been studied in detail. The reaction is known to involve a double-displacement mechanism with an acyl-enzyme intermediate, which can be attacked by water, specific amino acids, peptides, and other acyl acceptors. We describe in this paper an investigation of acyl acceptor specificity and assess the need for general base catalysis in the deacylation transition state of the Streptomyces R61 DD-peptidase. We show, by the criterion of solvent deuterium kinetic isotope effect measurements and proton inventories, that the transition states of specific and nonspecific substrates are very similar, at least with respect to proton motion. The transition states for attack (tetrahedral intermediate formation) by d-amino acids and Gly-l-Xaa dipeptides do not include a general base catalyst, while such catalysis is essential for reaction with water and d-alpha-hydroxy acids. D-Alpha-hydroxy acids act as acyl acceptors for glycyl substrates but not for more specific d-alanyl substrates; hydroxy acids actually behave, more generally, as mixed inhibitors of the DD-peptidase. The structural and mechanistic bases of these observations are discussed; they should inform transition state analogue design.

Optical absorption in planar graphene superlattice: The role of structural parameters

NASA Astrophysics Data System (ADS)

Azadi, L.; Shojaei, S.

2018-04-01

We theoretically studied the optically driven interband transitions in a planar graphene superlattices (PGSL) formed by patterning graphene sheet on laterally hetrostructured substrate as Sio2/hBN. A tunable optical transitions between minibands is observed based on engineering structural parameters. We derive analytically expression for optical absorption from two-band model. Considerable optical absorption is obtained for different ratios between widths of heterostructured substrate and is explained analytically from the view point of wavefunction engineering and miniband dispersion, in details. The role of different statuses of polarization as circular and linear are considered. Our study paves a way toward the control of optical properties of PGSLs to be implemented in optoelectronics devices.

Optical and structural properties in type-II InAlAs/AlGaAs quantum dots observed by photoluminescence, X-ray diffraction and transmission electron microscopy

NASA Astrophysics Data System (ADS)

Ben Daly, A.; Craciun, D.; Laura Ursu, E.; Lemaître, A.; Maaref, M. A.; Iacomi, F.; Vasile, B. S.; Craciun, V.

2017-10-01

We present the effects of AlGaAs alloy composition on InAlAs quantum dots (QDs) optical and structural properties. Photoluminescence (PL) analysis of samples having a variety of aluminium composition values covering type-II transitions clearly in QDs showed the presence of two transitions X-Sh and X-Ph. High-resolution X-ray diffraction (HRXRD) investigations showed that the layers grew epitaxially on the GaAs substrate, with no relaxation regardless the Al content of AlGaAs layer. From the reciprocal space map (RSM) investigation around (004) and (115) diffraction peaks, it was shown that the InAlAs layer is fully strained, the in-plane lattice parameters (a and b, a = b) being identical to those of GaAs substrate, while the c lattice parameter was dependent on the In and Al concentrations, being larger than that of the substrate. High-resolution transmission electronic microscopy (HRTEM) investigations confirmed that films grew epitaxially on the GaAs substrate with no visible dislocations or other major defects within the InAlAs/GaAlAs QDs structure.

Entropically Driven Layering Near a Substrate: A Fluids DFT Study

NASA Astrophysics Data System (ADS)

McGarrity, Erin; Frischknecht, Amalie; Mackay, Michael

2008-03-01

We employ a fluids density functional theory to study the phase behavior of athermal polymer/nanoparticle blends near a hard substrate. These blends exhibit two types of first order, entropically driven layering transitions. In the first type of transition, the nanoparticles order to form a layer which is a fixed distance from the surface. The structure and location of this layer depends on nanoparticle radius. In the second type of transition, which occurs at melt-like densities, the nanoparticles and polymers form laminar structures which resemble colloidal crystals. We examine the effects of packing density, chain length and nanoparticle radius on the system and show that the transitions are first order. In addition we show that the crystalline phase is nucleated by the presence of the surface. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Sapphire substrate-induced effects in VO{sub 2} thin films grown by oxygen plasma-assisted pulsed laser deposition

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

Skuza, J. R., E-mail: jrskuza@nsu.edu, E-mail: apradhan@nsu.edu; Scott, D. W.; Pradhan, A. K., E-mail: jrskuza@nsu.edu, E-mail: apradhan@nsu.edu

2015-11-21

We investigate the structural and electronic properties of VO{sub 2} thin films on c-plane sapphire substrates with three different surface morphologies to control the strain at the substrate-film interface. Only non-annealed substrates with no discernible surface features (terraces) provided a suitable template for VO{sub 2} film growth with a semiconductor-metal transition (SMT), which was much lower than the bulk transition temperature. In addition to strain, oxygen vacancy concentration also affects the properties of VO{sub 2}, which can be controlled through deposition conditions. Oxygen plasma-assisted pulsed laser deposition allows favorable conditions for VO{sub 2} film growth with SMTs that can bemore » easily tailored for device applications.« less

Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design

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

Miao, Yi; Tenor, Jennifer L.; Toffaletti, Dena L.

ABSTRACT The disaccharide trehalose is critical to the survival of pathogenic fungi in their human host. Trehalose-6-phosphate synthase (Tps1) catalyzes the first step of trehalose biosynthesis in fungi. Here, we report the first structures of eukaryotic Tps1s in complex with substrates or substrate analogues. The overall structures of Tps1 fromCandida albicansandAspergillus fumigatusare essentially identical and reveal N- and C-terminal Rossmann fold domains that form the glucose-6-phosphate and UDP-glucose substrate binding sites, respectively. These Tps1 structures with substrates or substrate analogues reveal key residues involved in recognition and catalysis. Disruption of these key residues severely impaired Tps1 enzymatic activity. Subsequent cellularmore » analyses also highlight the enzymatic function of Tps1 in thermotolerance, yeast-hypha transition, and biofilm development. These results suggest that Tps1 enzymatic functionality is essential for the fungal stress response and virulence. Furthermore, structures of Tps1 in complex with the nonhydrolyzable inhibitor, validoxylamine A, visualize the transition state and support an internal return-like catalytic mechanism that is generalizable to other GT-B-fold retaining glycosyltransferases. Collectively, our results depict key Tps1-substrate interactions, unveil the enzymatic mechanism of these fungal proteins, and pave the way for high-throughput inhibitor screening buttressed and guided by the current structures and those of high-affinity ligand-Tps1 complexes. IMPORTANCEInvasive fungal diseases have emerged as major threats, resulting in more than 1.5 million deaths annually worldwide. This epidemic has been further complicated by increasing resistance to all major classes of antifungal drugs in the clinic. Trehalose biosynthesis is essential for the fungal stress response and virulence. Critically, this biosynthetic pathway is absent in mammals, and thus, the two enzymes that carry out trehalose biosynthesis, namely, trehalose-6-phosphate synthase (Tps1) and trehalose-6-phosphate phosphatase (Tps2), are prominent targets for antifungal intervention. Here, we report the first eukaryotic Tps1 structures from the pathogenic fungiCandida albicansandAspergillus fumigatusin complex with substrates, substrate analogues, and inhibitors. These structures reveal key protein-substrate interactions, providing atomic-level scaffolds for structure-guided drug design of novel antifungals that target Tps1.« less

Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design.

PubMed

Miao, Yi; Tenor, Jennifer L; Toffaletti, Dena L; Maskarinec, Stacey A; Liu, Jiuyu; Lee, Richard E; Perfect, John R; Brennan, Richard G

2017-07-25

The disaccharide trehalose is critical to the survival of pathogenic fungi in their human host. Trehalose-6-phosphate synthase (Tps1) catalyzes the first step of trehalose biosynthesis in fungi. Here, we report the first structures of eukaryotic Tps1s in complex with substrates or substrate analogues. The overall structures of Tps1 from Candida albicans and Aspergillus fumigatus are essentially identical and reveal N- and C-terminal Rossmann fold domains that form the glucose-6-phosphate and UDP-glucose substrate binding sites, respectively. These Tps1 structures with substrates or substrate analogues reveal key residues involved in recognition and catalysis. Disruption of these key residues severely impaired Tps1 enzymatic activity. Subsequent cellular analyses also highlight the enzymatic function of Tps1 in thermotolerance, yeast-hypha transition, and biofilm development. These results suggest that Tps1 enzymatic functionality is essential for the fungal stress response and virulence. Furthermore, structures of Tps1 in complex with the nonhydrolyzable inhibitor, validoxylamine A, visualize the transition state and support an internal return-like catalytic mechanism that is generalizable to other GT-B-fold retaining glycosyltransferases. Collectively, our results depict key Tps1-substrate interactions, unveil the enzymatic mechanism of these fungal proteins, and pave the way for high-throughput inhibitor screening buttressed and guided by the current structures and those of high-affinity ligand-Tps1 complexes. IMPORTANCE Invasive fungal diseases have emerged as major threats, resulting in more than 1.5 million deaths annually worldwide. This epidemic has been further complicated by increasing resistance to all major classes of antifungal drugs in the clinic. Trehalose biosynthesis is essential for the fungal stress response and virulence. Critically, this biosynthetic pathway is absent in mammals, and thus, the two enzymes that carry out trehalose biosynthesis, namely, trehalose-6-phosphate synthase (Tps1) and trehalose-6-phosphate phosphatase (Tps2), are prominent targets for antifungal intervention. Here, we report the first eukaryotic Tps1 structures from the pathogenic fungi Candida albicans and Aspergillus fumigatus in complex with substrates, substrate analogues, and inhibitors. These structures reveal key protein-substrate interactions, providing atomic-level scaffolds for structure-guided drug design of novel antifungals that target Tps1. Copyright © 2017 Miao et al.

Molecular modeling studies of substrate binding by penicillin acylase.

PubMed

Chilov, G G; Stroganov, O V; Svedas, V K

2008-01-01

Molecular modeling has revealed intimate details of the mechanism of binding of natural substrate, penicillin G (PG), in the penicillin acylase active center and solved questions raised by analysis of available X-ray structures, mimicking Michaelis complex, which substantially differ in the binding pattern of the PG leaving group. Three MD trajectories were launched, starting from PDB complexes of the inactive mutant enzyme with PG (1FXV) and native penicillin acylase with sluggishly hydrolyzed substrate analog penicillin G sulfoxide (1GM9), or from the complex obtained by PG docking. All trajectories converged to a similar PG binding mode, which represented the near-to-attack conformation, consistent with chemical criteria of how reactive Michaelis complex should look. Simulated dynamic structure of the enzyme-substrate complex differed significantly from 1FXV, resembling rather 1GM9; however, additional contacts with residues bG385, bS386, and bN388 have been found, which were missing in X-ray structures. Combination of molecular docking and molecular dynamics also clarified the nature of extremely effective phenol binding in the hydrophobic pocket of penicillin acylase, which lacked proper explanation from crystallographic experiments. Alternative binding modes of phenol were probed, and corresponding trajectories converged to a single binding pattern characterized by a hydrogen bond between the phenol hydroxyl and the main chain oxygen of bS67, which was not evident from the crystal structure. Observation of the trajectory, in which phenol moved from its steady bound to pre-dissociation state, mapped the consequence of molecular events governing the conformational transitions in a coil region a143-a146 coupled to substrate binding and release of the reaction products. The current investigation provided information on dynamics of the conformational transitions accompanying substrate binding and significance of poorly structured and flexible regions in maintaining catalytic framework.

Effects of different binders on microstructure and phase composition of hydroxyapatite Nd-YAG laser clad coatings

NASA Astrophysics Data System (ADS)

Chien, C. S.; Hong, T. F.; Han, T. J.; Kuo, T. Y.; Liao, T. Y.

2011-01-01

The laser clad coating technique can help to produce metallurgical bonding with high bonding strength between the coating layer and the substrate, which has been gradually applied for hydroxyapatite (HA) coating on metallic substrates. In this study, HA powder is mixed with two different binders, namely water glass (WG) and polyvinyl alcohol (PVA), respectively, and is then clad on Ti-6Al-4V substrates using an Nd:YAG laser system under various processing conditions. The microstructure, chemical composition and hardness of the coating layer and transition layer of the various samples are then systematically explored. The experimental results show that the coating layers of the various samples all contain both cellular dendrites and rod-like piled structures, while the transition layers contain only cellular dendrites. For all samples, the coating layer consists mostly of CaTiO 3, Ca 2P 2O 7, CaO and HA phases, whereas the transition layer contains primarily CaTiO 3, Ca 2P 2O 7, Ti 3P, Ti and HA phases. In addition, the transition layer of the WG samples also contains SiO 2 and Si 2Ti phases. In all of the specimens, the transition layer has a higher average hardness than the substrate or coating layer. Moreover, the transition layer in the WG sample is harder than that in the PVA sample.

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

Structure-based analysis of catalysis and substrate definition in the HIT protein family.

PubMed

Lima, C D; Klein, M G; Hendrickson, W A

1997-10-10

The histidine triad (HIT) protein family is among the most ubiquitous and highly conserved in nature, but a biological activity has not yet been identified for any member of the HIT family. Fragile histidine triad protein (FHIT) and protein kinase C interacting protein (PKCI) were used in a structure-based approach to elucidate characteristics of in vivo ligands and reactions. Crystallographic structures of apo, substrate analog, pentacovalent transition-state analog, and product states of both enzymes reveal a catalytic mechanism and define substrate characteristics required for catalysis, thus unifying the HIT family as nucleotidyl hydrolases, transferases, or both. The approach described here may be useful in identifying structure-function relations between protein families identified through genomics.

Comparison of molecular orientation and phase transition behaviors in the two kinds of ordered ultrathin films of reversed duckweed polymer ES-3 studied by infrared grazing reflection-absorption spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Qiang; Xu, Weiqing; Zhao, Bing

2003-03-01

A multilayer LB film and a casting film of reversed duckweed polymer ES-3 on Au-evaporated glass slides were investigated by Fourier Transform infrared grazing reflection-absorption spectroscopy. It is found that the two kinds of ordered ultrathin films have different orientation of alkyl chains, nearly perpendicular to the substrate surface for the LB film while rather tilted for the casting film. The studies on their thermal transition behaviors indicate that both of the films have three phase transition processes, respectively, occurring near 65, 105 and 140 °C for the former while near 80, 105 and 140 °C for the latter, but show different transition behavior in the each corresponding transition process. It is referred that at room temperature there are island-like domain structures formed in the LB film, but no ones in the casting film; however, the latter can form the domain structures between the first two transition points due to the desorption of solvents. The formation of domain structure seems to play two important roles, one of which is to make alkyl chains more perpendicular to the substrate surface, and the other to make alkyl chains more packed closely. Thermal cyclic experiments reveal that neither of the films could return to its original state after thermal cyclic treatment up to the temperature, which is above the third transition point, although its alkyl chain becomes highly ordered again.

Intermediate surface structure between step bunching and step flow in SrRuO3 thin film growth

NASA Astrophysics Data System (ADS)

Bertino, Giulia; Gura, Anna; Dawber, Matthew

We performed a systematic study of SrRuO3 thin films grown on TiO2 terminated SrTiO3 substrates using off-axis magnetron sputtering. We investigated the step bunching formation and the evolution of the SRO film morphology by varying the step size of the substrate, the growth temperature and the film thickness. The thin films were characterized using Atomic Force Microscopy and X-Ray Diffraction. We identified single and multiple step bunching and step flow growth regimes as a function of the growth parameters. Also, we clearly observe a stronger influence of the step size of the substrate on the evolution of the SRO film surface with respect to the other growth parameters. Remarkably, we observe the formation of a smooth, regular and uniform ``fish skin'' structure at the transition between one regime and another. We believe that the fish skin structure results from the merging of 2D flat islands predicted by previous models. The direct observation of this transition structure allows us to better understand how and when step bunching develops in the growth of SrRuO3 thin films.

Evolution of optical properties and band structure from amorphous to crystalline Ga2O3 films

NASA Astrophysics Data System (ADS)

Zhang, Fabi; Li, Haiou; Cui, Yi-Tao; Li, Guo-Ling; Guo, Qixin

2018-04-01

The optical properties and band structure evolution from amorphous to crystalline Ga2O3 films was investigated in this work. Amorphous and crystalline Ga2O3 films were obtained by changing the growth substrate temperatures of pulsed laser deposition and the crystallinity increase with the rising of substrate temperature. The bandgap value and ultraviolet emission intensity of the films increase with the rising of crystallinity as observed by means of spectrophotometer and cathodoluminescence spectroscopy. Abrupt bandgap value and CL emission variations were observed when amorphous to crystalline transition took place. X-ray photoelectron spectroscopy core level spectra reveal that more oxygen vacancies and disorders exist in amorphous Ga2O3 film grown at lower substrate temperature. The valence band spectra of hard X-ray photoelectron spectroscopy present the main contribution from Ga 4sp for crystalline film deposited at substrate temperature of 500 oC, while extra subgap states has been observed in amorphous film deposited at 300 oC. The oxygen vacancy and the extra subgap density of states are suggested to be the parts of origin of bandgap and CL spectra variations. The experimental data above yields a realistic picture of optical properties and band structure variation for the amorphous to crystalline transition of Ga2O3 films.

Structure-based Insights into the Catalytic Power and Conformational Dexterity of Peroxiredoxins

PubMed Central

Hall, Andrea; Nelson, Kimberly; Poole, Leslie B.

2011-01-01

Abstract Peroxiredoxins (Prxs), some of nature's dominant peroxidases, use a conserved Cys residue to reduce peroxides. They are highly expressed in organisms from all kingdoms, and in eukaryotes they participate in hydrogen peroxide signaling. Seventy-two Prx structures have been determined that cover much of the diversity of the family. We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied catalytic structural transitions and highlight how they differ depending on the location of the resolving Cys. We also review new insights into the question of how Prxs are such effective catalysts: the enzyme activates not only the conserved Cys thiolate but also the peroxide substrate. Moreover, the hydrogen-bonding network created by the four residues conserved in all Prx active sites stabilizes the transition state of the peroxidatic SN2 displacement reaction. Strict conservation of the peroxidatic active site along with the variation in structural transitions provides a fascinating picture of how the diverse Prxs function to break down peroxide substrates rapidly. Antioxid. Redox Signal. 15, 795–815. PMID:20969484

Ordered to isotropic morphology transition in pattern-directed dewetting of polymer thin films on substrates with different feature heights.

PubMed

Roy, Sudeshna; Mukherjee, Rabibrata

2012-10-24

Controlled dewetting of a thin polymer film on a topographically patterned substrate is an interesting approach for aligning isotropic dewetted structures. In this article, we investigate the influence of substrate feature height (H(S)) on the dewetting pathway and final pattern morphology by studying the dewetting of polystyrene (PS) thin films on grating substrates with identical periodicity (λ(P) = 1.5 μm), but H(S) varying between 10 nm and 120 nm. We identify four distinct categories of final dewetted morphology, with different extent of ordering: (1) array of aligned droplets (H(S) ≈ 120 nm); (2) aligned undulating ribbons (H(S) ≈ 70-100 nm); (3) multilength scale structures with coexisting large droplets uncorrelated to the substrate and smaller droplets/ribbons aligned along the stripes (H(S) ≈ 40-60 nm); and (4) large droplets completely uncorrelated to the substrate (H(S) < 25 nm). The distinct morphologies across the categories are attributed to two major factors: (a) whether the as-cast film is continuous (H(S)≤ 80 nm) or discontinuous (H(S)≥ 100 nm) and (b) in case of a continuous film, whether the film ruptures along each substrate stripe (H(S)≥ 70 nm) or with nucleation of random holes that are not correlated to the substrate features (H(S)≤ 60 nm). While the ranges of H(S) values indicated in the parentheses are valid for PS films with an equivalent thickness (h(E)) ≈ 50.3 nm on a flat substrate, a change in h(E) merely alters the cut-off values of H(S), as the final dewetted morphologies and transition across categories remain generically unaltered. We finally show that the structures obtained by dewetting on different H(S) substrates exhibits different levels of hydrophobicity because of combined spatial variation of chemical and topographic contrast along the surface. Thus, the work reported in this article can find potential application in fabricating surfaces with controlled wettability.

Conformational transitions in DNA polymerase I revealed by single-molecule FRET

PubMed Central

Santoso, Yusdi; Joyce, Catherine M.; Potapova, Olga; Le Reste, Ludovic; Hohlbein, Johannes; Torella, Joseph P.; Grindley, Nigel D. F.; Kapanidis, Achillefs N.

2010-01-01

The remarkable fidelity of most DNA polymerases depends on a series of early steps in the reaction pathway which allow the selection of the correct nucleotide substrate, while excluding all incorrect ones, before the enzyme is committed to the chemical step of nucleotide incorporation. The conformational transitions that are involved in these early steps are detectable with a variety of fluorescence assays and include the fingers-closing transition that has been characterized in structural studies. Using DNA polymerase I (Klenow fragment) labeled with both donor and acceptor fluorophores, we have employed single-molecule fluorescence resonance energy transfer to study the polymerase conformational transitions that precede nucleotide addition. Our experiments clearly distinguish the open and closed conformations that predominate in Pol-DNA and Pol-DNA-dNTP complexes, respectively. By contrast, the unliganded polymerase shows a broad distribution of FRET values, indicating a high degree of conformational flexibility in the protein in the absence of its substrates; such flexibility was not anticipated on the basis of the available crystallographic structures. Real-time observation of conformational dynamics showed that most of the unliganded polymerase molecules sample the open and closed conformations in the millisecond timescale. Ternary complexes formed in the presence of mismatched dNTPs or complementary ribonucleotides show unique FRET species, which we suggest are relevant to kinetic checkpoints that discriminate against these incorrect substrates. PMID:20080740

Twin-induced phase transition from β-Ga2O3 to α-Ga2O3 in Ga2O3 thin films

NASA Astrophysics Data System (ADS)

Choi, Byeongdae; Allabergenov, Bunyod; Lyu, Hong-Kun; Lee, Seong Eui

2018-06-01

We deposited a 300-nm-thick Ga2O3 thin film on an amorphous SiO2/Si substrate via pulsed laser deposition. X-ray diffraction patterns revealed the formation of β-Ga2O3 phase at a substrate temperature of 700 °C. X-ray photoelectron spectra indicated that the degree of oxidation increased after annealing at 700 °C. Further annealings at higher temperatures led to a transition of the β-Ga2O3 phase to the α-Ga2O3 phase; this transition was caused by the twin structure formed during the crystallinity improvement process. In addition, we discuss the mechanism of the transition from the β phase to the α phase in the β-Ga2O3 thin films.

Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis

PubMed Central

Chi, Young-In; Martick, Monika; Lares, Monica; Kim, Rosalind; Scott, William G; Kim, Sung-Hou

2008-01-01

We have obtained precatalytic (enzyme–substrate complex) and postcatalytic (enzyme–product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme–substrate and enzyme–product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures. PMID:18834200

The structural and optical properties of GaSb/InGaAs type-II quantum dots grown on InP (100) substrate

PubMed Central

2012-01-01

We have investigated the structural and optical properties of type-II GaSb/InGaAs quantum dots [QDs] grown on InP (100) substrate by molecular beam epitaxy. Rectangular-shaped GaSb QDs were well developed and no nanodash-like structures which could be easily found in the InAs/InP QD system were formed. Low-temperature photoluminescence spectra show there are two peaks centered at 0.75eV and 0.76ev. The low-energy peak blueshifted with increasing excitation power is identified as the indirect transition from the InGaAs conduction band to the GaSb hole level (type-II), and the high-energy peak is identified as the direct transition (type-I) of GaSb QDs. This material system shows a promising application on quantum-dot infrared detectors and quantum-dot field-effect transistor. PMID:22277096

How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations

PubMed Central

Kirmizialtin, Serdal; Nguyen, Virginia; Johnson, Kenneth A.; Elber, Ron

2012-01-01

Summary Nearly every enzyme undergoes a significant change in structure after binding it’s substrate. New experimental and theoretical analyses of the role of changes in HIV reverse transcriptase structure in selecting a correct substrate are presented. Atomically detailed simulations using the Milestoning method predict a rate and free energy profile of the conformational change commensurate with experimental data. A large conformational change occurring on a ms timescale locks the correct nucleotide at the active site, but promotes release of a mismatched nucleotide. The positions along the reaction coordinate that decide the yield of the reaction are not determined by the chemical step. Rather, the initial steps of weak substrate binding and protein conformational transition significantly enrich the yield of a reaction with a correct substrate, while the same steps diminish the reaction probability of an incorrect substrate. PMID:22483109

Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM).

PubMed

Wu, Heng-Liang; Tong, Yujin; Peng, Qiling; Li, Na; Ye, Shen

2016-01-21

The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.

Magneto-electric transition in nickel-gallium arsenide-nickel multiferroic structure

NASA Astrophysics Data System (ADS)

Galichyan, T. A.; Filippov, D. A.; Laletin, V. M.; Firsova, T. O.; Poddubnaya, N. N.

2018-04-01

Experimental studies of the magnetoelectric effect are presented in structures manufactured by electrolytic deposition of nickel on a substrate of gallium arsenide. It is shown that the use of gold-germanium-nickel sublayer, when sprayed on a substrate, significantly improves the adhesion between electrolytically deposited nickel and substrate. Linear and nonlinear magnetoelectric effects on the alternating magnetic field are observed in these structures. Both effects have resonant character and the resonance frequency of the nonlinear effect is twice less than that of the linear effect. In weak fields, the value of the nonlinear magnetoelectric effect is in quadratic dependence on the alternating magnetic field and unlike the linear magnetoelectric effect, it does not depend on the bias field.

Change in the magnetic structure of (Bi,Sm)FeO3 thin films at the morphotropic phase boundary probed by neutron diffraction

NASA Astrophysics Data System (ADS)

Maruyama, Shingo; Anbusathaiah, Varatharajan; Fennell, Amy; Enderle, Mechthild; Takeuchi, Ichiro; Ratcliff, William D.

2014-11-01

We report on the evolution of the magnetic structure of BiFeO3 thin films grown on SrTiO3 substrates as a function of Sm doping. We determined the magnetic structure using neutron diffraction. We found that as Sm increases, the magnetic structure evolves from a cycloid to a G-type antiferromagnet at the morphotropic phase boundary, where there is a large piezoelectric response due to an electric-field induced structural transition. The occurrence of the magnetic structural transition at the morphotropic phase boundary offers another route towards room temperature multiferroic devices.

Friction transition in polyimide films as related to molecular relaxations and structure

NASA Technical Reports Server (NTRS)

Fusaro, R. L.

1975-01-01

The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were correlated to molecular structure and the results of torsional braid analysis (TBA). A large friction transition (0.23 to 0.03) was found to occur at 45 C + or - 5 C. It was postulated that this transition was initiated by some molecular relaxation, which gave the molecules a degree of freedom by which an external mechanical stress could rearrange the molecules into a structure, such as an extended chain, which is conducive to easy shear. Above 300 C the friction characteristics were found to be dependent on the thermal prehistory of the film.

Germanene on single-layer ZnSe substrate: novel electronic and optical properties.

PubMed

Ye, H Y; Hu, F F; Tang, H Y; Yang, L W; Chen, X P; Wang, L G; Zhang, G Q

2018-06-01

In this work, the structural, electronic and optical properties of germanene and ZnSe substrate nanocomposites have been investigated using first-principles calculations. We found that the large direct-gap ZnSe semiconductors and zero-gap germanene form a typical orbital hybridization heterostructure with a strong binding energy, which shows a moderate direct band gap of 0.503 eV in the most stable pattern. Furthermore, the heterostructure undergoes semiconductor-to-metal band gap transition when subjected to external out-of-plane electric field. We also found that applying external strain and compressing the interlayer distance are two simple ways of tuning the electronic structure. An unexpected indirect-direct band gap transition is also observed in the AAII pattern via adjusting the interlayer distance. Quite interestingly, the calculated results exhibit that the germanene/ZnSe heterobilayer structure has perfect optical absorption in the solar spectrum as well as the infrared and UV light zones, which is superior to that of the individual ZnSe substrate and germanene. The staggered interfacial gap and tunability of the energy band structure via interlayer distance and external electric field and strain thus make the germanene/ZnSe heterostructure a promising candidate for field effect transistors (FETs) and nanoelectronic applications.

Templating effect of the substrate on the structure of Cu-phthalocyanine thin film

NASA Astrophysics Data System (ADS)

Pierantozzi, Gian Marco; Sbroscia, Marco; Ruocco, Alessandro

2018-03-01

An experimental study of electronic properties, structure and morphology of Copper-phthalocyanine films deposited onto Al(100) and Au(110), as a function of thickness up to tens of nanometers, is presented. The monolayers grown on these two model substrates are already known to exhibit very different behavior for what concerns both the degree of interaction with the substrate and the formation of long range order; in this experiment, by means of low energy electron scattering and Electron Energy Loss Spectroscopy (EELS), remarkable differences are revealed also in the successive growth. Exploiting the link between the crystal structure and the lineshape of HOMO-LUMO transition in EELS spectrum, two different structural phases are identified, compatible with α and β phases, respectively in the case of the film grown on aluminum and on gold. Besides, the evolution of the specular reflection elastic peak indicates the formation of islands on the gold substrate and a more homogeneous growth on the aluminum one.

Growth and Structure of Strontium Doped LaGaO3

DTIC Science & Technology

2001-01-01

Sandstrom, E.A. Giess, W.J. Gallagher, A. Segmifler, E.I. Cooper, M.F. Chisholm, A. Gupta, S. Shinole, R.B. Laibowitz," Lanthanum gallate substrates...that a structural phase transition occurs at -150 °C 5. The phase transition is the most serious drawback of many lanthanide gallates and aluminates5 for...and C.D. Brandle, "Thermal analysis of rare earth gallates and aluminates", J Mater. Res. 5, p. 183, 1990. 6. S. Miyazawa," Surface roughening

A theoretical study of the structure and stability of borohydride on 3d transition metals

NASA Astrophysics Data System (ADS)

Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

2012-12-01

The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

Nanomechanics of Ferroelectric Thin Films and Heterostructures

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

Li, Yulan; Hu, Shenyang Y.; Chen , L.Q.

2016-08-31

The focus of this chapter is to provide basic concepts of how external strains/stresses altering ferroelectric property of a material and how to evaluate quantitatively the effect of strains/stresses on phase stability, domain structure, and material ferroelectric properties using the phase-field method. The chapter starts from a brief introduction of ferroelectrics and the Landau-Devinshire description of ferroelectric transitions and ferroelectric phases in a homogeneous ferroelectric single crystal. Due to the fact that ferroelectric transitions involve crystal structure change and domain formation, strains and stresses can be produced inside of the material if a ferroelectric transition occurs and it is confined.more » These strains and stresses affect in turn the domain structure and material ferroelectric properties. Therefore, ferroelectrics and strains/stresses are coupled to each other. The ferroelectric-mechanical coupling can be used to engineer the material ferroelectric properties by designing the phase and structure. The followed section elucidates calculations of the strains/stresses and elastic energy in a thin film containing a single domain, twinned domains to complicated multidomains constrained by its underlying substrate. Furthermore, a phase field model for predicting ferroelectric stable phases and domain structure in a thin film is presented. Examples of using substrate constraint and temperature to obtain interested ferroelectric domain structures in BaTiO3 films are demonstrated b phase field simulations.« less

Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

PubMed Central

Miller, Bill R.; Parish, Carol A.; Wu, Eugene Y.

2014-01-01

During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although X-ray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme∶DNA) state to better understand its dynamics. We have applied long time-scale, unbiased molecular dynamics to investigate the opening process of the fingers domain in the absence of substrate for B. stearothermophilis DNA polymerase in silico. These simulations are biologically and/or physiologically relevant as they shed light on the transitions between states in this important enzyme. All closed and ajar simulations successfully transitioned into the fully open conformation, which is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic studies. Furthermore, we have detailed the key stages in the opening process starting from the open and ajar crystal structures, including the observation of a previously unknown key intermediate structure. Four backbone dihedrals were identified as important during the opening process, and their movements provide insight into the recognition of dNTP substrate molecules by the polymerase binary state. In addition to revealing the opening mechanism, this study also demonstrates our ability to study biological events of DNA polymerase using current computational methods without biasing the dynamics. PMID:25474643

Molecular dynamics study of the melting of a supported 887-atom Pd decahedron.

PubMed

Schebarchov, D; Hendy, S C; Polak, W

2009-04-08

We employ classical molecular dynamics simulations to investigate the melting behaviour of a decahedral Pd(887) cluster on a single layer of graphite (graphene). The interaction between Pd atoms is modelled with an embedded-atom potential, while the adhesion of Pd atoms to the substrate is approximated with a Lennard-Jones potential. We find that the decahedral structure persists at temperatures close to the melting point, but that just below the melting transition, the cluster accommodates to the substrate by means of complete melting and then recrystallization into an fcc structure. These structural changes are in qualitative agreement with recently proposed models, and they verify the existence of an energy barrier preventing softly deposited clusters from 'wetting' the substrate at temperatures below the melting point.

Photoluminescence spectroscopy and the effective mass theory of strained (In,Ga)As/GaAs heterostructures grown on (112)B GaAs substrates

NASA Technical Reports Server (NTRS)

Henderson, R. H.; Sun, D.; Towe, E.

1995-01-01

The photoluminescence characteristics of pseudomorphic In(0.19)Ga(0.81)As/GaAs quantum well structures grown on both the conventional (001) and the unconventional (112)B GaAs substrate are investigated. It is found that the emission spectra of the structures grown on the (112)B surface exhibit some spectral characteristics not observed on similar structures grown on the (001) surface. A spectral blue shift of the e yields hh1 transition with increasing optical pump intensity is observed for the quantum wells on the (112) surface. This shift is interpreted to be evidence of a strain-induced piezoelectric field. A second spectral feature located within the band gap of the In(0.19)Ga(0.81)As layer is also observed for the (112) structure; this feature is thought to be an impurity-related emission. The expected transition energies of the quantum well structures are calculated using the effective mass theory based on the 4 x 4 Luttinger valence band Hamiltonian, and related strain Hamiltonian.

Tuning the metal-insulator transition of VO2 by introducing W dopants via a combinatorial approach

NASA Astrophysics Data System (ADS)

Liang, Yangang; Lee, Seunghun; Zhang, Xiaohang; Takeuchi, Ichiro

We have systematically studied the structural phase transition and the electronic properties of composition spread V1-xWxO2 (0 <= x <= 0.037) thin films fabricated on silicon (001) and c-cut sapphire substrates through combinatorial pulsed laser deposition of a V2O5 target and a WO3 target. Our in-situ temperature-dependent x-ray diffraction measurements reveal a gradual change in the film structure from a monoclinic phase to a tetragonal phase via an intermediate mixture of the two as the concentration of tungsten increases from 0% to 3.7% at 300 K. At 358 K, the film is found to be in a tetragonal phase for the entire composition range we studied. The results also suggest that the volume of the unit cell increases as the concentration of tungsten increases. Electrical transport results further show that both the phase transition temperature and the width of the hysteresis loop decrease with the increasing of the concentration of tungsten. Especially, epitaxial V1-xWxO2 films fabricated on c-cut sapphire substrates show narrower hysteresis loop compared to textured V1-xWxO2 films fabricated on Si (100) substrates. In addition, the Hall effect measurements on the epitaxial V1-xWxO2 thin films at various temperature points provide important information for the change in the electronic structure upon increasing the concentration of tungsten. This work was supported by CNAM.

Thermopower analysis of the electronic structure around the metal-insulator transition in V1-xWxO2

NASA Astrophysics Data System (ADS)

Katase, Takayoshi; Endo, Kenji; Ohta, Hiromichi

2014-10-01

The electronic structure across the metal-insulator (MI) transition of electron-doped V1-xWxO2 epitaxial films (x =0-0.06) grown on α-Al2O3 substrates was studied by means of thermopower (S) measurements. Significant increase of |S | values accompanied by MI transition was observed, and the transition temperatures of S (TS) decreased with x in a good linear relation with MI transition temperatures. |S| values of V1-xWxO2 films at T>TS were constant at low values of 23μVK-1 independently of x, which reflects a metallic electronic structure, whereas those at T

Optical properties of epitaxial BiFeO3 thin film grown on SrRuO3-buffered SrTiO3 substrate.

PubMed

Xu, Ji-Ping; Zhang, Rong-Jun; Chen, Zhi-Hui; Wang, Zi-Yi; Zhang, Fan; Yu, Xiang; Jiang, An-Quan; Zheng, Yu-Xiang; Wang, Song-You; Chen, Liang-Yao

2014-01-01

The BiFeO3 (BFO) thin film was deposited by pulsed-laser deposition on SrRuO3 (SRO)-buffered (111) SrTiO3 (STO) substrate. X-ray diffraction pattern reveals a well-grown epitaxial BFO thin film. Atomic force microscopy study indicates that the BFO film is rather dense with a smooth surface. The ellipsometric spectra of the STO substrate, the SRO buffer layer, and the BFO thin film were measured, respectively, in the photon energy range 1.55 to 5.40 eV. Following the dielectric functions of STO and SRO, the ones of BFO described by the Lorentz model are received by fitting the spectra data to a five-medium optical model consisting of a semi-infinite STO substrate/SRO layer/BFO film/surface roughness/air ambient structure. The thickness and the optical constants of the BFO film are obtained. Then a direct bandgap is calculated at 2.68 eV, which is believed to be influenced by near-bandgap transitions. Compared to BFO films on other substrates, the dependence of the bandgap for the BFO thin film on in-plane compressive strain from epitaxial structure is received. Moreover, the bandgap and the transition revealed by the Lorentz model also provide a ground for the assessment of the bandgap for BFO single crystals.

Structural phase transitions in SrTiO 3 nanoparticles

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

Zhang, Han; Liu, Sizhan; Scofield, Megan E.

2017-07-31

Pressure dependent structural measurements on monodispersed nanoscale SrTiO3 samples with average diameters of 10 to ~80 nm were conducted to enhance the understanding of the structural phase diagram of nanoscale SrTiO3. A robust pressure independent polar structure was found in the 10 nm sample for pressures up to 13 GPa, while a size dependent cubic to tetragonal transition occurs (at P = Pc) for larger particle sizes. The results suggest that the growth of ~10 nm STO particles on substrates with significant lattice mismatch may maintain a polar state for a large range of strain values, possibly enabling device use.

Effect of film thickness on soft magnetic behavior of Fe2CoSi Heusler alloy for spin transfer torque device applications

NASA Astrophysics Data System (ADS)

Asvini, V.; Saravanan, G.; Kalaiezhily, R. K.; Raja, M. Manivel; Ravichandran, K.

2018-04-01

Fe2CoSi based Heusler alloy thin films were deposited on Si (111) wafer (substrate) of varying thickness using ultra high vacuum DC magnetron sputtering. The structural behavior was observed and found to be hold the L21 structure. The deposited thin films were characterized magnetic properties using vibrating sample magnetometer; the result shows a very high saturated magnetization (Ms), lowest coercivity (Hc), high curie transition temperature (Tc) and low hysteresis loss. Thin film thickness of 75 nm Fe2CoSi sample maintained at substrate temperature 450°C shows the lowest coercivity (Hc=7 Oe). In general, Fe2CoSi Heusler alloys curie transition temperature is very high, due to strong exchange interaction between the Fe and Co atoms. The substrate temperature was kept constant at 450°C for varying thickness (e.g. 5, 20, 50, 75 and 100 nm) of thin film sample. The 75 nm thickness thin film sample shows well crystallanity and good magnetic properties, further squareness ratio in B-H loop increases with the increase in film thickness.

Highly organized smectic-like packing in vapor-deposited glasses of a liquid crystal

DOE PAGES

Gujral, Ankit; Gomez, Jaritza; Jiang, Jing; ...

2016-12-26

Glasses of a model smectic liquid crystal-forming molecule, itraconazole, were prepared by vapor deposition onto substrates with temperatures ranging from T substrate = 0.78T g to 1.02T g, where T g (=330 K) is the glass transition temperature. The films were characterized using X-ray scattering techniques. For T substrate near and below T g, glasses with layered smectic-like structures can be prepared and the layer spacing can be tuned by 16% through the choice of T substrate. Remarkably, glasses prepared with T substrate values above T g exhibit levels of structural organization much higher than that of a thermally annealedmore » film. These results are explained by a mechanism based upon a preferred molecular orientation and enhanced molecular motion at the free surface, indicating that molecular organization in the glass is independent of the anchoring preferred at the substrate. Furthermore, these results suggest new strategies for optimizing molecular packing within active layers of organic electronic and optoelectronic devices.« less

Defect-related photoluminescence in Mg-doped GaN nanostructures

NASA Astrophysics Data System (ADS)

Reshchikov, M. A.; Shahedipour-Sandvik, F.; Messer, B. J.; Jindal, V.; Tripathi, N.; Tungare, M.

2009-12-01

Thin film of GaN:Mg, pyramidal GaN:Mg on GaN, sapphire and AlN substrates were grown in a MOCVD system under same growth conditions and at the same time. In samples with Mg-doped GaN pyramids on GaN:Si template a strong ultraviolet (UVL) band with few phonon replicas dominated at low temperature and was attributed to transitions from shallow donors to shallow Mg acceptor. In samples grown on sapphire and AlN substrates the UVL band appeared as a structureless band with the maximum at about 3.25 eV. There is a possibility that the structureless UVL band and the UVL band with phonon structure have different origin. In addition to the UVL band, the blue luminescence (BL) band peaking at 2.9 eV was observed in samples representing GaN:Mg pyramids on GaN:Si substrate. It is preliminary attributed to transitions from shallow donors to Zn acceptor in GaN:Si substrate.

Electronic and geometric structure of thin CoO(100) films studied by angle-resolved photoemission spectroscopy and Auger electron diffraction

NASA Astrophysics Data System (ADS)

Heiler, M.; Chassé, A.; Schindler, K.-M.; Hollering, M.; Neddermeyer, H.

2000-05-01

We have prepared ordered thin films of CoO by evaporating cobalt in an O 2 atmosphere on to a heated (500 K) Ag(100) substrate. The geometric and electronic structure of the films was characterized by means of Auger electron diffraction (AED) and angle-resolved photoemission spectroscopy (ARUPS), respectively. The experimental AED results were compared with simulated data, which showed that the film grows in (100) orientation on the Ag(100) substrate. Synchrotron-radiation-induced photoemission investigations were performed in the photon energy range from 25 eV to 67 eV. The dispersion of the transitions was found to be similar to that of previous results on a single-crystal CoO(100) surface. The resonance behaviour of the photoemission lines in the valence-band region was investigated by constant-initial-state (CIS) spectroscopy. The implications of this behaviour for assignment of the photoemission lines to specific electronic transitions is discussed and compared with published theoretical models of the electronic structure.

Substrate-induced ubiquitylation and endocytosis of yeast amino acid permeases.

PubMed

Ghaddar, Kassem; Merhi, Ahmad; Saliba, Elie; Krammer, Eva-Maria; Prévost, Martine; André, Bruno

2014-12-01

Many plasma membrane transporters are downregulated by ubiquitylation, endocytosis, and delivery to the lysosome in response to various stimuli. We report here that two amino acid transporters of Saccharomyces cerevisiae, the general amino acid permease (Gap1) and the arginine-specific permease (Can1), undergo ubiquitin-dependent downregulation in response to their substrates and that this downregulation is not due to intracellular accumulation of the transported amino acids but to transport catalysis itself. Following an approach based on permease structural modeling, mutagenesis, and kinetic parameter analysis, we obtained evidence that substrate-induced endocytosis requires transition of the permease to a conformational state preceding substrate release into the cell. Furthermore, this transient conformation must be stable enough, and thus sufficiently populated, for the permease to undergo efficient downregulation. Additional observations, including the constitutive downregulation of two active Gap1 mutants altered in cytosolic regions, support the model that the substrate-induced conformational transition inducing endocytosis involves remodeling of cytosolic regions of the permeases, thereby promoting their recognition by arrestin-like adaptors of the Rsp5 ubiquitin ligase. Similar mechanisms might control many other plasma membrane transporters according to the external concentrations of their substrates. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Key Mutations Alter the Cytochrome P450 BM3 Conformational Landscape and Remove Inherent Substrate Bias*

PubMed Central

Butler, Christopher F.; Peet, Caroline; Mason, Amy E.; Voice, Michael W.; Leys, David; Munro, Andrew W.

2013-01-01

Cytochrome P450 monooxygenases (P450s) have enormous potential in the production of oxychemicals, due to their unparalleled regio- and stereoselectivity. The Bacillus megaterium P450 BM3 enzyme is a key model system, with several mutants (many distant from the active site) reported to alter substrate selectivity. It has the highest reported monooxygenase activity of the P450 enzymes, and this catalytic efficiency has inspired protein engineering to enable its exploitation for biotechnologically relevant oxidations with structurally diverse substrates. However, a structural rationale is lacking to explain how these mutations have such effects in the absence of direct change to the active site architecture. Here, we provide the first crystal structures of BM3 mutants in complex with a human drug substrate, the proton pump inhibitor omeprazole. Supported by solution data, these structures reveal how mutation alters the conformational landscape and decreases the free energy barrier for transition to the substrate-bound state. Our data point to the importance of such “gatekeeper” mutations in enabling major changes in substrate recognition. We further demonstrate that these mutants catalyze the same 5-hydroxylation reaction as performed by human CYP2C19, the major human omeprazole-metabolizing P450 enzyme. PMID:23828198

Allosteric Inhibition via R-state Destabilization in ATP Sulfurylase from Penicillium chrysogenum

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

MacRae, I. J.

2002-01-01

The structure of the cooperative hexameric enzyme ATP sulfurylase from Penicillium chrysogenum bound to its allosteric inhibitor, 3'-phosphoadenosine-5'-phosphosulfate (PAPS), was determined to 2.6 {angstrom} resolution. This structure represents the low substrate-affinity T-state conformation of the enzyme. Comparison with the high substrate-affinity R-state structure reveals that a large rotational rearrangement of domains occurs as a result of the R-to-T transition. The rearrangement is accompanied by the 17 {angstrom} movement of a 10-residue loop out of the active site region, resulting in an open, product release-like structure of the catalytic domain. Binding of PAPS is proposed to induce the allosteric transition bymore » destabilizing an R-state-specific salt linkage between Asp 111 in an N-terminal domain of one subunit and Arg 515 in the allosteric domain of a trans-triad subunit. Disrupting this salt linkage by site-directed mutagenesis induces cooperative inhibition behavior in the absence of an allosteric effector, confirming the role of these two residues.« less

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Synthesis of sub-micro-flakes CrSe2 on glass and (110) Si substrates by solvothermal method

NASA Astrophysics Data System (ADS)

Tang, Qingkai; Liu, Changyou; Zhang, Binbin; Jie, Wanqi

2018-06-01

Layered structure MX2 (M = transition metal, X = S, Se and Te) chalcogenides have rich physic properties and potential applications. While it is still a challenge to prepare the chalcogenides by solvothermal method. In this work, we reported a new solution method to prepare CrSe2 sub-micro-flakes on different substrates. The surface morphologies, structures and compositions of the precursor CrSe2(en)1/2 and CrSe2 were investigated by SEM, XRD, thermogravimetric, IR and Raman spectra. The CrSe2 flakes with the sizes of 5-15 μm were obtained on both glass and (110) Si crystalline substrates. The formation mechanism of CrSe2 sub-micro-flakes is suggested.

Epitaxy, strain, and composition effects on metal-insulator transition characteristics of SmNiO{sub 3} thin films

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

Aydogdu, Gulgun H.; Ha, Sieu D.; Viswanath, B.

SmNiO{sub 3} (SNO) thin films were deposited on LaAlO{sub 3} (LAO), SrTiO{sub 3}, SrLaAlO{sub 4}, Si, and Al{sub 2}O{sub 3} (sapphire) substrates by RF magnetron sputtering and studies were conducted to understand how film structure and composition influence the insulator-metal transition properties. It is observed that the compressive strain induces the insulator to metal transition (MIT), while tensile strain suppresses it. In the case of non-epitaxial films, semiconducting behavior is obtained on sapphire over a broad temperature range, while on heavily-doped Si substrate; an MIT is seen in out-of-plane resistance measurement. In addition, thickness dependence on the resistance behavior andmore » nickel oxidation state has been examined for epitaxial SNO films on LAO substrates. Fine control of the MIT by modifications to the mismatch strain and thickness provides insights to enhance the performance and the functionality of these films for emerging electron devices.« less

Enantioselectivity in Candida antarctica lipase B: A molecular dynamics study

PubMed Central

Raza, Sami; Fransson, Linda; Hult, Karl

2001-01-01

A major problem in predicting the enantioselectivity of an enzyme toward substrate molecules is that even high selectivity toward one substrate enantiomer over the other corresponds to a very small difference in free energy. However, total free energies in enzyme-substrate systems are very large and fluctuate significantly because of general protein motion. Candida antarctica lipase B (CALB), a serine hydrolase, displays enantioselectivity toward secondary alcohols. Here, we present a modeling study where the aim has been to develop a molecular dynamics-based methodology for the prediction of enantioselectivity in CALB. The substrates modeled (seven in total) were 3-methyl-2-butanol with various aliphatic carboxylic acids and also 2-butanol, as well as 3,3-dimethyl-2-butanol with octanoic acid. The tetrahedral reaction intermediate was used as a model of the transition state. Investigative analyses were performed on ensembles of nonminimized structures and focused on the potential energies of a number of subsets within the modeled systems to determine which specific regions are important for the prediction of enantioselectivity. One category of subset was based on atoms that make up the core structural elements of the transition state. We considered that a more favorable energetic conformation of such a subset should relate to a greater likelihood for catalysis to occur, thus reflecting higher selectivity. The results of this study conveyed that the use of this type of subset was viable for the analysis of structural ensembles and yielded good predictions of enantioselectivity. PMID:11266619

Conformational Dynamics of a Y-Family DNA Polymerase during Substrate Binding and Catalysis As Revealed by Interdomain Förster Resonance Energy Transfer

PubMed Central

2015-01-01

Numerous kinetic, structural, and theoretical studies have established that DNA polymerases adjust their domain structures to enclose nucleotides in their active sites and then rearrange critical active site residues and substrates for catalysis, with the latter conformational change acting to kinetically limit the correct nucleotide incorporation rate. Additionally, structural studies have revealed a large conformational change between the apoprotein and the DNA–protein binary state for Y-family DNA polymerases. In previous studies [Xu, C., Maxwell, B. A., Brown, J. A., Zhang, L., and Suo, Z. (2009) PLoS Biol.7, e1000225], a real-time Förster resonance energy transfer (FRET) method was developed to monitor the global conformational transitions of DNA polymerase IV from Sulfolobus solfataricus (Dpo4), a prototype Y-family enzyme, during nucleotide binding and incorporation by measuring changes in distance between locations on the enzyme and the DNA substrate. To elucidate further details of the conformational transitions of Dpo4 during substrate binding and catalysis, in this study, the real-time FRET technique was used to monitor changes in distance between various pairs of locations in the protein itself. In addition to providing new insight into the conformational changes as revealed in previous studies, the results here show that the previously described conformational change between the apo and DNA-bound states of Dpo4 occurs in a mechanistic step distinct from initial formation or dissociation of the binary complex of Dpo4 and DNA. PMID:24568554

Band structure dynamics in indium wires

NASA Astrophysics Data System (ADS)

Chávez-Cervantes, M.; Krause, R.; Aeschlimann, S.; Gierz, I.

2018-05-01

One-dimensional indium wires grown on Si(111) substrates, which are metallic at high temperatures, become insulating below ˜100 K due to the formation of a charge density wave (CDW). The physics of this transition is not conventional and involves a multiband Peierls instability with strong interband coupling. This CDW ground state is readily destroyed with femtosecond laser pulses resulting in a light-induced insulator-to-metal phase transition. The current understanding of this transition remains incomplete, requiring measurements of the transient electronic structure to complement previous investigations of the lattice dynamics. Time- and angle-resolved photoemission spectroscopy with extreme ultraviolet radiation is applied to this end. We find that the transition from the insulating to the metallic band structure occurs within ˜660 fs, which is a fraction of the amplitude mode period. The long lifetime of the transient state (>100 ps) is attributed to trapping in a metastable state in accordance with previous work.

Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.

PubMed

Pereira, Jose H; Goh, Ee-Been; Keasling, Jay D; Beller, Harry R; Adams, Paul D

2012-10-01

Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.

A metal-insulator transition study of VO 2 thin films grown on sapphire substrates

DOE PAGES

Yu, Shifeng; Wang, Shuyu; Lu, Ming; ...

2017-12-15

In this paper, vanadium thin films were deposited on sapphire substrates by DC magnetron sputtering and then oxidized in a tube furnace filled with oxygen under different temperatures and oxygen flow rates. The significant influence of the oxygen flow rate and oxidation temperature on the electrical and structural properties of the vanadium oxide thin films were investigated systematically. It shows the pure vanadium dioxide (VO 2) state can only be obtained in a very narrow temperature and oxygen flow rate range. The resistivity change during the metal-insulator transition varies from 0.2 to 4 orders of magnitude depending on the oxidationmore » condition. Large thermal hysteresis during the metal-insulator phase transition was observed during the transition compared to the results in literature. Proper oxidation conditions can significantly reduce the thermal hysteresis. Finally, the fabricated VO 2 thin films showed the potential to be applied in the development of electrical sensors and other smart devices.« less

Strain effect in epitaxial VO2 thin films grown on sapphire substrates using SnO2 buffer layers

NASA Astrophysics Data System (ADS)

Kim, Heungsoo; Bingham, Nicholas S.; Charipar, Nicholas A.; Piqué, Alberto

2017-10-01

Epitaxial VO2/SnO2 thin film heterostructures were deposited on m-cut sapphire substrates via pulsed laser deposition. By adjusting SnO2 (150 nm) growth conditions, we are able to control the interfacial strain between the VO2 film and SnO2 buffer layer such that the semiconductor-to-metal transition temperature (TC) of VO2 films can be tuned without diminishing the magnitude of the transition. It is shown that in-plane tensile strain and out-of-plane compressive strain of the VO2 film leads to a decrease of Tc. Interestingly, VO2 films on SnO2 buffer layers exhibit a structural phase transition from tetragonal-like VO2 to tetragonal-VO2 during the semiconductor-to-metal transition. These results suggest that the strain generated by SnO2 buffer provides an effective way for tuning the TC of VO2 films.

Collective transport for active matter run-and-tumble disk systems on a traveling-wave substrate

DOE PAGES

Sándor, Csand; Libál, Andras; Reichhardt, Charles; ...

2017-01-17

Here, we examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of themore » substrate speed, maximum substrate force, disk run time, and disk density. Since variation of the disk activity parameters produces different disk drift rates for a fixed traveling-wave speed on the substrate, the system we consider could be used as an efficient method for active matter species separation. Within the cluster phase, we find that in some regimes the motion of the cluster center of mass is in the opposite direction to that of the traveling wave, while when the maximum substrate force is increased, the cluster drifts in the direction of the traveling wave. This suggests that swarming or clustering motion can serve as a method by which an active system can collectively move against an external drift.« less

Collective transport for active matter run-and-tumble disk systems on a traveling-wave substrate

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

Sándor, Csand; Libál, Andras; Reichhardt, Charles

Here, we examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of themore » substrate speed, maximum substrate force, disk run time, and disk density. Since variation of the disk activity parameters produces different disk drift rates for a fixed traveling-wave speed on the substrate, the system we consider could be used as an efficient method for active matter species separation. Within the cluster phase, we find that in some regimes the motion of the cluster center of mass is in the opposite direction to that of the traveling wave, while when the maximum substrate force is increased, the cluster drifts in the direction of the traveling wave. This suggests that swarming or clustering motion can serve as a method by which an active system can collectively move against an external drift.« less

Structures with Reconfigurable Circulatory Systems

DTIC Science & Technology

2008-05-16

chemical groups ( cinnamates , etc.) may be explored as they may result in faster kinetics which will facilitate transition between solid and liquid...Cysteine, an amino acid , is a critical substrate in biosynthesis of proteins, glutathione, taurine sulfate and the exceptionally metabolically active

Structural phase transitions in SrTiO 3 nanoparticles

DOE PAGES

Zhang, Han; Liu, Sizhan; Scofield, Megan E.; ...

2017-08-04

We present that pressure dependent structural measurements on monodispersed nanoscale SrTiO 3 samples with average diameters of 10 to ~80 nm were conducted to enhance the understanding of the structural phase diagram of nanoscale SrTiO 3. A robust pressure independent polar structure was found in the 10 nm sample for pressures up to 13 GPa, while a size dependent cubic to tetragonal transition occurs (at P = P c) for larger particle sizes. In conclusion, the results suggest that the growth of ~10 nm STO particles on substrates with significant lattice mismatch may maintain a polar state for a largemore » range of strain values, possibly enabling device use.« less

Dual-Color Emission in Hybrid III-Nitride/ZnO Light Emitting Diodes

NASA Astrophysics Data System (ADS)

Namkoong, Gon; Trybus, Elaissa; Cheung, Maurice C.; Doolittle, W. Alan; Cartwright, Alexander N.; Ferguson, Ian; Seong, Tae-Yeon; Nause, Jeff

2010-02-01

We report dual-color production of the blue and green regions using hybrid nitride/ZnO light emitting diode (LED) structures grown on ZnO substrates. The blue emission is ascribed to the near-band edge transition in InGaN while green emission is related to Zn-related defect levels formed by the unintentional interdiffusion of Zn into the InGaN active layer from the ZnO substrates.

Pattern-induced anchoring transitions in nematic liquid crystals

NASA Astrophysics Data System (ADS)

Rojas-Gómez, Óscar A.; Romero-Enrique, José M.; Silvestre, Nuno M.; Telo da Gama, Margarida M.

2017-02-01

In this paper we revisit the problem of a nematic liquid crystal in contact with patterned substrates. The substrate is modelled as a periodic array of parallel infinite grooves of well-defined cross-section sculpted on a chemically homogeneous substrate which favours local homeotropic anchoring of the nematic. We consider three cases: a sawtooth, a crenellated and a sinusoidal substrate. We analyse this problem within the modified Frank-Oseen formalism. We argue that, for substrate periodicities much larger than the extrapolation length, the existence of different nematic textures with distinct far-field orientations, as well as the anchoring transitions between them, are associated with the presence of topological defects either on or close to the substrate. For the sawtooth and sinusoidal cases, we observe a homeotropic to planar anchoring transition as the substrate roughness increases. On the other hand, a homeotropic to oblique anchoring transition is observed for crenellated substrates. In this case, the anchoring phase diagram shows a complex dependence on the substrate roughness and substrate anchoring strength.

Direct observation of the lattice precursor of the metal-to-insulator transition in V2O3 thin films by surface acoustic waves

NASA Astrophysics Data System (ADS)

Kündel, J.; Pontiller, P.; Müller, C.; Obermeier, G.; Liu, Z.; Nateprov, A. A.; Hörner, A.; Wixforth, A.; Horn, S.; Tidecks, R.

2013-03-01

A surface acoustic wave (SAW) delay line is used to study the metal-to-insulator (MI) transition of V2O3 thin films deposited on a piezoelectric LiNbO3 substrate. Effects contributing to the sound velocity shift of the SAW which are caused by elastic properties of the lattice of the V2O3 films when changing the temperature are separated from those originating from the electrical conductivity. For this purpose the electric field accompanying the elastic wave of the SAW has been shielded by growing the V2O3 film on a thin metallic Cr interlayer (coated with Cr2O3), covering the piezoelectric substrate. Thus, the recently discovered lattice precursor of the MI transition can be directly observed in the experiments, and its fine structure can be investigated.

Verwey transition in a magnetite ultrathin film by resonant x-ray scattering

NASA Astrophysics Data System (ADS)

Grenier, S.; Bailly, A.; Ramos, A. Y.; De Santis, M.; Joly, Y.; Lorenzo, J. E.; Garaudée, S.; Frericks, M.; Arnaud, S.; Blanc, N.; Boudet, N.

2018-03-01

We report a detailed study of the Verwey transition in a magnetite ultrathin film (UTF) grown on Ag(001) using resonant x-ray scattering (RXS). RXS was measured at the Fe K-edge on the crystal truncation rod of the substrate, increasing the sensitivity to the film thanks to the cross-interference, thereby obtaining an x-ray phase-shift reference and a polarization analyzer. The spectra were interpreted with ad hoc calculations based on density functional theory within a surface-scattering formalism. We observed that the UTF has a relatively sharp transition temperature TV=120 K and is remarkably close to the bulk temperature for such thickness. We determined the specific Fe stacking at the interface with the substrate below TV, and detected a spectroscopic signal evolving with temperature from TV up to at least TV+80 K, hinting that the RT crystallographic structure does not set at TV in the UTF.

A Two-Dimensional 'Zigzag' Silica Polymorph on a Metal Support.

PubMed

Kuhness, David; Yang, Hyun Jin; Klemm, Hagen W; Prieto, Mauricio; Peschel, Gina; Fuhrich, Alexander; Menzel, Dietrich; Schmidt, Thomas; Yu, Xin; Shaikhutdinov, Shamil; Lewandowski, Adrian; Heyde, Markus; Kelemen, Anna; Włodarczyk, Radosław; Usvyat, Denis; Schütz, Martin; Sauer, Joachim; Freund, Hans-Joachim

2018-05-16

We present a new polymorph of the two-dimensional (2D) silica film with a characteristic 'zigzag' line structure and a rectangular unit cell which forms on a Ru(0001) metal substrate. This new silica polymorph may allow for important insights into growth modes and transformations of 2D silica films as a model system for the study of glass transitions. Based on scanning tunneling microscopy, low energy electron diffraction, infrared reflection absorption spectroscopy, and X-ray photoelectron spectroscopy measurements on the one hand, and density functional theory calculations on the other, a structural model for the 'zigzag' polymorph is proposed. In comparison to established monolayer and bilayer silica, this 'zigzag' structure system has intermediate characteristics in terms of coupling to the substrate and stoichiometry. The silica 'zigzag' phase is transformed upon reoxidation at higher annealing temperature into a SiO 2 silica bilayer film which is chemically decoupled from the substrate.

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

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

Xiang, Yong; Karaveg, Khanita; Moremen, Kelley W.

2016-11-17

Asn-linked glycosylation of newly synthesized polypeptides occurs in the endoplasmic reticulum of eukaryotic cells. Glycan structures are trimmed and remodeled as they transit the secretory pathway, and processing intermediates play various roles as ligands for folding chaperones and signals for quality control and intracellular transport. Key steps for the generation of these trimmed intermediates are catalyzed by glycoside hydrolase family 47 (GH47) α-mannosidases that selectively cleave α1,2-linked mannose residues. Despite the sequence and structural similarities among the GH47 enzymes, the molecular basis for residue-specific cleavage remains obscure. The present studies reveal enzyme–substrate complex structures for two related GH47 α-mannosidases andmore » provide insights into how these enzymes recognize the same substrates differently and catalyze the complementary glycan trimming reactions necessary for glycan maturation.« less

Superconductors

DOEpatents

Newkirk, Lawrence R.; Valencia, Flavio A.

1977-02-01

The structural quality of niobium germanide as a high-transition-temperature superconducting material is substantially improved by the presence of about 5 at. % oxygen. Niobium germanide having this oxygen content may readily be prepared as a bulk coating bonded to a metallic substrate by chemical vapor deposition techniques.

Cuboidal-to-pyramidal shape transition of a strained island on a substrate

NASA Astrophysics Data System (ADS)

Abbes, Fatima Z.; Durinck, Julien; Talea, Mohamed; Grilhé, Jean; Colin, Jérôme

2017-10-01

The stability of a strained cuboidal island deposited on a substrate has been numerically investigated by means of finite element simulations in the case where the structure is submitted to misfit strain resulting from the lattice mismatch between the island and the substrate. In the hypothesis where the surface energy is isotropic, it is found that, depending on the island volume, the formation of a truncated or inverted truncated pyramid can be favored by the misfit strain with respect to the cuboidal shape. A shape diagram is finally provided as a function of the misfit strain and island volume.

Magnus-induced dynamics of driven skyrmions on a quasi-one-dimensional periodic substrate

DOE PAGES

Reichhardt, Charles; Reichhardt, Cynthia Jane

2016-09-13

Here we numerically examine driven skyrmions interacting with a periodic quasi-one-dimensional substrate where the driving force is applied either parallel or perpendicular to the substrate periodicity direction. For perpendicular driving, the particles in a purely overdamped system simply slide along the substrate minima; however, for skyrmions where the Magnus force is relevant, we find that a rich variety of dynamics can arise. In the single skyrmion limit, the skyrmion motion is locked along the driving or longitudinal direction for low drives, while at higher drives a transition occurs to a state in which the skyrmion moves both transverse and longitudinalmore » to the driving direction. Within the longitudinally locked phase we find a pronounced speedup effect that occurs when the Magnus force aligns with the external driving force, while at the transition to transverse and longitudinal motion, the skyrmion velocity drops, producing negative differential conductivity. For collectively interacting skyrmion assemblies, the speedup effect is still present and we observe a number of distinct dynamical phases, including a sliding smectic phase, a disordered or moving liquid phase, a moving hexatic phase, and a moving crystal phase. The transitions between the dynamic phases produce distinct features in the structure of the skyrmion lattice and in the velocity-force curves. Lastly, we map these different phases as a function of the ratio of the Magnus term to the dissipative term, the substrate strength, the commensurability ratio, and the magnitude of the driving force.« less

Magnus-induced dynamics of driven skyrmions on a quasi-one-dimensional periodic substrate

NASA Astrophysics Data System (ADS)

Reichhardt, C.; Reichhardt, C. J. Olson

2016-09-01

We numerically examine driven skyrmions interacting with a periodic quasi-one-dimensional substrate where the driving force is applied either parallel or perpendicular to the substrate periodicity direction. For perpendicular driving, the particles in a purely overdamped system simply slide along the substrate minima; however, for skyrmions where the Magnus force is relevant, we find that a rich variety of dynamics can arise. In the single skyrmion limit, the skyrmion motion is locked along the driving or longitudinal direction for low drives, while at higher drives a transition occurs to a state in which the skyrmion moves both transverse and longitudinal to the driving direction. Within the longitudinally locked phase we find a pronounced speedup effect that occurs when the Magnus force aligns with the external driving force, while at the transition to transverse and longitudinal motion, the skyrmion velocity drops, producing negative differential conductivity. For collectively interacting skyrmion assemblies, the speedup effect is still present and we observe a number of distinct dynamical phases, including a sliding smectic phase, a disordered or moving liquid phase, a moving hexatic phase, and a moving crystal phase. The transitions between the dynamic phases produce distinct features in the structure of the skyrmion lattice and in the velocity-force curves. We map these different phases as a function of the ratio of the Magnus term to the dissipative term, the substrate strength, the commensurability ratio, and the magnitude of the driving force.

Key feature of the catalytic cycle of TNF-α converting enzyme involves communication between distal protein sites and the enzyme catalytic core

PubMed Central

Solomon, Ariel; Akabayov, Barak; Frenkel, Anatoly; Milla, Marcos E.; Sagi, Irit

2007-01-01

Despite their key roles in many normal and pathological processes, the molecular details by which zinc-dependent proteases hydrolyze their physiological substrates remain elusive. Advanced theoretical analyses have suggested reaction models for which there is limited and controversial experimental evidence. Here we report the structure, chemistry and lifetime of transient metal–protein reaction intermediates evolving during the substrate turnover reaction of a metalloproteinase, the tumor necrosis factor-α converting enzyme (TACE). TACE controls multiple signal transduction pathways through the proteolytic release of the extracellular domain of a host of membrane-bound factors and receptors. Using stopped-flow x-ray spectroscopy methods together with transient kinetic analyses, we demonstrate that TACE's catalytic zinc ion undergoes dynamic charge transitions before substrate binding to the metal ion. This indicates previously undescribed communication pathways taking place between distal protein sites and the enzyme catalytic core. The observed charge transitions are synchronized with distinct phases in the reaction kinetics and changes in metal coordination chemistry mediated by the binding of the peptide substrate to the catalytic metal ion and product release. Here we report key local charge transitions critical for proteolysis as well as long sought evidence for the proposed reaction model of peptide hydrolysis. This study provides a general approach for gaining critical insights into the molecular basis of substrate recognition and turnover by zinc metalloproteinases that may be used for drug design. PMID:17360351

Classification of Phase Transitions by Microcanonical Inflection-Point Analysis

NASA Astrophysics Data System (ADS)

Qi, Kai; Bachmann, Michael

2018-05-01

By means of the principle of minimal sensitivity we generalize the microcanonical inflection-point analysis method by probing derivatives of the microcanonical entropy for signals of transitions in complex systems. A strategy of systematically identifying and locating independent and dependent phase transitions of any order is proposed. The power of the generalized method is demonstrated in applications to the ferromagnetic Ising model and a coarse-grained model for polymer adsorption onto a substrate. The results shed new light on the intrinsic phase structure of systems with cooperative behavior.

Thickness dependent properties of CMR Manganite thin films on lattice mismatched substrates: Distinguishing Strain and Interface Effects

NASA Astrophysics Data System (ADS)

Davidson, Anthony, III; Kolagani, Rajeswari; Bacharova, Ellisaveta; Yong, Grace; Smolyaninova, Vera; Schaefer, David; Mundle, Rajeh

2007-03-01

Epitaxial thin films of CMR manganite materials have been known to show thickness dependent electrical and magnetic properties on lattice mismatched substrates. Below a critical thickness, insulator-metal transition is suppressed. These effects have been largely attributed to the role of bi-axial lattice mismatch strain. Our recent results of epitaxial thin films of La0.67Ca0.33MnO3 (LCMO) on two substrates with varying degrees of compressive lattice mismatch indicate that, in addition to the effect of lattice mismatch strain, the thickness dependence of the properties are influenced by other factors possibly related to the nature of the film substrate interface and defects such as twin boundaries. We have compared the properties of LCMO films on (100) oriented LaAlO3 and (001) oriented NdCaAlO4 both of which induce compressive bi-axial strain. Interestingly, the suppression of the insulator-metal transition is less in films on NCAO which has a larger lattice mismatch. We will present results correlating the electrical and magneto transport properties with the structure and morphology of the films.

Scaling of elongation transition thickness during thin-film growth on weakly interacting substrates

NASA Astrophysics Data System (ADS)

Lü, B.; Souqui, L.; Elofsson, V.; Sarakinos, K.

2017-08-01

The elongation transition thickness ( θElong) is a central concept in the theoretical description of thin-film growth dynamics on weakly interacting substrates via scaling relations of θElong with respect to rates of key atomistic film-forming processes. To date, these scaling laws have only been confirmed quantitatively by simulations, while experimental proof has been left ambiguous as it has not been possible to measure θElong. Here, we present a method for determining experimentally θElong for Ag films growing on amorphous SiO2: an archetypical weakly interacting film/substrate system. Our results confirm the theoretically predicted θElong scaling behavior, which then allow us to calculate the rates of adatom diffusion and island coalescence completion, in good agreement with the literature. The methodology presented herein casts the foundation for studying growth dynamics and cataloging atomistic-process rates for a wide range of weakly interacting film/substrate systems. This may provide insights into directed growth of metal films with a well-controlled morphology and interfacial structure on 2D crystals—including graphene and MoS2—for catalytic and nanoelectronic applications.

Dielectric properties of betaine phosphite and deuterated betaine phosphite films

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

Balashova, E. V., E-mail: balashova@mail.ioffe.ru; Krichevtsov, B. B.; Zaitseva, N. V.

2011-01-15

Polycrystalline films of betaine phosphite (BPI) and deuterated BPI have been grown by evaporation on LiNbO{sub 3}, {alpha}-SiO{sub 2}, {alpha}-Al{sub 2}O{sub 3}, and NdGaO{sub 3} substrates. These films consist of large single-crystal blocks in which the polar axis (b) lies in the substrate plane. The results of studying the dielectric properties of the films using interdigital electrodes, X-ray diffraction, and block images in a polarized-light microscope in reflection are reported. The film transition into the ferroelectric state at T = T{sub c} is accompanied by strong anomalies of the capacitance of the film/interdigital structure/substrate structure. The deuteration of BPI filmsmore » leads to an increase in their temperature T{sub c}: from T{sub c} = 200 K for BPI-based structures to T{sub c} = 280 K for structures with a high degree of deuteration (d {approx} 90%).« less

In situ probing of doping- and stress-mediated phase transitions in a single-crystalline VO2 nanobeam by spatially resolved Raman spectroscopy

NASA Astrophysics Data System (ADS)

Chang, Sung-Jin; Park, Jong Bae; Lee, Gaehang; Kim, Hae Jin; Lee, Jin-Bae; Bae, Tae-Sung; Han, Young-Kyu; Park, Tae Jung; Huh, Yun Suk; Hong, Woong-Ki

2014-06-01

We demonstrate an experimental in situ observation of the temperature-dependent evolution of doping- and stress-mediated structural phase transitions in an individual single-crystalline VO2 nanobeam on a Au-coated substrate under exposure to hydrogen gas using spatially resolved Raman spectroscopy. The nucleation temperature of the rutile R structural phase in the VO2 nanobeam upon heating under hydrogen gas was lower than that under air. The spatial structural phase evolution behavior along the length of the VO2 nanobeam under hydrogen gas upon heating was much more inhomogeneous than that along the length of the same nanobeam under air. The triclinic T phase of the VO2 nanobeam upon heating under hydrogen gas transformed to the R phase and this R phase was stabilized even at room temperature in air after sample cooling. In particular, after the VO2 nanobeam with the R phase was annealed at approximately 250 °C in air, it exhibited the monoclinic M1 phase (not the T phase) at room temperature during heating and cooling cycles. These results were attributed to the interplay between hydrogen doping and stress associated with nanobeam-substrate interactions. Our study has important implications for engineering metal-insulator transition properties and developing functional devices based on VO2 nanostructures through doping and stress.We demonstrate an experimental in situ observation of the temperature-dependent evolution of doping- and stress-mediated structural phase transitions in an individual single-crystalline VO2 nanobeam on a Au-coated substrate under exposure to hydrogen gas using spatially resolved Raman spectroscopy. The nucleation temperature of the rutile R structural phase in the VO2 nanobeam upon heating under hydrogen gas was lower than that under air. The spatial structural phase evolution behavior along the length of the VO2 nanobeam under hydrogen gas upon heating was much more inhomogeneous than that along the length of the same nanobeam under air. The triclinic T phase of the VO2 nanobeam upon heating under hydrogen gas transformed to the R phase and this R phase was stabilized even at room temperature in air after sample cooling. In particular, after the VO2 nanobeam with the R phase was annealed at approximately 250 °C in air, it exhibited the monoclinic M1 phase (not the T phase) at room temperature during heating and cooling cycles. These results were attributed to the interplay between hydrogen doping and stress associated with nanobeam-substrate interactions. Our study has important implications for engineering metal-insulator transition properties and developing functional devices based on VO2 nanostructures through doping and stress. Electronic supplementary information (ESI) available: Illustration, photograph, Raman data, and EDX spectra. See DOI: 10.1039/c4nr01118j

Dielectric and structural properties of ferroelectric betaine arsenate films

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Zaitseva, N. V.; Yurko, E. I.; Svinarev, F. B.

2014-12-01

Ferroelectric films of betaine arsenate and partially deuterated betaine arsenate have been grown by evaporation on LiNbO3, α-Al2O3, and NdGaO3 substrates with a preliminarily deposited structure of interdigitated electrodes, as well as on the Al/glass substrate. This paper presents the results of the examination of the block structure of the films in a polarizing microscope, the X-ray diffraction analysis of their crystal structure, and the investigation of the dielectric properties in a measuring field oriented both parallel and perpendicular to the plane of the film. The transition of the films to the ferroelectric state at T = T c is accompanied by anomalies of the capacitance of the structure, an increase in the dielectric loss, and the appearance of dielectric hysteresis loops. The growth of the films from a solution of betaine arsenate in a heavy water leads to an increase in the ferroelectric transition temperature from T c = 119 K in the films without deuterium to T c = 149 K, which corresponds to the degree of deuteration of approximately 60-70%. The dielectric and structural properties of the films are compared with those of the betaine arsenate single crystals and the previously studied films of betaine phosphite and glycine phosphite.

Effect of substrate orientation on CdS homoepitaxy by molecular dynamics

DOE PAGES

Almeida, S.; Chavez, J. J.; Zhou, X. W.; ...

2016-02-10

CdS homoepitaxy growth was performed by molecular dynamics using different substrate orientations and structures in order to analyze the CdS crystallinity. As anticipated from thermodynamics of homoepitaxy, highly crystalline films with only point defects were obtained on substrates with rectangular surface geometries, including View the MathML source[112¯] zinc blende (ZB), [101¯0] wurtzite (WZ), [112¯0] WZ, [110][110] ZB, [010][010] ZB, and View the MathML source[1101110] ZB. In contrast, films grown on substrates with hexagonal surface geometries, corresponding to the [0001][0001] WZ and [111][111] ZB growth directions, showed structures with a large number of defects including; anti-sites, vacancies, stacking faults, twinning, andmore » polytypism. WZ and ZB transitions and grain boundaries are identified using a lattice identification algorithm and represented graphically in a structural map. A dislocation analysis was performed to detect, identify, and quantify linear defects within the atomistic data. Systematic simulations using different temperatures, deposition rates, and substrate polarities were perform to analyze the trends of dislocation densities on [0001][0001] WZ direction and showed persistent polytypism. As a result, the polytypism observed in the films grown on the substrates with hexagonal surface geometry is attributed to the similar formation energies of the WZ and ZB phases.« less

Atomic mechanism for the growth of wafer-scale single-crystal graphene: theoretical perspective and scanning tunneling microscopy investigations

NASA Astrophysics Data System (ADS)

Niu, Tianchao; Zhang, Jialin; Chen, Wei

2017-12-01

Chemical vapor deposition (CVD) is the most promising approach for producing low-cost, high-quality, and large area graphene. Revealing the graphene growth mechanism at the atomic-scale is of great importance for realizing single crystal graphene (SCG) over wafer scale. Density functional theoretical (DFT) calculations are playing an increasingly important role in revealing the structure of the most stable carbon species, understanding the evolution processes, and disclosing the active sites. Scanning tunneling microscopy (STM) is a powerful surface characterization tool to illustrate the real space distribution and atomic structures of growth intermediates during the CVD process. Combining them together can provide valuable information to improve the atomically controlled growth of SCG. Starting from a basic concept of the substrate effect on realizing SCG, this review covers the progress made in theoretical investigations on various carbon species during graphene growth on different transition metal substrates, in the STM study of the structural intermediates on transition metal surfaces, and in synthesizing graphene nanoribbons with atomic-precise width and edge structure, ending with a perspective on the future development of 2D materials beyond graphene.

Structural Studies of the Initial Stages of Fluoride Epitaxy on Silicon and GERMANIUM(111)

NASA Astrophysics Data System (ADS)

Denlinger, Jonathan David

The epitaxial growth of ionic insulators on semiconductor substrates is of interest due to fundamental issues of interface bonding and structure as well as to potential technological applications. The initial stages of Group IIa fluoride insulator growth on (111) Si and Ge substrates by molecular beam epitaxy are studied with the in situ combination of X-ray Photoelectron Spectroscopy (XPS) and Diffraction (XPD). While XPS probes the electronic structure, XPD reveals atomic structure. In addition, low energy electron diffraction (LEED) is used to probe surface order and a separate study using X-ray standing wave (XSW) fluorescence reveals interface cation bonding sites. Following the formation of a chemically-reacted interface layer in CaF_2 epitaxy on Si(111), the morphology of the subsequent bulk layers is found to be dependent on substrate temperature and incident flux rate. At temperatures >=600 ^circC a transition from three -dimensional island formation at low flux to laminar growth at higher flux is observed with bulk- and interface-resolved XPD. At lower substrate temperatures, laminar growth is observed at all fluxes, but with different bulk nucleation behavior due to changes in the stoichiometry of the interface layer. This new observation of kinetic effects on the initial nucleation in CaF_2 epitaxy has important ramifications for the formation of thicker heterostructures for scientific or device applications. XPS and XPD are also used to identify for the first time, surface core-level species of Ca and F, and a secondary interface-shifted F Auger component arising from a second-layer site directly above interface-layer Ca atoms. The effects of lattice mismatch (from -3% to 8%) are investigated with various growths of Ca_{rm x}Sr _{rm 1-x}F_2 on Si and Ge (111) substrates. Triangulation of (111) and (220) XSW indicates a predominance of 3-fold hollow Sr bonding sites coexisting with 4-fold top sites for monolayers of SrF_2 on Si. XSW and LEED reveal a lateral discommensuration of the overlayer for lattice mismatches of >5% relative to the substrate. XPD also reveals a transition from single - to mixed-domains of overlayer crystallographic orientation for mismatches >=3.5%.

High performance YBCO films. Report for 1 August-31 October 1992

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

Denlinger, E.J.; Fathy, A.; Kalokitis, D.

1992-10-31

The objective of this program is to identify suitable low loss, low dielectric constant substrates and develop and optimize deposition processes for high quality YBCO films including the necessary buffer layers. Ultimate goals are large area substrates having double-sided HTS coating with a surface resistance ten times lower than copper at 40 GHz. High quality HTS films on low dielectric constant substrates are expected to find widespread use in advanced millimeter wave components, in extending the power handling capability of microwave and millimeter wave circuitry, and in facilitating high speed computer interconnects. Sample demonstration circuits will be built toward themore » end of the program. We have successfully deposited a high quality YBCO film on a good low loss and low dielectric constant substrate, magnesium fluoride (e=5). With the use of two buffer layers (magnesium oxide and strontium titanate) between the YBCO and the substrate, transition temperatures of 89 deg K and transition widths of about 0.5 deg K were achieved. The critical current density Jc of 4 x 10 6 A/cm2 at 77K in zero field is among the highest reported for YBCO films. The magnesium fluoride (MgF2) substrate has a tetragonal structure with a dielectric constant of 5.2 in the plane of the substrate and 4.6 perpendicular to the substrate surface. It has a good harness (-575 Knoop) and a linear thermal expansion coefficient that closely matches YBCO and the buffer layers.« less

Excavated substrate modulates growth instability during nest building in ants

PubMed Central

Toffin, Etienne; Kindekens, Jonathan; Deneubourg, Jean-Louis

2010-01-01

In social insects, the nests of the same species can show a large difference in size and shape. Despite these large variations, the nests share the same substructures, some appearing during nest growth. In ants, the interplay between nest size and digging activity leads to two successive morphological transitions from circular to branched shapes (budding along the perimeter of the circular cavity and tunnelling of the galleries). Like several other self-organized collective behaviours, this phenomenon, as well as the entire nest-digging process, is thought to be modulated by environmental properties. The present study investigates the effect of excavated substrate on the nest morphogenesis and the morphological transitions by using two materials with different cohesions. Here, we show that the two morphological transitions occur more frequently with a cohesive substrate than with a granular one: 96 per cent of cohesive experiments showed both transitions, whereas only 50 per cent did in granular experiments. We found that transitions and excavation cessation follow area–response thresholds: the shape transitions take place and the digging activity stops when the dug area reaches the corresponding threshold values. The shape transition thresholds are lower with the cohesive substrate and that of stopping digging is independent of nest shape and material. According to simulations, the experimental frequencies of transitions found their origin in the competition between transitions and activity cessation and in the difference between the transition threshold values of each substrate. Our results demonstrate how the substrate properties modulate the collective response and lead to various patterns. Considering the non-specific mechanisms at work, such effects of substrate coarseness have their counterparts in various collective behaviours, generating alternative patterns to colonize and exploit the environment. PMID:20410036

Enhanced doping effect on tuning structural phases of monolayer antimony

NASA Astrophysics Data System (ADS)

Wang, Jizhang; Yang, Teng; Zhang, Zhidong; Yang, Li

2018-05-01

Doping is capable to control the atomistic structure, electronic structure, and even to dynamically realize a semiconductor-metal transition in two-dimensional (2D) transition metal dichalcogenides (TMDs). However, the high critical doping density (˜1014 electron/cm2), compound nature, and relatively low carrier mobility of TMDs limits broader applications. Using first-principles calculations, we predict that, via a small transition potential, a substantially lower hole doping density (˜6 × 1012 hole/cm2) can switch the ground-state structure of monolayer antimony from the hexagonal β-phase, a 2D semiconductor with excellent transport performance and air stability but an indirect bandgap, to the orthorhombic α phase with a direct bandgap and potentially better carrier mobility. We further show that this structural engineering can be achieved by the established electrostatic doping, surface functional adsorption, or directly using graphene substrate. This gives hope to dynamically tuning and large-scale production of 2D single-element semiconductors that simultaneously exhibit remarkable transport and optical performance.

Strain-induced magnetization control in an oxide multiferroic heterostructure

NASA Astrophysics Data System (ADS)

Motti, Federico; Vinai, Giovanni; Petrov, Aleksandr; Davidson, Bruce A.; Gobaut, Benoit; Filippetti, Alessio; Rossi, Giorgio; Panaccione, Giancarlo; Torelli, Piero

2018-03-01

Controlling magnetism by using electric fields is a goal of research towards novel spintronic devices and future nanoelectronics. For this reason, multiferroic heterostructures attract much interest. Here we provide experimental evidence, and supporting density functional theory analysis, of a transition in L a0.65S r0.35Mn O3 thin film to a stable ferromagnetic phase, that is induced by the structural and strain properties of the ferroelectric BaTi O3 (BTO) substrate, which can be modified by applying external electric fields. X-ray magnetic circular dichroism measurements on Mn L edges with a synchrotron radiation show, in fact, two magnetic transitions as a function of temperature that correspond to structural changes of the BTO substrate. We also show that ferromagnetism, absent in the pristine condition at room temperature, can be established by electrically switching the BTO ferroelectric domains in the out-of-plane direction. The present results confirm that electrically induced strain can be exploited to control magnetism in multiferroic oxide heterostructures.

Symmetry of Highly-Strained BiFeO3 Films in the Ultrathin Regime

NASA Astrophysics Data System (ADS)

Yang, Yongsoo; Senabulya, Nancy; Clarke, Roy; Schlepütz, Christian M.; Beekman, Christianne; Siemons, Wolter; Christen, Hans M.

2014-03-01

At room temperature, highly-strained BiFeO3 (BFO) films grown on LaAlO3 substrates exhibit a monoclinic structure with a giant c/a ratio (~1.3) when the films are thicker than 4 nm. Their structural symmetry can be controlled by adjusting the temperature [Appl. Phys. Express 4, 095801 (2011), Adv. Mater. 25, 5561 (2013)], with a high-temperature tetragonal phase being observed. We report that a structural phase transition can also be achieved by controlling the film thickness: synchrotron x-ray diffraction data shows that the Bragg peak splitting associated with the monoclinic phase disappears as the film thickness decreases below 3 nm, indicating a tetragonal symmetry, but still maintaining the giant c/a ratio. Unlike a similar transition reported for moderately strained BFO grown on SrTiO3 [APL Mater. 1, 052102 (2013)], the half-order Bragg peaks indicate that this transition does not involve a significant change in the octahedral tilt pattern of the film. This suggests that the structural evolution of highly-strained BFO films should be understood in terms of the unique (non-octahedral) oxygen coordination of the Fe ion in this highly-strained BFO, not the corner-connectivity of the oxygen octahedra between the film and the substrate. Funding: U.S. Department of Energy, BES-MSED (U. Michigan: DE-FG02-06ER46273, and at ORNL). Measurements: 13-BMC, 33-IDD, 33-BMC of the Advanced Photon Source, ANL (DE-AC02-06CH11357).

Waveguide Transition for Submillimeter-Wave MMICs

NASA Technical Reports Server (NTRS)

Leong, Kevin M.; Deal, William R.; Radisic, Vesna; Mei, Xiaobing; Uyeda, Jansen; Lai, Richard; Fung, King Man; Gaier, Todd C.

2009-01-01

An integrated waveguide-to-MMIC (monolithic microwave integrated circuit) chip operating in the 300-GHz range is designed to operate well on high-permittivity semiconductor substrates typical for an MMIC amplifier, and allows a wider MMIC substrate to be used, enabling integration with larger MMICs (power amplifiers). The waveguide-to- CBCPW (conductor-backed coplanar waveguide) transition topology is based on an integrated dipole placed in the E-plane of the waveguide module. It demonstrates low loss and good impedance matching. Measurement and simulation demonstrate that the loss of the transition and waveguide loss is less than 1-dB over a 340-to-380-GHz bandwidth. A transition is inserted along the propagation direction of the waveguide. This transition uses a planar dipole aligned with the maximum E-field of the TE10 waveguide mode as an inter face between the waveguide and the MMIC. Mode conversion between the coplanar striplines (CPS) that feed the dipole and the CBCPW transmission line is accomplished using a simple air-bridge structure. The bottom side ground plane is truncated at the same reference as the top-side ground plane, leaving the end of the MMIC suspended in air.

Preparation and investigation of sputtered vanadium dioxide films with large phase-transition hysteresis loops

NASA Astrophysics Data System (ADS)

Zhang, Huafu; Wu, Zhiming; He, Qiong; Jiang, Yadong

2013-07-01

Vanadium dioxide (VO2) films with large phase-transition hysteresis loops were fabricated on glass substrates by reactive direct current (DC) magnetron sputtering in Ar/O2 atmosphere and subsequent in situ annealing process in pure oxygen. The crystal structure, chemical composition, morphology and metal-insulator transition (MIT) properties of the deposited films were investigated. The results reveal that the films show a polycrystalline nature with a (0 1 1) preferred orientation and consist of small spheroidal nanoparticles. All the deposited VO2 films show large hysteresis loops due to the small density of nucleating defects and the large interfacial energies, which are determined by the characteristics of the particles in the films, namely the small transversal grain size and the spheroidal shape. The film comprising the smallest spheroidal nanoparticles not only shows a large hysteresis width of 36.3 °C but also shows a low transition temperature of 32.2 °C upon cooling. This experiment facilitates the civilian applications of the VO2 films on glass substrates in optical storage-type devices.

Phosphoryl transfer reaction snapshots in crystals: Insights into the mechanism of protein kinase a catalytic subunit

DOE PAGES

Das, Amit; Gerlits, Oksana O.; Heller, William T.; ...

2015-06-19

To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal structures of the Michaelis complex mimics of the PKA catalytic subunit (PKAc) were obtained with either peptide inhibitors or ATP analogs. Here we utilized Ca 2+ ions and sulfur in place of the nucleophilic oxygen in a 20-residue pseudo-substrate peptide (CP20) and ATP to produce a close mimic of the Michaelis complex. In the ternary reactant complex,more » the thiol group of Cys-21 of the peptide is facing Asp-166 and the sulfur atom is positioned for an in-line phosphoryl transfer. Replacement of Ca 2+ cations with Mg 2+ ions resulted in a complex with trapped products of ATP hydrolysis: phosphate ion and ADP. As a result, the present structural results in combination with the previously reported structures of the transition state mimic and phosphorylated product complexes complete the snapshots of the phosphoryl transfer reaction by PKAc, providing us with the most thorough picture of the catalytic mechanism to date.« less

Structure and Electronic Properties of Interface-Confined Oxide Nanostructures

DOE PAGES

Liu, Yun; Ning, Yanxiao; Yu, Liang; ...

2017-09-16

The controlled fabrication of nanostructures has often made use of a substrate template to mediate and control the growth kinetics. Electronic substrate-mediated interactions have been demonstrated to guide the assembly of organic molecules or the nucleation of metal atoms but usually at cryogenic temperatures, where the diffusion has been limited. Combining STM, STS, and DFT studies, we report that the strong electronic interaction between transition metals and oxides could indeed govern the growth of low-dimensional oxide nanostructures. As a demonstration, a series of FeO triangles, which are of the same structure and electronic properties but with different sizes (side lengthmore » >3 nm), are synthesized on Pt(111). The strong interfacial interaction confines the growth of FeO nanostructures, leading to a discrete size distribution and a uniform step structure. Given the same interfacial configuration, as-grown FeO nanostructures not only expose identical edge/surface structure but also exhibit the same electronic properties, as manifested by the local density of states and local work functions. We expect the interfacial confinement effect can be generally applied to control the growth of oxide nanostructures on transition metal surfaces. These oxide nanostructures of the same structure and electronic properties are excellent models for studies of nanoscale effects and applications.« less

Structure and Electronic Properties of Interface-Confined Oxide Nanostructures

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

Liu, Yun; Ning, Yanxiao; Yu, Liang

The controlled fabrication of nanostructures has often made use of a substrate template to mediate and control the growth kinetics. Electronic substrate-mediated interactions have been demonstrated to guide the assembly of organic molecules or the nucleation of metal atoms but usually at cryogenic temperatures, where the diffusion has been limited. Combining STM, STS, and DFT studies, we report that the strong electronic interaction between transition metals and oxides could indeed govern the growth of low-dimensional oxide nanostructures. As a demonstration, a series of FeO triangles, which are of the same structure and electronic properties but with different sizes (side lengthmore » >3 nm), are synthesized on Pt(111). The strong interfacial interaction confines the growth of FeO nanostructures, leading to a discrete size distribution and a uniform step structure. Given the same interfacial configuration, as-grown FeO nanostructures not only expose identical edge/surface structure but also exhibit the same electronic properties, as manifested by the local density of states and local work functions. We expect the interfacial confinement effect can be generally applied to control the growth of oxide nanostructures on transition metal surfaces. These oxide nanostructures of the same structure and electronic properties are excellent models for studies of nanoscale effects and applications.« less

The t-Butylsulfinamide Lynchpin in Transition Metal-Mediated Multiscaffold Library Synthesis

PubMed Central

Bauer, Renato A.; DiBlasi, Christine M.; Tan, Derek S.

2010-01-01

A unified synthetic approach to diverse polycyclic scaffolds has been developed using transition metal-mediated cycloaddition and cyclization reactions of enynes and diynes. The t-butylsulfinamide group has been identified as a particularly versatile lynchpin in these reactions, with a reactivity profile uniquely suited for efficient, stereoselective substrate synthesis and downstream transformations. This approach provides ten distinct, functionalized scaffold classes related to common core structures in alkaloid and terpenoid natural products. PMID:20356070

Quantum mechanical hydrogen tunneling in bacterial copper amine oxidase reaction

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

Murakawa, Takeshi; Okajima, Toshihide; Kuroda, Shun'ichi

A key step decisively affecting the catalytic efficiency of copper amine oxidase is stereospecific abstraction of substrate {alpha}-proton by a conserved Asp residue. We analyzed this step by pre-steady-state kinetics using a bacterial enzyme and stereospecifically deuterium-labeled substrates, 2-phenylethylamine and tyramine. A small and temperature-dependent kinetic isotope effect (KIE) was observed with 2-phenylethylamine, whereas a large and temperature-independent KIE was observed with tyramine in the {alpha}-proton abstraction step, showing that this step is driven by quantum mechanical hydrogen tunneling rather than the classical transition-state mechanism. Furthermore, an Arrhenius-type preexponential factor ratio approaching a transition-state value was obtained in the reactionmore » of a mutant enzyme lacking the critical Asp. These results provide strong evidence for enzyme-enhanced hydrogen tunneling. X-ray crystallographic structures of the reaction intermediates revealed a small difference in the binding mode of distal parts of substrates, which would modulate hydrogen tunneling proceeding through either active or passive dynamics.« less

Stabilization of ultrathin (hydroxy)oxide films on transition metal substrates for electrochemical energy conversion

DOE PAGES

Zeng, Zhenhua; Chang, Kee-Chul; Kubal, Joseph; ...

2017-05-08

Design of cost-effective electrocatalysts with enhanced stability and activity is of paramount importance for the next generation of energy conversion systems, including fuel cells and electrolyzers. However, electrocatalytic materials generally improve one of these properties at the expense of the other. Here, using Density Functional Theory calculations and electrochemical surface science measurements, we explore atomic-level features of ultrathin (hydroxy)oxide films on transition metal substrates and demonstrate that these films exhibit both excellent stability and activity for electrocatalytic applications. The films adopt structures with stabilities that significantly exceed bulk Pourbaix limits, including stoichiometries not found in bulk and properties that aremore » tunable by controlling voltage, film composition, and substrate identity. Using nickel (hydroxy)oxide/Pt(111) as an example, we further show how the films enhance activity for hydrogen evolution through a bifunctional effect. Finally, the results suggest design principles for a new class of electrocatalysts with simultaneously enhanced stability and activity for energy conversion.« less

Stabilization of ultrathin (hydroxy)oxide films on transition metal substrates for electrochemical energy conversion

NASA Astrophysics Data System (ADS)

Zeng, Zhenhua; Chang, Kee-Chul; Kubal, Joseph; Markovic, Nenad M.; Greeley, Jeffrey

2017-06-01

Design of cost-effective electrocatalysts with enhanced stability and activity is of paramount importance for the next generation of energy conversion systems, including fuel cells and electrolysers. However, electrocatalytic materials generally improve one of these properties at the expense of the other. Here, using density functional theory calculations and electrochemical surface science measurements, we explore atomic-level features of ultrathin (hydroxy)oxide films on transition metal substrates and demonstrate that these films exhibit both excellent stability and activity for electrocatalytic applications. The films adopt structures with stabilities that significantly exceed bulk Pourbaix limits, including stoichiometries not found in bulk and properties that are tunable by controlling voltage, film composition, and substrate identity. Using nickel (hydroxy)oxide/Pt(111) as an example, we further show how the films enhance activity for hydrogen evolution through a bifunctional effect. The results suggest design principles for this class of electrocatalysts with simultaneously enhanced stability and activity for energy conversion.

Ambiguous Role of Growth-Induced Defects on the Semiconductor-to-Metal Characteristics in Epitaxial VO2/TiO2 Thin Films.

PubMed

Mihailescu, Cristian N; Symeou, Elli; Svoukis, Efthymios; Negrea, Raluca F; Ghica, Corneliu; Teodorescu, Valentin; Tanase, Liviu C; Negrila, Catalin; Giapintzakis, John

2018-04-25

Controlling the semiconductor-to-metal transition temperature in epitaxial VO 2 thin films remains an unresolved question both at the fundamental as well as the application level. Within the scope of this work, the effects of growth temperature on the structure, chemical composition, interface coherency and electrical characteristics of rutile VO 2 epitaxial thin films grown on TiO 2 substrates are investigated. It is hereby deduced that the transition temperature is lower than the bulk value of 340 K. However, it is found to approach this value as a function of increased growth temperature even though it is accompanied by a contraction along the V 4+ -V 4+ bond direction, the crystallographic c-axis lattice parameter. Additionally, it is demonstrated that films grown at low substrate temperatures exhibit a relaxed state and a strongly reduced transition temperature. It is suggested that, besides thermal and epitaxial strain, growth-induced defects may strongly affect the electronic phase transition. The results of this work reveal the difficulty in extracting the intrinsic material response to strain, when the exact contribution of all strain sources cannot be effectively determined. The findings also bear implications on the limitations in obtaining the recently predicted novel semi-Dirac point phase in VO 2 /TiO 2 multilayer structures.

Giant Controllable Magnetization Changes Induced by Structural Phase Transitions in a Metamagnetic Artificial Multiferroic

PubMed Central

Bennett, S. P.; Wong, A. T.; Glavic, A.; Herklotz, A.; Urban, C.; Valmianski, I.; Biegalski, M. D.; Christen, H. M.; Ward, T. Z.; Lauter, V.

2016-01-01

The realization of a controllable metamagnetic transition from AFM to FM ordering would open the door to a plethora of new spintronics based devices that, rather than reorienting spins in a ferromagnet, harness direct control of a materials intrinsic magnetic ordering. In this study FeRh films with drastically reduced transition temperatures and a large magneto-thermal hysteresis were produced for magnetocaloric and spintronics applications. Remarkably, giant controllable magnetization changes (measured to be as high has ~25%) are realized by manipulating the strain transfer from the external lattice when subjected to two structural phase transitions of BaTiO3 (001) single crystal substrate. These magnetization changes are the largest seen to date to be controllably induced in the FeRh system. Using polarized neutron reflectometry we reveal how just a slight in plane surface strain change at ~290C results in a massive magnetic transformation in the bottom half of the film clearly demonstrating a strong lattice-spin coupling in FeRh. By means of these substrate induced strain changes we show a way to reproducibly explore the effects of temperature and strain on the relative stabilities of the FM and AFM phases in multi-domain metamagnetic systems. This study also demonstrates for the first time the depth dependent nature of a controllable magnetic order using strain in an artificial multiferroic heterostructure. PMID:26940159

Giant Controllable Magnetization Changes Induced by Structural Phase Transitions in a Metamagnetic Artificial Multiferroic

DOE PAGES

Bennett, S. P.; Wong, A. T.; Glavic, A.; ...

2016-03-04

We realize that a controllable metamagnetic transition from AFM to FM ordering would open the door to a plethora of new spintronics based devices that, rather than reorienting spins in a ferromagnet, harness direct control of a materials intrinsic magnetic ordering. In this study FeRh films with drastically reduced transition temperatures and a large magneto-thermal hysteresis were produced for magnetocaloric and spintronics applications. Remarkably, giant controllable magnetization changes (measured to be as high has ~25%) are realized and by manipulating the strain transfer from the external lattice when subjected to two structural phase transitions of BaTiO3 (001) single crystal substrate.more » These magnetization changes are the largest seen to date to be controllably induced in the FeRh system. Using polarized neutron reflectometry we reveal how just a slight in plane surface strain change at ~290C results in a massive magnetic transformation in the bottom half of the film clearly demonstrating a strong lattice-spin coupling in FeRh. By means of these substrate induced strain changes we show a way to reproducibly explore the effects of temperature and strain on the relative stabilities of the FM and AFM phases in multi-domain metamagnetic systems. In our study also demonstrates for the first time the depth dependent nature of a controllable magnetic order using strain in an artificial multiferroic heterostructure.« less

Dewetting and spreading transitions for active matter on random pinning substrates.

PubMed

Sándor, Cs; Libál, A; Reichhardt, C; Olson Reichhardt, C J

2017-05-28

We show that sterically interacting self-propelled disks in the presence of random pinning substrates exhibit transitions among a variety of different states. In particular, from a phase separated cluster state, the disks can spread out and homogeneously cover the substrate in what can be viewed as an example of an active matter wetting transition. We map the location of this transition as a function of activity, disk density, and substrate strength, and we also identify other phases including a cluster state, coexistence between a cluster and a labyrinth wetted phase, and a pinned liquid. Convenient measures of these phases include the cluster size, which dips at the wetting-dewetting transition, and the fraction of sixfold coordinated particles, which drops when dewetting occurs.

Geometric confinement effects on the metal-insulator transition temperature and stress relaxation in VO2 thin films grown on silicon

NASA Astrophysics Data System (ADS)

Viswanath, Changhyun Ko, B.; Yang, Zheng; Ramanathan, Shriram

2011-03-01

VO2 undergoes a sharp metal-insulator transition at ˜67 °C with several orders of change in conductivity and optical transmittance. Understanding and control of the properties of vanadium oxide layers grown on technologically relevant substrates such as Si (100) single crystals is therefore of great interest. In this work, we show tunability of metal-insulator transition temperature as well as recoverable stress in VO2 thin films grown on Si substrate by introducing nanoscale atomic layer deposited HfO2 interfacial layers with no degradation in the resistance ratio. For a confined VO2 film, the metal-insulator transition temperature is suppressed by ˜16 °C and the recoverable stress is 150 MPa, compared to 400 MPa for a bare film. These observations are further correlated with in situ variable temperature measurement of stress changes occurring during the phase transition. Structural and microstructural studies on the various samples have been carried out by x ray diffraction and cross-sectional transmission electron microscopy. The strategy of tuning the metal-insulator transition characteristics by nanoscale interfacial dielectrics is of broader relevance in design of programmable materials and integration into solid state devices for electronics.

Polar phase transitions in heteroepitaxial stabilized La0.5Y0.5AlO3 thin films

NASA Astrophysics Data System (ADS)

Liu, Shenghua; Zhang, Chunfeng; Zhu, Mengya; He, Qian; Chakhalian, Jak; Liu, Xiaoran; Borisevich, Albina; Wang, Xiaoyong; Xiao, Min

2017-10-01

We report on the fabrication of epitaxial La0.5Y0.5AlO3 ultrathin films on (001) LaAlO3 substrates. Structural characterizations by scanning transmission electron microscopy and x-ray diffraction confirm the high quality of the film with a - b + c - AlO6 octahedral tilt pattern. Unlike either of the nonpolar parent compound, LaAlO3 and YAlO3, second harmonic generation measurements on the thin films suggest a nonpolar-polar phase transition at T c near 500 K, and a polar-polar phase transition at T a near 160 K. By fitting the angular dependence of the second harmonic intensities, we further propose that the two polar structures can be assigned to the Pmc2 1 and Pmn2 1 space group, while the high temperature nonpolar structure belongs to the Pbnm space group.

Observation of structure transition as a function of temperature in depositing hydrogenated sp2-rich carbon films

NASA Astrophysics Data System (ADS)

Wang, Yongfu; Gao, Kaixiong; Zhang, Junyan

2018-05-01

In this study, we carried out the transition experiments of graphite-like (GL) to fullerene-like (FL) structures by placing high temperature steel substrates in the depositing environment which can form FL hydrogenated carbon films. We investigated the changes of bond mixtures, H content, aromatic clusters and internal stress at the transition process, and proposed the transformation mechanism inferred from Raman, TEM cross-section, FTIR and XPS results. It was found that the size of aromatic clusters and accordingly graphene planes and the formation of edge dangling bonds were the key steps. H+ bombardment leaded to the splitting of large graphene planes (at GL stage) into more and smaller planes (at FL stage) and the formation of edge dangling bonds; Some of these dangling bonds were reduced by the formation of pentagons and subsequent curving of the smaller planes, which were an indicator of FL structures.

X-ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides

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

M Gleghorn; E Davydova; R Basu

2011-12-31

We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groupsmore » of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.« less

Strain driven sequential magnetic transitions in strained GdTiO3 on compressive substrates: a first-principles study.

PubMed

Yang, Li-Juan; Weng, Ya-Kui; Zhang, Hui-Min; Dong, Shuai

2014-11-26

The compressive strain effect on the magnetic ground state and electronic structure of strained GdTiO3 has been studied using the first-principles method. Unlike the cases of congeneric YTiO3 and LaTiO3, both of which become the A-type antiferromagnetism on the (0 0 1) LaAlO3 substrate despite their contrastive magnetism, the ground state of strained GdTiO3 on the LaAlO3 substrate changes from the original ferromagnetism to a G-type antiferromagnetim, instead of the A-type one although Gd(3+) is between Y(3+) and La(3+). It is only when the in-plane compressive strain is large enough, e.g. on the (0 0 1) YAlO3 substrate, that the ground state finally becomes the A-type. The band structure calculation shows that the compressive strained GdTiO3 remains insulating, although the band gap changes a little in the strained GdTiO3.

Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT.

PubMed

Merkle, Patrick S; Gotfryd, Kamil; Cuendet, Michel A; Leth-Espensen, Katrine Z; Gether, Ulrik; Loland, Claus J; Rand, Kasper D

2018-05-01

LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na + - and K + -dependent manner. The results suggest that partial unwinding of transmembrane helices 1/5/6/7 drives LeuT from a substrate-bound, outward-facing occluded conformation toward an inward-facing open state. These hitherto unknown, large-scale conformational changes in functionally important transmembrane segments, observed for LeuT in detergent-solubilized form and when embedded in a native-like phospholipid bilayer, could be of physiological relevance for the translocation process.

Tuning metal-insulator transitions in epitaxial V2O3 thin films

NASA Astrophysics Data System (ADS)

Thorsteinsson, Einar B.; Shayestehaminzadeh, Seyedmohammad; Arnalds, Unnar B.

2018-04-01

We present a study of the synthesis of epitaxial V2O3 films on c-plane Al2O3 substrates by reactive dc-magnetron sputtering. The results reveal a temperature window, at substantially lower values than previously reported, wherein epitaxial films can be obtained when deposited on [0001] oriented surfaces. The films display a metal-insulator transition with a change in the resistance of up to four orders of magnitude, strongly dependent on the O2 partial pressure during deposition. While the electronic properties of the films show sensitivity to the amount of O2 present during deposition of the films, their crystallographic structure and surface morphology of atomically flat terraced structures with up to micrometer dimensions are maintained. The transition temperature, as well as the scale of the metal-insulator transition, is correlated with the stoichiometry and local strain in the films controllable by the deposition parameters.

Photo-crystallization in a-Se layer structures: Effects of film-substrate interface-rigidity

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

Lindberg, G. P.; Gross, N.; Weinstein, B. A.

Amorphous selenium (a-Se) films deposited on rigid substrates can undergo photo-induced crystallization (PC) even at temperatures (T) well below the glass transition, T{sub g} ∼ 313 K. Substrate-generated shear strain is known to promote the PC process. In the present work, we explore the influence of different substrates (Si and glass), and different film-layer-substrate combinations, on the PC in a variety of a-Se films and film-structures. The intermediate layers (indium tin oxide and polyimide) are chosen to promote conductivity and/or to be a buffer against interface strain in structures of interest for digital imaging applications. The PC characteristics in these samples are evaluatedmore » and compared using optical microscopy, atomic-force microscopy, Raman mapping, and T-dependent Raman spectroscopy. Both the presence of a soft intermediate layer, and the thermal softening that occurs for T increasing through T{sub g}, inhibit the tendency for the onset of PC. The extensive PC mapping results in the wide range of samples studied here, as well as the suppression of PC near T{sub g} in this array of samples, strongly support the generality of this behavior. As a consequence, one may expect that the stability of a-Se films against PC can be enhanced by decreasing the rigidity of the film-substrate interface. In this regard, advanced film structures that employ flexible substrates, soft intermediate layers, and/or are designed to be operated near T{sub g} should be explored.« less

Design of Strain-Limiting Substrate Materials for Stretchable and Flexible Electronics

PubMed Central

Ma, Yinji; Jang, Kyung-In; Wang, Liang; Jung, Han Na; Kwak, Jean Won; Xue, Yeguang; Chen, Hang; Yang, Yiyuan; Shi, Dawei; Feng, Xue

2017-01-01

Recently developed classes of electronics for biomedical applications exploit substrates that offer low elastic modulus and high stretchability, to allow intimate, mechanically biocompatible integration with soft biological tissues. A challenge is that such substrates do not generally offer protection of the electronics from high peak strains that can occur upon large-scale deformation, thereby creating a potential for device failure. The results presented here establish a simple route to compliant substrates with strain-limiting mechanics based on approaches that complement those of recently described alternatives. Here, a thin film or mesh of a high modulus material transferred onto a prestrained compliant substrate transforms into wrinkled geometry upon release of the prestrain. The structure formed by this process offers a low elastic modulus at small strain due to the small effective stiffness of the wrinkled film or mesh; it has a high tangent modulus (e.g., >1000 times the elastic modulus) at large strain, as the wrinkles disappear and the film/mesh returns to a flat geometry. This bilinear stress–strain behavior has an extremely sharp transition point, defined by the magnitude of the prestrain. A theoretical model yields analytical expressions for the elastic and tangent moduli and the transition strain of the bilinear stress–strain relation, with quantitative correspondence to finite element analysis and experiments. PMID:29033714

Design of Strain-Limiting Substrate Materials for Stretchable and Flexible Electronics.

PubMed

Ma, Yinji; Jang, Kyung-In; Wang, Liang; Jung, Han Na; Kwak, Jean Won; Xue, Yeguang; Chen, Hang; Yang, Yiyuan; Shi, Dawei; Feng, Xue; Rogers, John A; Huang, Yonggang

2016-08-02

Recently developed classes of electronics for biomedical applications exploit substrates that offer low elastic modulus and high stretchability, to allow intimate, mechanically biocompatible integration with soft biological tissues. A challenge is that such substrates do not generally offer protection of the electronics from high peak strains that can occur upon large-scale deformation, thereby creating a potential for device failure. The results presented here establish a simple route to compliant substrates with strain-limiting mechanics based on approaches that complement those of recently described alternatives. Here, a thin film or mesh of a high modulus material transferred onto a prestrained compliant substrate transforms into wrinkled geometry upon release of the prestrain. The structure formed by this process offers a low elastic modulus at small strain due to the small effective stiffness of the wrinkled film or mesh; it has a high tangent modulus (e.g., >1000 times the elastic modulus) at large strain, as the wrinkles disappear and the film/mesh returns to a flat geometry. This bilinear stress-strain behavior has an extremely sharp transition point, defined by the magnitude of the prestrain. A theoretical model yields analytical expressions for the elastic and tangent moduli and the transition strain of the bilinear stress-strain relation, with quantitative correspondence to finite element analysis and experiments.

Protecting the properties of monolayer MoS 2 on silicon based substrates with an atomically thin buffer

DOE PAGES

Man, Michael K. L.; Deckoff-Jones, Skylar; Winchester, Andrew; ...

2016-02-12

Semiconducting 2D materials, like transition metal dichalcogenides (TMDs), have gained much attention for their potential in opto-electronic devices, valleytronic schemes, and semi-conducting to metallic phase engineering. However, like graphene and other atomically thin materials, they lose key properties when placed on a substrate like silicon, including quenching of photoluminescence, distorted crystalline structure, and rough surface morphology. The ability to protect these properties of monolayer TMDs, such as molybdenum disulfide (MoS 2), on standard Si-based substrates, will enable their use in opto-electronic devices and scientific investigations. Here we show that an atomically thin buffer layer of hexagonal-boron nitride (hBN) protects themore » range of key opto-electronic, structural, and morphological properties of monolayer MoS 2 on Si-based substrates. The hBN buffer restores sharp diffraction patterns, improves monolayer flatness by nearly two-orders of magnitude, and causes over an order of magnitude enhancement in photoluminescence, compared to bare Si and SiO 2 substrates. Lastly, our demonstration provides a way of integrating MoS 2 and other 2D monolayers onto standard Si-substrates, thus furthering their technological applications and scientific investigations.« less

Substrate Binding Drives Active-Site Closing of Human Blood Group B Galactosyltransferase as Revealed by Hot-Spot Labeling and NMR Spectroscopy Experiments.

PubMed

Weissbach, Sophie; Flügge, Friedemann; Peters, Thomas

2018-05-04

Crystallography has shown that human blood group A (GTA) and B (GTB) glycosyltransferases undergo transitions between "open", "semiclosed", and "closed" conformations upon substrate binding. However, the timescales of the corresponding conformational reorientations are unknown. Crystal structures show that the Trp and Met residues are located at "conformational hot spots" of the enzymes. Therefore, we utilized 15 N side-chain labeling of Trp residues and 13 C-methyl labeling of Met residues to study substrate-induced conformational transitions of GTB. Chemical-shift perturbations (CSPs) of Met and Trp residues in direct contact with substrate ligands reflect binding kinetics, whereas the CSPs of Met and Trp residues at remote sites reflect conformational changes of the enzyme upon substrate binding. Acceptor binding is fast on the chemical-shift timescale with rather small CSPs in the range of less than approximately 20 Hz. Donor binding matches the intermediate exchange regime to yield an estimate for exchange rate constants of approximately 200-300 Hz. Donor or acceptor binding to GTB saturated with acceptor or donor substrate, respectively, is slow (<10 Hz), as are coupled protein motions, reflecting mutual allosteric control of donor and acceptor binding. Remote CSPs suggest that substrate binding drives the enzyme into the closed state required for catalysis. These findings should contribute to better understanding of the mechanism of glycosyl transfer of GTA and GTB. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A comparison study of Co and Cu doped MgO diluted magnetic thin films

NASA Astrophysics Data System (ADS)

Sarıtaş, S.; ćakıcı, T.; Muǧlu, G. Merhan; Kundakcı, M.; Yıldırım, M.

2017-02-01

Transition metal-doped MgO diluted magnetic thin films are appropriate candidates for spintronic applications and designing magnetic devices and sensors. Therefore, MgO:Co and MgO:Cu films were deposited on glass substrates by Chemical Spray Pyrolysis (CSP) method different thin film deposition parameters. Deposited different transition metal doped MgO thin films were compared in terms of optic and structural properties. Comparison optic analysis of the films was investigated spectral absorption and transmittance measurements by UV-Vis double beam spectrophotometer technique. Comparison structural analysis of the thin films was examined by using XRD, Raman Analysis, SEM, EDX and AFM techniques. The transition metal-doped; MgO:Co and MgO:Cu thin films maybe have potential applications in spintronics and magnetic data storage.

Interfacial coupling and polarization of perovskite ABO3 heterostructures

NASA Astrophysics Data System (ADS)

Wu, Lijun; Wang, Zhen; Zhang, Bangmin; Yu, Liping; Chow, G. M.; Tao, Jing; Han, Myung-Geun; Guo, Hangwen; Chen, Lina; Plummer, E. W.; Zhang, Jiandi; Zhu, Yimei

2017-02-01

Interfaces with subtle difference in atomic and electronic structures in perovskite ABO3 heterostructures often yield intriguingly different properties, yet their exact roles remain elusive. In this article, we report an integrated study of unusual transport, magnetic, and structural properties of Pr0.67Sr0.33MnO3 (PSMO) films and La0.67Sr0.33MnO3 (LSMO) films of various thicknesses on SrTiO3 (STO) substrate. In particular, using atomically resolved imaging and electron energy-loss spectroscopy (EELS), we measured interface related local lattice distortion, BO6 octahedral rotation and cation-anion displacement induced polarization. In the very thin PSMO film, an unexpected interface-induced ferromagnetic polaronic insulator phase was observed during the cubic-to-tetragonal phase transition of the substrate STO, due to the enhanced electron-phonon interaction and atomic disorder in the film. On the other hand, for the very thin LSMO films we observed a remarkably deep polarization in non-ferroelectric STO substrate near the interface. Combining the experimental results with first principles calculations, we propose that the observed deep polarization is induced by an electric field originating from oxygen vacancies that extend beyond a dozen unit-cells from the interface, thus providing important evidence of the role of defects in the emergent interface properties of transition metal oxides.

Mechanistic Basis for High Stereoselectivity and Broad Substrate Scope in the (salen)Co(III)-Catalyzed Hydrolytic Kinetic Resolution

PubMed Central

Ford, David D.; Nielsen, Lars P. C.; Zuend, Stephan J.; Jacobsen, Eric N.

2013-01-01

In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic, rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR. PMID:24041239

Mechanistic basis for high stereoselectivity and broad substrate scope in the (salen)Co(III)-catalyzed hydrolytic kinetic resolution.

PubMed

Ford, David D; Nielsen, Lars P C; Zuend, Stephan J; Musgrave, Charles B; Jacobsen, Eric N

2013-10-16

In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR.

Edge Delamination of Monolayer Transition Metal Dichalcogenides.

PubMed

Ly, Thuc Hue; Yun, Seok Joon; Thi, Quoc Huy; Zhao, Jiong

2017-07-25

Delamination of thin films from the supportive substrates is a critical issue within the thin film industry. The emergent two-dimensional, atomic layered materials, including transition metal dichalcogenides, are highly flexible; thus buckles and wrinkles can be easily generated and play vital roles in the corresponding physical properties. Here we introduce one kind of patterned buckling behavior caused by the delamination from a substrate initiated at the edges of the chemical vapor deposition synthesized monolayer transition metal dichalcogenides, led by thermal expansion mismatch. The atomic force microscopy and optical characterizations clearly showed the puckered structures associated with the strain, whereas the transmission electron microscopy revealed the special sawtooth-shaped edges, which break the geometrical symmetry for the buckling behavior of hexagonal samples. The condition of the edge delamination is in accordance with the fracture behavior of thin film interfaces. This edge delamination and buckling process is universal for most ultrathin two-dimensional materials, which requires more attention in various future applications.

Fabrication of large tungsten structures by chemical vapor deposition

NASA Technical Reports Server (NTRS)

Kahle, V. E.; Lewis, W. J.; Stubbs, V. R.

1971-01-01

Process is accomplished by reducing tungsten hexafluoride with hydrogen. Metallic tungsten of essentially 100 percent purity and density is produced and built up as dense deposit on heated mandrel assembly. Process variations are building up, sealing or bonding refractory metals at temperatures below transition temperatures of base metal substrates.

Low energy electron catalyst: the electronic origin of catalytic strategies.

PubMed

Davis, Daly; Sajeev, Y

2016-10-12

Using a low energy electron (LEE) as a catalyst, the electronic origin of the catalytic strategies corresponding to substrate selectivity, reaction specificity and reaction rate enhancement is investigated for a reversible unimolecular elementary reaction. An electronic energy complementarity between the catalyst and the substrate molecule is the origin of substrate selectivity and reaction specificity. The electronic energy complementarity is induced by tuning the electronic energy of the catalyst. The energy complementarity maximizes the binding forces between the catalyst and the molecule. Consequently, a new electronically metastable high-energy reactant state and a corresponding new low barrier reaction path are resonantly created for a specific reaction of the substrate through the formation of a catalyst-substrate transient adduct. The LEE catalysis also reveals a fundamental structure-energy correspondence in the formation of the catalyst-substrate transient adduct. Since the energy complementarities corresponding to the substrate molecules of the forward and the backward steps of the reversible reactions are not the same due to their structural differences, the LEE catalyst exhibits a unique one-way catalytic strategy, i.e., the LEE catalyst favors the reversible reaction more effectively in one direction. A characteristic stronger binding of the catalyst to the transition state of the reaction than in the initial reactant state and the final product state is the molecular origin of barrier lowering.

Growth and phase transformations of Ir on Ge(111)

NASA Astrophysics Data System (ADS)

Mullet, C. H.; Stenger, B. H.; Durand, A. M.; Morad, J. A.; Sato, Y.; Poppenheimer, E. C.; Chiang, S.

2017-12-01

The growth of Ir on Ge(111) as a function of temperature between 23 °C and 820 °C is characterized with low energy electron microscopy (LEEM), low energy electron diffraction (LEED), scanning tunneling microscopy (STM), and x-ray photoemission spectroscopy (XPS). Deposition onto a substrate at 350 °C revealed a novel growth mode consisting of multilayer Ir islands with (√3 × √3)R30° (abbreviated as √3) structure interconnected by ;bridges; of single-layer Ir several atoms wide. For deposition onto substrates above 500 °C, the √3 Ir phase grows with dendritic morphology, and substrate step bunches act as barriers to √3 Ir growth. LEEM images showed Stranski-Krastanov growth for 650-820 °C: after the √3 phase covers the surface, corresponding to 2 monolayers (ML) Ir coverage, multilayer hexagonal-shaped Ir islands form, surrounded by regions of IrGe alloy. Hexagonal-shaped Ir islands also formed upon heating 1.2 ML of √3 Ir beyond 830 °C, which resulted in the elimination of √3 structure from the surface. The transformation from √3 to (1 × 1) structure upon heating to 830 °C was an irreversible surface phase transition. Annealing > 2.0 ML of Ir in the √3 phase above the 830 °C disorder temperature, followed by cooling, produced a (3 × 1) structure. Subsequent heating and cooling through 830 °C give evidence for a reversible (3 × 1) to (1 × 1) phase transition.

Studies of lysine cyclodeaminase from Streptomyces pristinaespiralis: Insights into the complex transition NAD+ state.

PubMed

Ying, Hanxiao; Wang, Jing; Shi, Ting; Zhao, Yilei; Wang, Xin; Ouyang, Pingkai; Chen, Kequan

2018-01-01

Lysine cyclodeaminase (LCD) catalyzes the piperidine ring formation in macrolide-pipecolate natural products metabolic pathways from a lysine substrate through a combination of cyclization and deamination. This enzyme belongs to a unique enzyme class, which uses NAD + as the catalytic prosthetic group instead of as the co-substrate. To understand the molecular details of NAD + functions in lysine cyclodeaminase, we have determined four ternary crystal structure complexes of LCD-NAD + with pipecolic acid (LCD-PA), lysine (LCD-LYS), and an intermediate (LCD-INT) as ligands at 2.26-, 2.00-, 2.17- and 1.80 Å resolutions, respectively. By combining computational studies, a NAD + -mediated "gate keeper" function involving NAD + /NADH and Arg49 that control the binding and entry of the ligand lysine was revealed, confirming the critical roles of NAD + in the substrate access process. Further, in the gate opening form, a substrate delivery tunnel between ε-carboxyl moiety of Glu264 and the α-carboxyl moiety of Asp236 was observed through a comparison of four structure complexes. The LCD structure details including NAD + -mediated "gate keeper" and substrate tunnel may assist in the exploration the NAD + function in this unique enzyme class, and in regulation of macrolide-pipecolate natural product synthesis. Copyright © 2017 Elsevier Inc. All rights reserved.

Tracking polaron generation in electrochemically doped polyaniline thin films

NASA Astrophysics Data System (ADS)

Kalagi, S. S.; Patil, P. S.

2018-04-01

Electrochemically deposited polyaniline films on ITO substrates have been studied for their optical properties. π-π*transitions inducing the formation of polarons and bipolarons have been studied from the optical spectra. The generation of these quasiparticles and the corresponding quantum of energy stored has been analysed and calculated from the experimental data. The evolution of polaron with increased levels of protonation has been identified and the necessary energy required for the transitions have been explained with the help of band structure diagram.

Shape transition of endotaxial islands growth from kinetically constrained to equilibrium regimes

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

Li, Zhi-Peng, E-mail: LI.Zhipeng@nims.go.jp; Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044; Tok, Engsoon

2013-09-01

Graphical abstract: - Highlights: • All Fe{sub 13}Ge{sub 8} islands will grow into Ge(0 0 1) substrate at temperatures from 350 to 675 °C. • Shape transition occurred from kinetically constrained to equilibrium regime. • All endotaxial islands can be clarified into two types. • The mechanisms of endotaxial growth and shape transition have been rationalized. - Abstract: A comprehensive study of Fe grown on Ge(0 0 1) substrates has been conducted at elevated temperatures, ranging from 350 to 675 °C. All iron germinide islands, with the same Fe{sub 13}Ge{sub 8} phase, grow into the Ge substrate with the samemore » epitaxial relationship. Shape transition occurs from small square islands (low temperatures), to elongated orthogonal islands or orthogonal nanowires (intermediate temperatures), and then finally to large square orthogonal islands (high temperatures). According to both transmission electron microscopy (TEM) and atomic force microscopy (AFM) investigations, all islands can be defined as either type-I or type-II. Type-I islands usually form at kinetically constrained growth regimes, like truncated pyramids. Type-II islands usually appear at equilibrium growth regimes forming a dome-like shape. Based on a simple semi-quantitative model, type-II islands have a lower total energy per volume than type-I, which is considered as the dominant mechanism for this type of shape transition. Moreover, this study not only elucidates details of endotaxial growth in the Fe–Ge system, but also suggests the possibility of controlled fabrication of temperature-dependent nanostructures, especially in materials with dissimilar crystal structures.« less

Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state.

PubMed

Gu, Jiali; Liu, Min; Guo, Fei; Xie, Wenping; Lu, Wenqiang; Ye, Lidan; Chen, Zhirong; Yuan, Shenfeng; Yu, Hongwei

2014-02-05

Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k(cat)/K(m)) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme. Copyright © 2013 Elsevier Inc. All rights reserved.

Effects of a Ta interlayer on the phase transition of TiSi2 on Si(111)

NASA Astrophysics Data System (ADS)

Jeon, Hyeongtag; Jung, Bokhee; Kim, Young Do; Yang, Woochul; Nemanich, R. J.

2000-09-01

This study examines the effects of a thin Ta interlayer on the formation of TiSi2 on Si(111) substrate. The Ta interlayer was introduced by depositing Ta and Ti films sequentially on an atomically clean Si(111) substrate in an ultrahigh vacuum (UHV) system. Samples of 100 Å Ti with 5 and 10 Å Ta interlayers were compared to similar structures without an interlayer. After deposition, the substrates were annealed for 10 min, in situ, at temperatures between 500 and 750 °C in 50 °C increments. The TiSi2 formation with and without the Ta interlayer was analyzed with an X-ray diffractometer, Auger electron spectroscopy (AES), Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and a four-point probe. The AES analysis data showed a 1:2 ratio of Ti:Si in the Ti-silicide layer and indicated that the Ta layer remained at the interface between TiSi2 and the Si(111) substrate. The C 49-C 54 TiSi2 phase transition temperature was lowered by ˜200 °C. The C 49-C 54 TiSi2 phase transition temperature was 550 °C for the samples with a Ta interlayer and was 750 °C for the samples with no Ta interlayer. The sheet resistance of the Ta interlayered Ti silicide showed lower values of resistivity at low temperatures which indicated the change in phase transition temperature. The C 54 TiSi2 displayed different crystal orientation when the Ta interlayer was employed. The SEM and TEM micrographs showed that the TiSi2 with a Ta interlayer significantly suppressed the tendency to islanding and surface agglomeration.

Supramolecular control of transition metal complexes in water by a hydrophobic cavity: a bio-inspired strategy.

PubMed

Bistri, Olivia; Reinaud, Olivia

2015-03-14

Supramolecular chemistry in water is a very challenging research area. In biology, water is the universal solvent where transition metal ions play major roles in molecular recognition and catalysis. In enzymes, it participates in substrate binding and/or activation in the heart of a pocket defined by the folded protein. The association of a hydrophobic cavity with a transition metal ion is thus a very appealing strategy for controlling the metal ion properties in the very competitive water solvent. Various systems based on intrinsically water-soluble macrocyclic structures such as cyclodextrins, cucurbituryls, and metallo-cages have been reported. Others use calixarenes and resorcinarenes functionalized with hydrophilic substituents. One approach for connecting a metal complex to these cavities is to graft a ligand for metal ion binding at their edge. Early work with cyclodextrins has shown Michaelis-Menten like catalysis displaying enhanced kinetics and substrate-selectivity. Remarkable examples of regio- and stereo-selective transformation of substrates have been reported as well. Dynamic two-phase systems for transition metal catalysis have also been developed. They rely on either water-transfer of the metal complex through ligand embedment or synergistic coordination of a metal ion and substrate hosting. Another strategy consists in using metallo-cages, which provide a well-defined hydrophobic space, to stabilize metal complexes in water. When the cages can host simultaneously a substrate and a reactive metal complex, size- and regio-selective catalysis was obtained. Finally, construction of a polydentate coordination site closely interlocked with a calixarene or resorcinarene macrocycle has been shown to be a very fruitful strategy for obtaining metal complexes with remarkable hosting properties. For each of these systems, the synergism resulting from the biomimetic association of a hydrophobic cavity and a metal ion is discussed within the objective of developing new tools for either selective molecular recognition (with analytical perspectives) or performant catalysis, in water.

Empty substrate integrated waveguide technology for E plane high-frequency and high-performance circuits

NASA Astrophysics Data System (ADS)

Belenguer, Angel; Cano, Juan Luis; Esteban, Héctor; Artal, Eduardo; Boria, Vicente E.

2017-01-01

Substrate integrated circuits (SIC) have attracted much attention in the last years because of their great potential of low cost, easy manufacturing, integration in a circuit board, and higher-quality factor than planar circuits. A first suite of SIC where the waves propagate through dielectric have been first developed, based on the well-known substrate integrated waveguide (SIW) and related technological implementations. One step further has been made with a new suite of empty substrate integrated waveguides, where the waves propagate through air, thus reducing the associated losses. This is the case of the empty substrate integrated waveguide (ESIW) or the air-filled substrate integrated waveguide (air-filled SIW). However, all these SIC are H plane structures, so classical H plane solutions in rectangular waveguides have already been mapped to most of these new SIC. In this paper a novel E plane empty substrate integrated waveguide (ESIW-E) is presented. This structure allows to easily map classical E plane solutions in rectangular waveguide to this new substrate integrated solution. It is similar to the ESIW, although more layers are needed to build the structure. A wideband transition (covering the frequency range between 33 GHz and 50 GHz) from microstrip to ESIW-E is designed and manufactured. Measurements are successfully compared with simulation, proving the validity of this new SIC. A broadband high-frequency phase shifter (for operation from 35 GHz to 47 GHz) is successfully implemented in ESIW-E, thus proving the good performance of this new SIC in a practical application.

Porous silicon-VO{sub 2} based hybrids as possible optical temperature sensor: Wavelength-dependent optical switching from visible to near-infrared range

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

Antunez, E. E.; Salazar-Kuri, U.; Estevez, J. O.

Morphological properties of thermochromic VO{sub 2}—porous silicon based hybrids reveal the growth of well-crystalized nanometer-scale features of VO{sub 2} as compared with typical submicron granular structure obtained in thin films deposited on flat substrates. Structural characterization performed as a function of temperature via grazing incidence X-ray diffraction and micro-Raman demonstrate reversible semiconductor-metal transition of the hybrid, changing from a low-temperature monoclinic VO{sub 2}(M) to a high-temperature tetragonal rutile VO{sub 2}(R) crystalline structure, coupled with a decrease in phase transition temperature. Effective optical response studied in terms of red/blue shift of the reflectance spectra results in a wavelength-dependent optical switching withmore » temperature. As compared to VO{sub 2} film over crystalline silicon substrate, the hybrid structure is found to demonstrate up to 3-fold increase in the change of reflectivity with temperature, an enlarged hysteresis loop and a wider operational window for its potential application as an optical temperature sensor. Such silicon based hybrids represent an exciting class of functional materials to display thermally triggered optical switching culminated by the characteristics of each of the constituent blocks as well as device compatibility with standard integrated circuit technology.« less

Role of surface energy on the morphology and optical properties of GaP micro & nano structures grown on polar and non-polar substrates

NASA Astrophysics Data System (ADS)

Roychowdhury, R.; Kumar, Shailendra; Wadikar, A.; Mukherjee, C.; Rajiv, K.; Sharma, T. K.; Dixit, V. K.

2017-10-01

Role of surface energy on the morphology, crystalline quality, electronic structure and optical properties of GaP layer grown on Si (001), Si (111), Ge (111) and GaAs (001) is investigated. GaP layers are grown on four different substrates under identical growth kinetics by metal organic vapour phase epitaxy. The atomic force microscopy images show that GaP layer completely covers the surface of GaAs substrate. On the other hand, the surfaces of Si (001), Si (111), Ge (111) substrates are partially covered with crystallographically morphed GaP island type micro and nano-structures. Origin of these crystallographically morphed GaP island is explained by the theoretical calculation of surface energy of the layer and corresponding substrates respectively. The nature of GaP island type micro and nano-structures and layers are single crystalline with existence of rotational twins on Si and Ge (111) substrates which is confirmed by the phi, omega and omega/2theta scans of high resolution x-ray diffraction. The electronic valence band offsets between the GaP and substrates have been determined from the valence band spectra of ultraviolet photoelectron spectroscopy. The valence electron plasmon of GaP are investigated by studying the energy values of Ga (3d) core level along with loss peaks in the energy dependent photoelectron spectra. The peak observed within the range of 3-6 eV from the Ga (3d) core level in the photoelectron spectra are associated to inter band transitions as their energy values are estimated from the pseudo dielectric function by the spectroscopic ellipsometry.

Surface segregation on Fe3%Si0.04%VC(100) single crystal surfaces

NASA Astrophysics Data System (ADS)

Uebing, C.; Viefhaus, H.

1990-10-01

Surface segregation phenomena on (100) oriented single crystal surfaces of the ferritic Fe-3%Si-0.04%V-C alloy were investigated by AES and LEED. At temperatures below 635 °C vanadium and carbon cosegregation is observed after prolonged heating. At thermodynamic equilibrium the substrate surface is saturated with the binary surface compound VC. The two-dimensional VC is epitaxially arranged on the substrate surface as indicated by LEED investigations. Its structure corresponds to the (100) plane of the three-dimensional VC with rocksalt structure. Sharp above 635 °C the surface compound VC is dissolved into the bulk. At higher temperatures the substrate surface is covered with segregated silicon forming a c(2 × 2) structure. This surface phase transition is reversible. Because of the low concentration and slow diffusion of vanadium, non-equilibrium surface states are formed as intermediates upon segregation of silicon and carbon. Below 500 °C a disordered graphite layer with a characteristical asymmetrical C Auger peak is observed on the substrate surface. Above 500 °C carbon segregation leads to the formation of an ordered c(2 × 2) structure with a symmetrical C Auger peak being characteristic for carbidic or atomically adsorbed species. At increasing temperatures silicon segregation takes place leading to a c(2 × 2) structure. Between silicon and carbon site competition is effective.

Electron crystallography reveals that substrate release from the PTS IIC glucose transporter is coupled to a subtle conformational change.

PubMed

Kalbermatter, David; Chiu, Po-Lin; Jeckelmann, Jean-Marc; Ucurum, Zöhre; Walz, Thomas; Fotiadis, Dimitrios

2017-07-01

The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a structurally and functionally complex system that mediates sugar uptake in bacteria. Besides several soluble subunits, the glucose-specific PTS includes the integral membrane protein IICB that couples the transmembrane transport of glucose to its phosphorylation. Here, we used electron crystallography of sugar-embedded tubular crystals of the glucose-specific IIC transport domain from Escherichia coli (ecIIC glc ) to visualize the structure of the transporter in the presence and absence of its substrate. Using an in vivo transport assay and binding competition experiments, we first established that, while it transports d-glucose, ecIIC glc does not bind l-glucose. We then determined the projection structure of ecIIC glc from tubular crystals embedded in d- and l-glucose and found a subtle conformational change. From comparison of the ecIIC glc projection maps with crystal structures of other IIC transporters, we can deduce that the transporter adopts an inward-facing conformation, and that the maps in the presence and absence of the substrate reflect the transporter before and after release of the transported glucose into the cytoplasm. The transition associated with substrate release appears to require a subtle structural rearrangement in the region that includes hairpin 1. Copyright © 2017 Elsevier Inc. All rights reserved.

Controlling major cellular processes of human mesenchymal stem cells using microwell structures.

PubMed

Xu, Xun; Wang, Weiwei; Kratz, Karl; Fang, Liang; Li, Zhengdong; Kurtz, Andreas; Ma, Nan; Lendlein, Andreas

2014-12-01

Directing stem cells towards a desired location and function by utilizing the structural cues of biomaterials is a promising approach for inducing effective tissue regeneration. Here, the cellular response of human adipose-derived mesenchymal stem cells (hADSCs) to structural signals from microstructured substrates comprising arrays of square-shaped or round-shaped microwells is explored as a transitional model between 2D and 3D systems. Microwells with a side length/diameter of 50 μm show advantages over 10 μm and 25 μm microwells for accommodating hADSCs within single microwells rather than in the inter-microwell area. The cell morphologies are three-dimensionally modulated by the microwell structure due to differences in focal adhesion and consequent alterations of the cytoskeleton. In contrast to the substrate with 50 μm round-shaped microwells, the substrate with 50 μm square-shaped microwells promotes the proliferation and osteogenic differentiation potential of hADSCs but reduces the cell migration velocity and distance. Such microwell shape-dependent modulatory effects are highly associated with Rho/ROCK signaling. Following ROCK inhibition, the differences in migration, proliferation, and osteogenesis between cells on different substrates are diminished. These results highlight the possibility to control stem cell functions through the use of structured microwells combined with the manipulation of Rho/ROCK signaling. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural and physical properties of InAlAs quantum dots grown on GaAs

NASA Astrophysics Data System (ADS)

Vasile, B. S.; Daly, A. Ben; Craciun, D.; Alexandrou, I.; Lazar, S.; Lemaître, A.; Maaref, M. A.; Iacomi, F.; Craciun, V.

2018-04-01

Quantum dots (QDs), which have particular physical properties due to the three dimensions confinement effect, could be used in many advanced optoelectronic applications. We investigated the properties of InAlAs/AlGaAs QDs grown by molecular beam epitaxy on GaAs/Al0.5Ga0.5As layers. The optical properties of QDs were studied by low-temperature photoluminescence (PL). Two bandgap transitions corresponding to the X-Sh and X-Ph energy structure were observed. The QDs structure was investigated using high-resolution X-ray diffraction (HRXRD) and high-resolution transmission electron microscopy (HRTEM). HRXRD investigations showed that the layers grew epitaxially on the substrate, with no relaxation. HRTEM investigations confirmed the epitaxial nature of the grown structures. In addition, it was revealed that the In atoms aggregated in some prismatic regions, forming areas of high In concentration, that were still in perfect registry with the substrate.

State transitions and feedback mechanisms control hydrology in the constructed catchment ´Chicken Creeḱ

NASA Astrophysics Data System (ADS)

Schaaf, Wolfgang; Gerwin, Werner; Hinz, Christoph; Zaplata, Markus

2016-04-01

Landscapes and ecosystems are complex systems with many feedback mechanisms acting between the various abiotic and biotic components. The knowledge about these interacting processes is mainly derived from mature ecosystems. The initial development of ecosystem complexity may involve state transitions following catastrophic shifts, disturbances or transgression of thresholds. The Chicken Creek catchment was constructed in 2005 in the mining area of Lusatia/Germany to study processes and feedback mechanisms during ecosystem evolution. The hillslope-shaped 6 ha site has defined boundary conditions and well-documented inner structures. The dominating substrate above the underlying clay layer is Pleistocene sandy material representing mainly the lower C horizon of the former landscape. Since 2005, the unrestricted, unmanaged development of the catchment was intensively monitored. During the ten years since then, we observed characteristic state transitions in catchment functioning driven by feedbacks between original substrate properties, surface structures, soil development and vegetation succession. Whereas surface runoff induced by surface crusting and infiltration dominated catchment hydrology in the first years, the impact of vegetation on hydrological pathways and groundwater levels became more and more evident during the last years. Discharge from the catchment changed from episodic events driven by precipitation and surface runoff to groundwater driven. This general picture is overlain by spatial patterns and single episodic events of external drivers. The scientific value of the Chicken Creek site with known boundary conditions and structure information could help in disentangling general feedback mechanisms between hydrologic, pedogenic, biological and geomorphological processes as well as a in gaining a more integrative view of succession and its drivers during the transition from initial, less complex systems to more mature ecosystems. Long-term time series of data are a key for a better understanding of these processes and the effects on ecosystem resilience and self-organization.

Bandgap engineering in van der Waals heterostructures of blue phosphorene and MoS{sub 2}: A first principles calculation

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

Zhang, Z.Y.; Si, M.S., E-mail: sims@lzu.edu.cn; Peng, S.L.

2015-11-15

Blue phosphorene (BP) was theoretically predicted to be thermally stable recently. Considering its similar in-layer hexagonal lattice to MoS{sub 2}, MoS{sub 2} could be an appropriate substrate to grow BP in experiments. In this work, the van der Waals (vdW) heterostructures are constructed by stacking BP on top of MoS{sub 2}. The thermal stability and electronic structures are evaluated based on first principles calculations with vdW-corrected exchange-correlation functional. The formation of the heterostructures is demonstrated to be exothermic and the most stable stacking configuration is confirmed. The heterostructures BP/MoS{sub 2} preserve both the properties of BP and MoS{sub 2} butmore » exhibit relatively narrower bandgaps due to the interlayer coupling effect. The band structures can be further engineered by applying external electric fields. An indirect–direct bandgap transition in bilayer BP/MoS{sub 2} is demonstrated to be controlled by the symmetry property of the built-in electric dipole fields. - Graphical abstract: An indirect-direct band gap transition occurs in van der Waals heterostructure of MoS{sub 2}/BP under external electric fields which is demonstrated to be controlled by the symmetry of the built-in electric dipole fields. - Highlights: • The stacking of heterostructures of BP/MoS{sub 2} is demonstrated to be exothermic. • This suggests that it is possible to grow BP using MoS{sub 2} as the substrate. • The band structures of the heterostructures are exploited. • It realizes an indirect–direct gap transition under external electric fields. • The symmetry of the built-in electric dipole fields controls such gap transition.« less

The optical properties and photocatalytic activity of CdS-ZnS-TiO{sub 2}/Graphite for isopropanol degradation under visible light irradiation

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

Rahmawati, Fitria, E-mail: fitria@mipa.uns.ac.id; Wulandari, Rini, E-mail: riniwulandari55@yahoo.com; Murni, Irvinna M., E-mail: irvinna-mutiara@yahoo.com

2016-02-08

This research prepared a photocatalyst tablet of CdS-ZnS-TiO{sub 2} on a graphite substrate. The synthesis was conducted through chemical bath deposition method. The graphite substrate used was a waste graphite rod from primary batteries. The aims of this research are studying the crystal structure, the optical properties and the photocatalytic activity of the prepared material. The photocatalytic activity was determined through isopropanol degradation. The result shows that the TiO{sub 2}/Graphite provide direct transition gap energy at 2.91 eV and an indirect transition gap energy at 3.21 eV. Deposition of CdS-ZnS changed the direct transition gap energy to 3.01 eV andmore » the indirect transition gap energy to 3.22 eV. Isopropanol degradation with the prepared catalyst produced new peaks at 223-224 nm and 265-266 nm confirming the production of acetone. The degradation follows first order with rate constant of 2.4 × 10{sup −2} min{sup −1}.« less

LaAlO3: A substrate material with unusual ferroelastic properties

NASA Astrophysics Data System (ADS)

Kustov, S.; Liubimova, Iu.; Salje, E. K. H.

2018-01-01

Twin boundary dynamics in LaAlO3 is associated with non-linear anelasticity. Ultrasonic studies of non-linear twin boundary dynamics between 80 and 520 K show that cooling substrates from temperatures near the ferroelastic transition at 813 K generate three characteristic thermal regimes with different non-linear dynamics. Twin boundaries are initially highly mobile. Anelastic strain amplitudes versus stress are power law distributed with an exponent of 2.5. No de-pinning was found down to elastic strain amplitudes of ɛ0 ˜ 10-7. The power law is gradually replaced between 370 K and 280 K by few large singularities (jerks) due to massive rearrangements of the domain structure for ɛ0 larger than ca. 5 × 10-5. At lower temperatures, the domain structure is pinned with well-defined thresholds for de-pinning. The de-pinning is not accompanied by global rearrangements of twin patterns below room temperature. Unexpectedly, the low-temperature critical de-pinning strain amplitude decreases with decreasing temperature, which may indicate an additional, so far unknown phase transition near 40 K.

Structure of Irreversibly Adsorbed Star Polymers

NASA Astrophysics Data System (ADS)

Akgun, Bulent; Aykan, Meryem Seyma; Canavar, Seda; Satija, Sushil K.; Uhrig, David; Hong, Kunlun

Formation of irreversibly adsorbed polymer chains on solid substrates have a huge impact on the wetting, glass transition, aging and polymer chain mobility in thin films. In recent years there has been many reports on the formation, kinetics and dynamics of these layers formed by linear homopolymers. Recent studies showed that by varying the number of polymer arms and arm molecular weight one can tune the glass transition temperature of thin polymer films. Using polymer architecture as a tool, the behavior of thin films can be tuned between the behavior of linear chains and soft colloids. We have studied the effect of polymer chain architecture on the structure of dead layer using X-ray reflectivity (XR) and atomic force microscopy. Layer thicknesses and densities of flattened and loosely adsorbed chains has been measured for linear, 4-arm, and 8-arm star polymers with identical total molecular weight as a function of substrate surface energy, annealing temperature and annealing time. Star polymers have been synthesized using anionic polymerization. XR measurements showed that 8-arm star PS molecules form the densest and the thickest dead layers among these three molecules.

Method of preparing electrodes with porous current collector structures and solid reactants for secondary electrochemical cells

DOEpatents

Gay, Eddie C.; Martino, Fredric J.

1976-01-01

Particulate electrode reactants, for instance transition metal sulfides for the positive electrodes and lithium alloys for the negative electrodes, are vibratorily compacted into porous, electrically conductive structures. Structures of high porosity support sufficient reactant material to provide high cell capacity per unit weight while serving as an electrical current collector to improve the utilization of reactant materials. Pore sizes of the structure and particle sizes of the reactant material are selected to permit uniform vibratory loading of the substrate without settling of the reactant material during cycling.

Strain driven sequential magnetic transitions in strained GdTiO3 on compressive substrates: a first-principles study

NASA Astrophysics Data System (ADS)

Yang, Li-Juan; Weng, Ya-Kui; Zhang, Hui-Min; Dong, Shuai

2014-11-01

The compressive strain effect on the magnetic ground state and electronic structure of strained GdTiO3 has been studied using the first-principles method. Unlike the cases of congeneric YTiO3 and LaTiO3, both of which become the A-type antiferromagnetism on the (0 0 1) LaAlO3 substrate despite their contrastive magnetism, the ground state of strained GdTiO3 on the LaAlO3 substrate changes from the original ferromagnetism to a G-type antiferromagnetim, instead of the A-type one although Gd3+ is between Y3+ and La3+. It is only when the in-plane compressive strain is large enough, e.g. on the (0 0 1) YAlO3 substrate, that the ground state finally becomes the A-type. The band structure calculation shows that the compressive strained GdTiO3 remains insulating, although the band gap changes a little in the strained GdTiO3.

Strain-engineered growth of two-dimensional materials

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

Ahn, Geun Ho; Amani, Matin; Rasool, Haider

The application of strain to semiconductors allows for controlled modification of their band structure. This principle is employed for the manufacturing of devices ranging from high-performance transistors to solid-state lasers. Traditionally, strain is typically achieved via growth on lattice-mismatched substrates. For two-dimensional (2D) semiconductors, this is not feasible as they typically do not interact epitaxially with the substrate. Here in this paper, we demonstrate controlled strain engineering of 2D semiconductors during synthesis by utilizing the thermal coefficient of expansion mismatch between the substrate and semiconductor. Using WSe 2 as a model system, we demonstrate stable built-in strains ranging from 1%more » tensile to 0.2% compressive on substrates with different thermal coefficient of expansion. Consequently, we observe a dramatic modulation of the band structure, manifested by a strain-driven indirect-to-direct bandgap transition and brightening of the dark exciton in bilayer and monolayer WSe 2, respectively. The growth method developed here should enable flexibility in design of more sophisticated devices based on 2D materials.« less

Strain-engineered growth of two-dimensional materials

DOE PAGES

Ahn, Geun Ho; Amani, Matin; Rasool, Haider; ...

2017-09-20

The application of strain to semiconductors allows for controlled modification of their band structure. This principle is employed for the manufacturing of devices ranging from high-performance transistors to solid-state lasers. Traditionally, strain is typically achieved via growth on lattice-mismatched substrates. For two-dimensional (2D) semiconductors, this is not feasible as they typically do not interact epitaxially with the substrate. Here in this paper, we demonstrate controlled strain engineering of 2D semiconductors during synthesis by utilizing the thermal coefficient of expansion mismatch between the substrate and semiconductor. Using WSe 2 as a model system, we demonstrate stable built-in strains ranging from 1%more » tensile to 0.2% compressive on substrates with different thermal coefficient of expansion. Consequently, we observe a dramatic modulation of the band structure, manifested by a strain-driven indirect-to-direct bandgap transition and brightening of the dark exciton in bilayer and monolayer WSe 2, respectively. The growth method developed here should enable flexibility in design of more sophisticated devices based on 2D materials.« less

Microscopic aspects of wetting using classical density functional theory

NASA Astrophysics Data System (ADS)

Yatsyshin, P.; Durán-Olivencia, M.-A.; Kalliadasis, S.

2018-07-01

Wetting is a rather efficient mechanism for nucleation of a phase (typically liquid) on the interface between two other phases (typically solid and gas). In many experimentally accessible cases of wetting, the interplay between the substrate structure, and the fluid–fluid and fluid–substrate intermolecular interactions brings about an entire ‘zoo’ of possible fluid configurations, such as liquid films with a thickness of a few nanometers, liquid nanodrops and liquid bridges. These fluid configurations are often associated with phase transitions occurring at the solid–gas interface and at lengths of just several molecular diameters away from the substrate. In this special issue article, we demonstrate how a fully microscopic classical density-functional framework can be applied to the efficient, rational and systematic exploration of the rich phase space of wetting phenomena. We consider a number of model prototype systems such as wetting on a planar wall, a chemically patterned wall and a wedge. Through density-functional computations we demonstrate that for these simply structured substrates the behaviour of the solid–gas interface is already highly complex and non-trivial.

Spatially resolved mapping of electrical conductivity across individual domain (grain) boundaries in graphene.

PubMed

Clark, Kendal W; Zhang, X-G; Vlassiouk, Ivan V; He, Guowei; Feenstra, Randall M; Li, An-Ping

2013-09-24

All large-scale graphene films contain extended topological defects dividing graphene into domains or grains. Here, we spatially map electronic transport near specific domain and grain boundaries in both epitaxial graphene grown on SiC and CVD graphene on Cu subsequently transferred to a SiO2 substrate, with one-to-one correspondence to boundary structures. Boundaries coinciding with the substrate step on SiC exhibit a significant potential barrier for electron transport of epitaxial graphene due to the reduced charge transfer from the substrate near the step edge. Moreover, monolayer-bilayer boundaries exhibit a high resistance that can change depending on the height of substrate step coinciding at the boundary. In CVD graphene, the resistance of a grain boundary changes with the width of the disordered transition region between adjacent grains. A quantitative modeling of boundary resistance reveals the increased electron Fermi wave vector within the boundary region, possibly due to boundary induced charge density variation. Understanding how resistance change with domain (grain) boundary structure in graphene is a crucial first step for controlled engineering of defects in large-scale graphene films.

Phase stability tuning in the NbxZr1-xN thin-film system for large stacking fault density and enhanced mechanical strength

NASA Astrophysics Data System (ADS)

Joelsson, T.; Hultman, L.; Hugosson, H. W.; Molina-Aldareguia, J. M.

2005-03-01

The phase stability of hexagonal WC-structure and cubic NaCl-structure 4d transition metal nitrides was calculated using first-principles density functional theory. It is predicted that there is a multiphase or polytypic region for the 4d transition metal nitrides with a valence electron concentration around 9.5 to 9.7 per formula unit. For verification, epitaxial NbxZr1-xN (0⩽x⩽1) was grown by reactive magnetron sputter deposition on MgO(001) substrates and analyzed with transmission electron microscopy (TEM) and x-ray diffraction. The defects observed in the films were threading dislocations due to nucleation and growth on the lattice-mismatched substrate and planar defects (stacking faults) parallel to the substrate surface. The highest defect density was found at the x =0.5 composition. The nanoindentation hardness of the films varied between 21GPa for the binary nitrides, and 26GPa for Nb0.5Zr0.5N. Unlike the cubic binary nitrides, no slip on the preferred ⟨11¯0⟩{110} slip system was observed. The increase in hardness is attributed to the increase in defect density at x =0.5, as the defects act as obstacles for dislocation glide during deformation. The findings present routes for the design of wear-resistant nitride coatings by phase stability tuning.

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release

PubMed Central

Koldsø, Heidi; Noer, Pernille; Grouleff, Julie; Autzen, Henriette Elisabeth; Sinning, Steffen; Schiøtt, Birgit

2011-01-01

Monoamine transporters are responsible for termination of synaptic signaling and are involved in depression, control of appetite, and anxiety amongst other neurological processes. Despite extensive efforts, the structures of the monoamine transporters and the transport mechanism of ions and substrates are still largely unknown. Structural knowledge of the human serotonin transporter (hSERT) is much awaited for understanding the mechanistic details of substrate translocation and binding of antidepressants and drugs of abuse. The publication of the crystal structure of the homologous leucine transporter has resulted in homology models of the monoamine transporters. Here we present extended molecular dynamics simulations of an experimentally supported homology model of hSERT with and without the natural substrate yielding a total of more than 1.5 µs of simulation of the protein dimer. The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central substrate binding site becomes fully exposed to the cytoplasm leaving both the Na+-ion in the Na2-site and the substrate in direct contact with the cytoplasm through water interactions. The simulations reveal how sodium is released and show indications of early events of substrate transport. The notion that ion dissociation from the Na2-site drives translocation is supported by experimental studies of a Na2-site mutant. Transmembrane helices (TMs) 1 and 6 are identified as the helices involved in the largest movements during transport. PMID:22046120

Chloride ions induce order-disorder transition at water-oxide interfaces

NASA Astrophysics Data System (ADS)

Deshmukh, Sanket; Kamath, Ganesh; Ramanathan, Shriram; Sankaranarayanan, Subramanian K. R. S.

2013-12-01

Water can form quasi-two-dimensional ordered layers near a solid interface. The solvation dynamics and ionic transport phenomena through this ordered water structure is of direct relevance to a variety of problems in interface science. Molecular dynamics simulations are used to study the impact of local fluctuation of the chloride ion density in the vicinity of an oxide surface on the structure and dynamics of water layers. We demonstrate that local increase in chloride ions beyond a threshold concentration near the water-MgO (100) interface introduces an order-disorder transition of this two-dimensional layered network into bulklike water, leading to increased diffusional characteristics and reduced hydrogen bonding lifetimes. We find that the extent of this order-disorder transition can be tuned by modifying the defect chemistry and nature of the underlying substrate. The kinetic fluidity resulting from order-disorder transition at high chloride ion concentration has significance for a broad range of phenomena, ranging from freezing point depression of brine to onset of aqueous corrosion.

δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

PubMed Central

2015-01-01

The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

Correlation of Critical Temperatures and Electrical Properties in Titanium Films

NASA Astrophysics Data System (ADS)

Gandini, C.; Lacquaniti, V.; Monticone, E.; Portesi, C.; Rajteri, M.; Rastello, M. L.; Pasca, E.; Ventura, G.

Recently transition-edge sensors (TES) have obtained an increasing interest as light detectors due to their high energy resolution and broadband response. Titanium (Ti), with transition temperature up to 0.5 K, is among the suitable materials for TES application. In this work we investigate Ti films obtained from two materials of different purity deposited by e-gun on silicon nitride. Films with different thickness and deposition substrate temperature have been measured. Critical temperatures, electrical resistivities and structural properties obtained from x-ray are related to each other.

Nano- and microcrystalline diamond deposition on pretreated WC-Co substrates: structural properties and adhesion

NASA Astrophysics Data System (ADS)

Fraga, M. A.; Contin, A.; Rodríguez, L. A. A.; Vieira, J.; Campos, R. A.; Corat, E. J.; Trava Airoldi, V. J.

2016-02-01

Many developments have been made to improve the quality and adherence of CVD diamond films onto WC-Co hard metal tools by the removing the cobalt from the substrate surface through substrate pretreatments. Here we compare the efficiency of three chemical pretreatments of WC-Co substrates for this purpose. First, the work was focused on a detailed study of the composition and structure of as-polished and pretreated substrate surfaces to characterize the effects of the substrate preparation. Considering this objective, a set of WC-9% Co substrates, before and after pretreatment, was analyzed by FEG-SEM, EDS and x-ray diffraction (XRD). The second stage of the work was devoted to the evaluation of the influence of seeding process, using 4 nm diamond nanoparticles, on the morphology and roughness of the pretreated substrates. The last and most important stage was to deposit diamond coatings with different crystallite sizes (nano and micro) by hot-filament CVD to understand fully the mechanism of growth and adhesion of CVD diamond films on pretreated WC-Co substrates. The transition from nano to microcrystalline diamond was achieved by controlling the CH4/H2 gas ratio. The nano and microcrystalline samples were grown under same time at different substrate temperatures 600 °C and 800 °C, respectively. The different substrate temperatures allowed the analysis of the cobalt diffusion from the bulk to the substrate surface during CVD film growth. Furthermore, it was possible to evaluate how the coating adhesion is affected by the diffusion. The diamond coatings were characterized by Raman spectroscopy, XRD, EDS, FEG-SEM, atomic force microscope and 1500 N Rockwell indentation to evaluate the adhesion.

Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.

PubMed

Lu, Jun; Koo, Selene C; Weissman, Benjamin P; Harris, Michael E; Li, Nan-Sheng; Piccirilli, Joseph A

2018-06-26

Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p K a , consistent with the expected electron-withdrawing effect. In HDV ribozyme reactions, we observed that the RNA substrates undergo transphosphorylation relatively efficiently, suggesting that the conformational constraints imposed by a ribofuranose ring are not strictly required for ribozyme catalysis. In contrast to the nonenzymatic reactions, however, substrate fluorination modestly increases the ribozyme reaction rate, consistent with a mechanism in which (1) the 2'-hydroxyl nucleophile exists predominantly in its neutral, protonated form in the ground state and (2) the 2'-hydroxyl bears some negative charge in the rate-determining step, consistent with a transition state in which the extent of 2'-OH deprotonation exceeds the extent of P-O bond formation.

Microstructure characteristics of Ni/WC composite cladding coatings

NASA Astrophysics Data System (ADS)

Yang, Gui-rong; Huang, Chao-peng; Song, Wen-ming; Li, Jian; Lu, Jin-jun; Ma, Ying; Hao, Yuan

2016-02-01

A multilayer tungsten carbide particle (WCp)-reinforced Ni-based alloy coating was fabricated on a steel substrate using vacuum cladding technology. The morphology, microstructure, and formation mechanism of the coating were studied and discussed in different zones. The microstructure morphology and phase composition were investigated by scanning electron microscopy, optical microscopy, X-ray diffraction, and energy-dispersive X-ray spectroscopy. In the results, the coating presents a dense and homogeneous microstructure with few pores and is free from cracks. The whole coating shows a multilayer structure, including composite, transition, fusion, and diffusion-affected layers. Metallurgical bonding was achieved between the coating and substrate because of the formation of the fusion and diffusion-affected layers. The Ni-based alloy is mainly composed of γ-Ni solid solution with finely dispersed Cr7C3/Cr23C6, CrB, and Ni+Ni3Si. WC particles in the composite layer distribute evenly in areas among initial Ni-based alloying particles, forming a special three-dimensional reticular microstructure. The macrohardness of the coating is HRC 55, which is remarkably improved compared to that of the substrate. The microhardness increases gradually from the substrate to the composite zone, whereas the microhardness remains almost unchanged in the transition and composite zones.

Insect adhesion on rough surfaces: analysis of adhesive contact of smooth and hairy pads on transparent microstructured substrates

PubMed Central

Zhou, Yanmin; Robinson, Adam; Steiner, Ullrich; Federle, Walter

2014-01-01

Insect climbing footpads are able to adhere to rough surfaces, but the details of this capability are still unclear. To overcome experimental limitations of randomly rough, opaque surfaces, we fabricated transparent test substrates containing square arrays of 1.4 µm diameter pillars, with variable height (0.5 and 1.4 µm) and spacing (from 3 to 22 µm). Smooth pads of cockroaches (Nauphoeta cinerea) made partial contact (limited to the tops of the structures) for the two densest arrays of tall pillars, but full contact (touching the substrate in between pillars) for larger spacings. The transition from partial to full contact was accompanied by a sharp increase in shear forces. Tests on hairy pads of dock beetles (Gastrophysa viridula) showed that setae adhered between pillars for larger spacings, but pads were equally unable to make full contact on the densest arrays. The beetles' shear forces similarly decreased for denser arrays, but also for short pillars and with a more gradual transition. These observations can be explained by simple contact models derived for soft uniform materials (smooth pads) or thin flat plates (hairy-pad spatulae). Our results show that microstructured substrates are powerful tools to reveal adaptations of natural adhesives for rough surfaces. PMID:24990289

Insect adhesion on rough surfaces: analysis of adhesive contact of smooth and hairy pads on transparent microstructured substrates.

PubMed

Zhou, Yanmin; Robinson, Adam; Steiner, Ullrich; Federle, Walter

2014-09-06

Insect climbing footpads are able to adhere to rough surfaces, but the details of this capability are still unclear. To overcome experimental limitations of randomly rough, opaque surfaces, we fabricated transparent test substrates containing square arrays of 1.4 µm diameter pillars, with variable height (0.5 and 1.4 µm) and spacing (from 3 to 22 µm). Smooth pads of cockroaches (Nauphoeta cinerea) made partial contact (limited to the tops of the structures) for the two densest arrays of tall pillars, but full contact (touching the substrate in between pillars) for larger spacings. The transition from partial to full contact was accompanied by a sharp increase in shear forces. Tests on hairy pads of dock beetles (Gastrophysa viridula) showed that setae adhered between pillars for larger spacings, but pads were equally unable to make full contact on the densest arrays. The beetles' shear forces similarly decreased for denser arrays, but also for short pillars and with a more gradual transition. These observations can be explained by simple contact models derived for soft uniform materials (smooth pads) or thin flat plates (hairy-pad spatulae). Our results show that microstructured substrates are powerful tools to reveal adaptations of natural adhesives for rough surfaces.

Mechanical exfoliation of two-dimensional materials

NASA Astrophysics Data System (ADS)

Gao, Enlai; Lin, Shao-Zhen; Qin, Zhao; Buehler, Markus J.; Feng, Xi-Qiao; Xu, Zhiping

2018-06-01

Two-dimensional materials such as graphene and transition metal dichalcogenides have been identified and drawn much attention over the last few years for their unique structural and electronic properties. However, their rise begins only after these materials are successfully isolated from their layered assemblies or adhesive substrates into individual monolayers. Mechanical exfoliation and transfer are the most successful techniques to obtain high-quality single- or few-layer nanocrystals from their native multi-layer structures or their substrate for growth, which involves interfacial peeling and intralayer tearing processes that are controlled by material properties, geometry and the kinetics of exfoliation. This procedure is rationalized in this work through theoretical analysis and atomistic simulations. We propose a criterion to assess the feasibility for the exfoliation of two-dimensional sheets from an adhesive substrate without fracturing itself, and explore the effects of material and interface properties, as well as the geometrical, kinetic factors on the peeling behaviors and the torn morphology. This multi-scale approach elucidates the microscopic mechanism of the mechanical processes, offering predictive models and tools for the design of experimental procedures to obtain single- or few-layer two-dimensional materials and structures.

Oligomerization of a molecular chaperone modulates its activity

PubMed Central

Kawagoe, Soichiro; Ishimori, Koichiro

2018-01-01

Molecular chaperones alter the folding properties of cellular proteins via mechanisms that are not well understood. Here, we show that Trigger Factor (TF), an ATP-independent chaperone, exerts strikingly contrasting effects on the folding of non-native proteins as it transitions between a monomeric and a dimeric state. We used NMR spectroscopy to determine the atomic resolution structure of the 100 kDa dimeric TF. The structural data show that some of the substrate-binding sites are buried in the dimeric interface, explaining the lower affinity for protein substrates of the dimeric compared to the monomeric TF. Surprisingly, the dimeric TF associates faster with proteins and it exhibits stronger anti-aggregation and holdase activity than the monomeric TF. The structural data show that the dimer assembles in a way that substrate-binding sites in the two subunits form a large contiguous surface inside a cavity, thus accounting for the observed accelerated association with unfolded proteins. Our results demonstrate how the activity of a chaperone can be modulated to provide distinct functional outcomes in the cell. PMID:29714686

Ring resonator optical modes in InGaN/GaN structures grown on micro-cone-patterned sapphire substrates

NASA Astrophysics Data System (ADS)

Kazanov, D. R.; Pozina, G.; Jmerik, V. N.; Shubina, T. V.

2018-03-01

Molecular beam epitaxy (MBE) of III-nitride compounds on specially prepared cone-shaped patterned substrates is being actively developed nowadays, especially for nanophotonic applications. This type of substrates enables the successful growth of hexagonal nanorods (NRs). The insertion of an active quantum-sized region of InGaN inside a GaN NR allows us to enhance the rate of optical transitions by coupling them with resonant optical modes in the NR. However, we have observed the enhancement of emission not only from the NR but also around the circumference region of the cone-shaped base. We have studied this specific feature and demonstrated its impact on the output signal.

VO2 Thermochromic Films on Quartz Glass Substrate Grown by RF-Plasma-Assisted Oxide Molecular Beam Epitaxy

PubMed Central

Zhang, Dong; Sun, Hong-Jun; Wang, Min-Huan; Miao, Li-Hua; Liu, Hong-Zhu; Zhang, Yu-Zhi; Bian, Ji-Ming

2017-01-01

Vanadium dioxide (VO2) thermochromic thin films with various thicknesses were grown on quartz glass substrates by radio frequency (RF)-plasma assisted oxide molecular beam epitaxy (O-MBE). The crystal structure, morphology and chemical stoichiometry were investigated systemically by X-ray diffraction (XRD), atomic force microscopy (AFM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) analyses. An excellent reversible metal-to-insulator transition (MIT) characteristics accompanied by an abrupt change in both electrical resistivity and optical infrared (IR) transmittance was observed from the optimized sample. Remarkably, the transition temperature (TMIT) deduced from the resistivity-temperature curve was reasonably consistent with that obtained from the temperature-dependent IR transmittance. Based on Raman measurement and XPS analyses, the observations were interpreted in terms of residual stresses and chemical stoichiometry. This achievement will be of great benefit for practical application of VO2-based smart windows. PMID:28772673

Achieving high aspect ratio wrinkles by modifying material network stress.

PubMed

Chen, Yu-Cheng; Wang, Yan; McCarthy, Thomas J; Crosby, Alfred J

2017-06-07

Wrinkle aspect ratio, or the amplitude divided by the wavelength, is hindered by strain localization transitions when an increasing global compressive stress is applied to synthetic material systems. However, many examples from living organisms show extremely high aspect ratios, such as gut villi and flower petals. We use three experimental approaches to demonstrate that these high aspect ratio structures can be achieved by modifying the network stress in the wrinkle substrate. We modify the wrinkle stress and effectively delay the strain localization transition, such as folding, to larger aspect ratios by using a zero-stress initial wavy substrate, creating a secondary network with post-curing, or using chemical stress relaxation materials. A wrinkle aspect ratio as high as 0.85, almost three times higher than common values of synthetic wrinkles, is achieved, and a quantitative framework is presented to provide understanding the different strategies and predictions for future investigations.

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

PubMed Central

Sigala, Paul A.; Kraut, Daniel A.; Caaveiro, Jose M. M.; Pybus, Brandon; Ruben, Eliza A.; Ringe, Dagmar; Petsko, Gregory A.; Herschlag, Daniel

2009-01-01

Enzymes are classically proposed to accelerate reactions by binding substrates within active site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1 – 1 Å scale of most substrate rearrangements. The flexibility of active site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together high resolution X-ray crystallography, 1H and 19F NMR spectroscopy, quantum mechanical calculations, and transition state analog binding measurements to test the distance scale on which non-covalent forces can constrain side chain and ligand relaxation or translation along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side chain reorientation and prevent hydrogen bond shortening by 0.1 Å or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function. PMID:18808119

Strain tuning of electronic structure in Bi 4Ti 3O 12-LaCoO 3 epitaxial thin films

DOE PAGES

Choi, Woo Seok; Lee, Ho Nyung

2015-05-08

In this study, we investigated the crystal and electronic structures of ferroelectric Bi 4Ti 3O 12 single-crystalline thin films site-specifically substituted with LaCoO 3 (LCO). The epitaxial films were grown by pulsed laser epitaxy on NdGaO 3 and SrTiO 3 substrates to vary the degree of strain. With increasing the LCO substitution, we observed a systematic increase in the c-axis lattice constant of the Aurivillius phase related with the modification of pseudo-orthorhombic unit cells. These compositional and structural changes resulted in a systematic decrease in the band gap, i.e., the optical transition energy between the oxygen 2p and transition-metal 3dmore » states, based on a spectroscopic ellipsometry study. In particular, the Co 3d state seems to largely overlap with the Ti t 2g state, decreasing the band gap. Interestingly, the applied tensile strain facilitates the band-gap narrowing, demonstrating that epitaxial strain is a useful tool to tune the electronic structure of ferroelectric transition-metal oxides.« less

Nanotwinning and structural phase transition in CdS quantum dots

NASA Astrophysics Data System (ADS)

Kumar, Pragati; Saxena, Nupur; Chandra, Ramesh; Gupta, Vinay; Agarwal, Avinash; Kanjilal, Dinakar

2012-10-01

Nanotwin structures are observed in high-resolution transmission electron microscopy studies of cubic phase CdS quantum dots in powder form by chemical co-precipitation method. The deposition of thin films of nanocrystalline CdS is carried out on silicon, glass, and TEM grids keeping the substrates at room temperature (RT) and 200°C by pulsed laser ablation. These films are then subjected to thermal annealing at different temperatures. Glancing angle X-ray diffraction results confirm structural phase transitions after thermal annealing of films deposited at RT and 200°C. The variation of average particle size and ratio of intensities in Raman peaks I 2LO/ I 1LO with annealing temperature are studied. It is found that electron-phonon interaction is a function of temperature and particle size and is independent of the structure. Besides Raman modes LO, 2LO and 3LO of CdS at approximately 302, 603, and 903 cm-1 respectively, two extra Raman modes at approximately 390 and 690 cm-1 are studied for the first time. The green and orange emissions observed in photoluminescence are correlated with phase transition.

Nanotwinning and structural phase transition in CdS quantum dots.

PubMed

Kumar, Pragati; Saxena, Nupur; Chandra, Ramesh; Gupta, Vinay; Agarwal, Avinash; Kanjilal, Dinakar

2012-10-23

Nanotwin structures are observed in high-resolution transmission electron microscopy studies of cubic phase CdS quantum dots in powder form by chemical co-precipitation method. The deposition of thin films of nanocrystalline CdS is carried out on silicon, glass, and TEM grids keeping the substrates at room temperature (RT) and 200°C by pulsed laser ablation. These films are then subjected to thermal annealing at different temperatures. Glancing angle X-ray diffraction results confirm structural phase transitions after thermal annealing of films deposited at RT and 200°C. The variation of average particle size and ratio of intensities in Raman peaks I2LO/I1LO with annealing temperature are studied. It is found that electron-phonon interaction is a function of temperature and particle size and is independent of the structure. Besides Raman modes LO, 2LO and 3LO of CdS at approximately 302, 603, and 903 cm-1 respectively, two extra Raman modes at approximately 390 and 690 cm-1 are studied for the first time. The green and orange emissions observed in photoluminescence are correlated with phase transition.

Comparison of structural and optical properties of TeO2 nanostructures synthesized using various substrate conditions

NASA Astrophysics Data System (ADS)

Jung, Taek-Kyun; Ryou, Min; Lee, Ji-Woon; Hyun, Soong-Keun; Na, Han Gil; Jin, Changhyun

2017-11-01

Several TeO2 low-dimensional nanostructures were prepared by thermal evaporation using four substrate conditions: (1) a bare substrate, (2) a scratched substrate, (3) a Au-catalyst-assisted substrate, and (4) a multi-walled carbon nanotube (MWCNT)-assisted substrate. Scanning electron microscopy and transmission electron microscopy analysis reveals that the morphologies of the nanostructures synthesized using these methods gradually changed from nanoparticles to ultra-thin nanowires with single tetragonal-type TeO2. Photoluminescence (PL) spectra reveal that the PL intensities of the TeO2 nanomaterials obtained using methods (1) and (2) are slightly increased, whereas the intensities of the TeO2 nanostructures obtained using methods (3) and (4) differ significantly depending on the initial substrate conditions. The emission peak is also blue-shifted from 440 nm to 430 nm for the scratched surface condition due to an excitonic transition. The increase in the blue emission for the MWCNT-assisted condition is attributed to the degree and type of excitons and defects in the TeO2 nanostructures.

Effect of Trisodium Citrate Concentration on the Structural and Photodiode Performance of CdO Thin Films

NASA Astrophysics Data System (ADS)

Ravikumar, M.; Valanarasu, S.; Chandramohan, R.; Jacob, S. Santhosh Kumar; Kathalingam, A.

2015-08-01

CdO thin films were deposited on glass and silicon substrates by simple perfume atomizer at 350°C using cadmium acetate and trisodium citrate (TSC). The effect of the TSC concentration on the structural, morphological, optical, and photoconductive properties of the prepared CdO thin films was investigated. X-Ray diffraction (XRD) studies of the deposited films revealed improvement in crystalline nature with increase of TSC concentration. Films prepared without TSC showed porous nature, not fully covering the substrate, whereas films prepared using TSC exhibited full coverage of the substrate with uniform particles. Optical transmittance study of the films showed high transmittance (50% to 60%), and the absorption edge was found to shift towards the red region depending on the TSC concentration. The films exhibited a direct band-to-band transition with bandgap varying between 2.31 eV and 2.12 eV. Photoconductivity studies of the n-CdO/ p-Si structure for various TSC concentrations were also carried out. I- V characteristics of this n-CdO/ p-Si structure revealed the formation of rectifying junctions, and its photoconductivity was found to increase with the TSC concentration.

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

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

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed endsmore » at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.« less

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.

PubMed

Shi, Yuqian; Hellinga, Homme W; Beese, Lorena S

2017-06-06

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'-3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

Thermoinactivation analysis of vacuolar H(+)-pyrophosphatase.

PubMed

Yang, Su J; Jiang, Shih S; Hsiao, Yi Y; Van, Ru C; Pan, Yih J; Pan, Rong L

2004-06-07

Vacuolar H(+)-translocating pyrophosphatase (H(+)-PPase; EC 3.6.1.1) catalyzes both the hydrolysis of PP(i) and the electrogenic translocation of proton from the cytosol to the lumen of the vacuole. Vacuolar H(+)-PPase, purified from etiolated hypocotyls of mung bean (Vigna radiata L.), is a homodimer with a molecular mass of 145 kDa. To investigate the relationship between structure and function of this H(+)-translocating enzyme, thermoinactivation analysis was employed. Thermoinactivation studies suggested that vacuolar H(+)-PPase consists of two distinct states upon heat treatment and exhibited different transition temperatures in the presence and absence of ligands (substrate and inhibitors). Substrate protection of H(+)-PPase stabilizes enzyme structure by increasing activation energy from 54.9 to 70.2 kJ/mol. We believe that the conformation of this enzyme was altered in the presence of substrate to protect against the thermoinactivation. In contrast, the modification of H(+)-PPase by inhibitor (fluorescein 5'-isothiocyanate; FITC) augmented the inactivation by heat treatment. The native, substrate-bound, and FITC-labeled vacuolar H(+)-PPases possess probably distinct conformation and show different modes of susceptibility to thermoinactivation. Our results also indicate that the structure of one subunit of this homodimer exerts long distance effect on the other, suggesting a specific subunit-subunit interaction in vacuolar H(+)-PPase. A working model was proposed to interpret the relationship of the structure and function of vacuolar H(+)-PPase.

Probing long-range structural order in SnPc/Ag(111) by umklapp process assisted low-energy angle-resolved photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Jauernik, Stephan; Hein, Petra; Gurgel, Max; Falke, Julian; Bauer, Michael

2018-03-01

Laser-based angle-resolved photoelectron spectroscopy is performed on tin-phthalocyanine (SnPc) adsorbed on silver Ag(111). Upon adsorption of SnPc, strongly dispersing bands are observed which are identified as secondary Mahan cones formed by surface umklapp processes acting on photoelectrons from the silver substrate as they transit through the ordered adsorbate layer. We show that the photoemission data carry quantitative structural information on the adsorbate layer similar to what can be obtained from a conventional low-energy electron diffraction (LEED) study. More specifically, we compare photoemission data and LEED data probing an incommensurate-to-commensurate structural phase transition of the adsorbate layer. Based on our results we propose that Mahan-cone spectroscopy operated in a pump-probe configuration can be used in the future to probe structural dynamics at surfaces with a temporal resolution in the sub-100-fs regime.

Numerical simulation of the alloying process during impulse induction heating of the metal substrate

NASA Astrophysics Data System (ADS)

Popov, V. N.

2017-10-01

2D numerical modeling of the processes during the alloying of the substrate surface metal layer is carried out. Heating, phase transition, heat and mass transfer in the molten metal, solidification of the melt are considered with the aid the proposed mathematical model. Under study is the applicability of the high-frequency electromagnetic field impulse for metal heating and melting. The distribution of the electromagnetic energy in the metal is described by empirical formulas. According to the results of numerical experiments, the flow structure in the melt and distribution of the alloying substances is evaluated.

Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh

PubMed Central

Lezon, Timothy R.; Bahar, Ivet

2012-01-01

Substrate transport in sodium-coupled amino acid symporters involves a large-scale conformational change that shifts the access to the substrate-binding site from one side of the membrane to the other. The structural change is particularly substantial and entails a unique piston-like quaternary rearrangement in glutamate transporters, as evidenced by the difference between the outward-facing and inward-facing structures resolved for the archaeal aspartate transporter GltPh. These structural changes occur over time and length scales that extend beyond the reach of current fully atomic models, but are regularly explored with the use of elastic network models (ENMs). Despite their success with other membrane proteins, ENM-based approaches for exploring the collective dynamics of GltPh have fallen short of providing a plausible mechanism. This deficiency is attributed here to the anisotropic constraints imposed by the membrane, which are not incorporated into conventional ENMs. Here we employ two novel (to our knowledge) ENMs to demonstrate that one can largely capture the experimentally observed structural change using only the few lowest-energy modes of motion that are intrinsically accessible to the transporter, provided that the surrounding lipid molecules are incorporated into the ENM. The presence of the membrane reduces the overall energy of the transition compared with conventional models, showing that the membrane not only guides the selected mechanism but also acts as a facilitator. Finally, we show that the dynamics of GltPh is biased toward transitions of individual subunits of the trimer rather than cooperative transitions of all three subunits simultaneously, suggesting a mechanism of transport that exploits the intrinsic dynamics of individual subunits. Our software is available online at http://www.membranm.csb.pitt.edu. PMID:22455916

Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.

PubMed

Lezon, Timothy R; Bahar, Ivet

2012-03-21

Substrate transport in sodium-coupled amino acid symporters involves a large-scale conformational change that shifts the access to the substrate-binding site from one side of the membrane to the other. The structural change is particularly substantial and entails a unique piston-like quaternary rearrangement in glutamate transporters, as evidenced by the difference between the outward-facing and inward-facing structures resolved for the archaeal aspartate transporter Glt(Ph). These structural changes occur over time and length scales that extend beyond the reach of current fully atomic models, but are regularly explored with the use of elastic network models (ENMs). Despite their success with other membrane proteins, ENM-based approaches for exploring the collective dynamics of Glt(Ph) have fallen short of providing a plausible mechanism. This deficiency is attributed here to the anisotropic constraints imposed by the membrane, which are not incorporated into conventional ENMs. Here we employ two novel (to our knowledge) ENMs to demonstrate that one can largely capture the experimentally observed structural change using only the few lowest-energy modes of motion that are intrinsically accessible to the transporter, provided that the surrounding lipid molecules are incorporated into the ENM. The presence of the membrane reduces the overall energy of the transition compared with conventional models, showing that the membrane not only guides the selected mechanism but also acts as a facilitator. Finally, we show that the dynamics of Glt(Ph) is biased toward transitions of individual subunits of the trimer rather than cooperative transitions of all three subunits simultaneously, suggesting a mechanism of transport that exploits the intrinsic dynamics of individual subunits. Our software is available online at http://www.membranm.csb.pitt.edu. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.

PubMed

Cao, Nan; Tan, Kemin; Annamalai, Thirunavukkarasu; Joachimiak, Andrzej; Tse-Dinh, Yuk-Ching

2018-06-14

We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.

The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates.

PubMed

Henriksen, A; Smith, A T; Gajhede, M

1999-12-03

We have solved the x-ray structures of the binary horseradish peroxidase C-ferulic acid complex and the ternary horseradish peroxidase C-cyanide-ferulic acid complex to 2.0 and 1.45 A, respectively. Ferulic acid is a naturally occurring phenolic compound found in the plant cell wall and is an in vivo substrate for plant peroxidases. The x-ray structures demonstrate the flexibility and dynamic character of the aromatic donor binding site in horseradish peroxidase and emphasize the role of the distal arginine (Arg(38)) in both substrate oxidation and ligand binding. Arg(38) hydrogen bonds to bound cyanide, thereby contributing to the stabilization of the horseradish peroxidase-cyanide complex and suggesting that the distal arginine will be able to contribute with a similar interaction during stabilization of a bound peroxy transition state and subsequent O-O bond cleavage. The catalytic arginine is additionally engaged in an extensive hydrogen bonding network, which also includes the catalytic distal histidine, a water molecule and Pro(139), a proline residue conserved within the plant peroxidase superfamily. Based on the observed hydrogen bonding network and previous spectroscopic and kinetic work, a general mechanism of peroxidase substrate oxidation is proposed.

Strain Phase Diagram of SrTiO3 Thin Films

NASA Astrophysics Data System (ADS)

He, Feizhou; Shapiro, S. M.

2005-03-01

SrTiO3 thin films were used as a model system to study the effects of strain and epitaxial constraint on structural phase transitions of oxide films. The basic phenomena revealed will apply to a variety of important structural transitions including the ferroelectric transition. Highly strained, epitaxial films of SrTiO3 were grown on different substrates. The structural phase transition temperature Tc increases from 105 K in bulk STO to 167 K for films under tensile strain and 330 K for films with compressive strain. The measured temperature-strain phase diagram is qualitatively consistent with theory [1], however the increase in Tc is much larger than predicted in all cases. The symmetry of the phases involved in the transition is different from the corresponding bulk structures largely because of epitaxial constraint, the clamping effect. Thus the shape of the STO unit cell is tetragonal at all temperatures. The possibility exists of a very unique low temperature phase with orthorhombic symmetry (Cmcm) but tetragonal unit cell shape. More generally, we have characterized at least three different manifestations of the clamping effect, showing it is much more subtle than usually recognized. This work is supported through NSF DMR-0239667, DMR-0132918, by the Research Corp, and at BNL by the US DOE DE-AC02-98CH10886. [1] N. A. Pertsev, A. K. Tagantsev and N. Setter, Phys. Rev. B61, R825 (2000).

Biochemical profiling in silico--predicting substrate specificities of large enzyme families.

PubMed

Tyagi, Sadhna; Pleiss, Juergen

2006-06-25

A general high-throughput method for in silico biochemical profiling of enzyme families has been developed based on covalent docking of potential substrates into the binding sites of target enzymes. The method has been tested by systematically docking transition state--analogous intermediates of 12 substrates into the binding sites of 20 alpha/beta hydrolases from 15 homologous families. To evaluate the effect of side chain orientations to the docking results, 137 crystal structures were included in the analysis. A good substrate must fulfil two criteria: it must bind in a productive geometry with four hydrogen bonds between the substrate and the catalytic histidine and the oxyanion hole, and a high affinity of the enzyme-substrate complex as predicted by a high docking score. The modelling results in general reproduce experimental data on substrate specificity and stereoselectivity: the differences in substrate specificity of cholinesterases toward acetyl- and butyrylcholine, the changes of activity of lipases and esterases upon the size of the acid moieties, activity of lipases and esterases toward tertiary alcohols, and the stereopreference of lipases and esterases toward chiral secondary alcohols. Rigidity of the docking procedure was the major reason for false positive and false negative predictions, as the geometry of the complex and docking score may sensitively depend on the orientation of individual side chains. Therefore, appropriate structures have to be identified. In silico biochemical profiling provides a time efficient and cost saving protocol for virtual screening to identify the potential substrates of the members of large enzyme family from a library of molecules.

Modulation of magnetic interaction in Bismuth ferrite through strain and spin cycloid engineering

NASA Astrophysics Data System (ADS)

Yadav, Rama Shanker; Reshi, Hilal Ahmad; Pillai, Shreeja; Rana, D. S.; Shelke, Vilas

2016-12-01

Bismuth ferrite, a widely studied room temperature multiferroic, provides new horizons of multifunctional behavior in phase transited bulk and thin film forms. Bismuth ferrite thin films were deposited on lattice mismatched LaAlO3 substrate using pulsed laser deposition technique. X-ray diffraction confirmed nearly tetragonal (T-type) phase of thin film involving role of substrate induced strain. The film thickness of 56 nm was determined by X-ray reflectivity measurement. The perfect coherence and epitaxial nature of T- type film was observed through reciprocal space mapping. The room temperature Raman measurement of T-type bismuth ferrite thin film also verified phase transition with appearance of only few modes. In parallel, concomitant La and Al substituted Bi1-xLaxFe0.95Al0.05O3 (x = 0.1, 0.2, 0.3) bulk samples were synthesized using solid state reaction method. A structural phase transition into orthorhombic (Pnma) phase at x = 0.3 was observed. The structural distortion at x = 0.1, 0.2 and phase transition at x = 0.3 substituted samples were also confirmed by changes in Raman active modes. The remnant magnetization moment of 0.199 emu/gm and 0.28 emu/gm were observed for x = 0.2 and 0.3 bulk sample respectively. The T-type bismuth ferrite thin film also showed high remnant magnetization of around 20emu/cc. The parallelism in magnetic behavior between T-type thin film and concomitant La and Al substituted bulk samples is indication of modulation, frustration and break in continuity of spiral spin cycloid.

Structural, magnetic and magnetocaloric properties of sputtered Gd films

NASA Astrophysics Data System (ADS)

Kumar, N. Pavan; Shaleni, V.; Satyanarayana, L.; Manorama, S. V.; Raja, M. Manivel

2018-05-01

Gd films with different thicknesses varying from 100 nm to 750 nm have been deposited on single crystal Si (100) substrate by ultra high vacuum magnetron sputtering system. X-ray diffraction analysis reveals the crystalline nature and hcp crystal structure of the films. Microstructure investigations have been carried to study the surface morphology of the films. Thermo magnetic studies confirm the magnetic transition of the films and are ˜275 K, close to bulk. Magnetocaloric effect (MCE) has been studied from magnetic isotherms measured around magnetic transition and the maximum isothermal entropy change of 2.0 J/kg-K is achieved for a magnetic field change of 2 T for the 750 nm film. The sputtered Gd films are useful for micro cooling device applications.

Structural and optical properties of GaAs(100) with a thin surface layer doped with chromium

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

Seredin, P. V., E-mail: paul@phys.vsu.ru; Fedyukin, A. V.; Arsentyev, I. N.

The aim of this study is to explore the structural and optical properties of single-crystal GaAs(100) doped with Cr atoms by burning them into the substrate at high temperatures. The diffusion of chromium into single-crystal GaAs(100) substrates brings about the formation of a thin (~20–40 μm) GaAs:Cr transition layer. In this case, chromium atoms are incorporated into the gallium-arsenide crystal lattice and occupy the regular atomic sites of the metal sublattice. As the chromium diffusion time is increased, such behavior of the dopant impurity yields changes in the energy structure of GaAs, a decrease in the absorption at free chargemore » carriers, and a lowering of the surface recombination rate. As a result, the photoluminescence signal from the sample is significantly enhanced.« less

Crystallographic Snapshots of the Complete Catalytic Cycle of the Unregulated Aspartate Transcarbamoylase from Bacillus subtilis

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

K Harris; G Cockrell; D Puleo

2011-12-31

Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in the absence of ligands, in the presence of the substrate carbamoyl phosphate, and in the presence of the bisubstrate/transition state analog N-phosphonacetyl-L-aspartate. Combining the structural data with in silico docking and electrostatic calculations, we have been able to visualize each step in the catalytic cycle of ATCase, from the ordered binding of the substrates, to the formation and decomposition of the tetrahedral intermediate, to the ordered releasemore » of the products from the active site. Analysis of the conformational changes associated with these steps provides a rationale for the lack of cooperativity in trimeric ATCases that do not possess regulatory subunits.« less

Semiconductor to Metal Transition Characteristics of VO2/NiO Epitaxial Heterostructures Integrated with Si(100)

NASA Astrophysics Data System (ADS)

Molaei, Roya

The novel functionalities of Vanadium dioxide (VO2), such as, several orders of magnitude transition in resistivity and IR transmittance, provide the exciting opportunity for the development of next generation memory, sensor, and field-effect based devices. A critical issue in the development of practical devices based on metal oxides is the integration of high quality epitaxial oxide thin films with the existing silicon technology which is based on silicon (100) substrates. However, silicon is not suitable for epitaxial growth of oxides owing to its tendency to readily form an amorphous oxide layer or silicide at the film-substrate interface. The oxide films deposited directly on silicon exhibit poor crystallinity and are not suitable for device applications. To overcome this challenge, appropriate substrate templates must be developed for the growth of oxide thin films on silicon substrates. The primary objective of this dissertation was to develop an integration methodology of VO2 with Si (100) substrates so they could be used in "smart" sensor type of devices along with other multifunctional devices on the same silicon chip. This was achieved by using a NiO/c- YSZ template layer deposited in situ. It will be shown that if the deposition conditions are controlled properly. This approach was used to integrate VO 2 thin films with Si (100) substrates using pulsed laser deposition (PLD) technique. The deposition methodology of integrating VO2 thin films on silicon using various other template layers will also be discussed. Detailed epitaxial relationship of NiO/c-YSZ/Si(100) heterostructures as a template to growth of VO2 as well as were studied. We also were able to create a p-n junction within a single NiO epilayer through subsequent nanosecond laser annealing, as well as established a structure-property correlation in NiO/c-YSZ/Si(100) thin film epitaxial heterostructures with especial emphasis on the stoichiometry and crystallographic characteristics. NiO/c-YSZ/Si(100) heterostructures were used as template to grow fully relaxed VO2 thin films. The detailed x-ray diffraction, transmission electron microscopy (TEM), electrical characterization results for the deposited films will be presented. In the framework on domain matching epitaxy, epitaxial growth of VO2 (tetragonal crystal structure at growth temperature) on NiO has been explained. Our detailed phi-scan X-ray diffraction measurements corroborate our understanding of the epitaxial growth and in-plane atomic arrangements at the interface. It was observed that the transition characteristics (sharpness, over which electrical property changes are completed, amplitude, transition temperature, and hysteresis) are a strong function of microstructure, strain, and stoichiometry. We have shown that by the choosing the right template layer, strain in the VO2 thin films can be fully relaxed and near-bulk VO2 transition temperatures can be achieved. Finally, I will present my research work on modification of semiconductor-to-metal transition characteristics and effect on room temperature magnetic properties of VO2 thin films upon laser annealing. While the microstructure (epitaxy, crystalline quality etc.) and phase were preserved, we envisage these changes to occur as a result of introduction of oxygen vacancies upon laser treatment.

Multiphase nanodomains in a strained BaTiO3 film on a GdScO3 substrate

NASA Astrophysics Data System (ADS)

Kobayashi, Shunsuke; Inoue, Kazutoshi; Kato, Takeharu; Ikuhara, Yuichi; Yamamoto, Takahisa

2018-02-01

Controlling the crystal structure of ferroelectric materials via epitaxial strain, which is a well-known technique in strain engineering, can lead to the formation of unique domain structures generating non-intrinsic phenomena such as electronic conductivity, photovoltages, and enhanced piezoelectric characteristics. Strained BaTiO3 films are promising ferroelectric materials as theoretical modeling predicts that different domain morphologies can introduce additional properties not observed in conventional BaTiO3 ceramics. To rationally design materials for practical application, a thorough understanding of the formation mechanisms and stabilities of different domain structures in strained BaTiO3 films is required. However, there have been very few experimental reports on this topic, and details about the domain structures in strained BaTiO3 films are currently lacking. In this paper, we report multiphase nanodomains in a strained BaTiO3 film deposited on an orthorhombic GdScO3 substrate. The phase-transition behavior of the strained BaTiO3 film reveals that it contains multiple phases at room temperature; the film first undergoes a phase-transition upon heating at around 550 K, and then a paraelectric phase forms at temperatures above 690 K. A picometer-scale analysis of the Ti ion displacements, using an advanced scanning transmission electron microscopy technique, is used to characterize the complex multiphase nanodomains, providing useful insights into the control of domain structures in BaTiO3 films by applying epitaxial strain.

Strained multilayer structures with pseudomorphic GeSiSn layers

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

Timofeev, V. A., E-mail: Vyacheslav.t@isp.nsc.ru; Nikiforov, A. I.; Tuktamyshev, A. R.

2016-12-15

The temperature and composition dependences of the critical thickness of the 2D–3D transition for a GeSiSn film on Si(100) have been studied. The regularities of the formation of multilayer structures with pseudomorphic GeSiSn layers directly on a Si substrate, without relaxed buffer layers, were investigated for the first time. The possibility of forming multilayer structures based on pseudomorphic GeSiSn layers has been shown and the lattice parameters have been determined using transmission electron microscopy. The grown structures demonstrate photoluminescence for Sn contents from 3.5 to 5% in GeSiSn layers.

Superconducting articles of manufacture and method of producing same

DOEpatents

Newkirk, Lawrence R.; Valencia, Flavio A.

1980-01-01

Bulk coatings of Nb.sub.3 Ge with high superconducting transition temperatures bonded to metallic substrates and a chemical vapor deposition method for producing such coatings on metallic substrates are disclosed. In accordance with the method, a Nb.sub.3 Ge coating having a transition temperature in excess of 21.5 K may be tightly bonded to a copper substrate.

Mesophotic bioerosion: Variability and structural impact on U.S. Virgin Island deep reefs

NASA Astrophysics Data System (ADS)

Weinstein, David K.; Smith, Tyler B.; Klaus, James S.

2014-10-01

Mesophotic reef corals, found 30-150 m below sea level, build complex structures that provide habitats for diverse ecosystems. Whereas bioerosion is known to impact the development and persistence of shallow reef structures, little is known regarding the extent of mesophotic bioerosion or how it might affect deeper reef geomorphology and carbonate accretion. Originally pristine experimental coral substrates and collected coral rubble were both used to investigate the variation and significance of mesophotic coral reef bioerosion south of St. Thomas, U.S. Virgin Islands. Bioerosion rates were calculated from experimental coral substrates exposed as framework for 1 and 2 years at four structurally distinct mesophotic coral reef habitats (between 30 and 45 m) as well as at a mid-shelf patch reef (21 m) and a shallow fringing patch reef (9 m). The long-term effects of macroboring were assessed by examining coral rubble collected at all sites. Overall, differences in bioerosional processes were found between shallow and mesophotic reefs. Increases in bioerosion on experimental substrates (amount of weight lost) were related to both decreasing seawater depth and increasing biomass of bioeroding parrotfish. Significant differences in coral skeleton bioerosion rates were also found between the transitional mesophotic reef zone (30-35 m) and the upper mesophotic reef zone (35-50 m) after 2 years of exposure, ranging from - 19.6 to 3.7 g/year. Total coral rubble macroboring was greater at most deep sites compared to shallower sites. Bioerosional grazing was found to dominate initial substrate modification in reefs 30.7 m and shallower, but sponges are believed to act as the main time-averaged long-term substrate bioeroders in reefs between 35 and 50 m. Although initial substrate bioerosion rates of a uniform substrate were relatively homogeneous in the 35-50 m depth zone, comparison of site composition suggests that mesophotic bioerosion will vary depending on the amount, location, and type of available substrate, and the duration both coral rubble and in situ coral framework are exposed on the seafloor. These variations may exaggerate pronounced structural differences in mesophotic reef habitats that experience few other methods of erosion.

Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells

PubMed Central

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate. PMID:25202990

Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells.

PubMed

Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

2014-01-01

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.

Structural Basis for Substrate Specificity in Phosphate Binding (beta/alpha)8-Barrels: D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K-12

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

Chan,K.; Fedorov, A.; Almo, S.

2008-01-01

Enzymes that share the ({beta}/{alpha})8-barrel fold catalyze a diverse range of reactions. Many utilize phosphorylated substrates and share a conserved C-terminal ({beta}/a)2-quarter barrel subdomain that provides a binding motif for the dianionic phosphate group. We recently reported functional and structural studies of d-ribulose 5-phosphate 3-epimerase (RPE) from Streptococcus pyogenes that catalyzes the equilibration of the pentulose 5-phosphates d-ribulose 5-phosphate and d-xylulose 5-phosphate in the pentose phosphate pathway [J. Akana, A. A. Fedorov, E. Fedorov, W. R. P. Novack, P. C. Babbitt, S. C. Almo, and J. A. Gerlt (2006) Biochemistry 45, 2493-2503]. We now report functional and structural studies ofmore » d-allulose 6-phosphate 3-epimerase (ALSE) from Escherichia coli K-12 that catalyzes the equilibration of the hexulose 6-phosphates d-allulose 6-phosphate and d-fructose 6-phosphate in a catabolic pathway for d-allose. ALSE and RPE prefer their physiological substrates but are promiscuous for each other's substrate. The active sites (RPE complexed with d-xylitol 5-phosphate and ALSE complexed with d-glucitol 6-phosphate) are superimposable (as expected from their 39% sequence identity), with the exception of the phosphate binding motif. The loop following the eighth {beta}-strand in ALSE is one residue longer than the homologous loop in RPE, so the binding site for the hexulose 6-phosphate substrate/product in ALSE is elongated relative to that for the pentulose 5-phosphate substrate/product in RPE. We constructed three single-residue deletion mutants of the loop in ALSE, ?T196, ?S197 and ?G198, to investigate the structural bases for the differing substrate specificities; for each, the promiscuity is altered so that d-ribulose 5-phosphate is the preferred substrate. The changes in kcat/Km are dominated by changes in kcat, suggesting that substrate discrimination results from differential transition state stabilization. In both ALSE and RPE, the phosphate group hydrogen bonds not only with the conserved motif but also with an active site loop following the sixth {beta}-strand, providing a potential structural mechanism for coupling substrate binding with catalysis.« less

Ferroelectric domain structure of anisotropically strained NaNbO3 epitaxial thin films

NASA Astrophysics Data System (ADS)

Schwarzkopf, J.; Braun, D.; Schmidbauer, M.; Duk, A.; Wördenweber, R.

2014-05-01

NaNbO3 thin films have been grown under anisotropic biaxial strain on several oxide substrates by liquid-delivery spin metalorganic chemical vapor deposition. Compressive lattice strain of different magnitude, induced by the deposition of NaNbO3 films with varying film thickness on NdGaO3 single crystalline substrates, leads to modifications of film orientation and phase symmetry, which are similar to the phase transitions in Pb-containing oxides near the morphotropic phase boundary. Piezoresponse force microscopy measurements exhibit large out-of-plane polarization components, but no distinctive domain structure, while C-V measurements indicate relaxor properties in these films. When tensile strain is provoked by the epitaxial growth on DyScO3, TbScO3, and GdScO3 single crystalline substrates, NaNbO3 films behave rather like a normal ferroelectric. The application of these rare-earth scandate substrates yields well-ordered ferroelectric stripe domains of the type a1/a2 with coherent domain walls aligned along the [001] substrate direction as long as the films are fully strained. With increasing plastic lattice relaxation, initially, a 2D domain pattern with still exclusively in-plane electric polarization, and finally, domains with in-plane and out-of-plane polar components evolve.

Retinoic acid biosynthesis catalyzed by retinal dehydrogenases relies on a rate-limiting conformational transition associated with substrate recognition

PubMed Central

Bchini, Raphaël; Vasiliou, Vasilis; Branlant, Guy; Talfournier, François; Rahuel-Clermont, Sophie

2012-01-01

Retinoic acid (RA), a metabolite of vitamin A, exerts pleiotropic effects throughout life in vertebrate organisms. Thus, RA action must be tightly regulated through the coordinated action of biosynthetic and degradating enzymes. The last step of retinoic acid biosynthesis is irreversibly catalyzed by the NAD-dependent retinal dehydrogenases (RALDH), which are members of the aldehyde dehydrogenase (ALDH) superfamily. Low intracellular retinal concentrations imply efficient substrate molecular recognition to ensure high affinity and specificity of RALDHs for retinal. This study addresses the molecular basis of retinal recognition in human ALDH1A1 (or RALDH1) and rat ALDH1A2 (or RALDH2), through the comparison of the catalytic behavior of retinal analogs and use of the fluorescence properties of retinol. We show that, in contrast to long chain unsaturated substrates, the rate-limiting step of retinal oxidation by RALDHs is associated with acylation. Use of the fluorescence resonance energy transfer upon retinol interaction with RALDHs provides evidence that retinal recognition occurs in two steps: binding into the substrate access channel, and a slower structural reorganization with a rate constant of the same magnitude as the kcat for retinal oxidation: 0.18 vs. 0.07 s−1 and 0.25 vs. 0.1 s−1 for ALDH1A1 and ALDH1A2, respectively. This suggests that the conformational transition of the RALDH-retinal complex significantly contributes to the rate-limiting step that controls the kinetics of retinal oxidation, as a prerequisite for the formation of a catalytically competent Michaelis complex. This conclusion is consistent with the general notion that structural flexibility within the active site of ALDH enzymes has been shown to be an integral component of catalysis. PMID:23220587

Wetting Behavior in Colloid-Polymer Mixtures at Different Substrates.

PubMed

Wijting, Willem K; Besseling, Nicolaas A M; Cohen Stuart, Martien A

2003-09-25

We present experimental observations on wetting phenomena in depletion interaction driven, phase separated colloidal dispersions. The contact angle of the colloidal liquid-gas interface at a solid substrate was determined for a series of compositions. Upon approach to the critical point, a transition occurs from partial to complete wetting. The interaction with the substrate was manipulated by modifying the substrate with a polymer. In that case, a transition from partial to complete drying is observed upon approach to the critical point.

Strain and Structure Heterogeneity in MoS2 Atomic Layers Grown by Chemical Vapour Deposition

DTIC Science & Technology

2014-11-18

substrate and material. To better explain the experimental results and estimate the strain transferred to MoS2 layer under such tensile tests, a 3D... ACS Nano 7, 7126 7131 (2013). 29. He, K., Poole, C., Mak, K. F. & Shan, J. Experimental demonstration of continuous electronic structure tuning via...transition as it is thinned down from multi layer to monolayer, producing a significant enhancement of photoluminescence (PL) quantum yield as a result of the

Evaluation of Graphene/WO3 and Graphene/CeO x Structures as Electrodes for Supercapacitor Applications

NASA Astrophysics Data System (ADS)

Chaitoglou, Stefanos; Amade, Roger; Bertran, Enric

2017-12-01

The combination of graphene with transition metal oxides can result in very promising hybrid materials for use in energy storage applications thanks to its intriguing properties, i.e., highly tunable surface area, outstanding electrical conductivity, good chemical stability, and excellent mechanical behavior. In the present work, we evaluate the performance of graphene/metal oxide (WO3 and CeO x ) layered structures as potential electrodes in supercapacitor applications. Graphene layers were grown by chemical vapor deposition (CVD) on copper substrates. Single and layer-by-layer graphene stacks were fabricated combining graphene transfer techniques and metal oxides grown by magnetron sputtering. The electrochemical properties of the samples were analyzed and the results suggest an improvement in the performance of the device with the increase in the number of graphene layers. Furthermore, deposition of transition metal oxides within the stack of graphene layers further improves the areal capacitance of the device up to 4.55 mF/cm2, for the case of a three-layer stack. Such high values are interpreted as a result of the copper oxide grown between the copper substrate and the graphene layer. The electrodes present good stability for the first 850 cycles before degradation.

Growth optimization and electronic structure of ultrathin CoO films on Ag(001): A LEED and photoemission study

NASA Astrophysics Data System (ADS)

Barman, Sukanta; Menon, Krishnakumar S. R.

2018-04-01

We present here a detailed growth optimization of CoO thin film on Ag(001) involving the effects of different growth parameters on the electronic structure. A well-ordered stoichiometric growth of 5 ML CoO film has been observed at 473 K substrate temperature and 1 × 10-6 mbar oxygen partial pressure. The growth at lower substrate temperature and oxygen partial pressure show non-stoichiometric impurity phases which have been investigated further to correlate the growth parameters with surface electronic structure. The coverage dependent valence band electronic structure of the films grown at optimized condition reveals the presence of interfacial states near the Fermi edge (EF) for lower film coverages. Presence of interfacial states in the stoichiometric films rules out their defect-induced origin. We argue that this is an intrinsic feature of transition metal monoxides like NiO, CoO, MnO in the low coverage regime.

Structure of the Deactive State of Mammalian Respiratory Complex I.

PubMed

Blaza, James N; Vinothkumar, Kutti R; Hirst, Judy

2018-02-06

Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Interfaces between hexagonal and cubic oxides and their structure alternatives

DOE PAGES

Zhou, Hua; Wu, Lijun; Wang, Hui-Qiong; ...

2017-11-14

Multi-layer structure of functional materials often involves the integration of different crystalline phases. The film growth orientation thus frequently exhibits a transformation, owing to multiple possibilities caused by incompatible in-plane structural symmetry. Nevertheless, the detailed mechanism of the transformation has not yet been fully explored. Here we thoroughly probe the heteroepitaxially grown hexagonal zinc oxide (ZnO) films on cubic (001)-magnesium oxide (MgO) substrates using advanced scanning transition electron microscopy, X-ray diffraction and first principles calculations, revealing two distinct interface models of (001) ZnO/(001) MgO and (100) ZnO/(001) MgO. Here we have found that the structure alternatives are controlled thermodynamically bymore » the nucleation, while kinetically by the enhanced Zn adsorption and O diffusion upon the phase transformation. Finally, this work not only provides a guideline for the interface fabrication with distinct crystalline phases but also shows how polar and non-polar hexagonal ZnO films might be manipulated on the same cubic substrate.« less

Expression and purification of isotopically labeled peptide inhibitors and substrates of cAMP-dependant protein kinase A for NMR analysis.

PubMed

Masterson, Larry R; Bortone, Nadia; Yu, Tao; Ha, Kim N; Gaffarogullari, Ece C; Nguyen, Oanh; Veglia, Gianluigi

2009-04-01

Extensive X-ray crystallographic studies carried out on the catalytic-subunit of protein kinase A (PKA-C) enabled the atomic characterization of inhibitor and/or substrate peptide analogues trapped at its active site. Yet, the structural and dynamic transitions of these peptides from the free to the bound state are missing. These conformational transitions are central to understanding molecular recognition and the enzymatic cycle. NMR spectroscopy allows one to study these phenomena under functionally relevant conditions. However, the amounts of isotopically labeled peptides required for this technique present prohibitive costs for solid-phase peptide synthesis. To enable NMR studies, we have optimized both expression and purification of isotopically enriched substrate/inhibitor peptides using a recombinant fusion protein system. Three of these peptides correspond to the cytoplasmic regions of the wild-type and lethal mutants of the membrane protein phospholamban, while the fourth peptide correspond to the binding epitope of the heat-stable protein kinase inhibitor (PKI(5-24)). The target peptides were fused to the maltose binding protein (MBP), which is further purified using a His(6) tag approach. This convenient protocol allows for the purification of milligram amounts of peptides necessary for NMR analysis.

Metal-Insulator Transition of strained SmNiO3 Thin Films: Structural, Electrical and Optical Properties

PubMed Central

Torriss, B.; Margot, J.; Chaker, M.

2017-01-01

Samarium nickelate (SmNiO3) thin films were successfully synthesized on LaAlO3 and SrTiO3 substrates using pulsed-laser deposition. The Mott metal-insulator (MI) transition of the thin films is sensitive to epitaxial strain and strain relaxation. Once the strain changes from compressive to tensile, the transition temperature of the SmNiO3 samples shifts to slightly higher values. The optical conductivity reveals the strong dependence of the Drude spectral weight on the strain relaxation. Actually, compressive strain broadens the bandwidth. In contrast, tensile strain causes the effective number of free carriers to reduce which is consistent with the d-band narrowing. PMID:28098240

High-intensity pulse light sintering of silver nanowire transparent films on polymer substrates: the effect of the thermal properties of substrates on the performance of silver films.

PubMed

Jiu, Jinting; Sugahara, Tohru; Nogi, Masaya; Araki, Teppei; Suganuma, Katsuaki; Uchida, Hiroshi; Shinozaki, Kenji

2013-12-07

Silver nanowire (AgNW) films with a random mesh structure have attracted considerable attention as high-performance flexible transparent electrodes that can replace the expensive and brittle ITO-sputtered films widely used in displays, touch screens, and solar cells. Methods such as heating, pressure treatment, and light treatment are usually used to obtain an optically transparent and electrically conductive film comparable to those of commercial ITO. However, the adhesion between the AgNW film and the substrate is so weak that other overcoatings or extra treatments are necessary. Here, a high-intensity pulsed light (HIPL) sintering technique was developed to rapidly and simply sinter the AgNW film and thus achieve strong adhesion and even high conductivity on these flexible polymer substrates which will be widely applied to the printing of electronic devices. The conductivity of the AgNW film closely depended on the thermal performance of substrates, and the adhesion was determined by the soft state of the substrate surface originating from the glass transition or melting of substrates with light intensity. The rapid sintering technique can be popularized to fabricate new devices on these polymer substrates by considering the thermal properties of the substrate to improve the performance of devices.

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

PubMed Central

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

2017-01-01

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5′-nuclease superfamily. Its dominant, processive 5′–3′ exonuclease and secondary 5′-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5′-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5′ flaps. Their distinctive 5′ ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5′ flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity. PMID:28533382

Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis.

PubMed

Richard, John P; Amyes, Tina L; Reyes, Archie C

2018-04-17

The mystery associated with catalysis by what were once regarded as protein black boxes, diminished with the X-ray crystallographic determination of the three-dimensional structures of enzyme-substrate complexes. The report that several high-resolution X-ray crystal structures of orotidine 5'-monophosphate decarboxylase (OMPDC) failed to provide a consensus mechanism for enzyme-catalyzed decarboxylation of OMP to form uridine 5'-monophosphate, therefore, provoked a flurry of controversy. This controversy was fueled by the enormous 10 23 -fold rate acceleration for this enzyme, which had " jolted many biochemists' assumptions about the catalytic potential of enzymes." Our studies on the mechanism of action of OMPDC provide strong evidence that catalysis by this enzyme is not fundamentally different from less proficient catalysts, while highlighting important architectural elements that enable a peak level of performance. Many enzymes undergo substrate-induced protein conformational changes that trap their substrates in solvent occluded protein cages, but the conformational change induced by ligand binding to OMPDC is incredibly complex, as required to enable the development of 22 kcal/mol of stabilizing binding interactions with the phosphodianion and ribosyl substrate fragments of OMP. The binding energy from these fragments is utilized to activate OMPDC for catalysis of decarboxylation at the orotate fragment of OMP, through the creation of a tight, catalytically active, protein cage from the floppy, open, unliganded form of OMPDC. Such utilization of binding energy for ligand-driven conformational changes provides a general mechanism to obtain specificity in transition state binding. The rate enhancement that results from the binding of carbon acid substrates to enzymes is partly due to a reduction in the carbon acid p K a that is associated with ligand binding. The binding of UMP to OMPDC results in an unusually large >12 unit decrease in the p K a = 29 for abstraction of the C-6 substrate hydrogen, due to stabilization of an enzyme-bound vinyl carbanion, which is also an intermediate of OMPDC-catalyzed decarboxylation. The protein-ligand interactions operate to stabilize the vinyl carbanion at the enzyme active site compared to aqueous solution, rather than to stabilize the transition state for the concerted electrophilic displacement of CO 2 by H + that avoids formation of this reaction intermediate. There is evidence that OMPDC induces strain into the bound substrate. The interaction between the amide side chain of Gln-215 from the phosphodianion gripper loop and the hydroxymethylene side chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion of OMP. There are no direct stabilizing interactions between dianion gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the pyrimidine ring at the decarboxylation transition state. Rather these side chains function solely to hold OMPDC in the catalytically active closed conformation. The hydrophobic side chains that line the active site of OMPDC in the region of the departing CO 2 product may function to stabilize the decarboxylation transition state by providing hydrophobic solvation of this product.

Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase–an Essential Enzyme of the Polyamine Metabolism

PubMed Central

Krossa, Sebastian; Faust, Annette; Ober, Dietrich; Scheidig, Axel J.

2016-01-01

The highly conserved bacterial homospermidine synthase (HSS) is a key enzyme of the polyamine metabolism of many proteobacteria including pathogenic strains such as Legionella pneumophila and Pseudomonas aeruginosa; The unique usage of NAD(H) as a prosthetic group is a common feature of bacterial HSS, eukaryotic HSS and deoxyhypusine synthase (DHS). The structure of the bacterial enzyme does not possess a lysine residue in the active center and thus does not form an enzyme-substrate Schiff base intermediate as observed for the DHS. In contrast to the DHS the active site is not formed by the interface of two subunits but resides within one subunit of the bacterial HSS. Crystal structures of Blastochloris viridis HSS (BvHSS) reveal two distinct substrate binding sites, one of which is highly specific for putrescine. BvHSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism. The proposed reaction steps for the catalysis of BvHSS emphasize cation-π interaction through a conserved Trp residue as a key stabilizer of high energetic transition states. PMID:26776105

Development of GaAs/Si and GaAs/Si monolithic structures for future space solar cells

NASA Technical Reports Server (NTRS)

Spitzer, M. B.; Vernon, S. M.; Wolfson, R. G.; Tobin, S. P.

1984-01-01

The results of heteroepitaxial growth of GaAs and GaAlAs directly on Si are presented, and applications to new cell structures are suggested. The novel feature is the elimination of a Ge lattice transition region. This feature not only reduces the cost of substrate preparation, but also makes possible the fabrication of high efficiency monolithic cascade structures. All films to be discussed were grown by organometallic chemical vapor deposition at atmospheric pressure. This process yielded reproducible, large-area films of GaAs, grown directly on Si, that are tightly adherent and smooth, and are characterized by a defect density of 5 x 10(6) power/sq cm. Preliminary studies indicate that GaAlAs can also be grown in this way. A number of promising applications are suggested. Certainly these substrates are ideal for low-weight GaAs space solar ells. For very high efficiency, the absence of Ge makes the technology attractive for GaAlAs/Si monolithic cascades, in which the Si substrates would first be provided with a suitable p/n junction. An evaluation of a three bandgap cascade consisting of appropriately designed GaAlAs/GaAs/Si layers is also presented.

Temperature-assisted morphological transition in CuPc thin films

NASA Astrophysics Data System (ADS)

Bae, Yu Jeong; Pham, Thi Kim Hang; Kim, Tae Hee

2016-05-01

Ex-situ and in-situ morphological analyses were performed for Cu-phthalocyanine (CuPc) organic semiconductor films by using atomic force microscopy (AFM) and reflection high-energy electron diffraction (RHEED). The focus was the effects of post-annealing on the structural characteristics of CuPc films grown on MgO(001) layers by using an ultra-high-vacuum thermal evaporator. Sphere-to-nanofibril and 2-D to 3-D morphological transitions were observed with increasing CuPc thickness beyond 3 nm. The surface morphology and the crystallinity were drastically improved after an additional cooling of the post-annealed CuPc films thinner than 3 nm. Our results highlight that molecular orientation and structural ordering can be effectively controlled by using different temperature treatments and a proper combination of material, film thickness, and substrate.

QM/MM Investigation of Substrate and Product Specificities of Suv4-20h2: How Does This Enzyme Generate Dimethylated H4K20 from Monomethylated Substrate?

PubMed

Qian, Ping; Guo, Haobo; Wang, Liang; Guo, Hong

2017-06-13

Protein lysine methyltransferases (PKMTs) catalyze the methylation of lysine residues on histone proteins in the regulation of chromatin structure and gene expression. In contrast to many other PKMTs for which unmodified lysine is the methylation target, the enzymes in the Suv4-20 family are able to generate dimethylated product (H4K20me2) based exclusively on the monomethylated H4K20 substrate (H4K20me1). The origin of such substrate/product specificity is still not clear. Here, molecular dynamics (MD) and free energy (potential of mean force) simulations are undertaken using quantum mechanical/molecular mechanical (QM/MM) potentials to understand the substrate/product specificities of Suv4-20h2, a member of the Suv4-20 family. The free energy barriers for mono-, di-, and trimethylation in Suv4-20h2 obtained from the simulations are found to be well correlated with the specificities observed experimentally with the allowed dimethylation based on the H4K20me1 substrate and prohibited monomethylation and trimethylation based on H4K20 and H4K20me2, respectively. It is demonstrated that the reason for the relatively efficient dimethylation is an effective transition state (TS) stabilization through strengthening the CH···O interactions as well as the presence of a cation-π interaction at the transition state. The simulations also show that the failures of Suv4-20h2 to catalyze monomethylation and trimethylation are due, respectively, to a less effective TS stabilization and inability of the reactant complex containing H4K20me2 to adopt a reactive (near attack) configuration for methyl transfer. The results suggest that care must be exercised in the prediction of the substrate specificity based only on the existence of near attack configurations in substrate complexes.

Nanotwinning and structural phase transition in CdS quantum dots

PubMed Central

2012-01-01

Nanotwin structures are observed in high-resolution transmission electron microscopy studies of cubic phase CdS quantum dots in powder form by chemical co-precipitation method. The deposition of thin films of nanocrystalline CdS is carried out on silicon, glass, and TEM grids keeping the substrates at room temperature (RT) and 200°C by pulsed laser ablation. These films are then subjected to thermal annealing at different temperatures. Glancing angle X-ray diffraction results confirm structural phase transitions after thermal annealing of films deposited at RT and 200°C. The variation of average particle size and ratio of intensities in Raman peaks I2LO/I1LO with annealing temperature are studied. It is found that electron-phonon interaction is a function of temperature and particle size and is independent of the structure. Besides Raman modes LO, 2LO and 3LO of CdS at approximately 302, 603, and 903 cm−1 respectively, two extra Raman modes at approximately 390 and 690 cm−1 are studied for the first time. The green and orange emissions observed in photoluminescence are correlated with phase transition. PMID:23092351

Roles of strain and domain boundaries on the phase transition stability of VO2 thin films

NASA Astrophysics Data System (ADS)

Jian, Jie; Chen, Aiping; Chen, Youxing; Zhang, Xinghang; Wang, Haiyan

2017-10-01

The fundamental phase transition mechanism and the stability of the semiconductor-to-metal phase transition properties during multiple thermal cycles have been investigated on epitaxial vanadium dioxide (VO2) thin films via both ex situ heating and in situ heating by transmission electron microscopy (TEM). VO2 thin films were deposited on c-cut sapphire substrates by pulsed laser deposition. Ex situ studies show the broadening of transition sharpness (ΔT) and the width of thermal hysteresis (ΔH) after 60 cycles. In situ TEM heating studies reveal that during thermal cycles, large strain was accumulated around the domain boundaries, which was correlated with the phase transition induced lattice constant change and the thermal expansion. It suggests that the degradation of domain boundary structures in the VO2 films not only caused the transition property reduction (e.g., the decrease in ΔT and ΔH) but also played an important role in preventing the film from fracture during thermal cycles.

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

PubMed

Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

2010-06-03

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

PubMed Central

Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

2010-01-01

The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590

DFT+DMFT study of strain and interface effects in d1 and d2 t2 g-perovskites

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dymkowski, Krzysztof; Ederer, Claude

2015-03-01

Metal-insulator transitions in thin films of early-transition metal correlated oxides are linked to both epitaxial strain and electronic reconstruction at the film/substrate interface. We separately address these two key factors for LaTiO3 and LaVO3 through density functional theory plus dynamical mean-field theory (DFT+DMFT). We find that mere epitaxial strain suffices to induce an insulator-to-metal transition in LaTiO3, but not in LaVO3, in agreement with recent experiments. We show that this difference can be explained by the combined effect of strain-induced changes in the crystal field splitting of t2 g orbitals and different orbital filling in these two materials. The role of the interface is investigated through DFT+DMFT simulations of LaVO3/SrTiO3 heterostructures with varying superlattice periodicities and substrate terminations. Our aim is to assess whether the metallicity observed at the LaVO3/SrTiO3 interface could be driven by pure electronic reconstruction effects, rather than structural or stoichiometric reasons (such as, e.g., O-related defects).

The magnetic transition temperature tuned by strain in YMn0.9Ru0.1O3 thin films

NASA Astrophysics Data System (ADS)

Yang, L. P.; Zhang, A. M.; Wang, K.; Wu, X. S.; Zhai, Z. Y.

2018-05-01

Epitaxial orthorhombic YMn0.9Ru0.1O3 films with different thickness have been grown on (001)-SrTiO3 substrates by pulsed laser deposition (PLD). The crystal structure is well investigated by X-ray Diffraction. It is found that the out-of-plane parameter c slowly increases with decreasing thickness of samples because of the tensile strain between the films and substrates along c axis. The lengths of in-plane Mn-O bonds expand with the enhancement of strains, which is proved by Raman scatting. The magnetic measurements reveal that there exist two magnetic transition temperatures TN1 and TN2. The TN1 is close to that of orthorhombic YMnO3 bulk. With decreasing thickness of the films, TN1 keeps almost constant because of the small stain along c-axis. TN2, however, obviously increases from 117 K to 134 K, which could be related to the expansion of in-plane Mn-O bonds. Results show that the magnetic transition temperature of YMn0.9Ru0.1O3 films can be sensitively manipulated by the strain of the films.

Ferroelectric films of deuterated glycine phosphite: Structure and dielectric properties

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Svinarev, F. B.; Lemanov, V. V.

2013-05-01

Polycrystalline textured films of deuterated glycine phosphite consisting of single-crystal blocks with lateral dimensions ˜(50-100) μm and a thickness d ˜ (1-5) μm have been grown by evaporation on NdGaO3(100) and α-Al2O3 substrates with preliminarily deposited interdigitated electrodes, as well as on Al substrates. The c* ( Z) crystallographic axis in the blocks is normal to the film plane, and the a ( X) axis and the polar axis b ( Y) are oriented in the film plane. The temperature dependences of the capacitance of the structures measured with the interdigitated electrode system reveal a strong dielectric anomaly at the film transition to the ferroelectric state. The phase transition temperature T c depends on the degree of deuteration D of the glycine phosphite. The maximum value T c = 275 K obtained in the structures studied corresponds to a degree of deuteration of the glycine phosphite D ˜ 50%. The frequency behavior of the dielectric hysteresis loops in glycine phosphite films differs radically from that of the previously studied films of deuterated betaine phosphite, which evidences that polarization switching in these structures proceeds by different mechanisms. It has been that application of a dc bias to the electrodes changes the shape of the dielectric hysteresis loops and shifts them along the electric field axis. The shift of the loops depends on the sign, magnitude, and time of application of the bias. Possible mechanisms underlying the induced unipolarity are discussed.

Structure and energetics of hydrogen-bonded networks of methanol on close packed transition metal surfaces

NASA Astrophysics Data System (ADS)

Murphy, Colin J.; Carrasco, Javier; Lawton, Timothy J.; Liriano, Melissa L.; Baber, Ashleigh E.; Lewis, Emily A.; Michaelides, Angelos; Sykes, E. Charles H.

2014-07-01

Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogen-bonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbate-substrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanol-methanol and methanol-surface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells.

The influence of doping element on structural and luminescent characteristics of ZnS thin films

NASA Astrophysics Data System (ADS)

Kryshtab, T.; Khomchenko, V. S.; Andraca-Adame, J. A.; Rodionov, V. E.; Khachatryan, V. B.; Tzyrkunov, Yu. A.

2006-10-01

For the fabrication of green and blue emitting ZnS structures the elements of I, III, and VII groups (Cu, Al, Ga, Cl) are used as dopants. The influence of type of impurity, doping technique, and type of substrate on crystalline structure and surface morphology together with luminescent properties was investigated. The doping of thin films was realized during the growth process and/or post-deposition thermal treatment. ZnS thin films were deposited by physical (EBE) and chemical (MOCVD) methods onto glass or ceramic (BaTiO 3) substrates. Closed spaced evaporation and thermodiffusion methods were used for the post-deposition doping of ZnS films. X-ray diffraction (XRD) techniques, atomic force microscopy (AFM), and measurements of photoluminescent (PL) spectra were used for the investigations. It was shown that the doping by the elements of I (Cu) and III (Al, Ga) groups does not change the crystal structure during the thermal treatment up to 1000 ∘C, whereas simultaneous use of the elements of I (Cu) and VII (Cl) groups leads to decrease of the phase transition temperature to 800 ∘C. The presence of impurities in the growth process leads to a grain size increase. At post-deposition treatment Ga and Cl act as activators of recrystallization process. The transition of ZnS sphalerite lattice to wurtzite one leads to the displacement of the blue emission band position towards the short-wavelength range by 10 nm.

Spectroscopic study of native defects in the semiconductor to metal phase transition in V2O5 nanostructure

NASA Astrophysics Data System (ADS)

Basu, Raktima; Dhara, Sandip

2018-04-01

Vanadium is a transition metal with multiple oxidation states and V2O5 is the most stable form among them. Besides catalysis, chemical sensing, and photo-chromatic applications, V2O5 is also reported to exhibit a semiconductor to metal transition (SMT) at a temperature range of 530-560 K. Even though there are debates in using the term "SMT" for V2O5, the metallic behavior above the transition temperature and its origin are of great interest in the scientific community. In this study, V2O5 nanostructures were deposited on a SiO2/Si substrate by the vapour transport method using Au as a catalyst. Temperature dependent electrical measurement confirms the SMT in V2O5 without any structural change. Temperature dependent photoluminescence analysis proves the appearance of oxygen vacancy related peaks due to reduction of V2O5 above the transition temperature, as also inferred from temperature dependent Raman spectroscopic studies. The newly evolved defect levels in the V2O5 electronic structure with increasing temperature are also understood from the downward shift of the bottom most split-off conduction bands due to breakdown of pdπ bonds leading to metallic behavior in V2O5 above the transition temperature.

Effect of chemical pressure on the electronic phase transition in Ca 1-x Sr x Mn 7 O 12 films

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

Huon, A.; Lee, D.; Herklotz, A.

Here, we demonstrate how chemical pressure affects the structural and electronic phase transitions of the quadruple perovskite CaMn 7O 12 by Sr doping, a compound that exhibits a charge-ordering transition above room temperature making it a candidate for oxide electronics. We also have synthesized Ca 1-xSr xMn 7O 12 (0 ≤ x ≤ 0.6) thin films by oxide molecular beam epitaxy on (LaAlO 3) 0.3(SrAl 0.5Ta 0.5O 3) 0.7 (LSAT) substrates. The substitution of Sr for Ca results in a linear expansion of the lattice, as revealed by X-ray diffraction. Temperature-dependent resistivity and X-ray diffraction measurements are used to demonstratemore » that the coupled charge-ordering and structural phase transitions can be tuned with Sr doping. An increase in Sr concentration acts to decrease the phase transition temperature (T*) from 426 K at x = 0 to 385 K at x = 0.6. Furthemore, the presence of a tunable electronic phase transition, above room temperature, points to the potential applicability of Ca 1-xSr xMn 7O 12 in sensors or oxide electronics, for example, via charge doping.« less

Effect of chemical pressure on the electronic phase transition in Ca 1-x Sr x Mn 7 O 12 films

DOE PAGES

Huon, A.; Lee, D.; Herklotz, A.; ...

2017-09-18

Here, we demonstrate how chemical pressure affects the structural and electronic phase transitions of the quadruple perovskite CaMn 7O 12 by Sr doping, a compound that exhibits a charge-ordering transition above room temperature making it a candidate for oxide electronics. We also have synthesized Ca 1-xSr xMn 7O 12 (0 ≤ x ≤ 0.6) thin films by oxide molecular beam epitaxy on (LaAlO 3) 0.3(SrAl 0.5Ta 0.5O 3) 0.7 (LSAT) substrates. The substitution of Sr for Ca results in a linear expansion of the lattice, as revealed by X-ray diffraction. Temperature-dependent resistivity and X-ray diffraction measurements are used to demonstratemore » that the coupled charge-ordering and structural phase transitions can be tuned with Sr doping. An increase in Sr concentration acts to decrease the phase transition temperature (T*) from 426 K at x = 0 to 385 K at x = 0.6. Furthemore, the presence of a tunable electronic phase transition, above room temperature, points to the potential applicability of Ca 1-xSr xMn 7O 12 in sensors or oxide electronics, for example, via charge doping.« less

Morphological Evolution of Gyroid-Forming Block Copolymer Thin Films with Varying Solvent Evaporation Rate.

PubMed

Wu, Yi-Hsiu; Lo, Ting-Ya; She, Ming-Shiuan; Ho, Rong-Ming

2015-08-05

In this study, we aim to examine the morphological evolution of block copolymer (BCP) nanostructured thin films through solvent evaporation at different rates for solvent swollen polystyrene-block-poly(l-lactide) (PS-PLLA). Interesting phase transitions from disorder to perpendicular cylinder and then gyroid can be found while using a partially selective solvent for PS to swell PS-PLLA thin film followed by solvent evaporation. During the transitions, gyroid-forming BCP thin film with characteristic crystallographic planes of (111)G, (110)G, and (211)G parallel to air surface can be observed, and will gradually transform into coexisting (110)G and (211)G planes, and finally transforms to (211)G plane due to the preferential segregation of constituted block to the surface (i.e., the thermodynamic origin for self-assembly) that affects the relative amount of each component at the air surface. With the decrease on the evaporation rate, the disorder phase will transform to parallel cylinder and then directly to (211)G without transition to perpendicular cylinder phase. Most importantly, the morphological evolution of PS-PLLA thin films is strongly dependent upon the solvent removal rate only in the initial stage of the evaporation process due to the anisotropy of cylinder structure. Once the morphology is transformed back to the isotropic gyroid structure after long evaporation, the morphological evolution will only relate to the variation of the surface composition. Similar phase transitions at the substrate can also be obtained by controlling the ratio of PLLA-OH to PS-OH homopolymers to functionalize the substrate. As a result, the fabrication of well-defined nanostructured thin films with controlled orientation can be achieved by simple swelling and deswelling with controlled evaporation rate.

mTOR kinase structure, mechanism and regulation by the rapamycin-binding domain

PubMed Central

Yang, Haijuan; Rudge, Derek G.; Koos, Joseph D.; Vaidialingam, Bhamini; Yang, Hyo J.; Pavletich, Nikola P.

2015-01-01

The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a truncated mTOR-mLST8 complex with an ATP transition state mimic and with ATP-site inhibitors. The structures reveal an intrinsically active kinase conformation, with catalytic residues and mechanism remarkably similar to canonical protein kinases. The active site is highly recessed due to the FKBP12-Rapamycin binding (FRB) domain and an inhibitory helix protruding from the catalytic cleft. mTOR activating mutations map to the structural framework that holds these elements in place, indicating the kinase is controlled by restricted access. In vitro biochemistry indicates that the FRB domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. FKBP12-rapamycin inhibits by directly blocking substrate recruitment and by further restricting active site access. The structures also reveal active site residues and conformational changes that underlie inhibitor potency and specificity. PMID:23636326

Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations

PubMed Central

Deng, Hua

2017-01-01

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis. PMID:24018325

The "Transport Specificity Ratio": a structure-function tool to search the protein fold for loci that control transition state stability in membrane transport catalysis

PubMed Central

King, Steven C

2004-01-01

Background In establishing structure-function relationships for membrane transport proteins, the interpretation of phenotypic changes can be problematic, owing to uncertainties in protein expression levels, sub-cellular localization, and protein-folding fidelity. A dual-label competitive transport assay called "Transport Specificity Ratio" (TSR) analysis has been developed that is simple to perform, and circumvents the "expression problem," providing a reliable TSR phenotype (a constant) for comparison to other transporters. Results Using the Escherichia coli GABA (4-aminobutyrate) permease (GabP) as a model carrier, it is demonstrated that the TSR phenotype is largely independent of assay conditions, exhibiting: (i) indifference to the particular substrate concentrations used, (ii) indifference to extreme changes (40-fold) in transporter expression level, and within broad limits (iii) indifference to assay duration. The theoretical underpinnings of TSR analysis predict all of the above observations, supporting that TSR has (i) applicability in the analysis of membrane transport, and (ii) particular utility in the face of incomplete information on protein expression levels and initial reaction rate intervals (e.g., in high-throughput screening situations). The TSR was used to identify gab permease (GabP) variants that exhibit relative changes in catalytic specificity (kcat/Km) for [14C]GABA (4-aminobutyrate) versus [3H]NA (nipecotic acid). Conclusions The TSR phenotype is an easily measured constant that reflects innate molecular properties of the transition state, and provides a reliable index of the difference in catalytic specificity that a carrier exhibits toward a particular pair of substrates. A change in the TSR phenotype, called a Δ(TSR), represents a specificity shift attributable to underlying changes in the intrinsic substrate binding energy (ΔGb) that translocation catalysts rely upon to decrease activation energy (). TSR analysis is therefore a structure-function tool that enables parsimonious scanning for positions in the protein fold that couple to the transition state, creating stability and thereby serving as functional determinants of catalytic power (efficiency, or specificity). PMID:15548327

Carrier Localization in Confined Vanadate Superlattices

NASA Astrophysics Data System (ADS)

Eaton, Craig; Zhang, Lei; Engel-Herbert, Roman

2015-03-01

Perovskite oxide heterostructures have attracted attention due to the wealth of phenomena emerging at the interface, as well as the presence of strong electron correlations with potential applications as active electronic material for logic application utilizing the metal-to-insulator transition. Successful monolithic integration of perovskite oxides with Si makes them an ideal material choice. Here we present the growth of cubic SrTiO3/SrVO3/SrTiO3 heterostructures on (La0.3Sr0.7) (Al0.65Ta0.35) O3 substrates and orthorhombically distorted CaTiO3/CaVO3/CaTiO3 heterostructures on (LaSrAlTa4) O3 substrates by hybrid molecular beam epitaxy, where alkaline earth metals were supplied using conventional effusion cells and the transition metals from the metal-organic precursor titanium-isopropoxide and vanadium oxi-tri-isopropoxide. Here, the interfaces are non-polar and carrier confinement in the correlated vanadate metals (d1 configuration, 1 electron per unit cell) is achieved using insulating titanates as barrier material. Growth challenges associated with optimizing conditions for cation and oxygen stoichiometry are discussed. Confined structures down to 2 ML have been studied to demonstrate the potential for tuning incipient 2D Mott transition from 3D correlated metal. Room temperature hall measurements revealed carrier concentration in SrVO3 films are 2 × 1022 cm-3 in thick films and decreases to 8 × 1020 cm-3 at 3 ML confinement, revealing the onset of strong carrier localization. Direct comparison between SrVO3 and CaVO3 structures are presented to elucidate the role of dimensional confinement and structural distortion.

RICIN-inhibitor design. Final report, 15 April 1993-14 April 1996

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

Schramm, V.L.

1996-05-01

The purpose of this proposal was to provide information which will permit the design of transition state inhibitors for ricin A-chain. The original goals were to solve the transition state structure based on kinetic isotope effects. Substrates were synthesized and the conditions for assays optimized to provide catalytic rates at least 1000 fold greater than those published prior to this work. Reliable assay methods have been established to permit routine assays for ricin A-chain. Substrate analogues for N-ribohydrolase reactions have been designed to establish whether the reaction involves leaving-group activation or oxycarbonium ion formation. Based on these results, leaving groupmore » activation is a major contributor and oxycarbonium-ion formation is a secondary contribution in the mechanism of catalysis by ricin A-chain. Using this information, the first submicromolar inhibitor of ricin A-chain has been synthesized, tested and kinetically characterized. The development of powerful inhibitors will be a direct extrapolation of these results.« less

The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

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

Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.

2011-09-20

Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamermore » with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.« less

Ferroelectric and structural properties of stress-constrained and stress-relaxed polycrystalline BiFeO3 thin films

NASA Astrophysics Data System (ADS)

Nakashima, Seiji; Ricinschi, Dan; Park, Jung Min; Kanashima, Takeshi; Fujisawa, Hironori; Shimizu, Masaru; Okuyama, Masanori

2009-03-01

The stress influence of the structural and ferroelectric properties of polycrystalline BiFeO3 (BFO) thin films has been investigated using a membrane substrate for relaxing stress. Reciprocal space mapping (RSM) measurement has been performed to confirm the stress dependence of the crystal structure of polycrystalline BFO thin films on the Pt (200 nm)/TiO2 (50 nm)/SiO2 (600 nm)/Si (625 μm) substrate (stress-constrained BFO film) and the Pt (200 nm)/TiO2 (50 nm)/SiO2 (600 nm)/Si (15 μm) membrane substrate (stress-relaxed BFO film). The BFO thin films prepared by pulsed laser deposition were polycrystalline and mainly exhibit a texture with (001) and (110) plane orientations. From the RSM results, the crystal structure of the (001)-oriented domain changes from Pm monoclinic to Cm monoclinic or to R3c rhombohedral due to stress relaxation. Moreover, at room temperature as well as at 150 K, remanent polarization (Pr) increases and double coercive field (2Ec) decreases (in the latter case from 88 to 94 μC/cm2 and from 532 to 457 kV/cm, respectively) due to relaxing stress. The enhancement of ferroelectricity is attributed to the crystal structural deformation and/or transition and angle change between the polarization direction and film plane.

Metal-semiconductor phase transition of order arrays of VO2 nanocrystals

NASA Astrophysics Data System (ADS)

Lopez, Rene; Suh, Jae; Feldman, Leonard; Haglund, Richard

2004-03-01

The study of solid-state phase transitions at nanometer length scales provides new insights into the effects of material size on the mechanisms of structural transformations. Such research also opens the door to new applications, either because materials properties are modified as a function of particle size, or because the nanoparticles interact with a surrounding matrix material, or with each other. In this paper, we describe the formation of vanadium dioxide nanoparticles in silicon substrates by pulsed laser deposition of ion beam lithographically selected sites and thermal processing. We observe the collective behavior of 50 nm diameter VO2 oblate nanoparticles, 10 nm high, and ordered in square arrays with arbitrary lattice constant. The metal-semiconductor-transition of the VO2 precipitates shows different features in each lattice spacing substrate. The materials are characterized by electron microscopy, x-ray diffraction, Rutherford backscattering. The features of the phase transition are studied via infrared optical spectroscopy. Of particular interest are the enhanced scattering and the surface plasmon resonance when the particles reach the metallic state. This resonance amplifies the optical contrast in the range of near-infrared optical communication wavelengths and it is altered by the particle-particle coupling as in the case of noble metals. In addition the VO2 nanoparticles exhibit sharp transitions with up to 50 K of hysteresis, one of the largest values ever reported for this transition. The optical properties of the VO2 nanoarrays are correlated with the size of the precipitates and their inter-particle distance. Nonlinear and ultra fast optical measurements have shown that the transition is the fastest known solid-solid transformation. The VO2 nanoparticles show the same bulk property, transforming in times shorter than 150 fs. This makes them remarkable candidates for ultrafast optical and electronic switching applications.

High Quantum Efficiency OLED Lighting Systems

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

Shiang, Joseph

The overall goal of the program was to apply improvements in light outcoupling technology to a practical large area plastic luminaire, and thus enable the product vision of an extremely thin form factor high efficiency large area light source. The target substrate was plastic and the baseline device was operating at 35 LPW at the start of the program. The target LPW of the program was a >2x improvement in the LPW efficacy and the overall amount of light to be delivered was relatively high 900 lumens. Despite the extremely difficult challenges associated with scaling up a wet solution processmore » on plastic substrates, the program was able to make substantial progress. A small molecule wet solution process was successfully implemented on plastic substrates with almost no loss in efficiency in transitioning from the laboratory scale glass to large area plastic substrates. By transitioning to a small molecule based process, the LPW entitlement increased from 35 LPW to 60 LPW. A further 10% improvement in outcoupling efficiency was demonstrated via the use of a highly reflecting cathode, which reduced absorptive loss in the OLED device. The calculated potential improvement in some cases is even larger, ~30%, and thus there is considerable room for optimism in improving the net light coupling efficacy, provided absorptive loss mechanisms are eliminated. Further improvements are possible if scattering schemes such as the silver nanowire based hard coat structure are fully developed. The wet coating processes were successfully scaled to large area plastic substrate and resulted in the construction of a 900 lumens luminaire device.« less

Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.

PubMed

Ehrnstorfer, Ines A; Geertsma, Eric R; Pardon, Els; Steyaert, Jan; Dutzler, Raimund

2014-11-01

Members of the SLC11 (NRAMP) family transport iron and other transition-metal ions across cellular membranes. These membrane proteins are present in all kingdoms of life with a high degree of sequence conservation. To gain insight into the determinants of ion selectivity, we have determined the crystal structure of Staphylococcus capitis DMT (ScaDMT), a close prokaryotic homolog of the family. ScaDMT shows a familiar architecture that was previously identified in the amino acid permease LeuT. The protein adopts an inward-facing conformation with a substrate-binding site located in the center of the transporter. This site is composed of conserved residues, which coordinate Mn2+, Fe2+ and Cd2+ but not Ca2+. Mutations of interacting residues affect ion binding and transport in both ScaDMT and human DMT1. Our study thus reveals a conserved mechanism for transition-metal ion selectivity within the SLC11 family.

Transition from Reconstruction toward Thin Film on the (110) Surface of Strontium Titanate

PubMed Central

2016-01-01

The surfaces of metal oxides often are reconstructed with a geometry and composition that is considerably different from a simple termination of the bulk. Such structures can also be viewed as ultrathin films, epitaxed on a substrate. Here, the reconstructions of the SrTiO3 (110) surface are studied combining scanning tunneling microscopy (STM), transmission electron diffraction, and X-ray absorption spectroscopy (XAS), and analyzed with density functional theory calculations. Whereas SrTiO3 (110) invariably terminates with an overlayer of titania, with increasing density its structure switches from n × 1 to 2 × n. At the same time the coordination of the Ti atoms changes from a network of corner-sharing tetrahedra to a double layer of edge-shared octahedra with bridging units of octahedrally coordinated strontium. This transition from the n × 1 to 2 × n reconstructions is a transition from a pseudomorphically stabilized tetrahedral network toward an octahedral titania thin film with stress-relief from octahedral strontia units at the surface. PMID:26954064

On the growth mechanisms of polar (100) surfaces of ceria on copper (100)

NASA Astrophysics Data System (ADS)

Hackl, Johanna; Duchoň, Tomáš; Gottlob, Daniel M.; Cramm, Stefan; Veltruská, Kateřina; Matolín, Vladimír; Nemšák, Slavomír; Schneider, Claus M.

2018-05-01

We present a study of temperature dependent growth of nano-sized ceria islands on a Cu (100) substrate. Low-energy electron microscopy, micro-electron diffraction, X-ray absorption spectroscopy, and photoemission electron microscopy are used to determine the morphology, shape, chemical state, and crystal structure of the grown islands. Utilizing real-time observation capabilities, we reveal a three-way interaction between the ceria, substrate, and local oxygen chemical potential. The interaction manifests in the reorientation of terrace boundaries on the Cu (100) substrate, characteristic of the transition between oxidized and metallic surface. The reorientation is initiated at nucleation sites of ceria islands, whose growth direction is influenced by the proximity of the terrace boundaries. The grown ceria islands were identified as fully stoichiometric CeO2 (100) surfaces with a (2 × 2) reconstruction.

Size and shape dependence of CO adsorption sites on sapphire supported Fe microcrystals

NASA Technical Reports Server (NTRS)

Papageorgopoulos, C.; Heinemann, K.

1985-01-01

The surface structure and stoichiometry of alumina substrates, as well as the size, growth characteristics, and shape of Fe deposits on sapphire substrates have been investigated by low energy electron diffraction (LEED), Auger electron spectroscopy, electron energy loss spectroscopy, and X-ray photoemission spectroscopy (XPS), as well as work function measurements, in conjunction with transition electron microscopy observations. The substrates used in this work were the following: (1) new, clean Al2O3; (2) same surface amorphized by Ar ion bombardment; (3) same surface regenerated by 650 C annealing; (4) amorphous alumina films on Ta slab; and (5) polycrystal alumina films, obtained by heating amorphous films to 600 C. Substrate cleaning was found to be most effective in producing a reproducible surface upon oxygen RF plasma treatment. The Fe nucleation and growth process was found to depend strongly on the type of substrate surface and deposition conditions. Ar ion bombardment under beam flooding, and subsequent annealing at 650 C was found an effective means to restore the original Al2O3 (1102) surface for renewed Fe deposition.

Ultrafast far-infrared studies of vanadates &mdash Multiple routes for an insulator to metal transition

NASA Astrophysics Data System (ADS)

Liu, Mengkun

The metal insulator transition in vanadates has been studied for decades and yet new discoveries still spring up revealing new physics, especially among two of the most studied members: Vanadium sesquioxide (V20 3) and Vanadium dioxide (VO2). Although subtleties abound, both of the materials have first order insulator to metal phase transitions that are considered to be related to strong electron-electron (e-e) correlation. Further, ultrafast spectroscopy of strongly correlated materials has generated great interest in the field given the potential to dynamically distinguish the difference between electronic (spin) response versus lattice responses due to the associated characteristic energy and time scales. In this thesis, I mainly focus on utilizing ultrafast optical and THz spectroscopy to study phase transition dynamics in high quality V20 3 and VO2 thin films epitaxially grown on different substrates. The main findings of the thesis are: (1) Despite the fact that the insulator to metal transition (IMT) in V203 is electron-correlation driven, lattice distortion plays an important role. Coherent oscillations in the far-infrared conductivity are observed resulting from coherent acoustic phonon modulation of the bandwidth W. The same order of lattice distortion induces less of an effect on the electron transport in VO2 in comparison to V203. This is directly related to the difference in latent heat of the phase transitions in VO2 and V203. (2) It is possible for the IMT to occur with very little structural change in epitaxial strained VO2 films, like in the case of Cr doped or strained V203. However, in V02, this necessitates a large strain which is only possible by clamping to a substrate with larger c axis parameter through epitaxial growth. This is demonstrated for VO 2 films on TiO2 substrates. (3) Initiating an ultrafast photo-induced insulator-to-metal transition (IMT) is not only possible with above bandgap excitation, but also possible with high-field far-infrared excitation. With the help of the field enhancement in metamaterial split ring resonator gaps, we obtain picosecond THz electric field transients of several MV/cm which is sufficient to drive the insulator to metal transition in V02.

Phase-field model of domain structures in ferroelectric thin films

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

Li, Y. L.; Hu, S. Y.; Liu, Z. K.

A phase-field model for predicting the coherent microstructure evolution in constrained thin films is developed. It employs an analytical elastic solution derived for a constrained film with arbitrary eigenstrain distributions. The domain structure evolution during a cubic{r_arrow}tetragonal proper ferroelectric phase transition is studied. It is shown that the model is able to simultaneously predict the effects of substrate constraint and temperature on the volume fractions of domain variants, domain-wall orientations, domain shapes, and their temporal evolution. {copyright} 2001 American Institute of Physics.

Scalable hydrothermal synthesis of free-standing VO₂ nanowires in the M1 phase.

PubMed

Horrocks, Gregory A; Singh, Sujay; Likely, Maliek F; Sambandamurthy, G; Banerjee, Sarbajit

2014-09-24

VO2 nanostructures derived from solution-phase methods are often plagued by broadened and relatively diminished metal-insulator transitions and adventitious doping due to imperfect control of stoichiometry. Here, we demonstrate a stepwise scalable hydrothermal and annealing route for obtaining VO2 nanowires exhibiting almost 4 orders of magnitude abrupt (within 1 °C) metal-insulator transitions. The prepared nanowires have been characterized across their structural and electronic phase transitions using single-nanowire Raman microprobe analysis, ensemble differential scanning calorimetry, and single-nanowire electrical transport measurements. The electrical band gap is determined to be 600 meV and is consistent with the optical band gap of VO2, and the narrowness of differential scanning calorimetry profiles indicates homogeneity of stoichiometry. The preparation of high-quality free-standing nanowires exhibiting pronounced metal-insulator transitions by a solution-phase process allows for scalability, further solution-phase processing, incorporation within nanocomposites, and integration onto arbitrary substrates.

Two-dimensional tantalum disulfide: controlling structure and properties via synthesis

NASA Astrophysics Data System (ADS)

Zhao, Rui; Grisafe, Benjamin; Krishna Ghosh, Ram; Holoviak, Stephen; Wang, Baoming; Wang, Ke; Briggs, Natalie; Haque, Aman; Datta, Suman; Robinson, Joshua

2018-04-01

Tantalum disulfide (TaS2) is a transition metal dichalcogenide (TMD) that exhibits phase transition induced electronic property modulation at low temperature. However, the appropriate phase must be grown to enable the semiconductor/metal transition that is of interest for next generation electronic applications. In this work, we demonstrate direct and controllable synthesis of ultra-thin 1T-TaS2 and 2H-TaS2 on a variety of substrates (sapphire, SiO2/Si, and graphene) via powder vapor deposition. The synthesis process leads to single crystal domains ranging from 20 to 200 nm thick and 1-10 µm on a side. The TaS2 phase (1T or 2H) is controlled by synthesis temperature, which subsequently is shown to control the electronic properties. Furthermore, this work constitutes the first demonstration of a metal-insulator phase transition in directly synthesized 1T-TaS2 films and domains by electronic means.

Communication: Orientational structure manipulation in nematic liquid crystal droplets induced by light excitation of azodendrimer dopant

NASA Astrophysics Data System (ADS)

Shvetsov, Sergey A.; Emelyanenko, Alexander V.; Boiko, Natalia I.; Liu, Jui-Hsiang; Khokhlov, Alexei R.

2017-06-01

Reversible orientational transitions in the droplets of a nematic liquid crystal (NLC) caused by the change of boundary conditions under the low intensity diode illumination are investigated. Photosensitivity of NLC is achieved by the addition of the dendrimer compound with azobenzene terminal groups. Two types of NLC droplets in glycerol are considered: the spherical droplets in the bulk of glycerol and the droplets laid-down onto the solid substrate. In the second case, the first order phase transition is revealed. The effects described can be useful for the development of highly sensitive chemical detectors and microsized photo-tunable optical devices.

Broad Frequency LTCC Vertical Interconnect Transition for Multichip Modules and System on Package Applications

NASA Technical Reports Server (NTRS)

Decrossas, Emmanuel; Glover, Michael D.; Porter, Kaoru; Cannon, Tom; Mantooth, H. Alan; Hamilton, M. C.

2013-01-01

Various stripline structures and flip chip interconnect designs for high-speed digital communication systems implemented in low temperature co-fired ceramic (LTCC) substrates are studied in this paper. Specifically, two different transition designs from edge launch 2.4 millimeter connectors to stripline transmission lines embedded in LTCC are discussed. After characterizing the DuPont (sup trademark) 9K7 green tape, different designs are proposed to improve signal integrity for high-speed digital data. The full-wave simulations and experimental data validate the presented designs over a broad frequency band from Direct Current to 50 gigahertz and beyond.

Aqueous solution epitaxy of CdS layers on CuInSe 2

NASA Astrophysics Data System (ADS)

Furlong, M. J.; Froment, M.; Bernard, M. C.; Cortès, R.; Tiwari, A. N.; Krejci, M.; Zogg, H.; Lincot, D.

1998-09-01

Epitaxial CdS thin films have been deposited from an aqueous ammonia solution containing cadmium ions and thiourea as precursors on single crystalline CuInSe 2 films prepared by MBE on Si(1 1 1) and GaAs(1 0 0) substrates. The structure and quality of the films were investigated by RHEED, glancing angle XRD and HRTEM in cross-section. The films are cubic on (1 0 0) substrates, and mixed cubic and hexagonal on (1 1 1) substrates due to the presence of stacking faults parallel to the substrate. The growth is under surface kinetic control with an activation energy of 85 kJ mol -1. Epitaxy improves with increasing temperature and an epitaxial transition temperature at approx. 60°C is demonstrated in the selected experimental conditions. The epitaxy is very sensitive to the preparation of the surface. Beneficial effects of in situ or ex situ chemical etching are found. Similarities between aqueous solution and vapor-phase chemical depositions are pointed out.

Epitaxial Ni-Mn-Ga-Co thin films on PMN-PT substrates for multicaloric applications

NASA Astrophysics Data System (ADS)

Schleicher, B.; Niemann, R.; Diestel, A.; Hühne, R.; Schultz, L.; Fähler, S.

2015-08-01

Multicaloric stacks consisting of a magnetocaloric film on a piezoelectric substrate promise improved caloric properties as the transition temperature can be controlled by both magnetic and electric fields. We present epitaxially grown magnetocaloric Ni-Mn-Ga-Co thin films on ferroelectric Pb(Mg1/3Nb2/3)0.72Ti0.28O3 substrates. Structure and microstructure of two samples, being in the austenitic and martensitic state at room temperature, are investigated by X-ray diffraction in two- and four-circle geometry and by atomic force microscopy. In addition, high temperature magnetometry was performed on the latter sample. The combination of these methods allows separating the influence of epitaxial growth and martensitic transformation. A preferential alignment of twin boundaries is observed already in the as-deposited state, which indicates the presence of prestress, without applying an electric field to the substrate. A temperature-magnetic field phase diagram is presented, which demonstrates the inverse magnetocaloric effect of the epitaxial Ni-Mn-Ga-Co film.

Method for applying a diffusion barrier interlayer for high temperature components

DOEpatents

Wei, Ronghua; Cheruvu, Narayana S.

2016-03-08

A coated substrate and a method of forming a diffusion barrier coating system between a substrate and a MCrAl coating, including a diffusion barrier coating deposited onto at least a portion of a substrate surface, wherein the diffusion barrier coating comprises a nitride, oxide or carbide of one or more transition metals and/or metalloids and a MCrAl coating, wherein M includes a transition metal or a metalloid, deposited on at least a portion of the diffusion barrier coating, wherein the diffusion barrier coating restricts the inward diffusion of aluminum of the MCrAl coating into the substrate.

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

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

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

Structural and electrical properties of large area epitaxial VO2 films grown by electron beam evaporation

NASA Astrophysics Data System (ADS)

Théry, V.; Boulle, A.; Crunteanu, A.; Orlianges, J. C.; Beaumont, A.; Mayet, R.; Mennai, A.; Cosset, F.; Bessaudou, A.; Fabert, M.

2017-02-01

Large area (up to 4 squared inches) epitaxial VO2 films, with a uniform thickness and exhibiting an abrupt metal-insulator transition with a resistivity ratio as high as 2.85 × 10 4 , have been grown on (001)-oriented sapphire substrates by electron beam evaporation. The lattice distortions (mosaicity) and the level of strain in the films have been assessed by X-ray diffraction. It is demonstrated that the films grow in a domain-matching mode where the distortions are confined close to the interface which allows growth of high-quality materials despite the high film-substrate lattice mismatch. It is further shown that a post-deposition high-temperature oxygen annealing step is crucial to ensure the correct film stoichiometry and provide the best structural and electrical properties. Alternatively, it is possible to obtain high quality films with a RF discharge during deposition, which hence do not require the additional annealing step. Such films exhibit similar electrical properties and only slightly degraded structural properties.

Filtered pulsed cathodic arc deposition of fullerene-like carbon and carbon nitride films

NASA Astrophysics Data System (ADS)

Tucker, Mark D.; Czigány, Zsolt; Broitman, Esteban; Näslund, Lars-Åke; Hultman, Lars; Rosen, Johanna

2014-04-01

Carbon and carbon nitride films (CNx, 0 ≤ x ≤ 0.26) were deposited by filtered pulsed cathodic arc and were investigated using transmission electron microscopy and X-ray photoelectron spectroscopy. A "fullerene-like" (FL) structure of ordered graphitic planes, similar to that of magnetron sputtered FL-CNx films, was observed in films deposited at 175 °C and above, with N2 pressures of 0 and 0.5 mTorr. Higher substrate temperatures and significant nitrogen incorporation are required to produce similar FL structure by sputtering, which may, at least in part, be explained by the high ion charge states and ion energies characteristic of arc deposition. A gradual transition from majority sp3-hybridized films to sp2 films was observed with increasing substrate temperature. High elastic recovery, an attractive characteristic mechanical property of FL-CNx films, is evident in arc-deposited films both with and without nitrogen content, and both with and without FL structure.

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

NASA Astrophysics Data System (ADS)

Deng, Zengqin; Wang, Qing; Liu, Zhao; Zhang, Manfeng; Machado, Ana Carolina Dantas; Chiu, Tsu-Pei; Feng, Chong; Zhang, Qi; Yu, Lin; Qi, Lei; Zheng, Jiangge; Wang, Xu; Huo, Xinmei; Qi, Xiaoxuan; Li, Xiaorong; Wu, Wei; Rohs, Remo; Li, Ying; Chen, Zhongzhou

2015-07-01

Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.

In situ TEM observation of heterogeneous phase transition of a constrained single-crystalline Ag2Te nanowire.

PubMed

In, Juneho; Yoo, Youngdong; Kim, Jin-Gyu; Seo, Kwanyong; Kim, Hyunju; Ihee, Hyotchel; Oh, Sang Ho; Kim, Bongsoo

2010-11-10

Laterally epitaxial single crystalline Ag2Te nanowires (NWs) are synthesized on sapphire substrates by the vapor transport method. We observed the phase transitions of these Ag2Te NWs via in situ transmission electron microscopy (TEM) after covering them with Pt layers. The constrained NW shows phase transition from monoclinic to a body-centered cubic (bcc) structure near the interfaces, which is ascribed to the thermal stress caused by differences in the thermal expansion coefficients. Furthermore, we observed the nucleation and growth of bcc phase penetrating into the face-centered cubic matrix at 200 °C by high-resolution TEM in real time. Our results would provide valuable insight into how compressive stresses imposed by overlayers affect behaviors of nanodevices.

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

PubMed

Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

2017-01-17

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4 O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S 1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S 1 state is exposed to light, the S 1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S 1 → S 2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the "narrow" channel through a "carousel" rearrangement of waters around Mn4 upon the S 2 → S 3 transition. An alternative hypothesis suggests water delivery through the "large" channel on the Ca side. However, both water delivery paths lead to a similar S 3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O 2 evolution.

The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

DOE PAGES

Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

2016-12-21

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S 1 state is exposed to light, the S 1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S 1 → S 2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the “narrow” channel through a “carousel” rearrangement of waters around Mn4 upon the S 2 → S 3 transition. An alternative hypothesis suggests water delivery through the “large” channel on the Ca side. However, both water delivery paths lead to a similar S 3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O 2 evolution.« less

The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

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

Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S 1 state is exposed to light, the S 1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S 1 → S 2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the “narrow” channel through a “carousel” rearrangement of waters around Mn4 upon the S 2 → S 3 transition. An alternative hypothesis suggests water delivery through the “large” channel on the Ca side. However, both water delivery paths lead to a similar S 3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O 2 evolution.« less

Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation.

PubMed

Jamshidi, Shirin; Jalili, Seifollah; Rafii-Tabar, Hashem

2015-01-01

Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.

Anomalous fast dynamics of adsorbate overlayers near an incommensurate structural transition.

PubMed

Granato, Enzo; Ying, S C; Elder, K R; Ala-Nissila, T

2013-09-20

We investigate the dynamics of a compressively strained adsorbed layer on a periodic substrate via a simple two-dimensional model that admits striped and hexagonal incommensurate phases. We show that the mass transport is superfast near the striped-hexagonal phase boundary and in the hexagonal phase. For an initial step profile separating a bare substrate region (or "hole") from the rest of a striped incommensurate phase, the superfast domain wall dynamics leads to a bifurcation of the initial step profile into two interfaces or profiles propagating in opposite directions with a hexagonal phase in between. This yields a theoretical understanding of the recent experiments for the Pb/Si(111) system.

Epitaxial Ba2IrO4 thin-films grown on SrTiO3 substrates by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Nichols, J.; Korneta, O. B.; Terzic, J.; Cao, G.; Brill, J. W.; Seo, S. S. A.

2014-03-01

We have synthesized epitaxial Ba2IrO4 (BIO) thin-films on SrTiO3 (001) substrates by pulsed laser deposition and studied their electronic structure by dc-transport and optical spectroscopic experiments. We have observed that BIO thin-films are insulating but close to the metal-insulator transition boundary with significantly smaller transport and optical gap energies than its sister compound, Sr2IrO4. Moreover, BIO thin-films have both an enhanced electronic bandwidth and electronic-correlation energy. Our results suggest that BIO thin-films have great potential for realizing the interesting physical properties predicted in layered iridates.

Effect of annealing on optical properties and structure of the vanadium dioxide thin films

NASA Astrophysics Data System (ADS)

Zhu, Huiqun; Li, Yi; Li, Yuming; Huang, Yize; Tong, Guoxiang; Fang, Baoying; Zheng, Qiuxin; Li, Liu; Shen, Yujian

2012-10-01

VO2 thin films were prepared on soda-lime glass substrates by DC magnetron sputtering at room temperature using vanadium target and post annealing in air. X-ray diffraction and FTIR spectroscopy analyses showed that the films obtained at the optimized parameters have high VO2 (011) orientation. Both low temperature deposition and post annealing method were beneficial to grow the nano-films with pure VO2 phase-structure and composition. Metalinsulator transition properties of the VO2 films in terms of infrared transmittance, transmittance variation and film thickness were investigated under varying annealing temperature. Results showed that infrared transmittance variation and transition temperature of the nano-films were significantly improved and reduced respectively. Therefore, this study was able to develop practical low-cost preparation methods for high-performance intelligent energy-saving thin films.

The Challenge of Producing Fiber-Based Organic Electronic Devices

PubMed Central

Könyves-Toth, Tobias; Gassmann, Andrea; von Seggern, Heinz

2014-01-01

The implementation of organic electronic devices on fibers is a challenging task, not yet investigated in detail. As was shown earlier, a direct transition from a flat device structure to a fiber substrate is in principle possible. However, a more detailed investigation of the process reveals additional complexities than just the transition in geometry. It will be shown, that the layer formation of evaporated materials behaves differently due to the multi-angled incidence on the fibers surface. In order to achieve homogenous layers the evaporation process has to be adapted. Additionally, the fiber geometry itself facilitates damaging of its surface due to mechanical impact and leads to a high surface roughness, thereby often hindering commercial fibers to be used as substrates. In this article, a treatment of commercial polymer-coated glass fibers will be demonstrated that allows for the fabrication of rather flexible organic light-emitting diodes (OLEDs) with cylindrical emission characteristics. Since OLEDs rely the most on a smooth substrate, fibers undergoing the proposed treatment are applicable for other organic electronic devices such as transistors and solar cells. Finally, the technique also supports the future fabrication of organic electronics not only in smart textiles and woven electronics but also in bent surfaces, which opens a wide range of applications. PMID:28788128

Neutron irradiation and high temperature effects on amorphous Fe-based nano-coatings on steel - A macroscopic assessment

NASA Astrophysics Data System (ADS)

Simos, N.; Zhong, Z.; Dooryhee, E.; Ghose, S.; Gill, S.; Camino, F.; Şavklıyıldız, İ.; Akdoğan, E. K.

2017-06-01

The study revealed that loss of ductility in an amorphous Fe-alloy coating on a steel substrate composite structure was essentially prevented from occurring, following radiation with modest neutron doses of ∼2 × 1018 n/cm2. At the higher neutron dose of ∼2 × 1019, macroscopic stress-strain analysis showed that the amorphous Fe-alloy nanostructured coating, while still amorphous, experienced radiation-induced embrittlement, no longer offering protection against ductility loss in the coating-substrate composite structure. Neutron irradiation in a corrosive environment revealed exemplary oxidation/corrosion resistance of the amorphous Fe-alloy coating, which is attributed to the formation of the Fe2B phase in the coating. To establish the impact of elevated temperatures on the amorphous-to-crystalline transition in the amorphous Fe-alloy, electron microscopy was carried out which confirmed the radiation-induced suppression of crystallization in the amorphous Fe-alloy nanostructured coating.

Optimization of a growth process for as-grown 2D materials-based devices

NASA Astrophysics Data System (ADS)

Lindquist, Miles; Khadka, Sudiksha; Aleithan, Shrouq; Blumer, Ari; Wickramasinghe, Thushan; Thorat, Ruhi; Kordesch, Martin; Stinaff, Eric

We will present the effects of varying key parameters of a deterministic growth method for producing self-contacted 2D transition metal dichalcogenides. Chemical vapor deposition is used to grow a film of 2D material nucleated around and seeded from metallic features prepared by photolithography and sputtering on a Si/SiO2 substrate prior to growth. We will focus on a particular method of growing variable MoS2 based device structures. The goal of this work is to arrive at robust platform for growing a variety of device structures by systematically altering parameters such as the amount of reactants used, the heat of the substrate and oxide powder, and the flow rate of argon gas used. These results will help advance a comprehensive process for the scalable production of as-grown, complex, 2D materials-based device architectures.

CVD growth of large-area and high-quality HfS2 nanoforest on diverse substrates

NASA Astrophysics Data System (ADS)

Zheng, Binjie; Wang, Zegao; Qi, Fei; Wang, Xinqiang; Yu, Bo; Zhang, Wanli; Chen, Yuanfu

2018-03-01

Two-dimensional layered transition metal dichalcogenides (TMDs) have attracted burgeoning attention due to their various properties and wide potential applications. As a new TMD, hafnium disulfide (HfS2) is theoretically predicted to have better electrical performance than widely studied MoS2. The experimental researches also confirmed the extraordinary feature in electronics and optoelectronics. However, the maximal device performance may not be achieved due to its own limitation of planar structure and challenge of transfer without contamination. Here, through the chemical vapor deposition (CVD) technique, inch-size HfS2 nanoforest has been directly grown on diverse objective substrates covering insulating, semiconducting and conducting substrates. This direct CVD growth without conventional transfer process avoids contamination and degradation in quality, suggesting its promising and wide applications in high-quality and multifarious devices. It is noted that all the HfS2 nanoforests grown on diverse substrates are constructed with vertically aligned few-layered HfS2 nanosheets with high crystalline quality and edge orientation. Moreover, due to its unique structure, the HfS2 nanoforest owns abundant exposed edge sites and large active surface area, which is essential to apply in high-performance catalyst, sensor, and energy storage or field emitter.

Functionalized carbon nanostructures for hydrogen catalysis

NASA Astrophysics Data System (ADS)

Hu, Lung-Hao

Sodium borohydride, NaBH4, is widely used as a source of pure hydrogen. Hydrogen is of interest because it is a source of clean energy. It can be converted directly into electrical energy by means of fuel cells. One of the objectives of this thesis was to develop a new catalytic process to (i) enhance the rate of hydrogen generation, and (ii) to achieve hydrogen generation equal to 100% of the theoretically expected value. The catalyst investigated in this research is constructed by starting from single wall carbon nanotubes (SWNT). This material has a very high specific surface area and good conductivity. The SWNT were formed into a paper by a special filtration process. Polysilazane, a polymeric precursor (Ceraset(TM)-SN from KiON Corp., Wiesbaden, Germany) was diluted by acetone and then layered onto SWNT paper. The Ceraset coated SWNT was then pyrolyzed at 1100°C for three hours to form a silicon carbonitride (SiCN), polymer derived ceramic (PDC), layer on the surface of SWNT filtered paper. This functionalized SiCN carbon nanotube paper (SiCN/CNT) was used as the substrate for catalyst dispersions. The catalyst consisted of transition metals, Pt/Pd/Ru. Suspension solutions of Pt, Pd and Ru were impregnated onto the SiCN/CNT paper with the expectation of creating a monolayer of these transition metals on surface of the SiCN/CNT substrate. It is likely that an interaction could occur between the transition metals and the silicon atoms present in the SiCN layer on the surface of the carbon nanotubes. It is known that transition metals and silicon react to form silicides, suggesting the formation of a strong Si-transition metal bond. Therefore, it is possible that this bond could provide good wetting of metal atoms on SiCN functionalized carbon nanotube substrate. In the limit a monolayer of the transition metals may be achieved, which would correspond to a near zero dihedral angle between the substrate and the cluster of transition metals. In such a scenario a very high activity of the catalyst can be achieved raising the figure of merit for hydrogen generation nearly to its highest possible value. The catalytic performance is also related to the intrinsic activity of chemical composition of the catalyst. In the present work, the use of catalysts of a ternary composition has been discovered to enhance the activity of the catalyst. The experiments presented in this work use Pt/Pd/Ru catalyzed SiCN/CNT as the catalyst to react with sodium borohydride for the hydrogen generation. The thickness of SiCN/CNT paper is one of the factors, which influences the hydrogen generation rate: thinner papers produce higher rates of hydrogen generation. The likely reason for this phenomenon is that hydrogen bubbles can become trapped within the mesh of carbon nanotubes that constitute the paper-like structure of the catalyst. It is hypothesized that hydrogen bubbles can escape more easily from the interior of the paper if the paper is thinner. The effect of the paper thickness on the hydrogen generation rate forms the first part of the thesis. In the next phase of the thesis, thin film structures of carbon nanotubes, about 300 nm high, were created to serve as the catalyst substrates. Transition metals were deposited on to these substrates by an electrophoretic process. In these catalysts huge increases in hydrogen generation rates, relative to the CNT-paper architecture, were achieved. Indeed the Figure of Merit (FOM), expressed as liters per minute of hydrogen generated per gram of the precious metals, per unit molar concentration of NaBH4, (Lmin-1g met-1[NaBH4]-1), of these "thin film CNT" catalysts was up to three orders of magnitude greater than could be achieved with the thick CNT paper, as described in the first part of the thesis. These values for the FOM are more than two orders of magnitude greater than the highest values for hydrogen generation from NaBH4 reported in the literature. The reaction mechanism and the catalytic efficiency in the present work is described in terms of an electric charge transfer, as has been proposed in the literature. In this mechanism the negative charge on the BH4 - ion is transferred with one hydrogen atom via SiCN/CNT structure, which increases the catalytic activity. (Abstract shortened by UMI.)

Low-pressure large-area magnetron sputter deposition of YBa2Cu3O7-δ films for industrial applications

NASA Astrophysics Data System (ADS)

Wördenweber, Roger; Hollmann, Eugen; Poltiasev, Michael; Neumüller, Heinz-Werner

2003-05-01

This paper addresses the development of a technically relevant sputter-deposition process for YBa2Cu3O7-delta films. First, the simulation of the particle transport from target to substrate indicates that only at a reduced pressure of p approx 1-10 Pa can a sufficiently large deposition rate and homogeneous stoichiometric distribution of the particles during large-area deposition be expected. The results of the simulations are generally confirmed by deposition experiments on CeO2 buffered sapphire and LaAlO3 substrates using a magnetron sputtering system suitable for large-area deposition. However, it is shown that in addition to the effect of scattering during particle transport, the conditions at the substrate lead to a selective growth of Y-Ba-Cu-O phases that, among others, strongly affect the growth rate. For example, the growth rate is more than three times larger for optimized parameters compared to the same set of parameters but at 100 K lower substrate temperature. Stoichiometrical and structural perfect films can be grown at low pressure (p < 10 Pa). However, the superconducting transition temperature of these films is reduced. The Tc reduction seems to be correlated with the c-axis length of YBa2Cu3O7-delta. Two possible explanations for the increased c-axis length and the correlated reduced transition temperature are discussed, i.e. reduced oxygen content and strong cation site disorder due to the heavy particle bombardment.

Vibrational Studies of Adsorbate-Induced Reconstruction on Molybdenum Surfaces.

NASA Astrophysics Data System (ADS)

Lopinski, Gregory Peter

Adsorbate-induced rearrangement of the substrate structure strongly modifies the adsorbate-substrate and adsorbate-adsorbate interactions, leading to the complex behavior observed in many chemisorption systems. In this thesis the H/Mo(211), O/Mo(211) and Na/Mo(100) systems have been studied using high resolution electron energy loss spectroscopy (HREELS) to observe vibrations of the adsorbed atoms. The vibrational data is correlated with observations of the long-range order probed by LEED as well as the work function changes induced by adsorption. Adsorbate -induced substrate reconstruction plays an important role in all three of these systems. Studies of the coadsorption systems O+H/Mo(211) and Na+O/Mo(100) indicate how these effects can influence interactions between adsorbates. For H/Mo(211), above 1ML a (1 x 1) to (1 x 2) transition is observed and attributed to modification of the substrate periodicity. Below 1ML, H atoms are bridge bonded and induce local distortions of the substrate. The transition to the (1 x 2) phase involves the ordering of these displacements and occupation of three-fold sites partially populated by conversion of the bridge bonded species. This conversion accounts for the sawtooth-like coverage dependence of the work function. The structural model proposed for this system is also supported by the desorption parameters and partial molar entropy extracted from adsorption isobars. Oxygen adsorption on Mo(211) involves the occupation of multiple binding sites, with both the long-range order and the local geometry of the adsorbate phases strongly temperature dependent. Coadsorption of low coverages of oxygen and hydrogen leads to segregation of the two adsorbates which can be understood in terms of a substrate-mediated repulsive interaction between O and H. For Na/Mo(100), the frequency of the Na-Mo symmetric stretch mode does not shift with coverage although the mode intensity is strongly coverage dependent. The absence of a frequency shift as well as the form of the observed coverage dependence differ from the predictions of the traditional charge transfer model of alkali adsorption. The relevance of the vibrational results to the Na-induced structural changes observed on this surface are also discussed. Na adsorption has been found to dramatically alter the interaction of oxygen with this surface, due to the presence of a strong attractive interaction between Na and O that forces O atoms to occupy a different binding site than on a clean surface.

Strain engineering of atomic and electronic structures of few-monolayer-thick GaN

NASA Astrophysics Data System (ADS)

Kolobov, A. V.; Fons, P.; Saito, Y.; Tominaga, J.; Hyot, B.; André, B.

2017-07-01

Two-dimensional (2D) semiconductors possess the potential to ultimately minimize the size of devices and concomitantly drastically reduce the corresponding energy consumption. In addition, materials in their atomic-scale limit often possess properties different from their bulk counterparts paving the way to conceptually novel devices. While graphene and 2D transition-metal dichalcogenides remain the most studied materials, significant interest also exists in the fabrication of atomically thin structures from traditionally 3D semiconductors such as GaN. While in the monolayer limit GaN possesses a graphenelike structure and an indirect band gap, it was recently demonstrated that few-layer GaN acquires a Haeckelite structure in the direction of growth with an effectively direct gap. In this work, we demonstrate the possibility of strain engineering of the atomic and electronic structure of few-monolayer-thick GaN structures, which opens new avenues for their practical application in flexible nanoelectronics and nano-optoelectronics. Our simulations further suggest that due to the weak van der Waals-like interaction between a substrate and an overlayer, the use of a MoS2 substrate may be a promising route to fabricate few-monolayer Haeckelite GaN experimentally.

A New Structural Form in the SAM/Metal-Dependent O;#8209;Methyltransferase Family: MycE from the Mycinamicin Biosynthetic Pathway

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

Akey, David L.; Li, Shengying; Konwerski, Jamie R.

2012-08-01

O-linked methylation of sugar substituents is a common modification in the biosynthesis of many natural products and is catalyzed by multiple families of S-adenosyl-l-methionine (SAM or AdoMet)-dependent methyltransferases (MTs). Mycinamicins, potent antibiotics from Micromonospora griseorubida, can be methylated at two positions on a 6-deoxyallose substituent. The first methylation is catalyzed by MycE, a SAM- and metal-dependent MT. Crystal structures were determined for MycE bound to the product S-adenosyl-l-homocysteine (AdoHcy) and magnesium, both with and without the natural substrate mycinamicin VI. This represents the first structure of a natural product sugar MT in complex with its natural substrate. MycE is amore » tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding. The symmetric MycE tetramer has a novel MT organization in which each of the four active sites is formed at the junction of three monomers within the tetramer. The active-site structure supports a mechanism in which a conserved histidine acts as a general base, and the metal ion helps to position the methyl acceptor and to stabilize a hydroxylate intermediate. A conserved tyrosine is suggested to support activity through interactions with the transferred methyl group from the SAM methyl donor. The structure of the free enzyme reveals a dramatic order-disorder transition in the active site relative to the S-adenosyl-L-homocysteine complexes, suggesting a mechanism for product/substrate exchange through concerted movement of five loops and the polypeptide C-terminus.« less

Self-Assembled Structures of Benzoic Acid on Au(111) Surface

NASA Astrophysics Data System (ADS)

Vu, Thu-Hien; Wandlowski, Thomas

2017-06-01

Electrochemical scanning tunneling microscopy combined with cyclic voltammetry were employed to explore the self-assembly of benzoic acid (BA) on a Au(111) substrate surface in a 0.1-M HClO4 solution. At the negatively charged surface, BA molecules form two highly ordered physisorbed adlayers with their phenyl rings parallel to the substrate surface. High-resolution scanning tunneling microscopy images reveal the packing arrangement and internal molecular structures. The striped pattern and zigzag structure of the BA adlayers are composed of parallel rows of dimers, in which two BA molecules are bound through a pair of O-H···O hydrogen bonds. Increasing the electrode potential further to positive charge densities of Au(111) leads to the desorption of the physisorbed hydrogen-bonded networks and the formation of a chemisorbed adlayer. BA molecules change their orientation from planar to upright fashion, which is accompanied by the deprotonation of the carboxyl group. Furthermore, potential-induced formation and dissolution of BA adlayers were also investigated. Structural transitions between the various types of ordered adlayers occur according to a nucleation and growth mechanism.

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

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

Sullivan, Sarah M.; Holyoak, Todd

2008-09-17

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection

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

Sullivan, S.M.; Holyoak, T.

2009-05-26

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Dynamic-compliance and viscosity of PET and PEN

NASA Astrophysics Data System (ADS)

Weick, Brian L.

2016-05-01

Complex dynamic-compliance and in-phase dynamic-viscosity data are presented and analyzed for PET and PEN advanced polyester substrates used for magnetic tapes. Frequency-temperature superposition is used to predict long-term behavior. Temperature and frequency ranges for the primary glass transition and secondary transitions are discussed and compared for PET and PEN. Shift factors from frequency-temperature superposition are used to determine activation energies for the transitions, and WLF parameters are determined for the polyester substrates.

Dynamic-compliance and viscosity of PET and PEN

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

Weick, Brian L.

Complex dynamic-compliance and in-phase dynamic-viscosity data are presented and analyzed for PET and PEN advanced polyester substrates used for magnetic tapes. Frequency-temperature superposition is used to predict long-term behavior. Temperature and frequency ranges for the primary glass transition and secondary transitions are discussed and compared for PET and PEN. Shift factors from frequency-temperature superposition are used to determine activation energies for the transitions, and WLF parameters are determined for the polyester substrates.

High-resolution structural studies of ultra-thin magnetic, transition metal overlayers and two-dimensional transition metal oxides using synchrotron radiation

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

Kellar, S.A.

This thesis report the surface-structure determination of three, ultra-thin magnetic transition-metal films, Fe/Au(100), Mn/Ni(100), and Mn/Cu(100) using Angle-Resolved Photoemission Extended Fine Structure (ARPEFS) and photoelectron holography. These structural studies are the first to use non-s initial states in the ARPEFS procedure. This thesis also reports an ARPEFS surface-structure determination of a two-dimensional transition-metal oxide, [(1 x 1)O/W(110)] x 12. The authors have analyzed the ARPFES signal from the Au 4f{sub 7/5} core level of the Au(1 ML)/Fe(15 ML)/Au(100) system. The analysis shows that the Fe grows layer by layer with one monolayer of gold, acting as a surfactant, remaining onmore » top of the growing Fe layers. These surface gold atoms sit in the four-fold hollow site, 1.67 {+-} 0.02 A above the iron surface. The grown Fe layer is very much like the bulk, bcc iron, with an interlayer spacing of 1.43 {+-} 0.03 A. Analysis of the Mn 3p ARPEFS signals from c(2 x 2)Mn/Ni(100) and c(2 x 2)Mn/Cu(100) shows that the Mn forms highly corrugated surface alloys. The corrugation of the Mn/Ni(100) and Mn/Cu(100) systems are 0.24 {+-} 0.02 A and 0.30 {+-} 0.04 A respectively. In both cases the Mn is sticking above the plane of the surface substrate atoms. For the Mn/Ni(100) system the first layer Ni is contracted 4% from the bulk value. The Mn/Cu(100) system shows bulk spacing for the substrate Cu. Photoelectron holography shows that the Mn/Ni interface is very abrupt with very little Mn leaking into the second layer, while the Mn/Cu(100) case has a significant amount of Mn leaking into the second layer. A new, five-element electrostatic electron lens was developed for hemispherical electron-energy analyzers. This lens system can be operated at constant transverse or constants angular magnification, and has been optimized for use with the very small photon-spot sizes. Improvements to the hemispherical electron-energy analyzer are also discussed.« less

Rifampin phosphotransferase is an unusual antibiotic resistance kinase

PubMed Central

Stogios, Peter J.; Cox, Georgina; Spanogiannopoulos, Peter; Pillon, Monica C.; Waglechner, Nicholas; Skarina, Tatiana; Koteva, Kalinka; Guarné, Alba; Savchenko, Alexei; Wright, Gerard D.

2016-01-01

Rifampin (RIF) phosphotransferase (RPH) confers antibiotic resistance by conversion of RIF and ATP, to inactive phospho-RIF, AMP and Pi. Here we present the crystal structure of RPH from Listeria monocytogenes (RPH-Lm), which reveals that the enzyme is comprised of three domains: two substrate-binding domains (ATP-grasp and RIF-binding domains); and a smaller phosphate-carrying His swivel domain. Using solution small-angle X-ray scattering and mutagenesis, we reveal a mechanism where the swivel domain transits between the spatially distinct substrate-binding sites during catalysis. RPHs are previously uncharacterized dikinases that are widespread in environmental and pathogenic bacteria. These enzymes are members of a large unexplored group of bacterial enzymes with substrate affinities that have yet to be fully explored. Such an enzymatically complex mechanism of antibiotic resistance augments the spectrum of strategies used by bacteria to evade antimicrobial compounds. PMID:27103605

Cooperative catalysis by tertiary amino-thioureas: mechanism and basis for enantioselectivity of ketone cyanosilylation.

PubMed

Zuend, Stephan J; Jacobsen, Eric N

2007-12-26

The mechanism of the enantioselective cyanosilylation of ketones catalyzed by tertiary amino-thiourea derivatives was investigated using a combination of experimental and theoretical methods. The kinetic analysis is consistent with a cooperative mechanism in which both the thiourea and the tertiary amine of the catalyst are involved productively in the rate-limiting cyanide addition step. Density functional theory calculations were used to distinguish between mechanisms involving thiourea activation of ketone or of cyanide in the enantioselectivity-determining step. The strong correlation obtained between experimental and calculated ee's for a range of substrates and catalysts provides support for the most favorable calculated transition structures involving amine-bound HCN adding to thiourea-bound ketone. The calculations suggest that enantioselectivity arises from direct interactions between the ketone substrate and the amino-acid derived portion of the catalyst. On the basis of this insight, more enantioselective catalysts with broader substrate scope were prepared and evaluated experimentally.

Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites

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

Radka, Christopher D.; DeLucas, Lawrence J.; Wilson, Landon S.

2017-06-30

Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. InYersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA ismore » polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.« less

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

PubMed Central

Skjaerven, Lars; Grant, Barry; Muga, Arturo; Teigen, Knut; McCammon, J. Andrew; Reuter, Nathalie; Martinez, Aurora

2011-01-01

GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant “opening” of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition. PMID:21423709

Single crystalline electronic structure and growth mechanism of aligned square graphene sheets

NASA Astrophysics Data System (ADS)

Yang, H. F.; Chen, C.; Wang, H.; Liu, Z. K.; Zhang, T.; Peng, H.; Schröter, N. B. M.; Ekahana, S. A.; Jiang, J.; Yang, L. X.; Kandyba, V.; Barinov, A.; Chen, C. Y.; Avila, J.; Asensio, M. C.; Peng, H. L.; Liu, Z. F.; Chen, Y. L.

2018-03-01

Recently, commercially available copper foil has become an efficient and inexpensive catalytic substrate for scalable growth of large-area graphene films for fundamental research and applications. Interestingly, despite its hexagonal honeycomb lattice, graphene can be grown into large aligned square-shaped sheets on copper foils. Here, by applying angle-resolved photoemission spectroscopy with submicron spatial resolution (micro-ARPES) to study the three-dimensional electronic structures of square graphene sheets grown on copper foils, we verified the high quality of individual square graphene sheets as well as their merged regions (with aligned orientation). Furthermore, by simultaneously measuring the graphene sheets and their substrate copper foil, we not only established the (001) copper surface structure but also discovered that the square graphene sheets' sides align with the ⟨110⟩ copper direction, suggesting an important role of copper substrate in the growth of square graphene sheets—which will help the development of effective methods to synthesize high-quality large-size regularly shaped graphene sheets for future applications. This work also demonstrates the effectiveness of micro-ARPES in exploring low-dimensional materials down to atomic thickness and sub-micron lateral size (e.g., besides graphene, it can also be applied to transition metal dichalcogenides and various van der Waals heterostructures)

Nonlinear dielectric properties of planar structures based on ferroelectric betaine phosphite films

NASA Astrophysics Data System (ADS)

Balashova, E. V.; Krichevtsov, B. B.; Svinarev, F. B.; Yurko, E. I.

2014-02-01

Ferroelectric films of partly deuterated betaine phosphite are grown on NdGaO3(001) substrates with an interdigitated system of electrodes on their surfaces by evaporation at room temperature. These films have a high capacitance in the ferroelectric phase transition range. The dielectric nonlinearity of the grown structures is studied in small-signal and strong-signal response modes and in the intermediate region between these two modes by measuring the capacitance in a dc bias field, dielectric hysteresis loops, and the Fourier spectra of an output signal in the Sawyer-Tower circuit. In the phase transition range, the capacitance control ratio at a bias voltage U bias = 40 V is K ≅ 7. The dielectric nonlinearity of the structures in the paraelectric phase is described by the Landau theory of second-order phase transitions. The additional contribution to the nonlinearity in the ferroelectric phase is related to the motion of domain walls and manifests itself when the input signal amplitude is higher than U st ˜ 0.7-1.0 V. The relaxation times of domain walls are determined from an analysis of the frequency dependences of the dielectric hysteresis.

Influence of Al content on the properties of ternary Al{sub 2x}In{sub 2−2x}O{sub 3} alloy films prepared on YSZ (1 1 1) substrates by MOCVD

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

Feng, Xianjin; Zhao, Cansong; Li, Zhao

2015-10-15

Highlights: • Al{sub 2x}In{sub 2−2x}O{sub 3} films were prepared on the Y-stabilized ZrO{sub 2} (1 1 1) substrates by MOCVD at 700 °C. • A phase transition from the bixbyite In{sub 2}O{sub 3} structure to the amorphous structure was observed. • The lowest resistivity of 4.7 × 10{sup −3} Ω cm was obtained for the Al{sub 0.4}In{sub 1.6}O{sub 3} film. • Tunable optical band gap from 3.7 to 4.8 eV was obtained. - Abstract: The ternary Al{sub 2x}In{sub 2−2x}O{sub 3} films with different Al contents of x [Al/(Al + In) atomic ratio] have been fabricated on the Y-stabilized ZrO{sub 2}more » (1 1 1) substrates by metal organic chemical vapor deposition at 700 °C. The structural, electrical and optical properties of the films as a result of different Al contents (x = 0.1–0.9) were investigated in detail. With the increase of Al content from 10% to 90%, a phase transition from the bixbyite In{sub 2}O{sub 3} structure with a single orientation along (1 1 1) to the amorphous structure was observed. The minimum resistivity of 4.7 × 10{sup −3} Ω cm, a carrier concentration of 1.4 × 10{sup 20} cm{sup −3} and a Hall mobility of 9.8 cm{sup 2} v{sup −1} s{sup −1} were obtained for the sample with x = 0.2. The average transmittances for the Al{sub 2x}In{sub 2−2x}O{sub 3} films in the visible range were all over 78% and the optical band gap of the films could be tuned from 3.7 to 4.8 eV.« less

Specificity in transition state binding: the Pauling model revisited.

PubMed

Amyes, Tina L; Richard, John P

2013-03-26

Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared with that of the free enzyme. Evidence is presented that supports a model in which the binding energy of the phosphite dianion piece, or the phosphodianion group of the whole substrate, is utilized to drive an enzyme conformational change from an inactive open form E(O) to an active closed form E(C), by closure of a phosphodianion gripper loop. Members of the enolase and haloalkanoic acid dehalogenase superfamilies use variable capping domains to interact with nonreacting portions of the substrate and sequester the substrate from interaction with bulk solvent. Interactions of this capping domain with the phenyl group of mandelate have been shown to activate mandelate racemase for catalysis of deprotonation of α-carbonyl carbon. We propose that an important function of these capping domains is to utilize the binding interactions with nonreacting portions of the substrate to activate the enzyme for catalysis.

Specificity in Transition State Binding: The Pauling Model Revisited

PubMed Central

Amyes, Tina L.; Richard, John P.

2013-01-01

Linus Pauling proposed that the large rate accelerations for enzymes are due to the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogs of the transition states for enzymatic reactions often act as tight-binding binding inhibitors provided early support for this simple and elegant proposal. We review experimental results which support the proposal that Pauling’s model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of CoA are responsible for a rate increase of 3 × 1012-fold, which is close to the estimated total 5 × 1013-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide a ca. 12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5′-monophosphate decarboxylase and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6 – 8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared with the free enzyme. Evidence is presented that supports a model in which the binding energy of the phosphite dianion piece, or the phosphodianion group of the whole substrate, is utilized to drive an enzyme conformational change from an inactive open form EO to an active closed form EC, by closure of a phosphodianion gripper loop. Members of the enolase and haloalkanoic acid dehalogenase superfamilies use variable capping domains to interact with nonreacting portions of the substrate and sequester the substrate from interaction with bulk solvent. Interactions of this capping domain with the phenyl group of mandelate have been shown to activate mandelate racemase for catalysis of deprotonation of α-carbonyl carbon. We propose that an important function of these capping domains is to utilize the binding interactions with nonreacting portions of the substrate to activate the enzyme for catalysis. PMID:23327224

A simulation study on the constancy of cardiac energy metabolites during workload transition.

PubMed

Saito, Ryuta; Takeuchi, Ayako; Himeno, Yukiko; Inagaki, Nobuya; Matsuoka, Satoshi

2016-12-01

The cardiac energy metabolites such as ATP, phosphocreatine, ADP and NADH are kept relatively constant during physiological cardiac workload transition. How this is accomplished is not yet clarified, though Ca 2+ has been suggested to be one of the possible mechanisms. We constructed a detailed mathematical model of cardiac mitochondria based on experimental data and studied whether known Ca 2+ -dependent regulation mechanisms play roles in the metabolite constancy. Model simulations revealed that the Ca 2+ -dependent regulation mechanisms have important roles under the in vitro condition of isolated mitochondria where malate and glutamate were mitochondrial substrates, while they have only a minor role and the composition of substrates has marked influence on the metabolite constancy during workload transition under the simulated in vivo condition where many substrates exist. These results help us understand the regulation mechanisms of cardiac energy metabolism during physiological cardiac workload transition. The cardiac energy metabolites such as ATP, phosphocreatine, ADP and NADH are kept relatively constant over a wide range of cardiac workload, though the mechanisms are not yet clarified. One possible regulator of mitochondrial metabolism is Ca 2+ , because it activates several mitochondrial enzymes and transporters. Here we constructed a mathematical model of cardiac mitochondria, including oxidative phosphorylation, substrate metabolism and ion/substrate transporters, based on experimental data, and studied whether the Ca 2+ -dependent activation mechanisms play roles in metabolite constancy. Under the in vitro condition of isolated mitochondria, where malate and glutamate were used as mitochondrial substrates, the model well reproduced the Ca 2+ and inorganic phosphate (P i ) dependences of oxygen consumption, NADH level and mitochondrial membrane potential. The Ca 2+ -dependent activations of the aspartate/glutamate carrier and the F 1 F o -ATPase, and the P i -dependent activation of Complex III were key factors in reproducing the experimental data. When the mitochondrial model was implemented in a simple cardiac cell model, simulation of workload transition revealed that cytoplasmic Ca 2+ concentration ([Ca 2+ ] cyt ) within the physiological range markedly increased NADH level. However, the addition of pyruvate or citrate attenuated the Ca 2+ dependence of NADH during the workload transition. Under the simulated in vivo condition where malate, glutamate, pyruvate, citrate and 2-oxoglutarate were used as mitochondrial substrates, the energy metabolites were more stable during the workload transition and NADH level was almost insensitive to [Ca 2+ ] cyt . It was revealed that mitochondrial substrates have a significant influence on metabolite constancy during cardiac workload transition, and Ca 2+ has only a minor role under physiological conditions. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Structural and phase transitions of one and two polymer mushrooms in poor solvent

NASA Astrophysics Data System (ADS)

Yang, Delian; Wang, Qiang

2014-05-01

Using the recently proposed fast lattice Monte Carlo (FLMC) simulations and the corresponding lattice self-consistent field (LSCF) calculations based on the same model system, where multiple occupancy of lattice sites is allowed [Q. Wang, Soft Matter 5, 4564 (2009); Q. Wang, Soft Matter 5, 6206 (2010)], we studied the coil-globule transition (CGT) of one-mushroom systems and the fused-separated transition (FST) of two-mushroom systems, where a polymer mushroom is formed by a group of n homopolymer chains each of N segments end-grafted at the same point onto a flat substrate and immersed in a poor solvent. With our soft potential that allows complete particle overlapping, LSCF theory neglecting the system fluctuations/correlations becomes exact in the limit of n → ∞, and FLMC results approach LSCF predictions with increasing n. Using LSCF calculations, we systematically constructed the phase diagrams of one- and two-mushroom systems. A second-order symmetric-asymmetric transition (SAT) was found in the globule state of one-mushroom systems, where the rotational symmetry around the substrate normal passing through the grafting point is broken in each individual configuration but preserved by the degeneracy of different orientations of these asymmetric configurations. Three different states were also found in two-mushroom systems: separated coils, separated globules, and fused globule. We further studied the coupling between FST in two-mushroom systems and CGT and SAT of each mushroom. Finally, direct comparisons between our simulation and theoretical results, without any parameter-fitting, unambiguously and quantitatively revealed the fluctuation/correlation effects on these phase transitions.

Molecular Dynamics Simulation of the Allosteric Regulation of eIF4A Protein from the Open to Closed State, Induced by ATP and RNA Substrates

PubMed Central

Meng, Hongqing; Li, Chaoqun; Wang, Yan; Chen, Guangju

2014-01-01

Background Eukaryotic initiation factor 4A (eIF4A) plays a key role in the process of protein translation initiation by facilitating the melting of the 5′ proximal secondary structure of eukaryotic mRNA for ribosomal subunit attachment. It was experimentally postulated that the closed conformation of the eIF4A protein bound by the ATP and RNA substrates is coupled to RNA duplex unwinding to promote protein translation initiation, rather than an open conformation in the absence of ATP and RNA substrates. However, the allosteric process of eIF4A from the open to closed state induced by the ATP and RNA substrates are not yet fully understood. Methodology In the present work, we constructed a series of diplex and ternary models of the eIF4A protein bound by the ATP and RNA substrates to carry out molecular dynamics simulations, free energy calculations and conformation analysis and explore the allosteric properties of eIF4A. Results The results showed that the eIF4A protein completes the conformational transition from the open to closed state via two allosteric processes of ATP binding followed by RNA and vice versa. Based on cooperative allosteric network analysis, the ATP binding to the eIF4A protein mainly caused the relative rotation of two domains, while the RNA binding caused the proximity of two domains via the migration of RNA bases in the presence of ATP. The cooperative binding of ATP and RNA for the eIF4A protein plays a key role in the allosteric transition. PMID:24465900

Unusually sharp paramagnetic phase transition in thin film Fe3Pt invar

NASA Astrophysics Data System (ADS)

Drisko, Jasper; Cumings, John

2013-03-01

Invar alloys, typically 3d transition metal rich systems, are most commonly known for their extremely low coefficients of thermal expansion (CTE) over a wide range of temperatures close to room temperature. This anomalous behavior in the CTE lends Invar to a variety of important applications in precision mechanical devices, scientific instruments, and sensors, among others. Many theoretical models of Invar have been proposed over the years, the most promising of which is a system described by two coexisting phases, one high-spin high-volume and the other low-spin low-volume, that compete to stabilize the volume of the material as the temperature is changed. However, no theory has yet been able to explain all experimental observations across the range of Invar alloys, especially at finite temperature. We have fabricated thin films of a Fe3Pt Invar alloy and investigate them using Lorentz Transmission Electron Microscopy (TEM). 23nm films are deposited onto SiN membrane substrates via radio-frequency magnetron sputtering from a pure Fe target decorated with Pt pieces. We observe novel magnetic domain structures and an unusually sharp phase transition between ferromagnetic (FM) and paramagnetic (PM) regions of the film under a temperature gradient. This sharp transition suggests that the FM-to-PM transition may be first order, perhaps containing a structural-elastic component to the order parameter. However, electron diffraction reveals that both the FM and PM regions have the same FCC crystal structure.

The behavior of commensurate-incommensurate transitions using the phase field crystal model

NASA Astrophysics Data System (ADS)

Zhang, Tinghui; Lu, Yanli; Chen, Zheng

2018-02-01

We study the behavior of the commensurate-incommensurate (CI) transitions by using a phase field crystal model. The model is capable of modeling both elastic and plastic deformation and can simulate the evolution of the microstructure of the material at the atomic scale and the diffusive time scale, such as for adsorbed monolayer. Specifically, we study the behavior of the CI transitions as a function of lattice mismatch and the amplitude of substrate pinning potential. The behavior of CI phase transitions is revealed with the increase of the amplitude of pinning potential in some certain lattice mismatches. We find that for the negative lattice mismatch absorbed monolayer undergoes division, reorganization and displacement as increasing the amplitude of substrate pinning potential. In addition, for the positive mismatch absorbed monolayer undergoes a progress of phase transformation after a complete grain is split. Our results accord with simulations for atomic models of absorbed monolayer on a substrate surface.

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: A review

DOE PAGES

Reichhardt, Charles; Olson Reichhardt, Cynthia Jane

2016-12-20

Here, we review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic andmore » plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.« less

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: a review

NASA Astrophysics Data System (ADS)

Reichhardt, C.; Olson Reichhardt, C. J.

2017-02-01

We review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic and plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.

Freezing and melting of salt hydrates next to solid surfaces probed by infrared-visible sum frequency generation spectroscopy.

PubMed

Anim-Danso, Emmanuel; Zhang, Yu; Dhinojwala, Ali

2013-06-12

Understanding the freezing of salt solutions near solid surfaces is important in many scientific fields. Here we use sum frequency generation (SFG) spectroscopy to study the freezing of a NaCl solution next to a sapphire substrate. During cooling we observe two transitions. The first corresponds to segregation of concentrated brine next to the sapphire surface as we cool the system down to the region where ice and brine phases coexist. At this transition, the intensity of the ice-like peak decreases, suggesting the disruption of hydrogen-bonding by sodium ions. The second transition corresponds to the formation of NaCl hydrates with abrupt changes in both the SFG intensity and the sharpness of spectral peaks. The similarity in the position of the SFG peaks with those observed using IR and Raman spectroscopy indicates the formation of NaCl·2H2O crystals next to the sapphire substrate. The melting temperatures of the hydrates are very similar to those reported for bulk NaCl·2H2O. This study enhances our understanding of nucleation and freezing of salt solutions on solid surfaces and the effects of salt ions on the structure of interfacial ice.

Synthesis and characterization of poly[d(G-z5C)]. B-Z transition and inhibition of DNA methylase.

PubMed

McIntosh, L P; Zielinski, W S; Kalisch, B W; Pfeifer, G P; Sprinzl, M; Drahovsky, D; van de Sande, J H; Jovin, T M

1985-08-27

Deoxy-5-azacytidine 5'-triphosphate was synthesized and used as a substrate for the enzymatic synthesis of the polynucleotide poly[d(G-z5C)]. Whereas the triphosphate decomposes in solution, the azacytosine analogue incorporated into DNA is stable under conditions preserving the double-helical structure. Poly[d(G-z5C)] undergoes the transition to the left-handed Z conformation at salt (NaCl and MgCl2) concentrations approximately 30% higher than those required for unsubstituted poly[d(G-C)]. However, the incorporation of azacytidine potentiates the formation at room temperature of the Z helix stabilized by the transition metal Mn2+; in the case of poly[d(G-C)], a heating step is required. The spectral properties of the two polymers in the B and Z forms are similar. Both left-handed forms are recognized by anti-Z DNA immunoglobulins, indicating that the DNAs bear common antigenic features. Poly[d(G-z5C)] is not a substrate for the DNA cytosine 5-methyltransferase from human placenta. It is a potent inhibitor of the enzyme when tested in a competitive binding assay. These results are compatible with a very strong, possibly covalent, mode of interaction between methyltransferases and DNA containing 5-azacytosine.

Synchrotron radiation topography studies of the phase transition in LaGaO 3 crystals

NASA Astrophysics Data System (ADS)

Yao, G.-D.; Dudley, M.; Wang, Y.; Liu, X.; Liebermann, R. C.

1991-05-01

An investigation of the orthorhombic to rhombohedral phase transformation occurring at 145°C in lanthanum gallate has been conducted using white beam synchrotron X-ray topography (WBSXRT). The existence of the first order transition was confirmed by differential thermal analysis and X-ray diffractometer powder analysis. Subsequent to this, synchrotron white beam Laue patterns were recorded in situ as a function of temperature, during the transition. Before the transition point was reached, (112) orth type reflection twinning was found to be dominant although a small amount of (110) orth type twinning was also observed in the same crystal. Beyond the transition point, not only did the structural change become evident but also reflection twinning on the (110) rhom planes was observed. The scale of this twinning became finer as the temperature was increased beyond the transition temperature. The twinning observed in both the low and high temperature phases gives rise to deformation of the (011) rhom surface plane which creates problems for the potential use of this material as a substrate for growing high Tc superconducting epitaxial layers.

QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity

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

Yao, Jianzhuang; Xu, Qin; Chen, Feng

2010-01-01

Salicylic acid methyltransferases (SAMTs) synthesize methyl salicylate (MeSA) using salicylate as the substrate. MeSA synthesized in plants may function as an airborne signal to activate the expression of defense-related genes and could also be a critical mobile signaling molecule that travels from the site of plant infection to establish systemic immunity in the induction of disease resistance. Here the results of QM/MM free energy simulations for the methyl transfer process in Clarkia breweri SAMT (CbSAMT) are reported to determine the origin of the substrate specificity of SAMTs. The free energy barrier for the methyl transfer from S-adenosyl-l-methionine (AdoMet) to 4-hydroxybenzoatemore » in CbSAMT is found to be about 5 kcal/mol higher than that from AdoMet to salicylate, consistent with the experimental observations. It is suggested that the relatively high efficiency for the methylation of salicylate compared to 4-hydroxybenzoate is due, at least in part, to the reason that a part of the stabilization of the transition state (TS) configuration is already reflected in the reactant complex, presumably, through the binding. The results seem to indicate that the creation of the substrate complex (e.g., through mutagenesis and substrate modifications) with its structure closely resembling TS might be fruitful for improving the catalytic efficiency for some enzymes. The results show that the computer simulations may provide important insights into the origin of the substrate specificity for the SABATH family and could be used to help experimental efforts in generating engineered enzymes with altered substrate specificity.« less

Electric field induced metal-insulator transition in VO2 thin film based on FTO/VO2/FTO structure

NASA Astrophysics Data System (ADS)

Hao, Rulong; Li, Yi; Liu, Fei; Sun, Yao; Tang, Jiayin; Chen, Peizu; Jiang, Wei; Wu, Zhengyi; Xu, Tingting; Fang, Baoying

2016-03-01

A VO2 thin film has been prepared using a DC magnetron sputtering method and annealing on an F-doped SnO2 (FTO) conductive glass substrate. The FTO/VO2/FTO structure was fabricated using photolithography and a chemical etching process. The temperature dependence of the I-V hysteresis loop for the FTO/VO2/FTO structure has been analyzed. The threshold voltage decreases with increasing temperature, with a value of 9.2 V at 20 °C. The maximum transmission modulation value of the FTO/VO2/FTO structure is 31.4% under various temperatures and voltages. Optical modulation can be realized in the structure by applying an electric field.

Consolidation of hydrophobic transition criteria by using an approximate energy minimization approach.

PubMed

Patankar, Neelesh A

2010-06-01

Recent experimental work has successfully revealed pressure induced transition from Cassie to Wenzel state on rough hydrophobic substrates. Formulas, based on geometric considerations and imposed pressure, have been developed as transition criteria. In the past, transition has also been considered as a process of overcoming the energy barrier between the Cassie and Wenzel states. A unified understanding of the various considerations of transition has not been apparent. To address this issue, in this work, we consolidate the transition criteria with a homogenized energy minimization approach. This approach decouples the problem of minimizing the energy to wet the rough substrate, from the energy of the macroscopic drop. It is seen that the transition from Cassie to Wenzel state, due to depinning of the liquid-air interface, emerges from the approximate energy minimization approach if the pressure-volume energy associated with the impaled liquid in the roughness is included. This transition can be viewed as a process in which the work done by the pressure force is greater than the barrier due to the surface energy associated with wetting the roughness. It is argued that another transition mechanism, due to a sagging liquid-air interface that touches the bottom of the roughness grooves, is not typically relevant if the substrate roughness is designed such that the Cassie state is at lower energy compared to the Wenzel state.

Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding

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

Wang, Huanchen; Falck, J.R.; Hall, Traci M. Tanaka

2012-01-11

Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domainmore » of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF{sub 3}{sup -} transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.« less

Substrate induced changes in atomically thin 2-dimensional semiconductors: Fundamentals, engineering, and applications

NASA Astrophysics Data System (ADS)

Sun, Yinghui; Wang, Rongming; Liu, Kai

2017-03-01

Substrate has great influences on materials syntheses, properties, and applications. The influences are particularly crucial for atomically thin 2-dimensional (2D) semiconductors. Their thicknesses are less than 1 nm; however, the lateral sizes can reach up to several inches or more. Therefore, these materials must be placed onto a variety of substrates before subsequent post-processing techniques for final electronic or optoelectronic devices. Recent studies reveal that substrates have been employed as ways to modulate the optical, electrical, mechanical, and chemical properties of 2D semiconductors. In this review, we summarize recent progress upon the effects of substrates on properties of 2D semiconductors, mostly focused on 2D transition metal dichalcogenides, through viewpoints of both fundamental physics and device applications. First, we discuss various effects of substrates, including interface strain, charge transfer, dielectric screening, and optical interference. Second, we show the modulation of 2D semiconductors by substrate engineering, including novel substrates (patterned substrates, 2D-material substrates, etc.) and active substrates (phase transition materials, ferroelectric materials, flexible substrates, etc.). Last, we present prospectives and challenges in this research field. This review provides a comprehensive understanding of the substrate effects, and may inspire new ideas of novel 2D devices based on substrate engineering.

Chemical structure of interfaces

NASA Technical Reports Server (NTRS)

Grunthaner, F. J.

1985-01-01

The interfacial structure of silicon/dielectric and silicon/metal systems is particularly amenable to analysis using a combination of surface spectroscopies together with a variety of chemical structures of Si/SiO2, Si/SiO2Si3N4, Si/Si2N2O, Si/SiO2/Al, and Si/Native Oxide interfaces using high resolution (0.350 eV FWHM) X ray photoelectron spectroscopy. The general structure of these dielectric interfaces entails a monolayer chemical transition layer at the Si/dielectric boundary. Amorphous Si substrates show a wide variety of hydrogenated Si and Si(OH) sub x states that are not observed in thermal oxidation of single crystal material. Extended SiO2 layers greater than 8 A in thickness are shown to be stoichiometric SiO2, but to exhibit a wide variety of local network structures. In the nitrogen containing systems, an approach to stoichiometric oxynitride compounds with interesting impurity and electron trapping properties are seen. In native oxides, substantial topographical nonuniformity in oxide thickness and composition are found. Analysis of metal/oxide interfacial layers is accomplished by analytical removal of the Si substrate by UHV XeF2 dry etching methods.

Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation

PubMed Central

Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

2006-01-01

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33→Ala33, Asp60→Ala60, Ser62→Ala62, and Thr220→Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (ΔΔGT). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the Km values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations. PMID:16411898

Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

PubMed

Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

2006-05-01

Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33-->Ala33, Asp60-->Ala60, Ser62-->Ala62, and Thr220-->Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (DeltaDeltaG(T)). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the K(m) values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.

Relationships between substrate, surface characteristics, and vegetation in an initial ecosystem

NASA Astrophysics Data System (ADS)

Biber, P.; Seifert, S.; Zaplata, M. K.; Schaaf, W.; Pretzsch, H.; Fischer, A.

2013-12-01

We investigated surface and vegetation dynamics in the artificial initial ecosystem "Chicken Creek" (Lusatia, Germany) in the years 2006-2011 across a wide spectrum of empirical data. We scrutinized three overarching hypotheses concerning (1) the relations between initial geomorphological and substrate characteristics with surface structure and terrain properties, (2) the effects of the latter on the occurrence of grouped plant species, and (3) vegetation density effects on terrain surface change. Our data comprise and conflate annual vegetation monitoring results, biennial terrestrial laser scans (starting in 2008), annual groundwater levels, and initially measured soil characteristics. The empirical evidence mostly confirms the hypotheses, revealing statistically significant relations for several goal variables: (1) the surface structure properties, local rill density, local relief energy and terrain surface height change; (2) the cover of different plant groups (annual, herbaceous, grass-like, woody, Fabaceae), and local vegetation height; and (3) terrain surface height change showed significant time-dependent relations with a variable that proxies local plant biomass. Additionally, period specific effects (like a calendar-year optimum effect for the occurrence of Fabaceae) were proven. Further and beyond the hypotheses, our findings on the spatiotemporal dynamics during the system's early development grasp processes which generally mark the transition from a geo-hydro-system towards a bio-geo-hydro system (weakening geomorphology effects on substrate surface dynamics, while vegetation effects intensify with time), where pure geomorphology or substrate feedbacks are changing into vegetation-substrate feedback processes.

Dynamically Babinet-invertible metasurface: a capacitive-inductive reconfigurable filter for terahertz waves using vanadium-dioxide metal-insulator transition

NASA Astrophysics Data System (ADS)

Urade, Yoshiro; Nakata, Yosuke; Okimura, Kunio; Nakanishi, Toshihiro; Miyamaru, Fumiaki; Takeda, Mitsuo W.; Kitano, Masao

2016-03-01

This paper proposes a reconfigurable planar metamaterial that can be switched between capacitive and inductive responses using local changes in the electrical conductivity of its constituent material. The proposed device is based on Babinet's principle and exploits the singular electromagnetic responses of metallic checkerboard structures, which are dependent on the local electrical conductivity. Utilizing the heating-induced metal-insulator transition of vanadium dioxide ($\\mathrm{VO}_2$), the proposed metamaterial is designed to compensate for the effect of the substrate and is experimentally characterized in the terahertz regime. This reconfigurable metamaterial can be utilized as a switchable filter and as a switchable phase shifter for terahertz waves.

Dynamically Babinet-invertible metasurface: a capacitive-inductive reconfigurable filter for terahertz waves using vanadium-dioxide metal-insulator transition.

PubMed

Urade, Yoshiro; Nakata, Yosuke; Okimura, Kunio; Nakanishi, Toshihiro; Miyamaru, Fumiaki; Takeda, Mitsuo W; Kitano, Masao

2016-03-07

This paper proposes a reconfigurable planar metamaterial that can be switched between capacitive and inductive responses using local changes in the electrical conductivity of its constituent material. The proposed device is based on Babinet's principle and exploits the singular electromagnetic responses of metallic checkerboard structures, which are dependent on the local electrical conductivity. Utilizing the heating-induced metal-insulator transition of vanadium dioxide (VO 2 ), the proposed meta-material is designed to compensate for the effect of the substrate and is experimentally characterized in the terahertz regime. This reconfigurable metamaterial can be utilized as a switchable filter and as a switchable phase shifter for terahertz waves.

IR visible sum-frequency vibrational spectroscopy of Biphenyl-3 methylene thiol monolayer on gold and silver: effect of the visible wavelength on the SFG spectrum

NASA Astrophysics Data System (ADS)

Humbert, C.; Dreesen, L.; Mani, A. A.; Caudano, Y.; Lemaire, J.-J.; Thiry, P. A.; Peremans, A.

2002-04-01

We measured IR-visible sum-frequency generation spectra of CH 3-(C 6H 4) 2-(CH 2) 3-S-H (Biphenyl-3) self-assembled monolayers on a silver and a gold substrate. For the latter substrate, we observed different interference patterns between the resonant signal of the CH vibration and the non-resonant contribution of the substrate as a function of the visible beam wavelength. The non-linear response of the gold substrate is enhanced around 480 nm corresponding to the s-d interband transition. Such effect is not observed for the silver substrate the interband transition of which is located out of the investigated visible spectral range of 450-700 nm.

Intersubband absorption of p-type wurtzite GaN/AlN quantum well for fiber-optics telecommunication

NASA Astrophysics Data System (ADS)

Park, Seoung-Hwan; Ahn, Doyeol; Park, Chan-Yong

2017-11-01

The intersubband transition of wurtzite (WZ) p-type GaN/AlN quantum well (QW) structures grown on GaN substrate was investigated theoretically using the multiband effective-mass theory. The peak value of the TE-polarization absorption spectrum is found to be similar to that of the TM-polarization absorption spectrum. The absorption coefficients for TE- and TM-polarizations are mainly attributed to the absorption from the ground state (m1 = 1) because holes are mainly confined in ground states near the band-edge in an investigated range of the carrier density. We observe that a transition wavelength of 1.55 μm can be obtained for the QW structure with a relatively thin (˜16 Å) well width. Thus, we expect that a p-type WZ AlN/GaN heterostructure is applicable for a photodetector application for fiber-optic communications with normal incidence of wave.

Structural and Magnetic Properties of Sputter-Deposited Polycrystalline Ni-Mn-Ga Ferromagnetic Shape-Memory Thin Films

NASA Astrophysics Data System (ADS)

Vinodh Kumar, S.; Seenithurai, S.; Manivel Raja, M.; Mahendran, M.

2015-10-01

Polycrystalline Ni-Mn-Ga ferromagnetic shape-memory thin films have been deposited on Si (100) substrates using a direct-current magnetron sputtering technique. The microstructure and the temperature dependence of magnetic properties of the films have been investigated by x-ray diffraction, scanning electron microscopy, and thermomagnetic measurements. As-deposited Ni50.2Mn30.6Ga19.2 film showed quasi-amorphous structure with paramagnetic nature at room temperature. When annealed at 873 K, the quasi-amorphous film attained crystallinity and possessed L21 cubic ordering with high magnetic transition temperature. Saturation magnetization and coercivity values for the annealed film were found to be 220 emu/cm3 and 70 Oe, respectively, indicating soft ferromagnetic character with low magnetocrystalline anisotropy. The magnetic transitions of the film deposited at 100 W were above room temperature, making this a potential candidate for use in microelectromechanical system devices.

Preparation and modification of VO2 thin film on R-sapphire substrate by rapid thermal process

NASA Astrophysics Data System (ADS)

Zhu, Nai-Wei; Hu, Ming; Xia, Xiao-Xu; Wei, Xiao-Ying; Liang, Ji-Ran

2014-04-01

The VO2 thin film with high performance of metal-insulator transition (MIT) is prepared on R-sapphire substrate for the first time by magnetron sputtering with rapid thermal process (RTP). The electrical characteristic and THz transmittance of MIT in VO2 film are studied by four-point probe method and THz time domain spectrum (THz-TDS). X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and search engine marketing (SEM) are employed to analyze the crystalline structure, valence state, surface morphology of the film. Results indicate that the properties of VO2 film which is oxidized from the metal vanadium film in oxygen atmosphere are improved with a follow-up RTP modification in nitrogen atmosphere. The crystallization and components of VO2 film are improved and the film becomes compact and uniform. A better phase transition performance is shown that the resistance changes nearly 3 orders of magnitude with a 2-°C hysteresis width and the THz transmittances are reduced by 64% and 60% in thermal and optical excitation respectively.

Functionalization of Carbon-Hydrogen Bonds Through Transition Metal Carbenoid Insertion

NASA Astrophysics Data System (ADS)

Davies, Huw M. L.; Dick, Allison R.

The functionalization of carbon-hydrogen bonds through transition metal carbenoid insertion is becoming a powerful method for the construction of new carbon-carbon bonds in organic synthesis. This chapter will highlight recent developments in this field, while placing it within its historical context. Intramolecular carbenoid C-H insertion will be covered first, focusing on formation of three- and six-membered rings, as well as the use of nontraditional substrates. Additionally, the most recent progress in asymmetric catalysis will be discussed. The bulk of the chapter will concentrate on intermolecular transformations, emphasizing both the effect of substrate structure and the influence of carbene substituent electronics on the regioselectivity of the reactions. Vinyldiazoacetates will be covered as a distinct class of carbenoid precursor, as they have been shown to initiate a variety of unique transformations, such as the combined C-H activation/Cope rearrangement. Finally, the synthetic utility of carbenoid C-H insertion reactions, both intra- and intermolecular, will be displayed through their use in the total syntheses of a number of natural products and pharmaceuticals.

Functionalization of carbon-hydrogen bonds through transition metal carbenoid insertion.

PubMed

Davies, Huw M L; Dick, Allison R

2010-01-01

The functionalization of carbon-hydrogen bonds through transition metal carbenoid insertion is becoming a powerful method for the construction of new carbon-carbon bonds in organic synthesis. This chapter will highlight recent developments in this field, while placing it within its historical context. Intramolecular carbenoid C-H insertion will be covered first, focusing on formation of three- and six-membered rings, as well as the use of nontraditional substrates. Additionally, the most recent progress in asymmetric catalysis will be discussed. The bulk of the chapter will concentrate on intermolecular transformations, emphasizing both the effect of substrate structure and the influence of carbene substituent electronics on the regioselectivity of the reactions. Vinyldiazoacetates will be covered as a distinct class of carbenoid precursors, as they have been shown to initiate a variety of unique transformations, such as the combined C-H activation/Cope rearrangement. Finally, the synthetic utility of carbenoid C-H insertion reactions, both intra- and intermolecular, will be displayed through their use in the total syntheses of a number of natural products and pharmaceuticals.

Temperature dependence of the interband critical points of bulk Ge and strained Ge on Si

NASA Astrophysics Data System (ADS)

Fernando, Nalin S.; Nunley, T. Nathan; Ghosh, Ayana; Nelson, Cayla M.; Cooke, Jacqueline A.; Medina, Amber A.; Zollner, Stefan; Xu, Chi; Menendez, Jose; Kouvetakis, John

2017-11-01

Epitaxial Ge layers on a Si substrate experience a tensile biaxial stress due to the difference between the thermal expansion coefficients of the Ge epilayer and the Si substrate, which can be measured using asymmetric X-ray diffraction reciprocal space maps. This stress depends on temperature and affects the band structure, interband critical points, and optical spectra. This manuscripts reports careful measurements of the temperature dependence of the dielectric function and the interband critical point parameters of bulk Ge and Ge epilayers on Si using spectroscopic ellipsometry from 80 to 780 K and from 0.8 to 6.5 eV. The authors find a temperature-dependent redshift of the E1 and E1 + Δ1 critical points in Ge on Si (relative to bulk Ge). This redshift can be described well with a model based on thermal expansion coefficients, continuum elasticity theory, and the deformation potential theory for interband transitions. The interband transitions leading to E0‧ and E2 critical points have lower symmetry and therefore are not affected by the stress.

Influence of transition metal doping on the structural, optical, and magnetic properties of TiO2 films deposited on Si substrates by a sol–gel process

PubMed Central

2013-01-01

Transition metal (TM)-doped TiO2 films (TM = Co, Ni, and Fe) were deposited on Si(100) substrates by a sol–gel method. With the same dopant content, Co dopants catalyze the anatase-to-rutile transformation (ART) more obviously than Ni and Fe doping. This is attributed to the different strain energy induced by the different dopants. The optical properties of TM-doped TiO2 films were studied with spectroscopic ellipsometry data. With increasing dopant content, the optical band gap (EOBG) shifts to lower energy. With the same dopant content, the EOBG of Co-doped TiO2 film is the smallest and that of Fe-doped TiO2 film is the largest. The results are related to electric disorder due to the ART. Ferromagnetic behaviors were clearly observed for TM-doped TiO2 films except the undoped TiO2 film which is weakly magnetic. Additionally, it is found that the magnetizations of the TM-doped TiO2 films decrease with increasing dopant content. PMID:24350904

Transition from reconstruction toward thin film on the (110) surface of strontium titanate

DOE PAGES

Wang, Z.; Loon, A.; Subramanian, A.; ...

2016-03-08

The surfaces of metal oxides often are reconstructed with a geometry and composition that is considerably different from a simple termination of the bulk. Such structures can also be viewed as ultrathin films, epitaxed on a substrate. Here, the reconstructions of the SrTiO 3 (110) surface are studied combining scanning tunneling microscopy (STM), transmission electron diffraction, and X-ray absorption spectroscopy (XAS), and analyzed with density functional theory calculations. Whereas SrTiO 3 (110) invariably terminates with an overlayer of titania, with increasing density its structure switches from n × 1 to 2 × n. At the same time the coordination ofmore » the Ti atoms changes from a network of corner-sharing tetrahedra to a double layer of edge-shared octahedra with bridging units of octahedrally coordinated strontium. Furthermore, this transition from the n × 1 to 2 × n reconstructions is a transition from a pseudomorphically stabilized tetrahedral network toward an octahedral titania thin film with stress-relief from octahedral strontia units at the surface.« less

Dielectric response and structure of in-plane tensile strained BaTiO3 thin films grown on the LaNiO3 buffered Si substrate

NASA Astrophysics Data System (ADS)

Qiao, Liang; Bi, Xiaofang

2008-02-01

Highly (001)-textured BaTiO3 films were grown epitaxially on the LaNiO3 buffered Si substrate. A strong in-plane tensile strain has been revealed by using x-ray diffraction and high resolution transmission electron microscopy. The BaTiO3 film has exhibited a small remnant polarization, indicating the presence of ca1/ca2/ca1/ca2 polydomain state in the film. Temperature dependent dielectric permittivity has demonstrated that two phase transitions occurred at respective temperatures of 170 and 30°C. The result was discussed in detail based on the misfit strain-temperature phase diagrams theory.

Quantum mechanical approaches to in silico enzyme characterization and drug design

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

Nilmeier, J P; Fattebert, J L; Jacobson, M P

2012-01-17

The astonishing, exponentially increasing rates of genome sequencing has led to one of the most significant challenges for the biological and computational sciences in the 21st century: assigning the likely functions of the encoded proteins. Enzymes represent a particular challenge, and a critical one, because the universe of enzymes is likely to contain many novel functions that may be useful for synthetic biology, or as drug targets. Current approaches to protein annotation are largely based on bioinformatics. At the simplest level, this annotation involves transferring the annotations of characterized enzymes to related sequences. In practice, however, there is no simple,more » sequence based criterion for transferring annotations, and bioinformatics alone cannot propose new enzymatic functions. Structure-based computational methods have the potential to address these limitations, by identifying potential substrates of enzymes, as we and others have shown. One successful approach has used in silico 'docking' methods, more commonly applied in structure-based drug design, to identify possible metabolite substrates. A major limitation of this approach is that it only considers substrate binding, and does not directly assess the potential of the enzyme to catalyze a particular reaction using a particular substrate. That is, substrate binding affinity is necessary but not sufficient to assign function. A reaction profile is ultimately what is needed for a more complete quantitative description of function. To address this rather fundamental limitation, they propose to use quantum mechanical methods to explicitly compute transition state barriers that govern the rates of catalysis. Although quantum mechanical, and mixed quantum/classical (QM/MM), methods have been used extensively to investigate enzymatic reactions, the focus has been primarily on elucidating complex reaction mechanisms. Here, the key catalytic steps are known, and they use these methods quantify substrate specificity. That is, we bring the power of quantum mechanics to bear on the problem of annotating enzyme function, which is a novel approach. Although it has been clear to us at the Jacobson group for some time that enzyme specificity may be encoded in transition states, rather than simply substrate recognition, the main limitation has always been computational expense. Using a hierarchy of different methods, they can reduce the list of plausible substrates of an enzyme to a small number in most cases, but even identifying the transition states for a dozen plausible substrates requires significant computational effort, beyond what is practical using standard QM/MM methods. For this project, they have chosen two enzyme superfamilies which they have used as 'model systems' for functional assignment. The enolase superfamily is a large group of {alpha}-{beta} barrel enzymes with highly diverse substrates and chemical transformations. Despite decades of work, over a third of the superfamily remains unassigned, which means that the remaining cases are by definition difficult to assign. They have focused on acid sugar dehydratases, and have considerable expertise on the matter. They are also interested in the isoprenoid synthase superfamily, which is of central interest to the synthetic biology community, because these enzymes are used by nature to create complex rare natural products of medicinal value. the most notable example of this is the artemisinin, an antimalarial compound that is found in trace amounts in the wormwod root. From the standpoint of enzyme function assignment, these enzymes are intriguing because they use a small number of chemically simple substrates to generate, potentially, tens of thousands of different products. Hence, substrate binding specificity is only a small part of the challenge; the key is determining how the enzyme directs the carbocation chemistry to specific products. These more complex modeling approaches clearly require quantum mechanical methods.« less

Transition between 'base' and 'tip' carbon nanofiber growth modes

NASA Astrophysics Data System (ADS)

Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Guillorn, Michael A.; Simpson, Michael L.

2002-04-01

Carbon nanofibers (CNFs) have been synthesized by catalytically controlled dc glow discharge plasma-enhanced chemical vapor deposition (PECVD). Both base-type and tip-type nanofibers have been produced on identical substrates. We have observed a sharp transition between these two growth modes by controlling the kinetics of the growth process without changing the substrate and catalyst materials. This transition is brought about by changing the parameters used in the deposition process such as the flow ratio of the carbonaceous and etchant gasses and others. This study of the initial growth stages as a function of time for both regimes provides a basis for a model of the growth mode transition.

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis.

PubMed

Burschowsky, Daniel; van Eerde, André; Ökvist, Mats; Kienhöfer, Alexander; Kast, Peter; Hilvert, Donald; Krengel, Ute

2014-12-09

For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.

Enzyme activation through the utilization of intrinsic dianion binding energy.

PubMed

Amyes, T L; Malabanan, M M; Zhai, X; Reyes, A C; Richard, J P

2017-03-01

We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Adhesion and Wetting of Soft Nanoparticles on Textured Surfaces: Transition between Wenzel and Cassie-Baxter States

DOE PAGES

Cao, Zhen; Stevens, Mark J.; Carrillo, Jan-Michael Y.; ...

2015-01-16

We use a combination of the molecular dynamics simulations and scaling analysis to study interactions between gel-like nanoparticles and substrates covered with rectangular shape posts. Our simulations have shown that nanoparticle in contact with substrate undergo first order transition between Wenzel and Cassie-Baxter state which location depends on nanoparticle shear modulus, the strength of nanoparticle-substrate interactions, height of the substrate posts and nanoparticle size, R p. There is a range of system parameters where these two states coexist such that the average indentation δ produced by substrate posts changes monotonically with nanoparticle shear modulus, G p. We have developed amore » scaling model that describes deformation of nanoparticle in contact with patterned substrate. In the framework of this model the effect of the patterned substrate can be taken into account by introducing an effective work of adhesion, W eff, which describes the first order transition between Wenzel and Cassie-Baxter states. There are two different shape deformation regimes for nanoparticles with shear modulus G p and surface tension γ p. Shape of small nanoparticles with size R p < γ p 3/2G p -1 W eff -1/2 is controlled by capillary forces while deformation of large nanoparticles, R p > γ p 3/2G p -1 W eff -1/2« less

Structure-Reactivity Relationships in Multi-Component Transition Metal Oxide Catalysts FINAL Report

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

Altman, Eric I.

2015-10-06

The focus of the project was on developing an atomic-level understanding of how transition metal oxide catalysts function. Over the course of several renewals the specific emphases shifted from understanding how local structure and oxidation state affect how molecules adsorb and react on the surfaces of binary oxide crystals to more complex systems where interactions between different transition metal oxide cations in an oxide catalyst can affect reactivity, and finally to the impact of cluster size on oxide stability and reactivity. Hallmarks of the work were the use of epitaxial growth methods to create surfaces relevant to catalysis yet tractablemore » for fundamental surface science approaches, and the use of scanning tunneling microscopy to follow structural changes induced by reactions and to pinpoint adsorption sites. Key early findings included the identification of oxidation and reduction mechanisms on a tungsten oxide catalyst surface that determine the sites available for reaction, identification of C-O bond cleavage as the rate limiting step in alcohol dehydration reactions on the tungsten oxide surface, and demonstration that reduction does not change the favored reaction pathway but rather eases C-O bond cleavage and thus reduces the reaction barrier. Subsequently, a new reconstruction on the anatase phase of TiO 2 relevant to catalysis was discovered and shown to create sites with distinct reactivity compared to other TiO 2 surfaces. Building on this work on anatase, the mechanism by which TiO 2 enhances the reactivity of vanadium oxide layers was characterized and it was found that the TiO 2 substrate can force thin vanadia layers to adopt structures they would not ordinarily form in the bulk which in turn creates differences in reactivity between supported layers and bulk samples. From there, the work progressed to studying well-defined ternary oxides where synergistic effects between the two cations can induce catalytic properties not seen for the individual binary oxides and to the structure and properties of transition metal oxide clusters. For the latter, surprising results were found including the observation that small clusters can actually be orders of magnitude more difficult than bulk materials to oxidize and that even weak substrate interactions can dictate the structure and reactivity of the oxide clusters. It was shown that these results could be explained in terms of simple thermodynamic arguments that extend to materials beyond the Co oxide system studied.« less

Latest Researches Advances of Plasma Spraying: From Splat to Coating Formation

NASA Astrophysics Data System (ADS)

Fauchais, P.; Vardelle, M.; Goutier, S.

2016-12-01

The plasma spray process with solid feedstock, mainly ceramics powders, studied since the sixties is now a mature technology. The plasma jet and particle in-flight characterizations are now well established. The use of computer-aided robot trajectory allows spraying on industrial parts with complex geometries. Works about splat formation have shown the importance of: the substrate preheating over the transition temperature to get rid of adsorbates and condensates, substrate chemistry, crystal structure and substrate temperature during the whole coating process. These studies showed that coating properties strongly depend on the splat formation and layering. The first part of this work deals with a summary of conventional plasma spraying key points. The second part presents the current knowledge in plasma spraying with liquid feedstock, technology developed for about two decades with suspensions of particles below micrometers or solutions of precursors that form particles a few micrometers sized through precipitation. Coatings are finely structured and even nanostructured with properties arousing the interest of researchers. However, the technology is by far more complex than the conventional ones. The main conclusions are that models should be developed further, plasma torches and injection setups adapted, and new measuring techniques to reliably characterize these small particles must be designed.

Crystal Structure of the Golgi-Associated Human Nα-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation.

PubMed

Støve, Svein Isungset; Magin, Robert S; Foyn, Håvard; Haug, Bengt Erik; Marmorstein, Ronen; Arnesen, Thomas

2016-07-06

N-Terminal acetylation is a common and important protein modification catalyzed by N-terminal acetyltransferases (NATs). Six human NATs (NatA-NatF) contain one catalytic subunit each, Naa10 to Naa60, respectively. In contrast to the ribosome-associated NatA to NatE, NatF/Naa60 specifically associates with Golgi membranes and acetylates transmembrane proteins. To gain insight into the molecular basis for the function of Naa60, we developed an Naa60 bisubstrate CoA-peptide conjugate inhibitor, determined its X-ray structure when bound to CoA and inhibitor, and carried out biochemical experiments. We show that Naa60 adapts an overall fold similar to that of the catalytic subunits of ribosome-associated NATs, but with the addition of two novel elongated loops that play important roles in substrate-specific binding. One of these loops mediates a dimer to monomer transition upon substrate-specific binding. Naa60 employs a catalytic mechanism most similar to Naa50. Collectively, these data reveal the molecular basis for Naa60-specific acetyltransferase activity with implications for its Golgi-specific functions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Disordered Phase of the 3x3 Pb/Ge(111) structure at low temperature

NASA Astrophysics Data System (ADS)

Guo, Jiandong; Bolorizadeh, Mehdi; Plummer, E. W.

2003-03-01

* Dept. of Phys., Univ. of Tenn., Knoxville, TN 37996. ** Condensed Matter Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831. At a metal surface or a thin metallic film on a semiconductor there is a competition between the long-range adatom-adatom interactions and the local stress fields imposed by the substrate bulk structure. In interesting cases this leads to a structural phase transition. In this talk we present a STM investigation of the two-dimensional structure at different temperatures for the 1/3 monolayer of Pb on Ge(111) system. When the temperature is lowered the interface undergoes a (3x3)R30^o to (3x3) phase transition at roughly 110 K. Substitutional Ge defects play a crucial role in the phase transition as has been reported for the isoelectronic Sn/Ge system. However, unlike Sn/Ge, as the temperature is lowed below 80 K the (3x3) structure in Pb/Ge is broken and a disordered glassy-like structure is observed. This is very similar to the glassy phase predicted by Shi et al. in a model calculation for the Sn/Ge system. The question we address is, is this disordered low temperature phase inherent to the ideal Pb/Ge system or a consequence of the Ge substitutional defects? This work was funded by NSF DMR-0105232 and Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U.S. Dept. of Energy under contract DE-AC05-00OR22725.

Characterization of a new transparent-conducting material of ZnO doped ITO thin films

NASA Astrophysics Data System (ADS)

Ali, H. M.

2005-11-01

Thin films of indium tin oxide (ITO) doped with zinc oxide have the remarkable properties of being conductive yet still highly transparent in the visible and near-IR spectral ranges. The Electron beam deposi- tion technique is one of the simplest and least expensive ways of preparing. High-quality ITO thin films have been deposited on glass substrates by Electron beam evaporation technique. The effect of doping and substrate deposition temperature was found to have a significant effect on the structure, electrical and optical properties of ZnO doped ITO films. The average optical transmittance has been increased with in- creasing the substrate temperature. The maximum value of transmittance is greater than 84% in the visible region and 85% in the NIR region obtained for film with Zn/ITO = 0.13 at substrate temperature 200 °C. The dielectric constant, average excitation energy for electronic transitions (E o), the dispersion energy (E d), the long wavelength refractive index (n ), average oscillator wave length ( o) and oscillator strength S _o for the thin films were determined and presented in this work.

Microstructure evolution of Al-doped zinc oxide films prepared by in-line reactive mid-frequency magnetron sputtering

NASA Astrophysics Data System (ADS)

Hong, R. J.; Jiang, X.

2006-07-01

Aluminium-doped zinc oxide (ZnO:Al or AZO) thin films were deposited on glass substrates by reactive mid-frequency (MF) magnetron sputtering from Zn/Al metallic targets. Strong (002) preferred orientation was detected by X-ray diffraction (XRD). It was observed by plan-view transmission electron microscopy (TEM) that an AZO film deposited at low substrate temperature was composed of irregular large grains; but the film prepared at high temperature was composed of moderate sized grains with a regular shape. A secondary phase of ZnO2 was also observed for the film deposited at low substrate temperature. The cross-sectional TEM study of the AZO film showed that prior to the well-aligned columnar growth an initial interfacial zone with nano crystallites were formed. The nano crystallites formed initially with a large tilt angle normal to the substrate surface and during the growth of the transition zone, the tilt angle decreased until it vanished. The evolution of the film structure is discussed in terms of evolutionary selection model and the dynamic deposition process.

Epitaxial Ni-Mn-Ga-Co thin films on PMN-PT substrates for multicaloric applications

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

Schleicher, B., E-mail: b.schleicher@ifw-dresden.de; Niemann, R.; Schultz, L.

2015-08-07

Multicaloric stacks consisting of a magnetocaloric film on a piezoelectric substrate promise improved caloric properties as the transition temperature can be controlled by both magnetic and electric fields. We present epitaxially grown magnetocaloric Ni-Mn-Ga-Co thin films on ferroelectric Pb(Mg{sub 1/3}Nb{sub 2/3}){sub 0.72}Ti{sub 0.28}O{sub 3} substrates. Structure and microstructure of two samples, being in the austenitic and martensitic state at room temperature, are investigated by X-ray diffraction in two- and four-circle geometry and by atomic force microscopy. In addition, high temperature magnetometry was performed on the latter sample. The combination of these methods allows separating the influence of epitaxial growth andmore » martensitic transformation. A preferential alignment of twin boundaries is observed already in the as-deposited state, which indicates the presence of prestress, without applying an electric field to the substrate. A temperature-magnetic field phase diagram is presented, which demonstrates the inverse magnetocaloric effect of the epitaxial Ni-Mn-Ga-Co film.« less

Ideal glass transitions in thin films: An energy landscape perspective

NASA Astrophysics Data System (ADS)

Truskett, Thomas M.; Ganesan, Venkat

2003-07-01

We introduce a mean-field model for the potential energy landscape of a thin fluid film confined between parallel substrates. The model predicts how the number of accessible basins on the energy landscape and, consequently, the film's ideal glass transition temperature depend on bulk pressure, film thickness, and the strength of the fluid-fluid and fluid-substrate interactions. The predictions are in qualitative agreement with the experimental trends for the kinetic glass transition temperature of thin films, suggesting the utility of landscape-based approaches for studying the behavior of confined fluids.

Spectroscopic analysis of phase constitution of high quality VO2 thin film prepared by facile sol-gel method

NASA Astrophysics Data System (ADS)

Wu, Y. F.; Fan, L. L.; Chen, S. M.; Chen, S.; Zou, C. W.; Wu, Z. Y.

2013-04-01

VO2 thin films with large-area were prepared on Al2O3 substrates by a simple sol-gel method. After an annealing treatment under low vacuum condition, all the VO2 films showed a preferred growth direction and exhibited excellent semiconductor-metal transition (SMT) characteristics. The structure and electrical properties of the obtained VO2 films were investigated systematically. Raman spectra, X-ray diffraction and X-ray absorption spectra measurements pointed out that the VO2 film on Al_2 O_3 ( {10overline 1 0}) substrate showed a M1 phase instead of M2 phase as reported in previous studies. Based on the experiment results, it was suggested that the strained structure of oriented VO2 films could be a mechanism for the formation of the intermediate M2 phase, whereas it is difficult to access the pure M2 phase of undoped VO2 films. VO2 film on Al_2 O_3 ( {10overline 1 0} ) substrate showed a lower SMT temperature compared to VO2 film on Al2O3 (0001), which can be mostly attributed to the differences of both lattice mismatch and thermal stress. The present results confirm and make clear the relevance of the substrate orientation in the growth of VO2 film and their different contributions to the SMT characteristics in vanadate systems.

Exosites in the substrate specificity of blood coagulation reactions.

PubMed

Bock, P E; Panizzi, P; Verhamme, I M A

2007-07-01

The specificity of blood coagulation proteinases for substrate, inhibitor, and effector recognition is mediated by exosites on the surfaces of the catalytic domains, physically separated from the catalytic site. Some thrombin ligands bind specifically to either exosite I or II, while others engage both exosites. The involvement of different, overlapping constellations of exosite residues enables binding of structurally diverse ligands. The flexibility of the thrombin structure is central to the mechanism of complex formation and the specificity of exosite interactions. Encounter complex formation is driven by electrostatic ligand-exosite interactions, followed by conformational rearrangement to a stable complex. Exosites on some zymogens are in low affinity proexosite states and are expressed concomitant with catalytic site activation. The requirement for exosite expression controls the specificity of assembly of catalytic complexes on the coagulation pathway, such as the membrane-bound factor Xa*factor Va (prothrombinase) complex, and prevents premature assembly. Substrate recognition by prothrombinase involves a two-step mechanism with initial docking of prothrombin to exosites, followed by a conformational change to engage the FXa catalytic site. Prothrombin and its activation intermediates bind prothrombinase in two alternative conformations determined by the zymogen to proteinase transition that are hypothesized to involve prothrombin (pro)exosite I interactions with FVa, which underpin the sequential activation pathway. The role of exosites as the major source of substrate specificity has stimulated development of exosite-targeted anticoagulants for treatment of thrombosis.

Hairy and Slippery Polyoxazoline-Based Copolymers on Model and Cartilage Surfaces.

PubMed

Morgese, Giulia; Ramakrishna, Shivaprakash N; Simic, Rok; Zenobi-Wong, Marcy; Benetti, Edmondo M

2018-02-12

Comb-like polymers presenting a hydroxybenzaldehyde (HBA)-functionalized poly(glutamic acid) (PGA) backbone and poly(2-methyl-2-oxazoline) (PMOXA) side chains chemisorb on aminolized substrates, including cartilage surfaces, forming layers that reduce protein contamination and provide lubrication. The structure, physicochemical, biopassive, and tribological properties of PGA-PMOXA-HBA films are finely determined by the copolymer architecture, its reactivity toward the surface, i.e. PMOXA side-chain crowding and HBA density, and by the copolymer solution concentration during assembly. Highly reactive species with low PMOXA content form inhomogeneous layers due to the limited possibility of surface rearrangements by strongly anchored copolymers, just partially protecting the functionalized surface from protein contamination and providing a relatively weak lubrication on cartilage. Biopassivity and lubrication can be improved by increasing copolymer concentration during assembly, leading to a progressive saturation of surface defects across the films. In a different way, less reactive copolymers presenting high PMOXA side-chain densities form uniform, biopassive, and lubricious films, both on model aminolized silicon oxide surfaces, as well as on cartilage substrates. When assembled at low concentrations these copolymers adopt a "lying down" conformation, i.e. adhering via their backbones onto the substrates, while at high concentrations they undergo a conformational transition, assuming a more densely packed, "standing up" structure, where they stretch perpendicularly from the substrate. This specific arrangement reduces protein contamination and improves lubrication both on model as well as on cartilage surfaces.

Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study.

PubMed

McClory, James; Timson, David J; Singh, Warispreet; Zhang, Jian; Huang, Meilan

2017-12-14

Isopentenyl phosphate kinase (IPK) catalyzes the Mg 2+ -ATP dependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the catalytically competent structure in complex with the metal ion Mg 2+ and elucidate the phosphorylation reaction mechanism using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99). Comparing the substrate-bound and substrate-free IPK complexes, we observed that substrate binding results in significant conformational change of three residues Lys204, Glu207, and Lys211 located on the αG helix to form a strong salt bridge network with Asp145, which in turn tethers the invariant Ser142 via H-bond interaction. The conformational change shuts the subtrate entrance channel formed between the αG and αE helices. Further, we demonstrate the phosphorylation reaction occurs with a reaction barrier of 17.58 kcal/mol, which is in agreement with the previous experimental kinetic data. We found that a highly conserved Gly8 on a glycine-rich loop, together with Lys14, stabilizes the transition state.

CVD synthesis of large-area, highly crystalline MoSe2 atomic layers on diverse substrates and application to photodetectors.

PubMed

Xia, Jing; Huang, Xing; Liu, Ling-Zhi; Wang, Meng; Wang, Lei; Huang, Ben; Zhu, Dan-Dan; Li, Jun-Jie; Gu, Chang-Zhi; Meng, Xiang-Min

2014-08-07

Synthesis of large-area, atomically thin transition metal dichalcogenides (TMDs) on diverse substrates is of central importance for the large-scale fabrication of flexible devices and heterojunction-based devices. In this work, we successfully synthesized a large area of highly-crystalline MoSe2 atomic layers on SiO2/Si, mica and Si substrates using a simple chemical vapour deposition (CVD) method at atmospheric pressure. Atomic force microscopy (AFM) and Raman spectroscopy reveal that the as-grown ultrathin MoSe2 layers change from a single layer to a few layers. Photoluminescence (PL) spectroscopy demonstrates that while the multi-layer MoSe2 shows weak emission peaks, the monolayer has a much stronger emission peak at ∼ 1.56 eV, indicating the transition from an indirect to a direct bandgap. Transmission electron microscopy (TEM) analysis confirms the single-crystallinity of MoSe2 layers with a hexagonal structure. In addition, the photoresponse performance of photodetectors based on MoSe2 monolayer was studied for the first time. The devices exhibit a rapid response of ∼ 60 ms and a good photoresponsivity of ∼ 13 mA/W (using a 532 nm laser at an intensity of 1 mW mm(-2) and a bias of 10 V), suggesting that MoSe2 monolayer is a promising material for photodetection applications.

Filtered pulsed cathodic arc deposition of fullerene-like carbon and carbon nitride films

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

Tucker, Mark D., E-mail: martu@ifm.liu.se; Broitman, Esteban; Näslund, Lars-Åke

Carbon and carbon nitride films (CN{sub x}, 0 ≤ x ≤ 0.26) were deposited by filtered pulsed cathodic arc and were investigated using transmission electron microscopy and X-ray photoelectron spectroscopy. A “fullerene-like” (FL) structure of ordered graphitic planes, similar to that of magnetron sputtered FL-CN{sub x} films, was observed in films deposited at 175 °C and above, with N{sub 2} pressures of 0 and 0.5 mTorr. Higher substrate temperatures and significant nitrogen incorporation are required to produce similar FL structure by sputtering, which may, at least in part, be explained by the high ion charge states and ion energies characteristic of arc deposition. A gradualmore » transition from majority sp{sup 3}-hybridized films to sp{sup 2} films was observed with increasing substrate temperature. High elastic recovery, an attractive characteristic mechanical property of FL-CN{sub x} films, is evident in arc-deposited films both with and without nitrogen content, and both with and without FL structure.« less

Structural basis for the mechanism and substrate specificity of glycocyamine kinase, a phosphagen kinase family member

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

Lim, Kap; Pullalarevu, Sadhana; Surabian, Karen Talin

2010-03-12

Glycocyamine kinase (GK), a member of the phosphagen kinase family, catalyzes the Mg{sup 2+}-dependent reversible phosphoryl group transfer of the N-phosphoryl group of phosphoglycocyamine to ADP to yield glycocyamine and ATP. This reaction helps to maintain the energy homeostasis of the cell in some multicelullar organisms that encounter high and variable energy turnover. GK from the marine worm Namalycastis sp. is heterodimeric, with two homologous polypeptide chains, {alpha} and {beta}, derived from a common pre-mRNA by mutually exclusive N-terminal alternative exons. The N-terminal exon of GK{beta} encodes a peptide that is different in sequence and is 16 amino acids longermore » than that encoded by the N-terminal exon of GK{alpha}. The crystal structures of recombinant GK{alpha}{beta} and GK{beta}{beta} from Namalycastis sp. were determined at 2.6 and 2.4 {angstrom} resolution, respectively. In addition, the structure of the GK{beta}{beta} was determined at 2.3 {angstrom} resolution in complex with a transition state analogue, Mg{sup 2+}-ADP-NO{sub 3}{sup -}-glycocyamine. Consistent with the sequence homology, the GK subunits adopt the same overall fold as that of other phosphagen kinases of known structure (the homodimeric creatine kinase (CK) and the monomeric arginine kinase (AK)). As with CK, the GK N-termini mediate the dimer interface. In both heterodimeric and homodimeric GK forms, the conformations of the two N-termini are asymmetric, and the asymmetry is different than that reported previously for the homodimeric CKs from several organisms. The entire polypeptide chains of GK{alpha}{beta} are structurally defined, and the longer N-terminus of the {beta} subunit is anchored at the dimer interface. In GK{beta}{beta} the 24 N-terminal residues of one subunit and 11 N-terminal residues of the second subunit are disordered. This observation is consistent with a proposal that the GK{alpha}{beta} amino acids involved in the interface formation were optimized once a heterodimer emerged as the physiological form of the enzyme. As a consequence, the homodimer interface (either solely {alpha} or solely {beta} chains) has been corrupted. In the unbound state, GK exhibits an open conformation analogous to that observed with ligand-free CK or AK. Upon binding the transition state analogue, both subunits of GK undergo the same closure motion that clasps the transition state analogue, in contrast to the transition state analogue complexes of CK, where the corresponding transition state analogue occupies only one subunit, which undergoes domain closure. The active site environments of the GK, CK, and AK at the bound states reveal the structural determinants of substrate specificity. Despite the equivalent binding in both active sites of the GK dimer, the conformational asymmetry of the N-termini is retained. Thus, the coupling between the structural asymmetry and negative cooperativity previously proposed for CK is not supported in the case of GK.« less

Molecular beam epitaxy of quasi-freestanding transition metal disulphide monolayers on van der Waals substrates: a growth study

NASA Astrophysics Data System (ADS)

Hall, Joshua; Pielić, Borna; Murray, Clifford; Jolie, Wouter; Wekking, Tobias; Busse, Carsten; Kralj, Marko; Michely, Thomas

2018-04-01

Based on an ultra-high vacuum compatible two-step molecular beam epitaxy synthesis with elemental sulphur, we grow clean, well-oriented, and almost defect-free monolayer islands and layers of the transition metal disulphides MoS2, TaS2 and WS2. Using scanning tunneling microscopy and low energy electron diffraction we investigate systematically how to optimise the growth process, and provide insight into the growth and annealing mechanisms. A large band gap of 2.55 eV and the ability to move flakes with the scanning tunneling microscope tip both document the weak interaction of MoS2 with its substrate consisting of graphene grown on Ir(1 1 1). As the method works for the synthesis of a variety of transition metal disulphides on different substrates, we speculate that it could be of great use for providing hitherto unattainable high quality monolayers of transition metal disulphides for fundamental spectroscopic investigations.

High process yield rates of thermoplastic nanofluidic devices using a hybrid thermal assembly technique.

PubMed

Uba, Franklin I; Hu, Bo; Weerakoon-Ratnayake, Kumuditha; Oliver-Calixte, Nyote; Soper, Steven A

2015-02-21

Over the past decade, thermoplastics have been used as alternative substrates to glass and Si for microfluidic devices because of the diverse and robust fabrication protocols available for thermoplastics that can generate high production rates of the desired structures at low cost and with high replication fidelity, the extensive array of physiochemical properties they possess, and the simple surface activation strategies that can be employed to tune their surface chemistry appropriate for the intended application. While the advantages of polymer microfluidics are currently being realized, the evolution of thermoplastic-based nanofluidic devices is fraught with challenges. One challenge is assembly of the device, which consists of sealing a cover plate to the patterned fluidic substrate. Typically, channel collapse or substrate dissolution occurs during assembly making the device inoperable resulting in low process yield rates. In this work, we report a low temperature hybrid assembly approach for the generation of functional thermoplastic nanofluidic devices with high process yield rates (>90%) and with a short total assembly time (16 min). The approach involves thermally sealing a high T(g) (glass transition temperature) substrate containing the nanofluidic structures to a cover plate possessing a lower T(g). Nanofluidic devices with critical feature sizes ranging between 25-250 nm were fabricated in a thermoplastic substrate (T(g) = 104 °C) and sealed with a cover plate (T(g) = 75 °C) at a temperature significantly below the T(g) of the substrate. Results obtained from sealing tests revealed that the integrity of the nanochannels remained intact after assembly and devices were useful for fluorescence imaging at high signal-to-noise ratios. The functionality of the assembled devices was demonstrated by studying the stretching and translocation dynamics of dsDNA in the enclosed thermoplastic nanofluidic channels.

Atomic Scale Control of Competing Electronic Phases in Ultrathin Correlated Oxides

NASA Astrophysics Data System (ADS)

Shen, Kyle

2015-03-01

Ultrathin epitaxial thin films offer a number of unique advantages for engineering the electronic properties of correlated transition metal oxides. For example, atomically thin films can be synthesized to artificially confine electrons in two dimensions. Furthermore, using a substrate with a mismatched lattice constant can impose large biaxial strains of larger than 3% (Δa / a), much larger than can achieved in bulk single crystals. Since these dimensionally confined or strained systems may necessarily be less than a few unit cells thick, investigating their properties and electronic structure can be particularly challenging. We employ a combination of reactive oxide molecular beam epitaxy (MBE) and angle-resolved photoemission spectroscopy (ARPES) to investigate how dimensional confinement and epitaxial strain can be used to manipulate electronic properties and structure in correlated transition metal oxide thin films. We describe some of our recent work manipulating and studying the electronic structure of ultrathin LaNiO3 through a thickness-driven metal-insulator transition between three and two unit cells (Nature Nanotechnology 9, 443, 2014), where coherent Fermi liquid-like quasiparticles are suppressed at the metal-insulator transition observed in transport. We also will describe some recent unpublished work using epitaxial strain to drive a Lifshitz transition in atomically thin films of the spin-triplet ruthenate superconductor Sr2RuO4, where we also can dramatically alter the quasiparticle scattering rates and drive the system towards non-Fermi liquid behavior near the critical point (B. Burganov, C. Adamo, in preparation). Funding provided by the Office of Naval Research and Air Force Office of Scientific Research.

Anopheles gambiae Purine Nucleoside Phosphorylase: Catalysis, Structure, and Inhibition

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

Taylor,E.; Rinaldo-Matthis, A.; Li, L.

The purine salvage pathway of Anopheles gambiae, a mosquito that transmits malaria, has been identified in genome searches on the basis of sequence homology with characterized enzymes. Purine nucleoside phosphorylase (PNP) is a target for the development of therapeutic agents in humans and purine auxotrophs, including malarial parasites. The PNP from Anopheles gambiae (AgPNP) was expressed in Escherichia coli and compared to the PNPs from Homo sapiens (HsPNP) and Plasmodium falciparum (PfPNP). AgPNP has kcat values of 54 and 41 s-1 for 2'-deoxyinosine and inosine, its preferred substrates, and 1.0 s-1 for guanosine. However, the chemical step is fast formore » AgPNP at 226 s-1 for guanosine in pre-steady-state studies. 5'-Deaza-1'-aza-2'-deoxy-1'-(9-methylene)-Immucillin-H (DADMe-ImmH) is a transition-state mimic for a 2'-deoxyinosine ribocation with a fully dissociated N-ribosidic bond and is a slow-onset, tight-binding inhibitor with a dissociation constant of 3.5 pM. This is the tightest-binding inhibitor known for any PNP, with a remarkable Km/Ki* of 5.4 x 107, and is consistent with enzymatic transition state predictions of enhanced transition-state analogue binding in enzymes with enhanced catalytic efficiency. Deoxyguanosine is a weaker substrate than deoxyinosine, and DADMe-Immucillin-G is less tightly bound than DADMe-ImmH, with a dissociation constant of 23 pM for AgPNP as compared to 7 pM for HsPNP. The crystal structure of AgPNP was determined in complex with DADMe-ImmH and phosphate to a resolution of 2.2 Angstroms to reveal the differences in substrate and inhibitor specificity. The distance from the N1' cation to the phosphate O4 anion is shorter in the AgPNP{center_dot}DADMe-ImmH{center_dot}PO4 complex than in HsPNP{center_dot}DADMe-ImmH{center_dot}SO4, offering one explanation for the stronger inhibitory effect of DADMe-ImmH for AgPNP.« less

Evolution of sp{sup 2} networks with substrate temperature in amorphous carbon films: Experiment and theory

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

Gago, R.; Centro de Micro-Analisis de Materiales, Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid; Vinnichenko, M.

2005-07-01

The evolution of sp{sup 2} hybrids in amorphous carbon (a-C) films deposited at different substrate temperatures was studied experimentally and theoretically. The bonding structure of a-C films prepared by filtered cathodic vacuum arc was assessed by the combination of visible Raman spectroscopy, x-ray absorption, and spectroscopic ellipsometry, while a-C structures were generated by molecular-dynamics deposition simulations with the Brenner interatomic potential to determine theoretical sp{sup 2} site distributions. The experimental results show a transition from tetrahedral a-C (ta-C) to sp{sup 2}-rich structures at {approx}500 K. The sp{sup 2} hybrids are mainly arranged in chains or pairs whereas graphitic structures aremore » only promoted for sp{sup 2} fractions above 80%. The theoretical analysis confirms the preferred pairing of isolated sp{sup 2} sites in ta-C, the coalescence of sp{sup 2} clusters for medium sp{sup 2} fractions, and the pronounced formation of rings for sp{sup 2} fractions >80%. However, the dominance of sixfold rings is not reproduced theoretically, probably related to the functional form of the interatomic potential used.« less

Electrodeposition of biaxially textured layers on a substrate

DOEpatents

Bhattacharya, Raghu N; Phok, Sovannary; Spagnol, Priscila; Chaudhuri, Tapas

2013-11-19

Methods of producing one or more biaxially textured layer on a substrate, and articles produced by the methods, are disclosed. An exemplary method may comprise electrodepositing on the substrate a precursor material selected from the group consisting of rare earths, transition metals, actinide, lanthanides, and oxides thereof. An exemplary article (150) may comprise a biaxially textured base material (130), and at least one biaxially textured layer (110) selected from the group consisting of rare earths, transition metals, actinides, lanthanides, and oxides thereof. The at least one biaxially textured layer (110) is formed by electrodeposition on the biaxially textured base material (130).

Framework for scalable adsorbate–adsorbate interaction models

DOE PAGES

Hoffmann, Max J.; Medford, Andrew J.; Bligaard, Thomas

2016-06-02

Here, we present a framework for physically motivated models of adsorbate–adsorbate interaction between small molecules on transition and coinage metals based on modifications to the substrate electronic structure due to adsorption. We use this framework to develop one model for transition and one for coinage metal surfaces. The models for transition metals are based on the d-band center position, and the models for coinage metals are based on partial charges. The models require no empirical parameters, only two first-principles calculations per adsorbate as input, and therefore scale linearly with the number of reaction intermediates. By theory to theory comparison withmore » explicit density functional theory calculations over a wide range of adsorbates and surfaces, we show that the root-mean-squared error for differential adsorption energies is less than 0.2 eV for up to 1 ML coverage.« less

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

Yu, Shifeng; Wang, Shuyu; Lu, Ming

In this paper, vanadium thin films were deposited on sapphire substrates by DC magnetron sputtering and then oxidized in a tube furnace filled with oxygen under different temperatures and oxygen flow rates. The significant influence of the oxygen flow rate and oxidation temperature on the electrical and structural properties of the vanadium oxide thin films were investigated systematically. It shows the pure vanadium dioxide (VO 2) state can only be obtained in a very narrow temperature and oxygen flow rate range. The resistivity change during the metal-insulator transition varies from 0.2 to 4 orders of magnitude depending on the oxidationmore » condition. Large thermal hysteresis during the metal-insulator phase transition was observed during the transition compared to the results in literature. Proper oxidation conditions can significantly reduce the thermal hysteresis. Finally, the fabricated VO 2 thin films showed the potential to be applied in the development of electrical sensors and other smart devices.« less

The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase

PubMed Central

Bauer, Robert J.; Evans, Thomas C.; Lohman, Gregory J. S.

2016-01-01

DNA ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. Prior characterization of DNA ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsDNA substrate, with no interaction evident on dsDNA lacking a nick. In the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation and nick-sealing steps of T4 DNA ligase by non-nicked, non-substrate dsDNA. Inhibition by non-substrate DNA was dependent only on the total DNA concentration rather than the structure; with 1 μg/mL of 40-mers, 75-mers, or circular plasmid DNA all inhibiting ligation equally. A >15-fold reduction in T4 DNA ligase self-adenylylation rate when in the presence of high non-nicked dsDNA concentrations was observed. Finally, EMSAs were utilized to demonstrate that non-substrate dsDNA can compete with nicked dsDNA substrates for enzyme binding. Based upon these data, we hypothesize the inhibition of T4 DNA ligase by non-nicked dsDNA is direct evidence for a two-step nick-binding mechanism, with an initial, nick-independent, transient dsDNA-binding event preceding a transition to a stable binding complex in the presence of a nick site. PMID:26954034

The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase.

PubMed

Bauer, Robert J; Evans, Thomas C; Lohman, Gregory J S

2016-01-01

DNA ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. Prior characterization of DNA ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsDNA substrate, with no interaction evident on dsDNA lacking a nick. In the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation and nick-sealing steps of T4 DNA ligase by non-nicked, non-substrate dsDNA. Inhibition by non-substrate DNA was dependent only on the total DNA concentration rather than the structure; with 1 μg/mL of 40-mers, 75-mers, or circular plasmid DNA all inhibiting ligation equally. A >15-fold reduction in T4 DNA ligase self-adenylylation rate when in the presence of high non-nicked dsDNA concentrations was observed. Finally, EMSAs were utilized to demonstrate that non-substrate dsDNA can compete with nicked dsDNA substrates for enzyme binding. Based upon these data, we hypothesize the inhibition of T4 DNA ligase by non-nicked dsDNA is direct evidence for a two-step nick-binding mechanism, with an initial, nick-independent, transient dsDNA-binding event preceding a transition to a stable binding complex in the presence of a nick site.

Wetting Transitions in ^4He/^3He Mixtures on Cesium

NASA Astrophysics Data System (ADS)

Ross, David

1997-03-01

Over the last several years, helium on cesium has proven to be an ideal model system for the study of wetting and wetting transitions(E. Cheng, M.W. Cole, W.F. Saam, and J. Treiner, Phys. Rev. Lett. 67), 1007 (1991).^,(J.E. Rutledge and P. Taborek, Phys. Rev. Lett. 69), 937 (1992).^,(D. Ross, J.E. Rutledge, and P. Taborek, Phys. Rev. Lett. 76), 2350 (1996).. This presentation will focus on the adsorption of binary liquid mixtures of the helium isotopes, ^3He and ^4He, on cesium substrates over a range of temperatures extending from 0.2 K to 1.0 K. The results, spanning ^3He concentrations from 0 to 1, constitute the first experimentally constructed complete wetting phase diagram for a two component liquid at a weakly binding substrate. The wetting behavior is particularly interesting in the vicinity of bulk liquid phase separation. A wetting transition of the ^4He rich liquid between the ^3He rich liquid and the cesium substrate has been found with Tw = 0.53 K. The surface phase transition line associated with this wetting transition is found to extend to both sides of the bulk phase separation line. On the ^3He rich side it is a prewetting line, and on the ^4He rich side it becomes a line of triple point induced dewetting transitions. General arguments indicate that this behavior should be typical of a large class of binary liquid mixtures at weakly binding substrates.

Structural Characterization of the Molecular Events during a Slow Substrate-Product Transition in Orotidine 5'-Monophosphate Decarboxylase

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

Fujihashi, Masahiro; Wei, Lianhu; Kotra, Lakshmi P

2009-04-06

Crystal structures of substrate-product complexes of Methanobacterium thermoautotrophicum orotidine 5'-monophosphate decarboxylase, obtained at various steps in its catalysis of the unusual transformation of 6-cyano-uridine 5'-monophosphate (UMP) into barbituric acid ribosyl monophosphate, show that the cyano substituent of the substrate, when bound to the active site, is first bent significantly from the plane of the pyrimidine ring and then replaced by an oxygen atom. Although the K72A and D70A/K72A mutants are either catalytically impaired or even completely inactive, they still display bending of the C6 substituent. Interestingly, high-resolution structures of the D70A and D75N mutants revealed a covalent bond between C6more » of UMP and the Lys72 side chain after the -CN moiety's release. The same covalent bond was observed when the native enzyme was incubated with 6-azido-UMP and 6-iodo-UMP; in contrast, the K72A mutant transformed 6-iodo-UMP to barbituric acid ribosyl 5'-monophosphate. These results demonstrate that, given a suitable environment, native orotidine 5'-monophosphate decarboxylase and several of its mutants are not restricted to the physiologically relevant decarboxylation; they are able to catalyze even nucleophilic substitution reactions but consistently maintain distortion on the C6 substituent as an important feature of catalysis.« less

Orotidine Monophosphate Decarboxylase--A Fascinating Workhorse Enzyme with Therapeutic Potential.

PubMed

Fujihashi, Masahiro; Mnpotra, Jagjeet S; Mishra, Ram Kumar; Pai, Emil F; Kotra, Lakshmi P

2015-05-20

Orotidine 5'-monophosphate decarboxylase (ODCase) is known as one of the most proficient enzymes. The enzyme catalyzes the last reaction step of the de novo pyrimidine biosynthesis, the conversion from orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate. The enzyme is found in all three domains of life, Bacteria, Eukarya and Archaea. Multiple sequence alignment of 750 putative ODCase sequences resulted in five distinct groups. While the universally conserved DxKxxDx motif is present in all the groups, depending on the groups, several characteristic motifs and residues can be identified. Over 200 crystal structures of ODCases have been determined so far. The structures, together with biochemical assays and computational studies, elucidated that ODCase utilized both transition state stabilization and substrate distortion to accelerate the decarboxylation of its natural substrate. Stabilization of the vinyl anion intermediate by a conserved lysine residue at the catalytic site is considered the largest contributing factor to catalysis, while bending of the carboxyl group from the plane of the aromatic pyrimidine ring of OMP accounts for substrate distortion. A number of crystal structures of ODCases complexed with potential drug candidate molecules have also been determined, including with 6-iodo-uridine, a potential antimalarial agent. Copyright © 2015 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase.

PubMed

Fujihashi, Masahiro; Wei, Lianhu; Kotra, Lakshmi P; Pai, Emil F

2009-04-17

Crystal structures of substrate-product complexes of Methanobacterium thermoautotrophicum orotidine 5'-monophosphate decarboxylase, obtained at various steps in its catalysis of the unusual transformation of 6-cyano-uridine 5'-monophosphate (UMP) into barbituric acid ribosyl monophosphate, show that the cyano substituent of the substrate, when bound to the active site, is first bent significantly from the plane of the pyrimidine ring and then replaced by an oxygen atom. Although the K72A and D70A/K72A mutants are either catalytically impaired or even completely inactive, they still display bending of the C6 substituent. Interestingly, high-resolution structures of the D70A and D75N mutants revealed a covalent bond between C6 of UMP and the Lys72 side chain after the -CN moiety's release. The same covalent bond was observed when the native enzyme was incubated with 6-azido-UMP and 6-iodo-UMP; in contrast, the K72A mutant transformed 6-iodo-UMP to barbituric acid ribosyl 5'-monophosphate. These results demonstrate that, given a suitable environment, native orotidine 5'-monophosphate decarboxylase and several of its mutants are not restricted to the physiologically relevant decarboxylation; they are able to catalyze even nucleophilic substitution reactions but consistently maintain distortion on the C6 substituent as an important feature of catalysis.

Photoreflectance and photoluminescence spectroscopy of the lattice-matched InGaAs/InAlAs single quantum well

NASA Astrophysics Data System (ADS)

Wang, Y. C.; Tyan, S. L.; Juang, Y. D.

2002-07-01

A lattice-matched In0.53Ga0.47As/In0.52Al0.48As single quantum well (SQW) structure grown by gas source molecular beam epitaxy has been investigated by photoreflectance (PR) and photoluminescence (PL). The PR measurements allowed the observation of interband transitions from the heavy- and light-hole valence subbands to the conduction subbands. The transition energies measured from the PR spectra agree with those calculated theoretically. Two features corresponding to the ground state transition coming from the SQW and the band gap transition generated from the buffer layer are observed in the PL spectra and are in good agreement with the PR data. The effect of the temperature on the transition energies is essentially same as that in the gap transition of the bulk structure. The values of the Varshni coefficients of InGaAs/InAlAs were obtained from the relation between the exciton transition energy and the temperature. The built-in electric field could be determined and located from a series of PR spectra by sequential etching processes. The phase spectra obtained from the PR spectra by the Kramers-Kronig transformation were analyzed in terms of the two-ray model, and calculated the etching depth in each etching, and thus leading to the etching rate. The etching rate obtained from phase shift analysis agrees with that measured by atomic force microscopy. The etching results suggest that a built-in electric field exists at the buffer/substrate interface and it also enables us to determine the etching rate.

Reduced-Amide Inhibitor of Pin1 Binds in a Conformation Resembling a Twisted-Amide Transition State†

PubMed Central

Xu, Guoyan G.; Zhang, Yan; Mercedes-Camacho, Ana Y.; Etzkorn, Felicia A.

2011-01-01

The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R–pSer–Ψ[CH2N]–Pro–2-(indol-3-yl)-ethylamine, 1 (R = fluorenylmethoxycarbonyl, Fmoc), and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC50 value of 6.3 μM, which is 4.5-fold better inhibition for Pin1 than our comparable ground state analogue, a cis-amide alkene isostere containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination, and resulted in an IC50 value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser, and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1. PMID:21980916

A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

PubMed

Xu, Guoyan G; Zhang, Yan; Mercedes-Camacho, Ana Y; Etzkorn, Felicia A

2011-11-08

The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.

Switchable vanadium dioxide (VO2) metamaterials fabricated from tungsten doped vanadia-based colloidal nanocrystals

NASA Astrophysics Data System (ADS)

Paik, Taejong; Hong, Sung-Hoon; Gordon, Thomas; Gaulding, Ashley; Kagan, Cherie; Murray, Christopher

2013-03-01

We report the fabrication of thermochromic VO2-based metamaterials using solution-processable colloidal nanocrystals. Vanadium-based nanoparticles are prepared through a non-hydrolytic reaction, resulting in stable colloidal dispersions in solution. Thermochromic nanocrystalline VO2 thin-films are prepared via rapid thermal annealing of colloidal nanoparticles coated on a variety of substrates. Nanostructured VO2 can be patterned over large areas by nanoimprint lithography. Precise control of tungsten (W) doping concentration in colloidal nanoparticles enables tuning of the phase transition temperature of the nanocrystalline VO2 thin-films. W-doped VO2 films display a sharp temperature dependent phase transition, similar to the undoped VO2 film, but at lower temperatures tunable with the doping level. By sequential coating of doped VO2 with different doping concentrations, we fabricate ?smart? multi-layered VO2 films displaying multiple phase transition temperatures within a single structure, allowing for dynamic modulation of the metal-dielectric layered structure. The optical properties programmed into the layered structure are switchable with temperature, which provides additional degrees of freedom to design tunable optical metamaterials. This work is supported by the US Office of Naval Research Multidisciplinary University Research Initiative (MURI) program grant number ONR-N00014-10-1-0942.

Tactile friction of topical formulations.

PubMed

Skedung, L; Buraczewska-Norin, I; Dawood, N; Rutland, M W; Ringstad, L

2016-02-01

The tactile perception is essential for all types of topical formulations (cosmetic, pharmaceutical, medical device) and the possibility to predict the sensorial response by using instrumental methods instead of sensory testing would save time and cost at an early stage product development. Here, we report on an instrumental evaluation method using tactile friction measurements to estimate perceptual attributes of topical formulations. Friction was measured between an index finger and an artificial skin substrate after application of formulations using a force sensor. Both model formulations of liquid crystalline phase structures with significantly different tactile properties, as well as commercial pharmaceutical moisturizing creams being more tactile-similar, were investigated. Friction coefficients were calculated as the ratio of the friction force to the applied load. The structures of the model formulations and phase transitions as a result of water evaporation were identified using optical microscopy. The friction device could distinguish friction coefficients between the phase structures, as well as the commercial creams after spreading and absorption into the substrate. In addition, phase transitions resulting in alterations in the feel of the formulations could be detected. A correlation was established between skin hydration and friction coefficient, where hydrated skin gave rise to higher friction. Also a link between skin smoothening and finger friction was established for the commercial moisturizing creams, although further investigations are needed to analyse this and correlations with other sensorial attributes in more detail. The present investigation shows that tactile friction measurements have potential as an alternative or complement in the evaluation of perception of topical formulations. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I

NASA Astrophysics Data System (ADS)

Venditti, Vincenzo; Tugarinov, Vitali; Schwieters, Charles D.; Grishaev, Alexander; Clore, G. Marius

2015-01-01

Enzyme I (EI), the first component of the bacterial phosphotransfer signal transduction system, undergoes one of the largest substrate-induced interdomain rearrangements documented to date. Here we characterize the perturbations generated by two small molecules, the natural substrate phosphoenolpyruvate and the inhibitor α-ketoglutarate, on the structure and dynamics of EI using NMR, small-angle X-ray scattering and biochemical techniques. The results indicate unambiguously that the open-to-closed conformational switch of EI is triggered by complete suppression of micro- to millisecond dynamics within the C-terminal domain of EI. Indeed, we show that a ligand-induced transition from a dynamic to a more rigid conformational state of the C-terminal domain stabilizes the interface between the N- and C-terminal domains observed in the structure of the closed state, thereby promoting the resulting conformational switch and autophosphorylation of EI. The mechanisms described here may be common to several other multidomain proteins and allosteric systems.

Neutron irradiation and high temperature effects on amorphous Fe-based nano-coatings on steel – A macroscopic assessment

DOE PAGES

Simos, N.; Zhong, Z.; Dooryhee, E.; ...

2017-03-23

Here, this study revealed that loss of ductility in an amorphous Fe-alloy coating on a steel substrate composite structure was essentially prevented from occurring, following radiation with modest neutron doses of ~2 x 10 18 n/cm 2. At the higher neutron dose of ~2 x 10 19, macroscopic stress-strain analysis showed that the amorphous Fe-alloy nanostructured coating, while still amorphous, experienced radiation-induced embrittlement, no longer offering protection against ductility loss in the coating-substrate composite structure. Neutron irradiation in a corrosive environment revealed exemplary oxidation/corrosion resistance of the amorphous Fe-alloy coating, which is attributed to the formation of the Fe 2Bmore » phase in the coating. To establish the impact of elevated temperatures on the amorphous-to-crystalline transition in the amorphous Fe-alloy, electron microscopy was carried out which confirmed the radiation-induced suppression of crystallization in the amorphous Fe-alloy nanostructured coating.« less

Chemical strain engineering of magnetism in PrVO3 thin films

NASA Astrophysics Data System (ADS)

Prellier, Wilfrid; Copie, Olivier; Varignon, Julien; Rotella, Helene; Steciuk, Gwladys; Boullay, Philippe; Pautrat, Alain; David, Adrian; Mercey, Bernard; Ghosez, Philippe

Transition metal oxides having a perovskite structure present a wide range of functional properties ranging from insulator-to-metal, ferroelectricity, colossal magnetoresistance, high-temperature superconductivity and multiferroicity. Such systems are generally characterized by strong electronic correlations, complex phase diagrams and competing ground states. In addition, small perturbation induced by external stimuli (electric or magnetic field, temperature, strain, pressure..) may change structure, and ultimately modify the physical properties. Here, we synthetize an orthorhombic perovskite praseodymium vanadate (PrVO3), which is grown on strontium titanate substrate. We show that the control of the content of oxygen vacancies, the so-called chemical strain, can indeed result in unexpected properties. We further demonstrate that the Néel temperature can be tuned using the same substrate in agreement with first-principles calculations, and demonstrate that monitoring the concentration of oxygen vacancies through the oxygen partial pressure or the growth temperature can produce a substantial macroscopic tensile strain of a few percents.

Combined strain and composition-induced effects in the metal-insulator transition of epitaxial VO2 films

NASA Astrophysics Data System (ADS)

Théry, V.; Boulle, A.; Crunteanu, A.; Orlianges, J. C.

2017-12-01

The role of epitaxial strain, thermal strain, and bulk (strain-free) lattice parameters in the metal-insulator transition (MIT) and the structural phase transition (SPT) of VO2 is investigated for the case of epitaxial films grown on (001)-oriented TiO2 substrates. Temperature-resolved X-ray reciprocal space mapping has been used to determine the absolute state of strain as well as the bulk lattice parameters of VO2 at 100 °C. For the thinnest film (15 nm), the state of strain is dominated by the film/substrate lattice mismatch yielding an in-plane tensile strain which, in turn, shifts both the MIT and the SPT towards lower temperatures. Conversely, for the thickest film (100 nm), the epitaxial strain is relaxed, so that the state of strain is dominated by the VO2/TiO2 thermal expansion mismatch which is responsible for a compressive in-plane strain. In all cases, a swelling of the strain-free VO2 unit-cell is observed which indicates the presence of interfacial oxygen vacancies and/or Ti diffusion into the VO2 films. The presence of oxygen vacancies stabilizes the metallic rutile phase and counterbalances the action of thermal strain on the MIT and the SPT and degrades the electric properties for the thinnest film. For the thickest film, the resistivity ratio is 6.4 × 104.

Polymer brushes: a controllable system with adjustable glass transition temperature of fragile glass formers.

PubMed

Xie, Shi-Jie; Qian, Hu-Jun; Lu, Zhong-Yuan

2014-01-28

We present results of molecular dynamics simulations for coarse-grained polymer brushes in a wide temperature range to investigate the factors that affect the glass transition in these systems. We focus on the influences of free surface, polymer-substrate interaction strength, grafting density, and chain length not only on the change of glass transition temperature Tg, but also the fragility D of the glass former. It is found that the confinement can enhance the dependence of the Tg on the cooling rate as compared to the bulk melt. Our layer-resolved analysis demonstrates that it is possible to control the glass transition temperature Tg of polymer brushes by tuning the polymer-substrate interaction strength, the grafting density, and the chain length. Moreover, we find quantitative differences in the influence range of the substrate and the free surface on the density and dynamics. This stresses the importance of long range cooperative motion in glass formers near the glass transition temperature. Furthermore, the string-like cooperative motion analysis demonstrates that there exists a close relation among glass transition temperature Tg, fragility D, and string length ⟨S⟩. The polymer brushes that possess larger string length ⟨S⟩ tend to have relatively higher Tg and smaller D. Our results suggest that confining a fragile glass former through forming polymer brushes changes not only the glass transition temperature Tg, but also the very nature of relaxation process.

Accurate identification of layer number for few-layer WS2 and WSe2 via spectroscopic study.

PubMed

Li, Yuanzheng; Li, Xinshu; Yu, Tong; Yang, Guochun; Chen, Heyu; Zhang, Cen; Feng, Qiushi; Ma, Jiangang; Liu, Weizhen; Xu, Haiyang; Liu, Yichun; Liu, Xinfeng

2018-03-23

Transition metal dichalcogenides (TMDs) with a typical layered structure are highly sensitive to their layer number in optical and electronic properties. Seeking a simple and effective method for layer number identification is very important to low-dimensional TMD samples. Herein, a rapid and accurate layer number identification of few-layer WS 2 and WSe 2 is proposed via locking their photoluminescence (PL) peak-positions. As the layer number of WS 2 /WSe 2 increases, it is found that indirect transition emission is more thickness-sensitive than direct transition emission, and the PL peak-position differences between the indirect and direct transitions can be regarded as fingerprints to identify their layer number. Theoretical calculation confirms that the notable thickness-sensitivity of indirect transition derives from the variations of electron density of states of W atom d-orbitals and chalcogen atom p-orbitals. Besides, the PL peak-position differences between the indirect and direct transitions are almost independent of different insulating substrates. This work not only proposes a new method for layer number identification via PL studies, but also provides a valuable insight into the thickness-dependent optical and electronic properties of W-based TMDs.

Direct observation of bi-alkali antimonide photocathodes growth via in operando x-ray diffraction studies

DOE PAGES

Ruiz-Osés, M.; Schubert, S.; Attenkofer, K.; ...

2014-12-01

Alkali antimonides have a long history as visible-light-sensitive photocathodes. This study focuses on the process of fabrication of the bi-alkali photocathodes, K 2CsSb. In-situ synchrotron x-ray diffraction and photoresponse measurements were used to monitor phase evolution during sequential photocathode growth mode on Si(100) substrates. The amorphous-to-crystalline transition for the initial antimony layer was observed at a film thickness of 40 Å . The antimony crystalline structure dissolved upon potassium deposition, eventually recrystallizing upon further deposition into K-Sb crystalline modifications. This transition, as well as the conversion of potassium antimonide to K 2CsSb upon cesium deposition, is correlated with changes inmore » the quantum efficiency.« less

A Forty Year Odyssey in Metallo-Organic Chemistry.

PubMed

Nicholas, Kenneth M

2015-07-17

In this invited Perspective, I provide a personal account highlighting several of my group's research contributions in metallo-organic chemistry over the past 40 years. Our early work focused primarily in stoichiometric structure/reactivity of transition metal-organic compounds and their use in organic synthesis. More recent efforts have centered on the discovery and development of new metal-catalyzed organic reactions via reactive metal-organic intermediates. The major research findings that are described here include (1) propargyl-cobalt complexes as electrophilic agents for C-C and C-Nu coupling; (2) the activation of carbon dioxide by metal complexes; (3) metal-promoted C-H nitrogenation reactions; (4) oxo-metal catalyzed deoxygenation reactions; and (5) catalyst discovery via dynamic templating with substrate- and transition-state analogues.

A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase.

PubMed

Jimenez-Sandoval, Pedro; Vique-Sanchez, Jose Luis; Hidalgo, Marisol López; Velazquez-Juarez, Gilberto; Diaz-Quezada, Corina; Arroyo-Navarro, Luis Fernando; Moran, Gabriela Montero; Fattori, Juliana; Jessica Diaz-Salazar, A; Rudiño-Pinera, Enrique; Sotelo-Mundo, Rogerio; Figueira, Ana Carolina Migliorini; Lara-Gonzalez, Samuel; Benítez-Cardoza, Claudia G; Brieba, Luis G

2017-11-01

The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer. Copyright © 2017 Elsevier B.V. All rights reserved.

Resistive spectroscopy coupled with non-contacting oscillator for detecting discontinuous-continuous transition of metallic films

NASA Astrophysics Data System (ADS)

Nakamura, N.; Ogi, H.

2017-09-01

In spectroscopic measurements, one measures responses of specimens to oscillating fields (including electric, magnetic, and stress fields) at different frequencies for characterizing the samples. In contrast, we develop spectroscopy where the response (loss) is measured by changing the electric resistance, named the resistive spectroscopy. In the resistive spectroscopy, an energy-loss peak appears when the resistance is changed. We here apply it for studying the morphological change of thin films. When a metallic material is deposited on a substrate, the morphological transition from discontinuous islands to the continuous film occurs. It accompanies a drastic change in the resistance of the deposited material because of the transition from an insulator to a conductor. We find that the energy-loss peak appears at the transition moment during deposition of Ag. The resistive spectroscopy we develop uses no electrodes; it adopts the electric field generated by a piezoelectric material vibrating at its resonant frequency beneath the substrate. It is observed that the full width at half maximum (FWHM) of the resonance shows the peak during the deposition for high resistance substrates. The FWHM peak fails to be found for low resistance substrates, but it appears when the resonance frequency is increased. We propose an electrical-circuit model for explaining these observations.

Entropic factors provide unusual reactivity and selectivity in epoxide-opening reactions promoted by water

PubMed Central

Byers, Jeffery A.; Jamison, Timothy F.

2013-01-01

Despite the myriad of selective enzymatic reactions that occur in water, chemists have rarely capitalized on the unique properties of this medium to govern selectivity in reactions. Here we report detailed mechanistic investigations of a water-promoted reaction that displays high selectivity for what is generally a disfavored product. A combination of structural and kinetic data indicates not only that synergy between substrate and water suppresses undesired pathways but also that water promotes the desired pathway by stabilizing charge in the transition state, facilitating proton transfer, doubly activating the substrate for reaction, and perhaps most remarkably, reorganizing the substrate into a reactive conformation that leads to the observed product. This approach serves as an outline for a general strategy of exploiting solvent-solute interactions to achieve unusual reactivity in chemical reactions. These findings may also have implications in the biosynthesis of the ladder polyether natural products, such as the brevetoxins and ciguatoxins. PMID:24046369

Electrical manipulation of perpendicular magnetic anisotropy in a Pt/Co/Pt trilayer grown on PMN-PT(0 1 1) substrate

NASA Astrophysics Data System (ADS)

Xiao, X.; Sun, L.; Luo, Y. M.; Zhang, D.; Liang, J. H.; Wu, Y. Z.

2018-03-01

Strain-induced modulation of perpendicular magnetic anisotropy (PMA) is demonstrated in a wedge-shaped Pt/Co/Pt sandwich grown on PMN-PT(0 1 1) substrate using magnetic torque measurements. An anisotropic in-plane strain is generated by applying an electric field across the PMN-PT substrate and transferred to the ferromagnetic Pt/Co/Pt sandwich. The critical thickness of spin reorientation transition is tuned to the thicker region of the Pt/Co/Pt wedge. The strain-induced change of PMA is quantitatively extracted. Only the first order anisotropy term is tuned by the electric field, while the second order anisotropy term has negligible electric field-dependence. Both of the volume and interface contributions of the first order anisotropy term show tunable electric field modulation. These results may benefit the understanding of strain-mediated magnetoelectric coupling effect in artificial multiferroic structures containing a ferromagnetic layer with PMA.

Migration speed and directionality switch of normal epithelial cells after TGF-β1-induced EMT (tEMT) on micro-structured polydimethylsiloxane (PDMS) substrates with variations in stiffness and topographic patterning.

PubMed

Wu, Tsung-Hsien; Li, Chia-Hui; Tang, Ming-Jer; Liang, Jen-I; Chen, Chia-Hsin; Yeh, Ming-Long

2013-10-01

The epithelial to mesenchymal transition (EMT) involves several physiological and pathological phenomena and endows cells with invasive and migratory properties. However, the effects of substrate stiffness and topography on the migration of cells before or after transforming growth factor-β1 (TGF-β1)-induced EMT (tEMT) are unknown. Herein, we seed control or tEMT NMuMG cells on the 2D patterns consisted of 1 μm or 5 μm line-widths and groove or cone patterns on either 2 MPa (1.96 ± 0.48 MPa) or 4 MPa (3.70 ± 0.74 MPa) polydimethylsiloxane (PDMS) substrates. After tEMT, the increased expression of α-SMA with vinculin in focal adhesion (FA) sites led to an acceleration of tEMT cell motility. On the 2 MPa substrate, the most influenced substrate was the 1 μm, cone-patterned substrate, where the tEMT cells' motility decelerated by 0.13 μm/min (36% slower than the cells on groove pattern). However, on the 5 μm, groove-patterned substrate, where the tEMT cells demonstrated the most rapid motility relative to the control cells, with an increment of 0.18 μm/min (100%). Among the different physical cues from substrate, the cone pattern could impede the migration speed of tEMT cells. Furthermore, we recommend the groove-patterned with a 5 μm line-width substrate as a useful tool to differentiate control and tEMT cells by migration speed.

Investigating the nature of palladium chain-walking in the enantioselective redox-relay Heck reaction of alkenyl alcohols.

PubMed

Hilton, Margaret J; Xu, Li-Ping; Norrby, Per-Ola; Wu, Yun-Dong; Wiest, Olaf; Sigman, Matthew S

2014-12-19

The mechanism of the redox-relay Heck reaction was investigated using deuterium-labeled substrates. Results support a pathway through a low energy palladium-alkyl intermediate that immediately precedes product formation, ruling out a tautomerization mechanism. DFT calculations of the relevant transition structures at the M06/LAN2DZ+f/6-31+G* level of theory show that the former pathway is favored by 5.8 kcal/mol. Palladium chain-walking toward the alcohol, following successive β-hydride eliminations and migratory insertions, is also supported in this study. The stereochemistry of deuterium labels is determined, lending support that the catalyst remains bound to the substrate during the relay process and that both cis- and trans-alkenes form from β-hydride elimination.

Biaxial stress driven tetragonal symmetry breaking and high-temperature ferromagnetic semiconductor from half-metallic CrO2

NASA Astrophysics Data System (ADS)

Xiao, Xiang-Bo; Liu, Bang-Gui

2018-03-01

It is highly desirable to combine the full spin polarization of carriers with modern semiconductor technology for spintronic applications. For this purpose, one needs good crystalline ferromagnetic (or ferrimagnetic) semiconductors with high Curie temperatures. Rutile CrO2 is a half-metallic spintronic material with Curie temperature 394 K and can have nearly full spin polarization at room temperature. Here, we find through first-principles investigation that when a biaxial compressive stress is applied on rutile CrO2, the density of states at the Fermi level decreases with the in-plane compressive strain, there is a structural phase transition to an orthorhombic phase at the strain of -5.6 % , and then appears an electronic phase transition to a semiconductor phase at -6.1 % . Further analysis shows that this structural transition, accompanying the tetragonal symmetry breaking, is induced by the stress-driven distortion and rotation of the oxygen octahedron of Cr, and the half-metal-semiconductor transition originates from the enhancement of the crystal field splitting due to the structural change. Importantly, our systematic total-energy comparison indicates the ferromagnetic Curie temperature remains almost independent of the strain, near 400 K. This biaxial stress can be realized by applying biaxial pressure or growing the CrO2 epitaxially on appropriate substrates. These results should be useful for realizing full (100%) spin polarization of controllable carriers as one uses in modern semiconductor technology.

Imaging the Dynamics of the Ferroelectric Stripe Phase Near a Field-Driven Phase Transition in Bismuth Ferrite

NASA Astrophysics Data System (ADS)

Laanait, Nouamane; Li, Qian; Zhang, Zhan; Kalinin, Sergei

Electric field-driven phase transitions in multiferroic systems such as Bismuth Ferrite could potentially host interesting domain dynamics due to the coexistence of multiple order parameters. Structural imaging of these dynamics under a host of elastic and electric boundary conditions is therefore of interest. Here, we present X-ray diffraction microscopy (XDM) studies of the domain wall dynamics in a bismuth ferrite thin-film near the field-driven transition from rhombohedral to monoclinic (R to M). XDM is a novel full-field imaging technique that uses Bragg diffraction contrast to image structural configurations with sub-100nm lateral resolutions and fast acquisition times (milliseconds to seconds per image). We find that under electric fields 100 kV/cm, a bismuth ferrite thin-film (100 nm BiFeO3/DyScO3 (110)) undergoes a structural phase transition but that this new phase (M) is pinned by the preexisting ferroelectric/ferroelastic stripe phase (R). At higher fields ( 300 kV/cm), we observe unusually slow domain wall dynamics in the stripe phase, consisting of periodicity doubling, domain wall roughening and crowding. These observed ferroelastic domain wall spatial dynamics are weakly constrained by the crystal symmetry of the orthorhombic substrate but exhibit nonlinear dynamics more commonly associated with disordered nematic systems. This work was supported by the Eugene P. Wigner Fellowship program at Oak Ridge National Laboratory, a U.S. Department of Energy facility.

Coalescence of 3-phenyl-propynenitrile on Cu(111) into interlocking pinwheel chains

NASA Astrophysics Data System (ADS)

Luo, Miaomiao; Lu, Wenhao; Kim, Daeho; Chu, Eric; Wyrick, Jon; Holzke, Connor; Salib, Daniel; Cohen, Kamelia D.; Cheng, Zhihai; Sun, Dezheng; Zhu, Yeming; Einstein, T. L.; Bartels, Ludwig

2011-10-01

3-phenyl-propynenitrile (PPN) adsorbs on Cu(111) in a hexagonal network of molecular trimers formed through intermolecular interaction of the cyano group of one molecule with the aromatic ring of its neighbor. Heptamers of trimers coalesce into interlocking pinwheel-shaped structures that, by percolating across islands of the original trimer coverage, create the appearance of gear chains. Density functional theory aids in identifying substrate stress associated with the chemisorption of PPN's acetylene group as the cause of this transition.

Directional and magnetic field enhanced emission of Cu-doped ZnO nanowires/p-GaN heterojunction light-emitting diodes

NASA Astrophysics Data System (ADS)

Viana, Bruno; Lupan, Oleg; Pauporté, Thierry

2011-01-01

The electrochemical deposition technique was used for the preparation of Cu-doped ZnO-nanowire-based emitters. Nanowires of high structural and optical quality were epitaxially grown on p-GaN single crystalline film substrates. We found that the emission is directional with a wavelength that is tuned and redshifted toward the visible region by doping with Cu in nanowires. Furthermore, Cu-doped ZnO-nanowires show an enhancement of the transition probability under magnetic field.

Theoretical reflections on the structural polymorphism of the oxygen-evolving complex in the S2 state and the correlations to substrate water exchange and water oxidation mechanism in photosynthesis.

PubMed

Guo, Yu; Li, Hui; He, Lan-Lan; Zhao, Dong-Xia; Gong, Li-Dong; Yang, Zhong-Zhi

2017-10-01

The structural polymorphism of the oxygen-evolving complex is of great significance to photosynthetic water oxidation. Employing density functional theory calculations, we have made further advisement on the interconversion mechanism of O5 transfer in the S 2 state, mainly focusing on the potentiality of multi-state reactivity and spin transitions. Then, O5 protonation is proven impossible in S 2 for irreversibility of the interconversion, which serves as an auxiliary judgment for the protonation state of O5 in S 1 . Besides, the structural polymorphism could also be archived by alternative mechanisms involving Mn3 ligand exchange, one of which with Mn3(III) makes sense to substrate water exchange in S 2 , although being irresponsible for the derivations of the observed EPR signals. During the water exchange, high-spin states would prevail to facilitate electron transfer between the ferromagnetically coupled Mn centers. In addition, water exchange in S 1 could account for the closed-cubane structure as the initial form entering S 2 at cryogenic temperatures. With regard to water oxidation, the structural flexibility and variability in both S 2 and S 3 guarantee smooth W2-O5 coupling in S 4 , according to the substrate assignments from water exchange kinetics. Within this theoretical framework, the new XFEL findings on S 1 -S 3 can be readily rationalized. Finally, an alternative mechanistic scenario for OO bond formation with ·OH radical near O4 is presented, followed by water binding to the pivot Mn4(III) from O4 side during S 4 -S 0 . This may diversify the substrate sources combined with the Ca channel in water delivery for the forthcoming S-cycle. Copyright © 2017. Published by Elsevier B.V.

Constructing honeycomb micropatterns on nonplanar substrates with high glass transition temperature polymers.

PubMed

Ding, Jianyun; Gong, Jianliang; Bai, Hua; Li, Lei; Zhong, Yawen; Ma, Zhi; Svrcek, Vladimir

2012-08-15

In Qiao's previous report, only star polymers with T(g) (glass transition temperature) below 48°C were found forming homogeneous honeycomb coatings on the nonplanar substrates. The polymers with high T(g) are believed not able to duplicate nonplanar substrate due to their brittleness. This article presents a comprehensive study on the construction of macroporous polymeric films on various nonplanar substrates with static breath figure (BF) technique, using linear polymers with high T(g). Two kinds of linear polymers with high T(g), polystyrene-b-poly(acrylic acid) and polystyrene without polar end groups, are employed to prepare 3-dimensional macroporous films on different nonplanar substrates. Scanning electronic microscopy views on the side wall in addition to views in-plane prove that polymer films with BF array perfectly replicated the surface features of these substrates. The formation processes of macropores on these substrates are analyzed in detail, and it demonstrates that neither molecular topography nor T(g) of polymers is the critical factor contouring nonplanar substrate. A new hypothesis involving polymer plasticization and conformation during the solvent evaporation is formulated. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

Method of boronizing transition metal surfaces

DOEpatents

Koyama, Koichiro; Shimotake, Hiroshi

1983-01-01

A method is presented for preparing a boride layer on a transition metal substrate for use in corrosive environments or as a harden surface in machine applications. This method is particularly useful in treating current collectors for use within a high temperature and corrosive electrochemical cell environment. A melt of a alkali metal boride tetrafluoride salt including such as KF to lower its melting point is prepared including a dissolved boron containing material, for instance NiB, MnB.sub.2, or CrB.sub.2. A transition metal to be coated is immersed in the melt at a temperature of no more than 700.degree. C. and a surface boride layer of that transition metal is formed within a period of about 24 hours on the substrate surface.

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

Sokolov, Andrei; Kirianov, Eugene; Zlenko, Albina

The effect of substrates on the magnetic and transport properties of Ni{sub 2}Mn{sub 1.5}In{sub 0.5} ultra-thin films were studied theoretically and experimentally. High quality 8-nm films were grown by laser-assisted molecular beam epitaxy deposition. Magneto-transport measurements revealed that the films undergo electronic structure transformation similar to those of bulk materials at the martensitic transformation. The temperature of the transformation depends strongly on lattice parameters of the substrate. To explain this behavior, we performed DFT calculations on the system and found that different substrates change the relative stability of the ferromagnetic (FM) austenite and ferrimagnetic (FiM) martensite states. We conclude thatmore » the energy difference between the FM austenite and FiM martensite states in Ni{sub 2}Mn{sub 1.5}In{sub 0.5} films grown on MgO (001) substrates is ΔE = 0.20 eV per NiMnIn f.u, somewhat lower compared to ΔE = 0.24 eV in the bulk material with the same lattice parameters. When the lattice parameters of Ni{sub 2}Mn{sub 1.5}In{sub 0.5} film have values close to those of the MgO substrate, the energy difference becomes ΔE = 0.08 eV per NiMnIn f.u. These results suggest the possibility to control the martensitic transition in thin films through substrate engineering.« less

Correction of the exciton Bohr radius in monolayer transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Li, Run-Ze; Dong, Xi-Ying; Li, Zhi-Qing; Wang, Zi-Wu

2018-07-01

We theoretically investigate the correction of exciton Bohr radius in monolayer transition metal dichalcogenides (TMDCs) on different polar substrates arising from the exciton-optical phonon coupling, in which both the intrinsic longitudinal optical phonon and surface optical phonon modes couple with the exciton are taken into account. We find that the exciton Bohr radius is enlarged markedly due to these coupling. Moreover, it can be changed on a large scale by modulating the polarizability of polar substrate and the internal distance between the monolayer TMDCs and polar substrate. Theoretical result provides a potential explanation for the variation of the exciton Bohr radius in experimental measurement.

Structure and Properties of VO2 and Titanium Dioxide Based Epitaxial Heterostructures Integrated with Silicon and Sapphire Substrates

NASA Astrophysics Data System (ADS)

Bayati, Mohammad Reza

The main focus of this study was placed on structure-property correlation in TiO2 and VO2 based epitaxial heterostructures where the photochemical and electrical properties were tuned through microstructural engineering. In the framework of domain matching epitaxy, epitaxial growth of TiO2 and VO2 heterostructures on different substrates were explained. The theta-2theta and ϕ scan X-ray diffraction measurements and detailed high resolution electron microscopy studies corroborated our understanding of the epitaxial growth and the crystallographic arrangement across the interfaces. The influence of the laser and substrate variables on structural characteristics of the films was investigated using X-ray photoelectron spectroscopy, room temperature photoluminescence spectroscopy, and UV-Vis spectrophotometry. In addition, morphological studies were performed by atomic force microscopy. Photochemical properties of the heterostructures were assessed through measuring surface wettability characteristics and photocatalytic reaction rate constant of degradation of 4-chlorophenol under ultraviolet and visible irradiations. We also studied electrical properties employing 4-probe measurement technique. The effect of post treatment processes, such as vacuum annealing and laser treatment, on structure and properties was investigated as well. The role of point defects and deviation from the stoichiometry on photochemical and electrical properties was addressed. In this research, TiO2 epilayers with controlled phase structure, defect content, and crystallographic alignments were grown on sapphire and silicon substrates. Integration with silicon was achieved using cubic and tetragonal yttria-stabilized zirconia buffer layers. I was able to tune the phase structure of the TiO2 based heterostructures from pure rutile to pure anatase and establish an epitaxial relationship across the interfaces in each case. These heterostructures were used for two different purposes. First, their application in environmental remediation was taken into account. The photochemical efficiency of the samples was evaluated under ultraviolet and visible illuminations. I was able to establish a correlation between the growth conditions and the photocatalytic activity of single crystalline TiO 2 thin films. Visible-light-responsive TiO2 films were fabricated via vacuum annealing of the samples where point defects, namely oxygen vacancies and titanium interstitial, are surmised to play a critical role. An ultrafast switching was observed in wetting characteristics of the single crystalline rutile TiO2 films from a hydrophobic state to a superhydrophilic state by single pulsed excimer laser annealing. It was observed that the laser annealing almost doubles the photocatalytic efficiency of the anatase epitaxial thin films. I was able to measure the photochemical properties of the rutile and the anatase TiO2 heterostructures in a controlled way due to the single crystalline nature of the films. Second, the rutile TiO2 epilayers with different out-of-plane orientations were deposited and used as a platform for VO2 based epitaxial heterostructures with the aim of manipulating of microstructure and electrical properties of the VO 2 films. Vanadium dioxide (VO2) is an interesting material due to the abrupt change in electrical resistivity and infrared transmittance at about 68 °C. The transition temperature can be tuned through microstructural engineering. It was the idea behind using rutile TiO2 with different crystallographic orientations as a template to tune the semiconductor to metal transition characteristics of the VO2 top layer. I successfully grew VO2(001), VO2(100), and VO2(2¯01) epitaxial thin films on TiO2(100)/c-sapphire, TiO2(101)/r-sapphire, and TiO2(001)/ m-sapphire platforms, respectively. It was observed that tetragonal phase of VO2 was stabilized at lower temperatures leading to a significant decrease in the semiconductor to metal transition temperature. In other words, we were able to tune the transition temperature of the VO 2 epitaxial heterostructures. This achievement introduces the VO 2 based single crystalline heterostructures as a promising candidate for a wide range of applications where different transition temperatures are required. The epitaxial relationships were established and atomic arrangement across the interfaces was studied in detail.

Identification of key residues for protein conformational transition using elastic network model.

PubMed

Su, Ji Guo; Xu, Xian Jin; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin

2011-11-07

Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

Metal-insulator transition properties of sputtered silicon-doped and un-doped vanadium dioxide films at terahertz range

NASA Astrophysics Data System (ADS)

Zhang, Huafu; Wu, Zhiming; Niu, Ruihua; Wu, Xuefei; he, Qiong; Jiang, Yadong

2015-03-01

Silicon-doped and un-doped vanadium dioxide (VO2) films were synthesized on high-purity single-crystal silicon substrates by means of reactive direct current magnetron sputtering followed by thermal annealing. The structure, morphology and metal-insulator transition properties of silicon-doped VO2 films at terahertz range were measured and compared to those of un-doped VO2 films. X-ray diffraction and scanning electron microscopy indicated that doping the films with silicon significantly affects the preferred crystallographic orientation and surface morphologies (grain size, pores and characteristics of grain boundaries). The temperature dependence of terahertz transmission shows that the transition temperature, hysteresis width and transition sharpness greatly depend on the silicon contents while the transition amplitude was relatively insensitive to the silicon contents. Interestingly, the VO2 film doped with a silicon content of 4.6 at.% shows excellent terahertz switching characteristics, namely a small hysteresis width of 4.5 °C, a giant transmission modulation ratio of about 82% and a relatively low transition temperature of 56.1 °C upon heating. This work experimentally indicates that silicon doping can effectively control not only the surface morphology but also the metal-insulator transition characteristics of VO2 films at terahertz range.

Prospects of Two-Dimensional Devices: Electrical and Optical Characterization of Transition Metal Dichalcogenide Films

NASA Astrophysics Data System (ADS)

Klee, Velveth

Understanding the electrical and optical properties of 2D materials down to their monolayer limit is important for establishing their potential for novel applications. Prominent among 2D materials are transition metal dichalcogenides (TMDs), such as MoS2 and MoSe2. These materials have attracted attention because of their intriguing properties, such as a transition from an indirect bandgap for few layers to a direct bandgap for monolayers. New synthetic routes like chemical vapor deposition (CVD) allow for high-quality, centimeter-scale growth and tuning of the direct optical gap continuously between the values of single-layer MoS2 (1.87eV) and MoSe 2 (1.55eV). In the first part of this work, we perform optoelectronic measurements of alloy devices fabricated on CVD-grown, monolayer MoS2, MoS 2(1-x)Se2x, and MoSe2 islands. For all alloy compositions there is an unusual superlinear dependence of the photocurrent on light intensity. We also establish the photoconductive nature of the photoresponse, with the photocurrent originating from recombination and field-induced carrier separation in the channel. The study of transport characteristics of TMDs is extended to explore the effects of devices on a piezoelectric substrate as a route towards establishing fabrication processes suited for industry. In this work, we show that CVD-growth of MoS2 monolayer films onto periodically poled lithium niobate is possible while maintaining the substrate polarization pattern. Electrical transport measurements indicate an inversion of the MoS2 from n-type to p-type behavior under application of an external voltage depending on the domain orientation of the ferroelectric substrate. Sensitivity to ferroelectric substrate polarization opens the possibility for ferroelectric nonvolatile gating of TMDs in scalable devices fabricated free of exfoliation and transfer. Optimizing CVD techniques allows for preparation of TMD films in different phases that are reported to exhibit semiconducting and metallic properties. Here, we show optical and electronic characterization of few-layer films of MoTe2 in three distinct structural phases: 2H, 1T' and 1T. Depending on process parameters, either of the phases can be prepared using MoO3 and elemental tellurium precursors. Experimental and computed Raman spectra are presented for each phase. Transport measurements validate predictions from DFT-based band structure calculations on the metallic character of the centrosymmetric 1T phase.

Assessing the Location of Surface Plasmons Over Nanotriangle and Nanohole Arrays of Different Size and Periodicity

PubMed Central

Correia-Ledo, Debby; Gibson, Kirsty F.; Dhawan, Anuj; Couture, Maxime; Vo-Dinh, Tuan; Graham, Duncan; Masson, Jean-Francois

2012-01-01

The increasing popularity of surface plasmon resonance (SPR) and surface enhanced Raman scattering (SERS) sensor design based on nanotriangle or nanohole arrays, and the possibility to manufacture substrates at the transition between these plasmonic substrates, makes them ideal candidates for the establishment of structure-property relationships. This work features near diffraction-limited Raman images and FDTD simulations of nanotriangle and nanohole arrays substrates, which clearly demonstrate that the localization of the hot spot on these SERS substrates is significantly influenced by the ratio of diameter/periodicity (D/P). The experimental and simulation data reveal that the hot spots are located around nanotriangles (D/P = 1), characteristic of localized SPR. Decreasing the D/P ratio to 0.75-0.7 led to the creation of nanohole arrays, which promoted the excitation of a propagating surface plasmon (SP) delocalized over the metal network. The optimal SERS intensity was consistently achieved at this transition from nanotriangles to nanoholes, for every periodicity (650 nm to 1.5 μm) and excitation wavelength (633 and 785 nm) investigated, despite the presence or absence of a plasmonic band near the laser excitation. Further decreasing the D/P ratio led to excitation of a localized SP located around the rim of nanohole arrays for D/P of 0.5-0.6, in agreement with previous reports. In addition, this manuscript provides the first evidence that the hot spots are positioned inside the hole for D/P of 0.4, with the center being the region of highest electric field and Raman intensity. The compelling experimental evidence and FDTD simulations offer an overall understanding of the plasmonic properties of nanohole arrays as SERS and SPR sensors, which is of significant value in advancing the diversity of applications from such surfaces. PMID:23977402

Heteroepitaxial growth of Pt and Au thin films on MgO single crystals by bias-assisted sputtering

DOE PAGES

Tolstova, Yulia; Omelchenko, Stefan T.; Shing, Amanda M.; ...

2016-03-17

The crystallographic orientation of a metal affects its surface energy and structure, and has profound implications for surface chemical reactions and interface engineering, which are important in areas ranging from optoelectronic device fabrication to catalysis. However, it can be very difficult and expensive to manufacture, orient, and cut single crystal metals along different crystallographic orientations, especially in the case of precious metals. One approach is to grow thin metal films epitaxially on dielectric substrates. In this work, we report on growth of Pt and Au films on MgO single crystal substrates of (100) and (110) surface orientation for use asmore » epitaxial templates for thin film photovoltaic devices. We develop bias-assisted sputtering for deposition of oriented Pt and Au films with sub-nanometer roughness. We show that biasing the substrate decreases the substrate temperature necessary to achieve epitaxial orientation, with temperature reduction from 600 to 350 °C for Au, and from 750 to 550 °C for Pt, without use of transition metal seed layers. Additionally, this temperature can be further reduced by reducing the growth rate. Biased deposition with varying substrate bias power and working pressure also enables control of the film morphology and surface roughness.« less

Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases

PubMed Central

Kim, J. Dongun; Senn, Stefan; Harel, Arye; Jelen, Benjamin I.; Falkowski, Paul G.

2013-01-01

Oxidoreductases play a central role in catalysing enzymatic electron-transfer reactions across the tree of life. To first order, the equilibrium thermodynamic properties of these proteins are governed by protein folds associated with specific transition metals and ligands at the active site. A global analysis of holoenzyme structures and functions suggests that there are fewer than approximately 500 fundamental oxidoreductases, which can be further clustered into 35 unique groups. These catalysts evolved in prokaryotes early in the Earth's history and are largely responsible for the emergence of non-equilibrium biogeochemical cycles on the planet's surface. Although the evolutionary history of the amino acid sequences in the oxidoreductases is very difficult to reconstruct due to gene duplication and horizontal gene transfer, the evolution of the folds in the catalytic sites can potentially be used to infer the history of these enzymes. Using a novel, yet simple analysis of the secondary structures associated with the ligands in oxidoreductases, we developed a structural phylogeny of these enzymes. The results of this ‘composome’ analysis suggest an early split from a basal set of a small group of proteins dominated by loop structures into two families of oxidoreductases, one dominated by α-helices and the second by β-sheets. The structural evolutionary patterns in both clades trace redox gradients and increased hydrogen bond energy in the active sites. The overall pattern suggests that the evolution of the oxidoreductases led to decreased entropy in the transition metal folds over approximately 2.5 billion years, allowing the enzymes to use increasingly oxidized substrates with high specificity. PMID:23754810

Magnetic orders of LaTiO3 under epitaxial strain: A first-principles study

NASA Astrophysics Data System (ADS)

Weng, Yakui; Huang, Xin; Tang, Yankun; Dong, Shuai

2014-05-01

Perovskite LaTiO3 bulk is a typical Mott-insulator with G-type antiferromagnetic order. In this work, the biaxial strain effects on the ground magnetic order of LaTiO3 films grown on various substrates have been studied. For the compressive strain, LaTiO3 films grown on LaAlO3, LaGaO3, and SrTiO3 substrates undergo a phase transition from the original G-type antiferromagnet to A-type antiferromagnet. The underlying physical mechanisms are the lattice distortions tunned by strain. While for the tensile strain, the BaTiO3 and LaScO3 substrates have been tested, which show a tendency to transit the LaTiO3 to the C-type antiferromagnet. Furthermore, our calculations find that the magnetic transitions under epitaxial strain do not change the insulating fact of LaTiO3.

Study of the impurity photoconductivity in p-InSb using epitaxial p{sup +} contacts

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

Eminov, Sh. O., E-mail: shikhamirem@gmail.com

2016-08-15

The optical absorption coefficient α in p{sup +}-InSb layers (with hole concentrations of p ≈ 1 × 10{sup 17}–1.2 × 10{sup 19} cm{sup –3}), grown by liquid-phase epitaxy on p-InSb substrates, is measured in the spectral range of 5-12 µm at 90 K, and the impurity photoconductivity is measured (at 60 and 90 K) in p{sup +}–p structures. It is found that a in the p{sup +} layers reaches a value of 7000 cm{sup –1} (at p ≈ 2 × 10{sup 19} cm{sup –1}). It is shown that the measured substrate value of (α ≈1–3 cm{sup –1}) is overestimated inmore » comparison with estimates (α ≈ 0.1 cm{sup –1}) based on comparing the photoconductivity data. This discrepancy is explained by the fact that the optical transitions of holes responsible for photoconductivity are obscured by the excitation of electrons to the conduction band. The photoionization cross section for these transitions does not exceed 1 × 10{sup –15} cm{sup 2}.« less

Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase*

PubMed Central

Chen, Yaozong; Sun, Yueru; Song, Haigang; Guo, Zhihong

2015-01-01

o-Succinylbenzoyl-CoA synthetase, or MenE, is an essential adenylate-forming enzyme targeted for development of novel antibiotics in the menaquinone biosynthesis. Using its crystal structures in a ligand-free form or in complex with nucleotides, a conserved pattern is identified in the interaction between ATP and adenylating enzymes, including acyl/aryl-CoA synthetases, adenylation domains of nonribosomal peptide synthetases, and luciferases. It involves tight gripping interactions of the phosphate-binding loop (P-loop) with the ATP triphosphate moiety and an open-closed conformational change to form a compact adenylation active site. In MenE catalysis, this ATP-enzyme interaction creates a new binding site for the carboxylate substrate, allowing revelation of the determinants of substrate specificities and in-line alignment of the two substrates for backside nucleophilic substitution reaction by molecular modeling. In addition, the ATP-enzyme interaction is suggested to play a crucial catalytic role by mutation of the P-loop residues hydrogen-bonded to ATP. Moreover, the ATP-enzyme interaction has also clarified the positioning and catalytic role of a conserved lysine residue in stabilization of the transition state. These findings provide new insights into the adenylation half-reaction in the domain alteration catalytic mechanism of the adenylate-forming enzymes. PMID:26276389

Highly Stretchable Superhydrophobic Composite Coating Based on Self-Adaptive Deformation of Hierarchical Structures.

PubMed

Hu, Xin; Tang, Changyu; He, Zhoukun; Shao, Hong; Xu, Keqin; Mei, Jun; Lau, Woon-Ming

2017-05-01

With the rapid development of stretchable electronics, functional textiles, and flexible sensors, water-proof protection materials are required to be built on various highly flexible substrates. However, maintaining the antiwetting of superhydrophobic surface under stretching is still a big challenge since the hierarchical structures at hybridized micro-nanoscales are easily damaged following large deformation of the substrates. This study reports a highly stretchable and mechanically stable superhydrophobic surface prepared by a facile spray coating of carbon black/polybutadiene elastomeric composite on a rubber substrate followed by thermal curing. The resulting composite coating can maintain its superhydrophobic property (water contact angle ≈170° and sliding angle <4°) at an extremely large stretching strain of up to 1000% and can withstand 1000 stretching-releasing cycles without losing its superhydrophobic property. Furthermore, the experimental observation and modeling analysis reveal that the stable superhydrophobic properties of the composite coating are attributed to the unique self-adaptive deformation ability of 3D hierarchical roughness of the composite coating, which delays the Cassie-Wenzel transition of surface wetting. In addition, it is first observed that the damaged coating can automatically recover its superhydrophobicity via a simple stretching treatment without incorporating additional hydrophobic materials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Creation and Ordering of Oxygen Vacancies at WO 3-δ and Perovskite Interfaces

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

Zhang, Kelvin H. L.; Li, Guoqiang; Spurgeon, Steven R.

Changes in structure and composition resulting from oxygen deficiency can strongly impact the physical and chemical properties of transition metal oxides, which may lead to new functionalities for novel electronic devices. Oxygen vacancies (V o) can be readily formed to accomodate the lattice mismatch during epitixial thin film growth. In this paper, the effects of substrate strain and oxidizing power on the creation and distribution of V o in WO 3-δ thin films are investigated in detail. An 18O 2 isotope labeled time-of-flight secondary ion mass spectrometry study reveals that WO 3-δ films grown on SrTiO 3 substrates display amore » significantly larger oxygen vacancy gradient along the growth direction compared to those grown on LaAlO 3 substrates. This result is corroborated by scanning transmission electron microscopy imaging which reveals a large number of defects close to the interface to accommodate interfacial tensile strain, leading to the ordering of V o and the formation of semi-aligned Magnéli phases. The strain is gradually released and tetragonal phase with much better crystallinity is observed at the film/vacuum interface. The changes in structure resulting from oxygen defect creation are shown to have a direct impact on the electronic and optical properties of the films.« less

In-plane x-ray diffraction for characterization of monolayer and few-layer transition metal dichalcogenide films

NASA Astrophysics Data System (ADS)

Chubarov, Mikhail; Choudhury, Tanushree H.; Zhang, Xiaotian; Redwing, Joan M.

2018-02-01

There is significant interest in the growth of single crystal monolayer and few-layer films of transition metal dichalcogenides (TMD) and other 2D materials for scientific exploration and potential applications in optics, electronics, sensing, catalysis and others. The characterization of these materials is crucial in determining the properties and hence the applications. The ultra-thin nature of 2D layers presents a challenge to the use of x-ray diffraction (XRD) analysis with conventional Bragg-Brentano geometry in analyzing the crystallinity and epitaxial orientation of 2D films. To circumvent this problem, we demonstrate the use of in-plane XRD employing lab scale equipment which uses a standard Cu x-ray tube for the analysis of the crystallinity of TMD monolayer and few-layer films. The applicability of this technique is demonstrated in several examples for WSe2 and WS2 films grown by chemical vapor deposition on single crystal substrates. In-plane XRD was used to determine the epitaxial relation of WSe2 grown on c-plane sapphire and on SiC with an epitaxial graphene interlayer. The evolution of the crystal structure orientation of WS2 films on sapphire as a function of growth temperature was also examined. Finally, the epitaxial relation of a WS2/WSe2 vertical heterostructure deposited on sapphire substrate was determined. We observed that WSe2 grows epitaxially on both substrates employed in this work under all conditions studied while WS2 exhibits various preferred orientations on sapphire substrate which are temperature dependent. In contrast to the sapphire substrate, WS2 deposited on WSe2 exhibits only one preferred orientation which may provide a route to better control the orientation and crystal quality of WS2. In the case of epitaxial graphene on SiC, no graphene-related peaks were observed in in-plane XRD while its presence was confirmed using Raman spectroscopy. This demonstrates the limitation of the in-plane XRD technique for characterizing low electron density materials.

Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation

PubMed Central

Śledź, Paweł; Unverdorben, Pia; Beck, Florian; Pfeifer, Günter; Schweitzer, Andreas; Förster, Friedrich; Baumeister, Wolfgang

2013-01-01

The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. PMID:23589842

Boron doped bcc-W films: Achieving excellent mechanical properties and tribological performance by regulating substrate bias voltage

NASA Astrophysics Data System (ADS)

Yang, Lina; Zhang, Kan; Zeng, Yi; Wang, Xin; Du, Suxuan; Tao, Chuanying; Ren, Ping; Cui, Xiaoqiang; Wen, Mao

2017-11-01

Boron doped bcc-W (WBx, x = B/W) films were deposited on Si(100) substrates by magnetron co-sputtering pure W and B targets. Our results reveal that when the absolute value of substrate bias voltage (Vb) increases from floating to 240 V, the value of x monotonously decreases from 0.18 to 0.04, accompanied by a phase transition from a mixture of tetragonal γ-W2B and body-centered cubic α-W(B) phase (-Vb ≤ 60 V) to α-W(B) single phase (-Vb > 60 V). Hardness, depending on Vb, increases first and then drops, where the maximum hardness of 30.8 GPa was obtained at -Vb = 60 V and far higher than pure W and W2B theoretical value. In the mixed phase structure, the grain boundaries strengthening, Hall-Petch effect and solid-solution strengthening induced by B dominate the strengthening mechanism. Astonishingly, the film grown at -Vb = 120 V still possesses twice higher hardness than pure W, wherein unexpectedly low (6.7 at.%) B concentration and only the single α-W(B) phase can be identified. In this case, both Hall-Petch effect and solid-solution strengthening work. Besides, low friction coefficient of ∼0.18 can be obtained for the films with α-W(B) phase, which is competitive to that of reported B-rich transition-metal borides, such as TiB2, CrB and CrB2.

Unexpected metal-insulator transition in thick Ca1-xSrxVO3 film on SrTiO3 (100) single crystal

NASA Astrophysics Data System (ADS)

Takayanagi, Makoto; Tsuchiya, Takashi; Namiki, Wataru; Ueda, Shigenori; Minohara, Makoto; Horiba, Koji; Kumigashira, Hiroshi; Terabe, Kazuya; Higuchi, Tohru

2018-03-01

Epitaxial Ca1-xSrxVO3 (0 ≦ x ≦ 1) thin films were grown on (100)-oriented SrTiO3 substrates by using the pulsed laser deposition technique. In contrast to the previous report that metal-insulator transition (MIT) in Ca1-xSrxVO3 (CSVO) was achieved only for extremely thin films (several nm thick), MIT was observed at 39, 72, and 113 K for films with a thickness of 50 nm. The electronic structure was investigated by hard and soft X-ray photoemission spectroscopy (HX-PES and SX-PES). The difference between these PES results was significant due to the variation in an escape depth of photoelectrons of PES. While HX-PES showed that the V 2p3/2 spectra consisted of four peaks (V5+, V4+, V3+, and V2+/1+), SX-PES showed only three peaks (V5+, V4+, and V3+). This difference can be caused by a strain from the substrate, which leads to the chemical disorder (V5+, V4+, V3+, and V2+/1+). The thin film near the substrate is affected by the strain. The positive magnetoresistance is attributed to the effect of electron-electron interactions in the disorder system. Therefore, the emergence of MIT can be explained by the electron-electron interactions from the chemical disorder due to the strain.

Semiconductor-insulator transition in VO{sub 2} (B) thin films grown by pulsed laser deposition

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

Rúa, Armando; Díaz, Ramón D.; Lysenko, Sergiy

2015-09-28

Thin films of B-phase VO{sub 2} were grown by pulsed-laser deposition on glass and (100)-cut MgO substrates in a temperature range from 375 to 425 °C and at higher gas pressures than usual for this technique. The films were strongly oriented, with ab-planes parallel to the substrate surface. Detailed study of surface morphology through Atomic Force Microscopy images suggest significant differences in evolution as a function of growth temperature for films on the two types of substrates. Measurements of electrical conductivities through cooling-heating cycles from room temperature to 120 K showed changes of five orders of magnitude, with steeper changes between roommore » temperature and ∼150 K, which corresponds with the extended and reversible phase transition known to occur for this material. At lower temperatures conductivities exhibited Arrhenius behavior, indicating that no further structural change was occurring and that conduction is thermally activated. In this lower temperature range, conductivity of the samples can be described by the near-neighbor hopping model. No hysteresis was found between the cooling and heating braches of the cycles, which is at variance with previous results published for VO{sub 2} (B). This apparent lack of hysteresis for thin films grown in the manner described and the large conductivity variation as a function of temperature observed for the samples suggests this material could be of interest for infrared sensing applications.« less

Thermally Strained Band Gap Engineering of Transition-Metal Dichalcogenide Bilayers with Enhanced Light-Matter Interaction toward Excellent Photodetectors.

PubMed

Wang, Sheng-Wen; Medina, Henry; Hong, Kuo-Bin; Wu, Chun-Chia; Qu, Yindong; Manikandan, Arumugam; Su, Teng-Yu; Lee, Po-Tsung; Huang, Zhi-Quan; Wang, Zhiming; Chuang, Feng-Chuan; Kuo, Hao-Chung; Chueh, Yu-Lun

2017-09-26

Integration of strain engineering of two-dimensional (2D) materials in order to enhance device performance is still a challenge. Here, we successfully demonstrated the thermally strained band gap engineering of transition-metal dichalcogenide bilayers by different thermal expansion coefficients between 2D materials and patterned sapphire structures, where MoS 2 bilayers were chosen as the demonstrated materials. In particular, a blue shift in the band gap of the MoS 2 bilayers can be tunable, displaying an extraordinary capability to drive electrons toward the electrode under the smaller driven bias, and the results were confirmed by simulation. A model to explain the thermal strain in the MoS 2 bilayers during the synthesis was proposed, which enables us to precisely predict the band gap-shifted behaviors on patterned sapphire structures with different angles. Furthermore, photodetectors with enhancement of 286% and 897% based on the strained MoS 2 on cone- and pyramid-patterned sapphire substrates were demonstrated, respectively.

Electronic structure at transition metal phthalocyanine-transition metal oxide interfaces: Cobalt phthalocyanine on epitaxial MnO films

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

Glaser, Mathias; Peisert, Heiko, E-mail: heiko.peisert@uni-tuebingen.de; Adler, Hilmar

2015-03-14

The electronic structure of the interface between cobalt phthalocyanine (CoPc) and epitaxially grown manganese oxide (MnO) thin films is studied by means of photoemission (PES) and X-ray absorption spectroscopy (XAS). Our results reveal a flat-lying adsorption geometry of the molecules on the oxide surface which allows a maximal interaction between the π-system and the substrate. A charge transfer from MnO, in particular, to the central metal atom of CoPc is observed by both PES and XAS. The change of the shape of N-K XAS spectra at the interface points, however, to the involvement of the Pc macrocycle in the chargemore » transfer process. As a consequence of the charge transfer, energetic shifts of MnO related core levels were observed, which are discussed in terms of a Fermi level shift in the semiconducting MnO films due to interface charge redistribution.« less

Gadolinium nanoparticle based switchable mirrors: quenching of hydrogenation-dehydrogenation hysteresis.

PubMed

Aruna, I; Mehta, B R; Malhotra, L K

2007-06-01

A continuous and reversible 'structural, optical, and electronic' transition between the reflecting metallic dihydride and transparent semiconducting trihydride states observed in rare earth metals on hydrogenation make these materials and their hydrides suitable for switchable mirror, sensing, and other technological applications. Recently Pd capped Gd nanoparticle based 'new generation' switchable mirrors have been fabricated with extended color neutrality, better optical contrast, and faster kinetics in comparison to the polycrystalline, epitaxial, alloy, and multilayer films. The present report aims at investigating the effect of nanoparticle nature on the hydrogenation-dehydrogenation hysteresis in switchable mirrors by carrying out in situ measurement of optical transmittance and electrode potentials during electrochemical hydrogen loading-deloading of Gd nanoparticle samples. Interestingly, Gd nanoparticle samples were observed to exhibit quenched hysteresis. The quenching of hysteresis in hydrogen-induced properties has been attributed to the absence of structural transition upon hydrogenation, reduction in topographical interlocking of the grains and elimination of lateral clamping of the slack nanoparticle layer to the substrate.

Monolayer PtSe₂, a New Semiconducting Transition-Metal-Dichalcogenide, Epitaxially Grown by Direct Selenization of Pt.

PubMed

Wang, Yeliang; Li, Linfei; Yao, Wei; Song, Shiru; Sun, J T; Pan, Jinbo; Ren, Xiao; Li, Chen; Okunishi, Eiji; Wang, Yu-Qi; Wang, Eryin; Shao, Yan; Zhang, Y Y; Yang, Hai-tao; Schwier, Eike F; Iwasawa, Hideaki; Shimada, Kenya; Taniguchi, Masaki; Cheng, Zhaohua; Zhou, Shuyun; Du, Shixuan; Pennycook, Stephen J; Pantelides, Sokrates T; Gao, Hong-Jun

2015-06-10

Single-layer transition-metal dichalcogenides (TMDs) receive significant attention due to their intriguing physical properties for both fundamental research and potential applications in electronics, optoelectronics, spintronics, catalysis, and so on. Here, we demonstrate the epitaxial growth of high-quality single-crystal, monolayer platinum diselenide (PtSe2), a new member of the layered TMDs family, by a single step of direct selenization of a Pt(111) substrate. A combination of atomic-resolution experimental characterizations and first-principle theoretic calculations reveals the atomic structure of the monolayer PtSe2/Pt(111). Angle-resolved photoemission spectroscopy measurements confirm for the first time the semiconducting electronic structure of monolayer PtSe2 (in contrast to its semimetallic bulk counterpart). The photocatalytic activity of monolayer PtSe2 film is evaluated by a methylene-blue photodegradation experiment, demonstrating its practical application as a promising photocatalyst. Moreover, circular polarization calculations predict that monolayer PtSe2 has also potential applications in valleytronics.

From wrinkling to global buckling of a ring on a curved substrate

NASA Astrophysics Data System (ADS)

Lagrange, R.; López Jiménez, F.; Terwagne, D.; Brojan, M.; Reis, P. M.

2016-04-01

We present a combined analytical approach and numerical study on the stability of a ring bound to an annular elastic substrate, which contains a circular cavity. The system is loaded by depressurizing the inner cavity. The ring is modeled as an Euler-Bernoulli beam and its equilibrium equations are derived from the mechanical energy which takes into account both stretching and bending contributions. The curvature of the substrate is considered explicitly to model the work done by its reaction force on the ring. We distinguish two different instabilities: periodic wrinkling of the ring or global buckling of the structure. Our model provides an expression for the critical pressure, as well as a phase diagram that rationalizes the transition between instability modes. Towards assessing the role of curvature, we compare our results for the critical stress and the wrinkling wavelength to their planar counterparts. We show that the critical stress is insensitive to the curvature of the substrate, while the wavelength is only affected due to the permissible discrete values of the azimuthal wavenumber imposed by the geometry of the problem. Throughout, we contrast our analytical predictions against finite element simulations.

Wetting of heterogeneous substrates. A classical density-functional-theory approach

NASA Astrophysics Data System (ADS)

Yatsyshin, Peter; Parry, Andrew O.; Rascón, Carlos; Duran-Olivencia, Miguel A.; Kalliadasis, Serafim

2017-11-01

Wetting is a nucleation of a third phase (liquid) on the interface between two different phases (solid and gas). In many experimentally accessible cases of wetting, the interplay between the substrate structure, and the fluid-fluid and fluid-substrate intermolecular interactions leads to the appearance of a whole ``zoo'' of exciting interface phase transitions, associated with the formation of nano-droplets/bubbles, and thin films. Practical applications of wetting at small scales are numerous and include the design of lab-on-a-chip devices and superhydrophobic surfaces. In this talk, we will use a fully microscopic approach to explore the phase space of a planar wall, decorated with patches of different hydrophobicity, and demonstrate the highly non-trivial behaviour of the liquid-gas interface near the substrate. We will present fluid density profiles, adsorption isotherms and wetting phase diagrams. Our analysis is based on a formulation of statistical mechanics, commonly known as classical density-functional theory. It provides a computationally-friendly and rigorous framework, suitable for probing small-scale physics of classical fluids and other soft-matter systems. EPSRC Grants No. EP/L027186,EP/K503733;ERC Advanced Grant No. 247031.

Effect of vacuum annealing and substrate temperature on structural and optical properties of ZnIn2Se4 thin films

NASA Astrophysics Data System (ADS)

El-Nahass, M. M.; Attia, A. A.; Salem, G. F.; Ali, H. A. M.; Ismail, M. I.

2013-09-01

Zinc indium selenide (ZnIn2Se4) thin films were prepared by the thermal evaporation technique with high deposition rate. The effect of thermal annealing in vacuum on the crystallinity of the as-deposited films was studied at different temperatures (523, 573 and 623 K). The effect of substrate temperature (623 K) for different thickness values (173, 250, 335 and 346 nm) on the optical parameters of ZnIn2Se4 was also studied. The structural studies showed nanocrystalline nature of the room temperature (300 K) deposited films with crystallite size of about a few nanometers. The crystallite size increased up to 31 nm with increasing the annealing temperature in vacuum. From the reflection and transmission data, the refractive index n and the extinction coefficient k were estimated for ZnIn2Se4 thin films and they were found to be independent of film thickness. Analysis of the absorption coefficient data of the as-deposited films revealed the existence of allowed direct and indirect transitions with optical energy gaps of 2.21 eV and 1.71 eV, respectively. These values decreased with increasing annealing temperature. At substrate temperature of 623 K, the direct band gap increased to 2.41 eV whereas the value of indirect band gap remained nearly unchanged. The dispersion analysis showed that the values of the oscillator energy Eo, dispersion energy Ed, dielectric constant at infinite frequency ε∞, and lattice dielectric constant εL were changed appreciably under the effect of annealing and substrate temperature. The covalent nature of structure was studied as a function of the annealing and substrate temperature using an empirical relation for the dispersion energy Ed. Generalized Miller's rule and linear refractive index were used to estimate the nonlinear susceptibility and nonlinear refractive index of the thin films.

Magneto-optical study of holmium iron garnet Ho3Fe5O12

NASA Astrophysics Data System (ADS)

Kalashnikova, A. M.; Pavlov, V. V.; Kimel, A. V.; Kirilyuk, A.; Rasing, Th.; Pisarev, R. V.

2012-09-01

Bulk holmium iron garnet Ho3Fe5O12 is a cubic ferrimagnet with Curie temperature TC = 567 K and magnetization compensation point in the range 130-140 K. The magneto-optical data are presented for a holmium iron garnet Ho3Fe5O12 film, ˜10 μm thick, epitaxially grown on a (111)-type gadolinium-gallium garnet Gd3Ga5O12 substrate. A specific feature of this structure is that the parameters of the bulk material, from which the film was grown, closely match the substrate ones. The temperature and field dependences of Faraday rotation as well as the temperature dependence of the domain structure in zero field were investigated. The compensation point of the structure was found to be Tcomp = 127 K. It was shown that the temperature dependence of the characteristic size of domain structure diverges at this point. Based on the obtained results we established that the magnetic anisotropy of the material is determined by both uniaxial and cubic contributions, each characterized by different temperature dependence. A complex shape of hysteresis loops and sharp changes of the domain pattern with temperature indicate the presence of collinear-noncollinear phase transitions. Study of the optical second harmonic generation was carried out using 100 fs laser pulses with central photon energy E = 1.55 eV. The electric dipole contribution (both crystallographic and magnetic) to the second harmonic generation was observed with high reliability despite a small mismatch of the film and substrate parameters.

Enzyme architecture: optimization of transition state stabilization from a cation-phosphodianion pair.

PubMed

Reyes, Archie C; Koudelka, Astrid P; Amyes, Tina L; Richard, John P

2015-04-29

The side chain cation of R269 lies at the surface of l-glycerol 3-phosphate dehydrogenase (GPDH) and forms an ion pair to the phosphodianion of substrate dihydroxyacetone phosphate (DHAP), which is buried at the nonpolar protein interior. The R269A mutation of GPDH results in a 110-fold increase in K(m) (2.8 kcal/mol effect) and a 41,000-fold decrease in k(cat) (6.3 kcal/mol effect), which corresponds to a 9.1 kcal/mol destabilization of the transition state for GPDH-catalyzed reduction of DHAP by NADH. There is a 6.7 kcal/mol stabilization of the transition state for the R269A mutant GPDH-catalyzed reaction by 1.0 M guanidinium ion, and the transition state for the reaction of the substrate pieces is stabilized by an additional 2.4 kcal/mol by their covalent attachment at wildtype GPDH. These results provide strong support for the proposal that GPDH invests the 11 kcal/mol intrinsic phosphodianion binding energy of DHAP in trapping the substrate at a nonpolar active site, where strong electrostatic interactions are favored, and obtains a 9 kcal/mol return from stabilizing interactions between the side chain cation and transition state trianion. We propose a wide propagation for the catalytic motif examined in this work, which enables strong transition state stabilization from enzyme-phosphodianion pairs.

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

PubMed Central

Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.

2009-01-01

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742

Preparation of multilayered nanocrystalline thin films with composition-modulated interfaces

NASA Astrophysics Data System (ADS)

Biro, D.; Barna, P. B.; Székely, L.; Geszti, O.; Hattori, T.; Devenyi, A.

2008-06-01

The properties of multilayer thin film structures depend on the morphology and structure of interfaces. A broad interface, in which the composition is varying, can enhance, e.g., the hardness of multilayer thin films. In the present experiments multilayers of TiAlN and CrN as well as TiAlN, CrN and MoS 2 were studied by using unbalanced magnetron sputter sources. The sputter sources were arranged side by side on an arc. This arrangement permits development of a transition zone between the layers, where the composition changes continuously. The multilayer system was deposited by one-fold oscillating movement of substrates in front of sputter sources. Thicknesses of layers could be changed both by oscillation frequency and by the power applied to sputter sources. Ti/Al: 50/50 at%, pure chromium and MoS 2 targets were used in the sputter sources. The depositions were performed in an Ar-N 2 mixture at 0.22 Pa working pressure. The sputtering power of the TiAl source was feed-back adjusted in fuzzy-logic mode in order to avoid fluctuation of the TiAl target sputter rate due to poisoning of the target surface. Structure characterization of films deposited on <1 0 0> Si wafers covered by thermally grown SiO 2 was performed by cross-sectional transmission electron microscopy. At first a 100 nm thick Cr base layer was deposited on the substrate to improve adhesion, which was followed by a CrN transition layer. The CrN transition layer was followed by a 100 nm thick TiAlN/CrN multilayer system. The TiAlN/CrN/MoS 2 multilayer system was deposited on the surface of this underlayer system. The underlayer systems Cr, CrN and TiAlN/CrN were crystalline with columnar structure according to the morphology of zone T of the structure zone models. The column boundaries contained segregated phases showing up in the under-focused TEM images. The surface of the underlayer system was wavy due to dome-shaped columns. The nanometer-scaled TiAlN/CrN/MoS 2 multilayer system followed this waviness. Crystallinity of the TiAlN and CrN layers in the multilayer system decreases with increasing thickness of the MoS 2 layer.

Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery

DOE PAGES

Rodionova, Irina A.; Zuccola, Harmon J.; Sorci, Leonardo; ...

2015-01-28

Nicotinate mononucleotide adenylyltransferase NadD is an essential enzyme in the biosynthesis of the NAD cofactor, which has been implicated as a target for developing new antimycobacterial therapies. Here we report the crystal structure of Mycobacterium tuberculosis NadD ( MtNadD) at a resolution of 2.4 Å. A remarkable new feature of the MtNadD structure, compared with other members of this enzyme family, is a 310 helix that locks the active site in an over-closed conformation. As a result, MtNadD is rendered inactive as it is topologically incompatible with substrate binding and catalysis. Directed mutagenesis was also used to further dissect themore » structural elements that contribute to the interactions of the two MtNadD substrates, i.e. ATP and nicotinic acid mononucleotide (NaMN). For inhibitory profiling of partially active mutants and wild type MtNadD, we used a small molecule inhibitor of MtNadD with moderate affinity ( Ki ~ 25 μM) and antimycobacterial activity (MIC 80) ~ 40-80 μM). This analysis revealed interferences with some of the residues in the NaMN binding subsite consistent with the competitive inhibition observed for the NaMN substrate (but not ATP). A detailed steady-state kinetic analysis of MtNadD suggests that ATP must first bind to allow efficient NaMN binding and catalysis. This sequential mechanism is consistent with the requirement of transition to catalytically competent (open) conformation hypothesized from structural modeling. A possible physiological significance of this mechanism is to enable the down-regulation of NAD synthesis under ATP-limiting dormancy conditions. Lastly, these findings point to a possible new strategy for designing inhibitors that lock the enzyme in the inactive over-closed conformation.« less

Recycling nicotinamide. The transition-state structure of human nicotinamide phosphoribosyltransferase

PubMed Central

Burgos, Emmanuel S.; Vetticatt, Mathew J.; Schramm, Vern L.

2013-01-01

Human nicotinamide phosphoribosyltransferase (NAMPT) replenishes the NAD pool and controls the activities of sirtuins (SIRT), mono- and poly-(ADP-ribose) polymerases (PARP) and NAD nucleosidase (CD38). The nature of the enzymatic transition-state (TS) is central to understanding the function of NAMPT. We determined the TS structure for pyrophosphorolysis of nicotinamide mononucleotide (NMN) by kinetic isotope effects (KIEs). With the natural substrates, NMN and pyrophosphate (PPi), the intrinsic KIEs of [1′-14C], [1-15N], [1′-3H] and [2′-3H] are 1.047, 1.029, 1.154 and 1.093, respectively. A unique quantum computational approach was used for TS analysis that included structural elements of the catalytic site. Without constraints (e.g. imposed torsion angles), the theoretical and experimental data are in good agreement. The quantum-mechanical calculations incorporated a crucial catalytic site residue (D313), two magnesium atoms and coordinated water molecules. The transition state model predicts primary 14C, α-secondary 3H, β-secondary 3H and primary 15N KIE close to the experimental values. The analysis reveals significant ribocation character at the TS. The attacking PPi nucleophile is weakly interacting (rC-O = 2.60 Å) and the N-ribosidic C1′-N bond is highly elongated at the TS (rC-N = 2.35 Å), consistent with an ANDN mechanism. Together with the crystal structure of the NMN•PPi•Mg2•enzyme complex, the reaction coordinate is defined. The enzyme holds the nucleophile and leaving group in relatively fixed positions to create a reaction coordinate with C1′-anomeric migration from nicotinamide to the PPi. The transition state is reached by a 0.85 Å migration of C1′. PMID:23373462

Enzyme Architecture: Erection of Active Orotidine 5'-Monophosphate Decarboxylase by Substrate-Induced Conformational Changes.

PubMed

Reyes, Archie C; Amyes, Tina L; Richard, John P

2017-11-15

Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the decarboxylation of 5-fluoroorotate (FO) with k cat /K m = 1.4 × 10 -7 M -1 s -1 . Combining this and related kinetic parameters shows that the 31 kcal/mol stabilization of the transition state for decarboxylation of OMP provided by OMPDC represents the sum of 11.8 and 10.6 kcal/mol stabilization by the substrate phosphodianion and the ribosyl ring, respectively, and an 8.6 kcal/mol stabilization from the orotate ring. The transition state for OMPDC-catalyzed decarboxylation of FO is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively, by 1.0 M phosphite dianion, d-glycerol 3-phosphate and d-erythritol 4-phosphate. The stabilization is due to the utilization of binding interactions of the substrate fragments to drive an enzyme conformational change, which locks the orotate ring of the whole substrate, or the substrate pieces in a caged complex. We propose that enzyme-activation is a possible, and perhaps probable, consequence of any substrate-induced enzyme conformational change.

Transport Mechanisms in Organic Thin-Film Transistors

NASA Astrophysics Data System (ADS)

Fung, A. W. P.

1996-03-01

Recent success in fabricating field-effect transistors with polycrystalline α-sexithiophene (α-6T) has allowed us to study charge transport in this organic semiconductor. The appealing structural property that the oligomer chains are seated almost perpendicular to the substrate provides a model π-conjugated system which we find exhibits band transport at low temperatures. We observe a behavioral transition around 50K which is consistent with the metal-insulator transition in Holstein's small-polaron theory. The fact that we can observe intrinsic behavior means that the ambient-temperature mobility obtained in these transistors is optimal for α-6T. Agreement with the Holstein theory provides us with a prescription for rational design of materials for organic transistor applications. Work done in collaboration with L. Torsi, A. Dodabalapur, L. J. Rothberg and H. E. Katz.

Spontaneous formation of nanostructures inside inkjet-printed colloidal drops

NASA Astrophysics Data System (ADS)

Yang, Xin; Thorne, Nathaniel; Sun, Ying

2013-11-01

Nanostructures formed in inkjet-printed colloidal drops are systematically examined with different substrates and ink formulations. Various deposition patterns from multi-ring, radial spoke, firework to spider web, foam and island structures are observed. With a high particle loading, deposition transitions from multi-ring near the drop edge to spider web and finally to foam and islands in the center of the drop with 20 nm sulfate-modified polystyrene particles. At the same particle loading, 200 nm particles self-assemble into radial spokes at the drop edge and islands in the center, due to reduced contact line pinning resulted from less particles. In drops with a low particle concentration, due to fingering instability of the contact line, 20 nm particles form radial spokes enclosed by a ring, while 200 nm particles assemble into firework-like structures without a ring. Moreover, at a high particle loading, ruptures are observed on the multi-ring structure formed by 20 nm carboxylic-modified particles, due to stronger capillary forces from the contact line. Furthermore, for a drop printed on a less hydrophilic substrate, the interparticle interactions enable a more uniform deposition rather than complex nanostructures.

Localized to itinerant transition of f electrons in ordered Ce films on W(110)

NASA Astrophysics Data System (ADS)

Chen, Q. Y.; Feng, W.; Xie, D. H.; Lai, X. C.; Zhu, X. G.; Huang, L.

2018-04-01

A key issue to understand the driving force and underlying physics in the isostructural γ -α transition in Cerium is the character of the 4 f states, whether it is localized or itinerant. Here the surface topography and electronic structure of the well-ordered Ce metal films on a W(110) substrate were investigated by using scanning tunneling microscopy, angle-resolved photoemission spectroscopy and density functional theory, and single-site dynamical mean-field theory calculations. Three nearly flat f bands can be observed, and a weakly dispersive quasiparticle band near the Fermi level has been directly observed at low temperature, indicating the hybridization between f electrons and conduction electrons in the low-temperature α phase. The hybridization strength becomes weaker upon increasing temperature, and the f electrons become almost fully localized at 300 K in the high-temperature γ phase. The observed localized-to-itinerant transition of the f electrons with decreasing temperature gives direct experimental proof for the changes of the 4 f character in the isostructural γ -α phase transition. Our results suggest that the character of the f electrons plays a crucial role during the γ -α phase transition.

Method of boronizing transition metal surfaces

DOEpatents

Koyama, Koichiro; Shimotake, Hiroshi.

1983-08-16

A method is presented for preparing a boride layer on a transition metal substrate for use in corrosive environments or as a harden surface in machine applications. This method is particularly useful in treating current collectors for use within a high temperature and corrosive electrochemical cell environment. A melt of a alkali metal boride tetrafluoride salt including such as KF to lower its melting point is prepared including a dissolved boron containing material, for instance NiB, MnB[sub 2], or CrB[sub 2]. A transition metal to be coated is immersed in the melt at a temperature of no more than 700 C and a surface boride layer of that transition metal is formed within a period of about 24 hours on the substrate surface. 4 figs.

Symmetry of Epitaxial BiFeO3 Films in the Ultrathin Regime

NASA Astrophysics Data System (ADS)

Yang, Yongsoo; Schlep&üTz, Christian; Adamo, Carolina; Schlom, Darrell; Clarke, Roy

2013-03-01

BiFeO3 (BFO) films grown on SrTiO3 (STO) with a SrRuO3 buffer layer exhibit a monoclinic structure at thicknesses greater than 40 nm, but higher structural symmetry can be observed for thinner films [Phys. Rev. B 81, 144115 (2010)]. We report a structural phase transition from monoclinic to tetragonal in ultra-thin BFO films grown directly on (100)-oriented STO. X-ray diffraction measurements of 3-dimensional reciprocal space maps reveal half-integer order peaks due to oxygen octahedral tilting. When the film thickness is decreased below 20 unit cells, the integer-order Bragg peak splitting associated with the presence of multiple domains of the monoclinic phase disappears. Instead, a single peak that is commensurate with the STO substrate lattice appears. The diffraction pattern has four-fold symmetry, ruling out the presence of a single monoclinic domain in favor of a tetragonal film structure. The evolution of the oxygen octahedra tilt pattern inferred from the intensities of half-order peaks suggests that this transition originates from the corner-connectivity of oxygen atoms at the interface between BFO and STO, and also strongly supports this monoclinic to tetragonal transition. Supported in part by the U.S. Department of Energy (DE-FG02-06ER46273). Measurements performed at Sectors 13-BMC, 33-IDD, 33-BMC of the Advanced Photon Source, Argonne National Laboratory, USA (DOE contract No. DE-AC02-06CH11357).

Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development

PubMed Central

Ruzanski, Christian; Krucewicz, Katarzyna; Meier, Sebastian; Hägglund, Per; Svensson, Birte; Palcic, Monica M.

2017-01-01

The production of starch is essential for human nutrition and represents a major metabolic flux in the biosphere. The biosynthesis of starch in storage organs like barley endosperm operates via two main pathways using different substrates: starch synthases use ADP-glucose to produce amylose and amylopectin, the two major components of starch, whereas starch phosphorylase (Pho1) uses glucose-1-phosphate (G1P), a precursor for ADP-glucose production, to produce α-1,4 glucans. The significance of the Pho1 pathway in starch biosynthesis has remained unclear. To elucidate the importance of barley Pho1 (HvPho1) for starch biosynthesis in barley endosperm, we analyzed HvPho1 protein production and enzyme activity levels throughout barley endosperm development and characterized structure-function relationships of HvPho1. The molecular mechanisms underlying the initiation of starch granule biosynthesis, that is, the enzymes and substrates involved in the initial transition from simple sugars to polysaccharides, remain unclear. We found that HvPho1 is present as an active protein at the onset of barley endosperm development. Notably, purified recombinant protein can catalyze the de novo production of α-1,4-glucans using HvPho1 from G1P as the sole substrate. The structural properties of HvPho1 provide insights into the low affinity of HvPho1 for large polysaccharides like starch or amylopectin. Our results suggest that HvPho1 may play a role during the initiation of starch biosynthesis in barley. PMID:28407006

Functional mapping and implications of substrate specificity of the yeast high-affinity leucine permease Bap2.

PubMed

Usami, Yuki; Uemura, Satsohi; Mochizuki, Takahiro; Morita, Asami; Shishido, Fumi; Inokuchi, Jin-ichi; Abe, Fumiyoshi

2014-07-01

Leucine is a major amino acid in nutrients and proteins and is also an important precursor of higher alcohols during brewing. In Saccharomyces cerevisiae, leucine uptake is mediated by multiple amino acid permeases, including the high-affinity leucine permease Bap2. Although BAP2 transcription has been extensively analyzed, the mechanisms by which a substrate is recognized and moves through the permease remain unknown. Recently, we determined 15 amino acid residues required for Tat2-mediated tryptophan import. Here we introduced homologous mutations into Bap2 amino acid residues and showed that 7 residues played a role in leucine import. Residues I109/G110/T111 and E305 were located within the putative α-helix break in TMD1 and TMD6, respectively, according to the structurally homologous Escherichia coli arginine/agmatine antiporter AdiC. Upon leucine binding, these α-helix breaks were assumed to mediate a conformational transition in Bap2 from an outward-open to a substrate-binding occluded state. Residues Y336 (TMD7) and Y181 (TMD3) were located near I109 and E305, respectively. Bap2-mediated leucine import was inhibited by some amino acids according to the following order of severity: phenylalanine, leucine>isoleucine>methionine, tyrosine>valine>tryptophan; histidine and asparagine had no effect. Moreover, this order of severity clearly coincided with the logP values (octanol-water partition coefficients) of all amino acids except tryptophan. This result suggests that the substrate partition efficiency to the buried Bap2 binding pocket is the primary determinant of substrate specificity rather than structural amino acid side chain recognition. Copyright © 2014 Elsevier B.V. All rights reserved.

Manipulation of morphology and structure of the top of GaAs nanowires grown by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Li, Lixia; Pan, Dong; Yu, Xuezhe; So, Hyok; Zhao, Jianhua

2017-10-01

Self-catalyzed GaAs nanowires (NWs) are grown on Si (111) substrates by molecular-beam epitaxy. The effect of different closing sequences of the Ga and As cell shutters on the morphology and structural phase of GaAs NWs is investigated. For the sequences of closing the Ga and As cell shutters simultaneously or closing the As cell shutter 1 min after closing the Ga cell shutter, the NWs grow vertically to the substrate surface. In contrast, when the As cell shutter is closed first, maintaining the Ga flux is found to be critical for the following growth of GaAs NWs, which can change the growth direction from [111] to < 11\\bar{1}> . The evolution of the morphology and structural phase transition at the tips of these GaAs NWs confirm that the triple-phase-line shift mode is at work even for the growth with different cell shutter closing sequences. Our work will provide new insights for better understanding of the growth mechanism and realizing of the morphology and structure control of the GaAs NWs. Project supported partly by the MOST of China (No. 2015CB921503), the National Natural Science Foundation of China (Nos. 61504133, 61334006, 61404127), and Youth Innovation Promotion Association, CAS (No. 2017156).

Selective-area growth and controlled substrate coupling of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Bersch, Brian M.; Eichfeld, Sarah M.; Lin, Yu-Chuan; Zhang, Kehao; Bhimanapati, Ganesh R.; Piasecki, Aleksander F.; Labella, Michael, III; Robinson, Joshua A.

2017-06-01

Developing a means for true bottom-up, selective-area growth of two-dimensional (2D) materials on device-ready substrates will enable synthesis in regions only where they are needed. Here, we demonstrate seed-free, site-specific nucleation of transition metal dichalcogenides (TMDs) with precise control over lateral growth by utilizing an ultra-thin polymeric surface functionalization capable of precluding nucleation and growth. This polymer functional layer (PFL) is derived from conventional photoresists and lithographic processing, and is compatible with multiple growth techniques, precursors (metal organics, solid-source) and TMDs. Additionally, we demonstrate that the substrate can play a major role in TMD transport properties. With proper TMD/substrate decoupling, top-gated field-effect transistors (FETs) fabricated with selectively-grown monolayer MoS2 channels are competitive with current reported MoS2 FETs. The work presented here demonstrates that substrate surface engineering is key to realizing precisely located and geometrically-defined 2D layers via unseeded chemical vapor deposition techniques.

Metastable bcc phase formation in 3d ferromagnetic transition metal thin films sputter-deposited on GaAs(100) substrates

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

Minakawa, Shigeyuki, E-mail: s-minakawa@futamoto.elect.chuo-u.ac.jp; Ohtake, Mitsuru; Futamoto, Masaaki

2015-05-07

Co{sub 100−x}Fe{sub x} and Ni{sub 100−y}Fe{sub y} (at. %, x = 0–30, y = 0–60) films of 10 nm thickness are prepared on GaAs(100) substrates at room temperature by using a radio-frequency magnetron sputtering system. The detailed growth behavior is investigated by in-situ reflection high-energy electron diffraction. (100)-oriented Co and Ni single-crystals with metastable bcc structure are formed in the early stage of film growth, where the metastable structure is stabilized through hetero-epitaxial growth. With increasing the thickness up to 2 nm, the Co and the Ni films start to transform into more stable hcp and fcc structures through atomic displacements parallel to bcc(110) slide planes,more » respectively. The stability of bcc phase is improved by adding a small volume of Fe atoms into a Co film. The critical thickness of bcc phase formation is thicker than 10 nm for Co{sub 100−x}Fe{sub x} films with x ≥ 10. On the contrary, the stability of bcc phase for Ni-Fe system is less than that for Co-Fe system. The critical thicknesses for Ni{sub 100−y}Fe{sub y} films with y = 20, 40, and 60 are 1, 3, and 5 nm, respectively. The Co{sub 100−x}Fe{sub x} single-crystal films with metastable bcc structure formed on GaAs(100) substrates show in-plane uniaxial magnetic anisotropies with the easy direction along GaAs[011], similar to the case of Fe film epitaxially grown on GaAs(100) substrate. A Co{sub 100−x}Fe{sub x} film with higher Fe content shows a higher saturation magnetization and a lower coercivity.« less

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

DOE PAGES

Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi; ...

2016-03-19

The S 3 state of the Mn 4CaO 5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S 2 to S 3 transition that becomes a substrate water, we examined if the water insertion is essential for the S 3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S 3 stage. The novel S 3 state structure consisting of only short 2.7–2.8 Å MnMn distances was discussed.

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

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

Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi

The S 3 state of the Mn 4CaO 5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S 2 to S 3 transition that becomes a substrate water, we examined if the water insertion is essential for the S 3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S 3 stage. The novel S 3 state structure consisting of only short 2.7–2.8 Å MnMn distances was discussed.

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

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

Nithianantham, Stanley; Shilton, Brian H

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

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

Nithianantham, Stanley; Shilton, Brian H

2011-09-28

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motifmore » V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.« less

Orientation-adjusted anomalous insulator-metal transition in NdNiO3/LaMnO3 bilayers

NASA Astrophysics Data System (ADS)

Pan, S. Y.; Shi, L.; Zhao, J. Y.; Zhou, S. M.; Xu, X. M.

2018-04-01

NdNiO3/LaMnO3 (NNO/LMO) bilayers were epitaxially grown on SrTiO3 (STO) substrates with different orientations by the polymer-assisted deposition technique. A well crystallization quality of the bilayers is confirmed by X-ray diffraction. Two consecutive transitions, an anomalous insulator-metal transition at ˜100 K followed by the typical metal-insulator transition at ˜171 K, are observed in the (001)-oriented NNO/LMO/STO bilayer. The anomalous insulator-metal transition temperature increases to 142 K for the (111)-oriented NNO/LMO/STO bilayer. Meanwhile, the magnetic properties of the NNO/LMO bilayers show an obvious difference with [100] and [111] orientations. Considering the different strain directions and the related oxygen octahedral distortion/rotation, it is suggested that the magnetic changes and the low-temperature anomalous insulator-metal transition in the NNO/LMO bilayers are attributed to the strong interlayer exchange coupling and charge transfer adjusted by the substrate orientation, which can be an effective technique to tune the properties of transition-metal oxide films.

Substrate specificity of sheep liver sorbitol dehydrogenase.

PubMed Central

Lindstad, R I; Köll, P; McKinley-McKee, J S

1998-01-01

The substrate specificity of sheep liver sorbitol dehydrogenase has been studied by steady-state kinetics over the range pH 7-10. Sorbitol dehydrogenase stereo-selectively catalyses the reversible NAD-linked oxidation of various polyols and other secondary alcohols into their corresponding ketones. The kinetic constants are given for various novel polyol substrates, including L-glucitol, L-mannitol, L-altritol, D-altritol, D-iditol and eight heptitols, as well as for many aliphatic and aromatic alcohols. The maximum velocities (kcat) and the substrate specificity-constants (kcat/Km) are positively correlated with increasing pH. The enzyme-catalysed reactions occur by a compulsory ordered kinetic mechanism with the coenzyme as the first, or leading, substrate. With many substrates, the rate-limiting step for the overall reaction is the enzyme-NADH product dissociation. However, with several substrates there is a transition to a mechanism with partial rate-limitation at the ternary complex level, especially at low pH. The kinetic data enable the elucidation of new empirical rules for the substrate specificity of sorbitol dehydrogenase. The specificity-constants for polyol oxidation vary as a function of substrate configuration with D-xylo> D-ribo > L-xylo > D-lyxo approximately L-arabino > D-arabino > L-lyxo. Catalytic activity with a polyol or an aromatic substrate and various 1-deoxy derivatives thereof varies with -CH2OH > -CH2NH2 > -CH2OCH3 approximately -CH3. The presence of a hydroxyl group at each of the remaining chiral centres of a polyol, apart from the reactive C2, is also nonessential for productive ternary complex formation and catalysis. A predominantly nonpolar enzymic epitope appears to constitute an important structural determinant for the substrate specificity of sorbitol dehydrogenase. The existence of two distinct substrate binding regions in the enzyme active site, along with that of the catalytic zinc, is suggested to account for the lack of stereospecificity at C2 in some polyols. PMID:9461546

High Tc bolometer developments for planetary missions

NASA Technical Reports Server (NTRS)

Brasunas, J.; Lakew, B.

1991-01-01

A simple polishing technique was developed for thinning the LaAlO3 substrates for high-quality Tc bolometer films, and thus reducing their heat capacity. A 150-ms bolometer was made on a LaAlO3 substrate with a 5-Hz D* value of 1.5 x 10 exp 8. It is shown that passive temperature stabilization is adequate for operation at the transition. There remained excess noise at the transition, but this noise appears to be of nonbolometric origin.

Structural and Mechanistic Insights into C-P Bond Hydrolysis by Phosphonoacetate Hydrolase

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

Agarwal, Vinayak; Borisova, Svetlana A.; Metcalf, William W.

2011-12-22

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 {angstrom} resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformatemore » inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.« less

Characterization of pulsed laser deposition grown V2O3 converted VO2

NASA Astrophysics Data System (ADS)

Majid, Suhail; Shukla, D. K.; Rahman, F.; Gautam, Kamini; Sathe, V. G.; Choudhary, R. J.; Phase, D. M.

2016-10-01

Controllable tuning of Metal-insulator transition in VxOy thin film has been a field of extensive research. However controlled synthesis of desired Vanadium oxide phase is a challenging task. We have successfully achieved VO2 phase on Silicon substrate after post deposition annealing treatment to the PLD grown as deposited V2O3 thin films. The annealed thin film was characterized by x-ray diffraction (XRD), resistivity, Raman spectroscopy, X-ray absorption spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS) measurements. XRD confirms the crystalline nature and growth of VO2 phase in thin film. The characteristic MIT was observed from resistivity measurements and transition temperature appeared at lower value around 336 K, compared to bulk VO2. The structural transition accompanied with MIT from lower temperature monoclinic phase to higher temperature Rutile phase became evident from temperature dependent Raman measurements. Chemical state of vanadium was examined using XAS and XPS measurements which confirm the presence of +4 oxidation state of vanadium in thin film.

Semiconductor-metal phase transition of vanadium dioxide nanostructures on silicon substrate: Applications for thermal control of spacecraft

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

Leahu, G. L., E-mail: roberto.livoti@uniroma1.it; Li Voti, R., E-mail: roberto.livoti@uniroma1.it; Larciprete, M. C., E-mail: roberto.livoti@uniroma1.it

2014-06-19

We present a detailed infrared study of the semiconductor-to-metal transition (SMT) in a vanadium dioxide (VO2) film deposited on silicon wafer. The VO2 phase transition is studied in the mid-infrared (MIR) region by analyzing the transmittance and the reflectance measurements, and the calculated emissivity. The temperature behaviour of the emissivity during the SMT put into evidence the phenomenon of the anomalous absorption in VO2 which has been explained by applying the Maxwell Garnett effective medium approximation theory, together with a strong hysteresis phenomenon, both useful to design tunable thermal devices to be applied for the thermal control of spacecraft. Wemore » have also applied the photothermal radiometry in order to study the changes in the modulated emissivity induced by laser. Experimental results show how the use of these techniques represent a good tool for a quantitative measurement of the optothermal properties of vanadium dioxide based structures.« less

Synthesis of molybdenum carbide superconducting compounds by microwave-plasma chemical vapor deposition

NASA Astrophysics Data System (ADS)

Zhao, Hongyang; Cai, Kang; Ma, Zhibin; Cheng, Zhenxiang; Jia, Tingting; Kimura, Hideo; Fu, Qiuming; Tao, Hong; Xiong, Liwei

2018-02-01

A method to synthesize molybdenum carbides has been developed based on microwave plasma treatment with methane and hydrogen mixed gases, using a microwave-plasma chemical vapor deposition device. The device framework and its mechanism are described in detail. Two-dimensional α-Mo2C has been directly synthesized by a plate-to-plate substrate holder structure with a microwave power of 920 W and a partial pressure of 20 kPa. In-situ optical emission spectroscopy was used to measure the radical types in the plasma ball during glow discharge. The as-grown α-Mo2C samples were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy and Raman spectroscopy to determine their phases, purity and chemical groups. The superconducting transition temperature was measured, and the transition temperatures of the relevant phases are discussed in detail. The results confirmed that this method is an efficient way to obtain molybdenum carbides and inspire new research interest in transition metal carbides, which have many intrinsic local properties and applications.

Surface structuring in polypropylene using Ar+ beam sputtering: Pattern transition from ripples to dot nanostructures

NASA Astrophysics Data System (ADS)

Goyal, Meetika; Aggarwal, Sanjeev; Sharma, Annu; Ojha, Sunil

2018-05-01

Temporal variations in nano-scale surface morphology generated on Polypropylene (PP) substrates utilizing 40 keV oblique argon ion beam have been presented. Due to controlled variation of crucial beam parameters i.e. ion incidence angle and erosion time, formation of ripple patterns and further its transition into dot nanostructures have been realized. Experimental investigations have been supported by evaluation of Bradley and Harper (B-H) coefficients estimated using SRIM (The Stopping and Range of Ions in Matter) simulations. Roughness of pristine target surfaces has been accredited to be a crucial factor behind the early time evolution of nano-scale patterns over the polymeric surface. Study of Power spectral density (PSD) spectra reveals that smoothing mechanism switch from ballistic drift to ion enhanced surface diffusion (ESD) which can be the most probable cause for such morphological transition under given experimental conditions. Compositional analysis and depth profiling of argon ion irradiated specimens using Rutherford Backscattering Spectroscopy (RBS) has also been correlated with the AFM findings.

Pump-probe STM light emission spectroscopy for detection of photo-induced semiconductor-metal phase transition of VO2

NASA Astrophysics Data System (ADS)

Sakai, Joe; Katano, Satoshi; Kuwahara, Masashi; Uehara, Yoichi

2017-10-01

We attempted to observe pump-probe scanning tunneling microscopy (STM)-light emission (LE) from a VO2 thin film grown on a rutile TiO2(0 0 1) substrate, with an Ag tip fixed over a semiconducting domain. Laser pulses from a Ti:sapphire laser (wavelength 920 nm pulse width less than 1.5 ps) irradiated the tip-sample gap as pump and probe light sources. With a photon energy of 2.7 eV, suggesting phase transition from semiconducting monoclinic (M) to metallic rutile (R) phases in relation to the electronic band structure, faint LE was observed roughly 30 ps after the irradiation of the pump pulse, followed by retention for roughly 20 ps. The incident energy fluence of the pump pulse at the gap was five orders of magnitude lower than the threshold value for reported photo-induced M-R phase transition. The mechanism that makes it possible to reduce the threshold fluence is discussed.

Pump-probe STM light emission spectroscopy for detection of photo-induced semiconductor-metal phase transition of VO2.

PubMed

Sakai, Joe; Katano, Satoshi; Kuwahara, Masashi; Uehara, Yoichi

2017-10-11

We attempted to observe pump-probe scanning tunneling microscopy (STM)-light emission (LE) from a VO 2 thin film grown on a rutile TiO 2 (0 0 1) substrate, with an Ag tip fixed over a semiconducting domain. Laser pulses from a Ti:sapphire laser (wavelength 920 nm; pulse width less than 1.5 ps) irradiated the tip-sample gap as pump and probe light sources. With a photon energy of 2.7 eV, suggesting phase transition from semiconducting monoclinic (M) to metallic rutile (R) phases in relation to the electronic band structure, faint LE was observed roughly 30 ps after the irradiation of the pump pulse, followed by retention for roughly 20 ps. The incident energy fluence of the pump pulse at the gap was five orders of magnitude lower than the threshold value for reported photo-induced M-R phase transition. The mechanism that makes it possible to reduce the threshold fluence is discussed.

Electrical properties of CZTS thin films

NASA Astrophysics Data System (ADS)

Rao, M. C.; Kumar, M. Seshu; Lakshmi, K.; Rao, K. Koteswara; Parimala, M. P. D.; Basha, S. K. Shahenoor

2018-05-01

CZTS (Cu2ZnSnS4) thin films have been coated on to FTO and MO glass substrates by single step electro deposition process. Different characterization techniques were performed on to the prepared samples such as DSC and Raman studies. The Phase transition and weight loss of the precursors can be measured by DSC analysis. Raman spectrum is used to identify the functional groups and chemical structure involved in the materials. Electrical measurements confirm the nature of the film and also depend on the charge concentration present in the samples.

Micromagnetic structure in Co-alloy thin films and its correlation with microstructure

NASA Astrophysics Data System (ADS)

Tang, Kai

The development of magnetic hard disk recording has resulted in an increase of recording density in an accelerated pace. How to maintain the increasingly smaller bits with low noise presents a tremendous challenge to the recording media, which requires detailed study of micromagnetic structure of the media to understand the noise mechanism, and elucidation of the correlation between the micromagnetic structure and microstructure to systematically develop media materials and tailor their microstructure. Lorentz transmission electron microscopy (LTEM) is a high-resolution magnetic imaging technique. However, it requires uniformly thin specimens, which cannot be produced by conventional TEM specimen preparation methods. Consequently, its application to real computer magnetic hard disks has been limited. In this dissertation, a combined dimpling and chemical etching method is introduced to prepare specimens directly from the unmodified hard disks with the typical C/Co alloy/Cr/NiP/Al (substrate) structure. The specimens typically have 2000 μmsp2 or larger electron transparent areas of Co alloy/Cr films with uniform thickness, which are suitable for LTEM observation. This method is applicable to disks with both smooth and mechanically textured substrates. In this work, LTEM has been employed to study recorded patterns in real hard disks. Magnetic recording was performed on a standard spin stand. Bits of densities from 15 to 100 kfci were examined with head skew angles of 0sp° and 20sp°, respectively. We also compared tracks recorded on dc-erased disks with those on as-deposited disks. We observed magnetic ripples within the tracks and the inter-track regions, magnetic vortices of 0.1-0.2 mum in diameter at the bit-transitions, and curved magnetic domain walls in the track-edge regions resulting from the "dog-bone" shaped head field profile. Our results also indicate that the micromagnetic structure at the track edges is influenced by head skew and magnetization direction in the inter-track regions. The LTEM results are combined with MFM observations to provide further understanding. The study has concentrated on isotropic media on smooth substrates since low head-to-medium spacing required by high recording density demonstrates the need for this type of media. The recorded tracks are remanent magnetic states after a strong (head) magnetic field was applied. We also examined an ac-erased state, in which the effect of external field is removed. Magnetic vortices are identified, in which small crystal grains form magnetic clusters and these clusters then form closed-fluxed vortices. The size of these vortices is estimated to be around 1.0-1.5 mum, about 10 times larger than that found in the bit-transition regions. The smaller vortex sizes in the bit-transition regions may result from constraints from adjacent bits as well as the difference in magnetic processes generating these states. (Abstract shortened by UMI.)

Adsorbed Polymer Nanolayers on Solids: Mechanism, Structure and Applications

NASA Astrophysics Data System (ADS)

Sen, Mani Kuntal

In this thesis, by combining various advanced x-ray scattering, spectroscopic and other surface sensitive characterization techniques, I report the equilibrium polymer chain conformations, structures, dynamics and properties of polymeric materials at the solid-polymer melt interfaces. Following the introduction, in chapter 2, I highlight that the backbone chains (constituted of CH and CH2 groups) of the flattened polystyrene (PS) chains preferentially orient normal to the weakly interactive substrate surface via thermal annealing regardless of the initial chain conformations, while the orientation of the phenyl rings becomes randomized, thereby increasing the number of surface-segmental contacts (i.e., enthalpic gain) which is the driving force for the flattening process of the polymer chains even onto a weakly interactive solid. In chapter 3, I elucidate the flattened structures in block copolymer (BCP) thin films where both blocks lie flat on the substrate, forming a 2D randomly phase-separated structure irrespective of their microdomain structures and interfacial energetics. In chapter 4, I reveal the presence of an irreversibly adsorbed BCP layer which showed suppressed dynamics even at temperatures far above the individual glass transition temperatures of the blocks. Furthermore, this adsorbed BCP layer plays a crucial role in controlling the microdomain orientation in the entire film. In chapter 5, I report a radically new paradigm of designing a polymeric coating layer of a few nanometers thick ("polymer nanolayer") with anti-biofouling properties.

Transition from stripe-like patterns to a particulate film using driven evaporating menisci.

PubMed

Noguera-Marín, Diego; Moraila-Martínez, Carmen L; Cabrerizo-Vílchez, Miguel A; Rodríguez-Valverde, Miguel A

2014-07-01

Better control of colloidal assembly by convective deposition is particularly helpful in particle templating. However, knowledge of the different factors that can alter colloidal patterning mechanisms is still insufficient. Deposit morphology is strongly ruled by contact line dynamics, but the wettability properties of the substrate can alter it drastically. In this work, we experimentally examined the roles of substrate contact angle hysteresis and receding contact angle using driven evaporating menisci similar to the dip-coating technique but at a low capillary number. We used smooth substrates with very different wettability properties and nanoparticles of different sizes. For fixed withdrawal velocity, evaporation conditions, and nanoparticle concentration, we analyzed the morphology of the deposits formed on each substrate. A gradual transition from stripe-like patterns to a film was observed as the contact angle hysteresis and receding contact angle were lowered.

Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase

PubMed Central

Monroe, Nicole; Han, Han; Shen, Peter S; Sundquist, Wesley I; Hill, Christopher P

2017-01-01

Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP·BeFx, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating. The final Vps4 subunit completes a notched-washer configuration as if transitioning between the ends of the helix. We propose that ATP binding propagates growth at one end of the helix while hydrolysis promotes disassembly at the other end, so that Vps4 ‘walks’ along ESCRT-III until it encounters the ordered N-terminal domain to destabilize the ESCRT-III lattice. This model may be generally applicable to other protein-translocating AAA ATPases. DOI: http://dx.doi.org/10.7554/eLife.24487.001 PMID:28379137

Incident flux angle induced crystal texture transformation in nanostructured molybdenum films

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

Chen, L.; Lu, T.-M.; Wang, G.-C.

2012-07-15

Molybdenum films were observed to undergo a dramatic change in crystal texture orientation when the incident flux angle was varied in an oblique angle sputter deposition on amorphous substrates. Reflection high-energy electron diffraction pole figure and scanning electron microscopy were used to analyze in detail the texture orientation of the films. The normal incident deposition resulted in a fiber texture film with the minimum energy (110) crystal plane parallel to the substrate surface. A (110)[110] biaxial texture was observed for the samples grown with low incident angles of less than 45 Degree-Sign , with respect to the surface normal. Onmore » the other hand, for an oblique angle deposition of larger than 60 Degree-Sign , a (111)[112] biaxial texture was observed and appeared to be consistent with a zone T structure where the geometrically fastest growth [001] direction of a crystal plays a dominant role in defining the texture. We argue that a structural transition had occurred when the incident flux was varied from near normal incidence to a large angle.« less

X-Ray Reflectometry of DMPS Monolayers on a Water Substrate

NASA Astrophysics Data System (ADS)

Tikhonov, A. M.; Asadchikov, V. E.; Volkov, Yu. O.; Roshchin, B. S.; Ermakov, Yu. A.

2017-12-01

The molecular structure of dimyristoyl phosphatidylserine (DMPS) monolayers on a water substrate in different phase states has been investigated by X-ray reflectometry with a photon energy of 8 keV. According to the experimental data, the transition from a two-dimensional expanded liquid state to a solid gel state (liquid crystal) accompanied by the ordering of the hydrocarbon tails C14H27 of the DMPS molecule occurs in the monolayer as the surface pressure rises. The monolayer thickness is 20 ± 3 and 28 ± 2 Å in the liquid and solid phases, respectively, with the deflection angle of the molecular tail axis from the normal to the surface in the gel phase being 26° ± 8°. At least a twofold decrease in the degree of hydration of the polar lipid groups also occurs under two-dimensional monolayer compression. The reflectometry data have been analyzed using two approaches: under the assumption about the presence of two layers with different electron densities in the monolayer and without any assumptions about the transverse surface structure. Both approaches demonstrate satisfactory agreement between themselves in describing the experimental results.

Pyroelectric property of SrTiO3/Si ferroelectric-semiconductor heterojunctions near room temperature

NASA Astrophysics Data System (ADS)

Bai, Gang; Wu, Dongmei; Xie, Qiyun; Guo, Yanyan; Li, Wei; Deng, Licheng; Liu, Zhiguo

2015-12-01

A nonlinear thermodynamic formalism is developed to calculate the pyroelectric property of epitaxial single domain SrTiO3/Si heterojunctions by taking into account the thermal expansion misfit strain at different temperatures. It has been demonstrated that the crucial role was played by the contribution associated with the structure order parameter arising from the rotations of oxygen octahedral on pyroelectricity. A dramatic decrease in the pyroelectric coefficient due to the strong coupling between the polarization and the structure order parameter is found at ferroelectric TF1-TF2 phase transition. At the same time, the thermal expansion mismatch between film and substrate is also found to provide an additional weak decrease of pyroelectricity. The analytic relationship of the out-of-plane pyroelectric coefficient and dielectric constant of ferroelectric phases by considering the thermal expansion of thin films and substrates has been determined for the first time. Our research provides another avenue for the investigation of the pyroelectric effects of ferroic thin films, especially, such as antiferroelectric and multiferroic materials having two or more order parameters.

Influence of heat treatment on bond strength and corrosion resistance of sol-gel derived bioglass-ceramic coatings on magnesium alloy.

PubMed

Shen, Sibo; Cai, Shu; Xu, Guohua; Zhao, Huan; Niu, Shuxin; Zhang, Ruiyue

2015-05-01

In this study, bioglass-ceramic coatings were prepared on magnesium alloy substrates through sol-gel dip-coating route followed by heat treatment at the temperature range of 350-500°C. Structure evolution, bond strength and corrosion resistance of samples were studied. It was shown that increasing heat treatment temperature resulted in denser coating structure as well as increased interfacial residual stress. A failure mode transition from cohesive to adhesive combined with a maximum on the measured bond strength together suggested that heat treatment enhanced the cohesion strength of coating on the one hand, while deteriorated the adhesion strength of coating/substrate on the other, thus leading to the highest bond strength of 27.0MPa for the sample heat-treated at 450°C. This sample also exhibited the best corrosion resistance. Electrochemical tests revealed that relative dense coating matrix and good interfacial adhesion can effectively retard the penetration of simulated body fluid through the coating, thus providing excellent protection for the underlying magnesium alloy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of lattice-gas atoms on the adsorption behaviour of thioether molecules.

PubMed

Pan, Yi; Yang, Bing; Hulot, Catherine; Blechert, Siegfried; Nilius, Niklas; Freund, Hans-Joachim

2012-08-21

Using STM topographic imaging and spectroscopy, we have investigated the adsorption of two thioether molecules, 1,2-bis(phenylthio)benzene and (bis(3-phenylthio)-phenyl)sulfane, on noble and transition metal surfaces. The two substrates show nearly antipodal behaviour. Whereas complexes with one or two protruding centres are observed on Au(111), only flat and uniform ad-structures are found on NiAl(110). The difference is ascribed to the possibility of the thioethers to form metal-organic complexes by coordinating lattice-gas atoms on the Au(111), while only the pristine molecules adsorb on the alloy surface. The metal coordination in the first case is driven by the formation of strong Au-S bonds and enables the formation of characteristic monomer, dimer and chain-like structures of the thioethers, using the Au atoms as linkers. A similar mechanism is not available on the NiAl, because no lattice gas develops at this surface at room temperature. Our work demonstrates how surface properties, i.e. the availability of mobile ad-species, determine the interaction of organic molecules with metallic substrates.

Ultra-confined surface phonon polaritons in molecular layers of van der Waals dielectrics.

PubMed

Dubrovkin, Alexander M; Qiang, Bo; Krishnamoorthy, Harish N S; Zheludev, Nikolay I; Wang, Qi Jie

2018-05-02

Improvements in device density in photonic circuits can only be achieved with interconnects exploiting highly confined states of light. Recently this has brought interest to highly confined plasmon and phonon polaritons. While plasmonic structures have been extensively studied, the ultimate limits of phonon polariton squeezing, in particular enabling the confinement (the ratio between the excitation and polariton wavelengths) exceeding 10 2 , is yet to be explored. Here, exploiting unique structure of 2D materials, we report for the first time that atomically thin van der Waals dielectrics (e.g., transition-metal dichalcogenides) on silicon carbide substrate demonstrate experimentally record-breaking propagating phonon polaritons confinement resulting in 190-times squeezed surface waves. The strongly dispersive confinement can be potentially tuned to greater than 10 3 near the phonon resonance of the substrate, and it scales with number of van der Waals layers. We argue that our findings are a substantial step towards infrared ultra-compact phonon polaritonic circuits and resonators, and would stimulate further investigations on nanophotonics in non-plasmonic atomically thin interface platforms.

Porous silicon formation during Au-catalyzed etching

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

Algasinger, Michael; Bernt, Maximilian; Koynov, Svetoslav

2014-04-28

The formation of “black” nano-textured Si during the Au-catalyzed wet-chemical etch process was investigated with respect to photovoltaic applications. Cross-sectional scanning electron microscopy (SEM) images recorded at different stages of the etch process exhibit an evolution of a two-layer structure, consisting of cone-like Si hillocks covered with a nano-porous Si (np-Si) layer. Optical measurements confirm the presence of a np-Si phase which appears after the first ∼10 s of the etch process and continuously increases with the etch time. Furthermore, the etch process was investigated on Si substrates with different doping levels (∼0.01–100 Ω cm). SEM images show a transition frommore » the two-layer morphology to a structure consisting entirely of np-Si for higher doping levels (<0.1 Ω cm). The experimental results are discussed on the basis of the model of a local electrochemical etch process. A better understanding of the metal-catalyzed etch process facilitates the fabrication of “black” Si on various Si substrates, which is of significant interest for photovoltaic applications.« less

Replacement of Asp-162 by Ala prevents the cooperative transition by the substrates while enhancing the effect of the allosteric activator ATP on E. coli aspartate transcarbamoylase

PubMed Central

Fetler, L.; Tauc, P.; Baker, D.P.; Macol, C.P.; Kantrowitz, E.R.; Vachette, P.

2002-01-01

The available crystal structures of Escherichia coli aspartate transcarbamoylase (ATCase) show that the conserved residue Asp-162 from the catalytic chain interacts with essentially the same residues in both the T- and R-states. To study the role of Asp-162 in the regulatory properties of the enzyme, this residue has been replaced by alanine. The mutant D162A shows a 7700-fold reduction in the maximal observed specific activity, a twofold decrease in the affinity for aspartate, a loss of homotropic cooperativity, and decreased activation by the nucleotide effector adenosine triphosphate (ATP) compared with the wild-type enzyme. Small-angle X-ray scattering (SAXS) measurements reveal that the unliganded mutant enzyme adopts the T-quaternary structure of the wild-type enzyme. Most strikingly, the bisubstrate analog N-phosphonacetyl-L-aspartate (PALA) is unable to induce the T to R quaternary structural transition, causing only a small alteration of the scattering pattern. In contrast, addition of the activator ATP in the presence of PALA causes a significant increase in the scattering amplitude, indicating a large quaternary structural change, although the mutant does not entirely convert to the wild-type R structure. Attempts at modeling this new conformation using rigid body movements of the catalytic trimers and regulatory dimers did not yield a satisfactory solution. This indicates that intra- and/or interchain rearrangements resulting from the mutation bring about domain movements not accounted for in the simple model. Therefore, Asp-162 appears to play a crucial role in the cooperative structural transition and the heterotropic regulatory properties of ATCase. PMID:11967364

Facile fabrication of uniaxial nanopatterns on shape memory polymer substrates using a complete bottom-up approach

NASA Astrophysics Data System (ADS)

Chen, Zhongbi; Krishnaswamy, Sridhar

2014-03-01

In earlier work, we have demonstrated an assisted self-assembly fabrication method for unidirectional submicron patterns using pre-programmed shape memory polymers (SMP) as the substrate in an organic/inorganic bilayer structure. In this paper, we propose a complete bottom-up method for fabrication of uniaxial wrinkles whose wavelength is below 300 nm. The method starts with using the aforementioned self-assembled bi-layer wrinkled surface as the template to make a replica of surface wrinkles on a PDMS layer which is spin-coated on a pre-programmed SMP substrate. When the shape recovery of the substrate is triggered by heating it to its transition temperature, the substrate has been programmed in such a way that it shrinks uniaxially to return to its permanent shape. Consequently, the wrinkle wavelength on PDMS reduces accordingly. A subsequent contact molding process is carried out on the PDMS layer spin-coated on another pre-programmed SMP substrate, but using the wrinkled PDMS surface obtained in the previous step as the master. By activating the shape recovery of the substrate, the wrinkle wavelength is further reduced a second time in a similar fashion. Our experiments showed that the starting wavelength of 640 nm decreased to 290 nm after two cycles of recursive molding. We discuss the advantages and limitations of our recursive molding approach compared to the prevalent top-down fabrication methods represented by lithography. The present study is expected to o er a simple and cost-e ective fabrication method of nano-scale uniaxial wrinkle patterns with the potential for large-scale mass-production.

Poison Domains Block Transit of Translocated Substrates via the Legionella pneumophila Icm/Dot System

PubMed Central

Amyot, Whitney M.; deJesus, Dennise

2013-01-01

Legionella pneumophila uses the Icm/Dot type 4B secretion system (T4BSS) to deliver translocated protein substrates to the host cell, promoting replication vacuole formation. The conformational state of the translocated substrates within the bacterial cell is unknown, so we sought to determine if folded substrates could be translocated via this system. Fusions of L. pneumophila Icm/Dot-translocated substrates (IDTS) to dihydrofolate reductase (DHFR) or ubiquitin (Ub), small proteins known to fold rapidly, resulted in proteins with low translocation efficiencies. The folded moieties did not cause increased aggregation of the IDTS and did not impede interaction with the adaptor protein complex IcmS/IcmW, which is thought to form a soluble complex that promotes translocation. The translocation defect was alleviated with a Ub moiety harboring mutations known to destabilize its structure, indicating that unfolded proteins are preferred substrates. Real-time analysis of translocation, following movement during the first 30 min after bacterial contact with host cells, revealed that the folded moiety caused a kinetic defect in IDTS translocation. Expression of an IDTS fused to a folded moiety interfered with the translocation of other IDTS, consistent with it causing a blockage of the translocation channel. Furthermore, the folded protein fusions also interfered with intracellular growth, consistent with inefficient or impaired translocation of proteins critical for L. pneumophila intracellular growth. These studies indicate that substrates of the Icm/Dot T4SS are translocated to the host cytosol in an unfolded conformation and that folded proteins are stalled within the translocation channel, impairing the function of the secretion system. PMID:23798536

VTVH-MCD and DFT studies of thiolate bonding to [FeNO]7/[FeO2]8 complexes of isopenicillin N synthase: substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes.

PubMed

Brown, Christina D; Neidig, Michael L; Neibergall, Matthew B; Lipscomb, John D; Solomon, Edward I

2007-06-13

Isopenicillin N synthase (IPNS) is a unique mononuclear nonheme Fe enzyme that catalyzes the four-electron oxidative double ring closure of its substrate ACV. A combination of spectroscopic techniques including EPR, absorbance, circular dichroism (CD), magnetic CD, and variable-temperature, variable-field MCD (VTVH-MCD) were used to evaluate the geometric and electronic structure of the [FeNO]7 complex of IPNS coordinated with the ACV thiolate ligand. Density Function Theory (DFT) calculations correlated to the spectroscopic data were used to generate an experimentally calibrated bonding description of the Fe-IPNS-ACV-NO complex. New spectroscopic features introduced by the binding of the ACV thiolate at 13 100 and 19 800 cm-1 are assigned as the NO pi*(ip) --> Fe dx2-y2 and S pi--> Fe dx2-y2 charge transfer (CT) transitions, respectively. Configuration interaction mixes S CT character into the NO pi*(ip) --> Fe dx2-y2 CT transition, which is observed experimentally from the VTVH-MCD data from this transition. Calculations on the hypothetical {FeO2}8 complex of Fe-IPNS-ACV reveal that the configuration interaction present in the [FeNO]7 complex results in an unoccupied frontier molecular orbital (FMO) with correct orientation and distal O character for H-atom abstraction from the ACV substrate. The energetics of NO/O2 binding to Fe-IPNS-ACV were evaluated and demonstrate that charge donation from the ACV thiolate ligand renders the formation of the FeIII-superoxide complex energetically favorable, driving the reaction at the Fe center. This single center reaction allows IPNS to avoid the O2 bridged binding generally invoked in other nonheme Fe enzymes that leads to oxygen insertion (i.e., oxygenase function) and determines the oxidase activity of IPNS.

Tailoring the electronic transitions of NdNiO{sub 3} films through (111){sub pc} oriented interfaces

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

Catalano, S., E-mail: sara.catalano@unige.ch; Gibert, M.; Zubko, P.

2015-06-01

Bulk NdNiO{sub 3} and thin films grown along the pseudocubic (001){sub pc} axis display a 1st order metal to insulator transition (MIT) together with a Néel transition at T = 200 K. Here, we show that for NdNiO{sub 3} films deposited on (111){sub pc} NdGaO{sub 3}, the MIT occurs at T = 335 K and the Néel transition at T = 230 K. By comparing transport and magnetic properties of layers grown on substrates with different symmetries and lattice parameters, we demonstrate a particularly large tuning when the epitaxy is realized on (111){sub pc} surfaces. We attribute this effect tomore » the specific lattice matching conditions imposed along this direction when using orthorhombic substrates.« less

Glass transition in thin supported polystyrene films probed by temperature-modulated ellipsometry in vacuum.

PubMed

Efremov, Mikhail Yu; Kiyanova, Anna V; Last, Julie; Soofi, Shauheen S; Thode, Christopher; Nealey, Paul F

2012-08-01

Glass transition in thin (1-200 nm thick) spin-cast polystyrene films on silicon surfaces is probed by ellipsometry in a controlled vacuum environment. A temperature-modulated modification of the method is used alongside a traditional linear temperature scan. A clear glass transition is detected in films with thicknesses as low as 1-2 nm. The glass transition temperature (T(g)) shows no substantial dependence on thickness for coatings greater than 20 nm. Thinner films demonstrate moderate T(g) depression achieving 18 K for thicknesses 4-7 nm. Less than 4 nm thick samples are excluded from the T(g) comparison due to significant thickness nonuniformity (surface roughness). The transition in 10-20 nm thick films demonstrates excessive broadening. For some samples, the broadened transition is clearly resolved into two separate transitions. The thickness dependence of the glass transition can be well described by a simple 2-layer model. It is also shown that T(g) depression in 5 nm thick films is not sensitive to a wide range of experimental factors including molecular weight characteristics of the polymer, specifications of solvent used for spin casting, substrate composition, and pretreatment of the substrate surface.

Deduced catalytic mechanism of d-amino acid amidase from Ochrobactrum anthropi SV3

PubMed Central

Okazaki, Seiji; Suzuki, Atsuo; Komeda, Hidenobu; Asano, Yasuhisa; Yamane, Takashi

2008-01-01

d-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Ω loop, and a ground state with a disordered Ω loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oη, Ser60 Oγ and Lys63 Nζ revealed that Tyr149 Oη donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oη donates an H atom to Ser60 Oγ or Lys63 Nζ in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oη, Ser60 Oγ and Lys63 Nζ, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oη in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. PMID:18421151

Reduction of α,β-Unsaturated Ketones by Old Yellow Enzymes: Mechanistic Insights from Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Lonsdale, Richard; Reetz, Manfred T

2015-11-25

Enoate reductases catalyze the reduction of activated C═C bonds with high enantioselectivity. The oxidative half-reaction, which involves the addition of a hydride and a proton to opposite faces of the C═C bond, has been studied for the first time by hybrid quantum mechanics/molecular mechanics (QM/MM). The reduction of 2-cyclohexen-1-one by YqjM from Bacillus subtilis was selected as the model system. Two-dimensional QM/MM (B3LYP-D/OPLS2005) reaction pathways suggest that the hydride and proton are added as distinct steps, with the former step preceding the latter. Furthermore, we present interesting insights into the reactivity of this enzyme, including the weak binding of the substrate in the active site, the role of the two active site histidine residues for polarization of the substrate C═O bond, structural details of the transition states to hydride and proton transfer, and the role of Tyr196 as proton donor. The information presented here will be useful for the future design of enantioselective YqjM mutants for other substrates.

Strain induced superconductivity in the parent compound BaFe2As2

NASA Astrophysics Data System (ADS)

Engelmann, J.; Grinenko, V.; Chekhonin, P.; Skrotzki, W.; Efremov, D. V.; Oswald, S.; Iida, K.; Hühne, R.; Hänisch, J.; Hoffmann, M.; Kurth, F.; Schultz, L.; Holzapfel, B.

2013-12-01

The discovery of superconductivity with a transition temperature, Tc, up to 65 K in single-layer FeSe (bulk Tc=8 K) films grown on SrTiO3 substrates has attracted special attention to Fe-based thin films. The high Tc is a consequence of the combined effect of electron transfer from the oxygen-vacant substrate to the FeSe thin film and lattice tensile strain. Here we demonstrate the realization of superconductivity in the parent compound BaFe2As2 (no bulk Tc) just by tensile lattice strain without charge doping. We investigate the interplay between strain and superconductivity in epitaxial BaFe2As2 thin films on Fe-buffered MgAl2O4 single crystalline substrates. The strong interfacial bonding between Fe and the FeAs sublattice increases the Fe-Fe distance due to the lattice misfit, which leads to a suppression of the antiferromagnetic spin density wave and induces superconductivity with bulk Tc≈10 K. These results highlight the role of structural changes in controlling the phase diagram of Fe-based superconductors.

Quantum chemical study of leaving group activation in T. vivax nucleoside hydrolase

NASA Astrophysics Data System (ADS)

Loverix, Stefan; Versees, Wim; Steyaert, Jan; Geerlings, Paul

General acid catalysis is a powerful and widely used strategy in enzymatic nucleophilic displacement reactions. However, in the nucleoside hydrolase of the parasite Trypanosoma vivax, crystallographic and mutagenesis studies failed to identify a general acid. The only groups in the vicinity of the leaving group that contribute to catalysis are (i) the indole side chain of Trp260, and (ii) the 5'-group of the substrate's ribose moiety. The x-ray structure of the slow Asp10Ala mutant of nucleoside hydrolase with the substrate inosine bound in the active site displays a face-to-face aromatic stacking interaction between Trp260 and the purine base of the substrate, as well as a peculiar C4'-endo ribose pucker that allows the 5'-OH group to accept an intramolecular hydrogen bond from the C8 of the purine. The first interaction (aromatic stacking) has been shown to raise the pKa of the leaving purine. Here, we present a DFT study showing that the 5'-OH group of ribose fulfills a similar role, rather than stabilizing the oxocarbenium-like transition state.

Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover

PubMed Central

McGowan, Lauren C.; Hamelberg, Donald

2013-01-01

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. PMID:23332074

Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover.

PubMed

McGowan, Lauren C; Hamelberg, Donald

2013-01-08

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Defect structures and growth mechanisms of boron arsenide epilayers grown on 6H-silicon carbide and 15R-silicon carbide substrates

NASA Astrophysics Data System (ADS)

Chen, Hui

B12As2 possesses the extraordinary properties, such as wide bandgap of 3.47eV and unique 'self heal' ability from electron irradiation damage, which make it attractive for the applications in space electronics, high temperature semiconductors and in particular, beta cells, devices capable of producing electrical energy by coupling a radioactive beta emitter to a semiconductor junction. Due to the absence of native substrates, B12As2 has been grown on substrates with compatible structural parameters via chemical vapor deposition. To date, growth on Si with (100), (110) and (111) orientation and (0001) 6H-SiC has been attempted. However, structural variants, including rotational and translational variants, have been observed in the epilayers and are expected to have a detrimental effect on device performance which has severely hindered progress of this material to date. In addition, none of the earlier reports provide a detailed atomic level study of defect structures in the films and growth mechanisms remain obscure. The focus of this thesis is to study defect structures in B12As2 films grown on different SiC substrates using synchrotron x-ray topography, high resolution transmission microscopy as well as other characterization techniques. The goals of the studies are to understand the generations of the defects present in B12As 2 films and their growth mechanisms so as to develop strategies to reduce defect densities and obtain better film quality for future device fabrication. The following detailed studies have been carried out: (1) The microstructures in B12As2 epitaxial layers grown on on-axis c-plane (0001) 6H-SiC substrates were analyzed in detail. Synchrotron white beam X-ray topography (SWBXT) and scanning electron microscopy (SEM) revealed a mosaic structure consisting of a solid solution of twin and matrix epilayer domains. The epitaxial relationship was determined to be (0001)B12As2<112¯0> B12As2||(0001)6H-SiC<112¯0>6H-SiC. B 12As2 twinned domains were found in the epilayer and the twin relationship consisted of a 180° rotation about [0001]B12As2 . High resolution transmission electron microscopy (HRTEM) observation revealed an evolution of the film microstructure from an ˜200nm thick disordered mosaic transition layer to a more ordered structure. Observing the structural projections of the film lower surface and the substrate upper surface, generated by CaRine 4.0 crystal visualization software, eight possible nucleation sites were found to be available on the substrate surface by considering the stable bonding configurations between the boron triangles at the bottom of the boron icosahedra, and the Si dangling bonds on the Si oriented (0001) 6H-SiC substrate surface. The transition layer was suggested to arise from the coalescence of translationally and rotationally variant domains nucleated at the various nucleation sites on the (0001) 6H-SiC surface. Boundaries between translationally variant domains were shown to have unfavorable high-energy bonding configurations while the formation of a 1/3[0001]B12As2 Frank partial dislocation enabled elimination of these high energy boundaries during mutual overgrowth. In consequence, the film quality beyond thicknesses of ˜200nm can be improved as the translational variants grow out leaving only the twin variants. (0003) twin boundaries in the regions beyond 200nm are shown to possess fault vectors such as 1/6[11¯00]B12As2 which originates from the mutual shift between the nucleation sites of the respective domains. (2) The effect off-cut angle on substrate surface on the growth of B12As2 epitaxial layer was studied using a 3.5° off-cut (0001) 6H-SiC substrate. A combined characterized technique composed of SWBXT, SEM, conventional and HRTEM was employed. Similar to the growth on on-axis c-plane 6H-SiC, the epitaxial relationship is identified to be (0001)B12As2<112¯0>B12As2||(0001) 6H-SiC<1120>6H-SiC. It is also revealed that the epilayer consists of a solid solution of B12As2 twinned domains. The 3.5° off-cut angle breaks the surface symmetry of c-plane 6H-SiC, however, the width of each single terrace is large enough to provide eight possible nonequivalent nucleation sites for the growth of B12As 2. In consequence, there could be eight possible structural variants in the film which indicates that the 3.5° offcut angle has little effect in the reduction of possible structural variants in the epilayer and thus may not be an excellent substrate to grow high quality B12As 2 film. (3) Investigation of the microstructures of B12As 2 epitaxial layers grown on m-plane 6H-SiC substrates has been studied. A mosaic structure formed by six types of domains, including (1-21) B 12As2, (2-12) B12As2, (353) B 12As2 and their respective {111} twins, was found in the epilayer. The choice of the various growth orientations in the B12As 2 film were proposed to arise from the following factors: (1) the tendency for B12As2 to grow with {1-21} low energy surface facets; (2) the tendency to minimize the in-plane lattice mismatch between B 12As2 planes oriented approximately parallel to the SiC (0001) planes so as to alleviate local strain in the film/substrate interface; (3) the tendency to nucleate on 3-3 symmetric closed-packed atomic steps exposed on the substrate surface after hydrogen etching. (4) Epitaxial growth of single crystalline B12As2 was discovered and investigated on m-plane 15R-SiC inclusions in a 6H-SiC substrate wafer. SEM showed only one type of triangular feature on the smooth surface of the film which indicated single growth orientation of B12As2. This is confirmed by SWBXT and cross-sectional HRTEM which revealed untwinned (353) orientated B12As2, with significantly improved macroscopic properties as confirmed by Raman spectroscopy. The corresponding growth model involving the bonding configuration between the film and the substrate was developed. It was found that the choice of the unique film orientation substantially resulted from the tendency to nucleate in (111)B12As2 orientation on (474)15R-SiC close-packed facets that are exposed on the m-plane 15R-SiC surface. This indicates that m-plane 15R-SiC could be a potentially excellent substrate to grow high quality B12As2 for future device fabrication.

Transport properties and c/a ratio of V{sub 2}O{sub 3} thin films grown on C- and R-plane sapphire substrates by pulsed laser deposition

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

Sakai, Joe; Limelette, Patrice; Funakubo, Hiroshi

2015-12-14

We prepared V{sub 2}O{sub 3} thin films on C- or R-plane sapphire (Al{sub 2}O{sub 3}) substrates by a pulsed laser deposition method. X-ray diffraction analyses confirmed that single-phase V{sub 2}O{sub 3} films were epitaxially grown on both C- and R-planes under an Ar gas ambient of 2 × 10{sup −2} mbar at a substrate temperature of 873 K. Depending on the deposition conditions, c/a ratios at room temperature of (0001)-oriented V{sub 2}O{sub 3} films widely ranged from 2.79 to 2.88. Among them, the films of 2.81 ≤ c/a ≤ 2.84 showed complex metal (M)–insulator (I)–M transition during cooling from 300 to 10 K, while those of larger c/a ratiosmore » were accompanied by metallic properties throughout this temperature range. All the films on R-plane substrates underwent simple M-I transition at ∼150 K, which was more abrupt than the films on C-plane, whereas their c/a ratios were narrowly distributed. The distinct difference of M-I transition properties between C- and R-plane films is explained by the intrinsic a- and c-axes evolution through the transition from M to I phases.« less

Polaron effect on the bandgap modulation in monolayer transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Xiao, Yao; Li, Zhi-Qing; Wang, Zi-Wu

2017-12-01

We theoretically study the bandgap modulation in monolayer transition metal dichalcogenides (TMDs) originating from the carrier-optical phonon coupling in the Fröhlich polaron model, in which both of the surface optical phonons modes induced by the polar substrate and the intrinsic longitudinal optical phonons modes have been taken into account. We find that the modulated magnitude of the bandgap is in the range of 100-500 meV by altering different polar substrates and tuning the internal distance between TMDs and polar substrate. The large tunability of the bandgap not only provides a possible explanation for the experimental measurements regarding the dielectric environmental sensitivity of the bandgap, but also holds promise for potential applications in optoelectronics and photovoltaics.

Geometric and electronic structure contributions to function in non-heme iron enzymes.

PubMed

Solomon, Edward I; Light, Kenneth M; Liu, Lei V; Srnec, Martin; Wong, Shaun D

2013-11-19

Mononuclear non-heme Fe (NHFe) enzymes play key roles in DNA repair, the biosynthesis of antibiotics, the response to hypoxia, cancer therapy, and many other biological processes. These enzymes catalyze a diverse range of oxidation reactions, including hydroxylation, halogenation, ring closure, desaturation, and electrophilic aromatic substitution (EAS). Most of these enzymes use an Fe(II) site to activate dioxygen, but traditional spectroscopic methods have not allowed researchers to insightfully probe these ferrous active sites. We have developed a methodology that provides detailed geometric and electronic structure insights into these NHFe(II) active sites. Using these data, we have defined a general mechanistic strategy that many of these enzymes use: they control O2 activation (and limit autoxidation and self-hydroxylation) by allowing Fe(II) coordination unsaturation only in the presence of cosubstrates. Depending on the type of enzyme, O2 activation either involves a 2e(-) reduced Fe(III)-OOH intermediate or a 4e(-) reduced Fe(IV)═O intermediate. Nuclear resonance vibrational spectroscopy (NRVS) has provided the geometric structure of these intermediates, and magnetic circular dichroism (MCD) has defined the frontier molecular orbitals (FMOs), the electronic structure that controls reactivity. This Account emphasizes that experimental spectroscopy is critical in evaluating the results of electronic structure calculations. Therefore these data are a key mechanistic bridge between structure and reactivity. For the Fe(III)-OOH intermediates, the anticancer drug activated bleomycin (BLM) acts as the non-heme Fe analog of compound 0 in heme (e.g., P450) chemistry. However BLM shows different reactivity: the low-spin (LS) Fe(III)-OOH can directly abstract a H atom from DNA. The LS and high-spin (HS) Fe(III)-OOHs have fundamentally different transition states. The LS transition state goes through a hydroxyl radical, but the HS transition state is activated for EAS without O-O cleavage. This activation is important in one class of NHFe enzymes that utilizes a HS Fe(III)-OOH intermediate in dioxygenation. For Fe(IV)═O intermediates, the LS form has a π-type FMO activated for attack perpendicular to the Fe-O bond. However, the HS form (present in the NHFe enzymes) has a π FMO activated perpendicular to the Fe-O bond and a σ FMO positioned along the Fe-O bond. For the NHFe enzymes, the presence of π and σ FMOs enables enzymatic control in determining the type of reactivity: EAS or H-atom extraction for one substrate with different enzymes and halogenation or hydroxylation for one enzyme with different substrates.

Dry-spray deposition of TiO2 for a flexible dye-sensitized solar cell (DSSC) using a nanoparticle deposition system (NPDS).

PubMed

Kim, Min-Saeng; Chun, Doo-Man; Choi, Jung-Oh; Lee, Jong-Cheon; Kim, Yang Hee; Kim, Kwang-Su; Lee, Caroline Sunyong; Ahn, Sung-Hoon

2012-04-01

TiO2 powders were deposited on indium tin oxide (ITO) coated polyethylene terephthalate (PET) substrates for application to the photoelectrode of a dye-sensitized solar cell (DSSC). In the conventional DSSC manufacturing process, a semiconductor oxide such as TiO2 powder requires a sintering process at higher temperature than the glass transition temperature (T(g)) of polymers, and thus utilization of flexible polymer substrates in DSSC research has been constrained. To overcome this restriction related to sintering, we used a nanoparticle deposition system (NPDS) that could produce a thin coating layer through a dry-spray method under atmospheric pressure at room temperature. The powder was sprayed through a slit-type nozzle having a 0.4 x 10 mm2 rectangular outlet. In order to determine the deposited TiO2 thickness, five kinds of TiO2 layered specimens were prepared, where the specimens have single and double layer structures. Deposited powders on the ITO coated PET substrates were observed using FE-SEM and a scan profiler The thicker TiO2 photoelectrode with a DSSC having a double layer structure showed higher energy efficiency than the single layer case. The highest fabricated flexible DSSC displayed a short circuit current density J(sc) = 1.99 mA cm(-2), open circuit voltage V(oc) = 0.71 V, and energy efficiency eta = 0.94%. These results demonstrate the possibility of utilizing the dry-spray method to fabricate a TiO2 layer on flexible polymer substrates at room temperature under atmospheric pressure.

Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids.

PubMed

Lu, Zhibing; Feng, Xiaohua; Song, Ling; Han, Ying; Kim, Alexander; Herzberg, Osnat; Woodson, William R; Martin, Brian M; Mariano, Patrick S; Dunaway-Mariano, Debra

2005-12-20

The work described in this paper was carried out to define the chemical function a new member of the isocitrate lyase enzyme family derived from the flowering plant Dianthus caryophyllus. This protein (Swiss-Prot entry Q05957) is synthesized in the senescent flower petals and is named the "petal death protein" or "PDP". On the basis of an analysis of the structural contexts of sequence markers common to the C-C bond lyases of the isocitrate lyase/phosphoenolpyruvate mutase superfamily, a substrate screen that employed a (2R)-malate core structure was designed. Accordingly, stereochemically defined C(2)- and C(3)-substituted malates were synthesized and tested as substrates for PDP-catalyzed cleavage of the C(2)-C(3) bond. The screen identified (2R)-ethyl, (3S)-methylmalate, and oxaloacetate [likely to bind as the hydrate, C(2)(OH)(2) gem-diol] as the most active substrates (for each, k(cat)/K(m) = 2 x 10(4) M(-)(1) s(-)(1)). In contrast to the stringent substrate specificities previously observed for the Escherichia coli isocitrate and 2-methylisocitrate lyases, the PDP tolerated hydrogen, methyl, and to a much lesser extent acetate substituents at the C(3) position (S configuration only) and hydoxyl, methyl, ethyl, propyl, and to a much lesser extent isobutyl substituents at C(2) (R configuration only). It is hypothesized that PDP functions in oxalate production in Ca(2+) sequestering and/or in carbon scavenging from alpha-hydroxycarboxylate catabolites during the biochemical transition accompanying petal senescence.

Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on monooxo Mo(IV) and bisoxo Mo(VI) bis-dithiolenes: insights into the mechanism of oxo transfer in sulfite oxidase and its relation to the mechanism of DMSO reductase.

PubMed

Ha, Yang; Tenderholt, Adam L; Holm, Richard H; Hedman, Britt; Hodgson, Keith O; Solomon, Edward I

2014-06-25

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [Mo(IV)O(bdt)2](2-) and [Mo(VI)O2(bdt)2](2-) (bdt = benzene-1,2-dithiolate(2-)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of previously studied dimethyl sulfoxide reductase (DMSOr) models. DFT calculations supported by the data are extended to evaluate the reaction coordinate for oxo transfer to a phosphite ester substrate. Three possible transition states are found with the one at lowest energy, stabilized by a P-S interaction, in good agreement with experimental kinetics data. Comparison of both oxo transfer reactions shows that in DMSOr, where the oxo is transferred from the substrate to the metal ion, the oxo transfer induces electron transfer, while in SO, where the oxo transfer is from the metal site to the substrate, the electron transfer initiates oxo transfer. This difference in reactivity is related to the difference in frontier molecular orbitals (FMO) of the metal-oxo and substrate-oxo bonds. Finally, these experimentally related calculations are extended to oxo transfer by sulfite oxidase. The presence of only one dithiolene at the enzyme active site selectively activates the equatorial oxo for transfer, and allows facile structural reorganization during turnover.

Specific features of the spectra and relaxation kinetics of long-wavelength photoconductivity in narrow-gap HgCdTe epitaxial films and heterostructures with quantum wells

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

Rumyantsev, V. V., E-mail: rumyantsev@ipmras.ru; Ikonnikov, A. V.; Antonov, A. V.

2013-11-15

The spectra and relaxation kinetics of interband photoconductivity are investigated in narrow-gap Hg{sub 1-x}Cd{sub x}Te epitaxial films with x = 0.19-0.23 and in structures with HgCdTe-based quantum wells (QWs), having an interband-transition energy in the range of 30-90 meV, grown by molecular-beam epitaxy on GaAs (013) substrates. A long-wavelength sensitivity band caused by impurities or defects is found in the spectra of the structures with quantum wells in addition to the interband photoconductivity. It is shown that the lifetimes of nonequilibrium carriers in the structures with QWs is less than in bulk samples at the same optical-transition energy. From themore » measured carrier lifetimes, the ampere-watt responsivity and the equivalent noise power for a film with x = 0.19 at a wavelength of 19 {mu}m are estimated. When investigating the relaxation kinetics of the photoconductivity at 4.2 K in high excitation regime, it is revealed that radiative recombination is dominant over other mechanisms of nonequilibrium-carrier recombination.« less

Mammals of Australia's Tropical Savannas: A Conceptual Model of Assemblage Structure and Regulatory Factors in the Kimberley Region

PubMed Central

Radford, Ian J.; Dickman, Christopher R.; Start, Antony N.; Palmer, Carol; Carnes, Karin; Everitt, Corrin; Fairman, Richard; Graham, Gordon; Partridge, Thalie; Thomson, Allan

2014-01-01

We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011) were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:- low numbers of mammals, State II:- dominated by omnivorous rodents and State III:- dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I) did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but—unlike arid regions—were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the already-articulated cat-habitat structure hypothesis for mammal declines, and we suggest approaches for explicit testing of transition triggers for competing hypotheses. PMID:24670997

Mammals of Australia's tropical savannas: a conceptual model of assemblage structure and regulatory factors in the Kimberley region.

PubMed

Radford, Ian J; Dickman, Christopher R; Start, Antony N; Palmer, Carol; Carnes, Karin; Everitt, Corrin; Fairman, Richard; Graham, Gordon; Partridge, Thalie; Thomson, Allan

2014-01-01

We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011) were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:--low numbers of mammals, State II:--dominated by omnivorous rodents and State III:--dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I) did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but-unlike arid regions-were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the already-articulated cat-habitat structure hypothesis for mammal declines, and we suggest approaches for explicit testing of transition triggers for competing hypotheses.

Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer.

PubMed

Ross, Breyan; Krapp, Stephan; Augustin, Martin; Kierfersauer, Reiner; Arciniega, Marcelino; Geiss-Friedlander, Ruth; Huber, Robert

2018-02-13

Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.

Subnanometer to nanometer transition metal CO oxidation catalysts

DOEpatents

Vajda, Stefan; Fortunelli, Alessandro; Yasumatsu, Hisato

2017-12-26

The present invention provides a catalyst defined in part by a conductive substrate; a film overlaying a surface of the substrate; and a plurality of metal clusters supported by the layer, wherein each cluster comprises between 8 and 11 atoms. Further provided is a catalyst defined in part by a conductive substrate; a layer overlaying a surface of the substrate; and a plurality of metal clusters supported by the layer, wherein each cluster comprises at least two metals.

A new structural framework for integrating replication protein A into DNA processing machinery

PubMed Central

Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.; Heller, William T.; Rambo, Robert P.; Tainer, John A.; Ivanov, Ivaylo; Chazin, Walter J.

2013-01-01

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA’s DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA’s DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways. PMID:23303776

A new structural framework for integrating replication protein A into DNA processing machinery

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

Brosey, Chris; Yan, Chunli; Tsutakawa, Susan

2013-01-17

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamicmore » on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.« less

Magnetic stripe domains of [Pt/Co/Cu]{sub 10} multilayer near spin reorientation transition

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

Sun, L.; Liang, J. H.; Xiao, X.

The dependence of magnetic anisotropy, magnetic domain patterns and magnetization reversal processes in [Pt/Co(t{sub Co})/Cu]{sub 10} film stack epitaxied on Cu (111) substrate have been studied as a function of the Co layer thickness t{sub Co}, by magneto-optic polar Kerr magnetometry and microscopy. We find the film undergoes spin reorientation transition from out-of-plane to in-plane as t{sub Co} increases. The SRT thickness is verified by Rotating-field Magneto-Optic Kerr effect method. The film exhibits the stripe domain structures at remanence with the width decreasing while t{sub Co} approaches SRT. As demonstrated by the first order reversal curve measurement, the magnetization reversalmore » process encompasses irreversible domain nucleation, domain annihilation at large field and reversible domain switching near remanence.« less

Physical vapor deposition as a route to hidden amorphous states

PubMed Central

Dawson, Kevin J.; Kearns, Kenneth L.; Yu, Lian; Steffen, Werner; Ediger, M. D.

2009-01-01

Stable glasses of indomethacin (IMC) were prepared by using physical vapor deposition. Wide-angle X-ray scattering measurements were performed to characterize the average local structure. IMC glasses prepared at a substrate temperature of 0.84 Tg (where Tg is the glass transition temperature) and a deposition rate of 0.2 nm/s show a broad, high-intensity peak at low q values that is not present in the supercooled liquid or melt-quenched glasses. When annealed slightly above Tg, the new WAXS pattern transforms into the melt-quenched glass pattern, but only after very long annealing times. For a series of samples prepared at the lowest deposition rate, the new local packing arrangement is present only for deposition temperatures below Tg −20 K, suggesting an underlying first-order liquid-to-liquid phase transition. PMID:19666494

Formaldehyde in the Diffuse Interstellar Cloud MBM40

NASA Astrophysics Data System (ADS)

Joy, Mackenzie; Magnani, Loris A.

2018-06-01

MBM40, a high-latitude molecular cloud, has been extensively studied using different molecular tracers. It appears that MBM40 is composed of a relatively dense, helical filament embedded in a more diffuse substrate of low density molecular gas. In order to study the transition between the two regimes, this project presents the first high-resolution mapping of MBM40 using the 110-111 hyperfine transition of formaldehyde (H2CO) at 4.83 GHz. We used H2CO spectra obtained with the Arecibo telescope more than a decade ago to construct this map. The results can be compared to previous maps made from the CO(1-0) transition to gain further understanding of the structure of the cloud. The intensity of the H2CO emission was compared to the CO emission. Although a correlation exists between the H2CO and CO emissivity, there seems to be a saturation of H2CO line strength for stronger CO emissivity. This is probably a radiative transfer effect of the CO emission. We have also found that the velocity dispersion of H2CO in the lower ridge of the cloud is significantly lower than in the rest of the cloud. This may indicate that this portion of the cloud is a coherent structure (analogous to an eddy) in a turbulent flow.

Direct Observation of the Thickness-Induced Crystallization and Stress Build-Up during Sputter-Deposition of Nanoscale Silicide Films.

PubMed

Krause, Bärbel; Abadias, Gregory; Michel, Anny; Wochner, Peter; Ibrahimkutty, Shyjumon; Baumbach, Tilo

2016-12-21

The kinetics of phase transitions during formation of small-scale systems are essential for many applications. However, their experimental observation remains challenging, making it difficult to elucidate the underlying fundamental mechanisms. Here, we combine in situ and real-time synchrotron X-ray diffraction (XRD) and X-ray reflectivity (XRR) experiments with substrate curvature measurements during deposition of nanoscale Mo and Mo 1-x Si x films on amorphous Si (a-Si). The simultaneous measurements provide direct evidence of a spontaneous, thickness-dependent amorphous-to-crystalline (a-c) phase transition, associated with tensile stress build-up and surface roughening. This phase transformation is thermodynamically driven, the metastable amorphous layer being initially stabilized by the contributions of surface and interface energies. A quantitative analysis of the XRD data, complemented by simulations of the transformation kinetics, unveils an interface-controlled crystallization process. This a-c phase transition is also dominating the stress evolution. While stress build-up can significantly limit the performance of devices based on nanostructures and thin films, it can also trigger the formation of these structures. The simultaneous in situ access to the stress signal itself, and to its microstructural origins during structure formation, opens new design routes for tailoring nanoscale devices.

Preparation of dilute magnetic semiconductor films by metalorganic chemical vapor deposition

NASA Technical Reports Server (NTRS)

Nouhi, Akbar (Inventor); Stirn, Richard J. (Inventor)

1988-01-01

A method for preparation of a dilute magnetic semiconductor (DMS) film is provided, in which a Group II metal source, a Group VI metal source and a transition metal magnetic ion source are pyrolyzed in the reactor of a metalorganic chemical vapor deposition (MOCVD) system by contact with a heated substrate. As an example, the preparation of films of Cd(sub 1-x)Mn(sub x)Te, in which 0 is less than or equal to x less than or equal to 0.7, on suitable substrates (e.g., GaAs) is described. As a source of manganese, tricarbonyl (methylcyclopentadienyl) manganese (TCPMn) is employed. To prevent TCPMn condensation during its introduction into the reactor, the gas lines, valves and reactor tubes are heated. A thin-film solar cell of n-i-p structure, in which the i-type layer comprises a DMS, is also described; the i-type layer is suitably prepared by MOCVD.

Preparation of dilute magnetic semiconductor films by metalorganic chemical vapor deposition

NASA Technical Reports Server (NTRS)

Nouhi, Akbar (Inventor); Stirn, Richard J. (Inventor)

1990-01-01

A method for preparation of a dilute magnetic semiconductor (DMS) film is provided, wherein a Group II metal source, a Group VI metal source and a transition metal magnetic ion source are pyrolyzed in the reactor of a metalorganic chemical vapor deposition (MOCVD) system by contact with a heated substrate. As an example, the preparation of films of Cd.sub.1-x Mn.sub.x Te, wherein 0.ltoreq..times..ltoreq.0.7, on suitable substrates (e.g., GaAs) is described. As a source of manganese, tricarbonyl (methylcyclopentadienyl) maganese (TCPMn) is employed. To prevent TCPMn condensation during the introduction thereof int the reactor, the gas lines, valves and reactor tubes are heated. A thin-film solar cell of n-i-p structure, wherein the i-type layer comprises a DMS, is also described; the i-type layer is suitably prepared by MOCVD.

Graphene-silicon layered structures on single-crystalline Ir(111) thin films

DOE PAGES

Que, Yande D.; Tao, Jing; Zhang, Yong; ...

2015-01-20

Epitaxial growth of graphene on transition metal crystals, such as Ru,⁽¹⁻³⁾ Ir,⁽⁴⁻⁶⁾ and Ni,⁽⁷⁾ provides large-area, uniform graphene layers with controllable defect density, which is crucial for practical applications in future devices. To decrease the high cost of single-crystalline metal bulks, single-crystalline metal films are strongly suggested as the substrates for epitaxial growth large-scale high-quality graphene.⁽⁸⁻¹⁰⁾ Moreover, in order to weaken the interactions of graphene with its metal host, which may result in a suppression of the intrinsic properties of graphene,⁽¹¹ ¹²⁾ the method of element intercalation of semiconductors at the interface between an epitaxial graphene layer and a transitionmore » metal substrate has been successfully realized.⁽¹³⁻¹⁶⁾« less

Yeast Droplets

NASA Astrophysics Data System (ADS)

Nguyen, Baochi; Upadhyaya, Arpita; van Oudenaarden, Alexander; Brenner, Michael

2002-11-01

It is well known that the Young's law and surface tension govern the shape of liquid droplets on solid surfaces. Here we address through experiments and theory the shape of growing aggregates of yeast on agar substrates, and assess whether these ideas still hold. Experiments are carried out on Baker's yeast, with different levels of expressions of an adhesive protein governing cell-cell and cell-substrate adhesion. Changing either the agar concentration or the expression of this protein modifies the local contact angle of a yeast droplet. When the colony is small, the shape is a spherical cap with the contact angle obeying Young's law. However, above a critical volume this structure is unstable, and the droplet becomes nonspherical. We present a theoretical model where this instability is caused by bulk elastic effects. The model predicts that the transition depends on both volume and contact angle, in a manner quantitatively consistent with our experiments.