Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

2017-11-01

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (Cd) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of Cd with positive and negative surface potentials.

Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study.

PubMed

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K

2017-11-21

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (C d ) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of C d with positive and negative surface potentials.

Density functional theory calculations of III-N based semiconductors with mBJLDA

NASA Astrophysics Data System (ADS)

Gürel, Hikmet Hakan; Akıncı, Özden; Ünlü, Hilmi

2017-02-01

In this work, we present first principles calculations based on a full potential linear augmented plane-wave method (FP-LAPW) to calculate structural and electronic properties of III-V based nitrides such as GaN, AlN, InN in a zinc-blende cubic structure. First principles calculation using the local density approximation (LDA) and generalized gradient approximation (GGA) underestimate the band gap. We proposed a new potential called modified Becke-Johnson local density approximation (MBJLDA) that combines modified Becke-Johnson exchange potential and the LDA correlation potential to get better band gap results compared to experiment. We compared various exchange-correlation potentials (LSDA, GGA, HSE, and MBJLDA) to determine band gaps and structural properties of semiconductors. We show that using MBJLDA density potential gives a better agreement with experimental data for band gaps III-V nitrides based semiconductors.

A Sand Fly Salivary Protein Vaccine Shows Efficacy Against Vector-Transmitted Cutaneous Leishmaniasis in Nonhuman Primates

DTIC Science & Technology

2015-06-03

demonstrating its immunogenicity in humans. PdSP15 sequence and structure show no homol- ogy to mammalian proteins, further demonstrating its potential...sequence or structure homology to known human proteins The protective salivary antigen PdSP15 shares sequence homology only to the small odorant binding...salivary proteins PpSP15 and PsSP15, respectively (Fig. 4B). To exclude any structural similarities to human pro teins, the crystal structure of PdPS15

An interatomic pair potential for cadmium selenide

NASA Astrophysics Data System (ADS)

Rabani, Eran

2002-01-01

We have developed a set of interatomic pair potentials for cadmium selenide based on a form similar to the Born-Mayer model. We show that this simple form of the pair potential, which has been used to describe the properties of alkali halides in the sixfold-coordinate structure, provides a realistic description of the properties of cadmium selenide in all three crystal structures: wurtzite, zinc blende, and rocksalt. Using the new pair potential we have studied the pressure-induced phase transition from the fourfold-coordinate wurtzite structure to the sixfold-coordinate rocksalt structure. The pressure transformation and the equation of state are in good agreement with experimental observations. Using the dispersion term in our pair potential we have also calculated the Hamaker constant for cadmium selenide within the framework of the original microscopic approach due to Hamaker. The results indicate that for ionic materials many-body terms that are included in the Lifshitz theory are well captured by the simple pair potential.

Vortices in a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential

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

Zhang, Xiao-Fei, E-mail: xfzhang@ntsc.ac.cn; Du, Zhi-Jing; Tan, Ren-Bing

We consider a pair of coupled nonlinear Schrödinger equations modeling a rotating two-component Bose–Einstein condensate with tunable interactions and harmonic potential, with emphasis on the structure of vortex states by varying the strength of inter-component interaction, rotational frequency, and the aspect ratio of the harmonic potential. Our results show that the inter-component interaction greatly enhances the effect of rotation. For the case of isotropic harmonic potential and small inter-component interaction, the initial vortex structure remains unchanged. As the ratio of inter- to intra-component interactions increases, each component undergoes a transition from a vortex lattice (vortex line) in an isotropic (anisotropic)more » harmonic potential to an alternatively arranged stripe pattern, and eventually to the interwoven “serpentine” vortex sheets. Moreover, in the case of anisotropic harmonic potential the system can develop to a rotating droplet structure. -- Highlights: •Different vortex structures are obtained within the full parameter space. •Effects of system parameters on the ground state structure are discussed. •Phase transition between different vortex structures is also examined. •Present one possible way to obtain the rotating droplet structure. •Provide many possibilities to manipulate vortex in two-component BEC.« less

Foraging on the potential energy surface: a swarm intelligence-based optimizer for molecular geometry.

PubMed

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D; Sebastiani, Daniel

2012-11-21

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry

NASA Astrophysics Data System (ADS)

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D.; Sebastiani, Daniel

2012-11-01

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Head-on collision of multistate ultralight BEC dark matter configurations

NASA Astrophysics Data System (ADS)

Guzmán, F. S.; Avilez, Ana A.

2018-06-01

Density profiles of ultralight Bose-condensate dark matter inferred from numerical simulations of structure formation, ruled by the Gross-Pitaevskii-Poisson (GPP) system of equations, have a core-tail structure. Multistate equilibrium configurations of the GPP system, on the other hand, have a similar core-tail density profile. We now submit these multistate configurations to highly dynamical scenarios and show their potential as providers of appropriate density profiles of structures. We present the simulation of head-on collisions between two equilibrium configurations of the GPP system of equations, including the collision of ground state with multistate configurations. We study the regimes of solitonic and merger behavior and show generic properties of the dynamics of the system, including the relaxation process and attractor density profiles. We show that the merger of multistate configurations has the potential to produce core-tail density profiles, with the core dominated by the ground state and the halo dominated by an additional state.

Numerical impact simulation of gradually increased kinetic energy transfer has the potential to break up folded protein structures resulting in cytotoxic brain tissue edema.

PubMed

von Holst, Hans; Li, Xiaogai

2013-07-01

Although the consequences of traumatic brain injury (TBI) and its treatment have been improved, there is still a substantial lack of understanding the mechanisms. Numerical simulation of the impact can throw further lights on site and mechanism of action. A finite element model of the human head and brain tissue was used to simulate TBI. The consequences of gradually increased kinetic energy transfer was analyzed by evaluating the impact intracranial pressure (ICP), strain level, and their potential influences on binding forces in folded protein structures. The gradually increased kinetic energy was found to have the potential to break apart bonds of Van der Waals in all impacts and hydrogen bonds at simulated impacts from 6 m/s and higher, thereby superseding the energy in folded protein structures. Further, impacts below 6 m/s showed none or very slight increase in impact ICP and strain levels, whereas impacts of 6 m/s or higher showed a gradual increase of the impact ICP and strain levels reaching over 1000 KPa and over 30%, respectively. The present simulation study shows that the free kinetic energy transfer, impact ICP, and strain levels all have the potential to initiate cytotoxic brain tissue edema by unfolding protein structures. The definition of mild, moderate, and severe TBI should thus be looked upon as the same condition and separated only by a gradual severity of impact.

Temperature dependent structural and vibrational properties of liquid indium

NASA Astrophysics Data System (ADS)

Patel, A. B.; Bhatt, N. K.

2018-05-01

The influence of the temperature effect on both the structure factor and the phonon dispersion relation of liquid indium have been investigated by means of pseudopotential theory. The Percus-Yevick Hard Sphere reference system is applied to describe the structural calculation. The effective electron-ion interaction is explained by using modified empty core potential due to Hasegawa et al. along with a local field correction function due to Ichimaru-Utsumi (IU). The temperature dependence of pair potential needed at higher temperatures was achieved by multiplying the damping factor exp(- π/kBT2k F r ) in the pair potential. Very close agreement of static structure factor, particularly, at elevated temperatures confirms the validity of the local potential. A positive dispersion is found in low-q region and the correct trend of phonon dispersion branches like the experimental; shows all broad features of collective excitations in liquid metals.

Robust optical properties of sandwiched lateral composition modulation GaInP structure grown by molecular beam epitaxy

DOE PAGES

Park, Kwangwook; Kang, Seokjin; Ravindran, Sooraj; ...

2016-12-26

Double-hetero structure lateral composition modulated (LCM) GaInP and sandwiched LCM GaInP having the same active layer thickness were grown and their optical properties were compared. Sandwiched LCM GaInP showed robust optical properties due to periodic potential nature of the LCM structure, and the periodicity was undistorted even for thickness far beyond the critical layer thickness. A thick LCM GaInP structure with undistorted potential that could preserve the properties of native LCM structure was possible by stacking thin LCM GaInP structures interspaced with strain compensating GaInP layers. Furthermore, the sandwiched structure could be beneficial in realizing the LCM structure embedded highmore » efficiency solar cells.« less

Efficient Geometry Minimization and Transition Structure Optimization Using Interpolated Potential Energy Surfaces and Iteratively Updated Hessians.

PubMed

Zheng, Jingjing; Frisch, Michael J

2017-12-12

An efficient geometry optimization algorithm based on interpolated potential energy surfaces with iteratively updated Hessians is presented in this work. At each step of geometry optimization (including both minimization and transition structure search), an interpolated potential energy surface is properly constructed by using the previously calculated information (energies, gradients, and Hessians/updated Hessians), and Hessians of the two latest geometries are updated in an iterative manner. The optimized minimum or transition structure on the interpolated surface is used for the starting geometry of the next geometry optimization step. The cost of searching the minimum or transition structure on the interpolated surface and iteratively updating Hessians is usually negligible compared with most electronic structure single gradient calculations. These interpolated potential energy surfaces are often better representations of the true potential energy surface in a broader range than a local quadratic approximation that is usually used in most geometry optimization algorithms. Tests on a series of large and floppy molecules and transition structures both in gas phase and in solutions show that the new algorithm can significantly improve the optimization efficiency by using the iteratively updated Hessians and optimizations on interpolated surfaces.

Dibenzo[a,f]perylene bisimide: effects of introducing two fused rings.

PubMed

Chaolumen; Enno, Hiroki; Murata, Michihisa; Wakamiya, Atsushi; Murata, Yasujiro

2014-11-01

Perylene bisimides (PBIs) are fascinating dyes with various potential applications. To study the effects of introducing a dibenzo-fused structure to the perylene moiety, π-extended PBI derivatives with a dibenzo-fused structure at both of the a and f bonds were synthesized. The twisted structure was characterized by X-ray crystal structure analysis. In the cyclic voltammograms, the dibenzo[a,f]-fused PBI showed a reversible oxidation wave at much less positive potential, relative to a dibenzo[a,o]-fused PBI derivative. These data indicated that two ring fusions at both sides of a naphthalene moiety, which construct a tetracene core, effectively raise the HOMO level compared to fusion of one ring at each naphthalene moiety (two anthracene cores). The dibenzo[a,f]-fused PBI derivative showed an absorption band at 735 nm with a shoulder band reaching 900 nm. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relationship between Chemical Structure and Antimicrobial Activities of Isothiocyanates from Cruciferous Vegetables against Oral Pathogens.

PubMed

Ko, Mi-Ok; Kim, Mi-Bo; Lim, Sang-Bin

2016-12-28

We evaluated the potentials of 10 isothiocyanates (ITCs) from cruciferous vegetables and radish root hydrolysate for inhibiting the growth of oral pathogens, with an emphasis on assessing any structure-function relationship. Structural differences in ITCs impacted their antimicrobial activities against oral pathogens differently. The indolyl ITC (indol-3-carbinol) was the most potent inhibitor of the growth of oral pathogens, followed by aromatic ITCs (benzyl ITC (BITC) and phenylethyl ITC (PEITC)) and aliphatic ITCs (erucin, iberin, and sulforaphene). Sulforaphene, which is similar in structure, but has one double bond, showed higher antimicrobial activity than sulforaphane. Erucin, which has a thiol group, showed higher antimicrobial activity than sulforaphane, which has a sulfinyl group. BITC and iberin with a short chain exhibited higher antimicrobial potential than PEITC and sulforaphane with a longer chain, respectively. ITCs have strong antimicrobial activities and may be useful in the prevention and management of dental caries.

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

Osipiuk, J.; Gornicki, P.; Maj, L.

The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 Angstroms. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 Angstroms from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer {alpha}/{beta} sandwich with the overall shape of a cylinder and shows no structural homology to proteins of knownmore » structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the {alpha}-{beta} plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.« less

The Potential for Imaging in Situ Damage in Inflatable Space Structures

NASA Technical Reports Server (NTRS)

Madaras, Eric I.; Anastasi, Robert F.; Seebo, Jeffrey P.; Studor, George; McMakin, Douglas L.; Nellums, Robert; Winfree, William P.

2007-01-01

NASA is investigating the use of inflatable habitat structures for orbital transfer and planetary applications. Since space structures are vulnerable to damage from micrometeoroid and orbital debris, it is important to investigate means of detecting such damage. This study is an investigation into methods for performing non-destructive evaluation (NDE) on inflatable habitat modules. Results of this work showed that various electromagnetic imaging modalities from microwaves to terahertz imaging have the greatest potential for a viable, portable, NDE tool which could possibly be deployed aboard an inflatable habitat module.

A Gaussian Approximation Potential for Silicon

NASA Astrophysics Data System (ADS)

Bernstein, Noam; Bartók, Albert; Kermode, James; Csányi, Gábor

We present an interatomic potential for silicon using the Gaussian Approximation Potential (GAP) approach, which uses the Gaussian process regression method to approximate the reference potential energy surface as a sum of atomic energies. Each atomic energy is approximated as a function of the local environment around the atom, which is described with the smooth overlap of atomic environments (SOAP) descriptor. The potential is fit to a database of energies, forces, and stresses calculated using density functional theory (DFT) on a wide range of configurations from zero and finite temperature simulations. These include crystalline phases, liquid, amorphous, and low coordination structures, and diamond-structure point defects, dislocations, surfaces, and cracks. We compare the results of the potential to DFT calculations, as well as to previously published models including Stillinger-Weber, Tersoff, modified embedded atom method (MEAM), and ReaxFF. We show that it is very accurate as compared to the DFT reference results for a wide range of properties, including low energy bulk phases, liquid structure, as well as point, line, and plane defects in the diamond structure.

Design and synthesis of some new 2,3'-bipyridine-5-carbonitriles as potential anti-inflammatory/antimicrobial agents.

PubMed

Elzahhar, Perihan A; Elkazaz, Salwa; Soliman, Raafat; El-Tombary, Alaa A; Shaltout, Hossam A; El-Ashmawy, Ibrahim M; Abdel Wahab, Abeer E; El-Hawash, Soad A

2017-08-01

Inflammation may cause accumulation of fluid in the injured area, which may promote bacterial growth. Other reports disclosed that non-steroidal anti-inflammatory drugs may enhance progression of bacterial infection. This work describes synthesis of new series of 2,3'-bipyridine-5-carbonitriles as structural analogs of etoricoxib, linked at position-6 to variously substituted thio or oxo moieties. Biological screening results revealed that compounds 2b, 4b, 7e and 8 showed significant acute and chronic AI activities and broad spectrum of antimicrobial activity. In addition, similarity ensemble approach was applied to predict potential biological targets of the tested compounds. Then, pharmacophore modeling study was employed to determine the most important structural parameters controlling bioactivity. Moreover, title compounds showed physicochemical properties within those considered adequate for drug candidates. This study explored the potential of such series of compounds as structural leads for further modification to develop a new class of dual AI-antimicrobial agents.

Study of low dimensional SiGe island on Si for potential visible Metal-Semiconductor-Metal photodetector

NASA Astrophysics Data System (ADS)

Rahim, Alhan Farhanah Abd; Zainal Badri, Nur'Amirah; Radzali, Rosfariza; Mahmood, Ainorkhilah

2017-11-01

In this paper, an investigation of design and simulation of silicon germanium (SiGe) islands on silicon (Si) was presented for potential visible metal semiconductor metal (MSM) photodetector. The characterization of the performances in term of the structural, optical and electrical properties of the structures was analyzed from the simulation results. The project involves simulation using SILVACO Technology Computer Aided Design (TCAD) tools. The different structures of the silicon germanium (SiGe) island on silicon substrate were created, which were large SiGe, small SiGe, combination SiGe and bulk Ge. All the structures were tested for potential Metal Semiconductor Metal (MSM) photodetector. The extracted data such as current versus voltage characteristic, current gain and spectral response were obtained using ATLAS SILVACO tools. The performance of SiGe island structures and bulk Ge on Si substrate as (MSM) photodetector was evaluated by photo and dark current-voltage (I-V) characteristics. It was found that SiGe islands exhibited higher energy band gap compared to bulk Ge. The SiGe islands current-voltage characteristics showed improved current gain compared to bulk Ge. Specifically the enhancement of the islands gain was contributed by the enhanced photo currents and lower dark currents. The spectral responses of the SiGe islands showed peak response at 590 nm (yellow) which is at the visible wavelength. This shows the feasibility of the SiGe islands to be utilized for visible photodetections.

High-temperature annealing of graphite: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Petersen, Andrew; Gillette, Victor

2018-05-01

A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

Investigation of structural and mechanical properties of rare-earth bismuthide (RBi, R=Ce & Pr) with the NaCl structure at high pressure

NASA Astrophysics Data System (ADS)

Yaduvanshi, Namrata; Kapoor, Shilpa; Singh, Sadhna

2018-05-01

We have investigated the structural and mechanical properties of Cerium and Praseodymium Bismuthides under pressure by means of a three body interaction potential model which includes long range columbic interaction, three body interactions and short range overlap repulsive interaction operative up to second nearest neighbor. These compounds shows transition from NaCl structure to body-centered tetragonal (BCT) structure (distorted CsCl-type P4/mmm). The elastic constants and their properties are also reported. Our calculated results of phase transitions and volume collapses of these compounds show a good agreement with available theoretical and experimental results.

The validity of the potential model in predicting the structural, dynamical, thermodynamic properties of the unary and binary mixture of water-alcohol: Methanol-water case

NASA Astrophysics Data System (ADS)

Obeidat, Abdalla; Abu-Ghazleh, Hind

2018-06-01

Two intermolecular potential models of methanol (TraPPE-UA and OPLS-AA) have been used in order to examine their validity in reproducing the selected structural, dynamical, and thermodynamic properties in the unary and binary systems. These two models are combined with two water models (SPC/E and TIP4P). The temperature dependence of density, surface tension, diffusion and structural properties for the unary system has been computed over specific range of temperatures (200-300K). The very good performance of the TraPPE-UA potential model in predicting surface tension, diffusion, structure, and density of the unary system led us to examine its accuracy and performance in its aqueous solution. In the binary system the same properties were examined, using different mole fractions of methanol. The TraPPE-UA model combined with TIP4P-water shows a very good agreement with the experimental results for density and surface tension properties; whereas the OPLS-AA combined with SPCE-water shows a very agreement with experimental results regarding the diffusion coefficients. Two different approaches have been used in calculating the diffusion coefficient in the mixture, namely the Einstein equation (EE) and Green-Kubo (GK) method. Our results show the advantageous of applying GK over EE in reproducing the experimental results and in saving computer time.

Examining porous bio-active glass as a potential osteo-odonto-keratoprosthetic skirt material.

PubMed

Huhtinen, Reeta; Sandeman, Susan; Rose, Susanna; Fok, Elsie; Howell, Carol; Fröberg, Linda; Moritz, Niko; Hupa, Leena; Lloyd, Andrew

2013-05-01

Bio-active glass has been developed for use as a bone substitute with strong osteo-inductive capacity and the ability to form strong bonds with soft and hard tissue. The ability of this material to enhance tissue in-growth suggests its potential use as a substitute for the dental laminate of an osteo-odonto-keratoprosthesis. A preliminary in vitro investigation of porous bio-active glass as an OOKP skirt material was carried out. Porous glass structures were manufactured from bio-active glasses 1-98 and 28-04 containing varying oxide formulation (1-98, 28-04) and particle size range (250-315 μm for 1-98 and 28-04a, 315-500 μm for 28-04b). Dissolution of the porous glass structure and its effect on pH was measured. Structural 2D and 3D analysis of porous structures were performed. Cell culture experiments were carried out to study keratocyte adhesion and the inflammatory response induced by the porous glass materials. The dissolution results suggested that the porous structure made out of 1-98 dissolves faster than the structures made from glass 28-04. pH experiments showed that the dissolution of the porous glass increased the pH of the surrounding solution. The cell culture results showed that keratocytes adhered onto the surface of each of the porous glass structures, but cell adhesion and spreading was greatest for the 98a bio-glass. Cytokine production by all porous glass samples was similar to that of the negative control indicating that the glasses do not induce a cytokine driven inflammatory response. Cell culture results support the potential use of synthetic porous bio-glass as an OOKP skirt material in terms of limited inflammatory potential and capacity to induce and support tissue ingrowth.

Methanol oxidation reaction on core-shell structured Ruthenium-Palladium nanoparticles: Relationship between structure and electrochemical behavior

NASA Astrophysics Data System (ADS)

Kübler, Markus; Jurzinsky, Tilman; Ziegenbalg, Dirk; Cremers, Carsten

2018-01-01

In this work the relationship between structural composition and electrochemical characteristics of Palladium(Pd)-Ruthenium(Ru) nanoparticles during alkaline methanol oxidation reaction is investigated. The comparative study of a standard alloyed and a precisely Ru-core-Pd-shell structured catalyst allows for a distinct investigation of the electronic effect and the bifunctional mechanism. Core-shell catalysts benefit from a strong electronic effect and an efficient Pd utilization. It is found that core-shell nanoparticles are highly active towards methanol oxidation reaction for potentials ≥0.6 V, whereas alloyed catalysts show higher current outputs in the lower potential range. However, differential electrochemical mass spectrometry (DEMS) experiments reveal that the methanol oxidation reaction on core-shell structured catalysts proceeds via the incomplete oxidation pathway yielding formaldehyde, formic acid or methyl formate. Contrary, the alloyed catalyst benefits from the Ru atoms at its surface. Those are found to be responsible for high methanol oxidation activity at lower potentials as well as for complete oxidation of CH3OH to CO2 via the bifunctional mechanism. Based on these findings a new Ru-core-Pd-shell-Ru-terrace catalyst was synthesized, which combines the advantages of the core-shell structure and the alloy. This novel catalyst shows high methanol electrooxidation activity as well as excellent selectivity for the complete oxidation pathway.

Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing.

PubMed

Campa, Maria Fernanda; Techtmann, Stephen M; Gibson, Caleb M; Zhu, Xiaojuan; Patterson, Megan; Garcia de Matos Amaral, Amanda; Ulrich, Nikea; Campagna, Shawn R; Grant, Christopher J; Lamendella, Regina; Hazen, Terry C

2018-05-15

The environmental impacts of hydraulic fracturing, particularly those of surface spills in aquatic ecosystems, are not fully understood. The goals of this study were to (1) understand the effect of previous exposure to hydraulic fracturing fluids on aquatic microbial community structure and (2) examine the impacts exposure has on biodegradation potential of the biocide glutaraldehyde. Microcosms were constructed from hydraulic fracturing-impacted and nonhydraulic fracturing-impacted streamwater within the Marcellus shale region in Pennsylvania. Microcosms were amended with glutaraldehyde and incubated aerobically for 56 days. Microbial community adaptation to glutaraldehyde was monitored using 16S rRNA gene amplicon sequencing and quantification by qPCR. Abiotic and biotic glutaraldehyde degradation was measured using ultra-performance liquid chromatography--high resolution mass spectrometry and total organic carbon. It was found that nonhydraulic fracturing-impacted microcosms biodegraded glutaraldehyde faster than the hydraulic fracturing-impacted microcosms, showing a decrease in degradation potential after exposure to hydraulic fracturing activity. Hydraulic fracturing-impacted microcosms showed higher richness after glutaraldehyde exposure compared to unimpacted streams, indicating an increased tolerance to glutaraldehyde in hydraulic fracturing impacted streams. Beta diversity and differential abundance analysis of sequence count data showed different bacterial enrichment for hydraulic fracturing-impacted and nonhydraulic fracturing-impacted microcosms after glutaraldehyde addition. These findings demonstrated a lasting effect on microbial community structure and glutaraldehyde degradation potential in streams impacted by hydraulic fracturing operations.

Evaluation of thermal stability in spectrally selective few-layer metallo-dielectric structures for solar thermophotovoltaics

NASA Astrophysics Data System (ADS)

Shimizu, Makoto; Kohiyama, Asaka; Yugami, Hiroo

2018-06-01

The thermal stability of spectrally selective few-layer metallo-dielectric structures is evaluated to analyze their potential as absorber and emitter materials in solar thermophotovoltaic (STPV) systems. High-efficiency (e.g., STPV) systems require materials with spectrally selective properties, especially at high temperatures (>1273 K). Aiming to develop such materials for high-temperature applications, we propose a few-layer structure composed of a refractory metal (i.e., Mo) nanometric film sandwiched between the layers of a dielectric material (i.e., hafnium oxide, HfO2) deposited on a Mo bulk substrate. In vacuum conditions (<5 × 10-2 Pa), the few-layer structure shows thermal stability at 1423 K for at least 1 h. At 1473 K, the spectral selectivity was degraded. This could have been caused by the oxidation of the Mo thin film by the residual oxygen through the grain boundaries of the upper HfO2 layer. This experiment showed the potential stability of few-layer structures for applications working at temperatures greater than 1273 K as well as the degradation mechanism of the few-layer structure. This characteristic is expected to help improve the thermal stability in few-layer structures further.

Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

NASA Astrophysics Data System (ADS)

Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

2018-05-01

Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

PubMed

Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

2016-05-01

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

Waterlike anomalies in a two-dimensional core-softened potential

NASA Astrophysics Data System (ADS)

Bordin, José Rafael; Barbosa, Marcia C.

2018-02-01

We investigate the structural, thermodynamic, and dynamic behavior of a two-dimensional (2D) core-corona system using Langevin dynamics simulations. The particles are modeled by employing a core-softened potential which exhibits waterlike anomalies in three dimensions. In previous studies in a quasi-2D system a new region in the pressure versus temperature phase diagram of structural anomalies was observed. Here we show that for the two-dimensional case two regions in the pressure versus temperature phase diagram with structural, density, and diffusion anomalies are observed. Our findings indicate that, while the anomalous region at lower densities is due the competition between the two length scales in the potential at higher densities, the anomalous region is related to the reentrance of the melting line.

Functionalized coronenes: synthesis, solid structure, and properties.

PubMed

Wu, Di; Zhang, Hua; Liang, Jinhua; Ge, Haojie; Chi, Chunyan; Wu, Jishan; Liu, Sheng Hua; Yin, Jun

2012-12-21

The construction of coronenes using simple building blocks is a challenging task. In this work, triphenylene was used as a building block to construct functionalized coronenes, and their solid structures and optoelectronic properties were investigated. The single crystal structures showed that coronenes have different packing motifs. Their good solubility and photostability make them potential solution-processable candidates for organic devices.

Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel

PubMed Central

Sauguet, Ludovic; Howard, Rebecca J.; Malherbe, Laurie; Lee, Ui S.; Corringer, Pierre-Jean; Harris, R. Adron; Delarue, Marc

2014-01-01

Ethanol alters nerve signalling by interacting with proteins in the central nervous system, particularly pentameric ligand-gated ion channels. A recent series of mutagenesis experiments on Gloeobacter violaceus ligand-gated ion channel, a prokaryotic member of this family, identified a single-site variant that is potentiated by pharmacologically relevant concentrations of ethanol. Here we determine crystal structures of the ethanol-sensitized variant in the absence and presence of ethanol and related modulators, which bind in a transmembrane cavity between channel subunits and may stabilize the open form of the channel. Structural and mutagenesis studies defined overlapping mechanisms of potentiation by alcohols and anaesthetics via the inter-subunit cavity. Furthermore, homology modelling show this cavity to be conserved in human ethanol-sensitive glycine and GABA(A) receptors, and to involve residues previously shown to influence alcohol and anaesthetic action on these proteins. These results suggest a common structural basis for ethanol potentiation of an important class of targets for neurological actions of ethanol. PMID:23591864

Observation of ion acceleration and heating during collisionless magnetic reconnection in a laboratory plasma.

PubMed

Yoo, Jongsoo; Yamada, Masaaki; Ji, Hantao; Myers, Clayton E

2013-05-24

The ion dynamics in a collisionless magnetic reconnection layer are studied in a laboratory plasma. The measured in-plane plasma potential profile, which is established by electrons accelerated around the electron diffusion region, shows a saddle-shaped structure that is wider and deeper towards the outflow direction. This potential structure ballistically accelerates ions near the separatrices toward the outflow direction. Ions are heated as they travel into the high-pressure downstream region.

Single-layer group IV-V and group V-IV-III-VI semiconductors: Structural stability, electronic structures, optical properties, and photocatalysis

NASA Astrophysics Data System (ADS)

Lin, Jia-He; Zhang, Hong; Cheng, Xin-Lu; Miyamoto, Yoshiyuki

2017-07-01

Recently, single-layer group III monochalcogenides have attracted both theoretical and experimental interest at their potential applications in photonic devices, electronic devices, and solar energy conversion. Excited by this, we theoretically design two kinds of highly stable single-layer group IV-V (IV =Si ,Ge , and Sn; V =N and P) and group V-IV-III-VI (IV =Si ,Ge , and Sn; V =N and P; III =Al ,Ga , and In; VI =O and S) compounds with the same structures with single-layer group III monochalcogenides via first-principles simulations. By using accurate hybrid functional and quasiparticle methods, we show the single-layer group IV-V and group V-IV-III-VI are indirect bandgap semiconductors with their bandgaps and band edge positions conforming to the criteria of photocatalysts for water splitting. By applying a biaxial strain on single-layer group IV-V, single-layer group IV nitrides show a potential on mechanical sensors due to their bandgaps showing an almost linear response for strain. Furthermore, our calculations show that both single-layer group IV-V and group V-IV-III-VI have absorption from the visible light region to far-ultraviolet region, especially for single-layer SiN-AlO and SnN-InO, which have strong absorption in the visible light region, resulting in excellent potential for solar energy conversion and visible light photocatalytic water splitting. Our research provides valuable insight for finding more potential functional two-dimensional semiconductors applied in optoelectronics, solar energy conversion, and photocatalytic water splitting.

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

Morris, J.R.; Lu, Z.; Ring, D.M.

We have examined a variety of structures for the {l_brace}510{r_brace} symmetric tilt boundary in Si and Ge, using tight-binding and first-principles calculations. These calculations show that the observed structure in Si is the lowest-energy structure, despite the fact that it is more complicated than what is necessary to preserve fourfold coordination. Contrary to calculations using a Tersoff potential, first-principles calculations show that the energy depends strongly upon the structure. A recently developed tight-binding model for Si produces results in very good agreement with the first-principles calculations. Electronic density of states calculations based upon this model show no evidence of midgapmore » states and little evidence of electronic states localized to the grain boundary. {copyright} {ital 1998} {ital The American Physical Society}« less

An empirical potential for simulating vacancy clusters in tungsten.

PubMed

Mason, D R; Nguyen-Manh, D; Becquart, C S

2017-12-20

We present an empirical interatomic potential for tungsten, particularly well suited for simulations of vacancy-type defects. We compare energies and structures of vacancy clusters generated with the empirical potential with an extensive new database of values computed using density functional theory, and show that the new potential predicts low-energy defect structures and formation energies with high accuracy. A significant difference to other popular embedded-atom empirical potentials for tungsten is the correct prediction of surface energies. Interstitial properties and short-range pairwise behaviour remain similar to the Ackford-Thetford potential on which it is based, making this potential well-suited to simulations of microstructural evolution following irradiation damage cascades. Using atomistic kinetic Monte Carlo simulations, we predict vacancy cluster dissociation in the range 1100-1300 K, the temperature range generally associated with stage IV recovery.

Tunable multi-band absorption in metasurface of graphene ribbons based on composite structure

NASA Astrophysics Data System (ADS)

Ning, Renxia; Jiao, Zheng; Bao, Jie

2017-05-01

A tunable multiband absorption based on a graphene metasurface of composite structure at mid-infrared frequency was investigated by the finite difference time domain method. The composite structure were composed of graphene ribbons and a gold-MgF2 layer which was sandwiched in between two dielectric slabs. The permittivity of graphene is discussed with different chemical potential to obtain tunable absorption. And the absorption of the composite structure can be tuned by the chemical potential of graphene at certain frequencies. The impedance matching was used to study the perfect absorption of the structure in our paper. The results show that multi-band absorption can be obtained and some absorption peaks of the composite structure can be tuned through the changing not only of the width of graphene ribbons and gaps, but also the dielectric and the chemical potential of graphene. However, another peak was hardly changed by parameters due to a different resonant mechanism in proposed structure. This flexibily tunable multiband absorption may be applied to optical communications such as optical absorbers, mid infrared stealth devices and filters.

Functional and Structural Impact of Target Uridine Substitutions on the H/ACA Ribonucleoprotein Particle Pseudouridine Synthase

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

Zhou, Jing; Liang, Bo; Li, Hong

2010-09-17

Box H/ACA ribonucleoprotein protein particles catalyze the majority of pseudouridylation in functional RNA. Different from stand alone pseudouridine synthases, the RNP pseudouridine synthase comprises multiple protein subunits and an RNA subunit. Previous studies showed that each subunit, regardless its location, is sensitive to the step of subunit placement at the catalytic center and potentially to the reaction status of the substrate. Here we describe the impact of chemical substitutions of target uridine on enzyme activity and structure. We found that 3-methyluridine in place of uridine inhibited its isomerization while 2{prime}-deoxyuridine or 4-thiouridine did not. Significantly, crystal structures of an archaealmore » box H/ACA RNP bound with the nonreactive and the two postreactive substrate analogues showed only subtle structural changes throughout the assembly except for a conserved tyrosine and a substrate anchoring loop of Cbf5. Our results suggest a potential role of these elements and the subunit that contacts them in substrate binding and product release.« less

Effect of pH shifts on IgE-binding capacity and conformational structure of tropomyosin from short-neck clam (Ruditapes philippinarum).

PubMed

Lin, Haixin; Li, Zhenxing; Lin, Hong; Song, Yongna; Lv, Liangtao; Hao, Zina

2015-12-01

The aim of the present study was to assess pH-induced changes in conformational structures and potential allergenicity of tropomyosin from short-neck clams. As defined with circular dichroism (CD), an unfolded structure was found at pH values ranging from 2.0 to 5.0, followed by the loss of secondary structure at pH of 1.0. Correspondingly, surface hydrophobicity was reduced by 97.7% when pH was reduced from 7.0 to 1.0. Further indirect ELISA and dot-blot results of pH shifted tropomyosin showed that potential allergenicity correlated well with structural changes, as well as with SGF digestibility. Allergenicity decreased significantly with unfolding of the protein and was stable when surface hydrophobicity recovered back to neutral conditions. These results showed that conformational changes in tropomyosin induced by pH shifting significantly influenced the allergenicity of tropomyosin, and that the resulting changes occurred predominately in the acidic pH range. Copyright © 2015 Elsevier Ltd. All rights reserved.

Strongly Modulated Friction of a Film-Terminated Ridge-Channel Structure.

PubMed

He, Zhenping; Hui, Chung-Yuen; Levrard, Benjamin; Bai, Ying; Jagota, Anand

2016-05-26

Natural contacting surfaces have remarkable surface mechanical properties, which has led to the development of bioinspired surface structures using rubbery materials with strongly enhanced adhesion and static friction. However, sliding friction of structured rubbery surfaces is almost always significantly lower than that of a flat control, often due to significant loss of contact. Here we show that a film-terminated ridge-channel structure can strongly enhance sliding friction. We show that with properly chosen materials and geometrical parameters the near surface structure undergoes mechanical instabilities along with complex folding and sliding of internal interfaces, which is responsible for the enhancement of sliding friction. Because this structure shows no enhancement of adhesion under normal indentation by a sphere, it breaks the connection between energy loss during normal and shear loading. This makes it potentially interesting in many applications, for instance in tires, where one wishes to minimize rolling resistance (normal loading) while maximizing sliding friction (shear loading).

Magnetic field effects on charge structure factors of gapped graphene structure

NASA Astrophysics Data System (ADS)

Rezania, Hamed; Tawoose, Nasrin

2018-02-01

We present the behaviors of dynamical and static charge susceptibilities of undoped gapped graphene using the Green's function approach in the context of tight binding model Hamiltonian. Specially, the effects of magnetic field on the plasmon modes of gapped graphene structure are investigated via calculating correlation function of charge density operators. Our results show the increase of magnetic field leads to disappear high frequency plasmon mode for gapped case. We also show that low frequency plasmon mode has not affected by increase of magnetic field and chemical potential. Finally the temperature dependence of static charge structure factor of gapp graphene structure is studied. The effects of both magnetic field and gap parameter on the static structure factor are discusses in details.

Chiral lactic hydrazone derivatives as potential bioactive antibacterial agents: Synthesis, spectroscopic, structural and molecular docking studies

NASA Astrophysics Data System (ADS)

Noshiranzadeh, Nader; Heidari, Azam; Haghi, Fakhri; Bikas, Rahman; Lis, Tadeusz

2017-01-01

A series of novel chiral lactic-hydrazone derivatives were synthesized by condensation of (S)-lactic acid hydrazide with salicylaldehyde derivatives and characterized by elemental analysis and spectroscopic studies (FT-IR, 1H NMR and 13C NMR spectroscopy). The structure of one compound was determined by single crystal X-ray analysis. Antibacterial activity of the synthesized compounds was studied against Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli and Pseudomonas aeruginosa as bacterial cultures by broth microdilution method. All of the synthesized compounds showed good antibacterial activity with MIC range of 64-512 μg/mL. Compounds (S,E)-2-hydroxy-N-(2-hydroxy-5-nitrobenzylidene)propanehydrazide (5) and (S,E)-2-hydroxy-N-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propanehydrazide (7) were the most effective antibacterial derivatives against S. aureus and E. coli respectively with a MIC value of 64 μg/mL. Bacterial biofilm formation assay showed that these compounds significantly inhibited biofilm formation of P. aeruginosa. Also, in silico molecular docking studies were performed to show lipoteichoic acid synthase (LtaS) inhibitory effect of lactic hydrazone derivatives. The association between electronic and structural effects of some substituents on the benzylidene moiety and the biological activity of these chiral compounds were studied. Structural studies show that compound with higher hydrogen bonding interactions show higher antibacterial activity. The results show chiral hydrazone derivatives based on lactic acid hydrazide could be used as potential lead compounds for developing novel antibacterial agents.

Patching the Exchange-Correlation Potential in Density Functional Theory.

PubMed

Huang, Chen

2016-05-10

A method for directly patching exchange-correlation (XC) potentials in materials is derived. The electron density of a system is partitioned into subsystem densities by dividing its Kohn-Sham (KS) potential among the subsystems. Inside each subsystem, its projected KS potential is required to become the total system's KS potential. This requirement, together with the nearsightedness principle of electronic matters, ensures that the electronic structures inside subsystems can be good approximations to the total system's electronic structure. The nearsightedness principle also ensures that subsystem densities could be well localized in their regions, making it possible to use high-level methods to invert the XC potentials for subsystem densities. Two XC patching methods are developed. In the local XC patching method, the total system's XC potential is improved in the cluster region. We show that the coupling between a cluster and its environment is important for achieving a fast convergence of the electronic structure in the cluster region. In the global XC patching method, we discuss how to patch the subsystem XC potentials to construct the XC potential in the total system, aiming to scale up high-level quantum mechanics simulations of materials. Proof-of-principle examples are given.

Compositional bowing of band energies and their deformation potentials in strained InGaAs ternary alloys: A first-principles study

NASA Astrophysics Data System (ADS)

Khomyakov, Petr A.; Luisier, Mathieu; Schenk, Andreas

2015-08-01

Using first-principles calculations, we show that the conduction and valence band energies and their deformation potentials exhibit a non-negligible compositional bowing in strained ternary semiconductor alloys such as InGaAs. The electronic structure of these compounds has been calculated within the framework of local density approximation and hybrid functional approach for large cubic supercells and special quasi-random structures, which represent two kinds of model structures for random alloys. We find that the predicted bowing effect for the band energy deformation potentials is rather insensitive to the choice of the functional and alloy structural model. The direction of bowing is determined by In cations that give a stronger contribution to the formation of the InxGa1-xAs valence band states with x ≳ 0.5, compared to Ga cations.

Metagenomes reveal microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor.

PubMed

Ma, Jinxing; Wang, Zhiwei; Li, Huan; Park, Hee-Deung; Wu, Zhichao

2016-06-01

Metagenomic sequencing was used to investigate the microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor (MBR). The results showed that the microbial community in the MBR was highly diverse. Notably, function analysis of the dominant genera indicated that common genes from different phylotypes were identified for important functional potentials with the observation of variation of abundances of genes in a certain taxon (e.g., Dechloromonas). Despite maintaining similar metabolic functional potentials with a parallel full-scale conventional activated sludge (CAS) system due to treating the identical wastewater, the MBR had more abundant nitrification-related bacteria and coding genes of ammonia monooxygenase, which could well explain its excellent ammonia removal in the low-temperature period. Furthermore, according to quantification of the genes involved in exopolysaccharide and extracellular polymeric substance (EPS) protein metabolism, the MBR did not show a much different potential in producing EPS compared to the CAS system, and bacteria from the membrane biofilm had lower abundances of genes associated with EPS biosynthesis and transport compared to the activated sludge in the MBR.

X-ray diffraction, crystal structure, and spectral features of the optical susceptibilities of single crystals of the ternary borate oxide lead bismuth tetraoxide, PbBiBO4.

PubMed

Reshak, Ali Hussain; Kityk, I V; Auluck, S; Chen, Xuean

2009-05-14

The all-electron full-potential linearized augmented plane-wave method has been used for an ab initio theoretical study of the band structure, the spectral features of the optical susceptibilities, the density of states, and the electron charge density for PbBiBO4. Our calculations show that the valence-band maximum (VBM) and conduction-band minimum (CBM) are located at the center of the Brillouin zone, resulting in a direct energy gap of about 3.2 eV. We have synthesized the PbBiBO4 crystal by employing a conventional solid-state reaction method. The theoretical calculations in this work are based on the structure built from our measured atomic parameters. We should emphasize that the observed experimental X-ray diffraction (XRD) pattern is in good agreement with the theoretical one, confirming that our structural model is valid. Our calculated bond lengths show excellent agreement with the experimental data. This agreement is attributed to our use of full-potential calculations. The spectral features of the optical susceptibilities show a small positive uniaxial anisotropy.

Effect of Varying Pnictogen Elements (Pn=N, P, As, Sb, Bi) on the Optoelectronic Properties of SrZn2Pn2

NASA Astrophysics Data System (ADS)

Murtaza, G.; Yousaf, N.; Laref, A.; Yaseen, M.

2018-03-01

Pnictogen-based Zintl compounds have fascinating properties. Nowadays these compounds have gained exceptional interest in thermoelectric and optoelectronic fields. Therefore, in this work the structural, electronic and optical properties of SrZn2Pn2 (Pn=N, P, As, Sb, Bi) compounds were studied using state-of-the-art density functional theory. The optimised lattice parameters (ɑ, c, c/ɑ and bond lengths) are consistent with the experimental results. The bulk moduli and c/a showed a decrease when changing the Pnictogen (Pn) anion from N to Bi in SrZn2Pn2 (Pn=N, P, As, Sb, Bi). The modified Becke-Johnson potential is used for band structure calculations. All compounds show semiconducting behaviour except SrZn2Bi2, which is metallic. Pn-p, Zn-d and Sr-d play an important role in defining the electronic structure of the compounds. The optical conductivity and absorption coefficient strength are high in visible and ultraviolet regions. These band structures and optical properties clearly show that SrZn2Pn2 compounds are potential candidates in the fields of optoelectronic and photonic devices.

Electrophysiological responses to argument structure violations in healthy adults and individuals with agrammatic aphasia

PubMed Central

Kielar, Aneta; Meltzer-Asscher, Aya; Thompson, Cynthia

2012-01-01

Sentence comprehension requires processing of argument structure information associated with verbs, i.e. the number and type of arguments that they select. Many individuals with agrammatic aphasia show impaired production of verbs with greater argument structure density. The extent to which these participants also show argument structure deficits during comprehension, however, is unclear. Some studies find normal access to verb arguments, whereas others report impaired ability. The present study investigated verb argument structure processing in agrammatic aphasia by examining event-related potentials associated with argument structure violations in healthy young and older adults as well as aphasic individuals. A semantic violation condition was included to investigate possible differences in sensitivity to semantic and argument structure information during sentence processing. Results for the healthy control participants showed a negativity followed by a positive shift (N400-P600) in the argument structure violation condition, as found in previous ERP studies (Friederici & Frisch, 2000; Frisch, Hahne, & Friederici, 2004). In contrast, individuals with agrammatic aphasia showed a P600, but no N400, response to argument structure mismatches. Additionally, compared to the control groups, the agrammatic participants showed an attenuated, but relatively preserved, N400 response to semantic violations. These data show that agrammatic individuals do not demonstrate normal real-time sensitivity to verb argument structure requirements during sentence processing. PMID:23022079

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Well-ordered structure of methylene blue monolayers on Au(111) surface: electrochemical scanning tunneling microscopy studies.

PubMed

Song, Yonghai; Wang, Li

2009-02-01

Well-ordered structure of methylene blue (MB) monolayers on Au(111) surface has been successfully obtained by controlling the substrate potential. Electrochemical scanning tunneling microscopy (ECSTM) examined the monolayers of MB on Au(111) in 0.1 M HClO(4) and showed long-range ordered, interweaved arrays of MB with quadratic symmetry on the substrate in the potential range of double-layer charging. High-resolution ECSTM image further revealed the details of the MB monolayers structure of c(5 x 5 radical 3)rect and the flat-lying orientation of ad-molecules. The dependence of molecular organization on the substrate potential and the formation mechanism of well-ordered structure on Au(111) surface were investigated in detail. The obtained well-ordered structure at the interface between a metal and an aqueous electrolyte might possibly be used as high-density device for signal memory and templates for the advanced nanopatterning of surfaces. (c) 2008 Wiley-Liss, Inc.

Andreev reflection enhancement in semiconductor-superconductor structures

NASA Astrophysics Data System (ADS)

Bouscher, Shlomi; Winik, Roni; Hayat, Alex

2018-02-01

We develop a theoretical approach for modeling a wide range of semiconductor-superconductor structures with arbitrary potential barriers and a spatially dependent superconducting order parameter. We demonstrate asymmetry in the conductance spectrum as a result of a Schottky barrier shape. We further show that the Andreev reflection process can be significantly enhanced through resonant tunneling with appropriate barrier configuration, which can incorporate the Schottky barrier as a contributing component of the device. Moreover, we show that resonant tunneling can be achieved in superlattice structures as well. These theoretically demonstrated effects along with our modeling approach enable much more efficient Cooper pair injection into semiconductor-superconductor structures, including superconducting optoelectronic devices.

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

Lima, Jonas R. F., E-mail: jonas.iasd@gmail.com

We study the electronic and transport properties of a graphene-based superlattice theoretically by using an effective Dirac equation. The superlattice consists of a periodic potential applied on a single-layer graphene deposited on a substrate that opens an energy gap of 2Δ in its electronic structure. We find that extra Dirac points appear in the electronic band structure under certain conditions, so it is possible to close the gap between the conduction and valence minibands. We show that the energy gap E{sub g} can be tuned in the range 0 ≤ E{sub g} ≤ 2Δ by changing the periodic potential. We analyze the low energymore » electronic structure around the contact points and find that the effective Fermi velocity in very anisotropic and depends on the energy gap. We show that the extra Dirac points obtained here behave differently compared to previously studied systems.« less

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

PubMed

Lätzer, Joachim; Shen, Tongye; Wolynes, Peter G

2008-02-19

We investigate how post-translational phosphorylation modifies the global conformation of a protein by changing its free energy landscape using two test proteins, cystatin and NtrC. We first examine the changes in a free energy landscape caused by phosphorylation using a model containing information about both structural forms. For cystatin the free energy cost is fairly large indicating a low probability of sampling the phosphorylated conformation in a perfectly funneled landscape. The predicted barrier for NtrC conformational transition is several times larger than the barrier for cystatin, indicating that the switch protein NtrC most probably follows a partial unfolding mechanism to move from one basin to the other. Principal component analysis and linear response theory show how the naturally occurring conformational changes in unmodified proteins are captured and stabilized by the change of interaction potential. We also develop a partially guided structure prediction Hamiltonian which is capable of predicting the global structure of a phosphorylated protein using only knowledge of the structure of the unphosphorylated protein or vice versa. This algorithm makes use of a generic transferable long-range residue contact potential along with details of structure short range in sequence. By comparing the results obtained with this guided transferable potential to those from the native-only, perfectly funneled Hamiltonians, we show that the transferable Hamiltonian correctly captures the nature of the global conformational changes induced by phosphorylation and can sample substantially correct structures for the modified protein with high probability.

Orientation-dependent potential of mean force for protein folding

NASA Astrophysics Data System (ADS)

Mukherjee, Arnab; Bhimalapuram, Prabhakar; Bagchi, Biman

2005-07-01

We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model, the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other sites through an orientation-dependent interaction potential which we construct in the following fashion. First, the site-site potential of mean force (PMF) between heavy atoms is calculated [following F. Melo and E. Feytsman, J. Mol. Biol. 267, 207 (1997)] from statistics of their distance separation obtained from crystal structures. These site-site potentials are then used to calculate the distance and the orientation-dependent potential between side chains of all the amino acid residues (AAR). The distance and orientation dependencies show several interesting results. For example, we find that the PMF between two hydrophobic AARs, such as phenylalanine, is strongly attractive at short distances (after the obvious repulsive region at very short separation) and is characterized by a deep minimum, for specific orientations. For the interaction between two hydrophilic AARs, such a deep minimum is absent and in addition, the potential interestingly reveals the combined effect of polar (charge) and hydrophobic interactions among some of these AARs. The effectiveness of our potential has been tested by calculating the Z-scores for a large set of proteins. The calculated Z-scores show high negative values for most of them, signifying the success of the potential to identify the native structure from among a large number of its decoy states.

Descriptive and network analyses of the equine contact network at an equestrian show in Ontario, Canada and implications for disease spread.

PubMed

Spence, Kelsey L; O'Sullivan, Terri L; Poljak, Zvonimir; Greer, Amy L

2017-06-21

Identifying the contact structure within a population of horses attending a competition is an important element towards understanding the potential for the spread of equine pathogens as the horses subsequently travel from location to location. However, there is limited information in Ontario, Canada to quantify contact patterns of horses. The objective of this study was to describe the network of potential contacts associated with an equestrian show to determine how this network structure may influence potential disease transmission. This was a descriptive study of horses attending an equestrian show in southern Ontario, Canada on July 6 and 7, 2014. Horse show participants completed a questionnaire about their horse, travel patterns, and infection control practices. Questionnaire responses were received from horse owners of 79.7% (55/69) of the horses attending the show. Owners reported that horses attending the show were vaccinated for diseases such as rabies, equine influenza, and equine herpesvirus. Owners demonstrated high compliance with most infection control practices by reporting reduced opportunities for direct and indirect contact while away from home. The two-mode undirected network consisted of 820 nodes (41 locations and 779 horses). Eight percent of nodes in the network represented horses attending the show, 87% of nodes represented horses not attending the show, but boarded at individual home facilities, and 5% represented locations. The median degree of a horse in the network was 33 (range: 1-105). Developing disease management strategies without the explicit consideration of horses boarded at individual home facilities would underestimate the connectivity of horses in the population. The results of this study provides information that can be used by equestrian show organizers to configure event management in such a way that can limit the extent of potential disease spread.

Ab - initio study of rare earth magnesium alloy: TbMg

NASA Astrophysics Data System (ADS)

Kumari, Meena; Yadav, Priya; Nautiyal, Shashank; Verma, U. P.

2018-05-01

The structural, electronic and magnetic properties of TbMg were analyzed by using full-potential linearized augmented plane wave method. This intermetallic is stable in structure CsCl (B2 phase) with space group Pm-3m. In electronic properties, we show the electronic band structure and density of states plots. These plots show that this alloy have metallic character because there is no band gap between the valance band and conduction band at Fermi level. The structural properties, i.e. equilibrium lattice constant, bulk modulus and its pressure derivative, energy and volume show good agreement with available data. In this paper, we also present the total magnetic moment along with the magnetic moment on the atomic and interstitial sites of TbMg intermetallic in B2 phase.

An analytical bond-order potential for carbon

DOE PAGES

Zhou, Xiaowang; Ward, Donald K.; Foster, Michael E.

2015-05-27

Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, themore » potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. The potential must predict the crystalline growth of the correct phases during direct MD simulations of synthesis to achieve a predictive simulation of defect formation. An unlimited number of structures not included in the potential parameterization are encountered, thus the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We also demonstrate that our potential reasonably captures the property trends of important carbon phases. As a result, stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure.« less

An analytical bond-order potential for carbon.

PubMed

Zhou, X W; Ward, D K; Foster, M E

2015-09-05

Carbon is the most widely studied material today because it exhibits special properties not seen in any other materials when in nano dimensions such as nanotube and graphene. Reduction of material defects created during synthesis has become critical to realize the full potential of carbon structures. Molecular dynamics (MD) simulations, in principle, allow defect formation mechanisms to be studied with high fidelity, and can, therefore, help guide experiments for defect reduction. Such MD simulations must satisfy a set of stringent requirements. First, they must employ an interatomic potential formalism that is transferable to a variety of carbon structures. Second, the potential needs to be appropriately parameterized to capture the property trends of important carbon structures, in particular, diamond, graphite, graphene, and nanotubes. Most importantly, the potential must predict the crystalline growth of the correct phases during direct MD simulations of synthesis to achieve a predictive simulation of defect formation. Because an unlimited number of structures not included in the potential parameterization are encountered, the literature carbon potentials are often not sufficient for growth simulations. We have developed an analytical bond order potential for carbon, and have made it available through the public MD simulation package LAMMPS. We demonstrate that our potential reasonably captures the property trends of important carbon phases. Stringent MD simulations convincingly show that our potential accounts not only for the crystalline growth of graphene, graphite, and carbon nanotubes but also for the transformation of graphite to diamond at high pressure. © 2015 Wiley Periodicals, Inc.

Quantum resonance of nanometre-scale metal-ZnO-metal structure and its application in sensors

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

Li, Lijie, E-mail: L.Li@swansea.ac.uk; Rees, Paul

2016-01-15

Analysis of the thickness dependence of the potential profile of the metal-ZnO-metal (MZM) structure has been conducted based on Poisson’s equation and Schottky theory. Quantum scattering theory is then used to calculate the transmission probability of an electron passing through the MZM structure. Results show that the quantum resonance (QR) effect becomes pronounced when the thickness of the ZnO film reaches to around 6 nm. Strain induced piezopotentials are considered as biases to the MZM, which significantly changes the QR according to the analysis. This effect can be potentially employed as nanoscale strain sensors.

48 CFR 2452.209-70 - Potential organizational conflicts of interest.

Code of Federal Regulations, 2011 CFR

2011-10-01

... conflicts of interest. 2452.209-70 Section 2452.209-70 Federal Acquisition Regulations System DEPARTMENT OF... relevant facts that show how its organizational structure and/or management systems limit its knowledge of... and how that structure or system would avoid or mitigate such organizational conflict. (d) No award...

Synthesis of ordered mesoporous carbon monoliths with bicontinuous cubic pore structure of Ia3d symmetry.

PubMed

Yang, Haifeng; Shi, Qihui; Liu, Xiaoying; Xie, Songhai; Jiang, Decheng; Zhang, Fuqiang; Yu, Chengzhong; Tu, Bo; Zhao, Dongyuan

2002-12-07

Large-diameter-sized mesoporous carbon monoliths with bicontinuous cubic structure of Ia3d symmetry have been synthesized by using mesoporous silica monoliths as hard templates; such carbon monoliths show potential application of advanced electrodes and electrochemical double layer capacitors.

Interlayer interactions in graphites.

PubMed

Chen, Xiaobin; Tian, Fuyang; Persson, Clas; Duan, Wenhui; Chen, Nan-xian

2013-11-06

Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Möbius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

Tight-binding calculation studies of vacancy and adatom defects in graphene

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

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

Structure of AA5056 after friction drilling

NASA Astrophysics Data System (ADS)

Eliseev, A. A.; Kalashnikova, T. A.; Fortuna, S. V.

2017-12-01

Here we present data on the structure of AA5056 alloy after friction drilling to unveil potentials of the process for use in model experiments on friction stir welding. Our analysis of the average size and volume content of precipitates shows that their content decreases immediately beneath the friction surface and that the structure of this zone is the same as the structure of stirring zones formed in friction stir welding. The data suggest that both processes provide similar metal structures.

Electronic structure and properties of lanthanum

NASA Astrophysics Data System (ADS)

Nixon, Lane; Papaconstantopoulos, Dimitrios

2008-03-01

The total energy and electronic structure of lanthanum have been calculated in the bcc, fcc, hcp and dhcp structures for pressures up to 50 GPa. The full potential linearized-augmented-planewave method was used with both the local-density and general-gradient approximations. The correct phase ordering has been found, with lattice parameters and bulk moduli in good agreement with experimental data. The GGA method shows excellent agreement overall while the LDA results show larger discrepancies. The calculated strain energies for the fcc and bcc structures demonstrate the respective stable and unstable configurations at ambient conditions. The calculated superconductivity properties under pressure for the fcc structure are also found to agree well with measurements. Both LDA and GGA, with minor differences, reproduce well the experimental results for Tc.

Transport induced by large scale convective structures in a dipole-confined plasma.

PubMed

Grierson, B A; Mauel, M E; Worstell, M W; Klassen, M

2010-11-12

Convective structures characterized by E×B motion are observed in a dipole-confined plasma. Particle transport rates are calculated from density dynamics obtained from multipoint measurements and the reconstructed electrostatic potential. The calculated transport rates determined from the large-scale dynamics and local probe measurements agree in magnitude, show intermittency, and indicate that the particle transport is dominated by large-scale convective structures.

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization.

PubMed

Sheng, Jia; Hassan, Abdalla E A; Zhang, Wen; Zhou, Jianfeng; Xu, Bingqian; Soares, Alexei S; Huang, Zhen

2011-05-01

We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNA duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation. © The Author(s) 2011. Published by Oxford University Press.

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

PubMed Central

Sheng, Jia; Hassan, Abdalla E. A.; Zhang, Wen; Zhou, Jianfeng; Xu, Bingqian; Soares, Alexei S.; Huang, Zhen

2011-01-01

We report here the first synthesis of 5-phenyl–telluride–thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNA duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation. PMID:21245037

Synthesis Structure and Imaging of Oligodeoxyribonucleotides with Tellurium-nucleobase Derivatization

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

J Sheng; A Hassan; W Zhang

2011-12-31

We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNAmore » duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation.« less

Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

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

Sheng, J.; Soares, A.; Hassan, A. E. A.

2011-05-01

We report here the first synthesis of 5-phenyl-telluride-thymidine derivatives and the Te-phosphoramidite. We also report here the synthesis, structure and STM current-imaging studies of DNA oligonucleotides containing the nucleobases (thymine) derivatized with 5-phenyl-telluride functionality (5-Te). Our results show that the 5-Te-DNA is stable, and that the Te-DNA duplex has the thermo-stability similar to the corresponding native duplex. The crystal structure indicates that the 5-Te-DNA duplex structure is virtually identical to the native one, and that the Te-modified T and native A interact similarly to the native T and A pair. Furthermore, while the corresponding native showed weak signals, the DNAmore » duplex modified with electron-rich tellurium functionality showed strong topographic and current peaks by STM imaging, suggesting a potential strategy to directly image DNA without structural perturbation.« less

Dynamics of climate-based malaria transmission model with age-structured human population

NASA Astrophysics Data System (ADS)

Addawe, Joel; Pajimola, Aprimelle Kris

2016-10-01

In this paper, we proposed to study the dynamics of malaria transmission with periodic birth rate of the vector and an age-structure for the human population. The human population is divided into two compartments: pre-school (0-5 years) and the rest of the human population. We showed the existence of a disease-free equilibrium point. Using published epidemiological parameters, we use numerical simulations to show potential effect of climate change in the dynamics of age-structured malaria transmission. Numerical simulations suggest that there exists an asymptotically attractive solution that is positive and periodic.

Potential collapse due to geological structures influence in Seropan Cave, Gunung Kidul, Yogyakarta, Indonesia

NASA Astrophysics Data System (ADS)

Nugroho, B.; Pranantya, P. A.; Witjahjati, R.; Rofinus

2018-01-01

This study aims to estimate the potential collapse in the Seropan cave, based on the existing geological structure conditions in the cave. This is very necessary because in the Seropan cave will be built Microhydro installation for power plants. The electricity will be used to raise the underground river water in the cave to a barren soil surface, which can be used for surface irrigation. The method used is analysis the quality of rock mass along the cave. Analysis of rock mass quality using Geomechanical Classification or Rock Mass Rating (RMR), to determine the magnitude of the effect of geological structure on rock mass stability. The research path is divided into several sections and quality analysis is performed on each section. The results show that the influence of geological structure is very large and along the cave where the research there are several places that have the potential to collapse, so need to get serious attention in handling it. Nevertheless, the construction of this Microhydro installation can still be carried out by making a reinforcement on potentially collapsing parts

Composition and Structure of Microalgae Indicated in Raman and Hyperspectral Spectra and Scanning Electron Microscopy: from Cyanobacteria to Isolates from Coal-bed Methane Water Ponds

NASA Astrophysics Data System (ADS)

Zhou, X.; Zhou, Z.; Apple, M. E.; Spangler, L.

2017-12-01

Microalgae can be used for many potential applications for human's benefits. These potential applications included biofuel production from microalgae, biofiltering to cleaning water, chemical extraction as nutrients, etc. However, exploration for such applications is still in the early stages. For instance, many species and strains of microalgae have been investigated for their lipid content and growing conditions for efficient productions of lipids, but no specific species have yet been chosen as a fuel source for commercial production because of the huge biodiversity and subsequently a wide range of species that can potentially be exploited for biodiesel production, the great variability between species in their fuel precursor producing capabilities. Numerous coal-bed methane water ponds were established in the world as a consequence of coal-bed methane production from deep coal seams. Microalgae were isolated from such ponds and potentially these ponds can be used as venues for algal production. In this study, we characterized chemical composition and structure of the Cyanobacteria Anabaena cylindrica (UTEX # 1611) and isolates from coal-bed methane ponds Nannochloropsis gaditana and PW95 using Laser Raman Spectroscopy (LRS), hyperspectral spectra, and Scanning Electron Microscope (SEM). The objective is to seek bio-indicators for potential applications of these microalgae species. For instance, indicator of rich content lips shows the great potential for biofuel production. Fig.1 shows an example of the Raman spectra of the three species in desiccated form. The spectral peaks were isolated and the corresponding composition was identified. The insert at the right hand of the Raman spectrum of each species is the micrograph of the cell morphology under a microscope. The Raman spectra of cells in aquatic solutions were also obtained and compared with the desiccated form. The hyperspectral reflectances of the three species show quite different characteristics and the main absorption bands and scattering bands were located and their association with composition and structure were analyzed and discussed. SEM micrographs will be collected and the composition and structure derived from the SEM micrographs will be discussed and compared with those derived from the Raman spectra and hyperspectral spectra.

Perfect narrow band absorber for sensing applications.

PubMed

Luo, Shiwen; Zhao, Jun; Zuo, Duluo; Wang, Xinbing

2016-05-02

We design and numerically investigate a perfect narrow band absorber based on a metal-metal-dielectric-metal structure which consists of periodic metallic nanoribbon arrays. The absorber presents an ultra narrow absorption band of 1.11 nm with a nearly perfect absorption of over 99.9% in the infrared region. For oblique incidence, the absorber shows an absorption more than 95% for a wide range of incident angles from 0 to 50°. Structure parameters to the influence of the performance are investigated. The structure shows high sensing performance with a high sensitivity of 1170 nm/RIU and a large figure of merit of 1054. The proposed structure has great potential as a biosensor.

Crystal structure and superconductivity in atomic hydrogen: Deformation between I41/amd and Fddd

NASA Astrophysics Data System (ADS)

Ishikawa, T.; Nagara, H.; Oda, T.; Suzuki, N.; Shimizu, K.

2017-10-01

We investigated crystal structures of solid metallic hydrogen using the potential energy surface trekking for structure search. We applied this technique to a tetragonal I41/amd structure at pressures of 500 and 600 GPa and obtained the transformation into multiple orthorhombic Fddd structures, which are formed by distortions in the ab plane of I41/amd. The potential barriers are easily surmounted by few trekking steps, which indicates that in solid metallic hydrogen crystal structure is softened with respect to the distortion and is easily fluctuated among the I41/amd and Fddd structures. Calculated superconducting critical temperatures show 269 K for I41/amd and 263 K for Fddd at 500 GPa. The structures are softened and the electron-phonon coupling are enhanced with pressurization to 600 GPa. As the results, the superconducting critical temperature is increased to 281 K for I41/amd, whereas it is decreased to 252 K for Fddd owing to its larger phonon softening than that of I41/amd.

Full-Potential Calculation of Structural, Electronic, and Thermodynamic Properties of Fluoroperovskite { CsMF}3 (M = Be and Mg)

NASA Astrophysics Data System (ADS)

Harmel, M.; Khachai, H.; Ameri, A.; Baki, N.; Haddou, A.; Khalfa, M.; Abbar, B.; Omran, S. Bin; Uğur, G.; Uğur, Ş.; Khenata, R.

2012-12-01

The structural and electronic properties of the cubic fluoroperoveskite { CsBeF}3 and { CsMgF}3 have been investigated using the full-potential-linearized augmented plane wave method within the density functional theory. The exchange-correlation potential was treated with the local density approximation and the generalized gradient approximation. The calculations of the electronic band structures show that { CsBeF}_{3 } has an indirect bandgap, whereas { CsMgF}3 has a direct bandgap. Through the quasi-harmonic Debye model, in which the phononic effects are considered, the effect of pressure P and temperature T on the lattice parameter, bulk modulus, thermal expansion coefficient, Debye temperature, and the heat capacity for { CsBeF}3 and { CsMgF}3 compounds are investigated for the first time.

Effect of pulsed electric field (PEF) on structures and antioxidant activity of soybean source peptides-SHCMN.

PubMed

Lin, Songyi; Liang, Rong; Li, Xingfang; Xing, Jie; Yuan, Yuan

2016-12-15

Recently, high-intensity pulsed electric field (PEF) has successfully used in improvement of antioxidant activity. Ser-His-Cys-Met-Asn (SHCMN) obtained from soybean protein was chosen to investigate the phenomenon of antioxidant activity improvement. Effects of PEF treatment on antioxidant activity of SHCMN were evaluated by DPPH radical inhibition. Nuclear magnetic resonance (NMR), mid-infrared (MIR), circular dichroism (CD) were used to analyze structures of SHCMN. Two-factor-at-a-time results show that DPPH radical inhibition of SHCMN is significantly (P<0.05) increased to 94.35±0.03% at conditions of electric field intensity of 5kV/cm, pulse frequency of 2400Hz, and retention time of 2h. In addition, MIR and NMR spectra show that the basic structure of peptides SHCMN is stable by PEF treatment. But the secondary structures (α-helix, β-turn, and random coil) can be affected and zeta potential of PEF-treated SHCNM was reduced to 0.59±0.03mV. The antioxidant activity improvement of SHCMN might result from the changes of secondary structures and zeta potential. Copyright © 2016 Elsevier Ltd. All rights reserved.

Does Inquiry Based Learning Affect Students' Beliefs and Attitudes towards Mathematics?

ERIC Educational Resources Information Center

McGregor, Darren

2014-01-01

Ill-structured tasks presented in an inquiry learning environment have the potential to affect students' beliefs and attitudes towards mathematics. This empirical research followed a Design Experiment approach to explore how aspects of using ill-structured tasks may have affected students' beliefs and attitudes. Results showed this task type and…

Correlation of Emulsion Structure with Cellular Uptake Behavior of Encapsulated Bioactive Nutrients: Influence of Droplet Size and Interfacial Structure.

PubMed

Lu, Wei; Kelly, Alan L; Maguire, Pierce; Zhang, Hongzhou; Stanton, Catherine; Miao, Song

2016-11-16

In this study, an in vitro Caco-2 cell culture assay was employed to evaluate the correlation between emulsion structure and cellular uptake of encapsulated β-carotene. After 4 h of incubation, an emulsion stabilized with whey protein isolate showed the highest intracellular accumulation of β-carotene (1.06 μg), followed by that stabilized with sodium caseinate (0.60 μg) and Tween 80 (0.20 μg), which are 13-, 7.5-, and 2.5-fold higher than that of free β-carotene (0.08 μg), respectively. Emulsions with small droplet size (239 ± 5 nm) showed a higher cellular uptake of β-carotene (1.56 μg) than emulsiond with large droplet size (489 ± 9 nm) (0.93 μg) (p < 0.01). The results suggested that delivery in an emulsion significantly improved the cellular uptake of β-carotene and thus potentially its bioavailability; uptake was closely correlated with the interfacial composition and droplet size of emulsions. The findings support the potential for achieving optimal controlled and targeted delivery of bioactive nutrients by structuring emulsions.

Giant magnetoresistance and anomalous transport in phosphorene-based multilayers with noncollinear magnetization

NASA Astrophysics Data System (ADS)

Zare, Moslem; Majidi, Leyla; Asgari, Reza

2017-03-01

We theoretically investigate the unusual features of the magnetotransport in a monolayer phosphorene ferromagnetic/normal/ferromagnetic (F/N/F) hybrid structure. We find that the charge conductance can feature a minimum at parallel (P) configuration and a maximum near the antiparallel (AP) configuration of magnetization in the F/N/F structure with n -doped F and p -doped N regions and also a finite conductance in the AP configuration with the N region of n -type doping. In particular, the proposed structure exhibits giant magnetoresistance, which can be tuned to unity. This perfect switching is found to show strong robustness with respect to increasing the contact length and tuning the chemical potential of the N region with a gate voltage. We also explore the oscillatory behavior of the charge conductance or magnetoresistance in terms of the size of the N region. We further demonstrate the penetration of the spin-transfer torque into the right F region and show that, unlike graphene structure, the spin-transfer torque is very sensitive to the chemical potential of the N region as well as the exchange field of the F region.

Path-integral molecular dynamics simulations of hydrated hydrogen chloride cluster HCl(H 2O) 4 on a semiempirical potential energy surface

NASA Astrophysics Data System (ADS)

Takayanagi, Toshiyuki; Takahashi, Kenta; Kakizaki, Akira; Shiga, Motoyuki; Tachikawa, Masanori

2009-04-01

Path-integral molecular dynamics simulations for the HCl(H 2O) 4 cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H 2O) 4 cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.

Precise replication of antireflective nanostructures from biotemplates

NASA Astrophysics Data System (ADS)

Gao, Hongjun; Liu, Zhongfan; Zhang, Jin; Zhang, Guoming; Xie, Guoyong

2007-03-01

The authors report herein a new type of nanonipple structures on the cicada's eye and the direct structural replication of the complex micro- and nanostructures for potential functional emulation. A two-step direct molding process is developed to replicate these natural micro- and nanostructures using epoxy resin with high fidelity, which demonstrates a general way of fabricating functional nanostructures by direct replication of natural biotemplates via a suitable physicochemical process. Measurements of spectral reflectance showed that this kind of replicated nanostructure has remarkable antireflective property, suggestive of its potential applications to optical devices.

Pressure induced phase transition and elastic properties of cerium mono-nitride (CeN)

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

Yaduvanshi, Namrata, E-mail: namrata-yaduvanshi@yahoo.com; Singh, Sadhna

2016-05-23

In the present paper, we have investigated the high-pressure structural phase transition and elastic properties of cerium mono-nitride. We studied theoretically the structural properties of this compound (CeN) by using the improved interaction potential model (IIPM) approach. This compound exhibits first order crystallographic phase transition from NaCl (B{sub 1}) to tetragonal (BCT) phase at 37 GPa. The phase transition pressures and associated volume collapse obtained from present potential model (IIPM) show a good agreement with available theoretical data.

Albumin-based nanoparticle trehalose lyophilisation stress-down to preserve structure/function and enhanced binding.

PubMed

Siri, Macarena; Grasselli, Mariano; Alonso, Silvia Del V

2016-07-15

The aim of this study was to preserve albumin nanoparticle structure/function during the lyophilisation process. Bovine serum albumin nanoparticles were obtained by γ-irradiation. Nanoparticles were lyophilised in buffer, miliQ water or in trehalose/miliQ solution. The size and charge of the nanoparticles were tested after lyophilisation by light scattering and Z potential. The most relevant results in size of BSA nanoparticle were those lyophilised in PBS between 20 and 350nm, assembled in different aggregates, and negative Z potential obtained was 37±8mV in all, and those nanoparticles lyophilised with trehalose had a size range of 70±2nm and a negative Z potential of 20±5mV. Structure determination of surface aminoacids SH groups in the BSA NP lyophilised in PBS showed an increase in the free SH groups. Different aggregates had different amount of SH groups exposure from 55 to 938 (from smaller to bigger aggregates), whereas BSA NP lyophilised with trehalose showed no significant difference if compared with BSA NP. The binding properties of the BSA nanoparticle with a theragnostic probe (merocyanine 540) were studied after lyophilisation. Results showed more affinity between the BSA NP lyophilised with trehalose than that observed with non lyophilised BSA NP. As a result, the lyophilisation condition in trehalose 100μM solution is the best one to preserve the BSA NP structure/function and the one with the enhance binding affinity of the BSA NP. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor

PubMed Central

Bertaccini, Edward J.; Yoluk, Ozge; Lindahl, Erik R.; Trudell, James R.

2013-01-01

Background Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). While its molecular structure remains unknown, significant progress has been made towards understanding its interactions with anesthetics via molecular modeling. Methods The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50’s. Results Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between alpha and beta subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Conclusion Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed correlation of ligand docking scores with experimentally measured GABAaR potentiation. PMID:23770602

Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor.

PubMed

Bertaccini, Edward J; Yoluk, Ozge; Lindahl, Erik R; Trudell, James R

2013-11-01

Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). Although its molecular structure remains unknown, significant progress has been made toward understanding its interactions with anesthetics via molecular modeling. The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH-sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50s. Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between α and β subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed a correlation of ligand docking scores with experimentally measured GABAaR potentiation.

Fast iodide-SAD phasing for high-throughput membrane protein structure determination

PubMed Central

Melnikov, Igor; Polovinkin, Vitaly; Kovalev, Kirill; Gushchin, Ivan; Shevtsov, Mikhail; Shevchenko, Vitaly; Mishin, Alexey; Alekseev, Alexey; Rodriguez-Valera, Francisco; Borshchevskiy, Valentin; Cherezov, Vadim; Leonard, Gordon A.; Gordeliy, Valentin; Popov, Alexander

2017-01-01

We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide–single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins—the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein–coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques. PMID:28508075

Fast iodide-SAD phasing for high-throughput membrane protein structure determination.

PubMed

Melnikov, Igor; Polovinkin, Vitaly; Kovalev, Kirill; Gushchin, Ivan; Shevtsov, Mikhail; Shevchenko, Vitaly; Mishin, Alexey; Alekseev, Alexey; Rodriguez-Valera, Francisco; Borshchevskiy, Valentin; Cherezov, Vadim; Leonard, Gordon A; Gordeliy, Valentin; Popov, Alexander

2017-05-01

We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.

Omnidirectional polarization insensitive tunable absorption in graphene metamaterial of nanodisk structure

NASA Astrophysics Data System (ADS)

Ning, Renxia; Bao, Jie; Jiao, Zheng; Xu, Yuan

2015-11-01

Tunable absorption based on graphene metamaterial with nanodisk structure at near-infrared frequency was investigated using the finite difference time domain method. The absorption of the nanodisk structure which consisting of Au-MgF2-graphene-Au-polyimide (from bottom to top) can be tuned by the chemical potential of graphene at certain diameter of nanodisk. The permittivity of graphene is discussed with different chemical potential to obtain tunable absorption. It is shown that the increased value of the chemical potential of graphene can lead to blue-shifted of the absorption peaks and the values decreased. Moreover, dual-band and triple-band absorption can be achieved for resonance frequencies at normal incidence. Compared with diameter of nanodisks, the multilayer structure shows multi-band absorber, and an omnidirectional absorption at 195.25 THz is insensitive to TE/TM polarization. This omnidirectional polarization insensitive absorption may be applied by optical communications such as optical absorber, near infrared stealth, and filter.

Advances and applications of ABCI

NASA Astrophysics Data System (ADS)

Chin, Y. H.

1993-05-01

ABCI (Azimuthal Beam Cavity Interaction) is a computer program which solves the Maxwell equations directly in the time domain when a Gaussian beam goes through an axi-symmetrical structure on or off axis. Many new features have been implemented in the new version of ABCI (presently version 6.6), including the 'moving mesh' and Napoly's method of calculation of wake potentials. The mesh is now generated only for the part of the structure inside a window and moves together with the window frame. This moving mesh option reduces the number of mesh points considerably, and very fine meshes can be used. Napoly's integration method makes it possible to compute wake potentials in a structure such as a collimator, where parts of the cavity material are at smaller radii than that of the beam pipes, in such a way that the contribution from the beam pipes vanishes. For the monopole wake potential, ABCI can be applied even to structures with unequal beam pipe radii. Furthermore, the radial mesh size can be varied over the structure, permitting use a fine mesh only where actually needed. With these improvements, the program allows computation of wake fields for structures far too complicated for older codes. Plots of a cavity shape and wake potentials can be obtained in the form of a Top Drawer file. The program can also calculate and plot the impedance of a structure and/or the distribution of the deposited energy as a function of the frequency from Fourier transforms of wake potentials. Its usefulness is illustrated by showing some numerical examples.

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

Hormain, Laureline; Monnerville, Maurice, E-mail: maurice.monnerville@univ-lille1.fr; Toubin, Céline

The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by themore » comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.« less

A Group 6 Late Embryogenesis Abundant Protein from Common Bean Is a Disordered Protein with Extended Helical Structure and Oligomer-forming Properties*

PubMed Central

Rivera-Najera, Lucero Y.; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O.; García-Hernández, Enrique; Solórzano, Rosa M.; Reyes, José L.; Covarrubias, Alejandra A.

2014-01-01

Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

NASA Astrophysics Data System (ADS)

Dragoni, Daniele; Daff, Thomas D.; Csányi, Gábor; Marzari, Nicola

2018-01-01

We show that the Gaussian Approximation Potential (GAP) machine-learning framework can describe complex magnetic potential energy surfaces, taking ferromagnetic iron as a paradigmatic challenging case. The training database includes total energies, forces, and stresses obtained from density-functional theory in the generalized-gradient approximation, and comprises approximately 150,000 local atomic environments, ranging from pristine and defected bulk configurations to surfaces and generalized stacking faults with different crystallographic orientations. We find the structural, vibrational, and thermodynamic properties of the GAP model to be in excellent agreement with those obtained directly from first-principles electronic-structure calculations. There is good transferability to quantities, such as Peierls energy barriers, which are determined to a large extent by atomic configurations that were not part of the training set. We observe the benefit and the need of using highly converged electronic-structure calculations to sample a target potential energy surface. The end result is a systematically improvable potential that can achieve the same accuracy of density-functional theory calculations, but at a fraction of the computational cost.

The time course of syntactic activation during language processing: a model based on neuropsychological and neurophysiological data.

PubMed

Friederici, A D

1995-09-01

This paper presents a model describing the temporal and neurotopological structure of syntactic processes during comprehension. It postulates three distinct phases of language comprehension, two of which are primarily syntactic in nature. During the first phase the parser assigns the initial syntactic structure on the basis of word category information. These early structural processes are assumed to be subserved by the anterior parts of the left hemisphere, as event-related brain potentials show this area to be maximally activated when phrase structure violations are processed and as circumscribed lesions in this area lead to an impairment of the on-line structural assignment. During the second phase lexical-semantic and verb-argument structure information is processed. This phase is neurophysiologically manifest in a negative component in the event-related brain potential around 400 ms after stimulus onset which is distributed over the left and right temporo-parietal areas when lexical-semantic information is processed and over left anterior areas when verb-argument structure information is processed. During the third phase the parser tries to map the initial syntactic structure onto the available lexical-semantic and verb-argument structure information. In case of an unsuccessful match between the two types of information reanalyses may become necessary. These processes of structural reanalysis are correlated with a centroparietally distributed late positive component in the event-related brain potential.(ABSTRACT TRUNCATED AT 250 WORDS)

Energy-absorption spectroscopy of unitary Fermi gases in a uniform potential

NASA Astrophysics Data System (ADS)

Zhang, Pengfei; Yu, Zhenhua

2018-04-01

We propose to use the energy absorption spectroscopy to measure the kinetic coefficients of unitary Fermi gases in a uniform potential. We show that, in our scheme, the energy absorption spectrum is proportional to the dynamic structure factor of the system. The profile of the spectrum depends on the shear viscosity η , the thermal conductivity κ , and the superfluid bulk viscosity ξ3. We show that extraction of these coefficients from the spectrum is achievable in present experiments.

Vlasov Simulation of Electrostatic Solitary Structures in Multi-Component Plasmas

NASA Technical Reports Server (NTRS)

Umeda, Takayuki; Ashour-Abdalla, Maha; Pickett, Jolene S.; Goldstein, Melvyn L.

2012-01-01

Electrostatic solitary structures have been observed in the Earth's magnetosheath by the Cluster spacecraft. Recent theoretical work has suggested that these solitary structures are modeled by electron acoustic solitary waves existing in a four-component plasma system consisting of core electrons, two counter-streaming electron beams, and one species of background ions. In this paper, the excitation of electron acoustic waves and the formation of solitary structures are studied by means of a one-dimensional electrostatic Vlasov simulation. The present result first shows that either electron acoustic solitary waves with negative potential or electron phase-space holes with positive potential are excited in four-component plasma systems. However, these electrostatic solitary structures have longer duration times and higher wave amplitudes than the solitary structures observed in the magnetosheath. The result indicates that a high-speed and small free energy source may be needed as a fifth component. An additional simulation of a five-component plasma consisting of a stable four-component plasma and a weak electron beam shows the generation of small and fast electron phase-space holes by the bump-on-tail instability. The physical properties of the small and fast electron phase-space holes are very similar to those obtained by the previous theoretical analysis. The amplitude and duration time of solitary structures in the simulation are also in agreement with the Cluster observation.

Structural Design for a Neptune Aerocapture Mission

NASA Technical Reports Server (NTRS)

Dyke, R. Eric; Hrinda, Glenn A.

2004-01-01

A multi-center study was conducted in 2003 to assess the feasibility of and technology requirements for using aerocapture to insert a scientific platform into orbit around Neptune. The aerocapture technique offers a potential method of greatly reducing orbiter mass and thus total spacecraft launch mass by minimizing the required propulsion system mass. This study involved the collaborative efforts of personnel from Langley Research Center (LaRC), Johnson Space Flight Center (JSFC), Marshall Space Flight Center (MSFC), Ames Research Center (ARC), and the Jet Propulsion Laboratory (JPL). One aspect of this effort was the structural design of the full spacecraft configuration, including the ellipsled aerocapture orbiter and the in-space solar electric propulsion (SEP) module/cruise stage. This paper will discuss the functional and structural requirements for each of these components, some of the design trades leading to the final configuration, the loading environments, and the analysis methods used to ensure structural integrity. It will also highlight the design and structural challenges faced while trying to integrate all the mission requirements. Component sizes, materials, construction methods and analytical results, including masses and natural frequencies, will be presented, showing the feasibility of the resulting design for use in a Neptune aerocapture mission. Lastly, results of a post-study structural mass optimization effort on the ellipsled will be discussed, showing potential mass savings and their influence on structural strength and stiffness

Spatio-temporal patterns of major bacterial groups in alpine waters.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2014-01-01

Glacial alpine landscapes are undergoing rapid transformation due to changes in climate. The loss of glacial ice mass has directly influenced hydrologic characteristics of alpine floodplains. Consequently, hyporheic sediment conditions are likely to change in the future as surface waters fed by glacial water (kryal) become groundwater dominated (krenal). Such environmental shifts may subsequently change bacterial community structure and thus potential ecosystem functioning. We quantitatively investigated the structure of major bacterial groups in glacial and groundwater-fed streams in three alpine floodplains during different hydrologic periods. Our results show the importance of several physico-chemical variables that reflect local geological characteristics as well as water source in structuring bacterial groups. For instance, Alpha-, Betaproteobacteria and Cytophaga-Flavobacteria were influenced by pH, conductivity and temperature as well as by inorganic and organic carbon compounds, whereas phosphorous compounds and nitrate showed specific influence on single bacterial groups. These results can be used to predict future bacterial group shifts, and potential ecosystem functioning, in alpine landscapes under environmental transformation.

Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

NASA Astrophysics Data System (ADS)

Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

2013-11-01

The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.

PubMed

Marín, Mario Alejandro; López, Andrés; Uribe, Sandra Inés

2012-06-01

The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.

Evaluation of Advanced Composite Structures Technologies for Application to NASA's Vision for Space Exploration

NASA Technical Reports Server (NTRS)

Tenney, Darrel R.

2008-01-01

AS&M performed a broad assessment survey and study to establish the potential composite materials and structures applications and benefits to the Constellation Program Elements. Trade studies were performed on selected elements to determine the potential weight or performance payoff from use of composites. Weight predictions were made for liquid hydrogen and oxygen tanks, interstage cylindrical shell, lunar surface access module, ascent module liquid methane tank, and lunar surface manipulator. A key part of this study was the evaluation of 88 different composite technologies to establish their criticality to applications for the Constellation Program. The overall outcome of this study shows that composites are viable structural materials which offer from 20% to 40% weight savings for many of the structural components that make up the Major Elements of the Constellation Program. NASA investment in advancing composite technologies for space structural applications is an investment in America's Space Exploration Program.

First principle study of UHTC ternary diboride, Cr2AlB2

NASA Astrophysics Data System (ADS)

Rastogi, Anugya; Rajpoot, Priyanka; Verma, U. P.

2018-04-01

In this paper ab-initio study of the structural, electronic and optical properties of ternary metal boride Cr2AlB2 using full potential linear augmented plane wave (FP-LAPW) method based on the density functional theory (DFT). The study of structural properties shows that Cr2AlB2 is metallic in nature and have orthorhombic crystal structure. The optical properties show that it possess anisotropic behavior, which have wide applications in electricity production through concentration of solar power (CSP) technology. To the best of our knowledge, theoretical study of the optical properties of Cr2AlB2 is reported for the first time.

Bend-resistant large mode area fiber with novel segmented cladding

NASA Astrophysics Data System (ADS)

Ma, Shaoshuo; Ning, Tigang; Pei, Li; Li, Jing; Zheng, Jingjing

2018-01-01

A novel structure of segment cladding fiber (SCF) with characteristics of bend-resistance and large-mode-area (LMA) is proposed. In this new structure, the high refractive index (RI) core is periodically surrounded by high RI fan-segmented claddings. Numerical investigations show that effective single-mode operation of the proposed fiber with mode field area of 700 μm2 can be achieved when the bending radius is 15 cm. Besides, this fiber is insensitive to the bending orientation at the ranging of [-180°, 180°]. The proposed design shows great potential in high power fiber lasers and amplifiers with compact structure.

Conformational Sampling of a Biomolecular Rugged Energy Landscape.

PubMed

Rydzewski, Jakub; Jakubowski, Rafal; Nicosia, Giuseppe; Nowak, Wieslaw

2018-01-01

The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.

Discovery of a Phosphodiesterase 9A Inhibitor as a Potential Hypoglycemic Agent

PubMed Central

2015-01-01

Phosphodiesterase 9 (PDE9) inhibitors have been studied as potential therapeutics for treatment of diabetes and Alzheimer’s disease. Here we report a potent PDE9 inhibitor 3r that has an IC50 of 0.6 nM and >150-fold selectivity over other PDEs. The HepG2 cell-based assay shows that 3r inhibits the mRNA expression of phosphoenolpyruvate carboxykinase and glucose 6-phosphatase. These activities of 3r, together with the reasonable pharmacokinetic properties and no acute toxicity at 1200 mg/kg dosage, suggest its potential as a hypoglycemic agent. The crystal structure of PDE9-3r reveals significantly different conformation and hydrogen bonding pattern of 3r from those of previously published 28s. Both 3r and 28s form a hydrogen bond with Tyr424, a unique PDE9 residue (except for PDE8), but 3r shows an additional hydrogen bond with Ala452. This structure information might be useful for design of PDE9 inhibitors. PMID:25432025

Hydrophobic potential of mean force as a solvation function for protein structure prediction.

PubMed

Lin, Matthew S; Fawzi, Nicolas Lux; Head-Gordon, Teresa

2007-06-01

We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.

Spectroscopic investigation, vibrational assignments, HOMO-LUMO, NBO, MEP analysis and molecular docking studies of oxoaporphine alkaloid liriodenine

NASA Astrophysics Data System (ADS)

Costa, Renyer A.; Pitt, Priscilla Olliveira; Pinheiro, Maria Lucia B.; Oliveira, Kelson M. T.; Salomé, Kahlil Schwanka; Barison, Andersson; Costa, Emmanoel Vilaça

2017-03-01

A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of liriodenine is presented using B3LYP function with 6-311G (2d, p) basis set. The theoretical geometry optimization data were compared with the X-ray data for a similar structure in the associated literature, showing similar values. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap, mapped molecular Electrostatic Potential (MEP) surface calculation, first and second order hyperpolarizabilities were also performed with the same calculation level. Theoretical UV spectrum agreed well with the measured experimental data, with transitions assigned. The molecular electrostatic potential map shows opposite potentials regions that forms hydrogen bonds that stabilize the dimeric form, which were confirmed by the close values related to the C dbnd O bond stretching between the dimeric form and the experimental IR spectra (1654 cm- 1 for the experimental, 1700 cm- 1 for the dimer form). Calculated HOMO/LUMO gaps shows the excitation energy for Liriodenine, justifying its stability and kinetics reaction. Molecular docking studies with Candida albicans dihydrofolate reductase (DHFR) and Candida albicans secreted aspartic protease (SAP) showed binding free energies values of - 8.5 and - 8.3 kcal/mol, suggesting good affinity between the liriodenine and the target macromolecules.

Double layer zinc-UDP coordination polymers: structure and properties.

PubMed

Qiu, Qi-Ming; Gu, Leilei; Ma, Hongwei; Yan, Li; Liu, Minghua; Li, Hui

2018-05-17

A homochiral Zn-UDP coordination polymer with an alternating parallel ABAB sequence was constructed and studied by X-ray single crystal diffraction analysis. Its crystal structure shows that there are potentially open sites in the 2D layers. The activation of the sites makes the coordination polymer a fluorescent sensor for novel heterogeneous detection of amino acids.

Peierls potential of screw dislocations in bcc transition metals: Predictions from density functional theory

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

Weinberger, Christopher R.; Tucker, Garritt J.; Foiles, Stephen M.

2013-02-01

It is well known that screw dislocation motion dominates the plastic deformation in body-centered-cubic metals at low temperatures. The nature of the nonplanar structure of screw dislocations gives rise to high lattice friction, which results in strong temperature and strain rate dependence of plastic flow. Thus the nature of the Peierls potential, which is responsible for the high lattice resistance, is an important physical property of the material. However, current empirical potentials give a complicated picture of the Peierls potential. Here, we investigate the nature of the Peierls potential using density functional theory in the bcc transition metals. The resultsmore » show that the shape of the Peierls potential is sinusoidal for every material investigated. Furthermore, we show that the magnitude of the potential scales strongly with the energy per unit length of the screw dislocation in the material.« less

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

Chesny, D. L.; Oluseyi, H. M.; Orange, N. B.

We report on the identification of dynamic flaring non-potential structures on quiet Sun (QS) supergranular network scales. Data from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory allow for the high spatial and temporal resolution of this diverse class of compact structures. The rapidly evolving non-potential events presented here, with lifetimes <10 minutes, are on the order of 10″ in length. Thus, they contrast significantly with well-known active region (AR) non-potential structures such as high-temperature X-ray and EUV sigmoids (>100″) and micro-sigmoids (>10″) with lifetimes on the order of hours to days. The photospheric magnetic field environment derivedmore » from the Helioseismic and Magnetic Imager shows a lack of evidence for these flaring non-potential fields being associated with significant concentrations of bipolar magnetic elements. Of much interest to our events is the possibility of establishing them as precursor signatures of eruptive dynamics, similar to notions for AR sigmoids and micro-sigmoids, but associated with uneventful magnetic network regions. We suggest that the mixed network flux of QS-like magnetic environments, though unresolved, can provide sufficient free magnetic energy for flaring non-potential plasma structuring. The appearance of non-potential magnetic fields could be a fundamental process leading to self-organized criticality in the QS-like supergranular network and contribute to coronal heating, as these events undergo rapid helicial and vortical relaxations.« less

Synthesis and applications of titania nanotubes: Drug delivery and ionomer composites

NASA Astrophysics Data System (ADS)

Kulkarni, Harsha Prabhakar

In this dissertation, the potential of a tubular form of titania (titanium dioxide) has been explored for two diverse applications, in the field of targeted drug delivery for medical applications and in the field of composite materials for structural applications. We introduce the tubular form of titania, a material well known for its catalytic properties. The tubes are synthesized by hydrothermal procedure and are nanometers in dimension, with an inside diameter of 5-6 nm, outside diameter of 10-12, and an aspect ratio of ˜100:1 (l:d), structures both chemically and thermally stable. Biocompatible titania nanotubes with large catalytic surface area are used as vehicles for carrying Doxorubicin, an anticancer chemotherapeutic drug, to explore its potential in targeted drug delivery. Optical properties of Doxorubicin are used to study adsorption and release of the drug molecule from the nanotube surface. Pilot experiments show strong adsorption of 4 wt% of doxorubicin on the nanotube surface characterized by the quenching of its absorption centered at 490 nm. Quinone and protonated amino groups on the drug molecule, involved in protonation and deprotonation with the surface hydroxyls and molecular water on the nanotube surface, are responsible for adsorption. Doxorubicin adsorbed on the nanotube surface show pH specific release, with 40% release at a physiological pH of 7.4 as compared to 4% and 10% at pH values of 3.4 and 5.7 respectively under sink conditions. In vitro cytotoxicity experiments, used to characterize the anticancer potential of the nanotube-drug conjugate, shows comparable toxicity for the conjugates as the free drug. Nanotubes with strong adsorption of doxorubicin, large surface area, pH controlled release, and effective toxicity, demonstrate its potential as a vehicle for targeted drug delivery. If nanotube-drug conjugates with reversible bonds between them, and a pH controlled release in an aqueous solution are promising for medical applications, nanotube-polymer conjugates with nanotubes as reinforcing structures in a polymer matrix with improved mechanical properties are equally promising for structural applications. Nanotubes are used as reinforcing structures in Surlyn, a polyethylene-co-methacrylic acid polymer containing ions. When cooled from the melt, Surlyn shows strong aging effects on mechanical properties over periods of several days to months. Structures in the matrix of the polymer which form with time are responsible for these aging effects on mechanical properties. Aging at short times after cooling from the melt reveal subtle contributions from these structures not fully formed and mechanical properties not fully recovered. Nanotubes are used as reinforcing structures to improve the mechanical properties at short aging times, a property desired for high temperature applications demanding a quick recovery of mechanical properties. A unique Atomic Force Microscope (AFM) based Local Thermal Analysis (LTA) probe is used to study the mechanical properties of Surlyn and Nanotube-Surlyn composite. Nanotube-Surlyn composites show superior mechanical properties at both short and long aging times after cooling from the melt, as the structures in the matrix continue to form at long aging times.

Structure-property relationships in hybrid dental nanocomposite resins containing monofunctional and multifunctional polyhedral oligomeric silsesquioxanes.

PubMed

Wang, Weiguo; Sun, Xiang; Huang, Li; Gao, Yu; Ban, Jinghao; Shen, Lijuan; Chen, Jihua

2014-01-01

Organic-inorganic hybrid materials, such as polyhedral oligomeric silsesquioxanes (POSS), have the potential to improve the mechanical properties of the methacrylate-based composites and resins used in dentistry. In this article, nanocomposites of methacryl isobutyl POSS (MI-POSS [bears only one methacrylate functional group]) and methacryl POSS (MA-POSS [bears eight methacrylate functional groups]) were investigated to determine the effect of structures on the properties of dental resin. The structures of the POSS-containing networks were determined by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy. Monofunctional POSS showed a strong tendency toward aggregation and crystallization, while multifunctional POSS showed higher miscibility with the dimethacrylate monomer. The mechanical properties and wear resistance decreased with increasing amounts of MI-POSS, indicating that the MI-POSS agglomerates act as the mechanical weak point in the dental resins. The addition of small amounts of MA-POSS improved the mechanical and shrinkage properties. However, samples with a higher MA-POSS concentration showed lower flexural strength and flexural modulus, indicating that there is a limited range in which the reinforcement properties of MA-POSS can operate. This concentration dependence is attributed to phase separation at higher concentrations of POSS, which affects the structural integrity, and thus, the mechanical and shrinkage properties of the dental resin. Our results show that resin with 3% MA-POSS is a potential candidate for resin-based dental materials.

Fiber Diffraction of the Prion-Forming Domain HET-s(218-289) Shows Dehydration-Induced Deformation of a Complex Amyloid Structure

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

Wan, William; Stubbs, Gerald

2014-05-01

Amyloids are filamentous protein aggregates that can be formed by many different proteins and are associated with both disease and biological functions. The pathogenicities or biological functions of amyloids are determined by their particular molecular structures, making accurate structural models a requirement for understanding their biological effects. One potential factor that can affect amyloid structures is hydration. Previous studies of simple stacked β-sheet amyloids have suggested that dehydration does not impact structure, but other studies indicated dehydration-related structural changes of a putative water-filled nanotube. Our results show that dehydration significantly affects the molecular structure of the fungal prion-forming domain HET-s(218–289),more » which forms a β-solenoid with no internal solvent-accessible regions. The dehydration-related structural deformation of HET-s(218–289) indicates that water can play a significant role in complex amyloid structures, even when no obvious water-accessible cavities are present.« less

Recognition of LPS by TLR4: Potential for Anti-Inflammatory Therapies

PubMed Central

Nijland, Reindert; Hofland, Tom; van Strijp, Jos A. G.

2014-01-01

LPS molecules of marine bacteria show structures distinct from terrestrial bacteria, due to the different environment that marine bacteria live in. Because of these different structures, lipid A molecules from marine bacteria are most often poor stimulators of the Toll-like receptor 4 (TLR4) pathway. Due to their low stimulatory potential, these lipid A molecules are suggested to be applicable as antagonists of TLR4 signaling in sepsis patients, where this immune response is amplified and unregulated. Antagonizing lipid A molecules might be used for future therapies against sepsis, therapies that currently do not exist. In this review, we will discuss these differences in lipid A structures and their recognition by the immune system. The modifications present in marine lipid A structures are described, and their potential as LPS antagonists will be discussed. Finally, since clinical trials built on antagonizing lipid A molecules have proven unsuccessful, we propose to also focus on different aspects of the TLR4 signaling pathway when searching for new potential drugs. Furthermore, we put forward the notion that bacteria probably already produce inhibitors of TLR4 signaling, making these bacterial products interesting molecules to investigate for future sepsis therapies. PMID:25056632

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

The multifunctional wound dressing with core-shell structured fibers prepared by coaxial electrospinning

NASA Astrophysics Data System (ADS)

Wei, Qilin; Xu, Feiyang; Xu, Xingjian; Geng, Xue; Ye, Lin; Zhang, Aiying; Feng, Zengguo

2016-06-01

The non-woven wound dressing with core-shell structured fibers was prepared by coaxial electrospinning. The polycaprolactone (PCL) was electrospun as the fiber's core to provide mechanical strength whereas collagen was fabricated into the shell in order to utilize its good biocompatibility. Simultaneously, the silver nanoparticles (Ag-NPs) as anti-bacterial agent were loaded in the shell whereas the vitamin A palmitate (VA) as healing-promoting drug was encapsulated in the core. Resulting from the fiber's core-shell structure, the VA released from the core and Ag-NPs present in the shell can endow the dressing both heal-promoting and anti-bacteria ability simultaneously, which can greatly enhance the dressing's clinical therapeutic effect. The dressing can maintain high swelling ratio of 190% for 3 d indicating its potential application as wet dressing. Furthermore, the dressing's anti-bacteria ability against Staphylococcus aureus was proved by in vitro anti-bacteria test. The in vitro drug release test showed the sustainable release of VA within 72 h, while the cell attachment showed L929 cells can well attach on the dressing indicating its good biocompatibility. In conclusion, the fabricated nanofibrous dressing possesses multiple functions to benefit wound healing and shows promising potential for clinical application.

Elimination of resistive losses in large-area LEDs by new diffusion-driven devices

NASA Astrophysics Data System (ADS)

Kivisaari, Pyry; Kim, Iurii; Suihkonen, Sami; Oksanen, Jani

2017-02-01

High-power operation of conventional GaN-based light-emitting diodes (LEDs) is severely limited by current crowding, which increases the bias voltage of the LED, concentrates light emission close to the p-type contact edge, and aggravates the efficiency droop. Fabricating LEDs on thick n-GaN substrates alleviates current crowding but requires the use of expensive bulk GaN substrates and fairly large n-contacts, which take away a large part of the active region (AR). In this work, we demonstrate through comparative simulations how the recently introduced diffusion-driven charge transport (DDCT) concept can be used to realize lateral heterojunction (LHJ) structures, which eliminate most of the lateral current crowding. Specifically in this work, we analyze how using a single-side graded AR can both facilitate electron and hole diffusion in DDCT and increase the effective AR thickness. Our simulations show that the increased effective AR thickness allows a substantial reduction in the efficiency droop at large currents, and that unlike conventional 2D LEDs, the LHJ structure shows practically no added efficiency loss or differential resistance due to current crowding. Furthermore, as both electrons and holes enter the AR from the same side without any notable potential barriers in the LHJ structure, the LHJ structure shows an additional wall-plug efficiency gain over the conventional structures under comparison. This injection from the same side is expected to be even more interesting in multiple quantum well structures, where carriers typically need to surpass several potential barriers in conventional LEDs before recombining. In addition to simulations, we also demonstrate selective-area growth of a finger structure suitable for operation as an LHJ device with 2µm distance between n- and p-GaN regions.

Dark gap solitons in exciton-polariton condensates in a periodic potential.

PubMed

Cheng, Szu-Cheng; Chen, Ting-Wei

2018-03-01

We show that dark spatial gap solitons can occur inside the band gap of an exciton-polariton condensate (EPC) in a one-dimensional periodic potential. The energy dispersions of an EPC loaded into a periodic potential show a band-gap structure. Using the effective-mass model of the complex Gross-Pitaevskii equation with pump and dissipation in an EPC in a periodic potential, dark gap solitons are demonstrated near the minimum energy points of the band center and band edge of the first and second bands, respectively. The excitation energies of dark gap solitons are below these minimum points and fall into the band gap. The spatial width of a dark gap soliton becomes smaller as the pump power is increased.

Dark gap solitons in exciton-polariton condensates in a periodic potential

NASA Astrophysics Data System (ADS)

Cheng, Szu-Cheng; Chen, Ting-Wei

2018-03-01

We show that dark spatial gap solitons can occur inside the band gap of an exciton-polariton condensate (EPC) in a one-dimensional periodic potential. The energy dispersions of an EPC loaded into a periodic potential show a band-gap structure. Using the effective-mass model of the complex Gross-Pitaevskii equation with pump and dissipation in an EPC in a periodic potential, dark gap solitons are demonstrated near the minimum energy points of the band center and band edge of the first and second bands, respectively. The excitation energies of dark gap solitons are below these minimum points and fall into the band gap. The spatial width of a dark gap soliton becomes smaller as the pump power is increased.

Electronic, ductile, phase transition and mechanical properties of Lu-monopnictides under high pressures.

PubMed

Gupta, Dinesh C; Bhat, Idris Hamid

2013-12-01

The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (B2 phase) with space group Pm-3m. Hubbard-U and spin-orbit coupling were included to predict correctly the semiconducting band gap of LuN. Under compression, these materials undergo first-order structural transitions from B1 to B2 phases at 241, 98, 56.82, 25.2 and 32.3 GPa, respectively. The computed elastic properties show that LuBi is ductile by nature. The electronic structure calculations show that LuN is semiconductor at ambient conditions with an indirect band gap of 1.55 eV while other Lu-pnictides are metallic. It was observed that LuN shows metallization at high pressures. The structural properties, viz, equilibrium lattice constant, bulk modulus and its pressure derivative, transition pressure, equation of state, volume collapse, band gap and elastic moduli, show good agreement with available data.

On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization

NASA Astrophysics Data System (ADS)

Jacobsen, T. L.; Jørgensen, M. S.; Hammer, B.

2018-01-01

Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO2 (110 )-(4 ×1 ) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.

Comparative study of the pentamodal property of four potential pentamode microstructures

NASA Astrophysics Data System (ADS)

Huang, Yan; Lu, Xuegang; Liang, Gongying; Xu, Zhuo

2017-03-01

In this paper, a numerical comparative study is presented on the pentamodal property of four potential pentamode microstructures (three based on simple cubic and one on body-centered cubic structures) based on phonon band calculations. The finite-element method is employed to calculate the band structures, and the two essential factors of the ratio of bulk modulus B to shear modulus G and the single-mode band gap (SBG) are analyzed to quantitatively evaluate the pentamodal property. The results show that all four structures possess a higher B/G ratio than traditional materials. One of the simple cubic structures exhibits the incomplete SBG, while the three other structures exhibit complete SBG to decouple the compression and shear waves in all propagation directions. Further parametric analyses are presented investigating the effects of geometrical and material parameters on the pentamodal property of these structures. This study provides guidelines for the future design of novel pentamode microstructures possessing a high B/G ratio and a low-frequency broadband SBG.

Lone pair effect, structural distortions, and potential for superconductivity in Tl perovskites.

PubMed

Schoop, Leslie M; Müchler, Lukas; Felser, Claudia; Cava, R J

2013-05-06

Drawing the analogy to BaBiO3, we investigate via ab initio electronic structure calculations potential new superconductors of the type ATlX3 with A = Rb and Cs and X = F, Cl, and Br, with a particular emphasis on RbTlCl3. On the basis of chemical reasoning, supported by the calculations, we show that Tl-based perovskites have structural and charge instabilities driven by the lone pair effect, similar to the case of BaBiO3, effectively becoming A2Tl(+)Tl(3+)X6. We find that upon hole doping of RbTlCl3, structures without Tl(+) and Tl(3+) charge disproportionation become more stable, although the ideal cubic perovskite, often viewed as the best host for superconductivity, should not be the most stable phase in the system. The known superconductor (Sr,K)BiO3 and hole doped RbTlCl3, predicted to be most stable in the same tetragonal structure, display highly analogous calculated electronic band structures.

Structural, magnetic and transport properties of 2D structured perovskite oxychalcogenides

NASA Astrophysics Data System (ADS)

Berthebaud, David; Lebedev, Oleg I.; Pelloquin, Denis; Maignan, Antoine

2014-10-01

We have been looking for new potential thermoelectric materials in the family of 2D structured perovskite oxychalcogenides containing [Cu2Ch2]2- blocks (Ch = S or Se). Using high temperature syntheses, a new oxyselenide Sr2CuFeO3Se has been isolated and its structure has been compared to the isotypes sulfides, Ca2CuFeO3S and Sr2CuFeO3S, prepared by the same technique. By combining powder XRD and TEM analyses their composition and structure were analyzed. They all three crystallize in the Sr2CuGaO3S-type structure, with only the oxyselenide showing a Fe deficiency which is related to the stacking faults evidenced by high resolution TEM. Transport and magnetic properties of the samples have been studied; especially their electrical resistivity is characterized by high values in the range from 1 to 10 kΩ cm at 300 K. Thermoelectric potential of these materials is also discussed.

Parameter and Structure Inference for Nonlinear Dynamical Systems

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

2006-01-01

A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

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

Zhang, Y.; Ashcraft, R.; Mendelev, M. I.

The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni62Nb38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation. This simulation also showed that the FS potential well reproduces the bond angle distributions. The FS potential was then employed to elongate themore » AIMD PPCFs and determine the total structure factor (TSF) which was found to be in excellent agreement with X-ray TSF obtained within the present study demonstrating the reliability of the AIMD for the simulation of the structure of the liquid Ni–Nb alloys as well as the reliability of the developed FS potential. The glass structure obtained with the developed potential was also found to be in excellent agreement with the X-ray data. The analysis of the structure revealed that a network of the icosahedra clusters centered on Ni atoms is forming during cooling the liquid alloy down to T g and the Nb Z14, Z15, and Z16 clusters are attached to this network. This network is the main feature of the Ni 62Nb 38 alloy and further investigations of the properties of this alloy should be based on study of the behavior of this network.« less

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

NASA Astrophysics Data System (ADS)

Meyer, Sam; Everaers, Ralf

2015-02-01

The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

Full depth reclamation : workshop materials.

DOT National Transportation Integrated Search

2011-01-01

Rehabilitating an old pavement by pulverizing and stabilizing the existing pavement is a process referred to as Full Depth Reclamation (FDR). This process shows great potential as an economical rehabilitation alternative that provides deep structural...

Ba 2TeO as an optoelectronic material: First-principles study

DOE PAGES

Sun, Jifeng; Shi, Hongliang; Du, Mao-Hua; ...

2015-05-21

The band structure, optical and defects properties of Ba 2TeO are systematically investigated using density functional theory with a view to understanding its potential as an optoelectronic or transparent conducting material. Ba 2TeO crystallizes with tetragonal structure (space group P4/nmm) and with a 2.93 eV optical band gap1. We find relatively modest band masses for both electrons and holes suggesting applications. Optical properties show a infrared-red absorption when doped. This could potentially be useful for combining wavelength filtering and transparent conducting functions. Furthermore, our defect calculations show that Ba 2TeO is intrinsically p-type conducting under Ba-poor condition. However, the spontaneousmore » formation of the donor defects may constrain the p-type transport properties and would need to be addressed to enable applications.« less

Modeling photovoltaic performance in periodic patterned colloidal quantum dot solar cells.

PubMed

Fu, Yulan; Dinku, Abay G; Hara, Yukihiro; Miller, Christopher W; Vrouwenvelder, Kristina T; Lopez, Rene

2015-07-27

Colloidal quantum dot (CQD) solar cells have attracted tremendous attention mostly due to their wide absorption spectrum window and potentially low processability cost. The ultimate efficiency of CQD solar cells is highly limited by their high trap state density. Here we show that the overall device power conversion efficiency could be improved by employing photonic structures that enhance both charge generation and collection efficiencies. By employing a two-dimensional numerical model, we have calculated the characteristics of patterned CQD solar cells based of a simple grating structure. Our calculation predicts a power conversion efficiency as high as 11.2%, with a short circuit current density of 35.2 mA/cm2, a value nearly 1.5 times larger than the conventional flat design, showing the great potential value of patterned quantum dot solar cells.

Electrochemical, Structural and Magnetic Analysis of Electrodeposited CoCu/Cu Multilayers: Influence of Cu Layer Deposition Potential

NASA Astrophysics Data System (ADS)

Tekgül, Atakan; Kockar, Hakan; Kuru, Hilal; Alper, Mürsel; ÜnlÜ, C. Gökhan

2018-03-01

The electrochemical, structural and magnetic properties of CoCu/Cu multilayers electrodeposited at different cathode potentials were investigated from a single bath. The Cu layer deposition potentials were selected as - 0.3, V - 0.4 V, and - 0.5 V with respect to saturated calomel electrode (SCE) while the Co layer deposition potential was constant at - 1.5 V versus SCE. For the electrochemical analysis, the current-time transients were obtained. The amount of noble non-magnetic (Cu) metal materials decreased with the increase of deposition potentials due to anomalous codeposition. Further, current-time transient curves for the Co layer deposition and capacitance were calculated. In the structural analysis, the multilayers were found to be polycrystalline with both Co and Cu layers adopting the face-centered cubic structure. The (111) peak shifts towards higher angle with the increase of the deposition potentials. Also, the lattice parameters of the multilayers decrease from 0.3669 nm to 0.3610 nm with the increase of the deposition potentials from - 0.3 V to - 0.5 V, which corresponds to the bulk values of Cu and Co, respectively. The electrochemical and structural results demonstrate that the amount of Co atoms increased and the Cu atoms decreased in the layers with the increase of deposition potentials due to anomalous codeposition. For magnetic measurements, the saturation magnetizations, M_s obtained from the magnetic curves of the multilayers were obtained as 212 kA/m, 276 kA/m, and 366 kA/m with - 0.3 V, - 0.4 V, and - 0.5 V versus SCE, respectively. It is seen that the M_s values increased with the increase of the deposition potentials confirming the increase of the Co atoms and decrease of the Cu amount. The results of electrochemical and structural analysis show that the deposition potentials of non-magnetic layers plays important role on the amount of magnetic and non-magnetic materials in the layers and thus on the magnetic properties of the multilayers.

Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

NASA Astrophysics Data System (ADS)

Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

2018-05-01

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

Microwave-assisted synthesis, structural characterization, DFT studies, antibacterial and antioxidant activity of 2-methyl-4-oxo-1,2,3,4-tetrahydroquinazoline-2-carboxylic acid

NASA Astrophysics Data System (ADS)

Obafemi, Craig A.; Fadare, Olatomide A.; Jasinski, Jerry P.; Millikan, Sean P.; Obuotor, Efere M.; Iwalewa, Ezekiel O.; Famuyiwa, Samson O.; Sanusi, Kayode; Yilmaz, Yusuf; Ceylan, Ümit

2018-03-01

In the present study a new tetrahydroquinazoline-2-carboxylic, C10H10N2O3, 1‧, was synthesized and its structure was characterized by elemental analysis, IR, 1H NMR, 13C NMR data and high-resolution mass spectrometry. The spectral results are in line with the proposed structure. Single crystal X-ray structural analysis of the compound showed that the crystal structure adopts a monoclinic space group P21/c, with the packing of the molecule stabilized by Cdbnd O … …Hsbnd O, Nsbnd H … ….Odbnd Csbnd Osbnd intermolecular hydrogen bonding. The theoretical geometrical parameters of the compound have been calculated using density functional (DFT) and time-dependent density functional (TD-DFT) theory methods and have been used to predict the thermodynamic one-electron redox potential and the electronic absorption property of the compound. The theoretical characterization matched the experimental measurements, showing a good correlation. The calculated HOMO-LUMO gap (4.79 eV) suggests that compound 1‧ could be a potential antioxidant. The synthesized compound was screened for its in vitro antimicrobial activity against selected bacterial strains and antioxidant activity using the TAC, FRAP, NO and ABTS models. In vitro antioxidant activity of 1' showed a moderate activity, but weaker scavenging activity than the standards of ascorbic acid and trolox. Results of the antibacterial activity of the tested compound showed that it possesses a higher activity against Bacillus anthracis, Bacillus cereus, Bacillus polymyxa, Bacillus subtilis and Staphylococcus aureus than the two standard drugs, streptomycin and tetracycline, and better activity than tetracycline against Escherichia coli.

Detailed interpretation of aeromagnetic data from the Patagonia Mountains area, southeastern Arizona

USGS Publications Warehouse

Bultman, Mark W.

2015-01-01

Euler deconvolution depth estimates derived from aeromagnetic data with a structural index of 0 show that mapped faults on the northern margin of the Patagonia Mountains generally agree with the depth estimates in the new geologic model. The deconvolution depth estimates also show that the concealed Patagonia Fault southwest of the Patagonia Mountains is more complex than recent geologic mapping represents. Additionally, Euler deconvolution depth estimates with a structural index of 2 locate many potential intrusive bodies that might be associated with known and unknown mineralization.

Vision-Based Precision Landings of a Tailsitter UAV

DTIC Science & Technology

2010-04-01

2.2: Schematic of the controller used in simulation. The block diagram shown in Figure 2.2 shows the simulation structure used to simulate the vision...the structure of the flight facility walls, any vibration applied to the structure would potentially change the pose of the cameras. Each camera’s pose...relative to the target in Chap- ter 4, a flat earth assumption was made. In several situations the approximation that the ground over which the UAV is

Relationships between structure and function: System structure matters whether you are in a wetland or a college classroom

NASA Astrophysics Data System (ADS)

Andrews, Sarah Elizabeth

Part I of this dissertation describes two research projects I undertook to understand how structure influences function in freshwater wetlands. In the first study I tested the hypothesis that wetland structure (created versus natural) would influence function (methane cycling). Created wetlands had reduced rates of potential methane production and potential methane oxidation compared to natural wetlands; this was most likely explained by differences in edaphic factors that characterized each wetland, particularly soil moisture and soil organic matter. In the second study (Andrews et al. 2013), I tested the hypothesis that plant community structure (functional group composition, richness, presence/absence) would influence function (methane and iron cycling) in wetland mesocosms. Plant functional group richness was less important than the type of vegetation present: the presence of perennial vegetation (reeds or tussocks) led to increased rates of potential iron reduction compared to when only annual vegetation was present. Part II of this dissertation describes research I undertook to understand how structure influences function in an undergraduate soil science course. In the first study I tested the hypothesis that course structure (traditional versus studio) would influence function (student performance) in the course. Students in the studio course outperformed students in the traditional course; there was also a decrease in the fail rate. In the second study I looked at students' perspectives on their learning and experiences (function) in the studio course and asked whether students' epistemological development influenced this function. Interviews with students revealed that active learning, the integrated nature of the course, community, and variety of learning and assessment methods helped student learning. Students' epistemological development (interpreted from the Measure of Epistemological Reflection) permeated much of what they spoke about during the interviews. There was also evidence that the studio structure may help promote epistemological growth via "sneaky learning" and an expanded role of peers. The studies in Part I show that differences in structure affect function in freshwater wetland systems and the studies in Part II show that structure affects function in an undergraduate introductory soil science course. Thus, system structure matters whether you are in a wetland or a college classroom.

Device applications and structural and optical properties of Indigo - A biodegradable, low-cost organic semiconductor

NASA Astrophysics Data System (ADS)

Wang, Zhengjun; Pisane, Kelly L.; Sierros, Konstantinos; Seehra, Mohindar S.; Korakakis, Dimitris

2015-03-01

Currently, memory devices based on organic materials are attracting great attention due to their simplicity in device structure, mechanical flexibility, potential for scalability, low-cost potential, low-power operation, and large capacity for data storage. In a recent paper from our group, Indigo-based nonvolatile organic write-once-read-many-times (WORM) memory device, consisting of a 100nm layer of indigo sandwiched between an indium tin oxide (ITO) cathode and an Al anode, has been reported. This device is found to be at its low resistance state (ON state) and can be switched to high resistance state (OFF state) by applying a positive bias with ON/OFF current ratio of the device being up to 1.02 × e6. A summary of these results along with the structural and optical properties of indigo powder will be reported. Analysis of x-ray diffraction shows a monoclinic structure with lattice parameters a(b)[c] = 0.924(0.577)[0.1222]nm and β =117° . Optical absorption shows a band edge at 1.70 eV with peak of absorption occurring at 1.90 eV. These results will be interpreted in terms of the HOMO-LUMO bands of Indigo.

Impact of Solar Array Position on ISS Vehicle Charging

NASA Technical Reports Server (NTRS)

Alred, John; Mikatarian, Ronald; Koontz, Steve

2006-01-01

The International Space Station (ISS), because of its large structure and high voltage solar arrays, has a complex plasma interaction with the ionosphere in low Earth orbit (LEO). This interaction of the ISS US Segment photovoltaic (PV) power system with the LEO ionospheric plasma produces floating potentials on conducting elements of the ISS structure relative to the local plasma environment. To control the ISS floating potentials, two Plasma Contactor Units (PCUs) are installed on the Z1 truss. Each PCU discharges accumulated electrons from the Space Station structure, thus reducing the potential difference between the ISS structure and the surrounding charged plasma environment. Operations of the PCUs were intended to keep the ISS floating potential to 40 Volts (Reference 1). Exposed dielectric surfaces overlying conducting structure on the Space Station will collect an opposite charge from the ionosphere as the ISS charges. In theory, when an Extravehicular Activity (EVA) crewmember is tethered to structure via the crew safety tether or when metallic surfaces of the Extravehicular Mobility Unit (EMU) come in contact with conducting metallic surfaces of the ISS, the EMU conducting components, including the perspiration-soaked crewmember inside, can become charged to the Space Station floating potential. The concern is the potential dielectric breakdown of anodized aluminum surfaces on the EMU producing an arc from the EMU to the ambient plasma, or nearby ISS structure. If the EMU arcs, an electrical current of an unknown magnitude and duration may conduct through the EVA crewmember, producing an unacceptable condition. This electrical current may be sufficient to startle or fatally shock the EVA crewmember (Reference 2). Hence, as currently defined by the EVA community, the ISS floating potential for all nominal and contingency EVA worksites and translation paths must have a magnitude less than 40 volts relative to the local ionosphere at all times during EVA. Arcing from the EMU is classified as a catastrophic hazard, which requires two-failure tolerant controls, i.e., three hazard controls. Each PCU is capable of maintaining the ISS floating potential below the requirement during EVA. The two PCUs provide a single failure tolerant control of ISS floating potential. In the event of the failure of one or two PCUs, a combination of solar array shunting and turning the solar arrays into their own wakes will be used to supply control of the plasma hazard (Reference 3). The purpose of this paper is to present on-orbit information that shows that ISS solar array placement with respect to the ISS velocity vector can control solar array plasma charging, and hence, provide an operational control for the plasma hazard. Also, this paper will present on-orbit information that shows that shunting of the ISS solar arrays can control solar array plasma charging, and hence, provide an additional operational control for the plasma hazard.

Magnetophoresis of flexible DNA-based dumbbell structures

NASA Astrophysics Data System (ADS)

Babić, B.; Ghai, R.; Dimitrov, K.

2008-02-01

Controlled movement and manipulation of magnetic micro- and nanostructures using magnetic forces can give rise to important applications in biomedecine, diagnostics, and immunology. We report controlled magnetophoresis and stretching, in aqueous solution, of a DNA-based dumbbell structure containing magnetic and diamagnetic microspheres. The velocity and stretching of the dumbbell were experimentally measured and correlated with a theoretical model based on the forces acting on individual magnetic beads or the entire dumbbell structures. The results show that precise and predictable manipulation of dumbbell structures is achievable and can potentially be applied to immunomagnetic cell separators.

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

MHD Equilibrium with Reversed Current Density and Magnetic Islands Revisited: the Vacuum Vector Potential Calculus

NASA Astrophysics Data System (ADS)

L. Braga, F.

2013-10-01

The solution of Grad-Shafranov equation determines the stationary behavior of fusion plasma inside a tokamak. To solve the equation it is necessary to know the toroidal current density profile. Recent works show that it is possible to determine a magnetohydrodynamic (MHD) equilibrium with reversed current density (RCD) profiles that presents magnetic islands. In this work we show analytical MHD equilibrium with a RCD profile and analyze the structure of the vacuum vector potential associated with these equilibria using the virtual casing principle.

MgB2 thick films on three-dimensional structures fabricated by HPCVD

NASA Astrophysics Data System (ADS)

Guo, Zhengshan; Cai, Xingwei; Liao, Xuebin; Chen, Yiling; Yang, Can; Niu, Ruirui; Luo, Wenhao; Huang, Zigeng; Feng, Qingrong; Gan, Zizhao

2018-06-01

Magnetic shielding has been a key factor in the measurement of ultra-weak magnetic fields, especially for shielding from low frequency electromagnetic noise. With the recent development of superconducting quantum interference devices, superconducting magnetic shielding has become an important area of research. MgB2 has shown great potential in magnetic shielding for its remarkable superconducting properties, the feasibility of its use in this capacity having been demonstrated by MgB2 bulk samples. However, the potential for application of such bulk samples is limited. In this work, we have investigated the possibility of the fabrication of MgB2 films on three-dimensional (3D) structures using a hybrid physical‑chemical vapor deposition system. MgB2 films 10 μm thick have been fabricated on the outer surface of a polycrystalline Al2O3 cylinder. The deposited film showed a transition temperature (TC) of 39 K and J C of 5.1 × 105 A · cm‑2, which are comparable to those of planar MgB2 films. This work shows the feasibility of depositing MgB2 films onto a 3D structure, and sheds light on the potential use of MgB2 films in superconducting magnetic shielding.

Surface and structure modification induced by high energy and highly charged uranium ion irradiation in monocrystal spinel

NASA Astrophysics Data System (ADS)

Yang, Yitao; Zhang, Chonghong; Song, Yin; Gou, Jie; Zhang, Liqing; Meng, Yancheng; Zhang, Hengqing; Ma, Yizhun

2014-05-01

Due to its high temperature properties and relatively good behavior under irradiation, magnesium aluminate spinel (MgAl2O4) is considered as a possible material to be used as inert matrix for the minor actinides burning. In this case, irradiation damage is an unavoidable problem. In this study, high energy and highly charged uranium ions (290 MeV U32+) were used to irradiate monocrystal spinel to the fluence of 1.0 × 1013 ions/cm2 to study the modification of surface and structure. Highly charged ions carry large potential energy, when they interact with a surface, the release of potential energy results in the modification of surface. Atomic force microscopy (AFM) results showed the occurrence of etching on surface after uranium ion irradiation. The etching depth reached 540 nm. The surprising efficiency of etching is considered to be induced by the deposition of potential energy with high density. The X-ray diffraction results showed that the (4 4 0) diffraction peak obviously broadened after irradiation, which indicated that the distortion of lattice has occurred. After multi-peak Gaussian fitting, four Gaussian peaks were separated, which implied that a structure with different damage layers could be formed after irradiation.

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

PubMed Central

2012-01-01

Background Post-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) of mRNAs, in collaboration with specific binding proteins and RNAs. In several well characterized cases, these RNA elements are known to form stable secondary structures. RNA secondary structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance of lncRNAs in brain development and function. However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts. Results By comprehensive spatial expression analysis of the adult mouse in situ hybridization data of the Allen Mouse Brain Atlas, we show that transcripts (coding as well as non-coding) associated with in silico predicted structured probes are highly and significantly enriched in almost all analyzed brain regions. Functional implications of these RNA structures and their role in the brain are discussed in detail along with specific examples. We observe that mRNAs with a structure prediction in their UTRs are enriched for binding, transport and localization gene ontology categories. In addition, after manual examination we observe agreement between RNA binding protein interaction sites near the 3’ UTR structures and correlated expression patterns. Conclusions Our results show a potential use for RNA structures in expressed coding as well as noncoding transcripts in the adult mouse brain, and describe the role of structured RNAs in the context of intracellular signaling pathways and regulatory networks. Based on this data we hypothesize that RNA structure is widely involved in transcriptional and translational regulatory mechanisms in the brain and ultimately plays a role in brain function. PMID:22651826

Climate limits across space and time on European forest structure

NASA Astrophysics Data System (ADS)

Moreno, A. L. S.; Neumann, M.; Hasenauer, H.

2017-12-01

The impact climate has on forests has been extensively studied. However, the large scale effect climate has on forest structures, such as average diameters, heights and basal area are understudied in a spatially explicit manner. The limits, tipping points and thresholds that climate places on forest structures dictate the services a forest may provide, the vulnerability of a forest to mortality and the potential value of the timber there within. The majority of current research either investigates climate impacts on forest pools and fluxes, on a tree physiological scale or on case studies that are used to extrapolate results and potential impacts. A spatially explicit study on how climate affects forest structure over a large region would give valuable information to stakeholders who are more concerned with ecosystem services that cannot be described by pools and fluxes but require spatially explicit information - such as biodiversity, habitat suitability, and market values. In this study, we quantified the limits that climate (maximum, minimum temperature and precipitation) places on 3 forest structures, diameter at breast height, height, and basal area throughout Europe. Our results show clear climatic zones of high and low upper limits for each forest structure variable studied. We also spatially analyzed how climate restricts the potential bio-physical upper limits and creates tipping points of each forest structure variable and which climate factors are most limiting. Further, we demonstrated how the climate change has affected 8 individual forests across Europe and then the continent as a whole. We find that diameter, height and basal area are limited by climate in different ways and that areas may have high upper limits in one structure and low upper limits in another limitted by different climate variables. We also found that even though individual forests may have increased their potential upper limit forest structure values, European forests as a whole have lost, on average, 5.0%, 1.7% and 6.5% in potential mean forest diameter, height and basal area, respectively.

Citrinamides, new potentiators of antifungal miconazole activity, produced by Penicillium sp. FKI-1938.

PubMed

Fukuda, Takashi; Hasegawa, Yoko; Sakabe, Yasunari; Tomoda, Hiroshi; Omura, Satoshi

2008-09-01

Two new aromatic alkaloids, designated citrinamides A and B, were isolated from the culture broth of Penicillium sp. FKI-1938 by solvent extraction, silica gel column chromatography and HPLC. Their structures were elucidated by spectroscopic analysis, including NMR and amino acid analysis. Citrinamides A and B showed moderate potentiation of miconazole activity against Candida albicans.

Geologic Insights and Suggestions on Mineral Potential Based on Analyses of Geophysical Data of the Southern Toquima Range, Nye County, Nevada

USGS Publications Warehouse

Shawe, D.R.; Kucks, R.P.; Hildenbrand, T.G.

2004-01-01

Aeromagnetic and gravity data provide confirmation of major structural and lithologic units in the southern Toquima Range, Nevada. These units include Cretaceous granite plutons and Tertiary calderas. In addition, the geophysical maps pinpoint numerous faults and lesser intrusions, and they suggest locations of several inferred subsurface intrusions. They also corroborate a system of northwesterly and northeasterly conjugate structures that probably are fundamental to the structural framework of the Toquima Range. A combination of geophysical, geochemical, and geologic data available for the widely mineralized and productive area suggests additional mineral resource potential, especially in and (or) adjacent to the Round Mountain, Jefferson, Manhattan, and Belmont mining districts. Also, evidence for mineral potential exists for areas near the Flower mercury mine south of Mount Jefferson caldera, and in the Bald Mountain Canyon belt of gold-quartz veins in the Manhattan caldera. A few other areas also show potential for mineral resources. The various geologic environments indicated within the map area suggest base- and precious-metal potential in porphyry deposits as well as in quartz-vein and skarn deposits associated with intrusive stocks.

A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase

PubMed Central

Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R.; Yang, Shaoqing; Jiang, Zhengqiang

2015-01-01

Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions — a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins. PMID:26669854

A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase.

PubMed

Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R; Yang, Shaoqing; Jiang, Zhengqiang

2015-12-16

Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions--a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins.

Electrostatic Structure and Double-Probe Performance in Tenuous Plasmas

NASA Astrophysics Data System (ADS)

Cully, C. M.; Ergun, R. E.

2006-12-01

Many in-situ plasma instruments are affected by the local electrostatic structure surrounding the spacecraft. In order to better understand this structure, we have developed a fully 3-dimensional self-consistent model that uses realistic spacecraft geometry, including thin (<1 mm) wires and long (>100m) booms, with open boundary conditions. One of the more surprising results is that in tenuous plasmas, the charge on the booms can dominate over the charge on the spacecraft body. For instruments such as electric field double probes and boom-mounted low-energy particle detectors, this challenges the existing paradigm: long booms do not allow the probes to escape the spacecraft potential. Instead, the potential structure simply expands as the boom is deployed. We then apply our model to the double-probe Electric Field and Waves (EFW) instruments on Cluster, and predict the magnitudes of the main error sources. The overall error budget is consistent with experiment, and the model yields some additional interesting insights. We show that the charge in the photoelectron cloud is relatively unimportant, and that the spacecraft potential is typically underestimated by about 20% by double-probe experiments.

Ab Initio -Based Bond Order Potential to Investigate Low Thermal Conductivity of Stanene Nanostructures

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

Cherukara, Mathew J.; Narayanan, Badri; Kinaci, Alper

2016-08-28

We introduce a bond order potential (BOP) for stanene based on an ab initio derived training data set. The potential is optimized to accurately describe the energetics, as well as thermal and mechanical properties of a free-standing sheet, and used to study diverse nanostructures of stanene, including tubes and ribbons. As a representative case study, using the potential, we perform molecular dynamics simulations to study stanene’s structure and temperature-dependent thermal conductivity. We find that the structure of stanene is highly rippled, far in excess of other 2-D materials (e.g., graphene), owing to its low in-plane stiffness (stanene: ~ 25 N/m;more » graphene: ~ 480 N/ m). The extent of stanene’s rippling also shows stronger temperature dependence compared to that in graphene. Furthermore, we find that stanene based nanostructures have significantly lower thermal conductivity compared to graphene based structures owing to their softness (i.e., low phonon group velocities) and high anharmonic response. Our newly developed BOP will facilitate the exploration of stanene based low dimensional heterostructures for thermoelectric and thermal management applications.« less

Whole Protein Native Fitness Potentials

NASA Astrophysics Data System (ADS)

Faraggi, Eshel; Kloczkowski, Andrzej

2013-03-01

Protein structure prediction can be separated into two tasks: sample the configuration space of the protein chain, and assign a fitness between these hypothetical models and the native structure of the protein. One of the more promising developments in this area is that of knowledge based energy functions. However, standard approaches using pair-wise interactions have shown shortcomings demonstrated by the superiority of multi-body-potentials. These shortcomings are due to residue pair-wise interaction being dependent on other residues along the chain. We developed a method that uses whole protein information filtered through machine learners to score protein models based on their likeness to native structures. For all models we calculated parameters associated with the distance to the solvent and with distances between residues. These parameters, in addition to energy estimates obtained by using a four-body-potential, DFIRE, and RWPlus were used as training for machine learners to predict the fitness of the models. Testing on CASP 9 targets showed that our method is superior to DFIRE, RWPlus, and the four-body potential, which are considered standards in the field.

Mechanisms of action of ligands of potential-dependent sodium channels.

PubMed

Tikhonov, D B

2008-06-01

Potential-dependent sodium channels play a leading role in generating action potentials in excitable cells. Sodium channels are the site of action of a variety of modulator ligands. Despite numerous studies, the mechanisms of action of many modulators remain incompletely understood. The main reason that many important questions cannot be resolved is that there is a lack of precise data on the structures of the channels themselves. Structurally, potential-dependent sodium channels are members of the P-loop channel superfamily, which also include potassium and calcium channels and glutamate receptor channels. Crystallization of a series of potassium channels showed that it was possible to analyze the structures of different members of the superfamily using the "homologous modeling" method. The present study addresses model investigations of the actions of ligands of sodium channels, including tetrodotoxin and batrachotoxin, as well as local anesthetics. Comparison of experimental data on sodium channel ligands with x-ray analysis data allowed us to reach a new level of understanding of the mechanisms of channel modulation and to propose a series of experimentally verifiable hypotheses.

Theoretical investigation of the structural stabilities, optoelectronic properties and thermodynamic characteristics of GaPxSb1-x ternary alloys

NASA Astrophysics Data System (ADS)

Oumelaz, F.; Nemiri, O.; Boumaza, A.; Ghemid, S.; Meradji, H.; Bin Omran, S.; El Haj Hassan, F.; Rai, D. P.; Khenata, R.

2018-06-01

In this theoretical study, we have investigated the structural, phase transition, electronic, thermodynamic and optical properties of GaPxSb1-x ternary alloys. Our calculations are performed with the WIEN2k code based on density functional theory using the full-potential linearized augmented plane wave method. For the electron exchange-correlation potential, a generalized gradient approximation within Wu-Cohen scheme is considered. The recently developed Tran-Blaha modified Becke-Johnson potential has also been used to improve the underestimated band gap. The structural properties, including the lattice constants, the bulk moduli and their pressure derivatives are in very good agreement with the available experimental data and theoretical results. Several structural phase transitions were studied here to establish the stable structure and to predict the phase transition under hydrostatic pressure. The computed transition pressure (Pt) of the material of our interest from the zinc blende (B3) to the rock salt (B1) phase has been determined and found to agree well with the experimental and theoretical data. The calculated band structure shows that GaSb binary compound and the ternary alloys are direct band gap semiconductors. Optical parameters such as the dielectric constants and the refractive indices are calculated and analyzed. The thermodynamic results are also interpreted and analyzed.

Short- and medium-range structure of multicomponent bioactive glasses and melts: An assessment of the performances of shell-model and rigid-ion potentials.

PubMed

Tilocca, Antonio

2008-08-28

Classical and ab initio molecular dynamics (MD) simulations have been carried out to investigate the effect of a different treatment of interatomic forces in modeling the structural properties of multicomponent glasses and melts. The simulated system is a soda-lime phosphosilicate composition with bioactive properties. Because the bioactivity of these materials depends on their medium-range structural features, such as the network connectivity and the Q(n) distribution (where Q(n) is a tetrahedral species bonded to n bridging oxygens) of silicon and phosphorus network formers, it is essential to assess whether, and up to what extent, classical potentials can reproduce these properties. The results indicate that the inclusion of the oxide ion polarization through a shell-model (SM) approach provides a more accurate representation of the medium-range structure compared to rigid-ion (RI) potentials. Insight into the causes of these improvements has been obtained by comparing the melt-and-quench transformation of a small sample of the same system, modeled using Car-Parrinello MD (CPMD), to the classical MD runs with SM and RI potentials. Both classical potentials show some limitations in reproducing the highly distorted structure of the melt denoted by the CPMD runs; however, the inclusion of polarization in the SM potential results in a better and qualitatively correct dynamical balance between the interconversion of Q(n) species during the cooling of the melt. This effect seems to reflect the slower decay of the fraction of structural defects during the cooling with the SM potential. Because these transient defects have a central role in mediating the Q(n) transformations, as previously proposed and confirmed by the current simulations, their presence in the melt is essential to produce an accurate final distribution of Q(n) species in the glass.

Diffusion mechanism of non-interacting Brownian particles through a deformed substrate

NASA Astrophysics Data System (ADS)

Arfa, Lahcen; Ouahmane, Mehdi; El Arroum, Lahcen

2018-02-01

We study the diffusion mechanism of non-interacting Brownian particles through a deformed substrate. The study is done at low temperature for different values of the friction. The deformed substrate is represented by a periodic Remoissenet-Peyrard potential with deformability parameter s. In this potential, the particles (impurity, adatoms…) can diffuse. We ignore the interactions between these mobile particles consider them merely as non-interacting Brownian particles and this system is described by a Fokker-Planck equation. We solve this equation numerically using the matrix continued fraction method to calculate the dynamic structure factor S(q , ω) . From S(q , ω) some relevant correlation functions are also calculated. In particular, we determine the half-width line λ(q) of the peak of the quasi-elastic dynamic structure factor S(q , ω) and the diffusion coefficient D. Our numerical results show that the diffusion mechanism is described, depending on the structure of the potential, either by a simple jump diffusion process with jump length close to the lattice constant a or by a combination of a jump diffusion model with jump length close to lattice constant a and a liquid-like motion inside the unit cell. It shows also that, for different friction regimes and various potential shapes, the friction attenuates the diffusion mechanism. It is found that, in the high friction regime, the diffusion process is more important through a deformed substrate than through a non-deformed one.

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

PubMed

de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

2016-02-02

The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem-also called "microbiome"-is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. Copyright © 2016 de Steenhuijsen Piters and Bogaert.

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

PubMed Central

de Steenhuijsen Piters, Wouter A. A.

2016-01-01

ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

Crystal structure of a β-aminopeptidase from an Australian Burkholderia sp.

PubMed

John-White, Marietta; Dumsday, Geoff J; Johanesen, Priscilla; Lyras, Dena; Drinkwater, Nyssa; McGowan, Sheena

2017-07-01

β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.

Effect of attractive interactions on the water-like anomalies of a core-softened model potential.

PubMed

Pant, Shashank; Gera, Tarun; Choudhury, Niharendu

2013-12-28

It is now well established that water-like anomalies can be reproduced by a spherically symmetric potential with two length scales, popularly known as core-softened potential. In the present study we aim to investigate the effect of attractive interactions among the particles in a model fluid interacting with core-softened potential on the existence and location of various water-like anomalies in the temperature-pressure plane. We employ extensive molecular dynamic simulations to study anomalous nature of various order parameters and properties under isothermal compression. Order map analyses have also been done for all the potentials. We observe that all the systems with varying depth of attractive wells show structural, dynamic, and thermodynamic anomalies. As many of the previous studies involving model water and a class of core softened potentials have concluded that the structural anomaly region encloses the diffusion anomaly region, which in turn, encloses the density anomaly region, the same pattern has also been observed in the present study for the systems with less depth of attractive well. For the systems with deeper attractive well, we observe that the diffusion anomaly region shifts toward higher densities and is not always enclosed by the structural anomaly region. Also, density anomaly region is not completely enclosed by diffusion anomaly region in this case.

Chemical and structural indicators for large redox potentials in Fe-based positive electrode materials.

PubMed

Melot, Brent C; Scanlon, David O; Reynaud, Marine; Rousse, Gwenaëlle; Chotard, Jean-Noël; Henry, Marc; Tarascon, Jean-Marie

2014-07-23

Li-ion batteries have enabled a revolution in the way portable consumer-electronics are powered and will play an important role as large-scale electrochemical storage applications like electric vehicles and grid-storage are developed. The ability to identify and design promising new positive insertion electrodes will be vital in continuing to push Li-ion technology to its fullest potential. Utilizing a combination of computational tools and structural analysis, we report new indicators which will facilitate the recognition of phases with the desired redox potential. Most importantly of these, we find there is a strong correlation between the presence of Li ions sitting in close-proximity to the redox center of polyanionic phases and the open circuit voltage in Fe-based cathodes. This common structural feature suggests that the bonding associated with Li may have a secondary inductive effect which increases the ionic character of Fe bonds beyond what is typically expected based purely on arguments of electronegativity associated with the polyanionic group. This correlation is supported by ab initio calculations which show the Bader charge increases (reflecting an increased ionicity) in a nearly linear fashion with the experimental cell potentials. These features are demonstrated to be consistent across a wide variety of compositions and structures and should help to facilitate the design of new, high-potential, and environmentally sustainable insertion electrodes.

Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd 2Ti 2O 7

DOE PAGES

Aidhy, Dilpuneet S.; Sachan, Ritesh; Zarkadoula, Eva; ...

2015-11-10

In this research, the structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd 2Ti 2O 7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region ismore » predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. From these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.« less

Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions.

PubMed

Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

2018-04-06

Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions

NASA Astrophysics Data System (ADS)

Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

2018-04-01

Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

Investigation of surface potentials in reduced graphene oxide flake by Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Negishi, Ryota; Takashima, Kai; Kobayashi, Yoshihiro

2018-06-01

The surface potential (SP) of reduced graphene oxide (rGO) flakes prepared by thermal treatments of GO under several conditions was analyzed by Kelvin probe force microscopy. The low-crystalline rGO flakes in which a significant amount of oxygen functional groups and structural defects remain have a much lower SP than mechanically exfoliated graphene free from oxygen and defects. On the other hand, the highly crystalline rGO flake after a thermal treatment for the efficient removal of oxygen functional groups and healing of structural defects except for domain boundary shows SP equivalent to that of the mechanically exfoliated graphene. These results indicate that the work function of rGO is sensitively modulated by oxygen functional groups and structural defects remaining after the thermal reduction process, but is not affected significantly by the domain boundary remaining after the healing of structural defects through the thermal treatment at high temperature.

Centrifugal photovoltaic and photogalvanic effects driven by structured light

PubMed Central

Wätzel, J.; Berakdar, J.

2016-01-01

Much efforts are devoted to material structuring in a quest to enhance the photovoltaic effect. We show that structuring light in a way it transfers orbital angular momentum to semiconductor-based rings results in a steady charge accumulation at the outer boundaries that can be utilized for the generation of an open circuit voltage or a photogalvanic (bulk photovoltaic) type current. This effect which stems both from structuring light and matter confinement potentials, can be magnified even at fixed moderate intensities, by increasing the orbital angular momentum of light which strengthens the effective centrifugal potential that repels the charge outwards. Based on a full numerical time propagation of the carriers wave functions in the presence of light pulses we demonstrate how the charge buildup leads to a useable voltage or directed photocurrent whose amplitudes and directions are controllable by the light pulse parameters. PMID:26900105

NiCd battery electrodes

NASA Technical Reports Server (NTRS)

Holleck, G.; Turchan, M.; Hopkins, J.

1972-01-01

The objective of this research program was to develop and evaluate electrodes for a negative limited nickel-cadmium cell and to prove its feasibility. The program consisted of three phases: (1) the development of cadmium electrodes with high hydrogen overvoltage characteristics, (2) the testing of positive and negative plates, and (3) the fabrication and testing of complete negative limited NiCd cells. The following electrode structures were manufactured and their physical and electrochemical characteristics were evaluated: (1) silver sinter-based Cd electrodes, (2) Teflon-bonded Cd electrodes, (3) electrodeposited Cd sponge, and (4) Cd-sinter structures. All cadmium electrode structures showed a sharp increase in potential at the end of charge, with the advent of hydrogen evolution occurring at approximately -1.3 V versus Hg/HgO. The hydrogen advent potentials on pure cadmium structures were 50 to 70 mV more cathodic than those of their silver-containing counterparts.

Variable stiffness corrugated composite structure with shape memory polymer for morphing skin applications

NASA Astrophysics Data System (ADS)

Gong, Xiaobo; Liu, Liwu; Scarpa, Fabrizio; Leng, Jinsong; Liu, Yanju

2017-03-01

This work presents a variable stiffness corrugated structure based on a shape memory polymer (SMP) composite with corrugated laminates as reinforcement that shows smooth aerodynamic surface, extreme mechanical anisotropy and variable stiffness for potential morphing skin applications. The smart composite corrugated structure shows a low in-plane stiffness to minimize the actuation energy, but also possess high out-of-plane stiffness to transfer the aerodynamic pressure load. The skin provides an external smooth aerodynamic surface because of the one-sided filling with the SMP. Due to variable stiffness of the shape memory polymer the morphing skin exhibits a variable stiffness with a change of temperature, which can help the skin adjust its stiffness according different service environments and also lock the temporary shape without external force. Analytical models related to the transverse and bending stiffness are derived and validated using finite element techniques. The stiffness of the morphing skin is further investigated by performing a parametric analysis against the geometry of the corrugation and various sets of SMP fillers. The theoretical and numerical models show a good agreement and demonstrate the potential of this morphing skin concept for morphing aircraft applications. We also perform a feasibility study of the use of this morphing skin in a variable camber morphing wing baseline. The results show that the morphing skin concept exhibits sufficient bending stiffness to withstand the aerodynamic load at low speed (less than 0.3 Ma), while demonstrating a large transverse stiffness variation (up to 191 times) that helps to create a maximum mechanical efficiency of the structure under varying external conditions.

Structural and electronic properties of in-plane phase engineered WSe2: A DFT study

NASA Astrophysics Data System (ADS)

Bhart, Ankush; Kapoor, Pooja; Sharma, Munish; Sharma, Raman; Ahluwalia, P. K.

2018-04-01

We present first principal investigations on structural and electronic properties of in-plane phase engineered WSe2 with armchair type interface. The 2H and 1T phases of WSe2, joined along x-direction is a natural metal-semiconductor heterostructure and therefore shows potential for applications in 2D electronics and opto-electronics. The electronic properties transit towards metallic 1T region. No inflections across interface shows negligible mismatch strain which is unlike what has been reported for MoS2. Charge density analysis shows charge accumulation on 1T domain. This can lead to reduction of Schottky barrier heights at the metal-semiconductor junction. STM analysis confirms transition of 1T phase towards distorted 1T' structure. The present results provide essential insights for nano-devices using 2D hybrid materials.

Morphing wing structure with controllable twist based on adaptive bending-twist coupling

NASA Astrophysics Data System (ADS)

Raither, Wolfram; Heymanns, Matthias; Bergamini, Andrea; Ermanni, Paolo

2013-06-01

A novel semi-passive morphing airfoil concept based on variable bending-twist coupling induced by adaptive shear center location and torsional stiffness is presented. Numerical parametric studies and upscaling show that the concept relying on smart materials permits effective twist control while offering the potential of being lightweight and energy efficient. By means of an experimental characterization of an adaptive beam and a scaled adaptive wing structure, effectiveness and producibility of the structural concept are demonstrated.

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

PubMed Central

Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce; Nichols, Scott P; Wisniewski, Natalie A; Villa, Max M; Durand, Heather K; Jiang, Sharon; Midani, Firas S; Nimmagadda, Sai N; O'Connell, Thomas M; Wright, Justin P; Deshusses, Marc A

2018-01-01

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. PMID:29916366

Structural and vibrational analyses of new potential anticancer drug 2-(phenylmethyl)-2-azaspiro[5.11]heptadecane-1,3,7-trione

NASA Astrophysics Data System (ADS)

Vitnik, Željko J.; Popović-Đorđević, Jelena B.; Vitnik, Vesna D.

2017-06-01

The establishment of the most stable structures of 2-(phenylmethyl)-2-azaspiro[5.11]heptadecane-1,3,7-trione, potential anticancer and antimicrobial drug has been investigated in this work. A detailed interpretation of experimental and calculated IR, UV and NMR spectra were reported. The equilibrium geometry, harmonic vibrational frequencies and electronic properties have been investigated with Density Functional Theory using B3LYP/6-311++G(d,p) method. The scaled theoretical wavenumber showed very good agreement with the experimental values. The charge transfer in the molecule was confirmed with NBO analysis. Ultraviolet-visible spectrum was calculated using TD-DFT method and compared with experimental spectrum. The calculated energy and oscillator strength well reproduce the experimental data. The molecular electrostatic potential surface map portrays potential binding sites of the title molecule.

Ground penetrating radar imaging of cap rock, caliche and carbonate strata

USGS Publications Warehouse

Kruse, S.E.; Schneider, J.C.; Campagna, D.J.; Inman, J.A.; Hickey, T.D.

2000-01-01

Field experiments show ground penetrating radar (GPR) can be used to image shallow carbonate stratigraphy effectively in a variety of settings. In south Florida, the position and structure of cap rock cover on limestone can be an important control on surface water flow and vegetation, but larger scale outcrops (tens of meters) of cap rock are sparse. GPR mapping through south Florida prairie, cypress swamp and hardwood hammock resolves variations in thickness and structure of cap rock to ~3 m and holds the potential to test theories for cap rock-vegetation relationships. In other settings, carbonate strata are mapped to test models for the formation of local structural anomalies. A test of GPR imaging capabilities on an arid caliche (calcrete) horizon in southeastern Nevada shows depth penetration to ~2 m with resolution of the base of caliche. GPR profiling also succeeds in resolving more deeply buried (~5 m) limestone discontinuity surfaces that record subaerial exposure in south Florida. (C) 2000 Elsevier Science B.V. All rights reserved.Field experiments show ground penetrating radar (GPR) can be used to image shallow carbonate stratigraphy effectively in a variety of settings. In south Florida, the position and structure of cap rock cover on limestone can be an important control on surface water flow and vegetation, but larger scale outcrops (tens of meters) of cap rock are sparse. GPR mapping through south Florida prairie, cypress swamp and hardwood hammock resolves variations in thickness and structure of cap rock to approx. 3 m and holds the potential to test theories for cap rock-vegetation relationships. In other settings, carbonate strata are mapped to test models for the formation of local structural anomalies. A test of GPR imaging capabilities on an arid caliche (calcrete) horizon in southeastern Nevada shows depth penetration to approx. 2 m with resolution of the base of caliche. GPR profiling also succeeds in resolving more deeply buried (approx. 5 m) limestone discontinuity surfaces that record subaerial exposure in south Florida.

Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.

PubMed

Lin, Lianyun; Liu, Chen; Qin, Juan; Wang, Jie; Dong, Shengjie; Chen, Wei; He, Weiyi; Gao, Qingzhi; You, Minsheng; Yuchi, Zhiguang

2018-01-01

Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 Å resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide. Copyright © 2017 Elsevier Ltd. All rights reserved.

In vitro developmental model of the gastrointestinal tract from mouse embryonic stem cells.

PubMed

Torihashi, Shigeko; Kuwahara, Masaki; Kurahashi, Masaaki

2007-10-01

Mouse embryonic stem (ES) cells are pluripotent and retain their potential to form cells, tissues and organs originated from three embryonic germ layers. Recently, we developed in vitro organ--gut-like structures--from mouse ES cells. They had basically similar morphological features to a mouse gastrointestinal tract in vivo composed of three distinct layers (i.e., epithelium, connective tissue and musculature). Gut-like structures showed spontaneous contractions derived from pacemaker cells (interstitial cells of Cajal) in the musculature. We also examined their formation process and expression pattern of transcription factors crucial for gut organogenesis such as Id2, Sox17, HNF3beta/Foxa2 and GATA4. We found that they mimic the development of embryonic gut in vivo and showed a similar expression pattern of common transcription factors. They also maintain their developmental potential after transplantation to a renal capsule. Therefore, gut-like structures are suitable for in vitro models of gastrointestinal tracts and their development. In addition, we pointed out several unique features different from gut in vivo that provide useful and advantageous tools to investigate the developmental mechanism of the gastrointestinal tract.

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

PubMed

Noori Tahneh, Akram; Bagheri Novir, Samaneh; Balali, Ebrahim

2017-11-25

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

Amyloid formation and inhibition of an all-beta protein: A study on fungal polygalacturonase

NASA Astrophysics Data System (ADS)

Chinisaz, Maryam; Ghasemi, Atiyeh; Larijani, Bagher; Ebrahim-Habibi, Azadeh

2014-02-01

Theoretically, all proteins can adopt the nanofibrillar structures known as amyloid, which contain cross-beta structures. The all-beta folded proteins are particularly interesting in this regard, since they appear to be naturally more predisposed toward this structural arrangement. In this study, methanol has been used to drive the beta-helix protein polygalacturonase (PG), toward amyloid fibril formation. Congo red absorbance, thioflavin T fluorescence, circular dichroism (CD) and transmission electron microscopy have been used to characterize this process. Similar to other all-beta proteins, PG shows a non-cooperative fibrillation mechanism, but the structural changes that are monitored by CD indicate a different pattern. Furthermore, several compounds containing aromatic components were tested as potential inhibitors of amyloid formation. Another protein predominantly composed of alpha-helices (human serum albumin) was also targeted by these ligands, in order to get an insight into their potential anti-aggregation property toward structurally different proteins. Among tested compounds, silibinin and chlorpropamide were able to considerably affect both proteins fibrillation process.

Structural insight to mutation effects uncover a common allosteric site in class C GPCRs.

PubMed

Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian; Bräuner-Osborne, Hans; Gloriam, David E

2017-04-15

Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry. Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. We uncover one common site for both positive and negative modulators with different amino acid layouts that can be utilized to obtain selectivity. Additionally, we show a large potential for structure-based modulator design, especially for four orphan receptors with high similarity to the crystal structures. All collated mutagenesis data is available in the GPCRdb mutation browser at http://gpcrdb.org/mutations/ and can be analyzed online or downloaded in excel format. david.gloriam@sund.ku.dk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Potential energy surface of cyclooctatetraene

NASA Astrophysics Data System (ADS)

Andrés, José L.; Castaño, Obis; Morreale, Antonio; Palmeiro, Raul; Gomperts, Roberto

1998-01-01

We present a theoretical study of the cyclooctatetraene (COT) molecule. Seven COT structures are located on the singlet ground state potential energy surface. Four of them, which present D2d (tub), Cs (bicyclo[4.2.0]octa-2,4,7-triene or BOT), C2h (chair) and D4 (crown) symmetries are stable species, and the other three are transition state structures showing Cs, D4h, and D8h symmetry. We discuss the symmetry of wave functions for these stationary points. Geometries, energies, and harmonic vibrational frequencies of these structures, and energy gaps between singlet-triplet states and low-lying singlets are presented. For the planar D4h and D8h structures, Jahn-Teller and tunneling effects have also been discussed. Ring inversion, bond shifting and valence isomerization reactive channels from the tub COT conformer are discussed from the point of view of the corresponding transition state structures. Where possible, in order to lend support to this theoretical information comparisons with recent transition state spectroscopy data are made.

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.

Vibrational spectroscopic study of pH dependent solvation at a Ge(100)-water interface during an electrode potential triggered surface termination transition

NASA Astrophysics Data System (ADS)

Niu, Fang; Rabe, Martin; Nayak, Simantini; Erbe, Andreas

2018-06-01

The charge-dependent structure of interfacial water at the n-Ge(100)-aqueous perchlorate interface was studied by controlling the electrode potential. Specifically, a joint attenuated total reflection infrared spectroscopy and electrochemical experiment was used in 0.1M NaClO4 at pH ≈ 1-10. The germanium surface transformation to an H-terminated surface followed the thermodynamic Nernstian pH dependence and was observed throughout the entire pH range. A singular value decomposition-based spectra deconvolution technique coupled to a sigmoidal transition model for the potential dependence of the main components in the spectra shows the surface transformation to be a two-stage process. The first stage was observed together with the first appearance of Ge-H stretching modes in the spectra and is attributed to the formation of a mixed surface termination. This transition was reversible. The second stage occurs at potentials ≈0.1-0.3 V negative of the first one, shows a hysteresis in potential, and is attributed to the formation of a surface with maximum Ge-H coverage. During the surface transformation, the surface becomes hydrophobic, and an effective desolvation layer, a "hydrophobic gap," developed with a thickness ≈1-3 Å. The largest thickness was observed near neutral pH. Interfacial water IR spectra show a loss of strongly hydrogen-bound water molecules compared to bulk water after the surface transformation, and the appearance of "free," non-hydrogen bound OH groups, throughout the entire pH range. Near neutral pH at negative electrode potentials, large changes at wavenumbers below 1000 cm-1 were observed. Librational modes of water contribute to the observed changes, indicating large changes in the water structure.

Reactivity of Ala-Gly dipeptide with β-turn secondary structure

NASA Astrophysics Data System (ADS)

Yu, Craig P.; Gerlei, Klára Z.; Rágyanszki, Anita; Jensen, Svend J. Knak; Viskolcz, Béla; Csizmadia, Imre G.

2018-01-01

The conformational space of β-turns of Ala-Gly dipeptide is analyzed theoretically using quantum mechanical methods. A number of potential minima are obtained and characterized. The potential energy surface suggests that β-turn conformers are susceptible to rapid radical formation, which leads to potential L and D epimerization. The calculated thermodynamics show that the radical mediated epimerization is possible and that the estimated barrier height for hydrogen abstraction on the Cα is the lowest for the Gly residue.

Reconciling tensor and scalar observables in G-inflation

NASA Astrophysics Data System (ADS)

Ramírez, Héctor; Passaglia, Samuel; Motohashi, Hayato; Hu, Wayne; Mena, Olga

2018-04-01

The simple m2phi2 potential as an inflationary model is coming under increasing tension with limits on the tensor-to-scalar ratio r and measurements of the scalar spectral index ns. Cubic Galileon interactions in the context of the Horndeski action can potentially reconcile the observables. However, we show that this cannot be achieved with only a constant Galileon mass scale because the interactions turn off too slowly, leading also to gradient instabilities after inflation ends. Allowing for a more rapid transition can reconcile the observables but moderately breaks the slow-roll approximation leading to a relatively large and negative running of the tilt αs that can be of order ns‑1. We show that the observables on CMB and large scale structure scales can be predicted accurately using the optimized slow-roll approach instead of the traditional slow-roll expansion. Upper limits on |αs| place a lower bound of rgtrsim 0.005 and, conversely, a given r places a lower bound on |αs|, both of which are potentially observable with next generation CMB and large scale structure surveys.

Synthesis and Characterization of a Novel Phenolic Lipid for Use as Potential Lipophilic Antioxidant and as a Prodrug of Butyric Acid.

PubMed

Kaki, Shiva Shanker; Kunduru, Konda Reddy; Kanjilal, Sanjit; Narayana Prasad, Rachapudi Badari

2015-01-01

Ferulic acid was modified to produce a novel phenolipid containing butyl chains. Ferulic acid was esterified with butanol to produce butyl ferulate which was further dihydroxylated followed by esterification with butyric anhydride to produce the phenolipid containing butyric acid. IR, NMR and MS techniques confirmed the structure of the synthesized structured lipophilic phenolic compound. The synthesized compound was tested for in vitro antioxidant and antimicrobial activities. The produced phenolipid showed moderate antioxidant activity in DPPH (2, 2-diphenyl-1-picrylhydrazyl) radical scavenging assay but in linoleic acid oxidation method, it exhibited good activity compared with the parent compound and the reference compounds. The prepared derivative could find applications as antioxidant in lipophilic systems and also as a potential prodrug of butyric acid. It also showed antibacterial effect against the four bacterial strains studied. The drug-likeness properties of the prepared molecule calculated were in the acceptable ranges according to Lipinski's rule of 5 and suggest that it has potential to cross the blood-brain barrier.

Antibiofilm potential of synthetic 2-amino-5-chlorobenzophenone Schiff bases and its confirmation through fluorescence microscopy.

PubMed

Arshia; Khan, Anum Khalid; Khan, Khalid Mohammed; Ahmed, Ayaz; Taha, Muhammad; Perveen, Shahnaz

2017-09-01

Antibacterial/antibiofilm potential of microwave-assisted synthetic thirty-three 2-amino-5-chloro benzophenone Schiff bases have been carried out against four bacterial strains i.e. Klebsiella pneumoniae, Proteus mirabilis, Staphylococcus aureus and Streptococcus mutans. Among them compounds 5, 6, 8, 9, 14, 16, 22, 24, 26, and 30-32 showed antibiofilm activities against isolates at less than 100 μg/ml concentrations. These compounds showed enhanced antibiofilm activity against S. aureus as compared to cefixime used as control. However, remaining compounds were found to be active but at higher concentration. Fluorescence microscopy has been employed for confirmation of antibiofilm results. The structures of all synthetic molecules have been characterized on the basis of spectroscopic techniques including 1 H NMR, 13 C NMR, EI-MS, HREI-MS, and IR spectroscopy and their structure-activity relationship have been established. Copyright © 2017 Elsevier Ltd. All rights reserved.

The growth and perfection of β-cyclotetramethylene-tetranitramine (HMX) studied by laboratory and synchrotron X-ray topography

NASA Astrophysics Data System (ADS)

Gallagher, H. G.; Sherwood, J. N.; Vrcelj, R. M.

2017-10-01

An examination has been made of the defect structure of crystals of the energetic material β-cyclotetramethylene-tetranitramine (HMX) using both Laboratory (Lang method) and Synchrotron (Bragg Reflection and Laue method) techniques. The results of the three methods are compared with particular attention to the influence of potential radiation damage caused to the samples by the latter, more energetic, technique. The comparison shows that both techniques can be confidently used to evaluate the defect structures yielding closely similar results. The results show that, even under the relatively casual preparative methods used (slow evaporation of unstirred solutions at constant temperature), HMX crystals of high perfection can be produced. The crystals show well defined bulk defect structures characteristic of organic materials in general: growth dislocations, twins, growth sector boundaries, growth banding and solvent inclusions. The distribution of the defects in specific samples is correlated with the morphological variation of the grown crystals. The results show promise for the further evaluation and characterisation of the structure and properties of dislocations and other defects and their involvement in mechanical and energetic processes in this material.

Parameter optimization on the convergence surface of path simulations

NASA Astrophysics Data System (ADS)

Chandrasekaran, Srinivas Niranj

Computational treatments of protein conformational changes tend to focus on the trajectories themselves, despite the fact that it is the transition state structures that contain information about the barriers that impose multi-state behavior. PATH is an algorithm that computes a transition pathway between two protein crystal structures, along with the transition state structure, by minimizing the Onsager-Machlup action functional. It is rapid but depends on several unknown input parameters whose range of different values can potentially generate different transition-state structures. Transition-state structures arising from different input parameters cannot be uniquely compared with those generated by other methods. I outline modifications that I have made to the PATH algorithm that estimates these input parameters in a manner that circumvents these difficulties, and describe two complementary tests that validate the transition-state structures found by the PATH algorithm. First, I show that although the PATH algorithm and two other approaches to computing transition pathways produce different low-energy structures connecting the initial and final ground-states with the transition state, all three methods agree closely on the configurations of their transition states. Second, I show that the PATH transition states are close to the saddle points of free-energy surfaces connecting initial and final states generated by replica-exchange Discrete Molecular Dynamics simulations. I show that aromatic side-chain rearrangements create similar potential energy barriers in the transition-state structures identified by PATH for a signaling protein, a contractile protein, and an enzyme. Finally, I observed, but cannot account for, the fact that trajectories obtained for all-atom and Calpha-only simulations identify transition state structures in which the Calpha atoms are in essentially the same positions. The consistency between transition-state structures derived by different algorithms for unrelated protein systems argues that although functionally important protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. In the end, I outline the strategies that could enhance the efficiency and applicability of PATH.

Multi-Lagrangians for integrable systems

NASA Astrophysics Data System (ADS)

Nutku, Y.; Pavlov, M. V.

2002-03-01

We propose a general scheme to construct multiple Lagrangians for completely integrable nonlinear evolution equations that admit multi-Hamiltonian structure. The recursion operator plays a fundamental role in this construction. We use a conserved quantity higher/lower than the Hamiltonian in the potential part of the new Lagrangian and determine the corresponding kinetic terms by generating the appropriate momentum map. This leads to some remarkable new developments. We show that nonlinear evolutionary systems that admit N-fold first order local Hamiltonian structure can be cast into variational form with 2N-1 Lagrangians which will be local functionals of Clebsch potentials. This number increases to 3N-2 when the Miura transformation is invertible. Furthermore we construct a new Lagrangian for polytropic gas dynamics in 1+1 dimensions which is a free, local functional of the physical field variables, namely density and velocity, thus dispensing with the necessity of introducing Clebsch potentials entirely. This is a consequence of bi-Hamiltonian structure with a compatible pair of first and third order Hamiltonian operators derived from Sheftel's recursion operator.

New Disulfide-Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating Properties.

PubMed

Logashina, Yulia A; Solstad, Runar Gjerp; Mineev, Konstantin S; Korolkova, Yuliya V; Mosharova, Irina V; Dyachenko, Igor A; Palikov, Victor A; Palikova, Yulia A; Murashev, Arkadii N; Arseniev, Alexander S; Kozlov, Sergey A; Stensvåg, Klara; Haug, Tor; Andreev, Yaroslav A

2017-04-29

A novel bioactive peptide named τ-AnmTx Ueq 12-1 (short name Ueq 12-1) was isolated and characterized from the sea anemone Urticina eques. Ueq 12-1 is unique among the variety of known sea anemone peptides in terms of its primary and spatial structure. It consists of 45 amino acids including 10 cysteine residues with an unusual distribution and represents a new group of sea anemone peptides. The 3D structure of Ueq 12-1, determined by NMR spectroscopy, represents a new disulfide-stabilized fold partly similar to the defensin-like fold. Ueq 12-1 showed the dual activity of both a moderate antibacterial activity against Gram-positive bacteria and a potentiating activity on the transient receptor potential ankyrin 1 (TRPA1). Ueq 12-1 is a unique peptide potentiator of the TRPA1 receptor that produces analgesic and anti-inflammatory effects in vivo . The antinociceptive properties allow us to consider Ueq 12-1 as a potential analgesic drug lead with antibacterial properties.

An EQT-cDFT approach to determine thermodynamic properties of confined fluids.

PubMed

Mashayak, S Y; Motevaselian, M H; Aluru, N R

2015-06-28

We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.

Mapping Topographic Structure in White Matter Pathways with Level Set Trees

PubMed Central

Kent, Brian P.; Rinaldo, Alessandro; Yeh, Fang-Cheng; Verstynen, Timothy

2014-01-01

Fiber tractography on diffusion imaging data offers rich potential for describing white matter pathways in the human brain, but characterizing the spatial organization in these large and complex data sets remains a challenge. We show that level set trees–which provide a concise representation of the hierarchical mode structure of probability density functions–offer a statistically-principled framework for visualizing and analyzing topography in fiber streamlines. Using diffusion spectrum imaging data collected on neurologically healthy controls (N = 30), we mapped white matter pathways from the cortex into the striatum using a deterministic tractography algorithm that estimates fiber bundles as dimensionless streamlines. Level set trees were used for interactive exploration of patterns in the endpoint distributions of the mapped fiber pathways and an efficient segmentation of the pathways that had empirical accuracy comparable to standard nonparametric clustering techniques. We show that level set trees can also be generalized to model pseudo-density functions in order to analyze a broader array of data types, including entire fiber streamlines. Finally, resampling methods show the reliability of the level set tree as a descriptive measure of topographic structure, illustrating its potential as a statistical descriptor in brain imaging analysis. These results highlight the broad applicability of level set trees for visualizing and analyzing high-dimensional data like fiber tractography output. PMID:24714673

Development and characterization of a novel lipohydrogel nanocarrier: repaglinide as a lipophilic model drug.

PubMed

Ebrahimi, Hossein Ali; Javadzadeh, Yousef; Hamidi, Mehrdad; Barzegar Jalali, Mohammad

2016-04-01

Solid lipid nanoparticles (SLNs) are highly susceptible to phagocytosis by reticuloendothelial system (RES). To overcome this problem, a novel hydrogel-coated SLNs structure was developed and evaluated in this study. Solid lipid nanoparticles surface was coated with chitosan, via electrostatic attraction with the negatively charged SLNs surface. The resulting polymer-coated SLNs then hosted an inorganic poly-anionic agent, tripolyphosphate, to form the final lipohydrogel structure. Compared with the bare SLNs, lipohydrogel nanoparticles (LHNs) showed a significant increase in size and zeta potential. The release profile showed lower burst release and lower release rate for LHNs compared with SLNs. LHNs nanoparticles released the model antidiabetic drug, repaglinide, in a more sustained manner with lower burst effect compared with the corresponding SLN structure. Cytotoxicity studies via cell culture and MTT assay revealed no bio-toxicity of the SLNs and LHNs. In addition, intravenous administration of repaglinide-loaded SLNs and LHNs in rats showed longer drug residence time in circulation for LHNs, a trend also evident for the blood glucose level-time profile. The particle size, zeta potential, FTIR and microscopy data demonstrated the formation of the supposed lipohydrogel nanoparticles. All these benefits of LHNs propose it as a promising candidate for controlled release of the drugs. © 2016 Royal Pharmaceutical Society, Journal of Pharmacy and Pharmacology.

Energy dispersive-EXAFS of Pd nucleation at a liquid/liquid interface

NASA Astrophysics Data System (ADS)

Chang, S.-Y.; Booth, S. G.; Uehara, A.; Mosselmans, J. F. W.; Cibin, G.; Pham, V.-T.; Nataf, L.; Dryfe, R. A. W.; Schroeder, S. L. M.

2016-05-01

Energy dispersive extended X-ray absorption fine structure (EDE) has been applied to Pd nanoparticle nucleation at a liquid/liquid interface under control over the interfacial potential and thereby the driving force for nucleation. Preliminary analysis focusing on Pd K edge-step height determination shows that under supersaturated conditions the concentration of Pd near the interface fluctuate over a period of several hours, likely due to the continuous formation and dissolution of sub-critical nuclei. Open circuit potential measurements conducted ex-situ in a liquid/liquid electrochemical cell support this view, showing that the fluctuations in Pd concentration are also visible as variations in potential across the liquid/liquid interface. By decreasing the interfacial potential through inclusion of a common ion (tetraethylammonium, TEA+) the Pd nanoparticle growth rate could be slowed down, resulting in a smooth nucleation process. Eventually, when the TEA+ ions reached an equilibrium potential, Pd nucleation and particle growth were inhibited.

Double-layer interlaced nested multi-ring array metallic mesh for high-performance transparent electromagnetic interference shielding.

PubMed

Wang, Heyan; Lu, Zhengang; Liu, Yeshu; Tan, Jiubin; Ma, Limin; Lin, Shen

2017-04-15

We report a nested multi-ring array metallic mesh (NMA-MM) that shows a highly uniform diffraction pattern theoretically and experimentally. Then a high-performance transparent electromagnetic interference (EMI) shielding structure is constituted by the double-layer interlaced NMA-MMs separated by transparent quartz-glass substrate. Experimental results show that double-layer interlaced NMA-MM structure exhibits a shielding effectiveness (SE) of over 27 dB in the Ku-band, with a maximal SE of 37 dB at 12 GHz, normalized optical transmittance of 90%, and minimal image quality degradation due to the interlaced arrangement. It thus shows great potential for practical applications in transparent EMI shielding devices.

Cryptococcus neoformans ADS lyase is an enzyme essential for virulence whose crystal structure reveals features exploitable in antifungal drug design.

PubMed

Chitty, Jessica L; Blake, Kirsten L; Blundell, Ross D; Koh, Y Q Andre E; Thompson, Merinda; Robertson, Avril A B; Butler, Mark S; Cooper, Matthew A; Kappler, Ulrike; Williams, Simon J; Kobe, Bostjan; Fraser, James A

2017-07-14

There is significant clinical need for new antifungal agents to manage infections with pathogenic species such as Cryptococcus neoformans Because the purine biosynthesis pathway is essential for many metabolic processes, such as synthesis of DNA and RNA and energy generation, it may represent a potential target for developing new antifungals. Within this pathway, the bifunctional enzyme adenylosuccinate (ADS) lyase plays a role in the formation of the key intermediates inosine monophosphate and AMP involved in the synthesis of ATP and GTP, prompting us to investigate ADS lyase in C. neoformans. Here, we report that ADE13 encodes ADS lyase in C. neoformans. We found that an ade13 Δ mutant is an adenine auxotroph and is unable to successfully cause infections in a murine model of virulence. Plate assays revealed that production of a number of virulence factors essential for dissemination and survival of C. neoformans in a host environment was compromised even with the addition of exogenous adenine. Purified recombinant C. neoformans ADS lyase shows catalytic activity similar to its human counterpart, and its crystal structure, the first fungal ADS lyase structure determined, shows a high degree of structural similarity to that of human ADS lyase. Two potentially important amino acid differences are identified in the C. neoformans crystal structure, in particular a threonine residue that may serve as an additional point of binding for a fungal enzyme-specific inhibitor. Besides serving as an antimicrobial target, C. neoformans ADS lyase inhibitors may also serve as potential therapeutics for metabolic disease; rather than disrupt ADS lyase, compounds that improve the stability the enzyme may be used to treat ADS lyase deficiency disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Starch Granule Re-Structuring by Starch Branching Enzyme and Glucan Water Dikinase Modulation Affects Caryopsis Physiology and Metabolism

PubMed Central

Shaik, Shahnoor S.; Obata, Toshihiro; Hebelstrup, Kim H.; Schwahn, Kevin; Fernie, Alisdair R.; Mateiu, Ramona V.; Blennow, Andreas

2016-01-01

Starch is of fundamental importance for plant development and reproduction and its optimized molecular assembly is potentially necessary for correct starch metabolism. Re-structuring of starch granules in-planta can therefore potentially affect plant metabolism. Modulation of granule micro-structure was achieved by decreasing starch branching and increasing starch-bound phosphate content in the barley caryopsis starch by RNAi suppression of all three Starch Branching Enzyme (SBE) isoforms or overexpression of potato Glucan Water Dikinase (GWD). The resulting lines displayed Amylose-Only (AO) and Hyper-Phosphorylated (HP) starch chemotypes, respectively. We studied the influence of these alterations on primary metabolism, grain composition, starch structural features and starch granule morphology over caryopsis development at 10, 20 and 30 days after pollination (DAP) and at grain maturity. While HP showed relatively little effect, AO showed significant reduction in starch accumulation with re-direction to protein and β-glucan (BG) accumulation. Metabolite profiling indicated significantly higher sugar accumulation in AO, with re-partitioning of carbon to accumulate amino acids, and interestingly it also had high levels of some important stress-related metabolites and potentially protective metabolites, possibly to elude deleterious effects. Investigations on starch molecular structure revealed significant increase in starch phosphate and amylose content in HP and AO respectively with obvious differences in starch granule morphology at maturity. The results demonstrate that decreasing the storage starch branching resulted in metabolic adjustments and re-directions, tuning to evade deleterious effects on caryopsis physiology and plant performance while only little effect was evident by increasing starch-bound phosphate as a result of overexpressing GWD. PMID:26891365

Electronic structure and bonding of intergranular glassy films in polycrystalline Si3 N4 : Ab initio studies and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of β-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline β-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

Probing the electronic and local structural changes across the pressure-induced insulator-to-metal transition in VO2

NASA Astrophysics Data System (ADS)

Marini, C.; Bendele, M.; Joseph, B.; Kantor, I.; Mitrano, M.; Mathon, O.; Baldini, M.; Malavasi, L.; Pascarelli, S.; Postorino, P.

2014-11-01

Local and electronic structures of vanadium in \\text{VO}2 are studied across the high-pressure insulator-to-metal (IMT) transition using V K-edge x-ray absorption spectroscopy. Unlike the temperature-induced IMT, pressure-induced metallization leads to only subtle changes in the V K-edge prepeak structure, indicating a different mechanism involving smaller electronic spectral weight transfer close to the chemical potential. Intriguingly, upon application of the hydrostatic pressure, the electronic structure begins to show substantial changes well before the occurrence of the IMT and the associated structural transition to an anisotropic compression of the monoclinic metallic phase.

Stretchable and semitransparent conductive hybrid hydrogels for flexible supercapacitors.

PubMed

Hao, Guang-Ping; Hippauf, Felix; Oschatz, Martin; Wisser, Florian M; Leifert, Annika; Nickel, Winfried; Mohamed-Noriega, Nasser; Zheng, Zhikun; Kaskel, Stefan

2014-07-22

Conductive polymers showing stretchable and transparent properties have received extensive attention due to their enormous potential in flexible electronic devices. Here, we demonstrate a facile and smart strategy for the preparation of structurally stretchable, electrically conductive, and optically semitransparent polyaniline-containing hybrid hydrogel networks as electrode, which show high-performances in supercapacitor application. Remarkably, the stability can extend up to 35,000 cycles at a high current density of 8 A/g, because of the combined structural advantages in terms of flexible polymer chains, highly interconnected pores, and excellent contact between the host and guest functional polymer phase.

Study of Aggregation of Janus Ellipsoids

NASA Astrophysics Data System (ADS)

Ruth, Donovan; Li, Wei; Khadka, Shreeya; Rickman, Jeffrey; Gunton, James

2013-03-01

We perform numerical simulations of a quasi-square well potential model of one-patch colloidal particles to investigate the collective structure of a system of Janus ellipsoids. We show that for Janus ellipsoids such that one half is an attractive patch, while the entire ellipsoid has a hardcore repulsion, the system organizes into a distribution of orientationally ordered micelles and vesicles. We analyze the cluster distribution at several temperatures and low densities and show that below certain temperatures the system is populated by stable clusters and depending on temperature and density the system is populated by either vesicles or micelle structures.

Boron/aluminum graphite/resin advanced fiber composite hybrids

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Lark, R. F.; Sullivan, T. L.

1975-01-01

Fabrication feasibility and potential of an adhesively bonded metal and resin matrix fiber-composite hybrid are determined as an advanced material for aerospace and other structural applications. The results show that using this hybrid concept makes possible a composite design which, when compared with nonhybrid composites, has greater transverse strength, transverse stiffness, and impact resistance with only a small penalty on density and longitudinal properties. The results also show that laminate theory is suitable for predicting the structural response of such hybrids. The sequence of fracture modes indicates that these types of hybrids can be readily designed to meet fail-safe requirements.

Synthesis and structure elucidation of fluoro substituted guanidines as potential therapeutic agents

NASA Astrophysics Data System (ADS)

Ullah, Waseem; Imtiaz-ud-Din; Raheel, Ahmad; Badshah, Amin; Tahir, Muhammad Nawaz

2017-09-01

Six new fluoro -substituted guanidines (1-6) were synthesized and characterized by 1H and 13C NMR spectroscopy to ascertain the structures in solution (DMSO) besides the solid state information collected through FT IR and single crystal X-ray spectroscopy. The XRD data for (1-3) show that molecules are stabilized by strong intramolecular hydrogen bonding. The compounds were also preliminary bio-assayed for anti-microbial studies and show good to moderate activities. The anti-oxidant data revealed that o and p-substituted fluoro-guanidines enhances their DPPH scavenging ability significantly.

Ensemble modelling and structured decision-making to support Emergency Disease Management.

PubMed

Webb, Colleen T; Ferrari, Matthew; Lindström, Tom; Carpenter, Tim; Dürr, Salome; Garner, Graeme; Jewell, Chris; Stevenson, Mark; Ward, Michael P; Werkman, Marleen; Backer, Jantien; Tildesley, Michael

2017-03-01

Epidemiological models in animal health are commonly used as decision-support tools to understand the impact of various control actions on infection spread in susceptible populations. Different models contain different assumptions and parameterizations, and policy decisions might be improved by considering outputs from multiple models. However, a transparent decision-support framework to integrate outputs from multiple models is nascent in epidemiology. Ensemble modelling and structured decision-making integrate the outputs of multiple models, compare policy actions and support policy decision-making. We briefly review the epidemiological application of ensemble modelling and structured decision-making and illustrate the potential of these methods using foot and mouth disease (FMD) models. In case study one, we apply structured decision-making to compare five possible control actions across three FMD models and show which control actions and outbreak costs are robustly supported and which are impacted by model uncertainty. In case study two, we develop a methodology for weighting the outputs of different models and show how different weighting schemes may impact the choice of control action. Using these case studies, we broadly illustrate the potential of ensemble modelling and structured decision-making in epidemiology to provide better information for decision-making and outline necessary development of these methods for their further application. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Polyhydroxy surfactants for the formulation of lipid nanoparticles (SLN and NLC): effects on size, physical stability and particle matrix structure.

PubMed

Kovacevic, A; Savic, S; Vuleta, G; Müller, R H; Keck, C M

2011-03-15

The two polyhydroxy surfactants polyglycerol 6-distearate (Plurol(®)Stearique WL1009 - (PS)) and caprylyl/capryl glucoside (Plantacare(®) 810 - (PL)) are a class of PEG-free stabilizers, made from renewable resources. They were investigated for stabilization of aqueous solid lipid nanoparticle (SLN) and nanostructured lipid carrier (NLC) dispersions. Production was performed by high pressure homogenization, analysis by photon correlation spectroscopy (PCS), laser diffraction (LD), zeta potential measurements and differential scanning calorimetry (DSC). Particles were made from Cutina CP as solid lipid only (SLN) and its blends with Miglyol 812 (NLC, the blends containing increasing amounts of oil from 20% to 60%). The obtained particle sizes were identical for both surfactants, about 200 nm with polydispersity indices below 0.20 (PCS), and unimodal size distribution (LD). All dispersions with both surfactants were physically stable for 3 months at room temperature, but Plantacare (PL) showing a superior stability. The melting behaviour and crystallinity of bulk lipids/lipid blends were compared to the nanoparticles. Both were lower for the nanoparticles. The crystallinity of dispersions stabilized with PS was higher, the zeta potential decreased with storage time associated with this higher crystallinity, and leading to a few, but negligible larger particles. The lower crystallinity particles stabilized with PL remained unchanged in zeta potential (about -50 mV) and in size. These data show that surfactants have a distinct influence on the particle matrix structure (and related stability and drug loading), to which too little attention was given by now. Despite being from the same surfactant class, the differences on the structure are pronounced. They are attributed to the hydrophobic-lipophilic tail structure with one-point anchoring in the interface (PL), and the loop conformation of PS with two hydrophobic anchor points, i.e. their molecular structure and its interaction with the matrix surface and matrix bulk. Analysis of the effects of the surfactants on the particle matrix structure could potentially be used to further optimization of stability, drug loading and may be drug release. Copyright © 2011 Elsevier B.V. All rights reserved.

Quantitative Acoustic Model for Adhesion Evaluation of Pmma/silicon Film Structures

NASA Astrophysics Data System (ADS)

Ju, H. S.; Tittmann, B. R.

2010-02-01

A Poly-methyl-methacrylate (PMMA) film on a silicon substrate is a main structure for photolithography in semiconductor manufacturing processes. This paper presents a potential of scanning acoustic microscopy (SAM) for nondestructive evaluation of the PMMA/Si film structure, whose adhesion failure is commonly encountered during the fabrication and post-fabrication processes. A physical model employing a partial discontinuity in displacement is developed for rigorously quantitative evaluation of the interfacial weakness. The model is implanted to the matrix method for the surface acoustic wave (SAW) propagation in anisotropic media. Our results show that variations in the SAW velocity and reflectance are predicted to show their sensitivity to the adhesion condition. Experimental results by the v(z) technique and SAW velocity reconstruction verify the prediction.

Topochemical Reduction of YMnO3 into a Composite Structure.

PubMed

Kabbour, Houria; Gauthier, Gilles H; Tessier, Franck; Huvé, Marielle; Pussacq, Tanguy; Roussel, Pascal; Hayward, Michael A; Moreno B, Zulma L; Marinova, Maya; Colmont, Marie; Colis, Silviu; Mentré, Olivier

2017-07-17

Topochemical modification methods for solids have shown great potential in generating metastable structures inaccessible through classical synthetic routes. Here, we present the enhanced topotactic reduction of the multiferroic compound YMnO 3 . At moderate temperature in ammonia flow, the most reduced YMnO 3-δ (δ = 0.5) phase could be stabilized. XRD, PND, and HREM results show that phase separation occurs into two intimately intergrown layered sublattices with nominal compositions ∞ [YMn 2+ O 2+x ] (1-2x)+ and ∞ [YMn 2+ O 3-x ] (1-2x)- containing versatile Mn 2+ coordinations. The former sublattice shows original AA stacking between Mn layers, while AB stacking in the latter results from oxygen removal from the parent YMnO 3 crystal structure.

[Application research of DEI technique based on synchrotron X-ray source in imaging rabbit eyeball in vitro].

PubMed

Yin, Hong-xia; Huang, Zhi-feng; Wang, Zhen-chang; Liu, Zhao-hui; Li, Yong; Zhu, Pei-ping

2010-03-23

To study the application of DEI technique in imaging the small structures of rabbit eyeball. DEI technique was used to image the eyeball of New Zealand white rabbit in vitro. The experiments were performed using beamline 4W1A at the topography station of Beijing Synchrotron Radiation Facility (BSRF). DEI image showed clearly the fine structures of the rabbit eyeball, such as the transparent cornea, the sclera, the ciliaris, and the ciliary body. DEI is a new X-ray imaging modality which achieves high contrast and spatial resolution. It also showed obvious effect of edge enhancement. DEI has good potential in observing the micro-structures of eyeballs and other small organs.

Structural, Electronic and Elastic Properties of Half-Heusler Alloys CrNiZ (Z = Al, Si, Ge and As)

NASA Astrophysics Data System (ADS)

Zitouni, A.; Benstaali, W.; Abbad, A.; Lantri, T.; Bouadjemi, B.; Aziz, Z.

2018-06-01

In the present work, a self-consistent ab-initio calculation using the full- potential linearized augmented plane wave (FP-LAPW) method within the framework of the spin-polarized density functional theory (DFT) was used to study the structural, electronic, magnetic and elastic properties of the half Heusler alloys CrNiZ (Z = Al, Si, Ge and As) in three phases ( α, β and γ phases). The generalized gradient approximation (GGA) described by Perdew-Burke-Ernzerhof (PBE) was used. The results obtained for the spin-polarized band structure and the density of states show a halfmetallic behavior for the four compounds. The elastic constants ( C ij ) show that our compounds are ductile, stiff and anisotropic.

A THEORETICAL STUDY OF BISTABILITY OF POLYDIACETYLENE:. TCDU(poly(5,7-dodecadiyne-1,12-diyl-bis-phenylurethane)

NASA Astrophysics Data System (ADS)

Katagiri, Hideki; Shimoi, Yukihiro; Abe, Shuji

2001-08-01

We performed a first-principles calculation of typical polydiacetylene (PDA), TCDU (poly(5,7-dodecadiyne-1,12-diyl-bis-phenylurethane)). Potential energy curves (PEC's) as a function of two bond lengths of the backbone chain are presented. The present PEC's show that TCDU has only an acetylene-type stable structure and a butatriene-type structure is unstable, consistent with our previous calculations with a geometry optimization procedure. This result is in contrast to the case of a hypothetical hydrogen-substituted PDA where a butatriene-type structure is obtained as a meta-stable structure.

A THEORETICAL STUDY OF BISTABILITY OF POLYDIACETYLENE:. TCDU(poly(5,7-dodecadiyne-1,12-diyl-bis-phenylurethane)

NASA Astrophysics Data System (ADS)

Katagiri, Hideki; Shimoi, Yukihiro; Abe, Shuji

We performed a first-principles calculation of typical polydiacetylene (PDA), TCDU (poly(5,7-dodecadiyne-1,12-diyl-bis-phenylurethane)). Potential energy curves (PEC's) as a function of two bond lengths of the backbone chain are presented. The present PEC's show that TCDU has only an acetylene-type stable structure and a butatriene-type structure is unstable, consistent with our previous calculations with a geometry optimization procedure. This result is in contrast to the case of a hypothetical hydrogen-substituted PDA where a butatriene-type structure is obtained as a meta-stable structure.

Structural insight into the antagonistic action of diarylheptanoid on human estrogen receptor alpha.

PubMed

Geetha Rani, Yuvaraj; Lakshmi, Baddireddi Subhadra

2018-03-30

Estrogen receptor α (ER α) is an important therapeutic target in the regulation of ligand dependent signaling in breast cancer. The current study investigates the anti-estrogenic potential of the Diarylheptanoid, 5-hydroxy-7-(4-hydroxy-3 methoxyphenyl)-1-phenyl-3-heptanone (DAH) in silico. Rigid Docking analysis of DAH at the ligand binding domain (LBD) of ER α showed hydrogen bond interactions with Arg394 and Glu353 at the active site, similar to the positive controls 4-Hydroxy Tamoxifen (4-OHT) and Fulvestrant (FUL). The protein and the protein-DAH complexes were further analyzed using molecular dynamics simulations for a time scale of 50 ns using GROMACS. Root mean square fluctuation (RMSF) analysis showed large fluctuations at the N-terminal region of Helices (H) 3, 9 and at the C-terminal region of H11, which could be involved in the antagonistic conformational change. Interestingly, H12 appeared to move away from the ligand binding pocket and occupy the co-activator binding groove at the LBD of ER α. Secondary structure analysis of the protein upon binding of DAH and CUR showed structural change from α-helix to Turn conformation at H4. We hypothesize that this structural change at H4, similar to the positive control, could hinder the activity of AF-2 by blocking the binding of co-activator. These conformational changes in ER α indicate an anti-estrogenic and therapeutic potential of the DAH.

Vibrational, structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: A theoretical approach for potentially bioactive molecules

NASA Astrophysics Data System (ADS)

Costa, Renyer A.; Oliveira, Kelson M. T.; Costa, Emmanoel Vilaça; Pinheiro, Maria L. B.

2017-10-01

A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline is presented using the Becke three-parameter Lee-Yang-Parr function (B3LYP) and 6-311G(2d,p) basis set. The theoretical geometry optimization data were compared with the X-ray data for a similar structure in the associated literature, showing close values. The calculated HOMO-LUMO gap values showed that the presence of substituents in the benzene ring influences the quantum properties which are directly related to the reactive properties. Theoretical UV spectra agreed well with the measured experimental data, with bands assigned. In addition, Natural Bond Orbitals (NBOs), Mapped molecular electrostatic potential surface (MEPS) and NLO calculations were also performed at the same theory level. The theoretical vibrational analysis revealed several characteristic vibrations that may be used as a diagnostic tool for other strychnobrasiline type alkaloids, simplifying their identification and structural characterization. Molecular docking calculations with DNA Topoisomerase II-DNA complex showed binding free energies values of -8.0 and -9.5 kcal/mol for strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of -10.0 kcal/mol, suggesting that strychnobrasiline derivative alkaloids might exhibit an antineoplastic activity.

Structural, electronic and photocatalytic properties of atomic defective BiI3 monolayers

NASA Astrophysics Data System (ADS)

Yan, Huang; Ziyu, Hu; Xu, Gong; Xiaohong, Shao

2018-01-01

The structural, electronic and photocatalytic properties of five vacancy-containing 2D BiI3 monolayers are investigated by the first-principle calculations. The electronic structures show that the five structures are stable and have comparable binding energies to that of the pristine BiI3 monolayer, and the defects can tune the band gaps. Optical spectra indicate that the five structures retain high absorption capacity for visible light. The spin-orbit coupling (SOC) effect is found to play an important role in the band edge of defective structures, and the VBi and VBi-I3 defective BiI3 monolayers can make absolute band edges straddle water redox potentials more easily.

Structural Asymmetry of Dorsolateral Prefrontal Cortex Correlates with Depressive Symptoms: Evidence from Healthy Individuals and Patients with Major Depressive Disorder.

PubMed

Liu, Wei; Mao, Yu; Wei, Dongtao; Yang, Junyi; Du, Xue; Xie, Peng; Qiu, Jiang

2016-06-01

In this study, we investigated the role of structural asymmetry of the dorsolateral prefrontal cortex (DLPFC) in the continuum of depression from healthy individuals to patients. Structural magnetic resonance imaging was performed in 70 patients with major depressive disorder (MDD), 49 matched controls, and 349 healthy university students to calculate structural asymmetry indexes of the DLPFC. First-episode, treatment-naive MDD patients showed a relatively lower asymmetry index than healthy controls, and their asymmetry index was negatively correlated with the depressive symptoms. This abnormality was normalized by antidepressants in medicated MDD patients. Furthermore, the asymmetry index was negatively correlated with the depressive symptoms in university students; this was replicated at two time points in a subgroup of students, suggesting good test-retest reliability. Our findings are consistent with previous studies that support the imbalance hypothesis of MDD and suggest a potential structural basis underlying the functional asymmetry of the DLPFC in depression. In future, the structural index of the DLPFC may become a potential biomarker to evaluate individuals' risk for the onset of MDD.

New Coarse-Grained Model and Its Implementation in Simulations of Graphene Assemblies.

PubMed

Shang, Jun-Jun; Yang, Qing-Sheng; Liu, Xia

2017-08-08

Graphene is a one-atom thick layer of carbon atoms arranged in a hexagonal pattern, which makes it the strongest material in the world. The Tersoff potential is a suitable potential for simulating the mechanical behavior of the complex covalently bonded system of graphene. In this paper, we describe a new coarse-grained (CG) potential, TersoffCG, which is based on the function form of the Tersoff potential. The TersoffCG applies to a CG model of graphene that uses the same hexagonal pattern as the atomistic model. The parameters of the TersoffCG potential are determined using structural feature and potential-energy fitting between the CG model and the atomic model. The modeling process of graphene is highly simplified using the present CG model as it avoids the necessity to define bonds/angles/dihedrals connectivity. What is more, the present CG model provides a new perspective of coarse-graining scheme for crystal structures of nanomaterials. The structural changes and mechanical properties of multilayer graphene were calculated using the new potential. Furthermore, a CG model of a graphene aerogel was built in a specific form of assembly. The chemical bonding in the joints of graphene-aerogel forms automatically during the energy relaxation process. The compressive and recover test of the graphene aerogel was reproduced to study its high elasticity. Our computational examples show that the TersoffCG potential can be used for simulations of graphene and its assemblies, which have many applications in areas of environmental protection, aerospace engineering, and others.

Structure and stability of pyrophyllite edge surfaces: Effect of temperature and water chemical potential

NASA Astrophysics Data System (ADS)

Kwon, Kideok D.; Newton, Aric G.

2016-10-01

The surfaces of clay minerals, which are abundant in atmospheric mineral dust, serve as an important medium to catalyze ice nucleation. The lateral edge surface of 2:1 clay minerals is postulated to be a potential site for ice nucleation. However, experimental investigations of the edge surface structure itself have been limited compared to the basal planes of clay minerals. Density functional theory (DFT) computational studies have provided insights into the pyrophyllite edge surface. Pyrophyllite is an ideal surrogate mineral for the edge surfaces of 2:1 clay minerals as it possesses no or little structural charge. Of the two most-common hydrated edge surfaces, the AC edge, (1 1 0) surface in the monoclinic polytype notation, is predicted to be more stable than the B edge, (0 1 0) surface. These stabilities, however, were determined based on the total energies calculated at 0 K and did not consider environmental effects such as temperature and humidity. In this study, atomistic thermodynamics based on periodic DFT electronic calculations was applied to examine the effects of environmental variables on the structure and thermodynamic stability of the common edge surfaces in equilibrium with bulk pyrophyllite and water vapor. We demonstrate that the temperature-dependent vibrational energy of sorbed water molecules at the edge surface is a significant component of the surface free energy and cannot be neglected when determining the surface stability of pyrophyllite. The surface free energies were calculated as a function of temperature from 240 to 600 K and water chemical potential corresponding to conditions from ultrahigh vacuum to the saturation vapor pressure of water. We show that at lower water chemical potentials (dry conditions), the AC and B edge surfaces possessed similar stabilities; at higher chemical potentials (humid conditions) the AC edge surface was more stable than the B edge surface. At high temperatures, both surfaces showed similar stabilities regardless of the water chemical potential. The equilibrium morphology of pyrophyllite crystals is also expected to be dependent on these two environmental variables. Surface defects may impact the surface reactivity. We discuss the thermodynamic stability of a possible Si cation vacancy defect which provides additional hydroxyl group on the surface.

Composition, structure and functional properties of protein concentrates and isolates produced from walnut (Juglans regia L.).

PubMed

Mao, Xiaoying; Hua, Yufei

2012-01-01

In this study, composition, structure and the functional properties of protein concentrate (WPC) and protein isolate (WPI) produced from defatted walnut flour (DFWF) were investigated. The results showed that the composition and structure of walnut protein concentrate (WPC) and walnut protein isolate (WPI) were significantly different. The molecular weight distribution of WPI was uniform and the protein composition of DFWF and WPC was complex with the protein aggregation. H(0) of WPC was significantly higher (p < 0.05) than those of DFWF and WPI, whilst WPI had a higher H(0) compared to DFWF. The secondary structure of WPI was similar to WPC. WPI showed big flaky plate like structures; whereas WPC appeared as a small flaky and more compact structure. The most functional properties of WPI were better than WPC. In comparing most functional properties of WPI and WPC with soybean protein concentrate and isolate, WPI and WPC showed higher fat absorption capacity (FAC). Emulsifying properties and foam properties of WPC and WPI in alkaline pH were comparable with that of soybean protein concentrate and isolate. Walnut protein concentrates and isolates can be considered as potential functional food ingredients.

Regulation of Complement and Contact System Activation via C1 Inhibitor Potentiation and Factor XIIa Activity Modulation by Sulfated Glycans – Structure-Activity Relationships

PubMed Central

Schoenfeld, Ann-Kathrin; Lahrsen, Eric; Alban, Susanne

2016-01-01

The serpin C1 inhibitor (C1-INH) is the only regulator of classical complement activation as well as the major regulator of the contact system. Its importance is demonstrated by hereditary angioedema (HAE), a severe disease with potentially life-threatening attacks due to deficiency or dysfunction of C1-INH. C1-INH replacement is the therapy of choice in HAE. In addition, C1-INH showed to have beneficial effects in other diseases characterized by inappropriate complement and contact system activation. Due to some limitations of its clinical application, there is a need for improving the efficacy of therapeutically applied C1-INH or to enhance the activity of endogenous C1-INH. Given the known potentiating effect of heparin on C1-INH, sulfated glycans (SG) may be such candidates. The aim of this study was to characterize suitable SG by evaluating structure-activity relationships. For this, more than 40 structurally distinct SG were examined for their effects on C1-INH, C1s and FXIIa. The SG turned out to potentiate the C1s inhibition by C1-INH without any direct influence on C1s. Their potentiating activity proved to depend on their degree of sulfation, molecular mass as well as glycan structure. In contrast, the SG had no effect on the FXIIa inhibition by C1-INH, but structure-dependently modulated the activity of FXIIa. Among the tested SG, β-1,3-glucan sulfates with a Mr ≤ 10 000 were identified as most promising lead candidates for the development of a glycan-based C1-INH amplifier. In conclusion, the obtained information on structural characteristics of SG favoring C1-INH potentiation represent an useful elementary basis for the development of compounds improving the potency of C1-INH in diseases and clinical situations characterized by inappropriate activation of complement and contact system. PMID:27783665

Synthesis and Characterization of Composite Membranes made of Graphene and Polymers of Intrinsic Microporosity

DTIC Science & Technology

2016-02-16

group of polymers with molecular sieve behaviour due to their rigid, contorted macromolecular backbones. They show great potential in organophilic...ageing is expected by adding graphene as a nanofiller. Little is experimentally known about how the material disperses in the polymer. Here we used Raman...effective understanding of the structure-property relationships of the composite. Obtaining such structural infor- mation, however, is experimentally

CD4-binding site alterations in CCR5-using HIV-1 envelopes influencing gp120-CD4 interactions and fusogenicity

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

Sterjovski, Jasminka; Churchill, Melissa J.; Roche, Michael

2011-02-20

CD4-binding site (CD4bs) alterations in gp120 contribute to different pathophysiological phenotypes of CCR5-using (R5) HIV-1 strains, but the potential structural basis is unknown. Here, we characterized functionally diverse R5 envelope (Env) clones (n = 16) to elucidate potential structural alterations within the gp120 CD4bs that influence Env function. Initially, we showed that the magnitude of gp120-CD4-binding correlates with increased fusogenicity and reduced CD4 dependence. Analysis of three-dimensional gp120 structural models revealed two CD4bs variants, D279 and N362, that were associated with reduced CD4 dependence. Further structural analysis showed that a wider aperture of the predicted CD4bs cavity, as constrained bymore » the inner-most atoms at the gp120 V1V2 stem and the V5 loop, was associated with amino acid alterations within V5 and correlated with increased gp120-CD4 binding and increased fusogenicity. Our results provide evidence that the gp120 V5 loop may alter CD4bs conformation and contribute to increased gp120-CD4 interactions and Env fusogenicity.« less

Effect of disorder on the magnetic and electronic structure of a prospective spin-gapless semiconductor MnCrVAl

DOE PAGES

Kharel, P.; Herran, J.; Lukashev, P.; ...

2016-12-19

Recent discovery of a new class of materials, spin-gapless semiconductors (SGS), has attracted considerable attention in the last few years, primarily due to potential applications in the emerging field of spin-based electronics (spintronics). Here, we investigate structural, electronic, and magnetic properties of one potential SGS compound, MnCrVAl, using various experimental and theoretical techniques. Our calculations show that this material exhibits ≈ 0.5 eV band gap for the majority-spin states, while for the minority-spin it is nearly gapless. The calculated magnetic moment for the completely ordered structure is 2.9 μB/f.u., which is different from our experimentally measured value of almost zero.more » Here, this discrepancy is explained by the structural disorder. In particular, A2 type disorder, where Mn or Cr atoms exchange their positions with Al atoms, results in induced antiferromagnetic exchange coupling, which, at a certain level of disorder, effectively reduces the total magnetic moment to zero. This is consistent with our x-ray diffraction measurements which indicate the presence of A2 disorder in all of our samples. In addition, we also show that B2 disorder does not result in antiferromagnetic exchange coupling and therefore does not significantly reduce the total magnetic moment.« less

C-terminal Lysine-Linked Magainin 2 with Increased Activity Against Multidrug-Resistant Bacteria.

PubMed

Lorenzón, Esteban N; Santos-Filho, Norival A; Ramos, Matheus A S; Bauab, Tais M; Camargo, Ilana L B C; Cilli, Eduardo M

2016-01-01

Due to the growing problem of antibiotic-resistant microorganisms, the development of novel antimicrobial agents is a very important challenge. Dimerization of cationic antimicrobial peptides (cAMPs) is a potential strategy for enhancing antimicrobial activity. Here, we studied the effects of magainin 2 (MG2) dimerization on its structure and biological activity. Lysine and glutamic acid were used to synthesize the C- and N-terminal dimers of MG2, respectively, in order to evaluate the impact of linker position used to obtain the dimers. Both MG2 and its dimeric versions showed a random coil structure in aqueous solution. However, in the presence of a structure-inducing solvent or a membrane mimetic, all peptides acquired helical structure. N-terminal dimerization did not affect the biological activity of the peptide. On the other hand, the C-terminal dimer, (MG2)2K, showed antimicrobial activity 8-16 times higher than that of MG2, and the time required to kill Escherichia coli was lower. The enhanced antimicrobial activity was related to membrane permeabilization. (MG2)2K was also more active against multidrug-resistant bacteria of clinical origin. Overall, the results presented here demonstrate that C-terminal lysine-linked dimerization improve the activity of MG2, and (MG2)2K can be considered as a potential antimicrobial agent.

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

Mahajan, Mani, E-mail: manimahajan86@gmail.com; Singla, Gourav, E-mail: gsinghla@gmail.com; Singh, K., E-mail: kusingh@thapar.edu

Carbon nanospheres of grape-like structure (CNS) with diameter ranging from 40 to 50 nm and wall thickness of 6–8 nm were synthesized by solvothermal route. The phase structure, morphology, microstructure, thermal stability, disorder and optical properties of synthesized CNS were investigated by various characterization techniques. The possible formation and growth mechanism for CNS were discussed on the basis of the in-build reaction conditions. The degradation study of organic pollutants (methylene blue) in UV light in the presence of synthesized CNS was done. The stability of the CNS in electrochemical performance was also discussed at the different potential window and comparedmore » its electrocatalytic activity with platinum supported on CNS which shows the better response for oxygen reduction reactions (ORR) at an optimized potential window (–0.2 to 1.0 V vs SCE). - Graphical abstract: A representative synthesis mechanism of carbon nano sphere (CNS) showing spherical morphology with its photo as well as electrocatalyst properties. - Highlights: • Carbon nanospheres (CNS) have been synthesized using in situ chemical-reduction route. • The bare CNS shows good luminescence and photocatalytic applications. • The Pt/CNS shows better electrochemical performance than the reported Pt/C.« less

Computational segmentation of collagen fibers in bone matrix indicates bone quality in ovariectomized rat spine.

PubMed

Daghma, Diaa Eldin S; Malhan, Deeksha; Simon, Paul; Stötzel, Sabine; Kern, Stefanie; Hassan, Fathi; Lips, Katrin Susanne; Heiss, Christian; El Khassawna, Thaqif

2018-05-01

Bone loss varies according to disease and age and these variations affect bone cells and extracellular matrix. Osteoporosis rat models are widely investigated to assess mechanical and structural properties of bone; however, bone matrix proteins and their discrepant regulation of diseased and aged bone are often overlooked. The current study considered the spine matrix properties of ovariectomized rats (OVX) against control rats (Sham) at 16 months of age. Diseased bone showed less compact structure with inhomogeneous distribution of type 1 collagen (Col1) and changes in osteocyte morphology. Intriguingly, demineralization patches were noticed in the vicinity of blood vessels in the OVX spine. The organic matrix structure was investigated using computational segmentation of collagen fibril properties. In contrast to the aged bone, diseased bone showed longer fibrils and smaller orientation angles. The study shows the potential of quantifying transmission electron microscopy images to predict the mechanical properties of bone tissue.

Bioinformatics analysis of the predicted polyprenol reductase genes in higher plants

NASA Astrophysics Data System (ADS)

Basyuni, M.; Wati, R.

2018-03-01

The present study evaluates the bioinformatics methods to analyze twenty-four predicted polyprenol reductase genes from higher plants on GenBank as well as predicted the structure, composition, similarity, subcellular localization, and phylogenetic. The physicochemical properties of plant polyprenol showed diversity among the observed genes. The percentage of the secondary structure of plant polyprenol genes followed the ratio order of α helix > random coil > extended chain structure. The values of chloroplast but not signal peptide were too low, indicated that few chloroplast transit peptide in plant polyprenol reductase genes. The possibility of the potential transit peptide showed variation among the plant polyprenol reductase, suggested the importance of understanding the variety of peptide components of plant polyprenol genes. To clarify this finding, a phylogenetic tree was drawn. The phylogenetic tree shows several branches in the tree, suggested that plant polyprenol reductase genes grouped into divergent clusters in the tree.

Oxygen Reduction Reaction on Platinum-Terminated “Onion-structured” Alloy Catalysts

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

Herron, Jeffrey A.; Jiao, Jiao; Hahn, Konstanze

Using periodic, self-consistent density functional theory (GGA-PW91) calculations, a series of onion-structured metal alloys have been investigated for their catalytic performance towards the oxygen reduction reaction (ORR). The onion-structures consist of a varying number of atomic layers of one or two metals each, pseudomorphically deposited on top of one another to form the overall structure. All catalysts studied feature a Pt overlayer, and often consist of at least one Pd layer below the surface. Three distinct ORR mechanisms were analyzed on the close-packed facets of all the structures considered. These mechanisms include a direct route of O2 dissociation and twomore » hydrogen-assisted routes of O–O bond-breaking in peroxyl (OOH) and in hydrogen peroxide (HOOH) intermediates. A thermochemical analysis of the elementary steps provides information on the operating potential, and thereby energy efficiency of each electrocatalyst. A Sabatier analysis of catalytic activity based on thermochemistry of proton/electron transfer steps and activation energy barrier for O–O bond-breaking steps leads to a “volcano” relation between the surfaces’ activity and the binding energy of O. Several of the onion-structured alloys studied here show promise for achieving energy efficiency higher than that of Pt, by being active at potentials higher than the operating potential of Pt. Furthermore, some have at least as good activity as pure Pt at that operating potential. Thus, a number of the onion-structured alloys studied here are promising as cathode electrocatalysts in proton exchange membrane fuel cells.« less

New Robust Design Guideline forImperfection Sensitive Composite Launcher Structures- The Desicos Project

NASA Astrophysics Data System (ADS)

Degenhardt, Richard

2014-06-01

Space industry demands for reduced development and operating costs. Structural weight reduction by exploitation of structural reserves in composite space and aerospace structures contributes to this aim, however, it requires accurate and experimentally validated stability analysis. Currently, the potential of composite light weight structures, which are prone to buckling, is not fully exploited as appropriate guidelines in the field of space applications do not exist. This paper deals with the state-of-the-art advances and challenges related to coupled stability analysis of composite structures which show very complex stability behaviour. Improved design guidelines for composites structures are still under development. This paper gives a short state-of-the-art and presents a proposal for a future design guideline.

Microscopically derived potential energy surfaces from mostly structural considerations

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

Ermamatov, M.J.; Institute of Nuclear Physics, Ulughbek, Tashkent 100214; Hess, Peter O., E-mail: hess@nucleares.unam.mx

2016-08-15

A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. Wemore » will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.« less

Correlation Between Microstructure and Optical Properties of Cu (In0.7, Ga0.3) Se2 Grown by Electrodeposition Technique

NASA Astrophysics Data System (ADS)

Chihi, Adel; Bessais, Brahim

2017-01-01

Polycrystalline thin films Cu (In0.7, Ga0.3) Se2 (CIGSe) were grown on copper foils at various cathodic potentials by using an electrodeposition technique. Scanning electron microscopy showed that the average diameter of CIGSe grains increase from 0.1 μm to 1 μm when the cathodic potential decreases. The structure and surface morphology were investigated by x-ray diffraction and atomic force microscopy (AFM) techniques. This structure study shows that the thin films were well crystallized in a chalcopyrite structure without unwanted secondary phases with a preferred orientation along (112) plane. Energy-dispersive x-ray analyses confirms the existence of CIGSe single phase on a copper substrate. AFM analysis indicated that the root mean square roughness decreases from 64.28 to 27.42 when the potential deposition increases from -0.95 V to -0.77 V. Using Raman scattering spectroscopy, the A1 optical phonon mode was observed in 173 cm-1 and two other weak peaks were detected at 214 cm-1 and 225 cm-1 associated with the B2 and E modes of the CIGSe phase. Through spectroscopy ellipsometry analysis, a three-layer optical model was exploited to derive the optical properties and layer thickness of the CIGSe film by least-squares fitting the measured variation in polarization light versus the obtained microstructure.

Pump-probe imaging of pigmented cutaneous melanoma primary lesions gives insight into metastatic potential

PubMed Central

Robles, Francisco E.; Deb, Sanghamitra; Wilson, Jesse W.; Gainey, Christina S.; Selim, M. Angelica; Mosca, Paul J.; Tyler, Douglas S.; Fischer, Martin C.; Warren, Warren S.

2015-01-01

Metastatic melanoma is associated with a poor prognosis, but no method reliably predicts which melanomas of a given stage will ultimately metastasize and which will not. While sentinel lymph node biopsy (SLNB) has emerged as the most powerful predictor of metastatic disease, the majority of people dying from metastatic melanoma still have a negative SLNB. Here we analyze pump-probe microscopy images of thin biopsy slides of primary melanomas to assess their metastatic potential. Pump-probe microscopy reveals detailed chemical information of melanin with subcellular spatial resolution. Quantification of the molecular signatures without reference standards is achieved using a geometrical representation of principal component analysis. Melanin structure is analyzed in unison with the chemical information by applying principles of mathematical morphology. Results show that melanin in metastatic primary lesions has lower chemical diversity than non-metastatic primary lesions, and contains two distinct phenotypes that are indicative of aggressive disease. Further, the mathematical morphology analysis reveals melanin in metastatic primary lesions has a distinct “dusty” quality. Finally, a statistical analysis shows that the combination of the chemical information with spatial structures predicts metastatic potential with much better sensitivity than SLNB and high specificity, suggesting pump-probe microscopy can be an important tool to help predict the metastatic potential of melanomas. PMID:26417529

Spectroscopic and quantum chemical analysis of a natural product - Hayatin hydrochloride

NASA Astrophysics Data System (ADS)

Mishra, Rashmi; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

2015-08-01

Majority of drugs in use today are natural products, natural product mimics or semi synthetic derivatives. Therefore in recent times, focus on plant research has increased all over the world and large body of evidence has been collected to show immense potential of medicinal plants used in various traditional systems. Therefore, in the present communication to aid that research, structural and spectroscopic analysis of a natural product, an alkaloid Hayatin hydrochloride was performed. Both ab initio Hartree-Fock and density functional theory employing B3LYP with complete relaxation in the potential energy surface using 6-311G (d,p) basis set were used for the calculations. The vibrational frequencies were calculated and scaled values were compared with experimental FT-IR and micro-Raman spectra. The complete assignments were performed on the basis of potential energy distribution. The structure-activity relationship has also been interpreted by mapping electrostatic potential surface, which are valuable information for the quality control of medicines and drug-receptor interactions. Electronic properties have been analysed employing TD-DFT for both gaseous and solvent phase. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

Exploration of Al-Doped ZnO in Photovoltaic Thin Films

NASA Astrophysics Data System (ADS)

Ciccarino, Christopher; Sahiner, M. Alper

The electrical properties of Al doped ZnO-based thin films represent a potential advancement in the push for increasing solar cell efficiency. Doping with Aluminum will theoretically decrease resistivity of the film and therefore achieve this potential as a viable option in the P-N junction phase of photovoltaic cells. The n-type semi-conductive characteristics of the ZnO layer will theoretically be optimized with the addition of Aluminum carriers. In this study, Aluminum doping concentrations ranging from 1-3% by mass were produced, analyzed, and compared. Films were developed onto ITO coated glass using the Pulsed Laser Deposition technique. Target thickness was 250 nm and ellipsometry measurements showed uniformity and accuracy in this regard. Active dopant concentrations were determined using Hall Effect measurements. Efficiency measurements showed possible applications of this doped compound, with upwards of 7% efficiency measured, using a Keithley 2602 SourceMeter set-up. XRD scans showed highly crystalline structures, with effective Al intertwining of the hexagonal wurtzile ZnO molecular structure. This alone indicates a promising future of collaboration between these two materials.

Design, synthesis and biological evaluation of multifunctional tacrine-curcumin hybrids as new cholinesterase inhibitors with metal ions-chelating and neuroprotective property.

PubMed

Liu, Zhikun; Fang, Lei; Zhang, Huan; Gou, Shaohua; Chen, Li

2017-04-15

Total sixteen tacrine-curcumin hybrid compounds were designed and synthesized for the purpose of searching for multifunctional anti-Alzheimer agents. In vitro studies showed that these hybrid compounds showed good cholinesterase inhibitory activity. Particularly, the potency of K 3-2 is even beyond tacrine. Some of the compounds exhibited different selectivity on acetylcholinesterase or butyrylcholinesterase due to the structural difference. Thus, the structure and activity relationship is summarized and further discussed based on molecular modeling studies. The ORAC and MTT assays indicated that the hybrid compounds possessed pronounced antioxidant activity and could effectively protect PC12 cells from the H 2 O 2 /Aβ42-induced toxicity. Moreover, the hybrid compounds also showed positive metal ions-chelating ability in vitro, suggesting a potential to halt ion-induced Aβ aggregation. All the obtained results demonstrated that the tacrine-curcumin hybrid compounds, in particular compound K 3-2 , can be considered as potential therapeutic agents for Alzheimer's disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rainbows in rotationally inelastic scattering: a comparative study of different model potential surfaces and dynamical approximations

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

Schinke, R.; Korsch, H.J.; Poppe, D.

1982-12-15

Rainbow structures in rotationally elastic and inelastic differential cross sections in atom--diatom collisions are investigated by comparison of three model potential energy surfaces labeled I, II, and III which are represented by V(R,..gamma..) = V/sub 0/(R)+V/sub 2/(R)P/sub 2/(cos ..gamma..). The cross sections are calculated within the quantal infinite-order-sudden (IOS) approximation. The anisotropic part V/sub 2/ is the same for all potentials and purely repulsive. The isotropic part V/sub 0/ for potential I is also repulsive and the differential cross sections show the well-studied rotational rainbow structures. Structural changes occur for collisions in potential II and III which have V/sub 0/more » terms being attractive at intermediate and large atom--molecule separations and having well depths of 10% and 25% of the collision energy, respectively. For example, the elastic cross section has no classical rainbow in the case of potential I but three in the case of potential III. The rainbow structures are analyzed within the classical and semiclassical versions of the IOS approximation and interpreted in terms of catastrophe theory. The quantitative comparison of the classical with the quantal IOS cross sections manifests possible quantum effects, i.e., tunneling into nonclassical regions and interference effects due to the superposition of several contributions (up to six in the present study). They can be very prominent and thus we conclude that much caution is needed if experimental data are compared with classical calculations. The accuracy of the IOS approximation is tested by comparison of classical IOS cross sections with cross sections obtained from exact classical trajectory calculations. The agreement is generally good with the exemption of the rainbow region and small angle, rotationally elastic scattering.« less

Predicted facies, sedimentary structures and potential resources of Jurassic petroleum complex in S-E sWestern Siberia (based on well logging data)

NASA Astrophysics Data System (ADS)

Prakojo, F.; Lobova, G.; Abramova, R.

2015-11-01

This paper is devoted to the current problem in petroleum geology and geophysics- prediction of facies sediments for further evaluation of productive layers. Applying the acoustic method and the characterizing sedimentary structure for each coastal-marine-delta type was determined. The summary of sedimentary structure characteristics and reservoir properties (porosity and permeability) of typical facies were described. Logging models SP, EL and GR (configuration, curve range) in interpreting geophysical data for each litho-facies were identified. According to geophysical characteristics these sediments can be classified as coastal-marine-delta. Prediction models for potential Jurassic oil-gas bearing complexes (horizon J11) in one S-E Western Siberian deposit were conducted. Comparing forecasting to actual testing data of layer J11 showed that the prediction is about 85%.

Study of local currents in low dimension materials using complex injecting potentials

NASA Astrophysics Data System (ADS)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Combining network analysis with Cognitive Work Analysis: insights into social organisational and cooperation analysis.

PubMed

Houghton, Robert J; Baber, Chris; Stanton, Neville A; Jenkins, Daniel P; Revell, Kirsten

2015-01-01

Cognitive Work Analysis (CWA) allows complex, sociotechnical systems to be explored in terms of their potential configurations. However, CWA does not explicitly analyse the manner in which person-to-person communication is performed in these configurations. Consequently, the combination of CWA with Social Network Analysis provides a means by which CWA output can be analysed to consider communication structure. The approach is illustrated through a case study of a military planning team. The case study shows how actor-to-actor and actor-to-function mapping can be analysed, in terms of centrality, to produce metrics of system structure under different operating conditions. In this paper, a technique for building social network diagrams from CWA is demonstrated.The approach allows analysts to appreciate the potential impact of organisational structure on a command system.

Half-metallicity and electronic structures for carbon-doped group III-nitrides: Calculated with a modified Becke-Johnson potential

NASA Astrophysics Data System (ADS)

Fan, Shuai-wei; Wang, Ri-gao; Xu, Pemg

2016-09-01

The electronic structures and magnetism for carbon-doped group III-nitrides are investigated by utilizing the first principle method with the modified Becke-Johnson potential. Calculations show that carbon substituting cations (anions) would induce the group III-nitrides to be paramagnetic metals (half-metallic ferromagnets). Single carbon substituting nitrogen could produce 1.00μB magnetic moment. Electronic structures indicate that the carriers-mediated double-exchange interaction plays a crucial role in forming the ferromagnetism. Based on the mean-field theory, the Curie temperature for carbon-doped group III-nitrides would be above the room temperature. Negative chemical pair interactions imply that carbon dopants tend to form clustering distribution in group III-nitrides. The nitrogen vacancy would make the carbon-doped group III-nitrides lose the half-metallic ferromagnetism.

Formation of non-spherical polymersomes driven by hydrophobic directional aromatic perylene interactions.

PubMed

Wong, Chin Ken; Mason, Alexander F; Stenzel, Martina H; Thordarson, Pall

2017-11-01

Polymersomes, made up of amphiphilic block copolymers, are emerging as a powerful tool in drug delivery and synthetic biology due to their high stability, chemical versatility, and surface modifiability. The full potential of polymersomes, however, has been hindered by a lack of versatile methods for shape control. Here we show that a range of non-spherical polymersome morphologies with anisotropic membranes can be obtained by exploiting hydrophobic directional aromatic interactions between perylene polymer units within the membrane structure. By controlling the extent of solvation/desolvation of the aromatic side chains through changes in solvent quality, we demonstrate facile access to polymersomes that are either ellipsoidal or tubular-shaped. Our results indicate that perylene aromatic interactions have a great potential in the design of non-spherical polymersomes and other structurally complex self-assembled polymer structures.

Structure-based conformational preferences of amino acids

PubMed Central

Koehl, Patrice; Levitt, Michael

1999-01-01

Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for α-helices and β-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion. PMID:10535955

Multiscale tomography of buried magnetic structures: its use in the localization and characterization of archaeological structures

NASA Astrophysics Data System (ADS)

Saracco, Ginette; Moreau, Frédérique; Mathé, Pierre-Etienne; Hermitte, Daniel; Michel, Jean-Marie

2007-10-01

We have previously developed a method for characterizing and localizing `homogeneous' buried sources, from the measure of potential anomalies at a fixed height above ground (magnetic, electric and gravity). This method is based on potential theory and uses the properties of the Poisson kernel (real by definition) and the continuous wavelet theory. Here, we relax the assumption on sources and introduce a method that we call the `multiscale tomography'. Our approach is based on the harmonic extension of the observed magnetic field to produce a complex source by use of a complex Poisson kernel solution of the Laplace equation for complex potential field. A phase and modulus are defined. We show that the phase provides additional information on the total magnetic inclination and the structure of sources, while the modulus allows us to characterize its spatial location, depth and `effective degree'. This method is compared to the `complex dipolar tomography', extension of the Patella method that we previously developed. We applied both methods and a classical electrical resistivity tomography to detect and localize buried archaeological structures like antique ovens from magnetic measurements on the Fox-Amphoux site (France). The estimates are then compared with the results of excavations.

The structure of the NO(X (2)Pi)-N(2) complex: A joint experimental-theoretical study.

PubMed

Wen, B; Meyer, H; Kłos, J

2010-04-21

We report the first measurement of the spectrum of the NO-N(2) complex in the region of the first vibrational NO overtone transition. The origin band of the complex is blueshifted by 0.30 cm(-1) from the corresponding NO monomer frequency. The observed spectrum consists of three bands assigned to the origin band, the excitation of one quantum of z-axis rotation and one associated hot band. The spacing of the bands and the rotational structure indicate a T-shaped vibrationally averaged structure with the NO molecule forming the top of the T. These findings are confirmed by high level ab initio calculations of the potential energy surfaces in planar symmetry. The deepest minimum is found for a T-shaped geometry on the A(")-surface. As a result the sum potential also has the global minimum for this structure. The different potential surfaces show several additional local minima at slightly higher energies indicating that the complex most likely will perform large amplitude motion even in its ground vibrational state. Nevertheless, as suggested by the measured spectra, the complex must, on average, spend a substantial amount of time near the T-shaped configuration.

Liquid 4He at Zero Temperature and the STLS Scheme

NASA Astrophysics Data System (ADS)

Doroudi, A.

2007-07-01

Within the framework of the self-consistent scheme proposed by Singwi, Tosi, Land and Sjölander (STLS) for an interacting system we study the properties of superfluid liquid 4He. By employing the Aziz potential (HFD-B) as the interaction potential between helium atoms, we have calculated the static structure factor, the pair-correlation function, the elementary excitation spectrum and the effective two-body interaction as a function of wave-vector, for different densities. Our results show considerable improvement over the Ng-Singwi’s model potential of a hard core plus an attractive tail and are comparable with experimental data. We have compared our results with experimental data and with the results of some theoretical models. Agreement between our results and the experimental data for the static structure factor for the small k values is fairly good.

Gravity localization in sine-Gordon braneworlds

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

Cruz, W.T., E-mail: wilamicruz@gmail.com; Maluf, R.V., E-mail: r.v.maluf@fisica.ufc.br; Sousa, L.J.S., E-mail: luisjose@fisica.ufc.br

2016-01-15

In this work we study two types of five-dimensional braneworld models given by sine-Gordon potentials. In both scenarios, the thick brane is generated by a real scalar field coupled to gravity. We focus our investigation on the localization of graviton field and the behaviour of the massive spectrum. In particular, we analyse the localization of massive modes by means of a relative probability method in a Quantum Mechanics context. Initially, considering a scalar field sine-Gordon potential, we find a localized state to the graviton at zero mode. However, when we consider a double sine-Gordon potential, the brane structure is changedmore » allowing the existence of massive resonant states. The new results show how the existence of an internal structure can aid in the emergence of massive resonant modes on the brane.« less

Boron doped GaN and InN: Potential candidates for spintronics

NASA Astrophysics Data System (ADS)

Fan, S. W.; Huang, X. N.; Yao, K. L.

2017-02-01

The full potential linearized augmented plane wave method together with the Tran-Blaha modified Becke-Johnson potential is utilized to investigate the electronic structures and magnetism for boron doped GaN and InN. Calculations show the boron substituting nitrogen (BN defects) could induce the GaN and InN to be half-metallic ferromagnets. The magnetic moments mainly come from the BN defects, and each BN defect would produce the 2.00 μB total magnetic moment. The electronic structures indicate the carriers-mediated double exchange interaction plays a crucial role in forming the ferromagnetism. Positive chemical pair interactions imply the BN defects would form the homogeneous distribution in GaN and InN matrix. Moderate formation energies suggest that GaN and InN with BN defects could be fabricated experimentally.

Better band gaps for wide-gap semiconductors from a locally corrected exchange-correlation potential that nearly eliminates self-interaction errors

DOE PAGES

Singh, Prashant; Harbola, Manoj K.; Johnson, Duane D.

2017-09-08

Here, this work constitutes a comprehensive and improved account of electronic-structure and mechanical properties of silicon-nitride (more » $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ ) polymorphs via van Leeuwen and Baerends (LB) exchange-corrected local density approximation (LDA) that enforces the exact exchange potential asymptotic behavior. The calculated lattice constant, bulk modulus, and electronic band structure of $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ polymorphs are in good agreement with experimental results. We also show that, for a single electron in a hydrogen atom, spherical well, or harmonic oscillator, the LB-corrected LDA reduces the (self-interaction) error to exact total energy to ~10%, a factor of three to four lower than standard LDA, due to a dramatically improved representation of the exchange-potential.« less

Collective Modes of Dust Helical Clusters

NASA Astrophysics Data System (ADS)

Tsytovich, V. N.; Gousein-Zade, N. G.; Morfill, G. E.

2005-10-01

The helical structures are the simplest 3D crystal-like cylindrical structures with radius R being a system of 2D clusters equally separated along the cylindrical axis with a relative rotation on constant angle φ0. For mean free path for grain charging much larger than the separation of the grains, the total energy of grain interaction is a sum of all pair grain interactions. The helical structures have been found experimentally for ions in laser traps in cylindrical gas discharges at very low temperatures (in both case as ``warms''). The equilibrium criterion and the criteria of stability including the absence of saddle points show that in the plane ρ, φ the bifurcation points are often present with new branches appearing (stable and unstable). Numerical MD simulations show that for cylindrical symmetry any random distributions of grains is developing into helical structures. The theory of collective modes of helical structures is developed for arbitrary grain interactions. The dispersion relation for frequencies of the collective modes for different branches of helical structures is derived and solved numerically for interaction including different type of screened grain potentials including the grain attraction. The dispersion relation in the first Brillouin zone for the square of the frequency ω2 is shown to be a be-cubic equation and gives the square of frequency ω2 > 0 for stable modes and the square of the growth rates for the unstable modes ω2 < 0. Modes for helical structures in parabolic external confining potential well perpendicular to cylindrical axis are found. Stabile self-confined structures without external confinement are discovered in presence of both non-collective and collective grain attractions.

Structure–property relationships in hybrid dental nanocomposite resins containing monofunctional and multifunctional polyhedral oligomeric silsesquioxanes

PubMed Central

Wang, Weiguo; Sun, Xiang; Huang, Li; Gao, Yu; Ban, Jinghao; Shen, Lijuan; Chen, Jihua

2014-01-01

Organic-inorganic hybrid materials, such as polyhedral oligomeric silsesquioxanes (POSS), have the potential to improve the mechanical properties of the methacrylate-based composites and resins used in dentistry. In this article, nanocomposites of methacryl isobutyl POSS (MI-POSS [bears only one methacrylate functional group]) and methacryl POSS (MA-POSS [bears eight methacrylate functional groups]) were investigated to determine the effect of structures on the properties of dental resin. The structures of the POSS-containing networks were determined by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy. Monofunctional POSS showed a strong tendency toward aggregation and crystallization, while multifunctional POSS showed higher miscibility with the dimethacrylate monomer. The mechanical properties and wear resistance decreased with increasing amounts of MI-POSS, indicating that the MI-POSS agglomerates act as the mechanical weak point in the dental resins. The addition of small amounts of MA-POSS improved the mechanical and shrinkage properties. However, samples with a higher MA-POSS concentration showed lower flexural strength and flexural modulus, indicating that there is a limited range in which the reinforcement properties of MA-POSS can operate. This concentration dependence is attributed to phase separation at higher concentrations of POSS, which affects the structural integrity, and thus, the mechanical and shrinkage properties of the dental resin. Our results show that resin with 3% MA-POSS is a potential candidate for resin-based dental materials. PMID:24550674

Structural and opto-electronic properties of 2D AlSb monolayer

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

Singh, Deobrat, E-mail: deobratsingh9@gmail.com; Sonvane, Yogesh; Gupta, Sanjeev K.

2016-05-23

We have investigated dielectric function related optical properties such as refractive index, absorption coefficient of two-dimensional hexagonal system of aluminum antimony (AlSb). We have also find structural and electronic properties of AlSb which show direct/indirect band gap with planar structure, employing the density functional theory using the generalized gradient approximation (GGA) given by Perdew-Burke-Ernzerhof (PBE) functional for exchange-correlation potential. The refractive index n(ω) increases with frequency in the near infrared region but in visible region n(ω) increasing after decrease.

DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

PubMed

Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

2013-09-10

A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

Plasmon mediated inverse Faraday effect in a graphene-dielectric-metal structure.

PubMed

Bychkov, Igor V; Kuzmin, Dmitry A; Tolkachev, Valentine A; Plaksin, Pavel S; Shavrov, Vladimir G

2018-01-01

This Letter shows the features of inverse Faraday effect (IFE) in a graphene-dielectric-metal (GDM) structure. The constants of propagation and attenuation of the surface plasmon-polariton modes are calculated. The effective magnetic field induced by surface plasmon modes in the dielectric due to the IFE is estimated to reach above 1 tesla. The possibility to control the distribution of the magnetic field by chemical potential of graphene is shown. The concept of strain-driven control of the IFE in the structure has been proposed and investigated.

Rapid search for tertiary fragments reveals protein sequence–structure relationships

PubMed Central

Zhou, Jianfu; Grigoryan, Gevorg

2015-01-01

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure. PMID:25420575

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.

PubMed

Yang, Yunfeng; Wu, Linwei; Lin, Qiaoyan; Yuan, Mengting; Xu, Depeng; Yu, Hao; Hu, Yigang; Duan, Jichuang; Li, Xiangzhen; He, Zhili; Xue, Kai; van Nostrand, Joy; Wang, Shiping; Zhou, Jizhong

2013-02-01

Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes. © 2012 Blackwell Publishing Ltd.

Inhibitors of enzymes catalyzing modifications to histone lysine residues: structure, function and activity.

PubMed

Lillico, Ryan; Stesco, Nicholas; Khorshid Amhad, Tina; Cortes, Claudia; Namaka, Mike P; Lakowski, Ted M

2016-05-01

Gene expression is partly controlled by epigenetic mechanisms including histone-modifying enzymes. Some diseases are caused by changes in gene expression that can be mitigated by inhibiting histone-modifying enzymes. This review covers the enzyme inhibitors targeting histone lysine modifications. We summarize the enzymatic mechanisms of histone lysine acetylation, deacetylation, methylation and demethylation and discuss the biochemical roles of these modifications in gene expression and in disease. We discuss inhibitors of lysine acetylation, deacetylation, methylation and demethylation defining their structure-activity relationships and their potential mechanisms. We show that there are potentially indiscriminant off-target effects on gene expression even with the use of selective epigenetic enzyme inhibitors.

Electrical conduction at domain walls in multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Seidel, Jan; Martin, Lane; He, Qing; Zhan, Qian; Chu, Ying-Hao; Rother, Axel; Hawkridge, Michael; Maksymovych, Peter; Yu, Pu; Gajek, Martin; Balke, Nina; Kalinin, Sergei; Gemming, Sybille; Wang, Feng; Catalán, Gustau; Scott, James; Spaldin, Nicola; Orenstein, Joseph; Ramesh, Ramamoorthy

2009-03-01

We report the observation of room temperature electronic conductivity at ferroelectric domain walls in BiFeO3. The origin and nature of the observed conductivity is probed using a combination of conductive atomic force microscopy, high resolution transmission electron microscopy and first-principles density functional computations. We show that a structurally driven change in both the electrostatic potential and local electronic structure (i.e., a decrease in band gap) at the domain wall leads to the observed electrical conductivity. We estimate the conductivity in the wall to be several orders of magnitude higher than for the bulk material. Additionally we demonstrate the potential for device applications of such conducting nanoscale features.

Switching of the direction of reflectionless light propagation at exceptional points in non-PT-symmetric structures using phase-change materials.

PubMed

Huang, Yin; Shen, Yuecheng; Min, Changjun; Veronis, Georgios

2017-10-30

We introduce a non-parity-time-symmetric three-layer structure, consisting of a gain medium layer sandwiched between two phase-change medium layers for switching of the direction of reflectionless light propagation. We show that for this structure unidirectional reflectionlessness in the forward direction can be switched to unidirectional reflectionlessness in the backward direction at the optical communication wavelength by switching the phase-change material Ge 2 Sb 2 Te 5 (GST) from its amorphous to its crystalline phase. We also show that it is the existence of exceptional points for this structure with GST in both its amorphous and crystalline phases which leads to unidirectional reflectionless propagation in the forward direction for GST in its amorphous phase, and in the backward direction for GST in its crystalline phase. Our results could be potentially important for developing a new generation of compact active free-space optical devices.

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

Tyson, T. A.; Gao, W.; Chen, Y. -S.

Solar cells based on hybrid perovskites have shown high efficiency while possessing simple processing methods. To gain a fundamental understanding of their properties on an atomic level, we investigate single crystals of CH 3NH 3PbI 3 with a narrow transition (~5 K) near 327 K. Temperature dependent structural measurements reveal a persistent tetragonal structure with smooth changes in the atomic displacement parameters (ADPs) on crossing T*. We show that the ADPs for I ions yield extended flat regions in the potential wells consistent with the measured large thermal expansion parameter. Molecular dynamics simulations reveal that this material exhibits significant asymmetriesmore » in the Pb-I pair distribution functions. We also show that the intrinsically enhanced freedom of motion of the iodine atoms enables large deformations. This flexibility (softness) of the atomic structure results in highly localized atomic relaxation about defects and hence accounts for both the high carrier mobility as well as the structural instability.« less

Influence of trapping potentials on the phase diagram of bosonic atoms in optical lattices

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

Giampaolo, S.M.; Illuminati, F.; Mazzarella, G.

2004-12-01

We study the effect of external trapping potentials on the phase diagram of bosonic atoms in optical lattices. We introduce a generalized Bose-Hubbard Hamiltonian that includes the structure of the energy levels of the trapping potential, and show that these levels are in general populated both at finite and zero temperature. We characterize the properties of the superfluid transition for this situation and compare them with those of the standard Bose-Hubbard description. We briefly discuss similar behaviors for fermionic systems.

Vulnerability assessment of RC frames considering the characteristic of pulse-like ground motions

NASA Astrophysics Data System (ADS)

Xu, Chao; Wen, Zengping

2017-04-01

Pulse-like ground motions are a special class of ground motions that are particularly challenging to characterize for earthquake hazard assessment. These motions are characterized by a "pulse" in the velocity time history of the motion, and they are typically very intense and have been observed to cause severe damage to structures in past earthquakes. So it is particularly important to characterize these ground motions. Previous studies show that the severe response of structure is not entirely accounted for by measuring the intensity of the ground motion using spectral acceleration of the elastic first-mode period of a structure (Sa(T1)). This paper will use several alternative intensity measures to characterize the effect of pulse-like ground motions in vulnerability assessment. The ability of these intensity measures to characterize pulse-like ground motions will be evaluated. Pulse-like ground motions and ordinary ground motions are selected as input to carry out incremental dynamic analysis. Structural response and vulnerability are estimated by using Sa(T1) as the intensity measure. The impact of pulse period on structural response is studied through residual analysis. By comparing the difference between the structural response and vulnerability curves using pulse-like ground motions and ordinary ground motions as the input, the impact of velocity pulse on vulnerability is investigated and the shortcoming of using Sa(T1) to characterize pulse-like ground motion is analyzed. Then, vector-valued ground motion intensity measures(Sa(T1)&RT1,T2, Sa(T1)&RPGV,Sa) and inelastic displacement spectra(Sdi(T1)) are used to characterize the damage potential of pulse-like ground motions, the efficiency and sufficiency of these intensity measures are evaluated. The study shows that: have strong the damage potential of near fault ground motions with velocity pulse is closely related to the pulse period of strong motion as well as first mode period of vibration and nonlinear features of the structure. The above factors should be taken into account when choosing a reasonable ground motion parameter to characterize the damage potential of pulse-like ground motions. Vulnerability curves based on Sa(T1) show obvious differences between using near fault ground motions and ordinary ground motions, as well as pulse-like ground motions with different pulse periods as the input. When using vector-valued intensity measures such as Sa(T1)&RT1,T2, Sa(T1)&RPGV,Sa and inelastic displacement spectra, the results of vulnerability analysis are roughly the same. These ground motion intensity measures are more efficient and sufficient to characterize the damage potential of near fault ground motions with velocity pulse.

Density Functional Theory Study of Oxygen Reduction Activity on Ultrathin Platinum Nanotubes

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

Matanovic, Ivana; Kent, Paul; Garzon, Fernando

2012-07-13

The structure, stability, and catalytic activity of a number of single- and double-wall platinum (n,m) nanotubes ranging in diameter from 0.3 to 2.0 nm were studied using plane-wave based density functional theory in the gas phase and water environment. The change in the catalytic activity toward the oxygen reduction reaction (ORR) with the size and chirality of the nanotube was studied by calculating equilibrium adsorption potentials for ORR intermediates and by constructing free energy diagrams in the ORR dissociative mechanism network. In addition, the stability of the platinum nanotubes is investigated in terms of electrochemical dissolution potentials and by determiningmore » the most stable state of the material as a function of pH and potential, as represented in Pourbaix diagrams. Our results show that the catalytic activity and the stability toward electrochemical dissolution depend greatly on the diameter and chirality of the nanotube. On the basis of the estimated overpotentials for ORR, we conclude that smaller, approximately 0.5 nm in diameter single-wall platinum nanotubes consistently show a huge, up to 400 mV larger overpotential than platinum, indicating very poor catalytic activity toward ORR. This is the result of substantial structural changes induced by the adsorption of any chemical species on these tubes. Single-wall n = m platinum nanotubes with a diameter larger than 1 nm have smaller ORR overpotentials than bulk platinum for up to 180 mV and thus show improved catalytic activity relative to bulk. We also predict that these nanotubes can endure the highest cell potentials but dissolution potentials are still for 110 mV lower than for the bulk, indicating a possible corrosion problem.« less

Control of Bacteriophage T4 Tail Lysozyme Activity During the Infection Process

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

Kanamaru, Shuji; Ishiwata, Yasutaka; Suzuki, Toshiharu

2010-07-19

Bacteriophage T4 has an efficient mechanism for injecting the host Escherichia coli cell with genomic DNA. Its gene product 5 (gp5) has a needle-like structure attached to the end of a tube through which the DNA passes on its way out of the head and into the host. The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space. gp5 is normally post-translationally cleaved between residues 351 and 352. The function of this process in controlling the lysozyme activity of gp5 has now been investigated. When gp5 is over-expressed in E. coli,more » two mutants (S351H and S351A) showed a reduction of cleavage products and five other mutants (S351L, S351K, S351Y, S351Q, and S351T) showed no cleavage. Furthermore, in a complementation assay at 20 C, the mutants that had no cleavage of gp5 produced a reduced number of plaques compared to wild-type T4. The crystal structure of the non-cleavage phenotype mutant of gp5, S351L, complexed with gene product 27, showed that the 18 residues in the vicinity of the potential cleavage site (disordered in the wild-type structure) had visible electron density. The polypeptide around the potential cleavage site is exposed, thus allowing access for an E. coli protease. The lysozyme activity is inhibited in the wild-type structure by a loop from the adjacent gp5 monomer that binds into the substrate-binding site. The same inhibition is apparent in the mutant structure, showing that the lysozyme is inhibited before gp5 is cleaved and, presumably, the lysozyme is activated only after gp5 has penetrated the outer membrane.« less

Application of guided acoustic waves to delamination detection

NASA Technical Reports Server (NTRS)

Sun, Keun J.

1992-01-01

Guided plate waves are able to interact with structural flaws such as delaminations and cracks due to their propagation properties highly sensitive to the thickness change in materials. A technique which employs an acoustic damper to probe the results of this interaction and then to locate flaws in a relatively short period of time is developed. With its technical advantages, this technique shows its potential application to large area structural integrity assessment.

Arginine-based poly(ester amide) nanoparticle platform: From structure-property relationship to nucleic acid delivery.

PubMed

You, Xinru; Gu, Zhipeng; Huang, Jun; Kang, Yang; Chu, Chih-Chang; Wu, Jun

2018-05-25

Many different types of polycations have been vigorously studied for nucleic acid delivery, but a systematical investigation of the structure-property relationships of polycations for nucleic acid delivery is still lacking. In this study, a new library of biodegradable and biocompatible arginine-based poly(ester amide) (Arg-PEA) biomaterials was designed and synthesized with a tunable structure for such a comprehensive structure-property research. Nanoparticle (NP) complexes were formed through the electrostatic interactions between the polycationic Arg-PEAs and anionic nucleic acids. The following structure effects of the Arg-PEAs on the transfection efficiency of nucleic acids were investigated: 1) the linker/spacer length (length effect and odd-even effect); 2) salt type of arginine; 3) the side chain; 4) chain stiffness; 5) molecular weight (MW). The data obtained revealed that a slight change in the Arg-PEA structure could finely tune its physicochemical property such as hydrophobicity, and this could subsequently affect the nanoparticle size and zeta potential, which, in turn, regulate the transfection efficiency and silencing outcomes. A further study of the Arg-PEA/CpG oligodeoxynucleotide NP complexes indicated that the polymer structure could precisily regulate the immune response of CpG, thus providing a new potential nano-immunotherapy strategy. The in vitro data have further confirmed that the Arg-PEA NPs showed a satisfactory delivery performance for a variety of nucleic acids. Therefore, the data from the current study provide comprehensive information about the Arg-PEA structure-transfection property relationship; the tunable property of the library of Arg-PEA biomaterials can be one of the promising candidates for nucleic acid delivery and other biomedical applications. Polycations have being intensive utilized for nucleic acid delivery. However, there has not been elucidated about the relationship between polycation's structure and the physicochemical properties/biological function. In this timely report, an arginine based poly(ester amide) (Arg-PEA) library was prepared with finely tunable structure to systematically investigate the structure-property relationships of polycations for nucleic acid delivery. The results revealed that slight change of Arg-PEA structure could finely tune the physicochemical property (such as hydrophobicity), which subsequently affect the size and zeta potential of Arg-PEA/nucleic acid nanoparticles(NPs), and finally regulate the resulting transfection or silencing outcomes. Further study of Arg-PEA/CpG NPs indicated that the polymer structure could precisely regulate immuno response of CpG, providing new potential nano-immunotherapy strategy. In vitro evaluations confirmed that the NPs showed satisfied delivery performance for a variety types of nucleic acids. Therefore, these studies provide comprehensive information of Arg-PEA structure-property relationship, and the tunable properties of Arg-PEAs make them promising candidates for nucleic acid delivery and other biomedical applications. Overall, we have shown enough significance and novelty in terms of nucleic acid delivery, biomaterials, pharmaceutical science and nanomedicine. Copyright © 2018. Published by Elsevier Ltd.

The Ulam Index: Methods of Theoretical Computer Science Help in Identifying Chemical Substances

NASA Technical Reports Server (NTRS)

Beltran, Adriana; Salvador, James

1997-01-01

In this paper, we show how methods developed for solving a theoretical computer problem of graph isomorphism are used in structural chemistry. We also discuss potential applications of these methods to exobiology: the search for life outside Earth.

Terahertz pulsed imaging for the monitoring of dental caries: a comparison with x-ray imaging

NASA Astrophysics Data System (ADS)

Karagoz, Burcu; Kamburoglu, Kıvanc; Altan, Hakan

2017-07-01

Dental caries in sliced samples are investigated using terahertz pulsed imaging. Frequency domain terahertz response of these structures consistent with X-ray imaging results show the potential of this technique in the detection of early caries.

Tuning wettability of hydrogen titanate nanowire mesh by Na+ irradiation

NASA Astrophysics Data System (ADS)

Das, Pritam; Chatterjee, Shyamal

2018-04-01

Hydrogen titanate (HT) nanowires have been widely studied for remarkable properties and various potential applications. However, a handful studies are available related to ion beam induced structural changes and influence on wetting behavior of the HT nanowire surface. In this work, we exposed HT nanowires to 5 keV Na+ at an ion fluence of 1×1016 ions.cm-2. Scanning electron microscope shows that at this ion fluence nanowires are bent arbitrarily and they are welded to each other forming an interlinked network structure. Computer simulation shows that ion beam induces defect formation in the nanowires, which plays major role in such structural modifications. An interesting alteration of surface wetting property is observed due to ion irradiation. The hydrophilic pristine surface turns into hydrophobic after ion irradiation.

Advanced design for lightweight structures: Review and prospects

NASA Astrophysics Data System (ADS)

Braga, Daniel F. O.; Tavares, S. M. O.; da Silva, Lucas F. M.; Moreira, P. M. G. P.; de Castro, Paulo M. S. T.

2014-08-01

Current demand for fuel efficient aircraft has been pushing the aeronautical sector to develop ever more lightweight designs while keeping safe operation and required structural strength. Along with light-weighting, new structural design concepts have also been established in order to maintain the aircraft in service for longer periods of time, with high reliability levels. All these innovations and requirements have led to deeply optimized aeronautical structures contributing to more sustainable air transport. This article reviews the major design philosophies which have been employed in aircraft structures, including safe-life, fail-safe and damage tolerance taking into account their impact on the structural design. A brief historical review is performed in order to analyse what led to the development of each philosophy. Material properties are related to each of the design philosophies. Damage tolerant design has emerged as the main structural design philosophy in aeronautics, requiring deep knowledge on materials fatigue and corrosion strength, as well as potential failure modes and non-destructive inspection techniques, particularly minimum detectable defect and scan times. A discussion on the implementation of structural health monitoring and self-healing structures within the current panorama of structures designed according to the damage tolerant philosophy is presented. This discussion is aided by a review of research on these two subjects. These two concepts show potential for further improving safety and durability of aircraft structures.

Structure and Sequence Search on Aptamer-Protein Docking

NASA Astrophysics Data System (ADS)

Xiao, Jiajie; Bonin, Keith; Guthold, Martin; Salsbury, Freddie

2015-03-01

Interactions between proteins and deoxyribonucleic acid (DNA) play a significant role in the living systems, especially through gene regulation. However, short nucleic acids sequences (aptamers) with specific binding affinity to specific proteins exhibit clinical potential as therapeutics. Our capillary and gel electrophoresis selection experiments show that specific sequences of aptamers can be selected that bind specific proteins. Computationally, given the experimentally-determined structure and sequence of a thrombin-binding aptamer, we can successfully dock the aptamer onto thrombin in agreement with experimental structures of the complex. In order to further study the conformational flexibility of this thrombin-binding aptamer and to potentially develop a predictive computational model of aptamer-binding, we use GPU-enabled molecular dynamics simulations to both examine the conformational flexibility of the aptamer in the absence of binding to thrombin, and to determine our ability to fold an aptamer. This study should help further de-novo predictions of aptamer sequences by enabling the study of structural and sequence-dependent effects on aptamer-protein docking specificity.

12-Chemokine Gene Signature Identifies Lymph Node-like Structures in Melanoma: Potential for Patient Selection for Immunotherapy?

NASA Astrophysics Data System (ADS)

Messina, Jane L.; Fenstermacher, David A.; Eschrich, Steven; Qu, Xiaotao; Berglund, Anders E.; Lloyd, Mark C.; Schell, Michael J.; Sondak, Vernon K.; Weber, Jeffrey S.; Mulé, James J.

2012-10-01

We have interrogated a 12-chemokine gene expression signature (GES) on genomic arrays of 14,492 distinct solid tumors and show broad distribution across different histologies. We hypothesized that this 12-chemokine GES might accurately predict a unique intratumoral immune reaction in stage IV (non-locoregional) melanoma metastases. The 12-chemokine GES predicted the presence of unique, lymph node-like structures, containing CD20+ B cell follicles with prominent areas of CD3+ T cells (both CD4+ and CD8+ subsets). CD86+, but not FoxP3+, cells were present within these unique structures as well. The direct correlation between the 12-chemokine GES score and the presence of unique, lymph nodal structures was also associated with better overall survival of the subset of melanoma patients. The use of this novel 12-chemokine GES may reveal basic information on in situ mechanisms of the anti-tumor immune response, potentially leading to improvements in the identification and selection of melanoma patients most suitable for immunotherapy.

Influence of hydrolysis behaviour and microfluidisation on the functionality and structural properties of collagen hydrolysates.

PubMed

Zhang, Yehui; Zhang, Yousheng; Liu, Xueming; Huang, Lihua; Chen, Zhiyi; Cheng, Jingrong

2017-07-15

The functionality and structural properties of pig skin hydrolysates with different degrees of hydrolysis (DH, 10% and 20%) and microfluidisation (120MPa), prepared by pepsin and Alcalase® have been investigated in this study. Extensive hydrolysis can significantly improve the absolute value of the zeta potential and surface hydrophobicity. The particle distribution of hydrolysates decreased with increasing DH. The numbers of free sulfhydryl (SH) and disulfide bonds (SS) were significantly increased with increasing DH (p<0.05). Hydrolysates with a lower DH showed a better emulsifying property than those with a higher DH. Microfluidisation led to the transformation of structural and interfacial properties of the hydrolysates and increased the value of the zeta potential, S 0 , and gel strength. Microfluidisation results in limited breakage of chemical bonds, the number of SS and SH bonds unchanged in the treatment. These results reflect the functionality and structural properties of collagen-rich pig skin hydrolysates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural refinement of vitreous silica bilayers

NASA Astrophysics Data System (ADS)

Sadjadi, Mahdi; Wilson, Mark; Thorpe, M. F.

The importance of glasses resides not only in their applications but in fundamental questions that they put forth. The continuous random network model can successfully describe the glass structure, but determining details, like ring statistics, has always been difficult using only diffraction data. But recent atomic images of 2D vitreous silica bilayers can offer valuable new insights which are hard to be observed directly in 3D silica models/experiments (for references see). However, the experimental results are prone to uncertainty in atomic positions, systematic errors, and being finite. We employ special boundary conditions developed for such networks to refine the experimental structures. We show the best structure can be found by using various potentials to maximize information gained from the experimental samples. We find a range of densities, the so-called flexibility window, in which tetrahedra are perfect. We compare results from simulations using harmonic potentials, MD with atomic polarizabilities included and DFT. We should thank David Drabold and Bishal Bhattarai for useful discussions. Support through NSF Grant # DMS 1564468 is gratefully acknowledged.

Structural Feasibility Analysis of a Robotically Assembled Very Large Aperture Optical Space Telescope

NASA Technical Reports Server (NTRS)

Wilkie, William Keats; Williams, R. Brett; Agnes, Gregory S.; Wilcox, Brian H.

2007-01-01

This paper presents a feasibility study of robotically constructing a very large aperture optical space telescope on-orbit. Since the largest engineering challenges are likely to reside in the design and assembly of the 150-m diameter primary reflector, this preliminary study focuses on this component. The same technology developed for construction of the primary would then be readily used for the smaller optical structures (secondary, tertiary, etc.). A reasonable set of ground and on-orbit loading scenarios are compiled from the literature and used to define the structural performance requirements and size the primary reflector. A surface precision analysis shows that active adjustment of the primary structure is required in order to meet stringent optical surface requirements. Two potential actuation strategies are discussed along with potential actuation devices at the current state of the art. The finding of this research effort indicate that successful technology development combined with further analysis will likely enable such a telescope to be built in the future.

Fiber Optic Bragg Grating Sensors for Thermographic Detection of Subsurface Anomalies

NASA Technical Reports Server (NTRS)

Allison, Sidney G.; Winfree, William P.; Wu, Meng-Chou

2009-01-01

Conventional thermography with an infrared imager has been shown to be an extremely viable technique for nondestructively detecting subsurface anomalies such as thickness variations due to corrosion. A recently developed technique using fiber optic sensors to measure temperature holds potential for performing similar inspections without requiring an infrared imager. The structure is heated using a heat source such as a quartz lamp with fiber Bragg grating (FBG) sensors at the surface of the structure to detect temperature. Investigated structures include a stainless steel plate with thickness variations simulated by small platelets attached to the back side using thermal grease. A relationship is shown between the FBG sensor thermal response and variations in material thickness. For comparison, finite element modeling was performed and found to agree closely with the fiber optic thermography results. This technique shows potential for applications where FBG sensors are already bonded to structures for Integrated Vehicle Health Monitoring (IVHM) strain measurements and can serve dual-use by also performing thermographic detection of subsurface anomalies.

Silica deposits on Mars with features resembling hot spring biosignatures at El Tatio in Chile

PubMed Central

Ruff, Steven W.; Farmer, Jack D.

2016-01-01

The Mars rover Spirit encountered outcrops and regolith composed of opaline silica (amorphous SiO2·nH2O) in an ancient volcanic hydrothermal setting in Gusev crater. An origin via either fumarole-related acid-sulfate leaching or precipitation from hot spring fluids was suggested previously. However, the potential significance of the characteristic nodular and mm-scale digitate opaline silica structures was not recognized. Here we report remarkably similar features within active hot spring/geyser discharge channels at El Tatio in northern Chile, where halite-encrusted silica yields infrared spectra that are the best match yet to spectra from Spirit. Furthermore, we show that the nodular and digitate silica structures at El Tatio that most closely resemble those on Mars include complex sedimentary structures produced by a combination of biotic and abiotic processes. Although fully abiotic processes are not ruled out for the Martian silica structures, they satisfy an a priori definition of potential biosignatures. PMID:27853166

Quasi-Static Compression and Low-Velocity Impact Behavior of Tri-Axial Bio-Composite Structural Panels Using a Spherical Head

PubMed Central

Li, Jinghao; Hunt, John F; Gong, Shaoqin; Cai, Zhiyong

2017-01-01

This paper presents experimental results of both quasi-static compression and low-velocity impact behavior for tri-axial bio-composite structural panels using a spherical load head. Panels were made having different core and face configurations. The results showed that panels made having either carbon fiber fabric composite faces or a foam-filled core had significantly improved impact and compressive performance over panels without either. Different localized impact responses were observed based on the location of the compression or impact relative to the tri-axial structural core; the core with a smaller structural element had better impact performance. Furthermore, during the early contact phase for both quasi-static compression and low-velocity impact tests, the panels with the same configuration had similar load-displacement responses. The experimental results show basic compression data could be used for the future design and optimization of tri-axial bio-composite structural panels for potential impact applications. PMID:28772542

Long range stress correlations in the inherent structures of liquids at rest

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

Chowdhury, Sadrul; Abraham, Sneha; Hudson, Toby

2016-03-28

Simulation studies of the atomic shear stress in the local potential energy minima (inherent structures) are reported for binary liquid mixtures in 2D and 3D. These inherent structure stresses are fundamental to slow stress relaxation and high viscosity in supercooled liquids. We find that the atomic shear stress in the inherent structures (IS’s) of both liquids at rest exhibits slowly decaying anisotropic correlations. We show that the stress correlations contribute significantly to the variance of the total shear stress of the IS configurations and consider the origins of the anisotropy and spatial extent of the stress correlations.

Insight into the optoelectronic and thermoelectric properties of Ca-based Zintl phase CaCd2X2 (X = P, As) from first principles calculation

NASA Astrophysics Data System (ADS)

Belfarh, T.; Batouche, M.; Seddik, T.; Uğur, G.; Omran, S. Bin; Bouhemadou, A.; Sandeep; Wang, Xiaotian; Sun, Xiao-Wei; Khenata, R.

2018-06-01

We have studied the structural, optical, electronic and thermoelectric properties of the CaCd2X2 (X = P, As) compounds by using the full-potential augmented plane wave plus local orbitals method (FP-APW + lo). The exchange-correlation potential was treated using both the gradient generalized approximation (WC-GGA) and local density approximation (LDA). The estimated structural parameters, including the lattice parameters and internal coordinates agree well with the available experimental data. Our computed band structure shows that both studied compounds are semiconductors, with direct band gaps (Γ-Γ) of approximately 1.78 eV and 1.2 eV for CaCd2P2 and CaCd2As2, respectively, using GGA-TB-mBJ approach. The calculated optical spectra reveal a strong response of these materials in the energy range between the visible light and extreme UV regions, making them a good candidate for optoelectronic devices. Thermoelectric parameters, such as thermal conductivity, electrical conductivity, Seebeck coefficient, power factor and figure of merit were calculated. We note that both the CaCd2P2 and CaCd2As2 compounds show promising thermoelectric properties.

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

Kharel, P.; Herran, J.; Lukashev, P.

Recent discovery of a new class of materials, spin-gapless semiconductors (SGS), has attracted considerable attention in the last few years, primarily due to potential applications in the emerging field of spin-based electronics (spintronics). Here, we investigate structural, electronic, and magnetic properties of one potential SGS compound, MnCrVAl, using various experimental and theoretical techniques. Our calculations show that this material exhibits ≈ 0.5 eV band gap for the majority-spin states, while for the minority-spin it is nearly gapless. The calculated magnetic moment for the completely ordered structure is 2.9 μB/f.u., which is different from our experimentally measured value of almost zero.more » Here, this discrepancy is explained by the structural disorder. In particular, A2 type disorder, where Mn or Cr atoms exchange their positions with Al atoms, results in induced antiferromagnetic exchange coupling, which, at a certain level of disorder, effectively reduces the total magnetic moment to zero. This is consistent with our x-ray diffraction measurements which indicate the presence of A2 disorder in all of our samples. In addition, we also show that B2 disorder does not result in antiferromagnetic exchange coupling and therefore does not significantly reduce the total magnetic moment.« less

Physicochemical characterization of native and modified sodium caseinate- Vitamin A complexes.

PubMed

Gupta, Chitra; Arora, Sumit; Syama, M A; Sharma, Apurva

2018-04-01

Native and modified sodium caseinate- Vitamin A complexes {Sodium caseinate- Vit A complex by stirring (NaCas-VA ST), succinylated sodium caseinate- Vit A complex by stirring (SNaCas-VA ST), reassembled sodium caseinate- Vit A complex (RNaCas-VA) and reassembled succinylated sodium caseinate- Vit A complex (RSNaCas-VA)} were prepared and characterized for their physicochemical characteristics e.g. particle size, zeta potential, turbidity analysis and tryptophan intensities which confirmed structural modification of both native (NaCas-VA ST) and modified (SNaCas-VA ST, RNaCas-VA and RSNaCas- VA) proteins upon complex formation with vitamin A. Binding of vitamin A to milk protein reduced the turbidity caused by vitamin A, however, the particle size and zeta potential of milk protein increased after complexation. Microstructure details of NaCas (spray dried) showed uniform spherical structure, however, other milk proteins and milk protein- Vit A complexes (freeze dried) showed broken glass and flaky structures. Tiny particles were observed on the surface of reassembled protein and reassembled protein- Vit A complexes. Binding of vitamin A to milk protein did not have an influence on the electrophoretic mobility and elution profile (RP-HPLC). Copyright © 2018 Elsevier Ltd. All rights reserved.

Isolation and in silico analysis of a novel H+-pyrophosphatase gene orthologue from the halophytic grass Leptochloa fusca

NASA Astrophysics Data System (ADS)

Rauf, Muhammad; Saeed, Nasir A.; Habib, Imran; Ahmed, Moddassir; Shahzad, Khurram; Mansoor, Shahid; Ali, Rashid

2017-02-01

Structure prediction can provide information about function and active sites of protein which helps to design new functional proteins. H+-pyrophosphatase is transmembrane protein involved in establishing proton motive force for active transport of Na+ across membrane by Na+/H+ antiporters. A full length novel H+-pyrophosphatase gene was isolated from halophytic grass Leptochloa fusca using RT-PCR and RACE method. Full length LfVP1 gene sequence of 2292 nucleotides encodes protein of 764 amino acids. DNA and protein sequences were used for characterization using bioinformatics tools. Various important potential sites were predicted by PROSITE webserver. Primary structural analysis showed LfVP1 as stable protein and Grand average hydropathy (GRAVY) indicated that LfVP1 protein has good hydrosolubility. Secondary structure analysis showed that LfVP1 protein sequence contains significant proportion of alpha helix and random coil. Protein membrane topology suggested the presence of 14 transmembrane domains and presence of catalytic domain in TM3. Three dimensional structure from LfVP1 protein sequence also indicated the presence of 14 transmembrane domains and hydrophobicity surface model showed amino acid hydrophobicity. Ramachandran plot showed that 98% amino acid residues were predicted in the favored region.

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

First-principles study of the structural, electronic and thermal properties of CaLiF3

NASA Astrophysics Data System (ADS)

Chouit, N.; Amara Korba, S.; Slimani, M.; Meradji, H.; Ghemid, S.; Khenata, R.

2013-09-01

Density functional theory calculations have been performed to study the structural, electronic and optical properties of CaLiF3 cubic fluoroperovskite. Our calculations were carried out by means of the full-potential linearized augmented plane-wave method. The exchange-correlation potential is treated by the local density approximation and the generalized gradient approximation (GGA) (Perdew, Burke and Ernzerhof). Moreover, the alternative form of GGA proposed by Engel and Vosko is also used for band structure calculations. The calculated total energy versus volume allows us to obtain structural properties such as the lattice constant (a0), bulk modulus (B0) and pressure derivative of the bulk modulus (B'0 ). Band structure, density of states and band gap pressure coefficients are also given. Our calculations show that CaLiF3 has an indirect band gap (R-Γ). Following the quasi-harmonic Debye model, in which the phononic effects are considered, the temperature and pressure effects on the lattice constant, bulk modulus, thermal expansion coefficient, Debye temperature and heat capacities are calculated.

Computed Energetics of Nucleotides in Spatial Ribozyme Structures: An Accurate Identification of Functional Regions from Structure

PubMed Central

Torshin, Ivan Y.

2004-01-01

Ribozymes are functionally diverse RNA molecules with intrinsic catalytic activity. Multiple structural and biochemical studies are required to establish which nucleotide bases are involved in the catalysis. The relative energetic properties of the nucleotide bases have been analyzed in a set of the known ribozyme structures. It was found that many of the known catalytic nucleotides can be identified using only the structure without any additional biochemical data. The results of the calculations compare well with the available biochemical data on RNA stability. Extensive in silico mutagenesis suggests that most of the nucleotides in ribozymes stabilize the RNA. The calculations show that relative contribution of the catalytic bases to RNA stability observably differs from contributions of the noncatalytic bases. Distinction between the concepts of “relative stability” and “mutational stability” is suggested. As results of prediction for several models of ribozymes appear to be in agreement with the published data on the potential active site regions, the method can potentially be used for prediction of functional nucleotides from nucleic sequence. PMID:15105962

Conceptual Design and Structural Analysis of an Open Rotor Hybrid Wing Body Aircraft

NASA Technical Reports Server (NTRS)

Gern, Frank H.

2013-01-01

Through a recent NASA contract, Boeing Research and Technology in Huntington Beach, CA developed and optimized a conceptual design of an open rotor hybrid wing body aircraft (HWB). Open rotor engines offer a significant potential for fuel burn savings over turbofan engines, while the HWB configuration potentially allows to offset noise penalties through possible engine shielding. Researchers at NASA Langley converted the Boeing design to a FLOPS model which will be used to develop take-off and landing trajectories for community noise analyses. The FLOPS model was calibrated using Boeing data and shows good agreement with the original Boeing design. To complement Boeing s detailed aerodynamics and propulsion airframe integration work, a newly developed and validated conceptual structural analysis and optimization tool was used for a conceptual loads analysis and structural weights estimate. Structural optimization and weight calculation are based on a Nastran finite element model of the primary HWB structure, featuring centerbody, mid section, outboard wing, and aft body. Results for flight loads, deformations, wing weight, and centerbody weight are presented and compared to Boeing and FLOPS analyses.

Restructuring of an Ir(210) electrode surface by potential cycling

PubMed Central

Soliman, Khaled A; Kolb, Dieter M; Jacob, Timo

2014-01-01

Summary This study addresses the electrochemical surface faceting and restructuring of Ir(210) single crystal electrodes. Cyclic voltammetry measurements and in situ scanning tunnelling microscopy are used to probe structural changes and variations in the electrochemical behaviour after potential cycling of Ir(210) in 0.1 M H2SO4. Faceted structures are obtained electrochemically as a function of time by cycling at a scanrate of 1 V·s−1 between −0.28 and 0.70 V vs SCE, i.e., between the onset of hydrogen evolution and the surface oxidation regime. The electrochemical behaviour in sulfuric acid solution is compared with that of thermally faceted Ir(210), which shows a sharp characteristic voltammetric peak for (311) facets. Structures similar to thermally-induced faceted Ir(210) are obtained electrochemically, which typically correspond to polyoriented facets at nano-pyramids. These structures grow anisotropically in a preferred direction and reach a height of about 5 nm after 4 h of cycling. The structural changes are reflected in variations of the electrocatalytic activity towards carbon monoxide adlayer oxidation. PMID:25247118

Restructuring of an Ir(210) electrode surface by potential cycling.

PubMed

Soliman, Khaled A; Kolb, Dieter M; Kibler, Ludwig A; Jacob, Timo

2014-01-01

This study addresses the electrochemical surface faceting and restructuring of Ir(210) single crystal electrodes. Cyclic voltammetry measurements and in situ scanning tunnelling microscopy are used to probe structural changes and variations in the electrochemical behaviour after potential cycling of Ir(210) in 0.1 M H2SO4. Faceted structures are obtained electrochemically as a function of time by cycling at a scanrate of 1 V·s(-1) between -0.28 and 0.70 V vs SCE, i.e., between the onset of hydrogen evolution and the surface oxidation regime. The electrochemical behaviour in sulfuric acid solution is compared with that of thermally faceted Ir(210), which shows a sharp characteristic voltammetric peak for (311) facets. Structures similar to thermally-induced faceted Ir(210) are obtained electrochemically, which typically correspond to polyoriented facets at nano-pyramids. These structures grow anisotropically in a preferred direction and reach a height of about 5 nm after 4 h of cycling. The structural changes are reflected in variations of the electrocatalytic activity towards carbon monoxide adlayer oxidation.

Leaf water relations during summer water deficit: differential responses in turgor maintenance and variation in leaf structure among different plant communities in south-western Australia.

PubMed

Mitchell, Patrick J; Veneklaas, Erik J; Lambers, Hans; Burgess, Stephen S O

2008-12-01

We measured leaf water relations and leaf structural traits of 20 species from three communities growing along a topographical gradient. Our aim was to assess variation in seasonal responses in leaf water status and leaf tissue physiology between sites and among species in response to summer water deficit. Species from a ridge-top heath community showed the greatest reductions in pre-dawn leaf water potentials (Psi(leaf)) and stomatal conductance during summer; species from a valley-floor woodland and a midslope mallee community showed less reductions in these parameters. Heath species also displayed greater seasonal reduction in turgor-loss point (Psi(TLP)) than species from woodland or mallee communities. In general, species that had larger reductions in Psi(leaf) during summer showed significant shifts in either their osmotic potential at full turgor (Psi(pi 100); osmotic adjustment) or in tissue elasticity (epsilon(max)). Psi(pi 100) and epsilon(max) were negatively correlated, during both spring and summer, suggesting a trade-off between these different mechanisms to cope with water stress. Specific leaf area varied greatly among species, and was significantly correlated with seasonal changes in Psi(TLP) and pre-dawn Psi(leaf). These correlations suggest that leaf structure is a prerequisite for cellular mechanisms to be effective in adjusting to water deficit.

LyeTxI-b, a Synthetic Peptide Derived From Lycosa erythrognatha Spider Venom, Shows Potent Antibiotic Activity in Vitro and in Vivo.

PubMed

Reis, Pablo V M; Boff, Daiane; Verly, Rodrigo M; Melo-Braga, Marcella N; Cortés, María E; Santos, Daniel M; Pimenta, Adriano M de C; Amaral, Flávio A; Resende, Jarbas M; de Lima, Maria E

2018-01-01

The antimicrobial peptide LyeTxI isolated from the venom of the spider Lycosa erythrognatha is a potential model to develop new antibiotics against bacteria and fungi. In this work, we studied a peptide derived from LyeTxI, named LyeTxI-b, and characterized its structural profile and its in vitro and in vivo antimicrobial activities. Compared to LyeTxI, LyeTxI-b has an acetylated N-terminal and a deletion of a His residue, as structural modifications. The secondary structure of LyeTxI-b is a well-defined helical segment, from the second amino acid to the amidated C-terminal, with no clear partition between hydrophobic and hydrophilic faces. Moreover, LyeTxI-b shows a potent antimicrobial activity against Gram-positive and Gram-negative planktonic bacteria, being 10-fold more active than the native peptide against Escherichia coli. LyeTxI-b was also active in an in vivo model of septic arthritis, reducing the number of bacteria load, the migration of immune cells, the level of IL-1β cytokine and CXCL1 chemokine, as well as preventing cartilage damage. Our results show that LyeTxI-b is a potential therapeutic model for the development of new antibiotics against Gram-positive and Gram-negative bacteria.

LyeTxI-b, a Synthetic Peptide Derived From Lycosa erythrognatha Spider Venom, Shows Potent Antibiotic Activity in Vitro and in Vivo

PubMed Central

Reis, Pablo V. M.; Boff, Daiane; Verly, Rodrigo M.; Melo-Braga, Marcella N.; Cortés, María E.; Santos, Daniel M.; Pimenta, Adriano M. de C.; Amaral, Flávio A.; Resende, Jarbas M.; de Lima, Maria E.

2018-01-01

The antimicrobial peptide LyeTxI isolated from the venom of the spider Lycosa erythrognatha is a potential model to develop new antibiotics against bacteria and fungi. In this work, we studied a peptide derived from LyeTxI, named LyeTxI-b, and characterized its structural profile and its in vitro and in vivo antimicrobial activities. Compared to LyeTxI, LyeTxI-b has an acetylated N-terminal and a deletion of a His residue, as structural modifications. The secondary structure of LyeTxI-b is a well-defined helical segment, from the second amino acid to the amidated C-terminal, with no clear partition between hydrophobic and hydrophilic faces. Moreover, LyeTxI-b shows a potent antimicrobial activity against Gram-positive and Gram-negative planktonic bacteria, being 10-fold more active than the native peptide against Escherichia coli. LyeTxI-b was also active in an in vivo model of septic arthritis, reducing the number of bacteria load, the migration of immune cells, the level of IL-1β cytokine and CXCL1 chemokine, as well as preventing cartilage damage. Our results show that LyeTxI-b is a potential therapeutic model for the development of new antibiotics against Gram-positive and Gram-negative bacteria. PMID:29681894

Structural and functional analysis of mouse Msx1 gene promoter: sequence conservation with human MSX1 promoter points at potential regulatory elements.

PubMed

Gonzalez, S M; Ferland, L H; Robert, B; Abdelhay, E

1998-06-01

Vertebrate Msx genes are related to one of the most divergent homeobox genes of Drosophila, the muscle segment homeobox (msh) gene, and are expressed in a well-defined pattern at sites of tissue interactions. This pattern of expression is conserved in vertebrates as diverse as quail, zebrafish, and mouse in a range of sites including neural crest, appendages, and craniofacial structures. In the present work, we performed structural and functional analyses in order to identify potential cis-acting elements that may be regulating Msx1 gene expression. To this end, a 4.9-kb segment of the 5'-flanking region was sequenced and analyzed for transcription-factor binding sites. Four regions showing a high concentration of these sites were identified. Transfection assays with fragments of regulatory sequences driving the expression of the bacterial lacZ reporter gene showed that a region of 4 kb upstream of the transcription start site contains positive and negative elements responsible for controlling gene expression. Interestingly, a fragment of 130 bp seems to contain the minimal elements necessary for gene expression, as its removal completely abolishes gene expression in cultured cells. These results are reinforced by comparison of this region with the human Msx1 gene promoter, which shows extensive conservation, including many consensus binding sites, suggesting a regulatory role for them.

Deposition of Crystalline Hydroxyapatite Nanoparticles on Y-TZP Ceramic: A Potential Solution to Enhance Bonding Characteristics of Y-TZP Ceramics.

PubMed

Azari, Abbas; Nikzad Jamnani, Sakineh; Yazdani, Arash; Atri, Faezeh; Rasaie, Vania; Fazel Anvari Yazdi, Abbas

2017-03-01

Many advantages have been attributed to dental zirconia ceramics in terms of mechanical and physical properties; however, the bonding ability of this material to dental structure and/or veneering ceramics has always been a matter of concern. On the other hand, hydroxyapatite (HA) shows excellent biocompatibility and good bonding ability to tooth structure, with mechanically unstable and brittle characteristics, that make it clinically unacceptable for use in high stress bearing areas. The main purpose of this study was to introduce two simple yet practical methods to deposit the crystalline HA nanoparticles on zirconia ceramics. zirconia blocks were treated with HA via two different deposition methods namely thermal coating and air abrasion. Specimens were analyzed by scanning electron microscopy, energy dispersive spectroscopy (EDS) and X-ray diffraction (XRD). In both groups, the deposition techniques used were successfully accomplished, while the substrate showed no structural change. However, thermal coating group showed a uniform deposition of crystalline HA but in air abrasion method, there were dispersed thin islands of HA. Thermal coating method has the potential to significantly alter the surface characteristics of zirconia. The simple yet practical nature of the proposed method may be able to shift the bonding paradigm of dental zirconia ceramics. This latter subject needs to be addressed in future investigations.

Blocking a Redundant Cue: What does it say about preschoolers’ causal competence?

PubMed Central

Kloos, Heidi; Sloutsky, Vladimir M.

2013-01-01

The current study investigates the degree to which preschoolers can engage in causal inferences in blocking paradigm, a paradigm in which a cue is consistently linked with a target, either alone (A-T) or paired with another cue (AB-T). Unlike previous blocking studies with preschoolers, we manipulated the causal structure of the events without changing the specific contingencies. In particular, cues were said to be either potential causes (prediction condition), or they were said to be potential effects (diagnosis condition). The causally appropriate inference is to block the redundant cue B when it is a potential cause of the target, but not when it is a potential effect. Findings show a stark difference in performance between preschoolers and adults: While adults blocked the redundant cue only in the prediction condition, children blocked the redundant cue indiscriminately across both conditions. Therefore, children, but not adults ignored the causal structure of the events. These findings challenge a developmental account that attributes sophisticated machinery of causal reasoning to young children. PMID:24033577

Role of structural relaxations and chemical substitutions on piezoelectric fields and potential lineup in GaN/Al junctions

NASA Astrophysics Data System (ADS)

Picozzi, S.; Profeta, G.; Continenza, A.; Massidda, S.; Freeman, A. J.

2002-04-01

First-principles full-potential linearized augmented plane wave calculations are performed to clarify the role of the interface geometry on piezoelectric fields and potential lineups in [0001] wurtzite and [111]-zincblende GaN/Al junctions. The electric field (polarity and magnitude) is found to be strongly affected by atomic relaxations in the interface region. A procedure is used to evaluate the Schottky-barrier height in the presence of electric fields, showing that their effect is relatively small (a few tenths of an eV). These calculations assess the rectifying behavior of the GaN/Al contact, in agreement with experimental values for the barrier. We disentangle chemical and structural effects on the relevant properties (such as the potential discontinuity and the electric field) by studying unrelaxed ideal nitride/metal systems. Using simple electronegativity arguments, we outline the leading mechanisms that define the values of the electric field and Schottky barrier in these ideal systems. Finally, the transitivity rule is proved to be well satisfied.

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum

PubMed Central

Rico, Y; Wagner, H H

2016-01-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations. PMID:27381322

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

PubMed

Rico, Y; Wagner, H H

2016-11-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

Cytotoxicity of ZnO Nanoparticles Can Be Tailored by Modifying Their Surface Structure: A Green Chemistry Approach for Safer Nanomaterials.

PubMed

Punnoose, Alex; Dodge, Kelsey; Rasmussen, John W; Chess, Jordan; Wingett, Denise; Anders, Catherine

2014-07-07

ZnO nanoparticles (NP) are extensively used in numerous nanotechnology applications; however, they also happen to be one of the most toxic nanomaterials. This raises significant environmental and health concerns and calls for the need to develop new synthetic approaches to produce safer ZnO NP, while preserving their attractive optical, electronic, and structural properties. In this work, we demonstrate that the cytotoxicity of ZnO NP can be tailored by modifying their surface-bound chemical groups, while maintaining the core ZnO structure and related properties. Two equally sized (9.26 ± 0.11 nm) ZnO NP samples were synthesized from the same zinc acetate precursor using a forced hydrolysis process, and their surface chemical structures were modified by using different reaction solvents. X-ray diffraction and optical studies showed that the lattice parameters, optical properties, and band gap (3.44 eV) of the two ZnO NP samples were similar. However, FTIR spectroscopy showed significant differences in the surface structures and surface-bound chemical groups. This led to major differences in the zeta potential, hydrodynamic size, photocatalytic rate constant, and more importantly, their cytotoxic effects on Hut-78 cancer cells. The ZnO NP sample with the higher zeta potential and catalytic activity displayed a 1.5-fold stronger cytotoxic effect on cancer cells. These results suggest that by modifying the synthesis parameters/conditions and the surface chemical structures of the nanocrystals, their surface charge density, catalytic activity, and cytotoxicity can be tailored. This provides a green chemistry approach to produce safer ZnO NP.

Green synthesis of silver nanoparticles using Achillea biebersteinii flower extract and its anti-angiogenic properties in the rat aortic ring model.

PubMed

Baharara, Javad; Namvar, Farideh; Ramezani, Tayebe; Hosseini, Nasrin; Mohamad, Rosfarizan

2014-04-15

Silver nanoparticles display unique physical and biological properties which have attracted intensive research interest because of their important medical applications. In this study silver nanoparticles (Ab.Ag-NPs) were synthesized for biomedical applications using a completely green biosynthetic method using Achillea biebersteinii flowers extract. The structure and properties of Ab.Ag-NPs were investigated using UV-visible spectroscopic techniques, transmission electron microscopy (TEM), zeta potential and energy dispersive X-ray spectrometers (EDS). The UV-visible spectroscopic analysis showed the absorbance peak at 460 nm, which indicates the synthesis of silver nanoparticles. The average particle diameter as determined by TEM was found to be 12±2 nm. The zeta potential analysis indicated that Ab.Ag-NPs have good stability EDX analysis also exhibits presentation of silver element. As angiogenesis is an important phenomenon and as growth factors imbalance in this process causes the acceleration of several diseases including cancer, the anti-angiogenic properties of Ab.Ag-NPs were evaluated using the rat aortic ring model. The results showed that Ab.Ag-NPs (200 μg/mL) lead to a 50% reduction in the length and number of vessel-like structures. The synthesized silver nanoparticles from the Achillea biebersteinii flowers extract, which do not involve any harmful chemicals were well-dispersed and stabilized through this green method and showed potential therapeutic benefits against angiogenesis.

X-ray photoelectron spectrum and electronic properties of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4): LDA, GGA, and EV-GGA.

PubMed

Reshak, Ali Hussain; Khenata, R; Kityk, I V; Plucinski, K J; Auluck, S

2009-04-30

An all electron full potential linearized augmented plane wave method has been applied for a theoretical study of the band structure, density of states, and electron charge density of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4) using three different approximations for the exchange correlation potential. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma resulting in a direct energy gap of about 2.0, 2.2, and 2.8 eV for local density approximation (LDA), generalized gradient approximation (GGA), and Engel-Vosko (EVGGA) compared to the experimental value of 2.84 eV. We notice that EVGGA shows excellent agreement with the experimental data. This agreement is attributed to the fact that the Engel-Vosko GGA formalism optimizes the corresponding potential for band structure calculations. We make a detailed comparison of the density of states deduced from the X-ray photoelectron spectra with our calculations. We find that there is a strong covalent bond between the Hg and S atoms and Ga and S atoms. The Hg-Hg, Ga-Ga, and S-S bonds are found to be weaker than the Hg-S and Ga-S bonds showing that a covalent bond exists between Hg and S atoms and Ga and S atoms.

Surface potential driven dissolution phenomena of [0 0 0 1]-oriented ZnO nanorods grown from ZnO and Pt seed layers

NASA Astrophysics Data System (ADS)

Seo, Youngmi; Kim, Jung Hyeun

2011-06-01

Highly oriented ZnO nanorods are synthesized hydrothermally on ZnO and Pt seed layers, and they are dissolved in KOH solution. The rods grown on ZnO seed layer show uniform dissolution, but those grown on Pt seed layer are rod-selectively dissolved. The ZnO nanorods from both seed layers show the same crystalline structure through XRD and Raman spectrometer data. However, the surface potential analysis reveals big difference for ZnO and Pt seed cases. The surface potential distribution is very uniform for the ZnO seed case, but it is much fluctuated on the Pt seed case. It suggests that the rod-selective dissolution phenomena on Pt seed case are likely due to the surface energy difference.

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

Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R., E-mail: aluru@illinois.edu

Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluidmore » mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.« less

Monte Carlo study of one-dimensional confined fluids with Gay-Berne intermolecular potential

NASA Astrophysics Data System (ADS)

Moradi, M.; Hashemi, S.

2011-11-01

The thermodynamic quantities of a one dimensional system of particles with Gay-Berne model potential confined between walls have been obtained by means of Monte Carlo computer simulations. For a number of temperatures, the systems were considered and their density profiles, order parameter, pressure, configurational temperature and average potential energy per particle are reported. The results show that by decreasing the temperature, the soft particles become more ordered and they align to the walls and also they don't show any tendency to be near the walls at very low temperatures. We have also changed the structure of the walls by embedding soft ellipses in them, this change increases the total density near the wall whereas, increasing or decreasing the order parameter depend on the angle of embedded ellipses.

Review of Repair Materials for Fire-Damaged Reinforced Concrete Structures

NASA Astrophysics Data System (ADS)

Zahid, MZA Mohd; Abu Bakar, BH; Nazri, FM; Ahmad, MM; Muhamad, K.

2018-03-01

Reinforced concrete (RC) structures perform well during fire and may be repaired after the fire incident because their low heat conductivity prevents the loss or degradation of mechanical strength of the concrete core and internal reinforcing steel. When an RC structure is heated to more than 500 °C, mechanical properties such as compressive strength, stiffness, and tensile strength start to degrade and deformations occur. Although the fire-exposed RC structure shows no visible damage, its residual strength decreases compared with that in the pre-fire state. Upon thorough assessment, the fire-damaged RC structure can be repaired or strengthened, instead of subjecting to partial or total demolition followed by reconstruction. The structure can be repaired using several materials, such as carbon fiber-reinforced polymer, glass fiber-reinforced polymer, normal strength concrete, fiber-reinforced concrete, ferrocement, epoxy resin mortar, and high-performance concrete. Selecting an appropriate repair material that must be compatible with the substrate or base material is a vital step to ensure successful repair. This paper reviews existing repair materials and factors affecting their performance. Of the materials considered, ultra-high-performance fiber-reinforced concrete (UHPFRC) exhibits huge potential for repairing fire-damaged RC structures but lack of information available. Hence, further studies must be performed to assess the potential of UHPFRC in rehabilitating fire-damaged RC structures.

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor.

PubMed

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI.

Structure of the Triatoma virus capsid

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

Squires, Gaëlle; Pous, Joan; Agirre, Jon

The crystallographic structure of TrV shows specific morphological and functional features that clearly distinguish it from the type species of the Cripavirus genus, CrPV. The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses ofmore » this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.« less

Controlling silk fibroin particle features for drug delivery

PubMed Central

Lammel, Andreas; Hu, Xiao; Park, Sang-Hyug; Kaplan, David L.; Scheibel, Thomas

2010-01-01

Silk proteins are a promising material for drug delivery due to their aqueous processability, biocompatibility, and biodegradability. A simple aqueous preparation method for silk fibroin particles with controllable size, secondary structure and zeta potential is reported. The particles were produced by salting out a silk fibroin solution with potassium phosphate. The effect of ionic strength and pH of potassium phosphate solution on the yield and morphology of the particles was determined. Secondary structure and zeta potential of the silk particles could be controlled by pH. Particles produced by salting out with 1.25 M potassium phosphate pH 6 showed a dominating silk II (crystalline) structure whereas particles produced at pH 9 were mainly composed of silk I (less crystalline). The results show that silk I rich particles possess chemical and physical stability and secondary structure which remained unchanged during post treatments even upon exposure to 100% ethanol or methanol. A model is presented to explain the process of particle formation based on intra- and intermolecular interactions of the silk domains, influenced by pH and kosmotrope salts. The reported silk fibroin particles can be loaded with small molecule model drugs, such as alcian blue, rhodamine B, and crystal violet, by simple absorption based on electrostatic interactions. In vitro release of these compounds from the silk particles depends on charge – charge interactions between the compounds and the silk. With crystal violet we demonstrated that the release kinetics are dependent on the secondary structure of the particles. PMID:20219241

The dynamics of interacting salt structures and associated fluid flow in the western Norwegian-Danish Basin

NASA Astrophysics Data System (ADS)

Olsen, Mikkel S.; Clausen, Ole R.; Andresen, Katrine J.; Korstgård, John A.

2015-04-01

Minor secondary structures observed along the flanks of major salt structures in the Norwegian-Danish Basin appear to be generated mainly during the early stages of halokinesis. Seismic anomalies in the cover sediments at the flanks of the major salt structures and in relation to one of the secondary structures show several circular patterns. The circular patterns are generally interpreted as faults related to collapsing salt, indicating a subtle and dynamic cannibalization relationship between the secondary structure and the main diapir. High-amplitude reflections interpreted as either entrapped gas along the circular faults or diagenetic changes induced by the fluids originating from the salt-sediment interface generally enhances the seismic appearance of the circular faults, but potentially also disturb the seismic imaging of the faults. Other secondary salt structures, with a similar geometry, do not show sign of collapse, apparently due to a greater distance from the main salt structures and therefore not within the reach of being cannibalized by these. The observations furthermore suggest a trend showing a more advanced development of the main salt structures when the secondary structures are cannibalized. The lateral distribution of the main salt structures thus appears to be controlled not only by the initial thickness of the Zechstein salt, and possible underlying structures, but also by subtle variations in the location and evolution of secondary structures. The secondary structures have a major impact on the drainage of the deep Mesozoic succession as indicated by the fluid flow pattern also observed in the study, which emphasizes that a detailed mapping of salt structures including secondary structures at the flanks is of major importance during evaluation of petroleum systems in areas dominated by halokinesis.

Transmembrane voltage: Potential to induce lateral microdomains.

PubMed

Malinsky, Jan; Tanner, Widmar; Opekarova, Miroslava

2016-08-01

Lateral segregation of plasma membrane lipids is a generally accepted phenomenon. Lateral lipid microdomains of specific composition, structure and biological functions are established as a result of simultaneous action of several competing mechanisms which contribute to membrane organization. Various lines of evidence support the conclusion that among those mechanisms, the membrane potential plays significant and to some extent unique role. Above all, clear differences in the microdomain structure as revealed by fluorescence microscopy could be recognized between polarized and depolarized membranes. In addition, recent fluorescence spectroscopy experiments reported depolarization-induced changes in a membrane lipid order. In the context of earlier findings showing that plasma membranes of depolarized cells are less susceptible to detergents and the cells less sensitive to antibiotics or antimycotics treatment we discuss a model, in which membrane potential-driven re-organization of the microdomain structure contributes to maintaining membrane integrity during response to stress, pathogen attack and other challenges involving partial depolarization of the plasma membrane. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon. Copyright © 2016 Elsevier B.V. All rights reserved.

The potential influence of morphology on the evolutionary divergence of an acoustic signal

PubMed Central

Pitchers, W. R.; Klingenberg, C.P.; Tregenza, Tom; Hunt, J.; Dworkin, I.

2014-01-01

The evolution of acoustic behaviour and that of the morphological traits mediating its production are often coupled. Lack of variation in the underlying morphology of signalling traits has the potential to constrain signal evolution. This relationship is particularly likely in field crickets, where males produce acoustic advertisement signals to attract females by stridulating with specialized structures on their forewings. In this study, we characterise the size and geometric shape of the forewings of males from six allopatric populations of the black field cricket (Teleogryllus commodus) known to have divergent advertisement calls. We sample from each of these populations using both wild-caught and common-garden reared cohorts, allowing us to test for multivariate relationships between wing morphology and call structure. We show that the allometry of shape has diverged across populations. However, there was a surprisingly small amount of covariation between wing shape and call structure within populations. Given the importance of male size for sexual selection in crickets, the divergence we observe among populations has the potential to influence the evolution of advertisement calls in this species. PMID:25223712

Carrier separation and transport in perovskite solar cells studied by nanometre-scale profiling of electrical potential

PubMed Central

Jiang, Chun-Sheng; Yang, Mengjin; Zhou, Yuanyuan; To, Bobby; Nanayakkara, Sanjini U.; Luther, Joseph M.; Zhou, Weilie; Berry, Joseph J.; van de Lagemaat, Jao; Padture, Nitin P.; Zhu, Kai; Al-Jassim, Mowafak M.

2015-01-01

Organometal–halide perovskite solar cells have greatly improved in just a few years to a power conversion efficiency exceeding 20%. This technology shows unprecedented promise for terawatt-scale deployment of solar energy because of its low-cost, solution-based processing and earth-abundant materials. We have studied charge separation and transport in perovskite solar cells—which are the fundamental mechanisms of device operation and critical factors for power output—by determining the junction structure across the device using the nanoelectrical characterization technique of Kelvin probe force microscopy. The distribution of electrical potential across both planar and porous devices demonstrates p–n junction structure at the TiO2/perovskite interfaces and minority-carrier diffusion/drift operation of the devices, rather than the operation mechanism of either an excitonic cell or a p-i-n structure. Combining the potential profiling results with solar cell performance parameters measured on optimized and thickened devices, we find that carrier mobility is a main factor that needs to be improved for further gains in efficiency of the perovskite solar cells. PMID:26411597

Carrier Separation and Transport in Perovskite Solar Cells Studied by Nanometre-Scale Profiling of Electrical Potential

DOE PAGES

Jiang, Chun-Sheng; Yang, Mengjin; Zhou, Yuanyuan; ...

2015-09-28

Organometal–halide perovskite solar cells have greatly improved in just a few years to a power conversion efficiency exceeding 20%. This technology shows unprecedented promise for terawatt-scale deployment of solar energy because of its low-cost, solution-based processing and earth-abundant materials. We have studied charge separation and transport in perovskite solar cells—which are the fundamental mechanisms of device operation and critical factors for power output—by determining the junction structure across the device using the nanoelectrical characterization technique of Kelvin probe force microscopy. Moreover, the distribution of electrical potential across both planar and porous devices demonstrates p–n junction structure at the TiO2/perovskite interfacesmore » and minority-carrier diffusion/drift operation of the devices, rather than the operation mechanism of either an excitonic cell or a p-i-n structure. When we combined the potential profiling results with solar cell performance parameters measured on optimized and thickened devices, we find that carrier mobility is a main factor that needs to be improved for further gains in efficiency of the perovskite solar cells.« less

Application potential of ATR-FT/IR molecular spectroscopy in animal nutrition: revelation of protein molecular structures of canola meal and presscake, as affected by heat-processing methods, in relationship with their protein digestive behavior and utilization for dairy cattle.

PubMed

Theodoridou, Katerina; Yu, Peiqiang

2013-06-12

Protein quality relies not only on total protein but also on protein inherent structures. The most commonly occurring protein secondary structures (α-helix and β-sheet) may influence protein quality, nutrient utilization, and digestive behavior. The objectives of this study were to reveal the protein molecular structures of canola meal (yellow and brown) and presscake as affected by the heat-processing methods and to investigate the relationship between structure changes and protein rumen degradations kinetics, estimated protein intestinal digestibility, degraded protein balance, and metabolizable protein. Heat-processing conditions resulted in a higher value for α-helix and β-sheet for brown canola presscake compared to brown canola meal. The multivariate molecular spectral analyses (PCA, CLA) showed that there were significant molecular structural differences in the protein amide I and II fingerprint region (ca. 1700-1480 cm(-1)) between the brown canola meal and presscake. The in situ degradation parameters, amide I and II, and α-helix to β-sheet ratio (R_a_β) were positively correlated with the degradable fraction and the degradation rate. Modeling results showed that α-helix was positively correlated with the truly absorbed rumen synthesized microbial protein in the small intestine when using both the Dutch DVE/OEB system and the NRC-2001 model. Concerning the protein profiles, R_a_β was a better predictor for crude protein (79%) and for neutral detergent insoluble crude protein (68%). In conclusion, ATR-FT/IR molecular spectroscopy may be used to rapidly characterize feed structures at the molecular level and also as a potential predictor of feed functionality, digestive behavior, and nutrient utilization of canola feed.

Versatile application of indirect Fourier transformation to structure factor analysis: from X-ray diffraction of molecular liquids to small angle scattering of protein solutions.

PubMed

Fukasawa, Toshiko; Sato, Takaaki

2011-02-28

We highlight versatile applicability of a structure-factor indirect Fourier transformation (IFT) technique, hereafter called SQ-IFT. The original IFT aims at the pair distance distribution function, p(r), of colloidal particles from small angle scattering of X-rays (SAXS) and neutrons (SANS), allowing the conversion of the experimental form factor, P(q), into a more intuitive real-space spatial autocorrelation function. Instead, SQ-IFT is an interaction potential model-free approach to the 'effective' or 'experimental' structure factor to yield the pair correlation functions (PCFs), g(r), of colloidal dispersions like globular protein solutions for small-angle scattering data as well as the radial distribution functions (RDFs) of molecular liquids in liquid diffraction (LD) experiments. We show that SQ-IFT yields accurate RDFs of liquid H(2)O and monohydric alcohol reflecting their local intermolecular structures, in which q-weighted structure function, qH(q), conventionally utilized in many LD studies out of necessity of performing direct Fourier transformation, is no longer required. We also show that SQ-IFT applied to theoretically calculated structure factors for uncharged and charged colloidal dispersions almost perfectly reproduces g(r) obtained as a solution of the Ornstein-Zernike (OZ) equation. We further demonstrate the relevance of SQ-IFT in its practical applications, using SANS effective structure factors of lysozyme solutions reported in recent literatures which revealed the equilibrium cluster formation due to coexisting long range electrostatic repulsion and short range attraction between the proteins. Finally, we present SAXS experiments on human serum albumin (HSA) at different ionic strength and protein concentration, in which we discuss the real space picture of spatial distributions of the proteins via the interaction potential model-free route.

Unjamming and cell shape in the asthmatic airway epithelium

NASA Astrophysics Data System (ADS)

Park, Jin-Ah; Kim, Jae Hun; Bi, Dapeng; Mitchel, Jennifer A.; Qazvini, Nader Taheri; Tantisira, Kelan; Park, Chan Young; McGill, Maureen; Kim, Sae-Hoon; Gweon, Bomi; Notbohm, Jacob; Steward, Robert, Jr.; Burger, Stephanie; Randell, Scott H.; Kho, Alvin T.; Tambe, Dhananjay T.; Hardin, Corey; Shore, Stephanie A.; Israel, Elliot; Weitz, David A.; Tschumperlin, Daniel J.; Henske, Elizabeth P.; Weiss, Scott T.; Manning, M. Lisa; Butler, James P.; Drazen, Jeffrey M.; Fredberg, Jeffrey J.

2015-10-01

From coffee beans flowing in a chute to cells remodelling in a living tissue, a wide variety of close-packed collective systems--both inert and living--have the potential to jam. The collective can sometimes flow like a fluid or jam and rigidify like a solid. The unjammed-to-jammed transition remains poorly understood, however, and structural properties characterizing these phases remain unknown. Using primary human bronchial epithelial cells, we show that the jamming transition in asthma is linked to cell shape, thus establishing in that system a structural criterion for cell jamming. Surprisingly, the collapse of critical scaling predicts a counter-intuitive relationship between jamming, cell shape and cell-cell adhesive stresses that is borne out by direct experimental observations. Cell shape thus provides a rigorous structural signature for classification and investigation of bronchial epithelial layer jamming in asthma, and potentially in any process in disease or development in which epithelial dynamics play a prominent role.

Identification of structural motifs as tunneling two-level systems in amorphous alumina at low temperatures

NASA Astrophysics Data System (ADS)

Paz, Alejandro Pérez; Lebedeva, Irina V.; Tokatly, Ilya V.; Rubio, Angel

2014-12-01

One of the most accepted models that describe the anomalous thermal behavior of amorphous materials at temperatures below 1 K relies on the quantum mechanical tunneling of atoms between two nearly equivalent potential energy wells forming a two-level system (TLS). Indirect evidence for TLSs is widely available. However, the atomistic structure of these TLSs remains an unsolved topic in the physics of amorphous materials. Here, using classical molecular dynamics, we found several hitherto unknown bistable structural motifs that may be key to understanding the anomalous thermal properties of amorphous alumina at low temperatures. We show through free energy profiles that the complex potential energy surface can be reduced to canonical TLSs. The tunnel splitting predicted from instanton theory, the number density, dipole moment, and coupling to external strain of the discovered motifs are consistent with experiments.

Cellulose/poly-(m-phenylene isophthalamide) porous film as a tissue-engineered skin bioconstruct

NASA Astrophysics Data System (ADS)

Lee, Jae Woong; Han, Sung Soo; Zo, Sum Mi; Choi, Soon Mo

2018-06-01

Regarding the porous structure, coagulated cellulose may not provide sufficient voids for cell proliferation, resulting in tissue growth. For this reason, it was blended with poly(m-phenylene isophthalamide) (PMIA), which could produce a porous structure in the resulting construct. The aim of this study was to confirm the potential of a novel cellulose/PMIA porous film as a tissue-engineered bioconstruct for impaired skin. The films were fabricated by a coagulation process added with a peel-off method, and the structural, mechanical properties were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, and capillary flow porometry. CRL-2310 human keratinocytes were used to determine the biocompatibility of the prepared films. The attachment and proliferation of cells were investigated by scanning electron microscopy, DAPI staining, and a cell viability assay. The results show that cellulose/PMIA porous films have potential use as wound matrices for skin tissue genesis.

Effects of Piezoelectric Potential of ZnO on Resistive Switching Characteristics of Flexible ZnO/TiO2 Heterojunction Cells

NASA Astrophysics Data System (ADS)

Li, Hongxia; Zhou, You; Du, Gang; Huang, Yanwei; Ji, Zhenguo

2018-03-01

Flexible resistance random access memory (ReRAM) devices with a heterojunction structure of PET/ITO/ZnO/TiO2/Au were fabricated on polyethylene terephthalate/indium tin oxide (PET/ITO) substrates by different physical and chemical preparation methods. X-ray diffraction, scanning electron microscopy and atomic force microscopy were carried out to investigate the crystal structure, surface topography and cross-sectional structure of the prepared films. X-ray photoelectron spectroscopy was also used to identify the chemical state of Ti, O and Zn elements. Theoretical and experimental analyses were conducted to identify the effect of piezoelectric potential of ZnO on resistive switching characteristics of flexible ZnO/TiO2 heterojunction cells. The results showed a pathway to enhance the performance of ReRAM devices by engineering the interface barrier, which is also feasible for other electronics, optoelectronics and photovoltaic devices.

Structure and stability of M6N8 clusters (M = Si, Ge, Sn, Ti).

PubMed

Davydova, Elena I; Timoshkin, Alexey Y; Frenking, Gernot

2010-06-10

The structures and stabilities of the M(6)N(8) clusters (M = Si, Ge, Sn, Ti) have been theoretically studied at DFT and ab initio levels of theory. Two new isomers have been considered: cage-like molecules and propeller-like molecules. It is shown that only for M = Si are both isomers true minima on the potential energy surface. The thermodynamics of the dissociation process (1/6)M(6)N(8) --> (1/3)M(3)N(4) is discussed. For each M(3)N(4) molecule, four structures with different multiplicity are considered. The thermodynamic analysis shows that independently of the multiplicity of M(3)N(4) nitrides all M(6)N(8) clusters are stable in the gas phase in a wide temperature range and could be potential intermediates in chemical vapor deposition of the nitride materials.

Using the shortwave infrared to image middle ear pathologies

PubMed Central

Valdez, Tulio A.; Bruns, Oliver T.; Bawendi, Moungi G.

2016-01-01

Visualizing structures deep inside opaque biological tissues is one of the central challenges in biomedical imaging. Optical imaging with visible light provides high resolution and sensitivity; however, scattering and absorption of light by tissue limits the imaging depth to superficial features. Imaging with shortwave infrared light (SWIR, 1–2 μm) shares many advantages of visible imaging, but light scattering in tissue is reduced, providing sufficient optical penetration depth to noninvasively interrogate subsurface tissue features. However, the clinical potential of this approach has been largely unexplored because suitable detectors, until recently, have been either unavailable or cost prohibitive. Here, taking advantage of newly available detector technology, we demonstrate the potential of SWIR light to improve diagnostics through the development of a medical otoscope for determining middle ear pathologies. We show that SWIR otoscopy has the potential to provide valuable diagnostic information complementary to that provided by visible pneumotoscopy. We show that in healthy adult human ears, deeper tissue penetration of SWIR light allows better visualization of middle ear structures through the tympanic membrane, including the ossicular chain, promontory, round window niche, and chorda tympani. In addition, we investigate the potential for detection of middle ear fluid, which has significant implications for diagnosing otitis media, the overdiagnosis of which is a primary factor in increased antibiotic resistance. Middle ear fluid shows strong light absorption between 1,400 and 1,550 nm, enabling straightforward fluid detection in a model using the SWIR otoscope. Moreover, our device is easily translatable to the clinic, as the ergonomics, visual output, and operation are similar to a conventional otoscope. PMID:27551085

Thieno[3,2-c]pyran-4-one based novel small molecules: their synthesis, crystal structure analysis and in vitro evaluation as potential anticancer agents.

PubMed

Nakhi, Ali; Adepu, Raju; Rambabu, D; Kishore, Ravada; Vanaja, G R; Kalle, Arunasree M; Pal, Manojit

2012-07-01

Novel thieno[3,2-c]pyran-4-one based small molecules were designed as potential anticancer agents. Expeditious synthesis of these compounds was carried out via a multi-step sequence consisting of few steps such as Gewald reaction, Sandmeyer type iodination, Sonogashira type coupling followed by iodocyclization and then Pd-mediated various C-C bond forming reactions. The overall strategy involved the construction of thiophene ring followed by the fused pyranone moiety and then functionalization at C-7 position of the resultant thieno[3,2-c]pyran-4-one framework. Some of the compounds synthesized showed selective growth inhibition of cancer cells in vitro among which two compounds for example, 5d and 6c showed IC(50) values in the range of 2.0-2.5 μM. The crystal structure analysis of an active compound along with hydrogen bonding patterns and molecular arrangement present within the molecule is described. Copyright © 2012 Elsevier Ltd. All rights reserved.

Synthesis of carbon-coated Na2MnPO4F hollow spheres as a potential cathode material for Na-ion batteries

NASA Astrophysics Data System (ADS)

Wu, Ling; Hu, Yong; Zhang, Xiaoping; Liu, Jiequn; Zhu, Xing; Zhong, Shengkui

2018-01-01

Hollow sphere structure Na2MnPO4F/C composite is synthesized through spray drying, following in-situ pyrolytic carbon coating process. XRD results indicate that the well crystallized composite can be successfully synthesized, and no other impurity phases are detected. SEM and TEM results reveal that the Na2MnPO4F/C samples show intact hollow spherical architecture, and the hollow spherical shells with an average thickness of 150 nm-250 nm are composed of nanosized primary particles. Furthermore, the amorphous carbon layer is uniformly coated on the surface of the hollow sphere, and the nanosized Na2MnPO4F particles are well embedded in the carbon networks. Consequently, the hollow sphere structure Na2MnPO4F/C shows enhanced electrochemical performance. Especially, it is the first time that the obvious potential platforms (∼3.6 V) are observed during the charge and discharge process at room temperature.

Distinct aggregation patterns and fluid porous phase in a 2D model for colloids with competitive interactions

NASA Astrophysics Data System (ADS)

Bordin, José Rafael

2018-04-01

In this paper we explore the self-assembly patterns in a two dimensional colloidal system using extensive Langevin Dynamics simulations. The pair potential proposed to model the competitive interaction have a short range length scale between first neighbors and a second characteristic length scale between third neighbors. We investigate how the temperature and colloidal density will affect the assembled morphologies. The potential shows aggregate patterns similar to observed in previous works, as clusters, stripes and porous phase. Nevertheless, we observe at high densities and temperatures a porous mesophase with a high mobility, which we name fluid porous phase, while at lower temperatures the porous structure is rigid. triangular packing was observed for the colloids and pores in both solid and fluid porous phases. Our results show that the porous structure is well defined for a large range of temperature and density, and that the fluid porous phase is a consequence of the competitive interaction and the random forces from the Langevin Dynamics.

Ion acoustic solitons and supersolitons in a magnetized plasma with nonthermal hot electrons and Boltzmann cool electrons

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

Rufai, O. R., E-mail: rajirufai@gmail.com; Bharuthram, R., E-mail: rbharuthram@uwc.ac.za; Singh, S. V., E-mail: satyavir@iigs.iigm.res.in

2014-08-15

Arbitrary amplitude, ion acoustic solitons, and supersolitons are studied in a magnetized plasma with two distinct groups of electrons at different temperatures. The plasma consists of a cold ion fluid, cool Boltzmann electrons, and nonthermal energetic hot electrons. Using the Sagdeev pseudo-potential technique, the effect of nonthermal hot electrons on soliton structures with other plasma parameters is studied. Our numerical computation shows that negative potential ion-acoustic solitons and double layers can exist both in the subsonic and supersonic Mach number regimes, unlike the case of an unmagnetized plasma where they can only exist in the supersonic Mach number regime. Formore » the first time, it is reported here that in addition to solitions and double layers, the ion-acoustic supersoliton solutions are also obtained for certain range of parameters in a magnetized three-component plasma model. The results show good agreement with Viking satellite observations of the solitary structures with density depletions in the auroral region of the Earth's magnetosphere.« less

Multicomponent polymeric nanoparticles enhancing intracellular drug release in cancer cells.

PubMed

Ahmed, Arsalan; Liu, Sen; Pan, Yutong; Yuan, Shanmei; He, Jian; Hu, Yong

2014-12-10

Three kinds of amphiphilic copolymer, that is, poly(ε-caprolactone)-SS-poly(ethylene glycol) (PCL-SS-PEG), poly(ε-caprolactone)-polyethylenimine (PCL-PEI), and poly(ε-caprolactone)-polyethylenimine-folate (PCL-PEI-Fol) were synthesized and self-assembled into surface engineered hybrid nanoparticles (NPs). Morphological studies elucidated the stable, spherical, and uniform sandwich structure of the NPs. PCL-PEI and PCL-SS-PEG segments have introduced pH and reduction responsive characteristics in these NPs, while PCL-PEI-FA copolymers could provide specific targeting capability to cancer cells. The stimuli responsive capabilities of these NPs were carried out. Negative-to-positive charge reversible property, in response to the pH change, was investigated by zeta potential and nuclear magnetic resonance (NMR) measurements. The structure cleavage, due to redox gradient, was studied by dynamic light scattering (DLS) and transmission electron microscopy (TEM). These NPs showed controlled degradation, better drug release, less toxicity, and effective uptake in MCF-7 breast cancer cells. These multifunctional NPs showed promising potential in the treatment of cancer.

MoTe2, A novel anode material for sodium ion battery

NASA Astrophysics Data System (ADS)

Panda, Manas Ranjan; Anish Raj, K.; Bao, Qiaoliang; Mitra, Sagar

2018-04-01

2D layered transition metal dichalcogenides are considered as a potential anode for sodium-ion batteries due to their high specific capacity, structural stability and its well-developed two-dimensional layers. 2D layered structure Molybdenum ditelluride (MoTe2) provides a superior Na-ion storage properties in sodium ion battery due to its comparative more interlayer spacing (0.699 nm). In the current study MoTe2 polycrystalline powder sample has been prepared by solid state reaction process, the structural and morphological studies have been carried out by XRD, FE-SEM and EDS etc. XRD study revealsthe well crystalline structure of the material having hexagonal structure. FE-SEM and EDS studies depict the uniformflakes like structure of the material. When it is tested as sodium-ion battery anode by applying a potential window 0.1-2.5 V, the material demonstrates a high capacity and high power performances. The as prepared MoTe2 shows an initial discharge capacity of 376 mA h g-1 and a corresponding discharge capacity of 303 mA h g-1 after the 50th cycle at a current density of 500 mA g-1.

Evolution in Stage-Structured Populations

PubMed Central

Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

2016-01-01

For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

On the application of accelerated molecular dynamics to liquid water simulations.

PubMed

de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew

2006-11-16

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.

Dependence of the 0.7 anomaly on the curvature of the potential barrier in quantum wires

NASA Astrophysics Data System (ADS)

Smith, L. W.; Al-Taie, H.; Lesage, A. A. J.; Sfigakis, F.; See, P.; Griffiths, J. P.; Beere, H. E.; Jones, G. A. C.; Ritchie, D. A.; Hamilton, A. R.; Kelly, M. J.; Smith, C. G.

2015-06-01

Ninety-eight one-dimensional channels defined using split gates fabricated on a GaAs/AlGaAs heterostructure are measured during one cooldown at 1.4 K. The devices are arranged in an array on a single chip and are individually addressed using a multiplexing technique. The anomalous conductance feature known as the "0.7 structure" is studied using statistical techniques. The ensemble of data shows that the 0.7 anomaly becomes more pronounced and occurs at lower values as the curvature of the potential barrier in the transport direction decreases. This corresponds to an increase in the effective length of the device. The 0.7 anomaly is not strongly influenced by other properties of the conductance related to density. The curvature of the potential barrier appears to be the primary factor governing the shape of the 0.7 structure at a given T and B .

Self-constrained inversion of potential fields

NASA Astrophysics Data System (ADS)

Paoletti, V.; Ialongo, S.; Florio, G.; Fedi, M.; Cella, F.

2013-11-01

We present a potential-field-constrained inversion procedure based on a priori information derived exclusively from the analysis of the gravity and magnetic data (self-constrained inversion). The procedure is designed to be applied to underdetermined problems and involves scenarios where the source distribution can be assumed to be of simple character. To set up effective constraints, we first estimate through the analysis of the gravity or magnetic field some or all of the following source parameters: the source depth-to-the-top, the structural index, the horizontal position of the source body edges and their dip. The second step is incorporating the information related to these constraints in the objective function as depth and spatial weighting functions. We show, through 2-D and 3-D synthetic and real data examples, that potential field-based constraints, for example, structural index, source boundaries and others, are usually enough to obtain substantial improvement in the density and magnetization models.

Controlling effect of geometrically defined local structural changes on chaotic Hamiltonian systems.

PubMed

Ben Zion, Yossi; Horwitz, Lawrence

2010-04-01

An effective characterization of chaotic conservative Hamiltonian systems in terms of the curvature associated with a Riemannian metric tensor derived from the structure of the Hamiltonian has been extended to a wide class of potential models of standard form through definition of a conformal metric. The geodesic equations reproduce the Hamilton equations of the original potential model through an inverse map in the tangent space. The second covariant derivative of the geodesic deviation in this space generates a dynamical curvature, resulting in (energy-dependent) criteria for unstable behavior different from the usual Lyapunov criteria. We show here that this criterion can be constructively used to modify locally the potential of a chaotic Hamiltonian model in such a way that stable motion is achieved. Since our criterion for instability is local in coordinate space, these results provide a minimal method for achieving control of a chaotic system.

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

NASA Astrophysics Data System (ADS)

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.; Jin, Wencan; Dadap, Jerry I.; Hybertsen, Mark S.; Osgood, Richard M.

2018-04-01

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n =1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energy and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. This opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.

ERP Evidence for the Activation of Syntactic Structure During Comprehension of Lexical Idiom.

PubMed

Zhang, Meichao; Lu, Aitao; Song, Pingfang

2017-10-01

The present study used event-related potentials to investigate whether the syntactic structure was activated in the comprehension of lexical idioms, and if so, whether it varied as a function of familiarity and semantic transparency. Participants were asked to passively read the "1+2" structural Chinese lexical idioms with each being presented following 3-5 contextual "1+2" (congruent-structure condition) or "2+1" structural Chinese phrases (incongruent-structure condition). The N400 ERP responses showed more positivity in congruent-structure condition relative to incongruent-structure condition in idioms with high familiarity and high semantic transparency, but less positivity in congruent-structure condition in idioms with high familiarity but low semantic transparency, idioms with low familiarity but high semantic transparency, and idioms with low familiarity and low semantic transparency. Our results suggest that syntactic structure, as the unnecessarity of lexical idiomatic words, was nevertheless activated, independent of familiarity and semantic transparency.

Compartments in a marine food web associated with phylogeny, body mass, and habitat structure.

PubMed

Rezende, Enrico L; Albert, Eva M; Fortuna, Miguel A; Bascompte, Jordi

2009-08-01

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.

Electron Beam Freeform Fabrication of Titanium Alloy Gradient Structures

NASA Technical Reports Server (NTRS)

Brice, Craig A.; Newman, John A.; Bird, Richard Keith; Shenoy, Ravi N.; Baughman, James M.; Gupta, Vipul K.

2014-01-01

Historically, the structural optimization of aerospace components has been done through geometric methods. A monolithic material is chosen based on the best compromise between the competing design limiting criteria. Then the structure is geometrically optimized to give the best overall performance using the single material chosen. Functionally graded materials offer the potential to further improve structural efficiency by allowing the material composition and/or microstructural features to spatially vary within a single structure. Thus, local properties could be tailored to the local design limiting criteria. Additive manufacturing techniques enable the fabrication of such graded materials and structures. This paper presents the results of a graded material study using two titanium alloys processed using electron beam freeform fabrication, an additive manufacturing process. The results show that the two alloys uniformly mix at various ratios and the resultant static tensile properties of the mixed alloys behave according to rule-of-mixtures. Additionally, the crack growth behavior across an abrupt change from one alloy to the other shows no discontinuity and the crack smoothly transitions from one crack growth regime into another.

Molecular dynamics simulations suggest changes in electrostatic interactions as a potential mechanism through which serine phosphorylation inhibits DNA Polymerase β's activity.

PubMed

Homouz, Dirar; Joyce-Tan, Kwee Hong; Shahir Shamsir, Mohd; Moustafa, Ibrahim M; Idriss, Haitham

2018-01-01

DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics. The simulations show drastic conformational changes of the polymerase structure as a result of S44 phosphorylation. Phosphorylation-induced conformational changes transform the closed (active) enzyme structure into an open one. Further analysis of the results points to a key hydrogen bond and newly formed salt bridges as potential drivers of these structural fluctuations. The changes observed with S44/55 and S55 phosphorylation were less dramatic than S44 and the integrity of the H-bond was not compromised. Thus the phosphorylation of S44 is likely the major contributor to structural fluctuations that lead to loss of enzymatic activity. Copyright © 2017. Published by Elsevier Inc.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

PubMed

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2015-03-20

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

Relationship between Structural and Functional Assessment of the Visual System in Mildly Disabled Relapsing-Remitting Multiple Sclerosis Patients

PubMed Central

Huseyinoglu, Nergiz; Ekinci, Metin; Ozben, Serkan; Buyukuysal, Cagatay

2014-01-01

Abstract Studies that explored the anterior visual pathway in the patients with multiple sclerosis (MS) have demonstrated contradictory results about the correlation between structural and functional status of optic nerve and retina. We aimed to investigate the functional and structural findings in our cohort of mildly disabled relapsing-remitting MS patients. A total of 134 eyes (80 eyes of the patients with MS and 54 eyes of the control group) were investigated. Eyes of MS patients were divided into two groups—as eyes with history of optic neuritis (ON group) and without history of optic neuritis (NON group). Ophthalmological investigation including visual evoked potentials, standard automated perimetry, and optical coherence tomography were performed for all participants. Retinal and macular thicknesses were significantly decreased in ON and NON groups compared with controls. Also, visual evoked potential latencies and visual field loss were worse in the both MS groups compared with control group. We did not find any correlation between visual evoked potentials and retinal or macular thickness values but visual field parameters were correlated between retinal and macular layer loss in the NON group. According to our results and some previous studies, although both functional and structural changes were detected in patients with MS, functional status markers do not always show parallelism (or synchrony) with structural changes, especially in eyes with history of optic neuritis. PMID:27928266

Modelling inhibition of avian aromatase by azole pesticides.

PubMed

Saxena, A K; Devillers, J; Bhunia, S S; Bro, E

2015-01-01

The potential effects of pesticides and their metabolites on the endocrine system are of major concern to wildlife and human health. In this context, the azole pesticides have earned special attention due to their cytochrome P450 aromatase inhibition potential. Cytochrome P450 aromatase (CYP19) catalyses the conversion of androstenedione and testosterone into oestrone and oestradiol, respectively. Thus, aromatase modulates the oestrogenic balance essential not only for females, but also for male physiology, including gonadal function. Its inhibition affects reproductive organs, fertility and sexual behaviour in humans and wildlife species. Several studies have shown that azole pesticides are able to inhibit human and fish aromatases but the information on birds is lacking. Consequently, it appeared to be of interest to estimate the aromatase inhibition of azoles in three different avian species, namely Gallus gallus, Coturnix coturnix japonica and Taeniopygia guttata. In the absence of the crystal structure of the aromatase enzyme in these bird species, homology models for the individual avian species were constructed using the crystal structure of human aromatase (hAr) (pdb: 3EQM) that showed high sequence similarity for G. gallus (82.0%), T. guttata (81.9%) and C. japonica (81.2%). A homology model with Oncorhynchus mykiss (81.9%) was also designed for comparison purpose. The homology-modelled aromatase for each avian and fish species and crystal structure of human aromatase were selected for docking 46 structurally diverse azoles and related compounds. We showed that the docking behaviour of the chemicals on the different aromatases was broadly the same. We also demonstrated that there was an acceptable level of correlation between the binding score values and the available aromatase inhibition data. This means that the homology models derived on bird and fish species can be used to approximate the potential inhibitory effects of azoles on their aromatase.

Influence of square wave anodization on the electronic properties and structures of the passive films on Ti in sulfuric acid solution

NASA Astrophysics Data System (ADS)

Long, Y.; Li, D. G.; Chen, D. R.

2017-12-01

Two types of square wave anodization (type 1 and type 2) were employed in this work to form a passive film on Ti in a 0.5 M H2SO4 solution. The influences of the anodization potential and duration on the electronic properties and structures of the passive films were studied by Mott-Schottky plots, auger electron spectroscopy (AES) and X-ray photoelectron spectroscopy (XPS). The results showed that the donor density, ND, of the passive film decreased and the flat band potential, EFB, shifted to the positive direction with the increase of the anodization duration and high anodization potential irrespective of whether type 1 or type 2 was used. Moreover, the passive film that formed on Ti using type 1 had a lower donor density and a more positive flat band potential than that on Ti using type 2 at one fixed anodization duration (only exchanging the anodization order of 1 V and the high potential). XPS analysis revealed that the outmost passive film was only composed of TiO2, the inner passive film was mainly composed of TiO2 with some amount of TiO and Ti2O3, and the TiO2 concentration in the outermost passive film increased with the increase of the anodization duration and the high potential in the case of using type 1 or type 2, implying an increased degree of crystallinity. The AES results showed that the O/Ti atomic ratio of the passive film obviously increased with the increasing anodization duration and high potential, demonstrating the increased homogeneous characteristic of the passive film; this was in agreement with the Mott-Schottky and XPS results.

Evidence for magnetic energy storage in coronal active regions

NASA Technical Reports Server (NTRS)

Krieger, A. S.; De Feiter, L. D.; Vaiana, G. S.

1976-01-01

Examination of X-ray images obtained by the S-054 X-ray spectrographic telescope on Skylab shows the presence of some atypical X-ray-emitting coronal structures in active regions which are not consistent with potential extrapolations of photospheric magnetic fields. Analysis of the observed temporal changes in the X-ray-emitting active-region structures demonstrates that the majority of these consist of brightness changes representing temperature (and perhaps density) variations of the material in the loops.

An Ultrastable Heterobimetallic Uranium(IV)/Vanadium(III) Solid Compound Protected by a Redox-Active Phosphite Ligand: Crystal Structure, Oxidative Dissolution, and First-Principles Simulation.

PubMed

Gui, Daxiang; Dai, Xing; Zheng, Tao; Wang, Xiangxiang; Silver, Mark A; Chen, Lanhua; Zhang, Chao; Diwu, Juan; Zhou, Ruhong; Chai, Zhifang; Wang, Shuao

2018-02-05

The first heterobimetallic uranium(IV)/vanadium(III) phosphite compound, Na 2 UV 2 (HPO 3 ) 6 (denoted as UVP), was synthesized via an in situ redox-active hydrothermal reaction. It exhibits superior hydrolytic and antioxidant stability compared to the majority of structures containing low-valent uranium or vanadium, further elucidated by first-principles simulations, and therefore shows potential applications in nuclear waste management.

Large-scale broadband absorber based on metallic tungsten nanocone structure

NASA Astrophysics Data System (ADS)

Wang, Jiaxing; Liang, Yuzhang; Huo, Pengcheng; Wang, Daopeng; Tan, Jun; Xu, Ting

2017-12-01

We report a broadband tungsten absorber based on a nanocone metallic resonant structure fabricated by self-assembly nanosphere lithography. In experimental demonstration, the fabricated absorber has more than 90% average absorption efficiency and shows superior angular tolerance in the entire visible and near-infrared spectral region. We envision that this large-scale nanostructured broadband optical absorber would find great potential in the applications of high performance optoelectronic platforms and solar-thermal energy harvesting systems.

Serotonin and the Brain's Rich Club-Association Between Molecular Genetic Variation on the TPH2 Gene and the Structural Connectome.

PubMed

Markett, Sebastian; de Reus, Marcel A; Reuter, Martin; Montag, Christian; Weber, Bernd; Schoene-Bake, Jan-Christoph; van den Heuvel, Martijn P

2017-03-01

The rich club comprises a densely mutually connected set of hub regions in the brain, thought to serve as a processing and integration core. We assessed the impact of normal variation of the tryptophane hydroxylase 2 gene's promotor region (TPH2 rs4570625) on structural connectivity of the rich club pathways by means of a candidate gene association design. Tryptophane hydroxylase 2 (TPH2) is a rate-limiting enzyme in the biosynthesis of serotonin and is known to inhibit, in addition to its role as a trans-synaptic messenger, axonal and dendritic growth. The TPH2 T-variant has been associated with reduced mRNA expression and reduced serotonin levels, which may particularly influence the development of macroscale anatomical connectivity. Here, we show larger mean connectivity in the rich club in carriers of the T-variant, suggesting potential effects of upregulation of neural connectivity growth in this central core system. In addition, by edge-removal statistics, we show that the TPH2-associated higher levels of rich club connectivity are of importance for the functioning of the total structural network. The observed association is speculated to result from an effect of serotonin levels on brain development, potentially leading to stronger structural connectivity in heavily interconnected hubs. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Design, synthesis, and biological evaluation of combretabenzodiazepines: a novel class of anti-tubulin agents.

PubMed

Galli, Ubaldina; Travelli, Cristina; Aprile, Silvio; Arrigoni, Elena; Torretta, Simone; Grosa, Giorgio; Massarotti, Alberto; Sorba, Giovanni; Canonico, Pier Luigi; Genazzani, Armando A; Tron, Gian Cesare

2015-02-12

In the present manuscript, starting from the 1,4-benzodiazepin-2-one nucleus, a privileged structure in medicinal chemistry, we have synthesized a novel class of cis-locked combretastatins named combreatabenzodiazepines. They show similar cytotoxic and antitubulin activity compared to combretastatin A-4 in neuroblastoma cells, showing a better pharmacokinetic profile. This class of compounds has therefore the potential for further development as antitubulin agents.

Structure and Dynamics of the Thermohaline Staircases in the Beaufort Gyre

DTIC Science & Technology

2007-09-01

diffusive layering created by heating a salt gradient from below, after Figure 6 (Kelley 2003) A is the first quasi - stationary interface. B is the...sources Crapper (1975), Turner (1965), and Newell (1984) from Kelley (1990). The solid line is the empirical fit....12 Figure 11. Schematic of Ice...Salinity, Potential Temperature and Density plots show thermohaline xi step characteristics. b) Sound velocity profiles showing the step data

Physical properties of molybdenum monoboride: Ab-initio study

NASA Astrophysics Data System (ADS)

Rajpoot, Priyanka; Rastogi, Anugya; Verma, U. P.

2018-02-01

The Ab initio investigations on structural, electronic, optical and thermal properties of MoB have been reported using full potential linearised-augmented plane wave method within the framework of density functional theory. The exchange and correlation potentials were calculated using the Perdew-Burke-Ernzerhof-Sol generalised gradient approximation. The calculated equilibrium lattice constants and cell volume are in excellent agreement with the experimental results as compared to the available theoretical data. Electronic band structure shows that MoB is metallic in nature. From the partial densities of states of MoB it has been found that major contribution on the Fermi level is due to Mo-4d states. Among the reported optical parameters the large value of reflectivity at low energy shows that MoB can be used as a coating material in IR region. Maximum absorption in extreme UV region shows that it can be used in production of electricity through solar power in space vehicles. Various thermal properties have been calculated in a wide temperature range at high pressures. Change in thermal expansion coefficient with respect to temperature shows that anharmonic effect in MoB is very weak at high temperature. The optical and thermal properties of MoB are presented for the first time in this work.

Metallic VS2 Monolayer Polytypes as Potential Sodium-Ion Battery Anode via ab Initio Random Structure Searching.

PubMed

Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai

2016-07-27

We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications.

Recent Progress of Microfluidics in Translational Applications

PubMed Central

Liu, Zongbin; Han, Xin

2016-01-01

Microfluidics, featuring microfabricated structures, is a technology for manipulating fluids at the micrometer scale. The small dimension and flexibility of microfluidic systems are ideal for mimicking molecular and cellular microenvironment, and show great potential in translational research and development. Here, the recent progress of microfluidics in biological and biomedical applications, including molecular analysis, cellular analysis, and chip-based material delivery and biomimetic design is presented. The potential future developments in the translational microfluidics field are also discussed. PMID:27091777

Electrospun Fibrous Scaffolds for Tissue Engineering: Viewpoints on Architecture and Fabrication.

PubMed

Jun, Indong; Han, Hyung-Seop; Edwards, James R; Jeon, Hojeong

2018-03-06

Electrospinning has been used for the fabrication of extracellular matrix (ECM)-mimicking fibrous scaffolds for several decades. Electrospun fibrous scaffolds provide nanoscale/microscale fibrous structures with interconnecting pores, resembling natural ECM in tissues, and showing a high potential to facilitate the formation of artificial functional tissues. In this review, we summarize the fundamental principles of electrospinning processes for generating complex fibrous scaffold geometries that are similar in structural complexity to the ECM of living tissues. Moreover, several approaches for the formation of three-dimensional fibrous scaffolds arranged in hierarchical structures for tissue engineering are also presented.

Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

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

Kryzhevich, Dmitrij S., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Zolnikov, Konstantin P., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Abdrashitov, Andrei V.

2014-11-14

A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

Electronic and structural properties of M3(HITP)2 (M = Ni, Cu and Co) metal-organic frameworks

NASA Astrophysics Data System (ADS)

Silveira, Orlando; Chacham, Helio; Alexandre, Simone

Theoretical and experimental works have demonstrated that electrical and structural properties of metal-organic frameworks (MOF) can be significantly changed by the identity of the metal center, leading to a potential strategy for tuning the selectivity of the material toward different types of technological applications. In this work, we use first principle calculations to investigate the electronic properties of 2D MOF M3(HITP)2 (M is Ni, Cu and Co and HITP = 2,3,6,7,10,11 - hexaiminotriphenylene). Our results show that for M=Ni and Co, the structures are perfect planar and there is a full charge delocalization in the 2D plane of stacking due to the predominance of π - π bonding. The band structure for M = Ni shows that this material is a semiconductor with an indirect band gap of 132 meV, whilst for M = Co the band structure shows that this material is a ferromagnetic semiconductor with a direct band gap of 386 meV for spin down and a indirect band gap of 246 meV for spin up. For M=Cu, the material is a metal and adopts a distorted structure due to a different hybridization of the metal atom in comparison with its counterparts. We also propose a tight binding model that can represent the electronic structure near the Fermi level of this family of MOF.

Superlattice-induced minigaps in graphene band structure due to underlying one-dimensional nanostructuration

NASA Astrophysics Data System (ADS)

Celis, A.; Nair, M. N.; Sicot, M.; Nicolas, F.; Kubsky, S.; Malterre, D.; Taleb-Ibrahimi, A.; Tejeda, A.

2018-05-01

We have studied the influence of one-dimensional periodic nanostructured substrates on graphene band structure. One-monolayer-thick graphene is extremely sensitive to periodic terrace arrays, as demonstrated on two different nanostructured substrates, namely Ir(332) and multivicinal curved Pt(111). Photoemission shows the presence of minigaps related to the spatial periodicity. The potential barrier strength of the one-dimensional periodic nanostructuration can be tailored with the step-edge type and the nature of the substrate. The minigap opening further demonstrates the presence of backward scattered electronic waves on the surface and the absence of Klein tunneling on the substrate, probably due to the fast variation of the potential, of a spatial extent of the order of the lattice parameter of graphene.

Mössbauer study of iron-based perovskite-type materials as potential catalysts for ethyl acetate oxidation

NASA Astrophysics Data System (ADS)

Paneva, D.; Dimitrov, M.; Velinov, N.; Kolev, H.; Kozhukharov, V.; Tsoncheva, T.; Mitov, I.

2010-03-01

La-Sr-Fe perovskite-type oxides were prepared by the nitrate-citrate method. The basic object of this study is layered Ruddlesden-Popper phase LaSr3Fe3O10. The phase composition and structural properties of the obtained materials are investigated by Mössbauer spectroscopy, X-ray diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS) and temperature programmed reduction (TPR). The preliminary catalytic tests show a high potential of these materials for volatile organic compounds (VOCs) elimination as they possess high conversion ability and selectivity to total oxidation of ethyl acetate. Catalytic performance of LaSr3Fe3O10 is depended on the stability of structure and Fe4+-oxidation state.

Molecular dynamics simulation of liquid structure for undercooled Zr-Nb alloys assisted with electrostatic levitation experiments

NASA Astrophysics Data System (ADS)

Yang, S. J.; Hu, L.; Wang, L.; Wei, B.

2018-06-01

The liquid structures of undercooled Zr90Nb10, Zr70Nb30 and Zr50Nb50 alloys were studied by molecular dynamics simulation combined with electrostatic levitation experiments. The densities of three alloys were measured by electrostatic levitation to modify the Zr-Nb potential functions by adjusting parameters in potential functions. In simulation, the atomic packing in Zr-Nb alloys was more ordered at lower temperatures. The Voronoi tessellation analyses indicated Nb-centered clusters were easier to form than Zr-centered clusters although the Nb content was less than 50%. The partial pair distribution functions showed that the interactions among Zr atoms are quite different to that among Nb atoms.

Sorption of lead ions on diatomite and manganese oxides modified diatomite.

PubMed

Al-Degs, Y; Khraisheh, M A; Tutunji, M F

2001-10-01

Naturally occurring diatomaceous earth (diatomite) has been tested as a potential sorbent for Pb(II) ions. The intrinsic exchange properties were further improved by modification with manganese oxides. Modified adsorbent (referred to as Mn-diatomite) showed a higher tendency for adsorbing lead ions from solution at pH 4. The high performance exhibited by Mn-diatomite was attributed to increased surface area and higher negative surface charge after modification. Scanning electron microscope pictures revealed a birnessite structure of manganese oxides, which was featured by a plate-like-crystal structure. Diatomite filtration quality was improved after modification by manganese oxides. Good filtration qualities combined with high exchange capacity emphasised the potential use of Mn-diatomite in filtration systems.

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

Singh, Prashant; Harbola, Manoj K.; Johnson, Duane D.

Here, this work constitutes a comprehensive and improved account of electronic-structure and mechanical properties of silicon-nitride (more » $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ ) polymorphs via van Leeuwen and Baerends (LB) exchange-corrected local density approximation (LDA) that enforces the exact exchange potential asymptotic behavior. The calculated lattice constant, bulk modulus, and electronic band structure of $${\\rm Si}_{3}$$ $${\\rm N}_{4}$$ polymorphs are in good agreement with experimental results. We also show that, for a single electron in a hydrogen atom, spherical well, or harmonic oscillator, the LB-corrected LDA reduces the (self-interaction) error to exact total energy to ~10%, a factor of three to four lower than standard LDA, due to a dramatically improved representation of the exchange-potential.« less

Conduction at domain walls in oxide multiferroics

NASA Astrophysics Data System (ADS)

Seidel, J.; Martin, L. W.; He, Q.; Zhan, Q.; Chu, Y.-H.; Rother, A.; Hawkridge, M. E.; Maksymovych, P.; Yu, P.; Gajek, M.; Balke, N.; Kalinin, S. V.; Gemming, S.; Wang, F.; Catalan, G.; Scott, J. F.; Spaldin, N. A.; Orenstein, J.; Ramesh, R.

2009-03-01

Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO3. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

Conduction at domain walls in oxide multiferroics.

PubMed

Seidel, J; Martin, L W; He, Q; Zhan, Q; Chu, Y-H; Rother, A; Hawkridge, M E; Maksymovych, P; Yu, P; Gajek, M; Balke, N; Kalinin, S V; Gemming, S; Wang, F; Catalan, G; Scott, J F; Spaldin, N A; Orenstein, J; Ramesh, R

2009-03-01

Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO(3). The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

Enhancement of minority carrier injection in ambipolar carbon nanotube transistors using double-gate structures

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

Kim, Bongjun; Liang, Kelly; Dodabalapur, Ananth, E-mail: ananth.dodabalapur@engr.utexas.edu

We show that double-gate ambipolar thin-film transistors can be operated to enhance minority carrier injection. The two gate potentials need to be significantly different for enhanced injection to be observed. This enhancement is highly beneficial in devices such as light-emitting transistors where balanced electron and hole injections lead to optimal performance. With ambipolar single-walled carbon nanotube semiconductors, we demonstrate that higher ambipolar currents are attained at lower source-drain voltages, which is desired for portable electronic applications, by employing double-gate structures. In addition, when the two gates are held at the same potential, the expected advantages of the double-gate transistors suchmore » as enhanced on-current are also observed.« less

SPACER: server for predicting allosteric communication and effects of regulation

PubMed Central

Goncearenco, Alexander; Mitternacht, Simon; Yong, Taipang; Eisenhaber, Birgit; Eisenhaber, Frank; Berezovsky, Igor N.

2013-01-01

The SPACER server provides an interactive framework for exploring allosteric communication in proteins with different sizes, degrees of oligomerization and function. SPACER uses recently developed theoretical concepts based on the thermodynamic view of allostery. It proposes easily tractable and meaningful measures that allow users to analyze the effect of ligand binding on the intrinsic protein dynamics. The server shows potential allosteric sites and allows users to explore communication between the regulatory and functional sites. It is possible to explore, for instance, potential effector binding sites in a given structure as targets for allosteric drugs. As input, the server only requires a single structure. The server is freely available at http://allostery.bii.a-star.edu.sg/. PMID:23737445

Early Adolescent Perceptions of Neighborhood: Strengths, Structural Disadvantage, and Relations to Outcomes

ERIC Educational Resources Information Center

Witherspoon, Dawn P.; Hughes, Diane L.

2014-01-01

Considerable evidence shows the detriments of neighborhood social disorganization for urban youth. Researchers have focused less on potential neighborhood strengths or on the interplay of neighborhood perceptions and objective neighborhood characteristics. The authors examined the presence and perception of positive and negative neighborhood…

Predicting Career Advancement with Structural Equation Modelling

ERIC Educational Resources Information Center

Heimler, Ronald; Rosenberg, Stuart; Morote, Elsa-Sofia

2012-01-01

Purpose: The purpose of this paper is to use the authors' prior findings concerning basic employability skills in order to determine which skills best predict career advancement potential. Design/methodology/approach: Utilizing survey responses of human resource managers, the employability skills showing the largest relationships to career…

Mechanism of Positive Allosteric Modulators Acting on AMPA Receptors

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

Jin,R.; Clark, S.; Weeks, A.

2005-01-01

Ligand-gated ion channels involved in the modulation of synaptic strength are the AMPA, kainate, and NMDA glutamate receptors. Small molecules that potentiate AMPA receptor currents relieve cognitive deficits caused by neurodegenerative diseases such as Alzheimer's disease and show promise in the treatment of depression. Previously, there has been limited understanding of the molecular mechanism of action for AMPA receptor potentiators. Here we present cocrystal structures of the glutamate receptor GluR2 S1S2 ligand-binding domain in complex with aniracetam [1-(4-methoxybenzoyl)-2-pyrrolidinone] or CX614 (pyrrolidino-1, 3-oxazino benzo-1, 4-dioxan-10-one), two AMPA receptor potentiators that preferentially slow AMPA receptor deactivation. Both potentiators bind within the dimermore » interface of the nondesensitized receptor at a common site located on the twofold axis of molecular symmetry. Importantly, the potentiator binding site is adjacent to the 'hinge' in the ligand-binding core 'clamshell' that undergoes conformational rearrangement after glutamate binding. Using rapid solution exchange, patch-clamp electrophysiology experiments, we show that point mutations of residues that interact with potentiators in the cocrystal disrupt potentiator function. We suggest that the potentiators slow deactivation by stabilizing the clamshell in its closed-cleft, glutamate-bound conformation.« less

Three reversible states controlled on a gold monoatomic contact by the electrochemical potential

NASA Astrophysics Data System (ADS)

Kiguchi, Manabu; Konishi, Tatsuya; Hasegawa, Kouta; Shidara, Satoshi; Murakoshi, Kei

2008-06-01

Conductance of a Au monoatomic contact was investigated under the electrochemical potential control. The Au contact showed three different behaviors depending on the potential: 1G0 (G0=2e2/h) , 0.5G0 , and not-well-defined values below 1G0 were shown when the potential of the contact was kept at -0.6V (double layer potential), -1.0V (hydrogen evolution potential), and 0.8 V (oxide formation potential) versus Ag/AgCl in 0.1M Na2SO4 solution, respectively. These three reversible states and their respective conductances could be fully controlled by the electrochemical potential. These changes in the conductance values are discussed based on the proposed structure models of hydrogen adsorbed and oxygen incorporated on a Au monoatomic contact.

Titanium doped LSCM anode for hydrocarbon fuelled SOFCs

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

Azad, Abul K.; Hakem, Afizul; Petra, Pg. M. Iskandar

2015-05-15

La{sub 0.75}Sr{sub 0.25}Cr{sub 0.5-x}Mn{sub 0.5}Ti{sub x}O{sub 3} (x = 0.1, 0.2) has been synthesized in solid state reaction method and tested as a potential anode material for solid oxide fuel cells. Rietveld refinement of X-ray powder diffraction data using Fullprof software shows that the materials crystallize in the rhombohedral symmetry in the R-3C space group. The cell parameters are: a = b = 5.5286 (4) Å, c = 13.408(1) Å, α = β = 90°, γ = 120°. Particle size distribution measurements show that the average particle size for x = 0.1 and 0.2 was 232.66 nm and 176.63 nm, respectively. Themore » potential on particles were found to be −22.86 mV and −27.73 mV, for x = 0.1 and x = 0.2, respectively. Thermal expansion measurement using thermo-mechanical analyzer shows that the thermal expansion coefficient is 13.96 × 10{sup −6}/°C which is close to the thermal expansion of the state-of–the art YSZ electrolyte. Microstructure has been observed from scanning electron microscopy which shows a porous structure. Energy dispersive X-ray shows that the percentage of the different cations and anions in the structure are close to the chemical occupancies.« less

Ion beam sputter deposited zinc telluride films

NASA Technical Reports Server (NTRS)

Gulino, D. A.

1986-01-01

Zinc telluride is of interest as a potential electronic device material, particularly as one component in an amorphous superlattice, which is a new class of interesting and potentially useful materials. Some structural and electronic properties of ZnTe films deposited by argon ion beam sputter deposition are described. Films (up to 3000 angstroms thick) were deposited from a ZnTe target. A beam energy of 1000 eV and a current density of 4 mA/sq cm resulted in deposition rates of approximately 70 angstroms/min. The optical band gap was found to be approximately 1.1 eV, indicating an amorphous structure, as compared to a literature value of 2.26 eV for crystalline material. Intrinsic stress measurements showed a thickness dependence, varying from tensile for thicknesses below 850 angstroms to compressive for larger thicknesses. Room temperature conductivity measurement also showed a thickness dependence, with values ranging from 1.86 x 10 to the -6th/ohm cm for 300 angstrom film to 2.56 x 10 to the -1/ohm cm for a 2600 angstrom film. Measurement of the temperature dependence of the conductivity for these films showed complicated behavior which was thickness dependent. Thinner films showed at least two distinct temperature dependent conductivity mechanisms, as described by a Mott-type model. Thicker films showed only one principal conductivity mechanism, similar to what might be expected for a material with more crystalline character.

Ion beam sputter deposited zinc telluride films

NASA Technical Reports Server (NTRS)

Gulino, D. A.

1985-01-01

Zinc telluride is of interest as a potential electronic device material, particularly as one component in an amorphous superlattice, which is a new class of interesting and potentially useful materials. Some structural and electronic properties of ZnTe films deposited by argon ion beam sputter depoairion are described. Films (up to 3000 angstroms thick) were deposited from a ZnTe target. A beam energy of 1000 eV and a current density of 4 mA/sq. cm. resulted in deposition rates of approximately 70 angstroms/min. The optical band gap was found to be approximately 1.1 eV, indicating an amorphous structure, as compared to a literature value of 2.26 eV for crystalline material. Intrinsic stress measurements showed a thickness dependence, varying from tensile for thicknesses below 850 angstroms to compressive for larger thicknesses. Room temperature conductivity measurement also showed a thickness dependence, with values ranging from 1.86 x to to the -6/ohm. cm. for 300 angstrom film to 2.56 x 10 to the -1/ohm. cm. for a 2600 angstrom film. Measurement of the temperature dependence of the conductivity for these films showed complicated behavior which was thickness dependent. Thinner films showed at least two distinct temperature dependent conductivity mechanisms, as described by a Mott-type model. Thicker films showed only one principal conductivity mechanism, similar to what might be expected for a material with more crystalline character.

Design and analysis of coplanar waveguide triple-band antenna based on defected ground structure

NASA Astrophysics Data System (ADS)

Lv, Hong; Chen, Wanli; Xia, Xinsheng; Qi, Peng; Sun, Quanling

2017-11-01

A kind of coplanar waveguide triple-band antenna based on defected ground structure is proposed, which has novel structure. Three batches with different frequency band are constructed by utilizing line combination, overlapping, and symmetry method. Stop band signals among three frequency bands are effectively suppressed by slots with different structures. More satisfactory impedance matching is realized by means of changing slot structure and improving return-loss. The presented antenna can operates simultaneously in various systems such as 3G / 4G wireless communication, Bluetooth, Worldwide Interoperability for Microwave Access, Wireless LAN. Test results show that the antenna has good radiation and gain in its working frequency band, and that it has great application potentials.

Damage Detection in Rotorcraft Composite Structures Using Thermography and Laser-Based Ultrasound

NASA Technical Reports Server (NTRS)

Anastasi, Robert F.; Zalameda, Joseph N.; Madaras, Eric I.

2004-01-01

New rotorcraft structural composite designs incorporate lower structural weight, reduced manufacturing complexity, and improved threat protection. These new structural concepts require nondestructive evaluation inspection technologies that can potentially be field-portable and able to inspect complex geometries for damage or structural defects. Two candidate technologies were considered: Thermography and Laser-Based Ultrasound (Laser UT). Thermography and Laser UT have the advantage of being non-contact inspection methods, with Thermography being a full-field imaging method and Laser UT a point scanning technique. These techniques were used to inspect composite samples that contained both embedded flaws and impact damage of various size and shape. Results showed that the inspection techniques were able to detect both embedded and impact damage with varying degrees of success.

Personality Inventory for DSM-5-Short Form (PID-5-SF): Reliability, Factorial Structure, and Relationship With Functional Impairment in Dual Diagnosis Patients.

PubMed

Díaz-Batanero, Carmen; Ramírez-López, Juan; Domínguez-Salas, Sara; Fernández-Calderón, Fermín; Lozano, Óscar M

2017-11-01

Section III of the Diagnostic and Statistical Manual of Mental Disorders-Fifth edition ( DSM-5) has generated a personality paradigm consisting of 25 personality facets identified in five domains. The developed assessment instrument Personality Inventory for DSM-5 (PID-5) has showed good psychometric properties, but the potential for certain improvements still remain. In this article, a sample of 282 dual diagnosis patients is used to provide evidence of the psychometric properties of the PID-5-Short Form. The mean value of Cronbach's alpha coefficients reached .73 on the facets and .84 for domains and test-retest values ranged between .57 to .83 for facets and .70 to .87 for the domains. Confirmatory factor analyses conducted showed good fit on both models tested: the five correlated factor structure and hierarchical structure of personality traits. The WHODAS 2.0 domains of understanding and communicating, and participating in society, appear to show the strongest relationship with personality facets. In general, the PID-5-Short Form shows adequate psychometric properties for use in dual diagnosis patients.

A complex study of 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate: A new low-molecular-weight immune response modifier

NASA Astrophysics Data System (ADS)

Ryng, Stanisław; Zimecki, Michał; Jezierska-Mazzarello, Aneta; Panek, Jarosław J.; Mączyński, Marcin; Głowiak, Tadeusz; Sawka-Dobrowolska, Wanda; Koll, Aleksander

2011-07-01

A new potential lead structure with immunological activity, 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate, was synthesized. A detailed description of synthesis is presented together with X-ray structural analysis. In vitro assays showed that the compound had a potent immunosuppressive activity. Next, Density Functional Theory (DFT) was employed to shed a light on molecular properties of the investigated isoxazole derivative. The molecular modeling part included geometric as well as electronic structure descriptions: (i) the conformational analysis was performed to localize the most appropriate conformation; (ii) the coordination energy and Basis Set Superposition Error (BSSE) were estimated for the complex of the isoxazole derivative interacting with water molecule; (iii) the potential energy distribution was used to assign molecular vibrations, and NBO population analysis served to describe the electronic structure; (iv) the electrostatic potential map was generated to provide the graphical presentation of regions exposed for intermolecular interactions. The contacts between the water molecule and the nitrogen atom of the isoxazole ring edge were present in the solid phase. On the other hand, the theoretical DFT prediction was that the oxygen atom of the edge should form a more stable complex with the water molecule.

Minimum stiffness criteria for ring frame stiffeners of space launch vehicles

NASA Astrophysics Data System (ADS)

Friedrich, Linus; Schröder, Kai-Uwe

2016-12-01

Frame stringer-stiffened shell structures show high load carrying capacity in conjunction with low structural mass and are for this reason frequently used as primary structures of aerospace applications. Due to the great number of design variables, deriving suitable stiffening configurations is a demanding task and needs to be realized using efficient analysis methods. The structural design of ring frame stringer-stiffened shells can be subdivided into two steps. One, the design of a shell section between two ring frames. Two, the structural design of the ring frames such that a general instability mode is avoided. For sizing stringer-stiffened shell sections, several methods were recently developed, but existing ring frame sizing methods are mainly based on empirical relations or on smeared models. These methods do not mandatorily lead to reliable designs and in some cases the lightweight design potential of stiffened shell structures can thus not be exploited. In this paper, the explicit physical behaviour of ring frame stiffeners of space launch vehicles at the onset of panel instability is described using mechanical substitute models. Ring frame stiffeners of a stiffened shell structure are sized applying existing methods and the method suggested in this paper. To verify the suggested method and to demonstrate its potential, geometrically non-linear finite element analyses are performed using detailed finite element models.

Spin-polarized structural, elastic, electronic and magnetic properties of half-metallic ferromagnetism in V-doped ZnSe

NASA Astrophysics Data System (ADS)

Monir, M. El Amine.; Baltache, H.; Murtaza, G.; Khenata, R.; Ahmed, Waleed K.; Bouhemadou, A.; Omran, S. Bin; Seddik, T.

2015-01-01

Based on first principles spin-polarized density functional theory, the structural, elastic electronic and magnetic properties of Zn1-xVxSe (for x=0.25, 0.50, 0.75) in zinc blende structure have been studied. The investigation was done using the full-potential augmented plane wave method as implemented in WIEN2k code. The exchange-correlation potential was treated with the generalized gradient approximation PBE-GGA for the structural and elastic properties. Moreover, the PBE-GGA+U approximation (where U is the Hubbard correlation terms) is employed to treat the "d" electrons properly. A comparative study between the band structures, electronic structures, total and partial densities of states and local moments calculated within both GGA and GGA+U schemes is presented. The analysis of spin-polarized band structure and density of states shows the half-metallic ferromagnetic character and are also used to determine s(p)-d exchange constants N0α (conduction band) and N0β (valence band) due to Se(4p)-V(3d) hybridization. It has been clearly evidence that the magnetic moment of V is reduced from its free space change value of 3 μB and the minor atomic magnetic moment on Zn and Se are generated.

A Global Comparison of the Human and T. brucei Degradomes Gives Insights about Possible Parasite Drug Targets

PubMed Central

Mashiyama, Susan T.; Koupparis, Kyriacos; Caffrey, Conor R.; McKerrow, James H.; Babbitt, Patricia C.

2012-01-01

We performed a genome-level computational study of sequence and structure similarity, the latter using crystal structures and models, of the proteases of Homo sapiens and the human parasite Trypanosoma brucei. Using sequence and structure similarity networks to summarize the results, we constructed global views that show visually the relative abundance and variety of proteases in the degradome landscapes of these two species, and provide insights into evolutionary relationships between proteases. The results also indicate how broadly these sequence sets are covered by three-dimensional structures. These views facilitate cross-species comparisons and offer clues for drug design from knowledge about the sequences and structures of potential drug targets and their homologs. Two protease groups (“M32” and “C51”) that are very different in sequence from human proteases are examined in structural detail, illustrating the application of this global approach in mining new pathogen genomes for potential drug targets. Based on our analyses, a human ACE2 inhibitor was selected for experimental testing on one of these parasite proteases, TbM32, and was shown to inhibit it. These sequence and structure data, along with interactive versions of the protein similarity networks generated in this study, are available at http://babbittlab.ucsf.edu/resources.html. PMID:23236535

Structural, electronic and magnetic properties of metal thiophosphate InPS4

NASA Astrophysics Data System (ADS)

Rajpoot, Priyanka; Nayak, Vikas; Kumari, Meena; Yadav, Priya; Nautiyal, Shashank; Verma, U. P.

2017-05-01

The non-centrosymmetric crystal, InPS4, has been investigated by means of density functional theory (DFT). In this paper we have calculated the structural parameters, electronic band structures, density of states plot and magnetic properties using full potential linearized augmented plane wave (FP-LAPW) method. The exchange correlation has been solved employing the generalised gradient approximation due to Perdew-Burke-Ernzerhof. The calculations are performed both without spin as well as spin polarized. The results show that InPS4 is an indirect band gap semiconductor with (N-Г) energy gap of 2.32eV (without spin) and 1.86eV in spin up and down channels.The obtained lattice parameters and energy gap agree well with the experimental results. Our reported magnetic moment results show that the property of InPS4is nonmagnetic.

Mix-and-diffuse serial synchrotron crystallography

DOE PAGES

Beyerlein, Kenneth R.; Dierksmeyer, Dennis; Mariani, Valerio; ...

2017-10-09

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzymemore » at a high level of detail. Here, the success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.« less

Mix-and-diffuse serial synchrotron crystallography

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

Beyerlein, Kenneth R.; Dierksmeyer, Dennis; Mariani, Valerio

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzymemore » at a high level of detail. Here, the success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.« less

Effect of the L499M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties

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

Osipov, Evgeny; Polyakov, Konstantin; Engelhardt Institute of Molecular Biology, Vavilova Str. 32, Moscow 119991

2014-11-01

The structures of the ascomycetous B. aclada laccase and its L499M T1-site mutant have been solved at 1.7 Å resolution. The mutant enzyme shows a 140 mV lower redox potential of the type 1 copper and altered kinetic behaviour. The wild type and the mutant have very similar structures, which makes it possible to relate the changes in the redox potential to the L499M mutation Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain fourmore » Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. The redox potential of the T1 copper ion influences the enzymatic reaction and is determined by the nature of the axial ligands and the structure of the second coordination sphere. In this work, the laccase from the ascomycete Botrytis aclada was studied, which contains conserved Ile491 and nonconserved Leu499 residues in the axial positions. The three-dimensional structures of the wild-type enzyme and the L499M mutant were determined by X-ray crystallography at 1.7 Å resolution. Crystals suitable for X-ray analysis could only be grown after deglycosylation. Both structures did not contain the T2 copper ion. The catalytic properties of the enzyme were characterized and the redox potentials of both enzyme forms were determined: E{sub 0} = 720 and 580 mV for the wild-type enzyme and the mutant, respectively. Since the structures of the wild-type and mutant forms are very similar, the change in the redox potential can be related to the L499M mutation in the T1 site of the enzyme.« less

Morphological and structural changes at the Merapi lava dome monitored using Unmanned Aerial Vehicles (UAVs)

NASA Astrophysics Data System (ADS)

Darmawan, H.; Walter, T. R.; Brotopuspito, K. S.; Subandriyo, S.; Nandaka, M. A.

2017-12-01

Six gas-driven explosions between 2012 and 2014 had changed the morphology and structures of the Merapi lava dome. The explosions mostly occurred during rainfall season and caused NW-SE elongated open fissures that dissected the lava dome. In this study, we conducted UAVs photogrammetry before and after the explosions to investigate the morphological and structural changes and to assess the quality of the UAV photogrammetry. The first UAV photogrammetry was conducted on 26 April 2012. After the explosions, we conducted Terrestrial Laser Scanning (TLS) survey on 18 September 2014 and repeated UAV photogrammetry on 6 October 2015. We applied Structure from Motion (SfM) algorithm to reconstruct 3D SfM point clouds and photomosaics of the 2012 and 2015 UAVs images. Topography changes has been analyzed by calculating height difference between the 2012 and 2015 SfM point clouds, while structural changes has been investigated by visual comparison between the 2012 and 2015 photo mosaics. Moreover, a quality assessment of the results of UAV photogrammetry has been done by comparing the 3D SfM point clouds to TLS dataset. Result shows that the 2012 and 2015 SfM point clouds have 0.19 and 0.57 m difference compared to the TLS point cloud. Furthermore, topography, and structural changes reveal that the 2012-14 explosions were controlled by pre-existing structures. The volume of the 2012-14 explosions is 26.400 ± 1320 m3 DRE. In addition, we find a structurally delineated unstable block at the southern front of the dome which potentially collapses in the future. We concluded that the 2012-14 explosions occurred due to interaction between magma intrusion and rain water and were facilitated by pre-existing structures. The unstable block potentially leads to a rock avalanche hazard. Furthermore, our drone photogrammetry results show very promising and therefore we recommend to use drone for topography mapping in lava dome building volcanoes.

Binding of Amphipathic Cell Penetrating Peptide p28 to Wild Type and Mutated p53 as studied by Raman, Atomic Force and Surface Plasmon Resonance spectroscopies.

PubMed

Signorelli, Sara; Santini, Simona; Yamada, Tohru; Bizzarri, Anna Rita; Beattie, Craig W; Cannistraro, Salvatore

2017-04-01

Mutations within the DNA binding domain (DBD) of the tumor suppressor p53 are found in >50% of human cancers and may significantly modify p53 secondary structure impairing its function. p28, an amphipathic cell-penetrating peptide, binds to the DBD through hydrophobic interaction and induces a posttranslational increase in wildtype and mutant p53 restoring functionality. We use mutation analyses to explore which elements of secondary structure may be critical to p28 binding. Molecular modeling, Raman spectroscopy, Atomic Force Spectroscopy (AFS) and Surface Plasmon Resonance (SPR) were used to identify which secondary structure of site-directed and naturally occurring mutant DBDs are potentially altered by discrete changes in hydrophobicity and the molecular interaction with p28. We show that specific point mutations that alter hydrophobicity within non-mutable and mutable regions of the p53 DBD alter specific secondary structures. The affinity of p28 was positively correlated with the β-sheet content of a mutant DBD, and reduced by an increase in unstructured or random coil that resulted from a loss in hydrophobicity and redistribution of surface charge. These results help refine our knowledge of how mutations within p53-DBD alter secondary structure and provide insight on how potential structural alterations in p28 or similar molecules improve their ability to restore p53 function. Raman spectroscopy, AFS, SPR and computational modeling are useful approaches to characterize how mutations within the p53DBD potentially affect secondary structure and identify those structural elements prone to influence the binding affinity of agents designed to increase the functionality of p53. Copyright © 2017 Elsevier B.V. All rights reserved.

MEFA (multiepitope fusion antigen)-Novel Technology for Structural Vaccinology, Proof from Computational and Empirical Immunogenicity Characterization of an Enterotoxigenic Escherichia coli (ETEC) Adhesin MEFA

PubMed Central

Duan, Qiangde; Lee, Kuo Hao; Nandre, Rahul M; Garcia, Carolina; Chen, Jianhan; Zhang, Weiping

2017-01-01

Vaccine development often encounters the challenge of virulence heterogeneity. Enterotoxigenic Escherichia coli (ETEC) bacteria producing immunologically heterogeneous virulence factors are a leading cause of children’s diarrhea and travelers’ diarrhea. Currently, we do not have licensed vaccines against ETEC bacteria. While conventional methods continue to make progress but encounter challenge, new computational and structure-based approaches are explored to accelerate ETEC vaccine development. In this study, we applied a structural vaccinology concept to construct a structure-based multiepitope fusion antigen (MEFA) to carry representing epitopes of the seven most important ETEC adhesins [CFA/I, CFA/II (CS1–CS3), CFA/IV (CS4–CS6)], simulated antigenic structure of the CFA/I/II/IV MEFA with computational atomistic modeling and simulation, characterized immunogenicity in mouse immunization, and examined the potential of structure-informed vaccine design for ETEC vaccine development. A tag-less recombinant MEFA protein (CFA/I/II/IV MEFA) was effectively expressed and extracted. Molecular dynamics simulations indicated that this MEFA immunogen maintained a stable secondary structure and presented epitopes on the protein surface. Empirical data showed that mice immunized with the tagless CFA/I/II/IV MEFA developed strong antigen-specific antibody responses, and mouse serum antibodies significantly inhibited in vitro adherence of bacteria expressing these seven adhesins. These results revealed congruence of antigen immunogenicity between computational simulation and empirical mouse immunization and indicated this tag-less CFA/I/II/IV MEFA potentially an antigen for a broadly protective ETEC vaccine, suggesting a potential application of MEFA-based structural vaccinology for vaccine design against ETEC and likely other pathogens. PMID:28944092

Cognitive control over learning: Creating, clustering and generalizing task-set structure

PubMed Central

Collins, Anne G.E.; Frank, Michael J.

2013-01-01

Executive functions and learning share common neural substrates essential for their expression, notably in prefrontal cortex and basal ganglia. Understanding how they interact requires studying how cognitive control facilitates learning, but also how learning provides the (potentially hidden) structure, such as abstract rules or task-sets, needed for cognitive control. We investigate this question from three complementary angles. First, we develop a new computational “C-TS” (context-task-set) model inspired by non-parametric Bayesian methods, specifying how the learner might infer hidden structure and decide whether to re-use that structure in new situations, or to create new structure. Second, we develop a neurobiologically explicit model to assess potential mechanisms of such interactive structured learning in multiple circuits linking frontal cortex and basal ganglia. We systematically explore the link betweens these levels of modeling across multiple task demands. We find that the network provides an approximate implementation of high level C-TS computations, where manipulations of specific neural mechanisms are well captured by variations in distinct C-TS parameters. Third, this synergism across models yields strong predictions about the nature of human optimal and suboptimal choices and response times during learning. In particular, the models suggest that participants spontaneously build task-set structure into a learning problem when not cued to do so, which predicts positive and negative transfer in subsequent generalization tests. We provide evidence for these predictions in two experiments and show that the C-TS model provides a good quantitative fit to human sequences of choices in this task. These findings implicate a strong tendency to interactively engage cognitive control and learning, resulting in structured abstract representations that afford generalization opportunities, and thus potentially long-term rather than short-term optimality. PMID:23356780

Identification of anomalous motion of thunderstorms using daily rainfall fields

NASA Astrophysics Data System (ADS)

del Moral, Anna; Llasat, Maria Carmen; Rigo, Tomeu

2016-04-01

Adverse weather phenomena in Catalonia (NE of the Iberian Peninsula) is commonly associated to heavy rains, large hail, strong winds, and/or tornados, all of them caused by thunderstorms. In most of the cases with adverse weather, thunderstorms vary sharply their trajectories in a concrete moment, changing completely the motion directions that have previously followed. Furthermore, it is possible that a breaking into several cells may be produced, or, in the opposite, it can be observed a joining of different thunderstorms into a bigger system. In order to identify the main features of the developing process of thunderstorms and the anomalous motions that these may follow in some cases, this contribution presents a classification of the events using daily rainfall fields, with the purpose of distinguishing quickly anomalous motion of thunderstorms. The methodology implemented allows classifying the daily rainfall fields in three categories by applying some thresholds related with the daily precipitation accumulated values and their extension: days with "no rain", days with "potentially convective" rain and days with "non-potentially convective" rain. Finally, for those "potentially convective" daily rainfall charts, it also allows a geometrical identification and classification of all the convective structures into "ellipse" and "non-ellipse", obtaining then the structures with "normal" or "anomalous" motion pattern, respectively. The work is focused on the period 2008-2015, and presents some characteristics of the rainfall behaviour in terms of the seasonal distribution of convective rainfall or the geographic variability. It shows that convective structures are mainly found during late spring and summer, even though they can be recorded in any time of the year. Consequently, the maximum number of convective structures with anomalous motion is recorded between July and November. Furthermore, the contribution shows the role of the orography of Catalonia in the development of convective structures. This work has been developed in the framework of the Spanish project HOPE.

Landau instability and mobility edges of the interacting one-dimensional Bose gas in weak random potentials

NASA Astrophysics Data System (ADS)

Cherny, Alexander Yu; Caux, Jean-Sébastien; Brand, Joachim

2018-01-01

We study the frictional force exerted on the trapped, interacting 1D Bose gas under the influence of a moving random potential. Specifically we consider weak potentials generated by optical speckle patterns with finite correlation length. We show that repulsive interactions between bosons lead to a superfluid response and suppression of frictional force, which can inhibit the onset of Anderson localisation. We perform a quantitative analysis of the Landau instability based on the dynamic structure factor of the integrable Lieb-Liniger model and demonstrate the existence of effective mobility edges.

The Floating Potential Probe (FPP) for ISS: Operations and Initial Results

NASA Technical Reports Server (NTRS)

Ferguson, Dale C.; Hillard, G. Barry; Morton, Thomas L.

2001-01-01

In this paper we report early results from the Floating Potential Probe (FPP) recently installed on the International Space Station (ISS). The data show that FPP properly measures the electrical potential of ISS structure with respect to the plasma it is flying through. FPP Langmuir probe data seem to give accurate measurements of the ambient plasma density, and are generally consistent with the IRI-90 model. FPP data are used to judge the performance of the ISS Plasma Contacting Units (PCUs), and to evaluate the extent of ISS charging in the absence of the PCUs.

Hydrocarbon Reservoir Identification in Volcanic Zone by using Magnetotelluric and Geochemistry Information

NASA Astrophysics Data System (ADS)

Firda, S. I.; Permadi, A. N.; Supriyanto; Suwardi, B. N.

2018-03-01

The resistivity of Magnetotelluric (MT) data show the resistivity mapping in the volcanic reservoir zone and the geochemistry information for confirm the reservoir and source rock formation. In this research, we used 132 data points divided with two line at exploration area. We used several steps to make the resistivity mapping. There are time series correction, crosspower correction, then inversion of Magnetotelluric (MT) data. Line-2 and line-3 show anomaly geological condition with Gabon fault. The geology structure from the resistivity mapping show the fault and the geological formation with the geological rock data mapping distribution. The geochemistry information show the maturity of source rock formation. According to core sample analysis information, we get the visual porosity for reservoir rock formation in several geological structure. Based on that, we make the geological modelling where the potential reservoir and the source rock around our interest area.

Auxin effects on ion transport in Chara corallina.

PubMed

Zhang, Suyun; de Boer, Albertus H; van Duijn, Bert

2016-04-01

The plant hormone auxin has been widely studied with regard to synthesis, transport, signaling and functions among the land plants while there is still a lack of knowledge about the possible role for auxin regulation mechanisms in algae with "plant-like" structures. Here we use the alga Chara corallina as a model to study aspects of auxin signaling. In this respect we measured auxin on membrane potential changes and different ion fluxes (K(+), H(+)) through the plasma membrane. Results showed that auxin, mainly IAA, could hyperpolarize the membrane potential of C. corallina internodal cells. Ion flux measurements showed that the auxin-induced membrane potential change may be based on the change of K(+) permeability and/or channel activity rather than through the activation of proton pumps as known in land plants. Copyright © 2016 Elsevier GmbH. All rights reserved.

Synthesis: Small library of hybrid scaffolds of benzothiazole having hydrazone and evaluation of their β-glucuronidase activity.

PubMed

Taha, Muhammad; Arbin, Mastura; Ahmat, Norizan; Imran, Syahrul; Rahim, Fazal

2018-04-01

Due to the great biological importance of β-glucuronidase inhibitors, here in this study, we have synthesized a library of novel benzothiazole derivatives (1-30), characterized by different spectroscopic methods and evaluated for β-glucuronidase inhibitory potential. Among the series sixteen compounds i.e.1-6, 8, 9, 11, 14, 15, 20-23 and 26 showed outstanding inhibitory potential with IC 50 value ranging in between 16.50 ± 0.26 and 59.45 ± 1.12 when compared with standard d-Saccharic acid 1,4-lactone (48.4 ± 1.25 µM). Except compound 8 and 23 all active analogs showed better potential than the standard. Structure activity relationship has been established. Copyright © 2018 Elsevier Inc. All rights reserved.

Hidden Entanglement and Unitarity at the Planck Scale

NASA Astrophysics Data System (ADS)

Arzano, Michele; Hamma, Alioscia; Severini, Simone

Attempts to go beyond the framework of local quantum field theory include scenarios in which the action of external symmetries on the quantum fields Hilbert space is deformed. We show how the Fock spaces of such theories exhibit a richer structure in their multi-particle sectors. When the deformation scale is proportional to the Planck energy, such new structure leads to the emergence of a "planckian" mode-entanglement, invisible to an observer that cannot probe the Planck scale. To the same observer, certain unitary processes would appear non-unitary. We show how entanglement transfer to the additional degrees of freedom can provide a potential way out of the black hole information paradox.

Dissociation of diatomic molecules and the exact-exchange Kohn-Sham potential: the case of LiF

NASA Astrophysics Data System (ADS)

Makmal, Adi; Kuemmel, Stephan; Kronik, Leeor

2011-03-01

The incorrect fractional-charge dissociation of stretched diatomic molecules, predicted by semi-local exchange-correlation functionals, is revisited. This difficulty can be overcome with asymptotically correct non-local potential operators, but should also be absent in exact Kohn-Sham theory, where the potential is local. Here, we show, for the illustrative case of the LiF dimer, that the exact-exchange local Kohn-Sham potential, constructed within the Krieger, Li, and Iafrate (KLI) approximation, can lead to binding energy and charge dissociation curves that are qualitatively correct. This correct behavior is traced back to a characteristic ``step'' structure in the local exchange potential and its relation to the Kohn-Sham eigenvalues is analyzed.

⁹⁹mTc/Re complexes bearing bisnitroimidazole or mononitroimidazole as potential bioreductive markers for tumor: synthesis, physicochemical characterization and biological evaluation.

PubMed

Mei, Lei; Wang, Yue; Chu, Taiwei

2012-12-01

Four monoamine-monoamide dithiol (MAMA) ligands containing two or one nitroimidazole moieties were synthesized and labeled with (99m)Tc (labeling yield > 95%). The proposed structures of (99m)Tc-complexes are identified by comparison with analogous Re-MAMA complexes. (99m)Tc-MAMA complexes show better physicochemical characters than (99m)TcO-(PnAO-1-(2-nitroimidazole)). Reduction potentials of nitro groups of the rhenium complexes are within the range for bioreductive compounds. As expected, biodistribution studies demonstrate that the 2-nitroimidazole complex shows better tumor-to-tissue ratios than 4-nitroimidazole analog for mononitroimidazole complexes, but not for MAMA-bisnitroimidazoles due to higher lipophilicity. Both the bisnitroimidazole compounds show rapider excretion, lower background activity in liver and higher tumor-to-tissue ratios than the mononitroimidazoles. Better biodistribution characteristic makes both the MAMA-bisnitroimidazole complexes, especially (99m)Tc-15, be potential tumor hypoxia marker. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Structural phase transition and 5f-electrons localization of PuSe explored by ab initio calculations

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

Cui Shouxin, E-mail: shouxincui@yahoo.co; Feng Wenxia; Hu Haiquan

2010-04-15

An investigation into the structural phase transformation, electronic and optical properties of PuSe under high pressure was conducted by using the full potential linearized augmented plane wave plus local orbitals (FP-LAPW+lo) method, in the presence and in the absence of spin-orbit coupling (SOC). Our results demonstrate that there exists a structural phase transition from rocksalt (B 1) structure to CsCl-type (B 2) structure at the transition pressure of 36.3 GPa (without SOC) and 51.3 GPa (with SOC). The electronic density of states (DOS) for PuSe show that the f-electrons of Pu are more localized and concentrated in a narrow peakmore » near the Fermi level, which is consistent with the experimental studies. The band structure shows that B 1-PuSe is metallic. A pseudogap appears around the Fermi level of the total density of states of B 1 phase PuSe, which may contribute to its stability. The calculated reflectivity R(omega) shows agreement with the available experimental results. Furthermore, the absorption spectrum, refractive index, extinction coefficient, energy-loss spectrum and dielectric function were calculated. The origin of the spectral peaks was interpreted based on the electronic structures. - Abstract: Graphical Abstract Legend (TOC Figure): 5f-electrons are more localized by the analysis of the density of states (SOC). The origin spectra peaks was interpreted based on electronic structures.« less

Studies of tin-transition metal-carbon and tin-cobalt-transition metal-carbon negative electrode materials prepared by mechanical attrition

NASA Astrophysics Data System (ADS)

Ferguson, P. P.; Martine, M. L.; George, A. E.; Dahn, J. R.

Samples of Sn 30TM 30C 40 and of Sn 30Co 15TM 15C 40, with TM = 3d transition metals, were prepared by vertical-axis attritor milling. The structure and performance of these samples were studied by X-ray diffraction (XRD) and by electrochemical testing. The XRD patterns of Sn 30TM 30C 40 show an amorphous-like diffraction pattern only for the sample with TM = Co. The other prepared samples show broadened Bragg peaks of their main starting material, along with an amorphous-like background, even after 32 h of milling. Samples with TM = Co and TM = Ni show stable differential capacity versus potential plots and stable cycling for at least 100 cycles with reversible capacities of 425 and 250 mAh g -1, respectively. All samples prepared with 15 at.% Co show good capacity retention for at least 100 cycles ranging from 270 mAh g -1 for samples with TM = Ni to 500 mAh g -1 for samples with TM = Ti. The differential capacity versus potential plots for all the prepared Sn 30Co 15TM 15C 40 samples show similar structure to that of Sn 30Co 30C 40 except when TM = Cu. This shows the possibility of preparing tin-based negative electrode materials using a combination of cobalt and TM, especially if one looks to reduce the cobalt content.

A nuclear-receptor-dependent phosphatidylcholine pathway with antidiabetic effects

USDA-ARS?s Scientific Manuscript database

Nuclear hormone receptors regulate diverse metabolic pathways and the orphan nuclear receptor LRH-1 (also known as NR5A2) regulates bile acid biosynthesis. Structural studies have identified phospholipids as potential LRH-1 ligands, but their functional relevance is unclear. Here we show that an unu...

Unidimensional Interpretations for Multidimensional Test Items

ERIC Educational Resources Information Center

Kahraman, Nilufer

2013-01-01

This article considers potential problems that can arise in estimating a unidimensional item response theory (IRT) model when some test items are multidimensional (i.e., show a complex factorial structure). More specifically, this study examines (1) the consequences of model misfit on IRT item parameter estimates due to unintended minor item-level…

AMPK activation by pterostilbene contributes to suppression of hepatic gluconeogenic gene expression and glucose production in H4IIE cells

USDA-ARS?s Scientific Manuscript database

Pterostilbene, a bioactive component of blueberries and grapes, shows structural similarity to resveratrol, and exhibits antioxidant, anti-inflammatory, anti-cancer, hypoglycemic, and cholesterol lowering effects. This study examined potential mechanisms that may contribute to its lipid- and glucose...

Synthesis of novel disulfide and sulfone hybrid scaffolds as potent β-glucuronidase inhibitor.

PubMed

Taha, Muhammad; Ismail, Nor Hadiani; Imran, Syahrul; Wadood, Abdul; Rahim, Fazal; Al Muqarrabin, Laode Muhammad Ramadhan; Zaki, Hamizah Mohd; Ahmat, Norizan; Nasir, Abdul; Khan, Fahad

2016-10-01

Novel series of disulfide and sulfone hybrid analogs (1-20) were synthesized and characterized through EI-MS and (1)H NMR and evaluated for β-glucuronidase inhibitory potential. All synthesized analogs except 13 and 15 showed excellent β-glucuronidase inhibitory potential with IC50 value ranging in between 2.20-88.16μM as compared to standard d-saccharic acid 1,4 lactone (48.4±1.25μM). Analogs 19, 16, 4, 1, 17, 6, 10, 3, 18, 2, 11, 14 and 5 showed many fold potent activity against β-glucuronidase inhibitor. Structure activity relationship showed that substitution of electron withdrawing groups at ortho as well as para position on phenyl ring increase potency. Electron withdrawing groups at meta position on phenyl ring showed slightly low potency as compared to ortho and para position. The binding interactions were confirmed through molecular docking studies. Copyright © 2016 Elsevier Inc. All rights reserved.

SYNTHESIS AND STUDY OF HALOGENATED BENZYLAMIDES OF SOME ISOCYCLIC AND HETEROCYCLIC ACIDS AS POTENTIAL ANTICONVULSANTS.

PubMed

Strupińska, Marzanna; Rostafińska-Suchar, Grażyna; Pirianowicz-Chaber, Elżbieta; Grabczuk, Mateusz; Józwenko, Magdalena; Kowalczyk, Hubert; Szuba, Joanna; Wójcicka, Monika; Chen, Tracy; Mazurek, Aleksander P

2015-01-01

A series of potential anticonvulsants have been synthesized. There are eight fluorobenzylamides and three chlorobenzylamides of isocyclic or heterocyclic acids. Two not halogenated benzylamides were also synthesized to compare the effect of halogenation. The aim of the research performed was to evaluate whether halogenation of the mother structure is able to improve its anticonvulsant activity. The compounds were tested in Anticonvulsant Screening Project (ASP) of Antiepileptic Drug Development Program (ADDP) of NIH. Compound 1 showed MES ED50 = 80.32 mg/kg, PI = 3.16. Compound 7 showed CKM ED50 = 56.72 mg/kg. Compound 8 showed MES ED50 = 34.23 mg/kg and scPTZ ED50 > 300 mg/kg, PI = 8.53.Compound 13 showed 6Hz ED50 = 78.96, PI = 3.37. The results indicate that fluorination does not improve activity, whereas chlorination in our experiment even reduces it.

Quasibound states in a triple Gaussian potential

NASA Astrophysics Data System (ADS)

Reichl, L. E.; Porter, Max D.

2018-04-01

We derive the transmission probabilities and delay times, and identify quasibound state structures in an open quantum system consisting of three Gaussian potential energy peaks, a system whose classical scattering dynamics we show to be chaotic. Such open quantum systems can serve as models for nanoscale quantum devices and their wave dynamics are similar to electromagnetic wave dynamics in optical microcavities. We use a quantum web to determine energy regimes for which the system exhibits the quantum manifestations of chaos, and we show that the classical scattering dynamics contains a significant amount of chaos. We also derive an exact expression for the non-Hermitian Hamiltonian whose eigenvalues give quasibound state energies and lifetimes of the system.

Cytotoxicity of ZnO Nanoparticles Can Be Tailored by Modifying Their Surface Structure: A Green Chemistry Approach for Safer Nanomaterials

PubMed Central

2015-01-01

ZnO nanoparticles (NP) are extensively used in numerous nanotechnology applications; however, they also happen to be one of the most toxic nanomaterials. This raises significant environmental and health concerns and calls for the need to develop new synthetic approaches to produce safer ZnO NP, while preserving their attractive optical, electronic, and structural properties. In this work, we demonstrate that the cytotoxicity of ZnO NP can be tailored by modifying their surface-bound chemical groups, while maintaining the core ZnO structure and related properties. Two equally sized (9.26 ± 0.11 nm) ZnO NP samples were synthesized from the same zinc acetate precursor using a forced hydrolysis process, and their surface chemical structures were modified by using different reaction solvents. X-ray diffraction and optical studies showed that the lattice parameters, optical properties, and band gap (3.44 eV) of the two ZnO NP samples were similar. However, FTIR spectroscopy showed significant differences in the surface structures and surface-bound chemical groups. This led to major differences in the zeta potential, hydrodynamic size, photocatalytic rate constant, and more importantly, their cytotoxic effects on Hut-78 cancer cells. The ZnO NP sample with the higher zeta potential and catalytic activity displayed a 1.5-fold stronger cytotoxic effect on cancer cells. These results suggest that by modifying the synthesis parameters/conditions and the surface chemical structures of the nanocrystals, their surface charge density, catalytic activity, and cytotoxicity can be tailored. This provides a green chemistry approach to produce safer ZnO NP. PMID:25068096

Exchange potential from the common energy denominator approximation for the Kohn-Sham Green's function: Application to (hyper)polarizabilities of molecular chains

NASA Astrophysics Data System (ADS)

Grüning, M.; Gritsenko, O. V.; Baerends, E. J.

2002-04-01

An approximate Kohn-Sham (KS) exchange potential vxσCEDA is developed, based on the common energy denominator approximation (CEDA) for the static orbital Green's function, which preserves the essential structure of the density response function. vxσCEDA is an explicit functional of the occupied KS orbitals, which has the Slater vSσ and response vrespσCEDA potentials as its components. The latter exhibits the characteristic step structure with "diagonal" contributions from the orbital densities |ψiσ|2, as well as "off-diagonal" ones from the occupied-occupied orbital products ψiσψj(≠1)σ*. Comparison of the results of atomic and molecular ground-state CEDA calculations with those of the Krieger-Li-Iafrate (KLI), exact exchange (EXX), and Hartree-Fock (HF) methods show, that both KLI and CEDA potentials can be considered as very good analytical "closure approximations" to the exact KS exchange potential. The total CEDA and KLI energies nearly coincide with the EXX ones and the corresponding orbital energies ɛiσ are rather close to each other for the light atoms and small molecules considered. The CEDA, KLI, EXX-ɛiσ values provide the qualitatively correct order of ionizations and they give an estimate of VIPs comparable to that of the HF Koopmans' theorem. However, the additional off-diagonal orbital structure of vxσCEDA appears to be essential for the calculated response properties of molecular chains. KLI already considerably improves the calculated (hyper)polarizabilities of the prototype hydrogen chains Hn over local density approximation (LDA) and standard generalized gradient approximations (GGAs), while the CEDA results are definitely an improvement over the KLI ones. The reasons of this success are the specific orbital structures of the CEDA and KLI response potentials, which produce in an external field an ultranonlocal field-counteracting exchange potential.

Recent Progress of Microfluidics in Translational Applications.

PubMed

Liu, Zongbin; Han, Xin; Qin, Lidong

2016-04-20

Microfluidics, featuring microfabricated structures, is a technology for manipulating fluids at the micrometer scale. The small dimension and flexibility of microfluidic systems are ideal for mimicking molecular and cellular microenvironment, and show great potential in translational research and development. Here, the recent progress of microfluidics in biological and biomedical applications, including molecular analysis, cellular analysis, and chip-based material delivery and biomimetic design is presented. The potential future developments in the translational microfluidics field are also discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perspective: n-type oxide thermoelectrics via visual search strategies

DOE PAGES

Xing, Guangzong; Sun, Jifeng; Ong, Khuong P.; ...

2016-02-12

We discuss and present search strategies for finding new thermoelectric compositions based on first principles electronic structure and transport calculations. We illustrate them by application to a search for potential n-type oxide thermoelectric materials. This includes a screen based on visualization of electronic energy isosurfaces. Lastly, we report compounds that show potential as thermoelectric materials along with detailed properties, including SrTiO 3, which is a known thermoelectric, and appropriately doped KNbO 3 and rutile TiO 2.

Ab initio SCF calculations on the potential energy surface of potassium cyanide (KCN)

NASA Astrophysics Data System (ADS)

Wormer, Paul E. S.; Tennyson, Jonathan

1981-08-01

The potential energy surface of KCN has been generated by ab initio SCF calculations in the region of equilibrium bond distances. An analytic representation of the surface is presented. The calculations show that the bonding between K and CN is ionic, and that the structure of KCN is triangular, which confirms recent experimental findings. The computed geometry is &KCN = 62.4°, rCK = 5.492a0, and rCN = 2.186a0.

Perspective: n-type oxide thermoelectrics via visual search strategies

NASA Astrophysics Data System (ADS)

Xing, Guangzong; Sun, Jifeng; Ong, Khuong P.; Fan, Xiaofeng; Zheng, Weitao; Singh, David J.

2016-05-01

We discuss and present search strategies for finding new thermoelectric compositions based on first principles electronic structure and transport calculations. We illustrate them by application to a search for potential n-type oxide thermoelectric materials. This includes a screen based on visualization of electronic energy isosurfaces. We report compounds that show potential as thermoelectric materials along with detailed properties, including SrTiO3, which is a known thermoelectric, and appropriately doped KNbO3 and rutile TiO2.

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor

PubMed Central

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

Context: A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. Objective: We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. Materials and Methods: CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. Results: The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. Discussion and Conclusion: The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI. PMID:28781485

Tunable electronic properties of CdS nanoribbons by edge effects

NASA Astrophysics Data System (ADS)

Ma, Ruican; Zhao, Hui; Wang, Yaping; Ji, Weixiao; Li, Ping

2017-08-01

Based on first-principles calculations, the electronic properties of Cadmium Sulfide nanoribbons (CdSNRs) have been studied with both zigzag (Z-CdSNRs) and armchair shaped edges (A-CdSNRs). For Z-CdSNRs, the structures with both edges decorated by H or F atoms show half-metallic or semiconducting properties, respectively. Only S-dominated edge decorated by H/F atoms, Z-CdSNRs show metallic properties. Only Cd-dominated edge is hydrogenated, Z-CdSNRs can be observed from a metallic to half metallic transition. But instead of fluorinated, the structures show the metallic properties. However, either edge or both edges are hydrogenated or fluorinated, A-CdSNRs exhibit semiconducting properties, and their band gap decreases monotonically with increasing ribbons width (n). When a stress is applied on the half-hydrogenated A-CdSNRs, their band gap displays a steady decrease trend. Moreover, A-CdSNRs are more stable than Z-CdSNRs, while the hydrogenated systems are more stable than fluorinated systems. The results show that different structures of CdSNRs decorated with the different edges can play different nature as semiconducting - half-metallic - metallic properties. The research has important theoretical significance for the electronic design and assembly of CdSNRs structures, and provides a new perspective for the potential application of CdSNRs in nanoelectronics.

Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.

PubMed

Zhou, Zhanping; Liu, Yang; Chang, Zhenying; Wang, Huilin; Leier, André; Marquez-Lago, Tatiana T; Ma, Yanhe; Li, Jian; Song, Jiangning

2017-04-01

Biotechnological applications of microbial pectate lyases (Pels) in plant fiber processing are promising, eco-friendly substitutes for conventional chemical degumming processes. However, to potentiate the enzymes' use for industrial applications, resolving the molecular structure to elucidate catalytic mechanisms becomes necessary. In this manuscript, we report the high resolution (1.45 Å) crystal structure of pectate lyase (pelN) from Paenibacillus sp. 0602 in apo form. Through sequence alignment and structural superposition with other members of the polysaccharide lyase (PL) family 1 (PL1), we determined that pelN shares the characteristic right-handed β-helix and is structurally similar to other members of the PL1 family, while exhibiting key differences in terms of catalytic and substrate binding residues. Then, based on information from structure alignments with other PLs, we engineered a novel pelN. Our rational design yielded a pelN mutant with a temperature for enzymatic activity optimally shifted from 67.5 to 60 °C. Most importantly, this pelN mutant displayed both higher specific activity and ramie fiber degumming ability when compared with the wild-type enzyme. Altogether, our rational design method shows great potential for industrial applications. Moreover, we expect the reported high-resolution crystal structure to provide a solid foundation for future rational, structure-based engineering of genetically enhanced pelNs.

Verbal and non-verbal intelligence changes in the teenage brain.

PubMed

Ramsden, Sue; Richardson, Fiona M; Josse, Goulven; Thomas, Michael S C; Ellis, Caroline; Shakeshaft, Clare; Seghier, Mohamed L; Price, Cathy J

2011-10-19

Intelligence quotient (IQ) is a standardized measure of human intellectual capacity that takes into account a wide range of cognitive skills. IQ is generally considered to be stable across the lifespan, with scores at one time point used to predict educational achievement and employment prospects in later years. Neuroimaging allows us to test whether unexpected longitudinal fluctuations in measured IQ are related to brain development. Here we show that verbal and non-verbal IQ can rise or fall in the teenage years, with these changes in performance validated by their close correlation with changes in local brain structure. A combination of structural and functional imaging showed that verbal IQ changed with grey matter in a region that was activated by speech, whereas non-verbal IQ changed with grey matter in a region that was activated by finger movements. By using longitudinal assessments of the same individuals, we obviated the many sources of variation in brain structure that confound cross-sectional studies. This allowed us to dissociate neural markers for the two types of IQ and to show that general verbal and non-verbal abilities are closely linked to the sensorimotor skills involved in learning. More generally, our results emphasize the possibility that an individual's intellectual capacity relative to their peers can decrease or increase in the teenage years. This would be encouraging to those whose intellectual potential may improve, and would be a warning that early achievers may not maintain their potential.

Passivation dynamics in the anisotropic deposition and stripping of bulk magnesium electrodes during electrochemical cycling

DOE PAGES

Wetzel, David J.; Malone, Marvin A.; Haasch, Richard T.; ...

2015-08-10

Rechargeable magnesium (Mg) batteries show promise for use as a next generation technology for high-density energy storage, though little is known about the Mg anode solid electrolyte interphase and its implications for the performance and durability of a Mg-based battery. We explore in this report passivation effects engendered during the electrochemical cycling of a bulk Mg anode, characterizing their influences during metal deposition and dissolution in a simple, nonaqueous, Grignard electrolyte solution (ethylmagnesium bromide, EtMgBr, in tetrahydrofuran). Scanning electron microscopy images of Mg foil working electrodes after electrochemical polarization to dissolution potentials show the formation of corrosion pits. The pitmore » densities so evidenced are markedly potential-dependent. When the Mg working electrode is cycled both potentiostatically and galvanostatically in EtMgBr these pits, formed due to passive layer breakdown, act as the foci for subsequent electrochemical activity. Detailed microscopy, diffraction, and spectroscopic data show that further passivation and corrosion results in the anisotropic stripping of the Mg {0001} plane, leaving thin oxide-comprising passivated side wall structures that demark the {0001} fiber texture of the etched Mg grains. Upon long-term cycling, oxide side walls formed due to the pronounced crystallographic anisotropy of the anodic stripping processes, leading to complex overlay anisotropic, columnar structures, exceeding 50 μm in height. Finally, the passive responses mediating the growth of these structures appear to be an intrinsic feature of the electrochemical growth and dissolution of Mg using this electrolyte.« less

Passivation dynamics in the anisotropic deposition and stripping of bulk magnesium electrodes during electrochemical cycling

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

Wetzel, David J.; Malone, Marvin A.; Haasch, Richard T.

Rechargeable magnesium (Mg) batteries show promise for use as a next generation technology for high-density energy storage, though little is known about the Mg anode solid electrolyte interphase and its implications for the performance and durability of a Mg-based battery. We explore in this report passivation effects engendered during the electrochemical cycling of a bulk Mg anode, characterizing their influences during metal deposition and dissolution in a simple, nonaqueous, Grignard electrolyte solution (ethylmagnesium bromide, EtMgBr, in tetrahydrofuran). Scanning electron microscopy images of Mg foil working electrodes after electrochemical polarization to dissolution potentials show the formation of corrosion pits. The pitmore » densities so evidenced are markedly potential-dependent. When the Mg working electrode is cycled both potentiostatically and galvanostatically in EtMgBr these pits, formed due to passive layer breakdown, act as the foci for subsequent electrochemical activity. Detailed microscopy, diffraction, and spectroscopic data show that further passivation and corrosion results in the anisotropic stripping of the Mg {0001} plane, leaving thin oxide-comprising passivated side wall structures that demark the {0001} fiber texture of the etched Mg grains. Upon long-term cycling, oxide side walls formed due to the pronounced crystallographic anisotropy of the anodic stripping processes, leading to complex overlay anisotropic, columnar structures, exceeding 50 μm in height. Finally, the passive responses mediating the growth of these structures appear to be an intrinsic feature of the electrochemical growth and dissolution of Mg using this electrolyte.« less

Passivation Dynamics in the Anisotropic Deposition and Stripping of Bulk Magnesium Electrodes During Electrochemical Cycling.

PubMed

Wetzel, David J; Malone, Marvin A; Haasch, Richard T; Meng, Yifei; Vieker, Henning; Hahn, Nathan T; Gölzhäuser, Armin; Zuo, Jian-Min; Zavadil, Kevin R; Gewirth, Andrew A; Nuzzo, Ralph G

2015-08-26

Although rechargeable magnesium (Mg) batteries show promise for use as a next generation technology for high-density energy storage, little is known about the Mg anode solid electrolyte interphase and its implications for the performance and durability of a Mg-based battery. We explore in this report passivation effects engendered during the electrochemical cycling of a bulk Mg anode, characterizing their influences during metal deposition and dissolution in a simple, nonaqueous, Grignard electrolyte solution (ethylmagnesium bromide, EtMgBr, in tetrahydrofuran). Scanning electron microscopy images of Mg foil working electrodes after electrochemical polarization to dissolution potentials show the formation of corrosion pits. The pit densities so evidenced are markedly potential-dependent. When the Mg working electrode is cycled both potentiostatically and galvanostatically in EtMgBr these pits, formed due to passive layer breakdown, act as the foci for subsequent electrochemical activity. Detailed microscopy, diffraction, and spectroscopic data show that further passivation and corrosion results in the anisotropic stripping of the Mg {0001} plane, leaving thin oxide-comprising passivated side wall structures that demark the {0001} fiber texture of the etched Mg grains. Upon long-term cycling, oxide side walls formed due to the pronounced crystallographic anisotropy of the anodic stripping processes, leading to complex overlay anisotropic, columnar structures, exceeding 50 μm in height. The passive responses mediating the growth of these structures appear to be an intrinsic feature of the electrochemical growth and dissolution of Mg using this electrolyte.

[Effects of biochar application on the abundance and structure of ammonia-oxidizer communities in coal-mining area.

PubMed

Liu, Yuan; Zhu, Ji Rong; Wu, Yu Chen; Shu, Liang Zuo

2017-10-01

As a new type of soil amendment, biochar can effectively improve soil fertility, structure and soil nitrogen transformation. We studied the effects of biochar application on soil properties, abundance and community structure of ammonia oxidizer in coal-mining area. The results showed that the biochar application significantly increased contents of soil NH4+-N, total nitrogen, available phosphorus and potassium. Compared with the control, no change in the abundance of ammonia-oxidizing archaea (AOA) was found under biochar treatment, but there was a significant increase in the abundance of ammonia-oxidizing bacteria (AOB). The analysis of T-RFLP profiles showed that biochar significantly increased the diversity indexes of AOA and AOB, and altered the community structure of both AOA and AOB. Improved soil nutrients as well as increased abundance and diversity of ammonia-oxidizing community to some extent indicated the potential of biochar application in reclamation of coal-mining area soil.

Ultrasound effects on the degradation kinetics, structure, and antioxidant activity of sea cucumber fucoidan.

PubMed

Guo, Xin; Ye, Xingqian; Sun, Yujing; Wu, Dan; Wu, Nian; Hu, Yaqin; Chen, Shiguo

2014-02-05

The effects of ultrasound on the molecular weight, structure, and antioxidant potential of a fucoidan found in Isostichopus badionotus were investigated. The results showed the molecular weight (Mw) of fucoidan decreased obviously after ultrasound treatment. Higher ultrasonic intensity, lower temperature, and lower fucoidan concentrations led to a more effective sonochemical effect. The kinetic model for fucoidan degradation fitted to 1/M(wt)-1/M(w0) = kt at the tested temperature. The optimized degradation conditions by response surface methodology (RSM) were temperature, 12 °C, and intensity, 508 W/cm². Structural analysis by FTIR and NMR indicated the fucoidan kept the linear tetrasaccharide repeating units as the original polysaccharides after the ultrasound treatment, with only slight destruction of the middle nonsulfated fucose units. Antioxidant activity assay showed the antioxidant activity was slightly improved by the ultrasound treatment. The results suggested that ultrasound treatment is an effective approach to decrease the M(w) of fucoidan with only minor structural destruction.

Inkjet Printing Based Mono-layered Photonic Crystal Patterning for Anti-counterfeiting Structural Colors.

PubMed

Nam, Hyunmoon; Song, Kyungjun; Ha, Dogyeong; Kim, Taesung

2016-08-04

Photonic crystal structures can be created to manipulate electromagnetic waves so that many studies have focused on designing photonic band-gaps for various applications including sensors, LEDs, lasers, and optical fibers. Here, we show that mono-layered, self-assembled photonic crystals (SAPCs) fabricated by using an inkjet printer exhibit extremely weak structural colors and multiple colorful holograms so that they can be utilized in anti-counterfeit measures. We demonstrate that SAPC patterns on a white background are covert under daylight, such that pattern detection can be avoided, but they become overt in a simple manner under strong illumination with smartphone flash light and/or on a black background, showing remarkable potential for anti-counterfeit techniques. Besides, we demonstrate that SAPCs yield different RGB histograms that depend on viewing angles and pattern densities, thus enhancing their cryptographic capabilities. Hence, the structural colorations designed by inkjet printers would not only produce optical holograms for the simple authentication of many items and products but also enable a high-secure anti-counterfeit technique.

Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain.

PubMed

Ali, Anjum A; Dale, Anders M; Badea, Alexandra; Johnson, G Allan

2005-08-15

We present the automated segmentation of magnetic resonance microscopy (MRM) images of the C57BL/6J mouse brain into 21 neuroanatomical structures, including the ventricular system, corpus callosum, hippocampus, caudate putamen, inferior colliculus, internal capsule, globus pallidus, and substantia nigra. The segmentation algorithm operates on multispectral, three-dimensional (3D) MR data acquired at 90-microm isotropic resolution. Probabilistic information used in the segmentation is extracted from training datasets of T2-weighted, proton density-weighted, and diffusion-weighted acquisitions. Spatial information is employed in the form of prior probabilities of occurrence of a structure at a location (location priors) and the pairwise probabilities between structures (contextual priors). Validation using standard morphometry indices shows good consistency between automatically segmented and manually traced data. Results achieved in the mouse brain are comparable with those achieved in human brain studies using similar techniques. The segmentation algorithm shows excellent potential for routine morphological phenotyping of mouse models.

Negative pressure driven phase transformation in Sr doped SmCoO₃.

PubMed

Arshad Farhan, M; Javed Akhtar, M

2010-02-24

Atomistic computer simulation techniques based on energy minimization procedures are utilized for the structural investigation of perovskite-type SmCoO(3). A reliable potential model is derived which reproduces both cubic as well as orthorhombic phases of SmCoO(3). We observe a negative chemical pressure induced structural phase transformation from distorted perovskite (orthorhombic) to perfect perovskite (cubic) due to the substitution of Sr(2 + ) at the Sm(3 + ) sites. However, external hydrostatic pressure shows isotropic compression and no pressure-induced structural transformation is observed up to 100 GPa. To maintain the electroneutrality of the system, charge compensation is through oxygen vacancies which results in the brownmillerite-type structure. A defect model is proposed, which is consistent with experimental results. The solution energies for divalent and trivalent cations are also calculated. These results show that the cations having ionic radii less than 0.75 Å will occupy the Co sites and those with ionic radii larger than 0.75 Å will substitute at the Sm sites.

Molecules Without Atoms

NASA Astrophysics Data System (ADS)

Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

Inkjet Printing Based Mono-layered Photonic Crystal Patterning for Anti-counterfeiting Structural Colors

NASA Astrophysics Data System (ADS)

Nam, Hyunmoon; Song, Kyungjun; Ha, Dogyeong; Kim, Taesung

2016-08-01

Photonic crystal structures can be created to manipulate electromagnetic waves so that many studies have focused on designing photonic band-gaps for various applications including sensors, LEDs, lasers, and optical fibers. Here, we show that mono-layered, self-assembled photonic crystals (SAPCs) fabricated by using an inkjet printer exhibit extremely weak structural colors and multiple colorful holograms so that they can be utilized in anti-counterfeit measures. We demonstrate that SAPC patterns on a white background are covert under daylight, such that pattern detection can be avoided, but they become overt in a simple manner under strong illumination with smartphone flash light and/or on a black background, showing remarkable potential for anti-counterfeit techniques. Besides, we demonstrate that SAPCs yield different RGB histograms that depend on viewing angles and pattern densities, thus enhancing their cryptographic capabilities. Hence, the structural colorations designed by inkjet printers would not only produce optical holograms for the simple authentication of many items and products but also enable a high-secure anti-counterfeit technique.

Molecular and electronic structure of terminal and alkali metal-capped uranium(V) nitride complexes

PubMed Central

King, David M.; Cleaves, Peter A.; Wooles, Ashley J.; Gardner, Benedict M.; Chilton, Nicholas F.; Tuna, Floriana; Lewis, William; McInnes, Eric J. L.; Liddle, Stephen T.

2016-01-01

Determining the electronic structure of actinide complexes is intrinsically challenging because inter-electronic repulsion, crystal field, and spin–orbit coupling effects can be of similar magnitude. Moreover, such efforts have been hampered by the lack of structurally analogous families of complexes to study. Here we report an improved method to U≡N triple bonds, and assemble a family of uranium(V) nitrides. Along with an isoelectronic oxo, we quantify the electronic structure of this 5f1 family by magnetometry, optical and electron paramagnetic resonance (EPR) spectroscopies and modelling. Thus, we define the relative importance of the spin–orbit and crystal field interactions, and explain the experimentally observed different ground states. We find optical absorption linewidths give a potential tool to identify spin–orbit coupled states, and show measurement of UV···UV super-exchange coupling in dimers by EPR. We show that observed slow magnetic relaxation occurs via two-phonon processes, with no obvious correlation to the crystal field. PMID:27996007

Acceleration of on-axis and ring-shaped electron beams in wakefields driven by Laguerre-Gaussian pulses

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

Zhang, Guo-Bo; Key Laboratory for Laser Plasmas; Chen, Min, E-mail: minchen@sjtu.edu.cn, E-mail: yanyunma@126.com

2016-03-14

The acceleration of electron beams with multiple transverse structures in wakefields driven by Laguerre-Gaussian pulses has been studied through three-dimensional (3D) particle-in-cell simulations. Under different laser-plasma conditions, the wakefield shows different transverse structures. In general cases, the wakefield shows a donut-like structure and it accelerates the ring-shaped hollow electron beam. When a lower plasma density or a smaller laser spot size is used, besides the donut-like wakefield, a central bell-like wakefield can also be excited. The wake sets in the center of the donut-like wake. In this case, both a central on-axis electron beam and a ring-shaped electron beam aremore » simultaneously accelerated. Further, reducing the plasma density or laser spot size leads to an on-axis electron beam acceleration only. The research is beneficial for some potential applications requiring special pulse beam structures, such as positron acceleration and collimation.« less

Large Thermal Motion in Halide Perovskites

DOE PAGES

Tyson, T. A.; Gao, W.; Chen, Y. -S.; ...

2017-08-24

Solar cells based on hybrid perovskites have shown high efficiency while possessing simple processing methods. To gain a fundamental understanding of their properties on an atomic level, we investigate single crystals of CH 3NH 3PbI 3 with a narrow transition (~5 K) near 327 K. Temperature dependent structural measurements reveal a persistent tetragonal structure with smooth changes in the atomic displacement parameters (ADPs) on crossing T*. We show that the ADPs for I ions yield extended flat regions in the potential wells consistent with the measured large thermal expansion parameter. Molecular dynamics simulations reveal that this material exhibits significant asymmetriesmore » in the Pb-I pair distribution functions. We also show that the intrinsically enhanced freedom of motion of the iodine atoms enables large deformations. This flexibility (softness) of the atomic structure results in highly localized atomic relaxation about defects and hence accounts for both the high carrier mobility as well as the structural instability.« less

Rheological properties in relation to molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2018-07-15

Quinoa starch granules are small (~0.5 - 3μm) with potentials for some food and other applications. To better exploit it as a new starch resource, this study investigates the steady shear and dynamic oscillatory properties of 9 quinoa starches varying in composition and structure. Steady shear analysis shows that the flow curves could be well described by 4 selected mathematic models. Temperature sweep analysis reveals that the quinoa starch encounters a 4-stage process including 2 phase transitions. Structure-function relationship analysis showed that composition as well as unit and internal chain length distribution of amylopectin have significant impact on the rheological properties (e.g., G' at 90°C) of quinoa starch. The roles of some individual unit chains and super-long unit chains of amylopectin in determining the rheological properties of quinoa starch were revealed. This study may stimulate further interest in understanding the structural basis of starch rheology. Copyright © 2018 Elsevier B.V. All rights reserved.

Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes

NASA Astrophysics Data System (ADS)

Kaushik, Aman C.; Kumar, Sanjay; Wei, Dong Q.; Sahi, Shakti

2018-02-01

GPR142 (G protein receptor 142) is a novel orphan GPCR (G protein coupled receptor) belonging to ‘Class A’ of GPCR family and expressed in beta cells of pancreas. In this study, we reported the structure based virtual screening to identify the hit compounds which can be developed as leads for potential agonists. The results were validated through induced fit docking, pharmacophore modeling and system biology approaches. Since, there is no solved crystal structure of GPR142, we attempted to predict the 3D structure followed by validation and then identification of active site using threading and ab initio methods. Also, structure based virtual screening was performed against a total of 1171519 compounds from different libraries and only top 20 best hit compounds were screened and analyzed. Moreover, the biochemical pathway of GPR142 complex with screened compound2 was also designed and compared with experimental data. Interestingly, compound2 showed an increase in insulin production via Gq mediated signaling pathway suggesting the possible role of novel GPR142 agonists in therapy against type 2 diabetes.

The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.

PubMed

Iwata, Momi; Lee, Yang; Yamashita, Tetsuo; Yagi, Takao; Iwata, So; Cameron, Alexander D; Maher, Megan J

2012-09-18

Bioenergy is efficiently produced in the mitochondria by the respiratory system consisting of complexes I-V. In various organisms, complex I can be replaced by the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the transfer of an electron from NADH via FAD to quinone, without proton pumping. The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the matrix. A number of studies have investigated the potential use of Ndi1 as a therapeutic agent against complex I disorders, and the NDH-2 enzymes have emerged as potential therapeutic targets for treatments against the causative agents of malaria and tuberculosis. Here we present the crystal structures of Ndi1 in its substrate-free, NAD(+)- and ubiquinone- (UQ2) complexed states. The structures reveal that Ndi1 is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure. Crucially, the structures of the Ndi1-NAD(+) and Ndi1-UQ2 complexes show overlapping binding sites for the NAD(+) and quinone substrates.

Application and Optimization of Stiffness Abruption Structures for Pressure Sensors with High Sensitivity and Anti-Overload Ability

PubMed Central

Xu, Tingzhong; Lu, Dejiang; Zhao, Libo; Jiang, Zhuangde; Wang, Hongyan; Guo, Xin; Li, Zhikang; Zhou, Xiangyang; Zhao, Yulong

2017-01-01

The influence of diaphragm bending stiffness distribution on the stress concentration characteristics of a pressure sensing chip had been analyzed and discussed systematically. According to the analysis, a novel peninsula-island-based diaphragm structure was presented and applied to two differenet diaphragm shapes as sensing chips for pressure sensors. By well-designed bending stiffness distribution of the diaphragm, the elastic potential energy induced by diaphragm deformation was concentrated above the gap position, which remarkably increased the sensitivity of the sensing chip. An optimization method and the distribution pattern of the peninsula-island based diaphragm structure were also discussed. Two kinds of sensing chips combined with the peninsula-island structures distributing along the side edge and diagonal directions of rectangular diaphragm were fabricated and analyzed. By bonding the sensing chips with anti-overload glass bases, these two sensing chips were demonstrated by testing to achieve not only high sensitivity, but also good anti-overload ability. The experimental results showed that the proposed structures had the potential to measure ultra-low absolute pressures with high sensitivity and good anti-overload ability in an atmospheric environment. PMID:28846599

[Characterization of microbial community in produced water from a petroleum reservoir subjected to alkali-surfactant-polymer ASP flooding].

PubMed

Hao, Qin Qin; Shi, Rong Jiu; Hao, Jin Sheng; Zhao, Jin Yi; Li, Guo Qiao; Zhao, Feng; Han, Si Qin; Zhang, Ying

2017-10-01

Injection of alkali, surfactant and polymer (ASP) into oil reservoir can substantially increase oil recovery compared with water-flooding strategy. However, the effects of these agents on the microbial diversity and community structure, which is important for water management and corrosion control in oil industry, are hitherto poorly understood. Here, we disclosed the microbial diversity and community structure in the produced water collected from four producing wells of an ASP-flooded oilfield at Daqing, China, using high-throughput sequencing technique. Results showed that the average pH in produced water was as high as 9.65. The microbial diversity varied from well to well, and the Shannon diversity index was between 2.00 to 3.56. The Proteobacteria (85.5%-98.3%), γ-proteobacteria (83.7%-97.8%), and alkaliphilic Nitrincola (51.8%-82.5%) were the most dominant phylogenetic taxa at the phylum, class, and genus levels, respectively. A total of 12 potentially sulfide-producing genera were detected, and the most abundant taxon was Sulfurospirillum (0.4%-7.4%). The microbial community of ASP-flooded petroleum reservoir was distinct, showing an alkaliphilic or alkalitolerant potential; a reduced diversity and more simple structure were observed compared with those of the water-flooded petroleum reservoirs that were previously reported.

Interfacial Effects on the Band Edges of Functionalized Si Surfaces in Liquid Water

DOE PAGES

Pham, Tuan Anh; Lee, Donghwa; Schwegler, Eric; ...

2014-11-17

By combining ab initio molecular dynamics simulations and many-body perturbation theory calculations of electronic energy levels, we determined the band edge positions of functionalized Si(111) surfaces in the presence of liquid water, with respect to vacuum and to water redox potentials. We considered surface terminations commonly used for Si photoelectrodes in water splitting experiments. We found that, when exposed to water, the semiconductor band edges were shifted by approximately 0.5 eV in the case of hydrophobic surfaces, irrespective of the termination. The effect of the liquid on band edge positions of hydrophilic surfaces was much more significant and determined bymore » a complex combination of structural and electronic effects. These include structural rearrangements of the semiconductor surfaces in the presence of water, changes in the orientation of interfacial water molecules with respect to the bulk liquid, and charge transfer at the interfaces, between the solid and the liquid. Our results showed that the use of many-body perturbation theory is key to obtain results in agreement with experiments; they also showed that the use of simple computational schemes that neglect the detailed microscopic structure of the solid–liquid interface may lead to substantial errors in predicting the alignment between the solid band edges and water redox potentials.« less

Human hemoglobin structural and functional alterations and heme degradation upon interaction with benzene: A spectroscopic study.

PubMed

Hosseinzadeh, Reza; Moosavi-Movahedi, Ali Akbar

2016-03-15

Here, the effect of benzene on hemoglobin structure, stability and heme prosthetic group integrity was studied by different methods. These included UV-vis absorption spectrophotometry, normal and synchronous fluorescence techniques, and differential scanning calorimetry (DSC). Our results indicated that benzene has high hemolytic potential even at low concentrations. The UV-vis spectroscopic results demonstrated that benzene altered both the globin chain and the heme prosthetic group of hemoglobin increasing met- and deoxy-Hb, while decreasing oxy-Hb. However, with increasing benzene the concentration of all species decreased due to heme destruction. The spectrophotometric results show that benzene has a high potential for penetrating the hydrophobic pocket of hemoglobin. These results were consistent with the molecular docking simulation results of benzene-hHb. Aggregation and thermal denaturation studies show that the increased benzene concentration induced hemoglobin aggregation with a decrease in stability, which is consistent with the DSC results. Conventional fluorescence spectroscopy revealed that the heme degradation species were produced in the presence of benzene. The results of constant wavelength synchronous fluorescence spectroscopy (CWSFS) indicated that at least five heme-degraded species were produced. Together, our results indicated that benzene has adverse effects on hemoglobin structure and function, and heme degradation. Copyright © 2015 Elsevier B.V. All rights reserved.

Effect of total and pair configurational entropy in determining dynamics of supercooled liquids over a range of densities

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

Banerjee, Atreyee; Nandi, Manoj Kumar; Bhattacharyya, Sarika Maitra, E-mail: mb.sarika@ncl.res.in

2016-07-21

In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in thismore » paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al., Phys. Rev. Lett. 113, 225701 (2014)] and shows that they are generic in nature, independent of density.« less

Some properties of solid helium and helium nanoclusters using the effective HFD-like interaction potential: Adsorption and desorption inside carbon nanotube

NASA Astrophysics Data System (ADS)

Abbaspour, M.; Akbarzadeh, H.; Banihashemi, S. Z.; Sotoudeh, A.

2018-02-01

We have calculated the zero equation of state of solid helium using a two-body Hartree-Fock dispersion (HFD)-like potential from molecular dynamics (MD) simulation. To take many-body forces into account, our simple and accurate empirical expression is used with the HFD-like potential without requiring an expensive three-body calculation. This potential model also includes the quantum effects for helium at low temperatures. The results indicate that our effective HFD-like potential improves the prediction of the classical two-body results to get better agreement with experiment than many other two-body and three-body potentials of helium reported in the literature. We have also simulated the adsorption and desorption processes of the (He)55, (He)147, (He)309, (He)561, and (He)923 icosahedral nanoclusters confined into the different armchair and zigzag CNTs from 0 to 50 K using our effective model. We have observed an interesting phenomenon at 0 K for helium. The nanoclusters adsorb to the inner CNT wall as a melting process. But, the heavier noble gas clusters (such as Ne and Xe) show the different behavior than the He clusters. They form a multilayered solid structure into the CNT at zero temperature and adsorb into the inner wall of the CNT at higher temperatures. Our results for He clusters show that the absolute value of the adsorption energy increases as the size of the nanocluster increases. The desorption process begins at a certain temperature and represents itself by a jump in the configurational energy values. We have also investigated the structural and dynamical properties of the confined helium nanoclusters during the adsorption and desorption processes at different temperatures.

Topic Structure Affects Semantic Integration: Evidence from Event-Related Potentials

PubMed Central

Yang, Xiaohong; Chen, Xuhai; Chen, Shuang; Xu, Xiaoying; Yang, Yufang

2013-01-01

This study investigated whether semantic integration in discourse context could be influenced by topic structure using event-related brain potentials. Participants read discourses in which the last sentence contained a critical word that was either congruent or incongruent with the topic established in the first sentence. The intervening sentences between the first and the last sentence of the discourse either maintained or shifted the original topic. Results showed that incongruent words in topic-maintained discourses elicited an N400 effect that was broadly distributed over the scalp while those in topic-shifted discourses elicited an N400 effect that was lateralized to the right hemisphere and localized over central and posterior areas. Moreover, a late positivity effect was only elicited by incongruent words in topic-shifted discourses, but not in topic-maintained discourses. This suggests an important role for discourse structure in semantic integration, such that compared with topic-maintained discourses, the complexity of discourse structure in topic-shifted condition reduces the initial stage of semantic integration and enhances the later stage in which a mental representation is updated. PMID:24348994

Secretion of RNA-Containing Extracellular Vesicles by the Porcine Whipworm, Trichuris suis.

PubMed

Hansen, Eline Palm; Kringel, Helene; Williams, Andrew R; Nejsum, Peter

2015-06-01

Trichuris suis is a common parasitic helminth of pigs. As with many other parasites, T. suis ensures its own survival by evading host immune responses, but little is known about how this is achieved. MicroRNAs (miRNA) have been shown to be involved in various immunological processes by post-transcriptional regulation of specific genes, and the potential of using these molecules as biomarkers of disease is currently being examined. It has recently been shown that parasites may secrete extracellular structures such as exosomes and microvesicles, containing proteins and miRNA. The fusion of these structures with host cells has been demonstrated, and a role of exosome-derived miRNA in host gene regulation has been suggested. In the present study, we show that exosome- and microvesicular-like structures are secreted by T. suis L1 larvae and also demonstrate the presence of miRNA-sized RNA inside these structures. A potential role of these molecules in host-parasite interactions is suggested. In addition, an electron-dense layer covering the surface of the larvae was observed, which may play a function in host immune evasion.

DFT calculations on spectroscopic and structural properties of a NLO chromophore

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

2016-03-01

The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

Application of X-ray micro-CT for micro-structural characterization of APCVD deposited SiC coatings on graphite conduit.

PubMed

Agrawal, A K; Sarkar, P S; Singh, B; Kashyap, Y S; Rao, P T; Sinha, A

2016-02-01

SiC coatings are commonly used as oxidation protective materials in high-temperature applications. The operational performance of the coating depends on its microstructure and uniformity. This study explores the feasibility of applying tabletop X-ray micro-CT for the micro-structural characterization of SiC coating. The coating is deposited over the internal surface of pipe structured graphite fuel tube, which is a prototype of potential components of compact high-temperature reactor (CHTR). The coating is deposited using atmospheric pressure chemical vapor deposition (APCVD) and properties such as morphology, porosity, thickness variation are evaluated. Micro-structural differences in the coating caused by substrate distance from precursor inlet in a CVD reactor are also studied. The study finds micro-CT a potential tool for characterization of SiC coating during its future course of engineering. We show that depletion of reactants at larger distances causes development of larger pores in the coating, which affects its morphology, density and thickness. Copyright © 2015 Elsevier Ltd. All rights reserved.

Parametric Modelling of As-Built Beam Framed Structure in Bim Environment

NASA Astrophysics Data System (ADS)

Yang, X.; Koehl, M.; Grussenmeyer, P.

2017-02-01

A complete documentation and conservation of a historic timber roof requires the integration of geometry modelling, attributional and dynamic information management and results of structural analysis. Recently developed as-built Building Information Modelling (BIM) technique has the potential to provide a uniform platform, which provides possibility to integrate the traditional geometry modelling, parametric elements management and structural analysis together. The main objective of the project presented in this paper is to develop a parametric modelling tool for a timber roof structure whose elements are leaning and crossing beam frame. Since Autodesk Revit, as the typical BIM software, provides the platform for parametric modelling and information management, an API plugin, able to automatically create the parametric beam elements and link them together with strict relationship, was developed. The plugin under development is introduced in the paper, which can obtain the parametric beam model via Autodesk Revit API from total station points and terrestrial laser scanning data. The results show the potential of automatizing the parametric modelling by interactive API development in BIM environment. It also integrates the separate data processing and different platforms into the uniform Revit software.

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.

PubMed

Mittal, Jeetain; Best, Robert B

2010-08-04

The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Topic structure affects semantic integration: evidence from event-related potentials.

PubMed

Yang, Xiaohong; Chen, Xuhai; Chen, Shuang; Xu, Xiaoying; Yang, Yufang

2013-01-01

This study investigated whether semantic integration in discourse context could be influenced by topic structure using event-related brain potentials. Participants read discourses in which the last sentence contained a critical word that was either congruent or incongruent with the topic established in the first sentence. The intervening sentences between the first and the last sentence of the discourse either maintained or shifted the original topic. Results showed that incongruent words in topic-maintained discourses elicited an N400 effect that was broadly distributed over the scalp while those in topic-shifted discourses elicited an N400 effect that was lateralized to the right hemisphere and localized over central and posterior areas. Moreover, a late positivity effect was only elicited by incongruent words in topic-shifted discourses, but not in topic-maintained discourses. This suggests an important role for discourse structure in semantic integration, such that compared with topic-maintained discourses, the complexity of discourse structure in topic-shifted condition reduces the initial stage of semantic integration and enhances the later stage in which a mental representation is updated.

Does lactobionic acid affect the colloidal structure and skin moisturizing potential of the alkyl polyglucoside-based emulsion systems?

PubMed

Tasic-Kostov, M Z; Reichl, S; Lukic, M Z; Jaksic, I N; Savic, S D

2011-11-01

Moisturizing creams are the most prescribed products in dermatology, essential in maintaining healthy skin as well as in the topical treatment of some diseases. The irritation potential of commonly used emulsifiers and moisturizing ingredients, but also their mutual interactions, could affect the functionality and safety of those dermopharmaceutics. The aim of this study was to promote moisturizing alkyl polyglucoside (APG)-based emulsion as vehicle for lactobionic acid (LA), advantageous representative of the alphahydroxyacids (AHAs)-multifunctional moisturizers, assessing the safety for use (in vitro acute skin irritation test using cytotoxicity assay compared with in vivo data obtained using skin bioengineering methods) and in vivo moisturizing capacity (bioengineering of the skin). In order to investigate possible interactions between APG mild natural emulsifier-based emulsion and LA, a deeper insight into the colloidal structure of the placebo and the emulsion with LA was given using polarization and transmission electron microscopy, rheology, thermal and texture analysis. This study showed that APG-based emulsions could be promoted as safe cosmetic/dermopharmaceutical vehicles and carriers for extremely acidic and hygroscopic AHA class of actives (specifically LA); prospective safety for human use of both APG and LA with the correlation between in vivo and in vitro findings was shown. However, it was revealed that LA strongly influenced the colloidal structure of the emulsion based on APGs and promoted the formation of lamellar structures which reflects onto the mode of water distribution within the cream. The advantageous skin hydrating potential of LA-containing emulsion vs. placebo was unlikely to be achieved, pointing that emulsions stabilized by lamellar liquid crystalline structures probably are not satisfying carriers for highly hygroscopic actives in order to reach the full moisturizing potential. Safe and effective use on dry skin is presumed.

An optimal transportation approach for nuclear structure-based pathology.

PubMed

Wang, Wei; Ozolek, John A; Slepčev, Dejan; Lee, Ann B; Chen, Cheng; Rohde, Gustavo K

2011-03-01

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g., normal versus cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers.

An optimal transportation approach for nuclear structure-based pathology

PubMed Central

Wang, Wei; Ozolek, John A.; Slepčev, Dejan; Lee, Ann B.; Chen, Cheng; Rohde, Gustavo K.

2012-01-01

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g. normal vs. cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers. PMID:20977984

Collisional excitation of CH2 rotational/fine-structure levels by helium

NASA Astrophysics Data System (ADS)

Dagdigian, P. J.; Lique, F.

2018-02-01

Accurate determination of the abundance of CH2 in interstellar media relies on both radiative and collisional rate coefficients. We investigate here the rotational/fine-structure excitation of CH2 induced by collisions with He. We employ a recoupling technique to generate fine-structure-resolved cross-sections and rate coefficients from close coupling spin-free scattering calculations. The calculations are based on a recent, high-accuracy CH2-He potential energy surface computed at the coupled clusters level of theory. The collisional cross-section calculations are performed for all fine-structure transitions among the first 22 and 24 energy levels of ortho- and para-CH2, respectively, and for temperatures up to 300 K. As a first application, we simulate the excitation of CH2 in typical molecular clouds. The excitation temperatures of the CH2 lines are found to be small at typical densities of molecular clouds, showing that the non-local thermodynamic equilibrium approach has to be used to analyse interstellar spectra. We also found that the fine-structure lines connected with the 404 - 313 and 505 - 414 rotational transitions show possible maser emissions so that they can be easily seen in emission. These calculations show that CH2 may have to be detected mainly through absorption spectra.

Field induced transient current in one-dimensional nanostructure

NASA Astrophysics Data System (ADS)

Sako, Tokuei; Ishida, Hiroshi

2018-07-01

Field-induced transient current in one-dimensional nanostructures has been studied by a model of an electron confined in a 1D attractive Gaussian potential subjected both to electrodes at the terminals and to an ultrashort pulsed oscillatory electric field with the central frequency ω and the FWHM pulse width Γ. The time-propagation of the electron wave packet has been simulated by integrating the time-dependent Schrödinger equation directly relying on the second-order symplectic integrator method. The transient current has been calculated as the flux of the probability density of the escaping wave packet emitted from the downstream side of the confining potential. When a static bias-field E0 is suddenly applied, the resultant transient current shows an oscillatory decay behavior with time followed by a minimum structure before converging to a nearly constant value. The ω-dependence of the integrated transient current induced by the pulsed electric field has shown an asymmetric resonance line-shape for large Γ while it shows a fringe pattern on the spectral line profile for small Γ. These observations have been rationalized on the basis of the energy-level structure and lifetime of the quasibound states in the bias-field modified confining potential obtained by the complex-scaling Fourier grid Hamiltonian method.

Calculations of the first frequency moment of the structure factor in the BCS model

NASA Astrophysics Data System (ADS)

Rendell, J. M.; Carbotte, J. P.

1998-03-01

We have calculated the first frequency moment of the dynamical structure factor, S(q,ω), known as the f-sum, using the BCS model of susceptibility, \\chi(q,ω), with phenomenological models of the normal state dispersion, tilde\\varepsilon_k, and the superconducting energy gap, Δ_k(T). We have found an explicit expression for the f-sum in both the normal state and the superconducting state. Numerically, we show that the f-sum is insensitive to temperature changes in the range 0 to the order of magnitude of T_c, to the state (normal or superconducting) and to the size and type of energy gap, Δ_k(T), in the superconducting state. The f-sum does depend intimately on the normal state dispersion model, tilde\\varepsilonk and on the filling in the first Brillouin zone. In addition, we show numerically that the f-sum is nearly constant for the Random Phase Approximation (RPA) of the susceptibility up to pseudo-potentials, U <= U_c, the critical potential. Thus, a large increase in Im \\chi(q_0,ω_0) at frequency ω0 and a potential U > 0 (e.g. examining the 41 meV peak at q0 = (π,π)), is compensated by commensurate reduction in Im \\chi(q_0,ω) at other frequencies.

Fish trypsins: potential applications in biomedicine and prospects for production.

PubMed

Jesús-de la Cruz, Kristal; Álvarez-González, Carlos Alfonso; Peña, Emyr; Morales-Contreras, José Antonio; Ávila-Fernández, Ángela

2018-04-01

In fishes, trypsins are adapted to different environmental conditions, and the biochemical and kinetic properties of a broad variety of native isoforms have been studied. Proteolytic enzymes remain in high demand in the detergent, food, and feed industries; however, our analysis of the literature showed that, in the last decade, some fish trypsins have been studied for the synthesis of industrial peptides and for specific biomedical uses as antipathogenic agents against viruses and bacteria, which have been recently patented. In addition, innovative strategies of trypsin administration have been studied to ensure that trypsins retain their properties until they exert their action. Biomedical uses require the production of high-quality enzymes. In this context, the production of recombinant trypsins is an alternative. For this purpose, E. coli -based systems have been tested for the production of fish trypsins; however, P. pastoris -based systems also seem to show great potential in the production of fish trypsins with higher production quality. On the other hand, there is a lack of information regarding the specific structures, biochemical and kinetic properties, and characteristics of trypsins produced using heterologous systems. This review describes the potential uses of fish trypsins in biomedicine and the enzymatic and structural properties of native and recombinant fish trypsins obtained to date, outlining some prospects for their study.

Synthesis, structural characterization, and pro-apoptotic activity of 1-indanone thiosemicarbazone platinum(II) and palladium(II) complexes: potential as antileukemic agents.

PubMed

Gómez, Natalia; Santos, Diego; Vázquez, Ramiro; Suescun, Leopoldo; Mombrú, Alvaro; Vermeulen, Monica; Finkielsztein, Liliana; Shayo, Carina; Moglioni, Albertina; Gambino, Dinorah; Davio, Carlos

2011-08-01

In the search for alternative chemotherapeutic strategies against leukemia, various 1-indanone thiosemicarbazones, as well as eight novel platinum(II) and palladium(II) complexes, with the formula [MCl₂(HL)] and [M(HL)(L)]Cl, derived from two 1-indanone thiosemicarbazones were synthesized and tested for antiproliferative activity against the human leukemia U937 cell line. The crystal structure of [Pt(HL1)(L1)]Cl·2MeOH, where L1=1-indanone thiosemicarbazone, was solved by X-ray diffraction. Free thiosemicarbazone ligands showed no antiproliferative effect, but the corresponding platinum(II) and palladium(II) complexes inhibited cell proliferation and induced apoptosis. Platinum(II) complexes also displayed selective apoptotic activity in U937 cells but not in peripheral blood monocytes or the human hepatocellular carcinoma HepG2 cell line used to screen for potential hepatotoxicity. Present findings show that, in U937 cells, 1-indanone thiosemicarbazones coordinated to palladium(II) were more cytotoxic than those complexed with platinum(II), although the latter were found to be more selective for leukemic cells suggesting that they are promising compounds with potential therapeutic application against hematological malignancies. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions.

PubMed

Bedford, Nicholas M; Hughes, Zak E; Tang, Zhenghua; Li, Yue; Briggs, Beverly D; Ren, Yang; Swihart, Mark T; Petkov, Valeri G; Naik, Rajesh R; Knecht, Marc R; Walsh, Tiffany R

2016-01-20

Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.

Electrochemical Control of Peptide Self-Organization on Atomically Flat Solid Surfaces: A Case Study with Graphite.

PubMed

Seki, Takakazu; So, Christopher R; Page, Tamon R; Starkebaum, David; Hayamizu, Yuhei; Sarikaya, Mehmet

2018-02-06

The nanoscale self-organization of biomolecules, such as proteins and peptides, on solid surfaces under controlled conditions is an important issue in establishing functional bio/solid soft interfaces for bioassays, biosensors, and biofuel cells. Electrostatic interaction between proteins and surfaces is one of the most essential parameters in the adsorption and self-assembly of proteins on solid surfaces. Although the adsorption of proteins has been studied with respect to the electrochemical surface potential, the self-assembly of proteins or peptides forming well-organized nanostructures templated by lattice structure of the solid surfaces has not been studied in the relation to the surface potential. In this work, we utilize graphite-binding peptides (GrBPs) selected by the phage display method to investigate the relationship between the electrochemical potential of the highly ordered pyrolytic graphite (HOPG) and peptide self-organization forming long-range-ordered structures. Under modulated electrical bias, graphite-binding peptides form various ordered structures, such as well-ordered nanowires, dendritic structures, wavy wires, amorphous (disordered) structures, and islands. A systematic investigation of the correlation between peptide sequence and self-organizational characteristics reveals that the presence of the bias-sensitive amino acid modules in the peptide sequence has a significant effect on not only surface coverage but also on the morphological features of self-assembled structures. Our results show a new method to control peptide self-assembly by means of applied electrochemical bias as well as peptide design-rules for the construction of functional soft bio/solid interfaces that could be integrated in a wide range of practical implementations.

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

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

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n = 1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energymore » and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. Finally, this opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.« less

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

DOE PAGES

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.; ...

2018-04-09

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n = 1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energymore » and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. Finally, this opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.« less

Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginosa.

PubMed

Wei, Yong; Zhang, Heng; Gao, Zeng-Qiang; Xu, Jian-Hua; Liu, Quan-Sheng; Dong, Yu-Hui

2013-01-01

The global metabolic regulator catabolite repression control (Crc) has recently been found to modulate the susceptibility to antibiotics and virulence in the opportunistic pathogen Pseudomonas aeruginosa and been suggested as a nonlethal target for novel antimicrobials. In P. aeruginosa, Crc couples with the CA motifs from the small RNA CrcZ to form a post-transcriptional regulator system and is removed from the 5'-end of the target mRNAs. In this study, we first reported the crystal structure of Crc from P. aeruginosa refined to 2.20 Å. The structure showed that it consists of two halves with similar overall topology and there are 11 β strands surrounded by 13 helices, forming a four-layered α/β-sandwich. The circular dichroism spectroscopy revealed that it is thermostable in solution and shares similar characteristics to that in crystal. Comprehensive structural analysis and comparison with the homologies of Crc showed high similarity with several known nucleases and consequently may be classified into a member exodeoxyribonuclease III. However, it shows distinct substrate specificity (RNA as the preferred substrate) compared to these DNA endonucleases. Structural comparisons also revealed potential RNA recognition and binding region mainly consisting of five flexible loops. Our structure study provided the basis for the future application of Crc as a target to develop new antibiotics. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

Thermoelectric properties of 2H-CuGaO2 for device applications: A first principle TB-mBJ potential study

NASA Astrophysics Data System (ADS)

Bhamu, K. C.; Praveen, C. S.

2017-12-01

Here we report the structural, electronic, optical, and thermoelectric properties of delafossite type 2H-CuGaO2 using first principles calculations. The present calculation predict an indirect band gap of 1.20 eV and a direct band gap of 3.48 eV. A detailed analysis of the electronic structure is provided based on atom and orbital projected density of states. Frequency dependent dielectric functions, refractive index, and absorption coefficient as a function of photon energy are discussed. The thermoelectric properties with power factor, and the figure of merit are reported as a function of chemical potential in the region ± 0.195 (μ -EF) eV at constant temperature of 300 and 800 K. The thermoelectric properties shows that 2H-CuGaO2 could be potential candidate for engineering devises operating at high temperature for the chemical potential in the range of ± 0.055 (μ -EF) eV and beyond this range the thermoelectric performance of 2H-CuGaO2 get reduced.

The inherent dynamics of a molecular liquid: geodesic pathways through the potential energy landscape of a liquid of linear molecules.

PubMed

Jacobson, Daniel; Stratt, Richard M

2014-05-07

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation-molecules largely thread their way through narrow channels available in the potential energy landscape.

The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

NASA Astrophysics Data System (ADS)

Jacobson, Daniel; Stratt, Richard M.

2014-05-01

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

An EQT-based cDFT approach for thermodynamic properties of confined fluid mixtures

NASA Astrophysics Data System (ADS)

Motevaselian, M. H.; Aluru, N. R.

2017-04-01

We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths. We show that the EQT-cDFT predictions for the structure, surface tension, solvation force, and local pressure tensor profiles are in good agreement with the molecular dynamics simulations. Moreover, we study the effect of different bulk compositions and channel widths on the thermodynamic properties. Our results reveal that the composition of methane in the mixture can significantly affect the ordering of molecules and thermodynamic properties under confinement. In addition, we find that graphene is selective to methane molecules.

Stable tetragonal phase and magnetic properties of Fe-doped HfO2 nanoparticles

NASA Astrophysics Data System (ADS)

Sales, T. S. N.; Cavalcante, F. H. M.; Bosch-Santos, B.; Pereira, L. F. D.; Cabrera-Pasca, G. A.; Freitas, R. S.; Saxena, R. N.; Carbonari, A. W.

2017-05-01

In this paper, the effect in structural and magnetic properties of iron doping with concentration of 20% in hafnium dioxide (HfO2) nanoparticles is investigated. HfO2 is a wide band gap oxide with great potential to be used as high-permittivity gate dielectrics, which can be improved by doping. Nanoparticle samples were prepared by sol-gel chemical method and had their structure, morphology, and magnetic properties, respectively, investigated by X-ray diffraction (XRD), transmission electron microscopy (TEM) and scanning electron microscopy (SEM) with electron back scattering diffraction (EBSD), and magnetization measurements. TEM and SEM results show size distribution of particles in the range from 30 nm to 40 nm with small dispersion. Magnetization measurements show the blocking temperature at around 90 K with a strong paramagnetic contribution. XRD results show a major tetragonal phase (94%).

Some factors affecting efficiencies of n-CdS/p-CdTe thin film solar cells

NASA Astrophysics Data System (ADS)

Morris, G. C.; Das, S. K.; Tanner, P. G.

1992-02-01

Electrodeposited CdS and CdTe thin films have been fabricated into solar cells with a CdS/CdTe heterojunction. The CdTe films were made by varying two parameters, viz. the concentration of tellurium ions in the deposition solution and the quasi-rest potential (QRP) of the deposit. The properties of the completed cells were examined as a function of those preparation variables. Cell efficiency varied with both QRP and tellurium ion concentration. Whilst chemical analytic methods showed no compositional variation between cells, morphological studies showed that the most efficient cells had the largest grain size. Electrical and capacitance measurements were used to show that the density of interband states and of junction interface states increased with structural imperfection. The major losses in the solar cell parameters increased with increased polycrystalline structure.

Structural Characterization of the Histone Variant macroH2A

PubMed Central

Chakravarthy, Srinivas; Gundimella, Sampath Kumar Y.; Caron, Cecile; Perche, Pierre-Yves; Pehrson, John R.; Khochbin, Saadi; Luger, Karolin

2005-01-01

macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold region of macroH2A impact the structure and potentially the function of nucleosomes. The 1.6-Å X-ray structure of the nonhistone region reveals an α/β fold which has previously been found in a functionally diverse group of proteins. This region associates with histone deacetylases and affects the acetylation status of nucleosomes containing macroH2A. Thus, the unusual domain structure of macroH2A integrates independent functions that are instrumental in establishing a structurally and functionally unique chromatin domain. PMID:16107708

Ballistic Puncture Self-Healing Polymeric Materials

NASA Technical Reports Server (NTRS)

Gordon, Keith L.; Siochi, Emilie J.; Yost, William T.; Bogert, Phil B.; Howell, Patricia A.; Cramer, K. Elliott; Burke, Eric R.

2017-01-01

Space exploration launch costs on the order of $10,000 per pound provide an incentive to seek ways to reduce structural mass while maintaining structural function to assure safety and reliability. Damage-tolerant structural systems provide a route to avoiding weight penalty while enhancing vehicle safety and reliability. Self-healing polymers capable of spontaneous puncture repair show promise to mitigate potentially catastrophic damage from events such as micrometeoroid penetration. Effective self-repair requires these materials to quickly heal following projectile penetration while retaining some structural function during the healing processes. Although there are materials known to possess this capability, they are typically not considered for structural applications. Current efforts use inexpensive experimental methods to inflict damage, after which analytical procedures are identified to verify that function is restored. Two candidate self-healing polymer materials for structural engineering systems are used to test these experimental methods.

Linear and nonlinear analysis of kinetic Alfven waves in quantum magneto-plasmas with arbitrary temperature degeneracy

NASA Astrophysics Data System (ADS)

Sadiq, Nauman; Ahmad, Mushtaq; Farooq, M.; Jan, Qasim

2018-06-01

Linear and nonlinear kinetic Alfven waves (KAWs) are studied in collisionless, non-relativistic two fluid quantum magneto-plasmas by considering arbitrary temperature degeneracy. A general coupling parameter is applied to discuss the range of validity of the proposed model in nearly degenerate and nearly non-degenerate plasma limits. Linear analysis of KAWs shows an increase (decrease) in frequency with the increase in parameter ζ ( δ ) for the nearly non-degenerate (nearly degenerate) plasma limit. The energy integral equation in the form of Sagdeev potential is obtained by using the approach of the Lorentz transformation. The analysis reveals that the amplitude of the Sagdeev potential curves and soliton structures remains the same, but the potential depth and width of soliton structure change for both the limiting cases. It is further observed that only density hump structures are formed in the sub-alfvenic region for value Kz 2 > 1 . The effects of parameters ζ, δ on the nonlinear properties of KAWs are shown in graphical plots. New results for comparison with earlier work have also been highlighted. The significance of this work to astrophysical plasmas is also emphasized.

Neural Correlate of Anterograde Amnesia in Wernicke-Korsakoff Syndrome.

PubMed

Nahum, Louis; Pignat, Jean-Michel; Bouzerda-Wahlen, Aurélie; Gabriel, Damien; Liverani, Maria Chiara; Lazeyras, François; Ptak, Radek; Richiardi, Jonas; Haller, Sven; Thorens, Gabriel; Zullino, Daniele F; Guggisberg, Adrian G; Schnider, Armin

2015-09-01

The neural correlate of anterograde amnesia in Wernicke-Korsakoff syndrome (WKS) is still debated. While the capacity to learn new information has been associated with integrity of the medial temporal lobe (MTL), previous studies indicated that the WKS is associated with diencephalic lesions, mainly in the mammillary bodies and anterior or dorsomedial thalamic nuclei. The present study tested the hypothesis that amnesia in WKS is associated with a disrupted neural circuit between diencephalic and hippocampal structures. High-density evoked potentials were recorded in four severely amnesic patients with chronic WKS, in five patients with chronic alcoholism without WKS, and in ten age matched controls. Participants performed a continuous recognition task of pictures previously shown to induce a left medial temporal lobe dependent positive potential between 250 and 350 ms. In addition, the integrity of the fornix was assessed using diffusion tensor imaging (DTI). WKS, but not alcoholic patients without WKS, showed absence of the early, left MTL dependent positive potential following immediate picture repetitions. DTI indicated disruption of the fornix, which connects diencephalic and hippocampal structures. The findings support an interpretation of anterograde amnesia in WKS as a consequence of a disconnection between diencephalic and MTL structures with deficient contribution of the MTL to rapid consolidation.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

PubMed Central

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

2015-01-01

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

Crystal structure of human esterase D: a potential genetic marker of retinoblastoma

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

Wu, Dong; Li, Yang; Song, Gaojie

2009-07-10

Retinoblastoma (RB), a carcinoma of the retina, is caused by mutations in the long arm of chromosome 13, band 13q14. The esterase D (ESD) gene maps at a similar location as the RB gene locus and therefore serves as a potential marker for the prognosis of retinoblastoma. Because very little is known about the structure and function of ESD, we determined the 3-dimensional structure of the enzyme at 1.5 {angstrom} resolution using X-ray crystallography. ESD shows a single domain with an {alpha}/{beta}-hydrolase fold. A number of insertions are observed in the canonical {alpha}/{beta}-hydrolase fold. The active site is located inmore » a positively charged, shallow cleft on the surface lined by a number of aromatic residues. Superimposition studies helped identify the typical catalytic triad residues -- Ser-153, His264, and Asp230 -- involved in catalysis. Mutagenesis of any of the catalytic triad residues to alanine abolished the enzyme activity. Backbone amides of Leu54 and Met150 are involved in the formation of the oxyanion hole. Interestingly, a M150A mutation increased the enzyme activity by 62%. The structure of human ESD determined in this study will aid the elucidation of the physiological role of the enzyme in the human body and will assist in the early diagnosis of retinoblastoma. Wu, D., Li, Y., Song, G., Zhang, D., Shaw, N., Liu, Z. J. Crystal structure of human esterase D: a potential genetic marker of retinoblastoma.« less

Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

DOE PAGES

Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

2007-08-21

Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

Engel-Vosko GGA calculations of the structural, electronic and optical properties of LiYO2

NASA Astrophysics Data System (ADS)

Muhammad, Nisar; Khan, Afzal; Haidar Khan, Shah; Sajjaj Siraj, Muhammad; Shah, Syed Sarmad Ali; Murtaza, Ghulam

2017-09-01

Structural, electronic and optical properties of lithium yttrium oxide (LiYO2) are investigated using density functional theory (DFT). These calculations are based on full potential linearized augmented plane wave (FP-LAPW) method implemented by WIEN2k. The generalized gradient approximation (GGA) is used as an exchange correlation potential with Perdew-Burk-Ernzerhof (PBE) and Engel-Vosko (EV) as exchange correlation functional. The structural properties are calculated with PBE-GGA as it gives the equilibrium lattice constants very close to the experimental values. While, the band structure and optical properties are calculated with EV-GGA obtain much closer results to their experimental values. Our calculations confirm LiYO2 as large indirect band gap semiconductor having band gap of 5.23 eV exhibiting the characteristics of ultrawide band gap materials showing the properties like higher critical breakdown field, higher temperature operation and higher radiation tolerance. In this article, we report the density of states (DOS) in terms of contribution from s, p, and d-states of the constituent atoms, the band structure, the electronic structure, and the frequency-dependent optical properties of LiYO2. The optical properties presented in this article reveal LiYO2 a suitable candidate for the field of optoelectronic and optical devices.

Composite corrugated structures for morphing wing skin applications

NASA Astrophysics Data System (ADS)

Thill, C.; Etches, J. A.; Bond, I. P.; Potter, K. D.; Weaver, P. M.

2010-12-01

Composite corrugated structures are known for their anisotropic properties. They exhibit relatively high stiffness parallel (longitudinal) to the corrugation direction and are relatively compliant in the direction perpendicular (transverse) to the corrugation. Thus, they offer a potential solution for morphing skin panels (MSPs) in the trailing edge region of a wing as a morphing control surface. In this paper, an overview of the work carried out by the present authors over the last few years on corrugated structures for morphing skin applications is first given. The second part of the paper presents recent work on the application of corrugated sandwich structures. Panels made from multiple unit cells of corrugated sandwich structures are used as MSPs in the trailing edge region of a scaled morphing aerofoil section. The aerofoil section features an internal actuation mechanism that allows chordwise length and camber change of the trailing edge region (aft 35% chord). Wind tunnel testing was carried out to demonstrate the MSP concept but also to explore its limitations. Suggestions for improvements arising from this study were deduced, one of which includes an investigation of a segmented skin. The overall results of this study show that the MSP concept exploiting corrugated sandwich structures offers a potential solution for local morphing wing skins for low speed and small air vehicles.

Structural optimization with approximate sensitivities

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Hopkins, D. A.; Coroneos, R.

1994-01-01

Computational efficiency in structural optimization can be enhanced if the intensive computations associated with the calculation of the sensitivities, that is, gradients of the behavior constraints, are reduced. Approximation to gradients of the behavior constraints that can be generated with small amount of numerical calculations is proposed. Structural optimization with these approximate sensitivities produced correct optimum solution. Approximate gradients performed well for different nonlinear programming methods, such as the sequence of unconstrained minimization technique, method of feasible directions, sequence of quadratic programming, and sequence of linear programming. Structural optimization with approximate gradients can reduce by one third the CPU time that would otherwise be required to solve the problem with explicit closed-form gradients. The proposed gradient approximation shows potential to reduce intensive computation that has been associated with traditional structural optimization.

Crystal structure and functional characterization of SF216 from Shigella flexneri.

PubMed

Kim, Ha-Neul; Seok, Seung-Hyeon; Lee, Yoo-Sup; Won, Hyung-Sik; Seo, Min-Duk

2017-11-01

Shigella flexneri is a Gram-negative anaerobic bacterium that causes highly infectious bacterial dysentery in humans. Here, we solved the crystal structure of SF216, a hypothetical protein from the S. flexneri 5a strain M90T, at 1.7 Å resolution. The crystal structure of SF216 represents a homotrimer stabilized by intersubunit interactions and ion-mediated electrostatic interactions. Each subunit consists of three β-strands and five α-helices with the β-β-β-α-α-α-α-α topology. Based on the structural information, we also demonstrate that SF216 shows weak ribonuclease activity by a fluorescence quenching assay. Furthermore, we identify potential druggable pockets (putative hot spots) on the surface of the SF216 structure by computational mapping. © 2017 Federation of European Biochemical Societies.

Asymmetry of Hemispheric Network Topology Reveals Dissociable Processes between Functional and Structural Brain Connectome in Community-Living Elders

PubMed Central

Sun, Yu; Li, Junhua; Suckling, John; Feng, Lei

2017-01-01

Human brain is structurally and functionally asymmetrical and the asymmetries of brain phenotypes have been shown to change in normal aging. Recent advances in graph theoretical analysis have showed topological lateralization between hemispheric networks in the human brain throughout the lifespan. Nevertheless, apparent discrepancies of hemispheric asymmetry were reported between the structural and functional brain networks, indicating the potentially complex asymmetry patterns between structural and functional networks in aging population. In this study, using multimodal neuroimaging (resting-state fMRI and structural diffusion tensor imaging), we investigated the characteristics of hemispheric network topology in 76 (male/female = 15/61, age = 70.08 ± 5.30 years) community-dwelling older adults. Hemispheric functional and structural brain networks were obtained for each participant. Graph theoretical approaches were then employed to estimate the hemispheric topological properties. We found that the optimal small-world properties were preserved in both structural and functional hemispheric networks in older adults. Moreover, a leftward asymmetry in both global and local levels were observed in structural brain networks in comparison with a symmetric pattern in functional brain network, suggesting a dissociable process of hemispheric asymmetry between structural and functional connectome in healthy older adults. Finally, the scores of hemispheric asymmetry in both structural and functional networks were associated with behavioral performance in various cognitive domains. Taken together, these findings provide new insights into the lateralized nature of multimodal brain connectivity, highlight the potentially complex relationship between structural and functional brain network alterations, and augment our understanding of asymmetric structural and functional specializations in normal aging. PMID:29209197

Electrostatic potential calculation for biomolecules--creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures.

PubMed

Rocchia, W; Neshich, G

2007-10-05

STING and Java Protein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and Java Protein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. BlueStar STING is available at http://www.cbi.cnptia.embrapa.br.

Electric potential structures of auroral acceleration region border from multi-spacecraft Cluster data

NASA Astrophysics Data System (ADS)

Sadeghi, S.; Emami, M. R.

2018-04-01

This paper studies an auroral event using data from three spacecraft of the Cluster mission, one inside and two at the poleward edge of the bottom of the Auroral Acceleration Region (AAR). The study reveals the three-dimensional profile of the region's poleward boundary, showing spatial segmentation of the electric potential structures and their decay in time. It also depicts localized magnetic field variations and field-aligned currents that appear to have remained stable for at least 80 s. Such observations became possible due to the fortuitous motion of the three spacecraft nearly parallel to each other and tangential to the AAR edge, so that the differences and variations can be seen when the spacecraft enter and exit the segmentations, hence revealing their position with respect to the AAR.

A Review of the Positive Influence of Crown Contours on Soft-Tissue Esthetics.

PubMed

Kinsel, Richard P; Pope, Bryan I; Capoferri, Daniele

2015-05-01

Successful crown restorations duplicate the natural tooth in hue, chroma, value, maverick colors, and surface texture. Equally important is the visual harmony of the facial and proximal soft-tissue contours, which requires the collaborative skills of the restorative dentist, periodontist, and dental technician. The treatment team must understand the biologic structures adjacent to natural dentition and dental implants. This report describes the potential for specifically designed restorative contours to dictate the optimal gingival profile for tooth-supported and implant-supported crowns. Showing several cases, the article explains how esthetic soft-tissue contours enhance the definitive crown restoration, highlights the importance of clinical evaluation of adjacent biologic structures, and discusses keys to predicting when the proximal papilla has the potential to return to a favorable height and shape.

Atomic interaction of the MEAM type for the study of intermetallics in the Al-U alloy

NASA Astrophysics Data System (ADS)

Pascuet, M. I.; Fernández, J. R.

2015-12-01

Interaction for both pure Al and Al-U alloys of the MEAM type are developed. The obtained Al interatomic potential assures its compatibility with the details of the framework presently adopted. The Al-U interaction fits various properties of the Al2U, Al3U and Al4U intermetallics. The potential verifies the stability of the intermetallic structures in a temperature range compatible with that observed in the phase diagram, and also takes into account the greater stability of these structures relative to others that are competitive in energy. The intermetallics are characterized by calculating elastic and thermal properties and point defect parameters. Molecular dynamics simulations show a growth of the Al3U intermetallic in the Al/U interface in agreement with experimental evidence.

Space-charge-sustained microbunch structure in the Los Alamos Proton Storage Ring

NASA Astrophysics Data System (ADS)

Cousineau, S.; Danilov, V.; Holmes, J.; Macek, R.

2004-09-01

We present experimental data from the Los Alamos Proton Storage Ring (PSR) showing long-lived linac microbunch structure during beam storage with no rf bunching. Analysis of the experimental data and particle-in-cell simulations of the experiments indicate that space charge, coupled with energy spread effects, is responsible for the sustained microbunch structure. The simulated longitudinal phase space of the beam reveals a well-defined separatrix in the phase space between linac microbunches, with particles executing unbounded motion outside of the separatrix. We show that the longitudinal phase space of the beam was near steady state during the PSR experiments, such that the separatrix persisted for long periods of time. Our simulations indicate that the steady state is very sensitive to the experimental conditions. Finally, we solve the steady-state problem in an analytic, self-consistent fashion for a set of periodic longitudinal space-charge potentials.

From protein sequence to dynamics and disorder with DynaMine.

PubMed

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F

2013-01-01

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

Complete fold annotation of the human proteome using a novel structural feature space.

PubMed

Middleton, Sarah A; Illuminati, Joseph; Kim, Junhyong

2017-04-13

Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.

Solar Coronal Loop Dynamics Near the Null Point Above Active Region NOAA 2666

NASA Astrophysics Data System (ADS)

Filippov, B.

2018-06-01

We analyse observations of a saddle-like structure in the corona above the western limb of the Sun on 2017 July 18. The structure was clearly outlined by coronal loops with typical coronal temperature no more than 1 MK. The dynamics of loops showed convergence towards the centre of the saddle in the vertical direction and divergence in the horizontal direction. The event is a clear example of smooth coronal magnetic field reconnection. No heating manifestations in the reconnection region or magnetically connected areas were observed. Potential magnetic field calculations, which use as the boundary condition the SDO/HMI magnetogram taken on July 14, showed the presence of a null point at the height of 122 arcsec above the photosphere just at the centre of the saddle structure. The shape of field lines fits the fan-spine magnetic configuration above NOAA 2666.

Detecting reactive islands using Lagrangian descriptors and the relevance to transition path sampling.

PubMed

Patra, Sarbani; Keshavamurthy, Srihari

2018-02-14

It has been known for sometime now that isomerization reactions, classically, are mediated by phase space structures called reactive islands (RI). RIs provide one possible route to correct for the nonstatistical effects in the reaction dynamics. In this work, we map out the reactive islands for the two dimensional Müller-Brown model potential and show that the reactive islands are intimately linked to the issue of rare event sampling. In particular, we establish the sensitivity of the so called committor probabilities, useful quantities in the transition path sampling technique, to the hierarchical RI structures. Mapping out the RI structure for high dimensional systems, however, is a challenging task. Here, we show that the technique of Lagrangian descriptors is able to effectively identify the RI hierarchy in the model system. Based on our results, we suggest that the Lagrangian descriptors can be useful for detecting RIs in high dimensional systems.

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.