3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

PubMed

Xiong, Yi; Esquivel-Rodriguez, Juan; Sael, Lee; Kihara, Daisuke

2014-01-01

The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITE (csc) . The server is available at http://kiharalab.org/3d-surfer/.

"Soft docking": matching of molecular surface cubes.

PubMed

Jiang, F; Kim, S H

1991-05-05

Molecular recognition is achieved through the complementarity of molecular surface structures and energetics with, most commonly, associated minor conformational changes. This complementarity can take many forms: charge-charge interaction, hydrogen bonding, van der Waals' interaction, and the size and shape of surfaces. We describe a method that exploits these features to predict the sites of interactions between two cognate molecules given their three-dimensional structures. We have developed a "cube representation" of molecular surface and volume which enables us not only to design a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. The present molecular docking procedure may be divided into two stages. The first is the selection of a population of complexes by geometric "soft docking", in which surface structures of two interacting molecules are matched with each other, allowing minor conformational changes implicitly, on the basis of complementarity in size and shape, close packing, and the absence of steric hindrance. The second is a screening process to identify a subpopulation with many favorable energetic interactions between the buried surface areas. Once the size of the subpopulation is small, one may further screen to find the correct complex based on other criteria or constraints obtained from biochemical, genetic, and theoretical studies, including visual inspection. We have tested the present method in two ways. First is a control test in which we docked the components of a molecular complex of known crystal structure available in the Protein Data Bank (PDB). Two molecular complexes were used: (1) a ternary complex of dihydrofolate reductase, NADPH and methotrexate (3DFR in PDB) and (2) a binary complex of trypsin and trypsin inhibitor (2PTC in PDB). The components of each complex were taken apart at an arbitrary relative orientation and then docked together again. The results show that the geometric docking alone is sufficient to determine the correct docking solutions in these ideal cases, and that the cube representation of the molecules does not degrade the docking process in the search for the correct solution. The second is the more realistic experiment in which we docked the crystal structures of uncomplexed molecules and then compared the structures of docked complexes with the crystal structures of the corresponding complexes. This is to test the capability of our method in accommodating the effects of the conformational changes in the binding sites of the molecules in docking.(ABSTRACT TRUNCATED AT 400 WORDS)

STUDY OF TURBULENT ENERGY OVER COMPLEX TERRAIN: STATE, 1978

EPA Science Inventory

The complex structure of the earth's surface influenced atmospheric parameters pertinent to modeling the diffusion process during the 1978 'STATE' field study. The Information Theory approach of statistics proved useful for analyzing the complex structures observed in the radiome...

Adsorption mechanisms of selenium oxyanions at the aluminum oxide/water interface

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

Peak, Derek

2008-06-09

Sorption processes at the mineral/water interface typically control the mobility and bioaccessibility of many inorganic contaminants such as oxyanions. Selenium is an important micronutrient for human and animal health, but at elevated concentrations selenium toxicity is a concern. The objective of this study was to determine the bonding mechanisms of selenate (SeO{sub 4}{sup 2-}) and selenite (SeO{sub 3}{sup 2-}) on hydrous aluminum oxide (HAO) over a wide range of reaction pH using extended X-ray absorption fine structure (EXAFS) spectroscopy. Additionally, selenate adsorption on corundum ({alpha}-Al{sub 2}O{sub 3}) was studied to determine if adsorption mechanisms change as the aluminum oxide surfacemore » structure changes. The overall findings were that selenite forms a mixture of outer-sphere and inner-sphere bidentate-binuclear (corner-sharing) surface complexes on HAO, selenate forms primarily outer-sphere surface complexes on HAO, and on corundum selenate forms outer-sphere surface complexes at pH 3.5 but inner-sphere monodentate surface complexes at pH 4.5 and above. It is possible that the lack of inner-sphere complex formation at pH 3.5 is caused by changes in the corundum surface at low pH or secondary precipitate formation. The results are consistent with a structure-based reactivity for metal oxides, wherein hydrous metal oxides form outer-sphere complexes with sulfate and selenate, but inner-sphere monodentate surface complexes are formed between sulfate and selenate and {alpha}-Me{sub 2}O{sub 3}.« less

Identifying structural styles in Colombia

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

Wilson, W.P.; Van Nieuwenhuise, R.E.; Steuer, M.R.

1996-08-01

Much of our understanding of the Earth is from the study of surface geology and seismic, but many surface structures are responses to deformation which occurred below sedimentary layers. The practice within the petroleum industry is to use top-down processes of analyzing the surface to understand the subsurface, and observed surface structural styles tend to influence seismic interpretations. Yet many conditions which influenced the structural styles seen at the surface are different at depth. Since seismic is a time representation of the Earth, many interpretation pitfalls may exist within areas of complex geology. Also, its reliability decreases with depth andmore » with increasing geologic complexity. Forward modeling and pre-stack depth migration technologies are used to provide true depth images of the seismic data. Even with these advances in seismic imaging technology, the interpreter needs to incorporate additional data into the interpretation. Accurate structural identification requires the interpreter to integrate seismic with surface geology, remote sensing, gravity, magnetic data, geochemistry, fault-plane solutions from earthquakes, and regional tectonic studies. Incorporating these types of data into the interpretation will help us learn how basement is involved in the deformation of overlying sediments. A study of the Eastern Cordillera of Colombia shows the deformation to be dominantly transpressional in style. Euler deconvolution of the areomagnetic data shows a highly fractured basement, steep fault lineaments, en echelon structures, and complex fault patterns, all of which would be typical of wrench-type deformation. Available surface geology, regional studies, earthquake data, and forward modeling support this interpretation.« less

Hydrous ferric oxide: evaluation of Cd-HFO surface complexation models combining Cd(K) EXAFS data, potentiometric titration results, and surface site structures identified from mineralogical knowledge.

PubMed

Spadini, Lorenzo; Schindler, Paul W; Charlet, Laurent; Manceau, Alain; Vala Ragnarsdottir, K

2003-10-01

The surface properties of ferrihydrite were studied by combining wet chemical data, Cd(K) EXAFS data, and a surface structure and protonation model of the ferrihydrite surface. Acid-base titration experiments and Cd(II)-ferrihydrite sorption experiments were performed within 3<-log[H(+)]<10.5 and 0.5<[Cd(t)]<12 mM in 0.3 M NaClO(4) at 25 degrees C, where [Cd(t)] refers to total Cd concentration. Measurements at -5.5triple bond Fe-OH(-1/2),logk((int))=-8.29, assuming the existence of a unique intrinsic microscopic constant, logk((int)), and consequently the existence of a single significant type of acid-base reactive functional groups. The surface structure model indicates that these groups are terminal water groups. The Cd(II) data were modeled assuming the existence of a single reactive site. The model fits the data set at low Cd(II) concentration and up to 50% surface coverage. At high coverage more Cd(II) ions than predicted are adsorbed, which is indicative of the existence of a second type of site of lower affinity. This agrees with the surface structure and protonation model developed, which indicates comparable concentrations of high- and low-affinity sites. The model further shows that for each class of low- and high-affinity sites there exists a variety of corresponding Cd surface complex structure, depending on the model crystal faces on which the complexes develop. Generally, high-affinity surface structures have surface coordinations of 3 and 4, as compared to 1 and 2 for low-affinity surface structures.

Numerical simulation of colloidal self-assembly of super-hydrophobic arachnid cerotegument structures.

PubMed

Filippov, Alexander É; Wolff, Jonas O; Seiter, Michael; Gorb, Stanislav N

2017-10-07

Certain arachnids exhibit complex coatings of their exoskeleton, consisting of globular structures with complex surface features. This, so-called, cerotegument is formed by a multi-component colloidal secretion that self-assembles and cures on the body surface, and leads to high water repellency. Previous ultrastructural studies revealed the involvement of different glandular cells that contribute different components to the secretion mixture, but the overall process of self-assembly into the complex regular structures observed remained highly unclear. Here we study this process from a theoretical point of view, starting from the so-called Tammes-problem. We show that slight changes of simple parameters lead to a variety of morphologies that are highly similar to the ones observed in the species specific cerotegument structures of whip-spiders. These results are not only important for our understanding of the formation of globular hierarchical structures in nature, but also for the fabrication of novel surface coatings by colloidal lithography. Copyright © 2017 Elsevier Ltd. All rights reserved.

Experimental and Theoretical Approaches for the Surface Interaction between Copper and Activated Sludge Microorganisms at Molecular Scale

NASA Astrophysics Data System (ADS)

Luo, Hong-Wei; Chen, Jie-Jie; Sheng, Guo-Ping; Su, Ji-Hu; Wei, Shi-Qiang; Yu, Han-Qing

2014-11-01

Interactions between metals and activated sludge microorganisms substantially affect the speciation, immobilization, transport, and bioavailability of trace heavy metals in biological wastewater treatment plants. In this study, the interaction of Cu(II), a typical heavy metal, onto activated sludge microorganisms was studied in-depth using a multi-technique approach. The complexing structure of Cu(II) on microbial surface was revealed by X-ray absorption fine structure (XAFS) and electron paramagnetic resonance (EPR) analysis. EPR spectra indicated that Cu(II) was held in inner-sphere surface complexes of octahedral coordination with tetragonal distortion of axial elongation. XAFS analysis further suggested that the surface complexation between Cu(II) and microbial cells was the distorted inner-sphere coordinated octahedra containing four short equatorial bonds and two elongated axial bonds. To further validate the results obtained from the XAFS and EPR analysis, density functional theory calculations were carried out to explore the structural geometry of the Cu complexes. These results are useful to better understand the speciation, immobilization, transport, and bioavailability of metals in biological wastewater treatment plants.

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.

Supported metallocene catalysts by surface organometallic chemistry. Synthesis, characterization, and reactivity in ethylene polymerization of oxide-supported mono- and biscyclopentadienyl zirconium alkyl complexes: establishment of structure/reactivity relationships.

PubMed

Jezequel, M; Dufaud, V; Ruiz-Garcia, M J; Carrillo-Hermosilla, F; Neugebauer, U; Niccolai, G P; Lefebvre, F; Bayard, F; Corker, J; Fiddy, S; Evans, J; Broyer, J P; Malinge, J; Basset, J M

2001-04-18

The reactions of CpZr(CH(3))(3), 1, and Cp(2)Zr(CH(3))(2), 2, with partially dehydroxylated silica, silica-alumina, and alumina surfaces have been carried out with careful identification of the resulting surface organometallic complexes in order to probe the relationship between catalyst structure and polymerization activity. The characterization of the supported complexes has been achieved in most cases by in situ infrared spectroscopy, surface microanalysis, qualitative and quantitative analysis of evolved gases during surface reactions with labeled surface, solid state (1)H and (13)C NMR using (13)C-enriched compounds, and EXAFS. 1 and 2 react with silica(500) and silica-alumina(500) by simple protonolysis of one Zr-Me bond by surface silanols with formation of a single well-defined neutral compound. In the case of silica-alumina, a fraction of the supported complexes exhibits some interactions with electronically unsaturated surface aluminum sites. 1 and 2 also react with the hydroxyl groups of gamma-alumina(500), leading to several surface structures. Correlation between EXAFS and (13)C NMR data suggests, in short, two main surface structures having different environments for the methyl group: [Al](3)-OZrCp(CH(3))(2) and [Al](2)-OZrCp(CH(3))(mu-CH(3))-[Al] for the monoCp series and [Al](2)-OZrCp(2)(CH(3)) and [Al]-OZrCp(2)(mu-CH(3))-[Al] for the bisCp series. Ethylene polymerization has been carried out with all the supported complexes under various reaction conditions. Silica-supported catalysts in the absence of any cocatalyst exhibited no activity whatsoever for ethylene polymerization. When the oxide contained Lewis acidic sites, the resulting surface species were active. The activity, although improved by the presence of additional cocatalysts, remained very low by comparison with that of the homogeneous metallocene systems. This trend has been interpreted on the basis of various possible parameters, including the (p-pi)-(d-pi) back-donation of surface oxygen atoms to the zirconium center.

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

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

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

DOE PAGES

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.; ...

2017-10-06

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Multiresolution Distance Volumes for Progressive Surface Compression

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

Laney, D E; Bertram, M; Duchaineau, M A

2002-04-18

We present a surface compression method that stores surfaces as wavelet-compressed signed-distance volumes. Our approach enables the representation of surfaces with complex topology and arbitrary numbers of components within a single multiresolution data structure. This data structure elegantly handles topological modification at high compression rates. Our method does not require the costly and sometimes infeasible base mesh construction step required by subdivision surface approaches. We present several improvements over previous attempts at compressing signed-distance functions, including an 0(n) distance transform, a zero set initialization method for triangle meshes, and a specialized thresholding algorithm. We demonstrate the potential of sampled distancemore » volumes for surface compression and progressive reconstruction for complex high genus surfaces.« less

[DNA complexes, formed on aqueous phase surfaces: new planar polymeric and composite nanostructures].

PubMed

Antipina, M N; Gaĭnutdinov, R V; Rakhnianskaia, A A; Sergeev-Cherenkov, A N; Tolstikhina, A L; Iurova, T V; Kislov, V V; Khomutov, G B

2003-01-01

The formation of DNA complexes with Langmuir monolayers of the cationic lipid octadecylamine (ODA) and the new amphiphilic polycation poly-4-vinylpyridine with 16% of cetylpyridinium groups (PVP-16) on the surface of an aqueous solution of native DNA of low ionic strength was studied. Topographic images of Langmuir-Blodgett films of DNA/ODA and DNA/PVP-16 complexes applied to micaceous substrates were investigated by the method of atomic force microscopy. It was found that films of the amphiphilic polycation have an ordered planar polycrystalline structure. The morphology of planar DNA complexes with the amphiphilic cation substantially depended on the incubation time and the phase state of the monolayer on the surface of the aqueous DNA solution. Complex structures and individual DNA molecules were observed on the surface of the amphiphilic monolayer. Along with quasi-linear individual bound DNA molecules, characteristic extended net-like structures and quasi-circular toroidal condensed conformations of planar DNA complexes were detected. Mono- and multilayer films of DNA/PVP-16 complexes were used as templates and nanoreactors for the synthesis of inorganic nanostructures via the binding of metal cations from the solution and subsequent generation of the inorganic phase. As a result, ultrathin polymeric composite films with integrated DNA building blocks and quasi-linear arrays of inorganic semiconductor (CdS) and iron oxide nanoparticles and nanowires were obtained. The nanostructures obtained were characterized by scanning probe microscopy and transmission electron microscopy techniques. The methods developed are promising for investigating the mechanisms of structural organization and transformation in DNA and polyelectrolyte complexes at the gas-liquid interface and for the design of new extremely thin highly ordered planar polymeric and composite materials, films, and coatings with controlled ultrastructure for applications in nanoelectronics and nanobiotechnology.

Effective mass and Fermi surface complexity factor from ab initio band structure calculations

NASA Astrophysics Data System (ADS)

Gibbs, Zachary M.; Ricci, Francesco; Li, Guodong; Zhu, Hong; Persson, Kristin; Ceder, Gerbrand; Hautier, Geoffroy; Jain, Anubhav; Snyder, G. Jeffrey

2017-02-01

The effective mass is a convenient descriptor of the electronic band structure used to characterize the density of states and electron transport based on a free electron model. While effective mass is an excellent first-order descriptor in real systems, the exact value can have several definitions, each of which describe a different aspect of electron transport. Here we use Boltzmann transport calculations applied to ab initio band structures to extract a density-of-states effective mass from the Seebeck Coefficient and an inertial mass from the electrical conductivity to characterize the band structure irrespective of the exact scattering mechanism. We identify a Fermi Surface Complexity Factor: Nv*K* from the ratio of these two masses, which in simple cases depends on the number of Fermi surface pockets (Nv* ) and their anisotropy K*, both of which are beneficial to high thermoelectric performance as exemplified by the high values found in PbTe. The Fermi Surface Complexity factor can be used in high-throughput search of promising thermoelectric materials.

Fabrication of meso- and nano-scale structures on surfaces of chalcogenide semiconductors by surface hydrodynamic interference patterning

NASA Astrophysics Data System (ADS)

Bilanych, V.; Komanicky, V.; Lacková, M.; Feher, A.; Kuzma, V.; Rizak, V.

2015-10-01

We observe the change of surface relief on amorphous Ge-As-Se thin films after irradiation with an electron beam. The beam softens the glass and induces various topological surface changes in the irradiated area. The film relief change depends on the film thickness, deposited charge, and film composition. Various structures are formed: Gausian-like cones, extremely sharp Taylor cones, deep craters, and craters with large spires grown on the side. Our investigation shows that these effects can be at least partially a result of electro-hydrodynamic material flow, but the observed phenomena are likely more complex. When we irradiated structural patterns formed by the electron beam with a red laser beam, we could not only fully relax the produced patterns, but also form very complex and intricate superstructures. These organized meso- and nano-scale structures are formed by a combination of photo-induced structural relaxation, light interference on structures fabricated by the e-beam, and photo-induced material flow.

Obtaining source current density related to irregularly structured electromagnetic target field inside human body using hybrid inverse/FDTD method.

PubMed

Han, Jijun; Yang, Deqiang; Sun, Houjun; Xin, Sherman Xuegang

2017-01-01

Inverse method is inherently suitable for calculating the distribution of source current density related with an irregularly structured electromagnetic target field. However, the present form of inverse method cannot calculate complex field-tissue interactions. A novel hybrid inverse/finite-difference time domain (FDTD) method that can calculate the complex field-tissue interactions for the inverse design of source current density related with an irregularly structured electromagnetic target field is proposed. A Huygens' equivalent surface is established as a bridge to combine the inverse and FDTD method. Distribution of the radiofrequency (RF) magnetic field on the Huygens' equivalent surface is obtained using the FDTD method by considering the complex field-tissue interactions within the human body model. The obtained magnetic field distributed on the Huygens' equivalent surface is regarded as the next target. The current density on the designated source surface is derived using the inverse method. The homogeneity of target magnetic field and specific energy absorption rate are calculated to verify the proposed method.

STEM-EELS analysis of multipole surface plasmon modes in symmetry-broken AuAg nanowire dimers

NASA Astrophysics Data System (ADS)

Schubert, Ina; Sigle, Wilfried; van Aken, Peter A.; Trautmann, Christina; Toimil-Molares, Maria Eugenia

2015-03-01

Surface plasmon coupling in nanowires separated by small gaps generates high field enhancements at the position of the gap and is thus of great interest for sensing applications. It is known that the nanowire dimensions and in particular the symmetry of the structures has strong influence on the plasmonic properties of the dimer structure. Here, we report on multipole surface plasmon coupling in symmetry-broken AuAg nanowire dimers. Our dimers, consisting of two nanowires with different lengths and separated by gaps of only 10 to 30 nm, were synthesized by pulsed electrochemical deposition in ion track-etched polymer templates. Electron energy-loss spectroscopy in scanning transmission electron microscopy allows us to resolve up to nine multipole order surface plasmon modes of these dimers spectrally separated from each other. The spectra evidence plasmon coupling between resonances of different multipole order, resulting in the generation of additional plasmonic modes. Since such complex structures require elaborated synthesis techniques, dimer structures with complex composition, morphology and shape are created. We demonstrate that finite element simulations on pure Au dimers can predict the generated resonances in the fabricated structures. The excellent agreement of our experiment on AuAg dimers with finite integration simulations using CST microwave studio manifests great potential to design complex structures for sensing applications.

Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis

DOEpatents

Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA

2008-04-29

The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

Biomimetic surface structuring using cylindrical vector femtosecond laser beams

NASA Astrophysics Data System (ADS)

Skoulas, Evangelos; Manousaki, Alexandra; Fotakis, Costas; Stratakis, Emmanuel

2017-03-01

We report on a new, single-step and scalable method to fabricate highly ordered, multi-directional and complex surface structures that mimic the unique morphological features of certain species found in nature. Biomimetic surface structuring was realized by exploiting the unique and versatile angular profile and the electric field symmetry of cylindrical vector (CV) femtosecond (fs) laser beams. It is shown that, highly controllable, periodic structures exhibiting sizes at nano-, micro- and dual- micro/nano scales can be directly written on Ni upon line and large area scanning with radial and azimuthal polarization beams. Depending on the irradiation conditions, new complex multi-directional nanostructures, inspired by the Shark’s skin morphology, as well as superhydrophobic dual-scale structures mimicking the Lotus’ leaf water repellent properties can be attained. It is concluded that the versatility and features variations of structures formed is by far superior to those obtained via laser processing with linearly polarized beams. More important, by exploiting the capabilities offered by fs CV fields, the present technique can be further extended to fabricate even more complex and unconventional structures. We believe that our approach provides a new concept in laser materials processing, which can be further exploited for expanding the breadth and novelty of applications.

Surface complexation studied via combined grazing-incidence EXAFS and surface diffraction: Arsenate on hematite (0001) and (10-12)

USGS Publications Warehouse

Waychunas, G.; Trainor, T.; Eng, P.; Catalano, J.; Brown, G.; Davis, J.; Rogers, J.; Bargar, J.

2005-01-01

X-ray diffraction [crystal-truncation-rod (CTR)] studies of the surface structure of moisture-equilibrated hematite reveal sites for complexation not present on the bulk oxygen-terminated surface, and impose constraints on the types of inner-sphere sorption topologies. We have used this improved model of the hematite surface to analyze grazing-incidence EXAFS results for arsenate sorption on the c(0001) and r(10-12) surfaces measured in two electric vector polarizations. This work shows that the reconfiguration of the surface under moist conditions is responsible for an increased adsorption density of arsenate complexes on the (0001) surface relative to predicted ideal termination, and an abundance of "edge-sharing" bidentate complexes on both studied surfaces. We consider possible limitations on combining the methods due to differing surface sensitivities, and discuss further analysis possibilities using both methods. ?? Springer-Verlag 2005.

The Silent Canyon caldera complex: a three-dimensional model based on drill-hole stratigraphy and gravity inversion

USGS Publications Warehouse

McKee, Edwin H.; Hildenbrand, Thomas G.; Anderson, Megan L.; Rowley, Peter D.; Sawyer, David A.

1999-01-01

The structural framework of Pahute Mesa, Nevada, is dominated by the Silent Canyon caldera complex, a buried, multiple collapse caldera complex. Using the boundary surface between low density Tertiary volcanogenic rocks and denser granitic and weakly metamorphosed sedimentary rocks (basement) as the outer fault surfaces for the modeled collapse caldera complex, it is postulated that the caldera complex collapsed on steeply- dipping arcuate faults two, possibly three, times following eruption of at least two major ash-flow tuffs. The caldera and most of its eruptive products are now deeply buried below the surface of Pahute Mesa. Relatively low-density rocks in the caldera complex produce one of the largest gravity lows in the western conterminous United States. Gravity modeling defines a steep sided, cup-shaped depression as much as 6,000 meters (19,800 feet) deep that is surrounded and floored by denser rocks. The steeply dipping surface located between the low-density basin fill and the higher density external rocks is considered to be the surface of the ring faults of the multiple calderas. Extrapolation of this surface upward to the outer, or topographic rim, of the Silent Canyon caldera complex defines the upper part of the caldera collapse structure. Rock units within and outside the Silent Canyon caldera complex are combined into seven hydrostratigraphic units based on their predominant hydrologic characteristics. The caldera structures and other faults on Pahute Mesa are used with the seven hydrostratigraphic units to make a three-dimensional geologic model of Pahute Mesa using the "EarthVision" (Dynamic Graphics, Inc.) modeling computer program. This method allows graphic representation of the geometry of the rocks and produces computer generated cross sections, isopach maps, and three-dimensional oriented diagrams. These products have been created to aid in visualizing and modeling the ground-water flow system beneath Pahute Mesa.

Enhanced lithium storage performance of hierarchical CuO nanomaterials with surface fractal characteristics

NASA Astrophysics Data System (ADS)

Li, Ang; He, Renyue; Bian, Zhuo; Song, Huaihe; Chen, Xiaohong; Zhou, Jisheng

2018-06-01

Self-assembled hierarchical CuO nanostructures with fractal structures were prepared by a mild method and exhibited excellent lithium storage properties, certain of which even demonstrated a high reversible capacity of 827 mAh g-1 at a rate of 0.1 C. An interesting phenomenon was observed that the electrochemical performance varies along with the structure complexity, and the products with higher surface factal dimensions exhibited larger capability and better cyclability. Structural and electrochemical analysis methods were used to explore the lithiation kinetics of the samples and the reasons for the outstanding electrochemical performances related to the complexities of hierarchical nanostructures and the irregularities of surface and mass distribution.

Atomic-scale visualization of oxide thin-film surfaces.

PubMed

Iwaya, Katsuya; Ohsawa, Takeo; Shimizu, Ryota; Okada, Yoshinori; Hitosugi, Taro

2018-01-01

The interfaces of complex oxide heterostructures exhibit intriguing phenomena not observed in their constituent materials. The oxide thin-film growth of such heterostructures has been successfully controlled with unit-cell precision; however, atomic-scale understandings of oxide thin-film surfaces and interfaces have remained insufficient. We examined, with atomic precision, the surface and electronic structures of oxide thin films and their growth processes using low-temperature scanning tunneling microscopy. Our results reveal that oxide thin-film surface structures are complicated in contrast to the general perception and that atomically ordered surfaces can be achieved with careful attention to the surface preparation. Such atomically ordered oxide thin-film surfaces offer great opportunities not only for investigating the microscopic origins of interfacial phenomena but also for exploring new surface phenomena and for studying the electronic states of complex oxides that are inaccessible using bulk samples.

Synthesis, crystal structures and Hirshfeld surface analyses of two new Salen type nickel/sodium heteronuclear complexes

NASA Astrophysics Data System (ADS)

Mahlooji, Niloofar; Behzad, Mahdi; Tarahhomi, Atekeh; Maroney, Michael; Rudbari, Hadi Amiri; Bruno, Giuseppe; Ghanbari, Bahram

2016-04-01

Two new heteronuclear Nickel(II)/Sodium(I) complexes of a side-off compartmental Schiff base ligand were synthesized and characterized by spectroscopic methods. Crystal structures of both of the complexes were also obtained. The Schiff base ligand was synthesized from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-3-methoxybenzaldehyde. In both of the complexes the Ni(II) ion is coordinated to the inner N2O2 coordination sphere with square-planar geometry and the Na(I) ion is coordinated to the outer O2 O2‧ coordination sphere. In Complex (1) with general formula [Ni(L)Na(CH3OH)(ClO4)] the sodium ion is seven coordinated while in (2) with general formula [{Ni(L)Na(OH2)}2(μ-Ni(CN)4)] the sodium ion is six coordinated. Intermolecular interactions in two studied complexes were analyzed using 3D Hirshfeld surfaces and corresponding 2D fingerprint plots. This analysis showed that the H … H and C … H/H … C contacts for both structures (altogether 67.5% of total Hirshfeld surface area for (1) and 77.6% for (2)) and the O … H/H … O (24.2%) for (1) and the N … H/H … N (8.1%) contacts for (2) were the characteristic intermolecular contacts in the related crystal structures.

Equivalent complex conductivities representing the effects of T-tubules and folded surface membranes on the electrical admittance and impedance of skeletal muscles measured by external-electrode method

NASA Astrophysics Data System (ADS)

Sekine, Katsuhisa

2017-12-01

In order to represent the effects of T-tubules and folded surface membranes on the electrical admittance and impedance of skeletal muscles measured by the external-electrode method, analytical relations for the equivalent complex conductivities of hypothetical smooth surface membranes were derived. In the relations, the effects of each tubule were represented by the admittance of a straight cable. The effects of the folding of a surface membrane were represented by the increased area of surface membranes. The equivalent complex conductivities were represented as summation of these effects, and the effects of the T-tubules were different between the transversal and longitudinal directions. The validity of the equivalent complex conductivities was supported by the results of finite-difference method (FDM) calculations made using three-dimensional models in which T-tubules and folded surface membranes were represented explicitly. FDM calculations using the equivalent complex conductivities suggested that the electrically inhomogeneous structure due to the existence of muscle cells with T-tubules was sufficient for explaining the experimental results previously obtained using the external-electrode method. Results of FDM calculations in which the structural changes caused by muscle contractions were taken into account were consistent with the reported experimental results.

Surface Structuring with Polarization-Singular Femtosecond Laser Beams Generated by a q-plate

PubMed Central

Nivas, Jijil JJ; Cardano, Filippo; Song, Zhenming; Rubano, Andrea; Fittipaldi, Rosalba; Vecchione, Antonio; Paparo, Domenico; Marrucci, Lorenzo; Bruzzese, Riccardo; Amoruso, Salvatore

2017-01-01

In the last few years femtosecond optical vortex beams with different spatial distributions of the state of polarization (e.g. azimuthal, radial, spiral, etc.) have been used to generate complex, regular surface patterns on different materials. Here we present an experimental investigation on direct femtosecond laser surface structuring based on a larger class of vector beams generated by means of a q-plate with topological charge q = +1/2. In fact, voltage tuning of q-plate optical retardation allows generating a family of ultrashort laser beams with a continuous spatial evolution of polarization and fluence distribution in the focal plane. These beams can be thought of as a controlled coherent superposition of a Gaussian beam with uniform polarization and a vortex beam with a radial or azimuthal state of polarization. The use of this family of ultrashort laser beams in surface structuring leads to a further extension of the achievable surface patterns. The comparison of theoretical predictions of the vector beam characteristics at the focal plane and the generated surface patterns is used to rationalize the dependence of the surface structures on the local state of the laser beam, thus offering an effective way to either design unconventional surface structures or diagnose complex ultrashort laser beams. PMID:28169342

Surface Structuring with Polarization-Singular Femtosecond Laser Beams Generated by a q-plate.

PubMed

Nivas, Jijil Jj; Cardano, Filippo; Song, Zhenming; Rubano, Andrea; Fittipaldi, Rosalba; Vecchione, Antonio; Paparo, Domenico; Marrucci, Lorenzo; Bruzzese, Riccardo; Amoruso, Salvatore

2017-02-07

In the last few years femtosecond optical vortex beams with different spatial distributions of the state of polarization (e.g. azimuthal, radial, spiral, etc.) have been used to generate complex, regular surface patterns on different materials. Here we present an experimental investigation on direct femtosecond laser surface structuring based on a larger class of vector beams generated by means of a q-plate with topological charge q = +1/2. In fact, voltage tuning of q-plate optical retardation allows generating a family of ultrashort laser beams with a continuous spatial evolution of polarization and fluence distribution in the focal plane. These beams can be thought of as a controlled coherent superposition of a Gaussian beam with uniform polarization and a vortex beam with a radial or azimuthal state of polarization. The use of this family of ultrashort laser beams in surface structuring leads to a further extension of the achievable surface patterns. The comparison of theoretical predictions of the vector beam characteristics at the focal plane and the generated surface patterns is used to rationalize the dependence of the surface structures on the local state of the laser beam, thus offering an effective way to either design unconventional surface structures or diagnose complex ultrashort laser beams.

Surface Structuring with Polarization-Singular Femtosecond Laser Beams Generated by a q-plate

NASA Astrophysics Data System (ADS)

Nivas, Jijil Jj; Cardano, Filippo; Song, Zhenming; Rubano, Andrea; Fittipaldi, Rosalba; Vecchione, Antonio; Paparo, Domenico; Marrucci, Lorenzo; Bruzzese, Riccardo; Amoruso, Salvatore

2017-02-01

In the last few years femtosecond optical vortex beams with different spatial distributions of the state of polarization (e.g. azimuthal, radial, spiral, etc.) have been used to generate complex, regular surface patterns on different materials. Here we present an experimental investigation on direct femtosecond laser surface structuring based on a larger class of vector beams generated by means of a q-plate with topological charge q = +1/2. In fact, voltage tuning of q-plate optical retardation allows generating a family of ultrashort laser beams with a continuous spatial evolution of polarization and fluence distribution in the focal plane. These beams can be thought of as a controlled coherent superposition of a Gaussian beam with uniform polarization and a vortex beam with a radial or azimuthal state of polarization. The use of this family of ultrashort laser beams in surface structuring leads to a further extension of the achievable surface patterns. The comparison of theoretical predictions of the vector beam characteristics at the focal plane and the generated surface patterns is used to rationalize the dependence of the surface structures on the local state of the laser beam, thus offering an effective way to either design unconventional surface structures or diagnose complex ultrashort laser beams.

Molecular recognition on a cavitand-functionalized silicon surface.

PubMed

Biavardi, Elisa; Favazza, Maria; Motta, Alessandro; Fragalà, Ignazio L; Massera, Chiara; Prodi, Luca; Montalti, Marco; Melegari, Monica; Condorelli, Guglielmo G; Dalcanale, Enrico

2009-06-03

A Si(100) surface featuring molecular recognition properties was obtained by covalent functionalization with a tetraphosphonate cavitand (Tiiii), able to complex positively charged species. Tiiii cavitand was grafted onto the Si by photochemical hydrosilylation together with 1-octene as a spatial spectator. The recognition properties of the Si-Tiiii surface were demonstrated through two independent analytical techniques, namely XPS and fluorescence spectroscopy, during the course of reversible complexation-guest exchange-decomplexation cycles with specifically designed ammonium and pyridinium salts. Control experiments employing a Si(100) surface functionalized with a structurally similar, but complexation inactive, tetrathiophosphonate cavitand (TSiiii) demonstrated no recognition events. This provides evidence for the complexation properties of the Si-Tiiii surface, ruling out the possibility of nonspecific interactions between the substrate and the guests. The residual Si-O(-) terminations on the surface replace the guests' original counterions, thus stabilizing the complex ion pairs. These results represent a further step toward the control of self-assembly of complex supramolecular architectures on surfaces.

Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes

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

Vasan, Neil; Hutagalung, Alex; Novick, Peter

2010-08-13

The Golgi-associated retrograde protein (GARP) complex is a membrane-tethering complex that functions in traffic from endosomes to the trans-Golgi network. Here we present the structure of a C-terminal fragment of the Vps53 subunit, important for binding endosome-derived vesicles, at a resolution of 2.9 {angstrom}. We show that the C terminus consists of two {alpha}-helical bundles arranged in tandem, and we identify a highly conserved surface patch, which may play a role in vesicle recognition. Mutations of the surface result in defects in membrane traffic. The fold of the Vps53 C terminus is strongly reminiscent of proteins that belong to threemore » other tethering complexes - Dsl1, conserved oligomeric Golgi, and the exocyst - thought to share a common evolutionary origin. Thus, the structure of the Vps53 C terminus suggests that GARP belongs to this family of complexes.« less

Fine tuning and orientation control of surface Cu complexes on TiO2(110) premodified with mercapto compounds: the effect of different mercapto group positions.

PubMed

Takakusagi, Satoru; Nojima, Hirotaka; Ariga, Hiroko; Uehara, Hiromitsu; Miyazaki, Kotaro; Chun, Wang-Jae; Iwasawa, Yasuhiro; Asakura, Kiyotaka

2013-09-07

Three-dimensional structures of vacuum-deposited Cu species formed on TiO2(110) surfaces premodified with three mercaptobenzoic acid (MBA) isomers were studied using polarization-dependent total reflection fluorescence X-ray absorption fine structure (PTRF-XAFS). We explored the possibility of fine tuning and orientation control of the surface Cu structures, including their coordination and configuration against the surface, according to the different mercapto group positions of the three MBA isomers (o-, m-, and p-MBA). Almost linear S-Cu-O (lattice O of TiO2) surface compounds were formed on the three MBA-modified TiO2(110) surfaces; however, the orientation of the Cu species on the o- and m-MBA-modified TiO2(110) surfaces (40-45° inclined from the surface normal) was different from that on the p-MBA-modified TiO2(110) surface (60° from the surface normal). This work suggests that the selection of a different MBA isomer for premodification of a single crystal TiO2(110) surface enables fine tuning and orientation control of surface Cu complexes.

On the anomalous adsorption of [Pd(edta)]2- at the water/Goethite interface: spectroscopic evidence for two types of surface complexes.

PubMed

Kaplun, Marina; Nordin, Agneta; Persson, Per

2008-01-15

The structure of palladium(II) ethylenediaminetetraacetate (edta) in aqueous solutions and its adsorption on the surface of goethite (alpha-FeOOH) were studied using extended X-ray absorption fine structure spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy. The obtained results show that in aqueous solutions, Pd-edta exists as a 1:1 complex, [Pd(edta)]2-, with edta acting as a quadridentate ligand. On the surface of goethite, [Pd(edta)]2- forms two different types of complexes over a pH range of 3.40-8.12. At pH < 5, [Pd(edta)]2- adsorbs as an outer-sphere species with possible hydrogen bonding. At higher pH values, the formation of inner-sphere complexes of the cation-type sets in after a cleavage of one glycinate ring and the formation of an (edta)Pd-O-Fe linkage.

Protein surface roughness accounts for binding free energy of Plasmepsin II-ligand complexes.

PubMed

Valdés-Tresanco, Mario E; Valdés-Tresanco, Mario S; Valiente, Pedro A; Cocho, Germinal; Mansilla, Ricardo; Nieto-Villar, J M

2018-01-01

The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high-resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x-ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave-one-out cross-validation showed that our model reproduced accurately the absolute binding free energies for our training set (R 2  = 0.76; <|error|> =0.55 kcal/mol; SD error  = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article. Copyright © 2017 John Wiley & Sons, Ltd.

Inner-sphere complexation of cations at the rutile-water interface: A concise surface structural interpretation with the CD and MUSIC model

NASA Astrophysics Data System (ADS)

Ridley, Moira K.; Hiemstra, Tjisse; van Riemsdijk, Willem H.; Machesky, Michael L.

2009-04-01

Acid-base reactivity and ion-interaction between mineral surfaces and aqueous solutions is most frequently investigated at the macroscopic scale as a function of pH. Experimental data are then rationalized by a variety of surface complexation models. These models are thermodynamically based which in principle does not require a molecular picture. The models are typically calibrated to relatively simple solid-electrolyte solution pairs and may provide poor descriptions of complex multi-component mineral-aqueous solutions, including those found in natural environments. Surface complexation models may be improved by incorporating molecular-scale surface structural information to constrain the modeling efforts. Here, we apply a concise, molecularly-constrained surface complexation model to a diverse suite of surface titration data for rutile and thereby begin to address the complexity of multi-component systems. Primary surface charging curves in NaCl, KCl, and RbCl electrolyte media were fit simultaneously using a charge distribution (CD) and multisite complexation (MUSIC) model [Hiemstra T. and Van Riemsdijk W. H. (1996) A surface structural approach to ion adsorption: the charge distribution (CD) model. J. Colloid Interf. Sci. 179, 488-508], coupled with a Basic Stern layer description of the electric double layer. In addition, data for the specific interaction of Ca 2+ and Sr 2+ with rutile, in NaCl and RbCl media, were modeled. In recent developments, spectroscopy, quantum calculations, and molecular simulations have shown that electrolyte and divalent cations are principally adsorbed in various inner-sphere configurations on the rutile 1 1 0 surface [Zhang Z., Fenter P., Cheng L., Sturchio N. C., Bedzyk M. J., Předota M., Bandura A., Kubicki J., Lvov S. N., Cummings P. T., Chialvo A. A., Ridley M. K., Bénézeth P., Anovitz L., Palmer D. A., Machesky M. L. and Wesolowski D. J. (2004) Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties. Langmuir20, 4954-4969]. Our CD modeling results are consistent with these adsorbed configurations provided adsorbed cation charge is allowed to be distributed between the surface (0-plane) and Stern plane (1-plane). Additionally, a complete description of our titration data required inclusion of outer-sphere binding, principally for Cl - which was common to all solutions, but also for Rb + and K +. These outer-sphere species were treated as point charges positioned at the Stern layer, and hence determined the Stern layer capacitance value. The modeling results demonstrate that a multi-component suite of experimental data can be successfully rationalized within a CD and MUSIC model using a Stern-based description of the EDL. Furthermore, the fitted CD values of the various inner-sphere complexes of the mono- and divalent ions can be linked to the microscopic structure of the surface complexes and other data found by spectroscopy as well as molecular dynamics (MD). For the Na + ion, the fitted CD value points to the presence of bidenate inner-sphere complexation as suggested by a recent MD study. Moreover, its MD dominance quantitatively agrees with the CD model prediction. For Rb +, the presence of a tetradentate complex, as found by spectroscopy, agreed well with the fitted CD and its predicted presence was quantitatively in very good agreement with the amount found by spectroscopy.

inner-sphere complexation of cations at the rutile-water interface: A concise surface structural interpretation with the CD and MUSIC model

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

Ridley, Mora K.; Hiemstra, T; Van Riemsdijk, Willem H.

Acid base reactivity and ion-interaction between mineral surfaces and aqueous solutions is most frequently investigated at the macroscopic scale as a function of pH. Experimental data are then rationalized by a variety of surface complexation models. These models are thermodynamically based which in principle does not require a molecular picture. The models are typically calibrated to relatively simple solid-electrolyte solution pairs and may provide poor descriptions of complex multicomponent mineral aqueous solutions, including those found in natural environments. Surface complexation models may be improved by incorporating molecular-scale surface structural information to constrain the modeling efforts. Here, we apply a concise,more » molecularly-constrained surface complexation model to a diverse suite of surface titration data for rutile and thereby begin to address the complexity of multi-component systems. Primary surface charging curves in NaCl, KCl, and RbCl electrolyte media were fit simultaneously using a charge distribution (CD) and multisite complexation (MUSIC) model [Hiemstra T. and Van Riemsdijk W. H. (1996) A surface structural approach to ion adsorption: the charge distribution (CD) model. J. Colloid Interf. Sci. 179, 488 508], coupled with a Basic Stern layer description of the electric double layer. In addition, data for the specific interaction of Ca2+ and Sr2+ with rutile, in NaCl and RbCl media, were modeled. In recent developments, spectroscopy, quantum calculations, and molecular simulations have shown that electrolyte and divalent cations are principally adsorbed in various inner-sphere configurations on the rutile 110 surface [Zhang Z., Fenter P., Cheng L., Sturchio N. C., Bedzyk M. J., Pr edota M., Bandura A., Kubicki J., Lvov S. N., Cummings P. T., Chialvo A. A., Ridley M. K., Be ne zeth P., Anovitz L., Palmer D. A., Machesky M. L. and Wesolowski D. J. (2004) Ion adsorption at the rutile water interface: linking molecular and macroscopic properties. Langmuir 20, 4954 4969]. Our CD modeling results are consistent with these adsorbed configurations provided adsorbed cation charge is allowed to be distributed between the surface (0-plane) and Stern plane (1-plane). Additionally, a complete description of our titration data required inclusion of outer-sphere binding, principally for Cl which was common to all solutions, but also for Rb+ and K+. These outer-sphere species were treated as point charges positioned at the Stern layer, and hence determined the Stern layer capacitance value. The modeling results demonstrate that a multi-component suite of experimental data can be successfully rationalized within a CD and MUSIC model using a Stern-based description of the EDL. Furthermore, the fitted CD values of the various inner-sphere complexes of the mono- and divalent ions can be linked to the microscopic structure of the surface complexes and other data found by spectroscopy as well as molecular dynamics (MD). For the Na+ ion, the fitted CD value points to the presence of bidenate inner-sphere complexation as suggested by a recent MD study. Moreover, its MD dominance quantitatively agrees with the CD model prediction. For Rb+, the presence of a tetradentate complex, as found by spectroscopy, agreed well with the fitted CD and its predicted presence was quantitatively in very good agreement with the amount found by spectroscopy.« less

Intercomparison of 7 Planetary Boundary-Layer/Surface-Layer Physics Schemes over Complex Terrain for Battlefield Situational Awareness

DTIC Science & Technology

This study considers the performance of 7 of the Weather Research and Forecast model boundary-layer (BL) parameterization schemes in a complex...schemes performed best. The surface parameters, planetary BL structure, and vertical profiles are important for US Army Research Laboratory

Complexation and phase evolution at dimethylformamide-Ag(111) interfaces

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

Song, Wentao; Leung, Kevin; Shao, Qian

The interaction of solvent molecules with metallic surfaces impacts many interfacial chemical processes. We investigate the chemical and structure evolution that follows adsorption of the polar solvent dimethylformamide (DMF) on Ag(111). An Ag(DMF) 2 coordination complex forms spontaneously by DMF etching of Ag(111), yielding mixed films of the complexes and DMF. Utilizing ultrahigh vacuum scanning tunneling microscopy (UHV-STM), in combination with X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) computations, we map monolayer phases from the 2-D gas regime, consisting of a binary mixture of DMF and Ag(DMF) 2, through the saturation monolayer limit, in which these two chemicalmore » species phase separate into ordered islands. Structural models for the near-square DMF phase and the chain-like Ag(DMF) 2 phase are presented and supported by DFT computation. Interface evolution is summarized in a surface pressure-composition phase diagram, which allows structure prediction over arbitrary experimental conditions. In conclusion, this work reveals new surface coordination chemistry for an important electrolyte-electrode system, and illustrates how surface pressure can be used to tune monolayer phases.« less

Complexation and phase evolution at dimethylformamide-Ag(111) interfaces

DOE PAGES

Song, Wentao; Leung, Kevin; Shao, Qian; ...

2016-09-15

The interaction of solvent molecules with metallic surfaces impacts many interfacial chemical processes. We investigate the chemical and structure evolution that follows adsorption of the polar solvent dimethylformamide (DMF) on Ag(111). An Ag(DMF) 2 coordination complex forms spontaneously by DMF etching of Ag(111), yielding mixed films of the complexes and DMF. Utilizing ultrahigh vacuum scanning tunneling microscopy (UHV-STM), in combination with X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) computations, we map monolayer phases from the 2-D gas regime, consisting of a binary mixture of DMF and Ag(DMF) 2, through the saturation monolayer limit, in which these two chemicalmore » species phase separate into ordered islands. Structural models for the near-square DMF phase and the chain-like Ag(DMF) 2 phase are presented and supported by DFT computation. Interface evolution is summarized in a surface pressure-composition phase diagram, which allows structure prediction over arbitrary experimental conditions. In conclusion, this work reveals new surface coordination chemistry for an important electrolyte-electrode system, and illustrates how surface pressure can be used to tune monolayer phases.« less

STRUCTURAL DYNAMICS OF METAL PARTITIONING TO MINERAL SURFACES

EPA Science Inventory

The conceptual understanding of surface complexation reactions that control trace element partitioning to mineral surfaces is limited by the assumption that the solid reactant possesses a finite, time-invariant population of surface functional groups. This assumption has limited...

Biomimetic surface structuring using cylindrical vector femtosecond laser beams

PubMed Central

Skoulas, Evangelos; Manousaki, Alexandra; Fotakis, Costas; Stratakis, Emmanuel

2017-01-01

We report on a new, single-step and scalable method to fabricate highly ordered, multi-directional and complex surface structures that mimic the unique morphological features of certain species found in nature. Biomimetic surface structuring was realized by exploiting the unique and versatile angular profile and the electric field symmetry of cylindrical vector (CV) femtosecond (fs) laser beams. It is shown that, highly controllable, periodic structures exhibiting sizes at nano-, micro- and dual- micro/nano scales can be directly written on Ni upon line and large area scanning with radial and azimuthal polarization beams. Depending on the irradiation conditions, new complex multi-directional nanostructures, inspired by the Shark’s skin morphology, as well as superhydrophobic dual-scale structures mimicking the Lotus’ leaf water repellent properties can be attained. It is concluded that the versatility and features variations of structures formed is by far superior to those obtained via laser processing with linearly polarized beams. More important, by exploiting the capabilities offered by fs CV fields, the present technique can be further extended to fabricate even more complex and unconventional structures. We believe that our approach provides a new concept in laser materials processing, which can be further exploited for expanding the breadth and novelty of applications. PMID:28327611

Non-interacting surface solvation and dynamics in protein-protein interactions.

PubMed

Visscher, Koen M; Kastritis, Panagiotis L; Bonvin, Alexandre M J J

2015-03-01

Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo binders with preferred interaction properties. At a structural and molecular level, interface and rim regions are not enough to fully account for the energetics of protein-protein binding, even for simple lock-and-key rigid binders. As we have recently shown, properties of the global surface might also play a role in protein-protein interactions. Here, we report on molecular dynamics simulations performed to understand solvent effects on protein-protein surfaces. We compare properties of the interface, rim, and non-interacting surface regions for five different complexes and their free components. Interface and rim residues become, as expected, less mobile upon complexation. However, non-interacting surface appears more flexible in the complex. Fluctuations of polar residues are always lower compared with charged ones, independent of the protein state. Further, stable water molecules are often observed around polar residues, in contrast to charged ones. Our analysis reveals that (a) upon complexation, the non-interacting surface can have a direct entropic compensation for the lower interface and rim entropy and (b) the mobility of the first hydration layer, which is linked to the stability of the protein-protein complex, is influenced by the local chemical properties of the surface. These findings corroborate previous hypotheses on the role of the hydration layer in shielding protein-protein complexes from unintended protein-protein interactions. © 2014 Wiley Periodicals, Inc.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Surface Modification and Nanojunction Fabrication with Molecular Metal Wires

DTIC Science & Technology

2014-02-17

Title: Transition Metal Complexes of a Super Rigid Anthyridine Ligand: Structural, Magnetic and DFT Studies. Transition metal complexes of iron ( II ...Compounds with Masked Diazonium Capping Groups (J. Organomet. Chem. 2013, 745, 93). (3) New Diruthenium( II ,III) Compounds Bearing Terminal Olefin Groups...2012, 36, 2340). (2) Synthesis , Structure, Magnetism, and Single Molecular Conductance of Linear Trinickel String Complexes with Sulfur-Containing

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Scale-free networks of the earth’s surface

NASA Astrophysics Data System (ADS)

Liu, Gang; He, Jing; Luo, Kaitian; Gao, Peichao; Ma, Lei

2016-06-01

Studying the structure of real complex systems is of paramount importance in science and engineering. Despite our understanding of lots of real systems, we hardly cognize our unique living environment — the earth. The structural complexity of the earth’s surface is, however, still unknown in detail. Here, we define the modeling of graph topology for the earth’s surface, using the satellite images of the earth’s surface under different spatial resolutions derived from Google Earth. We find that the graph topologies of the earth’s surface are scale-free networks regardless of the spatial resolutions. For different spatial resolutions, the exponents of power-law distributions and the modularity are both quite different; however, the average clustering coefficient is approximately equal to a constant. We explore the morphology study of the earth’s surface, which enables a comprehensive understanding of the morphological feature of the earth’s surface.

Hierarchical micro-nano structured Ti6Al4V surface topography via two-step etching process for enhanced hydrophilicity and osteoblastic responses.

PubMed

Moon, Byeong-Seok; Kim, Sungwon; Kim, Hyoun-Ee; Jang, Tae-Sik

2017-04-01

Hierarchical micro-nano (HMN) surface structuring of dental implants is a fascinating strategy for achieving fast and mechanically stable fixation due to the synergetic effect of micro- and nano-scale surface roughness with surrounding tissues. However, the introduction of a well-defined nanostructure on a microstructure having complex surface geometry is still challenging. As a means of fabricating HMN surface on Ti6Al4V-ELI, target-ion induced plasma sputtering (TIPS) was used onto a sand-blasted, large-grit and acid-etched substrate. The HMN surface topography was simply controlled by adjusting the tantalum (Ta) target power of the TIPS technique, which is directly related to the Ta ion flux and the surface chemical composition of the substrate. Characterization using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and laser scanning microscopy (LSM) verified that well-defined nano-patterned surface structures with a depth of ~300 to 400nm and a width of ~60 to 70nm were uniformly distributed and followed the complex micron-sized surface geometry. In vitro cellular responses of pre-osteoblast cells (MC3T3-E1) were assessed by attachment and proliferation of cells on flat, nano-roughened, micro-roughened, and an HMN surface structure of Ti6Al4V-ELI. Moreover, an in vivo dog mandible defect model study was used to investigate the biological effect of the HMN surface structure compared with the micro-roughened surface. The results showed that the surface nanostructure significantly increased the cellular activities of flat and micro-roughened Ti, and the bone-to-implant contact area and new bone volume were significantly improved on the HMN surface structured Ti. These results support the idea that an HMN surface structure on Ti6Al4V-ELI alloy has great potential for enhancing the biological performance of dental implants. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular-orbital models for the catalytic activity and selectivity of coordinatively unsaturated platinum surfaces and complexes

NASA Astrophysics Data System (ADS)

Balazs, A. C.; Johnson, K. H.

1982-01-01

Electronic structures have been calculated for 5-, 6-, and 10-atom Pt clusters, as well as for a Pt(PH 3) 4 coordination complex, using the self-consistent-field X-alpha scattered-wave (SCF-Xα-SW) molecular-orbital technique. The 10-atom cluster models the local geometry of a flat, unreconstructed Pt(100) surface, while the 5- and 6-atom clusters show features of a stepped Pt surface. Pt(PH 3) 4 resembles the chemically similar homogeneous catalyst Pt(PPh 3) 4. Common to all these coordinatively unsaturated complexes are orbitals lying near or coinciding with the highest occupied molecular orbital ("Fermi level") which show pronounced d lobes pointing directly into the vacuum. Under the hypothesis that these molecular orbitals are mainly responsible for the chemical activities of the above species, one can account for the relative similarities and differences in catalytic activity and selectivity displayed by unreconstructed Pt(100) surfaces, stepped Pt surfaces or particles, and isolated Pt(PPh 3) 4 coordination complexes. The relevance of these findings to catalyst-support interactions is also discussed. Finally, relativistic corrections to the electronic structures are calculated and their implications on catalytic properties discussed.

Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system.

PubMed

Cornilescu, Gabriel; Lee, Byeong Ryong; Cornilescu, Claudia C; Wang, Guangshun; Peterkofsky, Alan; Clore, G Marius

2002-11-01

The solution structure of the complex between the cytoplasmic A domain (IIA(Mtl)) of the mannitol transporter II(Mannitol) and the histidine-containing phosphocarrier protein (HPr) of the Escherichia coli phosphotransferase system has been solved by NMR, including the use of conjoined rigid body/torsion angle dynamics, and residual dipolar couplings, coupled with cross-validation, to permit accurate orientation of the two proteins. A convex surface on HPr, formed by helices 1 and 2, interacts with a complementary concave depression on the surface of IIA(Mtl) formed by helix 3, portions of helices 2 and 4, and beta-strands 2 and 3. The majority of intermolecular contacts are hydrophobic, with a small number of electrostatic interactions at the periphery of the interface. The active site histidines, His-15 of HPr and His-65 of IIA(Mtl), are in close spatial proximity, and a pentacoordinate phosphoryl transition state can be readily accommodated with no change in protein-protein orientation and only minimal perturbations of the backbone immediately adjacent to the histidines. Comparison with two previously solved structures of complexes of HPr with partner proteins of the phosphotransferase system, the N-terminal domain of enzyme I (EIN) and enzyme IIA(Glucose) (IIA(Glc)), reveals a number of common features despite the fact that EIN, IIA(Glc), and IIA(Mtl) bear no structural resemblance to one another. Thus, entirely different underlying structural elements can form binding surfaces for HPr that are similar in terms of both shape and residue composition. These structural comparisons illustrate the roles of surface and residue complementarity, redundancy, incremental build-up of specificity and conformational side chain plasticity in the formation of transient specific protein-protein complexes in signal transduction pathways.

Forced convection in the wakes of sliding bubbles

NASA Astrophysics Data System (ADS)

Meehan, O'Reilly; Donnelly, B.; Persoons, T.; Nolan, K.; Murray, D. B.

2016-09-01

Both vapour and gas bubbles are known to significantly increase heat transfer rates between a heated surface and the surrounding fluid, even with no phase change. However, the complex wake structures means that the surface cooling is not fully understood. The current study uses high speed infra-red thermography to measure the surface temperature and convective heat flux enhancement associated with an air bubble sliding under an inclined surface, with a particular focus on the wake. Enhancement levels of 6 times natural convection levels are observed, along with cooling patterns consistent with a possible hairpin vortex structure interacting with the thermal boundary layer. Local regions of suppressed convective heat transfer highlight the complexity of the bubble wake in two-phase applications.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

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

Collective evolution of submicron hillocks during the early stages of anisotropic alkaline wet chemical etching of Si(1 0 0) surfaces

NASA Astrophysics Data System (ADS)

Sana, P.; Vázquez, Luis; Cuerno, Rodolfo; Sarkar, Subhendu

2017-11-01

We address experimentally the large-scale dynamics of Si(1 0 0) surfaces during the initial stages of anisotropic wet (KOH) chemical etching, which are characterized through atomic force microscopy. These systems are known to lead to the formation of characteristic pyramids, or hillocks, of typical sizes in the nanometric/micrometer scales, thus with the potential for a large number of applications that can benefit from the nanotexturing of Si surfaces. The present pattern formation process is very strongly disordered in space. We assess the space correlations in such a type of rough surface and elucidate the existence of a complex and rich morphological evolution, featuring at least three different regimes in just 10 min of etching. Such a complex time behavior cannot be consistently explained within a single formalism for dynamic scaling. The pyramidal structure reveals itself as the basic morphological motif of the surface throughout the dynamics. A detailed analysis of the surface slope distribution with etching time reveals that the texturing process induced by the KOH etching is rather gradual and progressive, which accounts for the dynamic complexity. The various stages of the morphological evolution can be accurately reproduced by computer-generated surfaces composed by uncorrelated pyramidal structures. To reach such an agreement, the key parameters are the average pyramid size, which increases with etching time, its distribution and the surface coverage by the pyramidal structures.

Internal Structure of a Lobate Debris Apron Complex in Eastern Hellas: Evidence for Multiple Mid-Latitude Glaciations on Mars

NASA Astrophysics Data System (ADS)

Quartini, E.; Holt, J. W.; Brothers, T. C.

2011-03-01

The past depositional history of a lobate debris apron complex in eastern Hellas has been investigated by conducting a combined analysis of its surface morphology and subsurface structure using a CTX mosaic and orbital radar sounding data from SHARAD.

New five coordinated supramolecular structured cadmium complex as precursor for CdO nanoparticles: Synthesis, crystal structure, theoretical and 3D Hirshfeld surface analyses

NASA Astrophysics Data System (ADS)

Ghanbari Niyaky, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

2017-03-01

In this paper, a combined experimental and theoretical study on a new CdLBr2 complex (L = N1-(2-bromobenzylidene)-N2-(2-((E)-(2-bromobenzylidene) amino)ethyl) ethane-1,2-diamine) synthesized via template method, is described. The crystal structure analysis of the complex indicates that, the Cd(II) ion is centered in a distorted square pyramidal space constructed by three iminic nitrogens of the ligand as well as two bromide anions. More analysis of crystal packing proposed a supramolecular structure stabilized by some non-covalent interactions such as Br⋯Br and Xsbnd H⋯Br (X = N and C) in solid state. Furthermore, 3D Hirshfeld surface analyses and DFT studies were applied for theoretical investigation of the complexes. Theoretical achievements were found in a good agreement with respect to the experimental data. To evaluate the nature of bonding and the strength of the intra and inter-molecular interactions a natural bond orbital (NBO) analysis on the complex structure was performed. Time dependent density functional theory (TD-DFT) was also applied to predict the electronic spectral data of the complex as compared with the experimental ones. CdLBr2 complex as nano-structure compound was also prepared under ultrasonic conditions and characterized by scanning electron microscopy (SEM) and X-ray powder diffraction (XRPD). Finally, it was found that the cadmium complex can be used as a suitable precursor for preparation of CdO nanoparticles via calcination process at 600 °C under air atmosphere.

Thermal transformation of bioactive caffeic acid on fumed silica seen by UV-Vis spectroscopy, thermogravimetric analysis, temperature programmed desorption mass spectrometry and quantum chemical methods.

PubMed

Kulik, Tetiana V; Lipkovska, Natalia O; Barvinchenko, Valentyna M; Palyanytsya, Borys B; Kazakova, Olga A; Dudik, Olesia O; Menyhárd, Alfréd; László, Krisztina

2016-05-15

Thermochemical studies of hydroxycinnamic acid derivatives and their surface complexes are important for the pharmaceutical industry, medicine and for the development of technologies of heterogeneous biomass pyrolysis. In this study, structural and thermal transformations of caffeic acid complexes on silica surfaces were studied by UV-Vis spectroscopy, thermogravimetric analysis, temperature programmed desorption mass spectrometry (TPD MS) and quantum chemical methods. Two types of caffeic acid surface complexes are found to form through phenolic or carboxyl groups. The kinetic parameters of the chemical reactions of caffeic acid on silica surface are calculated. The mechanisms of thermal transformations of the caffeic chemisorbed surface complexes are proposed. Thermal decomposition of caffeic acid complex chemisorbed through grafted ester group proceeds via three parallel reactions, producing ketene, vinyl and acetylene derivatives of 1,2-dihydroxybenzene. Immobilization of phenolic acids on the silica surface improves greatly their thermal stability. Copyright © 2016 Elsevier Inc. All rights reserved.

Surface reaction of SnII on goethite (α-FeOOH): surface complexation, redox reaction, reductive dissolution, and phase transformation.

PubMed

Dulnee, Siriwan; Scheinost, Andreas C

2014-08-19

To elucidate the potential risk of (126)Sn migration from nuclear waste repositories, we investigated the surface reactions of Sn(II) on goethite as a function of pH and Sn(II) loading under anoxic condition with O2 level < 2 ppmv. Tin redox state and surface structure were investigated by Sn K edge X-ray absorption spectroscopy (XAS), goethite phase transformations were investigated by high-resolution transmission electron microscopy and selected area electron diffraction. The results demonstrate the rapid and complete oxidation of Sn(II) by goethite and formation of Sn(IV) (1)E and (2)C surface complexes. The contribution of (2)C complexes increases with Sn loading. The Sn(II) oxidation leads to a quantitative release of Fe(II) from goethite at low pH, and to the precipitation of magnetite at higher pH. To predict Sn sorption, we applied surface complexation modeling using the charge distribution multisite complexation approach and the XAS-derived surface complexes. Log K values of 15.5 ± 1.4 for the (1)E complex and 19.2 ± 0.6 for the (2)C complex consistently predict Sn sorption across pH 2-12 and for two different Sn loadings and confirm the strong retention of Sn(II) even under anoxic conditions.

White Light Used to Enable Enhanced Surface Topography, Geometry, and Wear Characterization of Oil-Free Bearings

NASA Technical Reports Server (NTRS)

Lucero, John M.

2003-01-01

A new optically based measuring capability that characterizes surface topography, geometry, and wear has been employed by NASA Glenn Research Center s Tribology and Surface Science Branch. To characterize complex parts in more detail, we are using a three-dimensional, surface structure analyzer-the NewView5000 manufactured by Zygo Corporation (Middlefield, CT). This system provides graphical images and high-resolution numerical analyses to accurately characterize surfaces. Because of the inherent complexity of the various analyzed assemblies, the machine has been pushed to its limits. For example, special hardware fixtures and measuring techniques were developed to characterize Oil- Free thrust bearings specifically. We performed a more detailed wear analysis using scanning white light interferometry to image and measure the bearing structure and topography, enabling a further understanding of bearing failure causes.

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

A novel protein-protein interaction in the RES (REtention and Splicing) complex.

PubMed

Tripsianes, Konstantinos; Friberg, Anders; Barrandon, Charlotte; Brooks, Mark; van Tilbeurgh, Herman; Seraphin, Bertrand; Sattler, Michael

2014-10-10

The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp(232) in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Photoexpulsion of surface-grafted ruthenium complexes and subsequent release of cytotoxic cargos to cancer cells from mesoporous silica nanoparticles.

PubMed

Frasconi, Marco; Liu, Zhichang; Lei, Juying; Wu, Yilei; Strekalova, Elena; Malin, Dmitry; Ambrogio, Michael W; Chen, Xinqi; Botros, Youssry Y; Cryns, Vincent L; Sauvage, Jean-Pierre; Stoddart, J Fraser

2013-08-07

Ruthenium(II) polypyridyl complexes have emerged both as promising probes of DNA structure and as anticancer agents because of their unique photophysical and cytotoxic properties. A key consideration in the administration of those therapeutic agents is the optimization of their chemical reactivities to allow facile attack on the target sites, yet avoid unwanted side effects. Here, we present a drug delivery platform technology, obtained by grafting the surface of mesoporous silica nanoparticles (MSNPs) with ruthenium(II) dipyridophenazine (dppz) complexes. This hybrid nanomaterial displays enhanced luminescent properties relative to that of the ruthenium(II) dppz complex in a homogeneous phase. Since the coordination between the ruthenium(II) complex and a monodentate ligand linked covalently to the nanoparticles can be cleaved under irradiation with visible light, the ruthenium complex can be released from the surface of the nanoparticles by selective substitution of this ligand with a water molecule. Indeed, the modified MSNPs undergo rapid cellular uptake, and after activation with light, the release of an aqua ruthenium(II) complex is observed. We have delivered, in combination, the ruthenium(II) complex and paclitaxel, loaded in the mesoporous structure, to breast cancer cells. This hybrid material represents a promising candidate as one of the so-called theranostic agents that possess both diagnostic and therapeutic functions.

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues

DOE PAGES

Nikolaienko, Roman M.; Hammel, Michal; Dubreuil, Véronique; ...

2016-08-18

Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptormore » cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling.« less

From chloroplasts to photosystems: in situ scanning force microscopy on intact thylakoid membranes

PubMed Central

Kaftan, David; Brumfeld, Vlad; Nevo, Reinat; Scherz, Avigdor; Reich, Ziv

2002-01-01

Envelope-free chloroplasts were imaged in situ by contact and tapping mode scanning force microscopy at a lateral resolution of 3–5 nm and vertical resolution of ∼0.3 nm. The images of the intact thylakoids revealed detailed structural features of their surface, including individual protein complexes over stroma, grana margin and grana-end membrane domains. Structural and immunogold-assisted assignment of two of these complexes, photosystem I (PS I) and ATP synthase, allowed direct determination of their surface density, which, for both, was found to be highest in grana margins. Surface rearrangements and pigment– protein complex redistribution associated with salt-induced membrane unstacking were followed on native, hydrated specimens. Unstacking was accompanied by a substantial increase in grana diameter and, eventually, led to their merging with the stroma lamellae. Concomitantly, PS IIα effective antenna size decreased by 21% and the mean size of membrane particles increased substantially, consistent with attachment of mobile light-harvesting complex II to PS I. The ability to image intact photosynthetic membranes at molecular resolution, as demonstrated here, opens up new vistas to investigate thylakoid structure and function. PMID:12426386

Unusual Complex Formation and Chemical Reaction of Haloacetate Anion on the Exterior Surface of Cucurbit[6]uril in the Gas Phase

NASA Astrophysics Data System (ADS)

Choi, Tae Su; Ko, Jae Yoon; Heo, Sung Woo; Ko, Young Ho; Kim, Kimoon; Kim, Hugh I.

2012-10-01

Noncovalent interactions of cucurbit[6]uril (CB[6]) with haloacetate and halide anions are investigated in the gas phase using electrospray ionization ion mobility mass spectrometry. Strong noncovalent interactions of monoiodoacetate, monobromoacetate, monochloroacetate, dichloroacetate, and trichloroacetate on the exterior surface of CB[6] are observed in the negative mode electrospray ionization mass spectra. The strong binding energy of the complex allows intramolecular SN2 reaction of haloacetate, which yields externally bound CB[6]-halide complex, by collisional activation. Utilizing ion mobility technique, structures of exteriorly bound CB[6] complexes of haloacetate and halide anions are confirmed. Theoretically determined low energy structures using density functional theory (DFT) further support results from ion mobility studies. The DFT calculation reveals that the binding energy and conformation of haloacetate on the CB[6] surface affect the efficiency of the intramolecular SN2 reaction of haloacetate, which correlate well with the experimental observation.

Molecular simulation of structure and diffusion at smectite-water interfaces: Using expanded clay interlayers as model nanopores

DOE PAGES

Greathouse, Jeffery A.; Hart, David; Bowers, Geoffrey M.; ...

2015-07-20

In geologic settings relevant to a number of extraction and potential sequestration processes, nanopores bounded by clay mineral surfaces play a critical role in the transport of aqueous species. Solution structure and dynamics at clay–water interfaces are quite different from their bulk values, and the spatial extent of this disruption remains a topic of current interest. We have used molecular dynamics simulations to investigate the structure and diffusion of aqueous solutions in clay nanopores approximately 6 nm thick, comparing the effect of clay composition with model Na-hectorite and Na-montmorillonite surfaces. In addition to structural properties at the interface, water andmore » ion diffusion coefficients were calculated within each aqueous layer at the interface, as well as in the central bulk-like region of the nanopore. The results show similar solution structure and diffusion properties at each surface, with subtle differences in sodium adsorption complexes and water structure in the first adsorbed layer due to different arrangements of layer hydroxyl groups in the two clay models. Interestingly, the extent of surface disruption on bulk-like solution structure and diffusion extends to only a few water layers. Additionally, a comparison of sodium ion residence times confirms similar behavior of inner-sphere and outer-sphere surface complexes at each clay surface, but ~1% of sodium ions adsorb in ditrigonal cavities on the hectorite surface. Thus, the presence of these anhydrous ions is consistent with highly immobile anhydrous ions seen in previous nuclear magnetic resonance spectroscopic measurements of hectorite pastes.« less

Genesis of femtosecond-induced nanostructures on solid surfaces.

PubMed

Varlamova, Olga; Martens, Christian; Ratzke, Markus; Reif, Juergen

2014-11-01

The start and evolution of the formation of laser-induced periodic surface structures (LIPSS, ripples) are investigated. The important role of irradiation dose (fluence×number of pulses) for the properties of the generated structures is demonstrated. It is shown how, with an increasing dose, the structures evolve from random surface modification to regular sub-wavelength ripples, then coalesce to broader LIPSS and finally form more complex shapes when ablation produces deep craters. First experiments are presented following this evolution in one single irradiated spot.

New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

NASA Astrophysics Data System (ADS)

Tabti, Salima; Djedouani, Amel; Aggoun, Djouhra; Warad, Ismail; Rahmouni, Samra; Romdhane, Samir; Fouzi, Hosni

2018-03-01

The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

Structural complexity and land-surface energy exchange along a gradient from arctic tundra to boreal forest

USGS Publications Warehouse

Thompson, C.; Beringer, J.; Chapin, F. S.; McGuire, A.D.

2004-01-01

Question: Current climate changes in the Alaskan Arctic, which are characterized by increases in temperature and length of growing season, could alter vegetation structure, especially through increases in shrub cover or the movement of treeline. These changes in vegetation structure have consequences for the climate system. What is the relationship between structural complexity and partitioning of surface energy along a gradient from tundra through shrub tundra to closed canopy forest? Location: Arctic tundra-boreal forest transition in the Alaskan Arctic. Methods: Along this gradient of increasing canopy complexity, we measured key vegetation characteristics, including community composition, biomass, cover, height, leaf area index and stem area index. We relate these vegetation characteristics to albedo and the partitioning of net radiation into ground, latent, and sensible heating fluxes. Results: Canopy complexity increased along the sequence from tundra to forest due to the addition of new plant functional types. This led to non-linear changes in biomass, cover, and height in the understory. The increased canopy complexity resulted in reduced ground heat fluxes, relatively conserved latent heat fluxes and increased sensible heat fluxes. The localized warming associated with increased sensible heating over more complex canopies may amplify regional warming, causing further vegetation change in the Alaskan Arctic.

CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin

PubMed Central

van Pee, Katharina; Neuhaus, Alexander; D'Imprima, Edoardo; Mills, Deryck J; Kühlbrandt, Werner; Yildiz, Özkan

2017-01-01

Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane. DOI: http://dx.doi.org/10.7554/eLife.23644.001 PMID:28323617

Water structure and aqueous uranyl(VI) adsorption equilibria onto external surfaces of beidellite, montmorillonite, and pyrophyllite: results from molecular simulations.

PubMed

Greathouse, Jeffery A; Cygan, Randall T

2006-06-15

Molecular dynamics simulations were performed to provide a systematic study of aqueous uranyl adsorption onto the external surface of 2:1 dioctahedral clays. Our understanding of this key process is critical in predicting the fate of radioactive contaminants in natural groundwaters. These simulations provide atomistic detail to help explain experimental trends in uranyl adsorption onto natural media containing smectite clays. Aqueous uranyl concentrations ranged from 0.027 to 0.162 M. Sodium ions and carbonate ions (0.027-0.243 M) were also present in the aqueous regions to more faithfully model a stream of uranyl-containing groundwater contacting a mineral system comprised of Na-smectite. No adsorption occurred near the pyrophyllite surface, and there was little difference in uranyl adsorption onto the beidellite and montmorillonite, despite the difference in location of clay layer charge between the two. At low uranyl concentration, the pentaaquouranyl complex dominates in solution and readily adsorbs to the clay basal plane. At higher uranyl (and carbonate) concentrations, the mono(carbonato) complex forms in solution, and uranyl adsorption decreases. Sodium adsorption onto beidellite occurred both as inner- and outer-sphere surface complexes, again with little effect on uranyl adsorption. Uranyl surface complexes consisted primarily of the pentaaquo cation (85%) and to a lesser extent the mono(carbonato) species (15%). Speciation diagrams of the aqueous region indicate that the mono(carbonato)uranyl complex is abundant at high ionic strength. Oligomeric uranyl complexes are observed at high ionic strength, particularly near the pyrophyllite and montmorillonite surfaces. Atomic density profiles of water oxygen and hydrogen atoms are nearly identical near the beidellite and montmorillonite surfaces. Water structure therefore appears to be governed by the presence of adsorbed ions and not by the location of layer charge associated with the substrate. The water oxygen density near the pyrophyllite surface is similar to the other cases, but the hydrogen density profile indicates reduced hydrogen bonding between adsorbed water molecules and the surface.

Structure of a Glomulin-RBX1-CUL1 complex: inhibition of a RING E3 ligase through masking of its E2-binding surface

PubMed Central

Duda, David M.; Olszewski, Jennifer L.; Tron, Adriana E.; Hammel, Michal; Lambert, Lester J.; Waddell, M. Brett; Mittag, Tanja; DeCaprio, James A.; Schulman, Brenda A.

2012-01-01

Summary The ~300 human Cullin-RING ligases (CRLs) are multisubunit E3s in which a RING protein, either RBX1 or RBX2, recruits an E2 to catalyze ubiquitination. RBX1-containing CRLs also can bind Glomulin (GLMN), which binds RBX1’s RING domain, regulates the RBX1-CUL1-containing SCFFBW7 complex, and is disrupted in the disease Glomuvenous Malformation. Here we report the crystal structure of a complex between GLMN, RBX1, and a fragment of CUL1. Structural and biochemical analyses reveal that GLMN adopts a HEAT-like repeat fold that tightly binds the E2-interacting surface of RBX1, inhibiting CRL-mediated chain formation by the E2 CDC34. The structure explains the basis for GLMN’s selectivity toward RBX1 over RBX2, and how disease-associated mutations disrupt GLMN-RBX1 interactions. Our study reveals a mechanism for RING E3 ligase regulation whereby an inhibitor blocks E2 access, and raises the possibility that other E3s are likewise controlled by cellular proteins that mask E2-binding surfaces to mediate inhibition. PMID:22748924

Sample-Based Surface Coloring

PubMed Central

Bürger, Kai; Krüger, Jens; Westermann, Rüdiger

2011-01-01

In this paper, we present a sample-based approach for surface coloring, which is independent of the original surface resolution and representation. To achieve this, we introduce the Orthogonal Fragment Buffer (OFB)—an extension of the Layered Depth Cube—as a high-resolution view-independent surface representation. The OFB is a data structure that stores surface samples at a nearly uniform distribution over the surface, and it is specifically designed to support efficient random read/write access to these samples. The data access operations have a complexity that is logarithmic in the depth complexity of the surface. Thus, compared to data access operations in tree data structures like octrees, data-dependent memory access patterns are greatly reduced. Due to the particular sampling strategy that is employed to generate an OFB, it also maintains sample coherence, and thus, exhibits very good spatial access locality. Therefore, OFB-based surface coloring performs significantly faster than sample-based approaches using tree structures. In addition, since in an OFB, the surface samples are internally stored in uniform 2D grids, OFB-based surface coloring can efficiently be realized on the GPU to enable interactive coloring of high-resolution surfaces. On the OFB, we introduce novel algorithms for color painting using volumetric and surface-aligned brushes, and we present new approaches for particle-based color advection along surfaces in real time. Due to the intermediate surface representation we choose, our method can be used to color polygonal surfaces as well as any other type of surface that can be sampled. PMID:20616392

Direct Femtosecond Laser Surface Structuring with Optical Vortex Beams Generated by a q-plate

PubMed Central

JJ Nivas, Jijil; He, Shutong; Rubano, Andrea; Vecchione, Antonio; Paparo, Domenico; Marrucci, Lorenzo; Bruzzese, Riccardo; Amoruso, Salvatore

2015-01-01

Creation of patterns and structures on surfaces at the micro- and nano-scale is a field of growing interest. Direct femtosecond laser surface structuring with a Gaussian-like beam intensity profile has already distinguished itself as a versatile method to fabricate surface structures on metals and semiconductors. Here we present an approach for direct femtosecond laser surface structuring based on optical vortex beams with different spatial distributions of the state of polarization, which are easily generated by means of a q-plate. The different states of an optical vortex beam carrying an orbital angular momentum ℓ = ±1 are used to demonstrate the fabrication of various regular surface patterns on silicon. The spatial features of the regular rippled and grooved surface structures are correlated with the state of polarization of the optical vortex beam. Moreover, scattered surface wave theory approach is used to rationalize the dependence of the surface structures on the local state of the laser beam characteristics (polarization and fluence). The present approach can be further extended to fabricate even more complex and unconventional surface structures by exploiting the possibilities offered by femtosecond optical vector fields. PMID:26658307

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Self-assembly of metal nanostructures on binary alloy surfaces

PubMed Central

Duguet, T.; Han, Yong; Yuen, Chad; Jing, Dapeng; Ünal, Barış; Evans, J. W.; Thiel, P. A.

2011-01-01

Deposition of metals on binary alloy surfaces offers new possibilities for guiding the formation of functional metal nanostructures. This idea is explored with scanning tunneling microscopy studies and atomistic-level analysis and modeling of nonequilibrium island formation. For Au/NiAl(110), complex monolayer structures are found and compared with the simple fcc(110) bilayer structure recently observed for Ag/NiAl(110). We also consider a more complex codeposition system, (Ni + Al)/NiAl(110), which offers the opportunity for fundamental studies of self-growth of alloys including deviations for equilibrium ordering. A general multisite lattice-gas model framework enables analysis of structure selection and morphological evolution in these systems. PMID:21097706

Crystal structure of botulinum neurotoxin type A in complex with the cell surface co-receptor GT1b-insight into the toxin-neuron interaction.

PubMed

Stenmark, Pål; Dupuy, Jérôme; Imamura, Akihiro; Kiso, Makoto; Stevens, Raymond C

2008-08-15

Botulinum neurotoxins have a very high affinity and specificity for their target cells requiring two different co-receptors located on the neuronal cell surface. Different toxin serotypes have different protein receptors; yet, most share a common ganglioside co-receptor, GT1b. We determined the crystal structure of the botulinum neurotoxin serotype A binding domain (residues 873-1297) alone and in complex with a GT1b analog at 1.7 A and 1.6 A, respectively. The ganglioside GT1b forms several key hydrogen bonds to conserved residues and binds in a shallow groove lined by Tryptophan 1266. GT1b binding does not induce any large structural changes in the toxin; therefore, it is unlikely that allosteric effects play a major role in the dual receptor recognition. Together with the previously published structures of botulinum neurotoxin serotype B in complex with its protein co-receptor, we can now generate a detailed model of botulinum neurotoxin's interaction with the neuronal cell surface. The two branches of the GT1b polysaccharide, together with the protein receptor site, impose strict geometric constraints on the mode of interaction with the membrane surface and strongly support a model where one end of the 100 A long translocation domain helix bundle swing into contact with the membrane, initiating the membrane anchoring event.

A novel diamond micro-/nano-machining process for the generation of hierarchical micro-/nano-structures

NASA Astrophysics Data System (ADS)

Zhu, Zhiwei; To, Suet; Ehmann, Kornel F.; Xiao, Gaobo; Zhu, Wule

2016-03-01

A new mechanical micro-/nano-machining process that combines rotary spatial vibrations (RSV) of a diamond tool and the servo motions of the workpiece is proposed and applied for the generation of multi-tier hierarchical micro-/nano-structures. In the proposed micro-/nano-machining system, the servo motion, as the primary cutting motion generated by a slow-tool-servo, is adopted for the fine generation of the primary surfaces with complex shapes. The RSV, as the tertiary cutting operation, is superimposed on the secondary fundamental rotary cutting motion to construct secondary nano-structures on the primary surface. Since the RSV system generally works at much higher frequencies and motion resolution than the primary and secondary motions, it leads to an inherent hierarchical cutting architecture. To investigate the machining performance, complex micro-/nano-structures were generated and explored by both numerical simulations and actual cutting tests. Rotary vibrations of the diamond tool at a constant rotational distance offer an inherent constant cutting velocity, leading to the ability for the generation of homogeneous micro-/nano-structures with fixed amplitudes and frequencies of the vibrations, even over large-scale surfaces. Furthermore, by deliberately combining the non-resonant three-axial vibrations and the servo motion, the generation of a variety of micro-/nano-structures with complex shapes and with flexibly tunable feature sizes can be achieved.

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

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

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

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

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

DOE PAGES

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

2017-06-12

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

Regular square planer bis-(4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione)/copper(II) complex: Trans/cis-DFT isomerization, crystal structure, thermal, solvatochromism, hirshfeld surface and DNA-binding analysis

NASA Astrophysics Data System (ADS)

Hema, M. K.; Karthik, C. S.; Warad, Ismail; Lokanath, N. K.; Zarrouk, Abdelkader; Kumara, Karthik; Pampa, K. J.; Mallu, P.

2018-04-01

Trans-[Cu(O∩O)2] complex, O∩O = 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione was reported with high potential toward CT-DNA binder. The solved XRD-structure of complex indicated a perfect regular square-planer geometry around the Cu(II) center. The trans/cis-DFT-isomerization calculation supported the XRD seen in reflecting the trans-isomer as the kinetic-favor isomer. The desired complex structure was also characterized by conductivity measurement, CHN-elemental analyses, MS, EDX, SEM, UV-Vis., FT-IR, HAS and TG/DTG. The Solvatochromism behavior of the complex was evaluated using four different polar solvents. MPE and Hirshfeld surface analysis (HSA) come to an agreement that fluoride and thiophene protons atoms are with suitable electro-potential environment to form non-classical H-bonds of type CThsbnd H⋯F. The DNA-binding properties were investigated by viscosity tests and spectrometric titrations, the results revealed the complex as strong calf-thymus DNA binder. High intrinsic-binding constants value ∼1.8 × 105 was collected.

Structural model of the p14/SF3b155 · branch duplex complex.

PubMed

Schellenberg, Matthew J; Dul, Erin L; MacMillan, Andrew M

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.

Structural model of the p14/SF3b155·branch duplex complex

PubMed Central

Schellenberg, Matthew J.; Dul, Erin L.; MacMillan, Andrew M.

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing. PMID:21062891

DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

PubMed

Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

2017-09-24

We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.

Adsorption of uranium(VI) to manganese oxides: X-ray absorption spectroscopy and surface complexation modeling.

PubMed

Wang, Zimeng; Lee, Sung-Woo; Catalano, Jeffrey G; Lezama-Pacheco, Juan S; Bargar, John R; Tebo, Bradley M; Giammar, Daniel E

2013-01-15

The mobility of hexavalent uranium in soil and groundwater is strongly governed by adsorption to mineral surfaces. As strong naturally occurring adsorbents, manganese oxides may significantly influence the fate and transport of uranium. Models for U(VI) adsorption over a broad range of chemical conditions can improve predictive capabilities for uranium transport in the subsurface. This study integrated batch experiments of U(VI) adsorption to synthetic and biogenic MnO(2), surface complexation modeling, ζ-potential analysis, and molecular-scale characterization of adsorbed U(VI) with extended X-ray absorption fine structure (EXAFS) spectroscopy. The surface complexation model included inner-sphere monodentate and bidentate surface complexes and a ternary uranyl-carbonato surface complex, which was consistent with the EXAFS analysis. The model could successfully simulate adsorption results over a broad range of pH and dissolved inorganic carbon concentrations. U(VI) adsorption to synthetic δ-MnO(2) appears to be stronger than to biogenic MnO(2), and the differences in adsorption affinity and capacity are not associated with any substantial difference in U(VI) coordination.

Structure of D-AKAP2:PKA RI complex: Insights into AKAP specificity and selectivity

PubMed Central

Sarma, Ganapathy N.; Kinderman, Francis S.; Kim, Choel; von Daake, Sventja; Chen, Lirong; Wang, Bi-Cheng; Taylor, Susan S.

2011-01-01

Summary A-kinase anchoring proteins (AKAPs) regulate cyclic AMP-dependent protein kinase (PKA) signaling in space and time. Dual-specific AKAP 2 (D-AKAP2) binds to the dimerization/docking (D/D) domain of both RI and RII regulatory subunits of PKA with high affinity. Here, we have determined the structures of the RIα D/D domain alone and in complex with D-AKAP2. The D/D domain presents an extensive surface for binding through a well-formed N-termina helix and this surface restricts the diversity of AKAPs that can interact. The structures also underscore the importance of a redox-sensitive disulfide in affecting AKAP binding. An unexpected shift in the helical register of D-AKAP2 compared to the RIIα:D-AKAP2 complex structure makes the mode of binding to RIα novel. Finally, the comparison allows us to deduce a molecular explanation for the sequence and spatial determinants of AKAP specificity. PMID:20159461

Structural changes of cytochrome c(552) from Thermus thermophilus adsorbed on anionic and hydrophobic surfaces probed by FTIR and 2D-FTIR spectroscopy.

PubMed

Lecomte, S; Hilleriteau, C; Forgerit, J P; Revault, M; Baron, M H; Hildebrandt, P; Soulimane, T

2001-03-02

The structural changes of cytochrome c(552) bound to anionic and hydrophobic clay surfaces have been investigated by Fourier transform infrared spectroscopy. Binding to the anionic surface of montmorillonite is controlled by electrostatic interactions since addition of electrolyte (0.5 mol L(-1) KCl) causes desorption of more than 2/3 of the protein molecules. Electrostatic binding occurs through the back side of the protein (i.e., remote from the heme site) and is associated only with subtle changes of the secondary structure. In contrast, adsorption to the hydrophobic surface of talc leads to a decrease in alpha-helical structure by ca. 5% and an increase in beta-sheet structure by ca. 6%. These structural changes are attributed to a hydrophobic region on the front surface of cytochrome c(552) close to the partially exposed heme edge. This part on the protein surface is identified as the interaction domain for talc and most likely also serves for binding to the natural reaction partner, a ba(3)-oxidase. Fourier transform infrared spectra of cytochrome c(552) and the clay-cytochrome c(552) complexes have been measured as a function of time following dissolution and suspension in deuterated buffer, respectively. A two-dimensional correlation analysis was applied to these spectra to investigate the dynamics of the structural changes in the protein. For both complexes, adsorption and subsequent unfolding processes in the binding domains are faster than the time resolution of the spectroscopic experiments. Thus, the processes that could be monitored are refolding of peptide segments and side chain rearrangements following the adsorption-induced perturbation of the protein structure and the solvation of the adsorbed protein. In each case, side chain alterations of solvent-exposed tyrosine, aspartate, and glutamate residues were observed. For the cytochrome c(552)-talc complex, these changes are followed by a slow refolding of the peptide chain in the binding domain and, subsequently, a further H/D exchange of amide group protons.

Stretchable ultrasonic transducer arrays for three-dimensional imaging on complex surfaces

PubMed Central

Zhu, Xuan; Li, Xiaoshi; Chen, Zeyu; Chen, Yimu; Lei, Yusheng; Li, Yang; Nomoto, Akihiro; Zhou, Qifa; di Scalea, Francesco Lanza

2018-01-01

Ultrasonic imaging has been implemented as a powerful tool for noninvasive subsurface inspections of both structural and biological media. Current ultrasound probes are rigid and bulky and cannot readily image through nonplanar three-dimensional (3D) surfaces. However, imaging through these complicated surfaces is vital because stress concentrations at geometrical discontinuities render these surfaces highly prone to defects. This study reports a stretchable ultrasound probe that can conform to and detect nonplanar complex surfaces. The probe consists of a 10 × 10 array of piezoelectric transducers that exploit an “island-bridge” layout with multilayer electrodes, encapsulated by thin and compliant silicone elastomers. The stretchable probe shows excellent electromechanical coupling, minimal cross-talk, and more than 50% stretchability. Its performance is demonstrated by reconstructing defects in 3D space with high spatial resolution through flat, concave, and convex surfaces. The results hold great implications for applications of ultrasound that require imaging through complex surfaces. PMID:29740603

The evolution of cerebellum structure correlates with nest complexity.

PubMed

Hall, Zachary J; Street, Sally E; Healy, Susan D

2013-01-01

Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulative skills. Here, we tested this hypothesis by investigating the relationship between cerebellar foliation and species-typical nest structure in birds. Increasing complexity of nest structure is a measure of a bird's ability to manipulate nesting material into the required shape. Consistent with our hypothesis, avian cerebellar foliation increases as the complexity of the nest built increases, setting the scene for the exploration of nest building at the neural level.

Electrostatic interactions guide the active site face of a structure-specific ribonuclease to its RNA substrate.

PubMed

Plantinga, Matthew J; Korennykh, Alexei V; Piccirilli, Joseph A; Correll, Carl C

2008-08-26

Restrictocin, a member of the alpha-sarcin family of site-specific endoribonucleases, uses electrostatic interactions to bind to the ribosome and to RNA oligonucleotides, including the minimal specific substrate, the sarcin/ricin loop (SRL) of 23S-28S rRNA. Restrictocin binds to the SRL by forming a ground-state E:S complex that is stabilized predominantly by Coulomb interactions and depends on neither the sequence nor structure of the RNA, suggesting a nonspecific complex. The 22 cationic residues of restrictocin are dispersed throughout this protein surface, complicating a priori identification of a Coulomb interacting surface. Structural studies have identified an enzyme-substrate interface, which is expected to overlap with the electrostatic E:S interface. Here, we identified restrictocin residues that contribute to binding in the E:S complex by determining the salt dependence [partial differential log(k 2/ K 1/2)/ partial differential log[KCl

Photoexpulsion of Surface-Grafted Ruthenium Complexes and Subsequent Release of Cytotoxic Cargos to Cancer Cells from Mesoporous Silica Nanoparticles

PubMed Central

Frasconi, Marco; Liu, Zhichang; Lei, Juying; Wu, Yilei; Strekalova, Elena; Malin, Dmitry; Ambrogio, Michael W.; Chen, Xinqi; Botros, Youssry Y.; Cryns, Vincent L.; Sauvage, Jean-Pierre; Stoddart, J. Fraser

2014-01-01

Ruthenium(II) polypyridyl complexes have emerged both as promising probes of DNA structure and as anticancer agents because of their unique photophysical and cytotoxic properties. A key consideration in the administration of those therapeutic agents is the optimization of their chemical reactivities to allow facile attack on the target sites, yet avoid unwanted side effects. Here, we present a drug delivery platform technology, obtained by grafting the surface of mesoporous silica nanoparticles (MSNPs) with ruthenium(II) dipyridophenazine (dppz) complexes. This hybrid nanomaterial displays enhanced luminescent properties relative to that of the ruthenium(II) dppz complex in a homogeneous phase. Since the coordination between the ruthenium(II) complex and a monodentate ligand linked covalently to the nanoparticles can be cleaved under irradiation with visible light, the ruthenium complex can be released from the surface of the nanoparticles by selective substitution of this ligand with a water molecule. Indeed, the modified MSNPs undergo rapid cellular uptake, and after activation with light, the release of an aqua ruthenium(II) complex is observed. We have delivered, in combination, the ruthenium(II) complex and paclitaxel, loaded in the mesoporous structure, to breast cancer cells. This hybrid material represents a promising candidate as one of the so-called theranostic agents that possess both diagnostic and therapeutic functions. PMID:23815127

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).

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues.

PubMed

Nikolaienko, Roman M; Hammel, Michal; Dubreuil, Véronique; Zalmai, Rana; Hall, David R; Mehzabeen, Nurjahan; Karuppan, Sebastian J; Harroch, Sheila; Stella, Salvatore L; Bouyain, Samuel

2016-10-07

Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptor cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterization of structural and electrostatic complexity in pentacene thin films by scanning probe microscopy

NASA Astrophysics Data System (ADS)

Puntambekar, Kanan Prakash

The advancement of organic electronics for applications in solar energy conversion, printed circuitry, displays, and solid-state lighting depends upon optimization of structure and properties for a variety of organic semiconductor interfaces. Organic semiconductor/insulator (O/I) and organic-metal (O/M) interfaces, in particular, are critical to the operation of organic thin film transistors (OTFTs) currently being developed for printed flexible electronics. Scanning probe microscopy (SPM) is a powerful tool to isolate and characterize the bottlenecks to charge transport at these interfaces. This thesis establishes a direct correlation between the structural disorder and electrical complexity at these interfaces, using various SPM based methods and discusses the implications of such complexity on device performance. To examine the O/M interfaces, surface potentials of operating pentacene TFTs with two different contact geometries (bottom or top) were mapped by Kelvin probe force microscopy (KFM). The surface potential distribution was used to isolate the potential drops at the source and drain contacts. Simultaneously obtained topography and surface potential maps elucidated the correlation between the morphology and contact resistance at the O/M interface; the bottom contact TFTs were observed to be contact limited at large gate voltages, while the top contact TFTs were not contact limited. A direct correlation between structural defects and electric potential variations at the pentacene and silicon dioxide, a common insulator, is demonstrated. Lateral force microscopy (LFM) generates striking images of the polycrystalline microstructure of a monolayer thick pentacene film, allowing clear visualization of the grain boundary network. Further more, surface potential wells localized at the grain boundaries were observed by KFM, suggesting that the grain boundaries may serve as charge carrier (hole) traps. Line dislocations were also revealed in the second monolayer by chemical etching and SPM and produce strong variations in the surface potential that must affect the interfacial charge conductance. Structural disorder at the O/I and O/M interfaces degrades both injection and transport of charge, and therefore needs to be minimized. Thus both visualization and correlation of structural and electrical complexity at these interfaces have important implications for understanding electrical transport in OTFTs and for defining strategies to improve device performance.

Enhanced removal of azo dye using modified PAN nanofibrous membrane Fe complexes with adsorption/visible-driven photocatalysis bifunctional roles

NASA Astrophysics Data System (ADS)

Li, Fu; Dong, Yongchun; Kang, Weimin; Cheng, Bowen; Cui, Guixin

2017-05-01

A series of polyacrylonitrile (PAN) nanofibrous membrane Fe complexes as the Fenton heterogeneous catalysts were fabricated through surface modification with different ratio of hydrazine hydrate (HH) and hydroxylamine (HA) and subsequent coordination with Fe3+ ions for the synergistic removal of a typical azo dye, Reactive Red 195 (RR 195) via adsorption and visible-driven photocatalytic oxidation. Effect of molar ratio of HH and HA on surface structure characteristics of the resulting complexes were examined. Their adsorptive or photocatalytic activity was also compared by changing molar ratio of HH and HA. The results indicated that three PAN nanofibrous membrane Fe complexes prepared with simultaneous modification of HA and HH exhibited much higher adsorption and visible photocatalytic activities than the complex modified solely with HA or HH due to their distinctive surface structures containing more active sites. Their adsorption and visible photocatalytic kinetics of RR 195 followed pseudo-second-order model equation. Their high photocatalytic rate constant and large amount of dye adsorption were regarded as the main reasons for better dye removal efficiency and durability in cyclic reuse by means of the synergistic adsorption-photocatalysis process.

Decay assessment through thermographic analysis in architectural and archaeological heritage

NASA Astrophysics Data System (ADS)

Gomez-Heras, Miguel; Martinez-Perez, Laura; Fort, Rafael; Alvarez de Buergo, Monica

2010-05-01

Any exposed stone-built structure is subject to thermal variations due to daily, seasonal and secular environmental temperature changes. Surface temperature is a function of air temperature (due to convective heat transfer) and of infrared radiation received through insolation. While convective heat transfer homogenizes surface temperature, stone response to insolation is much more complex and the temporal and spatial temperature differences across structures are enhanced. Surface temperature in stone-built structures will be affected by orientation, sunlight inclination and the complex patterns of light and shadows generated by the often intricate morphology of historical artefacts and structures. Surface temperature will also be affected by different material properties, such as albedo, thermal conductivity, transparency and absorbance to infrared radiation of minerals and rocks. Moisture and the occurrence of salts will also be a factor affecting surface temperatures. Surface temperatures may as well be affected by physical disruptions of rocks due to differences in thermal inertia generated by cracks and other discontinuities. Thermography is a non-invasive, non-destructive technique that measures temperature variations on the surface of a material. With this technique, surface temperature rates of change and their spatial variations can be analysed. This analysis may be used not only to evaluate the incidence of thermal decay as a factor that generates or enhances stone decay, but also to detect and evaluate other factors that affect the state of conservation of architectural and archaeological heritage, as for example moisture, salts or mechanical disruptions.

High-Resolution Scanning Electron Microscopy and Immuno-Gold Labeling of the Nuclear Lamina and Nuclear Pore Complex.

PubMed

Goldberg, Martin W

2016-01-01

Scanning electron microscopy (SEM) is a technique used to image surfaces. Field emission SEMs (feSEMs) can resolve structures that are ~0.5-1.5 nm apart. FeSEM, therefore is a useful technique for imaging molecular structures that exist at surfaces such as membranes. The nuclear envelope consists of four membrane surfaces, all of which may be accessible for imaging. Imaging of the cytoplasmic face of the outer membrane gives information about ribosomes and cytoskeletal attachments, as well as details of the cytoplasmic peripheral components of the nuclear pore complex, and is the most easily accessed surface. The nucleoplasmic face of the inner membrane is easily accessible in some cells, such as amphibian oocytes, giving valuable details about the organization of the nuclear lamina and how it interacts with the nuclear pore complexes. The luminal faces of both membranes are difficult to access, but may be exposed by various fracturing techniques. Protocols are presented here for the preparation, labeling, and feSEM imaging of Xenopus laevis oocyte nuclear envelopes.

Age-related differences in the structural complexity of subcortical and ventricular structures.

PubMed

Madan, Christopher R; Kensinger, Elizabeth A

2017-02-01

It has been well established that the volume of several subcortical structures decreases in relation to age. Different metrics of cortical structure (e.g., volume, thickness, surface area, and gyrification) have been shown to index distinct characteristics of interindividual differences; thus, it is important to consider the relation of age to multiple structural measures. Here, we compare age-related differences in subcortical and ventricular volume to those differences revealed with a measure of structural complexity, quantified as fractal dimensionality. Across 3 large data sets, totaling nearly 900 individuals across the adult lifespan (aged 18-94 years), we found greater age-related differences in complexity than volume for the subcortical structures, particularly in the caudate and thalamus. The structural complexity of ventricular structures was not more strongly related to age than volume. These results demonstrate that considering shape-related characteristics improves sensitivity to detect age-related differences in subcortical structures. Copyright © 2016 Elsevier Inc. All rights reserved.

A general method for computing the total solar radiation force on complex spacecraft structures

NASA Technical Reports Server (NTRS)

Chan, F. K.

1981-01-01

The method circumvents many of the existing difficulties in computational logic presently encountered in the direct analytical or numerical evaluation of the appropriate surface integral. It may be applied to complex spacecraft structures for computing the total force arising from either specular or diffuse reflection or even from non-Lambertian reflection and re-radiation.

Crystal structure of LGR4-Rspo1 complex: insights into the divergent mechanisms of ligand recognition by leucine-rich repeat G-protein-coupled receptors (LGRs).

PubMed

Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

2015-01-23

Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4-6) recognize R-spondin family proteins (Rspo1-4) to stimulate Wnt signaling. In this study, we successfully utilized the "hybrid leucine-rich repeat technique," which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4-6, suggesting that LGR4-6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4-6 in ligand recognition. The molecular mechanism of LGR4-6 is distinct from the two-step mechanism of group A receptors LGR1-3 and the multiple-interface binding model of group C receptors LGR7-8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Angle-resolved photoemission spectroscopy studies of metallic surface and interface states of oxide insulators

NASA Astrophysics Data System (ADS)

Plumb, Nicholas C.; Radović, Milan

2017-11-01

Over the last decade, conducting states embedded in insulating transition metal oxides (TMOs) have served as gateways to discovering and probing surprising phenomena that can emerge in complex oxides, while also opening opportunities for engineering advanced devices. These states are commonly realized at thin film interfaces, such as the well-known case of LaAlO3 (LAO) grown on SrTiO3 (STO). In recent years, the use of angle-resolved photoemission spectroscopy (ARPES) to investigate the k-space electronic structure of such materials led to the discovery that metallic states can also be formed on the bare surfaces of certain TMOs. In this topical review, we report on recent studies of low-dimensional metallic states confined at insulating oxide surfaces and interfaces as seen from the perspective of ARPES, which provides a direct view of the occupied band structure. While offering a fairly broad survey of progress in the field, we draw particular attention to STO, whose surface is so far the best-studied, and whose electronic structure is probably of the most immediate interest, given the ubiquitous use of STO substrates as the basis for conducting oxide interfaces. The ARPES studies provide crucial insights into the electronic band structure, orbital character, dimensionality/confinement, spin structure, and collective excitations in STO surfaces and related oxide surface/interface systems. The obtained knowledge increases our understanding of these complex materials and gives new perspectives on how to manipulate their properties.

Surface complexation and precipitate geometry for aqueous Zn(II) sorption on ferrihydrite I: X-ray absorption extended fine structure spectroscopy analysis

USGS Publications Warehouse

Waychunas, G.A.; Fuller, C.C.; Davis, J.A.

2002-01-01

"Two-line" ferrihydrite samples precipitated and then exposed to a range of aqueous Zn solutions (10-5 to 10-3 M), and also coprecipitated in similar Zn solutions (pH 6.5), have been examined by Zn and Fe K-edge X-ray absorption spectroscopy. Typical Zn complexes on the surface have Zn-O distances of 1.97(0.2) A?? and coordination numbers of about 4.0(0.5), consistent with tetrahedral oxygen coordination. This contrasts with Zn-O distances of 2.11(.02) A?? and coordination numbers of 6 to 7 in the aqueous Zn solutions used in sample preparation. X-ray absorption extended fine structure spectroscopy (EXAFS) fits to the second shell of cation neighbors indicate as many as 4 Zn-Fe neighbors at 3.44(.04) A?? in coprecipitated samples, and about two Zn-Fe neighbors at the same distance in adsorption samples. In both sets of samples, the fitted coordination number of second shell cations decreases as sorption density increases, indicating changes in the number and type of available complexing sites or the onset of competitive precipitation processes. Comparison of our results with the possible geometries for surface complexes and precipitates suggests that the Zn sorption complexes are inner sphere and at lowest adsorption densities are bidentate, sharing apical oxygens with adjacent edge-sharing Fe(O,OH)6 octahedra. Coprecipitation samples have complexes with similar geometry, but these are polydentate, sharing apices with more than two adjacent edge-sharing Fe(O,OH)6 polyhedra. The results are inconsistent with Zn entering the ferrihydrite structure (i.e., solid solution formation) or formation of other Zn-Fe precipitates. The fitted Zn-Fe coordination numbers drop with increasing Zn density with a minimum of about 0.8(.2) at Zn/(Zn + Fe) of 0.08 or more. This change appears to be attributable to the onset of precipitation of zinc hydroxide polymers with mainly tetrahedral Zn coordination. At the highest loadings studied, the nature of the complexes changes further, and a second type of precipitate forms. This has a structure based on a brucite layer topology, with mainly octahedral Zn coordination. Amorphous zinc hydroxide samples prepared for comparison had a closely similar local structure. Analysis of the Fe K-edge EXAFS is consistent with surface complexation reactions and surface precipitation at high Zn loadings with little or no Fe-Zn solid solution formation. The formation of Zn-containing precipitates at solution conditions two or more orders of magnitude below their solubility limit is compared with other sorption and spectroscopic studies that describe similar behavior. Copyright ?? 2002 Elsevier Science Ltd.

W-band EPR of vanadyl complexes aggregates on the surface of Al2O3

NASA Astrophysics Data System (ADS)

Mamin, G.; Gafurov, M.; Galukhin, A.; Gracheva, I.; Murzakhanov, F.; Rodionov, A.; Orlinskii, S.

2018-05-01

Structural characterization of metalloporphyrins, asphaltenes and their aggregates in complex systems such as native hydrocarbons is in the focus of scientific and industrial interests since many years. We present W-band (95 GHz) electron paramagnetic resonance (EPR) study in the magnetic field of about 3.4 T and temperature of 100 K for Karmalinskoe oil, asphaltens and asphaltenes deposited on the surface of Al2O3. Features of the obtained spectra are described. Shift to the higher frequencies allows to separate spectrally the contributions from paramagnetic complexes of different origin and define the EPR parameters more accurately comparing to the conventional X-band (9 GHz). Changes of the EPR parameters are tracked. We suggest that the proposed approach can be used for the investigation of structure of vanadyl complexes aggregates in crude oil and their fractions.

Tensorial Minkowski functionals of triply periodic minimal surfaces

PubMed Central

Mickel, Walter; Schröder-Turk, Gerd E.; Mecke, Klaus

2012-01-01

A fundamental understanding of the formation and properties of a complex spatial structure relies on robust quantitative tools to characterize morphology. A systematic approach to the characterization of average properties of anisotropic complex interfacial geometries is provided by integral geometry which furnishes a family of morphological descriptors known as tensorial Minkowski functionals. These functionals are curvature-weighted integrals of tensor products of position vectors and surface normal vectors over the interfacial surface. We here demonstrate their use by application to non-cubic triply periodic minimal surface model geometries, whose Weierstrass parametrizations allow for accurate numerical computation of the Minkowski tensors. PMID:24098847

Complex technology of vacuum-arc processing of structural material surface

NASA Astrophysics Data System (ADS)

Arustamov, V. N.; Ashurov, Kh. B.; Kadyrov, Kh. Kh.; Khudoikulov, I. Kh.

2015-08-01

The development of environmentally friendly and energy-resource-saving technologies based on vacuum arc discharge is a topical problem in science and engineering. In view of their unique properties, cathode spots of a vacuum arc induce cleaning of the surface of an article (cathode) from various contaminations and pulsed thermal action on the surface layers. These processes occur in complex with vacuum-arc deposition of coatings in the same technological cycle, which makes it possible to considerably increase the efficiency of methods for changing physical, mechanical, and chemical properties of the surface of steel articles, which considerably increase their service life. Analysis of the formation of the temperature regime of the surface during vacuum arc action and of the parameters of the deposited coating will make it possible to optimize the regimes of complex treatment of the surfaces of articles and is of considerable theoretical and practical importance.

Structure and Specificity of a Binary Tandem Domain F-Lectin from Striped Bass (Morone saxatilis)

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

Bianchet, M.; Odom, E; Vasta, J

2010-01-01

The plasma of the striped bass Morone saxatilis contains a fucose-specific lectin (MsaFBP32) that consists of two F-type carbohydrate recognition domains (CRDs) in tandem. The crystal structure of the complex of MsaFBP32 with l-fucose reported here shows a cylindrical 81-A-long and 60-A-wide trimer divided into two globular halves: one containing N-terminal CRDs (N-CRDs) and the other containing C-terminal CRDs (C-CRDs). The resulting binding surfaces at the opposite ends of the cylindrical trimer have the potential to cross-link cell surface or humoral carbohydrate ligands. The N-CRDs and C-CRDs of MsaFBP32 exhibit significant structural differences, suggesting that they recognize different glycans. Analysismore » of the carbohydrate binding sites provides the structural basis for the observed specificity of MsaFBP32 for simple carbohydrates and suggests that the N-CRD recognizes more complex fucosylated oligosaccharides and with a relatively higher avidity than the C-CRD. Modeling of MsaFBP32 complexed with fucosylated glycans that are widely distributed in prokaryotes and eukaryotes rationalizes the observation that binary tandem CRD F-type lectins function as opsonins by cross-linking 'non-self' carbohydrate ligands and 'self' carbohydrate ligands, such as sugar structures displayed by microbial pathogens and glycans on the surface of phagocytic cells from the host.« less

Structure of a Glomulin-RBX1-CUL1 Complex: Inhibition of a RING E3 Ligase through Masking of Its E2-Binding Surface

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

Duda, David M.; Olszewski, Jennifer L.; Tron, Adriana E.

2012-11-01

The approximately 300 human cullin-RING ligases (CRLs) are multisubunit E3s in which a RING protein, either RBX1 or RBX2, recruits an E2 to catalyze ubiquitination. RBX1-containing CRLs also can bind Glomulin (GLMN), which binds RBX1's RING domain, regulates the RBX1-CUL1-containing SCF{sup FBW7} complex, and is disrupted in the disease Glomuvenous Malformation. Here we report the crystal structure of a complex between GLMN, RBX1, and a fragment of CUL1. Structural and biochemical analyses reveal that GLMN adopts a HEAT-like repeat fold that tightly binds the E2-interacting surface of RBX1, inhibiting CRL-mediated chain formation by the E2 CDC34. The structure explains themore » basis for GLMN's selectivity toward RBX1 over RBX2, and how disease-associated mutations disrupt GLMN-RBX1 interactions. Our study reveals a mechanism for RING E3 ligase regulation, whereby an inhibitor blocks E2 access, and raises the possibility that other E3s are likewise controlled by cellular proteins that mask E2-binding surfaces to mediate inhibition.« less

Controllability of Surface Water Networks

NASA Astrophysics Data System (ADS)

Riasi, M. Sadegh; Yeghiazarian, Lilit

2017-12-01

To sustainably manage water resources, we must understand how to control complex networked systems. In this paper, we study surface water networks from the perspective of structural controllability, a concept that integrates classical control theory with graph-theoretic formalism. We present structural controllability theory and compute four metrics: full and target controllability, control centrality and control profile (FTCP) that collectively determine the structural boundaries of the system's control space. We use these metrics to answer the following questions: How does the structure of a surface water network affect its controllability? How to efficiently control a preselected subset of the network? Which nodes have the highest control power? What types of topological structures dominate controllability? Finally, we demonstrate the structural controllability theory in the analysis of a wide range of surface water networks, such as tributary, deltaic, and braided river systems.

Nano-Ag complexes prepared by γ-radiolysis and their structures and physical properties

NASA Astrophysics Data System (ADS)

Kim, Hwa-Jung; Choi, Seong-Ho; Park, Hae-Jun

2012-10-01

In this study, nano-silver (nano-Ag) complexes showing different properties have been synthesized as follows. Polypyrrolidone (PVP)-stabilized silver colloids (NAg), nano-Ag bound to silica (SiO2) (NSS), and nano-Ag bound to a complex of SiO2 and polyaniline (PANI) (NSSPAI) were prepared via γ-irradiation at room temperature. NAg and NSS used PVP as a colloidal stabilizer, while NSSPAI did not use PVP as a colloidal stabilizer. Interesting bonding properties occurred in the nano-Ag complex and anticipated structural changes were clearly shown through a surface analysis of x-ray photoelectron spectroscopy (XPS). The morphologies by field emission-scanning electron microscopy (FE-SEM) analysis showed that nano-Ag complexes have various particle sizes ranging from 10 to 30 nm. NSS (average, 10 nm) and NSSPAI (average, 30 nm) showed a uniformly spherical shape and size, while NAg did not. From the reflection peaks in the x-ray diffraction (XRD) patterns, surface crystallinity of the nano-Ag complexes was indicated to be in the same degree as that of NSSPAI>NSS>NAg. Also, in the contact angle (CA) determination, surface hydrophobicity of NSSPAI was stronger than those of NSS and NAg, relatively. The different nano-Ag complexes prepared by γ-irradiation can be applicable in various industry fields due to the increase in specific property.

Controlled evaporative self-assembly of confined microfluids: A route to complex ordered structures

NASA Astrophysics Data System (ADS)

Byun, Myunghwan

The evaporative self-assembly of nonvolatile solutes such as polymers, nanocrystals, and carbon nanotubes has been widely recognized as a non-lithographic means of producing a diverse range of intriguing complex structures. Due to the spatial variation of evaporative flux and possible convection, however, these non-equilibrium dissipative structures (e.g., fingering patterns and polygonal network structures) are often irregularly and stochastically organized. Yet for many applications in microelectronics, data storage devices, and biotechnology, it is highly desirable to achieve surface patterns having a well-controlled spatial arrangement. To date, only a few elegant studies have centered on precise control over the evaporation process to produce ordered structures. In a remarked comparison with conventional lithography techniques, surface patterning by controlled solvent evaporation is simple and cost-effective, offering a lithography- and external field-free means to organize nonvolatile materials into ordered microscopic structures over large surface areas. The ability to engineer an evaporative self-assembly process that yields a wide range of complex, self-organizing structures over large areas offers tremendous potential for applications in electronics, optoelectronics, and bio- or chemical sensors. We developed a facile, robust tool for evaporating polymer, nanoparticle, or DNA solutions in curve-on-flat geometries to create versatile, highly regular microstructures, including hierarchically structured polymer blend rings, conjugated polymer "snake-skins", block copolymer stripes, and punch-hole-like meshes, biomolecular microring arrays, etc. The mechanism of structure formation was elucidated both experimentally and theoretically. Our method further enhances current fabrication approaches to creating highly ordered structures in a simple and cost-effective manner, envisioning the potential to be tailored for use in photonics, optoelectronics, microfluidic devices, nanotechnology and biotechnology, etc.

Far-infrared BRDFs and reflectance spectra of candidate SOFIA telescope, cavity, and focal-plane instrument surfaces

NASA Astrophysics Data System (ADS)

Meyer, Allan W.; Smith, Sheldon M.; Koerber, Christopher T.

2000-06-01

The far-infrared reflectance and scattering properties of telescope surfaces, surrounding cavity walls, and surfaces within focal-plane instruments can be significant contributors to background noise. Radiation from sources well off-axis, such as the earth, moon or aircraft engines may be multiply scattered by the cavity walls and/or surface facets of a complex telescope structure. The Non-Specular Reflectometer at NASA Ames Research Center was reactivated and upgraded, and used to measure reflectance and Bi- directional Reflectance Distribution Functions for samples of planned telescope system structural materials and associated surface treatments.

Crystal Structure of Botulinum Neurotoxin Type a in Complex With the Cell Surface Co-Receptor GT1b-Insight Into the Toxin-Neuron Interaction

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

Stenmark, P.; Dupuy, J.; Inamura, A.

2009-05-26

Botulinum neurotoxins have a very high affinity and specificity for their target cells requiring two different co-receptors located on the neuronal cell surface. Different toxin serotypes have different protein receptors; yet, most share a common ganglioside co-receptor, GT1b. We determined the crystal structure of the botulinum neurotoxin serotype A binding domain (residues 873-1297) alone and in complex with a GT1b analog at 1.7 A and 1.6 A, respectively. The ganglioside GT1b forms several key hydrogen bonds to conserved residues and binds in a shallow groove lined by Tryptophan 1266. GT1b binding does not induce any large structural changes in themore » toxin; therefore, it is unlikely that allosteric effects play a major role in the dual receptor recognition. Together with the previously published structures of botulinum neurotoxin serotype B in complex with its protein co-receptor, we can now generate a detailed model of botulinum neurotoxin's interaction with the neuronal cell surface. The two branches of the GT1b polysaccharide, together with the protein receptor site, impose strict geometric constraints on the mode of interaction with the membrane surface and strongly support a model where one end of the 100 A long translocation domain helix bundle swing into contact with the membrane, initiating the membrane anchoring event.« less

A gravimetric analysis of protein-oligosaccharide interactions.

PubMed

Rudd, T; Gallagher, J T; Ron, D; Nichols, R J; Fernig, D G

2003-04-01

Interactions between an immobilized, heparin-derived octasaccharide and growth factors have been observed using a quartz crystal microbalance-dissipation (QCM-D). This device can measure the amount of growth factors binding to the octasaccharide surface and also the change of dissipation of the surface. Dissipation is a measure of how the adhered material 'damps' the surface vibrations. The octasaccharides were anchored through their reducing ends by the intermediary of the alkanethiol molecule, which covalently binds to the crystal surface through the thiol group. As expected, heparin sulphate binding growth factors bound to the octasaccharide, but the change in mass of growth factor bound per unit change in dissipation is different for the different growth factors. Suggesting that the structures of the various growth factor-octasaccharide complexes are different, therefore, indicates that the change in dissipation can give insights into the structure, orientation and packing of the oligosaccharide-growth factor complexes.

Facile modification of electrospun fibrous structures with antifouling zwitterionic hydrogels.

PubMed

Xu, Tong; Yang, Jing; Zhang, Jiamin; Zhu, Yingnan; Li, Qingsi; Pan, Chao; Zhang, Lei

2017-12-28

Electrospinning technology can easily produce different shaped fibrous structures, making them highly valuable to various biomedical applications. However, surface contamination of biomolecules, cells, or blood has emerged as a significant challenge to the success of electrospun devices, especially artificial blood vessels, catheters and wound dressings etc. Many efforts have been made to resist the surface non-specific biomolecules or cells adsorption, but most of them require complex pre-treatment processes, hard-to-remove metal catalysts or rigorous reaction conditions. In addition, the stability of antifouling coatings, especially in complex conditions, is still a major concern. In this work, inspired by the interpenetrating polymer network and reinforced concrete structure, an efficient and facile strategy for modifying hydrophobic electrospun meshes and tubes with antifouling zwitterionic hydrogels has been introduced. The resulting products could efficiently resist the adhesion of proteins, cells, or even fresh whole blood. Meanwhile, they could maintain the shapes and mechanical strength of the original electrospun structures. Furthermore, the hydrogel structures could retain stable in a physiological condition for at least 3 months. This paper provided a general antifouling and hydrophilicity surface modification strategy for various fibrous structures, and could be of great value for many biomedical applications where antifouling properties are critical.

Surface tension driven aggregation of organic nanowires via lab in a droplet.

PubMed

Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Feng, Man; Zhang, Ziming; Dong, Haiyun; Gao, Faming; Zhao, Yong Sheng

2018-06-05

Directing the architecture of complex organic nanostructures is desirable and still remains a challenge in areas of materials science due to their structure-dependent collective optoelectronic properties. Herein, we demonstrate a simple and versatile solution strategy that allows surface tension to drive low-dimensional nanostructures to aggregate into complex structures via a lab in a droplet technique. By selecting a suitable combination of a solvent and an anti-solvent with controllable surface tension difference, the droplets can be automatically cracked into micro-droplets, which provides an aggregation force directed toward the centre of the droplet to drive the low-dimensional building blocks to form the special aggregations during the self-assembly process. This synthetic strategy has been shown to be universal for organic materials, which is beneficial for further optimizing the optoelectronic properties. These results contribute to gaining an insightful understanding on the detailed growth mechanism of complex organic nanostructures and greatly promoting the development of organic nanophotonics.

Shrink-induced superhydrophobic and antibacterial surfaces in consumer plastics.

PubMed

Freschauf, Lauren R; McLane, Jolie; Sharma, Himanshu; Khine, Michelle

2012-01-01

Structurally modified superhydrophobic surfaces have become particularly desirable as stable antibacterial surfaces. Because their self-cleaning and water resistant properties prohibit bacteria growth, structurally modified superhydrophobic surfaces obviate bacterial resistance common with chemical agents, and therefore a robust and stable means to prevent bacteria growth is possible. In this study, we present a rapid fabrication method for creating such superhydrophobic surfaces in consumer hard plastic materials with resulting antibacterial effects. To replace complex fabrication materials and techniques, the initial mold is made with commodity shrink-wrap film and is compatible with large plastic roll-to-roll manufacturing and scale-up techniques. This method involves a purely structural modification free of chemical additives leading to its inherent consistency over time and successive recasting from the same molds. Finally, antibacterial properties are demonstrated in polystyrene (PS), polycarbonate (PC), and polyethylene (PE) by demonstrating the prevention of gram-negative Escherichia coli (E. coli) bacteria growth on our structured plastic surfaces.

Local structural ordering in surface-confined liquid crystals

NASA Astrophysics Data System (ADS)

Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

2017-06-01

The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

Surface topographical effects on the structural growth of thick sputtered metal and alloy coatings

NASA Technical Reports Server (NTRS)

Spalvins, T.; Brainard, W. A.

1974-01-01

Thick sputtered S-Monel, silver, and 304 stainless steel coatings were deposited on mica and metal substrates with various surface finishes to investigate the structural growth of the coating by scanning electron microscopy. The geometry and the surface structure of the nodules are characterized. Compositional changes within the coating were analyzed by X-ray dispersion miscroscopy. Defects in the surface finish act as preferential nucleation sites and form isolated and complex nodules and various surface overgrowths in the coating. The nodule boundaries are very vulnerable to chemical etching, and these nodules do not disappear after full annealing. Further, they have undesirable effects on mechanical properties; cracks are initiated at the nodules when the coating is stressed by mechanical forces.

Self-templated formation of uniform NiCo2O4 hollow spheres with complex interior structures for lithium-ion batteries and supercapacitors.

PubMed

Shen, Laifa; Yu, Le; Yu, Xin-Yao; Zhang, Xiaogang; Lou, Xiong Wen David

2015-02-02

Despite the significant advancement in preparing metal oxide hollow structures, most approaches rely on template-based multistep procedures for tailoring the interior structure. In this work, we develop a new generally applicable strategy toward the synthesis of mixed-metal-oxide complex hollow spheres. Starting with metal glycerate solid spheres, we show that subsequent thermal annealing in air leads to the formation of complex hollow spheres of the resulting metal oxide. We demonstrate the concept by synthesizing highly uniform NiCo2O4 hollow spheres with a complex interior structure. With the small primary building nanoparticles, high structural integrity, complex interior architectures, and enlarged surface area, these unique NiCo2O4 hollow spheres exhibit superior electrochemical performances as advanced electrode materials for both lithium-ion batteries and supercapacitors. This approach can be an efficient self-templated strategy for the preparation of mixed-metal-oxide hollow spheres with complex interior structures and functionalities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface morphological, structural, electrical and optical properties of GaN-based light-emitting diodes using submicron-scaled Ag islands and ITO thin films

NASA Astrophysics Data System (ADS)

Lee, Young-Woong; Reddy, M. Siva Pratap; Kim, Bo-Myung; Park, Chinho

2018-07-01

An ITO-Ag islands complex as a new transparent conducting electrode (TCE) structure (on the 5 nm-thick p-InGaN/90 nm-thick p-GaN) for achieving high-performance and more reliable GaN-based LEDs were fabricated. A normal LED with a conventional ITO TCE was also compared. The surface morphological, structural, electrical and optical properties of fabricated GaN-based light-emitting diodes using a complex electrode of submicron-scaled Ag islands and ITO thin films are explored by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), current-voltage (I-V) and output power-current (L-I) techniques. Surface morphology investigations revealed Ag islands formed uniformly on the p-InGaN/p-GaN surface during rapid thermal annealing at 400 °C for 1 min in N2 ambient. The ohmic properties and overall device-performance of the suggested contact and device structures were superior to those in the conventional ITO contact and normal ITO LED structures. Based on the results of XRD and XPS measurements, the formation of the intermetallic gallide phases (AgGa) is responsible for better performance characteristics of the ITO-Ag islands device. The significant improvements are described in terms of the conducting bridge influence, highly effective micro-mirror effect, and wider photon window via the roughened structure.

Fabrication of the replica templated from butterfly wing scales with complex light trapping structures

NASA Astrophysics Data System (ADS)

Han, Zhiwu; Li, Bo; Mu, Zhengzhi; Yang, Meng; Niu, Shichao; Zhang, Junqiu; Ren, Luquan

2015-11-01

The polydimethylsiloxane (PDMS) positive replica templated twice from the excellent light trapping surface of butterfly Trogonoptera brookiana wing scales was fabricated by a simple and promising route. The exact SiO2 negative replica was fabricated by using a synthesis method combining a sol-gel process and subsequent selective etching. Afterwards, a vacuum-aided process was introduced to make PDMS gel fill into the SiO2 negative replica, and the PDMS gel was solidified in an oven. Then, the SiO2 negative replica was used as secondary template and the structures in its surface was transcribed onto the surface of PDMS. At last, the PDMS positive replica was obtained. After comparing the PDMS positive replica and the original bio-template in terms of morphology, dimensions and reflectance spectra and so on, it is evident that the excellent light trapping structures of butterfly wing scales were inherited by the PDMS positive replica faithfully. This bio-inspired route could facilitate the preparation of complex light trapping nanostructure surfaces without any assistance from other power-wasting and expensive nanofabrication technologies.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

PubMed

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

A study on adsorption mechanism of organoarsenic compounds on ferrihydrite by XAFS

NASA Astrophysics Data System (ADS)

Tanaka, M.; Takahashi, Y.; Yamaguchi, N.

2013-04-01

Anthropogenic organoarsenic compounds which were used such as agrochemicals, pesticides, and herbicides can have a potential as a source of arsenic pollution in water. In the process, the adsorption of arsenic onto mineral surface in soil may play an important role to affect arsenic distribution in solid-water interface. However, adsorption structures of organoarsenic compounds on the iron-(oxyhydr)oxides are not well known. In this study, extended X-ray absorption fine structure (EXAFS) spectroscopy was employed to know the adsorption structure of methyl- and phenyl-substituted organoarsenic compounds (methylarsonic acid (MMA), dimethylarsinic acid (DMA), phenylarsonic acid (PAA), and diphenylarsinic acid (DPAA) onto ferrihydrite which can be a strong adsorbent of arsenic. EXAFS analysis suggests that the formation of inner-sphere surface complex for all organoarsenic compounds with ferrihydrite regardless of the organic functional groups and the number of substitution. The As-Fe distances are around 3.27 , which suggests both mono-and bi-dentate inner-sphere complexes by DFT calculations. The corresponding coordination numbers (CNs) are less than two, suggesting that coexistence of both structures of inner-sphere complexes.

Complex between α-bungarotoxin and an α7 nicotinic receptor ligand-binding domain chimaera

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

Huang, Sun; Li, Shu-Xing; Bren, Nina

2013-09-01

To identify high-affinity interactions between long-chain α-neurotoxins and nicotinic receptors, we determined the crystal structure of the complex between α-btx (α-bungarotoxin) and a pentameric ligand-binding domain constructed from the human α7 AChR (acetylcholine receptor) and AChBP (acetylcholine-binding protein). The complex buries ~2000 Å 2 (1 Å=0.1 nm) of surface area, within which Arg 36 and Phe 32 from finger II of α-btx form a π-cation stack that aligns edge-to-face with the conserved Tyr 184 from loop-C of α7, while Asp 30 of α-btx forms a hydrogen bond with the hydroxy group of Tyr 184. These inter-residue interactions diverge from thosemore » in a 4.2 Å structure of α-ctx (α-cobratoxin) bound to AChBP, but are similar to those in a 1.94 Å structure of α-btx bound to the monomeric α1 extracellular domain, although compared with the monomer-bound complex, the α-btx backbone exhibits a large shift relative to the protein surface. Mutational analyses show that replacing Tyr 184 with a threonine residue abolishes high-affinity α-btx binding, whereas replacing with a phenylalanine residue maintains high affinity. Comparison of the α-btx complex with that coupled to the agonist epibatidine reveals structural rearrangements within the binding pocket and throughout each subunit. The overall findings highlight structural principles by which α-neurotoxins interact with nicotinic receptors.« less

Structural tests and development of a laminar flow control wing surface composite chordwise joint

NASA Technical Reports Server (NTRS)

Lineberger, L. B.

1984-01-01

The dramatic increases in fuel costs and the potential for periods of limited fuel availability provided the impetus to explore technologies to reduce transport aircraft fuel consumption. NASA sponsored the Aircraft Energy Efficiency (ACEE) program beginning in 1976 to develop technologies to improve fuel efficiency. The Lockheed-Georgia Company accomplished under NAS1-16235 Laminar-Flow-Control (LFC) Wing Panel Structural Design and Development (WSSD); design, manufacturing, and testing activities. An in-depth preliminary design of the baseline 1993 LFC wing was accomplished. A surface panel using the Lockheed graphite/epoxy integrated LFC wing box structural concept was designed. The concept was shown by analysis to be structurally efficient and cost effective. Critical details of the surface and surface joint was demonstrated by fabricating and testing complex, concept selection specimens. The Lockheed-Georgia Company accomplishments, Development of LFC Wind Surface Composite Structures (WSCS), are documented. Tests were conducted on two CV2 panels to verify the static tension and fatigue strength of LFC wing surface chordwise joints.

Atomistic Simulations of Complex DNA DSBs and the Interactions with Ku70/80 Heterodimer

NASA Technical Reports Server (NTRS)

Hu, Shaowen; Cucinotta, Francis A.

2011-01-01

Compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex. Binding of Ku drastically reduces the structural disruption and flexibility caused by the complex lesions. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. Binding of Ku promotes the rigidity of DNA duplexes, due to the clamp structure of the inner surface of the rings of Ku70/80.

Generation of continuously rotating polarization by combining cross-polarizations and its application in surface structuring.

PubMed

Lam, Billy; Zhang, Jihua; Guo, Chunlei

2017-08-01

In this study, we develop a simple but highly effective technique that generates a continuously varying polarization within a laser beam. This is achieved by having orthogonal linear polarizations on each side of the beam. By simply focusing such a laser beam, we can attain a gradually and continuously changing polarization within the entire Rayleigh range due to diffraction. To demonstrate this polarization distribution, we apply this laser beam onto a metal surface and create a continuously rotating laser induced periodic surface structure pattern. This technique provides a very effective way to produce complex surface structures that may potentially find applications, such as polarization modulators and metasurfaces.

Aggregation behavior and complex structure between triblock copolymer and anionic surfactants

NASA Astrophysics Data System (ADS)

Li, Yiming; Bao, Mutai; Wang, Zhining; Zhang, Haixia; Xu, Guiying

2011-01-01

The aggregation behavior and complex structure of ABA triblock copolymer EO 76PO 30EO 76 (F68) with sodium dodecyl sulfate (SDS) and sodium bis(2-ethylhexyl)sulfonate (AOT) in aqueous solution were investigated by surface tension, fluorescence techniques and dynamic light-scattering (DLS) measurements. It is revealed that in certain regions of binding, surfactant/F68 complexes are formed. Structural informations and size of complexes are evaluated. When F68 is present in its nonassociated state, F68/micellar SDS complexes are formed at SDS concentrations above its critical aggregation concentration (cac). The cac is well below the critical micellar concentration (cmc) of pure SDS, and a model suggesting how complexes are formed at the cac in the presence of F68 is described. Experimental results show that SDS interacts with F68 mainly through hydrophobic forces, polypropylene oxide (PPO) groups of F68 are solubilized into SDS micellar cores and poly(ethylene oxide) (PEO) groups interact with SDS micelles. This interaction mechanism results in a "pearl-necklace" complex structure. However, a different structure occurs for F68/AOT complex at lower F68 concentrations, as nonassociated F68 interacts with AOT mainly through ion-dipole interactions. Complexes with a "wrapping" structure at lower F68 concentrations are formed.

Intercalation of Transition Metals into Stacked Benzene Rings: A Model Study of the Intercalation of Transition Metals into Bilayered Graphene.

PubMed

Youn, Il Seung; Kim, Dong Young; Singh, N Jiten; Park, Sung Woo; Youn, Jihee; Kim, Kwang S

2012-01-10

Structures of neutral metal-dibenzene complexes, M(C6H6)2 (M = Sc-Zn), are investigated by using Møller-Plesset second order perturbation theory (MP2). The benzene molecules change their conformation and shape upon complexation with the transition metals. We find two types of structures: (i) stacked forms for early transition metal complexes and (ii) distorted forms for late transition metal ones. The benzene molecules and the metal atom are bound together by δ bonds which originate from the interaction of π-MOs and d orbitals. The binding energy shows a maximum for Cr(C6H6)2, which obeys the 18-electron rule. It is noticeable that Mn(C6H6)2, a 19-electron complex, manages to have a stacked structure with an excess electron delocalized. For other late transition metal complexes having more than 19 electrons, the benzene molecules are bent or stray away from each other to reduce the electron density around a metal atom. For the early transition metals, the M(C6H6) complexes are found to be more weakly bound than M(C6H6)2. This is because the M(C6H6) complexes do not have enough electrons to satisfy the 18-electron rule, and so the M(C6H6)2 complexes generally tend to have tighter binding with a shorter benzene-metal length than the M(C6H6) complexes, which is quite unusual. The present results could provide a possible explanation of why on the Ni surface graphene tends to grow in a few layers, while on the Cu surface the weak interaction between the copper surface and graphene allows for the formation of a single layer of graphene, in agreement with chemical vapor deposition experiments.

Direct ambient noise tomography for 3-D near surface shear velocity structure: methodology and applications

NASA Astrophysics Data System (ADS)

Yao, H.; Fang, H.; Li, C.; Liu, Y.; Zhang, H.; van der Hilst, R. D.; Huang, Y. C.

2014-12-01

Ambient noise tomography has provided essential constraints on crustal and uppermost mantle shear velocity structure in global seismology. Recent studies demonstrate that high frequency (e.g., ~ 1 Hz) surface waves between receivers at short distances can be successfully retrieved from ambient noise cross-correlation and then be used for imaging near surface or shallow crustal shear velocity structures. This approach provides important information for strong ground motion prediction in seismically active area and overburden structure characterization in oil and gas fields. Here we propose a new tomographic method to invert all surface wave dispersion data for 3-D variations of shear wavespeed without the intermediate step of phase or group velocity maps.The method uses frequency-dependent propagation paths and a wavelet-based sparsity-constrained tomographic inversion. A fast marching method is used to compute, at each period, surface wave traveltimes and ray paths between sources and receivers. This avoids the assumption of great-circle propagation that is used in most surface wave tomographic studies, but which is not appropriate in complex media. The wavelet coefficients of the velocity model are estimated with an iteratively reweighted least squares (IRLS) algorithm, and upon iterations the surface wave ray paths and the data sensitivity matrix are updated from the newly obtained velocity model. We apply this new method to determine the 3-D near surface wavespeed variations in the Taipei basin of Taiwan, Hefei urban area and a shale and gas production field in China using the high-frequency interstation Rayleigh wave dispersion data extracted from ambient noisecross-correlation. The results reveal strong effects of off-great-circle propagation of high-frequency surface waves in these regions with above 30% shear wavespeed variations. The proposed approach is more efficient and robust than the traditional two-step surface wave tomography for imaging complex structures. In the future, approximate 3-D sensitivity kernels for dispersion data will be incorporated to account for finite-frequency effect of surface wave propagation. In addition, our approach provides a consistent framework for joint inversion of surface wave dispersion and body wave traveltime data for 3-D Vp and Vs structures.

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

Ballouz, Ronald-Louis; Richardson, Derek C.; Morishima, Ryuji

We study the B ring’s complex optical depth structure. The source of this structure may be the complex dynamics of the Keplerian shear and the self-gravity of the ring particles. The outcome of these dynamic effects depends sensitively on the collisional and physical properties of the particles. Two mechanisms can emerge that dominate the macroscopic physical structure of the ring: self-gravity wakes and viscous overstability. Here we study the interplay between these two mechanisms by using our recently developed particle collision method that allows us to better model the inter-particle contact physics. We find that for a constant ring surfacemore » density and particle internal density, particles with rough surfaces tend to produce axisymmetric ring features associated with the viscous overstability, while particles with smoother surfaces produce self-gravity wakes.« less

Structural Analysis of the Synaptic Protein Neuroligin and Its β-Neurexin Complex: Determinants for Folding and Cell Adhesion

PubMed Central

Fabrichny, Igor P.; Leone, Philippe; Sulzenbacher, Gerlind; Comoletti, Davide; Miller, Meghan T.; Taylor, Palmer; Bourne, Yves; Marchot, Pascale

2009-01-01

SUMMARY The neuroligins are postsynaptic cell adhesion proteins whose associations with presynaptic neurexins participate in synaptogenesis. Mutations in the neuroligin and neurexin genes appear to be associated with autism and mental retardation. The crystal structure of a neuroligin reveals features not found in its catalytically active relatives, such as the fully hydrophobic interface forming the functional neuroligin dimer; the conformations of surface loops surrounding the vestigial active center; the location of determinants that are critical for folding and processing; and the absence of a macromolecular dipole and presence of an electronegative, hydrophilic surface for neurexin binding. The structure of a β-neurexin-neuroligin complex reveals the precise orientation of the bound neurexin and, despite a limited resolution, provides substantial information on the Ca2+-dependent interactions network involved in trans-synaptic neurexin-neuroligin association. These structures exemplify how an α/β-hydrolase fold varies in surface topography to confer adhesion properties and provide templates for analyzing abnormal processing or recognition events associated with autism. PMID:18093521

Sorption of trivalent lanthanides and actinides onto montmorillonite: Macroscopic, thermodynamic and structural evidence for ternary hydroxo and carbonato surface complexes on multiple sorption sites.

PubMed

Fernandes, M Marques; Scheinost, A C; Baeyens, B

2016-08-01

The credibility of long-term safety assessments of radioactive waste repositories may be greatly enhanced by a molecular level understanding of the sorption processes onto individual minerals present in the near- and far-fields. In this study we couple macroscopic sorption experiments to surface complexation modelling and spectroscopic investigations, including extended X-ray absorption fine structure (EXAFS) and time-resolved laser fluorescence spectroscopies (TRLFS), to elucidate the uptake mechanism of trivalent lanthanides and actinides (Ln/An(III)) by montmorillonite in the absence and presence of dissolved carbonate. Based on the experimental sorption isotherms for the carbonate-free system, the previously developed 2 site protolysis non electrostatic surface complexation and cation exchange (2SPNE SC/CE) model needed to be complemented with an additional surface complexation reaction onto weak sites. The fitting of sorption isotherms in the presence of carbonate required refinement of the previously published model by reducing the strong site capacity and by adding the formation of Ln/An(III)-carbonato complexes both on strong and weak sites. EXAFS spectra of selected Am samples and TRLFS spectra of selected Cm samples corroborate the model assumptions by showing the existence of different surface complexation sites and evidencing the formation of Ln/An(III) carbonate surface complexes. In the absence of carbonate and at low loadings, Ln/An(III) form strong inner-sphere complexes through binding to three Al(O,OH)6 octahedra, most likely by occupying vacant sites in the octahedral layers of montmorillonite, which are exposed on {010} and {110} edge faces. At higher loadings, Ln/An(III) binds to only one Al octahedron, forming a weaker, edge-sharing surface complex. In the presence of carbonate, we identified a ternary mono- or dicarbonato Ln/An(III) complex binding directly to one Al(O,OH)6 octahedron, revealing that type-A ternary complexes form with the one or two carbonate groups pointing away from the surface into the solution phase. Within the spectroscopically observable concentration range these complexes could only be identified on the weak sites, in line with the small strong site capacity suggested by the refined sorption model. When the solubility of carbonates was exceeded, formation of an Am carbonate hydroxide could be identified. The excellent agreement between the thermodynamic model parameters obtained by fitting the macroscopic data, and the spectroscopically identified mechanisms, demonstrates the mature state of the 2SPNE SC/CE model for predicting and quantifying the retention of Ln/An(III) elements by montmorillonite-rich clay rocks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Facet-Dependent Cr(VI) Adsorption of Hematite Nanocrystals.

PubMed

Huang, Xiaopeng; Hou, Xiaojing; Song, Fahui; Zhao, Jincai; Zhang, Lizhi

2016-02-16

In this study, the adsorption process of Cr(VI) on the hematite facets was systematically investigated with synchrotron-based Cr K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy, in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, density-functional theory calculation, and surface complexation models. Structural model fitting of EXAFS spectroscopy suggested that the interatomic distances of Cr-Fe were, respectively, 3.61 Å for the chromate coordinated hematite nanoplates with exposed {001} facets, 3.60 and 3.30 Å for the chromate coordinated hematite nanorods with exposed {001} and {110} facets, which were characteristic of inner-sphere complexation. In situ ATR-FTIR spectroscopy analysis confirmed the presence of two inner-sphere surface complexes with C3ν and C2ν symmetry, while the C3ν and C2ν species were assigned to monodentate and bidentate inner-sphere surface complexes with average Cr-Fe interatomic distances of 3.60 and 3.30 Å, respectively. On the basis of these experimental and theoretical results, we concluded that HCrO4(-) as dominated Cr(VI) species was adsorbed on {001} and {110} facets in inner-sphere monodentate mononuclear and bidentate binuclear configurations, respectively. Moreover, the Cr(VI) adsorption performance of hematite facets was strongly dependent on the chromate complexes formed on the hematite facets.

Stacking and T-shape competition in aromatic-aromatic amino acid interactions.

PubMed

Chelli, Riccardo; Gervasio, Francesco Luigi; Procacci, Piero; Schettino, Vincenzo

2002-05-29

The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

Mimicking bug-like surface structures and their fluid transport produced by ultrashort laser pulse irradiation of steel

NASA Astrophysics Data System (ADS)

Kirner, S. V.; Hermens, U.; Mimidis, A.; Skoulas, E.; Florian, C.; Hischen, F.; Plamadeala, C.; Baumgartner, W.; Winands, K.; Mescheder, H.; Krüger, J.; Solis, J.; Siegel, J.; Stratakis, E.; Bonse, J.

2017-12-01

Ultrashort laser pulses with durations in the fs-to-ps range were used for large area surface processing of steel aimed at mimicking the morphology and extraordinary wetting behaviour of bark bugs (Aradidae) found in nature. The processing was performed by scanning the laser beam over the surface of polished flat sample surfaces. A systematic variation of the laser processing parameters (peak fluence and effective number of pulses per spot diameter) allowed the identification of different regimes associated with characteristic surface morphologies (laser-induced periodic surface structures, i.e., LIPSS, grooves, spikes, etc.). Moreover, different laser processing strategies, varying laser wavelength, pulse duration, angle of incidence, irradiation atmosphere, and repetition rates, allowed to achieve a range of morphologies that resemble specific structures found on bark bugs. For identifying the ideal combination of parameters for mimicking bug-like structures, the surfaces were inspected by scanning electron microscopy. In particular, tilted micrometre-sized spikes are the best match for the structure found on bark bugs. Complementary to the morphology study, the wetting behaviour of the surface structures for water and oil was examined in terms of philic/phobic nature and fluid transport. These results point out a route towards reproducing complex surface structures inspired by nature and their functional response in technologically relevant materials.

Electrospray deposition of organic molecules on bulk insulator surfaces.

PubMed

Hinaut, Antoine; Pawlak, Rémy; Meyer, Ernst; Glatzel, Thilo

2015-01-01

Large organic molecules are of important interest for organic-based devices such as hybrid photovoltaics or molecular electronics. Knowing their adsorption geometries and electronic structures allows to design and predict macroscopic device properties. Fundamental investigations in ultra-high vacuum (UHV) are thus mandatory to analyze and engineer processes in this prospects. With increasing size, complexity or chemical reactivity, depositing molecules by thermal evaporation becomes challenging. A recent way to deposit molecules in clean conditions is Electrospray Ionization (ESI). ESI keeps the possibility to work with large molecules, to introduce them in vacuum, and to deposit them on a large variety of surfaces. Here, ESI has been successfully applied to deposit triply fused porphyrin molecules on an insulating KBr(001) surface in UHV environment. Different deposition coverages have been obtained and characterization of the surface by in-situ atomic force microscopy working in the non-contact mode shows details of the molecular structures adsorbed on the surface. We show that UHV-ESI, can be performed on insulating surfaces in the sub-monolayer regime and to single molecules which opens the possibility to study a variety of complex molecules.

Different Effects of Roughness (Granularity) and Hydrophobicity

NASA Astrophysics Data System (ADS)

Shirtcliffe, Neil; McHale, Glen; Hamlett, Christopher; Newton, Michael

2010-05-01

With thanks to Stefan Doerr and Jorge Mataix-Solera for their invitation Superhydrophobicity is an interesting effect that appears to be simple on the outset; increased surface area from roughness increases interfacial area and therefore energy loss or gain. More extreme roughness prevents total wetting, resulting in gas pockets present at the surface and a drastic change in the properties of the system. Increases in complexity of the system, by adding porosity (granularity), allowing the structures to move, varying the shape of the roughness or the composition of the liquid used often has unexpected effects. Here we will consider a few of these related to complex topography. Overhanging features are commonly used in test samples as they perform better in some tests than simple roughness. It has been shown to be a prerequisite for superoleophobic surfaces as it allows liquids to be suspended for contact angles considerably below 90°. It also allows trapping of gas in lower layers even if the first layer is flooded. This is important in soils as a fixed bed of granules behaves just like a surface with overhanging roughness. Using simple geometry it is possible to predict at what contact angle penetration will occur. Plants have some structured superhydrophobic surfaces and we have shown that some use them in conjunction with other structured surfaces to control water flows. This allows some plants to survive in difficult environments and shows us how subtly different structures interact completely differently with water. Long fibres can either cause water droplets to roll over a plant surface or halt it in its tracks. Implications of this in soils include predicting when particles will adhere more strongly to water drops and why organic fibrous material may play a greater role in the behaviour of water in soils than may be expected from the amount present. The garden snail uses a biosurfactant that is very effective at wetting surfaces and can crawl over most superhydrophobic surfaces. There are some, however, that defeat even the snail's complex slime. Looking at these surfaces in more detail reveals that some superhydrophobic surfaces are much more resistant to the effects of surfactants than others. As mentioned above, overhanging structures, such as those found in granular materials are particularly effective at suspending liquids. This does not, however, always translate to them being more effective against surfactants, unfortunately, however, surfactants are not always as effective as we would like them to be, although drops do not skate across superhydrophobic surfaces they often do not penetrate into them fully either.

Silver nanoparticle deposition on inverse opal SiO2 films embedded in protective polypropylene micropits for SERS applications

NASA Astrophysics Data System (ADS)

Ammosova, Lena; Ankudze, Bright; Philip, Anish; Jiang, Yu; Pakkanen, Tuula T.; Pakkanen, Tapani A.

2018-01-01

Common methods to fabricate surface enhanced Raman scattering (SERS) substrates with controlled micro-nanohierarchy are often complex and expensive. In this study, we demonstrate a simple and cost effective method to fabricate SERS substrates with complex geometries. Microworking robot structuration is used to pattern a polypropylene (PP) substrate with micropits, facilitating protective microenvironment for brittle SiO2 inverse opal (IO) structure. Hierarchical SiO2 IO patterns were obtained using polystyrene (PS) spheres as a sacrificial template, and were selectively embedded into the hydrophilized PP micropits. The same microworking robot technique was subsequently used to deposit silver nanoparticle ink into the SiO2 IO cavities. The fabricated multi-level micro-nanohierarchy surface was studied to enhance Raman scattering of the 4-aminothiophenol (4-ATP) analyte molecule. The results show that the SERS performance of the micro-nanohierarchical substrate increases significantly the Raman scattering intensity compared to substrates with structured 2D surface geometries.

Shallow subsurface structure of the Wasatch fault, Provo segment, Utah, from integrated compressional and shear-wave seismic reflection profiles with implications for fault structure and development

USGS Publications Warehouse

McBride, J.H.; Stephenson, W.J.; Williams, R.A.; Odum, J.K.; Worley, D.M.; South, J.V.; Brinkerhoff, A.R.; Keach, R.W.; Okojie-Ayoro, A. O.

2010-01-01

Integrated vibroseis compressional and experimental hammer-source, shear-wave, seismic reflection profiles across the Provo segment of the Wasatch fault zone in Utah reveal near-surface and shallow bedrock structures caused by geologically recent deformation. Combining information from the seismic surveys, geologic mapping, terrain analysis, and previous seismic first-arrival modeling provides a well-constrained cross section of the upper ~500 m of the subsurface. Faults are mapped from the surface, through shallow, poorly consolidated deltaic sediments, and cutting through a rigid bedrock surface. The new seismic data are used to test hypotheses on changing fault orientation with depth, the number of subsidiary faults within the fault zone and the width of the fault zone, and the utility of integrating separate elastic methods to provide information on a complex structural zone. Although previous surface mapping has indicated only a few faults, the seismic section shows a wider and more complex deformation zone with both synthetic and antithetic normal faults. Our study demonstrates the usefulness of a combined shallow and deeper penetrating geophysical survey, integrated with detailed geologic mapping to constrain subsurface fault structure. Due to the complexity of the fault zone, accurate seismic velocity information is essential and was obtained from a first-break tomography model. The new constraints on fault geometry can be used to refine estimates of vertical versus lateral tectonic movements and to improve seismic hazard assessment along the Wasatch fault through an urban area. We suggest that earthquake-hazard assessments made without seismic reflection imaging may be biased by the previous mapping of too few faults. ?? 2010 Geological Society of America.

Multiple pickering emulsions stabilized by microbowls.

PubMed

Nonomura, Yoshimune; Kobayashi, Naoto; Nakagawa, Naoki

2011-04-19

Some researchers have focused on the adsorption of solid particles at fluid-fluid interfaces and prepared emulsions and foams called "Pickering emulsions/foams". However, while several reports exist on simple spherical emulsions, few reports are available on the formation of more complex structures. Here, we show that holes on particle surfaces are a key factor in establishing the variety and complexity of mesoscale structures. Microbowls, which are hollow particles with holes on their surfaces, form multiple emulsions (water-in-oil-in-water and oil-in-water-in-oil emulsions) by simply mixing them with water and oil. Furthermore, stable potato-like or coffee-bean-like emulsions are also obtained, although nonspherical emulsions are usually unstable because of their larger interfacial energies. These findings are useful in designing the building blocks of complex supracolloidal systems for pharmaceutical, food, and cosmetic products. © 2011 American Chemical Society

Examination of the effect of blowing on the near-surface flow structure over a dimpled surface

NASA Astrophysics Data System (ADS)

Borchetta, C. G.; Martin, A.; Bailey, S. C. C.

2018-03-01

The near surface flow over a dimpled surface with flow injection through it was documented using time-resolved particle image velocimetry. The instantaneous flow structure, time-averaged statistics, and results from snapshot proper orthogonal decomposition were used to examine the coherent structures forming near the dimpled surface. In particular, the modifications made to the flow structures by the addition of flow injection through the surface were studied. It was observed that without flow injection, inclined flow structures with alternating vorticity from neighboring dimples are generated by the dimples and advect downstream. This behavior is coupled with fluid becoming entrained inside the dimples, recirculating and ejecting away from the surface. When flow injection was introduced through the surface, the flow structures became more disorganized, but some of the features of the semi-periodic structures observed without flow injection were preserved. The structures with flow injection appear in multiple wall-normal layers, formed from vortical structures shed from upstream dimples, with a corresponding increase in the size of the advecting structures. As a result of the more complex flow field observed with flow injection, there was an increase in turbulent kinetic energy and Reynolds shear stress, with the Reynolds shear stress representing an increase in vertical transport of momentum by sweeping and ejecting motions that were not present without flow injection.

A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

PubMed

Zhou, Weiqiang; Yan, Hong

2010-10-15

Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.

PubMed

Liang, Shide; Zhang, Jian; Zhang, Shicui; Guo, Huarong

2004-11-15

We show that residues at the interfaces of protein-protein complexes have higher side-chain energy than other surface residues. Eight different sets of protein complexes were analyzed. For each protein pair, the complex structure was used to identify the interface residues in the unbound monomer structures. Side-chain energy was calculated for each surface residue in the unbound monomer using our previously developed scoring function.1 The mean energy was calculated for the interface residues and the other surface residues. In 15 of the 16 monomers, the mean energy of the interface residues was higher than that of other surface residues. By decomposing the scoring function, we found that the energy term of the buried surface area of non-hydrogen-bonded hydrophilic atoms is the most important factor contributing to the high energy of the interface regions. In spite of lacking hydrophilic residues, the interface regions were found to be rich in buried non-hydrogen-bonded hydrophilic atoms. Although the calculation results could be affected by the inaccuracy of the scoring function, patch analysis of side-chain energy on the surface of an isolated protein may be helpful in identifying the possible protein-protein interface. A patch was defined as 20 residues surrounding the central residue on the protein surface, and patch energy was calculated as the mean value of the side-chain energy of all residues in the patch. In 12 of the studied monomers, the patch with the highest energy overlaps with the observed interface. The results are more remarkable when only three residues with the highest energy in a patch are averaged to derive the patch energy. All three highest-energy residues of the top energy patch belong to interfacial residues in four of the eight small protomers. We also found that the residue with the highest energy score on the surface of a small protomer is very possibly the key interaction residue. (c) 2004 Wiley-Liss, Inc.

The effect of structural complexity, prey density, and "predator-free space" on prey survivorship at created oyster reef mesocosms

USGS Publications Warehouse

Humphries, Austin T.; La Peyre, Megan K.; Decossas, Gary A.

2011-01-01

Interactions between predators and their prey are influenced by the habitat they occupy. Using created oyster (Crassostrea virginica) reef mesocosms, we conducted a series of laboratory experiments that created structure and manipulated complexity as well as prey density and “predator-free space” to examine the relationship between structural complexity and prey survivorship. Specifically, volume and spatial arrangement of oysters as well as prey density were manipulated, and the survivorship of prey (grass shrimp, Palaemonetes pugio) in the presence of a predator (wild red drum, Sciaenops ocellatus) was quantified. We found that the presence of structure increased prey survivorship, and that increasing complexity of this structure further increased survivorship, but only to a point. This agrees with the theory that structural complexity may influence predator-prey dynamics, but that a threshold exists with diminishing returns. These results held true even when prey density was scaled to structural complexity, or the amount of “predator-free space” was manipulated within our created reef mesocosms. The presence of structure and its complexity (oyster shell volume) were more important in facilitating prey survivorship than perceived refugia or density-dependent prey effects. A more accurate indicator of refugia might require “predator-free space” measures that also account for the available area within the structure itself (i.e., volume) and not just on the surface of a structure. Creating experiments that better mimic natural conditions and test a wider range of “predator-free space” are suggested to better understand the role of structural complexity in oyster reefs and other complex habitats.

Straining and wrinkling processes during turbulence-premixed flame interaction measured using temporally-resolved diagnostics

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

Steinberg, Adam M.; Driscoll, James F.

2009-12-15

The dynamical processes of flame surface straining and wrinkling that occur as turbulence interacts with a premixed flame were measured using cinema-stereoscopic PIV (CS-PIV) and orthogonal-plane cinema-stereoscopic PIV (OPCS-PIV). These diagnostics provided temporally resolved measurements of turbulence-flame interaction at frame rates of up to 3 kHz and spatial resolutions as small as 280{mu} m. Previous descriptions of flame straining and wrinkling have typically been derived based on a canonical interaction between a pair of counter-rotating vortices and a planar flame surface. However, it was found that this configuration did not properly represent real turbulence-flame interaction. Interactions resembling the canonical configurationmore » were observed in less than 10% of the recorded frames. Instead, straining and wrinkling were generally caused more geometrically complex turbulence, consisting of large groups of structures that could be multiply curved and intertwined. The effect of the interaction was highly dependent on the interaction geometry. Furthermore, even when the turbulence did exist in the canonical geometry, the straining and wrinkling of the flame surface were not well characterized by the vortical structures. A new mechanistic description of the turbulence-flame interaction was therefore identified and confirmed by the measurements. In this description, flame surface straining is caused by coherent structures of fluid-dynamic strain-rate (strain-rate structures). The role of vortical structures is to curve existing flame surface, creating wrinkles. By simultaneously considering both forms of turbulent structure, turbulence-flame interactions in both the canonical configuration and more complex geometries could be understood. (author)« less

Frictional heterogeneities on carbonate-bearing normal faults: Insights from the Monte Maggio Fault, Italy

NASA Astrophysics Data System (ADS)

Carpenter, B. M.; Scuderi, M. M.; Collettini, C.; Marone, C.

2014-12-01

Observations of heterogeneous and complex fault slip are often attributed to the complexity of fault structure and/or spatial heterogeneity of fault frictional behavior. Such complex slip patterns have been observed for earthquakes on normal faults throughout central Italy, where many of the Mw 6 to 7 earthquakes in the Apennines nucleate at depths where the lithology is dominated by carbonate rocks. To explore the relationship between fault structure and heterogeneous frictional properties, we studied the exhumed Monte Maggio Fault, located in the northern Apennines. We collected intact specimens of the fault zone, including the principal slip surface and hanging wall cataclasite, and performed experiments at a normal stress of 10 MPa under saturated conditions. Experiments designed to reactivate slip between the cemented principal slip surface and cataclasite show a 3 MPa stress drop as the fault surface fails, then velocity-neutral frictional behavior and significant frictional healing. Overall, our results suggest that (1) earthquakes may readily nucleate in areas of the fault where the slip surface separates massive limestone and are likely to propagate in areas where fault gouge is in contact with the slip surface; (2) postseismic slip is more likely to occur in areas of the fault where gouge is present; and (3) high rates of frictional healing and low creep relaxation observed between solid fault surfaces could lead to significant aftershocks in areas of low stress drop.

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

PubMed

Comeau, Stephen R; Gatchell, David W; Vajda, Sandor; Camacho, Carlos J

2004-01-01

Predicting protein interactions is one of the most challenging problems in functional genomics. Given two proteins known to interact, current docking methods evaluate billions of docked conformations by simple scoring functions, and in addition to near-native structures yield many false positives, i.e. structures with good surface complementarity but far from the native. We have developed a fast algorithm for filtering docked conformations with good surface complementarity, and ranking them based on their clustering properties. The free energy filters select complexes with lowest desolvation and electrostatic energies. Clustering is then used to smooth the local minima and to select the ones with the broadest energy wells-a property associated with the free energy at the binding site. The robustness of the method was tested on sets of 2000 docked conformations generated for 48 pairs of interacting proteins. In 31 of these cases, the top 10 predictions include at least one near-native complex, with an average RMSD of 5 A from the native structure. The docking and discrimination method also provides good results for a number of complexes that were used as targets in the Critical Assessment of PRedictions of Interactions experiment. The fully automated docking and discrimination server ClusPro can be found at http://structure.bu.edu

Structure and Dynamics of Individual Diastereomeric Complexes on Platinum: Surface Studies Related to Heterogeneous Enantioselective Catalysis.

PubMed

Dong, Yi; Goubert, Guillaume; Groves, Michael N; Lemay, Jean-Christian; Hammer, Bjørk; McBreen, Peter H

2017-05-16

The modification of heterogeneous catalysts through the chemisorption of chiral molecules is a method to create catalytic sites for enantioselective surface reactions. The chiral molecule is called a chiral modifier by analogy to the terms chiral auxiliary or chiral ligand used in homogeneous asymmetric catalysis. While there has been progress in understanding how chirality transfer occurs, the intrinsic difficulties in determining enantioselective reaction mechanisms are compounded by the multisite nature of heterogeneous catalysts and by the challenges facing stereospecific surface analysis. However, molecular descriptions have now emerged that are sufficiently detailed to herald rapid advances in the area. The driving force for the development of heterogeneous enantioselective catalysts stems, at the minimum, from the practical advantages they might offer over their homogeneous counterparts in terms of process scalability and catalyst reusability. The broader rewards from their study lie in the insights gained on factors controlling selectivity in heterogeneous catalysis. Reactions on surfaces to produce a desired enantiomer in high excess are particularly challenging since at room temperature, barrier differences as low as ∼2 kcal/mol between pathways to R and S products are sufficient to yield an enantiomeric ratio (er) of 90:10. Such small energy differences are comparable to weak interadsorbate interaction energies and are much smaller than chemisorption or even most physisorption energies. In this Account, we describe combined experimental and theoretical surface studies of individual diastereomeric complexes formed between chiral modifiers and prochiral reactants on the Pt(111) surface. Our work is inspired by the catalysis literature on the enantioselective hydrogenation of activated ketones on cinchona-modified Pt catalysts. Using scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations, we probe the structures and relative abundances of non-covalently bonded complexes formed between three representative prochiral molecules and (R)-(+)-1-(1-naphthyl)ethylamine ((R)-NEA). All three prochiral molecules, 2,2,2-trifluoroacetophenone (TFAP), ketopantolactone (KPL), and methyl 3,3,3-trifluoropyruvate (MTFP), are found to form multiple complexation configurations around the ethylamine group of chemisorbed (R)-NEA. The principal intermolecular interaction is NH···O H-bonding. In each case, submolecularly resolved STM images permit the determination of the prochiral ratio (pr), pro-R to pro-S, proper to specific locations around the ethylamine group. The overall pr observed in experiments on large ensembles of KPL-(R)-NEA complexes is close to the er reported in the literature for the hydrogenation of KPL to pantolactone on (R)-NEA-modified Pt catalysts at 1 bar H 2 . The results of independent DFT and STM studies are merged to determine the geometries of the most abundant complexation configurations. The structures reveal the hierarchy of chemisorption and sometimes multiple H-bonding interactions operating in complexes. In particular, privileged complexes formed by KPL and MTFP reveal the participation of secondary CH···O interactions in stereocontrol. State-specific STM measurements on individual TFAP-(R)-NEA complexes show that complexation states interconvert through processes including prochiral inversion. The state-specific information on structure, prochirality, dynamics, and energy barriers delivered by the combination of DFT and STM provides insight on how to design better chiral modifiers.

Extended hierarchical solvent perturbations from curved surfaces of mesoporous silica particles in a deep eutectic solvent.

PubMed

Hammons, Joshua A; Zhang, Fan; Ilavsky, Jan

2018-06-15

Many applications of deep eutectic solvents (DES) rely on exploitation of their unique yet complex liquid structures. Due to the ionic nature of the DES components, their diffuse structures are perturbed in the presence of a charged surface. We hypothesize that it is possible to perturb the bulk DES structure far (>100 nm) from a curved, charged surface with mesoscopic dimensions. We performed in situ, synchrotron-based ultra-small angle X-ray scattering (USAXS) experiments to study the solvent distribution near the surface of charged mesoporous silica particles (MPS) (≈0.5 µm in diameter) suspended in both water and a common type of DES (1:2 choline Cl-:ethylene glycol). A careful USAXS analysis reveals that the perturbation of electron density distribution within the DES extends ≈1 μm beyond the particle surface, and that this perturbation can be manipulated by the addition of salt ions (AgCl). The concentration of the pore-filling fluid is greatly reduced in the DES. Notably, we extracted the real-space structures of these fluctuations from the USAXS data using a simulated annealing approach that does not require a priori knowledge about the scattering form factor, and can be generalized to a wide range of complex small-angle scattering problems. Copyright © 2018 Elsevier Inc. All rights reserved.

Reconstruction of 3d Models from Point Clouds with Hybrid Representation

NASA Astrophysics Data System (ADS)

Hu, P.; Dong, Z.; Yuan, P.; Liang, F.; Yang, B.

2018-05-01

The three-dimensional (3D) reconstruction of urban buildings from point clouds has long been an active topic in applications related to human activities. However, due to the structures significantly differ in terms of complexity, the task of 3D reconstruction remains a challenging issue especially for the freeform surfaces. In this paper, we present a new reconstruction algorithm which allows the 3D-models of building as a combination of regular structures and irregular surfaces, where the regular structures are parameterized plane primitives and the irregular surfaces are expressed as meshes. The extraction of irregular surfaces starts with an over-segmented method for the unstructured point data, a region growing approach based the adjacent graph of super-voxels is then applied to collapse these super-voxels, and the freeform surfaces can be clustered from the voxels filtered by a thickness threshold. To achieve these regular planar primitives, the remaining voxels with a larger flatness will be further divided into multiscale super-voxels as basic units, and the final segmented planes are enriched and refined in a mutually reinforcing manner under the framework of a global energy optimization. We have implemented the proposed algorithms and mainly tested on two point clouds that differ in point density and urban characteristic, and experimental results on complex building structures illustrated the efficacy of the proposed framework.

Synchrotron x-ray imaging visualization study of capillary-induced flow and critical heat flux on surfaces with engineered micropillars

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

Yu, Dong In; Kwak, Ho Jae; Noh, Hyunwoo

Over the past several decades, phenomena related to critical heat flux (CHF) on structured surfaces have received a large amount of attention from the research community. The purpose of such research has been to enhance the safety and efficiency of a variety of thermal systems. A number of theories have been put forward to explain the key CHF enhancement mechanisms on structured surfaces. However, these theories have not been confirmed experimentally due to limitations in the available visualization techniques and the complexity of the phenomena. To overcome the limitations of the previous visualization techniques and elucidate the CHF enhancement mechanismmore » on the structured surfaces, we introduce synchrotron X-ray imaging with high spatial (~2 μm) and time (~20,000 Hz) resolutions. Lastly, this technique has enabled us to confirm that capillary-induced flow is the key CHF enhancement mechanism on structured surfaces.« less

Synchrotron x-ray imaging visualization study of capillary-induced flow and critical heat flux on surfaces with engineered micropillars

DOE PAGES

Yu, Dong In; Kwak, Ho Jae; Noh, Hyunwoo; ...

2018-02-23

Over the past several decades, phenomena related to critical heat flux (CHF) on structured surfaces have received a large amount of attention from the research community. The purpose of such research has been to enhance the safety and efficiency of a variety of thermal systems. A number of theories have been put forward to explain the key CHF enhancement mechanisms on structured surfaces. However, these theories have not been confirmed experimentally due to limitations in the available visualization techniques and the complexity of the phenomena. To overcome the limitations of the previous visualization techniques and elucidate the CHF enhancement mechanismmore » on the structured surfaces, we introduce synchrotron X-ray imaging with high spatial (~2 μm) and time (~20,000 Hz) resolutions. Lastly, this technique has enabled us to confirm that capillary-induced flow is the key CHF enhancement mechanism on structured surfaces.« less

Theory and Application of Photoelectron Diffraction for Complex Oxide Systems

NASA Astrophysics Data System (ADS)

Chassé, Angelika; Chassé, Thomas

2018-06-01

X-ray photoelectron diffraction (XPD) has been used to investigate film structures and local sites of surface and dopant atoms in complex oxide materials. We have performed angular-resolved measurements of intensity distribution curves (ADCs) and patterns (ADPs) of elemental core level intensities from binary to quaternary mixed oxide samples and compared them to multiple-scattering cluster (MSC) calculations in order to derive information on structural models and related parameters. MSC calculations permitted to describe both bulk diffraction features of binary oxide MnO(001) and the thickness-dependence of the tetragonal distortion of epitaxial MnO films on Ag(001). XPD was further used to investigate the surface termination of perovskite SrTiO3 and BaTiO3 substrates in order to evaluate influence of different ex situ and in situ preparation procedures on the surface layers, which are crucial for quality of following film growth. Despite the similarity of local environments of Sr (Ba) and Ti atoms in the perovskite film structure an angular region in the ADCs was identified as a fingerprint with the help of MSC simulations which provided clear conclusions on the perovskite oxide surfaces. Dopant sites in quaternary perovskite manganites La1-xCaxMnO3, La1-xSrxMnO3, and La1-xCexMnO3 were studied with polar angle scans of the photoemission intensities of host and dopant atoms. Both direct comparison of experimental ADCs and to the simulations within MSC models confirm the occupation of A sites by the dopants and the structural quality of the complex oxide films.

Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

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

Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.

2010-09-07

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Crystal Structure and Functional Interpretation of the Erythrocyte spectrin Tetramerization Domain Complex

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

J Ipsaro; S Harper; T Messick

2011-12-31

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Colloids with high-definition surface structures

PubMed Central

Chen, Hsien-Yeh; Rouillard, Jean-Marie; Gulari, Erdogan; Lahann, Joerg

2007-01-01

Compared with the well equipped arsenal of surface modification methods for flat surfaces, techniques that are applicable to curved, colloidal surfaces are still in their infancy. This technological gap exists because spin-coating techniques used in traditional photolithographic processes are not applicable to the curved surfaces of spherical objects. By replacing spin-coated photoresist with a vapor-deposited, photodefinable polymer coating, we have now fabricated microstructured colloids with a wide range of surface patterns, including asymmetric and chiral surface structures, that so far were typically reserved for flat substrates. This high-throughput method can yield surface-structured colloidal particles at a rate of ≈107 to 108 particles per operator per day. Equipped with spatially defined binding pockets, microstructured colloids can engage in programmable interactions, which can lead to directed self-assembly. The ability to create a wide range of colloids with both simple and complex surface patterns may contribute to the genesis of previously unknown colloidal structures and may have important technological implications in a range of different applications, including photonic and phononic materials or chemical sensors. PMID:17592149

DYNAMICS OF MINERAL STRUCTURES AND THE FATE OF METALS IN SOILS AND SEDIMENTS

EPA Science Inventory

Significant progress has been made in elucidating sorption reactions that control the partitioning of metals from solution to mineral surfaces in contaminated soil/sediment systems. Surface complexation models have been developed to quantify the forward reaction with reasonable ...

Detection of warning surfaces in pedestrian environments: the importance for blind people of kerbs, depth, and structure of tactile surfaces.

PubMed

Ståhl, Agneta; Newman, Emma; Dahlin-Ivanoff, Synneve; Almén, Mai; Iwarsson, Sussane

2010-01-01

The overall purpose was to study whether and how persons with blindness detect warning surfaces with a long white cane in a real pedestrian environment after following a natural guidance surface to the warning surfaces. Of particular interest was the importance of kerb, depth, and structure of the warning surfaces. A concurrently mixed methods approach, with a combination of observation using a structured form together with 'think aloud' and a structured interview, was used. It was done with well-defined samples and study sites in an inter-disciplinary research context. The results show that the most important design characteristic for detection of the warning surfaces with a white cane is the structure of the surface, while the depth of the surface and availability of a kerb do not have any impact on the detection. A precondition was that there is a distinct natural guidance surface leading up to the warning surface. The probability among pedestrians with blindness to detect a tactile surface is not higher if the design solution has a kerb. This study also confirms the complexity of being a blind pedestrian in the traffic environment. The results can be used for evidence-based physical planning. The study also has implications for development of more efficient vision rehabilitation.

Plant Surfaces: Structures and Functions for Biomimetic Innovations

NASA Astrophysics Data System (ADS)

Barthlott, Wilhelm; Mail, Matthias; Bhushan, Bharat; Koch, Kerstin

2017-04-01

An overview of plant surface structures and their evolution is presented. It combines surface chemistry and architecture with their functions and refers to possible biomimetic applications. Within some 3.5 billion years biological species evolved highly complex multifunctional surfaces for interacting with their environments: some 10 million living prototypes (i.e., estimated number of existing plants and animals) for engineers. The complexity of the hierarchical structures and their functionality in biological organisms surpasses all abiotic natural surfaces: even superhydrophobicity is restricted in nature to living organisms and was probably a key evolutionary step with the invasion of terrestrial habitats some 350-450 million years ago in plants and insects. Special attention should be paid to the fact that global environmental change implies a dramatic loss of species and with it the biological role models. Plants, the dominating group of organisms on our planet, are sessile organisms with large multifunctional surfaces and thus exhibit particular intriguing features. Superhydrophilicity and superhydrophobicity are focal points in this work. We estimate that superhydrophobic plant leaves (e.g., grasses) comprise in total an area of around 250 million km2, which is about 50% of the total surface of our planet. A survey of structures and functions based on own examinations of almost 20,000 species is provided, for further references we refer to Barthlott et al. (Philos. Trans. R. Soc. A 374: 20160191, 1). A basic difference exists between aquatic non-vascular and land-living vascular plants; the latter exhibit a particular intriguing surface chemistry and architecture. The diversity of features is described in detail according to their hierarchical structural order. The first underlying and essential feature is the polymer cuticle superimposed by epicuticular wax and the curvature of single cells up to complex multicellular structures. A descriptive terminology for this diversity is provided. Simplified, the functions of plant surface characteristics may be grouped into six categories: (1) mechanical properties, (2) influence on reflection and absorption of spectral radiation, (3) reduction of water loss or increase of water uptake, moisture harvesting, (4) adhesion and non-adhesion (lotus effect, insect trapping), (5) drag and turbulence increase, or (6) air retention under water for drag reduction or gas exchange (Salvinia effect). This list is far from complete. A short overview of the history of bionics and the impressive spectrum of existing and anticipated biomimetic applications are provided. The major challenge for engineers and materials scientists, the durability of the fragile nanocoatings, is also discussed.

Self-assembled diatom substrates with plasmonic functionality

NASA Astrophysics Data System (ADS)

Kwon, Sun Yong; Park, Sehyun; Nichols, William T.

2014-04-01

Marine diatoms have an exquisitely complex exoskeleton that is promising for engineered surfaces such as sensors and catalysts. For such applications, creating uniform arrays of diatom frustules across centimeter scales will be necessary. Here, we present a simple, low-cost floating interface technique to self-assemble the diatom frustules. We show that well-prepared diatoms form floating hexagonal close-packed arrays at the air-water interface that can be transferred directly to a substrate. We functionalize the assembled diatom surfaces with gold and characterize the plasmonic functionality by using surface enhanced Raman scattering (SERS). Thin gold films conform to the complex, hierarchical diatom structure and produce a SERS enhancement factor of 2 × 104. Small gold nanoparticles attached to the diatom's surface produce a higher enhancement of 7 × 104 due to stronger localization of the surface plasmons. Taken together, the large-scale assembly and plasmonic functionalization represent a promising platform to control the energy and the material flows at a complex surface for applications such as sensors and plasmonic enhanced catalysts.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Zoete, V.; Michielin, O.; Karplus, M.

2003-12-01

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SAS bur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC 50 without reparametrization.

Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.

PubMed

Cohen, Gerson H; Silverton, Enid W; Padlan, Eduardo A; Dyda, Fred; Wibbenmeyer, Jamie A; Willson, Richard C; Davies, David R

2005-05-01

The structure of the complex between hen egg-white lysozyme and the Fab HyHEL-5 at 2.7 A resolution has previously been reported [Cohen et al. (1996), Acta Cryst. D52, 315-326]. With the availability of recombinant Fab, the X-ray structure of the complex has been re-evaluated at 1.7 A resolution. The refined structure has yielded a detailed picture of the Fab-lysozyme interface, showing the high complementarity of the protein surfaces as well as several water molecules within the interface that complete the good fit. The model of the full complex has improved significantly, yielding an R(work) of 19.5%. With this model, the structural results can be compared with the results of isothermal titration calorimetry. An attempt has been made to estimate the changes in bound waters that accompany complex formation and the difficulties inherent in using the crystal structures to provide the information necessary to make this calculation are discussed.

Geometrical effect, optimal design and controlled fabrication of bio-inspired micro/nanotextures for superhydrophobic surfaces

NASA Astrophysics Data System (ADS)

Ma, F. M.; Li, W.; Liu, A. H.; Yu, Z. L.; Ruan, M.; Feng, W.; Chen, H. X.; Chen, Y.

2017-09-01

Superhydrophobic surfaces with high water contact angles and low contact angle hysteresis or sliding angles have received tremendous attention for both academic research and industrial applications in recent years. In general, such surfaces possess rough microtextures, particularly, show micro/nano hierarchical structures like lotus leaves. Now it has been recognized that to achieve the artificial superhydrophobic surfaces, the simple and effective strategy is to mimic such hierarchical structures. However, fabrications of such structures for these artificial surfaces involve generally expensive and complex processes. On the other hand, the relationships between structural parameters of various surface topography and wetting properties have not been fully understood yet. In order to provide guidance for the simple fabrication and particularly, to promote practical applications of superhydrophobic surfaces, the geometrical designs of optimal microtextures or patterns have been proposed. In this work, the recent developments on geometrical effect, optimal design and controlled fabrication of various superhydrophobic structures, such as unitary, anisotropic, dual-scale hierarchical, and some other surface geometries, are reviewed. The effects of surface topography and structural parameters on wetting states (composite and noncomposite) and wetting properties (contact angle, contact angle hysteresis and sliding angle) as well as adhesive forces are discussed in detail. Finally, the research prospects in this field are briefly addressed.

Modeling Water Waves with Smoothed Particle Hydrodynamics

DTIC Science & Technology

2013-09-30

SPH Model for Water Waves and Other Free Surface Flows ...Lagrangian nature of SPH allows the modeling of wave breaking, surf zones, ship waves, and wave-structure interaction, where the free surface becomes...proving to be a competent modeling scheme for free surface flows in three dimensions including the complex flows of the surf zone. As the GPU

Linking morphology with activity through the lifetime of pretreated PtNi nanostructured thin film catalysts

DOE PAGES

Cullen, David A.; Lopez-Haro, Miguel; Bayle-Guillemaud, Pascale; ...

2015-04-10

In this study, the nanoscale morphology of highly active Pt 3Ni 7 nanostructured thin film fuel cell catalysts is linked with catalyst surface area and activity following catalyst pretreatments, conditioning and potential cycling. The significant role of fuel cell conditioning on the structure and composition of these extended surface catalysts is demonstrated by high resolution imaging, elemental mapping and tomography. The dissolution of Ni during fuel cell conditioning leads to highly complex, porous structures which were visualized in 3D by electron tomography. Quantification of the rendered surfaces following catalyst pretreatment, conditioning, and cycling shows the important role pore structure playsmore » in surface area, activity, and durability.« less

Gallium(III) adsorption on carbonates and oxides: X-ray absorption fine structure spectroscopy study and surface complexation modeling.

PubMed

Pokrovsky, O S; Pokrovski, G S; Schott, J

2004-11-15

Adsorption of Ga on calcite, magnesite, amorphous silica, and manganese oxide as a function of pH and gallium concentration in solution was studied using a batch adsorption technique. Adsorbed complexes of Ga on calcite, magnesite, and delta-MnO2 were further characterized using XAFS spectroscopy. At high surface loadings from supersaturated solutions, Ga is likely to form a polymeric network at the surface (edge- and corner-sharing octahedra). At low surface loadings, Ga presents as isolated octahedra, probably attached to the Me-O sites on the surface, and coordinated by water molecules and hydroxide groups at 1.90-1.94 A. At pH>6, Ga therefore changes its coordination from 4 to 6 when adsorbing from solution (Ga(OH)(-)4(aq)) onto metal surface sites (MeOGa(OH)n(H2O)2-n(5-n), Me = Ca, Mg, or Mn, and n=1 and 2 for carbonate minerals and MnO2, respectively). Because the EXAFS is not capable of seeing hydrogen atoms, the protonation of surface complexes was determined by fitting the experimental pH-dependent Ga adsorption edge. A surface complexation model which assumes the constant capacitance of the electric double layer (CCM) and postulates the formation of positively charged, neutral and negatively charged surface complexes for carbonates, manganese oxide and silica, respectively, was used to describe the dependence of adsorption equilibria on aqueous solution composition in a wide range of pH and Ga concentration.

Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface.

PubMed

Kastritis, Panagiotis L; Rodrigues, João P G L M; Folkers, Gert E; Boelens, Rolf; Bonvin, Alexandre M J J

2014-07-15

Protein-protein complexes orchestrate most cellular processes such as transcription, signal transduction and apoptosis. The factors governing their affinity remain elusive however, especially when it comes to describing dissociation rates (koff). Here we demonstrate that, next to direct contributions from the interface, the non-interacting surface (NIS) also plays an important role in binding affinity, especially polar and charged residues. Their percentage on the NIS is conserved over orthologous complexes indicating an evolutionary selection pressure. Their effect on binding affinity can be explained by long-range electrostatic contributions and surface-solvent interactions that are known to determine the local frustration of the protein complex surface. Including these in a simple model significantly improves the affinity prediction of protein complexes from structural models. The impact of mutations outside the interacting surface on binding affinity is supported by experimental alanine scanning mutagenesis data. These results enable the development of more sophisticated and integrated biophysical models of binding affinity and open new directions in experimental control and modulation of biomolecular interactions. Copyright © 2014. Published by Elsevier Ltd.

A model of the complex between human {beta}-microseminoprotein and CRISP-3 based on NMR data

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

Ghasriani, Houman; Fernlund, Per; Udby, Lene

2009-01-09

{beta}-Microseminoprotein (MSP), a 10 kDa seminal plasma protein, forms a tight complex with cysteine-rich secretory protein 3 (CRISP-3) from granulocytes. The 3D structure of human MSP has been determined but there is as yet no 3D structure for CRISP-3. We have now studied the complex between human MSP and CRISP-3 with multidimensional NMR. {sup 15}N-HSQC spectra show substantial differences between free and complexed hMSP. Using several 3D-NMR spectra of triply labeled hMSP in complex with a recombinant N-terminal domain of CRISP-3, most of the backbone of hMSP could be assigned. The data show that only one side of hMSP, comprisingmore » {beta}-strands 1, 4, 5, and 8 are affected by the complex formation, indicating that {beta}-strands 1 and 8 form the main binding surface. Based on this we present a tentative structure for the hMSP-CRISP-3 complex using the known crystal structure of triflin as a model of CRISP-3.« less

A nonviral DNA delivery system based on surface modified silica-nanoparticles can efficiently transfect cells in vitro.

PubMed

Kneuer, C; Sameti, M; Bakowsky, U; Schiestel, T; Schirra, H; Schmidt, H; Lehr, C M

2000-01-01

Diverse polycationic polymers have been used as nonviral transfection agents. Here we report the ability of colloidal silica particles with covalently attached cationic surface modifications to transfect plasmid DNA in vitro and make an attempt to describe the structure of the resulting transfection complexes. In analogy to the terms lipoplex and polyplex, we propose to describe the nanoparticle-DNA complexes by the term "nanoplex". Three batches, Si10E, Si100E, and Si26H, sized between 10 and 100 nm and with zeta potentials ranging from +7 to +31 mV at pH 7.4 were evaluated. The galactosidase expression plasmid DNA pCMVbeta was immobilized on the particle surface and efficiently transfected Cos-1 cells. The transfection activity was accompanied by very low cytotoxicity, with LD(50) values in the milligrams per milliliter range. The most active batch, Si26H, was produced by modification of commercially available silica particles with N-(6-aminohexyl)-3-aminopropyltrimethoxysilane, yielding spherical nanoparticles with a mean diameter of 26 nm and a zeta potential of +31 mV at pH 7.4. Complexes of Si26H and pCMVbeta plasmid DNA formed at w/w ratios of 10 were most effective in promoting transfection of Cos-1 cells in the absence of serum. At this ratio, >90% of the DNA was associated with the particles, yielding nanoplexes with a net negative surface charge. When the transfection medium was supplemented with 10% serum, maximum gene expression was observed at a w/w ratio of 30, at which the resulting particle-DNA complexes possessed a positive surface charge. Transfection was strongly increased in the presence of 100 microM chloroquine in the incubation medium and reached approximately 30% of the efficiency of a 60 kDa polyethylenimine. In contrast to polyethylenimine, no toxicity was observed at the concentrations required. Atomic force microscopy of Si26H-DNA complexes revealed a spaghetti-meatball-like structure. The surface of complexes prepared at a w/w ratio of 30 was dominated by particles half-spheres. Complex sizes correlated well with those determined previously by dynamic light scattering.

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

PubMed

Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

2007-07-01

We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

Magnetorheological Finishing for Imprinting Continuous Phase Plate Structure onto Optical Surfaces

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

Menapace, J A; Dixit, S N; Genin, F Y

2004-01-05

Magnetorheological finishing (MRF) techniques have been developed to manufacture continuous phase plates (CPP's) and custom phase corrective structures on polished fused silica surfaces. These phase structures are important for laser applications requiring precise manipulation and control of beam-shape, energy distribution, and wavefront profile. The MRF's unique deterministic-sub-aperture polishing characteristics make it possible to imprint complex topographical information onto optical surfaces at spatial scale-lengths approaching 1 mm. In this study, we present the results of experiments and model calculations that explore imprinting two-dimensional sinusoidal structures. Results show how the MRF removal function impacts and limits imprint fidelity and what must bemore » done to arrive at a high quality surface. We also present several examples of this imprinting technology for fabrication of phase correction plates and CPPs for use at high fluences.« less

Hierarchical and Well-Ordered Porous Copper for Liquid Transport Properties Control.

PubMed

Pham, Quang N; Shao, Bowen; Kim, Yongsung; Won, Yoonjin

2018-05-09

Liquid delivery through interconnected pore network is essential for various interfacial transport applications ranging from energy storage to evaporative cooling. The liquid transport performance in porous media can be significantly improved through the use of hierarchical morphology that leverages transport phenomena at different length scales. Traditional surface engineering techniques using chemical or thermal reactions often show nonuniform surface nanostructuring within three-dimensional pore network due to uncontrollable diffusion and reactivity in geometrically complex porous structures. Here, we demonstrate hierarchical architectures on the basis of crystalline copper inverse opals using an electrochemistry approach, which offers volumetric controllability of structural and surface properties within the complex porous metal. The electrochemical process sequentially combines subtractive and additive steps-electrochemical polishing and electrochemical oxidation-to improve surface wetting properties without sacrificing structural permeability. We report the transport performance of the hierarchical inverse opals by measuring the capillary-driven liquid rise. The capillary performance parameter of hierarchically engineered inverse opal ( K/ R eff = ∼5 × 10 -3 μm) is shown to be higher than that of a typical crystalline inverse opal ( K/ R eff = ∼1 × 10 -3 μm) owing to the enhancement in fluid permeable and hydrophilic pathways. The new surface engineering method presented in this work provides a rational approach in designing hierarchical porous copper for transport performance enhancements.

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

PubMed

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-12-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

PubMed Central

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-01-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit. PMID:12515387

Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

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

Park, Min-Sun; Park, Sung Yong; Miller, Keith R.

2013-11-01

Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformationalmore » changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.« less

Shrink-Induced Superhydrophobic and Antibacterial Surfaces in Consumer Plastics

PubMed Central

Freschauf, Lauren R.; McLane, Jolie; Sharma, Himanshu; Khine, Michelle

2012-01-01

Structurally modified superhydrophobic surfaces have become particularly desirable as stable antibacterial surfaces. Because their self-cleaning and water resistant properties prohibit bacteria growth, structurally modified superhydrophobic surfaces obviate bacterial resistance common with chemical agents, and therefore a robust and stable means to prevent bacteria growth is possible. In this study, we present a rapid fabrication method for creating such superhydrophobic surfaces in consumer hard plastic materials with resulting antibacterial effects. To replace complex fabrication materials and techniques, the initial mold is made with commodity shrink-wrap film and is compatible with large plastic roll-to-roll manufacturing and scale-up techniques. This method involves a purely structural modification free of chemical additives leading to its inherent consistency over time and successive recasting from the same molds. Finally, antibacterial properties are demonstrated in polystyrene (PS), polycarbonate (PC), and polyethylene (PE) by demonstrating the prevention of gram-negative Escherichia coli (E. coli) bacteria growth on our structured plastic surfaces. PMID:22916100

Applying Parallel Adaptive Methods with GeoFEST/PYRAMID to Simulate Earth Surface Crustal Dynamics

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Glasscoe, Margaret; Donnellan, Andrea; Li, Peggy

2006-01-01

This viewgraph presentation reviews the use Adaptive Mesh Refinement (AMR) in simulating the Crustal Dynamics of Earth's Surface. AMR simultaneously improves solution quality, time to solution, and computer memory requirements when compared to generating/running on a globally fine mesh. The use of AMR in simulating the dynamics of the Earth's Surface is spurred by future proposed NASA missions, such as InSAR for Earth surface deformation and other measurements. These missions will require support for large-scale adaptive numerical methods using AMR to model observations. AMR was chosen because it has been successful in computation fluid dynamics for predictive simulation of complex flows around complex structures.

Dissecting Arabidopsis G beta signal transduction on the protein surface

USDA-ARS?s Scientific Manuscript database

The heterotrimeric G protein complex provides signal amplification and target specificity. The Arabidopsis Gbeta subunit of this complex (AGB1) interacts with and modulates the activity of target cytoplasmic proteins. This specificity resides in the structure of the interface between AGB1 and its ta...

Surface-Sensitive and Bulk Studies on the Complexation and Photosensitized Degradation of Catechol by Iron(III) as a Model for Multicomponent Aerosol Systems

NASA Astrophysics Data System (ADS)

Al-abadleh, H. A.; Tofan-Lazar, J.; Situm, A.; Ruffolo, J.; Slikboer, S.

2013-12-01

Surface water plays a crucial role in facilitating or inhibiting surface reactions in atmospheric aerosols. Little is known about the role of surface water in the complexation of organic molecules to transition metals in multicomponent aerosol systems. We will show results from real time diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) experiments for the in situ complexation of catechol to Fe(III) and its photosensitized degradation under dry and humid conditions. Catechol was chosen as a simple model for humic-like substances (HULIS) in aerosols and aged polyaromatic hydrocarbons (PAH). It has also been detected in secondary organic aerosols (SOA) formed from the reaction of hydroxyl radicals with benzene. Given the importance of the iron content in aerosols and its biogeochemistry, our studies were conducted using FeCl3. For comparison, these surface-sensitive studies were complemented with bulk aqueous ATR-FTIR, UV-vis, and HPLC measurements for structural, quantitative and qualitative information about complexes in the bulk, and potential degradation products. The implications of our studies on understanding interfacial and condensed phase chemistry relevant to multicomponent aerosols, water thin islands on buildings, and ocean surfaces containing transition metals will be discussed.

Imprinting continuously varying topographical structure onto large-aperture optical surfaces using magnetorheological finishing

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

Menapace, J A; Davis, P J; Dixit, S

2007-03-07

Over the past four years we have advanced Magnetorheological Finishing (MRF) techniques and tools to imprint complex continuously varying topographical structures onto large-aperture (430 x 430 mm) optical surfaces. These optics, known as continuous phase plates (CPPs), are important for high-power laser applications requiring precise manipulation and control of beam-shape, energy distribution, and wavefront profile. MRF's unique deterministic-sub-aperture polishing characteristics make it possible to imprint complex topographical information onto optical surfaces at spatial scale-lengths approaching 1 mm and surface peak-to-valleys as high as 22 {micro}m. During this discussion, we will present the evolution of the MRF imprinting technology and themore » MRF tools designed to manufacture large-aperture 430 x 430 mm CPPs. Our results will show how the MRF removal function impacts and limits imprint fidelity and what must be done to arrive at a high-quality surface. We also present several examples of this imprinting technology for fabrication of phase correction plates and CPPs for use in high-power laser applications.« less

Structural Analysis of Der p 1–Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies

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

Osinski, Tomasz; Pomés, Anna; Majorek, Karolina A.

Der p 1 is a major allergen from the house dust mite, Dermatophagoides pteronyssinus, that belongs to the papain-like cysteine protease family. To investigate the antigenic determinants of Der p 1, we determined two crystal structures of Der p 1 in complex with the Fab fragments of mAbs 5H8 or 10B9. Epitopes for these two Der p 1–specific Abs are located in different, nonoverlapping parts of the Der p 1 molecule. Nevertheless, surface area and identity of the amino acid residues involved in hydrogen bonds between allergen and Ab are similar. The epitope for mAb 10B9 only showed a partialmore » overlap with the previously reported epitope for mAb 4C1, a cross-reactive mAb that binds Der p 1 and its homolog Der f 1 from Dermatophagoides farinae. Upon binding to Der p 1, the Fab fragment of mAb 10B9 was found to form a very rare α helix in its third CDR of the H chain. To provide an overview of the surface properties of the interfaces formed by the complexes of Der p 1–10B9 and Der p 1–5H8, along with the complexes of 4C1 with Der p 1 and Der f 1, a broad analysis of the surfaces and hydrogen bonds of all complexes of Fab–protein or Fab–peptide was performed. This work provides detailed insight into the cross-reactive and specific allergen–Ab interactions in group 1 mite allergens. The surface data of Fab–protein and Fab–peptide interfaces can be used in the design of conformational epitopes with reduced Ab binding for immunotherapy.« less

Planetary benchmarks. [structural design criteria for radar reference devices on planetary surfaces

NASA Technical Reports Server (NTRS)

Uphoff, C.; Staehle, R.; Kobrick, M.; Jurgens, R.; Price, H.; Slade, M.; Sonnabend, D.

1978-01-01

Design criteria and technology requirements for a system of radar reference devices to be fixed to the surfaces of the inner planets are discussed. Offshoot applications include the use of radar corner reflectors as landing beacons on the planetary surfaces and some deep space applications that may yield a greatly enhanced knowledge of the gravitational and electromagnetic structure of the solar system. Passive retroreflectors with dimensions of about 4 meters and weighing about 10 kg are feasible for use with orbiting radar at Venus and Mars. Earth-based observation of passive reflectors, however, would require very large and complex structures to be delivered to the surfaces. For Earth-based measurements, surface transponders offer a distinct advantage in accuracy over passive reflectors. A conceptual design for a high temperature transponder is presented. The design appears feasible for the Venus surface using existing electronics and power components.

Surface topographical effects on the structural growth of thick sputtered metal and alloy coatings

NASA Technical Reports Server (NTRS)

Spalvins, T.; Brainard, W. A.

1974-01-01

Thick sputtered S-Monel, silver, and 304 stainless steel coatings were deposited on mica and metal substrates with various surface finishes to investigate the structural growth of the coating by scanning electron microscopy. The geometry and the surface structure of the nodules are characterized. Compositional changes within the coating were analyzed by X-ray dispersion microscopy. Defects in the surface finish (i.e., scratches, inclusions, etc.) act as preferential nucleation sites and form isolated and complex nodules and various surface overgrowths in the coating. The nodule boundaries are very vulnerable to chemical etching and these nodules do not disappear after full annealing. Further, they have undesirable effects on mechanical properties; cracks are initiated at the nodules when the coating is stressed by mechanical forces. These effects are illustrated by micrographs. Nodular growth within a coating can be minimized or eliminated by reducing the surface roughness.

Structure of a Premicellar Complex of Alkyl Sulfates with the Interfacial Binding Surfaces of 4 Subunits of Phospholipase A2✰

PubMed Central

Pan, Ying H.; Bahnson, Brian J.

2010-01-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates has been characterized [Berg, O. G., et al., Biochemistry 43, 7999–8013, 2004]. Here we have solved the 2.7 Å crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in 3 of the 4 protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. PMID:20302975

Development of explosive welding procedures to fabricate channeled nozzle structures

NASA Technical Reports Server (NTRS)

Pattee, H. E.; Linse, V. D.

1976-01-01

Research was conducted to demonstrate the feasibility of fabricating a large contoured structure with complex internal channeling by explosive welding procedures. Structures or nozzles of this nature for wind tunnel applications were designed. Such nozzles vary widely in their complexity. However, in their simplest form, they consist of a grooved base section to which a cover sheet is attached to form a series of internal cooling passages. The cover sheet attachment can be accomplished in various ways: fusion welding, brazing, and diffusion welding. The cover sheet has also been electroformed in place. Of these fabrication methods, brazing has proved most successful in producing nozzles with complex contoured surfaces and a multiplicity of internal channels.

Global search in photoelectron diffraction structure determination using genetic algorithms

NASA Astrophysics Data System (ADS)

Viana, M. L.; Díez Muiño, R.; Soares, E. A.; Van Hove, M. A.; de Carvalho, V. E.

2007-11-01

Photoelectron diffraction (PED) is an experimental technique widely used to perform structural determinations of solid surfaces. Similarly to low-energy electron diffraction (LEED), structural determination by PED requires a fitting procedure between the experimental intensities and theoretical results obtained through simulations. Multiple scattering has been shown to be an effective approach for making such simulations. The quality of the fit can be quantified through the so-called R-factor. Therefore, the fitting procedure is, indeed, an R-factor minimization problem. However, the topography of the R-factor as a function of the structural and non-structural surface parameters to be determined is complex, and the task of finding the global minimum becomes tough, particularly for complex structures in which many parameters have to be adjusted. In this work we investigate the applicability of the genetic algorithm (GA) global optimization method to this problem. The GA is based on the evolution of species, and makes use of concepts such as crossover, elitism and mutation to perform the search. We show results of its application in the structural determination of three different systems: the Cu(111) surface through the use of energy-scanned experimental curves; the Ag(110)-c(2 × 2)-Sb system, in which a theory-theory fit was performed; and the Ag(111) surface for which angle-scanned experimental curves were used. We conclude that the GA is a highly efficient method to search for global minima in the optimization of the parameters that best fit the experimental photoelectron diffraction intensities to the theoretical ones.

How to Select the most Relevant Roughness Parameters of a Surface: Methodology Research Strategy

NASA Astrophysics Data System (ADS)

Bobrovskij, I. N.

2018-01-01

In this paper, the foundations for new methodology creation which provides solving problem of surfaces structure new standards parameters huge amount conflicted with necessary actual floors quantity of surfaces structure parameters which is related to measurement complexity decreasing are considered. At the moment, there is no single assessment of the importance of a parameters. The approval of presented methodology for aerospace cluster components surfaces allows to create necessary foundation, to develop scientific estimation of surfaces texture parameters, to obtain material for investigators of chosen technological procedure. The methods necessary for further work, the creation of a fundamental reserve and development as a scientific direction for assessing the significance of microgeometry parameters are selected.

Flow Structure and Surface Topology on a UCAV Planform

NASA Astrophysics Data System (ADS)

Elkhoury, Michel; Yavuz, Metin; Rockwell, Donald

2003-11-01

Flow past a X-45 UCAV planform involves the complex generation and interaction of vortices, their breakdown and occurrence of surface separation and stall. A cinema technique of high-image-density particle image velocimetry, in conjunction with dye visualization, allows characterization of the time-averaged and instantaneous states of the flow, in terms of critical points of the near-surface streamlines. These features are related to patterns of surface normal vorticity and velocity fluctuation. Spectral analysis of the naturally occurring unsteadiness of the flow allows definition of the most effective frequencies for small-amplitude perturbation of the wing, which leads to substantial alterations of the aforementioned patterns of flow structure and topology adjacent to the surface.

A closer look at the complex hydrophilic/hydrophobic interactions forces at the human hair surface

NASA Astrophysics Data System (ADS)

Baghdadli, N.; Luengo, G. S.; Recherche, L.

2008-03-01

The complex chemical structure of the hair surface is far from being completely understood. Current understanding is based on Rivett's model1 that was proposed to explain the macroscopic hydrophobic nature of the surface of natural hair. In this model covalently-linked fatty acids are chemically grafted to the amorphous protein (keratin) through a thio-ester linkage2,3. Nevertheless, experience like wetting and electrical properties of human hair surface4 shows that the complexity of the hair surface is not fully understand based on this model in literature. Recent studies in our laboratory show for the first time microscopic evidence of the heterogeneous physico-chemical character of the hair surface. By using Chemical Force Microscopy, the presence of hydrophobic and ionic species are detected and localized, before and after a cosmetic treatment (bleaching). Based on force curve analysis the mapping of the local distribution of hydrophilic and hydrophobic groups of hair surface is obtained. A discussion on a more plausible hair model and its implications will be presented based on these new results.

High-Resolution Seismic Velocity and Attenuation Models of the Caucasus-Caspian Region

DTIC Science & Technology

2009-09-30

region is part of the Alpine-Himalayan collision belt and is an area of complex structure accompanied by large variations in seismic wave velocities...velocity structure is developed using teleseismic receiver functions and surface waves. Joint inversion of surface wave group dispersion curves...Caucasus and the thinnest is in the Arabian Plate. Thin crust is also observed near the Caspian. The lithospheric mantle in the Greater Caucasus and the

Evolution of surface structure in laser-preheated, perturbed materials

DOE PAGES

Di Stefano, Carlos; Merritt, Elizabeth Catherine; Doss, Forrest William; ...

2017-02-03

Here, we report an experimental and computational study investigating the effects of laser preheat on the hydrodynamic behavior of a material layer. In particular, we find that perturbation of the surface of the layer results in a complex interaction, in which the bulk of the layer develops density, pressure, and temperature structure and in which the surface experiences instability-like behavior, including mode coupling. A uniform one-temperature preheat model is used to reproduce the experimentally observed behavior, and we find that this model can be used to capture the evolution of the layer, while also providing evidence of complexities in themore » preheat behavior. Lastly, this result has important consequences for inertially confined fusion plasmas, which can be difficult to diagnose in detail, as well as for laser hydrodynamics experiments, which generally depend on assumptions about initial conditions in order to interpret their results.« less

The Est3 protein associates with yeast telomerase through an OB-fold domain

PubMed Central

Lee, Jaesung S.; Mandell, Edward K.; Tucey, Timothy M.; Morris, Danna K.; Victoria, Lundblad

2009-01-01

The Est3 protein is a small regulatory subunit of yeast telomerase which is dispensable for enzyme catalysis but essential for telomere replication in vivo. Using structure prediction combined with in vivo characterization, we show here that Est3 consists of a predicted OB (oligo-saccharide/oligo-nucleotide binding) fold. Mutagenesis of predicted surface residues was used to generate a functional map of one surface of Est3, which identified a site that mediates association with the telomerase complex. Surprisingly, the predicted OB-fold of Est3 is structurally similar to the OB-fold of the mammalian TPP1 protein, despite the fact that Est3 and TPP1, as components of telomerase and a telomere capping complex, respectively, perform functionally distinct tasks at chromosome ends. The analysis performed on Est3 may be instructive in generating comparable missense mutations on the surface of the OB-fold domain of TPP1. PMID:19172754

Structures of Cu surfaces developing in benzotriazole solutions: Effect of pH

NASA Astrophysics Data System (ADS)

Kondoh, Eiichi; Kawakami, Tatsuya; Watanabe, Mitsuhiro; Jin, Linhua; Hamada, Satomi; Shima, Shohei; Hiyama, Hirokuni

2017-07-01

The effect of pH on layer formation onto clean Cu surfaces in benzotriazole (BTA) aqueous solutions was studied by in situ spectroscopic ellipsometry. The effect of H2O2 addition was also investigated. Time changes in the ellipsometric parameters Ψ and Δ, which correspond to the structural changes of the layers on Cu, were discussed. In acidic solutions, a BTA or a Cu-BTA complex layer grows directly on Cu. The out-diffusion of Cu is suppressed at the Cu layer interface. When H2O2 was mixed, the Cu surface is eroded in acidic solutions. In alkaline solutions, the BTA layer grows on the oxidized Cu layer, or no growth occurs, depending on the composition of the solutions. In neutral solutions, the Cu-BTA complex layer forms on Cu, and the uncovered part is oxidized in the presence of H2O2.

Surface speciation of phosphate on goethite as seen by InfraRed Surface Titrations (IRST)

NASA Astrophysics Data System (ADS)

Arroyave, Jeison Manuel; Puccia, Virginia; Zanini, Graciela P.; Avena, Marcelo J.

2018-06-01

Phosphate adsorption at the metal oxide-water interface has been intensely studied, and the system phosphate-goethite in aqueous media is normally used as a model system with abundant information regarding adsorption-desorption under very different conditions. In spite of this, there is still discussion on whether the main inner-sphere surface complexes that phosphate forms on goethite are monodentate or bidentate. A new spectroscopic technique, InfraRed Surface Titration (IRST), is presented here and used to systematically explore the surface speciation of phosphate on goethite in the pH range 4.5-9.5 at different surface coverages. IRST enabled to construct distribution curves of surface species and distribution curves of dissolved phosphate species. In combination with the CD-MUSIC surface complexation model it was possible to conclude that surface complexes are monodentate. Very accurate distribution curves were obtained, showing a crossing point at pH 5.5 at a surface coverage of 2.0 μmol m-2, with a mononuclear monoprotonated species predominating at pH > 5.5 and a mononuclear diprotonated species prevailing at pH < 5.5. On the contrary, at the low surface coverage of 0.7 μmol m-2 there is no crossing point, with the mononuclear monoprotonated species prevailing at all pH. IRST can become a powerful technique to investigate structure, properties and reactions of any IR-active surface complex at the solid-water interface.

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

Identification of Au–S complexes on Au(100)

DOE PAGES

Walen, Holly; Liu, Da -Jiang; Oh, Junepyo; ...

2016-01-25

In this study, using a combination of scanning tunneling microscopy and density functional theory (DFT) calculations, we have identified a set of related Au–S complexes that form on Au(100), when sulfur adsorbs and lifts the hexagonal surface reconstruction. The predominant complex is diamond-shaped with stoichiometry Au 4S 5. All of the complexes can be regarded as combinations of S–Au–S subunits. The complexes exist within, or at the edges of, p(2 × 2) sulfur islands that cover the unreconstructed Au regions, and are observed throughout the range of S coverage examined in this study, 0.009 to 0.12 monolayers. A qualitative modelmore » is developed which incorporates competitive formation of complexes, Au rafts, and p(2 × 2) sulfur islands, as Au atoms are released by the surface structure transformation.« less

Structural and functional organization of the ESCRT-I trafficking complex

PubMed Central

Kostelansky, Michael S.; Sun, Ji; Lee, Sangho; Kim, Jaewon; Ghirlando, Rodolfo; Hierro, Aitor; Emr, Scott D.; Hurley, James H.

2006-01-01

Summary The Endosomal Sorting Complex Required for Transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 Å resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEVdomain, the Vps28 C-domain, and other domains project to bind their partners. PMID:16615894

Self-assembled virus-membrane complexes

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

Yang, Lihua; Liang, Hongjun; Angelini, Thomas

Anionic polyelectrolytes and cationic lipid membranes can self-assemble into lamellar structures ranging from alternating layers of membranes and polyelectrolytes to 'missing layer' superlattice structures. We show that these structural differences can be understood in terms of the surface-charge-density mismatch between the polyelectrolyte and membrane components by examining complexes between cationic membranes and highly charged M13 viruses, a system that allowed us to vary the polyelectrolyte diameter independently of the charge density. Such virus-membrane complexes have pore sizes that are about ten times larger in area than DNA-membrane complexes, and can be used to package and organize large functional molecules; correlatedmore » arrays of Ru(bpy){sub 3}{sup 2+} macroionic dyes have been directly observed within the virus-membrane complexes using an electron-density reconstruction. These observations elucidate fundamental design rules for rational control of self-assembled polyelectrolyte-membrane structures, which have applications ranging from non-viral gene therapy to biomolecular templates for nanofabrication.« less

Discrete structural features among interface residue-level classes.

PubMed

Sowmya, Gopichandran; Ranganathan, Shoba

2015-01-01

Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of PPIs. Each PPI complex is specific, sensitive and selective to binding. Therefore, we have estimated the relative difference in percentage of polar residues between surface and the interface for each complex in a non-redundant heterodimer dataset of 278 complexes to understand the predominant forces driving binding. Our analysis showed ~60% of protein complexes with surface polarity greater than interface polarity (designated as class A). However, a considerable number of complexes (~40%) have interface polarity greater than surface polarity, (designated as class B), with a significantly different p-value of 1.66E-45 from class A. Comprehensive analyses of protein complexes show that interface features such as interface area, interface polarity abundance, solvation free energy gain upon interface formation, binding energy and the percentage of interface charged residue abundance distinguish among class A and class B complexes, while electrostatic visualization maps also help differentiate interface classes among complexes. Class A complexes are classical with abundant non-polar interactions at the interface; however class B complexes have abundant polar interactions at the interface, similar to protein surface characteristics. Five physicochemical interface features analyzed from the protein heterodimer dataset are discriminatory among the interface residue-level classes. These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs.

Discrete structural features among interface residue-level classes

PubMed Central

2015-01-01

Background Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of PPIs. Each PPI complex is specific, sensitive and selective to binding. Therefore, we have estimated the relative difference in percentage of polar residues between surface and the interface for each complex in a non-redundant heterodimer dataset of 278 complexes to understand the predominant forces driving binding. Results Our analysis showed ~60% of protein complexes with surface polarity greater than interface polarity (designated as class A). However, a considerable number of complexes (~40%) have interface polarity greater than surface polarity, (designated as class B), with a significantly different p-value of 1.66E-45 from class A. Comprehensive analyses of protein complexes show that interface features such as interface area, interface polarity abundance, solvation free energy gain upon interface formation, binding energy and the percentage of interface charged residue abundance distinguish among class A and class B complexes, while electrostatic visualization maps also help differentiate interface classes among complexes. Conclusions Class A complexes are classical with abundant non-polar interactions at the interface; however class B complexes have abundant polar interactions at the interface, similar to protein surface characteristics. Five physicochemical interface features analyzed from the protein heterodimer dataset are discriminatory among the interface residue-level classes. These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs. PMID:26679043

Modeling Water Waves with Smoothed Particle Hydrodynamics

DTIC Science & Technology

2011-09-30

Lagrangian nature of SPH allows the modeling of wave breaking, surf zones, ship waves, and wave-structure interaction, where the free surface becomes...particle detection--To study free surface flows and analyze their complex deformations, we need to know which particles are located on the free surface ...Hydrodynamics is proving to be a competent modeling scheme for free surface flows in two and three dimensions. As the GPU hardware improves, it is

Impact of cleaning methods on the structural properties and morphology of SrTiO3 surface

NASA Astrophysics Data System (ADS)

Arnay, Iciar; Rubio-Zuazo, Juan; Castro, German R.

2018-01-01

SrTiO3 is a widely used substrate for the epitaxial growth of complex systems. Nevertheless, in order to get good quality interface and avoid the formation of defects in the adsorbed layer it is essential to prepare the surface of the substrate prior to the deposition. Thermal and chemical treatments are mostly used to eliminate superficial contamination and improve the surface quality. However, there is a lack of information regarding the impact of these treatments on the formation of structural defects at the SrTiO3 surface. In this work we present a detailed characterization of the SrTiO3 surface for the different cleaning methods paying special attention to the formation of oxygen vacancies, large surface mosaicity and roughness. We prove that thermal treatment induces large surface roughness and that chemical etching produces important structural defects at the surface. Our results show that mechanical polishing provided the best compromise in terms of large surface domains, low roughness, absence of oxygen vacancies and absence of atomic structure modification, although with the presence of low level of contaminants at the SrTiO3 surface.

Studies of high coverage oxidation of the Cu(100) surface using low energy positrons

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Maddox, W. B.; Weiss, A. H.

2012-02-01

The study of oxidation of single crystal metal surfaces is important in understanding the corrosive and catalytic processes associated with thin film metal oxides. The structures formed on oxidized transition metal surfaces vary from simple adlayers of chemisorbed oxygen to more complex structures which result from the diffusion of oxygen into subsurface regions. In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. Calculations are performed for various high coverage missing row structures ranging between 0.50 and 1.50 ML oxygen coverage. The results of calculations of positron binding energy, positron work function, and annihilation characteristics of surface trapped positrons with relevant core electrons as function of oxygen coverage are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES).

Assembly of Reconfigurable Colloidal Structures by Multidirectional Field-Induced Interactions.

PubMed

Bharti, Bhuvnesh; Velev, Orlin D

2015-07-28

Field-directed colloidal assembly has shown remarkable recent progress in increasing the complexity, degree of control, and multiscale organization of the structures. This has largely been achieved by using particles of complex shapes and polarizabilites (Janus, patchy, shaped, and faceted). We review the fundamentals of the interactions leading to the directed assembly of such structures, the ways to simulate the dynamics of the process, and the effect of particle size, shape, and properties on the type of structure obtained. We discuss how directional polarization interactions induced by external electric and magnetic fields can be used to assemble complex particles or particle mixtures into lattices of tailored structure. Examples of such systems include isotropic and anisotropic shaped particles with surface patches, which form networks and crystals of unusual symmetry by dipolar, quadrupolar, and multipolar interactions in external fields. The emerging trends in making reconfigurable and dynamic structures are discussed.

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

NASA Astrophysics Data System (ADS)

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.; Davis, J. A.

2018-01-01

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonite edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites ('spillover' effect). A series of U(VI) - Na-montmorillonite batch adsorption experiments was conducted as a function of pH, with variable U(VI), Ca, and dissolved carbonate concentrations. Based on the experimental data, a new type of surface complexation model (SCM) was developed for montmorillonite, that specifically accounts for the spillover effect using the edge surface speciation model by Tournassat et al. (2016a). The SCM allows for a prediction of U(VI) adsorption under varying chemical conditions with a minimum number of fitting parameters, not only for our own experimental results, but also for a number of published data sets. The model agreed well with many of these datasets without introducing a second site type or including the formation of ternary U(VI)-carbonato surface complexes. The model predictions were greatly impacted by utilizing analytical measurements of dissolved inorganic carbon (DIC) concentrations in individual sample solutions rather than assuming solution equilibration with a specific partial pressure of CO2, even when the gas phase was laboratory air. Because of strong aqueous U(VI)-carbonate solution complexes, the measurement of DIC concentrations was even important for systems set up in the 'absence' of CO2, due to low levels of CO2 contamination during the experiment.

Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

PubMed

Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

2013-12-06

Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.

PubMed

Olechnovic, Kliment; Margelevicius, Mindaugas; Venclovas, Ceslovas

2011-03-01

We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure. Voroprot is available for Windows, Linux and Mac OS X operating systems and can be downloaded from http://www.ibt.lt/bioinformatics/voroprot/.

The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.

PubMed Central

Gomis-Rüth, F X; Gómez, M; Bode, W; Huber, R; Avilés, F X

1995-01-01

The metalloexozymogen procarboxypeptidase A is mainly secreted in ruminants as a ternary complex with zymogens of two serine endoproteinases, chymotrypsinogen C and proproteinase E. The bovine complex has been crystallized, and its molecular structure analysed and refined at 2.6 A resolution to an R factor of 0.198. In this heterotrimer, the activation segment of procarboxypeptidase A essentially clamps the other two subunits, which shield the activation sites of the former from tryptic attack. In contrast, the propeptides of both serine proproteinases are freely accessible to trypsin. This arrangement explains the sequential and delayed activation of the constituent zymogens. Procarboxypeptidase A is virtually identical to the homologous monomeric porcine form. Chymotrypsinogen C displays structural features characteristic for chymotrypsins as well as elastases, except for its activation domain; similar to bovine chymotrypsinogen A, its binding site is not properly formed, while its surface located activation segment is disordered. The proproteinase E structure is fully ordered and strikingly similar to active porcine elastase; its specificity pocket is occluded, while the activation segment is fixed to the molecular surface. This first structure of a native zymogen from the proteinase E/elastase family does not fundamentally differ from the serine proproteinases known so far. Images PMID:7556081

Complex and oriented ZnO nanostructures.

PubMed

Tian, Zhengrong R; Voigt, James A; Liu, Jun; McKenzie, Bonnie; McDermott, Matthew J; Rodriguez, Mark A; Konishi, Hiromi; Xu, Huifang

2003-12-01

Extended and oriented nanostructures are desirable for many applications, but direct fabrication of complex nanostructures with controlled crystalline morphology, orientation and surface architectures remains a significant challenge. Here we report a low-temperature, environmentally benign, solution-based approach for the preparation of complex and oriented ZnO nanostructures, and the systematic modification of their crystal morphology. Using controlled seeded growth and citrate anions that selectively adsorb on ZnO basal planes as the structure-directing agent, we prepared large arrays of oriented ZnO nanorods with controlled aspect ratios, complex film morphologies made of oriented nanocolumns and nanoplates (remarkably similar to biomineral structures in red abalone shells) and complex bilayers showing in situ column-to-rod morphological transitions. The advantages of some of these ZnO structures for photocatalytic decompositions of volatile organic compounds were demonstrated. The novel ZnO nanostructures are expected to have great potential for sensing, catalysis, optical emission, piezoelectric transduction, and actuations.

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro

2011-10-20

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.

Transmission X-ray scattering as a probe for complex liquid-surface structures

DOE PAGES

Fukuto, Masafumi; Yang, Lin; Nykypanchuk, Dmytro; ...

2016-01-28

The need for functional materials calls for increasing complexity in self-assembly systems. As a result, the ability to probe both local structure and heterogeneities, such as phase-coexistence and domain morphologies, has become increasingly important to controlling self-assembly processes, including those at liquid surfaces. The traditional X-ray scattering methods for liquid surfaces, such as specular reflectivity and grazing-incidence diffraction, are not well suited to spatially resolving lateral heterogeneities due to large illuminated footprint. A possible alternative approach is to use scanning transmission X-ray scattering to simultaneously probe local intermolecular structures and heterogeneous domain morphologies on liquid surfaces. To test the feasibilitymore » of this approach, transmission small- and wide-angle X-ray scattering (TSAXS/TWAXS) studies of Langmuir films formed on water meniscus against a vertically immersed hydrophilic Si substrate were recently carried out. First-order diffraction rings were observed in TSAXS patterns from a monolayer of hexagonally packed gold nanoparticles and in TWAXS patterns from a monolayer of fluorinated fatty acids, both as a Langmuir monolayer on water meniscus and as a Langmuir–Blodgett monolayer on the substrate. The patterns taken at multiple spots have been analyzed to extract the shape of the meniscus surface and the ordered-monolayer coverage as a function of spot position. These results, together with continual improvement in the brightness and spot size of X-ray beams available at synchrotron facilities, support the possibility of using scanning-probe TSAXS/TWAXS to characterize heterogeneous structures at liquid surfaces.« less

Preparation of anticoagulant PyC biomaterials with super-hydrophobic surface.

PubMed

Ze, Wang; Wen-Sheng, Tan; Ye-Xia; Ming, Zhang; Xiao-Ping, Li; Jian-Guo, Qiu; Xiao-Hong, Yang

2018-01-01

Pyrolytic carbon (PyC) is a kind of biomaterial which is chemically inert and has excellent biocompatibility. In order to obtain a super-hydrophobic PyC surface to improve anticoagulation and inhibit thrombus, this study prepares grating pair structure, microhole array structure, helix structure on PyC surface by nanoseconds laser etching. Rod-like ZnO film and ball-like ZnO film are prepared on the PyC surface by the hydrothermal method; polyvinyl pyrrolidone (PVP) nanofiber film and PVP/TiO 2 complex nanofiber film are prepared on the PyC surface by the electrospinning method; the PyC surface is silanized. Finally, surface microstructure and surface energy are characterized by scanning electron microscopy and contact angle meter (OCA20, German DataPhysics Co.). The periodical microstructures are formed respectively by nanoseconds laser etching. The surface roughness is increased by the hydrothermal and electrospinning method. Through infiltration experiment on rough and smooth PyC surfaces, rough PyC surface with microstructure is super-hydrophobic and has greater than 150° contact angle, which decreases blood flow resistance and inhibits thrombus.

Nanoscale surface modification of Li-rich layered oxides for high-capacity cathodes in Li-ion batteries

NASA Astrophysics Data System (ADS)

Lan, Xiwei; Xin, Yue; Wang, Libin; Hu, Xianluo

2018-03-01

Li-rich layered oxides (LLOs) have been developed as a high-capacity cathode material for Li-ion batteries, but the structural complexity and unique initial charging behavior lead to several problems including large initial capacity loss, capacity and voltage fading, poor cyclability, and inferior rate capability. Since the surface conditions are critical to electrochemical performance and the drawbacks, nanoscale surface modification for improving LLO's properties is a general strategy. This review mainly summarizes the surface modification of LLOs and classifies them into three types of surface pre-treatment, surface gradient doping, and surface coating. Surface pre-treatment usually introduces removal of Li2O for lower irreversible capacity while surface doping is aimed to stabilize the structure during electrochemical cycling. Surface coating layers with different properties, protective layers to suppress the interface side reaction, coating layers related to structural transformation, and electronic/ionic conductive layers for better rate capability, can avoid the shortcomings of LLOs. In addition to surface modification for performance enhancement, other strategies can also be investigated to achieve high-performance LLO-based cathode materials.

“Feathered” fractal surfaces to minimize secondary electron emission for a wide range of incident angles

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

Swanson, Charles; Kaganovich, Igor D.

Complex structures on a material surface can significantly reduce the total secondary electron emission from that surface. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at one point of the structure and intersecting another. We performed Monte Carlo calculations to demonstrate that fractal surfaces can reduce net secondary electron emission produced by the surface as compared to the flat surface. Specifically, we describe one surface, a “feathered” surface, which reduces the secondary electron emission yield more effectively than other previously considered configurations. Specifically, feathers grown onto a surface suppress secondary electron emission from shallow anglesmore » of incidence more effectively than velvet. Here, we find that, for the surface simulated, secondary electron emission yield remains below 20% of its un-suppressed value, even for shallow incident angles, where the velvet-only surface gives reduction factor of only 50%.« less

“Feathered” fractal surfaces to minimize secondary electron emission for a wide range of incident angles

DOE PAGES

Swanson, Charles; Kaganovich, Igor D.

2017-07-24

Complex structures on a material surface can significantly reduce the total secondary electron emission from that surface. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at one point of the structure and intersecting another. We performed Monte Carlo calculations to demonstrate that fractal surfaces can reduce net secondary electron emission produced by the surface as compared to the flat surface. Specifically, we describe one surface, a “feathered” surface, which reduces the secondary electron emission yield more effectively than other previously considered configurations. Specifically, feathers grown onto a surface suppress secondary electron emission from shallow anglesmore » of incidence more effectively than velvet. Here, we find that, for the surface simulated, secondary electron emission yield remains below 20% of its un-suppressed value, even for shallow incident angles, where the velvet-only surface gives reduction factor of only 50%.« less

"Feathered" fractal surfaces to minimize secondary electron emission for a wide range of incident angles

NASA Astrophysics Data System (ADS)

Swanson, Charles; Kaganovich, Igor D.

2017-07-01

Complex structures on a material surface can significantly reduce the total secondary electron emission from that surface. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at one point of the structure and intersecting another. We performed Monte Carlo calculations to demonstrate that fractal surfaces can reduce net secondary electron emission produced by the surface as compared to the flat surface. Specifically, we describe one surface, a "feathered" surface, which reduces the secondary electron emission yield more effectively than other previously considered configurations. Specifically, feathers grown onto a surface suppress secondary electron emission from shallow angles of incidence more effectively than velvet. We find that, for the surface simulated, secondary electron emission yield remains below 20% of its un-suppressed value, even for shallow incident angles, where the velvet-only surface gives reduction factor of only 50%.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

PubMed

Walzthoeni, Thomas; Joachimiak, Lukasz A; Rosenberger, George; Röst, Hannes L; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi

2015-12-01

Chemical cross-linking in combination with mass spectrometry generates distance restraints of amino acid pairs in close proximity on the surface of native proteins and protein complexes. In this study we used quantitative mass spectrometry and chemical cross-linking to quantify differences in cross-linked peptides obtained from complexes in spatially discrete states. We describe a generic computational pipeline for quantitative cross-linking mass spectrometry consisting of modules for quantitative data extraction and statistical assessment of the obtained results. We used the method to detect conformational changes in two model systems: firefly luciferase and the bovine TRiC complex. Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information.

Characterization of U(VI)-carbonato ternary complexes on hematite: EXAFS and electrophoretic mobility measurements

USGS Publications Warehouse

Bargar, John R.; Reitmeyer, Rebecca; Lenhart, John J.; Davis, James A.

2000-01-01

We have measured U(VI) adsorption on hematite using EXAFS spectroscopy and electrophoresis under conditions relevant to surface waters and aquifers (0.01 to 10 μM dissolved uranium concentrations, in equilibrium with air, pH 4.5 to 8.5). Both techniques suggest the existence of anionic U(VI)-carbonato ternary complexes. Fits to EXAFS spectra indicate that U(VI) is simultaneously coordinated to surface FeO6 octahedra and carbonate (or bicarbonate) ligands in bidentate fashions, leading to the conclusion that the ternary complexes have an inner-sphere metal bridging (hematite-U(VI)-carbonato) structure. Greater than or equal to 50% of adsorbed U(VI) was comprised of monomeric hematite-U(VI)-carbonato ternary complexes, even at pH 4.5. Multimeric U(VI) species were observed at pH ≥ 6.5 and aqueous U(VI) concentrations approximately an order of magnitude more dilute than the solubility of crystalline β-UO2(OH)2. Based on structural constraints, these complexes were interpreted as dimeric hematite-U(VI)-carbonato ternary complexes. These results suggest that Fe-oxide-U(VI)-carbonato complexes are likely to be important transport-limiting species in oxic aquifers throughout a wide range of pH values.

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

PubMed Central

Rahman, Masudur; Neff, David; Green, Nathaniel; Norton, Michael L.

2016-01-01

Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material. PMID:28335324

Incorporation of organometallic Ru complexes into apo-ferritin cage.

PubMed

Takezawa, Yusuke; Böckmann, Philipp; Sugi, Naoki; Wang, Ziyue; Abe, Satoshi; Murakami, Tatsuya; Hikage, Tatsuo; Erker, Gerhard; Watanabe, Yoshihito; Kitagawa, Susumu; Ueno, Takafumi

2011-03-14

Spherical protein cages such as an iron storage protein, ferritin, have great potential as nanometer-scale capsules to assemble and store metal ions and complexes. We report herein the synthesis of a composite of an apo-ferritin cage and Ru(p-cymene) complexes. Ru complexes were efficiently incorporated into the ferritin cavity without degradation of its cage structure. X-Ray crystallography revealed that the Ru complexes were immobilized on the interior surface of the cage mainly by the coordination of histidine residues.

Predictive Modeling in Actinide Chemistry and Catalysis

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

Yang, Ping

2016-05-16

These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

Acoustic emission source location in composite structure by Voronoi construction using geodesic curve evolution.

PubMed

Gangadharan, R; Prasanna, G; Bhat, M R; Murthy, C R L; Gopalakrishnan, S

2009-11-01

Conventional analytical/numerical methods employing triangulation technique are suitable for locating acoustic emission (AE) source in a planar structure without structural discontinuities. But these methods cannot be extended to structures with complicated geometry, and, also, the problem gets compounded if the material of the structure is anisotropic warranting complex analytical velocity models. A geodesic approach using Voronoi construction is proposed in this work to locate the AE source in a composite structure. The approach is based on the fact that the wave takes minimum energy path to travel from the source to any other point in the connected domain. The geodesics are computed on the meshed surface of the structure using graph theory based on Dijkstra's algorithm. By propagating the waves in reverse virtually from these sensors along the geodesic path and by locating the first intersection point of these waves, one can get the AE source location. In this work, the geodesic approach is shown more suitable for a practicable source location solution in a composite structure with arbitrary surface containing finite discontinuities. Experiments have been conducted on composite plate specimens of simple and complex geometry to validate this method.

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Computational characterization of ordered nanostructured surfaces

NASA Astrophysics Data System (ADS)

Mohieddin Abukhdeir, Nasser

2016-08-01

A vital and challenging task for materials researchers is to determine relationships between material characteristics and desired properties. While the measurement and assessment of material properties can be complex, quantitatively characterizing their structure is frequently a more challenging task. This issue is magnified for materials researchers in the areas of nanoscience and nanotechnology, where material structure is further complicated by phenomena such as self-assembly, collective behavior, and measurement uncertainty. Recent progress has been made in this area for both self-assembled and nanostructured surfaces due to increasing accessibility of imaging techniques at the nanoscale. In this context, recent advances in nanomaterial surface structure characterization are reviewed including the development of new theory and image processing methods.

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

NASA Astrophysics Data System (ADS)

Costa, Dominique; Pradier, Claire-Marie; Tielens, Frederik; Savio, Letizia

2015-12-01

Understanding the bio-physical-chemical interactions at nanostructured biointerfaces and the assembly mechanisms of so-called hybrid nano-composites is nowadays a key issue for nanoscience in view of the many possible applications foreseen. The contribution of surface science in this field is noteworthy since, using a bottom-up approach, it allows the investigation of the fundamental processes at the basis of complex interfacial phenomena and thus it helps to unravel the elementary mechanisms governing them. Nowadays it is well demonstrated that a wide variety of different molecular assemblies can form upon adsorption of small biomolecules at surfaces. The geometry of such self-organized structures can often be tuned by a careful control of the experimental conditions during the deposition process. Indeed an impressive number of studies exists (both experimental and - to a lesser extent - theoretical), which demonstrates the ability of molecular self-assembly to create different structural motifs in a more or less predictable manner, by tuning the molecular building blocks as well as the metallic substrate. In this frame, amino acids and small peptides at surfaces are key, basic, systems to be studied. The amino acids structure is simple enough to serve as a model for the chemisorption of biofunctional molecules, but their adsorption at surfaces has applications in surface functionalization, in enantiospecific catalysis, biosensing, shape control of nanoparticles or in emerging fields such as "green" corrosion inhibition. In this paper we review the most recent advances in this field. We shall start from the adsorption of amino acids at metal surfaces and we will evolve then in the direction of more complex systems, in the light of the latest improvements of surface science techniques and of computational methods. On one side, we will focus on amino acids adsorption at oxide surfaces, on the other on peptide adsorption both at metal and oxide substrates. Particular attention will be drawn to the added value provided by the combination of several experimental surface science techniques and to the precious contribution of advanced complementary computational methods to resolve the details of systems of increased complexity. Finally, some hints on experiments performed in presence of water and then characterized in UHV and on the related theoretical work will be presented. This is a further step towards a better approximation of real biological systems. However, since the methods employed are often not typical of surface science, this topic is not developed in detail.

New surface smoothing technologies for manufacturing of complex shaped glass components

NASA Astrophysics Data System (ADS)

Henkel, Sebastian; Schwager, Anne-Marie; Bliedtner, Jens; Götze, Kerstin; Rädlein, Edda; Schulze, Christian; Gerhardt, Martin; Fuhr, Michael

2017-10-01

The production of complex glass components with 2.5D or 3D-structures involves great effort and the need for advanced CNC-technology. Especially the final surface treatment, for generation of transparent surfaces, represents a timeconsuming and costly process. The ultrasonic-assisted grinding procedure is used to generate arbitrary shaped components and freeform-surfaces. The special kinematic principle, containing a high-frequency tool oscillation, enables efficient manufacturing processes. Surfaces produced in this way allow for application of novel smoothing methods, providing considerable advantages compared to classic polishing. It is shown, that manufacturing of transparent glass surfaces with low roughness down to Rq = 10 nm is possible, using an ultra-fine grinding process. By adding a CO2-laser polishing process, roughness can be reduced even further with a very short polishing time.

Crustal Seismic Structure beneath Portugal (Western Iberia) and the role of Variscan Inheritance

NASA Astrophysics Data System (ADS)

Veludo, Idalina; Afonso Dias, Nuno; Fonseca, Paulo; Matias, Luís; Carrilho, Fernando; Haberland, Christian; Villaseñor, Antonio

2017-04-01

Mainland Portugal comprises most of the Western portion of the Iberian Peninsula, in a geodynamic setting associated with the Africa-Eurasia plate boundary. The crustal structure in Portugal is the result of a complex assemblage history of continental collision and extension with most of the surface is covered by rocks dating to the Variscan orogeny, the coastal ranges dominated by Mesozoic structures and Mesocenozoic basins covering partially the mainland. The impact and extension of this complex tectonic in the structure of the Iberian Lithosphere is still a matter of discussion, especially in its western part beneath Portugal. The existing knowledge relating the observed surface geology and lithospheric structures is sparse and sometimes incoherent, the relation between shallow and deep structures and their lateral extension still widely undetermined. Some questions still pertinent are the role and influence of the several tectonic units and their contacts in the present tectonic regime and in the stress field observed today, and the relation between the anomalous seismicity and associated crustal deformation rates with the inherited structure from past orogenies. In this study we present the results of a local earthquake tomographic study, performed to image this complex crustal structure down to 20 km depth. The relocation of the onshore seismicity recorded in the period 2000-2014 with the new 3D model allows cleansing some of the alignments and their correlation with some of the main active structures in Portugal enabling for the first time to correlate a large number of tectonic features to the small magnitude seismicity pattern. The seismicity distribution also displays a complex pattern, mainly reflecting the interaction between inherited Variscan structures with more recent fault systems created during the rifting stages of the Atlantic and diapir magmatic intrusions. The complex history of the assemblage of the crust beneath Western Iberia is well-marked in the final models. The arcuate shape of the Ibero-Armorican Arc can be perceived over the general pattern of the Vp and Vp/Vs anomalies and the heterogeneity observed on the surface geology are clearly marked in the tomograms. Other significant features are the low Vp values associated with the Mesocenozoic rocks outcropping in the Lusitanian and Algarve basins, and the low Vp and high Vp/Vs values of the sedimentary cover of the Lower-Tagus and Sado Basin. Publication supported by FCT- project UID/GEO/50019/2013 - Instituto Dom Luiz.

Risk maps for navigation in liver surgery

NASA Astrophysics Data System (ADS)

Hansen, C.; Zidowitz, S.; Schenk, A.; Oldhafer, K.-J.; Lang, H.; Peitgen, H.-O.

2010-02-01

The optimal transfer of preoperative planning data and risk evaluations to the operative site is challenging. A common practice is to use preoperative 3D planning models as a printout or as a presentation on a display. One important aspect is that these models were not developed to provide information in complex workspaces like the operating room. Our aim is to reduce the visual complexity of 3D planning models by mapping surgically relevant information onto a risk map. Therefore, we present methods for the identification and classification of critical anatomical structures in the proximity of a preoperatively planned resection surface. Shadow-like distance indicators are introduced to encode the distance from the resection surface to these critical structures on the risk map. In addition, contour lines are used to accentuate shape and spatial depth. The resulting visualization is clear and intuitive, allowing for a fast mental mapping of the current resection surface to the risk map. Preliminary evaluations by liver surgeons indicate that damage to risk structures may be prevented and patient safety may be enhanced using the proposed methods.

The influence of the focus position on laser machining and laser micro-structuring monocrystalline diamond surface

NASA Astrophysics Data System (ADS)

Wu, Mingtao; Guo, Bing; Zhao, Qingliang; Fan, Rongwei; Dong, Zhiwei; Yu, Xin

2018-06-01

Micro-structured surface on diamond is widely used in microelectronics, optical elements, MEMS and NEMS components, ultra-precision machining tools, etc. The efficient micro-structuring of diamond material is still a challenging task. In this article, the influence of the focus position on laser machining and laser micro-structuring monocrystalline diamond surface were researched. At the beginning, the ablation threshold and its incubation effect of monocrystalline diamond were determined and discussed. As the accumulated laser pulses ranged from 40 to 5000, the laser ablation threshold decreased from 1.48 J/cm2 to 0.97 J/cm2. Subsequently, the variation of the ablation width and ablation depth in laser machining were studied. With enough pulse energy, the ablation width mainly depended on the laser propagation attributes while the ablation depth was a complex function of the focus position. Raman analysis was used to detect the variation of the laser machined diamond surface after the laser machining experiments. Graphite formation was discovered on the machined diamond surface and graphitization was enhanced after the defocusing quantity exceeded 45 μm. At last, several micro-structured surfaces were successfully fabricated on diamond surface with the defined micro-structure patterns and structuring ratios just by adjusting the defocusing quantity. The experimental structuring ratio was consistent with the theoretical analysis.

A Framework for Optimal Control Allocation with Structural Load Constraints

NASA Technical Reports Server (NTRS)

Frost, Susan A.; Taylor, Brian R.; Jutte, Christine V.; Burken, John J.; Trinh, Khanh V.; Bodson, Marc

2010-01-01

Conventional aircraft generally employ mixing algorithms or lookup tables to determine control surface deflections needed to achieve moments commanded by the flight control system. Control allocation is the problem of converting desired moments into control effector commands. Next generation aircraft may have many multipurpose, redundant control surfaces, adding considerable complexity to the control allocation problem. These issues can be addressed with optimal control allocation. Most optimal control allocation algorithms have control surface position and rate constraints. However, these constraints are insufficient to ensure that the aircraft's structural load limits will not be exceeded by commanded surface deflections. In this paper, a framework is proposed to enable a flight control system with optimal control allocation to incorporate real-time structural load feedback and structural load constraints. A proof of concept simulation that demonstrates the framework in a simulation of a generic transport aircraft is presented.

GridTool: A surface modeling and grid generation tool

NASA Technical Reports Server (NTRS)

Samareh-Abolhassani, Jamshid

1995-01-01

GridTool is designed around the concept that the surface grids are generated on a set of bi-linear patches. This type of grid generation is quite easy to implement, and it avoids the problems associated with complex CAD surface representations and associated surface parameterizations. However, the resulting surface grids are close to but not on the original CAD surfaces. This problem can be alleviated by projecting the resulting surface grids onto the original CAD surfaces. GridTool is designed primary for unstructured grid generation systems. Currently, GridTool supports VGRID and FELISA systems, and it can be easily extended to support other unstructured grid generation systems. The data in GridTool is stored parametrically so that once the problem is set up, one can modify the surfaces and the entire set of points, curves and patches will be updated automatically. This is very useful in a multidisciplinary design and optimization process. GridTool is written entirely in ANSI 'C', the interface is based on the FORMS library, and the graphics is based on the GL library. The code has been tested successfully on IRIS workstations running IRIX4.0 and above. The memory is allocated dynamically, therefore, memory size will depend on the complexity of geometry/grid. GridTool data structure is based on a link-list structure which allows the required memory to expand and contract dynamically according to the user's data size and action. Data structure contains several types of objects such as points, curves, patches, sources and surfaces. At any given time, there is always an active object which is drawn in magenta, or in their highlighted colors as defined by the resource file which will be discussed later.

Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins

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

Lok, Shee-Mei; Kostyuchenko, Victor; Nybakken, Grant E.

The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization ofmore » the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells.« less

Modeling the assembly order of multimeric heteroprotein complexes

PubMed Central

Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Shin, Woong-Hee

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes. PMID:29329283

Modeling the assembly order of multimeric heteroprotein complexes.

PubMed

Peterson, Lenna X; Togawa, Yoichiro; Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Roy, Amitava; Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.

Characterization of measurement errors using structure-from-motion and photogrammetry to measure marine habitat structural complexity.

PubMed

Bryson, Mitch; Ferrari, Renata; Figueira, Will; Pizarro, Oscar; Madin, Josh; Williams, Stefan; Byrne, Maria

2017-08-01

Habitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure-from-motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time. This study evaluated the accuracy, precision, and bias in measurements of marine habitat structural complexity derived from structure-from-motion and photogrammetric measurements using repeated surveys of artificial reefs (with known structure) as well as natural coral reefs. We quantified measurement errors as a function of survey image coverage, actual surface rugosity, and the morphological community composition of the habitat-forming organisms (reef corals). Our results indicated that measurements could be biased by up to 7.5% of the total observed ranges of structural complexity based on the environmental conditions present during any particular survey. Positive relationships were found between measurement errors and actual complexity, and the strength of these relationships was increased when coral morphology and abundance were also used as predictors. The numerous advantages of structure-from-motion and photogrammetry techniques for quantifying and investigating marine habitats will mean that they are likely to replace traditional measurement techniques (e.g., chain-and-tape). To this end, our results have important implications for data collection and the interpretation of measurements when examining changes in habitat complexity using structure-from-motion and photogrammetry.

Integration of Quartz Crystal Microbalance-Dissipation and Reflection-Mode Localized Surface Plasmon Resonance Sensors for Biomacromolecular Interaction Analysis.

PubMed

Ferhan, Abdul Rahim; Jackman, Joshua A; Cho, Nam-Joon

2016-12-20

The combination of label-free, surface-sensitive measurement techniques based on different physical principles enables detailed characterization of biomacromolecular interactions at solid-liquid interfaces. To date, most combined measurement systems have involved experimental techniques with similar probing volumes, whereas the potential of utilizing techniques with different surface sensitivities remains largely unexplored, especially for data interpretation. Herein, we report a combined measurement approach that integrates a conventional quartz crystal microbalance-dissipation (QCM-D) setup with a reflection-mode localized surface plasmon (LSPR) sensor. Using this platform, we investigate vesicle adsorption on a titanium oxide-coated sensing substrate along with the amphipathic, α-helical (AH) peptide-induced structural transformation of surface-adsorbed lipid vesicles into a supported lipid bilayer (SLB) as a model biomacromolecular interaction. While the QCM-D and LSPR signals both detected mass uptake arising from vesicle adsorption, tracking the AH peptide-induced structural transformation revealed more complex measurement responses based on the different surface sensitivities of the two techniques. In particular, the LSPR signal recorded an increase in optical mass near the sensor surface which indicated SLB formation, whereas the QCM-D signals detected a significant loss in net acoustic mass due to excess lipid and coupled solvent leaving the probing volume. Importantly, these measurement capabilities allowed us to temporally distinguish the process of SLB formation at the sensor surface from the overall structural transformation process. Looking forward, these label-free measurement capabilities to simultaneously probe adsorbates at multiple length scales will provide new insights into complex biomacromolecular interactions.

Stability of M 3S 3 complexes on fcc M(111) surfaces: M = Au, Ag, Cu, and Ni

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

Liu, Da-Jiang; Lee, Jiyoung; Windus, Theresa L.

Density Functional Theory is utilized to assess the stability of metal (M)-sulfur (S) complexes adsorbed on fcc M(111) surfaces, specifically considering S-decorated planar M trimers, M 3S 3. Scanning Tunneling Microscopy studies have identified structures proposed to be Ni 3S 3 on Ni(111), and Au 3S 3 on Au(111). In addition, Cu 3S 3 on Cu(111) has been suggested to facilitate enhanced Cu surface mass transport. Our analysis considers M 3S 3 complexes for M = Au, Ag, Cu, and Ni, assessing key measures of stability on surfaces, and also comparing behavior with trends in gas-phase stability. These surface andmore » gas-phase analyses are systematically related within the framework of Hess’s law, which allows elucidation of various contributions to the overall energetics. In all cases, the adsorbed complex is stable relative to its separated constituents adsorbed on the terrace. However, only for Ag does one find a negative energy of formation from excess S on terraces and M extracted from kink sites along step edges, implying spontaneous complex formation for this pathway. We interpret various experimental observations in the context of our results for energetics.« less

Stability of M 3S 3 complexes on fcc M(111) surfaces: M = Au, Ag, Cu, and Ni

DOE PAGES

Liu, Da-Jiang; Lee, Jiyoung; Windus, Theresa L.; ...

2018-02-08

Density Functional Theory is utilized to assess the stability of metal (M)-sulfur (S) complexes adsorbed on fcc M(111) surfaces, specifically considering S-decorated planar M trimers, M 3S 3. Scanning Tunneling Microscopy studies have identified structures proposed to be Ni 3S 3 on Ni(111), and Au 3S 3 on Au(111). In addition, Cu 3S 3 on Cu(111) has been suggested to facilitate enhanced Cu surface mass transport. Our analysis considers M 3S 3 complexes for M = Au, Ag, Cu, and Ni, assessing key measures of stability on surfaces, and also comparing behavior with trends in gas-phase stability. These surface andmore » gas-phase analyses are systematically related within the framework of Hess’s law, which allows elucidation of various contributions to the overall energetics. In all cases, the adsorbed complex is stable relative to its separated constituents adsorbed on the terrace. However, only for Ag does one find a negative energy of formation from excess S on terraces and M extracted from kink sites along step edges, implying spontaneous complex formation for this pathway. We interpret various experimental observations in the context of our results for energetics.« less

Effect of Surfaces on Amyloid Fibril Formation

PubMed Central

Moores, Bradley; Drolle, Elizabeth; Attwood, Simon J.; Simons, Janet; Leonenko, Zoya

2011-01-01

Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Aβ) (1–42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid with cell membrane surfaces. We compared the structure and density of Aβ fibrils on positively and negatively charged as well as hydrophobic chemically-modified surfaces at physiologically relevant conditions. We report that due to the complex distribution of charge and hydrophobicity amyloid oligomers bind to all types of surfaces investigated (CH3, COOH, and NH2) although the charge and hydrophobicity of surfaces affected the structure and size of amyloid deposits as well as surface coverage. Hydrophobic surfaces promote formation of spherical amorphous clusters, while charged surfaces promote protofibril formation. We used the nonlinear Poisson-Boltzmann equation (PBE) approach to analyze the electrostatic interactions of amyloid monomers and oligomers with modified surfaces to complement our AFM data. PMID:22016789

Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations.

PubMed

Jain, Vaibhav; Maiti, Prabal K; Bharatam, Prasad V

2016-09-28

Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH 2 ) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH 2 ) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH 2 ) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an important role in the stabilization of complex. Interestingly, it was observed from the equilibrated structures of dendrimer-drug complexes at low pH that encapsulated drug molecules in the G4 PAMAM(NH 2 ) formed cluster, while in the case of nontoxic G4 PAMAM(Ac) they were uniformly distributed inside the dendritic cavities. Thus, the latter dendrimer is suggested to be suitable nanovehicle for the delivery of Ntg. This computational analysis highlighted the importance of realistic molecular models of dendrimer-drug complexes (1:n) in order to obtain reliable results.

Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

NASA Astrophysics Data System (ADS)

Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

2016-09-01

Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an important role in the stabilization of complex. Interestingly, it was observed from the equilibrated structures of dendrimer-drug complexes at low pH that encapsulated drug molecules in the G4 PAMAM(NH2) formed cluster, while in the case of nontoxic G4 PAMAM(Ac) they were uniformly distributed inside the dendritic cavities. Thus, the latter dendrimer is suggested to be suitable nanovehicle for the delivery of Ntg. This computational analysis highlighted the importance of realistic molecular models of dendrimer-drug complexes (1:n) in order to obtain reliable results.

Toroidal surface complexes of bacteriophage {phi}12 are responsible for host-cell attachment

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

Leo-Macias, Alejandra; Katz, Garrett; Wei Hui

2011-06-05

Cryo-electron tomography and subtomogram averaging are utilized to determine that the bacteriophage {phi}12, a member of the Cystoviridae family, contains surface complexes that are toroidal in shape, are composed of six globular domains with six-fold symmetry, and have a discrete density connecting them to the virus membrane-envelope surface. The lack of this kind of spike in a reassortant of {phi}12 demonstrates that the gene for the hexameric spike is located in {phi}12's medium length genome segment, likely to the P3 open reading frames which are the proteins involved in viral-host cell attachment. Based on this and on protein mass estimatesmore » derived from the obtained averaged structure, it is suggested that each of the globular domains is most likely composed of a total of four copies of P3a and/or P3c proteins. Our findings may have implications in the study of the evolution of the cystovirus species in regard to their host specificity. - Research Highlights: > Subtomogram averaging reveals enhanced detail of a {phi}12 cystovirus surface protein complex. > The surface protein complex has a toroidal shape and six-fold symmetry. > It is encoded by the medium-size genome segment. > The proteins of the surface complex most likely are one copy of P3a and three copies of P3c.« less

Polychromatic microdiffraction characterization of defect gradients in severely deformed materials.

PubMed

Barabash, Rozaliya I; Ice, Gene E; Liu, Wenjun; Barabash, Oleg M

2009-01-01

This paper analyzes local lattice rotations introduced in severely deformed polycrystalline titanium by friction stir welding. Nondestructive three-dimensional (3D) spatially resolved polychromatic X-ray microdiffraction, is used to resolve the local crystal structure of the restructured surface from neighboring local structures in the sample material. The measurements reveal strong gradients of strain and geometrically necessary dislocations near the surface and illustrate the potential of polychromatic microdiffraction for the study of deformation in complex materials systems.

Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.

PubMed

Numata, Tomoyuki; Inanaga, Hideko; Sato, Chikara; Osawa, Takuo

2015-01-30

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3-Csm4 subcomplex at 3.1Å resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1-Csm4-Csm3 ternary complex, which provides insights into its role in the Csm interference complex. Copyright © 2014 Elsevier Ltd. All rights reserved.

Surface Segregation in Multicomponent Systems: Modeling of Surface Alloys and Alloy Surfaces

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John; Noebe, Ronald D.; Good, Brian; Honecy, Frank S.; Abel, Phillip

1999-01-01

The study of surface segregation, although of great technological importance, has been largely restricted to experimental work due to limitations associated with theoretical methods. However, recent improvements in both first-particle and semi-empirical methods are opening, the doors to an array of new possibilities for surface scientists. We apply one of these techniques, the Bozzolo, Ferrante and Smith (BFS) method for alloys, which is particularly suitable for complex systems, to several aspects of the computational modeling of surfaces and segregation, including alloy surface segregation, structure and composition of alloy surfaces, and the formation of surface alloys. We conclude with the study of complex NiAl-based binary, ternary and quaternary thin films (with Ti, Cr and Cu additions to NiAl). Differences and similarities between bulk and surface compositions are discussed, illustrated by the results of Monte Carlo simulations. For some binary and ternary cases, the theoretical predictions are compared to experimental results, highlighting the accuracy and value of this developing theoretical tool.

Strike-Slip Faulting Processes on Ganymede: Global Morphological Mapping and Structural Interpretation of Grooved and Transitional Terrains

NASA Astrophysics Data System (ADS)

Burkhard, L. M.; Cameron, M. E.; Smith-Konter, B. R.; Seifert, F.; Pappalardo, R. T.; Collins, G. C.

2015-12-01

Ganymede's fractured surface reveals many large-scale, morphologically distinct regions of inferred distributed shear and strike-slip faulting that may be important to the structural development of its surface and in the transition from dark to light (grooved) materials. To better understand the role of strike-slip tectonism in shaping Ganymede's complex icy surface, we perform a detailed mapping of key examples of strike-slip morphologies (i.e., en echelon structures, strike-slip duplexes, laterally offset pre-existing features, and possible strained craters) from Galileo and Voyager images. We focus on complex structures associated with grooved terrain (e.g. Nun Sulcus, Dardanus Sulcus, Tiamat Sulcus, and Arbela Sulcus) and terrains transitional from dark to light terrain (e.g. the boundary between Nippur Sulcus and Marius Regio, including Byblus Sulcus and Philus Sulcus). Detailed structural interpretations suggest strong evidence of strike-slip faulting in some regions (i.e., Nun and Dardanus Sulcus); however, further investigation of additional strike-slip structures is required of less convincing regions (i.e., Byblus Sulcus). Where applicable, these results are synthesized into a global database representing an inferred sense of shear for many of Ganymede's fractures. Moreover, when combined with existing observations of extensional features, these results help to narrow down the range of possible principal stress directions that could have acted at the regional or global scale to produce grooved terrain on Ganymede.

Drone based structural mapping at Holuhraun indicates fault reactivation and complexity

NASA Astrophysics Data System (ADS)

Mueller, Daniel; Walter, Thomas R.; Steinke, Bastian; Witt, Tanja; Schoepa, Anne; Duerig, Tobi; Gudmundsson, Magnus T.

2016-04-01

Accompanied by an intense seismic swarm in August 2014, a dike laterally formed, starting under Icelands Vatnajökull glacier, propagating over a distance of more than 45 km within only two weeks, leading to the largest eruption by volume since the 1783-84 Laki eruption. Along its propagation path, the dike caused intense surface displacements up to meters. Based on seismicity, GPS and InSAR, the propagation has already been analysed and described as segmented lateral dike growth. We now focus on few smaller regions of the dike. We consider the Terrasar-X tandem digital elevation map and aerial photos and find localized zones where structural fissures formed and curved. At these localized, regions we performed a field campaign in summer 2015, applying the close range remote sensing techniques Structure from Motion (SfM) and Terrestrial Laser Scanning (TLS). Over 4 TLS scan were collected, along with over 5,000 aerial images. Point clouds from SfM and TLS are merged and compared, and local structural lineaments analysed. As a result, we obtained an unprecedentedly high-resolution digital elevation map. With this map, we analyse the structural expression of the fissure eruption at the surface and improve understanding on the conditions that influenced the magma propagation path. We elaborate scenarios that lead to complexities of the surface structures and the link to the underlying dike intrusion.

Free-Surface Fluid-Object Interaction for the Large-Scale Computation of Ship Hydrodynamics Phenomena

DTIC Science & Technology

2014-05-21

simulating air-water free -surface flow, fluid-object interaction (FOI), and fluid-structure interaction (FSI) phenomena for complex geometries, and...with no limitations on the motion of the free surface, and with particular emphasis on ship hydrodynamics. The following specific research objectives...were identified for this project: 1) Development of a theoretical framework for free -surface flow, FOI and FSI that is a suitable starting point

Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

PubMed

Bausewein, Thomas; Mills, Deryck J; Langer, Julian D; Nitschke, Beate; Nussberger, Stephan; Kühlbrandt, Werner

2017-08-10

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. Copyright © 2017 Elsevier Inc. All rights reserved.

The molecular origins of specificity in the assembly of a multienzyme complex.

PubMed

Frank, René A W; Pratap, J Venkatesh; Pei, Xue Y; Perham, Richard N; Luisi, Ben F

2005-08-01

The pyruvate dehydrogenase (PDH) multienzyme complex is central to oxidative metabolism. We present the first crystal structure of a complex between pyruvate decarboxylase (E1) and the peripheral subunit binding domain (PSBD) of the dihydrolipoyl acetyltransferase (E2). The interface is dominated by a "charge zipper" of networked salt bridges. Remarkably, the PSBD uses essentially the same zipper to alternately recognize the dihydrolipoyl dehydrogenase (E3) component of the PDH assembly. The PSBD achieves this dual recognition largely through the addition of a network of interfacial water molecules unique to the E1-PSBD complex. These structural comparisons illuminate our observations that the formation of this water-rich E1-E2 interface is largely enthalpy driven, whereas that of the E3-PSBD complex (from which water is excluded) is entropy driven. Interfacial water molecules thus diversify surface complementarity and contribute to avidity, enthalpically. Additionally, the E1-PSBD structure provides insight into the organization and active site coupling within the approximately 9 MDa PDH complex.

The water-hydrophobic interface: neutral and charged solute adsorption at fluorocarbon and hydrocarbon self-assembled monolayers (SAMs).

PubMed

Hopkins, Adam J; Richmond, Geraldine L

2013-03-01

Adsorption of small molecular solutes in an aqueous solution to a soft hydrophobic surface is a topic relevant to many fields. In biological and industrial systems, the interfacial environment is often complex, containing an array of salts and organic compounds in the solution phase. Additionally, the surface itself can have a complex structure that can interact in unpredictable ways with small solutes in its vicinity. In this work, we studied model adsorption processes on hydrocarbon and fluorocarbon self-assembled monolayers by using vibrational sum frequency spectroscopy, with methanol and butylammonium chloride as adsorbates. The results indicate that differences in surface functionality have a significant impact on the organization of adsorbed organic species at hydrophobic surfaces.

3-D surface reconstruction of patient specific anatomic data using a pre-specified number of polygons.

PubMed

Aharon, S; Robb, R A

1997-01-01

Virtual reality environments provide highly interactive, natural control of the visualization process, significantly enhancing the scientific value of the data produced by medical imaging systems. Due to the computational and real time display update requirements of virtual reality interfaces, however, the complexity of organ and tissue surfaces which can be displayed is limited. In this paper, we present a new algorithm for the production of a polygonal surface containing a pre-specified number of polygons from patient or subject specific volumetric image data. The advantage of this new algorithm is that it effectively tiles complex structures with a specified number of polygons selected to optimize the trade-off between surface detail and real-time display rates.

Interaction of NaOH solutions with silica surfaces

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

Rimsza, Jessica M.; Jones, Reese E.; Criscenti, Louise J.

Sodium adsorption on silica surfaces depends on the solution counter-ion. Here, we use NaOH solutions to investigate basic environments. Sodium adsorption on hydroxylated silica surfaces from NaOH solutions were investigated through molecular dynamics with a dissociative force field, allowing for the development of secondary molecular species. Furthermore, across the NaOH concentrations (0.01 M – 1.0 M), ~50% of the Na + ions were concentrated in the surface region, developing silica surface charges between –0.01 C/m 2 (0.01 M NaOH) and –0.76 C/m 2 (1.0 M NaOH) due to surface site deprotonation. Five inner-sphere adsorption complexes were identified, including monodentate, bidentate,more » and tridentate configurations and two additional structures, with Na + ions coordinated by bridging oxygen and hydroxyl groups or water molecules. Coordination of Na + ions by bridging oxygen atoms indicates partial or complete incorporation of Na + ions into the silica surface. Residence time analysis identified that Na + ions coordinated by bridging oxygen atoms stayed adsorbed onto the surface four times longer than the mono/bi/tridentate species, indicating formation of relatively stable and persistent Na + ion adsorption structures. Such inner-sphere complexes form only at NaOH concentrations of > 0.5 M. Na + adsorption and lifetimes have implications for the stability of silica surfaces.« less

Interaction of NaOH solutions with silica surfaces

DOE PAGES

Rimsza, Jessica M.; Jones, Reese E.; Criscenti, Louise J.

2018-01-16

Sodium adsorption on silica surfaces depends on the solution counter-ion. Here, we use NaOH solutions to investigate basic environments. Sodium adsorption on hydroxylated silica surfaces from NaOH solutions were investigated through molecular dynamics with a dissociative force field, allowing for the development of secondary molecular species. Furthermore, across the NaOH concentrations (0.01 M – 1.0 M), ~50% of the Na + ions were concentrated in the surface region, developing silica surface charges between –0.01 C/m 2 (0.01 M NaOH) and –0.76 C/m 2 (1.0 M NaOH) due to surface site deprotonation. Five inner-sphere adsorption complexes were identified, including monodentate, bidentate,more » and tridentate configurations and two additional structures, with Na + ions coordinated by bridging oxygen and hydroxyl groups or water molecules. Coordination of Na + ions by bridging oxygen atoms indicates partial or complete incorporation of Na + ions into the silica surface. Residence time analysis identified that Na + ions coordinated by bridging oxygen atoms stayed adsorbed onto the surface four times longer than the mono/bi/tridentate species, indicating formation of relatively stable and persistent Na + ion adsorption structures. Such inner-sphere complexes form only at NaOH concentrations of > 0.5 M. Na + adsorption and lifetimes have implications for the stability of silica surfaces.« less

Stabilization of polar Mn3O4(001) film on Ag(001): Interplay between kinetic and structural stability

NASA Astrophysics Data System (ADS)

Kundu, Asish K.; Barman, Sukanta; Menon, Krishnakumar S. R.

2017-10-01

Stabilization processes of polar surfaces are often very complex and interesting. Understanding of these processes is crucial as it ultimately determines the properties of the film. Here, by the combined study of Low Energy Electron Diffraction (LEED), X-ray Photoelectron Spectroscopy (XPS) and Ultraviolet Photoemission Spectroscopy (UPS) techniques we show that, although there can be many processes involved in the stabilization of the polar surfaces, in case of Mn3O4(001)/Ag(001), it goes through different reconstructions of the Mn2O4 terminated surface which is in good agreements with the theoretical predictions. The complex surface phase diagram has been probed by LEED as a function of film thickness, oxygen partial pressure and substrate temperature during growth, while their chemical compositions have been probed by XPS. Below a critical film thickness of ∼ 1 unit cell height (8 sublayers or 3 ML) of Mn3O4 and oxygen partial pressure range of 2 × 10-8 mbar < P(O2) ≤ 5 × 10-7 mbar, different surface structures are detected and beyond this thickness a constant evolution of apparent p(2 × 2) structure have been observed due to the coexistence of p(2 × 1) and c(2 × 2) structures. Similar apparent p(2 × 2) structure has also observed by the oxidation of Ag(001)-supported MnO(001) surface. Our study also shows that the substrate temperature during growth plays a crucial role in determining the final structure of the polar Mn3O4 film and as a consequence of that a strong interplay between structural and kinetic stability in the Mn3O4 film has been observed. Further, stripe-like LEED pattern has been observed from the Mn3O4(001) surface, for the film grown at higher oxygen partial pressure (> 5 × 10-7 mbar) and higher temperature UHV annealing. The origin of these stripes has been explained with the help of UPS results.

Carbon nanotubes on nanoporous alumina: from surface mats to conformal pore filling

PubMed Central

2014-01-01

Control over nucleation and growth of multi-walled carbon nanotubes in the nanochannels of porous alumina membranes by several combinations of posttreatments, namely exposing the membrane top surface to atmospheric plasma jet and application of standard S1813 photoresist as an additional carbon precursor, is demonstrated. The nanotubes grown after plasma treatment nucleated inside the channels and did not form fibrous mats on the surface. Thus, the nanotube growth mode can be controlled by surface treatment and application of additional precursor, and complex nanotube-based structures can be produced for various applications. A plausible mechanism of nanotube nucleation and growth in the channels is proposed, based on the estimated depth of ion flux penetration into the channels. PACS 63.22.Np Layered systems; 68. Surfaces and interfaces; Thin films and nanosystems (structure and non-electronic properties); 81.07.-b Nanoscale materials and structures: fabrication and characterization PMID:25177216

Chemical cross-linking of the urease complex from Helicobacter pylori and analysis by Fourier transform ion cyclotron resonance mass spectrometry and molecular modeling

NASA Astrophysics Data System (ADS)

Carlsohn, Elisabet; Ångström, Jonas; Emmett, Mark R.; Marshall, Alan G.; Nilsson, Carol L.

2004-05-01

Chemical cross-linking of proteins is a well-established method for structural mapping of small protein complexes. When combined with mass spectrometry, cross-linking can reveal protein topology and identify contact sites between the peptide surfaces. When applied to surface-exposed proteins from pathogenic organisms, the method can reveal structural details that are useful in vaccine design. In order to investigate the possibilities of applying cross-linking on larger protein complexes, we selected the urease enzyme from Helicobacter pylori as a model. This membrane-associated protein complex consists of two subunits: [alpha] (26.5 kDa) and [beta] (61.7 kDa). Three ([alpha][beta]) heterodimers form a trimeric ([alpha][beta])3 assembly which further associates into a unique dodecameric 1.1 MDa complex composed of four ([alpha][beta])3 units. Cross-linked peptides from trypsin-digested urease complex were analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and molecular modeling. Two potential cross-linked peptides (present in the cross-linked sample but undetectable in [alpha], [beta], and native complex) were assigned. Molecular modeling of urease [alpha][beta] complex and trimeric urease units ([alpha][beta])3 revealed a linkage site between the [alpha]-subunit and the [beta]-subunit, and an internal cross-linkage in the [beta]-subunit.

Structural Controls of the Friction Constitutive Properties of Carbonate-bearing Faults

NASA Astrophysics Data System (ADS)

Carpenter, B. M.; Collettini, C.; Scuderi, M.; Marone, C.

2012-12-01

The identification of hetereogenous and complex post-seismic slip for the 2009, Mw = 6.3, L'Aquila earthquake highlights the importance of fault zone structure and frictional behavior. Many of the Mw 6 to 7 earthquakes that occur on normal faults in the active Apennines, such as L'Aquila, nucleate at depths where the lithology is dominated by carbonate rocks. Due to the complex structure observed in exhumed faults (i.e. the presence of highly polished principal slip surfaces, cemented cataclasites, and phyllosilicate-bearing, foliated fault gouge) as well as the large spectrum of fault slip behaviors identified world wide, we designed a suite of experiments using intact and powdered samples to better constrain the possible slip behaviors of these carbonate bearing faults. We collected samples from the exposed Rocchetta Fault, a ~10km long, normal fault with approximately 600m of total offset. The exposed principal slip surface cuts through the Calcare Massiccio formation, which is present throughout central Italy at depths of earthquake nucleation. We collected intact specimens of the natural slip surface and cemented cataclasite, as well as fragments of both which were later pulverized. Furthermore, we collected an intact sample of the hanging wall cataclasite and footwall limestone that contained the principal slip surface. We performed friction experiments in a variety of different configurations (slip surface on slip surface, slip surface on powdered cataclasite, etc.) in order to investigate heterogeneity in frictional behavior as controlled by fault structure. We sheared saturated samples at a constant normal stress of 10 MPa at room temperature. Velocity-stepping tests were performed from 1 to 300 μm/s to identify the friction constitutive parameters of this fault material. Furthermore, a series slide-hold-slide tests were performed (holds of 3 to 1000 seconds) to measure the amount of frictional healing and determine the frictional healing rate. Results from experiments designed to reactivate slip between the principal slip surface and cemented cataclasite show a peak friction value of ~0.95 followed by a ~3 MPa stress drop as the fault surface fails. Our other results suggest that earthquakes will easily nucleate in areas of the fault where two slip surfaces are in contact and are likely to propagate in areas where pulverized fault gouge is in contact with the slip surface. Our data show that samples collected from a single fault can exhibit a large range of slip behaviors. Heterogeneous frictional behavior documented in the lab must be combined with field observations of complex fault structure and seismological observations of the different modes of fault slip to further our understanding of fault slip. Future work will consist of thin section and XRD analysis of all experimental material.

Surface-attached and suspended bacterial community structure as affected by C/N ratios: relationship between bacteria and fish production.

PubMed

Yu, Ermeng; Xie, Jun; Wang, Jinlin; Ako, Harry; Wang, Guangjun; Chen, Zhanghe; Liu, Yongfeng

2016-07-01

Bacteria play crucial roles in the combined system of substrate addition and C/N control, which has been demonstrated to improve aquaculture production. However, the complexity of surface-attached bacteria on substrates and suspended bacteria in the water column hamper further application of this system. This study firstly applied this combined system into the culture of grass carp, and then explored the relationship between microbial complexes from surface-attached and suspended bacteria in this system and the production of grass carp. In addition, this study investigated bacterial community structures as affected by four C/N ratios using Illumina sequencing technology. The results demonstrated that the weight gain rate and specific growth rate of grass carp in the CN20 group (C/N ratio 20:1) were the highest (P < 0.05), and dietary supplementation of the microbial complex had positive effects on the growth of grass carp (P < 0.05). Sequencing data revealed that, (1) the proportions of Verrucomicrobiae and Rhodobacter (surface-attached), sediminibacterium (suspended), and emticicia (surface-attached and suspended) were much higher in the CN20 group compared with those in the other groups (P < 0.05); (2) Rhodobacter, Flavobacterium, Acinetobacter, Pseudomonas, Planctomyces, and Cloacibacterium might be important for the microbial colonization on substrates; (3) as the C/N ratio increased, proportions of Hydrogenophaga (surface-attached and suspended), Zoogloea, and Flectobacillus (suspended) increased, but proportions of Bacillus, Clavibacter, and Cellvibro (surface-attached and suspended) decreased. In summary, a combined system of substrate addition and C/N control increased the production of grass carp, and Verrucomicrobiae and Rhodobacter in the surface-attached bacterial community were potential probiotic bacteria that contributed to the enhanced growth of grass carp.

Tubular inverse opal scaffolds for biomimetic vessels

NASA Astrophysics Data System (ADS)

Zhao, Ze; Wang, Jie; Lu, Jie; Yu, Yunru; Fu, Fanfan; Wang, Huan; Liu, Yuxiao; Zhao, Yuanjin; Gu, Zhongze

2016-07-01

There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially oriented elliptical pattern microstructures on their surfaces. It is demonstrated that these tailored tubular scaffolds can effectively make endothelial cells to form an integrated hollow tubular structure on their inner surface and induce smooth muscle cells to form a circumferential orientation on their outer surface. These features of our tubular scaffolds make them highly promising for the construction of biomimetic blood vessels.There is a clinical need for tissue-engineered blood vessels that can be used to replace or bypass damaged arteries. The success of such grafts depends strongly on their ability to mimic native arteries; however, currently available artificial vessels are restricted by their complex processing, controversial integrity, or uncontrollable cell location and orientation. Here, we present new tubular scaffolds with specific surface microstructures for structural vessel mimicry. The tubular scaffolds are fabricated by rotationally expanding three-dimensional tubular inverse opals that are replicated from colloidal crystal templates in capillaries. Because of the ordered porous structure of the inverse opals, the expanded tubular scaffolds are imparted with circumferentially oriented elliptical pattern microstructures on their surfaces. It is demonstrated that these tailored tubular scaffolds can effectively make endothelial cells to form an integrated hollow tubular structure on their inner surface and induce smooth muscle cells to form a circumferential orientation on their outer surface. These features of our tubular scaffolds make them highly promising for the construction of biomimetic blood vessels. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03173k

Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations

NASA Astrophysics Data System (ADS)

Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.

2001-12-01

Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations. Characteristics of this complex propagation appear from the southern Sierra Nevada Mountains, in the west, to Death Valley in the east. The structure does not cross the Garlock fault to the south, but we are unsure of the structures northern extent.

Molecular-level spectroscopic investigations of the complexation and photodegradation of catechol to/by iron(III)

NASA Astrophysics Data System (ADS)

Al-Abadleh, Hind; Tofan-Lazar, Julia; Situm, Arthur; Slikboer, Samantha

2014-05-01

Surface water plays a crucial role in facilitating or inhibiting surface reactions in atmospheric aerosols. Little is known about the role of surface water in the complexation of organic molecules to transition metals in multicomponent aerosol systems. We will show results from real time diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) experiments for the in situ complexation of catechol to Fe(III) and its photosensitized degradation under dry and humid conditions. Catechol was chosen as a simple model for humic-like substances (HULIS) in aerosols and aged polyaromatic hydrocarbons (PAH). It has also been detected in secondary organic aerosols (SOA) formed from the reaction of hydroxyl radicals with benzene. Given the importance of the iron content in aerosols and its biogeochemistry, our studies were conducted using FeCl3. For comparison, these surface-sensitive studies were complemented with bulk aqueous ATR-FTIR, UV-vis, and HPLC measurements for structural, quantitative and qualitative information about complexes in the bulk, and potential degradation products. The implications of our studies on understanding interfacial and condensed phase chemistry relevant to multicomponent aerosols, water thin islands on buildings, and ocean surfaces containing transition metals will be discussed.

Complex dispersion relation of surface acoustic waves at a lossy metasurface

NASA Astrophysics Data System (ADS)

Schwan, Logan; Geslain, Alan; Romero-García, Vicente; Groby, Jean-Philippe

2017-01-01

The complex dispersion relation of surface acoustic waves (SAWs) at a lossy resonant metasurface is theoretically and experimentally reported. The metasurface consists of the periodic arrangement of borehole resonators in a rigid substrate. The theoretical model relies on a boundary layer approach that provides the effective metasurface admittance governing the complex dispersion relation in the presence of viscous and thermal losses. The model is experimentally validated by measurements in the semi-anechoic chamber. The complex SAW dispersion relation is experimentally retrieved from the analysis of the spatial Laplace transform of the pressure scanned along a line at the metasurface. The geometrical spreading of the energy from the speaker is accounted for, and both the real and imaginary parts of the SAW wavenumber are obtained. The results show that the strong reduction of the SAW group velocity occurs jointly with a drastic attenuation of the wave, leading to the confinement of the field close to the source and preventing the efficient propagation of such slow-sound surface modes. The method opens perspectives to theoretically predict and experimentally characterize both the dispersion and the attenuation of surface waves at structured surfaces.

DROPWISE CONDENSATION ON MICRO- AND NANOSTRUCTURED SURFACES

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

Enright, R; Miljkovic, N; Alvarado, JL

In this review we cover recent developments in the area of surface-enhanced dropwise condensation against the background of earlier work. The development of fabrication techniques to create surface structures at the micro-and nanoscale using both bottom-up and top-down approaches has led to increased study of complex interfacial phenomena. In the heat transfer community, researchers have been extensively exploring the use of advanced surface structuring techniques to enhance phase-change heat transfer processes. In particular, the field of vapor-to-liquid condensation and especially that of water condensation has experienced a renaissance due to the promise of further optimizing this process at the micro-andmore » nanoscale by exploiting advances in surface engineering developed over the last several decades.« less

Effect of surface topography on structural growth of thick sputtered films

NASA Technical Reports Server (NTRS)

Spalvins, T.; Brainard, W. A.

1974-01-01

Primarily thick sputtered S-Monel, silver, and 304 stainless steel coatings were deposited on mica, glass, and metal substrates with various surface finishes to investigate the structural growth of the coating by scanning electron microscopy. Compositional changes within the coating were analyzed by X-ray dispersion microscopy. Defects in the surface finish act as preferential nucleation sites and form isolated and complex nodules and various surface overgrowths in the coating. These nodules do not disappear after full annealing. Further, they have undesirable effects on mechanial properties; cracks are initiated at the nodules when the coating is stressed by mechanical forces. These effects are illustrated by micrographs. Nodular growth within a coating can be minimized or eliminated by reducing the surface roughness.

Control over the branched structures of platinum nanocrystals for electrocatalytic applications.

PubMed

Ma, Liang; Wang, Chengming; Gong, Ming; Liao, Lingwen; Long, Ran; Wang, Jinguo; Wu, Di; Zhong, Wei; Kim, Moon J; Chen, Yanxia; Xie, Yi; Xiong, Yujie

2012-11-27

Structural control of branched nanocrystals allows tuning two parameters that are critical to their catalytic activity--the surface-to-volume ratio, and the number of atomic steps, ledges, and kinks on surface. In this work, we have developed a simple synthetic system that allows tailoring the numbers of branches in Pt nanocrystals by tuning the concentration of additional HCl. In the synthesis, HCl plays triple functions in tuning branched structures via oxidative etching: (i) the crystallinity of seeds and nanocrystals; (ii) the number of {111} or {100} faces provided for growth sites; (iii) the supply kinetics of freshly formed Pt atoms in solution. As a result, tunable Pt branched structures--tripods, tetrapods, hexapods, and octopods with identical chemical environment--can be rationally synthesized in a single system by simply altering the etching strength. The controllability in branched structures enables to reveal that their electrocatalytic performance can be optimized by constructing complex structures. Among various branched structures, Pt octopods exhibit particularly high activity in formic acid oxidation as compared with their counterparts and commercial Pt/C catalysts. It is anticipated that this work will open a door to design more complex nanostructures and to achieve specific functions for various applications.

Exopolysaccharide microchannels direct bacterial motility and organize multicellular behavior

DOE PAGES

Berleman, James E.; Zemla, Marcin; Remis, Jonathan P.; ...

2016-05-06

The myxobacteria are a family of soil bacteria that form biofilms of complex architecture, aligned multilayered swarms or fruiting body structures that are simple or branched aggregates containing myxospores. Here, we examined the structural role of matrix exopolysaccharide (EPS) in the organization of these surface-dwelling bacterial cells. Using time-lapse light and fluorescence microscopy, as well as transmission electron microscopy and focused ion beam/scanning electron microscopy (FIB/SEM) electron microscopy, we found that Myxococcus xanthus cell organization in biofilms is dependent on the formation of EPS microchannels. Cells are highly organized within the three-dimensional structure of EPS microchannels that are required formore » cell alignment and advancement on surfaces. Mutants lacking EPS showed a lack of cell orientation and poor colony migration. Purified, cell-free EPS retains a channel-like structure, and can complement EPS - mutant motility defects. In addition, EPS provides the cooperative structure for fruiting body formation in both the simple mounds of M. xanthus and the complex, tree-like structures of Chondromyces crocatus. We furthermore investigated the possibility that EPS impacts community structure as a shared resource facilitating cooperative migration among closely related isolates of M. xanthus.« less

The hydration structure at yttria-stabilized cubic zirconia (110)-water interface with sub-Ångström resolution

DOE PAGES

Hou, Binyang; Kim, Seunghyun; Kim, Taeho; ...

2016-06-15

The interfacial hydration structure of yttria-stabilized cubic zirconia (110) surface in contact with water was determined with ~0.5 Å resolution by high-resolution X-ray reflectivity measurement. The terminal layer shows a reduced electron density compared to the following substrate lattice layers, which indicates there are additional defects generated by metal depletion as well as intrinsic oxygen vacancies, both of which are apparently filled by water species. Above this top surface layer, two additional adsorbed layers are observed forming a characteristic interfacial hydration structure. The first adsorbed layer shows abnormally high density as pure water and likely includes metal species, whereas themore » second layer consists of pure water. The observed interfacial hydration structure seems responsible for local equilibration of the defective surface in water and eventually regulating the long-term degradation processes. As a result, the multitude of water interactions with the zirconia surface results in the complex but highly ordered interfacial structure constituting the reaction front.« less

Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots.

PubMed

Kuttner, Yosef Y; Engel, Stanislav

2018-02-01

A rational design of protein complexes with defined functionalities and of drugs aimed at disrupting protein-protein interactions requires fundamental understanding of the mechanisms underlying the formation of specific protein complexes. Efforts to develop efficient small-molecule or protein-based binders often exploit energetic hot spots on protein surfaces, namely, the interfacial residues that provide most of the binding free energy in the complex. The molecular basis underlying the unusually high energy contribution of the hot spots remains obscure, and its elucidation would facilitate the design of interface-targeted drugs. To study the nature of the energetic hot spots, we analyzed the backbone dynamic properties of contact surfaces in several protein complexes. We demonstrate that, in most complexes, the backbone dynamic landscapes of interacting surfaces form complementary "stability patches," in which static areas from the opposing surfaces superimpose, and that these areas are predominantly located near the geometric center of the interface. We propose that a diminished enthalpy-entropy compensation effect augments the degree to which residues positioned within the complementary stability patches contribute to complex affinity, thereby giving rise to the energetic hot spots. These findings offer new insights into the nature of energetic hot spots and the role that backbone dynamics play in facilitating intermolecular recognition. Mapping the interfacial stability patches may provide guidance for protein engineering approaches aimed at improving the stability of protein complexes and could facilitate the design of ligands that target complex interfaces. © 2017 Wiley Periodicals, Inc.

Evaluation of a laser scanning sensor on detection of complex shaped targets for variable-rate sprayer development

USDA-ARS?s Scientific Manuscript database

Sensors that can accurately measure canopy structures are prerequisites for development of advanced variable-rate sprayers. A 270° radial range laser sensor was evaluated for its accuracy to measure dimensions of target surfaces with complex shapes and sizes. An algorithm for data acquisition and 3-...

The C-terminal region of Ge-1 presents conserved structural features required for P-body localization.

PubMed

Jinek, Martin; Eulalio, Ana; Lingel, Andreas; Helms, Sigrun; Conti, Elena; Izaurralde, Elisa

2008-10-01

The removal of the 5' cap structure by the DCP1-DCP2 decapping complex irreversibly commits eukaryotic mRNAs to degradation. In human cells, the interaction between DCP1 and DCP2 is bridged by the Ge-1 protein. Ge-1 contains an N-terminal WD40-repeat domain connected by a low-complexity region to a conserved C-terminal domain. It was reported that the C-terminal domain interacts with DCP2 and mediates Ge-1 oligomerization and P-body localization. To understand the molecular basis for these functions, we determined the three-dimensional crystal structure of the most conserved region of the Drosophila melanogaster Ge-1 C-terminal domain. The region adopts an all alpha-helical fold related to ARM- and HEAT-repeat proteins. Using structure-based mutants we identified an invariant surface residue affecting P-body localization. The conservation of critical surface and structural residues suggests that the C-terminal region adopts a similar fold with conserved functions in all members of the Ge-1 protein family.

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.

Structure of a premicellar complex of alkyl sulfates with the interfacial binding surfaces of four subunits of phospholipase A2.

PubMed

Pan, Ying H; Bahnson, Brian J

2010-07-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates have been characterized [Berg, O. G. et al., Biochemistry 43, 7999-8013, 2004]. Here we have solved the 2.7 A crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in three of the four protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Probing surface sites of TiO2: reactions with [HRe(CO)5] and [CH3Re(CO)5].

PubMed

Lobo-Lapidus, Rodrigo J; Gates, Bruce C

2010-10-04

Two carbonyl complexes of rhenium, [HRe(CO)(5)] and [CH(3)Re(CO)(5)], were used to probe surface sites of TiO(2) (anatase). These complexes were adsorbed from the gas phase onto anatase powder that had been treated in flowing O(2) or under vacuum to vary the density of surface OH sites. Infrared (IR) spectra demonstrate the variation in the number of sites, including Ti(+3)-OH and Ti(+4)-OH. IR and extended X-ray absorption fine structure (EXAFS) spectra show that chemisorption of the rhenium complexes led to their decarbonylation, with formation of surface-bound rhenium tricarbonyls, when [HRe(CO)(5)] was adsorbed, or rhenium tetracarbonyls, when [CH(3)Re(CO)(5)] was adsorbed. These reactions were accompanied by the formation of water and surface carbonates and removal of terminal hydroxyl groups associated with Ti(+3) and Ti(+4) ions on the anatase. Data characterizing the samples after adsorption of [HRe(CO)(5)] or [CH(3)Re(CO)(5)] determined a ranking of the reactivity of the surface OH sites, with the Ti(+3)-OH groups being the more reactive towards the rhenium complexes but the less likely to be dehydroxylated. The two rhenium pentacarbonyl probes provided complementary information, suggesting that the carbonate species originate from carbonyl ligands initially bonded to the rhenium and from hydroxyl groups of the titania surface, with the reaction leading to the formation of water and bridging hydroxyl groups on the titania. The results illustrate the value of using a family of organometallic complexes as probes of oxide surface sites.

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.

‘Action’ on structured freeform surfaces

NASA Astrophysics Data System (ADS)

Whitehouse, David J.

2018-06-01

Surfaces are becoming more complex partly due to the more complicated function required of them and partly due to the introduction of different manufacturing processes. These have thrown into relief the need to consider new ways of measuring and characterizing such surfaces and more importantly to make such characterization more relevant by tying together the geometry and the function more closely. The surfaces which have freeform and structure have been chosen to be a carrier for this investigation because so far there has been little work carried out in this neglected but potentially important area. This necessitates the development of a strategy for their characterization. In this article, some ways have been found of identifying possible strategies for tackling this characterization problem but also linking this characterization to performance and manufacture, based in part on the principles of least action and on the way that nature has evolved to solve the marriage of flexible freeform geometry, structure and function. Recommendations are made for the most suitable surface parameter to use which satisfies the requirement for characterizing structured freeform surfaces as well as utilizing ‘Action’ to predict functionality.

Image the heterogeneous structure of Colima volcano complex using ambient noise and teleseismic tomography

NASA Astrophysics Data System (ADS)

Dai, Y.; Yang, T.

2017-12-01

As one of the most active stratovolcano in present world, Colima volcano has aroused extensive researches about its structure and mechanism. Preceded studies have described the deep internal structure of Jalisco subduction zone and attributed the surface volcanism to the subduction of Rivera plate and Cocos plate here, but the image of crustal structure remains vague. Thus our work aims to depict the lithosphere structure and magma system, trying to understand the material transportation of Colima volcano. Two dense networks of temporary stations, CODEX and MARS, were deployed in the studying area during 2006-2007, collected adequate seismic data for tomography. We used ambient noise tomography to obtain both the phase velocity maps and azimuthal anisotropic character of crust. Those results show a shallow magma chamber right beneath the Colima volcano reaching a depth of 8km and its azimuthal anisotropic character ,which is of larger magnitude and northeast-ward in the connection part, indicates the material probably flow from central Mexico volcanic zone in the superficial crust. Hereafter, we combine the ambient noise tomography with surface wave tomography which corresponding to deeper structure. Phase velocity information from two methods are then used to invert a 3D heterogeneous model, which well presents the complex lithosphere structure of this area and shows the connection between the mantle window and magma chamber, giving the clues of how the magma materials transport from source to surface to support the constant eruption of Colima volcano.

Changes in spectrochemical and catalytic properties of biopolymer anchored Cu(II) and Ni(II) catalysts by electron beam irradiation.

PubMed

Antony, R; Suja Pon Mini, P S; Theodore David Manickam, S; Sanjeev, Ganesh; Mitu, Liviu; Balakumar, S

2015-01-01

Chitosan (a biopolymer) anchored Cu(II) and Ni(II) Schiff base complexes, [M(OIAC)Cl2] (M: Cu/Ni and OIAC: ([2-oxo-1H-indol-3-ylidene]amino)chitosan) were electron beam irradiated by different doses (100 Gy, 1 kGy and 10 kGy). The electron beam has shown potential impact on biopolymer's support, in detail chain linking and chain scissoring, as evidenced by viscosity studies, FT-IR and X-ray diffraction spectroscopic techniques. Due to these structural changes, thermal properties of the complexes were found to be changed. The surface of these heterogeneous complexes was also effectually altered by electron beam. As a consequence, pores and holes were created as probed by SEM technique. The catalytic activity of both non-irradiated and irradiated complexes was investigated in the aerobic oxidation of cyclohexane using hydrogen peroxide oxidant. The catalytic ability of the complexes was enhanced significantly after irradiation as the result of surface changes. The reusability of the complexes was also greatly affected because of the structural variations in polymeric support. In terms of both better catalytic activity along with the reusability, 1 kGy is suggested as the best dose to attain adequate increase in catalytic activity and good reusability. Copyright © 2015 Elsevier B.V. All rights reserved.

Three-dimensional structure of an antibody-antigen complex.

PubMed

Sheriff, S; Silverton, E W; Padlan, E A; Cohen, G H; Smith-Gill, S J; Finzel, B C; Davies, D R

1987-11-01

We have determined the three-dimensional structure of two crystal forms of an antilysozyme Fab-lysozyme complex by x-ray crystallography. The epitope on lysozyme consists of three sequentially separated subsites, including one long, nearly continuous, site from Gln-41 through Tyr-53 and one from Gly-67 through Pro-70. Antibody residues interacting with lysozyme occur in each of the six complementarity-determining regions and also include one framework residue. Arg-45 and Arg-68 form a ridge on the surface of lysozyme, which binds in a groove on the antibody surface. Otherwise the surface of interaction between the two proteins is relatively flat, although it curls at the edges. The surface of interaction is approximately 26 X 19 A. No water molecules are found in the interface. The positive charge on the two arginines is complemented by the negative charge of Glu-35 and Glu-50 from the heavy chain of the antibody. The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70. One side chain not in the epitope, Trp-63, undergoes a rotation of approximately 180 degrees about the C beta--C gamma bond. The Fab elbow bends in the two crystal forms differ by 7 degrees.

Theoretical aspects of studies of high coverage oxidation of the Cu(100) surface using low energy positrons

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Maddox, W. B.; Reed, J. A.

2011-03-01

The study of adsorption of oxygen on transition metal surface is important for the understanding of oxidation, heterogeneous catalysis, and metal corrosion. The structures formed on transition metal surfaces vary from simple adlayers of chemisorbed oxygen to more complex structures which results from diffusion of oxygen into the sub-surface regions. In this work we present the results of an ab-initio investigation of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the Cu(100) missing row reconstructed surface under conditions of high oxygen coverage. Calculations are performed for various surface and subsurface oxygen coverages ranging from 0.50 to 1.50 monolayers. Calculations are also performed for the on-surface adsorption of oxygen on the unreconstructed Cu(001) surface for coverages up to one monolayer to use for comparison. Estimates of the positron binding energy, positron work function, and annihilation characteristics reveal their sensitivity to atomic structure of the topmost layers of the surface and charge transfer. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy.

Effect of lattice-gas atoms on the adsorption behaviour of thioether molecules.

PubMed

Pan, Yi; Yang, Bing; Hulot, Catherine; Blechert, Siegfried; Nilius, Niklas; Freund, Hans-Joachim

2012-08-21

Using STM topographic imaging and spectroscopy, we have investigated the adsorption of two thioether molecules, 1,2-bis(phenylthio)benzene and (bis(3-phenylthio)-phenyl)sulfane, on noble and transition metal surfaces. The two substrates show nearly antipodal behaviour. Whereas complexes with one or two protruding centres are observed on Au(111), only flat and uniform ad-structures are found on NiAl(110). The difference is ascribed to the possibility of the thioethers to form metal-organic complexes by coordinating lattice-gas atoms on the Au(111), while only the pristine molecules adsorb on the alloy surface. The metal coordination in the first case is driven by the formation of strong Au-S bonds and enables the formation of characteristic monomer, dimer and chain-like structures of the thioethers, using the Au atoms as linkers. A similar mechanism is not available on the NiAl, because no lattice gas develops at this surface at room temperature. Our work demonstrates how surface properties, i.e. the availability of mobile ad-species, determine the interaction of organic molecules with metallic substrates.

Structural and Functional Analysis of the Interaction Between the Nucleoporin Nup98 and the mRNA Export Facto Rae1

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

Y Ren; H Seo; G Blobel

The export of mRNAs is a multistep process, involving the packaging of mRNAs into messenger ribonucleoprotein particles (mRNPs), their transport through nuclear pore complexes, and mRNP remodeling events prior to translation. Ribonucleic acid export 1 (Rae1) and Nup98 are evolutionarily conserved mRNA export factors that are targeted by the vesicular stomatitis virus matrix protein to inhibit host cell nuclear export. Here, we present the crystal structure of human Rae1 in complex with the Gle2-binding sequence (GLEBS) of Nup98 at 1.65 {angstrom} resolution. Rae1 forms a seven-bladed {beta}-propeller with several extensive surface loops. The Nup98 GLEBS motif forms an {approx}50-{angstrom}-long hairpinmore » that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the entire top face of the Rae1 {beta}-propeller. The C-terminal arm of the GLEBS hairpin is necessary and sufficient for Rae1 binding, and we identify a tandem glutamate element in this arm as critical for complex formation. The Rae1 {center_dot} Nup98{sup GLEBS} surface features an additional conserved patch with a positive electrostatic potential, and we demonstrate that the complex possesses single-stranded RNA-binding capability. Together, these data suggest that the Rae1 {center_dot} Nup98 complex directly binds to the mRNP at several stages of the mRNA export pathway.« less

A hybrid 3D SEM reconstruction method optimized for complex geologic material surfaces.

PubMed

Yan, Shang; Adegbule, Aderonke; Kibbey, Tohren C G

2017-08-01

Reconstruction methods are widely used to extract three-dimensional information from scanning electron microscope (SEM) images. This paper presents a new hybrid reconstruction method that combines stereoscopic reconstruction with shape-from-shading calculations to generate highly-detailed elevation maps from SEM image pairs. The method makes use of an imaged glass sphere to determine the quantitative relationship between observed intensity and angles between the beam and surface normal, and the detector and surface normal. Two specific equations are derived to make use of image intensity information in creating the final elevation map. The equations are used together, one making use of intensities in the two images, the other making use of intensities within a single image. The method is specifically designed for SEM images captured with a single secondary electron detector, and is optimized to capture maximum detail from complex natural surfaces. The method is illustrated with a complex structured abrasive material, and a rough natural sand grain. Results show that the method is capable of capturing details such as angular surface features, varying surface roughness, and surface striations. Copyright © 2017 Elsevier Ltd. All rights reserved.

A time-efficient algorithm for implementing the Catmull-Clark subdivision method

NASA Astrophysics Data System (ADS)

Ioannou, G.; Savva, A.; Stylianou, V.

2015-10-01

Splines are the most popular methods in Figure Modeling and CAGD (Computer Aided Geometric Design) in generating smooth surfaces from a number of control points. The control points define the shape of a figure and splines calculate the required number of points which when displayed on a computer screen the result is a smooth surface. However, spline methods are based on a rectangular topological structure of points, i.e., a two-dimensional table of vertices, and thus cannot generate complex figures, such as the human and animal bodies that their complex structure does not allow them to be defined by a regular rectangular grid. On the other hand surface subdivision methods, which are derived by splines, generate surfaces which are defined by an arbitrary topology of control points. This is the reason that during the last fifteen years subdivision methods have taken the lead over regular spline methods in all areas of modeling in both industry and research. The cost of executing computer software developed to read control points and calculate the surface is run-time, due to the fact that the surface-structure required for handling arbitrary topological grids is very complicate. There are many software programs that have been developed related to the implementation of subdivision surfaces however, not many algorithms are documented in the literature, to support developers for writing efficient code. This paper aims to assist programmers by presenting a time-efficient algorithm for implementing subdivision splines. The Catmull-Clark which is the most popular of the subdivision methods has been employed to illustrate the algorithm.

Reflections concerning triply-periodic minimal surfaces.

PubMed

Schoen, Alan H

2012-10-06

In recent decades, there has been an explosion in the number and variety of embedded triply-periodic minimal surfaces (TPMS) identified by mathematicians and materials scientists. Only the rare examples of low genus, however, are commonly invoked as shape templates in scientific applications. Exact analytic solutions are now known for many of the low genus examples. The more complex surfaces are readily defined with numerical tools such as Surface Evolver software or the Landau-Ginzburg model. Even though table-top versions of several TPMS have been placed within easy reach by rapid prototyping methods, the inherent complexity of many of these surfaces makes it challenging to grasp their structure. The problem of distinguishing TPMS, which is now acute because of the proliferation of examples, has been addressed by Lord & Mackay (Lord & Mackay 2003 Curr. Sci. 85, 346-362).

Reflections concerning triply-periodic minimal surfaces

PubMed Central

Schoen, Alan H.

2012-01-01

In recent decades, there has been an explosion in the number and variety of embedded triply-periodic minimal surfaces (TPMS) identified by mathematicians and materials scientists. Only the rare examples of low genus, however, are commonly invoked as shape templates in scientific applications. Exact analytic solutions are now known for many of the low genus examples. The more complex surfaces are readily defined with numerical tools such as Surface Evolver software or the Landau–Ginzburg model. Even though table-top versions of several TPMS have been placed within easy reach by rapid prototyping methods, the inherent complexity of many of these surfaces makes it challenging to grasp their structure. The problem of distinguishing TPMS, which is now acute because of the proliferation of examples, has been addressed by Lord & Mackay (Lord & Mackay 2003 Curr. Sci. 85, 346–362). PMID:24098851

Kinetics of Structural Changes on GaSb(001) Singular and Vicinal Surfaces During the UHV Annealing

NASA Astrophysics Data System (ADS)

Vasev, A. V.; Putyato, M. A.; Preobrazhenskii, V. V.; Bakarov, A. K.; Toropov, A. I.

2018-05-01

The dynamics of processes of antimony desorption was investigated on the singular and vicinal GaSb(001) surface by RHEED method. The role of the terraces edges was determined during antimony evaporation in Langmuir desorption mode. It is shown that the structural transition (2x5) -> (1x3) is a complex of two transitions - order -> disorder and disorder -> order. The influence of the degree of surface miscut from the singular face on the dimension of the transition (2x5) -> DO was studied. The activation energies of structural transitions ex(2x5) -> (2x5), (2x5) -> DO and DO -> (1x3) on singular and vicinal faces GaSb(001) were determined.

COMPUTER SIMULATIONS OF LUNG AIRWAY STRUCTURES USING DATA-DRIVEN SURFACE MODELING TECHNIQUES

EPA Science Inventory

ABSTRACT

Knowledge of human lung morphology is a subject critical to many areas of medicine. The visualization of lung structures naturally lends itself to computer graphics modeling due to the large number of airways involved and the complexities of the branching systems...

HYDRAULIC REDISTRIBUTION OF SOIL WATER BY ROOTS IN FORESTS OF THE PACIFIC NORTHWEST

EPA Science Inventory

One aspect of structural complexity of forest canopies is the root system structure belowground, which influences patterns of soil water utilization by trees. Deeply rooted trees and other plants can hydraulically lift water via their roots from several m below the soil surface ...

Reticulate Structures Reveal the Significance of Cell Motility in the Morphogenesis of Complex Microbial Structures in Pavilion Lake, British Columbia

NASA Astrophysics Data System (ADS)

Shepard, R.

2008-12-01

Microbial communities are architects of incredibly complex and diverse morphological structures. Each morphology is a snapshot that reflects the complex interactions within the microbial community and between the community and its environment. Characterizing morphology as an emergent property of microbial communities is thus relevant to understanding the evolution of multicellularity and complexity in developmental systems, to the identification of biosignatures, and to furthering our understanding of modern and ancient microbial ecology. Recently discovered cyanobacterial mats in Pavilion Lake, British Columbia construct unusual complex architecture on the scale of decimeters that incorporates significant void space. Fundamental mesoscale morphological elements include terraces, arches, bridges, depressions, domes, and pillars. The mats themselves also exhibit several microscale morphologies, with reticulate structures being the dominant example. The reticulate structures exhibit a diverse spectrum of morphologies with endmembers characterized by either angular or curvilinear ridges. In laboratory studies, aggregation into reticulate structures occurs as a result of the random gliding and colliding among motile cyanobacterial filaments. Likewise, when Pavilion reticulate mats were sampled and brought to the surface, cyanobacteria invariably migrated out of the mat onto surrounding surfaces. Filaments were observed to move rapidly in clumps, preferentially following paths of previous filaments. The migrating filaments organized into new angular and ropey reticulate biofilms within hours of sampling, demonstrating that cell motility is responsible for the reticulate patterns. Because the morphogenesis of reticulate structures can be linked to motility behaviors of filamentous cyanobacteria, the Willow Point mats provide a unique natural laboratory in which to elucidate the connections between a specific microbial behavior and the construction of complex microbial community morphology. To this end, we identified and characterized fundamental building blocks of the mesoscale morphologies, including bridges, anchors, and curved edges. These morphological building blocks were compared with the suite of motility behaviors and patterns observed in reticulate morphogenesis. Results of this comparison suggest that cyanobacterial motility plays a significant and often dominant role in the morphogenesis of the entire suite of morphologies observed in the microbial mats of Pavilion Lake.

Laser surface melting of 10 wt% Mo alloyed hardfacing Stellite 12 plasma transferred arc deposits: Structural evolution and high temperature wear performance

NASA Astrophysics Data System (ADS)

Dilawary, Shaikh Asad Ali; Motallebzadeh, Amir; Afzal, Muhammad; Atar, Erdem; Cimenoglu, Huseyin

2018-05-01

Laser surface melting (LSM) process has been applied on the plasma transferred arc (PTA) deposited Stellite 12 and 10 wt% Mo alloyed Stellite 12 in this study. Following the LSM process, structural and mechanical property comparison of the LSM'ed surfaces has been made. Hardness of the LSM'ed surfaces was measured as 549 HV and 623 HV for the Stellite 12 and Stellite 12 + 10 wt% Mo deposits, respectively. Despite their different hardness and structural features, the LSM'ed surfaces exhibited similar tribological performance at room temperature (RT), where fatigue wear mechanism operates. However, the wear at 500 °C promotes tribo-oxide layer formation whose composition depended on the alloying with Mo. Thus, addition of 10 wt% Mo into Stellite 12 PTA deposit has remarkably enhanced the high temperature wear performance of the LSM'ed surface as a result of participation of complex oxide (CoMoO4) in tribo-oxide layer.

From Laser Scanning to Finite Element Analysis of Complex Buildings by Using a Semi-Automatic Procedure.

PubMed

Castellazzi, Giovanni; D'Altri, Antonio Maria; Bitelli, Gabriele; Selvaggi, Ilenia; Lambertini, Alessandro

2015-07-28

In this paper, a new semi-automatic procedure to transform three-dimensional point clouds of complex objects to three-dimensional finite element models is presented and validated. The procedure conceives of the point cloud as a stacking of point sections. The complexity of the clouds is arbitrary, since the procedure is designed for terrestrial laser scanner surveys applied to buildings with irregular geometry, such as historical buildings. The procedure aims at solving the problems connected to the generation of finite element models of these complex structures by constructing a fine discretized geometry with a reduced amount of time and ready to be used with structural analysis. If the starting clouds represent the inner and outer surfaces of the structure, the resulting finite element model will accurately capture the whole three-dimensional structure, producing a complex solid made by voxel elements. A comparison analysis with a CAD-based model is carried out on a historical building damaged by a seismic event. The results indicate that the proposed procedure is effective and obtains comparable models in a shorter time, with an increased level of automation.

Using AFM to probe the complexation of DNA with anionic lipids mediated by Ca(2+): the role of surface pressure.

PubMed

Luque-Caballero, Germán; Martín-Molina, Alberto; Sánchez-Treviño, Alda Yadira; Rodríguez-Valverde, Miguel A; Cabrerizo-Vílchez, Miguel A; Maldonado-Valderrama, Julia

2014-04-28

Complexation of DNA with lipids is currently being developed as an alternative to classical vectors based on viruses. Most of the research to date focuses on cationic lipids owing to their spontaneous complexation with DNA. Nonetheless, recent investigations have revealed that cationic lipids induce a large number of adverse effects on DNA delivery. Precisely, the lower cytotoxicity of anionic lipids accounts for their use as a promising alternative. However, the complexation of DNA with anionic lipids (mediated by cations) is still in early stages and is not yet well understood. In order to explore the molecular mechanisms underlying the complexation of anionic lipids and DNA we proposed a combined methodology based on the surface pressure-area isotherms, Gibbs elasticity and Atomic Force Microscopy (AFM). These techniques allow elucidation of the role of the surface pressure in the complexation and visualization of the interfacial aggregates for the first time. We demonstrate that the DNA complexes with negatively charged model monolayers (DPPC/DPPS 4 : 1) only in the presence of Ca(2+), but is expelled at very high surface pressures. Also, according to the Gibbs elasticity plot, the complexation of lipids and DNA implies a whole fluidisation of the monolayer and a completely different phase transition map in the presence of DNA and Ca(2+). AFM imaging allows identification for the first time of specific morphologies associated with different packing densities. At low surface coverage, a branched net like structure is observed whereas at high surface pressure fibers formed of interfacial aggregates appear. In summary, Ca(2+) mediates the interaction between DNA and negatively charged lipids and also the conformation of the ternary system depends on the surface pressure. Such observations are important new generic features of the interaction between DNA and anionic lipids.

Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity

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

Gupta,Y.; Nair, D.; Wharton, R.

2008-01-01

Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycBreverse and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, inmore » effect, acting as a 'spacer.' The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.« less

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

PubMed Central

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-01-01

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root mean square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases. PMID:22417139

Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2012-06-14

A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.

Surface modification by electrolytic plasma processing for high Nb-TiAl alloys

NASA Astrophysics Data System (ADS)

Gui, Wanyuan; Hao, Guojian; Liang, Yongfeng; Li, Feng; Liu, Xiao; Lin, Junpin

2016-12-01

Metal surface modification by electrolytic plasma processing (EPP) is an innovative treatment widely commonly applied to material processing and pretreatment process of coating and galvanization. EPP involves complex processes and a great deal of parameters, such as preset voltage, current, solution temperature and processing time. Several characterization methods are presented in this paper for evaluating the micro-structure surfaces of Ti45Al8Nb alloys: SEM, EDS, XRD and 3D topography. The results showed that the oxide scale and other contaminants on the surface of Ti45Al8Nb alloys can be effectively removed via EPP. The typical micro-crater structure of the surface of Ti45Al8Nb alloys were observed by 3D topography after EPP to find that the mean diameter of the surface structure and roughness value can be effectively controlled by altering the processing parameters. The mechanical properties of the surface according to nanomechanical probe testing exhibited slight decrease in microhardness and elastic modulus after EPP, but a dramatic increase in surface roughness, which is beneficial for further processing or coating.

3D Numerical simulation of bed morphological responses to complex in-streamstructures

NASA Astrophysics Data System (ADS)

Xu, Y.; Liu, X.

2017-12-01

In-stream structures are widely used in stream restoration for both hydraulic and ecologicalpurposes. The geometries of the structures are usually designed to be extremely complex andirregular, so as to provide nature-like physical habitat. The aim of this study is to develop anumerical model to accurately predict the bed-load transport and the morphological changescaused by the complex in-stream structures. This model is developed in the platform ofOpenFOAM. In the hydrodynamics part, it utilizes different turbulence models to capture thedetailed turbulence information near the in-stream structures. The technique of immersedboundary method (IBM) is efficiently implemented in the model to describe the movable bendand the rigid solid body of in-stream structures. With IBM, the difficulty of mesh generation onthe complex geometry is greatly alleviated, and the bed surface deformation is able to becoupled in to flow system. This morphodynamics model is firstly validated by simple structures,such as the morphology of the scour in log-vane structure. Then it is applied in a more complexstructure, engineered log jams (ELJ), which consists of multiple logs piled together. Thenumerical results including turbulence flow information and bed morphological responses areevaluated against the experimental measurement within the exact same flow condition.

Crystal structures, DFT calculations, and Hirshfeld surface analyses of two new copper(II) and nickel(II) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

NASA Astrophysics Data System (ADS)

Seifikar Ghomi, Leila; Behzad, Mahdi; Tarahhomi, Atekeh; Arab, Ali

2017-12-01

Two new Ni(II) and Cu(II) complexes of a tetradentate Schiff base ligand (1 and 2, respectively), derived from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-6-methoxy benzaldehyde, were synthesized and characterized by IR, UV-Vis, 1H NMR spectroscopy, and X-Ray crystallography. The central metal ions in both complexes are coordinated via the N2O2 coordination sphere of the ligand with square-planar geometry. DFT results revealed that the Msbnd N and Msbnd O interactions (M = Ni, Cu) are weaker than the typical covalent single bond indicating that ionic and electrostatic interactions are dominated in Msbnd N and Msbnd O bonds. Hirshfeld surface (HS) analyses of the studied structures 1 and 2 have been performed. The study using 3D HSs and 2D fingerprint plots (FPs) highlighted the dominant contacts H⋯H, C⋯H/H⋯C and O⋯H/H⋯O in both structures, and H⋯Cl in 2. The molecular assemblies held by C⋯O/O⋯C (in 1) and C⋯C (in 1 and 2) type dipole-dipole interactions are also found in the crystal packing contributing towards stability. The significant contributions arising from the mentioned interactions in crystal packing are also revealed from the Hirshfeld surface FPs showing a major contribution to total HS area for the H⋯H contacts for both structures.

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Role of an Oxidant Mixture as Surface Modifier of Porous Silicon Microstructures Evaluated by Spectroscopic Ellipsometry

PubMed Central

Montiel-González, Zeuz; Escobar, Salvador; Nava, Rocío; del Río, J. Antonio; Tagüeña-Martínez, Julia

2016-01-01

Current research on porous silicon includes the construction of complex structures with luminescent and/or photonic properties. However, their preparation with both characteristics is still challenging. Recently, our group reported a possible method to achieve that by adding an oxidant mixture to the electrolyte used to produce porous silicon. This mixture can chemically modify their microstructure by changing the thickness and surface passivation of the pore walls. In this work, we prepared a series of samples (with and without oxidant mixture) and we evaluated the structural differences through their scanning electron micrographs and their optical properties determined by spectroscopic ellipsometry. The results showed that ellipsometry is sensitive to slight variations in the porous silicon structure, caused by changes in their preparation. The fitting process, based on models constructed from the features observed in the micrographs, allowed us to see that the mayor effect of the oxidant mixture is on samples of high porosity, where the surface oxidation strongly contributes to the skeleton thinning during the electrochemical etching. This suggests the existence of a porosity threshold for the action of the oxidant mixture. These results could have a significant impact on the design of complex porous silicon structures for different optoelectronic applications. PMID:27097767

Role of an Oxidant Mixture as Surface Modifier of Porous Silicon Microstructures Evaluated by Spectroscopic Ellipsometry.

PubMed

Montiel-González, Zeuz; Escobar, Salvador; Nava, Rocío; del Río, J Antonio; Tagüeña-Martínez, Julia

2016-04-21

Current research on porous silicon includes the construction of complex structures with luminescent and/or photonic properties. However, their preparation with both characteristics is still challenging. Recently, our group reported a possible method to achieve that by adding an oxidant mixture to the electrolyte used to produce porous silicon. This mixture can chemically modify their microstructure by changing the thickness and surface passivation of the pore walls. In this work, we prepared a series of samples (with and without oxidant mixture) and we evaluated the structural differences through their scanning electron micrographs and their optical properties determined by spectroscopic ellipsometry. The results showed that ellipsometry is sensitive to slight variations in the porous silicon structure, caused by changes in their preparation. The fitting process, based on models constructed from the features observed in the micrographs, allowed us to see that the mayor effect of the oxidant mixture is on samples of high porosity, where the surface oxidation strongly contributes to the skeleton thinning during the electrochemical etching. This suggests the existence of a porosity threshold for the action of the oxidant mixture. These results could have a significant impact on the design of complex porous silicon structures for different optoelectronic applications.

Sample entropy and regularity dimension in complexity analysis of cortical surface structure in early Alzheimer's disease and aging.

PubMed

Chen, Ying; Pham, Tuan D

2013-05-15

We apply for the first time the sample entropy (SampEn) and regularity dimension model for measuring signal complexity to quantify the structural complexity of the brain on MRI. The concept of the regularity dimension is based on the theory of chaos for studying nonlinear dynamical systems, where power laws and entropy measure are adopted to develop the regularity dimension for modeling a mathematical relationship between the frequencies with which information about signal regularity changes in various scales. The sample entropy and regularity dimension of MRI-based brain structural complexity are computed for early Alzheimer's disease (AD) elder adults and age and gender-matched non-demented controls, as well as for a wide range of ages from young people to elder adults. A significantly higher global cortical structure complexity is detected in AD individuals (p<0.001). The increase of SampEn and the regularity dimension are also found to be accompanied with aging which might indicate an age-related exacerbation of cortical structural irregularity. The provided model can be potentially used as an imaging bio-marker for early prediction of AD and age-related cognitive decline. Copyright © 2013 Elsevier B.V. All rights reserved.

P-polarized reflectance spectroscopy: A high sensitive real-time monitoring technique to study surface kinetics under steady state epitaxial deposition conditions

NASA Technical Reports Server (NTRS)

Dietz, Nikolaus; Bachmann, Klaus J.

1995-01-01

This paper describes the results of real-time optical monitoring of epitaxial growth processes by p-polarized reflectance spectroscopy (PRS) using a single wavelength application under pulsed chemical beam epitaxy (PCBE) condition. The high surface sensitivity of PRS allows the monitoring of submonolayer precursors coverage on the surface as shown for GaP homoepitaxy and GaP on Si heteroepitaxy as examples. In the case of heteroepitaxy, the growth rate and optical properties are revealed by PRS using interference oscillations as they occur during growth. Super-imposed on these interference oscillations, the PRS signal exhibits a fine structure caused by the periodic alteration of the surface chemistry by the pulsed supply of chemical precursors. This fine structure is modeled under conditions where the surface chemistry cycles between phosphorus supersaturated and phosphorus depleted surfaces. The mathematical model describes the fine structure using a surface layer that increases during the tertiarybutyl phosphine (TBP) supply and decreases during and after the triethylgallium (TEG) pulse, which increases the growing GaP film thickness. The imaginary part of the dielectric function of the surface layer is revealed from the turning points in the fine structure, where the optical response to the first precursor pulse in the cycle sequence changes sign. The amplitude of the fine structure is determined by the surface layer thickness and the complex dielectric functions for the surface layer with the underlying bulk film. Surface kinetic data can be obtained by analyzing the rise and decay transients of the fine structure.

Dissolution of Fe(III) (hydr) oxides by metal-EDTA complexes

NASA Astrophysics Data System (ADS)

Ngwack, Bernd; Sigg, Laura

1997-03-01

The dissolution of Fe(III)(hydr)oxides (goethite and hydrous ferric oxide) by metal-EDTA complexes occurs by ligand-promoted dissolution. The process is initiated by the adsorption of metal-EDTA complexes to the surface and is followed by the dissociation of the complex at the surface and the release of Fe(III)EDTA into solution. The dissolution rate is decreased to a great extent if EDTA is complexed by metals in comparison to the uncomplexed EDTA. The rate decreases in the order EDTA CaEDTA ≫ PbEDTA > ZnEDTA > CuEDTA > Co(II)EDTA > NiEDTA. Two different rate-limiting steps determine the dissolution process: (1) detachment of Fe(III) from the oxide-structure and (2) dissociation of the metal-EDTA complexes. In the case of goethite, step 1 is slower than step 2 and the dissolution rates by various metals are similar. In the case of hydrous ferric oxide, step 2 is rate-limiting and the effect of the complexed metal is very pronounced.

Role of annealing on the structural and optical properties of nanostructured diaceto bis-benzimidazole Mn(II) complex thin films

NASA Astrophysics Data System (ADS)

Praveen, P. A.; Babu, R. Ramesh; Ramamurthi, K.

2017-02-01

A coordination complex, manganese incorporated benzimidazole, thin films were prepared by chemical bath deposition method. Structural characterization of the deposited films, carried out by Fourier transform infrared spectroscopy, Raman and electron paramagnetic resonance spectral analyses, reveals the distorted tetrahedral environment of the metal ion with bis-benzimidazole ligand. Further the molecular composition of the deposited metal complex was estimated by energy-dispersive X-ray spectroscopy. The prepared thin films were thermally treated to study the effect of annealing temperature on the surface morphology and the results showed that the surface homogeneity of the films increased for thermally treated films up to 150 °C. But distortion and voids were observed for the films annealed at 200 °C. The Raman analysis reveals the molecular hydrogen bond distortion which leads to the evaporation of the metal complex from the thin film surface with respect to annealing temperature. The linear and nonlinear optical properties of the as prepared and annealed films were studied using ultraviolet-visible transmittance spectroscopy, second harmonic generation and Z-scan analyses. Films annealed at 150 °C show a better linear transmittance in the visible region and larger SHG efficiency and third order nonlinear susceptibility when compared with the other samples. Further, the film annealed at 150 °C was subjected to optical switching analysis and demonstrated to have an inverted switching behavior.

Effect of humic acid on nickel(II) sorption to Ca-montmorillonite by batch and EXAFS techniques study.

PubMed

Hu, Jun; Tan, Xiaoli; Ren, Xuemei; Wang, Xiangke

2012-09-21

The influence of humic acid (HA) on Ni(II) sorption to Ca-montmorillonite was examined by using a combination of batch sorption experiments and extended X-ray absorption fine structure (EXAFS) spectroscopy technique. The sorption of Ni(II) on HA-montmorillonite hybrids is strongly dependent on pH and temperature. At low pH, the sorption of Ni(II) is mainly dominated by Ni-HA-montmorillonite and outer-sphere surface complexation. The EXAFS results indicate that the first coordination shell of Ni(II) consists of ∼6 O atoms at the interatomic distances of ∼2.04 Å in an octahedral structure. At high pH, binary Ni-montmorillonite surface complexation is the dominant sorption mechanism. EXAFS analysis indicates the formation of mononuclear complexes located at the edges of Ca-montmorillonite platelets at pH 7.5, while a Ni-Al layered double hydroxide (LDH) phase at the Ca-montmorillonite surface formed with pH 8.5. At pH 10.0, the dissolved HA-Ni(II) complexation inhibits the precipitation of Ni hydroxide, and Ni-Al LDH phase forms. The rise of temperature increases the sorption capacity of Ni(II), and promotes Ni-Al LDH phase formation and the growth of crystallites. The results are important to evaluate the physicochemical behavior of Ni(II) in the natural environment.

Gaze shifts and fixations dominate gaze behavior of walking cats

PubMed Central

Rivers, Trevor J.; Sirota, Mikhail G.; Guttentag, Andrew I.; Ogorodnikov, Dmitri A.; Shah, Neet A.; Beloozerova, Irina N.

2014-01-01

Vision is important for locomotion in complex environments. How it is used to guide stepping is not well understood. We used an eye search coil technique combined with an active marker-based head recording system to characterize the gaze patterns of cats walking over terrains of different complexity: (1) on a flat surface in the dark when no visual information was available, (2) on the flat surface in light when visual information was available but not required, (3) along the highly structured but regular and familiar surface of a horizontal ladder, a task for which visual guidance of stepping was required, and (4) along a pathway cluttered with many small stones, an irregularly structured surface that was new each day. Three cats walked in a 2.5 m corridor, and 958 passages were analyzed. Gaze activity during the time when the gaze was directed at the walking surface was subdivided into four behaviors based on speed of gaze movement along the surface: gaze shift (fast movement), gaze fixation (no movement), constant gaze (movement at the body’s speed), and slow gaze (the remainder). We found that gaze shifts and fixations dominated the cats’ gaze behavior during all locomotor tasks, jointly occupying 62–84% of the time when the gaze was directed at the surface. As visual complexity of the surface and demand on visual guidance of stepping increased, cats spent more time looking at the surface, looked closer to them, and switched between gaze behaviors more often. During both visually guided locomotor tasks, gaze behaviors predominantly followed a repeated cycle of forward gaze shift followed by fixation. We call this behavior “gaze stepping”. Each gaze shift took gaze to a site approximately 75–80 cm in front of the cat, which the cat reached in 0.7–1.2 s and 1.1–1.6 strides. Constant gaze occupied only 5–21% of the time cats spent looking at the walking surface. PMID:24973656

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

NASA Astrophysics Data System (ADS)

D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

2015-03-01

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

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

Toczydlowska, Diana; Kedra-Krolik, Karolina; Nejbert, Krzysztof

The role of surface electrostatics on the reductive dissolution of iron (III) oxides is poorly understood, despite its importance in controlling the amount of mobilized iron. We report the potentiometric titration of the a; y -Fe2O3 oxides exposed to reductants and complexing ligands (Fe(II), ascorbate, oxalate, malonate). We monitored in situ surface and potentials, the ratio of mobilized ferric to ferrous ions, and periodically analyzed nanoparticle crystal structure using X-ray diffraction. We found that addition of Fe2+ ions produces a response consistent with the iron solubilityactivity curve, whereas the presence of ascorbate significantly decreases the amount of mobilized Fe(III) duemore » to reduction to Fe(II). In addition, XRD analysis proved that y-Fe2O3 particles remain structurally unchanged along the titration pathway despite iron cycling between aqueous and solid reservoirs. Our studies, suggest that the surface redoxactivity of iron oxides is primarily governed by the balance between Fe(III) and Fe(II) ions in aqueous phase, which may be easily altered by complexing and reducing agents.« less

Stiffness Matrix of Thin-Walled Open Bar Subject to Bending, Bending Torsion and Shift of Cross Section Middle Surface

NASA Astrophysics Data System (ADS)

Panasenko, N. N.; Sinelschikov, A. V.

2017-11-01

One of the main stages in the analysis of complex 3D structures and engineering constructions made of thin-walled open bars using FEM is a stiffness matrix developing. Taking into account middle surface shear deformation caused by the work of tangential stresses in the formula to calculate a potential energy of thin-walled open bars, the authors obtain an important correction at calculation of the bar deformation and fundamental frequencies. The results of the analysis of the free end buckling of a cantilever H-bar under plane bending differ from exact solution by 0.53%. In the course of comparison of the obtained results with the cantilever bar buckling regardless the middle surface shear deformation, an increase made 16.6%. The stiffness matrix of a thin-walled open bar developed in the present work can be integrated into any software suite using FEM for the analysis of complex 3-D structures and engineering constructions with n-freedoms.

Remote camera monitoring and a mark – recapture study of the wandering salamander in a redwood forest canopy

Treesearch

Jim Campbell-Spickler; Stephen C. Sillett

2017-01-01

Crowns of old redwoods (Sequoia sempervirens (D. Don) Endl.) are teaming with life. Storm damage followed by recovery via trunk reiteration increases the structural complexity of redwood crowns over time. Bark and wood surfaces within complex redwood crowns accumulate debris and become covered with epiphytes. Arboreal soils develop beneath...

The molecular shape and the field similarities as criteria to interpret SAR studies for fragment-based design of platinum(IV) anticancer agents. Correlation of physicochemical properties with cytotoxicity.

PubMed

Lorenzo, Julia; Montaña, Ángel M

2016-09-01

Molecular shape similarity and field similarity have been used to interpret, in a qualitative way, the structure-activity relationships in a selected series of platinum(IV) complexes with anticancer activity. MM and QM calculations have been used to estimate the electron density, electrostatic potential maps, partial charges, dipolar moments and other parameters to correlate the stereo-electronic properties with the differential biological activity of complexes. Extended Electron Distribution (XED) field similarity has been also evaluated for the free 1,4-diamino carrier ligands, in a fragment-based drug design approach, comparing Connolly solvent excluded surface, hydrophobicity field surface, Van der Waals field surface, nucleophilicity field surface, electrophilicity field surface and the extended electron-distribution maxima field points. A consistency has been found when comparing the stereo-electronic properties of the studied series of platinum(IV) complexes and/or the free ligands evaluated and their in vitro anticancer activity. Copyright © 2016 Elsevier Inc. All rights reserved.

Response surface method in geotechnical/structural analysis, phase 1

NASA Astrophysics Data System (ADS)

Wong, F. S.

1981-02-01

In the response surface approach, an approximating function is fit to a long running computer code based on a limited number of code calculations. The approximating function, called the response surface, is then used to replace the code in subsequent repetitive computations required in a statistical analysis. The procedure of the response surface development and feasibility of the method are shown using a sample problem in slop stability which is based on data from centrifuge experiments of model soil slopes and involves five random soil parameters. It is shown that a response surface can be constructed based on as few as four code calculations and that the response surface is computationally extremely efficient compared to the code calculation. Potential applications of this research include probabilistic analysis of dynamic, complex, nonlinear soil/structure systems such as slope stability, liquefaction, and nuclear reactor safety.

Analysis of complex elastic structures by a Rayleigh-Ritz component modes method using Lagrange multipliers. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Klein, L. R.

1974-01-01

The free vibrations of elastic structures of arbitrary complexity were analyzed in terms of their component modes. The method was based upon the use of the normal unconstrained modes of the components in a Rayleigh-Ritz analysis. The continuity conditions were enforced by means of Lagrange Multipliers. Examples of the structures considered are: (1) beams with nonuniform properties; (2) airplane structures with high or low aspect ratio lifting surface components; (3) the oblique wing airplane; and (4) plate structures. The method was also applied to the analysis of modal damping of linear elastic structures. Convergence of the method versus the number of modes per component and/or the number of components is discussed and compared to more conventional approaches, ad-hoc methods, and experimental results.

Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

PubMed Central

Roberts, Victoria A.; Pique, Michael E.; Hsu, Simon; Li, Sheng; Slupphaug, Geir; Rambo, Robert P.; Jamison, Jonathan W.; Liu, Tong; Lee, Jun H.; Tainer, John A.; Ten Eyck, Lynn F.; Woods, Virgil L.

2012-01-01

X-ray crystallography provides excellent structural data on protein–DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein–DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG–DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210–220 and 251–264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG–DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway. PMID:22492624

Secondary electron emission from textured surfaces

NASA Astrophysics Data System (ADS)

Huerta, C. E.; Patino, M. I.; Wirz, R. E.

2018-04-01

In this work, a Monte Carlo model is used to investigate electron induced secondary electron emission for varying effects of complex surfaces by using simple geometric constructs. Geometries used in the model include: vertical fibers for velvet-like surfaces, tapered pillars for carpet-like surfaces, and a cage-like configuration of interlaced horizontal and vertical fibers for nano-structured fuzz. The model accurately captures the secondary electron emission yield dependence on incidence angle. The model shows that unlike other structured surfaces previously studied, tungsten fuzz exhibits secondary electron emission yield that is independent of primary electron incidence angle, due to the prevalence of horizontally-oriented fibers in the fuzz geometry. This is confirmed with new data presented herein of the secondary electron emission yield of tungsten fuzz at incidence angles from 0-60°.

Surface characterization of ZnO/ZnMn{sub 2}O{sub 4} and Cu/Mn{sub 3}O{sub 4} powders obtained by thermal degradation of heterobimetallic complexes

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

Barrault, Joeel, E-mail: joel.barrault@univ-poitiers.fr; Makhankova, Valeriya G., E-mail: leram@univ.kiev.ua; Khavryuchenko, Oleksiy V.

2012-03-15

From the selective transformation of the heterometallic (Zn-Mn or Cu-Mn) carboxylate complexes with 2,2 Prime -bipyridyl by thermal degradation at relatively low (350 Degree-Sign C) temperature, it was possible to get either well defined spinel ZnMn{sub 2}O{sub 4} over zinc oxide or well dispersed copper particles surrounded by a manganese oxide (Mn{sub 3}O{sub 4}) in a core-shell like structure. Morphology of the powder surface was examined by scanning electron microscopy with energy dispersive X-ray microanalysis (SEM/EDX). Surface composition was determined by X-ray photoelectron spectroscopy (XPS). Specific surface of the powders by nitrogen adsorption was found to be 33{+-}0.2 and 9{+-}0.06more » m{sup 2} g{sup -1} for Zn-Mn and Cu-Mn samples, respectively, which is comparable to those of commercial products. - Graphical abstract: From the selective transformation of heterometallic (Zn-Mn or Cu-Mn) carboxylate complexes, it was possible to get either well defined spinel ZnMn{sub 2}O{sub 4} over zinc oxide or well dispersed copper particles surrounded by a manganese oxide (Mn{sub 3}O{sub 4}) in a core-shell like structure. Highlights: Black-Right-Pointing-Pointer Thermal degradation of heterometallic complexes results in fine disperse particles. Black-Right-Pointing-Pointer Core-shell Cu/Mn{sub 3}O{sub 4} particles are obtained. Black-Right-Pointing-Pointer ZnMn{sub 2}O{sub 4} spinel layer covers ZnO particles.« less

A new fabrication technique for complex refractive micro-optical systems

NASA Astrophysics Data System (ADS)

Tormen, Massimo; Carpentiero, Alessandro; Ferrari, Enrico; Cabrini, Stefano; Cojoc, Dan; Di Fabrizio, Enzo

2006-01-01

We present a new method that allows to fabricate structures with tightly controlled three-dimensional profiles in the 10 nm to 100 μm scale range. This consists of a sequence of lithographic steps such as Electron Beam (EB) or Focused Ion Beam (FIB) lithography, alternated with isotropic wet etching processes performed on a quartz substrate. Morphological characterization by SEM and AFM shows that 3D structures with very accurate shape control and nanometer scale surface roughness can be realized. Quartz templates have been employed as complex system of micromirrors after metal coating of the patterned surface or used as stamps in nanoimprint, hot embossing or casting processes to shape complex plastic elements. Compared to other 3D micro and nanostructuring methods, in which a hard material is directly "sculptured" by energetic beams, our technique requires a much less intensive use of expensive lithographic equipments, for comparable volumes of structured material, resulting in dramatic increase of throughput. Refractive micro-optical elements have been fabricated and characterized in transmission and reflection modes with white and monochromatic light. The elements produce a distribution of sharp focal spots and lines in the three dimensional space, opening the route for applications of image reconstruction based on refractive optics.

Influence of structural and surface properties of whey-derived peptides on zinc-chelating capacity, and in vitro gastric stability and bioaccessibility of the zinc-peptide complexes.

PubMed

Udechukwu, M Chinonye; Downey, Brianna; Udenigwe, Chibuike C

2018-02-01

Gastrointestinal stability of zinc-peptide complexes is essential for zinc delivery. As peptide surface charge can influence their metal complex stability, we evaluated the zinc-chelating capacity and stability of zinc complexes of whey protein hydrolysates (WPH), produced with Everlase (WPH-Ever; ζ-potential, -39mV) and papain (WPH-Pap; ζ-potential, -7mV), during simulated digestion. WPH-Ever had lower amount of zinc-binding amino acids but showed higher zinc-chelating capacity than WPH-Pap. This is attributable to the highly anionic surface charge of WPH-Ever for electrostatic interaction with zinc. Release of zinc during peptic digestion was lower for WPH-Ever-zinc, and over 50% of zinc remained bound in both peptide complexes after peptic-pancreatic digestion. Fourier transform infrared spectroscopy suggests the involvement of carboxylate ion, and sidechain carbon-oxygen of aspartate/glutamate and serine/threonine in zinc-peptide complexation. The findings indicate that strong zinc chelation can promote gastric stability and impede intestinal release, for peptides intended for use as dietary zinc carriers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Lithospheric Velocity Structure of the Anatolain plateau-Caucasus-Caspian Regions

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

Gok, R; Mellors, R J; Sandvol, E

Anatolian Plateau-Caucasus-Caspian region is an area of complex structure accompanied by large variations in seismic wave velocities. Despite the complexity of the region little is known about the detailed lithospheric structure. Using data from 29 new broadband seismic stations in the region, a unified velocity structure is developed using teleseismic receiver functions and surface waves. Love and Rayleigh surface waves dispersion curves have been derived from event-based analysis and ambient-noise correlation. We jointly inverted the receiver functions with the surface wave dispersion curves to determine absolute shear wave velocity and important discontinuities such as sedimentary layer, Moho, lithospheric-asthenospheric boundary. Wemore » combined these new station results with Eastern Turkey Seismic Experiment results (29 stations). Caspian Sea and Kura basin underlained by one of the thickest sediments in the world. Therefore, short-period surface waves are observed to be very slow. The strong crustal multiples in receiver functions and the slow velocities in upper crust indicate the presence of thick sedimentary unit (up to 20 km). Crustal thickness varies from 34 to 52 km in the region. The thickest crust is in Lesser Caucasus and the thinnest is in the Arabian Plate. The lithospheric mantle in the Greater Caucasus and the Kura depression is faster than the Anatolian Plateau and Lesser Caucasus. This possibly indicates the presence of cold lithosphere. The lower crust is slowest in the northeastern part of the Anatolian Plateau where Holocene volcanoes are located.« less

Superficial Macromolecular Arrays on the Cell Wall of Spirillum putridiconchylium

PubMed Central

Beveridge, T. J.; Murray, R. G. E.

1974-01-01

Electron microscopy of the cell envelope of Spirillum putridiconchylium, using negatively stained, thin-sectioned, and replicated freeze-etched preparations, showed two superficial wall layers forming a complex macromolecular pattern on the external surface. The outer structured layer was a linear array of particles overlying an inner tetragonal array of larger subunits. They were associated in a very regular fashion, and the complex was bonded to the outer, pitted surface of the lipopolysaccharide tripartite layer of the cell wall. The relationship of the components of the two structured layers was resolved with the aid of optical diffraction, combined with image filtering and reconstruction and linear and rotary integration techniques. The outer structural layer consisted of spherical 1.5-nm units set in double lines determined by the size and arrangement of 6- by 3-nm inner structural layer subunits, which bore one outer structural layer unit on each outer corner. The total effect of this arrangement was a double-ridged linear structure that was evident in surface replicas and negatively stained fragments of the whole wall. The packing of these units was not square but skewed by 2° off the perpendicular so that the “unit array” described by optical diffraction and linear integration appeared to be a deformed tetragon. The verity of the model was checked by using a photographically reduced image to produce an optical diffraction pattern for comparison with that of the actual layers. The correspondence was nearly perfect. Images PMID:4137219

Influence of LaFeO 3 Surface Termination on Water Reactivity

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

Stoerzinger, Kelsey A.; Comes, Ryan; Spurgeon, Steven R.

2017-02-17

The polarity of oxide surfaces can dramatically impact their surface reactivity, in particular with polar molecules such as water. The surface species that result from this interaction change the oxide electronic structure and chemical reactivity in applications such as photoelectrochemistry, but are challenging to probe experimentally with atomic-scale understanding. Here we report a detailed study of the surface chemistry and electronic structure of the perovskite LaFeO3 in humid conditions using ambient pressure X-ray photoelectron spectroscopy. Comparing the two possible terminations of the polar (001)-oriented surface, we find that the LaO surface is more reactive toward water, forming hydroxyl species andmore » adsorbing molecular water at lower relative humidity than its FeO2-terminated counterpart. Our results demonstrate how the termination of a complex oxide can dramatically impact its reactivity, providing insight into the design of catalyst materials.« less

Effects of Surface Structure and of Embedded-Atom Pair Functionals on Adatom Diffusion on FCC Metallic Surfaces

DTIC Science & Technology

1992-11-01

total-energy calculations that this complex mechanism for diffusion can be invoked for surface self-diffusion on the (100) surface ( Kellog and...Woodland Hills, CA 91364 National Science Foundation 3 SRI International ATIN: A.B. Harvey ATIN: G. Smith Washington, DC 20550 D. Crosley D. Golden...Aeronautics and Astronautics ATTN: H. Krier ATfN: J.R. Osborn 144MEB, 1206 W. Green St. Grissom Hall Urbana, IL 61801 West Lafayette, IN 47906 The Johns

Diffusion of MMPs on the Surface of Collagen Fibrils: The Mobile Cell Surface – Collagen Substratum Interface

PubMed Central

Collier, Ivan E.; Legant, Wesley; Marmer, Barry; Lubman, Olga; Saffarian, Saveez; Wakatsuki, Tetsuro; Elson, Elliot; Goldberg, Gregory I.

2011-01-01

Remodeling of the extracellular matrix catalyzed by MMPs is central to morphogenetic phenomena during development and wound healing as well as in numerous pathologic conditions such as fibrosis and cancer. We have previously demonstrated that secreted MMP-2 is tethered to the cell surface and activated by MT1-MMP/TIMP-2-dependent mechanism. The resulting cell-surface collagenolytic complex (MT1-MMP)2/TIMP-2/MMP-2 can initiate (MT1-MMP) and complete (MMP-2) degradation of an underlying collagen fibril. The following question remained: What is the mechanism of substrate recognition involving the two structures of relatively restricted mobility, the cell surface enzymatic complex and a collagen fibril embedded in the ECM? Here we demonstrate that all the components of the complex are capable of processive movement on a surface of the collagen fibril. The mechanism of MT1-MMP movement is a biased diffusion with the bias component dependent on the proteolysis of its substrate, not adenosine triphosphate (ATP) hydrolysis. It is similar to that of the MMP-1 Brownian ratchet we described earlier. In addition, both MMP-2 and MMP-9 as well as their respective complexes with TIMP-1 and -2 are capable of Brownian diffusion on the surface of native collagen fibrils without noticeable dissociation while the dimerization of MMP-9 renders the enzyme immobile. Most instructive is the finding that the inactivation of the enzymatic activity of MT1-MMP has a detectable negative effect on the cell force developed in miniaturized 3D tissue constructs. We propose that the collagenolytic complex (MT1-MMP)2/TIMP-2/MMP-2 represents a Mobile Cell Surface – Collagen Substratum Interface. The biological implications of MT1-MMP acting as a molecular ratchet tethered to the cell surface in complex with MMP-2 suggest a new mechanism for the role of spatially regulated peri-cellular proteolysis in cell-matrix interactions. PMID:21912660

Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

PubMed Central

Chikira, Makoto; Ng, Chew Hee; Palaniandavar, Mallayan

2015-01-01

The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements. PMID:26402668

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

Strickland, Madeleine; Stanley, Ann Marie; Wang, Guangshun

Paralogous enzymes arise from gene duplication events that confer a novel function, although it is unclear how cross-reaction between the original and duplicate protein interaction network is minimized. We investigated HPr:EIsugar and NPr:EINtr, the initial complexes of paralogous phosphorylation cascades involved in sugar import and nitrogen regulation in bacteria, respectively. Although the HPr:EIsugar interaction has been well characterized, involving multiple complexes and transient interactions, the exact nature of the NPr:EINtr complex was unknown. We set out to identify the key features of the interaction by performing binding assays and elucidating the structure of NPr in complex with the phosphorylation domainmore » of EINtr (EINNtr), using a hybrid approach involving X-ray, homology, and sparse nuclear magnetic resonance. We found that the overall fold and active-site structure of the two complexes are conserved in order to maintain productive phosphorylation, however, the interface surface potential differs between the two complexes, which prevents cross-reaction.« less

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Electronic structure of dense Pb overlayers on Si(111) investigated using angle-resolved photoemission

NASA Astrophysics Data System (ADS)

Choi, W. H.; Koh, H.; Rotenberg, E.; Yeom, H. W.

2007-02-01

Dense Pb overlayers on Si(111) are important as the wetting layer for anomalous Pb island growth as well as for their own complex “devil’s-staircase” phases. The electronic structures of dense Pb overlayers on Si(111) were investigated in detail by angle-resolved photoemission. Among the series of ordered phases found recently above one monolayer, the low-coverage 7×3 and the high-coverage 14×3 phases are studied; they are well ordered and form reproducibly in large areas. The band dispersions and Fermi surfaces of the two-dimensional (2D) electronic states of these overlayers are mapped out. A number of metallic surface-state bands are identified for both phases with complex Fermi contours. The basic features of the observed Fermi contours can be explained by overlapping 2D free-electron-like Fermi circles. This analysis reveals that the 2D electrons near the Fermi level of the 7×3 and 14×3 phases are mainly governed by strong 1×1 and 3×3 potentials, respectively. The origins of the 2D electronic states and their apparent Fermi surface shapes are discussed based on recent structure models.

The (FHCl)- molecular anion - Structural aspects, global surface, and vibrational eigenspectrum

NASA Technical Reports Server (NTRS)

Klepeis, Neil E.; East, Allan L. L.; Csaszar, Attila G.; Allen, Wesley D.; Lee, Timothy J.; Schwenke, David W.

1993-01-01

State of the art ab initio electronic structure methods have been used to investigate the (FHCl)- molecular anion. It is proposed that the geometric structure and binding energies of the complex are r(e)(H-F) = 0.963 +/- 0.003 A, R(e)(H-Cl) = 1.925 +/- 0.015 A, and D0(HF + Cl(-)) = 21.8 +/- 0.4 kcal/mol. A Morokuma decomposition of the ion-molecular bonding give the following electrostatic, polarization, exchange repulsion, dispersion, and charge-transfer plus higher-order mixing components of the vibrationless complexation energy: -27.3, -5.2, +18.3, -4.5, and -5.0 kcal/mol, respectively. A couples cluster single and doubles global surface is constructed from 208 and 228 energy points for linear and bent configurations, respectively, these being fit to rms errors of only 3.9 and 9.3/cm, respectively, below 8000/cm. Converged J = 0 and J = 1 variational eigenstates of the (FHCl)- surface to near the HF + Cl(-) dissociation threshold are determined. The fundamental vibrational frequencies are found to be nu1 = 247/cm, nu2 = 876/cm, and nu3 = 2884/cm. The complete vibrational eigenspectrum is analyzed.

Dispersion of single-wall carbon nanotubes with supramolecular Congo red - properties of the complexes and mechanism of the interaction.

PubMed

Jagusiak, Anna; Piekarska, Barbara; Pańczyk, Tomasz; Jemioła-Rzemińska, Małgorzata; Bielańska, Elżbieta; Stopa, Barbara; Zemanek, Grzegorz; Rybarska, Janina; Roterman, Irena; Konieczny, Leszek

2017-01-01

A method of dispersion of single-wall carbon nanotubes (SWNTs) in aqueous media using Congo red (CR) is proposed. Nanotubes covered with CR constitute the high capacity system that provides the possibility of binding and targeted delivery of different drugs, which can intercalate into the supramolecular, ribbon-like CR structure. The study revealed the presence of strong interactions between CR and the surface of SWNTs. The aim of the study was to explain the mechanism of this interaction. The interaction of CR and carbon nanotubes was studied using spectral analysis of the SWNT-CR complex, dynamic light scattering (DLS), differential scanning calorimetry (DSC) and microscopic methods: atomic force microscopy (AFM), transmission (TEM), scanning (SEM) and optical microscopy. The results indicate that the binding of supramolecular CR structures to the surface of the nanotubes is based on the "face to face stacking". CR molecules attached directly to the surface of the nanotubes can bind further, parallel-oriented molecules and form supramolecular and protruding structures. This explains the high CR binding capacity of carbon nanotubes. The presented system - containing SWNTs covered with CR - offers a wide range of biomedical applications.

Co-crystal formation between two organic solids on the surface of Titan

NASA Astrophysics Data System (ADS)

Cable, M. L.; Vu, T. H.; Maynard-Casely, H. E.; Hodyss, R. P.

2017-12-01

Laboratory experiments of Titan molecular materials, informed by modeling, can help us to understand the complex and dynamic surface processes occurring on this moon at cryogenic temperatures. We previously demonstrated that two common organic materials on Titan, ethane and benzene, form a unique and stable co-crystalline structure at Titan surface temperatures. We have now characterized a second co-crystal that is stable on Titan, this time between two solids: acetylene and ammonia. The co-crystal forms within minutes at Titan surface temperature, as evidenced by new Raman spectral features in the lattice vibration and C-H bending regions. In addition, a red shift of the C-H stretching mode suggests that the acetylene-ammonia co-crystal is stabilized by a network of C-H···N interactions. Thermal stability studies indicate that this co-crystal remains intact to >110 K, and experiments with liquid methane and ethane reveal the co-crystal to be resistant to fluvial or pluvial exposure. Non-covalently bound structures such as these co-crystals point to far more complex surface interactions than previously believed on Titan. New physical and mechanical properties (deformation, plasticity, density, etc.), differences in storage of key species (i.e., ethane versus methane), variations in surface transport and new chemical gradients can all result in diverse surface features and chemistries of astrobiological interest.

Structure of nerve growth factor complexed with the shared neurotrophin receptor p75.

PubMed

He, Xiao-Lin; Garcia, K Christopher

2004-05-07

Neurotrophins are secreted growth factors critical for the development and maintenance of the vertebrate nervous system. Neurotrophins activate two types of cell surface receptors, the Trk receptor tyrosine kinases and the shared p75 neurotrophin receptor. We have determined the 2.4 A crystal structure of the prototypic neurotrophin, nerve growth factor (NGF), complexed with the extracellular domain of p75. Surprisingly, the complex is composed of an NGF homodimer asymmetrically bound to a single p75. p75 binds along the homodimeric interface of NGF, which disables NGF's symmetry-related second p75 binding site through an allosteric conformational change. Thus, neurotrophin signaling through p75 may occur by disassembly of p75 dimers and assembly of asymmetric 2:1 neurotrophin/p75 complexes, which could potentially engage a Trk receptor to form a trimolecular signaling complex.

Structure, dynamics and biophysics of the cytoplasmic protein–protein complexes of the bacterial phosphoenolpyruvate: Sugar phosphotransferase system

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

Clore, G. Marius; Venditti, Vincenzo

2013-10-01

The bacterial phosphotransferase system (PTS) couples phosphoryl transfer, via a series of bimolecular protein–protein interactions, to sugar transport across the membrane. The multitude of complexes in the PTS provides a paradigm for studying protein interactions, and for understanding how the same binding surface can specifically recognize a diverse array of targets. Fifteen years of work aimed at solving the solution structures of all soluble protein–protein complexes of the PTS has served as a test bed for developing NMR and integrated hybrid approaches to study larger complexes in solution and to probe transient, spectroscopically invisible states, including encounter complexes. We reviewmore » these approaches, highlighting the problems that can be tackled with these methods, and summarize the current findings on protein interactions.« less

An efficient hybrid technique in RCS predictions of complex targets at high frequencies

NASA Astrophysics Data System (ADS)

Algar, María-Jesús; Lozano, Lorena; Moreno, Javier; González, Iván; Cátedra, Felipe

2017-09-01

Most computer codes in Radar Cross Section (RCS) prediction use Physical Optics (PO) and Physical theory of Diffraction (PTD) combined with Geometrical Optics (GO) and Geometrical Theory of Diffraction (GTD). The latter approaches are computationally cheaper and much more accurate for curved surfaces, but not applicable for the computation of the RCS of all surfaces of a complex object due to the presence of caustic problems in the analysis of concave surfaces or flat surfaces in the far field. The main contribution of this paper is the development of a hybrid method based on a new combination of two asymptotic techniques: GTD and PO, considering the advantages and avoiding the disadvantages of each of them. A very efficient and accurate method to analyze the RCS of complex structures at high frequencies is obtained with the new combination. The proposed new method has been validated comparing RCS results obtained for some simple cases using the proposed approach and RCS using the rigorous technique of Method of Moments (MoM). Some complex cases have been examined at high frequencies contrasting the results with PO. This study shows the accuracy and the efficiency of the hybrid method and its suitability for the computation of the RCS at really large and complex targets at high frequencies.

Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

PubMed

Shu, Qin; Krezel, Andrzej M; Cusumano, Zachary T; Pinkner, Jerome S; Klein, Roger; Hultgren, Scott J; Frieden, Carl

2016-06-28

Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel β-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation.

The effect of mechano-chemical treatment on structural properties of the drawn TiNi-based alloy wire

NASA Astrophysics Data System (ADS)

Anikeev, Sergey; Hodorenko, Valentina; Gunther, Victor; Chekalkin, Timofey; Kang, Ji-hoon; Kang, Seung-baik

2018-01-01

The rapid development of biomedical materials with the advanced functional characteristics is a challenging task because of the growing demands for better material properties in-clinically employed. Modern medical devices that can be implanted into humans have evolved steadily by replacing TiNi-based alloys for titanium and stainless steel. In this study, the effect of the mechano-chemical treatment on structural properties of the matrix and surface layer of the drawn TiNi-based alloy wire was assessed. A range of samples have been prepared using different drawing and etching procedures. It is clear from the results obtained that the fabricated samples show a composite structure comprising the complex matrix and textured oxycarbonitride spitted surface layer. The suggested method of surface treatment is a concept to increase the surface roughness for the enhanced bio-performance and better in vivo integration.

Electromers of the benzene dimer radical cation.

PubMed

Błoch-Mechkour, Anna; Bally, Thomas

2015-04-28

The well-studied benzene dimer radical cation, which is prototypical for this class of species, has been reinvestigated computationally. Thereby it turned out that both the σ-hemibonded and the half-shifted sandwich structures of the benzene dimer cation, which had been independently proposed, represent stationary points on the B2PLYP-D potential energy surfaces. However, these structures belong to distinct electronic states, both of which are associated with potential surfaces that are very flat with regard to rotation of the two benzene rings in an opposite sense relative to each other. The surfaces of these two "electromers" of the benzene dimer cation are separated by only 3-4 kcal mol(-1) and do not intersect along the rotation coordinate, which represents a rather unique electronic structure situation. When moving on either of the two surfaces the title complex is an extremely fluxional species, in spite of its being bound by over 20 kcal mol(-1).

Fabrication and characterization of magnesium and calcium trimesate complexes via ion-exchange and one-pot self-assembly reaction

NASA Astrophysics Data System (ADS)

Ozer, Demet; Oztas, Nursen Altuntas; Köse, Dursun A.; Şahin, Onur

2018-03-01

Using two different synthesis methods, two diversified magnesium and calcium complexes were successfully prepared. When the ion exchange method was used, C9H14MgO11.H2O and C18H30Ca3O24 complexes were obtained. When the one-pot self-assembly reaction was used, C18H34Mg3O26.4H2O and C9H12CaO10 complexes were produced. The structural characterizations were performed by using X-ray diffraction, FT-IR and elemental analyses. Thermal behavior of complexes were also determined via TGA method. The both complexes of magnesium and calcium trimesate have micro and mesoporosity with low porosity because of hydrogen bonds. Then hydrogen storage capacities of complexes were also determined. The differences in synthesis method result in the differences on complexes structure, morphology (shape, particle size and specific surface area) and hydrogen storage capacities.

Utility of charge-transfer complexation for the assessment of macrocyclic polyethers: Spectroscopic, thermal and surface morphology characteristics of two highly crown ethers complexed with acido acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Adam, Abdel Majid A.; Saad, Hosam A.

2015-04-01

The study of the complexing ability of macrocyclic compounds to organic and inorganic substances is of great interest. The aim of this work is to provide basic data that can be used to the assessment of macrocyclic crown ethers quantitatively based on charge-transfer (CT) complexation. This goal was achieved by preparing CT complexes of two interesting mixed nitrogen-oxygen crown ethers with acido acceptors (chloranilic and picric acid), which were fully structurally characterized. The crown ethers are 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane (HDHC) and 1,4,10-trioxa-7,13-diaza-cyclopentadecane (TDPD). The obtained complexes were structurally characterized via elemental analysis, IR, Raman, 1H NMR, and UV-visible spectroscopy. Thermal properties of these complexes were also studied, and their kinetic thermodynamic parameters were calculated. Furthermore, the microstructure properties of these complexes have also been investigated using X-ray diffraction (XRD) and scanning electron microscope (SEM).

Universal moduli spaces of Riemann surfaces

NASA Astrophysics Data System (ADS)

Ji, Lizhen; Jost, Jürgen

2017-04-01

We construct a moduli space for Riemann surfaces that is universal in the sense that it represents compact Riemann surfaces of any finite genus. This moduli space is a connected complex subspace of an infinite dimensional complex space, and is stratified according to genus such that each stratum has a compact closure, and it carries a metric and a measure that induce a Riemannian metric and a finite volume measure on each stratum. Applications to the Plateau-Douglas problem for minimal surfaces of varying genus and to the partition function of Bosonic string theory are outlined. The construction starts with a universal moduli space of Abelian varieties. This space carries a structure of an infinite dimensional locally symmetric space which is of interest in its own right. The key to our construction of the universal moduli space then is the Torelli map that assigns to every Riemann surface its Jacobian and its extension to the Satake-Baily-Borel compactifications.

Scale separation for multi-scale modeling of free-surface and two-phase flows with the conservative sharp interface method

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

Han, L.H., E-mail: Luhui.Han@tum.de; Hu, X.Y., E-mail: Xiangyu.Hu@tum.de; Adams, N.A., E-mail: Nikolaus.Adams@tum.de

In this paper we present a scale separation approach for multi-scale modeling of free-surface and two-phase flows with complex interface evolution. By performing a stimulus-response operation on the level-set function representing the interface, separation of resolvable and non-resolvable interface scales is achieved efficiently. Uniform positive and negative shifts of the level-set function are used to determine non-resolvable interface structures. Non-resolved interface structures are separated from the resolved ones and can be treated by a mixing model or a Lagrangian-particle model in order to preserve mass. Resolved interface structures are treated by the conservative sharp-interface model. Since the proposed scale separationmore » approach does not rely on topological information, unlike in previous work, it can be implemented in a straightforward fashion into a given level set based interface model. A number of two- and three-dimensional numerical tests demonstrate that the proposed method is able to cope with complex interface variations accurately and significantly increases robustness against underresolved interface structures.« less

Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes.

PubMed

Xu, Qingping; Traag, Bjørn A; Willemse, Joost; McMullan, Daniel; Miller, Mitchell D; Elsliger, Marc-André; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L; Bakolitsa, Constantina; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Chruszcz, Maksymilian; Clayton, Thomas; Das, Debanu; Deller, Marc C; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L; Feuerhelm, Julie; Grant, Joanna C; Grzechnik, Anna; Grzechnik, Slawomir K; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Klock, Heath E; Knuth, Mark W; Kozbial, Piotr; Krishna, S Sri; Kumar, Abhinav; Marciano, David; Minor, Wladek; Mommaas, A Mieke; Morse, Andrew T; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L; Sefcovic, Natasha; Tien, Henry J; Trame, Christine B; van den Bedem, Henry; Wang, Shuren; Weekes, Dana; Hodgson, Keith O; Wooley, John; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A; van Wezel, Gilles P

2009-09-11

SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex actinomycetes. We show that SsgB, a subfamily of SALPs, is the archetypal SALP that is functionally conserved in all sporulating actinomycetes. Sporulation-specific cell division of Streptomyces coelicolor ssgB mutants is restored by introduction of distant ssgB orthologues from other actinomycetes. Interestingly, the number of septa (and spores) of the complemented null mutants is dictated by the specific ssgB orthologue that is expressed. The crystal structure of the SsgB from Thermobifida fusca was determined at 2.6 A resolution and represents the first structure for this family. The structure revealed similarities to a class of eukaryotic "whirly" single-stranded DNA/RNA-binding proteins. However, the electro-negative surface of the SALPs suggests that neither SsgB nor any of the other SALPs are likely to interact with nucleotide substrates. Instead, we show that a conserved hydrophobic surface is likely to be important for SALP function and suggest that proteins are the likely binding partners.

Nonlinear periodic wavetrains in thin liquid films falling on a uniformly heated horizontal plate

NASA Astrophysics Data System (ADS)

Issokolo, Remi J. Noumana; Dikandé, Alain M.

2018-05-01

A thin liquid film falling on a uniformly heated horizontal plate spreads into fingering ripples that can display a complex dynamics ranging from continuous waves, nonlinear spatially localized periodic wave patterns (i.e., rivulet structures) to modulated nonlinear wavetrain structures. Some of these structures have been observed experimentally; however, conditions under which they form are still not well understood. In this work, we examine profiles of nonlinear wave patterns formed by a thin liquid film falling on a uniformly heated horizontal plate. For this purpose, the Benney model is considered assuming a uniform temperature distribution along the film propagation on the horizontal surface. It is shown that for strong surface tension but a relatively small Biot number, spatially localized periodic-wave structures can be analytically obtained by solving the governing equation under appropriate conditions. In the regime of weak nonlinearity, a multiple-scale expansion combined with the reductive perturbation method leads to a complex Ginzburg-Landau equation: the solutions of which are modulated periodic pulse trains which amplitude and width and period are expressed in terms of characteristic parameters of the model.

The birth and evolution of surface science: child of the union of science and technology.

PubMed

Duke, C B

2003-04-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10(-7) Pascal or 10(-9) Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid-liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes.

Combining 3D human in vitro methods for a 3Rs evaluation of novel titanium surfaces in orthopaedic applications

PubMed Central

Stevenson, G.; Rehman, S.; Draper, E.; Hernández‐Nava, E.; Hunt, J.

2016-01-01

ABSTRACT In this study, we report on a group of complementary human osteoblast in vitro test methods for the preclinical evaluation of 3D porous titanium surfaces. The surfaces were prepared by additive manufacturing (electron beam melting [EBM]) and plasma spraying, allowing the creation of complex lattice surface geometries. Physical properties of the surfaces were characterized by SEM and profilometry and 3D in vitro cell culture using human osteoblasts. Primary human osteoblast cells were found to elicit greater differences between titanium sample surfaces than an MG63 osteoblast‐like cell line, particularly in terms of cell survival. Surface morphology was associated with higher osteoblast metabolic activity and mineralization on rougher titanium plasma spray coated surfaces than smoother surfaces. Differences in osteoblast survival and metabolic activity on titanium lattice structures were also found, despite analogous surface morphology at the cellular level. 3D confocal microscopy identified osteoblast organization within complex titanium surface geometries, adhesion, spreading, and alignment to the biomaterial strut geometries. Mineralized nodule formation throughout the lattice structures was also observed, and indicative of early markers of bone in‐growth on such materials. Testing methods such as those presented are not traditionally considered by medical device manufacturers, but we suggest have value as an increasingly vital tool in efficiently translating pre‐clinical studies, especially in balance with current regulatory practice, commercial demands, the 3Rs, and the relative merits of in vitro and in vivo studies. Biotechnol. Bioeng. 2016;113: 1586–1599. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:26702609

Resonance Raman and surface-enhanced resonance Raman spectra of LH2 antenna complex from Rhodobacter sphaeroides and Ectothiorhodospira sp. excited in the Qx and Qy transitions.

PubMed

Chumanov, G; Picorel, R; Ortiz de Zarate, I; Cotton, T M; Seibert, M

2000-05-01

Well-resolved vibrational spectra of LH2 complex isolated from two photosynthetic bacteria, Rhodobacter sphaeroides and Ectothiorhodospira sp., were obtained using surface-enhanced resonance Raman scattering (SERRS) exciting into the Qx and the Qy transitions of bacteriochlorophyll a. High-quality SERRS spectra in the Qy region were accessible because the strong fluorescence background was quenched near the roughened Ag surface. A comparison of the spectra obtained with 590 nm and 752 nm excitation in the mid- and low-frequency regions revealed spectral differences between the two LH2 complexes as well as between the LH2 complexes and isolated bacteriochlorophyll a. Because peripheral modes of pigments contribute mainly to the low-frequency spectral region, frequencies and intensities of many vibrational bands in this region are affected by interactions with the protein. The results demonstrate that the microenvironment surrounding the pigments within the two LH2 complexes is somewhat different, despite the fact that the complexes exhibit similar electronic absorption spectra. These differences are most probably due to specific pigment-pigment and pigment-protein interactions within the LH2 complexes, and the approach might be useful for addressing subtle static and dynamic structural variances between pigment-protein complexes from different sources or in complexes altered chemically or genetically.

Mechanism for chelated sulfate formation from SO2 and bis (triphenylphosphine) platinum

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1985-01-01

Structure and energy surface calculations using the atom superposition and electron delocalization molecular orbital theory show that the first step in the reaction between SO2 and the dioxygen complex (PPh3)2PtO2 is the coordination of SO2 with one oxygen atom of the complex, followed by metal-oxygen bond breaking and reorientation, leading to a five-membered cyclic structure. This then rearranges to form the bidentate coordinated sulfate. Alternative pathways are considered and are found to be less favorable.

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation

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

Xu, Kai; Olsen, Olav; Tzvetkova-Robev, Dorothea

The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation

DOE PAGES

Xu, Kai; Olsen, Olav; Tzvetkova-Robev, Dorothea; ...

2015-04-02

The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

Preparation, characterization and luminescence properties of core-shell ternary terbium composites SiO2(600)@Tb(MABA-Si)•L

NASA Astrophysics Data System (ADS)

Ma, Yang-Yang; Li, Wen-Xian; Zheng, Yu-Shan; Bao, Jin-Rong; Li, Yi-Lian; Feng, Li-Na; Yang, Kui-Suo; Qiao, Yan; Wu, An-Ping

2018-03-01

Two novel core-shell structure ternary terbium composites SiO2(600)@Tb(MABA-Si)·L(L:dipy/phen) nanometre luminescence materials were prepared by ternary terbium complexes Tb(MABA-Si)·L2·(ClO4)3·2H2O shell grafted onto the surface of SiO2 microspheres. And corresponding ternary terbium complexes were synthesized using (CONH(CH2)3Si(OCH2CH3)3)2 (denoted as MABA-Si) as first ligand and L as second ligand coordinated with terbium perchlorate. The as-synthesized products were characterized by means of IR spectra, 1HNMR, element analysis, molar conductivity, SEM and TEM. It was found that the first ligand MABA-Si of terbium ternary complex hydrolysed to generate the Si-OH and the Si-OH condensate with the Si-OH on the surface of SiO2 microspheres; then ligand MABA-Si grafted onto the surface of SiO2 microspheres. The diameter of SiO2 core of SiO2(600)@Tb(MABA-Si)·L was approximately 600 nm. Interestingly, the luminescence properties demonstrate that the two core-shell structure ternary terbium composites SiO2(600)Tb(MABA-Si)·L(dipy/phen) exhibit strong emission intensities, which are 2.49 and 3.35 times higher than that of the corresponding complexes Tb(MABA-Si)·L2·(ClO4)3·2H2O, respectively. Luminescence decay curves show that core-shell structure ternary terbium composites have longer lifetime. Excellent luminescence properties enable the core-shell materials to have potential applications in medicine, industry, luminescent fibres and various biomaterials fields.

Preparation, characterization and luminescence properties of core-shell ternary terbium composites SiO2(600)@Tb(MABA-Si)•L.

PubMed

Ma, Yang-Yang; Li, Wen-Xian; Zheng, Yu-Shan; Bao, Jin-Rong; Li, Yi-Lian; Feng, Li-Na; Yang, Kui-Suo; Qiao, Yan; Wu, An-Ping

2018-03-01

Two novel core-shell structure ternary terbium composites SiO 2(600) @Tb(MABA-Si)·L(L:dipy/phen) nanometre luminescence materials were prepared by ternary terbium complexes Tb(MABA-Si)·L 2 ·(ClO 4 ) 3 ·2H 2 O shell grafted onto the surface of SiO 2 microspheres. And corresponding ternary terbium complexes were synthesized using (CONH(CH 2 ) 3 Si(OCH 2 CH 3 ) 3 ) 2 (denoted as MABA-Si) as first ligand and L as second ligand coordinated with terbium perchlorate. The as-synthesized products were characterized by means of IR spectra, 1 HNMR, element analysis, molar conductivity, SEM and TEM. It was found that the first ligand MABA-Si of terbium ternary complex hydrolysed to generate the Si-OH and the Si-OH condensate with the Si-OH on the surface of SiO 2 microspheres; then ligand MABA-Si grafted onto the surface of SiO 2 microspheres. The diameter of SiO 2 core of SiO 2(600) @Tb(MABA-Si)·L was approximately 600 nm. Interestingly, the luminescence properties demonstrate that the two core-shell structure ternary terbium composites SiO 2(600) Tb(MABA-Si)·L(dipy/phen) exhibit strong emission intensities, which are 2.49 and 3.35 times higher than that of the corresponding complexes Tb(MABA-Si)·L 2 ·(ClO 4 ) 3 ·2H 2 O, respectively. Luminescence decay curves show that core-shell structure ternary terbium composites have longer lifetime. Excellent luminescence properties enable the core-shell materials to have potential applications in medicine, industry, luminescent fibres and various biomaterials fields.

Preparation, characterization and luminescence properties of core–shell ternary terbium composites SiO2(600)@Tb(MABA-Si)•L

PubMed Central

Ma, Yang-Yang; Zheng, Yu-Shan; Bao, Jin-Rong; Li, Yi-Lian; Feng, Li-Na; Yang, Kui-Suo; Qiao, Yan; Wu, An-Ping

2018-01-01

Two novel core–shell structure ternary terbium composites SiO2(600)@Tb(MABA-Si)·L(L:dipy/phen) nanometre luminescence materials were prepared by ternary terbium complexes Tb(MABA-Si)·L2·(ClO4)3·2H2O shell grafted onto the surface of SiO2 microspheres. And corresponding ternary terbium complexes were synthesized using (CONH(CH2)3Si(OCH2CH3)3)2 (denoted as MABA-Si) as first ligand and L as second ligand coordinated with terbium perchlorate. The as-synthesized products were characterized by means of IR spectra, 1HNMR, element analysis, molar conductivity, SEM and TEM. It was found that the first ligand MABA-Si of terbium ternary complex hydrolysed to generate the Si–OH and the Si–OH condensate with the Si–OH on the surface of SiO2 microspheres; then ligand MABA-Si grafted onto the surface of SiO2 microspheres. The diameter of SiO2 core of SiO2(600)@Tb(MABA-Si)·L was approximately 600 nm. Interestingly, the luminescence properties demonstrate that the two core–shell structure ternary terbium composites SiO2(600)Tb(MABA-Si)·L(dipy/phen) exhibit strong emission intensities, which are 2.49 and 3.35 times higher than that of the corresponding complexes Tb(MABA-Si)·L2·(ClO4)3·2H2O, respectively. Luminescence decay curves show that core–shell structure ternary terbium composites have longer lifetime. Excellent luminescence properties enable the core–shell materials to have potential applications in medicine, industry, luminescent fibres and various biomaterials fields. PMID:29657773

XAFS studies of surface structures of TiO{sub 2} nanoparticles and photocatalytic reduction of metal ions.

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

Chen, L. X.; Rajh, T.; Wang, Z.

1997-01-01

To probe the origin of the unique functions of titanium dioxide (TiO{sub 2}) nanoparticles observed in photocatalytic reactions, structures of Ti atom sites in titanium dioxide (TiO{sub 2}) nanoparticles with different sizes were studied by Ti K-edge XAFS (X-ray absorption fine structure). Compared to the bulk TiO{sub 2} structure, a shorter Ti-O distance from surface TiO{sub 2} resulting from Ti-OH bonding was observed. The XAFS spectra also revealed an increasing disorder of the lattice with decreasing sizes of the nanoparticles based on a coordination number decrease for the third-shell O atoms as well as changes in relative intensities of pre-edgemore » peaks A1, A2, and A3. However, the Ti sites largely remain octahedral even in the 30 Angstrom diameter particles. These results imply that the increasing number of surface Ti sites as well as possible corner defects in small nanoparticles may be the main cause of the unique surface chemistry exhibited by nanoparticles of TiO{sub 2}. XAFS was also used in monitoring the photoreduction reaction products of Cu{sup 2+} and Hg{sup 2+} on TiO{sub 2} nanoparticle surfaces, with or without surface adsorbers, alanine (Ala) and thiolactic acid (TLA). Ala dramatically enhanced photoreduction of Cu{sup 2+} on TiO{sub 2} nanoparticle surfaces, whereas thiolactic acid did not affect or even hindered Hg{sup 2+} photoreduction. Although both surface adsorbers chelated with the metal ions in the absence of TiO{sub 2} nanoparticles, this chelation was drastically changed in the Cu-Ala complex but was largely retained in the Hg-TLA complex when TiO{sub 2} was present. This may correlate with the different effects of the adsorbers on the photoreduction of the metal. Our experimental results suggest that a proper balance between the affinities of the adsorber to the metal ions and to the surface Ti atoms of TiO{sub 2} may be one of the keys in selecting a surface adsorber for enhanced photoreduction efficiency.« less

Solution structure of the Legionella pneumophila Mip-rapamycin complex.

PubMed

Ceymann, Andreas; Horstmann, Martin; Ehses, Philipp; Schweimer, Kristian; Paschke, Anne-Katrin; Steinert, Michael; Faber, Cornelius

2008-03-17

Legionella pneumphila is the causative agent of Legionnaires' disease. A major virulence factor of the pathogen is the homodimeric surface protein Mip. It shows peptidyl-prolyl cis/trans isomerase activty and is a receptor of FK506 and rapamycin, which both inhibit its enzymatic function. Insight into the binding process may be used for the design of novel Mip inhibitors as potential drugs against Legionnaires' disease. We have solved the solution structure of free Mip77-213 and the Mip77-213-rapamycin complex by NMR spectroscopy. Mip77-213 showed the typical FKBP-fold and only minor rearrangements upon binding of rapamycin. Apart from the configuration of a flexible hairpin loop, which is partly stabilized upon binding, the solution structure confirms the crystal structure. Comparisons to the structures of free FKBP12 and the FKBP12-rapamycin complex suggested an identical binding mode for both proteins. The structural similarity of the Mip-rapamycin and FKBP12-rapamycin complexes suggests that FKBP12 ligands may be promising starting points for the design of novel Mip inhibitors. The search for a novel drug against Legionnaires' disease may therefore benefit from the large variety of known FKBP12 inhibitors.

Solution structure of the Legionella pneumophila Mip-rapamycin complex

PubMed Central

Ceymann, Andreas; Horstmann, Martin; Ehses, Philipp; Schweimer, Kristian; Paschke, Anne-Katrin; Steinert, Michael; Faber, Cornelius

2008-01-01

Background Legionella pneumphila is the causative agent of Legionnaires' disease. A major virulence factor of the pathogen is the homodimeric surface protein Mip. It shows peptidyl-prolyl cis/trans isomerase activty and is a receptor of FK506 and rapamycin, which both inhibit its enzymatic function. Insight into the binding process may be used for the design of novel Mip inhibitors as potential drugs against Legionnaires' disease. Results We have solved the solution structure of free Mip77–213 and the Mip77–213-rapamycin complex by NMR spectroscopy. Mip77–213 showed the typical FKBP-fold and only minor rearrangements upon binding of rapamycin. Apart from the configuration of a flexible hairpin loop, which is partly stabilized upon binding, the solution structure confirms the crystal structure. Comparisons to the structures of free FKBP12 and the FKBP12-rapamycin complex suggested an identical binding mode for both proteins. Conclusion The structural similarity of the Mip-rapamycin and FKBP12-rapamycin complexes suggests that FKBP12 ligands may be promising starting points for the design of novel Mip inhibitors. The search for a novel drug against Legionnaires' disease may therefore benefit from the large variety of known FKBP12 inhibitors. PMID:18366641

A Quantitative Measure of Conformational Changes in Apo, Holo and Ligand-Bound Forms of Enzymes.

PubMed

Singh, Satendra; Singh, Atul Kumar; Wadhwa, Gulshan; Singh, Dev Bukhsh; Dwivedi, Seema; Gautam, Budhayash; Ramteke, Pramod W

2016-06-01

Determination of the native geometry of the enzymes and ligand complexes is a key step in the process of structure-based drug designing. Enzymes and ligands show flexibility in structural behavior as they come in contact with each other. When ligand binds with active site of the enzyme, in the presence of cofactor some structural changes are expected to occur in the active site. Motivation behind this study is to determine the nature of conformational changes as well as regions where such changes are more pronounced. To measure the structural changes due to cofactor and ligand complex, enzyme in apo, holo and ligand-bound forms is selected. Enzyme data set was retrieved from protein data bank. Fifteen triplet groups were selected for the analysis of structural changes based on selection criteria. Structural features for selected enzymes were compared at the global as well as local region. Accessible surface area for the enzymes in entire triplet set was calculated, which describes the change in accessible surface area upon binding of cofactor and ligand with the enzyme. It was observed that some structural changes take place during binding of ligand in the presence of cofactor. This study will helps in understanding the level of flexibility in protein-ligand interaction for computer-aided drug designing.

A general strategy for hybrid thin film fabrication and transfer onto arbitrary substrates.

PubMed

Zhang, Yong; Magan, John J; Blau, Werner J

2014-04-28

The development of thin film-based structures/devices often requires thin films to be transferred onto arbitrary substrates/surfaces. Controllable and non-destructive transfer method, although highly desired, remains quite challenging. Here we report a general method for fabrication and transfer of hybrid (ultra)thin films. The proposed solution-based in-situ transfer method shows not only its robust ability for thin film transfer onto arbitrary substrates but also its highly controlled and non-destructive characteristic. With a hole structure as the support, fully-stretched free-standing thin film is prepared. The successful transfer to a curved surface demonstrates the possibility for production of thin film-coated complex optical components. Ultrathin (35 nm) hybrid film transferred onto PET (50 μm thick) shows high transparency (>90% in visible range), conductivity (1.54 × 10(4) S/m), and flexibility (radius of curvature down to mm scale). The reported transfer method would provide a powerful route towards complex thin film-based structures/devices.

A General Strategy for Hybrid Thin Film Fabrication and Transfer onto Arbitrary Substrates

PubMed Central

Zhang, Yong; Magan, John J.; Blau, Werner J.

2014-01-01

The development of thin film-based structures/devices often requires thin films to be transferred onto arbitrary substrates/surfaces. Controllable and non-destructive transfer method, although highly desired, remains quite challenging. Here we report a general method for fabrication and transfer of hybrid (ultra)thin films. The proposed solution-based in-situ transfer method shows not only its robust ability for thin film transfer onto arbitrary substrates but also its highly controlled and non-destructive characteristic. With a hole structure as the support, fully-stretched free-standing thin film is prepared. The successful transfer to a curved surface demonstrates the possibility for production of thin film-coated complex optical components. Ultrathin (35 nm) hybrid film transferred onto PET (50 μm thick) shows high transparency (>90% in visible range), conductivity (1.54 × 104 S/m), and flexibility (radius of curvature down to mm scale). The reported transfer method would provide a powerful route towards complex thin film-based structures/devices. PMID:24769689

Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels*

PubMed Central

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, Joelle; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-01-01

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5′ and 3′ flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. PMID:22431731

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

PubMed

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P; Khun, Joelle; Vos, Marten H; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-05-04

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

Structural brain aging and speech production: a surface-based brain morphometry study.

PubMed

Tremblay, Pascale; Deschamps, Isabelle

2016-07-01

While there has been a growing number of studies examining the neurofunctional correlates of speech production over the past decade, the neurostructural correlates of this immensely important human behaviour remain less well understood, despite the fact that previous studies have established links between brain structure and behaviour, including speech and language. In the present study, we thus examined, for the first time, the relationship between surface-based cortical thickness (CT) and three different behavioural indexes of sublexical speech production: response duration, reaction times and articulatory accuracy, in healthy young and older adults during the production of simple and complex meaningless sequences of syllables (e.g., /pa-pa-pa/ vs. /pa-ta-ka/). The results show that each behavioural speech measure was sensitive to the complexity of the sequences, as indicated by slower reaction times, longer response durations and decreased articulatory accuracy in both groups for the complex sequences. Older adults produced longer speech responses, particularly during the production of complex sequence. Unique age-independent and age-dependent relationships between brain structure and each of these behavioural measures were found in several cortical and subcortical regions known for their involvement in speech production, including the bilateral anterior insula, the left primary motor area, the rostral supramarginal gyrus, the right inferior frontal sulcus, the bilateral putamen and caudate, and in some region less typically associated with speech production, such as the posterior cingulate cortex.

Mapping spatial variation in rock properties in relationship to scale-dependent structure using spectral curvature

NASA Astrophysics Data System (ADS)

Stewart, S. A.; Wynn, T. J.

2000-08-01

Maps of the three-dimensional geometry of geologic surfaces show that structural curvature commonly varies with scale of observation: This fact can be viewed as superposition of structures at different wavelengths. Rock properties such as fracture density and orientation reflect the contribution of superimposed structures. For this reason, characterization of geologic surfaces is fundamentally different from purely geometrical characterization, for which local description of surface properties is sufficient. We show that measured curvature decays according to a power law with increasing size of measurement window, so short-wavelength curvatures do not obscure long-wavelength curvatures in the same data set. This property can be taken advantage of in a simple technique for automatically mapping multiwavelength curvatures. At each point on a surface, curvature is measured at a range of wavelengths. This curvature spectrum can be analyzed in map view or collapsed into a single value at each point in space. The results indicate that complex geologic surfaces can be characterized without any prior knowledge of structural wavelengths and orientation. The method should prove useful in applications requiring knowledge of spatial variation in rock properties from remotely sensed data, such as exploration for hydrocarbon reservoirs or nuclear waste repositories.

Polymeric material prepared from Schiff base based on O-carboxymethyl chitosan and its Cu(II) and Pd(II) complexes

NASA Astrophysics Data System (ADS)

Baran, Talat; Menteş, Ayfer

2016-07-01

In this study, a new eco-friendly Schiff base based on O-carboxymethyl chitosan ([OCMCS-7a]) and its copper(II) and palladium(II) complexes were synthesized. Characterizations of [OCMCS-7a] and its metal complexes were conducted using FTIR, 1H NMR, 13C NMR, TG/DTG, XRD, SEM-EDAX, ICP, UV-VIS, GC-MS, elemental analysis, magnetic moment and molar conductivity measurements. The degree of substitution (DS) of [OCMCS-7a] was determined by elemental analysis to be 0.44. It was shown by the solubility test that [OCMCS-7a] was completely soluble in water. Surface images of chitosan, [OCMCS-7a] and its Cu(II) and Pd(II) complexes were investigated using the SEM-EDAX technique. Their thermal behaviors and crystallinities of the synthesized complexes were determined by TG/DTG and X-ray powder diffraction techniques, respectively. The metal contents of the obtained complexes were determined using an ICP-OES instrument. From the analyses, it was noted that the thermal stabilities and crystallinities of [OCMCS-7a] and its complexes decreased compared to chitosan. As a consequence of surface screening, it was also noted that the surface structure of the chitosan was smoother than that of the obtained compounds.

Growth of carbon structured over Pd, Pt and Ni: A comparative DFT study

NASA Astrophysics Data System (ADS)

Quiroga, Matías Abel

2013-03-01

To elucidate the graphene-like structures mechanisms growth over the M(1 1 1) surface (M = Pd, Pt and Ni) we performed ab initio calculus in the frame of density functional theory with the exchange-correlation functional treated according to the Generalized Gradient Approximation (GGA). In order to avoid the problem that represent the complex interaction between the well formed graphene layer and the metallic surface, we recreate the carbon rings formation initial steps, by adding one by one carbon atoms over M(1 1 1) surface. With this strategy, the chemical bonding is always present until the graphene layer is well formed, in which case the GGA neglects van der Waals dispersive forces. We investigate the electronic properties by studying the band structure and the density of states.

Layer-by-Layer Assembly of Fluorine-Free Polyelectrolyte-Surfactant Complexes for the Fabrication of Self-Healing Superhydrophobic Films.

PubMed

Wu, Mengchun; An, Ni; Li, Yang; Sun, Junqi

2016-11-29

Fluorine-free self-healing superhydrophobic films are of significance for practical applications because of their extended service life and cost-effective and eco-friendly preparation process. In this study, we report the fabrication of fluorine-free self-healing superhydrophobic films by layer-by-layer (LbL) assembly of poly(sodium 4-styrenesulfonate) (PSS)-1-octadecylamine (ODA) complexes (PSS-ODA) and poly(allylamine hydrochloride) (PAH)-sodium dodecyl sulfonate (SDS) (PAH-SDS) complexes. The wettability of the LbL-assembled PSS-ODA/PAH-SDS films depends on the film structure and can be tailored by changing the NaCl concentration in aqueous dispersions of PSS-ODA complexes and the number of film deposition cycles. The freshly prepared PSS-ODA/PAH-SDS film with micro- and nanoscaled hierarchical structures is hydrophilic and gradually changes to superhydrophobic in air because the polyelectrolyte-complexed ODA and SDS surfactants tend to migrate to the film surface to cover the film with hydrophobic alkyl chains to lower its surface energy. The large amount of ODA and SDS surfactants loaded in the superhydrophobic PSS-ODA/PAH-SDS films and the autonomic migration of these surfactants to the film surface endow the resultant superhydrophobic films with an excellent self-healing ability to restore the damaged superhydrophobicity. The self-healing superhydrophobic PSS-ODA/PAH-SDS films are mechanically robust and can be deposited on various flat and nonflat substrates. The LbL assembly of oppositely charged polyelectrolyte-surfactant complexes provides a new way for the fabrication of fluorine-free self-healing superhydrophobic films with satisfactory mechanical stability, enhanced reliability, and extended service life.

The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease

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

Bunick, Christopher G.; Milstone, Leonard M.

Keratins 1 (K1) and 10 (K10) are the primary keratins expressed in differentiated epidermis. Mutations in K1/K10 are associated with human skin diseases. We determined the crystal structure of the complex between the distal (2B) helices of K1 and K10 to better understand how human keratin structure correlates with function. The 3.3 Å resolution structure confirms many features inferred by previous biochemical analyses, but adds unexpected insights. It demonstrates a parallel, coiled-coil heterodimer with a predominantly hydrophobic intermolecular interface; this heterodimer formed a higher order complex with a second K1-K10-2B heterodimer via a Cys401K10 disulfide link, although the bond anglemore » is unanticipated. The molecular surface analysis of K1-K10-2B identified several pockets, one adjacent to the disulfide linkage and conserved in K5-K14. The solvent accessible surface area of the K1-K10 structure is 20–25% hydrophobic. The 2B region contains mixed acidic and basic patches proximally (N-terminal), whereas it is largely acidic distally (C-terminal). Mapping of conserved and nonconserved residues between K1-K10 and K5-K14 onto the structure demonstrated the majority of unique residues align along the outer helical ridge. Finally, the structure permitted a fresh analysis of the deleterious effects caused by K1/K10 missense mutations found in patients with phenotypic skin disease.« less

Elucidating the role of surface chemistry on cationic phosphorus dendrimer-siRNA complexation.

PubMed

Deriu, Marco A; Tsapis, Nicolas; Noiray, Magali; Grasso, Gianvito; El Brahmi, Nabil; Mignani, Serge; Majoral, Jean-Pierre; Fattal, Elias; Danani, Andrea

2018-06-14

In the field of dendrimers targeting small interfering RNA (siRNA) delivery, dendrimer structural properties, such as the flexibility/rigidity ratio, play a crucial role in the efficiency of complexation. However, advances in organic chemistry have enabled the development of dendrimers that differ only by a single atom on their surface terminals. This is the case for cationic phosphorus dendrimers functionalized with either pyrrolidinium (DP) or morpholinium (DM) terminal groups. This small change was shown to strongly affect the dendrimer-siRNA complexation, leading to more efficient anti-inflammatory effects in the case of DP. Reasons for this different behavior can hardly be inferred only by biological in vitro and in vivo experiments due to the high number of variables and complexity of the investigated biological system. However, an understanding of how small chemical surface changes may completely modify the overall dendrimer-siRNA complexation is a significant breakthrough towards the design of efficient dendrimers for nucleic acid delivery. Herein, we present experimental and computational approaches based on isothermal titration calorimetry and molecular dynamics simulations to elucidate the molecular reasons behind different efficiencies and activities of DP and DM. Results of the present research highlight how chemical surface modifications may drive the overall dendrimer-siRNA affinity by influencing enthalpic and entropic contributions of binding free energy. Moreover, this study elucidates molecular reasons related to complexation stoichiometry that may be crucial in determining the dendrimer complexation efficiency.

Plasmonic complex fluids of nematiclike and helicoidal self-assemblies of gold nanorods with a negative order parameter.

PubMed

Liu, Qingkun; Senyuk, Bohdan; Tang, Jianwei; Lee, Taewoo; Qian, Jun; He, Sailing; Smalyukh, Ivan I

2012-08-24

We describe a soft matter system of self-organized oblate micelles and plasmonic gold nanorods that exhibit a negative orientational order parameter. Because of anisotropic surface anchoring interactions, colloidal gold nanorods tend to align perpendicular to the director describing the average orientation of normals to the discoidal micelles. Helicoidal structures of highly concentrated nanorods with a negative order parameter are realized by adding a chiral additive and are further controlled by means of confinement and mechanical stress. Polarization-sensitive absorption, scattering, and two-photon luminescence are used to characterize orientations and spatial distributions of nanorods. Self-alignment and effective-medium optical properties of these hybrid inorganic-organic complex fluids match predictions of a simple model based on anisotropic surface anchoring interactions of nanorods with the structured host medium.

Sea-town interactions over Marseille: 3D urban boundary layer and thermodynamic fields near the surface

NASA Astrophysics Data System (ADS)

Lemonsu, A.; Pigeon, G.; Masson, V.; Moppert, C.

2006-02-01

3D numerical simulations with the Meso-NH atmospheric model including the Town Energy Balance urban parameterization, are conducted over the south-east of France and the one million inhabitants city of Marseille in the frameworks of the ESCOMPTE-UBL program. The geographic situation of the area is relatively complex, because of the proximity of the Mediterranean Sea and the presence of numerous massifs, inducing complex meteorological flows. The present work is focused on six days of the campaign, characterized by the development of strong summer sea-breeze circulations. A complete evaluation of the model is initially realized at both regional- and city-scales, by using the large available database. The regional evaluation shows a good behavior of the model, during the six days of simulation, either for the parameters near the surface or for the vertical profiles describing the structure of the atmosphere. The urban-scale evaluation indicates that the fine structure of the horizontal fields of air temperature above the city is correctly simulated by the model. A specific attention is then pointed to the 250-m horizontal resolution outputs, focused on the Marseille area, for two days of the campaign. From the study of the vertical structure of the Urban Boundary Layer and the thermodynamic fields near the surface, one underscores the important differences due to the regional and local flows, and the complex interactions that occur between the urban effects and the effects of sea breezes.

Coordination of N,O-donor appended Schiff base ligand (H2L1) towards Zinc(II) in presence of pseudohalides: Syntheses, crystal structures, photoluminescence, antimicrobial activities and Hirshfeld surfaces

NASA Astrophysics Data System (ADS)

Majumdar, Dhrubajyoti; Biswas, Jayanta Kumar; Mondal, Monojit; Surendra Babu, M. S.; Metre, Ramesh K.; Das, Sourav; Bankura, Kalipada; Mishra, Dipankar

2018-03-01

A series of dinuclear Zn(II) complexes [Zn2 (L1) (CH3OH)2(SCN) (OAc)](1), [Zn2 (L1) (CH3OH)2(N3)2](2) and [Zn2 (L1) (Cl)2(CH3OH)]·CH3OH (3) have been synthesized by the reaction of compartmental Schiff base ligand (H2L1) [N,N‧-Bis(3-ethoxysalicylidenimino)-1,3-diaminopropane] with Zn(OAc)2·2H2O in presence of coligand like KSCN, NaN3 and NaCl respectively. X-ray diffraction analysis revealed that all the complexes are neutral and possess a 4-membered Zn2 (μ2-O)2 ring fastened by the unified coordination action of a doubly deprotonated ligand. In addition, solid state structure of the complexes display extensive intermolecular interaction which has been supported theoretically by Hirshfeld surface analysis with 2D Fingerprint plots. The synthesized Zn(II) metal complexes observed enhancement of luminescence emission compared to the parent Schiff base due to emanating ligand based intraligand (π→π∗) fluorescence. Additionally, Zn(II) metal complexes exhibited considerable antimicrobial potency against some important Gram +ve and Gram -ve bacteria.

Rb + adsorption at the quartz(101)-aqueous interface: comparison of resonant anomalous x-ray reflectivity with ab initio calculations

DOE PAGES

Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; ...

2015-01-29

We study adsorption of Rb + to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb + distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights ofmore » 1.8 ± 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb + between these two conditions. At pH 7, the lowest energy structure shows that Rb + adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb + coverage was -0.11 C/m 2, in good agreement with the range of the surface charge magnitudes reported in the literature.« less

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Control surfaces of aquatic vertebrates: active and passive design and function.

PubMed

Fish, Frank E; Lauder, George V

2017-12-01

Aquatic vertebrates display a variety of control surfaces that are used for propulsion, stabilization, trim and maneuvering. Control surfaces include paired and median fins in fishes, and flippers and flukes in secondarily aquatic tetrapods. These structures initially evolved from embryonic fin folds in fishes and have been modified into complex control surfaces in derived aquatic tetrapods. Control surfaces function both actively and passively to produce torque about the center of mass by the generation of either lift or drag, or both, and thus produce vector forces to effect rectilinear locomotion, trim control and maneuvers. In addition to fins and flippers, there are other structures that act as control surfaces and enhance functionality. The entire body can act as a control surface and generate lift for stability in destabilizing flow regimes. Furthermore, control surfaces can undergo active shape change to enhance their performance, and a number of features act as secondary control structures: leading edge tubercles, wing-like canards, multiple fins in series, finlets, keels and trailing edge structures. These modifications to control surface design can alter flow to increase lift, reduce drag and enhance thrust in the case of propulsive fin-based systems in fishes and marine mammals, and are particularly interesting subjects for future research and application to engineered systems. Here, we review how modifications to control surfaces can alter flow and increase hydrodynamic performance. © 2017. Published by The Company of Biologists Ltd.

Programmable thermal emissivity structures based on bioinspired self-shape materials

NASA Astrophysics Data System (ADS)

Athanasopoulos, N.; Siakavellas, N. J.

2015-12-01

Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable - and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (ɛEff_H/ɛEff_L) equal to 28.

Programmable thermal emissivity structures based on bioinspired self-shape materials

PubMed Central

Athanasopoulos, N.; Siakavellas, N. J.

2015-01-01

Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable – and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (εEff_H/εEff_L) equal to 28. PMID:26635316

Growth and structural evolution of Sn on Ag(001): Epitaxial monolayer to thick alloy film

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

Chakraborty, Suvankar; Menon, Krishnakumar S. R., E-mail: krishna.menon@saha.ac.in

The growth and structure of Sn on Ag(001), from submonolayer to thick film coverages at room temperature, are studied using low energy electron diffraction, x-ray photoemission spectroscopy and angle-resolved photoemission spectroscopy (ARPES) techniques. The authors observe different growth modes for submonolayer Sn coverages and for higher Sn coverages. Systematic surface structural evolution, consistent with the substitution of surface Ag atoms by Sn atoms, is observed for submonolayer Sn coverages while an ordered Ag-Sn bulk alloy film is formed for higher Sn coverages with an Ag overlayer. For monolayer coverage of Sn, a pseudomorphic growth of a Sn layer without alloyingmore » is determined. ARPES results also confirm the presence of an ordered Ag overlayer on the bulk Ag-Sn alloy film, suggesting the formation of an Ag/Ag{sub 3}Sn/Ag(001) sandwich structure at the surface for higher Sn coverages. The present results illustrate the complex interplay of atomic mobilities, surface free-energies, and alloy formation energies in determining the growth and structural properties of the system.« less

Measuring floodplain spatial patterns using continuous surface metrics at multiple scales

USGS Publications Warehouse

Scown, Murray W.; Thoms, Martin C.; DeJager, Nathan R.

2015-01-01

Interactions between fluvial processes and floodplain ecosystems occur upon a floodplain surface that is often physically complex. Spatial patterns in floodplain topography have only recently been quantified over multiple scales, and discrepancies exist in how floodplain surfaces are perceived to be spatially organised. We measured spatial patterns in floodplain topography for pool 9 of the Upper Mississippi River, USA, using moving window analyses of eight surface metrics applied to a 1 × 1 m2 DEM over multiple scales. The metrics used were Range, SD, Skewness, Kurtosis, CV, SDCURV,Rugosity, and Vol:Area, and window sizes ranged from 10 to 1000 m in radius. Surface metric values were highly variable across the floodplain and revealed a high degree of spatial organisation in floodplain topography. Moran's I correlograms fit to the landscape of each metric at each window size revealed that patchiness existed at nearly all window sizes, but the strength and scale of patchiness changed within window size, suggesting that multiple scales of patchiness and patch structure exist in the topography of this floodplain. Scale thresholds in the spatial patterns were observed, particularly between the 50 and 100 m window sizes for all surface metrics and between the 500 and 750 m window sizes for most metrics. These threshold scales are ~ 15–20% and 150% of the main channel width (1–2% and 10–15% of the floodplain width), respectively. These thresholds may be related to structuring processes operating across distinct scale ranges. By coupling surface metrics, multi-scale analyses, and correlograms, quantifying floodplain topographic complexity is possible in ways that should assist in clarifying how floodplain ecosystems are structured.

Geometry and active tectonics of the Los Osos-Hosgri Fault Intersection in Estero Bay, CA: Reconciling seismicity patterns with near-surface geology

NASA Astrophysics Data System (ADS)

Watt, J. T.; Hardebeck, J.; Johnson, S. Y.; Kluesner, J.

2016-12-01

Characterizing active structures within structurally complex fault intersections is essential for unraveling the deformational history and for assessing the importance of fault intersections in regional earthquake hazard assessments. We employ an integrative, multi-scale geophysical approach to describe the 3D geometry and active tectonics of the offshore Los Osos fault (LOF) in Estero Bay, California. The shallow structure of the LOF, as imaged with multibeam and high-resolution seismic-reflection data, reveals a complex west-diverging zone of active faulting that bends into and joins the Hosgri fault. The down-dip geometry of the LOF as revealed by gravity, magnetic, and industry multi-channel seismic data, is vertical to steeply-dipping and varies along strike. As the LOF extends offshore, it is characterized by SW-side-up motion on a series of W-NW trending, steeply SW-dipping reverse faults. The LOF bends to the north ( 23°) as it approaches the Hosgri fault and dips steeply to the NE along a magnetic basement block. Inversion of earthquake focal mechanisms within Estero Bay yields maximum compressive stress axes that are near-horizontal and trend approximately N15E. This trend is consistent with dextral strike-slip faulting along NW-SE trending structures such as the Hosgri fault and northern LOF, and oblique dip-slip motion along the W-NW trending section of the LOF. Notably, NW-SE trending structures illuminated by seismicity in Estero Bay coincide with, but also appear to cross-cut, LOF structures imaged in the near-surface. We suggest this apparent disconnect reflects ongoing fault reorganization at a dynamic and inherently unstable fault intersection, in which the seismicity reflects active deformation at depth that is not clearly expressed in the near-surface geology. Direct connectivity between the Hosgri and Los Osos faults suggests a combined earthquake rupture is possible; however, the geometrical complexity along the offshore LOF may limit the extent of rupture.

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

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

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

Electrolyte-induced surface transformation and transition-metal dissolution of fully delithiated LiNi 0.8Co 0.15Al 0.05O 2

DOE PAGES

Faenza, Nicholas V.; Lebens-Higgins, Zachary W.; Mukherjee, Pinaki; ...

2017-06-08

Here, enabling practical utilization of layered Rmore » $$\\bar{3}$$ m positive electrodes near full delithiation requires an enhanced understanding of the complex electrode–electrolyte interactions that often induce failure. Using Li[Ni 0.8Co 0.15Al 0.05]O 2 (NCA) as a model layered compound, the chemical and structural stability in a strenuous thermal and electrochemical environment was explored. Operando microcalorimetry and electrochemical impedance spectroscopy identified a fingerprint for a structural decomposition and transition-metal dissolution reaction that occurs on the positive electrode at full delithiation. Surface-sensitive characterization techniques, including X-ray absorption spectroscopy and high-resolution transmission electron microscopy, measured a structural and morphological transformation of the surface and subsurface regions of NCA. Despite the bulk structural integrity being maintained, NCA surface degradation at a high state of charge induces excessive transition-metal dissolution and significant positive electrode impedance development, resulting in a rapid decrease in electrochemical performance. Additionally, the impact of electrolyte salt, positive electrode surface area, and surface Li 2CO 3 content on the magnitude and character of the dissolution reaction was studied.« less

Electrolyte-Induced Surface Transformation and Transition-Metal Dissolution of Fully Delithiated LiNi0.8Co0.15Al0.05O2.

PubMed

Faenza, Nicholas V; Lebens-Higgins, Zachary W; Mukherjee, Pinaki; Sallis, Shawn; Pereira, Nathalie; Badway, Fadwa; Halajko, Anna; Ceder, Gerbrand; Cosandey, Frederic; Piper, Louis F J; Amatucci, Glenn G

2017-09-19

Enabling practical utilization of layered R3̅m positive electrodes near full delithiation requires an enhanced understanding of the complex electrode-electrolyte interactions that often induce failure. Using Li[Ni 0.8 Co 0.15 Al 0.05 ]O 2 (NCA) as a model layered compound, the chemical and structural stability in a strenuous thermal and electrochemical environment was explored. Operando microcalorimetry and electrochemical impedance spectroscopy identified a fingerprint for a structural decomposition and transition-metal dissolution reaction that occurs on the positive electrode at full delithiation. Surface-sensitive characterization techniques, including X-ray absorption spectroscopy and high-resolution transmission electron microscopy, measured a structural and morphological transformation of the surface and subsurface regions of NCA. Despite the bulk structural integrity being maintained, NCA surface degradation at a high state of charge induces excessive transition-metal dissolution and significant positive electrode impedance development, resulting in a rapid decrease in electrochemical performance. Additionally, the impact of electrolyte salt, positive electrode surface area, and surface Li 2 CO 3 content on the magnitude and character of the dissolution reaction was studied.

EARP, a multisubunit tethering complex involved in endocytic recycling

PubMed Central

Schindler, Christina; Chen, Yu; Pu, Jing; Guo, Xiaoli; Bonifacino, Juan S.

2015-01-01

Recycling of endocytic receptors to the cell surface involves passage through a series of membrane-bound compartments by mechanisms that are poorly understood. In particular, it is unknown if endocytic recycling requires the function of multisubunit tethering complexes, as is the case for other intracellular trafficking pathways. Herein we describe a tethering complex named Endosome-Associated Recycling Protein (EARP) that is structurally related to the previously described Golgi-Associated Retrograde Protein (GARP) complex. Both complexes share the Ang2, Vps52 and Vps53 subunits, but EARP comprises an uncharacterized protein, Syndetin, in place of the Vps54 subunit of GARP. This change determines differential localization of EARP to recycling endosomes and GARP to the Golgi complex. EARP interacts with the target-SNARE Syntaxin 6 and various cognate SNAREs. Depletion of Syndetin or Syntaxin 6 delays recycling of internalized transferrin to the cell surface. These findings implicate EARP in canonical membrane-fusion events in the process of endocytic recycling. PMID:25799061

Growth of two-dimensional decagonal colloidal quasicrystals

NASA Astrophysics Data System (ADS)

Martinsons, M.; Schmiedeberg, M.

2018-06-01

The growth of quasicrystals, i.e. structures with long-range positional order but no periodic translational symmetry, is more complex than the growth of periodic crystals. By employing Brownian dynamics simulations in two dimensions for colloidal particles that interact according to an isotropic pair potential with two incommensurate lengths, we study the growth of quasicrystalline structures by sequentially depositing particles at their surface. We quantify the occurrence of quasicrystalline order as a function of the temperature and the rate of added particles. In addition, we explore defects like local triangular order or gaps within the quasicrystalline structure. Furthermore, we analyze the shapes of the surfaces in grown structures which tend to build straight lines along the symmetry axes of the quasicrystal. Finally, we identify phasonic flips which are rearrangements of the particles due to additional degrees of freedom. The number of phasonic flips decreases with the distance to the surface.

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

Xia, Shuangluo; Vashishtha, Ashwani; Bulkley, David

During DNA synthesis, base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the penultimate base pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady-state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The efficiency of incorporation for incoming dNTPs opposite an abasic site varied between 2- and 210-fold dependingmore » on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporation were consistent with specific features of base stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated, so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex, and the incorporation efficiency of incoming dNTPs is reduced.« less

Peptide interfaces with graphene: an emerging intersection of analytical chemistry, theory, and materials.

PubMed

Russell, Shane R; Claridge, Shelley A

2016-04-01

Because noncovalent interface functionalization is frequently required in graphene-based devices, biomolecular self-assembly has begun to emerge as a route for controlling substrate electronic structure or binding specificity for soluble analytes. The remarkable diversity of structures that arise in biological self-assembly hints at the possibility of equally diverse and well-controlled surface chemistry at graphene interfaces. However, predicting and analyzing adsorbed monolayer structures at such interfaces raises substantial experimental and theoretical challenges. In contrast with the relatively well-developed monolayer chemistry and characterization methods applied at coinage metal surfaces, monolayers on graphene are both less robust and more structurally complex, levying more stringent requirements on characterization techniques. Theory presents opportunities to understand early binding events that lay the groundwork for full monolayer structure. However, predicting interactions between complex biomolecules, solvent, and substrate is necessitating a suite of new force fields and algorithms to assess likely binding configurations, solvent effects, and modulations to substrate electronic properties. This article briefly discusses emerging analytical and theoretical methods used to develop a rigorous chemical understanding of the self-assembly of peptide-graphene interfaces and prospects for future advances in the field.

Pore-scale study of effects of macroscopic pores and their distributions on reactive transport in hierarchical porous media

DOE PAGES

Chen, Li; Zhang, Ruiyuan; Min, Ting; ...

2018-05-19

For applications of reactive transport in porous media, optimal porous structures should possess both high surface area for reactive sites loading and low mass transport resistance. Hierarchical porous media with a combination of pores at different scales are designed for this purpose. In this paper, using the lattice Boltzmann method, pore-scale numerical studies are conducted to investigate diffusion-reaction processes in 2D hierarchical porous media generated by self-developed reconstruction scheme. Complex interactions between porous structures and reactive transport are revealed under different conditions. Simulation results show that adding macropores can greatly enhance the mass transport, but at the same time reducemore » the reactive surface, leading to complex change trend of the total reaction rate. Effects of gradient distribution of macropores within the porous medium are also investigated. It is found that a front-loose, back-tight (FLBT) hierarchical structure is desirable for enhancing mass transport, increasing total reaction rate, and improving catalyst utilization. Finally, on the whole, from the viewpoint of reducing cost and improving material performance, hierarchical porous structures, especially gradient structures with the size of macropores gradually decreasing along the transport direction, are desirable for catalyst application.« less

Pore-scale study of effects of macroscopic pores and their distributions on reactive transport in hierarchical porous media

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

Chen, Li; Zhang, Ruiyuan; Min, Ting

For applications of reactive transport in porous media, optimal porous structures should possess both high surface area for reactive sites loading and low mass transport resistance. Hierarchical porous media with a combination of pores at different scales are designed for this purpose. In this paper, using the lattice Boltzmann method, pore-scale numerical studies are conducted to investigate diffusion-reaction processes in 2D hierarchical porous media generated by self-developed reconstruction scheme. Complex interactions between porous structures and reactive transport are revealed under different conditions. Simulation results show that adding macropores can greatly enhance the mass transport, but at the same time reducemore » the reactive surface, leading to complex change trend of the total reaction rate. Effects of gradient distribution of macropores within the porous medium are also investigated. It is found that a front-loose, back-tight (FLBT) hierarchical structure is desirable for enhancing mass transport, increasing total reaction rate, and improving catalyst utilization. Finally, on the whole, from the viewpoint of reducing cost and improving material performance, hierarchical porous structures, especially gradient structures with the size of macropores gradually decreasing along the transport direction, are desirable for catalyst application.« less

Rapid on-site/in-situ detection of heavy metal ions in environmental water using a structure-switching DNA optical biosensor.

PubMed

Long, Feng; Zhu, Anna; Shi, Hanchang; Wang, Hongchen; Liu, Jingquan

2013-01-01

A structure-switching DNA optical biosensor for rapid on-site/in situ detection of heavy metal ions is reported. Mercury ions (Hg²⁺), highly toxic and ubiquitous pollutants, were selected as model target. In this system, fluorescence-labeled DNA containing T-T mismatch structure was introduced to bind with DNA probes immobilized onto the sensor surface. In the presence of Hg²⁺, some of the fluorescence-labeled DNAs bind with Hg²⁺ to form T-Hg²⁺-T complexes through the folding of themselves into a hairpin structure and dehybridization from the sensor surface, which leads to decrease in fluorescence signal. The total analysis time for a single sample was less than 10 min with detection limit of 1.2 nM. The rapid on-site/in situ determination of Hg²⁺ was readily performed in natural water. This sensing strategy can be extended in principle to other metal ions by substituting the T-Hg²⁺-T complexes with other specificity structures that selectively bind to other analytes.

Substrate Binding and Catalytic Mechanism of Human Choline Acetyltransferase

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

Kim,A.; Rylett, J.; Shilton, B.

2006-01-01

Choline acetyltransferase (ChAT) catalyzes the synthesis of the neurotransmitter acetylcholine from choline and acetyl-CoA, and its presence is a defining feature of cholinergic neurons. We report the structure of human ChAT to a resolution of 2.2 {angstrom} along with structures for binary complexes of ChAT with choline, CoA, and a nonhydrolyzable acetyl-CoA analogue, S-(2-oxopropyl)-CoA. The ChAT-choline complex shows which features of choline are important for binding and explains how modifications of the choline trimethylammonium group can be tolerated by the enzyme. A detailed model of the ternary Michaelis complex fully supports the direct transfer of the acetyl group from acetyl-CoAmore » to choline through a mechanism similar to that seen in the serine hydrolases for the formation of an acyl-enzyme intermediate. Domain movements accompany CoA binding, and a surface loop, which is disordered in the unliganded enzyme, becomes localized and binds directly to the phosphates of CoA, stabilizing the complex. Interactions between this surface loop and CoA may function to lower the K{sub M} for CoA and could be important for phosphorylation-dependent regulation of ChAT activity.« less

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

PubMed

Pérez, Serge; Tubiana, Thibault; Imberty, Anne; Baaden, Marc

2015-05-01

A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein-carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Location and magnetic relaxation properties of the stable tyrosine radical in photosystem II.

PubMed

Innes, J B; Brudvig, G W

1989-02-07

Dipolar interactions with neighboring metal ions can cause enhanced spin-lattice relaxation of free radicals. We have applied the theory of dipolar relaxation enhancement and shown that the dependence of the enhanced relaxation on the protein structure surrounding the free radical can be used to obtain distances from the free radical to the protein surface. To test the theoretical predictions, we have examined the effect of added Dy3+ complexes on the microwave power saturation of free radicals in two protein complexes of known structure: myoglobin nitroxide and the reaction center from Rhodobacter sphaeroides. Three cases have been considered: (1) metal ions bound to a specific site, (2) metal ions bound randomly over the protein surface, and (3) metal ions distributed randomly in solution. Only case 3, which assumes no specific binding, gave good agreement between the distances obtained by using the two model systems. The effect of added Dy3+ complexes on the microwave power saturation of signal IIslow from photosystem II (PSII) was used to determine the location of the stable tyrosine radical giving rise to signal IIslow. Assuming that the surface of a membrane-bound protein can be approximated as planar, we have obtained distances from the tyrosine radical to the membrane surface in thylakoids, in PSII membranes, and in Tris-washed PSII membranes. The distances we have determined are in good agreement with those predicted on the basis of a structural homology between the D1 and D2 subunits of PSII and the structurally characterized L and M subunits of the reaction center from purple non-sulfur bacteria. We have also examined the temperature dependence of the microwave power at half-saturation (P1/2) of signal IIslow from 4 to 200 K in dark-adapted PSII membranes. Above 70 K, the P1/2 increases as T2.5, which is consistent with a Raman relaxation mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)

Engineering yeast consortia for surface-display of complex cellulosome structures

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

Chen, Wilfred

As our society marches toward a more technologically advanced future, energy and environmental sustainability are some of the most challenging problems we face today. Biomass is one of the most abundant renewable-feedstock for sustainable production of biofuels. However, the main technological obstacle to more widespread uses of this resource is the lack of low-cost technologies to overcome the recalcitrant nature of the cellulosic structure, especially the hydrolysis step on highly ordered celluloses. In this proposal, we successfully engineered several efficient and inexpensive whole-cell biocatalysts in an effort to produce economically compatible and sustainable biofuels, namely cellulosic ethanol. Our approach wasmore » to display of a highly efficient cellulolytic enzyme complex, named cellulosome, on the surface of a historical ethanol producer Saccharomyces cerevisiae for the simultaneous and synergistic saccharification and fermentation of cellulose to ethanol. We first demonstrated the feasibility of assembling a mini-cellulosome by incubating E. coli lysates expressing three different cellulases. Resting cells displaying mini-cellulosomes produced 4-fold more ethanol from phosphoric acid-swollen cellulose (PASC) than cultures with only added enzymes. The flexibility to assemble the mini-cellulosome structure was further demonstrated using a synthetic yeast consortium through intracellular complementation. Direct ethanol production from PASC was demonstrated with resting cell cultures. To create a microorganism suitable for a more cost-effective process, called consolidated bioprocessing (CBP), a synthetic consortium capable of displaying mini-cellulosomes on the cell surface via intercellular complementation was created. To further improve the efficiency, a new adaptive strategy of employing anchoring and adaptor scaffoldins to amplify the number of enzymatic subunits was developed, resulting in the creation of an artificial tetravalent cellulosome on the yeast surface and a significant improvement in cellulosic ethanol production. Although this adaptive strategy is ideal for assembling more complex cellulosome for large-scale production of cellulosic ethanol, a substantially larger number of enzymes (up to 10 to 12) is needed to better mimic the natural cellulosome structures for practical usage of the technology.« less

Method for the thermal characterization, visualization, and integrity evaluation of conducting material samples or complex structures

DOEpatents

Ortiz, Marcos G.

1992-01-01

A method for modeling a conducting material sample or structure (herein called a system) as at least two regions which comprise an electrical network of resistances, for measuring electric resistance between at least two selected pairs of external leads attached to the surface of the system, wherein at least one external lead is attached to the surface of each of the regions, and, using basic circuit theory, for translating measured resistances into temperatures or thermophysical properties in corresponding regions of the system.

Method for the thermal characterization, visualization, and integrity evaluation of conducting material samples or complex structures

DOEpatents

Ortiz, M.G.

1992-11-24

Disclosed is a method for modeling a conducting material sample or structure (herein called a system) as at least two regions which comprise an electrical network of resistances, for measuring electric resistance between at least two selected pairs of external leads attached to the surface of the system, wherein at least one external lead is attached to the surface of each of the regions, and, using basic circuit theory, for translating measured resistances into temperatures or thermophysical properties in corresponding regions of the system. 16 figs.

A Chemical Approach to Understanding Oxide Surface Structure and Reactivity

NASA Astrophysics Data System (ADS)

Enterkin, James Andrew

Transmission electron microscopy and diffraction are powerful tools for solving complex structural problems. They complement other analytical techniques, such as x-ray diffraction, elucidating problems which cannot be solved by other techniques. One area where they are of particularly great value is in the determination of surface structures. The research presented herein uses electron microscopy and diffraction as the primary experimental techniques in the development of a chemistry of surface structures. High-resolution electron microscopy revealed that the La4Cu 3MoO12 structure has turbostratic disorder and a lower symmetry space group (Pm) than was previously found. The refinement of the x-ray data was significantly improved by using a disordered model and the Pm space group. A bond valence analysis confirmed that the disordered structure is the superior model. Strontium titanate, SrTiO3, single crystal surfaces were examined principally via transmission electron diffraction. A homologous series with intergrowths was discovered on the (110) surface of strontium titanate, marking the first time that these important concepts of solid state chemistry have been found at the surface. Atmospheric adsorbates, such as H2O and CO2, were found to help to stabilize undercoordinated surface structures on the (100) surface. It was shown that chemical bonding, bond valence, atomic coordination, and stoichiometry greatly influence the development of surface structures. Additionally, such chemistry based analysis was demonstrated to be able to predict surface structure stability and reactivity. Application of a modified Wulff construction to the observed shape of strontium titanate nanocuboids revealed that the surface structure and particle stoichiometry are interlinked, with control over one allowing equally precise control over the other. Platinum nanoparticles on the strontium titanate nanocuboids were shown via high resolution electron microscopy to have cube-on-cube epitaxy, with the shape of the platinum nanoparticles governed by the Winterbottom construction. Precise modification of the support surface will therefore allow engineering of supported metal particles with precise control over which facets are exposed. These results suggest that control over the support surface chemistry can be used to engineer thermodynamically stable, face selective catalysts.

Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-d-maltoside using small-angle neutron scattering and molecular dynamics simulation

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

Le, Rosemary K.; Harris, Bradley J.; Iwuchukwu, Ifeyinwa J.

2014-05-01

Small-angle neutron scattering (SANS) and molecular dynamics (MD) simulation were used to investigate the structure of trimeric photosystem I (PSI) from Thermosynechococcus elongatus (T. elongatus) stabilized in n-dodecyl-β-d-maltoside (DDM) detergent solution. Scattering curves of detergent and protein–detergent complexes were measured at 18% D2O, the contrast match point for the detergent, and 100% D2O, allowing observation of the structures of protein/detergent complexes. It was determined that the maximum dimension of the PSI–DDM complex was consistent with the presence of a monolayer belt of detergent around the periphery of PSI. A dummy-atom reconstruction of the shape of the complex from the SANSmore » data indicates that the detergent envelope has an irregular shape around the hydrophobic periphery of the PSI trimer rather than a uniform, toroidal belt around the complex. A 50 ns MD simulation model (a DDM ring surrounding the PSI complex with extra interstitial DDM) of the PSI–DDM complex was developed for comparison with the SANS data. The results suggest that DDM undergoes additional structuring around the membrane-spanning surface of the complex instead of a simple, relatively uniform belt, as is generally assumed for studies that use detergents to solubilize membrane proteins.« less

Software Development for a Three-Dimensional Gravity Inversion and Application to Study of the Border Ranges Fault System, South-Central Alaska

NASA Astrophysics Data System (ADS)

Cardenas, R.; Doser, D. I.; Baker, M. R.

2011-12-01

Summary The Border Ranges Fault (BRFS) system bounds the Cook Inlet and Susitna Basins, an important petroleum province within south-central Alaska. An initial research goal is to test several plausible models of structure along the Border Ranges Fault System by developing a novel, 3D inversion software package. The inversion utilizes gravity data constrained with geophysical, borehole, and surface geological information. The novel inversion approach involves directly modeling known geology, initially free-air corrected data, and revising a priori uncertainties on the geologic model to allow comparisons to alternative interpretations. This technique to evaluate 3D structure in regions of highly complex geology can be applied in other studies of energy resources. The software reads an ASCII text file containing the latitude, longitude, elevation, and Free Air anomalies of each gravity station as well as gridded surface files of known topology. The contributions of each node in the grid are computed in order to compare the theoretical gravity calculations from a forward model to the gravity observations. The computation of solutions to the "linearized" inversion yields a range of plausible densities. The user will have the option of varying body proportions and dimensions to compare variations in density for changing depths of the gridded surface. Introduction Previous modeling of the BRFS using geophysical data has been limited due to the complexity of local geology and structure, both of shallow crustal features and the deeper subduction zone. Since the inversion is based on a sequence of gridded surfaces, it is feasible to develop software to help build these gridded geologic models. Without a way to modify grid surface elevations, density, and magnetic susceptibility in real time, the inversion process for the geologist would be highly nonlinear and poorly constrained, especially in structural geology this complex. Without a basic understanding of the geometry of the BRFS, its role in the formation and petroleum generation processes of the upper Cook Inlet and Susitna Basins is poorly understood. Model Generation The gravitational contributions are computed using a geophysics formulation, namely the vertical line element. g = πR2Gρ(x2+y2+z2)-1/2 Each line element is semi-infinite and extends from the top to the bottom of each structural layer. The user may define a three-dimensional body at a location on the surface. Each vertex of the body will be represented as separate nodes in the grid. The contribution of the body to the gravity value will be computed as a volume integral and added to the overall gravity contributions of other nodes on the surface. The user will also be able to modify the elevation and density of the defined body in real time. The most noted effectiveness of the software is in the user-defined a priori information facilitating real time interpretations and the computational efficiency of the model solution by using vertical line elements to address structural bodies with complex geometry.

Thinking Forbidden Thoughts: The Oedipus Complex as a Complex of Knowing.

PubMed

Schein, Michael

2016-04-01

The Oedipus complex, considered by Freud the "nuclear complex of development," played a central role in the evolution of psychoanalytic thought. This paper returns to the point of transition from the seduction theory, Freud's initial theorem, to the oedipal model, and suggests that the Oedipus complex is first and foremost a text and as such contains a multiplicity of narratives. In particular, the author articulates the close relation between the Oedipus complex and the subject of knowing, postulating that underlying its surface level, the deep-level structure of this complex is one of knowing. As a complex of knowing it is of dual quality, both promoting and impeding the ability to know.

A method for surface topography measurement using a new focus function based on dual-tree complex wavelet transform

NASA Astrophysics Data System (ADS)

Li, Shimiao; Guo, Tong; Yuan, Lin; Chen, Jinping

2018-01-01

Surface topography measurement is an important tool widely used in many fields to determine the characteristics and functionality of a part or material. Among existing methods for this purpose, the focus variation method has proved high performance particularly in large slope scenarios. However, its performance depends largely on the effectiveness of focus function. This paper presents a method for surface topography measurement using a new focus measurement function based on dual-tree complex wavelet transform. Experiments are conducted on simulated defocused images to prove its high performance in comparison with other traditional approaches. The results showed that the new algorithm has better unimodality and sharpness. The method was also verified by measuring a MEMS micro resonator structure.

Medicaid's Complex Goals: Challenges for Managed Care and Behavioral Health

PubMed Central

Gold, Marsha; Mittler, Jessica

2000-01-01

The Medicaid program has become increasingly complex as policymakers use it to address various policy objectives, leading to structural tensions that surface with Medicaid managed care. In this article, we illustrate this complexity by focusing on the experience of three States with behavioral health carveouts—Maryland, Oregon, and Tennessee. Converting to Medicaid managed care forces policymakers to confront Medicaid's competing policy objectives, multiplicity of stakeholders, and diverse patients, many with complex needs. Emerging Medicaid managed care systems typically represent compromises in which existing inequities and fragmentation are reconfigured rather than eliminated. PMID:12500322

Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure.

PubMed

Lee, Tzong-Hsien; Hirst, Daniel J; Kulkarni, Ketav; Del Borgo, Mark P; Aguilar, Marie-Isabel

2018-06-13

The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.

Attachment dynamics of Photosystem I on nano-tailored surfaces for photovoltaic applications

NASA Astrophysics Data System (ADS)

Mukherjee, Dibyendu; Bruce, Barry D.; Khomami, Bamin

2010-03-01

Photosystem I (PSI), a biological photodiode, is a supra-molecular protein complex that charge separates upon exposure to light. Effective use of photo-electrochemical activities of PSI for hybrid photovoltaic (PV) device fabrications requires optimal encapsulation of these proteins onto organic/ inorganic substrates. Our results indicate that various experimental parameters alter the surface attachment dynamics of PSI deposited from colloidal aqueous buffer suspensions onto OH-terminated alkanethiolate/Au SAM substrates, thereby resulting in complex structural arrangements which affect the electron transfer and capture pathway of PSI. We present surface topographical, specific adsorption and polarization fluorescence characterizations of PSI/Au SAM substrates to elucidate the protein-surface interaction kinetics as well as the directional attachment dynamics of PSI. Our final goal is to enable site-specific homogeneous attachment of directionally aligned PSI onto chemically tailored nano-patterned substrates.

One-step volumetric additive manufacturing of complex polymer structures

DOE PAGES

Shusteff, Maxim; Browar, Allison E. M.; Kelly, Brett E.; ...

2017-12-01

Two limitations of additive manufacturing methods that arise from layer-based fabrication are slow speed and geometric constraints (which include poor surface quality). Both limitations are overcome in the work reported here, introducing a new volumetric additive fabrication paradigm that produces photopolymer structures with complex non-periodic 3D geometries on a timescale of seconds. We implement this approach using holographic patterning of light fields, demonstrate the fabrication of a variety of structures, and study the properties of the light patterns and photosensitive resins required for this fabrication approach. The results indicate that lowabsorbing resins containing ~0.1% photoinitiator, illuminated at modest powers (~10-100more » mW) may be successfully used to build full structures in ~1-10 s.« less

One-step volumetric additive manufacturing of complex polymer structures

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

Shusteff, Maxim; Browar, Allison E. M.; Kelly, Brett E.

Two limitations of additive manufacturing methods that arise from layer-based fabrication are slow speed and geometric constraints (which include poor surface quality). Both limitations are overcome in the work reported here, introducing a new volumetric additive fabrication paradigm that produces photopolymer structures with complex non-periodic 3D geometries on a timescale of seconds. We implement this approach using holographic patterning of light fields, demonstrate the fabrication of a variety of structures, and study the properties of the light patterns and photosensitive resins required for this fabrication approach. The results indicate that lowabsorbing resins containing ~0.1% photoinitiator, illuminated at modest powers (~10-100more » mW) may be successfully used to build full structures in ~1-10 s.« less

Rethinking cell structure.

PubMed Central

Penman, S

1995-01-01

Cell structure, emerging from behind the veil of conventional electron microscopy, appears far more complex than formerly realized. The standard plastic-embedded, ultrathin section can image only what is on the section surface and masks the elaborate networks of the cytoplasm and nucleus. Embedment-free electron microscopy gives clear, high-contrast micrographs of cell structure when combined with removal of obscuring material such as soluble proteins. The resinless ultrathin section is the technique of choice; it is simple and inexpensive, and it uses ordinary electron microscopes. The resulting pictures reveal a world of complex cell structure and function. These images necessarily change our conception of the cytoskeleton, nuclear matrix, mitosis, and the relation of membranes to cytostructure. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7777493

One-step volumetric additive manufacturing of complex polymer structures

PubMed Central

Shusteff, Maxim; Browar, Allison E. M.; Kelly, Brett E.; Henriksson, Johannes; Weisgraber, Todd H.; Panas, Robert M.; Fang, Nicholas X.; Spadaccini, Christopher M.

2017-01-01

Two limitations of additive manufacturing methods that arise from layer-based fabrication are slow speed and geometric constraints (which include poor surface quality). Both limitations are overcome in the work reported here, introducing a new volumetric additive fabrication paradigm that produces photopolymer structures with complex nonperiodic three-dimensional geometries on a time scale of seconds. We implement this approach using holographic patterning of light fields, demonstrate the fabrication of a variety of structures, and study the properties of the light patterns and photosensitive resins required for this fabrication approach. The results indicate that low-absorbing resins containing ~0.1% photoinitiator, illuminated at modest powers (~10 to 100 mW), may be successfully used to build full structures in ~1 to 10 s. PMID:29230437

One-step volumetric additive manufacturing of complex polymer structures.

PubMed

Shusteff, Maxim; Browar, Allison E M; Kelly, Brett E; Henriksson, Johannes; Weisgraber, Todd H; Panas, Robert M; Fang, Nicholas X; Spadaccini, Christopher M

2017-12-01

Two limitations of additive manufacturing methods that arise from layer-based fabrication are slow speed and geometric constraints (which include poor surface quality). Both limitations are overcome in the work reported here, introducing a new volumetric additive fabrication paradigm that produces photopolymer structures with complex nonperiodic three-dimensional geometries on a time scale of seconds. We implement this approach using holographic patterning of light fields, demonstrate the fabrication of a variety of structures, and study the properties of the light patterns and photosensitive resins required for this fabrication approach. The results indicate that low-absorbing resins containing ~0.1% photoinitiator, illuminated at modest powers (~10 to 100 mW), may be successfully used to build full structures in ~1 to 10 s.

Surface Immobilization of Molecular Electrocatalysts for Energy Conversion

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

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

2017-03-22

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

Capacitance-based damage detection sensing for aerospace structural composites

NASA Astrophysics Data System (ADS)

Bahrami, P.; Yamamoto, N.; Chen, Y.; Manohara, H.

2014-04-01

Damage detection technology needs improvement for aerospace engineering application because detection within complex composite structures is difficult yet critical to avoid catastrophic failure. Damage detection is challenging in aerospace structures because not all the damage detection technology can cover the various defect types (delamination, fiber fracture, matrix crack etc.), or conditions (visibility, crack length size, etc.). These defect states are expected to become even more complex with future introduction of novel composites including nano-/microparticle reinforcement. Currently, non-destructive evaluation (NDE) methods with X-ray, ultrasound, or eddy current have good resolutions (< 0.1 mm), but their detection capabilities is limited by defect locations and orientations and require massive inspection devices. System health monitoring (SHM) methods are often paired with NDE technologies to signal out sensed damage, but their data collection and analysis currently requires excessive wiring and complex signal analysis. Here, we present a capacitance sensor-based, structural defect detection technology with improved sensing capability. Thin dielectric polymer layer is integrated as part of the structure; the defect in the structure directly alters the sensing layer's capacitance, allowing full-coverage sensing capability independent of defect size, orientation or location. In this work, capacitance-based sensing capability was experimentally demonstrated with a 2D sensing layer consisting of a dielectric layer sandwiched by electrodes. These sensing layers were applied on substrate surfaces. Surface indentation damage (~1mm diameter) and its location were detected through measured capacitance changes: 1 to 250 % depending on the substrates. The damage detection sensors are light weight, and they can be conformably coated and can be part of the composite structure. Therefore it is suitable for aerospace structures such as cryogenic tanks and rocket fairings for example. The sensors can also be operating in space and harsh environment such as high temperature and vacuum.

Structure and function of complex I in animals and plants - a comparative view.

PubMed

Senkler, Jennifer; Senkler, Michael; Braun, Hans-Peter

2017-09-01

The mitochondrial NADH dehydrogenase complex (complex I) has a molecular mass of about 1000 kDa and includes 40-50 subunits in animals, fungi and plants. It is composed of a membrane arm and a peripheral arm and has a conserved L-like shape in all species investigated. However, in plants and possibly some protists it has a second peripheral domain which is attached to the membrane arm on its matrix exposed side at a central position. The extra domain includes proteins resembling prokaryotic gamma-type carbonic anhydrases. We here present a detailed comparison of complex I from mammals and flowering plants. Forty homologous subunits are present in complex I of both groups of species. In addition, five subunits are present in mammalian complex I, which are absent in plants, and eight to nine subunits are present in plant complex I which do not occur in mammals. Based on the atomic structure of mammalian complex I and biochemical insights into complex I architecture from plants we mapped the species-specific subunits. Interestingly, four of the five animal-specific and five of the eight to nine plant-specific subunits are localized at the inner surface of the membrane arm of complex I in close proximity. We propose that the inner surface of the membrane arm represents a workbench for attaching proteins to complex I, which are not directly related to respiratory electron transport, like nucleoside kinases, acyl-carrier proteins or carbonic anhydrases. We speculate that further enzyme activities might be bound to this micro-location in other groups of organisms. © 2017 Scandinavian Plant Physiology Society.

Influence of pea protein aggregates on the structure and stability of pea protein/soybean polysaccharide complex emulsions.

PubMed

Yin, Baoru; Zhang, Rujing; Yao, Ping

2015-03-20

The applications of plant proteins in the food and beverage industry have been hampered by their precipitation in acidic solution. In this study, pea protein isolate (PPI) with poor dispersibility in acidic solution was used to form complexes with soybean soluble polysaccharide (SSPS), and the effects of PPI aggregates on the structure and stability of PPI/SSPS complex emulsions were investigated. Under acidic conditions, high pressure homogenization disrupts the PPI aggregates and the electrostatic attraction between PPI and SSPS facilitates the formation of dispersible PPI/SSPS complexes. The PPI/SSPS complex emulsions prepared from the PPI containing aggregates prove to possess similar droplet structure and similar stability compared with the PPI/SSPS emulsions produced from the PPI in which the aggregates have been previously removed by centrifugation. The oil droplets are protected by PPI/SSPS complex interfacial films and SSPS surfaces. The emulsions show long-term stability against pH and NaCl concentration changes. This study demonstrates that PPI aggregates can also be used to produce stable complex emulsions, which may promote the applications of plant proteins in the food and beverage industry.

Effect of surface site interactions on potentiometric titration of hematite (α-Fe2O3) crystal faces.

PubMed

Chatman, Shawn; Zarzycki, P; Preočanin, T; Rosso, K M

2013-02-01

Time dependent potentiometric pH titrations were used to study the effect of atomic scale surface structure on the protonation behavior of the structurally well-defined hematite/electrolyte interfaces. Our recently proposed thermodynamic model [1,25] was applied to measured acidimetric and alkalimetric titration hysteresis loops, collected from highly organized (001), (012), and (113) crystal face terminations using pH equilibration times ranging from 15 to 30 min. Hysteresis loop areas indicate that (001) faces equilibrate faster than the (012) and (113) faces, consistent with the different expected ensembles of singly-, doubly-, and triply-coordinated surface sites on each face. Strongly non-linear hysteretic pH-potential relationships were found, with slopes exceeding Nernstian, collectively indicating that protonation and deprotonation is much more complex than embodied in present day surface complexation models. The asymmetrical shape of the acidimetric and alkalimetric titration branches were used to illustrate a proposed steric "leaky screen" repulsion/trapping interaction mechanism that stems from high affinity singly-coordinated sites electrostatically and sterically screening lower affinity doubly- and triply-coordinated sites. Our data indicate that site interaction is the dominant phenomenon defining surface potential accumulation behavior on single crystal faces of metal oxide minerals. Copyright © 2012 Elsevier Inc. All rights reserved.

Fracture Analysis of Semi-Elliptical Surface Cracks in Ductile Materials

NASA Technical Reports Server (NTRS)

Daniewicz, S. R.; Newman, J. C., Jr.; Leach, A. M.

2004-01-01

Accurate life assessment of structural components may require advanced life prediction criteria and methodologies. Structural components often exhibit several different types of defects, among the most prevalent being surface cracks. A semi-elliptical surface crack subjected to monotonic loading will exhibit stable crack growth until the crack has reached a critical size, at which the crack loses stability and fracture ensues (Newman, 2000). The shape and geometry of the flaw are among the most influential factors. When considering simpler crack configurations, such as a through-the-thickness crack, a three-dimensional (3D) geometry may be modeled under the approximation of two-dimensional (2D) plane stress or plane strain. The more complex surface crack is typically modeled numerically with the Finite Element Method (FEM). A semi-elliptical surface crack is illustrated in Figure 1-1.

Structure of the Repulsive Guidance Molecule (RGM)—Neogenin Signaling Hub

PubMed Central

Bell, Christian H.; Bishop, Benjamin; Tang, Chenxiang; Gilbert, Robert J.C.; Aricescu, A. Radu; Pasterkamp, R. Jeroen; Siebold, Christian

2016-01-01

Repulsive guidance molecule family members (RGMs) control fundamental and diverse cellular processes, including motility and adhesion, immune cell regulation, and systemic iron metabolism. However, it is not known how RGMs initiate signaling through their common cell-surface receptor, neogenin (NEO1). Here, we present crystal structures of the NEO1 RGM-binding region and its complex with human RGMB (also called dragon). The RGMB structure reveals a previously unknown protein fold and a functionally important autocatalytic cleavage mechanism and provides a framework to explain numerous disease-linked mutations in RGMs. In the complex, two RGMB ectodomains conformationally stabilize the juxtamembrane regions of two NEO1 receptors in a pH-dependent manner. We demonstrate that all RGM-NEO1 complexes share this architecture, which therefore represents the core of multiple signaling pathways. PMID:23744777

Polynuclear Aromatic Hydrocarbons with Curved Surfaces: Buckyballs

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

Sygula, Andrzej

The discovery of a new allotropic form of elemental carbon – the fullerenes – and subsequently other novel forms of elemental carbon with pyramidalized surfaces, most notably single-walled and multi-walled carbon nanotubes, introduced a novel structural motif to the polycyclic aromatic hydrocarbons (PAHs) with nonplanar surfaces. Our research program supported by BES DOE grant DE-FG02-04ER15514 has dealt with the synthesis, structural studies, and chemistry of the novel curved-surface PAHs with carbon frameworks structurally related to fullerenes. They are referred to as “buckybowls”. We prepared several new buckybowls and, even more importantly, developed the efficient, gram-scale synthetic methodologies for the preparationmore » of small buckybowls, most notably corannulene (C20H10) and its derivatives. In addition, the employment of the corannulene-based synthons previously developed in our laboratory led to a number of highly nonplanar molecular architectures with two or more corannulene subunits with a potential for the applications as novel materials in separation sciences, nanoelectronics, photovoltaics and catalysis. In collaboration with Professor Angelici (Iowa State) we prepared and characterized several transition metal complexes of corannulene, providing the first structural characterization of η6 metal complexes of buckybowls by a single crystal X-ray diffraction. In addition to the definitive structural characterization of the complexes we demonstrated that the (η6-C6Me6)Ru2+ unit in some relatively stable complexes activate the corannulene ligand to react with proper nucleophiles suggesting that such complexex may be used in catalysis. (Section C). We have explored the efficiency of the dispersion-based interactions of curved-surface conjugated carbon networks by high-level computational models. We showed that the curvature of such networks does not reduce the van der Waals attractions as compared to the planar systems of similar size. We than concentrated on the design, synthesis and testing of the previously unknown molecular receptors with corannulene pincers which are capable of forming the strong ball-and-socket inclusion complexes with fullerenes in solution and in the solid state. Buckycatcher I (a molecular receptor with two corannulene pincers preorganized on a tetrabensocyclooctatetraene tether) inclusion complexes with fullerenes provided the first experimental evidence for the importance of concave-convex π – π interactions in the supramolecular chemistry of fullerene carbon cages with buckybowls. C60@Buckycatcher I has become the prototypical supramolecular system formed by the relatively weak (on the atom-to-atom bases) and has been extensively used by the computational community to test the quality of the theoretical models. In addition, Buckycatcher I shows an exceptional ability to adopt other guest molecules and several its inclusion complexes and/or solvates have been structurally characterized. These unusual structures show the potential of the buckycatchers to be tested as novel organic materials. “Intelligent design” of molecular receptors with corannulene receptors using computational approach allowing for a priori prediction of their binding potentials led to the preparation of other buckycatchers. Both bi- and tridentate corannulene pincers were tested and two of the bidentate receptors (Buckycatchers II and III) exhibited the outstanding affinity toward fullerenes, significantly exciding Buckycatcher I performance. Careful tailoring of the tethers resulted in the optimization of binding energies of the receptors with guest carbon cages and in the reduction of the entropy/solvation penalties. Practical preparation of dicorannulenopentacene opens a new avenue for the synthesis of a pool of bis-corannulene receptors possessing polar groups on their dibenzobarrelene tether. The polar “anchors” can be used to attach these efficient fullerene receptors to solid supports in order to modify their surfaces with the potential applications in separation sciences, catalysis and photovoltaic materials. additionally, the presence of such groups will improve the solubility of the receptors in polar solvents, expanding the scope of their supramolecular chemistry in solutions. Rigorous studies of thermodynamics of host-guest association of molecular clips and tweezers in organic solvents with C60/C70 inclusion complexes with Buckycatcher I as a model system have provided a full set of thermodynamical data including ΔG, ΔH, and –TΔS, for the formation of the inclusion complexes over a range of temperatures and in several solvents. Both 1H NMR and Isothermal Calorimetry (ITC) titrations provide virtually identical association constants, confirming the reliability of the results. WE have shown that thermodynamics of the host-guest complex formation is more complicated than anticipated and proposed by the existing computational models. These data are of premium importance for the testing of the computational solvation models and for a deeper understanding of the supramolecular interactions in organic solvents.« less

Fuels planning: science synthesis and integration; forest structure and fire hazard fact sheet 05: fuel treatment principles for complex landscapes

Treesearch

Rocky Mountain Research Station USDA Forest Service

2004-01-01

Appropriate types of thinning and surface fuel treatments are clearly useful in reducing surface and crown fire hazards under a wide range of fuels and topographic situations. This paper provides well-established scientific principles and simulation tools that can be used to adjust fuel treatments to attain specific risk levels.

Predicting surface fuel models and fuel metrics using lidar and CIR imagery in a dense mixed conifer forest

Treesearch

Marek K. Jakubowksi; Qinghua Guo; Brandon Collins; Scott Stephens; Maggi Kelly

2013-01-01

We compared the ability of several classification and regression algorithms to predict forest stand structure metrics and standard surface fuel models. Our study area spans a dense, topographically complex Sierra Nevada mixed-conifer forest. We used clustering, regression trees, and support vector machine algorithms to analyze high density (average 9 pulses/m

Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

2018-03-01

The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

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

Chatman, Shawn ME; Zarzycki, Piotr P.; Preocanin, Tajana

Time dependent potentiometric pH titrations were used to study the effect of atomic scale surface structure on the protonation behavior of the structurally well defined hematite/aqueous electrolyte interfaces. Our recently proposed thermodynamic model [1,23] was applied to measured acidimetric and alkalimetric titration hysteresis loops, collected from highly organized (001), (012), and (113) crystal face terminations using pH equilibration times ranging from 15 to 30 mins. Hysteresis loop areas indicate that (001) faces equilibrate faster than the (012) and (113) faces, consistent with the different expected ensembles of singly, doubly, and triply coordinated surface sites on each face. Strongly non-linear hystereticmore » pH-potential relationships were found, with slopes exceeding Nernstian, collectively indicating that protonation and deprotonation is much more complex than embodied in present day surface complexation models. The asymmetrical shape of the acidimetric and alkalimetric titration branches were used to illustrate a proposed steric "leaky screen" repulsion/trapping interaction mechanism that stems from high affinity singly-coordinated sites electrostatically and sterically screening lower affinity doubly and triply coordinated sites. Our data indicate that site interaction is the dominant phenomenon defining surface potential accumulation behavior on single crystal faces of metal oxide minerals.« less

Glycine transporter dimers: evidence for occurrence in the plasma membrane.

PubMed

Bartholomäus, Ingo; Milan-Lobo, Laura; Nicke, Annette; Dutertre, Sébastien; Hastrup, Hanne; Jha, Alok; Gether, Ulrik; Sitte, Harald H; Betz, Heinrich; Eulenburg, Volker

2008-04-18

Different Na(+)/Cl(-)-dependent neurotransmitter transporters of the SLC6a family have been shown to form dimers or oligomers in both intracellular compartments and at the cell surface. In contrast, the glycine transporters (GlyTs) GlyT1 and -2 have been reported to exist as monomers in the plasma membrane based on hydrodynamic and native gel electrophoretic studies. Here, we used cysteine substitution and oxidative cross-linking to show that of GlyT1 and GlyT2 also form dimeric complexes within the plasma membrane. GlyT oligomerization at the cell surface was confirmed for both GlyT1 and GlyT2 by fluorescence resonance energy transfer microscopy. Endoglycosidase treatment and surface biotinylation further revealed that complex-glycosylated GlyTs form dimers located at the cell surface. Furthermore, substitution of tryptophan 469 of GlyT2 by an arginine generated a transporter deficient in dimerization that was retained intracellulary. Based on these results and GlyT structures modeled by using the crystal structure of the bacterial homolog LeuT(Aa), as a template, residues located within the extracellular loop 3 and at the beginning of transmembrane domain 6 are proposed to contribute to the dimerization interface of GlyTs.

Epoxy blanket protects milled part during explosive forming

NASA Technical Reports Server (NTRS)

1966-01-01

Epoxy blanket protects chemically milled or machined sections of large, complex structural parts during explosive forming. The blanket uniformly covers all exposed surfaces and fills any voids to support and protect the entire part.

Three-dimensional morphological and textural complexity of Archean putative microfossils from the Northeastern Pilbara Craton: indications of biogenicity of large (>15 microm) spheroidal and spindle-like structures.

PubMed

Sugitani, Kenichiro; Grey, Kathleen; Nagaoka, Tsutomu; Mimura, Koichi

2009-09-01

We recently reported a diverse assemblage of carbonaceous structures (thread-like, film-like, spheroidal, and spindle-like) from chert in the ca. 3.0 Ga Farrel Quartzite of the Gorge Creek Group in the Pilbara Craton, Western Australia. Results from a rigorous examination of occurrence, composition, morphological complexity, size distributions, and taphonomy provided presumptive evidence for biogenicity. In this study, we present new data of morphological and textural complexity of large (>15 microm) spheroidal and spindle-like structures, using an in-focus, 3-D image reconstruction system, which further raises the scale of credibility that these structures are microfossils. While many of the large spheroids are single-walled, and the wall is irregularly folded, a few specimens are partially blistered, double walled, or have a dimpled wall. The wall-surface texture varies from smooth and homogeneous (hyaline) to patchy, granular or reticulate. Such variation is best explained as resulting from taphonomic processes. Additionally, an inner solitary body, present in some large spheroids, is hollow and partially broken, which indicates a primary origin for this substructure. Spindle-like structures have two types of flange-like appendage; one is attached at the equatorial plane of the body, whereas the other appears to be attached peripherally. In both cases, the appendage tends to have a flat geometry, a tapering thickness, and constancy in shape, proportions, and dimensions. Spindle-wall surfaces are variously textured and heterogeneous. These morphological and textural complexities and heterogeneity refute potential abiogenic formation models for these structures, such as crystals coated with organic matter, fenestrae, and the diagenetic redistribution of carbonaceous matter. When coupled with other data from Raman spectroscopy, NanoSIMS analysis, and palynology, the evidence that these large carbonaceous structures are biogenic appears compelling, though it is still equivocal as to whether they are cells or outer envelopes of colonies of smaller cells.

Control the wettability of poly(n-isopropylacrylamide-co-1-adamantan-1-ylmethyl acrylate) modified surfaces: the more Ada, the bigger impact?

PubMed

Shi, Xiu-Juan; Chen, Gao-Jian; Wang, Yan-Wei; Yuan, Lin; Zhang, Qiang; Haddleton, David M; Chen, Hong

2013-11-19

Surface-initiated SET-LRP was used to synthesize polymer brush containing N-isopropylacrylamide and adamantyl acrylate using Cu(I)Cl/Me6-TREN as precursor catalyst and isopropanol/H2O as solvent. Different reaction conditions were explored to investigate the influence of different parameters (reaction time, catalyst concentration, monomer concentration) on the polymerization. Copolymers with variable 1-adamantan-1-ylmethyl acrylate (Ada) content and comparable thickness were synthesized onto silicon surfaces. Furthermore, the hydrophilic and bioactive molecule β-cyclodextrin-(mannose)7 (CDm) was synthesized and complexed with adamantane via host-guest interaction. The effect of adamantane alone and the effect of CDm together with adamantane on the wettability and thermoresponsive property of surface were investigated in detail. Experimental and molecular structure analysis showed that Ada at certain content together with CDm has the greatest impact on surface wettability. When Ada content was high (20%), copolymer-CDm surfaces showed almost no CDm complexed with Ada as the result of steric hindrance.

When lithography meets self-assembly: a review of recent advances in the directed assembly of complex metal nanostructures on planar and textured surfaces

NASA Astrophysics Data System (ADS)

Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana

2017-07-01

One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and employ a wide scope of chemical processes including redox reactions, alloying, dealloying, phase separation, galvanic replacement, preferential etching, template-mediated reactions, and facet-selective capping agents. Taken together, they highlight the diverse toolset available when fabricating organized surfaces of substrate-supported nanostructures.

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces.

PubMed

Lubin, Joseph H; Pacella, Michael S; Gray, Jeffrey J

2018-05-08

Although structures have been determined for many soluble proteins and an increasing number of membrane proteins, experimental structure determination methods are limited for complexes of proteins and solid surfaces. An economical alternative or complement to experimental structure determination is molecular simulation. Rosetta is one software suite that models protein-surface interactions, but Rosetta is normally benchmarked on soluble proteins. For surface interactions, the validity of the energy function is uncertain because it is a combination of independent parameters from energy functions developed separately for solution proteins and mineral surfaces. Here, we assess the performance of the RosettaSurface algorithm and test the accuracy of its energy function by modeling the adsorption of leucine/lysine (LK)-repeat peptides on methyl- and carboxy-terminated self-assembled monolayers (SAMs). We investigated how RosettaSurface predictions for this system compare with the experimental results, which showed that on both surfaces, LK-α peptides folded into helices and LK-β peptides held extended structures. Utilizing this model system, we performed a parametric analysis of Rosetta's Talaris energy function and determined that adjusting solvation parameters offered improved predictive accuracy. Simultaneously increasing lysine carbon hydrophilicity and the hydrophobicity of the surface methyl head groups yielded computational predictions most closely matching the experimental results. De novo models still should be interpreted skeptically unless bolstered in an integrative approach with experimental data.

From Laser Scanning to Finite Element Analysis of Complex Buildings by Using a Semi-Automatic Procedure

PubMed Central

Castellazzi, Giovanni; D’Altri, Antonio Maria; Bitelli, Gabriele; Selvaggi, Ilenia; Lambertini, Alessandro

2015-01-01

In this paper, a new semi-automatic procedure to transform three-dimensional point clouds of complex objects to three-dimensional finite element models is presented and validated. The procedure conceives of the point cloud as a stacking of point sections. The complexity of the clouds is arbitrary, since the procedure is designed for terrestrial laser scanner surveys applied to buildings with irregular geometry, such as historical buildings. The procedure aims at solving the problems connected to the generation of finite element models of these complex structures by constructing a fine discretized geometry with a reduced amount of time and ready to be used with structural analysis. If the starting clouds represent the inner and outer surfaces of the structure, the resulting finite element model will accurately capture the whole three-dimensional structure, producing a complex solid made by voxel elements. A comparison analysis with a CAD-based model is carried out on a historical building damaged by a seismic event. The results indicate that the proposed procedure is effective and obtains comparable models in a shorter time, with an increased level of automation. PMID:26225978

Surface active complexes formed between keratin polypeptides and ionic surfactants.

PubMed

Pan, Fang; Lu, Zhiming; Tucker, Ian; Hosking, Sarah; Petkov, Jordan; Lu, Jian R

2016-12-15

Keratins are a group of important proteins in skin and hair and as biomaterials they can provide desirable properties such as strength, biocompatibility, and moisture regaining and retaining. The aim of this work is to develop water-soluble keratin polypeptides from sheep wool and then explore how their surface adsorption behaves with and without surfactants. Successful preparation of keratin samples was demonstrated by identification of the key components from gel electrophoresis and the reproducible production of gram scale samples with and without SDS (sodium dodecylsulphate) during wool fibre dissolution. SDS micelles could reduce the formation of disulphide bonds between keratins during extraction, reducing inter-molecular crosslinking and improving keratin polypeptide solubility. However, Zeta potential measurements of the two polypeptide batches demonstrated almost identical pH dependent surface charge distributions with isoelectric points around pH 3.5, showing complete removal of SDS during purification by dialysis. In spite of different solubility from the two batches of keratin samples prepared, very similar adsorption and aggregation behavior was revealed from surface tension measurements and dynamic light scattering. Mixing of keratin polypeptides with SDS and C 12 TAB (dodecyltrimethylammonium bromide) led to the formation of keratin-surfactant complexes that were substantially more effective at reducing surface tension than the polypeptides alone, showing great promise in the delivery of keratin polypeptides via the surface active complexes. Neutron reflection measurements revealed the coexistence of surfactant and keratin polypeptides at the interface, thus providing the structural support to the observed surface tension changes associated with the formation of the surface active complexes. Copyright © 2016. Published by Elsevier Inc.

Properties of Self-Assembled Monolayers Revealed via Inverse Tensiometry.

PubMed

Chen, Jiahao; Wang, Zhengjia; Oyola-Reynoso, Stephanie; Thuo, Martin M

2017-11-28

Self-assembled monolayers (SAMs) have emerged as a simple platform technology and hence have been broadly studied. With advances in state-of-the-art fabrication and characterization methods, new insights into SAM structure and related properties have been delineated, albeit with some discrepancies and/or incoherencies. Some discrepancies, especially between experimental and theoretical work, are in part due to the misunderstanding of subtle structural features such as phase evolution and SAM quality. Recent work has, however, shown that simple techniques, such as the measurement of static contact angles, can be used to delineate otherwise complex properties of the SAM, especially when complemented by other more advanced techniques. In this article, we highlight the effect of nanoscale substrate asperities and molecular chain length on the SAM structure and associated properties. First, surfaces with tunable roughness are prepared on both Au and Ag, and their corresponding n-alkanethiolate SAMs are characterized through wetting and spectroscopy. From these data, chain-length- and substrate-morphology-dependent limits to the odd-even effect (structure and properties vary with the number of carbons in the molecules and the nature of the substrate), parametrization of gauche defect densities, and structural phase evolution (liquidlike, waxy, crystalline interfaces) are deduced. An evaluation of the correlation between the effect of roughness and the components of surface tension (polar-γ p and dispersive-γ d ) reveals that wetting, at nanoscale rough surfaces, evolves proportionally with the ratio of the two components of surface tension. The evolution of conformational order is captured over a range of molecular lengths and parametrized through a dimensionless number, χ c . By deploying a well-known tensiometry technique (herein the liquid is used to characterize the solid, hence the term inverse tensiometry) to characterize SAMs, we demonstrate that complex molecular-level phenomena in SAMs can be understood through simplicity.

Supramolecular structures on silica surfaces and their adsorptive properties.

PubMed

Belyakov, Vladimir N; Belyakova, Lyudmila A; Varvarin, Anatoly M; Khora, Olexandra V; Vasilyuk, Sergei L; Kazdobin, Konstantin A; Maltseva, Tetyana V; Kotvitskyy, Alexey G; Danil de Namor, Angela F

2005-05-01

The study of adsorptive and chemical immobilization of beta-cyclodextrin on a surface of hydroxylated silicas with various porous structure is described. Using IR spectroscopy, thermal gravimetrical analysis with a programmed heating, and chemical analysis of the silica surface, it is shown that the process of adsorption-desorption of beta-cyclodextrin depends on the porous structure of the silica. The reaction of esterification was used for chemical grafting of beta-cyclodextrin on the surface of hydroxylated silicas. Hydrolytic stability of silicas chemically modified by beta-cyclodextrin apparently is explained by simultaneous formation of chemical and hydrogen bonds between surface silanol groups and hydroxyl groups of beta-cyclodextrin. The uptake of the cations Cu(II), Cd(II), and Pb(II) and the anions Cr(VI) and As(V) by silicas modified with beta-cyclodextrin is investigated as a function of equilibrium ion concentrations. The increase of ion uptake and selectivity of ion extraction in comparison with starting silicas is established. It is due to the formation of surface inclusion complexes of the "host-guest" type in which one molecule of beta-cyclodextrin interacts simultaneously with several ions.

Structure and functional properties of TiNiZr surface layers obtained by high-velocity oxygen fuel spraying

NASA Astrophysics Data System (ADS)

Rusinov, P. O.; Blednova, Zh M.; Borovets, O. I.

2017-05-01

The authors studied a complex method of surface modification of steels for materials with shape memory effect (SME) Ti-Ni-Zr with a high-velocity oxygen-fuel spraying (HVOF) of mechanically activated (MA) powder in a protective medium. We assessed the functional properties and X-ray diffraction studies, which showed that the formation of surface layers according to the developed technology ensures the manifestation of the shape memory effect.

Variable-Domain Displacement Transfer Functions for Converting Surface Strains into Deflections for Structural Deformed Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2015-01-01

Variable-Domain Displacement Transfer Functions were formulated for shape predictions of complex wing structures, for which surface strain-sensing stations must be properly distributed to avoid jointed junctures, and must be increased in the high strain gradient region. Each embedded beam (depth-wise cross section of structure along a surface strain-sensing line) was discretized into small variable domains. Thus, the surface strain distribution can be described with a piecewise linear or a piecewise nonlinear function. Through discretization, the embedded beam curvature equation can be piece-wisely integrated to obtain the Variable-Domain Displacement Transfer Functions (for each embedded beam), which are expressed in terms of geometrical parameters of the embedded beam and the surface strains along the strain-sensing line. By inputting the surface strain data into the Displacement Transfer Functions, slopes and deflections along each embedded beam can be calculated for mapping out overall structural deformed shapes. A long tapered cantilever tubular beam was chosen for shape prediction analysis. The input surface strains were analytically generated from finite-element analysis. The shape prediction accuracies of the Variable- Domain Displacement Transfer Functions were then determined in light of the finite-element generated slopes and deflections, and were fofound to be comparable to the accuracies of the constant-domain Displacement Transfer Functions

Solid-State Synthesized Nanostructured Au Dendritic Aggregates Towards Surface-Enhanced Raman Spectroscopy

NASA Astrophysics Data System (ADS)

Gentile, A.; Ruffino, F.; D'Andrea, C.; Gucciardi, P. G.; Reitano, R.; Grimaldi, M. G.

2016-06-01

Micrometric Au structures, presenting a dendritic nano-structure, have been fabricated on a Si-based substrate. The fabrication method involves the deposition of a thin Au film on the substrate and a high-temperature annealing (1100°C) using fast heating and cooling ramps. The thermal process produces the growth, from the substrate, of Si micro-pillars whose top surfaces, covered by a crystalline Au layer, present a nanodendritic morphology. In addition to the micro-pillars, the sample surface presents a complex structural and chemical composition including Si3N4 regions due to the silicon-nitrogen intermixing during the heating stage. By studying the kinetic processes at the Au-Si interface during the thermal treatment, we describe the stages involved in the micro-pillars growth, in the dendritic morphology development, and in the Au atoms entrapment at the top of the dendritic surfaces. Finally, we present the analyses of the optical and surface enhanced Raman scattering properties of the Au dendritic aggregates. We show, in particular, that: (1) the Au dendrites aggregates act as effective scattering elements for the electromagnetic radiation in the infrared spectral region; and (2) the higher surface area due to the branched dendritic structure is responsible for the improvement in the sensitivity of the surface enhanced Raman scattering activity.

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

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

Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan

The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less

Structural Basis of HCV Neutralization by Human Monoclonal Antibodies Resistant to Viral Neutralization Escape

PubMed Central

Krey, Thomas; Meola, Annalisa; Keck, Zhen-yong; Damier-Piolle, Laurence; Foung, Steven K. H.; Rey, Felix A.

2013-01-01

The high mutation rate of hepatitis C virus allows it to rapidly evade the humoral immune response. However, certain epitopes in the envelope glycoproteins cannot vary without compromising virus viability. Antibodies targeting these epitopes are resistant to viral escape from neutralization and understanding their binding-mode is important for vaccine design. Human monoclonal antibodies HC84-1 and HC84-27 target conformational epitopes overlapping the CD81 receptor-binding site, formed by segments aa434–446 and aa610–619 within the major HCV glycoprotein E2. No neutralization escape was yet observed for these antibodies. We report here the crystal structures of their Fab fragments in complex with a synthetic peptide comprising aa434–446. The structures show that the peptide adopts an α-helical conformation with the main contact residues F442 and Y443 forming a hydrophobic protrusion. The peptide retained its conformation in both complexes, independently of crystal packing, indicating that it reflects a surface feature of the folded glycoprotein that is exposed similarly on the virion. The same residues of E2 are also involved in interaction with CD81, suggesting that the cellular receptor binds the same surface feature and potential escape mutants critically compromise receptor binding. In summary, our results identify a critical structural motif at the E2 surface, which is essential for virus propagation and therefore represents an ideal candidate for structure-based immunogen design for vaccine development. PMID:23696737

BiGGER: a new (soft) docking algorithm for predicting protein interactions.

PubMed

Palma, P N; Krippahl, L; Wampler, J E; Moura, J J

2000-06-01

A new computationally efficient and automated "soft docking" algorithm is described to assist the prediction of the mode of binding between two proteins, using the three-dimensional structures of the unbound molecules. The method is implemented in a software package called BiGGER (Bimolecular Complex Generation with Global Evaluation and Ranking) and works in two sequential steps: first, the complete 6-dimensional binding spaces of both molecules is systematically searched. A population of candidate protein-protein docked geometries is thus generated and selected on the basis of the geometric complementarity and amino acid pairwise affinities between the two molecular surfaces. Most of the conformational changes observed during protein association are treated in an implicit way and test results are equally satisfactory, regardless of starting from the bound or the unbound forms of known structures of the interacting proteins. In contrast to other methods, the entire molecular surfaces are searched during the simulation, using absolutely no additional information regarding the binding sites. In a second step, an interaction scoring function is used to rank the putative docked structures. The function incorporates interaction terms that are thought to be relevant to the stabilization of protein complexes. These include: geometric complementarity of the surfaces, explicit electrostatic interactions, desolvation energy, and pairwise propensities of the amino acid side chains to contact across the molecular interface. The relative functional contribution of each of these interaction terms to the global scoring function has been empirically adjusted through a neural network optimizer using a learning set of 25 protein-protein complexes of known crystallographic structures. In 22 out of 25 protein-protein complexes tested, near-native docked geometries were found with C(alpha) RMS deviations < or =4.0 A from the experimental structures, of which 14 were found within the 20 top ranking solutions. The program works on widely available personal computers and takes 2 to 8 hours of CPU time to run any of the docking tests herein presented. Finally, the value and limitations of the method for the study of macromolecular interactions, not yet revealed by experimental techniques, are discussed.

3D Thermomechanical Modeling of Rifted Margins with Coupled Surface Processes: the North West Shelf, Australia

NASA Astrophysics Data System (ADS)

Moresi, L. N.; Beucher, R.; Morón, S.; Rey, P. F.; Salles, T.; Brocard, G. Y.; Farrington, R.; Giordani, J.; Mansour, J.

2017-12-01

Thermo-mechanical numerical models and analogue experiments with a layered lithosphere have emphasised the role played by the composition and thermal state of the lithosphere on the style of extension. The variation in rheological properties and the coupling between lithospheric layers promote depth-dependent extension with the potential for complex rift evolution over space and time. Local changes in the stress field due to loading / unloading of the lithosphere can perturb the syn and post-rift stability of the margins. We investigate how erosion of the margins and sedimentation within the basins integrate with the thermo-mechanical processes involved in the structural and stratigraphic evolution of the North West Shelf (NWS), one of the most productive and prospective hydrocarbon provinces in Australia. The complex structural characteristics of the NWS include large-scale extensional detachments, difference between amounts of crustal and lithospheric extension and prolonged episodes of thermal sagging after rifting episodes. It has been proposed that the succession of different extensional styles mechanisms (Cambrian detachment faulting, broadly distributed Permo-Carboniferous extension and Late Triassic to Early Cretaceous localised rift development) is best described in terms of variation in deformation response of a lithosphere that has strengthened from one extensional episode to the next. However, previous models invoking large-scale detachments fail to explain changes in extensional styles and overestimate the structural importance of relatively local detachments. Here, we hypothesize that an initially weak lithosphere would distribute deformation by ductile flow within the lower crust and that the interaction between crustal flow, thermal-evolution and sediment loading/unloading could explain some of the structural complexities recorded by the NWS. We run a series of fully coupled 3D thermo-mechanical numerical experiments that include realistic thermal and mechanical properties, as well as surface processes (erosion, sediments transport and sedimentation). This modeling approach aims to provide insights into the thermal and structural history of the NWS, and a better understanding of the complex interactions between tectonics and surface processes at rifted margins.

A pediatric brain structure atlas from T1-weighted MR images

NASA Astrophysics Data System (ADS)

Shan, Zuyao Y.; Parra, Carlos; Ji, Qing; Ogg, Robert J.; Zhang, Yong; Laningham, Fred H.; Reddick, Wilburn E.

2006-03-01

In this paper, we have developed a digital atlas of the pediatric human brain. Human brain atlases, used to visualize spatially complex structures of the brain, are indispensable tools in model-based segmentation and quantitative analysis of brain structures. However, adult brain atlases do not adequately represent the normal maturational patterns of the pediatric brain, and the use of an adult model in pediatric studies may introduce substantial bias. Therefore, we proposed to develop a digital atlas of the pediatric human brain in this study. The atlas was constructed from T1 weighted MR data set of a 9 year old, right-handed girl. Furthermore, we extracted and simplified boundary surfaces of 25 manually defined brain structures (cortical and subcortical) based on surface curvature. Higher curvature surfaces were simplified with more reference points; lower curvature surfaces, with fewer. We constructed a 3D triangular mesh model for each structure by triangulation of the structure's reference points. Kappa statistics (cortical, 0.97; subcortical, 0.91) indicated substantial similarities between the mesh-defined and the original volumes. Our brain atlas and structural mesh models (www.stjude.org/BrainAtlas) can be used to plan treatment, to conduct knowledge and modeldriven segmentation, and to analyze the shapes of brain structures in pediatric patients.

Selective adsorption of a supramolecular structure on flat and stepped gold surfaces

NASA Astrophysics Data System (ADS)

Peköz, Rengin; Donadio, Davide

2018-04-01

Halogenated aromatic molecules assemble on surfaces forming both hydrogen and halogen bonds. Even though these systems have been intensively studied on flat metal surfaces, high-index vicinal surfaces remain challenging, as they may induce complex adsorbate structures. The adsorption of 2,6-dibromoanthraquinone (2,6-DBAQ) on flat and stepped gold surfaces is studied by means of van der Waals corrected density functional theory. Equilibrium geometries and corresponding adsorption energies are systematically investigated for various different adsorption configurations. It is shown that bridge sites and step edges are the preferred adsorption sites for single molecules on flat and stepped surfaces, respectively. The role of van der Waals interactions, halogen bonds and hydrogen bonds are explored for a monolayer coverage of 2,6-DBAQ molecules, revealing that molecular flexibility and intermolecular interactions stabilize two-dimensional networks on both flat and stepped surfaces. Our results provide a rationale for experimental observation of molecular carpeting on high-index vicinal surfaces of transition metals.

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

PubMed

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

2014-04-28

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

Gels of sodium alginate‒chitosan interpolyelectrolyte complexes

NASA Astrophysics Data System (ADS)

Brovko, O. S.; Palamarchuk, I. A.; Val'chuk, N. A.; Chukhchin, D. G.; Bogolitsyn, K. G.; Boitsova, T. A.

2017-08-01

Aspects of the formation of gels of interpolyelectrolyte complexes (IPECs) based on sodium alginate (NaAlg) and chitosan are studied. The effect the conditions of synthesis and complex composition have on the morphological structure and functional properties of these complexes is examined. It is established that complexation in this system proceeds according to a mechanism of electrostatic interaction between the oppositely charged carboxylic groups of the L-hyaluronic acid pyranose cycles of NaAlg proximal polymer chains and chitosan's amino groups, along with a multitude of hydrogen bonds and dispersion forces. We show that the mechanism of IPEC formation is strongly influenced by the conformational state of a lyophilizing component that is present in the system in excess. The inner surfaces of cryogels based on NaAlg‒chitosan IPECs is found to be strongly influenced by the degree of conversion between the parental polyelectrolytes. The most developed mesoporous structure is obtained when a denser gel forms in the system.

A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB.

PubMed

Schubot, Florian D; Waugh, David S

2004-11-01

Structural studies of a ternary complex composed of the Yersina pestis virulence factors YopN, SycN and YscB were initially hampered by poor solubility of the individual proteins. Co-expression of all three proteins in Escherichia coli yielded a well behaved complex, but this sample proved to be recalcitrant to crystallization. As crystallization efforts remained fruitless, even after the proteolysis-guided engineering of a truncated YopN polypeptide, reductive methylation of lysine residues was employed to alter the surface properties of the complex. The methylated complex yielded crystals that diffracted X-rays to a maximal resolution of 1.8 A. The potential utility of reductive methylation as a remedial strategy for high-throughput structural biology was further underscored by the successful modification of a selenomethionine-substituted sample.

Hydration Differences Explain the Large Variations in the Complexation Thermodynamics of Modified γ-Cyclodextrins with Bile Salts.

PubMed

Køhler, Jonatan; Schönbeck, Christian; Westh, Peter; Holm, René

2016-01-28

The structure and thermodynamics of inclusion complexes of seven different γ-cyclodextrins (γCDs) and three biologically relevant bile salts (BS) were investigated in the present study. Natural γCD and six modified γCDs [two methyl-γCDs, one sulfobutyl ether-γCD (SBEγCD), and three 2-hydroxypropyl-γCDs (HPγCD)] and their complexes with BS were investigated by isothermal titration calorimetry, NMR, and molecular dynamics simulations. With the exception of the fully methylated γCD, which did not bind the BSs investigated, all of the γCDs formed 1:1 complexes with the BS, and the structures were similar to those with natural γCD; i.e., the modifications of the γCD had limited structural impact on the formation of complexes. Isothermal titration calorimetry was carried out over in the temperature interval 5-55 °C to enable the calculation of the stability constant (K) and the thermodynamic parameters enthalpy (ΔH°), entropy (ΔS°), and heat capacity (ΔCp°). The stability constants decreased with an increased degree of substitution (DS), with methyl substituents having a lower effect on the stability constant than the sulfobutyl ether and hydroxypropyl substituents on the stability constants. Enthalpy-entropy compensation was observed, since both enthalpy and entropy increased with the degree of substitution, which may reflect dehydration of the hydrophobic surface on both CD and BS. Calculations based on ΔCp° data suggested that each of the substituents dehydrated 10-20 (hydroxypropyl), 22-33 (sulfobutyl ether), and 10-15 Å(2) (methyl) of the BS surface area, in reasonable agreement with estimates from the molecular dynamics simulations. Combined with earlier investigations on modified βCDs, these results indicate general trends of the substituents on the thermodynamics of complex formation.

Habitat complexity influences fine scale hydrological processes and the incidence of stormwater runoff in managed urban ecosystems.

PubMed

Ossola, Alessandro; Hahs, Amy Kristin; Livesley, Stephen John

2015-08-15

Urban ecosystems have traditionally been considered to be pervious features of our cities. Their hydrological properties have largely been investigated at the landscape scale and in comparison with other urban land use types. However, hydrological properties can vary at smaller scales depending upon changes in soil, surface litter and vegetation components. Management practices can directly and indirectly affect each of these components and the overall habitat complexity, ultimately affecting hydrological processes. This study aims to investigate the influence that habitat components and habitat complexity have upon key hydrological processes and the implications for urban habitat management. Using a network of urban parks and remnant nature reserves in Melbourne, Australia, replicate plots representing three types of habitat complexity were established: low-complexity parks, high-complexity parks, and high-complexity remnants. Saturated soil hydraulic conductivity in low-complexity parks was an order of magnitude lower than that measured in the more complex habitat types, due to fewer soil macropores. Conversely, soil water holding capacity in low-complexity parks was significantly higher compared to the two more complex habitat types. Low-complexity parks would generate runoff during modest precipitation events, whereas high-complexity parks and remnants would be able to absorb the vast majority of rainfall events without generating runoff. Litter layers on the soil surface would absorb most of precipitation events in high-complexity parks and high-complexity remnants. To minimize the incidence of stormwater runoff from urban ecosystems, land managers could incrementally increase the complexity of habitat patches, by increasing canopy density and volume, preserving surface litter and maintaining soil macropore structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Echanges, interventions et actes de langage dans la structure de la conversation (Exchanges, Turns at Talk and Speech Acts in the Structure of Conversation).

ERIC Educational Resources Information Center

Roulet, Eddy

1981-01-01

Attempts to show how the surface structure of conversation can be described by means of a few principles and simple categories, regardless of its level of complexity. Accordingly, proposes a model that emphasizes the pragmatic functions of certain connectors and markers in the context of conversation exchanges. Societe Nouvelle Didier Erudition,…

Role of annealing on the structural and optical properties of nanostructured diaceto bis-benzimidazole Mn(II) complex thin films.

PubMed

Praveen, P A; Babu, R Ramesh; Ramamurthi, K

2017-02-15

A coordination complex, manganese incorporated benzimidazole, thin films were prepared by chemical bath deposition method. Structural characterization of the deposited films, carried out by Fourier transform infrared spectroscopy, Raman and electron paramagnetic resonance spectral analyses, reveals the distorted tetrahedral environment of the metal ion with bis-benzimidazole ligand. Further the molecular composition of the deposited metal complex was estimated by energy-dispersive X-ray spectroscopy. The prepared thin films were thermally treated to study the effect of annealing temperature on the surface morphology and the results showed that the surface homogeneity of the films increased for thermally treated films up to 150°C. But distortion and voids were observed for the films annealed at 200°C. The Raman analysis reveals the molecular hydrogen bond distortion which leads to the evaporation of the metal complex from the thin film surface with respect to annealing temperature. The linear and nonlinear optical properties of the as prepared and annealed films were studied using ultraviolet-visible transmittance spectroscopy, second harmonic generation and Z-scan analyses. Films annealed at 150°C show a better linear transmittance in the visible region and larger SHG efficiency and third order nonlinear susceptibility when compared with the other samples. Further, the film annealed at 150°C was subjected to optical switching analysis and demonstrated to have an inverted switching behavior. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

PubMed Central

Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

2013-01-01

Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

RNA-dependent RNA polymerase complex of Brome mosaic virus: analysis of the molecular structure with monoclonal antibodies.

PubMed

Dohi, Koji; Mise, Kazuyuki; Furusawa, Iwao; Okuno, Tetsuro

2002-11-01

Viral RNA-dependent RNA polymerase (RdRp) plays crucial roles in the genomic replication and subgenomic transcription of Brome mosaic virus (BMV), a positive-stranded RNA plant virus. BMV RdRp is a complex of virus-encoded 1a and 2a proteins and some cellular factors, and associates with the endoplasmic reticulum at an infection-specific structure in the cytoplasm of host cells. In this study, we investigate the gross structure of the active BMV RdRp complex using monoclonal antibodies raised against the 1a and 2a proteins. Immunoprecipitation experiments showed that the intermediate region between the N-terminal methyltransferase-like domain and the C-terminal helicase-like domain of 1a protein, and the N terminus region of 2a protein are exposed on the surface of the solubilized RdRp complex. Inhibition assays for membrane-bound RdRp suggested that the intermediate region between the methyltransferase-like and the helicase-like domains of 1a protein is located at the border of the region buried within a membrane structure or with membrane-associated material.

Structural assembly of the signaling competent ERK2–RSK1 heterodimeric protein kinase complex

PubMed Central

Alexa, Anita; Gógl, Gergő; Glatz, Gábor; Garai, Ágnes; Zeke, András; Varga, János; Dudás, Erika; Jeszenői, Norbert; Bodor, Andrea; Hetényi, Csaba; Reményi, Attila

2015-01-01

Mitogen-activated protein kinases (MAPKs) bind and activate their downstream kinase substrates, MAPK-activated protein kinases (MAPKAPKs). Notably, extracellular signal regulated kinase 2 (ERK2) phosphorylates ribosomal S6 kinase 1 (RSK1), which promotes cellular growth. Here, we determined the crystal structure of an RSK1 construct in complex with its activator kinase. The structure captures the kinase–kinase complex in a precatalytic state where the activation loop of the downstream kinase (RSK1) faces the enzyme's (ERK2) catalytic site. Molecular dynamics simulation was used to show how this heterodimer could shift into a signaling-competent state. This structural analysis combined with biochemical and cellular studies on MAPK→MAPKAPK signaling showed that the interaction between the MAPK binding linear motif (residing in a disordered kinase domain extension) and the ERK2 “docking” groove plays the major role in making an encounter complex. This interaction holds kinase domains proximal as they “readjust,” whereas generic kinase domain surface contacts bring them into a catalytically competent state. PMID:25730857

Structural basis for the Nanos-mediated recruitment of the CCR4-NOT complex and translational repression.

PubMed

Bhandari, Dipankar; Raisch, Tobias; Weichenrieder, Oliver; Jonas, Stefanie; Izaurralde, Elisa

2014-04-15

The RNA-binding proteins of the Nanos family play an essential role in germ cell development and survival in a wide range of metazoan species. They function by suppressing the expression of target mRNAs through the recruitment of effector complexes, which include the CCR4-NOT deadenylase complex. Here, we show that the three human Nanos paralogs (Nanos1-3) interact with the CNOT1 C-terminal domain and determine the structural basis for the specific molecular recognition. Nanos1-3 bind CNOT1 through a short CNOT1-interacting motif (NIM) that is conserved in all vertebrates and some invertebrate species. The crystal structure of the human Nanos1 NIM peptide bound to CNOT1 reveals that the peptide opens a conserved hydrophobic pocket on the CNOT1 surface by inserting conserved aromatic residues. The substitutions of these aromatic residues in the Nanos1-3 NIMs abolish binding to CNOT1 and abrogate the ability of the proteins to repress translation. Our findings provide the structural basis for the recruitment of the CCR4-NOT complex by vertebrate Nanos, indicate that the NIMs are the major determinants of the translational repression mediated by Nanos, and identify the CCR4-NOT complex as the main effector complex for Nanos function.

Molecular metal catalysts on supports: organometallic chemistry meets surface science.

PubMed

Serna, Pedro; Gates, Bruce C

2014-08-19

Recent advances in the synthesis and characterization of small, essentially molecular metal complexes and metal clusters on support surfaces have brought new insights to catalysis and point the way to systematic catalyst design. We summarize recent work unraveling effects of key design variables of site-isolated catalysts: the metal, metal nuclearity, support, and other ligands on the metals, also considering catalysts with separate, complementary functions on supports. The catalysts were synthesized with the goal of structural simplicity and uniformity to facilitate incisive characterization. Thus, they are essentially molecular species bonded to porous supports chosen for their high degree of uniformity; the supports are crystalline aluminosilicates (zeolites) and MgO. The catalytic species are synthesized in reactions of organometallic precursors with the support surfaces; the precursors include M(L)2(acetylacetonate)1-2, with M = Ru, Rh, Ir, or Au and the ligands L = C2H4, CO, or CH3. Os3(CO)12 and Ir4(CO)12 are used as precursors of supported metal clusters, and some such catalysts are made by ship-in-a-bottle syntheses to trap the clusters in zeolite cages. The simplicity and uniformity of the supported catalysts facilitate precise structure determinations, even in reactive atmospheres and during catalysis. The methods of characterizing catalysts in reactive atmospheres include infrared (IR), extended X-ray absorption fine structure (EXAFS), X-ray absorption near edge structure (XANES), and nuclear magnetic resonance (NMR) spectroscopies, and complementary methods include density functional theory and atomic-resolution aberration-corrected scanning transmission electron microscopy for imaging of individual metal atoms. IR, NMR, XANES, and microscopy data demonstrate the high degrees of uniformity of well-prepared supported species. The characterizations determine the compositions of surface metal complexes and clusters, including the ligands and the metal-support bonding and structure, which identify the supports as ligands with electron-donor properties that influence reactivity and catalysis. Each of the catalyst design variables has been varied independently, illustrated by mononuclear and tetranuclear iridium on zeolite HY and on MgO and by isostructural rhodium and iridium (diethylene or dicarbonyl) complexes on these supports. The data provide examples resolving the roles of the catalyst design variables and place the catalysis science on a firm foundation of organometallic chemistry linked with surface science. Supported molecular catalysts offer the advantages of characterization in the absence of solvents and with surface-science methods that do not require ultrahigh vacuum. Families of supported metal complexes have been made by replacement of ligands with others from the gas phase. Spectroscopically identified catalytic reaction intermediates help to elucidate catalyst performance and guide design. The methods are illustrated for supported complexes and clusters of rhodium, iridium, osmium, and gold used to catalyze reactions of small molecules that facilitate identification of the ligands present during catalysis: alkene dimerization and hydrogenation, H-D exchange in the reaction of H2 with D2, and CO oxidation. The approach is illustrated with the discovery of a highly active and selective MgO-supported rhodium carbonyl dimer catalyst for hydrogenation of 1,3-butadiene to give butenes.

Nanocrystalline coating design for extreme applications based on the concept of complex adaptive behavior

NASA Astrophysics Data System (ADS)

Fox-Rabinovich, G. S.; Veldhuis, S. C.; Dosbaeva, G. K.; Yamamoto, K.; Kovalev, A. I.; Wainstein, D. L.; Gershman, I. S.; Shuster, L. S.; Beake, B. D.

2008-04-01

The development of effective hard coatings for high performance dry machining, which is associated with high stress/temperatures during friction, is a major challenge. Newly developed synergistically alloyed nanocrystalline adaptive Ti0.2Al0.55Cr0.2Si0.03Y0.02N plasma vapor deposited hard coatings exhibit excellent tool life under conditions of high performance dry machining of hardened steel, especially under severe and extreme cutting conditions. The coating is capable of sustaining cutting speeds as high as 600 m/min. Comprehensive investigation of the microstructure and properties of the coating was performed. The structure of the coating before and after service has been characterized by high resolution transmission electron microscopy. Micromechanical characteristics of the coating have been investigated at elevated temperatures. Oxidation resistance of the coating has been studied by using thermogravimetry within a temperature range of 25-1100 °C in air. The coefficient of friction of the coatings was studied within a temperature range of 25-1200 °C. To determine the causes of excellent tool life and improved wear behavior of the TiAlCrSiYN coatings, its surface structure characteristics after service have been investigated by using x-ray photoelectron spectroscopy and extended energy-loss fine spectroscopy. One of the major features of this coating is the dynamic formation of the protective tribo-oxide films (dissipative structures) on the surface during friction with a sapphire and mullite crystal structure. Aluminum- and silicon-rich tribofilms with dangling bonds form on the surface as well. These tribofilms act in synergy and protect the surface so efficiently that it is able to sustain extreme operating conditions. Moreover, the Ti0.2Al0.55Cr0.2Si0.03Y0.02N coating possesses some features of a complex adaptive behavior because it has a number of improved characteristics (tribological adaptability, ultrafine nanocrystalline structure, hot hardness and plasticity, and oxidation stability) that work synergistically as a whole. Due to the complex adaptive behavior, this coating represents a higher ordered system that has an ability to achieve unattainable wear resistance under strongly intensifying and extreme tribological conditions.

Engineering the cell surface display of cohesins for assembly of cellulosome-inspired enzyme complexes on Lactococcus lactis

PubMed Central

2010-01-01

Background The assembly and spatial organization of enzymes in naturally occurring multi-protein complexes is of paramount importance for the efficient degradation of complex polymers and biosynthesis of valuable products. The degradation of cellulose into fermentable sugars by Clostridium thermocellum is achieved by means of a multi-protein "cellulosome" complex. Assembled via dockerin-cohesin interactions, the cellulosome is associated with the cell surface during cellulose hydrolysis, forming ternary cellulose-enzyme-microbe complexes for enhanced activity and synergy. The assembly of recombinant cell surface displayed cellulosome-inspired complexes in surrogate microbes is highly desirable. The model organism Lactococcus lactis is of particular interest as it has been metabolically engineered to produce a variety of commodity chemicals including lactic acid and bioactive compounds, and can efficiently secrete an array of recombinant proteins and enzymes of varying sizes. Results Fragments of the scaffoldin protein CipA were functionally displayed on the cell surface of Lactococcus lactis. Scaffolds were engineered to contain a single cohesin module, two cohesin modules, one cohesin and a cellulose-binding module, or only a cellulose-binding module. Cell toxicity from over-expression of the proteins was circumvented by use of the nisA inducible promoter, and incorporation of the C-terminal anchor motif of the streptococcal M6 protein resulted in the successful surface-display of the scaffolds. The facilitated detection of successfully secreted scaffolds was achieved by fusion with the export-specific reporter staphylococcal nuclease (NucA). Scaffolds retained their ability to associate in vivo with an engineered hybrid reporter enzyme, E. coli β-glucuronidase fused to the type 1 dockerin motif of the cellulosomal enzyme CelS. Surface-anchored complexes exhibited dual enzyme activities (nuclease and β-glucuronidase), and were displayed with efficiencies approaching 104 complexes/cell. Conclusions We report the successful display of cellulosome-inspired recombinant complexes on the surface of Lactococcus lactis. Significant differences in display efficiency among constructs were observed and attributed to their structural characteristics including protein conformation and solubility, scaffold size, and the inclusion and exclusion of non-cohesin modules. The surface-display of functional scaffold proteins described here represents a key step in the development of recombinant microorganisms capable of carrying out a variety of metabolic processes including the direct conversion of cellulosic substrates into fuels and chemicals. PMID:20840763

Scanning electron microscope investigation of the structural growth in thick sputtered coatings

NASA Technical Reports Server (NTRS)

Spalvins, T.

1975-01-01

Sputtered S-Monel, silver, and 304 stainless steel coatings and molybdenum disulfide coatings were deposited on mica and metal substrates with various surface finishes to investigate the structural growth of the coating by scanning electron microscopy. The geometry and the surface morphology of the nodules are characterized. Compositional changes within the coating were analyzed by energy dispersive X-ray analysis. Defects in the surface finish act as preferential nucleation sites and form isolated overlapping and complex nodules and various unusual surface overgrowths on the coating. The nodule boundaries are very vulnerable to chemical etching and these nodules do not disappear after full annealing. Further, they have undesirable effects on mechanical properties; cracks are initiated at the nodules when the coating is stressed by mechanical forces.

Modeling laser-induced periodic surface structures: Finite-difference time-domain feedback simulations

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

Skolski, J. Z. P., E-mail: j.z.p.skolski@utwente.nl; Vincenc Obona, J.; Römer, G. R. B. E.

2014-03-14

A model predicting the formation of laser-induced periodic surface structures (LIPSSs) is presented. That is, the finite-difference time domain method is used to study the interaction of electromagnetic fields with rough surfaces. In this approach, the rough surface is modified by “ablation after each laser pulse,” according to the absorbed energy profile, in order to account for inter-pulse feedback mechanisms. LIPSSs with a periodicity significantly smaller than the laser wavelength are found to “grow” either parallel or orthogonal to the laser polarization. The change in orientation and periodicity follow from the model. LIPSSs with a periodicity larger than the wavelengthmore » of the laser radiation and complex superimposed LIPSS patterns are also predicted by the model.« less

Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.

PubMed

Ritchie, David W

2003-07-01

This article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein-protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e.g., Lactobacillus HPr kinase, hemagglutinin, bovine rotavirus VP6). Here we describe several enhancements to our original spherical polar Fourier docking correlation algorithm. For example, a novel surface sphere smothering algorithm is introduced to generate multiple local coordinate systems around the surface of a large receptor molecule, which may be used to define a small number of initial ligand-docking orientations distributed over the receptor surface. High-resolution spherical polar docking correlations are performed over the resulting receptor surface patches, and candidate docking solutions are refined by using a novel soft molecular mechanics energy minimization procedure. Overall, this approach identified two good solutions at rank 5 or less for two of the seven CAPRI complexes. Subsequent analysis of our results shows that Hex 3.1 is able to place good solutions within a list of

Sorbents based on asbestos with a layer of an hydroxyethylcyclam derivative of PVC containing aquacomplexes of sulfuric acid or sodium hydroxide with aza-crown groups

NASA Astrophysics Data System (ADS)

Tsivadze, A. Yu.; Fridman, A. Ya.; Morozova, E. M.; Sokolova, N. P.; Voloshchuk, A. M.; Petukhova, G. A.; Bardyshev, I. I.; Gorbunov, A. M.; Polyakova, I. Ya.; Titova, V. N.; Yavich, A. A.; Novikov, A. K.; Petrova, N. V.

2016-07-01

Aquacomplexes of sulfuric acid and sodium hydroxide with aza-crown groups are synthesized in cavities of a sorbent from the porous layer of a PVC cyclam-derivative grafted onto fibers of asbestos fabric. The structure of sorbents with complexes is studied and their adsorption characteristics are determined. It is shown that the affinity of the developed surface toward ethanol, benzene, and hexane depends on the nature of complexes in the pore walls, and the volume of cavities formed as a result of the pores on the developed asbestos surface being coated with networks of aza-crown groups is larger than that of cavities with walls of aza-crown groups in the layers of a PVC cyclam derivative. Indicators of H+- and OH--conductivity of sorbents with complexes as electrochemical bridges are determined. It is shown that the major part of H+- and OH--ions moves through complexes with aza-crown groups in the region of cavities formed of pores on the surface of asbestos.

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detection of Threat Materials Using Terahertz Waveguides and Long Pathlength Terahertz Spectroscopy

DTIC Science & Technology

2015-05-01

intramolecular modes. Therefore a complex spectrum is anticipated. In the range between 0.2 THz and 3.0 THz there have been several free space THz...narrowing. A more complex underlying spectrum is only suggested, but not resolved. A PETN layer was formed on an Au-coated PPWG surface by drop casting...structure of the analyte, or complex formation where metal ions incorporate into the lattice of the analyte. In each of these cases the resulting THz

Dielectric Response at THz Frequencies of Mg Water Complexes Interacting with O3 Calculated by Density Functional Theory

DTIC Science & Technology

2012-10-24

of the atoms in a chemical system , at the maximal peak of the energy surface separating reactants from products . In the transition state every normal...Hada, M. Ehara, K. Toyota , R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda , O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E...calculations of ground state resonance structure associated with water complexes of Mg and the interaction of these complexes with Ozone using DFT. The

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab.

PubMed

Zhang, Fei; Qi, Xiaoqiang; Wang, Xiaoxiao; Wei, Diyang; Wu, Jiawei; Feng, Lingling; Cai, Haiyan; Wang, Yugang; Zeng, Naiyan; Xu, Ting; Zhou, Aiwu; Zheng, Ying

2017-10-27

Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å 2 , which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface.

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab

PubMed Central

Wei, Diyang; Wu, Jiawei; Feng, Lingling; Cai, Haiyan; Wang, Yugang; Zeng, Naiyan; Xu, Ting; Zhou, Aiwu; Zheng, Ying

2017-01-01

Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å2, which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface. PMID:29163822

Estimation of effective aerodynamic roughness with altimeter measurements

NASA Technical Reports Server (NTRS)

Menenti, M.; Ritchie, J. C.

1992-01-01

A new method is presented for estimating the aerodynamic roughness length of heterogeneous land surfaces and complex landscapes using elevation measurements performed with an airborne laser altimeter and the Seasat radar altimeter. Land surface structure is characterized at increasing length scales by considering three basic landscape elements: (1) partial to complete canopies of herbaceous vegetation; (2) sparse obstacles (e.g., shrubs and trees); and (3) local relief. Measured parameters of land surface geometry are combined to obtain an effective aerodynamic roughness length which parameterizes the total atmosphere-land surface stress.

Remote optoelectronic sensors for monitoring of nonlinear surfaces

NASA Astrophysics Data System (ADS)

Petrochenko, Andrew V.; Konyakhin, Igor A.

2015-05-01

Actually during construction of the high building actively are used objects of various nonlinear surface, for example, sinuous (parabolic or hyperbolic) roofs of the sport complexes that require automatic deformation control [1]. This type of deformation has character of deflection that is impossible to monitor objectively with just one optoelectronic sensor (which is fixed on this surface). In this article is described structure of remote optoelectronic sensor, which is part of the optoelectronic monitoring system of nonlinear surface, and mathematical transformation of exterior orientation sensor elements in the coordinates of control points.

An XPS study on the chemical bond structure at the interface between SiO{sub x}N{sub y} and N doped polyethylene terephthalate

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

Ding Wanyu; Key Laboratory of Materials Modification by Laser, Ion and Electron Beams, Ministry of Education, Dalian University of Technology, Dalian 116024; Li Li

2013-03-14

The super-thin silicon oxynitride (SiO{sub x}N{sub y}) films were deposited onto the N doped polyethylene terephthalate (PET) surface. Varying the N doping parameters, the different chemical bond structures were obtained at the interface between the SiO{sub x}N{sub y} film and the PET surface. X-ray photoelectron spectra results showed that at the initial stage of SiO{sub x}N{sub y} film growth, the C=N bonds could be broken and C-N-Si crosslink bonds could be formed at the interface of SiO{sub x}N{sub y}/PET, which C=N bonds could be formed onto the PET surface during the N doping process. At these positions, the SiO{sub x}N{submore » y} film could be crosslinked well onto the PET surface. Meanwhile, the doped N could crosslink the [SiO{sub 4}] and [SiN{sub 4}] tetrahedrons, which could easily form the dense layer structure at the initial stage of SiO{sub x}N{sub y} film growth, instead of the ring and/or chain structures of [SiO{sub 4}] tetrahedrons crosslinked by O. Finally, from the point of applying SiO{sub x}N{sub y}/PET complex as the substrate, the present work reveals a simple way to crosslink them, as well as the crosslink model and physicochemical mechanism happened at the interface of complex.« less

Surface reactions of iron - enriched smectites: adsorption and transformation of hydroxy fatty acids and phenolic acids

NASA Astrophysics Data System (ADS)

Polubesova, Tamara; Olshansky, Yaniv; Eldad, Shay; Chefetz, Benny

2014-05-01

Iron-enriched smectites play an important role in adsorption and transformation of soil organic components. Soil organo-clay complexes, and in particular humin contain hydroxy fatty acids, which are derived from plant biopolymer cutin. Phenolic acids belong to another major group of organic acids detected in soil. They participate in various soil processes, and are of concern due to their allelopathic activity. We studied the reactivity of iron-enriched smectites (Fe(III)-montmorillonite and nontronite) toward both groups of acids. We used fatty acids- 9(10),16-dihydroxypalmitic acid (diHPA), isolated from curtin, and 9,10,16-trihydroxypalmitic acid (triHPA); the following phenolic acids were used: ferulic, p-coumaric, syringic, and vanillic. Adsorption of both groups of acids was measured. The FTIR spectra of fatty acid-mineral complexes indicated inner-sphere complexation of fatty acids with iron-enriched smectites (versus outer-sphere complexation with Ca(II)-montmorillonite). The LC-MS results demonstrated enhanced esterification of fatty acids on the iron-enriched smectite surfaces (as compared to Ca(II)-montmorillonite). This study suggests that fatty acids can be esterified on the iron-enriched smectite surfaces, which results in the formation of stable organo-mineral complexes. These complexes may serve as a model for the study of natural soil organo-clay complexes and humin. The reaction of phenolic acids with Fe(III)-montmorillonite demonstrated their oxidative transformation by the mineral surfaces, which was affected by molecular structure of acids. The following order of their transformation was obtained: ferulic >syringic >p-coumaric >vanillic. The LC-MS analysis demonstrated the presence of dimers, trimers, and tetramers of ferulic acid on the surface of Fe(III)-montmorillonite. Oxidation and transformation of ferulic acid were more intense on the surface of Fe(III)-montmorillonite as compared to Fe(III) in solution due to stronger complexation on the Fe(III)-motnomrillonite surface. Our study demonstrate the importance of iron-enriched minerals for the abiotic formation of humic materials and for the transformation of aromatic (phenolic) pollutants.

Structure of the Polycomb Group protein PCGF1 (NSPC1) in complex with BCOR reveals basis for binding selectivity of PCGF homologs

PubMed Central

Junco, Sarah E.; Wang, Renjing; Gaipa, John C.; Taylor, Alexander B.; Schirf, Virgil; Gearhart, Micah D.; Bardwell, Vivian J.; Demeler, Borries; Hart, P. John; Kim, Chongwoo A.

2014-01-01

Summary Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6) are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes. Here we identify a protein interaction domain in BCL6 co-repressor, BCOR, which binds the ubiquitin-like RAWUL domain of PCGF1 (NSPC1) and PCGF3 but not of PCGF2 (MEL18) or PCGF4 (BMI1). Because of the selective binding, we have named this domain PCGF Ub-like fold Discriminator (PUFD). The structure of BCOR PUFD bound to PCGF1 reveals 1. that PUFD binds to the same surfaces as observed for a different Polycomb Group RAWUL domain and 2. the ability of PUFD to discriminate among RAWULs stems from the identity of specific residues within these interaction surfaces. These data are the first to show the molecular basis for determining the binding preference for a PCGF homolog, which ultimately helps determine the identity of the larger PRC1-like assembly. PMID:23523425

Arsenic Re-Mobilization in Water Treatment Adsorbents Under Reducing Conditions: Part II, XAS and Modeling Study

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

Liu,S.; Jing, C.; Meng, X.

2008-01-01

The mechanism of arsenic re-mobilization in spent adsorbents under reducing conditions was studied using X-ray absorption spectroscopy and surface complexation model calculations. X-ray absorption near edge structure (XANES) spectroscopy demonstrated that As(V) was partially reduced to As(III) in spent granular ferric hydroxide (GFH), titanium dioxide (TiO2), activated alumina (AA) and modified activated alumina (MAA) adsorbents after 2 years of anaerobic incubation. As(V) was completely reduced to As(III) in spent granular ferric oxide (GFO) under 2-year incubation. The extended X-ray absorption fine structure (EXAFS) spectroscopy analysis showed that As(III) formed bidentate binuclear surface complexes on GFO as evidenced by an averagemore » As(III)-O bond distance of 1.78 Angstroms and As(III)-Fe distance of 3.34 Angstroms . The release of As from the spent GFO and TiO2 was simulated using the charge distribution multi-site complexation (CD-MUSIC) model. The observed redox ranges for As release and sulfate mobility were described by model calculations.« less

Preliminary results on complex ceramic layers deposition by atmospheric plasma spraying

NASA Astrophysics Data System (ADS)

Florea, Costel; Bejinariu, Costicǎ; Munteanu, Corneliu; Cimpoeşu, Nicanor

2017-04-01

In this article we obtain thin layers from complex ceramic powders using industrial equipment based on atmospheric plasma spraying. We analyze the influence of the substrate material roughness on the quality of the thin layers using scanning electron microscopy (SEM) and X-ray dispersive energy analyze (EDAX). Preliminary results present an important dependence between the surface state and the structural and chemical homogeneity.

About complex refractive index of black Si

NASA Astrophysics Data System (ADS)

Pinčík, Emil; Brunner, Robert; Kobayashi, Hikaru; Mikula, Milan

2017-12-01

The paper deals with the complex refractive index in the IR light region of two types of samples (i) as prepared black silicon, and (ii) thermally oxidized black silicon (BSi) nano-crystalline specimens produced both by the surface structure chemical transfer method using catalytic Ag evaporated spots (as prepared sample) and by the catalytic Pt catalytic mesh (thermally oxidized sample). We present, compare, and discuss the values of the IR complex refractive index obtained by calculation using the Kramers-Krönig transformation. Results indicate that small differences between optical properties of as prepared black Si and thermally oxidized BSi are given by: (i) - oxidation procedure, (ii) - thickness of the formed black Si layer, mainly, not by utilization of different catalytic metals, and by iii) the different thickness. Contamination of the surface by different catalytic metals contributes almost equally to the calculated values of the corresponding complex refractive index.

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

Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowedmore » us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.« less

Geological History of the Tyre Region of Europa: A Regional Perspective on Europan Surface Features and Ice Thickness

NASA Technical Reports Server (NTRS)

Kadel, Steven D.; Chuang, Frank C.; Greeley, Ronald; Moore, Jeffrey M.

2000-01-01

Galileo images of the Tyre Macula region of Europa at regional (170 m/pixel) and local (approx. 40 m/pixel) scales allow mapping and understanding of surface processes and landforms. Ridged plains, doublet and complex ridges, shallow pits, domes, "chaos" areas. impact structures, tilted blocks and massifs, and young fracture systems indicate a complex history of surface deformation on Europa. Regional and local morphologies of the Tyre region of Europa suggest that an impactor penetrated through several kilometers of water ice tc a mobile layer below. The surface morphology was initially dominated by formation of ridged plains, followed by development of ridge bands and doublet ridges, with chaos and fracture formation dominating the latter part of the geologic history of the Tyre region. Two distinct types of chaos have been identified which, along with upwarped dome materials, appear to represent a continuum of features (domes-play chaos-knobby chaos) resulting from increasing degree of surface disruption associated with local lithospheric heating and thinning. Local and regional stratigraphic relationships, block heights, and the morphology of the Tyre impact structure suggest the presence of low-viscosity ice or liquid water beneath a thin (severa1 kilometers) surface ice shell at the time of the impact. The very low impact crater density on the surface of Europa suggests that this thin shell has either formed or been thoroughly resurfaced in the very recent past.

Combining 3D human in vitro methods for a 3Rs evaluation of novel titanium surfaces in orthopaedic applications.

PubMed

Stevenson, G; Rehman, S; Draper, E; Hernández-Nava, E; Hunt, J; Haycock, J W

2016-07-01

In this study, we report on a group of complementary human osteoblast in vitro test methods for the preclinical evaluation of 3D porous titanium surfaces. The surfaces were prepared by additive manufacturing (electron beam melting [EBM]) and plasma spraying, allowing the creation of complex lattice surface geometries. Physical properties of the surfaces were characterized by SEM and profilometry and 3D in vitro cell culture using human osteoblasts. Primary human osteoblast cells were found to elicit greater differences between titanium sample surfaces than an MG63 osteoblast-like cell line, particularly in terms of cell survival. Surface morphology was associated with higher osteoblast metabolic activity and mineralization on rougher titanium plasma spray coated surfaces than smoother surfaces. Differences in osteoblast survival and metabolic activity on titanium lattice structures were also found, despite analogous surface morphology at the cellular level. 3D confocal microscopy identified osteoblast organization within complex titanium surface geometries, adhesion, spreading, and alignment to the biomaterial strut geometries. Mineralized nodule formation throughout the lattice structures was also observed, and indicative of early markers of bone in-growth on such materials. Testing methods such as those presented are not traditionally considered by medical device manufacturers, but we suggest have value as an increasingly vital tool in efficiently translating pre-clinical studies, especially in balance with current regulatory practice, commercial demands, the 3Rs, and the relative merits of in vitro and in vivo studies. Biotechnol. Bioeng. 2016;113: 1586-1599. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

The birth and evolution of surface science: Child of the union of science and technology

PubMed Central

Duke, C. B.

2003-01-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10−7 Pascal or 10−9 Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid–liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes. PMID:12651946

Architecture, Assembly, and Emerging Applications of Branched Functional Polyelectrolytes and Poly(ionic liquid)s.

PubMed

Xu, Weinan; Ledin, Petr A; Shevchenko, Valery V; Tsukruk, Vladimir V

2015-06-17

Branched polyelectrolytes with cylindrical brush, dendritic, hyperbranched, grafted, and star architectures bearing ionizable functional groups possess complex and unique assembly behavior in solution at surfaces and interfaces as compared to their linear counterparts. This review summarizes the recent developments in the introduction of various architectures and understanding of the assembly behavior of branched polyelectrolytes with a focus on functional polyelectrolytes and poly(ionic liquid)s with responsive properties. The branched polyelectrolytes and poly(ionic liquid)s interact electrostatically with small molecules, linear polyelectrolytes, or other branched polyelectrolytes to form assemblies of hybrid nanoparticles, multilayer thin films, responsive microcapsules, and ion-conductive membranes. The branched structures lead to unconventional assemblies and complex hierarchical structures with responsive properties as summarized in this review. Finally, we discuss prospectives for emerging applications of branched polyelectrolytes and poly(ionic liquid)s for energy harvesting and storage, controlled delivery, chemical microreactors, adaptive surfaces, and ion-exchange membranes.

Interrogation of bimetallic particle oxidation in three dimensions at the nanoscale

PubMed Central

Han, Lili; Meng, Qingping; Wang, Deli; Zhu, Yimei; Wang, Jie; Du, Xiwen; Stach, Eric A.; Xin, Huolin L.

2016-01-01

An understanding of bimetallic alloy oxidation is key to the design of hollow-structured binary oxides and the optimization of their catalytic performance. However, one roadblock encountered in studying these binary oxide systems is the difficulty in describing the heterogeneities that occur in both structure and chemistry as a function of reaction coordinate. This is due to the complexity of the three-dimensional mosaic patterns that occur in these heterogeneous binary systems. By combining real-time imaging and chemical-sensitive electron tomography, we show that it is possible to characterize these systems with simultaneous nanoscale and chemical detail. We find that there is oxidation-induced chemical segregation occurring on both external and internal surfaces. Additionally, there is another layer of complexity that occurs during the oxidation, namely that the morphology of the initial oxide surface can change the oxidation modality. This work characterizes the pathways that can control the morphology in binary oxide materials. PMID:27928998

Synthesis, crystal structure, photoluminescence and electrochemical properties of a sandwiched Ni2Ce complex

NASA Astrophysics Data System (ADS)

Güngör, Seyit Ali; Kose, Muhammet

2017-12-01

In this study, a Ni2Ce complex [(NiL)2Ce(NO3)2](NO3) was synthesized and characterized by spectroscopic and analytical methods. The structure of the complex was determined by single crystal X-ray diffraction study. In the structure of the complex, a Ce(III) ion is sandwiched between the two NiL units, which are virtually parallel to each other. The Ce(III) center is 12-coordinate, surrounded by 12 oxygen atoms; four are from phenolic groups, four from methoxy groups, and four from two bidentate nitrate ligands. Hirshfeld surface analysis was used to evaluate the inter-molecular interactions within the crystal packing. The complex molecules are linked by H⋯ONO2 interactions. The largest contribution is H⋯O/O⋯H with 41.6% contribution and followed by H⋯H contacts with 39.1%. The complex showed an excitation band in the range of 510-580 nm. A band in the range of 520-580 nm observed in the emission spectrum almost completely overlapped. This suggests that the band in the emission spectrum of the complex is not the actual fluorescence emission and is assigned to the Rayleigh scattering band. Electrochemical and thermal behaviours of the complex were also investigated.

Molecular Simulation of Cesium Adsorption at the Basal Surface of Phyllosilicate Minerals

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

Kerisit, Sebastien N.; Okumura, Masahiko; Rosso, Kevin M.

2016-08-16

A better understanding of the thermodynamics of radioactive cesium uptake at the surfaces of phyllosilicate minerals is needed to understand mechanisms of its selective adsorption and help guide the development of practical and inexpensive decontamination techniques. In this work, molecular dynamics simulations were carried out to determine the thermodynamics of adsorption of Cs + at the basal surface of six 2:1 phyllosilicate minerals, namely pyrophyllite, illite, muscovite, phlogopite, celadonite, and margarite. These minerals were selected to isolate the effects of the magnitude of the permanent layer charge (≤ 2), its location (tetrahedral versus octahedral sheet), and the structure of themore » octahedral sheet (dioctahedral versus trioctahedral). Good agreement was obtained with experiment in terms of the hydration free energy of Cs + and the structure and thermodynamics of Cs + adsorption at the muscovite basal surface, for which published data were available for comparison. With the exception of pyrophyllite, which did not exhibit an inner-sphere free energy minimum, all phyllosilicate minerals showed similar behavior with respect to Cs + adsorption; notably, Cs + adsorption was predominantly inner-sphere whereas outer-sphere adsorption was very weak with the simulations predicting the formation of an extended outer-sphere complex. For a given location of the layer charge, the free energy of adsorption as an inner-sphere complex was found to vary linearly with the magnitude of the layer charge. For a given location and magnitude of the layer charge, adsorption at phlogopite (trioctahedral sheet structure) was much less favorable than at muscovite (dioctahedral sheet structure) due to the electrostatic repulsion between the adsorbed Cs + and the hydrogen atom of the hydroxyl group directly below the six-membered siloxane ring cavity. For a given magnitude of the layer charge and structure of the octahedral sheet, adsorption at celadonite (layer charge located in the octahedral sheet) was favored over muscovite (layer charge located in the tetrahedral sheet) due to the increased distance with surface potassium ions.« less