Three new europium(III) methanetriacetate metal-organic frameworks: the influence of synthesis on the product topology.

PubMed

Cañadillas-Delgado, Laura; Fabelo, Oscar; Pasán, Jorge; Déniz, Mariadel; Martínez-Benito, Carla; Díaz-Gallifa, Pau; Martín, Tomás; Ruiz-Pérez, Catalina

2014-02-01

Three new metal-organic framework structures containing Eu(III) and the little explored methanetriacetate (C7H7O6(3-), mta(3-)) ligand have been synthesized. Gel synthesis yields a two-dimensional framework with the formula [Eu(mta)(H2O)3]n·2nH2O, (I), while two polymorphs of the three-dimensional framework material [Eu(mta)(H2O)]n·nH2O, (II) and (III), are obtained through hydrothermal synthesis at either 423 or 443 K. Compounds (I) and (II) are isomorphous with previously reported Gd(III) compounds, but compound (III) constitutes a new phase. Compound (I) can be described in terms of dinuclear [Eu2(H2O)4](6+) units bonded through mta(3-) ligands to form a two-dimensional framework with topology corresponding to a (6,3)-connected binodal (4(3))(4(6)6(6)8(3))-kgd net, where the dinuclear [Eu2(H2O)4](6+) units are considered as a single node. Compounds (II) and (III) have distinct three-dimensional topologies, namely a (4(12)6(3))(4(9)6(6))-nia net for (II) and a (4(10)6(5))(4(11)6(4))-K2O2; 36641 net for (III). The crystal density of (III) is greater than that of (II), consistent with the increase of temperature, and thereby autogeneous pressure, in the hydrothermal synthesis.

IM-19: a new flexible microporous gallium based-MOF framework with pressure- and temperature-dependent openings.

PubMed

Chaplais, Gérald; Simon-Masseron, Angélique; Porcher, Florence; Lecomte, Claude; Bazer-Bachi, Delphine; Bats, Nicolas; Patarin, Joël

2009-07-14

Five metal-organic frameworks (MOFs) based on the same three-dimensional gallium terephthalate network (IM-19) are described, and an incommensurate structure (for the as-synthesized form) as well as two remarkable guest-free polymorphs (open and closed) are highlighted.

Rod-like polyaniline supported on three-dimensional boron and nitrogen-co-doped graphene frameworks for high-performance supercapacitors

NASA Astrophysics Data System (ADS)

Liao, Kexuan; Gao, Jialu; Fan, Jinchen; Mo, Yao; Xu, Qunjie; Min, Yulin

2017-12-01

In this work, novel three-dimensional (3D) boron and nitrogen-co-doped three-dimensional (3D) graphene frameworks (BN-GFs) supporting rod-like polyaniline (PANI) are facilely prepared and used as electrodes for high-performance supercapacitors. The results demonstrated that BN-GFs with tuned electronic structure can not only provide a large surface area for rod-like PANI to anchor but also effectively facilitate the ion transfer and charge storage in the electrode. The PANI/BN-GF composite with wrinkled boron and nitrogen-co-doped graphene sheets interconnected by rod-like PANI exhibits excellent capacitive properties with a maximum specific capacitance of 596 F/g at a current density of 0.5 A/g. Notably, they also show excellent cycling stability with more than 81% capacitance retention after 5000 charge-discharge cycles.

Topology of three-dimensional separated flows

NASA Technical Reports Server (NTRS)

Tobak, M.; Peake, D. J.

1981-01-01

Based on the hypothesis that patterns of skin-friction lines and external streamlines reflect the properties of continuous vector fields, topology rules define a small number of singular points (nodes, saddle points, and foci) that characterize the patterns on the surface and on particular projections of the flow (e.g., the crossflow plane). The restricted number of singular points and the rules that they obey are considered as an organizing principle whose finite number of elements can be combined in various ways to connect together the properties common to all steady three dimensional viscous flows. Introduction of a distinction between local and global properties of the flow resolves an ambiguity in the proper definition of a three dimensional separated flow. Adoption of the notions of topological structure, structural stability, and bifurcation provides a framework to describe how three dimensional separated flows originate and succeed each other as the relevant parameters of the problem are varied.

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

Global/local methods research using the CSM testbed

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Ransom, Jonathan B.; Griffin, O. Hayden, Jr.; Thompson, Danniella M.

1990-01-01

Research activities in global/local stress analysis are described including both two- and three-dimensional analysis methods. These methods are being developed within a common structural analysis framework. Representative structural analysis problems are presented to demonstrate the global/local methodologies being developed.

Bi-directional evolutionary structural optimization for strut-and-tie modelling of three-dimensional structural concrete

NASA Astrophysics Data System (ADS)

Shobeiri, Vahid; Ahmadi-Nedushan, Behrouz

2017-12-01

This article presents a method for the automatic generation of optimal strut-and-tie models in reinforced concrete structures using a bi-directional evolutionary structural optimization method. The methodology presented is developed for compliance minimization relying on the Abaqus finite element software package. The proposed approach deals with the generation of truss-like designs in a three-dimensional environment, addressing the design of corbels and joints as well as bridge piers and pile caps. Several three-dimensional examples are provided to show the capabilities of the proposed framework in finding optimal strut-and-tie models in reinforced concrete structures and verifying its efficiency to cope with torsional actions. Several issues relating to the use of the topology optimization for strut-and-tie modelling of structural concrete, such as chequerboard patterns, mesh-dependency and multiple load cases, are studied. In the last example, a design procedure for detailing and dimensioning of the strut-and-tie models is given according to the American Concrete Institute (ACI) 318-08 provisions.

Three-Dimensional Geologic Framework Model for a Karst Aquifer System, Hasty and Western Grove Quadrangles, Northern Arkansas

USGS Publications Warehouse

Turner, Kenzie J.; Hudson, Mark R.; Murray, Kyle E.; Mott, David N.

2007-01-01

Understanding ground-water flow in a karst aquifer benefits from a detailed conception of the three-dimensional (3D) geologic framework. Traditional two-dimensional products, such as geologic maps, cross-sections, and structure contour maps, convey a mental picture of the area but a stronger conceptualization can be achieved by constructing a digital 3D representation of the stratigraphic and structural geologic features. In this study, a 3D geologic model was created to better understand a karst aquifer system in the Buffalo National River watershed in northern Arkansas. The model was constructed based on data obtained from recent, detailed geologic mapping for the Hasty and Western Grove 7.5-minute quadrangles. The resulting model represents 11 stratigraphic zones of Ordovician, Mississippian, and Pennsylvanian age. As a result of the highly dissected topography, stratigraphic and structural control from geologic contacts and interpreted structure contours were sufficient for effectively modeling the faults and folds in the model area. Combined with recent dye-tracing studies, the 3D framework model is useful for visualizing the various geologic features and for analyzing the potential control they exert on the ground-water flow regime. Evaluation of the model, by comparison to published maps and cross-sections, indicates that the model accurately reproduces both the surface geology and subsurface geologic features of the area.

Metal–Organic Nanosheets Formed via Defect-Mediated Transformation of a Hafnium Metal–Organic Framework

PubMed Central

2017-01-01

We report a hafnium-containing MOF, hcp UiO-67(Hf), which is a ligand-deficient layered analogue of the face-centered cubic fcu UiO-67(Hf). hcp UiO-67 accommodates its lower ligand:metal ratio compared to fcu UiO-67 through a new structural mechanism: the formation of a condensed “double cluster” (Hf12O8(OH)14), analogous to the condensation of coordination polyhedra in oxide frameworks. In oxide frameworks, variable stoichiometry can lead to more complex defect structures, e.g., crystallographic shear planes or modules with differing compositions, which can be the source of further chemical reactivity; likewise, the layered hcp UiO-67 can react further to reversibly form a two-dimensional metal–organic framework, hxl UiO-67. Both three-dimensional hcp UiO-67 and two-dimensional hxl UiO-67 can be delaminated to form metal–organic nanosheets. Delamination of hcp UiO-67 occurs through the cleavage of strong hafnium-carboxylate bonds and is effected under mild conditions, suggesting that defect-ordered MOFs could be a productive route to porous two-dimensional materials. PMID:28343394

Solvent-free synthesis of new metal phosphites with double-layered, pillared-layered, and framework structures

NASA Astrophysics Data System (ADS)

Liu, Lin; Zhang, Wei; Shi, Zhonghua; Chen, Yaoqiang; Lin, Zhien

2014-12-01

Three new metal phosphites, formulated as (H3O)2·Mn2(HPO3)3 (1), Co(bpy) (H2O) (HPO3) (2), and H2tmpda·Zn3(HPO3)4 (3), have been synthesized under solvent-free conditions, where bpy = 4,4‧-bipyridine, and tmpda = N,N,N‧,N‧-tetramethyl-1,3-propanediamine. Compound 1 has a double-layered structure with a thickness of 5.68 Å. Compound 2 has an inorganic-organic hybrid framework with cobalt phosphite layers pillared by bpy ligands. Compound 3 has a three-dimensional open-framework structure containing 8-ring channels. The temperature dependence of the magnetic susceptibility of compounds 1 and 2 were also investigated.

Casting inorganic structures with DNA molds

PubMed Central

Sun, Wei; Boulais, Etienne; Hakobyan, Yera; Wang, Wei Li; Guan, Amy; Bathe, Mark; Yin, Peng

2014-01-01

We report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff “nano-mold” that contains a user-specified three-dimensional cavity and encloses a nucleating gold “seed”. Under mild conditions, this seed grows into a larger cast structure that fills and thus replicates the cavity. We synthesized a variety of nanoparticles with three nanometer resolution: three distinct silver cuboids with three independently tunable dimensions, silver and gold nanoparticles with diverse cross sections, and composite structures with homo-/heterogeneous components. The designer equilateral silver triangular and spherical nanoparticles exhibited plasmonic properties consistent with electromagnetism-based simulations. Our framework is generalizable to more complex geometries and diverse inorganic materials, offering a range of applications in biosensing, photonics, and nanoelectronics. PMID:25301973

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

Chao, Tzu-Ling; Yang, Chen-I., E-mail: ciyang@thu.edu.tw

The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features amore » 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. -- Graphical abstract: The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. Highlights: • Three homochiral 3D coordination polymers were synthesized. • 1 and 2 are 3D structure with metal-D-cam helical chains pillared by pyrazine. • 3 shows a 3D homochiral framework involving 1D manganese-carboxylate chains. • Magnetic data analysis indicates that 1–3 exhibit weak antiferromagnetic coupling.« less

Three-dimensional microbubble streaming flows

NASA Astrophysics Data System (ADS)

Rallabandi, Bhargav; Marin, Alvaro; Rossi, Massimiliano; Kaehler, Christian; Hilgenfeldt, Sascha

2014-11-01

Streaming due to acoustically excited bubbles has been used successfully for applications such as size-sorting, trapping and focusing of particles, as well as fluid mixing. Many of these applications involve the precise control of particle trajectories, typically achieved using cylindrical bubbles, which establish planar flows. Using astigmatic particle tracking velocimetry (APTV), we show that, while this two-dimensional picture is a useful description of the flow over short times, a systematic three-dimensional flow structure is evident over long time scales. We demonstrate that this long-time three-dimensional fluid motion can be understood through asymptotic theory, superimposing secondary axial flows (induced by boundary conditions at the device walls) onto the two-dimensional description. This leads to a general framework that describes three-dimensional flows in confined microstreaming systems, guiding the design of applications that profit from minimizing or maximizing these effects.

Three-dimensional polypyrrole-derived carbon nanotube framework for dye adsorption and electrochemical supercapacitor

NASA Astrophysics Data System (ADS)

Xin, Shengchang; Yang, Na; Gao, Fei; Zhao, Jing; Li, Liang; Teng, Chao

2017-08-01

Three-dimensional carbon nanotube frameworks have been prepared via pyrolysis of polypyrrole nanotube aerogels that are synthesized by the simultaneous self-degraded template synthesis and hydrogel assembly followed by freeze-drying. The microstructure and composition of the materials are investigated by thermal gravimetric analysis, Raman spectrum, X-ray photoelectron spectroscopy, transmission electron microscopy, and specific surface analyzer. The results confirm the formation of three-dimensional carbon nanotube frameworks with low density, high mechanical properties, and high specific surface area. Compared with PPy aerogel precursor, the as-prepared three-dimensional carbon nanotube frameworks exhibit outstanding adsorption capacity towards organic dyes. Moreover, electrochemical tests show that the products possess high specific capacitance, good rate capability and excellent cycling performance with no capacitance loss over 1000 cycles. These characteristics collectively indicate the potential of three-dimensional polypyrrole-derived carbon nanotube framework as a promising macroscopic device for the applications in environmental and energy storages.

Complex structures from patterned cell sheets

PubMed Central

Misra, M.; Audoly, B.; Shvartsman, S. Y.

2017-01-01

The formation of three-dimensional structures from patterned epithelial sheets plays a key role in tissue morphogenesis. An important class of morphogenetic mechanisms relies on the spatio-temporal control of apical cell contractility, which can result in the localized bending of cell sheets and in-plane cell rearrangements. We have recently proposed a modified vertex model that can be used to systematically explore the connection between the two-dimensional patterns of cell properties and the emerging three-dimensional structures. Here we review the proposed modelling framework and illustrate it through the computational analysis of the vertex model that captures the salient features of the formation of the dorsal appendages during Drosophila oogenesis. This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’. PMID:28348251

Hydrothermal synthesis and structural characterization of a novel three-dimensional supramolecular framework constructed by zinc salt and pyridine-2,5-dicarboxylate

NASA Astrophysics Data System (ADS)

Wang, Xinlong; Qin, Chao; Wang, Enbo; Hu, Changwen; Xu, Lin

2004-07-01

A novel metal-organic coordination polymer, [Zn(PDB)(H 2O) 2] 4 n (H 2PDB=pyridine-2,5-dicarboxylic acid), has been hydrothermally synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. Colorless crystals crystallized in the triclinic system, space group P-1, a=7.0562(14) Å, b=7.38526(15) Å, c=18.4611(4) Å, α=90.01(3)°, β=96.98(3)°, γ=115.67(3)°, V=859.1(3) Å 3, Z=1 and R=0.0334. The structure of the compound exhibits a novel three-dimensional supramolecular network, mainly based on multipoint hydrogen bonds originated from within and outside of a large 24-membered ring. Interestingly, the three-dimensional network consists of one-dimensional parallelogrammic channels in which coordinated water molecules point into the channel wall.

Coarse-grained mechanics of viral shells

NASA Astrophysics Data System (ADS)

Klug, William S.; Gibbons, Melissa M.

2008-03-01

We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

PubMed

Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

2017-07-31

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

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

Ren, Yixia, E-mail: renyixia1@163.com; Chai, Hongmei; Tang, Long

Three novel coordination polymers, namely, [Cd(2-Hstp)(1,4-bbi)(H{sub 2}O){sub 2}]·3H{sub 2}O (1), [Cd{sub 1.5}(2-stp)(1,4-bbi)(H{sub 2}O){sub 2}]·H{sub 2}O (2) and [Zn{sub 2}(2-stp)(μ{sub 2}-OH)(1,4-bbi){sub 1.5}(H{sub 2}O)]·6H{sub 2}O (3) (2-H{sub 3}stp is equal to 2-sulfoterephthalate and 1,4-bisbenzimidazole is equal to 1,4-bbi), have been synthesized by hydrothermal reaction. The structural analyses show that 1 and 2 possess different structural features despite the same raw materials, which are 1D chain structure featuring 6-member-water H-bonds cluster and 3D bbi-pillared wavy-like layer framework, respectively. As changing the metal ion to zinc ion, 3 exhibits 3D stp-pillared layer architecture, which discovers the effect of the central metal ions on themore » formation of metal–organic frameworks. The fluorescence studies show that the emissions of the coordination polymers are attributed to the ligand π–π* transition, which means they could be potential fluorescence materials. - Graphical abstract: Three new Cd{sup II}/Zn{sup II} 2-sulfoterephthalate (2-H{sub 3}stp) complexes with 1,4-bisbenzimidazole (1,4-bbi) are described. Complex 1 exhibits one-dimensional chain-like structure, 2 is a three-dimensional bbi-pillared wavy-like layer framework, while 3 is a three-dimensional stp-pillared layer architecture. Fluorescence spectra exhibit the π–π* transition of two organic ligands. - Highlights: • Three Cd{sup II}/Mn{sup II} 2-sulfoterephthalate complexes containing 1,4-bisbenzimidazole. • Different structural features despite the same raw materials for 1 and 2. • Fluorescence spectra exhibit the π–π* transition of organic ligands.« less

Loading Ag nanoparticles on Cd(II) boron imidazolate framework for photocatalysis

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

Liu, Min; State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002; Zhang, De-Xiang

2016-05-15

An amine-functionalized Cd(II) boron imidazolate framework (BIF-77) with three-dimensional open structure has been successfully synthesized, which can load Ag nanoparticles (NPs) for photocatalytic degradation of methylene blue (MB). - Graphical abstract: An amine-functionalized neutral Cd(II) boron imidazolate framework can load Ag NPs and show excellent photocatalytic degradation behavious for MB. - Highlights: • Amine-functionalization. • Neutral boron imidazolate framework. • Loading Ag nanoparticles (NPs). • Photocatalytic degradation of methylene blue.

Casting inorganic structures with DNA molds

DOE PAGES

Sun, Wei; Boulais, Etienne; Hakobyan, Yera; ...

2014-10-09

Here we report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff “nano-mold” that contains a user-specified three-dimensional cavity and encloses a nucleating gold “seed”. Under mild conditions, this seed grows into a larger cast structure that fills and thus replicates the cavity. We synthesized a variety of nanoparticles with three nanometer resolution: three distinct silver cuboids with three independently tunable dimensions, silver and gold nanoparticles with diverse cross sections, and composite structures with homo-/heterogeneous components. The designer equilateral silver triangular and spherical nanoparticles exhibited plasmonic propertiesmore » consistent with electromagnetism-based simulations. Our framework is generalizable to more complex geometries and diverse inorganic materials, offering a range of applications in biosensing, photonics, and nanoelectronics.« less

Dimensional Effects on the Charge Density Waves in Ultrathin Films of TiSe 2

DOE PAGES

Chen, P.; Chan, Y. -H.; Wong, M. -H.; ...

2016-09-20

Charge density wave (CDW) formation in solids is a critical phenomenon involving the collective reorganization of the electrons and atoms in the system into a wave structure, and it is expected to be sensitive to the geometric constraint of the system at the nanoscale. Here, we study the CDW transition in TiSe 2, a quasi-two-dimensional layered material, to determine the effects of quantum confinement and changing dimensions in films ranging from a single layer to multilayers. Of key interest is the characteristic length scale for the transformation from a two-dimensional case to the three-dimensional limit. Angle-resolved photoemission (ARPES) measurements ofmore » films with thicknesses up to six layers reveal substantial variations in the energy structure of discrete quantum well states; however, the temperature-dependent band-gap renormalization converges at just three layers. The results indicate a layer-dependent mixture of two transition temperatures and a very-short-range CDW interaction within a three-dimensional framework.« less

The UPSF code: a metaprogramming-based high-performance automatically parallelized plasma simulation framework

NASA Astrophysics Data System (ADS)

Gao, Xiatian; Wang, Xiaogang; Jiang, Binhao

2017-10-01

UPSF (Universal Plasma Simulation Framework) is a new plasma simulation code designed for maximum flexibility by using edge-cutting techniques supported by C++17 standard. Through use of metaprogramming technique, UPSF provides arbitrary dimensional data structures and methods to support various kinds of plasma simulation models, like, Vlasov, particle in cell (PIC), fluid, Fokker-Planck, and their variants and hybrid methods. Through C++ metaprogramming technique, a single code can be used to arbitrary dimensional systems with no loss of performance. UPSF can also automatically parallelize the distributed data structure and accelerate matrix and tensor operations by BLAS. A three-dimensional particle in cell code is developed based on UPSF. Two test cases, Landau damping and Weibel instability for electrostatic and electromagnetic situation respectively, are presented to show the validation and performance of the UPSF code.

Casting inorganic structures with DNA molds.

PubMed

Sun, Wei; Boulais, Etienne; Hakobyan, Yera; Wang, Wei Li; Guan, Amy; Bathe, Mark; Yin, Peng

2014-11-07

We report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff "nanomold" that contains a user-specified three-dimensional cavity and encloses a nucleating gold "seed." Under mild conditions, this seed grows into a larger cast structure that fills and thus replicates the cavity. We synthesized a variety of nanoparticles with 3-nanometer resolution: three distinct silver cuboids with three independently tunable dimensions, silver and gold nanoparticles with diverse cross sections, and composite structures with homo- and heterogeneous components. The designer equilateral silver triangular and spherical nanoparticles exhibited plasmonic properties consistent with electromagnetism-based simulations. Our framework is generalizable to more complex geometries and diverse inorganic materials, offering a range of applications in biosensing, photonics, and nanoelectronics. Copyright © 2014, American Association for the Advancement of Science.

Dimensionality Alteration and Intra- versus Inter-SBU Void Encapsulation in Zinc Phosphate Frameworks.

PubMed

Dar, Aijaz A; Bhat, Gulzar A; Murugavel, Ramaswamy

2016-06-06

4,4'-Bipyridine-N-oxide (BIPYMO, 1), a less commonly employed coordination polymer linker, has been used as a ditopic spacer to bridge double-four-ring (D4R) zinc phosphate clusters to form novel framework coordination polymers. Zinc phosphate framework compounds [Zn4(X-dipp)4(BIPYMO)2]n·2MeOH [X = H (2), Cl (3), Br (4), I (5); dipp = 2,6-diisopropylphenyl phosphate] have been obtained by treating a methanol solution of zinc acetate with X-dippH2 and BIPYMO (in a 1:1:1 molar ratio) at ambient conditions. Framework phosphates 2-5 can also be obtained by treating the preformed D4R cubanes [Zn(X-dipp)(DMSO)]4 with required quantities of BIPYMO in methanol. Single-crystal X-ray diffraction studies reveal that these framework solids are two-dimensional (2D) networks as opposed to the diamondoid networks obtained when the parent unoxidized 4,4'-bipyridine is used as the linker (Inorg. Chem. 2014, 53, 8959). The two types of voids (viz., smaller intra-D4R and larger inter-D4R) present in these framework solids can be utilized for different types of encapsulation processes. For example, the in situ generated 2D framework 2 encapsulates fluoride ions accompanied by a change in the dimensionality of the framework to yield {[(nC4H9)4N][F@(Zn4(dipp)4(BIPYMO)2)]}n (6). The three-dimensional framework 6 represents the first structurally characterized example of a fluoride-ion-encapsulated polymeric coordination compound or a metal-organic framework. The possibility of utilizing inter-D4R voids as hosts for small organic molecules has been explored by treating in situ generated 2 with a series of organic molecules of appropriate size. Framework 2 has been found to be a selective host for benzil and not for other structurally similar molecules such as benzoquinone, benzidine, anthracene, naphthalene, α-pyridoin, etc. The benzil-occluded isolated framework [benzil@{Zn4(dipp)4(BIPYMO)2}]n (7) has been isolated as single crystals, and its crystal structure determination revealed the binding of benzil molecules to the framework through strong π-π interactions.

Pursuing Mirror Image Reconstruction in Unilateral Microtia: Customizing Auricular Framework by Application of Three-Dimensional Imaging and Three-Dimensional Printing.

PubMed

Chen, Hsin-Yu; Ng, Li-Shia; Chang, Chun-Shin; Lu, Ting-Chen; Chen, Ning-Hung; Chen, Zung-Chung

2017-06-01

Advances in three-dimensional imaging and three-dimensional printing technology have expanded the frontier of presurgical design for microtia reconstruction from two-dimensional curved lines to three-dimensional perspectives. This study presents an algorithm for combining three-dimensional surface imaging, computer-assisted design, and three-dimensional printing to create patient-specific auricular frameworks in unilateral microtia reconstruction. Between January of 2015 and January of 2016, six patients with unilateral microtia were enrolled. The average age of the patients was 7.6 years. A three-dimensional image of the patient's head was captured by 3dMDcranial, and virtual sculpture carried out using Geomagic Freeform software and a Touch X Haptic device for fabrication of the auricular template. Each template was tailored according to the patient's unique auricular morphology. The final construct was mirrored onto the defective side and printed out with biocompatible acrylic material. During the surgery, the prefabricated customized template served as a three-dimensional guide for surgical simulation and sculpture of the MEDPOR framework. Average follow-up was 10.3 months. Symmetric and good aesthetic results with regard to auricular shape, projection, and orientation were obtained. One case with severe implant exposure was salvaged with free temporoparietal fascia transfer and skin grafting. The combination of three-dimensional imaging and manufacturing technology with the malleability of MEDPOR has surpassed existing limitations resulting from the use of autologous materials and the ambiguity of two-dimensional planning. This approach allows surgeons to customize the auricular framework in a highly precise and sophisticated manner, taking a big step closer to the goal of mirror-image reconstruction for unilateral microtia patients. Therapeutic, IV.

Mesostructured Metal Germanium Sulfide and Selenide Materials Based on the Tetrahedral [Ge 4S 10] 4- and [Ge 4Se 10] 4- Units: Surfactant Templated Three-Dimensional Disordered Frameworks Perforated with Worm Holes

NASA Astrophysics Data System (ADS)

Wachhold, Michael; Kasthuri Rangan, K.; Lei, Ming; Thorpe, M. F.; Billinge, Simon J. L.; Petkov, Valeri; Heising, Joy; Kanatzidis, Mercouri G.

2000-06-01

The polymerization of [Ge4S10]4- and [Ge4Se10]4- unit clusters with the divalent metal ions Zn2+, Cd2+, Hg2+, Ni2+, and Co2+ in the presence of various surfactant cations leads to novel mesostructured phases. The surfactants are the quaternary ammonium salts C12H25NMe3Br, C14H29NMe3Br, C16H33NMe3Br, and C18H37NMe3Br, which play the role of templates, helping to assemble a three-dimensional mesostructured metal-germanium chalcogenide framework. These materials are stoichiometric in nature and have the formula of (R-NMe3)2[MGe4Q10] (Q=S, Se). The local atomic structure was probed by X-ray diffuse scattering and pair distribution function analysis methods and indicates that the adamantane clusters stay intact while the linking metal atoms possess a tetrahedral coordination environment. A model can be derived, from the comparison of measured and simulated X-ray powder diffraction patterns, describing the structure as an amorphous three-dimensional framework consisting of adamantane [Ge4Q10]4- units that are bridged by tetrahedral coordinated M2+ cations. The network structures used in the simulations were derived from corresponding disordered structures developed for amorphous silicon. The frameworks in (R-NMe3)2[MGe4Q10] are perforated with worm hole-like tunnels, occupied by the surfactant cations, which show no long-range order. This motif is supported by transmission electron microscopy images of these materials. The pore sizes of these channels were estimated to lie in the range of 20-30 Å, depending on the appointed surfactant cation length. The framework wall thickness of ca. 10 Å is thereby independent from the surfactant molecules used. Up to 80% of the surfactant molecules can be removed by thermal degradation under vacuum without loss of mesostructural integrity. Physical, chemical, and spectroscopic properties of these materials are discussed.

Synthesis, Structure and Thermal Behavior of Oxalato-Bridged Rb+ and H3O+ Extended Frameworks with Different Dimensionalities

PubMed Central

Kherfi, Hamza; Hamadène, Malika; Guehria-Laïdoudi, Achoura; Dahaoui, Slimane; Lecomte, Claude

2010-01-01

Correlative studies of three oxalato-bridged polymers, obtained under hydrothermal conditions for the two isostructural compounds {Rb(HC2O4)(H2C2O4)(H2O)2}∞1, 1, {H3O(HC2O4)(H2C2O4).2H2O}∞1, 2, and by conventional synthetic method for {Rb(HC2O4)}∞3, 3, allowed the identification of H-bond patterns and structural dimensionality. Ferroïc domain structures are confirmed by electric measurements performed on 3. Although 2 resembles one oxalic acid sesquihydrate, its structure determination doesn’t display any kind of disorder and leads to recognition of a supramolecular network identical to hybrid s-block series, where moreover, unusual H3O+ and NH4+ similarity is brought out. Thermal behaviors show that 1D frameworks with extended H-bonds, whether with or without a metal center, have the same stability. Inversely, despite the dimensionalities, the same metallic intermediate and final compounds are obtained for the two Rb+ ferroïc materials.

Protein Structure and Function: An Interdisciplinary Multimedia-Based Guided-Inquiry Education Module for the High School Science Classroom

ERIC Educational Resources Information Center

Bethel, Casey M.; Lieberman, Raquel L.

2014-01-01

Here we present a multidisciplinary educational unit intended for general, advanced placement, or international baccalaureate-level high school science, focused on the three-dimensional structure of proteins and their connection to function and disease. The lessons are designed within the framework of the Next Generation Science Standards to make…

Synthesis, structure and electrochemical behavior of a 3D crystalline copper(II) metal-organic framework

NASA Astrophysics Data System (ADS)

Bai, Hong-Ye; Fan, Wei-Qiang; Liu, Chun-Bo; Shi, Wei-Dong; Yan, Yong-Sheng

2014-05-01

Using an flexible amide-type tripodal ligand N,N‧,N″-tris(3-pyridyl)-1,3,5-benzenetricarboxamide (L) and 1,4-benzenedicarboxylic acid (H2bdc), a three-dimensional copper(II) metal-organic framework (MOF) formulated as [Cu(bdc)(L)]n has been hydrothermally synthesized and structurally characterized by IR, elemental, X-ray single-crystal diffraction and thermal analysis. The complex crystallizes in the triclinic, space group P - 1, a = 8.891(2) Å, b = 11.760(2) Å, c = 15.348(3) Å, α = 96.73(3)°, β = 105.96(3)°, γ = 106.47(3)°, V = 1446.2(5) Å3, Mr = 666.10, Dc = 1.530 g/cm3, Z = 2, F(000) = 682, GOOF = 1.0560, μ(MoKα) = 0.817 mm-1, R = 0.0366 and wR = 0.0885. The structural analyses reveal that the title compound consists of one Cu(II) atom, two halves of bdc, and one L ligand. Each Cu(II) atom is linked by two bdc ligands and three L ligands to form a three-dimensional network. In addition, the electrochemical behavior of title compound has been studied. CCDC No. 990526.

Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

NASA Astrophysics Data System (ADS)

Paul, Avijit Kumar

2018-04-01

One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

Tailoring thermal conductivity via three-dimensional porous alumina

PubMed Central

Abad, Begoña; Maiz, Jon; Ruiz-Clavijo, Alejandra; Caballero-Calero, Olga; Martin-Gonzalez, Marisol

2016-01-01

Three-dimensional anodic alumina templates (3D-AAO) are an astonishing framework with open highly ordered three-dimensional skeleton structures. Since these templates are architecturally different from conventional solids or porous templates, they teem with opportunities for engineering thermal properties. By establishing the mechanisms of heat transfer in these frameworks, we aim to create materials with tailored thermal properties. The effective thermal conductivity of an empty 3D-AAO membrane was measured. As the effective medium theory was not valid to extract the skeletal thermal conductivity of 3D-AAO, a simple 3D thermal conduction model was developed, based on a mixed series and parallel thermal resistor circuit, giving a skeletal thermal conductivity value of approximately 1.25 W·m−1·K−1, which matches the value of the ordinary AAO membranes prepared from the same acid solution. The effect of different filler materials as well as the variation of the number of transversal nanochannels and the length of the 3D-AAO membrane in the effective thermal conductivity of the composite was studied. Finally, the thermal conductivity of two 3D-AAO membranes filled with cobalt and bismuth telluride was also measured, which was in good agreement with the thermal model predictions. Therefore, this work proved this structure as a powerful approach to tailor thermal properties. PMID:27934930

[Zn(INO) 2(DMF)]·DMF: A new three-dimensional supramolecular open framework containing one-dimensional channels

NASA Astrophysics Data System (ADS)

Hong, Jun

2006-02-01

A three-dimensional supramolecular compound, [Zn(INO) 2(DMF)]·DMF (1) (INO=isonicotinic acid N-oxide), has been prepared in the DMF solution at room temperature, and characterized by elemental analysis, TG and single crystal X-ray diffraction. The three-dimensional supramolecular open framework of 1 contains rectangular channels with the dimensions of 9.02×10.15 Å, assembled from one-dimensional helical chains via hydrogen-bonding and π-π stacking interactions. Furthermore, compound 1 shows blue photoluminescence at room temperature.

Three-dimensional nitrogen doped holey reduced graphene oxide framework as metal-free counter electrodes for high performance dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Yu, Mei; Zhang, Jindan; Li, Songmei; Meng, Yanbing; Liu, Jianhua

2016-03-01

Three-dimensional nitrogen doped holey reduced graphene oxide framework (NHGF) with hierarchical porosity structure was developed as high-performance metal-free counter electrodes (CEs) for dye-sensitized solar cells (DSSCs). With plenty of exposed active sites, efficient electron and ion transport pathways as well as a high surface hydrophilicity, NHGF-CE exhibits good electrocatalytic performances for I- /I3- redox couple and a low charge transfer resistance (Rct). The Rct of NHGF-CE is 1.46 Ω cm2, which is much lower than that of Pt-CE (4.02 Ω cm2). The DSSC with NHGF-CE reaches a power conversion efficiency of 5.56% and a fill factor of 65.5%, while those of the DSSC with Pt-CE are only 5.45% and 62.3%, respectively. The achievement of the highly efficient 3D structure presents a potential way to fabricate low-cost and metal-free counter electrodes with excellent performance.

Aromatic carboxylate effect on dimensionality of three bis(benzimidazole)-based cobalt(II) coordination polymers: Syntheses, structures and properties

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

Zhang, Ju-Wen; Gong, Chun-Hua; Hou, Li-Li

2013-09-15

Three new metal-organic coordination polymers [Co(4-bbc){sub 2}(bbbm)] (1), [Co(3,5-pdc)(bbbm)]·2H{sub 2}O (2) and [Co(1,4-ndc)(bbbm)] (3) (4-Hbbc=4-bromobenzoic acid, 3,5-H{sub 2}pdc=3,5-pyridinedicarboxylic acid, 1,4-H{sub 2}ndc=1,4-naphthalenedicarboxylic acid and bbbm=1,1-(1,4-butanediyl)bis-1H-benzimidazole) were hydrothermally synthesized and structurally characterized. Polymer 1 is a 1D chain formed by the bbbm ligands and Co{sup II} ions. Polymer 2 exhibits a 2D network with a (3·4·5)(3{sup 2}·4·5·6{sup 2}·7{sup 4}) topology. Polymer 3 possesses a 3D three-fold interpenetrating framework. The versatile structures of title polymers indicate that the aromatic carboxylates have an important influence on the dimensionality of 1–3. Moreover, the thermal stability, electrochemical and luminescent properties of 1–3 were investigated. - graphicalmore » abstract: Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were hydrothermally synthesized and structurally characterized. The aromatic carboxylates play a key role in the dimensionality of three polymers. The electrochemical and luminescent properties of three polymers were investigated. Display Omitted - Highlights: • Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were obtained. • The aromatic carboxylates have an important influence on the dimensionality of three polymers. • The electrochemical and luminescent properties of three polymers were investigated.« less

Predictive framework for shape-selective separations in three-dimensional zeolites and metal-organic frameworks.

PubMed

First, Eric L; Gounaris, Chrysanthos E; Floudas, Christodoulos A

2013-05-07

With the growing number of zeolites and metal-organic frameworks (MOFs) available, computational methods are needed to screen databases of structures to identify those most suitable for applications of interest. We have developed novel methods based on mathematical optimization to predict the shape selectivity of zeolites and MOFs in three dimensions by considering the energy costs of transport through possible pathways. Our approach is applied to databases of over 1800 microporous materials including zeolites, MOFs, zeolitic imidazolate frameworks, and hypothetical MOFs. New materials are identified for applications in gas separations (CO2/N2, CO2/CH4, and CO2/H2), air separation (O2/N2), and chemicals (propane/propylene, ethane/ethylene, styrene/ethylbenzene, and xylenes).

Stress distribution in fixed-partial prosthesis and peri-implant bone tissue with different framework materials and vertical misfit levels: a three-dimensional finite element analysis.

PubMed

Bacchi, Ataís; Consani, Rafael L X; Mesquita, Marcelo F; dos Santos, Mateus B F

2013-09-01

The purpose of this study was to evaluate the influence of superstructure material and vertical misfits on the stresses created in an implant-supported partial prosthesis. A three-dimensional (3-D) finite element model was prepared based on common clinical data. The posterior part of a severely resorbed jaw with two osseointegrated implants at the second premolar and second molar regions was modeled using specific modeling software (SolidWorks 2010). Finite element models were created by importing the solid model into mechanical simulation software (ANSYS Workbench 11). The models were divided into groups according to the prosthesis framework material (type IV gold alloy, silver-palladium alloy, commercially pure titanium, cobalt-chromium alloy, or zirconia) and vertical misfit level (10 µm, 50 µm, and 100 µm) created at one implant-prosthesis interface. The gap of the vertical misfit was set to be closed and the stress values were measured in the framework, porcelain veneer, retention screw, and bone tissue. Stiffer materials led to higher stress concentration in the framework and increased stress values in the retention screw, while in the same circumstances, the porcelain veneer showed lower stress values, and there was no significant difference in stress in the peri-implant bone tissue. A considerable increase in stress concentration was observed in all the structures evaluated within the misfit amplification. The framework material influenced the stress concentration in the prosthetic structures and retention screw, but not that in bone tissue. All the structures were significantly influenced by the increase in the misfit levels.

A flexible metal-organic framework with a high density of sulfonic acid sites for proton conduction

NASA Astrophysics Data System (ADS)

Yang, Fan; Xu, Gang; Dou, Yibo; Wang, Bin; Zhang, Heng; Wu, Hui; Zhou, Wei; Li, Jian-Rong; Chen, Banglin

2017-11-01

The design of stable electrolyte materials with high proton conductivity for use in proton exchange membrane fuel cells remains a challenge. Most of the materials explored have good conductivity at high relative humidity (RH), but significantly decreased conductivity at reduced RH. Here we report a chemically stable and structurally flexible metal-organic framework (MOF), BUT-8(Cr)A, possessing a three-dimensional framework structure with one-dimensional channels, in which high-density sulfonic acid (-SO3H) sites arrange on channel surfaces for proton conduction. We propose that its flexible nature, together with its -SO3H sites, could allow BUT-8(Cr)A to self-adapt its framework under different humid environments to ensure smooth proton conduction pathways mediated by water molecules. Relative to other MOFs, BUT-8(Cr)A not only has a high proton conductivity of 1.27 × 10-1 S cm-1 at 100% RH and 80 °C but also maintains moderately high proton conductivity at a wide range of RH and temperature.

Three-dimensional geologic model of the southeastern Espanola Basin, Santa Fe County, New Mexico

USGS Publications Warehouse

Pantea, Michael P.; Hudson, Mark R.; Grauch, V.J.S.; Minor, Scott A.

2011-01-01

This multimedia model and report show and describe digital three-dimensional faulted surfaces and volumes of lithologic units that confine and constrain the basin-fill aquifers within the Espanola Basin of north-central New Mexico. These aquifers are the primary groundwater resource for the cities of Santa Fe and Espanola, six Pueblo nations, and the surrounding areas. The model presented in this report is a synthesis of geologic information that includes (1) aeromagnetic and gravity data and seismic cross sections; (2) lithologic descriptions, interpretations, and geophysical logs from selected drill holes; (3) geologic maps, geologic cross sections, and interpretations; and (4) mapped faults and interpreted faults from geophysical data. Modeled faults individually or collectively affect the continuity of the rocks that contain the basin aquifers; they also help define the form of this rift basin. Structure, trend, and dip data not previously published were added; these structures are derived from interpretations of geophysical information and recent field observations. Where possible, data were compared and validated and reflect the complex relations of structures in this part of the Rio Grande rift. This interactive geologic framework model can be used as a tool to visually explore and study geologic structures within the Espanola Basin, to show the connectivity of geologic units of high and low permeability between and across faults, and to show approximate dips of the lithologic units. The viewing software can be used to display other data and information, such as drill-hole data, within this geologic framework model in three-dimensional space.

Two sodium and lanthanide(III) MOFs based on oxalate and V-shaped 4,4‧-oxybis(benzoate) ligands: Hydrothermal synthesis, crystal structure, and luminescence properties

NASA Astrophysics Data System (ADS)

Wang, Chongchen; Guo, Guangliang; Wang, Peng

2013-01-01

Two lanthanide based metal-organic frameworks, [NaLn(oba)(ox)(H2O)] (Lndbnd6 Eu(1) and Sm(2)) were obtained from 4,4'-oxybisbenzoic acid, sodium oxalate and corresponding lanthanide salts by hydrothermal synthesis. They were characterized by single-crystal X-ray diffraction, IR spectra, and photoluminescent spectra. The crystallographic data reveals that complexes 1 and 2 are isomorphous and isostructural, composed of three-dimensional framework built up of distorted tricapped trigonal EuO9 units, distorted octahedron NaO6 units, 4,4'-oxybis(benzoate) and oxalate. The carboxylate oxygen atoms of the 4,4'-oxybis(benzoate) and oxalate ligand are coordinated to lanthanide ions and sodium ions, resulting into two-dimensional inorganic sheets, which are further linked into three-dimensional network by organic ligands. Thermogravimetric analyses of 1-2 display a considerable thermal stability. Photoluminescent measurements indicated that europium complex 1 displayed strong red emission.

A Dynamic Hydrology-Critical Zone Framework for Rainfall-triggered Landslide Hazard Prediction

NASA Astrophysics Data System (ADS)

Dialynas, Y. G.; Foufoula-Georgiou, E.; Dietrich, W. E.; Bras, R. L.

2017-12-01

Watershed-scale coupled hydrologic-stability models are still in their early stages, and are characterized by important limitations: (a) either they assume steady-state or quasi-dynamic watershed hydrology, or (b) they simulate landslide occurrence based on a simple one-dimensional stability criterion. Here we develop a three-dimensional landslide prediction framework, based on a coupled hydrologic-slope stability model and incorporation of the influence of deep critical zone processes (i.e., flow through weathered bedrock and exfiltration to the colluvium) for more accurate prediction of the timing, location, and extent of landslides. Specifically, a watershed-scale slope stability model that systematically accounts for the contribution of driving and resisting forces in three-dimensional hillslope segments was coupled with a spatially-explicit and physically-based hydrologic model. The landslide prediction framework considers critical zone processes and structure, and explicitly accounts for the spatial heterogeneity of surface and subsurface properties that control slope stability, including soil and weathered bedrock hydrological and mechanical characteristics, vegetation, and slope morphology. To test performance, the model was applied in landslide-prone sites in the US, the hydrology of which has been extensively studied. Results showed that both rainfall infiltration in the soil and groundwater exfiltration exert a strong control on the timing and magnitude of landslide occurrence. We demonstrate the extent to which three-dimensional slope destabilizing factors, which are modulated by dynamic hydrologic conditions in the soil-bedrock column, control landslide initiation at the watershed scale.

Multitopic ligand directed assembly of low-dimensional metal-chalcogenide organic frameworks.

PubMed

Liu, Yi; Ye, Kaiqi; Wang, Yue; Zhang, Qichun; Bu, Xianhui; Feng, Pingyun

2017-01-31

Despite tremendous progress in metal-organic frameworks, only limited success has been achieved with metal-chalcogenide organic frameworks. Metal-chalcogenide organic frameworks are desirable because they offer a promising route towards tunable semiconducting porous frameworks. Here, four novel semiconducting chalcogenide-organic hybrid compounds have been synthesized through a solvothermal method. Multitopic organic molecules, i.e., 1,2-di-(4-pyridyl)ethylene (L 1 ), 1,3,5-tris(4-pyridyl-trans-ethenyl)benzene (L 2 ) and tetrakis(4-pyridyloxymethylene)methane (L 3 ), have been used as linkers to assemble Zn(SAr) 2 or Zn 2 (SAr) 4 units to generate different patterns of spatial organizations. Single-crystal structural analyses indicate that compounds NTU-2, NTU-3 and NTU-4 possess two-dimensional layer structures, while compound NTU-1 adopts a one-dimensional coordination framework (NTU-n, where n is the number related to a specific structure). The diffuse-reflectance spectra demonstrate that these four compounds possess indirect bandgaps and their tunable bandgaps are correlated with their compositions and crystal structures.

The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

PubMed

Mir, Rafia; Jallu, Shais; Singh, T P

2015-06-01

The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

Accurate facade feature extraction method for buildings from three-dimensional point cloud data considering structural information

NASA Astrophysics Data System (ADS)

Wang, Yongzhi; Ma, Yuqing; Zhu, A.-xing; Zhao, Hui; Liao, Lixia

2018-05-01

Facade features represent segmentations of building surfaces and can serve as a building framework. Extracting facade features from three-dimensional (3D) point cloud data (3D PCD) is an efficient method for 3D building modeling. By combining the advantages of 3D PCD and two-dimensional optical images, this study describes the creation of a highly accurate building facade feature extraction method from 3D PCD with a focus on structural information. The new extraction method involves three major steps: image feature extraction, exploration of the mapping method between the image features and 3D PCD, and optimization of the initial 3D PCD facade features considering structural information. Results show that the new method can extract the 3D PCD facade features of buildings more accurately and continuously. The new method is validated using a case study. In addition, the effectiveness of the new method is demonstrated by comparing it with the range image-extraction method and the optical image-extraction method in the absence of structural information. The 3D PCD facade features extracted by the new method can be applied in many fields, such as 3D building modeling and building information modeling.

Synthesis, structure determination and properties of MIL-53as and MIL-53ht: the first CrIII hybrid inorganic-organic microporous solids: CrIII(OH).(O2C-C6H4-CO2).(HO2C-C6H4-CO2H)x.

PubMed

Millange, Franck; Serre, Christian; Férey, Gérard

2002-04-21

The first three-dimensional chromium(III) dicarboxylate compounds have been isolated and their structures solved from powder X-ray diffraction data; the flexible framework of these materials delimits large pores.

My daily constitutional in martinsried.

PubMed

Allen, James P

2004-01-01

The three-dimensional structures of bacterial reaction centers have served as the framework for much of our understanding of anoxygenic photosynthesis. A key step in the determination of the structure of the reaction center from Rhodobacter sphaeroides was the use the molecular replacement technique. For this technique, we made use of two sets of data. First, X-ray diffraction data had been measured from crystals of the reaction center from R. sphaeroides by our research group in California, led by George Feher and Douglas Rees. The second data set consisted of the coordinates of the three-dimensional structure of the reaction center from Rhodopseudomonas (now Blastochloris) viridis, which had been solved in the pioneering efforts of a group in Martinsried, led by Johann Deisenhofer, Robert Huber and Hartmut Michel. The collaborative efforts of these two groups to determine the structure of the reaction center from R. sphaeroides is described.

α-ScVSe2O8, β-ScVSe2O8, and ScVTe2O8: new quaternary mixed metal oxides composed of only second-order Jahn-Teller distortive cations.

PubMed

Kim, Yeong Hun; Lee, Dong Woo; Ok, Kang Min

2013-10-07

Three new quaternary scandium vanadium selenium/tellurium oxides, α-ScVSe2O8, β-ScVSe2O8, and ScVTe2O8 have been synthesized through hydrothermal and standard solid-state reactions. Although all three reported materials are stoichiometrically similar, they exhibit different crystal structures: α-ScVSe2O8 has a three-dimensional framework structure consisting of ScO6, VO6, and SeO3 groups. β-ScVSe2O8 reveals another three-dimensional framework composed of ScO7, VO5, and SeO3 polyhedra. ScVTe2O8 shows a layered structure with ScO6, VO4, and TeO4 polyhedra. Interestingly, the constituent cations, that is, Sc(3+), V(5+), Se(4+), and Te(4+) are all in a distorted coordination environment attributable to second-order Jahn-Teller (SOJT) effects. Complete characterizations including infrared spectroscopy, elemental analyses, thermal analyses, dipole moment calculation, and the magnitudes of out-of-center distortions for the compounds are reported. Transformation reactions suggest that α-ScVSe2O8 may change to β-ScVSe2O8, and then to Sc2(SeO3)3·H2O under hydrothermal conditions.

Three-dimensional protonic conductivity in porous organic cage solids.

PubMed

Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y; Little, Marc A; Hasell, Tom; Aldous, Iain M; Brown, Craig M; Smith, Martin W; Morrison, Carole A; Hardwick, Laurence J; Cooper, Andrew I

2016-09-13

Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10(-3) S cm(-1) at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores.

Three-dimensional protonic conductivity in porous organic cage solids

NASA Astrophysics Data System (ADS)

Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y.; Little, Marc A.; Hasell, Tom; Aldous, Iain M.; Brown, Craig M.; Smith, Martin W.; Morrison, Carole A.; Hardwick, Laurence J.; Cooper, Andrew I.

2016-09-01

Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10-3 S cm-1 at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores.

Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph.

PubMed

Mörschel, Konstantin; Breit, Markus; Queisser, Gillian

2017-07-01

Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.

Na7Cr4(P2O7)4PO4

PubMed Central

Bourguiba Fakhar, Noura; Zid, Mohamed Faouzi; Driss, Ahmed

2013-01-01

The title compound, hepta­sodium tetra­chromium(III) tetra­kis­(diphosphate) orthophosphate, was synthesized by solid-state reaction. Its structure is isotypic with that of Na7 M 4(P2O7)4PO4 (M = In, Al) compounds and is made up from a three-dimensional [(CrP2O7)4PO4]7− framework with channels running along [001]. The three Na+ cations are located in the voids of the framework. One of the cations is situated on a general position, one is equally disordered around a twofold rotation axis and one is on a fourfold rotoinversion axis. The isolated PO4 tetra­hedron of the anionic framework is also situated on the -4 axis. Structural relationships between the title compound and different diphosphates containing MP2O11 units (M = Mo, V) are discussed. PMID:23723751

Orthotropic Laminated Open-cell Frameworks Retaining Strong Auxeticity under Large Uniaxial Loading

NASA Astrophysics Data System (ADS)

Tanaka, Hiro; Suga, Kaito; Iwata, Naoki; Shibutani, Yoji

2017-01-01

Anisotropic materials form inside living tissue and are widely applied in engineered structures, where sophisticated structural and functional design principles are essential to employing these materials. This paper presents a candidate laminated open-cell framework, which is an anisotropic material that shows remarkable mechanical performance. Using additive manufacturing, artificial frameworks are fabricated by lamination of in-plane orthotropic microstructures made of elbowed beam and column members; this fabricated structure features orthogonal anisotropy in three-dimensional space. Uniaxial loading tests reveal strong auxeticity (high negative Poisson’s ratios) in the out-of-plane direction, which is retained reproducibly up to the nonlinear elastic region, and is equal under tensile and compressive loading. Finite element simulations support the observed auxetic behaviors for a unit cell in the periodic framework, which preserve the theoretical elastic properties of an orthogonal solid. These findings open the possibility of conceptual materials design based on geometry.

Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

NASA Astrophysics Data System (ADS)

Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

2017-12-01

Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

Three-dimensional thermocapillary flow regimes with evaporation

NASA Astrophysics Data System (ADS)

Bekezhanova, V. B.; Goncharova, O. N.

2017-10-01

A three-dimensional problem of evaporative convection in a system of the immiscible media with a common thermocapillary interface is studied. New exact solution, which is a generalization of the Ostroumov - Birikh solution of the Navier - Stokes equations in the Oberbeck - Boussinesq approximation, is presented in order to describe the joint flows of the liquid and gas - vapor mixture in an infinite channel with a rectangular cross-section. The motion occurs in the bulk force field under action of a constant longitudinal temperature gradient. The velocity components depend only on the transverse coordinates. The functions of pressure, temperature and concentration of vapor in the gas are characterized by the linear dependence on the longitudinal coordinate. In the framework of the problem statement, which takes into account diffusive mass flux through the interface and zero vapor flux at the upper boundary of the channel, the influence of the gravity and intensity of the thermal action on flow structure is studied. The original three-dimensional problem is reduced to a chain of two-dimensional problems which are solved numerically with help of modification of the method of alternating directions. Arising flows can be characterized as a translational-rotational motion, under that the symmetrical double, quadruple or sextuple vortex structures are formed. Quantity, shape and structure of the vortexes also depend on properties of the working media.

Tuning metal–carboxylate coordination in crystalline metal–organic frameworks through surfactant media

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

Gao, Junkuo; Ye, Kaiqi; State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012

Although it has been widely demonstrated that surfactants can efficiently control the size, shape and surface properties of micro/nanocrystals of metal–organic frameworks (MOFs) due to the strong interactions between surfactants and crystal facets of MOFs, the use of surfactants as reaction media to grow MOF single crystals is unprecedented. In addition, compared with ionic liquids, surfactants are much cheaper and can have multifunctional properties such as acidic, basic, neutral, cationic, anionic, or even block. These factors strongly motivate us to develop a new synthetic strategy: growing crystalline MOFs in surfactants. In this report, eight new two-dimensional (2D) or three-dimensional (3D)more » MOFs have been successfully synthesized in an industrially-abundant and environmentally-friendly surfactant: polyethylene glycol-200 (PEG-200). Eight different coordination modes of carboxylates, ranging from monodentate η{sup 1} mode to tetra-donor coordination µ{sub 3}-η{sup 1}:η{sup 2}:η{sup 1} mode, have been founded in our research. The magnetic properties of Co-based MOFs were investigated and MOF NTU-Z6b showed a phase transition with a Curie temperature (T{sub c}) at 5 K. Our strategy of growing crystalline MOFs in surfactant could offer exciting opportunities for preparing novel MOFs with diverse structures and interesting properties. - Graphical abstract: Surfactants have been used as reaction media to grow MOF single crystals for the first time. Eight new two-dimensional or three-dimensional MOFs were successfully synthesized in surfactant polyethylene glycol-200 (PEG-200). Coordination modes of carboxylates up to eight were founded. Our strategy of growing crystalline MOFs in surfactant could offer exciting opportunities for preparing novel MOFs with diverse structures and interesting properties. Display Omitted - Highlights: • Surfactant-thermal synthesis of crystalline metal–organic frameworks. • Eight new 2-D or 3-D metal–organic frameworks. • Eight different metal–carboxylate coordination modes.« less

A New Framework for Addressing Temporal Range Queries and Some Preliminary Results

DTIC Science & Technology

2003-01-29

dominance reporting problem, which canbe solved in O(log n + f(v)) time using the data structure of Makris and Tsakalidis [11],which we call the...SIGMODInternational Conference on Management of Data, pages 426{435, 1991.[11] C. Makris and A. K. Tsakalidis . Algorithms for three-dimensional dominance searchingin

Three-dimensional wide-field pump-probe structured illumination microscopy

PubMed Central

Kim, Yang-Hyo; So, Peter T.C.

2017-01-01

We propose a new structured illumination scheme for achieving depth resolved wide-field pump-probe microscopy with sub-diffraction limit resolution. By acquiring coherent pump-probe images using a set of 3D structured light illumination patterns, a 3D super-resolution pump-probe image can be reconstructed. We derive the theoretical framework to describe the coherent image formation and reconstruction scheme for this structured illumination pump-probe imaging system and carry out numerical simulations to investigate its imaging performance. The results demonstrate a lateral resolution improvement by a factor of three and providing 0.5 µm level axial optical sectioning. PMID:28380860

General flat four-dimensional world pictures and clock systems

NASA Technical Reports Server (NTRS)

Hsu, J. P.; Underwood, J. A.

1978-01-01

We explore the mathematical structure and the physical implications of a general four-dimensional symmetry framework which is consistent with the Poincare-Einstein principle of relativity for physical laws and with experiments. In particular, we discuss a four-dimensional framework in which all observers in different frames use one and the same grid of clocks. The general framework includes special relativity and a recently proposed new four-dimensional symmetry with a nonuniversal light speed as two special simple cases. The connection between the properties of light propagation and the convention concerning clock systems is also discussed, and is seen to be nonunique within the four-dimensional framework.

Variational asymptotic modeling of composite dimensionally reducible structures

NASA Astrophysics Data System (ADS)

Yu, Wenbin

A general framework to construct accurate reduced models for composite dimensionally reducible structures (beams, plates and shells) was formulated based on two theoretical foundations: decomposition of the rotation tensor and the variational asymptotic method. Two engineering software systems, Variational Asymptotic Beam Sectional Analysis (VABS, new version) and Variational Asymptotic Plate and Shell Analysis (VAPAS), were developed. Several restrictions found in previous work on beam modeling were removed in the present effort. A general formulation of Timoshenko-like cross-sectional analysis was developed, through which the shear center coordinates and a consistent Vlasov model can be obtained. Recovery relations are given to recover the asymptotic approximations for the three-dimensional field variables. A new version of VABS has been developed, which is a much improved program in comparison to the old one. Numerous examples are given for validation. A Reissner-like model being as asymptotically correct as possible was obtained for composite plates and shells. After formulating the three-dimensional elasticity problem in intrinsic form, the variational asymptotic method was used to systematically reduce the dimensionality of the problem by taking advantage of the smallness of the thickness. The through-the-thickness analysis is solved by a one-dimensional finite element method to provide the stiffnesses as input for the two-dimensional nonlinear plate or shell analysis as well as recovery relations to approximately express the three-dimensional results. The known fact that there exists more than one theory that is asymptotically correct to a given order is adopted to cast the refined energy into a Reissner-like form. A two-dimensional nonlinear shell theory consistent with the present modeling process was developed. The engineering computer code VAPAS was developed and inserted into DYMORE to provide an efficient and accurate analysis of composite plates and shells. Numerical results are compared with the exact solutions, and the excellent agreement proves that one can use VAPAS to analyze composite plates and shells efficiently and accurately. In conclusion, rigorous modeling approaches were developed for composite beams, plates and shells within a general framework. No such consistent and general treatment is found in the literature. The associated computer programs VABS and VAPAS are envisioned to have many applications in industry.

Three-dimensional periodic supramolecular organic framework ion sponge in water and microcrystals

DOE PAGES

Tian, Jia; Zhou, Tian-You; Zhang, Shao-Chen; ...

2014-12-02

Self-assembly has emerged as a powerful approach to generating complex supramolecular architectures. Despite there being many crystalline frameworks reported in the solid state, the construction of highly soluble periodic supramolecular networks in a three-dimensional space is still a challenge. In this paper we demonstrate that the encapsulation motif, which involves the dimerization of two aromatic units within cucurbit[8]uril, can be used to direct the co-assembly of a tetratopic molecular block and cucurbit[8]uril into a periodic three-dimensional supramolecular organic framework in water. The periodicity of the supramolecular organic framework is supported by solution-phase small-angle X-ray-scattering and diffraction experiments. Upon evaporating themore » solvent, the periodicity of the framework is maintained in porous microcrystals. Lastly, as a supramolecular 'ion sponge', the framework can absorb different kinds of anionic guests, including drugs, in both water and microcrystals, and drugs absorbed in microcrystals can be released to water with selectivity.« less

Calcium Coordination Solids for pH-Triggered Release of Olsalazine

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

Levine, Dana J.; Gonzalez, Miguel I.; Legendre, Christina M.

Here, calcium coordination solids were synthesized and evaluated for delivery of olsalazine (H 4olz), an anti-inflammatory compound used for treatment of ulcerative colitis. The materials include one-dimensional Ca(H 2olz)•4H 2O chains, two-dimensional Ca(H 2olz)•2H 2O sheets, and a three-dimensional metal-organic framework Ca(H 2olz)•2DMF (DMF= N,N-dimethylformamide). The framework undergoes structural changes in response to solvent, forming a dense Ca(H 2olz) phase when exposed to aqueous HCl. The compounds Ca(H 2olz)•xH 2O (x=0, 2, 4) were each pressed into pellets and exposed to simulated gastrointestinal fluids to mimic the passage of a pill from the acidic stomach to the pH-neutral intestines. Allmore » three calcium materials exhibited a delayed release of olsalazine relative to Na 2(H 2olz), the commercial formulation, illustrating how formulation of a drug within an extended coordination solid can serve to tune its solubility and performance.« less

Calcium Coordination Solids for pH-Triggered Release of Olsalazine

DOE PAGES

Levine, Dana J.; Gonzalez, Miguel I.; Legendre, Christina M.; ...

2017-09-12

Here, calcium coordination solids were synthesized and evaluated for delivery of olsalazine (H 4olz), an anti-inflammatory compound used for treatment of ulcerative colitis. The materials include one-dimensional Ca(H 2olz)•4H 2O chains, two-dimensional Ca(H 2olz)•2H 2O sheets, and a three-dimensional metal-organic framework Ca(H 2olz)•2DMF (DMF= N,N-dimethylformamide). The framework undergoes structural changes in response to solvent, forming a dense Ca(H 2olz) phase when exposed to aqueous HCl. The compounds Ca(H 2olz)•xH 2O (x=0, 2, 4) were each pressed into pellets and exposed to simulated gastrointestinal fluids to mimic the passage of a pill from the acidic stomach to the pH-neutral intestines. Allmore » three calcium materials exhibited a delayed release of olsalazine relative to Na 2(H 2olz), the commercial formulation, illustrating how formulation of a drug within an extended coordination solid can serve to tune its solubility and performance.« less

Foldable interpenetrated metal-organic frameworks/carbon nanotubes thin film for lithium-sulfur batteries

NASA Astrophysics Data System (ADS)

Mao, Yiyin; Li, Gaoran; Guo, Yi; Li, Zhoupeng; Liang, Chengdu; Peng, Xinsheng; Lin, Zhan

2017-03-01

Lithium-sulfur batteries are promising technologies for powering flexible devices due to their high energy density, low cost and environmental friendliness, when the insulating nature, shuttle effect and volume expansion of sulfur electrodes are well addressed. Here, we report a strategy of using foldable interpenetrated metal-organic frameworks/carbon nanotubes thin film for binder-free advanced lithium-sulfur batteries through a facile confinement conversion. The carbon nanotubes interpenetrate through the metal-organic frameworks crystal and interweave the electrode into a stratified structure to provide both conductivity and structural integrity, while the highly porous metal-organic frameworks endow the electrode with strong sulfur confinement to achieve good cyclability. These hierarchical porous interpenetrated three-dimensional conductive networks with well confined S8 lead to high sulfur loading and utilization, as well as high volumetric energy density.

Foldable interpenetrated metal-organic frameworks/carbon nanotubes thin film for lithium–sulfur batteries

PubMed Central

Mao, Yiyin; Li, Gaoran; Guo, Yi; Li, Zhoupeng; Liang, Chengdu; Peng, Xinsheng; Lin, Zhan

2017-01-01

Lithium–sulfur batteries are promising technologies for powering flexible devices due to their high energy density, low cost and environmental friendliness, when the insulating nature, shuttle effect and volume expansion of sulfur electrodes are well addressed. Here, we report a strategy of using foldable interpenetrated metal-organic frameworks/carbon nanotubes thin film for binder-free advanced lithium–sulfur batteries through a facile confinement conversion. The carbon nanotubes interpenetrate through the metal-organic frameworks crystal and interweave the electrode into a stratified structure to provide both conductivity and structural integrity, while the highly porous metal-organic frameworks endow the electrode with strong sulfur confinement to achieve good cyclability. These hierarchical porous interpenetrated three-dimensional conductive networks with well confined S8 lead to high sulfur loading and utilization, as well as high volumetric energy density. PMID:28262801

Lead(II) coordination polymers based on rigid-flexible 3,5-bis-oxyacetate-benzoic acid: Structural transition driven by temperature control

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

Chen, Yong-Qiang, E-mail: chenjzxy@126.com; Tian, Yuan

2017-03-15

Three Pb(II) complexes ([Pb{sub 3}(BOABA){sub 2}(H{sub 2}O)]·H{sub 2}O){sub n} (1), ([Pb{sub 4}(BOABA){sub 2}(µ{sub 4}-O)(H{sub 2}O){sub 2}]·H{sub 2}O){sub n} (2), and [Pb{sub 3}(BOABA){sub 2}(H{sub 2}O)]{sub n} (3) (H{sub 3}BOABA=3,5-bis-oxyacetate-benzoic acid) were obtained under the same reaction systems with different temperatures. Complexes 1 and 2 are two dimensional (2D) networks based on Pb-BOABA chains and Pb{sub 4}(µ{sub 4}-O)(COO){sub 6} SBUs, respectively. Complex 3 presents an interesting three dimensional (3D) framework, was obtained by increasing the reaction temperature. Structural transition of the crystallization products is largely dependent on the reaction temperature. Moreover, the fluorescence properties of complexes 1–3 have been investigated. - Graphicalmore » abstract: Three Pb(II) coordination polymers were obtained under the same reaction systems with different temperatures. Both of complexes 1 and 2 are 2D network. 3 presents a 3D framework based on Pb–O–C rods SBUs. The 2D to 3D structures transition between three complexes was achieved successfully by temperature control. - Highlights: • Three Pb(II) complexes were obtained under the same reaction systems with different temperatures. • Structural transition of the crystallization products is largely dependent on the reaction temperature. • The luminescence properties studies reveal that three complexes exhibit yellow fluorescence emission behavior, which might be good candidates for obtaining photoluminescent materials.« less

A FSI computational framework for vascular physiopathology: A novel flow-tissue multiscale strategy.

PubMed

Bianchi, Daniele; Monaldo, Elisabetta; Gizzi, Alessio; Marino, Michele; Filippi, Simonetta; Vairo, Giuseppe

2017-09-01

A novel fluid-structure computational framework for vascular applications is herein presented. It is developed by combining the double multi-scale nature of vascular physiopathology in terms of both tissue properties and blood flow. Addressing arterial tissues, they are modelled via a nonlinear multiscale constitutive rationale, based only on parameters having a clear histological and biochemical meaning. Moreover, blood flow is described by coupling a three-dimensional fluid domain (undergoing physiological inflow conditions) with a zero-dimensional model, which allows to reproduce the influence of the downstream vasculature, furnishing a realistic description of the outflow proximal pressure. The fluid-structure interaction is managed through an explicit time-marching approach, able to accurately describe tissue nonlinearities within each computational step for the fluid problem. A case study associated to a patient-specific aortic abdominal aneurysmatic geometry is numerically investigated, highlighting advantages gained from the proposed multiscale strategy, as well as showing soundness and effectiveness of the established framework for assessing useful clinical quantities and risk indexes. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3.

PubMed

Strutynska, Nataliia Yu; Bondarenko, Marina A; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2015-03-01

Potassium rubidium cobalt(II)/titanium(IV) tris-(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/Ti(IV))O6 octa-hedra (point group symmetry .3.) and PO4 tetra-hedra. The K(+) and Rb(+) cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms.

A Water-Stable Metal-Organic Framework for Highly Sensitive and Selective Sensing of Fe3+ Ion.

PubMed

Hou, Bing-Lei; Tian, Dan; Liu, Jiang; Dong, Long-Zhang; Li, Shun-Li; Li, Dong-Sheng; Lan, Ya-Qian

2016-10-17

A new metal-organic framework [Zn 5 (hfipbb) 4 (trz) 2 (H 2 O) 2 ] (NNU-1) [H 2 hfipbb = 4,4'-(hexafluoroisopropylidene)bis(benzoic acid), Htrz = 1H-1,2,3-triazole] was assembled by hydrothermal synthesis. Single-crystal X-ray diffraction analysis reveals that NNU-1 displays a twofold interpenetrating three-dimensional (3D) framework with a {4 24 ·6 4 }-bcu topology. Interestingly, the 3D framework contains a two-dimensional (2D) layered structure that consists of alternating left- and right-handed double helical chains. On the basis of the hydrophobic -CF 3 groups from H 2 hfipbb ligand, NNU-1 possesses excellent stability in water. It is worth noting that NNU-1 not only shows a highly selective fluorescence quenching effect to Fe 3+ ion in aqueous solution but also resists the interference of other metals including Fe 2+ ion. Accordingly, NNU-1 probably functions as a potential promising fluorescence sensor for detecting Fe 3+ ion with high sensitivity and selectivity.

Three-dimensional analysis of alveolar wall destruction in the early stage of pulmonary emphysema.

PubMed

Kobayashi, Yukihiro; Uehara, Takeshi; Kawasaki, Kenji; Sugano, Mitsutoshi; Matsumoto, Takehisa; Matsumoto, Gou; Honda, Takayuki

2015-03-01

The morphological mechanism of alveolar wall destruction during pulmonary emphysema has not been clarified. The aim of this study was to elucidate this process three-dimensionally. Lung specimens from five patients with pulmonary emphysema were used, and five controls with normal alveolar structure were also examined. Sections 150 μm thick were stained with hematoxylin and eosin, elastica, and silver impregnation, and immunostained with selected antibodies. We examined these sections three-dimensionally using a laser confocal microscope and a light microscope. There were only a few Kohn's pores and no fenestrae in the normal alveoli from the controls. In the lungs of the emphysema patients a small rupture appeared in the extremely thin alveolar wall among the alveolar capillaries. This rupture enlarged to form a circle surrounded by the capillaries, which was called an alveolar fenestra. Two neighboring fenestrae fused by breakdown of the collapsed or cord-like capillary between them to form a large fenestra. The large fenestrae fused repeatedly to become larger, and these were bordered by thick elastic fibers constructing an alveolar framework. Alveolar wall destruction during emphysema could start from small ruptures of the alveolar wall that become fenestrae surrounded by capillaries, which fuse repeatedly to become larger fenestrae rimmed with elastic fibers. The alveolar capillary network could initially prevent enlargement of the fenestrae, and the thick elastic fibers constituting the alveolar framework could secondarily prevent destruction of the alveolar wall structure. © 2014 Wiley Periodicals, Inc.

The Effect of Framework Design on Stress Distribution in Implant-Supported FPDs: A 3-D FEM Study

PubMed Central

Eraslan, Oguz; Inan, Ozgur; Secilmis, Asli

2010-01-01

Objectives: The biomechanical behavior of the superstructure plays an important role in the functional longevity of dental implants. However, information about the influence of framework design on stresses transmitted to the implants and supporting tissues is limited. The purpose of this study was to evaluate the effects of framework designs on stress distribution at the supporting bone and supporting implants. Methods: In this study, the three-dimensional (3D) finite element stress analysis method was used. Three types of 3D mathematical models simulating three different framework designs for implant-supported 3-unit posterior fixed partial dentures were prepared with supporting structures. Convex (1), concave (2), and conventional (3) pontic framework designs were simulated. A 300-N static vertical occlusal load was applied on the node at the center of occlusal surface of the pontic to calculate the stress distributions. As a second condition, frameworks were directly loaded to evaluate the effect of the framework design clearly. The Solidworks/Cosmosworks structural analysis programs were used for finite element modeling/analysis. Results: The analysis of the von Mises stress values revealed that maximum stress concentrations were located at the loading areas for all models. The pontic side marginal edges of restorations and the necks of implants were other stress concentration regions. There was no clear difference among models when the restorations were loaded at occlusal surfaces. When the veneering porcelain was removed, and load was applied directly to the framework, there was a clear increase in stress concentration with a concave design on supporting implants and bone structure. Conclusions: The present study showed that the use of a concave design in the pontic frameworks of fixed partial dentures increases the von Mises stress levels on implant abutments and supporting bone structure. However, the veneering porcelain element reduces the effect of the framework and compensates for design weaknesses. PMID:20922156

An Object-Oriented Serial DSMC Simulation Package

NASA Astrophysics Data System (ADS)

Liu, Hongli; Cai, Chunpei

2011-05-01

A newly developed three-dimensional direct simulation Monte Carlo (DSMC) simulation package, named GRASP ("Generalized Rarefied gAs Simulation Package"), is reported in this paper. This package utilizes the concept of simulation engine, many C++ features and software design patterns. The package has an open architecture which can benefit further development and maintenance of the code. In order to reduce the engineering time for three-dimensional models, a hybrid grid scheme, combined with a flexible data structure compiled by C++ language, are implemented in this package. This scheme utilizes a local data structure based on the computational cell to achieve high performance on workstation processors. This data structure allows the DSMC algorithm to be very efficiently parallelized with domain decomposition and it provides much flexibility in terms of grid types. This package can utilize traditional structured, unstructured or hybrid grids within the framework of a single code to model arbitrarily complex geometries and to simulate rarefied gas flows. Benchmark test cases indicate that this package has satisfactory accuracy for complex rarefied gas flows.

Highly Crystalline Multimetallic Nanoframes with Three-Dimensional Electrocatalytic Surfaces

DOE PAGES

Chen, Chen; Kang, Yijin; Huo, Ziyang; ...

2014-02-27

Control of structure at the atomic level can precisely and effectively tune catalytic properties of materials, enabling enhancement in both activity and durability. We synthesized a highly active and durable class of electrocatalysts by exploiting the structural evolution of platinum-nickel (Pt-Ni) bimetallic nanocrystals. The starting material, crystalline PtNi 3 polyhedra, transforms in solution by interior erosion into Pt 3Ni nanoframes with surfaces that offer three-dimensional molecular accessibility. The edges of the Pt-rich PtNi 3 polyhedra are maintained in the final Pt 3Ni nanoframes. Both the interior and exterior catalytic surfaces of this open-framework structure are composed of the nanosegregated Pt-skinmore » structure, which exhibits enhanced oxygen reduction reaction (ORR) activity. The Pt 3Ni nanoframe catalysts achieved a factor of 36 enhancement in mass activity and a factor of 22 enhancement in specific activity, respectively, for this reaction (relative to state-of-the-art platinum-carbon catalysts) during prolonged exposure to reaction conditions.« less

Crystal structure of 1-meth-oxy-2,2,2-tris-(pyrazol-1-yl)ethane.

PubMed

Lyubartseva, Ganna; Parkin, Sean; Coleman, Morgan D; Mallik, Uma Prasad

2014-09-01

The title compound, C12H14N6O, consists of three pyrazole rings bound via nitro-gen to the distal ethane carbon of meth-oxy ethane. The dihedral angles between the three pyrazole rings are 67.62 (14), 73.74 (14), and 78.92 (12)°. In the crystal, mol-ecules are linked by bifurcated C-H,H⋯N hydrogen bonds, forming double-stranded chains along [001]. The chains are linked via C-H⋯O hydrogen bonds, forming a three-dimensional framework structure. The crystal was refined as a perfect (0.5:0.5) inversion twin.

Method of fabricating free-form, high-aspect ratio components for high-current, high-speed microelectrics

DOEpatents

Maxwell, James L; Rose, Chris R; Black, Marcie R; Springer, Robert W

2014-03-11

Microelectronic structures and devices, and method of fabricating a three-dimensional microelectronic structure is provided, comprising passing a first precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures to enhance formation of a first portion of said three-dimensional microelectronic structure; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said first portion of a selected three-dimensional microelectronic structure is formed from said first precursor material; positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs; passing a second precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures whereby a second portion of said three-dimensional microelectronic structure formation is enhanced; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said second portion of a selected three-dimensional microelectronic structure is formed from said second precursor material; and, positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs.

Generalized Lorenz equations on a three-sphere

NASA Astrophysics Data System (ADS)

Saiki, Yoshitaka; Sander, Evelyn; Yorke, James A.

2017-06-01

Edward Lorenz is best known for one specific three-dimensional differential equation, but he actually created a variety of related N-dimensional models. In this paper, we discuss a unifying principle for these models and put them into an overall mathematical framework. Because this family of models is so large, we are forced to choose. We sample the variety of dynamics seen in these models, by concentrating on a four-dimensional version of the Lorenz models for which there are three parameters and the norm of the solution vector is preserved. We can therefore restrict our focus to trajectories on the unit sphere S 3 in ℝ4. Furthermore, we create a type of Poincaré return map. We choose the Poincaré surface to be the set where one of the variables is 0, i.e., the Poincaré surface is a two-sphere S 2 in ℝ3. Examining different choices of our three parameters, we illustrate the wide variety of dynamical behaviors, including chaotic attractors, period doubling cascades, Standard-Map-like structures, and quasiperiodic trajectories. Note that neither Standard-Map-like structure nor quasiperiodicity has previously been reported for Lorenz models.

Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling

NASA Astrophysics Data System (ADS)

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

2015-01-01

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations.

Development of a 3D cell printed construct considering angiogenesis for liver tissue engineering.

PubMed

Lee, Jin Woo; Choi, Yeong-Jin; Yong, Woon-Jae; Pati, Falguni; Shim, Jin-Hyung; Kang, Kyung Shin; Kang, In-Hye; Park, Jaesung; Cho, Dong-Woo

2016-01-12

Several studies have focused on the regeneration of liver tissue in a two-dimensional (2D) planar environment, whereas actual liver tissue is three-dimensional (3D). Cell printing technology has been successfully utilized for building 3D structures; however, the poor mechanical properties of cell-laden hydrogels are a major concern. Here, we demonstrate the printing of a 3D cell-laden construct and its application to liver tissue engineering using 3D cell printing technology through a multi-head tissue/organ building system. Polycaprolactone (PCL) was used as a framework material because of its excellent mechanical properties. Collagen bioink containing three different types of cells-hepatocytes (HCs), human umbilical vein endothelial cells , and human lung fibroblasts--was infused into the canals of a PCL framework to induce the formation of capillary--like networks and liver cell growth. A co-cultured 3D microenvironment of the three types of cells was successfully established and maintained. The vascular formation and functional abilities of HCs (i.e., albumin secretion and urea synthesis) demonstrated that the heterotypic interaction among HCs and nonparenchymal cells increased the survivability and functionality of HCs within the collagen gel. Therefore, our results demonstrate the prospect of using cell printing technology for the creation of heterotypic cellular interaction within a structure for liver tissue engineering.

3D annotation and manipulation of medical anatomical structures

NASA Astrophysics Data System (ADS)

Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

2009-02-01

Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

Solid State Chemistry of Clathrate Phases: Crystal Structure, Chemical Bonding and Preparation Routes

NASA Astrophysics Data System (ADS)

Baitinger, Michael; Böhme, Bodo; Ormeci, Alim; Grin, Yuri

Clathrates represent a family of inorganic materials called cage compounds. The key feature of their crystal structures is a three-dimensional (host) framework bearing large cavities (cages) with 20-28 vertices. These polyhedral cages bear—as a rule—guest species. Depending on the formal charge of the framework, clathrates are grouped in anionic, cationic and neutral. While the bonding in the framework is of (polar) covalent nature, the guest-host interaction can be ionic, covalent or even van-der Waals, depending on the chemical composition of the clathrates. The chemical composition and structural features of the cationic clathrates can be described by the enhanced Zintl concept, whereas the composition of the anionic clathrates deviates often from the Zintl counts, indicating additional atomic interactions in comparison with the ionic-covalent Zintl model. These interactions can be visualized and studied by applying modern quantum chemical approaches such as electron localizability.

pH-specific hydrothermal assembly of binary and ternary Pb(II)-(O,N-carboxylic acid) metal organic framework compounds: correlation of aqueous solution speciation with variable dimensionality solid-state lattice architecture and spectroscopic signatures.

PubMed

Gabriel, C; Perikli, M; Raptopoulou, C P; Terzis, A; Psycharis, V; Mateescu, C; Jakusch, T; Kiss, T; Bertmer, M; Salifoglou, A

2012-09-03

Hydrothermal pH-specific reactivity in the binary/ternary systems of Pb(II) with the carboxylic acids N-hydroxyethyl-iminodiacetic acid (Heida), 1,3-diamino-2-hydroxypropane-N,N,N',N'-tetraacetic acid (Dpot), and 1,10-phenanthroline (Phen) afforded the new well-defined crystalline compounds [Pb(Heida)](n)·nH(2)O(1), [Pb(Phen)(Heida)]·4H(2)O(2), and [Pb(3)(NO(3))(Dpot)](n)(3). All compounds were characterized by elemental analysis, FT-IR, solution or/and solid-state NMR, and single-crystal X-ray diffraction. The structures in 1-2 reveal the presence of a Pb(II) center coordinated to one Heida ligand, with 1 exhibiting a two-dimensional (2D) lattice extending to a three-dimensional (3D) one through H-bonding interactions. The concurrent aqueous speciation study of the binary Pb(II)-Heida system projects species complementing the synthetic efforts, thereby lending credence to a global structural speciation strategy in investigating binary/ternary Pb(II)-Heida/Phen systems. The involvement of Phen in 2 projects the significance of nature and reactivity potential of N-aromatic chelators, disrupting the binary lattice in 1 and influencing the nature of the ultimately arising ternary 3D lattice. 3 is a ternary coordination polymer, where Pb(II)-Dpot coordination leads to a 2D metal-organic-framework material with unique architecture. The collective physicochemical properties of 1-3 formulate the salient features of variable dimensionality metal-organic-framework lattices in binary/ternary Pb(II)-(hydroxy-carboxylate) structures, based on which new Pb(II) materials with distinct architecture and spectroscopic signature can be rationally designed and pursued synthetically.

Self-assembly of a binodal metal-organic framework exhibiting a demi-regular lattice.

PubMed

Yan, Linghao; Kuang, Guowen; Zhang, Qiushi; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2017-10-26

Designing metal-organic frameworks with new topologies is a long-standing quest because new topologies often accompany new properties and functions. Here we report that 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene molecules coordinate with Cu atoms to form a two-dimensional framework in which Cu adatoms form a nanometer-scale demi-regular lattice. The lattice is articulated by perfectly arranged twofold and threefold pyridyl-Cu coordination motifs in a ratio of 1 : 6 and features local dodecagonal symmetry. This structure is thermodynamically robust and emerges solely when the molecular density is at a critical value. In comparison, we present three framework structures that consist of semi-regular and regular lattices of Cu atoms self-assembled out of 1,3,5-tris[4-(pyridin-4-yl)phenyl]benzene and trispyridylbenzene molecules. Thus a family of regular, semi-regular and demi-regular lattices can be achieved by Cu-pyridyl coordination.

Hybrid metal–organic chalcogenide nanowires with electrically conductive inorganic core through diamondoid-directed assembly

DOE PAGES

Yan, Hao; Hohman, J. Nathan; Li, Fei Hua; ...

2016-12-26

Controlling inorganic structure and dimensionality through structure-directing agents is a versatile approach for new materials synthesis that has been used extensively for metal–organic frameworks and coordination polymers. However, the lack of ‘solid’ inorganic cores requires charge transport through single-atom chains and/or organic groups, limiting their electronic properties. Here, we report that strongly interacting diamondoid structure-directing agents guide the growth of hybrid metal–organic chalcogenide nanowires with solid inorganic cores having three-atom cross-sections, representing the smallest possible nanowires. The strong van der Waals attraction between diamondoids overcomes steric repulsion leading to a cis configuration at the active growth front, enabling face-on additionmore » of precursors for nanowire elongation. These nanowires have band-like electronic properties, low effective carrier masses and three orders-of-magnitude conductivity modulation by hole doping. Furthermore, this discovery highlights a previously unexplored regime of structure-directing agents compared with traditional surfactant, block copolymer or metal–organic framework linkers.« less

Hybrid Assembly of Different-Sized Supertetrahedral Clusters into a Unique Non-Interpenetrated Mn-In-S Open Framework with Large Cavity.

PubMed

Wang, Hongxiang; Wang, Wei; Hu, Dandan; Luo, Min; Xue, Chaozhuang; Li, Dongsheng; Wu, Tao

2018-06-04

Reported here is a unique crystalline semiconductor open-framework material built from the large-sized supertetrahedral T4 and T5 clusters with the Mn-In-S compositions. The hybrid assembly between T4 and T5 clusters by sharing terminal μ 2 -S 2- is for the first time observed among the cluster-based chalcogenide open frameworks. Such three-dimensional structure displays non-interpenetrated diamond-type topology with extra-large nonframework volume of 82%. Moreover, ion exchange, CO 2 adsorption, as well as photoluminescence properties of the title compound are also investigated.

Quantitative volumetric Raman imaging of three dimensional cell cultures

NASA Astrophysics Data System (ADS)

Kallepitis, Charalambos; Bergholt, Mads S.; Mazo, Manuel M.; Leonardo, Vincent; Skaalure, Stacey C.; Maynard, Stephanie A.; Stevens, Molly M.

2017-03-01

The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

Construction of 3-D geologic framework and textural models for Cuyama Valley groundwater basin, California

USGS Publications Warehouse

Sweetkind, Donald S.; Faunt, Claudia C.; Hanson, Randall T.

2013-01-01

Groundwater is the sole source of water supply in Cuyama Valley, a rural agricultural area in Santa Barbara County, California, in the southeasternmost part of the Coast Ranges of California. Continued groundwater withdrawals and associated water-resource management concerns have prompted an evaluation of the hydrogeology and water availability for the Cuyama Valley groundwater basin by the U.S. Geological Survey, in cooperation with the Water Agency Division of the Santa Barbara County Department of Public Works. As a part of the overall groundwater evaluation, this report documents the construction of a digital three-dimensional geologic framework model of the groundwater basin suitable for use within a numerical hydrologic-flow model. The report also includes an analysis of the spatial variability of lithology and grain size, which forms the geologic basis for estimating aquifer hydraulic properties. The geologic framework was constructed as a digital representation of the interpreted geometry and thickness of the principal stratigraphic units within the Cuyama Valley groundwater basin, which include younger alluvium, older alluvium, and the Morales Formation, and underlying consolidated bedrock. The framework model was constructed by creating gridded surfaces representing the altitude of the top of each stratigraphic unit from various input data, including lithologic and electric logs from oil and gas wells and water wells, cross sections, and geologic maps. Sediment grain-size data were analyzed in both two and three dimensions to help define textural variations in the Cuyama Valley groundwater basin and identify areas with similar geologic materials that potentially have fairly uniform hydraulic properties. Sediment grain size was used to construct three-dimensional textural models that employed simple interpolation between drill holes and two-dimensional textural models for each stratigraphic unit that incorporated spatial structure of the textural data.

Three-dimensional hydrogeological modelling application to the Alverà mudslide (Cortina d'Ampezzo, Italy)

NASA Astrophysics Data System (ADS)

Bonomi, Tullia; Cavallin, Angelo

1999-10-01

Within the framework of Geographic Information System (GIS), the distributed three-dimensional groundwater model MODFLOW has been applied to evaluate the groundwater processes of the hydrogeological system in the Alverà mudslide (Cortina d'Ampezzo, Italy; test site in the TESLEC Project of the European Union). The application of this model has permitted an analysis of the spatial distribution of the structure (DTM and landslide bottom) and the mass transfer elements of the hydrogeological system. The field survey suggested zoning the area on the basis of the recharge, groundwater fluctuation and drainage system. For each zone, a hydraulic conductivity value to simulate the different recharge and the drainage responses has been assigned. The effect of rainfall infiltration into the ground and its effect on the groundwater table, with different intensity related to different time periods, have been simulated to reproduce the real condition of the area. The applied model can simulate the positive fluctuations of the water table on the whole landslide, with a different response of the hydrogeological system in each zone. The spatial simulated water level distribution is in accordance with the real one, with very small difference between them. The application of distributed three-dimensional models, within the framework of GIS, is an approach which permits data to be continually updated, standardised and integrated.

Audiomagnetotelluric Data and Two-Dimensional Models from Spring, Snake, and Three Lakes Valleys, Nevada

USGS Publications Warehouse

McPhee, Darcy K.; Chuchel, Bruce A.; Pellerin, Louise

2007-01-01

Audiomagnetotelluric (AMT) data along thirteen profiles in Spring, Snake, and Three Lakes Valleys, and the corresponding two-dimensional (2-D) inverse models, are presented. The AMT method is a valuable tool for estimating the electrical resistivity of the Earth over depth ranges of a few meters to roughly one kilometer. It is important for revealing subsurface structure and stratigraphy within the Basin and Range province of eastern Nevada that can be used to define the geohydrologic framework of the region. We collected AMT data using the Geometrics StrataGem EH4 system. Profiles were 1.2 to 4.6 km in length with station spacing of 100-400 m. Data were recorded in a coordinate system parallel to and perpendicular to the assumed regional geologic strike direction. We show station locations, sounding curves of apparent resistivity, phase, and coherency, and 2-D models. The 2-D inverse models are computed from the transverse electric (TE), transverse magnetic (TM), and TE+TM mode data using the conjugate gradient, finite-difference method of Rodi and Mackie (2001). Preliminary interpretation of these models defines the structural framework of the basins and the resistivity contrasts between alluvial basin-fill, volcanic units, and carbonate/clastic rocks.

Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3

PubMed Central

Strutynska, Nataliia Yu.; Bondarenko, Marina A.; Ogorodnyk, Ivan V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2015-01-01

Potassium rubidium cobalt(II)/titanium(IV) tris­(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/TiIV)O6 octa­hedra (point group symmetry .3.) and PO4 tetra­hedra. The K+ and Rb+ cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms. PMID:25844179

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

PubMed Central

Pan, Keyao; Kim, Do-Nyun; Zhang, Fei; Adendorff, Matthew R.; Yan, Hao; Bathe, Mark

2014-01-01

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. PMID:25470497

Adagio 4.20 User’s Guide

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

Spencer, Benjamin Whiting; Crane, Nathan K.; Heinstein, Martin W.

2011-03-01

Adagio is a Lagrangian, three-dimensional, implicit code for the analysis of solids and structures. It uses a multi-level iterative solver, which enables it to solve problems with large deformations, nonlinear material behavior, and contact. It also has a versatile library of continuum and structural elements, and an extensive library of material models. Adagio is written for parallel computing environments, and its solvers allow for scalable solutions of very large problems. Adagio uses the SIERRA Framework, which allows for coupling with other SIERRA mechanics codes. This document describes the functionality and input structure for Adagio.

PARTONS: PARtonic Tomography Of Nucleon Software. A computing framework for the phenomenology of Generalized Parton Distributions

NASA Astrophysics Data System (ADS)

Berthou, B.; Binosi, D.; Chouika, N.; Colaneri, L.; Guidal, M.; Mezrag, C.; Moutarde, H.; Rodríguez-Quintero, J.; Sabatié, F.; Sznajder, P.; Wagner, J.

2018-06-01

We describe the architecture and functionalities of a C++ software framework, coined PARTONS, dedicated to the phenomenology of Generalized Parton Distributions. These distributions describe the three-dimensional structure of hadrons in terms of quarks and gluons, and can be accessed in deeply exclusive lepto- or photo-production of mesons or photons. PARTONS provides a necessary bridge between models of Generalized Parton Distributions and experimental data collected in various exclusive production channels. We outline the specification of the PARTONS framework in terms of practical needs, physical content and numerical capacity. This framework will be useful for physicists - theorists or experimentalists - not only to develop new models, but also to interpret existing measurements and even design new experiments.

Epi-Two-Dimensional Fluid Flow: A New Topological Paradigm for Dimensionality

NASA Astrophysics Data System (ADS)

Yoshida, Z.; Morrison, P. J.

2017-12-01

While a variety of fundamental differences are known to separate two-dimensional (2D) and three-dimensional (3D) fluid flows, it is not well understood how they are related. Conventionally, dimensional reduction is justified by an a priori geometrical framework; i.e., 2D flows occur under some geometrical constraint such as shallowness. However, deeper inquiry into 3D flow often finds the presence of local 2D-like structures without such a constraint, where 2D-like behavior may be identified by the integrability of vortex lines or vanishing local helicity. Here we propose a new paradigm of flow structure by introducing an intermediate class, termed epi-two-dimensional flow, and thereby build a topological bridge between 2D and 3D flows. The epi-2D property is local and is preserved in fluid elements obeying ideal (inviscid and barotropic) mechanics; a local epi-2D flow may be regarded as a "particle" carrying a generalized enstrophy as its charge. A finite viscosity may cause "fusion" of two epi-2D particles, generating helicity from their charges giving rise to 3D flow.

Clarifying the Conceptualization, Dimensionality, and Structure of Emotion: Response to Barrett and Colleagues.

PubMed

Cowen, Alan S; Keltner, Dacher

2018-04-01

We present a mathematically based framework distinguishing the dimensionality, structure, and conceptualization of emotion-related responses. Our recent findings indicate that reported emotional experience is high-dimensional, involves gradients between categories traditionally thought of as discrete (e.g., 'fear', 'disgust'), and cannot be reduced to widely used domain-general scales (valence, arousal, etc.). In light of our conceptual framework and findings, we address potential methodological and conceptual confusions in Barrett and colleagues' commentary on our work. Copyright © 2018 Elsevier Ltd. All rights reserved.

Parametric Geometry, Structured Grid Generation, and Initial Design Study for REST-Class Hypersonic Inlets

NASA Technical Reports Server (NTRS)

Ferlemann, Paul G.; Gollan, Rowan J.

2010-01-01

Computational design and analysis of three-dimensional hypersonic inlets with shape transition has been a significant challenge due to the complex geometry and grid required for three-dimensional viscous flow calculations. Currently, the design process utilizes an inviscid design tool to produce initial inlet shapes by streamline tracing through an axisymmetric compression field. However, the shape is defined by a large number of points rather than a continuous surface and lacks important features such as blunt leading edges. Therefore, a design system has been developed to parametrically construct true CAD geometry and link the topology of a structured grid to the geometry. The Adaptive Modeling Language (AML) constitutes the underlying framework that is used to build the geometry and grid topology. Parameterization of the CAD geometry allows the inlet shapes produced by the inviscid design tool to be generated, but also allows a great deal of flexibility to modify the shape to account for three-dimensional viscous effects. By linking the grid topology to the parametric geometry, the GridPro grid generation software can be used efficiently to produce a smooth hexahedral multiblock grid. To demonstrate the new capability, a matrix of inlets were designed by varying four geometry parameters in the inviscid design tool. The goals of the initial design study were to explore inviscid design tool geometry variations with a three-dimensional analysis approach, demonstrate a solution rate which would enable the use of high-fidelity viscous three-dimensional CFD in future design efforts, process the results for important performance parameters, and perform a sample optimization.

Honeycomb-shaped coordination polymers based on the self-assembly of long flexible ligands and alkaline-earth ions

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

Lian, Chen; Liu, Liu; Guo, Xu

2016-01-15

Two novel coordination polymers, namely, [Ca(NCP){sub 2}]{sub ∞} (I) and [Sr(NCP){sub 2}]{sub ∞} (II) were synthesized under hydrothermal conditions based on 2-(4-carboxyphenyl)imidazo(4,5-f)-(1,10)phenanthroline (HNCP) and characterized by elemental analysis, infrared spectrometry, X-ray powder diffraction and single crystal X-ray diffraction. Findings indicate that I and II are isomorphous and isostructural, containing the unit of M(NCP{sup −}){sub 4} (M=Ca(II) and Sr(II)), based on which to assemble into three-dimensional (3D) porous 4-fold interpenetration honeycomb-shaped neutral coordination polymers (CPs). Between the adjacent lamellar structures in I and II, there exist π–π interactions between the pyridine rings belonging to phenanthroline of NCP{sup −} which stabilize themore » frameworks. Both I and II display stronger fluorescence emissions as well as high thermal stability. - Graphical abstract: One-dimensional nanotubular channels with the cross dimension of 37.1959(20)×23.6141(11)Å{sup 2} in the three-dimensional honeycomb-shaped coordination network of II are observed. The topological analysis of II indicates that there exists a typical diamond framework possessing large adamantanoid cages, which containing four cyclohexane-shaped patterns in chair conformations. - Highlights: • Two isomorphous and isostructural coordination polymers based on flexible ligand and two alkaline-earth metal salts have been synthesized and characterized. • Structural analysis indicates that I and II are assembled into 3D porous honeycomb-shaped metal-organic frameworks. • Both I and II display stronger fluorescence emissions and higher thermal stability.« less

Supramolecular organic frameworks: engineering periodicity in water through host-guest chemistry.

PubMed

Tian, Jia; Chen, Lan; Zhang, Dan-Wei; Liu, Yi; Li, Zhan-Ting

2016-05-11

The development of homogeneous, water-soluble periodic self-assembled structures comprise repeating units that produce porosity in two-dimensional (2D) or three-dimensional (3D) spaces has become a topic of growing interest in the field of supramolecular chemistry. Such novel self-assembled entities, known as supramolecular organic frameworks (SOFs), are the result of programmed host-guest interactions, which allows for the thermodynamically controlled generation of monolayer sheets or a diamondoid architecture with regular internal cavities or pores under mild conditions. This feature article aims at propagating the conceptually novel SOFs as a new entry into conventional supramolecular polymers. In the first section, we will describe the background of porous solid frameworks and supramolecular polymers. We then introduce the self-assembling behaviour of several multitopic flexible molecules, which is closely related to the design of periodic SOFs from rigid multitopic building blocks. This is followed by a brief discussion of cucurbit[8]uril (CB[8])-encapsulation-enhanced aromatic stacking in water. The three-component host-guest pattern based on this stacking motif has been utilized to drive the formation of most of the new SOFs. In the following two sections, we will highlight the main advances in the construction of 2D and 3D SOFs and the related functional aspects. Finally, we will offer our opinions on future directions for both structures and functions. We hope that this article will trigger the interest of researchers in the field of chemistry, physics, biology and materials science, which should help accelerate the applications of this new family of soft self-assembled organic frameworks.

Three-dimensional thin film for lithium-ion batteries and supercapacitors.

PubMed

Yang, Yang; Peng, Zhiwei; Wang, Gunuk; Ruan, Gedeng; Fan, Xiujun; Li, Lei; Fei, Huilong; Hauge, Robert H; Tour, James M

2014-07-22

Three-dimensional heterogeneously nanostructured thin-film electrodes were fabricated by using Ta2O5 nanotubes as a framework to support carbon-onion-coated Fe2O3 nanoparticles along the surface of the nanotubes. Carbon onion layers function as microelectrodes to separate the two different metal oxides and form a nanoscale 3-D sandwich structure. In this way, space-charge layers were formed at the phase boundaries, and it provides additional energy storage by charge separation. These 3-D nanostructured thin films deliver both excellent Li-ion battery properties (stabilized at 800 mAh cm(–3)) and supercapacitor (up to 18.2 mF cm(–2)) performance owing to the synergistic effects of the heterogeneous structure. Thus, Li-ion batteries and supercapacitors are successfully assembled into the same electrode, which is promising for next generation hybrid energy storage and delivery devices.

Materials science. Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling.

PubMed

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G; Huang, Yonggang; Zhang, Yihui; Rogers, John A

2015-01-09

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations. Copyright © 2015, American Association for the Advancement of Science.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

PubMed

Glusman, Gustavo; Rose, Peter W; Prlić, Andreas; Dougherty, Jennifer; Duarte, José M; Hoffman, Andrew S; Barton, Geoffrey J; Bendixen, Emøke; Bergquist, Timothy; Bock, Christian; Brunk, Elizabeth; Buljan, Marija; Burley, Stephen K; Cai, Binghuang; Carter, Hannah; Gao, JianJiong; Godzik, Adam; Heuer, Michael; Hicks, Michael; Hrabe, Thomas; Karchin, Rachel; Leman, Julia Koehler; Lane, Lydie; Masica, David L; Mooney, Sean D; Moult, John; Omenn, Gilbert S; Pearl, Frances; Pejaver, Vikas; Reynolds, Sheila M; Rokem, Ariel; Schwede, Torsten; Song, Sicheng; Tilgner, Hagen; Valasatava, Yana; Zhang, Yang; Deutsch, Eric W

2017-12-18

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

NASA Astrophysics Data System (ADS)

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-01

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

PubMed

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-07

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Three-dimensionally ordered macroporous Li2FeSiO4/C composite as a high performance cathode for advanced lithium ion batteries

NASA Astrophysics Data System (ADS)

Ding, Zhengping; Liu, Jiatu; Ji, Ran; Zeng, Xiaohui; Yang, Shuanglei; Pan, Anqiang; Ivey, Douglas G.; Wei, Weifeng

2016-10-01

Li2MSiO4 (M = Mn, Fe, Co, Ni, et al.) has received great attention because of the theoretical possibility to reversibly deintercalate two Li+ ions from the structure. However, the silicates still suffer from low electronic conductivity, sluggish lithium ion diffusion and structural instability upon deep cycling. In order to solve these problems, a "hard-soft" templating method has been developed to synthesize three-dimensionally ordered macroporous (3DOM) Li2FeSiO4/C composites. The 3DOM Li2FeSiO4/C composites show a high reversible capacity (239 mAh g-1) with ∼1.50 lithium ion insertion/extraction, a capacity retention of nearly 100% after 420 cycles and excellent rate capability. The enhanced electrochemical performance is ascribed to the interconnected carbon framework that improves the electronic conductivity and the 3DOM structure that offers short Li ion diffusion pathways and restrains volumetric changes.

Solvothermal syntheses and characterization of three new silver(I)/copper(I)-thioarsenates based on As2+/As3+ ions

NASA Astrophysics Data System (ADS)

Yao, Hua-Gang; Tang, Cheng-Fei; An, Yong-Lin; Ou, Zi-Jian; Wu, Guo-Hao; Lan, Pei; Zheng, Yi-Long

2017-02-01

Three new silver(I)/copper(I)-thioarsenates KAgAsIIS2 (1), RbCu2AsIIIS3 (2) and RbCu4AsIIIS4 (3) have been solvothermally synthesized and structurally characterized. 1 exhibits a two-dimensional anionic network built up by As-As bond connecting the left- and right-handed helical [AgS2]4- chains, and represents the first examples of thioarsenates(II). The structure of 2 consists of two kinds of helical [Cu2S3]4- chains linked by the arsenic atoms to form double layers with rubidium ions between the layers. Compound 3 is built up of infinite [Cu2S2]2- chain and layered [Cu6As2S6] linked to form a three-dimensional anionic framework, [Cu4AsS4]-, and containing channels in which the rubidium cations reside. The optical properties of 1-3 have been investigated by UV-vis spectroscopy.

New family of lanthanide-based inorganic-organic hybrid frameworks: Ln2(OH)4[O3S(CH2)nSO3]·2H2O (Ln = La, Ce, Pr, Nd, Sm; n = 3, 4) and their derivatives.

PubMed

Liang, Jianbo; Ma, Renzhi; Ebina, Yasuo; Geng, Fengxia; Sasaki, Takayoshi

2013-02-18

We report the synthesis and structure characterization of a new family of lanthanide-based inorganic-organic hybrid frameworks, Ln(2)(OH)(4)[O(3)S(CH(2))(n)SO(3)]·2H(2)O (Ln = La, Ce, Pr, Nd, Sm; n = 3, 4), and their oxide derivatives. Highly crystallized samples were synthesized by homogeneous precipitation of Ln(3+) ions from a solution containing α,ω-organodisulfonate salts promoted by slow hydrolysis of hexamethylenetetramine. The crystal structure solved from powder X-ray diffraction data revealed that this material comprises two-dimensional cationic lanthanide hydroxide {[Ln(OH)(2)(H(2)O)](+)}(∞) layers, which are cross-linked by α,ω-organodisulfonate ligands into a three-dimensional pillared framework. This hybrid framework can be regarded as a derivative of UCl(3)-type Ln(OH)(3) involving penetration of organic chains into two {LnO(9)} polyhedra. Substitutional modification of the lanthanide coordination promotes a 2D arrangement of the {LnO(9)} polyhedra. A new hybrid oxide, Ln(2)O(2)[O(3)S(CH(2))(n)SO(3)], which is supposed to consist of alternating {[Ln(2)O(2)](2+)}(∞) layers and α,ω-organodisulfonate ligands, can be derived from the hydroxide form upon dehydration/dehydroxylation. These hybrid frameworks provide new opportunities to engineer the interlayer chemistry of layered structures and achieve advanced functionalities coupled with the advantages of lanthanide elements.

Crystalline Coordination Networks of Zero-Valent Metal Centers: Formation of a 3-Dimensional Ni(0) Framework with m-Terphenyl Diisocyanides.

PubMed

Agnew, Douglas W; DiMucci, Ida M; Arroyave, Alejandra; Gembicky, Milan; Moore, Curtis E; MacMillan, Samantha N; Rheingold, Arnold L; Lancaster, Kyle M; Figueroa, Joshua S

2017-12-06

A permanently porous, three-dimensional metal-organic material formed from zero-valent metal nodes is presented. Combination of ditopic m-terphenyl diisocyanide, [CNAr Mes2 ] 2 , and the d 10 Ni(0) precursor Ni(COD) 2 , produces a porous metal-organic material featuring tetrahedral [Ni(CNAr Mes2 ) 4 ] n structural sites. X-ray absorption spectroscopy provides firm evidence for the presence of Ni(0) centers, whereas gas-sorption and thermogravimetric analysis reveal the characteristics of a robust network with a microdomain N 2 -adsorption profile.

Crystalline Coordination Networks of Zero-Valent Metal Centers: Formation of a 3-Dimensional Ni(0) Framework with m-Terphenyl Diisocyanides

DOE PAGES

Agnew, Douglas W.; DiMucci, Ida M.; Arroyave, Alejandra; ...

2017-11-13

A permanently porous, three-dimensional metal–organic material formed from zero-valent metal nodes is presented. Combination of ditopic m-terphenyl diisocyanide, [CNAr Mes2] 2, and the d 10 Ni(0) precursor Ni(COD) 2, produces a porous metal–organic material featuring tetrahedral [Ni(CNAr Mes2) 4] n structural sites. X-ray absorption spectroscopy provides firm evidence for the presence of Ni(0) centers, whereas gas-sorption and thermogravimetric analysis reveal the characteristics of a robust network with a microdomain N 2-adsorption profile.

Numerical modeling of the exterior-to-interior transmission of impulsive sound through three-dimensional, thin-walled elastic structures

NASA Astrophysics Data System (ADS)

Remillieux, Marcel C.; Pasareanu, Stephanie M.; Svensson, U. Peter

2013-12-01

Exterior propagation of impulsive sound and its transmission through three-dimensional, thin-walled elastic structures, into enclosed cavities, are investigated numerically in the framework of linear dynamics. A model was developed in the time domain by combining two numerical tools: (i) exterior sound propagation and induced structural loading are computed using the image-source method for the reflected field (specular reflections) combined with an extension of the Biot-Tolstoy-Medwin method for the diffracted field, (ii) the fully coupled vibro-acoustic response of the interior fluid-structure system is computed using a truncated modal-decomposition approach. In the model for exterior sound propagation, it is assumed that all surfaces are acoustically rigid. Since coupling between the structure and the exterior fluid is not enforced, the model is applicable to the case of a light exterior fluid and arbitrary interior fluid(s). The structural modes are computed with the finite-element method using shell elements. Acoustic modes are computed analytically assuming acoustically rigid boundaries and rectangular geometries of the enclosed cavities. This model is verified against finite-element solutions for the cases of rectangular structures containing one and two cavities, respectively.

Liquid/vapor-induced reversible dynamic structural transformation of a three-dimensional Cu-based MOF to a one-dimensional MOF showing gate adsorption.

PubMed

Kondo, Atsushi; Suzuki, Takayuki; Kotani, Ryosuke; Maeda, Kazuyuki

2017-05-23

A new 3D metal-organic framework (MOF), in which 2D layers are interlaced to form a 3D architecture, was synthesized by a reaction of Cu(BF 4 ) 2 and 1,3-bis(4-pyridyl)propane (bpp) in a water/1-hexanol solvent system, and the crystal structure of the MOF was successfully solved. The MOF is reversibly transformed to a 1D chain MOF, which shows gate adsorption properties. The dynamic transformation gives crystal size reduction resulting in a slight change in CO 2 adsorption isotherms. The 1D MOF shows selective adsorption/separation properties on benzene and its analogues with similar sizes and shapes (benzene, toluene, and cyclohexane).

One-dimensional ferromagnetic array compound [Co3(SBA)2(OH)2(H2O)2]n, (SBA = 4-sulfobenzoate)

NASA Astrophysics Data System (ADS)

Honda, Zentaro; Nomoto, Naoyuki; Fujihara, Takashi; Hagiwara, Masayuki; Kida, Takanori; Sawada, Yuya; Fukuda, Takeshi; Kamata, Norihiko

2018-06-01

We report on the syntheses, crystal structure, and magnetic properties of the transition metal coordination polymer [Co3(SBA)2(OH)2(H2O)2]n, (SBA = 4-sulfobenzoate) in which CoO6 octahedra are linked through their edges, forming one-dimensional (1D) Co(II) arrays running along the crystal a-axis. These arrays are further perpendicularly bridged by SBA ligand to construct a three-dimensional framework. Its magnetic properties have been investigated, and ferromagnetic interactions within the arrays have been found. From heat capacity measurements, we have found that this compound exhibits a three-dimensional ferromagnetic phase transition at TC = 1.54 K, and the specific heat just above TC shows a Schottky anomaly which originates from an energy gap caused by uniaxial magnetic anisotropy. These results suggest that [Co3(SBA)2(OH)2(H2O)2]n consists of weakly coupled 1D ferromagnetic Ising arrays.

Plastic Surgery Applications Using Three-Dimensional Planning and Computer-Assisted Design and Manufacturing.

PubMed

Pfaff, Miles J; Steinbacher, Derek M

2016-03-01

Three-dimensional analysis and planning is a powerful tool in plastic and reconstructive surgery, enabling improved diagnosis, patient education and communication, and intraoperative transfer to achieve the best possible results. Three-dimensional planning can increase efficiency and accuracy, and entails five core components: (1) analysis, (2) planning, (3) virtual surgery, (4) three-dimensional printing, and (5) comparison of planned to actual results. The purpose of this article is to provide an overview of three-dimensional virtual planning and to provide a framework for applying these systems to clinical practice. Therapeutic, V.

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

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Bhadbhade, Mohan; Karatchevtseva, Inna

Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5more » Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.« less

Three-Dimensional, Solid-State Mixed Electron-Ion Conductive Framework for Lithium Metal Anode.

PubMed

Xu, Shaomao; McOwen, Dennis W; Wang, Chengwei; Zhang, Lei; Luo, Wei; Chen, Chaoji; Li, Yiju; Gong, Yunhui; Dai, Jiaqi; Kuang, Yudi; Yang, Chunpeng; Hamann, Tanner R; Wachsman, Eric D; Hu, Liangbing

2018-06-13

Solid-state electrolytes (SSEs) have been widely considered as enabling materials for the practical application of lithium metal anodes. However, many problems inhibit the widespread application of solid state batteries, including the growth of lithium dendrites, high interfacial resistance, and the inability to operate at high current density. In this study, we report a three-dimensional (3D) mixed electron/ion conducting framework (3D-MCF) based on a porous-dense-porous trilayer garnet electrolyte structure created via tape casting to facilitate the use of a 3D solid state lithium metal anode. The 3D-MCF was achieved by a conformal coating of carbon nanotubes (CNTs) on the porous garnet structure, creating a composite mixed electron/ion conductor that acts as a 3D host for the lithium metal. The lithium metal was introduced into the 3D-MCF via slow electrochemical deposition, forming a 3D lithium metal anode. The slow lithiation leads to improved contact between the lithium metal anode and garnet electrolyte, resulting in a low resistance of 25 Ω cm 2 . Additionally, due to the continuous CNT coating and its seamless contact with the garnet we observed highly uniform lithium deposition behavior in the porous garnet structure. With the same local current density, the high surface area of the porous garnet framework leads to a higher overall areal current density for stable lithium deposition. An elevated current density of 1 mA/cm 2 based on the geometric area of the cell was demonstrated for continuous lithium cycling in symmetric lithium cells. For battery operation of the trilayer structure, the lithium can be cycled between the 3D-MCF on one side and the cathode infused into the porous structure on the opposite side. The 3D-MCF created by the porous garnet structure and conformal CNT coating provides a promising direction toward new designs in solid-state lithium metal batteries.

Controlled growth and form of precipitating microsculptures

NASA Astrophysics Data System (ADS)

Kaplan, C. Nadir; Noorduin, Wim L.; Li, Ling; Sadza, Roel; Folkertsma, Laura; Aizenberg, Joanna; Mahadevan, L.

2017-03-01

Controlled self-assembly of three-dimensional shapes holds great potential for fabrication of functional materials. Their practical realization requires a theoretical framework to quantify and guide the dynamic sculpting of the curved structures that often arise in accretive mineralization. Motivated by a variety of bioinspired coprecipitation patterns of carbonate and silica, we develop a geometrical theory for the kinetics of the growth front that leaves behind thin-walled complex structures. Our theory explains the range of previously observed experimental patterns and, in addition, predicts unexplored assembly pathways. This allows us to design a number of functional base shapes of optical microstructures, which we synthesize to demonstrate their light-guiding capabilities. Overall, our framework provides a way to understand and control the growth and form of functional precipitating microsculptures.

Nonlinear analysis of structures. [within framework of finite element method

NASA Technical Reports Server (NTRS)

Armen, H., Jr.; Levine, H.; Pifko, A.; Levy, A.

1974-01-01

The development of nonlinear analysis techniques within the framework of the finite-element method is reported. Although the emphasis is concerned with those nonlinearities associated with material behavior, a general treatment of geometric nonlinearity, alone or in combination with plasticity is included, and applications presented for a class of problems categorized as axisymmetric shells of revolution. The scope of the nonlinear analysis capabilities includes: (1) a membrane stress analysis, (2) bending and membrane stress analysis, (3) analysis of thick and thin axisymmetric bodies of revolution, (4) a general three dimensional analysis, and (5) analysis of laminated composites. Applications of the methods are made to a number of sample structures. Correlation with available analytic or experimental data range from good to excellent.

Breakdown of lung framework and an increase in pores of Kohn as initial events of emphysema and a cause of reduction in diffusing capacity.

PubMed

Yoshikawa, Akira; Sato, Shuntaro; Tanaka, Tomonori; Hashisako, Mikiko; Kashima, Yukio; Tsuchiya, Tomoshi; Yamasaki, Naoya; Nagayasu, Takeshi; Yamamoto, Hiroshi; Fukuoka, Junya

2016-01-01

Pulmonary emphysema is the pathological prototype of chronic obstructive pulmonary disease and is also associated with other lung diseases. We considered that observation with different approaches may provide new insights for the pathogenesis of emphysema. We reviewed tissue blocks of the lungs of 25 cases with/without emphysema and applied a three-dimensional observation method to the blocks. Based on the three-dimensional characteristics of the alveolar structure, we considered one face of the alveolar polyhedron as a structural unit of alveoli and called it a framework unit (FU). We categorized FUs based on their morphological characteristics and counted their number to evaluate the destructive changes in alveoli. We also evaluated the number and the area of pores of Kohn in FUs. We performed linear regression analysis to estimate the effect of these data on pulmonary function tests. In multivariable regression analysis, a decrease in the number of FUs without an alveolar wall led to a significant decrease in the diffusing capacity of the lung for carbon monoxide (DLCO) and DLCO per unit alveolar volume, and an increase in the area of pores of Kohn had a significant effect on an increase in residual capacity. A breakdown in the lung framework and an increase in pores of Kohn are associated with a decrease in DLCO and DLCO per unit alveolar volume with/without emphysema.

Evolution of an adenine-copper cluster to a highly porous cuboidal framework: solution-phase ripening and gas-adsorption properties.

PubMed

Venkatesh, V; Pachfule, Pradip; Banerjee, Rahul; Verma, Sandeep

2014-09-15

The synthesis and directed evolution of a tetranuclear copper cluster, supported by 8-mercapto-N9-propyladenine ligand, to a highly porous three-dimensional cubic framework in the solid state is reported. The structure of this porous framework was unambiguously characterized by X-ray crystallography. The framework contains about 62 % solvent-accessible void; the presence of a free exocyclic amino group in the porous framework facilitates reversible adsorption of gas and solvent molecules. Oriented growth of framework in solution was also tracked by force and scanning electron microscopy studies, leading to identification of an intriguing ripening process, over a period of 30 days, which also revealed formation of cuboidal aggregates in solution. The elemental composition of these cuboidal aggregates was ascertained by EDAX analysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unusual and Tunable Negative Linear Compressibility in the Metal-Organic Framework MFM-133(M) (M = Zr, Hf).

PubMed

Yan, Yong; O'Connor, Alice E; Kanthasamy, Gopikkaa; Atkinson, George; Allan, David R; Blake, Alexander J; Schröder, Martin

2018-03-21

High-pressure single-crystal X-ray structural analyses of isostructural MFM-133(M) (M = Zr, Hf) of flu topology and incorporating the tetracarboxylate ligand TCHB 4- [H 4 TCHB = 3,3',5,5'-tetrakis(4-carboxyphenyl)-2,2',4,4',6,6'-hexamethyl-1,1'-biphenyl] and {M 6 (μ 3 -OH) 8 (OH) 8 (COO) 8 } clusters confirm negative linear compressibility (NLC) behavior along the c axis. This occurs via a three-dimensional wine-rack NLC mechanism leading to distortion of the octahedral cage toward a more elongated polyhedron under static compression. Despite the isomorphous nature of these two structures, MFM-133(Hf) shows a higher degree of NLC than the Zr(IV) analogue. Thus, for the first time, we demonstrate here that the NLC property can be effectively tuned in a framework material by simply varying the inorganic component of the frameworks without changing the network topology and structure.

Crystal growth, differential gas adsorption, high thermal stability, and reversible coordination of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O)

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

Halake, Shobha; Ok, Kang Min, E-mail: kmok@cau.ac.kr

2015-11-15

Single crystals of two barium-organic framework materials, Ba(SBA)(DMF){sub 4} (CAUMOF-15) and Ba{sub 2}(BTEC)(H{sub 2}O) (CAUMOF-16), have been grown through solvothermal reactions (H{sub 2}SBA=4,4′-sulfonyldibenzoic acid and H{sub 4}BTEC=1,2,4,5-benzenetetracarboxylic acid). The crystal structures of the reported frameworks have been determined by single-crystal X-ray diffraction. The materials have been fully characterized by powder X-ray diffraction (PXRD), elemental analyses, Infrared (IR) spectroscopy, and thermogravimetric analyses (TGA). CAUMOF-15 reveals a three-dimensional open-framework that comprises of an inorganic motif with one-dimensional chains and the SBA linkers. CAUMOF-16 shows another three-dimensional backbone consisting of layers of edge-shared BaO{sub 9} and BaO{sub 10} polyhedra, and BTEC pillars. Bothmore » of the 3D frameworks exhibit relatively high thermal stabilities. The PXRD and IR spectral data confirm that CAUMOF-15 and CAUMOF-16 reveal reversible coordinations of the respective solvent molecules, DMF and H{sub 2}O. Gas adsorption properties towards nitrogen, hydrogen, and carbon dioxide have been also investigated. - Graphical abstract: Crystals of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O), exhibiting a differential gas adsorption, a high thermal stability, and a reversible coordination of solvent molecules have been grown. - Highlights: • Crystals of two new 3D Ba-MOFs are grown. • The two Ba-MOFs reveal very high thermal stabilities up to ca. 400 °C. • Ba(SBA)(DMF){sub 4} exhibits differential gas adsorption properties. • The two Ba-MOFs show reversible coordination of the solvent molecules.« less

Three-dimensional reduced graphene oxide/polyaniline nanocomposite film prepared by diffusion driven layer-by-layer assembly for high-performance supercapacitors

NASA Astrophysics Data System (ADS)

Hong, Xiaodong; Zhang, Binbin; Murphy, Elizabeth; Zou, Jianli; Kim, Franklin

2017-03-01

As a simple and versatile method, diffusion driven Layer-by-Layer assembly (dd-LbL) is developed to assemble graphene oxide (GO) into three-dimensional (3D) structure. The assembled GO macrostructure can be reduced through a hydrothermal treatment and used as a high volumetric capacitance electrode in supercapacitors. In this report we use rGO framework created from dd-LbL as a scaffold for in situ polymerization of aniline within the pores of the framework to form rGO/polyaniline (rGO/PANI) composite. The rGO/PANI composite affords a robust and porous structure, which facilitates electrolyte diffusion and exhibits excellent electrochemical performance as binder-free electrodes in a sandwich-configuration supercapacitor. Combining electric double layer capacitance and pseudo-capacitance, rGO/PANI electrodes exhibit a specific capacitance of 438.8 F g-1 at discharge rate of 5 mA (mass of electrodes were 10.0 mg, 0.5 A g-1) in 1 mol L-1 H2SO4 electrolyte; furthermore, the generated PANI nanoparticles in rGO template achieve a higher capacitance of 763 F g-1. The rGO/PANI composite electrodes also show an improved recyclability, 76.5% of capacitance retains after recycled 2000 times.

A Distributed GPU-Based Framework for Real-Time 3D Volume Rendering of Large Astronomical Data Cubes

NASA Astrophysics Data System (ADS)

Hassan, A. H.; Fluke, C. J.; Barnes, D. G.

2012-05-01

We present a framework to volume-render three-dimensional data cubes interactively using distributed ray-casting and volume-bricking over a cluster of workstations powered by one or more graphics processing units (GPUs) and a multi-core central processing unit (CPU). The main design target for this framework is to provide an in-core visualization solution able to provide three-dimensional interactive views of terabyte-sized data cubes. We tested the presented framework using a computing cluster comprising 64 nodes with a total of 128GPUs. The framework proved to be scalable to render a 204GB data cube with an average of 30 frames per second. Our performance analyses also compare the use of NVIDIA Tesla 1060 and 2050GPU architectures and the effect of increasing the visualization output resolution on the rendering performance. Although our initial focus, as shown in the examples presented in this work, is volume rendering of spectral data cubes from radio astronomy, we contend that our approach has applicability to other disciplines where close to real-time volume rendering of terabyte-order three-dimensional data sets is a requirement.

Synthesis and Characterization Hierarchical Three-Dimensional TiO2 Structure via Hydrothermal Method

NASA Astrophysics Data System (ADS)

Syuhada, N.; Yuliarto, B.; Nugraha

2018-05-01

TiO2 is one of the most potential candidates due to its fascinating properties for multi-discipline fields. One dimensional nanostructure TiO2 such as nanotube and nanorods has been widely used for many devices technology. Compare with one-dimensional nanostructure TiO2; the hierarchical TiO2 has not been widely applied. Three dimensional TiO2 play a promising role for application in many different fields such as photovoltaics, photocatalytic and a gas sensor. Herein, we report that the hierarchically structures TiO2 have been successfully obtained by the one-pot Hydrothermal process. The growth mechanism of Titania was controlled by Titanium (IV) isopropoxide (TTIP). Ethylene glycol (EG). Hydrochloric acid (HCl). Hexadecyltrimethylammonium bromide (CTAB) molar ratio. TTIP was used as titanium source and CTAB as a soft template. The molar ratio of TTIP. EG. HCl. CTAB was 0.1:0.2:0.4:0.001. Those samples were synthesized using the hydrothermal method at 180 °C for 20 h. The purpose of this work was focused on investigating morphology, crystallite size, crystalline phase, and particle size. The properties of these materials were characterized by XRay Diffraction, Energy Dispersive Spectroscopy and Scanning Electron Microscope. It was found all particles exhibited unique spherical morphology which arranged by nanorods and good distribution nanoparticle. The Average size of the sphere has range 1 µm to 3 µm with diameter nanorods 60 nm to 100 nm. The TiO2 spheres were constructed of interconnected nanorods and formed a three dimensional (3D) porous framework. XRD analysis confirmed that sample consisted of pure rutile crystal structure with crystallite size was 50 nm, and EDS revealed an elemental content of Ti 61.03 % and O 38.97 %.

Crystal structure of the co-crystal fac-tri-aqua-tris(thio-cyanato-κN)iron(III)-2,3-di-methyl-pyrazine (1/3).

PubMed

Kucheriv, Olesia I; Shylin, Sergii I; Ilina, Tetiana A; Dechert, Sebastian; Gural'skiy, Il'ya A

2015-04-01

In the crystal of the title compound, [Fe(NCS)3(H2O)3]·3C6H8N2, the Fe(III) cation is located on a threefold rotation axis and is coordinated by three N atoms of the thiocyanate anions and three water mol-ecules in a fac arrangement, forming a slightly distorted N3O3 octa-hedron. Stabilization within the crystal structure is provided by O-H⋯N hydrogen bonds; the H atoms from coordinating water mol-ecules act as donors to the N atoms of guest 2,3-di-methyl-pyrazine mol-ecules, leading to a three-dimensional supra-molecular framework.

Mesoscale Eddies in the Northwestern Pacific Ocean: Three-Dimensional Eddy Structures and Heat/Salt Transports

NASA Astrophysics Data System (ADS)

Dong, Di; Brandt, Peter; Chang, Ping; Schütte, Florian; Yang, Xiaofeng; Yan, Jinhui; Zeng, Jisheng

2017-12-01

The region encompassing the Kuroshio Extension (KE) in the Northwestern Pacific Ocean (25°N-45°N and 130°E-180°E) is one of the most eddy-energetic regions of the global ocean. The three-dimensional structures and transports of mesoscale eddies in this region are comprehensively investigated by combined use of satellite data and Argo profiles. With the allocation of Argo profiles inside detected eddies, the spatial variations of structures of eddy temperature and salinity anomalies are analyzed. The results show that eddies predominantly have subsurface (near-surface) intensified temperature and salinity anomalies south (north) of the KE jet, which is related to different background stratifications between these regions. A new method based on eddy trajectories and the inferred three-dimensional eddy structures is proposed to estimate heat and salt transports by eddy movements in a Lagrangian framework. Spatial distributions of eddy transports are presented over the vicinity of the KE for the first time. The magnitude of eddy-induced meridional heat (freshwater volume) transport is on the order of 0.01 PW (103 m3/s). The eddy heat transport divergence results in an oceanic heat loss south and heat gain north of the KE, thereby reinforcing and counteracting the oceanic heat loss from air-sea fluxes south and north of the KE jet, respectively. It also suggests a poleward heat transport across the KE jet due to eddy propagation.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

1D helix, 2D brick-wall and herringbone, and 3D interpenetration d10 metal-organic framework structures assembled from pyridine-2,6-dicarboxylic acid N-oxide.

PubMed

Wen, Li-Li; Dang, Dong-Bin; Duan, Chun-Ying; Li, Yi-Zhi; Tian, Zheng-Fang; Meng, Qing-Jin

2005-10-03

Five novel interesting d(10) metal coordination polymers, [Zn(PDCO)(H2O)2]n (PDCO = pyridine-2,6-dicarboxylic acid N-oxide) (1), [Zn2(PDCO)2(4,4'-bpy)2(H2O)2.3H2O]n (bpy = bipyridine) (2), [Zn(PDCO)(bix)]n (bix = 1,4-bis(imidazol-1-ylmethyl)benzene) (3), [Zn(PDCO)(bbi).0.5H2O]n (bbi = 1,1'-(1,4-butanediyl)bis(imidazole)) (4), and [Cd(PDCO)(bix)(1.5).1.5H2O]n (5), have been synthesized under hydrothermal conditions and structurally characterized. Polymer 1 possesses a one-dimensional (1D) helical chainlike structure with 4(1) helices running along the c-axis with a pitch of 10.090 Angstroms. Polymer 2 has an infinite chiral two-dimensional (2D) brick-wall-like layer structure in the ac plane built from achiral components, while both 3 and 4 exhibit an infinite 2D herringbone architecture, respectively extended in the ac and ab plane. Polymer 5 features a most remarkable and unique three-dimensional (3D) porous framework with 2-fold interpenetration related by symmetry, which contains channels in the b and c directions, both distributed in a rectangular grid fashion. Compounds 1-5, with systematic variation in dimensionality from 1D to 2D to 3D, are the first examples of d(10) metal coordination polymers into which pyridinedicarboxylic acid N-oxide has been introduced. In addition, polymers 1, 4, and 5 display strong blue fluorescent emissions in the solid state. Polymer 3 exhibits a strong SHG response, estimated to be approximately 0.9 times that of urea.

Rich structural chemistry in new alkali metal yttrium tellurites: three-dimensional frameworks of NaYTe4O10, KY(TeO3)2, RbY(TeO3)2, and a novel variant of hexagonal tungsten bronze, CsYTe3O8.

PubMed

Kim, Youngkwon; Lee, Dong Woo; Ok, Kang Min

2015-01-05

Pure polycrystalline phases and single crystals of four new quaternary alkali metal yttrium tellurites, NaYTe4O10, KY(TeO3)2, RbY(TeO3)2, and CsYTe3O8, have been prepared by solid-state and hydrothermal reactions using A2CO3 (A = Na, K, Rb, and Cs), Y(NO3)3·6H2O, Y2O3, and TeO2 as starting reagents. X-ray diffraction analyses suggest that NaYTe4O10 exhibits a highly symmetric three-dimensional (3D) framework consisting of YO8 square antiprisms and chains of TeO4 polyhedra. Within the framework, six- (6-) and eight-membered ring (8-MR) channels are observed. KY(TeO3)2 and RbY(TeO3)2 are isostructural to each other and reveal another 3D framework with structures containing YO6 octahedra and TeO3 trigonal pyramids with 4-MR and 12-MR channels. CsYTe3O8 shows a hexagonal tungsten bronze (HTB)-like topology composed of hexagonal tungsten oxide-like layers of TeO4 polyhedra and YO6 octahedral linkers with 3-MR and 6-MR channels. Thermal analyses, elemental analyses, and spectroscopic characterizations, such as UV-vis diffuse reflectance and infrared spectra, are presented, as are local dipole moment calculations for the constituent asymmetric polyhedra TeO3 and TeO4.

Using subject-specific three-dimensional (3D) anthropometry data in digital human modelling: case study in hand motion simulation.

PubMed

Tsao, Liuxing; Ma, Liang

2016-11-01

Digital human modelling enables ergonomists and designers to consider ergonomic concerns and design alternatives in a timely and cost-efficient manner in the early stages of design. However, the reliability of the simulation could be limited due to the percentile-based approach used in constructing the digital human model. To enhance the accuracy of the size and shape of the models, we proposed a framework to generate digital human models using three-dimensional (3D) anthropometric data. The 3D scan data from specific subjects' hands were segmented based on the estimated centres of rotation. The segments were then driven in forward kinematics to perform several functional postures. The constructed hand models were then verified, thereby validating the feasibility of the framework. The proposed framework helps generate accurate subject-specific digital human models, which can be utilised to guide product design and workspace arrangement. Practitioner Summary: Subject-specific digital human models can be constructed under the proposed framework based on three-dimensional (3D) anthropometry. This approach enables more reliable digital human simulation to guide product design and workspace arrangement.

Hydrothermal synthesis, crystal structure and properties of 2-D and 3-D lanthanide sulfates

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

Xu Yan; Ding Shaohua; Zheng Xuefang

2007-07-15

Two new lanthanum sulfates DySO{sub 4}(OH) 1 and Eu{sub 2}(SO{sub 4}){sub 3}(H{sub 2}O){sub 8} 2 have been hydrothermally synthesized. The colorless crystals were characterized by IR, TGA, ICP and XRD. The structure was determined by single-crystal X-ray diffraction. 1 crystallizes with monoclinic symmetry, space group P2(1)/n [a=7.995(4) A, b=10.945(5) A, c=8.164(4) A, {alpha}=90{sup o}, {beta}=93.619(6){sup o}, {gamma}=90{sup o}, V=713.0(5) A{sup 3}, Z=8]. It displays a three-dimensional framework, based on the novel Dy-O chains connected by the sulfate groups through helical chains. 2 crystallizes with monoclinic symmetry, space group C2/c, [a=13.5605(17) A, b=6.7676(8) A, c=18.318(2) A, {alpha}=90{sup o}, {beta}=102.265(2){sup o}, {gamma}=90{supmore » o}, V=1642.7 (4) A{sup 3}, Z=4]. Its layered framework is attained by the europium atoms connected by the sulfate groups arranged in a helical manner. - Graphical abstract: Two new lanthanum sulfates DySO{sub 4}(OH) 1 and Eu{sub 2} (SO{sub 4}){sub 3} (H{sub 2}O){sub 8} 2 have been hydrothermally synthesized. The colorless crystals were characterized by IR, TGA, ICP and XRD. The structure was determined by single-crystal X-ray diffraction. It displays a three dimensional framework, based on the novel Dy-O chains connected by the sulfate groups through helical chains.« less

Assembly and property research on seven 0D-3D complexes derived from imidazole dicarboxylate and 1,2-bi(pyridin-4-yl)ethene

NASA Astrophysics Data System (ADS)

Mu, Bao; Li, Qian; Lv, Lei; Yang, Dan-Dan; Wang, Qing; Huang, Ru-Dan

2015-03-01

The hydrothermal reaction of transition metals, 1H-imidazole-4,5-dicarboxylic acid (H3ImDC) and 1,2-bi(pyridin-4-yl)ethene (bpe) affords a series of new complexes, namely, [Mn(HImDC)(bpe)(H2O)] (1), [M(H2ImDC)2(H2O)2]·(bpe) (M=Fe(2), Co(3), Zn(4), Cd(6)), [Zn3(ImDC)2(bpe)(H2O)]·3H2O (5) and [Cd(H2ImDC)(bpe)] (7), which are characterized by elemental analyses, IR, TG, XRPD and single crystal X-ray diffraction. Complex 1 exhibits a one dimensional (1D) zigzag chain with two types of irregular rings, and the 1D chains are linked to form a three dimensional (3D) supramolecular framework by the hydrogen bonding interactions (O-H•••O and O-H•••N). Complexes 2-4 and 6 are isomorphous, and they display the mononuclear structures. In these complexes, the O-H•••O and O-H•••N hydrogen bonds play an important role in sustaining the whole 3D supramolecular frameworks. Complex 5 shows a (3,3)-connected 3D framework with (103) topology, and the lattice water molecules as guest molecules exist in the 3D framework. Complex 7 is a wave-like two dimensional (2D) structure, in which the adjacent 1D chains point at the opposite directions. Moreover, the fluorescent properties of complexes 1-7 and the magnetic property of 1 have been investigated. The water vapor adsorption for complex 5 has been researched at 298 K.

Fabrication and Handling of 3D Scaffolds Based on Polymers and Decellularized Tissues.

PubMed

Shpichka, Anastasia; Koroleva, Anastasia; Kuznetsova, Daria; Dmitriev, Ruslan I; Timashev, Peter

2017-01-01

Polymeric, ceramic and hybrid material-based three-dimensional (3D) scaffold or matrix structures are important for successful tissue engineering. While the number of approaches utilizing the use of cell-based scaffold and matrix structures is constantly growing, it is essential to provide a framework of their typical preparation and evaluation for tissue engineering. This chapter describes the fabrication of 3D scaffolds using two-photon polymerization, decellularization and cell encapsulation methods and easy-to-use protocols allowing assessing the cell morphology, cytotoxicity and viability in these scaffolds.

Three-dimensional full-field X-ray orientation microscopy

PubMed Central

Viganò, Nicola; Tanguy, Alexandre; Hallais, Simon; Dimanov, Alexandre; Bornert, Michel; Batenburg, Kees Joost; Ludwig, Wolfgang

2016-01-01

A previously introduced mathematical framework for full-field X-ray orientation microscopy is for the first time applied to experimental near-field diffraction data acquired from a polycrystalline sample. Grain by grain tomographic reconstructions using convex optimization and prior knowledge are carried out in a six-dimensional representation of position-orientation space, used for modelling the inverse problem of X-ray orientation imaging. From the 6D reconstruction output we derive 3D orientation maps, which are then assembled into a common sample volume. The obtained 3D orientation map is compared to an EBSD surface map and local misorientations, as well as remaining discrepancies in grain boundary positions are quantified. The new approach replaces the single orientation reconstruction scheme behind X-ray diffraction contrast tomography and extends the applicability of this diffraction imaging technique to material micro-structures exhibiting sub-grains and/or intra-granular orientation spreads of up to a few degrees. As demonstrated on textured sub-regions of the sample, the new framework can be extended to operate on experimental raw data, thereby bypassing the concept of orientation indexation based on diffraction spot peak positions. This new method enables fast, three-dimensional characterization with isotropic spatial resolution, suitable for time-lapse observations of grain microstructures evolving as a function of applied strain or temperature. PMID:26868303

The three-dimensional structures of bacterial reaction centers.

PubMed

Olson, T L; Williams, J C; Allen, J P

2014-05-01

This review presents a broad overview of the research that enabled the structure determination of the bacterial reaction centers from Blastochloris viridis and Rhodobacter sphaeroides, with a focus on the contributions from Duysens, Clayton, and Feher. Early experiments performed in the laboratory of Duysens and others demonstrated the utility of spectroscopic techniques and the presence of photosynthetic complexes in both oxygenic and anoxygenic photosynthesis. The laboratories of Clayton and Feher led efforts to isolate and characterize the bacterial reaction centers. The availability of well-characterized preparations of pure and stable reaction centers allowed the crystallization and subsequent determination of the structures using X-ray diffraction. The three-dimensional structures of reaction centers revealed an overall arrangement of two symmetrical branches of cofactors surrounded by transmembrane helices from the L and M subunits, which also are related by the same twofold symmetry axis. The structure has served as a framework to address several issues concerning bacterial photosynthesis, including the directionality of electron transfer, the properties of the reaction center-cytochrome c 2 complex, and the coupling of proton and electron transfer. Together, these research efforts laid the foundation for ongoing efforts to address an outstanding question in oxygenic photosynthesis, namely the molecular mechanism of water oxidation.

Bi2(IO3)(IO6): First combination of [IO3]- and [IO6]5- anions in three-dimensional framework

NASA Astrophysics Data System (ADS)

Sun, Chuanling; Wu, Yuandong; Mei, Dajiang; Doert, Thomas

2018-03-01

A new bismuth (III) iodate periodate, Bi2(IO3)(IO6) was obtained from hydrothermal reactions using Bi(NO3)3·5H2O, and H5IO6 as starting materials. Bi2(IO3)(IO6) crystallizes in the monoclinic space group P21/c (No. 14) with lattice parameters ɑ = 8.1119(6), b = 5.4746(4), c = 16.357(1) Å, β = 99.187(2)°, V = 717.07(9) Å3, Z = 4. The structure of Bi2(IO3)(IO6) features a three-dimensional framework which is a combination of [Bi(1)O5] tetragonal pyramids, [Bi(2)O8] bicapped trigonal prisms and [IO3]- and [IO6]5- anions. Thermal analysis shows that the compound is thermally stable up to about 350 °C. The solid state UV-vis-NIR diffuse reflectance spectrum indicates that Bi2(IO3)(IO6) is a semiconductor with a band gap of 2.76 eV.

An unusual 2p-3d-4f heterometallic coordination polymer featuring Ln8Na and Cu8I clusters as nodes

NASA Astrophysics Data System (ADS)

Zhao, Mingjuan; Chen, Shimin; Huang, Yutian; Dan, Youmeng

2017-01-01

A new cluster-based three-dimensional 2p-3d-4f heterometallic framework {[Ho8Na(OH)6Cu16I2(CPT)24](NO3)9(H2O)6(CH3CN)18}n (1, HCPT = 4-(4-carboxyphenyl)-1,2,4 triazole) has been prepared under solvothermal condition by using a custom-designed bifunctional organic ligand. The single-crystal structure analysis reveals that this framework features novel Ln8Na and Cu8I clusters as nodes, these nodes are further connected by the CPT ligands to give rise to a (6,14)-connected network. The magnetic property of this framework has also been investigated.

Metal-organic framework assembled from erbium and a tetrapodal polyphosphonic acid organic linker.

PubMed

Mendes, Ricardo F; Firmino, Ana D G; Tomé, João P C; Almeida Paz, Filipe A

2018-06-01

A three-dimensional metal-organic framework (MOF), poly[[μ 6 -5'-pentahydrogen [1,1'-biphenyl]-3,3',5,5'-tetrayltetrakis(phosphonato)]erbium(III)] 2.5-hydrate], formulated as [Er(C 12 H 11 O 12 P 4 )]·2.5H 2 O or [Er(H 5 btp)]·2.5H 2 O (I) and isotypical with a Y 3+ -based MOF reported previously by our research group [Firmino et al. (2017b). Inorg. Chem. 56, 1193-1208], was constructed based solely on Er 3+ and on the polyphosphonic organic linker [1,1'-biphenyl]-3,3',5,5'-tetrakis(phosphonic acid) (H 8 btp). The present work describes our efforts to introduce lanthanide cations into the flexible network, demonstrating that, on the one hand, the compound can be obtained using three distinct experimental methods, i.e. hydro(solvo)thermal (Hy), microwave-assisted (MW) and one-pot (Op), and, on the other hand, that crystallite size can be approximately fine-tuned according to the method employed. MOF I contains hexacoordinated Er 3+ cations which are distributed in a zigzag inorganic chain running parallel to the [100] direction of the unit cell. The chains are, in turn, bridged by the anionic organic linker to form a three-dimensional 6,6-connected binodal network. This connectivity leads to the existence of one-dimensional channels (also running parallel to the [100] direction) filled with disordered and partially occupied water molecules of crystalization which are engaged in O-H...O hydrogen-bonding interactions with the [Er(H 5 btp)] framework. Additional weak π-π interactions [intercentroid distance = 3.957 (7) Å] exist between aromatic rings, which help to maintain the structural integrity of the network.

Fluid-structure interaction simulations of deformable structures with non-linear thin shell elements

NASA Astrophysics Data System (ADS)

Asgharzadeh, Hafez; Hedayat, Mohammadali; Borazjani, Iman; Scientific Computing; Biofluids Laboratory Team

2017-11-01

Large deformation of structures in a fluid is simulated using a strongly coupled partitioned fluid-structure interaction (FSI) approach which is stabilized with under-relaxation and the Aitken acceleration technique. The fluid is simulated using a recently developed implicit Newton-Krylov method with a novel analytical Jacobian. Structures are simulated using a triangular thin-shell finite element formulation, which considers only translational degrees of freedom. The thin-shell method is developed on the top of a previously implemented membrane finite element formulation. A sharp interface immersed boundary method is used to handle structures in the fluid domain. The developed FSI framework is validated against two three-dimensional experiments: (1) a flexible aquatic vegetation in the fluid and (2) a heaving flexible panel in fluid. Furthermore, the developed FSI framework is used to simulate tissue heart valves, which involve large deformations and non-linear material properties. This work was supported by American Heart Association (AHA) Grant 13SDG17220022 and the Center of Computational Research (CCR) of University at Buffalo.

A flexible Eu(III)-based metal-organic framework: turn-off luminescent sensor for the detection of Fe(III) and picric acid.

PubMed

Zhou, Xin-Hui; Li, Liang; Li, Hong-Hui; Li, Ao; Yang, Tao; Huang, Wei

2013-09-14

A metal-organic framework (MOF) {[Eu2(MFDA)2(HCOO)2(H2O)6]·H2O}n (1) (H2MFDA = 9,9-dimethylfluorene-2,7-dicarboxylic acid) has been solvothermally synthesized and structurally characterized. 1 possesses the three-dimensional pcu type rod-packing structure with one-dimensional rhombic channels. The framework of 1 can reversibly shrink/swell along the c axis upon partial/full release of the water molecules. Correspondingly, the rhombic channels become narrow/large and 1 transforms to narrow-pore 1a/large-pore 1b. 1, 1a and 1b have almost the same excitation and emission spectra with the strong characteristic red-light-emission of Eu(III). A high photoluminescence quantum yield of 77% and long luminescence lifetime of around 1.1 ms was observed for 1. The potential of 1b for Fe(3+) ions and PA sensing was studied in DMF through the luminescence quenching experiments, which show 1b is a potential turn-off luminescent sensory material for the selective detection of Fe(3+) ions and PA with detection limits of around 10(-7) M for both of them. The fluorescence quenching mechanism for Fe(3+) ions and PA was also investigated.

Three-Dimensional Networked Metal-Organic Frameworks with Conductive Polypyrrole Tubes for Flexible Supercapacitors.

PubMed

Xu, Xingtao; Tang, Jing; Qian, Huayu; Hou, Shujin; Bando, Yoshio; Hossain, Md Shahriar A; Pan, Likun; Yamauchi, Yusuke

2017-11-08

Metal-organic frameworks (MOFs) with high porosity and a regular porous structure have emerged as a promising electrode material for supercapacitors, but their poor electrical conductivity limits their utilization efficiency and capacitive performance. To increase the overall electrical conductivity as well as the efficiency of MOF particles, three-dimensional networked MOFs are developed via using preprepared conductive polypyrrole (PPy) tubes as the support for in situ growth of MOF particles. As a result, the highly conductive PPy tubes that run through the MOF particles not only increase the electron transfer between MOF particles and maintain the high effective porosity of the MOFs but also endow the MOFs with flexibility. Promoted by such elaborately designed MOF-PPy networks, the specific capacitance of MOF particles has been increased from 99.2 F g -1 for pristine zeolitic imidazolate framework (ZIF)-67 to 597.6 F g -1 for ZIF-PPy networks, indicating the importance of the design of the ZIF-PPy continuous microstructure. Furthermore, a flexible supercapacitor device based on ZIF-PPy networks shows an outstanding areal capacitance of 225.8 mF cm -2 , which is far above other MOFs-based supercapacitors reported up to date, confirming the significance of in situ synthetic chemistry as well as the importance of hybrid materials on the nanoscale.

Clarifying the Conceptualization, Dimensionality, and Structure of Emotion: Response to Barrett and Colleagues

PubMed Central

Cowen, Alan S.; Keltner, Dacher

2018-01-01

We present a mathematically based framework distinguishing the dimensionality, structure, and conceptualization of emotion-related responses. Our recent findings indicate that reported emotional experience is highdimensional, involves gradients between categories traditionally thought of as discrete (e.g., ‘fear’, ‘disgust’), and cannot be reduced to widely used domain-general scales (valence, arousal, etc.). In light of our conceptual framework and findings, we address potential methodological and conceptual confusions in Barrett and colleagues’ commentary on our work. PMID:29477775

Lanthanide coordination polymers based on multi-donor ligand containing pyridine and phthalate moieties: Structures, luminescence and magnetic properties

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

Feng, Xun; Liu, Lang; College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471022

2013-10-15

A new family of five lanthanide-organic coordination polymers incorporating multi-functional N-hetrocyclic dicarboxylate ligand, namely, [Ln{sub 2}(Hdpp){sub 2}(dpp){sub 2}]{sub n}Ln=Pr(1), Eu(2), Gd(3), Dy(4), Er(5) (H{sub 2}dpp=1-(3, 4-dicarboxyphenyl) pyridin-4-ol) have been fabricated successfully through solvothermal reaction of 1-(3,4-dicarboxyphenyl)-4-hydroxypyridin-1-ium chloride with trivalent lanthanide salts, and have been characterized systematically. The complexes 1–5 are isomorphous and isostructural. They all feature three dimensional (3D) frameworks based on the interconnection of 1D double chains composed of the binuclear moiety [Ln{sub 2}(Hdpp){sub 2}]{sup 4+} basic carboxylate as secondary building unit (SBU). The results of magnetic analysis shows the same bridging fashion of carboxylic group in this casemore » results in the different magnetic properties occurring within lanthanide polymers. Moreover, the Eu(III) and Dy(III) complexes display characteristic luminescence emission in the visible regions. - Graphical abstract: A new family of lanthanide-organic frameworks incorporating multi-donor twisted ligand has been fabricated successfully, and has been characterized systematically. The complexes 1–5 are isostructural, and all feather three dimensional (3D) frameworks based on the interconnection of 1D double stride chains composed of the binuclear moiety [Ln{sub 2}(Hdpp){sub 2}]{sup 2+} basic carboxylate as secondary building unit (SBU). Display Omitted - Highlights: • New family of lanthanide–organic coordination polymers incorporating multifunctional N-hetrocyclic dicarboxylate ligand has been fabricated. • They have been characterized systematically. • They all feather three dimensional frameworks based on the binuclear moiety of [Ln{sub 2}(Hdpp){sub 2}]{sup 2+}. • The Eu(III) and Dy(III) analogues exhibit intense photoluminescence.« less

Method for making a bio-compatible scaffold

DOEpatents

Cesarano, III, Joseph; Stuecker, John N [Albuquerque, NM; Dellinger, Jennifer G [Champaigne, IL; Jamison, Russell D [Urbana, IL

2006-01-31

A method for forming a three-dimensional, biocompatible, porous scaffold structure using a solid freeform fabrication technique (referred to herein as robocasting) that can be used as a medical implant into a living organism, such as a human or other mammal. Imaging technology and analysis is first used to determine the three-dimensional design required for the medical implant, such as a bone implant or graft, fashioned as a three-dimensional, biocompatible scaffold structure. The robocasting technique is used to either directly produce the three-dimensional, porous scaffold structure or to produce an over-sized three-dimensional, porous scaffold lattice which can be machined to produce the designed three-dimensional, porous scaffold structure for implantation.

Manganese(III) Formate: A Three-Dimensional Framework That Traps Carbon Dioxide Molecules.

PubMed

Cornia, Andrea; Caneschi, Andrea; Dapporto, Paolo; Fabretti, Antonio C; Gatteschi, Dante; Malavasi, Wanda; Sangregorio, Claudio; Sessoli, Roberta

1999-06-14

Carbon dioxide, formic acid, and water molecules are trapped in the crystal lattice of manganese(III) formate (see 1), which was obtained by reducing permanganate with formic acid. Each CO 2 guest molecule exhibits four C-H⋅⋅⋅O-C-O interactions with the three-dimensional host framework of Mn(HCOO) 3 units. Compound 1 undergoes an antiferromagnetic phase transition at 27 K. © 1999 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

PubMed

Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

2011-01-10

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

Polyaniline-encapsulated silicon on three-dimensional carbon nanotubes foam with enhanced electrochemical performance for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Zhou, Xiaoming; Liu, Yang; Du, Chunyu; Ren, Yang; Mu, Tiansheng; Zuo, Pengjian; Yin, Geping; Ma, Yulin; Cheng, Xinqun; Gao, Yunzhi

2018-03-01

Seeking free volume around nanostructures for silicon-based anodes has been a crucial strategy to improve cycling and rate performance in the next generation Li-ion batteries. Herein, through a simple pyrolysis and in-situ polymerization approach, the low cost commercially available melamine foam as a soft template converts carbon nanotubes into highly dispersed and three-dimensionally interconnected framework with encapsulated silicon/polyaniline hierarchical nanoarchitecture. This unique core-sheath structure based on carbon nanotubes foam integrates a large number of mesoporous, thus providing well-accessible space for electrolyte wetting, whereas the carbon nanotubes matrix serves as conductive thoroughfares for electron transport. Meanwhile, the outer polyaniline coated on silicon nanoparticles provides effective space for volume expansion of silicon, further inhibiting the active material escape from the current collector. As expected, the PANI-Si@CNTs foam exhibits a high initial specific capacity of 1954 mAh g-1 and retains 727 mAh g-1 after 100 cycles at 100 mA g-1, which can be attributed to highly electrical conductivity of carbon nanotubes and protective layer of polyaniline sheath, together with three-dimensionally interconnected porous skeleton. This facile structure can pave a way for large scale synthesis of high durable silicon-based anodes or other electrode materials with huge volume expansion.

Ligand combination strategy for the preparation of novel low-dimensional and open-framework metal cluster materials

NASA Astrophysics Data System (ADS)

Anokhina, Ekaterina V.

Low-dimensional and open-framework materials containing transition metals have a wide range of applications in redox catalysis, solid-state batteries, and electronic and magnetic devices. This dissertation reports on research carried out with the goal to develop a strategy for the preparation of low-dimensional and open-framework materials using octahedral metal clusters as building blocks. Our approach takes its roots from crystal engineering principles where the desired framework topologies are achieved through building block design. The key idea of this work is to induce directional bonding preferences in the cluster units using a combination of ligands with a large difference in charge density. This investigation led to the preparation and characterization of a new family of niobium oxychloride cluster compounds with original structure types exhibiting 1ow-dimensional or open-framework character. Most of these materials have framework topologies unprecedented in compounds containing octahedral clusters. Comparative analysis of their structural features indicates that the novel cluster connectivity patterns in these systems are the result of complex interplay between the effects of anisotropic ligand arrangement in the cluster unit and optimization of ligand-counterion electrostatic interactions. The important role played by these factors sets niobium oxychloride systems apart from cluster compounds with one ligand type or statistical ligand distribution where the main structure-determining factor is the total number of ligands. These results provide a blueprint for expanding the ligand combination strategy to other transition metal cluster systems and for the future rational design of cluster-based materials.

BIM-Sim: Interactive Simulation of Broadband Imaging Using Mie Theory

PubMed Central

Berisha, Sebastian; van Dijk, Thomas; Bhargava, Rohit; Carney, P. Scott; Mayerich, David

2017-01-01

Understanding the structure of a scattered electromagnetic (EM) field is critical to improving the imaging process. Mechanisms such as diffraction, scattering, and interference affect an image, limiting the resolution, and potentially introducing artifacts. Simulation and visualization of scattered fields thus plays an important role in imaging science. However, EM fields are high-dimensional, making them time-consuming to simulate, and difficult to visualize. In this paper, we present a framework for interactively computing and visualizing EM fields scattered by micro and nano-particles. Our software uses graphics hardware for evaluating the field both inside and outside of these particles. We then use Monte-Carlo sampling to reconstruct and visualize the three-dimensional structure of the field, spectral profiles at individual points, the structure of the field at the surface of the particle, and the resulting image produced by an optical system. PMID:29170738

Two novel FeII-oxalate architectures: Solvent-free synthesis, structures, thermal and magnetic studies

NASA Astrophysics Data System (ADS)

Li, Jin-Hua; Liu, Hui; Wei, Li; Wang, Guo-Ming

2015-10-01

Two novel FeII-oxalate framework with the formulas of [NH4][FeIILi3(C2O4)3] (1) and [NH4]2[FeII(C2O4)2]·H2O (2) have been prepared by an oxalic acid flux approach and structurally characterized by IR, elemental analysis, thermogravimetric analysis, single-crystal and powder X-ray diffraction. Heterometallic compound 1 displays a three-dimensional (3D) framework with a pto topology, while homometallic compound 2 features a pillar-layer architecture with a hms topology. Thermal analysis indicates that the two compounds can be stable up to 300 °C and 200 °C, respectively. Magnetic investigations suggest that the FeII ions in 1 and 2 exhibit weak magnetic exchange interactions.

Variable dimensionality and framework found in a series of quaternary zinc selenites, A{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}·xH{sub 2}O (A = Na, Rb, and Cs; 0≤x≤1) and Cs{sub 2}Zn{sub 2}(SeO{sub 3}){sub 3}·2H{sub 2}O

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

Lü, Minfeng; Jo, Hongil; Oh, Seung-Jin

Five new alkali metal zinc selenites, A{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}·xH{sub 2}O (A = Na, Rb, and Cs; 0≤x≤1) and Cs{sub 2}Zn{sub 2}(SeO{sub 3}){sub 3}·2H{sub 2}O have been synthesized by heating a mixture of ZnO, SeO{sub 2} and A{sub 2}CO{sub 3} (A = Na, Rb, and Cs), and characterized by X-ray diffraction (XRD) and spectroscopic analyses techniques. All of the reported materials revealed a rich structural chemistry with different frameworks and connection modes of Zn{sup 2+}. While Rb{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4} and Cs{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}·H{sub 2}O revealed three-dimensional frameworks consisting of isolated ZnO{sub 4} tetrahedra and SeO{submore » 3} polyhedra, Na{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}, Cs{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}, and Cs{sub 2}Zn{sub 2}(SeO{sub 3}){sub 3}·2H{sub 2}O contained two-dimensional [Zn{sub 3}(SeO{sub 3}){sub 4}]{sup 2-} layers. Specifically, whereas isolated ZnO{sub 4} tetrahedra and SeO{sub 3} polyhedra are arranged into two-dimensional [Zn{sub 3}(SeO{sub 3}){sub 4}]{sup 2-} layers in two cesium compounds, circular [Zn{sub 3}O{sub 10}]{sup 14-} chains and SeO{sub 3} linkers are formed in two-dimensional [Zn{sub 3}(SeO{sub 3}){sub 4}]{sup 2-} layers in Na{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}. Close structural examinations suggest that the size of alkali metal is significant in determining the framework geometry as well as connection modes of transition metal cations. - Graphical abstract: Variable dimensions and frameworks were found in a series of quaternary zinc selenites, A{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4} (A = Na, Rb and Cs). - Highlights: • Five novel quaternary zinc selenites are synthesized. • All the selenites with different structures contain polarizable d{sup 10} and lone pair cations. • The size of alkali metal cations is significant in determining the framework geometry.« less

Chiral Silver-Lanthanide Metal-Organic Frameworks Comprised of One-Dimensional Triple Right-Handed Helical Chains Based on [Ln7(μ3-OH)8]13+ Clusters.

PubMed

Guo, Yan; Zhang, Lijuan; Muhammad, Nadeem; Xu, Yan; Zhou, Yunshan; Tang, Fang; Yang, Shaowei

2018-02-05

Three new isostructural chiral silver-lanthanide heterometal-organic frameworks [Ag 3 Ln 7 (μ 3 -OH) 8 (bpdc) 6 (NO 3 ) 3 (H 2 O) 6 ](NO 3 )·2H 2 O [Ln = Eu (1), Tb (2, Sm (3); H 2 bpdc = 2,2'-bipyridine-3,3'-dicarboxylic acid] based on heptanuclear lanthanide clusters [Ln 7 (μ 3 -OH) 8 ] 13+ comprised of one-dimensional triple right-handed helical chains were hydrothermally synthesized. Various means such as UV-vis spectroscopy, IR spectroscopy, elemental analysis, powder X-ray diffraction, and thermogravimetric/differential thermal analysis were used to characterize the compounds, wherein compound 3 was crystallographically characterized. In the structure of compound 3, eight μ 3 -OH - groups link seven Sm 3+ ions, forming a heptanuclear cluster, [Sm 7 (μ 3 -OH) 8 ] 13+ , and the adjacent [Sm 7 (μ 3 -OH) 8 ] 13+ clusters are linked by the carboxylic groups of bpdc 2- ligands, leading to the formation of a one-dimensional triple right-handed helical chain. The adjacent triple right-handed helical chains are further joined together by coordinating the pyridyl N atoms of the bpdc 2- ligands with Ag + , resulting in a chiral three-dimensional silver(I)-lanthanide(III) heterometal-organic framework with one-dimensional channels wherein NO 3 - anions and crystal lattice H 2 O molecules are trapped. The compounds were studied systematically with respect to their photoluminescence properties and energy-transfer mechanism, and it was found that H 2 bpdc (the energy level for the triplet states of the ligand H 2 bpdc is 21505 cm -1 ) can sensitize Eu 3+ luminescence more effectively than Tb 3+ and Sm 3+ luminescence because of effective energy transfer from bpdc 2- to Eu 3+ under excitation in compound 1.

Self-assembly of polyhedral metal-organic framework particles into three-dimensional ordered superstructures

NASA Astrophysics Data System (ADS)

Avci, Civan; Imaz, Inhar; Carné-Sánchez, Arnau; Pariente, Jose Angel; Tasios, Nikos; Pérez-Carvajal, Javier; Alonso, Maria Isabel; Blanco, Alvaro; Dijkstra, Marjolein; López, Cefe; Maspoch, Daniel

2018-01-01

Self-assembly of particles into long-range, three-dimensional, ordered superstructures is crucial for the design of a variety of materials, including plasmonic sensing materials, energy or gas storage systems, catalysts and photonic crystals. Here, we have combined experimental and simulation data to show that truncated rhombic dodecahedral particles of the metal-organic framework (MOF) ZIF-8 can self-assemble into millimetre-sized superstructures with an underlying three-dimensional rhombohedral lattice that behave as photonic crystals. Those superstructures feature a photonic bandgap that can be tuned by controlling the size of the ZIF-8 particles and is also responsive to the adsorption of guest substances in the micropores of the ZIF-8 particles. In addition, superstructures with different lattices can also be assembled by tuning the truncation of ZIF-8 particles, or by using octahedral UiO-66 MOF particles instead. These well-ordered, sub-micrometre-sized superstructures might ultimately facilitate the design of three-dimensional photonic materials for applications in sensing.

Analysis of the Three-Dimensional Vector FAÇADE Model Created from Photogrammetric Data

NASA Astrophysics Data System (ADS)

Kamnev, I. S.; Seredovich, V. A.

2017-12-01

The results of the accuracy assessment analysis for creation of a three-dimensional vector model of building façade are described. In the framework of the analysis, analytical comparison of three-dimensional vector façade models created by photogrammetric and terrestrial laser scanning data has been done. The three-dimensional model built from TLS point clouds was taken as the reference one. In the course of the experiment, the three-dimensional model to be analyzed was superimposed on the reference one, the coordinates were measured and deviations between the same model points were determined. The accuracy estimation of the three-dimensional model obtained by using non-metric digital camera images was carried out. Identified façade surface areas with the maximum deviations were revealed.

Analytical computation of three-dimensional synthetic seismograms by Modal Summation: method, validation and applications

NASA Astrophysics Data System (ADS)

La Mura, Cristina; Gholami, Vahid; Panza, Giuliano F.

2013-04-01

In order to enable realistic and reliable earthquake hazard assessment and reliable estimation of the ground motion response to an earthquake, three-dimensional velocity models have to be considered. The propagation of seismic waves in complex laterally varying 3D layered structures is a complicated process. Analytical solutions of the elastodynamic equations for such types of media are not known. The most common approaches to the formal description of seismic wavefields in such complex structures are methods based on direct numerical solutions of the elastodynamic equations, e.g. finite-difference, finite-element method, and approximate asymptotic methods. In this work, we present an innovative methodology for computing synthetic seismograms, complete of the main direct, refracted, converted phases and surface waves in three-dimensional anelastic models based on the combination of the Modal Summation technique with the Asymptotic Ray Theory in the framework of the WKBJ - approximation. The three - dimensional models are constructed using a set of vertically heterogeneous sections (1D structures) that are juxtaposed on a regular grid. The distribution of these sections in the grid is done in such a way to fulfill the requirement of weak lateral inhomogeneity in order to satisfy the condition of applicability of the WKBJ - approximation, i.e. the lateral gradient of the parameters characterizing the 1D structure has to be small with respect to the prevailing wavelength. The new method has been validated comparing synthetic seismograms with the records available of three different earthquakes in three different regions: Kanto basin (Japan) triggered by the 1990 Odawara earthquake Mw= 5.1, Romanian territory triggered by the 30 May 1990 Vrancea intermediate-depth earthquake Mw= 6.9 and Iranian territory affected by the 26 December 2003 Bam earthquake Mw= 6.6. Besides the advantage of being a useful tool for assessment of seismic hazard and seismic risk reduction, it is characterized by high efficiency, in fact, once the study region is identified and the 3D model is constructed, the computation, at each station, of the three components of the synthetic signal (displacement, velocity, and acceleration) takes less than 3 hours on a 2 GHz CPU.

Unique Chiral Interpenetrating d-f Heterometallic MOFs as Luminescent Sensors.

PubMed

Wu, Zhi-Lei; Dong, Jie; Ni, Wei-Yan; Zhang, Bo-Wen; Cui, Jian-Zhong; Zhao, Bin

2015-06-01

One novel three-dimensional (3D) 3d-4f metal-organic framework (MOF), [TbZn(L)(CO3)2(H2O)]n (1) [HL = 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine], has been successfully synthesized and structurally characterized. Structural analysis shows that compound 1 features a unique chiral interpenetrating 3D framework for the first time. The resulting crystals of 1 are composed of enantiomers 1a (P41) and 1b (P43), as was clearly confirmed by the crystal structure and the corresponding circular dichroism (CD) analyses of eight randomly selected crystals. The investigations on CD spectra based on every single crystal clearly assigned the Cotton effect signals. The powder X-ray diffraction measurement of 1 after being immersed in common solvents reveals that 1 possess excellent solvent stability. Furthermore, luminescent studies imply that 1 displays highly selective luminescent sensing of aldehydes, such as formol, acetaldehyde, and propanal.

SUPIN: A Computational Tool for Supersonic Inlet Design

NASA Technical Reports Server (NTRS)

Slater, John W.

2016-01-01

A computational tool named SUPIN is being developed to design and analyze the aerodynamic performance of supersonic inlets. The inlet types available include the axisymmetric pitot, three-dimensional pitot, axisymmetric outward-turning, two-dimensional single-duct, two-dimensional bifurcated-duct, and streamline-traced inlets. The aerodynamic performance is characterized by the flow rates, total pressure recovery, and drag. The inlet flow-field is divided into parts to provide a framework for the geometry and aerodynamic modeling. Each part of the inlet is defined in terms of geometric factors. The low-fidelity aerodynamic analysis and design methods are based on analytic, empirical, and numerical methods which provide for quick design and analysis. SUPIN provides inlet geometry in the form of coordinates, surface angles, and cross-sectional areas. SUPIN can generate inlet surface grids and three-dimensional, structured volume grids for use with higher-fidelity computational fluid dynamics (CFD) analysis. Capabilities highlighted in this paper include the design and analysis of streamline-traced external-compression inlets, modeling of porous bleed, and the design and analysis of mixed-compression inlets. CFD analyses are used to verify the SUPIN results.

Trans-dimensional and hierarchical Bayesian approaches toward rigorous estimation of seismic sources and structures in the Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, Seongryong; Tkalčić, Hrvoje; Mustać, Marija; Rhie, Junkee; Ford, Sean

2016-04-01

A framework is presented within which we provide rigorous estimations for seismic sources and structures in the Northeast Asia. We use Bayesian inversion methods, which enable statistical estimations of models and their uncertainties based on data information. Ambiguities in error statistics and model parameterizations are addressed by hierarchical and trans-dimensional (trans-D) techniques, which can be inherently implemented in the Bayesian inversions. Hence reliable estimation of model parameters and their uncertainties is possible, thus avoiding arbitrary regularizations and parameterizations. Hierarchical and trans-D inversions are performed to develop a three-dimensional velocity model using ambient noise data. To further improve the model, we perform joint inversions with receiver function data using a newly developed Bayesian method. For the source estimation, a novel moment tensor inversion method is presented and applied to regional waveform data of the North Korean nuclear explosion tests. By the combination of new Bayesian techniques and the structural model, coupled with meaningful uncertainties related to each of the processes, more quantitative monitoring and discrimination of seismic events is possible.

Intellect: a theoretical framework for personality traits related to intellectual achievements.

PubMed

Mussel, Patrick

2013-05-01

The present article develops a theoretical framework for the structure of personality traits related to intellectual achievements. We postulate a 2-dimensional model, differentiating between 2 processes (Seek and Conquer) and 3 operations (Think, Learn, and Create). The framework was operationalized by a newly developed measure, which was validated based on 2 samples. Subsequently, in 3 studies (overall N = 1,478), the 2-dimensional structure of the Intellect framework was generally supported. Additionally, subdimensions of the Intellect framework specifically predicted conceptually related criteria, including scholastic performance, vocational interest, and leisure activities. Furthermore, results from multidimensional scaling and higher order confirmatory factor analyses show that the framework allows for the incorporation of several constructs that have been proposed on different theoretical backgrounds, such as need for cognition, typical intellectual engagement, curiosity, intrinsic motivation, goal orientation, and openness to ideas. It is concluded that based on the Intellect framework, these constructs, which have been researched separately in the literature, can be meaningfully integrated.

Comparative Evaluation of a Four-Implant-Supported Polyetherketoneketone Framework Prosthesis: A Three-Dimensional Finite Element Analysis Based on Cone Beam Computed Tomography and Computer-Aided Design.

PubMed

Lee, Ki-Sun; Shin, Sang-Wan; Lee, Sang-Pyo; Kim, Jong-Eun; Kim, Jee-Hwan; Lee, Jeong-Yol

The purpose of this pilot study was to evaluate and compare polyetherketoneketone (PEKK) with different framework materials for implant-supported prostheses by means of a three-dimensional finite element analysis (3D-FEA) based on cone beam computed tomography (CBCT) and computer-aided design (CAD) data. A geometric model that consisted of four maxillary implants supporting a prosthesis framework was constructed from CBCT and CAD data of a treated patient. Three different materials (zirconia, titanium, and PEKK) were selected, and their material properties were simulated using FEA software in the generated geometric model. In the PEKK framework (ie, low elastic modulus) group, the stress transferred to the implant and simulated adjacent tissue was reduced when compressive stress was dominant, but increased when tensile stress was dominant. This study suggests that the shock-absorbing effects of a resilient implant-supported framework are limited in some areas and that rigid framework material shows a favorable stress distribution and safety of overall components of the prosthesis.

Phenyl/Perfluorophenyl Stacking Interactions Enhance Structural Order in Two-Dimensional Covalent Organic Frameworks

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

Johnson, Justin C; Braunecker, Wade A; Hurst, Katherine E

A two-dimensional imine-based covalent organic framework (COF) was designed and synthesized such that phenyl and perfluorophenyl structural units can seamlessly alternate between layers of the framework. X-ray diffraction of the COF powders reveals a striking increase in crystallinity for the COF with self-complementary phenyl/perfluorophenyl interactions (FASt-COF). Whereas measured values of the Brunauer-Emmet-Teller (BET) surface areas for the nonfluorinated Base-COF and the COF employing hydrogen bonding were ~37% and 59%, respectively, of their theoretical Connolly surface areas, the BET value for FASt-COF achieves >90% of its theoretical value (~1700 m2/g). Transmission electron microscopy images also revealed unique micron-sized rodlike features inmore » FASt-COF that were not present in the other materials. The results highlight a promising approach for improving surface areas and long-range order in two-dimensional COFs.« less

Close-range laser scanning in forests: towards physically based semantics across scales.

PubMed

Morsdorf, F; Kükenbrink, D; Schneider, F D; Abegg, M; Schaepman, M E

2018-04-06

Laser scanning with its unique measurement concept holds the potential to revolutionize the way we assess and quantify three-dimensional vegetation structure. Modern laser systems used at close range, be it on terrestrial, mobile or unmanned aerial platforms, provide dense and accurate three-dimensional data whose information just waits to be harvested. However, the transformation of such data to information is not as straightforward as for airborne and space-borne approaches, where typically empirical models are built using ground truth of target variables. Simpler variables, such as diameter at breast height, can be readily derived and validated. More complex variables, e.g. leaf area index, need a thorough understanding and consideration of the physical particularities of the measurement process and semantic labelling of the point cloud. Quantified structural models provide a framework for such labelling by deriving stem and branch architecture, a basis for many of the more complex structural variables. The physical information of the laser scanning process is still underused and we show how it could play a vital role in conjunction with three-dimensional radiative transfer models to shape the information retrieval methods of the future. Using such a combined forward and physically based approach will make methods robust and transferable. In addition, it avoids replacing observer bias from field inventories with instrument bias from different laser instruments. Still, an intensive dialogue with the users of the derived information is mandatory to potentially re-design structural concepts and variables so that they profit most of the rich data that close-range laser scanning provides.

Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework.

PubMed

Austria, Cristina; Zhang, Jian; Valle, Henry; Zhang, Qichun; Chew, Emily; Nguyen, Dan-Tam; Gu, J Y; Feng, Pingyun; Bu, Xianhui

2007-08-06

Whereas open-framework materials have been made in a variety of chemical compositions, few are known in which 3-connected SO3(2)- anions serve as basic building units. Here, we report four new metal-sulfite polymeric structures, (ZnSO3)Py (1, py = pyridine), (ZnSO3)2(2,2'-bipy)H2O (2, 2,2'-bipy = 2,2'-bipyridine), (ZnSO3)2(TMDPy) (3, TMDPy = 4,4'-trimethylenedipyridine), and (MnSO3)2en (4, en = ethylenediamine) that have been synthesized hydrothermally and structurally characterized. In these compounds, low-dimensional 1D and 2D inorganic subunits are assembled into higher 2D or 3D covalent frameworks by organic ligands. In addition to the structure-directing effect of organic ligands, the flexible coordination chemistry of Zn2+ and SO3(2)- also contributes to the observed structural diversity. In compounds 1-3, Zn2+ sites alternate with trigonal pyramidal SO3(2)- anions to form three types of [ZnSO3]n chains, whereas in compound 4, a 2D-corrugated [MnSO3]n layer is present. Compound 1 features a rail-like chain with pendant pyridine rings. The pi-pi interaction between 2,2'-bipy ligands is found between adjacent chains in compound 2, resulting in 2D sheets that are further stacked through interlayer hydrogen bonds. Compound 3 exhibits a very interesting inorganic [(ZnSO3)2]n chain constructed from two chairlike subunits, and such chains are bridged by TMDPy ligands into a 2D sheet. In compound 4, side-by-side helical chains permeate through 2D-corrugated [MnSO3]n layers, which are pillared by neutral ethylenediamine molecules into a 3D framework that can be topologically represented as a (3,6)-connected net. The results presented here illustrate the rich structural chemistry of metal-sulfites and the potential of sulfite anions as a unique structural building block for the construction of novel open-framework materials, in particular, those containing polymeric inorganic subunits that may have interesting physical properties such as low-dimensional magnetism or electronic properties.

Thermal solitons as revealed by the static structure factor

NASA Astrophysics Data System (ADS)

Gawryluk, Krzysztof; Brewczyk, Mirosław; Rzążewski, Kazimierz

2017-04-01

We study, within a framework of the classical fields approximation, the static structure factor of a weakly interacting Bose gas at thermal equilibrium. As in a recent experiment [R. Schley et al., Phys. Rev. Lett. 111, 055301 (2013), 10.1103/PhysRevLett.111.055301], we find that the thermal distribution of phonons in a three-dimensional Bose gas follows the Planck distribution. On the other hand we find a disagreement between the Planck and phonon (calculated just as for the bulk gas) distributions in the case of elongated quasi-one-dimensional systems. We attribute this discrepancy to the existence of spontaneous dark solitons [i.e., thermal solitons as reported in T. Karpiuk et al., Phys. Rev. Lett. 109, 205302 (2012), 10.1103/PhysRevLett.109.205302] in an elongated Bose gas at thermal equilibrium.

Two novel zinc(II) coordination polymers constructed from in situ amidation ligands

NASA Astrophysics Data System (ADS)

Yu, Xiao-Yang; Fu, Yao; Fu, Jian-Tao; Xu, Jia-Ning; Luo, Ya-Nan; Yang, Yan-Yan; Qu, Xiao-Shu; Zhang, Jing; Lu, Shu-Lai

2018-04-01

Two novel coordination compounds, [Zn(Hbimh) (H2O)]·H2O (1) and [Zn(Hbimh)]·(4,4ʹ-bpy)0.5 (2) (H3bimh = benzimidazole-5,6-hydrazide, 4,4ʹ-bpy = 4,4ʹ-bipyridine), have been prepared from the hydrothermal in situ amidation cyclization reactions of H3bimdc (H3bimdc = benzimidazole-5,6-dicarboxylic acid) and hydrazine hydrate (N2H4·H2O). Compound 1 exhibits a one-dimensional (1D) hexagon channel structure. Compound 2 is a three-dimensional (3D) framework structure, with 4,4ʹ-bpy fill the channels. We also obtained the ligand H3bimh. The compounds were characterized by IR, PXRD, TGA and elemental analysis. The fluorescence properties in the solid state at room temperature were also investigated.

Three-dimensional hierarchical C-Co-N/Se derived from metal-organic framework as superior cathode for Li-Se batteries

NASA Astrophysics Data System (ADS)

He, Jiarui; Lv, Weiqiang; Chen, Yuanfu; Xiong, Jie; Wen, Kechun; Xu, Chen; Zhang, Wanli; Li, Yanrong; Qin, Wu; He, Weidong

2017-09-01

Three-dimensional, porous graphitic carbon co-doped with cobalt and nitrogen (C-Co-N) is prepared with metal-organic framework (MOF) and employed as Lewis base matrix to host selenium. Owing to the unique structure with abundant micro/meso-pores, the highly-conductive C-Co-N matrix provides highly-efficient channels for electron transfer and ionic diffusion, and sufficient surface area for loading of selenium nanoparticles while mitigating dissolution of polyselenides and suppressing volume expansion. The homogenous distribution of cobalt nanoparticles and nitrogen-group in C-Co-N composite immobilize polyselenides through strong chemical interaction in the operation of Li-Se batteries. With a very high Se loading of 76.5 wt%, the C-Co-N/Se cathode delivers superior electrochemical performance with an ultrahigh reversible capacity of 672.3 mAh g-1 (99.6% of the theoretical value) and a capacity of 574.2 mAh g-1 after 200 cycles, giving a capacity fading of only 0.07% per cycle and a nearly 100% Columbic efficiency. In-situ Raman spectroscopy and density functional theory simulations are employed to investigate the Se (de)lithiation mechanism at the electrolyte/cathode interface, and confirm that the structure and composition of C-Co-N scaffold give rise to efficient cathode host for high-performance Se-based cathodes with dramatically reduced capacity fading.

Ultrahigh Surface Area Three-Dimensional Porous Graphitic Carbon from Conjugated Polymeric Molecular Framework

PubMed Central

2015-01-01

Porous graphitic carbon is essential for many applications such as energy storage devices, catalysts, and sorbents. However, current graphitic carbons are limited by low conductivity, low surface area, and ineffective pore structure. Here we report a scalable synthesis of porous graphitic carbons using a conjugated polymeric molecular framework as precursor. The multivalent cross-linker and rigid conjugated framework help to maintain micro- and mesoporous structures, while promoting graphitization during carbonization and chemical activation. The above unique design results in a class of highly graphitic carbons at temperature as low as 800 °C with record-high surface area (4073 m2 g–1), large pore volume (2.26 cm–3), and hierarchical pore architecture. Such carbons simultaneously exhibit electrical conductivity >3 times more than activated carbons, very high electrochemical activity at high mass loading, and high stability, as demonstrated by supercapacitors and lithium–sulfur batteries with excellent performance. Moreover, the synthesis can be readily tuned to make a broad range of graphitic carbons with desired structures and compositions for many applications. PMID:27162953

Ultrahigh Surface Area Three-Dimensional Porous Graphitic Carbon from Conjugated Polymeric Molecular Framework

DOE PAGES

To, John W. F.; Chen, Zheng; Yao, Hongbin; ...

2015-05-18

Porous graphitic carbon is essential for many applications such as energy storage devices, catalysts, and sorbents. However, current graphitic carbons are limited by low conductivity, low surface area, and ineffective pore structure. Here we report a scalable synthesis of porous graphitic carbons using a conjugated polymeric molecular framework as precursor. The multivalent cross-linker and rigid conjugated framework help to maintain micro- and mesoporous structures, while promoting graphitization during carbonization and chemical activation. The above unique design results in a class of highly graphitic carbons at temperature as low as 800 °C with record-high surface area (4073 m 2 g –1),more » large pore volume (2.26 cm –3), and hierarchical pore architecture. Such carbons simultaneously exhibit electrical conductivity >3 times more than activated carbons, very high electrochemical activity at high mass loading, and high stability, as demonstrated by supercapacitors and lithium–sulfur batteries with excellent performance. Moreover, the synthesis can be readily tuned to make a broad range of graphitic carbons with desired structures and compositions for many applications.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

NASA Astrophysics Data System (ADS)

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-04-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

Electron delocalization and charge mobility as a function of reduction in a metal-organic framework.

PubMed

Aubrey, Michael L; Wiers, Brian M; Andrews, Sean C; Sakurai, Tsuneaki; Reyes-Lillo, Sebastian E; Hamed, Samia M; Yu, Chung-Jui; Darago, Lucy E; Mason, Jarad A; Baeg, Jin-Ook; Grandjean, Fernande; Long, Gary J; Seki, Shu; Neaton, Jeffrey B; Yang, Peidong; Long, Jeffrey R

2018-06-04

Conductive metal-organic frameworks are an emerging class of three-dimensional architectures with degrees of modularity, synthetic flexibility and structural predictability that are unprecedented in other porous materials. However, engendering long-range charge delocalization and establishing synthetic strategies that are broadly applicable to the diverse range of structures encountered for this class of materials remain challenging. Here, we report the synthesis of K x Fe 2 (BDP) 3 (0 ≤ x ≤ 2; BDP 2-  = 1,4-benzenedipyrazolate), which exhibits full charge delocalization within the parent framework and charge mobilities comparable to technologically relevant polymers and ceramics. Through a battery of spectroscopic methods, computational techniques and single-microcrystal field-effect transistor measurements, we demonstrate that fractional reduction of Fe 2 (BDP) 3 results in a metal-organic framework that displays a nearly 10,000-fold enhancement in conductivity along a single crystallographic axis. The attainment of such properties in a K x Fe 2 (BDP) 3 field-effect transistor represents the realization of a general synthetic strategy for the creation of new porous conductor-based devices.

A General Exponential Framework for Dimensionality Reduction.

PubMed

Wang, Su-Jing; Yan, Shuicheng; Yang, Jian; Zhou, Chun-Guang; Fu, Xiaolan

2014-02-01

As a general framework, Laplacian embedding, based on a pairwise similarity matrix, infers low dimensional representations from high dimensional data. However, it generally suffers from three issues: 1) algorithmic performance is sensitive to the size of neighbors; 2) the algorithm encounters the well known small sample size (SSS) problem; and 3) the algorithm de-emphasizes small distance pairs. To address these issues, here we propose exponential embedding using matrix exponential and provide a general framework for dimensionality reduction. In the framework, the matrix exponential can be roughly interpreted by the random walk over the feature similarity matrix, and thus is more robust. The positive definite property of matrix exponential deals with the SSS problem. The behavior of the decay function of exponential embedding is more significant in emphasizing small distance pairs. Under this framework, we apply matrix exponential to extend many popular Laplacian embedding algorithms, e.g., locality preserving projections, unsupervised discriminant projections, and marginal fisher analysis. Experiments conducted on the synthesized data, UCI, and the Georgia Tech face database show that the proposed new framework can well address the issues mentioned above.

Al(0.5)Nb(1.5)(PO(4))(3).

PubMed

Zhao, Dan; Liang, Peng; Su, Ling; Chang, Huan; Yan, Shi

2011-02-12

Single crystals of the title compound, aluminium niobium triphosphate, Al(0.5)Nb(1.5)(PO(4))(3), have been synthesized by a high-temperature reaction in a platinium crucible. The Al(III) and Nb(V) atoms occupy the same site on the axis, with disorder in the ratio of 1:3. The fundamental building units of the title structure are isolated Al/NbO(6) octa-hedra and PO(4) tetra-hedra (. 2 symmetry), which are further inter-locked by corner-sharing O atoms, leading to a three-dimensional framework structure with infinite channels along the a axis.

Syntheses, crystal structures and fluorescent properties of three metal- tris(4‧-carboxybiphenyl)amine frameworks

NASA Astrophysics Data System (ADS)

Yuan, Lv-Bing; He, Yan-Ping; Xu, Hai; Zhang, Jian

2017-11-01

Triphenylamine and its derivatives have been widely concerned because of their excellent performance in the area of the photoelectric functional material. In this work, we chose a nanosized tris(4‧-carboxybiphenyl)amine (H3TPA) as organic ligand. By employing the H3TPA ligand to assemble with M2+ (M = Zn, Cd, and Pb) ions, respectively, three metal-organic frameworks (FIR-43 to FIR-45, FIR denotes Fujian Institute of Research) have been synthesized under different solvent systems. FIR-43 exhibits a 3-connected two-dimensional (2D) network based on mononuclear [Zn(COO)3] second building unit (SBU). Unlike the anionic framework FIR-43, FIR-44 is a neutral 2D layer constructed by trinuclear [Cd3(COO)6] SBU and displays a (3,6)-NbSe2 topology structure. If the weak Pb-O interactions in the range of 2.79-2.88 Å are considered, FIR-45 is a neutral 3D framework built by hexanuclear [Pb6(DMAE)6(COO)6] SBU (DMAE = N,N-dimethylethanolamine) and represents a (3,6)-connected (4·82)2(42·811·102) topology. Thermogravimetric analyses (TGA) and X-ray powder diffraction (PXRD) patterns were used to evaluate their thermal stability and phase purity. Photoluminescence studies showed that they exhibited strong emitting bands in the visible region with high quantum yields and long luminescent lifetimes. The assembly between nanosized tris((4-carboxyl)phenylduryl)amine ligand and M2+ (M = Zn, Cd, and Pb) ions leads to three new metal-organic frameworks, which show excellent fluorescent properties.

Modeling drying of three-dimensional pulp molded structures. Part I, Experimental program

Treesearch

Heike Nyist; John F. Hunt; Margit Tamasy-Bano

1998-01-01

Researchers at the USDA Forest Products Laboratory have developed a new three-dimensional structural panel, called FPL Spaceboard. This panel is formed using a U.S. patented three-dimensional mold capable of using a variety of fibrous materials with either the wet- or dry-forming process. Structurally, the panel departs from the traditional two-dimensional panel by...

Synthesis, characterizations and catalytic studies of a new two-dimensional metal-organic framework based on Co-carboxylate secondary building units

NASA Astrophysics Data System (ADS)

Bagherzadeh, Mojtaba; Ashouri, Fatemeh; Đaković, Marijana

2015-03-01

A metal-organic framework [Co3(BDC)3(DMF)2(H2O)2] was synthesized and structurally characterized. X-ray single crystal analysis revealed that the framework contains a 2D polymeric chain through coordination of 1,4-benzenedicarboxylic acid linker ligand to cobalt centers. The polymer crystallize in monoclinic P21/n space group with a=13.989(3) Å, b=9.6728(17) Å, c=16.707(3) Å, and Z=2. The polymer features a framework based on the perfect octahedral Co-O6 secondary building units. The catalytic activities of [Co3(BDC)3(DMF)2(H2O)2]n for olefins oxidation was conducted. The heterogeneous catalyst could be facilely separated from the reaction mixture, and reused three times without significant degradation in catalytic activity. Furthermore, no contribution from homogeneous catalysis of active species leaching into reaction solution was detected.

Hidden impacts of ocean acidification to live and dead coral framework.

PubMed

Hennige, S J; Wicks, L C; Kamenos, N A; Perna, G; Findlay, H S; Roberts, J M

2015-08-22

Cold-water corals, such as Lophelia pertusa, are key habitat-forming organisms found throughout the world's oceans to 3000 m deep. The complex three-dimensional framework made by these vulnerable marine ecosystems support high biodiversity and commercially important species. Given their importance, a key question is how both the living and the dead framework will fare under projected climate change. Here, we demonstrate that over 12 months L. pertusa can physiologically acclimate to increased CO2, showing sustained net calcification. However, their new skeletal structure changes and exhibits decreased crystallographic and molecular-scale bonding organization. Although physiological acclimatization was evident, we also demonstrate that there is a negative correlation between increasing CO2 levels and breaking strength of exposed framework (approx. 20-30% weaker after 12 months), meaning the exposed bases of reefs will be less effective 'load-bearers', and will become more susceptible to bioerosion and mechanical damage by 2100. © 2015 The Authors.

The Scientist, Philosopher, and Rhetorician: The Three Dimensions of Technical Communication and Technology

ERIC Educational Resources Information Center

Garrison, Kevin

2014-01-01

Technical communication's attempt to prioritize theories of scholarship and pedagogy has resulted in several authors contributing a three-dimensional framework to approach technology: the instrumental perspective, the critical humanist perspective, and the user-centered perspective [1-3]. This article traces connections between this framework for…

Solvothermal synthesis and structure of 3D frameworks of Nd(III) and Y(III) with thiophene-2,5-dicarboxylate and N,N‧-diethylformamide

NASA Astrophysics Data System (ADS)

Sharma, Swati; Yawer, Mohd; Kariem, Mukaddus; Sheikh, Haq Nawaz

2016-08-01

Two new 3D MOFs [Nd2(TDA)3(DEF)2(H2O)]n (1) and [Y4(TDA)6(DEF)4]n (2) [Thiophene-2,5-dicarboxylic acid (H2TDA) and N,N‧-diethylformamide (DEF)] were synthesized by solvothermal method. They were characterized by elemental analyses, infrared spectroscopy and single crystal X-ray diffraction studies. The two MOFs (1) and (2) belong to the monoclinic system with space group P21/n and C 2 respectively. Structural characterizations by single-crystal X-ray crystallography reveal that 1 and 2 adopt three-dimensional frameworks constructed by cross-linking of rod shaped infinite chain secondary building unit (SBU) by thiophene-2,5-dicarboxylates as linker. These frameworks feature rhomboidal channels, inside which coordinated DEF/H2O solvent molecules are located. DEF plays pivotal role in reaction and design of MOFs. Thermogravimetric analysis shows that both MOFs are thermally robust.

Ultralight mesoporous magnetic frameworks by interfacial assembly of Prussian blue nanocubes.

PubMed

Kong, Biao; Tang, Jing; Wu, Zhangxiong; Wei, Jing; Wu, Hao; Wang, Yongcheng; Zheng, Gengfeng; Zhao, Dongyuan

2014-03-10

A facile approach for the synthesis of ultralight iron oxide hierarchical structures with tailorable macro- and mesoporosity is reported. This method entails the growth of porous Prussian blue (PB) single crystals on the surface of a polyurethane sponge, followed by in situ thermal conversion of PB crystals into three-dimensional mesoporous iron oxide (3DMI) architectures. Compared to previously reported ultralight materials, the 3DMI architectures possess hierarchical macro- and mesoporous frameworks with multiple advantageous features, including high surface area (ca. 117 m(2) g(-1)) and ultralow density (6-11 mg cm(-3)). Furthermore, they can be synthesized on a kilogram scale. More importantly, these 3DMI structures exhibit superparamagnetism and tunable hydrophilicity/hydrophobicity, thus allowing for efficient multiphase interfacial adsorption and fast multiphase catalysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional hydrogeologic framework model for use with a steady-state numerical ground-water flow model of the Death Valley regional flow system, Nevada and California

USGS Publications Warehouse

Belcher, Wayne R.; Faunt, Claudia C.; D'Agnese, Frank A.

2002-01-01

The U.S. Geological Survey, in cooperation with the Department of Energy and other Federal, State, and local agencies, is evaluating the hydrogeologic characteristics of the Death Valley regional ground-water flow system. The ground-water flow system covers an area of about 100,000 square kilometers from latitude 35? to 38?15' North to longitude 115? to 118? West, with the flow system proper comprising about 45,000 square kilometers. The Death Valley regional ground-water flow system is one of the larger flow systems within the Southwestern United States and includes in its boundaries the Nevada Test Site, Yucca Mountain, and much of Death Valley. Part of this study includes the construction of a three-dimensional hydrogeologic framework model to serve as the foundation for the development of a steady-state regional ground-water flow model. The digital framework model provides a computer-based description of the geometry and composition of the hydrogeologic units that control regional flow. The framework model of the region was constructed by merging two previous framework models constructed for the Yucca Mountain Project and the Environmental Restoration Program Underground Test Area studies at the Nevada Test Site. The hydrologic characteristics of the region result from a currently arid climate and complex geology. Interbasinal regional ground-water flow occurs through a thick carbonate-rock sequence of Paleozoic age, a locally thick volcanic-rock sequence of Tertiary age, and basin-fill alluvium of Tertiary and Quaternary age. Throughout the system, deep and shallow ground-water flow may be controlled by extensive and pervasive regional and local faults and fractures. The framework model was constructed using data from several sources to define the geometry of the regional hydrogeologic units. These data sources include (1) a 1:250,000-scale hydrogeologic-map compilation of the region; (2) regional-scale geologic cross sections; (3) borehole information, and (4) gridded surfaces from a previous three-dimensional geologic model. In addition, digital elevation model data were used in conjunction with these data to define ground-surface altitudes. These data, properly oriented in three dimensions by using geographic information systems, were combined and gridded to produce the upper surfaces of the hydrogeologic units used in the flow model. The final geometry of the framework model is constructed as a volumetric model by incorporating the intersections of these gridded surfaces and by applying fault truncation rules to structural features from the geologic map and cross sections. The cells defining the geometry of the hydrogeologic framework model can be assigned several attributes such as lithology, hydrogeologic unit, thickness, and top and bottom altitudes.

A Mechanism-based 3D-QSAR Approach for Classification ...

EPA Pesticide Factsheets

Organophosphate (OP) and carbamate esters can inhibit acetylcholinesterase (AChE) by binding covalently to a serine residue in the enzyme active site, and their inhibitory potency depends largely on affinity for the enzyme and the reactivity of the ester. Despite this understanding, there has been no mechanism-based in silico approach for classification and prediction of the inhibitory potency of ether OPs or carbamates. This prompted us to develop a three dimensional prediction framework for OPs, carbamates, and their analogs. Inhibitory structures of a compound that can form the covalent bond were identified through analysis of docked conformations of the compound and its metabolites. Inhibitory potencies of the selected structures were then predicted using a previously developed three dimensional quantitative structure-active relationship. This approach was validated with a large number of structurally diverse OP and carbamate compounds encompassing widely used insecticides and structural analogs including OP flame retardants and thio- and dithiocarbamate pesticides. The modeling revealed that: (1) in addition to classical OP metabolic activation, the toxicity of carbamate compounds can be dependent on biotransformation, (2) OP and carbamate analogs such as OP flame retardants and thiocarbamate herbicides can act as AChEI, (3) hydrogen bonds at the oxyanion hole is critical for AChE inhibition through the covalent bond, and (4) π–π interaction with Trp86

Industrially benign super-compressible piezoresistive carbon foams with predefined wetting properties: from environmental to electrical applications

NASA Astrophysics Data System (ADS)

Pham, Tung Ngoc; Samikannu, Ajaikumar; Kukkola, Jarmo; Rautio, Anne-Riikka; Pitkänen, Olli; Dombovari, Aron; Lorite, Gabriela Simone; Sipola, Teemu; Toth, Geza; Mohl, Melinda; Mikkola, Jyri-Pekka; Kordas, Krisztian

2014-11-01

In the present work electrically conductive, flexible, lightweight carbon sponge materials derived from open-pore structure melamine foams are studied and explored. Hydrophobic and hydrophilic surface properties - depending on the chosen treatment conditions - allow the separation and storage of liquid chemical compounds. Activation of the carbonaceous structures substantially increases the specific surface area from ~4 m2g-1 to ~345 m2g-1, while retaining the original three-dimensional, open-pore structure suitable for hosting, for example, Ni catalyst nanoparticles. In turn the structure is rendered suitable for hydrogenating acetone to 2-propanol and methyl isobutyl ketone as well for growing hierarchical carbon nanotube structures used as electric double-layer capacitor electrodes with specific capacitance of ~40 F/g. Mechanical stress-strain analysis indicates the materials are super-compressible (>70% volume reduction) and viscoelastic with excellent damping behavior (loss of 0.69 +/- 0.07), while piezoresistive measurements show very high gauge factors (from ~20 to 50) over a large range of deformations. The cost-effective, robust and scalable synthesis - in conjunction with their fascinating multifunctional utility - makes the demonstrated carbon foams remarkable competitors with other three-dimensional carbon materials typically based on pyrolyzed biopolymers or on covalently bonded graphene and carbon nanotube frameworks.

Industrially benign super-compressible piezoresistive carbon foams with predefined wetting properties: from environmental to electrical applications.

PubMed

Pham, Tung Ngoc; Samikannu, Ajaikumar; Kukkola, Jarmo; Rautio, Anne-Riikka; Pitkänen, Olli; Dombovari, Aron; Lorite, Gabriela Simone; Sipola, Teemu; Toth, Geza; Mohl, Melinda; Mikkola, Jyri-Pekka; Kordas, Krisztian

2014-11-06

In the present work electrically conductive, flexible, lightweight carbon sponge materials derived from open-pore structure melamine foams are studied and explored. Hydrophobic and hydrophilic surface properties - depending on the chosen treatment conditions - allow the separation and storage of liquid chemical compounds. Activation of the carbonaceous structures substantially increases the specific surface area from ~4 m(2)g(-1) to ~345 m(2)g(-1), while retaining the original three-dimensional, open-pore structure suitable for hosting, for example, Ni catalyst nanoparticles. In turn the structure is rendered suitable for hydrogenating acetone to 2-propanol and methyl isobutyl ketone as well for growing hierarchical carbon nanotube structures used as electric double-layer capacitor electrodes with specific capacitance of ~40 F/g. Mechanical stress-strain analysis indicates the materials are super-compressible (>70% volume reduction) and viscoelastic with excellent damping behavior (loss of 0.69 ± 0.07), while piezoresistive measurements show very high gauge factors (from ~20 to 50) over a large range of deformations. The cost-effective, robust and scalable synthesis - in conjunction with their fascinating multifunctional utility - makes the demonstrated carbon foams remarkable competitors with other three-dimensional carbon materials typically based on pyrolyzed biopolymers or on covalently bonded graphene and carbon nanotube frameworks.

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

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.

Uncovering a reconstructive solid-solid phase transition in a metal-organic framework.

PubMed

Longley, L; Li, N; Wei, F; Bennett, T D

2017-11-01

A nanoporous three-dimensional metal-organic framework (MOF), ZnPurBr undergoes a transition to a previously unreported high-temperature phase, ZnPurBr-ht. The transition, which proceeds without mass loss, is uncovered through the use of differential scanning calorimetry (DSC). The new crystal structure was solved using single-crystal X-ray diffraction, and the mechanical properties of both phases investigated by nanoindentation and density functional theory. The anisotropy of the calculated Young's moduli showed good agreement with the crystallographic alignment of the stiff purinate organic linker. The results provide a prototypical example of the importance of the use of DSC in the MOF field, where its use is not currently standard in characterization.

Effect of the cation size on the framework structures of magnesium tungstate, A4Mg(WO4)3 (A = Na, K), R2Mg2(WO4)3 (R = Rb, Cs).

PubMed

Han, Shujuan; Wang, Ying; Jing, Qun; Wu, Hongping; Pan, Shilie; Yang, Zhihua

2015-03-28

A series of alkali metal magnesium tungstates, A4Mg(WO4)3 (A = Na, K), R2Mg2(WO4)3 (R = Rb, Cs), were synthesized from a high temperature solution, and their structures were determined by single-crystal X-ray diffraction. Interestingly, Na4Mg(WO4)3 crystallizes in the monoclinic space group C2/c, while K4Mg(WO4)3 having an identical stoichiometry with Na4Mg(WO4)3, exhibits a different framework structure belonging to triclinic symmetry with the space group P1[combining macron]. Isostructural Rb2Mg2(WO4)3 and Cs2Mg2(WO4)3 crystallize in the space group P213 of cubic symmetry and reveal a three dimensional framework composed of isolated WO4 tetrahedra, MgO6 octahedra and RO12 (R = Rb, Cs) polyhedra. The effect of the alkali metal cation size on the framework structures of magnesium tungstate has been discussed in detail. In addition, the infrared spectra, as well as the UV-Vis-NIR diffuse reflectance spectroscopy data, are reported. The first-principles theoretical studies are also carried out to aid the understanding of electronic structures and linear optical properties.

Syntheses and crystal structures of two new hydrated borates, Zn{sub 8}[(BO{sub 3}){sub 3}O{sub 2}(OH){sub 3}] and Pb[B{sub 5}O{sub 8}(OH)].1.5H{sub 2}O

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

Chen Xuean; Zhao Yinghua; Chang Xinan

Two new hydrated borates, Zn{sub 8}[(BO{sub 3}){sub 3}O{sub 2}(OH){sub 3}] and Pb[B{sub 5}O{sub 8}(OH)].1.5H{sub 2}O, have been prepared by hydrothermal reactions at 170 {sup o}C. Single-crystal X-ray structural analyses showed that Zn{sub 8}[(BO{sub 3}){sub 3}O{sub 2}(OH){sub 3}] crystallizes in a non-centrosymmetric space group R32 with a=8.006(2) A, c=17.751(2) A, Z=3 and Pb[B{sub 5}O{sub 8}(OH)].1.5H{sub 2}O in a triclinic space group P1-bar with a=6.656(2) A, b=6.714(2) A, c=10.701(2) A, {alpha}=99.07(2){sup o}, {beta}=93.67(2){sup o}, {gamma}=118.87(1){sup o}, Z=2. Zn{sub 8}[(BO{sub 3}){sub 3}O{sub 2}(OH){sub 3}] represents a new structure type in which Zn-centered tetrahedra are connected via common vertices leading to helical ribbons {submore » {infinity}} {sup 1}[Zn{sub 8}O{sub 15}(OH){sub 3}]{sup 17-} that pack side by side and are further condensed through sharing oxygen atoms to form a three-dimensional {sub {infinity}} {sup 3}[Zn{sub 8}O{sub 11}(OH){sub 3}]{sup 9-} framework. The boron atoms are incorporated into the channels in the framework to complete the final structure. Pb[B{sub 5}O{sub 8}(OH)].1.5H{sub 2}O is a layered compound containing double ring [B{sub 5}O{sub 8}(OH)]{sup 2-} building units that share exocyclic oxygen atoms to form a two-dimensional layer. Symmetry-center-related layers are stacked along the c-axis and held together by interlayer Pb{sup 2+} ions and water molecules via electrostatic and hydrogen bonding interactions. The IR spectra further confirmed the existence of both triangular BO{sub 3} and OH groups in Zn{sub 8}[(BO{sub 3}){sub 3}O{sub 2}(OH){sub 3}], and BO{sub 3}, BO{sub 4}, OH groups as well as guest water molecules in Pb[B{sub 5}O{sub 8}(OH)].1.5H{sub 2}O. -- Zn{sub 8}[(BO{sub 3}){sub 3}O{sub 2}(OH){sub 3}] represents a new structure type in which Zn-centered tetrahedra are connected via common vertices to form a three-dimensional framework. The boron atoms are incorporated into the channels in the framework to strengen the structure via B-O bonds. Pb[B{sub 5}O{sub 8}(OH)].1.5H{sub 2}O is a new layered material containing double ring [B{sub 5}O{sub 8}(OH)]{sup 2-} building units that share exocyclic oxygen atoms to form a two-dimensional layer.« less

Beyond comorbidity: Toward a dimensional and hierarchal approach to understanding psychopathology across the lifespan

PubMed Central

Forbes, Miriam K.; Tackett, Jennifer L.; Markon, Kristian E.; Krueger, Robert F.

2016-01-01

In this review, we propose a novel developmentally informed framework to push research beyond a focus on comorbidity between discrete diagnostic categories, and to move towards research based on the well-validated dimensional and hierarchical structure of psychopathology. For example, a large body of research speaks to the validity and utility of the Internalizing and Externalizing (IE) spectra as organizing constructs for research on common forms of psychopathology. The IE spectra act as powerful explanatory variables that channel the psychopathological effects of genetic and environmental risk factors, predict adaptive functioning, and account for the likelihood of disorder-level manifestations of psychopathology. As such, our proposed theoretical framework uses the IE spectra as central constructs to guide future psychopathology research across the lifespan. The framework is particularly flexible, as any of the facets or factors from the dimensional and hierarchical structure of psychopathology can form the focus of research. We describe the utility and strengths of this framework for developmental psychopathology in particular, and explore avenues for future research. PMID:27739384

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Condom negotiation: findings and future directions.

PubMed

Peasant, Courtney; Parra, Gilbert R; Okwumabua, Theresa M

2015-01-01

The aim of this review was to summarize factors associated with condom negotiation among heterosexual men. Literature searches were conducted using multiple databases spanning several disciplines. Studies examining psychological, demographic, relational, communication, and environmental factors related to condom negotiation are described, and a three-dimensional framework of condom negotiation is proposed. This framework of condom negotiation may aid researchers in operationalizing this construct, organizing this literature, and facilitating measurement development. We used this three-dimensional framework to articulate the influence of gender, ethnicity, relationship type, partner characteristics, trauma history, post-traumatic stress, and alcohol use on condom negotiation. Areas for future research are outlined. More research is needed to understand how these factors interact to influence condom negotiation, as well as the interaction between gender and the identified factors.

Tuning the formations of metal-1,3,5-benzenetricarboxylate frameworks via the assistance of amino acids

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

Lei, Xiao-Ping; Lian, Ting-Ting; Chen, Shu-Mei, E-mail: csm@fzu.edu.cn

Seven new metal-1,3,5-benzenetricarboxylate coordination polymers have been synthesized by modification of auxiliary components during the assembly reactions. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by XRD and TGA. Interestingly, they show fascinating topological structures. Compounds 1 and 2 possess the undulating layer structure with 3-connected hcb network and (3,6)-connected kgd network. Compound 3 possesses three-dimensional (3D) pillared-layer structure with 3-connected 2-fold interpenetrating srs net. Compound 4 also has the 3D 2-fold interpenetrating pillared-layer structure; however, it has (3,5)-connected hms topology because the Cd(II) center is 5-connected. Compound 5 possess 3D structure through hydrogen bondingmore » interactions between ladder-like layers. Compounds 6 and 7 have the similar 3D frameworks with 4-connected umc net and (3,7)-connected (3.4.5)(3{sup 2}.4{sup 6}.5{sup 5}.6{sup 8}) topology, respectively. The photoluminescent properties of compounds 2–7 were also investigated. - Graphical abstract: Presented here are seven new metal-1,3,5-benzenetricarboxylate coordination polymers with diverse structures from 2D layers to 3D open frameworks. The synthesis and structural diversity of these compounds are determined by the additional amino acids as unusual buffering agents. - Highlights: • Structural diversity of metal-1,3,5-benzenetricarboxylate frameworks. • Tuning structural topologies of MOFs via the assistance of amino acids. • Amino acids as unusual buffering agents for the synthesis of MOFs.« less

Upon Generating (2+1)-dimensional Dynamical Systems

NASA Astrophysics Data System (ADS)

Zhang, Yufeng; Bai, Yang; Wu, Lixin

2016-06-01

Under the framework of the Adler-Gel'fand-Dikii(AGD) scheme, we first propose two Hamiltonian operator pairs over a noncommutative ring so that we construct a new dynamical system in 2+1 dimensions, then we get a generalized special Novikov-Veselov (NV) equation via the Manakov triple. Then with the aid of a special symmetric Lie algebra of a reductive homogeneous group G, we adopt the Tu-Andrushkiw-Huang (TAH) scheme to generate a new integrable (2+1)-dimensional dynamical system and its Hamiltonian structure, which can reduce to the well-known (2+1)-dimensional Davey-Stewartson (DS) hierarchy. Finally, we extend the binormial residue representation (briefly BRR) scheme to the super higher dimensional integrable hierarchies with the help of a super subalgebra of the super Lie algebra sl(2/1), which is also a kind of symmetric Lie algebra of the reductive homogeneous group G. As applications, we obtain a super 2+1 dimensional MKdV hierarchy which can be reduced to a super 2+1 dimensional generalized AKNS equation. Finally, we compare the advantages and the shortcomings for the three schemes to generate integrable dynamical systems.

Integrated Aeromechanics with Three-Dimensional Solid-Multibody Structures

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2014-01-01

A full three-dimensional finite element-multibody structural dynamic solver is coupled to a three-dimensional Reynolds-averaged Navier-Stokes solver for the prediction of integrated aeromechanical stresses and strains on a rotor blade in forward flight. The objective is to lay the foundations of all major pieces of an integrated three-dimensional rotor dynamic analysis - from model construction to aeromechanical solution to stress/strain calculation. The primary focus is on the aeromechanical solution. Two types of three-dimensional CFD/CSD interfaces are constructed for this purpose with an emphasis on resolving errors from geometry mis-match so that initial-stage approximate structural geometries can also be effectively analyzed. A three-dimensional structural model is constructed as an approximation to a UH-60A-like fully articulated rotor. The aerodynamic model is identical to the UH-60A rotor. For preliminary validation measurements from a UH-60A high speed flight is used where CFD coupling is essential to capture the advancing side tip transonic effects. The key conclusion is that an integrated aeromechanical analysis is indeed possible with three-dimensional structural dynamics but requires a careful description of its geometry and discretization of its parts.

Extreme Mechanics: Self-Folding Origami

NASA Astrophysics Data System (ADS)

Santangelo, Christian D.

2017-03-01

Origami has emerged as a tool for designing three-dimensional structures from flat films. Because they can be fabricated by lithographic or roll-to-roll processing techniques, they have great potential for the manufacture of complicated geometries and devices. This article discusses the mechanics of origami and kirigami with a view toward understanding how to design self-folding origami structures. Whether an origami structure can be made to fold autonomously depends strongly on the geometry and kinematics of the origami fold pattern. This article collects some of the results on origami rigidity into a single framework, and discusses how these aspects affect the foldability of origami. Despite recent progress, most problems in origami and origami design remain completely open.

Three-Dimensional Bayesian Geostatistical Aquifer Characterization at the Hanford 300 Area using Tracer Test Data

NASA Astrophysics Data System (ADS)

Chen, X.; Murakami, H.; Hahn, M. S.; Hammond, G. E.; Rockhold, M. L.; Rubin, Y.

2010-12-01

Tracer testing under natural or forced gradient flow provides useful information for characterizing subsurface properties, by monitoring and modeling the tracer plume migration in a heterogeneous aquifer. At the Hanford 300 Area, non-reactive tracer experiments, in addition to constant-rate injection tests and electromagnetic borehole flowmeter (EBF) profiling, were conducted to characterize the heterogeneous hydraulic conductivity field. A Bayesian data assimilation technique, method of anchored distributions (MAD), is applied to assimilate the experimental tracer test data and to infer the three-dimensional heterogeneous structure of the hydraulic conductivity in the saturated zone of the Hanford formation. In this study, the prior information of the underlying random hydraulic conductivity field was obtained from previous field characterization efforts using the constant-rate injection tests and the EBF data. The posterior distribution of the random field is obtained by further conditioning the field on the temporal moments of tracer breakthrough curves at various observation wells. The parallel three-dimensional flow and transport code PFLOTRAN is implemented to cope with the highly transient flow boundary conditions at the site and to meet the computational demand of the proposed method. The validation results show that the field conditioned on the tracer test data better reproduces the tracer transport behavior compared to the field characterized previously without the tracer test data. A synthetic study proves that the proposed method can effectively assimilate tracer test data to capture the essential spatial heterogeneity of the three-dimensional hydraulic conductivity field. These characterization results will improve conceptual models developed for the site, including reactive transport models. The study successfully demonstrates the capability of MAD to assimilate multi-scale multi-type field data within a consistent Bayesian framework. The MAD framework can potentially be applied to combine geophysical data with other types of data in site characterization.

Host-guest interaction between Acridine orange molecules and AFI or CHA zeolite crystals

NASA Astrophysics Data System (ADS)

Chen, Yanping; Fu, Ling; Xu, Xintong; Li, Irene Ling; Ruan, Shuangchen; Jian, Dunliang; Zhai, Jianpang

2017-02-01

Acridine orange (AO) molecules were incorporated in AlPO4-5, SAPO-5 and SAPO-47 single crystals by vapor-phase diffusion method. Polarized absorption spectra show that AO molecules are well aligned by the one-dimensional channel systems of AlPO4-5 and SAPO-5 matrices. While the orientation of AO molecules in SAPO-47 crystals is diverse owing to the three-dimensional cage structure of chabazite (structure code CHA). The absorption peak and emission peak of AO/SAPO-5 blue shift compared with that of AO/AlPO4-5 because the channel environment changes from non-polar medium to polar medium when Si substituted in the framework of AlPO4-5. The greater blue shift in absorption band and emission band of AO/SAPO-47 are expected to originate from the polar channel medium and smaller channel size of SAPO-47.

Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

PubMed

Olsen, Aaron M; Westneat, Mark W

2016-12-01

Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing geometries and configurations, enabling novel interpretations of the mechanics of force transmission across a diversity of vertebrate feeding mechanisms and enhancing our understanding of musculoskeletal function and evolution. J. Morphol. 277:1570-1583, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

BiSr3(YO)3(BO3)4: a new gaudefroyite-type rare-earth borate with moderate SHG response.

PubMed

Gao, Jianhua; Li, Shuai

2012-01-02

The synthesis, crystal structure, crystal growth, and characterization of a new noncentrosymmetric rare-earth borate BiSr(3)(YO)(3)(BO(3))(4) are reported. BiSr(3)(YO)(3)(BO(3))(4) belongs to gaudefroyite type of structure and crystallizes in the polar hexagonal space group P6(3) (no. 173) with a = 10.6975(16) Å and c = 6.7222(12) Å. In the structure, the YO(7) polyhedra share edges to form an one-dimensional chain along the [001] direction. These chains are interconnected by the BO(3) group to construct a three-dimensional framework, leaving two kinds of channels for Bi atoms and Sr atoms together with BO(3) groups, respectively. On the basis of the powder second-harmonic generation (SHG) measurement, BiSr(3)(YO)(3)(BO(3))(4) belongs to the phase-matchable class with a SHG response of about 3 × KDP.

BIM-Sim: Interactive Simulation of Broadband Imaging Using Mie Theory

NASA Astrophysics Data System (ADS)

Berisha, Sebastian; van Dijk, Thomas; Bhargava, Rohit; Carney, P. Scott; Mayerich, David

2017-02-01

Understanding the structure of a scattered electromagnetic (EM) field is critical to improving the imaging process. Mechanisms such as diffraction, scattering, and interference affect an image, limiting the resolution and potentially introducing artifacts. Simulation and visualization of scattered fields thus plays an important role in imaging science. However, the calculation of scattered fields is extremely time-consuming on desktop systems and computationally challenging on task-parallel systems such as supercomputers and cluster systems. In addition, EM fields are high-dimensional, making them difficult to visualize. In this paper, we present a framework for interactively computing and visualizing EM fields scattered by micro and nano-particles. Our software uses graphics hardware for evaluating the field both inside and outside of these particles. We then use Monte-Carlo sampling to reconstruct and visualize the three-dimensional structure of the field, spectral profiles at individual points, the structure of the field at the surface of the particle, and the resulting image produced by an optical system.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

Low-cost three-dimensional millimeter-wave holographic imaging system based on a frequency-scanning antenna.

PubMed

Amin Nili, Vahid; Mansouri, Ehsan; Kavehvash, Zahra; Fakharzadeh, Mohammad; Shabany, Mahdi; Khavasi, Amin

2018-01-01

In this paper, a closed-form two-dimensional reconstruction technique for hybrid frequency and mechanical scanning millimeter-wave (MMW) imaging systems is proposed. Although being commercially implemented in many imaging systems as a low-cost real-time solution, the results of frequency scanning systems have been reconstructed numerically or have been reported as the captured raw data with no clear details. Furthermore, this paper proposes a new framework to utilize the captured data of different frequencies for three-dimensional (3D) reconstruction based on novel proposed closed-form relations. The hybrid frequency and mechanical scanning structure, together with the proposed reconstruction method, yields a low-cost MMW imaging system with a satisfying performance. The extracted reconstruction formulations are validated through numerical simulations, which show comparable image quality with conventional MMW imaging systems, i.e., switched-array (SA) and phased-array (PA) structures. Extensive simulations are also performed in the presence of additive noise, demonstrating the acceptable robustness of the system against system noise compared to SA and comparable performance with PA. Finally, 3D reconstruction of the simulated data shows a depth resolution of better than 10 cm with minimum degradation of lateral resolution in the 10 GHz frequency bandwidth.

Hierarchical Metal-Organic Framework-Assembled Membrane Filter for Efficient Removal of Particulate Matter.

PubMed

Koo, Won-Tae; Jang, Ji-Soo; Qiao, Shaopeng; Hwang, Wontae; Jha, Gaurav; Penner, Reginald M; Kim, Il-Doo

2018-06-13

Here, we propose heterogeneous nucleation-assisted hierarchical growth of metal-organic frameworks (MOFs) for efficient particulate matter (PM) removal. The assembly of two-dimensional (2D) Zn-based zeolite imidazole frameworks (2D-ZIF-L) in deionized water over a period of time produced hierarchical ZIF-L (H-ZIF-L) on hydrophilic substrates. During the assembly, the second nucleation and growth of ZIF-L occurred on the surface of the first ZIF-L, leading to the formation of flowerlike H-ZIF-L on the substrate. The flowerlike H-ZIF-L was easily synthesized on various substrates, namely, glass, polyurethane three-dimensional foam, nylon microfibers, and nonwoven fabrics. We demonstrated H-ZIF-L-assembled polypropylene microfibers as a washable membrane filter with highly efficient PM removal property (92.5 ± 0.8% for PM 2.5 and 99.5 ± 0.2% for PM 10 ), low pressure drop (10.5 Pa at 25 L min -1 ), long-term stability, and superior recyclability. These outstanding particle filtering properties are mainly attributed to the unique structure of the 2D-shaped H-ZIF-L, which is tightly anchored on individual fibers comprising the membrane.

Reconstructing spatial organizations of chromosomes through manifold learning

PubMed Central

Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

2018-01-01

Abstract Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data. PMID:29408992

Reconstructing spatial organizations of chromosomes through manifold learning.

PubMed

Zhu, Guangxiang; Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

2018-05-04

Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data.

Three-dimensional interaction and movements of various dislocations in anisotropic bicrystals with semicoherent interfaces

NASA Astrophysics Data System (ADS)

Vattré, A.; Pan, E.

2018-07-01

Lattice dislocation interactions with semicoherent interfaces are investigated by means of anisotropic field solutions in metallic homo- and hetero-structures. The present framework is based on the mathematically elegant and computationally powerful Stroh formalism, combining further with the Fourier integral and series transforms, which cover different shapes and dimensions of various extrinsic and intrinsic dislocations. Two-dimensional equi-spaced arrays of straight lattice dislocations and finite arrangements of piled-up dislocations as well as any polygonal and elliptical dislocation loops in three dimensions are considered using a superposition scheme. Self, image and Peach-Koehler forces are derived to compute the equilibrium dislocation positions in pile-ups, including the internal structures and energetics of the interfacial dislocation networks. For illustration, the effects due to the elastic and misfit mismatches are discussed in the pure misfit Au/Cu and heterophase Cu/Nb systems, while discrepancies resulting from the approximation of isotropic elasticity are clearly exhibited. These numerical examples not only feature and enhance the existing works in anisotropic bimaterials, but also promote a novel opportunity of analyzing the equilibrium shapes of planar glide dislocation loops at nanoscale.

Resolvent analysis of shear flows using One-Way Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Rigas, Georgios; Schmidt, Oliver; Towne, Aaron; Colonius, Tim

2017-11-01

For three-dimensional flows, questions of stability, receptivity, secondary flows, and coherent structures require the solution of large partial-derivative eigenvalue problems. Reduced-order approximations are thus required for engineering prediction since these problems are often computationally intractable or prohibitively expensive. For spatially slowly evolving flows, such as jets and boundary layers, the One-Way Navier-Stokes (OWNS) equations permit a fast spatial marching procedure that results in a huge reduction in computational cost. Here, an adjoint-based optimization framework is proposed and demonstrated for calculating optimal boundary conditions and optimal volumetric forcing. The corresponding optimal response modes are validated against modes obtained in terms of global resolvent analysis. For laminar base flows, the optimal modes reveal modal and non-modal transition mechanisms. For turbulent base flows, they predict the evolution of coherent structures in a statistical sense. Results from the application of the method to three-dimensional laminar wall-bounded flows and turbulent jets will be presented. This research was supported by the Office of Naval Research (N00014-16-1-2445) and Boeing Company (CT-BA-GTA-1).

Scaling up Three-Dimensional Science Learning through Teacher-Led Study Groups across a State

ERIC Educational Resources Information Center

Reiser, Brian J.; Michaels, Sarah; Moon, Jean; Bell, Tara; Dyer, Elizabeth; Edwards, Kelsey D.; McGill, Tara A. W.; Novak, Michael; Park, Aimee

2017-01-01

The vision for science teaching in the Framework for K-12 Science Education and the Next Generation Science Standards requires a radical departure from traditional science teaching. Science literacy is defined as three-dimensional (3D), in which students engage in science and engineering practices to develop and apply science disciplinary ideas…

A Score of the Ability of a Three-Dimensional Protein Model to Retrieve Its Own Sequence as a Quantitative Measure of Its Quality and Appropriateness

PubMed Central

Martínez-Castilla, León P.; Rodríguez-Sotres, Rogelio

2010-01-01

Background Despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three-dimensional fold, and in turn determines its function remains an elusive question. Alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. However, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. Folding pattern diversity seems to be much narrower than sequence diversity, and the amino acid sequences of natural proteins have evolved under a selective pressure comprising structural and functional requirements acting in parallel. Principal Findings The approach described in this work begins by generating a large number of amino acid sequences using ROSETTA [Dantas G et al. (2003) J Mol Biol 332:449–460], a program with notable robustness in the assignment of amino acids to a known three-dimensional structure. The resulting sequence-sets showed no conservation of amino acids at active sites, or protein-protein interfaces. Hidden Markov models built from the resulting sequence sets were used to search sequence databases. Surprisingly, the models retrieved from the database sequences belonged to proteins with the same or a very similar function. Given an appropriate cutoff, the rate of false positives was zero. According to our results, this protocol, here referred to as Rd.HMM, detects fine structural details on the folding patterns, that seem to be tightly linked to the fitness of a structural framework for a specific biological function. Conclusion Because the sequence of the native protein used to create the Rd.HMM model was always amongst the top hits, the procedure is a reliable tool to score, very accurately, the quality and appropriateness of computer-modeled 3D-structures, without the need for spectroscopy data. However, Rd.HMM is very sensitive to the conformational features of the models' backbone. PMID:20830209

Porphyrin framework solids. Synthesis and structure of hybrid coordination polymers of tetra(carboxyphenyl)porphyrins and lanthanide-bridging ions.

PubMed

Muniappan, Sankar; Lipstman, Sophia; George, Sumod; Goldberg, Israel

2007-07-09

New types of porphyrin-based framework solids were constructed by reacting meso-tetra(3-carboxyphenyl)porphyrin and meso-tetra(4-carboxyphenyl)metalloporphyrins with common salts of lanthanide metal ions. The large size, high coordination numbers and strong affinity for oxo ligands of the latter, combined with favorable hydrothermal reaction conditions, allowed the formation of open three-dimensional single-framework architectures by coordination polymerization, in which the tetradentate porphyrin units are intercoordinated by multinuclear assemblies of the bridging metal ions. The latter serve as construction pillars of the supramolecular arrays, affording stable structures. Several modes of coordination polymerization were revealed by single-crystal X-ray diffraction. They differ by the spatial functionality of the porphyrin building blocks, the coordination patterns of the lanthanide-carboxylate assemblies, and the topology of the resulting frameworks. The seven new reported structures exhibit periodically spaced 0.4-0.6 nm wide channel voids that perforate the respective crystalline polymeric architectures and are accessible to solvent components. Materials based on the m-carboxyphenyl derivative reveal smaller channels than those based on the p-carboxyphenyl analogues. An additional complex of the former with a smaller third-row transition metal (Co) is characterized by coordination connectivity in two dimensions only. Thermal and powder-diffraction analyses confirm the stability of the lanthanide-TmCPP (TmCPP=tetra(m-carboxyphenyl)porphyrin) frameworks.

An application framework of three-dimensional reconstruction and measurement for endodontic research.

PubMed

Gao, Yuan; Peters, Ove A; Wu, Hongkun; Zhou, Xuedong

2009-02-01

The purpose of this study was to customize an application framework by using the MeVisLab image processing and visualization platform for three-dimensional reconstruction and assessment of tooth and root canal morphology. One maxillary first molar was scanned before and after preparation with ProTaper by using micro-computed tomography. With a customized application framework based on MeVisLab, internal and external anatomy was reconstructed. Furthermore, the dimensions of root canal and radicular dentin were quantified, and effects of canal preparation were assessed. Finally, a virtual preparation with risk analysis was performed to simulate the removal of a broken instrument. This application framework provided an economical platform and met current requirements of endodontic research. The broad-based use of high-quality free software and the resulting exchange of experience might help to improve the quality of endodontic research with micro-computed tomography.

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

Zhang, Shiyan; Mei, Dajiang, E-mail: meidajiang718@pku.edu.cn; Du, Xin

Ag{sub 1−x}Ga{sub 1−x}Si{sub x}Se{sub 2} solutions with high Si doping level (x=1/2) are considered and new compound AgGaSiSe{sub 4} has been synthesized. It crystallizes in space group Aea2 and possesses very long axis of a=63.06(1)Å. The three-dimensional framework in AgGaSiSe{sub 4} is composed of AgSe{sub 3} trigonal planar units, AgSe{sub 4} tetrahedra and MSe{sub 4}(M=Si, Ga) tetrahedra. AgGaSiSe{sub 4} is a congruently melting compound with the melt temperature of 759 °C. The diffuse reflectance measurements reveal the band gap of 2.63 eV in AgGaSiSe{sub 4} and the value is 0.33 eV larger than that of Ag{sub 3}Ga{sub 3}SiSe{sub 8} (2.30more » eV). - Graphical abstract: The Ag{sub 1−x}Ga{sub 1−x}Si{sub x}Se{sub 2} with high Si doping level (x=1/2) has been studied and the new compound AgGaSiSe{sub 4} was synthesized for the first time. AgGaSiSe{sub 4} crystallizes in a new structure type in space group Aea2 and adopts a three-dimensional framework consisting of AgSe{sub 3} trigonal planar units, AgSe{sub 4} tetrahedra and MSe{sub 4} (M=Si, Ge) tetrahedra. Display Omitted - Highlights: • Study of Ag{sub 1−x}Ga{sub 1−x}Si{sub x}Se{sub 2} with high Si doping level (x=1/2). • Successful synthesis of new compound named AgGaSiSe{sub 4}. • AgGaSiSe{sub 4} crystallizes in space group Aea2 and adopts a three-dimensional framework. • The energy band gap of AgGaSiSe{sub 4} is enlarged compared with Ag{sub 3}Ga{sub 3}SiSe{sub 8}.« less

Unravelling earth flow dynamics with 3-D time series derived from UAV-SfM models

NASA Astrophysics Data System (ADS)

Clapuyt, François; Vanacker, Veerle; Schlunegger, Fritz; Van Oost, Kristof

2017-12-01

Accurately assessing geo-hazards and quantifying landslide risks in mountainous environments are gaining importance in the context of the ongoing global warming. For an in-depth understanding of slope failure mechanisms, accurate monitoring of the mass movement topography at high spatial and temporal resolutions remains essential. The choice of the acquisition framework for high-resolution topographic reconstructions will mainly result from the trade-off between the spatial resolution needed and the extent of the study area. Recent advances in the development of unmanned aerial vehicle (UAV)-based image acquisition combined with the structure-from-motion (SfM) algorithm for three-dimensional (3-D) reconstruction make the UAV-SfM framework a competitive alternative to other high-resolution topographic techniques. In this study, we aim at gaining in-depth knowledge of the Schimbrig earthflow located in the foothills of the Central Swiss Alps by monitoring ground surface displacements at very high spatial and temporal resolution using the efficiency of the UAV-SfM framework. We produced distinct topographic datasets for three acquisition dates between 2013 and 2015 in order to conduct a comprehensive 3-D analysis of the landslide. Therefore, we computed (1) the sediment budget of the hillslope, and (2) the horizontal and (3) the three-dimensional surface displacements. The multitemporal UAV-SfM based topographic reconstructions allowed us to quantify rates of sediment redistribution and surface movements. Our data show that the Schimbrig earthflow is very active, with mean annual horizontal displacement ranging between 6 and 9 m. Combination and careful interpretation of high-resolution topographic analyses reveal the internal mechanisms of the earthflow and its complex rotational structure. In addition to variation in horizontal surface movements through time, we interestingly showed that the configuration of nested rotational units changes through time. Although there are major changes in the internal structure of the earthflow in the 2013-2015 period, the sediment budget of the drainage basin is nearly in equilibrium. As a consequence, our data show that the time lag between sediment mobilization by landslides and enhanced sediment fluxes in the river network can be considerable.

MollDE: a homology modeling framework you can click with.

PubMed

Canutescu, Adrian A; Dunbrack, Roland L

2005-06-15

Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. http://dunbrack.fccc.edu/molide/molide.php rl_dunbrack@fccc.edu.

An Automatic Segmentation and Classification Framework Based on PCNN Model for Single Tooth in MicroCT Images.

PubMed

Wang, Liansheng; Li, Shusheng; Chen, Rongzhen; Liu, Sze-Yu; Chen, Jyh-Cheng

2016-01-01

Accurate segmentation and classification of different anatomical structures of teeth from medical images plays an essential role in many clinical applications. Usually, the anatomical structures of teeth are manually labelled by experienced clinical doctors, which is time consuming. However, automatic segmentation and classification is a challenging task because the anatomical structures and surroundings of the tooth in medical images are rather complex. Therefore, in this paper, we propose an effective framework which is designed to segment the tooth with a Selective Binary and Gaussian Filtering Regularized Level Set (GFRLS) method improved by fully utilizing three dimensional (3D) information, and classify the tooth by employing unsupervised learning Pulse Coupled Neural Networks (PCNN) model. In order to evaluate the proposed method, the experiments are conducted on the different datasets of mandibular molars and the experimental results show that our method can achieve better accuracy and robustness compared to other four state of the art clustering methods.

Continuum modeling of three-dimensional truss-like space structures

NASA Technical Reports Server (NTRS)

Nayfeh, A. H.; Hefzy, M. S.

1978-01-01

A mathematical and computational analysis capability has been developed for calculating the effective mechanical properties of three-dimensional periodic truss-like structures. Two models are studied in detail. The first, called the octetruss model, is a three-dimensional extension of a two-dimensional model, and the second is a cubic model. Symmetry considerations are employed as a first step to show that the specific octetruss model has four independent constants and that the cubic model has two. The actual values of these constants are determined by averaging the contributions of each rod element to the overall structure stiffness. The individual rod member contribution to the overall stiffness is obtained by a three-dimensional coordinate transformation. The analysis shows that the effective three-dimensional elastic properties of both models are relatively close to each other.

Three-dimensional printed acrylonitrile butadiene styrene framework coated with Cu-BTC metal-organic frameworks for the removal of methylene blue.

PubMed

Wang, Zongyuan; Wang, Jiajun; Li, Minyue; Sun, Kaihang; Liu, Chang-jun

2014-08-04

Three-dimensional (3D) printing was applied for the fabrication of acrylonitrile butadiene styrene (ABS) framework. Functionalization of the ABS framework was then performed by coating of porous Cu-BTC (BTC = benzene tricarboxylic acid) metal-organic frameworks on it using a step-by-step in-situ growth. The size of the Cu-BTC particles on ABS was ranged from 200 nm to 900 nm. The Cu-BTC/ABS framework can take up most of the space of the tubular reactor that makes the adsorption effective with no need of stirring. Methylene blue (MB) can be readily removed from aqueous solution by this Cu-BTC/ABS framework. The MB removal efficiency for solutions with concentrations of 10 and 5 mg/L was 93.3% and 98.3%, respectively, within 10 min. After MB adsorption, the Cu-BTC/ABS composite can easily be recovered without the need for centrifugation or filtration and the composite is reusable. In addition the ABS framework can be recovered for subsequent reuse. A significant advantage of 3D-printed frameworks is that different frameworks can be easily fabricated to meet the needs of different applications. This is a promising strategy to synthesize new frameworks using MOFs and polymers to develop materials for applications beyond adsorption.

Towards a voxel-based geographic automata for the simulation of geospatial processes

NASA Astrophysics Data System (ADS)

Jjumba, Anthony; Dragićević, Suzana

2016-07-01

Many geographic processes evolve in a three dimensional space and time continuum. However, when they are represented with the aid of geographic information systems (GIS) or geosimulation models they are modelled in a framework of two-dimensional space with an added temporal component. The objective of this study is to propose the design and implementation of voxel-based automata as a methodological approach for representing spatial processes evolving in the four-dimensional (4D) space-time domain. Similar to geographic automata models which are developed to capture and forecast geospatial processes that change in a two-dimensional spatial framework using cells (raster geospatial data), voxel automata rely on the automata theory and use three-dimensional volumetric units (voxels). Transition rules have been developed to represent various spatial processes which range from the movement of an object in 3D to the diffusion of airborne particles and landslide simulation. In addition, the proposed 4D models demonstrate that complex processes can be readily reproduced from simple transition functions without complex methodological approaches. The voxel-based automata approach provides a unique basis to model geospatial processes in 4D for the purpose of improving representation, analysis and understanding their spatiotemporal dynamics. This study contributes to the advancement of the concepts and framework of 4D GIS.

The Effect of Three-Dimensional Simulations on the Understanding of Chemical Structures and Their Properties

ERIC Educational Resources Information Center

Urhahne, Detlef; Nick, Sabine; Schanze, Sascha

2009-01-01

In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer's generative theory of multimedia learning. Simulations might lead to a…

Metal-chelate dye-controlled organization of Cd32S14(SPh)40(4-) nanoclusters into three-dimensional molecular and covalent open architecture.

PubMed

Zheng, Nanfeng; Lu, Haiwei; Bu, Xianhui; Feng, Pingyun

2006-04-12

Chalcogenide II-VI nanoclusters are usually prepared as isolated clusters and have defied numerous efforts to join them into covalent open-framework architecture with conventional templating methods such as protonated amines or inorganic cations commonly used to direct the formation of porous frameworks. Herein, we report the first templated synthesis of II-VI covalent superlattices from large II-VI tetrahedral clusters (i.e., [Cd32S14(SPh)38]2-). Our method takes advantage of low charge density of metal-chelate dyes that is a unique match with three-dimensional II-VI semiconductor frameworks in charge density, surface hydrophilicity-hydrophobicity, and spatial organization. In addition, metal-chelate dyes also serve to tune the optical properties of resulting dye semiconductor composite materials.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

A one-dimensional zinc(II) coordination polymer with a three-dimensional supramolecular architecture incorporating 1-[(1H-benzimidazol-2-yl)methyl]-1H-tetrazole and adipate.

PubMed

Liu, Chun Li; Huang, Qiu Ying; Meng, Xiang Ru

2016-12-01

The synthesis of coordination polymers or metal-organic frameworks (MOFs) has attracted considerable interest owing to the interesting structures and potential applications of these compounds. It is still a challenge to predict the exact structures and compositions of the final products. A new one-dimensional coordination polymer, catena-poly[[[bis{1-[(1H-benzimidazol-2-yl)methyl]-1H-tetrazole-κN 3 }zinc(II)]-μ-hexane-1,6-dicarboxylato-κ 4 O 1 ,O 1' :O 6 ,O 6' ] monohydrate], {[Zn(C 6 H 8 O 4 )(C 9 H 8 N 6 ) 2 ]·H 2 O} n , has been synthesized by the reaction of Zn(Ac) 2 (Ac is acetate) with 1-[(1H-benzimidazol-2-yl)methyl]-1H-tetrazole (bimt) and adipic acid (H 2 adi) at room temperature. In the polymer, each Zn II ion exhibits an irregular octahedral ZnN 2 O 4 coordination geometry and is coordinated by two N atoms from two symmetry-related bimt ligands and four O atoms from two symmetry-related dianionic adipate ligands. Zn II ions are connected by adipate ligands into a one-dimensional chain which runs parallel to the c axis. The bimt ligands coordinate to the Zn II ions in a monodentate mode on both sides of the main chain. In the crystal, the one-dimensional chains are further connected through N-H...O hydrogen bonds, leading to a three-dimensional supramolecular architecture. In addition, the title polymer exhibits fluorescence, with emissions at 334 and 350 nm in the solid state at room temperature.

Topological identification of the first uninodal 8-connected lsz MOF built from 2,2'-difluorobiphenyl-4,4'-dicarboxylate pillars and cadmium(II)-triazolate layers.

PubMed

Zhang, Yuchi; Wu, Yuanhua; He, Xin; Ma, Junhan; Shen, Xuan; Zhu, Dunru

2018-03-01

Using polynuclear metal clusters as nodes, many high-symmetry high-connectivity nets, like 8-connnected bcu and 12-connected fcu, have been attained in metal-organic frameworks (MOFs). However, construction of low-symmetry high-connected MOFs with a novel topology still remains a big challenge. For example, a uninodal 8-connected lsz network, observed in inorganic ZrSiO 4 , has not been topologically identified in MOFs. Using 2,2'-difluorobiphenyl-4,4'-dicarboxylic acid (H 2 L) as a new linker and 1,2,4-triazole (Htrz) as a coligand, a novel three-dimensional Cd II -MOF, namely poly[tetrakis(μ 4 -2,2'-difluorobiphenyl-4,4'-dicarboxylato-κ 5 O 1 ,O 1' :O 1' :O 4 :O 4' )tetrakis(N,N-dimethylformamide-κO)tetrakis(μ 3 -1,2,4-triazolato-κ 3 N 1 :N 2 :N 4 )hexacadmium(II)], [Cd 6 (C 14 H 6 F 2 O 4 ) 4 (C 2 H 2 N 3 ) 4 (C 3 H 7 NO) 4 ] n , (I), has been prepared. Single-crystal structure analysis indicates that six different Cd II ions co-exist in (I) and each Cd II ion displays a distorted [CdO 4 N 2 ] octahedral geometry with four equatorial O atoms and two axial N atoms. Three Cd II ions are connected by four carboxylate groups and four trz - ligands to form a linear trinuclear [Cd 3 (COO) 4 (trz) 4 ] cluster, as do the other three Cd II ions. Two Cd 3 clusters are linked by trz - ligands in a μ 1,2,4 -bridging mode to produce a two-dimensional Cd II -triazolate layer with (6,3) topology in the ab plane. These two-dimensional layers are further pillared by the L 2- ligands along the c axis to generate a complicated three-dimensional framework. Topologically, regarding the Cd 3 cluster as an 8-connected node, the whole architecture of (I) is a uninodal 8-connected lsz framework with the Schläfli symbol (4 22 ·6 6 ). Complex (I) was further characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction, thermogravimetric analysis and a photoluminescence study. MOF (I) has a high thermal and water stability.

From Two- to Three-Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations.

PubMed

Getmanskii, Iliya V; Minyaev, Ruslan M; Steglenko, Dmitrii V; Koval, Vitaliy V; Zaitsev, Stanislav A; Minkin, Vladimir I

2017-08-14

With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two- and three-dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two- and three-layer systems resulted in the construction of a three-dimensional supertetrahedral borane crystal structure. The two-dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three-dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm -3 ) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Harnessing Sparse and Low-Dimensional Structures for Robust Clustering of Imagery Data

ERIC Educational Resources Information Center

Rao, Shankar Ramamohan

2009-01-01

We propose a robust framework for clustering data. In practice, data obtained from real measurement devices can be incomplete, corrupted by gross errors, or not correspond to any assumed model. We show that, by properly harnessing the intrinsic low-dimensional structure of the data, these kinds of practical problems can be dealt with in a uniform…

Assembly and property research on seven 0D–3D complexes derived from imidazole dicarboxylate and 1,2-bi(pyridin-4-yl)ethene

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

Mu, Bao; Li, Qian; Lv, Lei

2015-03-15

The hydrothermal reaction of transition metals, 1H-imidazole-4,5-dicarboxylic acid (H{sub 3}ImDC) and 1,2-bi(pyridin-4-yl)ethene (bpe) affords a series of new complexes, namely, [Mn(HImDC)(bpe)(H{sub 2}O)] (1), [M(H{sub 2}ImDC){sub 2}(H{sub 2}O){sub 2}]·(bpe) (M=Fe(2), Co(3), Zn(4), Cd(6)), [Zn{sub 3}(ImDC){sub 2}(bpe)(H{sub 2}O)]·3H{sub 2}O (5) and [Cd(H{sub 2}ImDC)(bpe)] (7), which are characterized by elemental analyses, IR, TG, XRPD and single crystal X-ray diffraction. Complex 1 exhibits a one dimensional (1D) zigzag chain with two types of irregular rings, and the 1D chains are linked to form a three dimensional (3D) supramolecular framework by the hydrogen bonding interactions (O–H∙∙∙O and O–H∙∙∙N). Complexes 2–4 and 6 are isomorphous, andmore » they display the mononuclear structures. In these complexes, the O–H∙∙∙O and O–H∙∙∙N hydrogen bonds play an important role in sustaining the whole 3D supramolecular frameworks. Complex 5 shows a (3,3)-connected 3D framework with (10{sup 3}) topology, and the lattice water molecules as guest molecules exist in the 3D framework. Complex 7 is a wave-like two dimensional (2D) structure, in which the adjacent 1D chains point at the opposite directions. Moreover, the fluorescent properties of complexes 1–7 and the magnetic property of 1 have been investigated. The water vapor adsorption for complex 5 has been researched at 298 K. - Graphical abstract: Seven new complexes based on different structural characteristics have been hydrothermally synthesized by the mixed ligands. The fluorescent properties, the magnetic property and the water vapor adsorption have been investigated. - Highlights: • The semi-rigid ligand with C=C bonds and imidazole dicarboxylates with some advantages have been used. • A series of new complexes with different structural characteristics have been discussed in detail. • The fluorescent properties, the magnetic property and the water vapor adsorption have been investigated.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

PubMed Central

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-01-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design. PMID:27109208

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

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

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

DOE PAGES

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; ...

2016-04-25

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

A 3D metal-organic framework with a pcu net constructed from lead(II) and thiophene-2, 5-dicarboxylic acid: Synthesis, structure and ferroelectric property

NASA Astrophysics Data System (ADS)

Lin, Jian-Di; Rong, Cheng; Lv, Ri-Xin; Wang, Zu-Jian; Long, Xi-Fa; Guo, Guo-Cong; Pan, Chun-Yang

2018-01-01

Self-assembly reaction of Pb(NO3)2 with thiophene-2, 5-dicarboxylic acid (H2TDC) led to an acentric three-dimensional (3D) metal-organic framework under solvothermal conditions, namely, Pb(TDC) (1). The 3D framework of 1 is a pillared-layer structure with the I2O1 type which is composed of a 2D inorganic Pb-O-Pb substructural layer and two independent μ6-TDC2- anions pillars. This 3D framework shows a six-connected pcu topological net according to the topological analysis. Compound 1 crystallizes in an acentric space group and displays potential ferroelectric property which could be due to the swing of the thiophene rings. The remnant polarization (Pr), coercive field (Ec) and saturation spontaneous polarization (Ps) of 1 are ca. 0.034 μC cm-2, 15.7 kV cm-1 and 0.0997 μC cm-2, respectively. Among the H2TDC-based MOFs, the present compound is the first example which shows ferroelectric property. In addition, 1 also exhibits photoluminescent property which can be attributed to ligand-to-metal charge transfer.

Reconstruction of three-dimensional ultrasound images based on cyclic Savitzky-Golay filters

NASA Astrophysics Data System (ADS)

Toonkum, Pollakrit; Suwanwela, Nijasri C.; Chinrungrueng, Chedsada

2011-01-01

We present a new algorithm for reconstructing a three-dimensional (3-D) ultrasound image from a series of two-dimensional B-scan ultrasound slices acquired in the mechanical linear scanning framework. Unlike most existing 3-D ultrasound reconstruction algorithms, which have been developed and evaluated in the freehand scanning framework, the new algorithm has been designed to capitalize the regularity pattern of the mechanical linear scanning, where all the B-scan slices are precisely parallel and evenly spaced. The new reconstruction algorithm, referred to as the cyclic Savitzky-Golay (CSG) reconstruction filter, is an improvement on the original Savitzky-Golay filter in two respects: First, it is extended to accept a 3-D array of data as the filter input instead of a one-dimensional data sequence. Second, it incorporates the cyclic indicator function in its least-squares objective function so that the CSG algorithm can simultaneously perform both smoothing and interpolating tasks. The performance of the CSG reconstruction filter compared to that of most existing reconstruction algorithms in generating a 3-D synthetic test image and a clinical 3-D carotid artery bifurcation in the mechanical linear scanning framework are also reported.

Private algebras in quantum information and infinite-dimensional complementarity

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

Crann, Jason, E-mail: jason-crann@carleton.ca; Laboratoire de Mathématiques Paul Painlevé–UMR CNRS 8524, UFR de Mathématiques, Université Lille 1–Sciences et Technologies, 59655 Villeneuve d’Ascq Cédex; Kribs, David W., E-mail: dkribs@uoguelph.ca

We introduce a generalized framework for private quantum codes using von Neumann algebras and the structure of commutants. This leads naturally to a more general notion of complementary channel, which we use to establish a generalized complementarity theorem between private and correctable subalgebras that applies to both the finite and infinite-dimensional settings. Linear bosonic channels are considered and specific examples of Gaussian quantum channels are given to illustrate the new framework together with the complementarity theorem.

Uncertainty quantification in volumetric Particle Image Velocimetry

NASA Astrophysics Data System (ADS)

Bhattacharya, Sayantan; Charonko, John; Vlachos, Pavlos

2016-11-01

Particle Image Velocimetry (PIV) uncertainty quantification is challenging due to coupled sources of elemental uncertainty and complex data reduction procedures in the measurement chain. Recent developments in this field have led to uncertainty estimation methods for planar PIV. However, no framework exists for three-dimensional volumetric PIV. In volumetric PIV the measurement uncertainty is a function of reconstructed three-dimensional particle location that in turn is very sensitive to the accuracy of the calibration mapping function. Furthermore, the iterative correction to the camera mapping function using triangulated particle locations in space (volumetric self-calibration) has its own associated uncertainty due to image noise and ghost particle reconstructions. Here we first quantify the uncertainty in the triangulated particle position which is a function of particle detection and mapping function uncertainty. The location uncertainty is then combined with the three-dimensional cross-correlation uncertainty that is estimated as an extension of the 2D PIV uncertainty framework. Finally the overall measurement uncertainty is quantified using an uncertainty propagation equation. The framework is tested with both simulated and experimental cases. For the simulated cases the variation of estimated uncertainty with the elemental volumetric PIV error sources are also evaluated. The results show reasonable prediction of standard uncertainty with good coverage.

Finite dimensional approximation of a class of constrained nonlinear optimal control problems

NASA Technical Reports Server (NTRS)

Gunzburger, Max D.; Hou, L. S.

1994-01-01

An abstract framework for the analysis and approximation of a class of nonlinear optimal control and optimization problems is constructed. Nonlinearities occur in both the objective functional and in the constraints. The framework includes an abstract nonlinear optimization problem posed on infinite dimensional spaces, and approximate problem posed on finite dimensional spaces, together with a number of hypotheses concerning the two problems. The framework is used to show that optimal solutions exist, to show that Lagrange multipliers may be used to enforce the constraints, to derive an optimality system from which optimal states and controls may be deduced, and to derive existence results and error estimates for solutions of the approximate problem. The abstract framework and the results derived from that framework are then applied to three concrete control or optimization problems and their approximation by finite element methods. The first involves the von Karman plate equations of nonlinear elasticity, the second, the Ginzburg-Landau equations of superconductivity, and the third, the Navier-Stokes equations for incompressible, viscous flows.

Design and synthesis of an exceptionally stable and highly porous metal-organic framework

NASA Astrophysics Data System (ADS)

Li, Hailian; Eddaoudi, Mohamed; O'Keeffe, M.; Yaghi, O. M.

1999-11-01

Open metal-organic frameworks are widely regarded as promising materials for applications in catalysis, separation, gas storage and molecular recognition. Compared to conventionally used microporous inorganic materials such as zeolites, these organic structures have the potential for more flexible rational design, through control of the architecture and functionalization of the pores. So far, the inability of these open frameworks to support permanent porosity and to avoid collapsing in the absence of guest molecules, such as solvents, has hindered further progress in the field. Here we report the synthesis of a metal-organic framework which remains crystalline, as evidenced by X-ray single-crystal analyses, and stable when fully desolvated and when heated up to 300°C. This synthesis is achieved by borrowing ideas from metal carboxylate cluster chemistry, where an organic dicarboxylate linker is used in a reaction that gives supertetrahedron clusters when capped with monocarboxylates. The rigid and divergent character of the added linker allows the articulation of the clusters into a three-dimensional framework resulting in a structure with higher apparent surface area and pore volume than most porous crystalline zeolites. This simple and potentially universal design strategy is currently being pursued in the synthesis of new phases and composites, and for gas-storage applications.

Softly-confined water cluster between freestanding graphene sheets

NASA Astrophysics Data System (ADS)

Agustian, Rifan; Akaishi, Akira; Nakamura, Jun

2018-01-01

Confined water could adopt new forms not seen in the open air, such as a two-dimensional (2D) square ice trapped between two graphene sheets [Algara-Siller et al., Nature 519, 443-445 (2015)]. In this study, in order to investigate how the flexibility of graphene affects the confined structure of water molecules, we employed classical molecular dynamics simulations with Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential to produce a soft-confining property of graphene. We discovered various solid-like structures of water molecules ranging from two-dimensional to three-dimensional structure encapsulated between two freestanding graphene sheets even at room temperature (300K). A small amount of water encapsulation leads to a layered two-dimensional form with triangular structure. On the other hand, large amounts of water molecules take a three-dimensional flying-saucer-like form with the square ice intra-layer structure. There is also a metastable state where both two-dimensional and three-dimensional structures coexist.

Conjugated Microporous Polymers for Heterogeneous Catalysis.

PubMed

Zhou, Yun-Bing; Zhan, Zhuang-Ping

2018-01-04

Conjugated microporous polymers (CMPs) are a class of crosslinked polymers that combine permanent micropores with π-conjugated skeletons and possess three-dimensional (3D) networks. Compared with conventional materials such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), CMPs usually have superior chemical and thermal stability. CMPs have made significant progress in heterogeneous catalysis in the past seven years. With a bottom-up strategy, catalytic moieties can be directly introduced into in the framework to produce heterogeneous CMP catalysts. Higher activity, stability, and selectivity can be obtained with heterogeneous CMP catalysts in comparison with their homogeneous analogs. In addition, CMP catalysts can be easily isolated and recycled. In this review, we focus on CMPs as an intriguing platform for developing various highly efficient and recyclable heterogeneous catalysts in organic reactions. The design, synthesis, and structure of these CMP catalysts are also discussed in this focus review. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experiments on an unsteady, three-dimensional separation

NASA Technical Reports Server (NTRS)

Henk, R. W.; Reynolds, W. C.; Reed, H. L.

1992-01-01

Unsteady, three-dimensional flow separation occurs in a variety of technical situations including turbomachinery and low-speed aircraft. An experimental program at Stanford in unsteady, three-dimensional, pressure-driven laminar separation has investigated the structure and time-scaling of these flows; of particular interest is the development, washout, and control of flow separation. Results reveal that a two-dimensional, laminar boundary layer passes through several stages on its way to a quasi-steady three-dimensional separation. The quasi-steady state of the separation embodies a complex, unsteady, vortical structure.

A Recyclable Metal-Organic Framework as a Dual Detector and Adsorbent for Ammonia.

PubMed

Gładysiak, Andrzej; Nguyen, Tu N; Navarro, Jorge A R; Rosseinsky, Matthew J; Stylianou, Kyriakos C

2017-10-04

Recyclable materials for simultaneous detection and uptake of ammonia (NH 3 ) are of great interest due to the hazardous nature of NH 3 . The structural versatility and porous nature of metal-organic frameworks (MOFs) make them ideal candidates for NH 3 capture. Herein, the synthesis of a water-stable and porous 3-dimensional Cu II -based MOF (SION-10) displaying a ship-in-a-bottle structure is reported; the pores of the host SION-10 framework accommodate mononuclear Cu II -complexes. SION-10 spontaneously uptakes NH 3 as a result of two concurrent mechanisms: chemisorption due to the presence of active Cu II sites and physisorption (bulk permanent porosity). The color of the material changes from green to blue upon NH 3 capture, with the shifts of the UV/Vis absorption bands clearly seen at NH 3 concentrations as low as 300 ppm. SION-10 can be recovered upon immersion of SION-10⊃NH 3 in water and can be further reused for NH 3 capture for at least three cycles. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemically Active, Porous 3D-Printed Thermoplastic Composites.

PubMed

Evans, Kent A; Kennedy, Zachary C; Arey, Bruce W; Christ, Josef F; Schaef, Herbert T; Nune, Satish K; Erikson, Rebecca L

2018-05-02

Metal-organic frameworks (MOFs) exhibit exceptional properties and are widely investigated because of their structural and functional versatility relevant to catalysis, separations, and sensing applications. However, their commercial or large-scale application is often limited by their powder forms which make integration into devices challenging. Here, we report the production of MOF-thermoplastic polymer composites in well-defined and customizable forms and with complex internal structural features accessed via a standard three-dimensional (3D) printer. MOFs (zeolitic imidazolate framework; ZIF-8) were incorporated homogeneously into both poly(lactic acid) (PLA) and thermoplastic polyurethane (TPU) matrices at high loadings (up to 50% by mass), extruded into filaments, and utilized for on-demand access to 3D structures by fused deposition modeling. Printed, rigid PLA/MOF composites display a large surface area (SA avg = 531 m 2 g -1 ) and hierarchical pore features, whereas flexible TPU/MOF composites achieve a high surface area (SA avg = 706 m 2 g -1 ) by employing a simple method developed to expose obstructed micropores postprinting. Critically, embedded particles in the plastic matrices retain their ability to participate in chemical interactions characteristic of the parent framework. The fabrication strategies were extended to other MOFs and illustrate the potential of 3D printing to create unique porous and high surface area chemically active structures.

A series of three-dimensional lanthanide coordination polymers with rutile and unprecedented rutile-related topologies.

PubMed

Qin, Chao; Wang, Xin-Long; Wang, En-Bo; Su, Zhong-Min

2005-10-03

The complexes of formulas Ln(pydc)(Hpydc) (Ln = Sm (1), Eu (2), Gd (3); H2pydc = pyridine-2,5-dicarboxylic acid) and Ln(pydc)(bc)(H2O) (Ln = Sm (4), Gd (5); Hbc = benzenecarboxylic acid) have been synthesized under hydrothermal conditions and characterized by elemental analysis, IR, TG analysis, and single-crystal X-ray diffraction. Compounds 1-3 are isomorphous and crystallize in the orthorhombic system, space group Pbcn. Their final three-dimensional racemic frameworks can be considered as being constructed by helix-linked scalelike sheets. Compounds 4 and 5 are isostructural and crystallize in the monoclinic system, space group P2(1)/c. pydc ligands bridge dinuclear lanthanide centers to form the three-dimensional frameworks featuring hexagonal channels along the a-axis that are occupied by one-end-coordinated bc ligands. From the topological point of view, the five three-dimensional nets are binodal with six- and three-connected nodes, the former of which exhibit a rutile-related (4.6(2))(2)(4(2).6(9).8(4)) topology that is unprecedented within coordination frames, and the latter two species display a distorted rutile (4.6(2))(2)(4(2).6(10).8(3)) topology. Furthermore, the luminescent properties of 2 were studied.

Corporate practices and health: a framework and mechanisms.

PubMed

Madureira Lima, Joana; Galea, Sandro

2018-02-15

The Global Burden of Disease estimates that approximately a third of deaths worldwide are attributable to behavioural risk factors that, at their core, have the consumption of unhealthful products and exposures produced by profit driven commercial entities. We use Steven Lukes' three-dimensional view of power to guide the study of the practices deployed by commercial interests to foster the consumption of these commodities. Additionally, we propose a framework to systematically study corporations and other commercial interests as a distal, structural, societal factor that causes disease and injury. Our framework offers a systematic approach to mapping corporate activity, allowing us to anticipate and prevent actions that may have a deleterious effect on population health. Our framework may be used by, and can have utility for, public health practitioners, researchers, students, activists and other members of civil society, policy makers and public servants in charge of policy implementation. It can also be useful to corporations who are interested in identifying key actions they can take towards improving population health.

Sn Nanoparticles Encapsulated in 3D Nanoporous Carbon Derived from a Metal–Organic Framework for Anode Material in Lithium-Ion Batteries

DOE PAGES

Guo, Yuanyuan; Zeng, Xiaoqiao; Zhang, Yu; ...

2017-05-04

Three-dimensional nanoporous carbon frameworks encapsulated Sn nanoparticles (Sn@3D-NPC) are developed by a facile method as an improved lithium ion battery anode. The Sn@3D-NPC delivers a reversible capacity of 740 mAh g –1 after 200 cycles at a current density of 200 mA g –1, corresponding to a capacity retention of 85% (against the second capacity) and high rate capability (300 mAh g –1 at 5 A g –1). Compared to the Sn nanoparticles (SnNPs), such improvements are attributed to the 3D porous and conductive framework. The whole structure can provide not only the high electrical conductivity that facilities the electronmore » transfer but also the elasticity that will suppress the volume expansion and aggregation of SnNPs during the charge and discharge process. Lastly, this work opens a new application of metal–organic frameworks in energy storage.« less

Sn Nanoparticles Encapsulated in 3D Nanoporous Carbon Derived from a Metal-Organic Framework for Anode Material in Lithium-Ion Batteries.

PubMed

Guo, Yuanyuan; Zeng, Xiaoqiao; Zhang, Yu; Dai, Zhengfei; Fan, Haosen; Huang, Ying; Zhang, Weina; Zhang, Hua; Lu, Jun; Huo, Fengwei; Yan, Qingyu

2017-05-24

Three-dimensional nanoporous carbon frameworks encapsulated Sn nanoparticles (Sn@3D-NPC) are developed by a facile method as an improved lithium ion battery anode. The Sn@3D-NPC delivers a reversible capacity of 740 mAh g -1 after 200 cycles at a current density of 200 mA g -1 , corresponding to a capacity retention of 85% (against the second capacity) and high rate capability (300 mAh g -1 at 5 A g -1 ). Compared to the Sn nanoparticles (SnNPs), such improvements are attributed to the 3D porous and conductive framework. The whole structure can provide not only the high electrical conductivity that facilities the electron transfer but also the elasticity that will suppress the volume expansion and aggregation of SnNPs during the charge and discharge process. This work opens a new application of metal-organic frameworks in energy storage.

Solvothermal syntheses and characterization of three new silver(I)/copper(I)-thioarsenates based on As{sup 2+}/As{sup 3+} ions

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

Yao, Hua-Gang, E-mail: hgyao@gdpu.edu.cn; Guangdong Cosmetics Engineering & Technology Research Center, Zhongshan 528458; Tang, Cheng-Fei

2017-02-15

Three new silver(I)/copper(I)-thioarsenates KAgAs{sup II}S{sub 2} (1), RbCu{sub 2}As{sup III}S{sub 3} (2) and RbCu{sub 4}As{sup III}S{sub 4} (3) have been solvothermally synthesized and structurally characterized. 1 exhibits a two-dimensional anionic network built up by As−As bond connecting the left- and right-handed helical [AgS{sub 2}]{sup 4−} chains, and represents the first examples of thioarsenates(II). The structure of 2 consists of two kinds of helical [Cu{sub 2}S{sub 3}]{sup 4–} chains linked by the arsenic atoms to form double layers with rubidium ions between the layers. Compound 3 is built up of infinite [Cu{sub 2}S{sub 2}]{sup 2–} chain and layered [Cu{sub 6}As{sub 2}S{submore » 6}] linked to form a three-dimensional anionic framework, [Cu{sub 4}AsS{sub 4}]{sup –}, and containing channels in which the rubidium cations reside. The optical properties of 1–3 have been investigated by UV–vis spectroscopy. - Graphical abstract: Three new silver(I)/copper(I)-thioarsenates have been solvothermally synthesized and structurally characterized. 1 represents the first examples of thioarsenates(II) while compounds 2 and 3 possess noncondensed pyramidal AsS{sub 3}{sup 3–} unit.« less

Tunable Crystallinity and Charge Transfer in Two-Dimensional G-Quadruplex Organic Frameworks.

PubMed

Wu, Yi-Lin; Bobbitt, N Scott; Logsdon, Jenna L; Powers-Riggs, Natalia E; Nelson, Jordan N; Liu, Xiaolong; Wang, Timothy C; Snurr, Randall Q; Hupp, Joseph T; Farha, Omar K; Hersam, Mark C; Wasielewski, Michael R

2018-04-03

DNA G-quadruplex structures were recently discovered to provide reliable scaffolding for two-dimensional organic frameworks due to the strong hydrogen-bonding ability of guanine. Herein, 2,7-diaryl pyrene building blocks with high HOMO energies and large optical gaps are incorporated into G-quadruplex organic frameworks. The adjustable substitution on the aryl groups provides an opportunity to elucidate the framework formation mechanism; molecular non-planarity is found to be beneficial for restricting interlayer slippage, and the framework crystallinity is highest when intermolecular interaction and non-planarity strike a fine balance. When guanine-functionalized pyrenes are co-crystallized with naphthalene diimide, charge-transfer (CT) complexes are obtained. The photophysical properties of the pyrene-only and CT frameworks are characterized by UV/Vis and steady-state and time-resolved photoluminescence spectroscopies, and by EPR spectroscopy for the CT complex frameworks. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and structure determination of new open-framework chromium carboxylate MIL-105 or Cr{sup III}(OH).{l_brace}O{sub 2}C-C{sub 6}(CH{sub 3}){sub 4}-CO{sub 2}{r_brace}.nH{sub 2}O

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

Serre, Christian; Millange, Franck; Devic, Thomas

2006-08-10

Two new three-dimensional chromium(III) dicarboxylate, MIL-105 or Cr{sup III}(OH).{l_brace}O{sub 2}C-C{sub 6}(CH{sub 3}){sub 4}-CO{sub 2}{r_brace}.nH{sub 2}O, have been obtained under hydrothermal conditions, and their structures solved using X-ray powder diffraction data. Both solids are structural analogs of the known Cr benzenedicarboxylate compound (MIL-53). Both contain trans corner-sharing CrO{sub 4}(OH){sub 2} octahedral chains connected by tetramethylterephthalate di-anions. Each chain is linked by the ligands to four other chains to form a three-dimensional framework with an array of 1D pores channels. The pores of the high temperature form of the solid, MIL-105ht, are empty. However, MIL-105ht re-hydrates at room temperature to finally givemore » MIL-105lt with pores channels filled with free water molecules (lt: low temperature form; ht: high temperature form). The thermal behaviour of the two solids has been investigated using TGA. Crystal data for MIL-105ht: monoclinic space group C2/c with a = 19.653(1) A, b = 9.984(1) A, c = 6.970(1) A, {beta} = 110.67(1){sup o} and Z = 4. Crystal data for MIL-105lt: orthorhombic space group Pnam with a = 17.892(1) A, b = 11.165(1) A, c = 6.916(1) A and Z = 4.« less

A two-dimensional layered Cd(II) coordination polymer with a three-dimensional supramolecular architecture incorporating mixed multidentate N- and O-donor ligands.

PubMed

Huang, Qiu-Ying; Su, Ming-Yang; Meng, Xiang-Ru

2015-06-01

The combination of N-heterocyclic and multicarboxylate ligands is a good choice for the construction of metal-organic frameworks. In the title coordination polymer, poly[bis{μ2-1-[(1H-benzimidazol-2-yl)methyl]-1H-tetrazole-κ(2)N(3):N(4)}(μ4-butanedioato-κ(4)O(1):O(1'):O(4):O(4'))(μ2-butanedioato-κ(2)O(1):O(4))dicadmium], [Cd(C4H4O4)(C9H8N6)]n, each Cd(II) ion exhibits an irregular octahedral CdO4N2 coordination geometry and is coordinated by four O atoms from three carboxylate groups of three succinate (butanedioate) ligands and two N atoms from two 1-[(1H-benzimidazol-2-yl)methyl]-1H-tetrazole (bimt) ligands. Cd(II) ions are connected by two kinds of crystallographically independent succinate ligands to generate a two-dimensional layered structure with bimt ligands located on each side of the layer. Adjacent layers are further connected by hydrogen bonding, leading to a three-dimensional supramolecular architecture in the solid state. Thermogravimetric analysis of the title polymer shows that it is stable up to 529 K and then loses weight from 529 to 918 K, corresponding to the decomposition of the bimt ligands and succinate groups. The polymer exhibits a strong fluorescence emission in the solid state at room temperature.

Simultaneous determination of the second-harmonic generation emission directionality and reduced scattering coefficient from three-dimensional imaging of thick tissues

PubMed Central

Hall, Gunnsteinn; Eliceiri, Kevin W.

2013-01-01

Abstract. Second-harmonic generation (SHG) microscopy has intrinsic contrast for imaging fibrillar collagen and has shown great promise for disease characterization and diagnostics. In addition to morphology, additional information is achievable as the initially emitted SHG radiation directionality is related to subresolution fibril size and distribution. We show that by two parameter fittings, both the emission pattern (FSHG/BSHG)creation and the reduced scattering coefficient μs′, can be obtained from the best fits between three-dimensional experimental data and Monte Carlo simulations. The improved simulation framework accounts for collection apertures for the detected forward and backward components. We apply the new simulation framework to mouse tail tendon for validation and show that the spectral slope of μs′ obtained is similar to that from bulk optical measurements and that the (FSHG/BSHG)creation values are also similar to previous results. Additionally, we find that the SHG emission becomes increasingly forward directed at longer wavelengths, which is consistent with decreased dispersion in refractive index between the laser and SHG wavelengths. As both the spectral slope of μs′ and (FSHG/BSHG)creation have been linked to the underlying tissue structure, simultaneously obtaining these parameters on a microscope platform from the same tissue provides a powerful method for tissue characterization. PMID:24220726

The application of 3D Zernike moments for the description of "model-free" molecular structure, functional motion, and structural reliability.

PubMed

Grandison, Scott; Roberts, Carl; Morris, Richard J

2009-03-01

Protein structures are not static entities consisting of equally well-determined atomic coordinates. Proteins undergo continuous motion, and as catalytic machines, these movements can be of high relevance for understanding function. In addition to this strong biological motivation for considering shape changes is the necessity to correctly capture different levels of detail and error in protein structures. Some parts of a structural model are often poorly defined, and the atomic displacement parameters provide an excellent means to characterize the confidence in an atom's spatial coordinates. A mathematical framework for studying these shape changes, and handling positional variance is therefore of high importance. We present an approach for capturing various protein structure properties in a concise mathematical framework that allows us to compare features in a highly efficient manner. We demonstrate how three-dimensional Zernike moments can be employed to describe functions, not only on the surface of a protein but throughout the entire molecule. A number of proof-of-principle examples are given which demonstrate how this approach may be used in practice for the representation of movement and uncertainty.

Three-dimensional reciprocal space x-ray coherent scattering tomography of two-dimensional object.

PubMed

Zhu, Zheyuan; Pang, Shuo

2018-04-01

X-ray coherent scattering tomography is a powerful tool in discriminating biological tissues and bio-compatible materials. Conventional x-ray scattering tomography framework can only resolve isotropic scattering profile under the assumption that the material is amorphous or in powder form, which is not true especially for biological samples with orientation-dependent structure. Previous tomography schemes based on x-ray coherent scattering failed to preserve the scattering pattern from samples with preferred orientations, or required elaborated data acquisition scheme, which could limit its application in practical settings. Here, we demonstrate a simple imaging modality to preserve the anisotropic scattering signal in three-dimensional reciprocal (momentum transfer) space of a two-dimensional sample layer. By incorporating detector movement along the direction of x-ray beam, combined with a tomographic data acquisition scheme, we match the five dimensions of the measurements with the five dimensions (three in momentum transfer domain, and two in spatial domain) of the object. We employed a collimated pencil beam of a table-top copper-anode x-ray tube, along with a panel detector to investigate the feasibility of our method. We have demonstrated x-ray coherent scattering tomographic imaging at a spatial resolution ~2 mm and momentum transfer resolution 0.01 Å -1 for the rotation-invariant scattering direction. For any arbitrary, non-rotation-invariant direction, the same spatial and momentum transfer resolution can be achieved based on the spatial information from the rotation-invariant direction. The reconstructed scattering profile of each pixel from the experiment is consistent with the x-ray diffraction profile of each material. The three-dimensional scattering pattern recovered from the measurement reveals the partially ordered molecular structure of Teflon wrap in our sample. We extend the applicability of conventional x-ray coherent scattering tomography to the reconstruction of two-dimensional samples with anisotropic scattering profile by introducing additional degree of freedom on the detector. The presented method has the potential to achieve low-cost, high-specificity material discrimination based on x-ray coherent scattering. © 2018 American Association of Physicists in Medicine.

Three-dimensional Printed Acrylonitrile Butadiene Styrene Framework Coated with Cu-BTC Metal-organic Frameworks for the Removal of Methylene Blue

PubMed Central

Wang, Zongyuan; Wang, Jiajun; Li, Minyue; Sun, Kaihang; Liu, Chang-jun

2014-01-01

Three-dimensional (3D) printing was applied for the fabrication of acrylonitrile butadiene styrene (ABS) framework. Functionalization of the ABS framework was then performed by coating of porous Cu-BTC (BTC = benzene tricarboxylic acid) metal-organic frameworks on it using a step-by-step in-situ growth. The size of the Cu-BTC particles on ABS was ranged from 200 nm to 900 nm. The Cu-BTC/ABS framework can take up most of the space of the tubular reactor that makes the adsorption effective with no need of stirring. Methylene blue (MB) can be readily removed from aqueous solution by this Cu-BTC/ABS framework. The MB removal efficiency for solutions with concentrations of 10 and 5 mg/L was 93.3% and 98.3%, respectively, within 10 min. After MB adsorption, the Cu-BTC/ABS composite can easily be recovered without the need for centrifugation or filtration and the composite is reusable. In addition the ABS framework can be recovered for subsequent reuse. A significant advantage of 3D-printed frameworks is that different frameworks can be easily fabricated to meet the needs of different applications. This is a promising strategy to synthesize new frameworks using MOFs and polymers to develop materials for applications beyond adsorption. PMID:25089616

Parallel computation of three-dimensional aeroelastic fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sadeghi, Mani

This dissertation presents a numerical method for the parallel computation of aeroelasticity (ParCAE). A flow solver is coupled to a structural solver by use of a fluid-structure interface method. The integration of the three-dimensional unsteady Navier-Stokes equations is performed in the time domain, simultaneously to the integration of a modal three-dimensional structural model. The flow solution is accelerated by using a multigrid method and a parallel multiblock approach. Fluid-structure coupling is achieved by subiteration. A grid-deformation algorithm is developed to interpolate the deformation of the structural boundaries onto the flow grid. The code is formulated to allow application to general, three-dimensional, complex configurations with multiple independent structures. Computational results are presented for various configurations, such as turbomachinery blade rows and aircraft wings. Investigations are performed on vortex-induced vibrations, effects of cascade mistuning on flutter, and cases of nonlinear cascade and wing flutter.

MPI-AMRVAC 2.0 for Solar and Astrophysical Applications

NASA Astrophysics Data System (ADS)

Xia, C.; Teunissen, J.; El Mellah, I.; Chané, E.; Keppens, R.

2018-02-01

We report on the development of MPI-AMRVAC version 2.0, which is an open-source framework for parallel, grid-adaptive simulations of hydrodynamic and magnetohydrodynamic (MHD) astrophysical applications. The framework now supports radial grid stretching in combination with adaptive mesh refinement (AMR). The advantages of this combined approach are demonstrated with one-dimensional, two-dimensional, and three-dimensional examples of spherically symmetric Bondi accretion, steady planar Bondi–Hoyle–Lyttleton flows, and wind accretion in supergiant X-ray binaries. Another improvement is support for the generic splitting of any background magnetic field. We present several tests relevant for solar physics applications to demonstrate the advantages of field splitting on accuracy and robustness in extremely low-plasma β environments: a static magnetic flux rope, a magnetic null-point, and magnetic reconnection in a current sheet with either uniform or anomalous resistivity. Our implementation for treating anisotropic thermal conduction in multi-dimensional MHD applications is also described, which generalizes the original slope-limited symmetric scheme from two to three dimensions. We perform ring diffusion tests that demonstrate its accuracy and robustness, and show that it prevents the unphysical thermal flux present in traditional schemes. The improved parallel scaling of the code is demonstrated with three-dimensional AMR simulations of solar coronal rain, which show satisfactory strong scaling up to 2000 cores. Other framework improvements are also reported: the modernization and reorganization into a library, the handling of automatic regression tests, the use of inline/online Doxygen documentation, and a new future-proof data format for input/output.

Cones of localized shear strain in incompressible elasticity with prestress: Green's function and integral representations

PubMed Central

Argani, L. P.; Bigoni, D.; Capuani, D.; Movchan, N. V.

2014-01-01

The infinite-body three-dimensional Green's function set (for incremental displacement and mean stress) is derived for the incremental deformation of a uniformly strained incompressible, nonlinear elastic body. Particular cases of the developed formulation are the Mooney–Rivlin elasticity and the J2-deformation theory of plasticity. These Green's functions are used to develop a boundary integral equation framework, by introducing an ad hoc potential, which paves the way for a boundary element formulation of three-dimensional problems of incremental elasticity. Results are used to investigate the behaviour of a material deformed near the limit of ellipticity and to reveal patterns of shear failure. In fact, within the investigated three-dimensional framework, localized deformations emanating from a perturbation are shown to be organized in conical geometries rather than in planar bands, so that failure is predicted to develop through curved and thin surfaces of intense shearing, as can for instance be observed in the cup–cone rupture of ductile metal bars. PMID:25197258

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

Synthesis, growth, structural and optical studies of a new organic three dimensional framework: 4-(aminocarbonyl)pyridine 4-(aminocarbonyl)pyridinium hydrogen L-malate

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

Vijayalakshmi, A.; Vidyavathy, B., E-mail: vidyavathybalraj@gmail.com; Peramaiyan, G.

2017-02-15

4-(aminocarbonyl)pyridine 4-(aminocarbonyl)pyridinium hydrogen L-malate [(4ACP)(4ACP).(LM)] a new organic nonlinear optical (NLO) crystal was grown by the slow evaporation method. Single crystal X-ray diffraction analysis revealed that the [(4ACP)(4ACP).(LM)] crystal belongs to monoclinic crystal system, space group P2{sub 1}/n, with a three dimensional network. Thermogravimetry (TG) and differential thermal (DT) analyses showed that [(4ACP)(4ACP).(LM)] is thermally stable up to 165 °C. The optical transmittance window and the lower cut-off wavelength of [(4ACP)(4ACP).(LM)] were found out by UV–vis–NIR spectral study. The molecular structure of [(4ACP)(4ACP).(LM)] was further confirmed by FTIR spectral studies. The relative dielectric permittivity and dielectric loss were determined asmore » function of frequency and temperature. The third order nonlinear optical property of [(4ACP)(4ACP).(LM)] was studied by the Z-scan technique using a 532 nm diode pumped CW Nd:YAG laser. Nonlinear refractive index, nonlinear absorption coefficient and third order nonlinear susceptibility of the grown crystal were found to be 7.38×10{sup −8} cm{sup 2}/W, 0.08×10{sup −4} cm/W and 5.36×10{sup −6} esu, respectively. The laser damage threshold value is found to be 1.75 GW/cm{sup 2} - Graphical abstract: In the crystal structure of the title complex, the asymmetric unit contains one hydrogen L-malate anion, 4-(aminocarbonyl)pyridinium cation and a neutral isonicotinamide molecule. It is stabilized by intermolecular N-H…O, C-H…O and O-H…O hydrogen bonds which generate a three dimensional network.« less

Multidisciplinary Design Optimization of A Highly Flexible Aeroservoelastic Wing

NASA Astrophysics Data System (ADS)

Haghighat, Sohrab

A multidisciplinary design optimization framework is developed that integrates control system design with aerostructural design for a highly-deformable wing. The objective of this framework is to surpass the existing aircraft endurance limits through the use of an active load alleviation system designed concurrently with the rest of the aircraft. The novelty of this work is two fold. First, a unified dynamics framework is developed to represent the full six-degree-of-freedom rigid-body along with the structural dynamics. It allows for an integrated control design to account for both manoeuvrability (flying quality) and aeroelasticity criteria simultaneously. Secondly, by synthesizing the aircraft control system along with the structural sizing and aerodynamic shape design, the final design has the potential to exploit synergies among the three disciplines and yield higher performing aircraft. A co-rotational structural framework featuring Euler--Bernoulli beam elements is developed to capture the wing's nonlinear deformations under the effect of aerodynamic and inertial loadings. In this work, a three-dimensional aerodynamic panel code, capable of calculating both steady and unsteady loadings is used. Two different control methods, a model predictive controller (MPC) and a 2-DOF mixed-norm robust controller, are considered in this work to control a highly flexible aircraft. Both control techniques offer unique advantages that make them promising for controlling a highly flexible aircraft. The control system works towards executing time-dependent manoeuvres along with performing gust/manoeuvre load alleviation. The developed framework is investigated for demonstration in two design cases: one in which the control system simply worked towards achieving or maintaining a target altitude, and another where the control system is also performing load alleviation. The use of the active load alleviation system results in a significant improvement in the aircraft performance relative to the optimum result without load alleviation. The results show that the inclusion of control system discipline along with other disciplines at early stages of aircraft design improves aircraft performance. It is also shown that structural stresses due to gust excitations can be better controlled by the use of active structural control systems which can improve the fatigue life of the structure.

Self-encapsulation of [MII(phen)2(H2O)2]2+ (M=Co, Zn) in one-dimensional nanochannels of [MII(H2O)6(BTC)2]4- (M=Co, Cu, Mn): a high HQ/CAT ratio catalyst for hydroxylation of phenols.

PubMed

Bi, Jianhong; Kong, Lingtao; Huang, Zixiang; Liu, Jinhuai

2008-06-02

Four novel three-dimensional (3D) microporous supramolecular compounds containing nanosized channels, namely, [Co(phen)2(H2O)2]2[Co(H2O)6].2BTC.21.5H2O (1), [Co(phen)2(H2O)2]2[Cu(H2O)6].2BTC.21.5H2O (2), [Co(phen)2(H2O)2]2[Mn(H2O)6].2BTC.18H2O (3), and [Zn(phen)2(H2O)2]2[Mn(H2O)6].2BTC.22.5H2O (4), were synthesized from 1,3,5-benzenetricarboxylate (BTC), 1,10-phenanthroline (phen), and the transition-metal salt(s) by self-assembly. Single-crystal X-ray structural analysis showed that the resulting 3D microporous supramolecular frameworks consist of a two-dimensional (2D) hydrogen-bonded host framework of [MII(H2O)6(BTC)2]4- (M=Co for 1, Cu for 2, Mn for 3, 4) with rectangular-shaped cavities containing [MII(phen)2(H2O)2]2+ (M=Co for 1-3, Zn for 4) guests. The guest complex is encapsulated in the 2D hydrogen-bonded host framework by hydrogen bonding and aromatic pi-pi stacking interactions, forming the 3D hydrogen-bonded framework. The catalytic activities of 1, 2, 3, and 4 were studied using hydroxylation of phenols with 30% aqueous H2O2 as a test reaction. The compounds displayed a good phenol conversion ratio and excellent channel selectivity in the hydroxylation reaction, with a maximum hydroquinone (HQ)/catechol (CAT) ratio of 3.9.

Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

ERIC Educational Resources Information Center

Lazarowitz, Reuven; Naim, Raphael

2014-01-01

The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular…

A unified effective-field renormalization-group framework approach for the quenched diluted Ising models

NASA Astrophysics Data System (ADS)

de Albuquerque, Douglas F.; Fittipaldi, I. P.

1994-05-01

A unified effective-field renormalization-group framework (EFRG) for both quenched bond- and site-diluted Ising models is herein developed by extending recent works. The method, as in the previous works, follows up the same strategy of the mean-field renormalization-group scheme (MFRG), and is achieved by introducing an alternative way for constructing classical effective-field equations of state, based on rigorous Ising spin identities. The concentration dependence of the critical temperature, Tc(p), and the critical concentrations of magnetic atoms, pc, at which the transition temperature goes to zero, are evaluated for several two- and three-dimensional lattice structures. The obtained values of Tc and pc and the resulting phase diagrams for both bond and site cases are much more accurate than those estimated by the standard MFRG approach. Although preserving the same level of simplicity as the MFRG, it is shown that the present EFRG method, even by considering its simplest size-cluster version, provides results that correctly distinguishes those lattices that have the same coordination number, but differ in dimensionality or geometry.

A Fast, Open EEG Classification Framework Based on Feature Compression and Channel Ranking

PubMed Central

Han, Jiuqi; Zhao, Yuwei; Sun, Hongji; Chen, Jiayun; Ke, Ang; Xu, Gesen; Zhang, Hualiang; Zhou, Jin; Wang, Changyong

2018-01-01

Superior feature extraction, channel selection and classification methods are essential for designing electroencephalography (EEG) classification frameworks. However, the performance of most frameworks is limited by their improper channel selection methods and too specifical design, leading to high computational complexity, non-convergent procedure and narrow expansibility. In this paper, to remedy these drawbacks, we propose a fast, open EEG classification framework centralized by EEG feature compression, low-dimensional representation, and convergent iterative channel ranking. First, to reduce the complexity, we use data clustering to compress the EEG features channel-wise, packing the high-dimensional EEG signal, and endowing them with numerical signatures. Second, to provide easy access to alternative superior methods, we structurally represent each EEG trial in a feature vector with its corresponding numerical signature. Thus, the recorded signals of many trials shrink to a low-dimensional structural matrix compatible with most pattern recognition methods. Third, a series of effective iterative feature selection approaches with theoretical convergence is introduced to rank the EEG channels and remove redundant ones, further accelerating the EEG classification process and ensuring its stability. Finally, a classical linear discriminant analysis (LDA) model is employed to classify a single EEG trial with selected channels. Experimental results on two real world brain-computer interface (BCI) competition datasets demonstrate the promising performance of the proposed framework over state-of-the-art methods. PMID:29713262

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.

PubMed

Jossinet, Fabrice; Westhof, Eric

2005-08-01

Efficient RNA sequence manipulations (such as multiple alignments) need to be constrained by rules of RNA structure folding. The structural knowledge has increased dramatically in the last years with the accumulation of several large RNA structures similar to those of the bacterial ribosome subunits. However, no tool in the RNA community provides an easy way to link and integrate progress made at the sequence level using the available three-dimensional information. Sequence to Structure (S2S) proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures. S2S has been implemented using the Java language and has been developed and tested under UNIX systems, such as Linux and MacOSX. S2S is available at http://bioinformatics.org/S2S/.

Towards Careful Practices for Automated Linguistic Analysis of Group Learning

ERIC Educational Resources Information Center

Howley, Iris; Rosé, Carolyn Penstein

2016-01-01

The multifaceted nature of collaborative learning environments necessitates theory to investigate the cognitive, motivational, and relational dimensions of collaboration. Several existing frameworks include aspects related to each of these three. This article explores the capability of multi-dimensional frameworks for analysis of collaborative…

Three Dimensional Immobilization of Beta-Galactosidase on a Silicon Surface (Preprint)

DTIC Science & Technology

2006-12-01

initial activity after 10 days at 24°C. The ability to generate three- dimensional structures with enhanced loading capacity for biosensing molecules...dimensional structures for biosensors (Charles et al. 2004). Silicon samples that had been washed but not activated with APTS did not retain any enzyme...preparation. The use of silica particles to build a 3-dimensional structure not only provides an increased capacity for the immobilization of β

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Direct Numerical Simulation of a Temporally Evolving Incompressible Plane Wake: Effect of Initial Conditions on Evolution and Topology

NASA Technical Reports Server (NTRS)

Sondergaard, R.; Cantwell, B.; Mansour, N.

1997-01-01

Direct numerical simulations have been used to examine the effect of the initial disturbance field on the development of three-dimensionality and the transition to turbulence in the incompressible plane wake. The simulations were performed using a new numerical method for solving the time-dependent, three-dimensional, incompressible Navier-Stokes equations in flows with one infinite and two periodic directions. The method uses standard Fast Fourier Transforms and is applicable to cases where the vorticity field is compact in the infinite direction. Initial disturbances fields examined were combinations of two-dimensional waves and symmetric pairs of 60 deg oblique waves at the fundamental, subharmonic, and sub-subharmonic wavelengths. The results of these simulations indicate that the presence of 60 deg disturbances at the subharmonic streamwise wavelength results in the development of strong coherent three-dimensional structures. The resulting strong three-dimensional rate-of-strain triggers the growth of intense fine scale motions. Wakes initiated with 60 deg disturbances at the fundamental streamwise wavelength develop weak coherent streamwise structures, and do not develop significant fine scale motions, even at high Reynolds numbers. The wakes which develop strong three-dimensional structures exhibit growth rates on par with experimentally observed turbulent plane wakes. Wakes which develop only weak three-dimensional structures exhibit significantly lower late time growth rates. Preliminary studies of wakes initiated with an oblique fundamental and a two-dimensional subharmonic, which develop asymmetric coherent oblique structures at the subharmonic wavelength, indicate that significant fine scale motions only develop if the resulting oblique structures are above an angle of approximately 45 deg.

Anhydrous 1:1 proton-transfer compounds of isonipecotamide with picric acid and 3,5-dinitrosalicylic acid: 4-carbamoylpiperidinium 2,4,6-trinitrophenolate and two polymorphs of 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate.

PubMed

Smith, Graham; Wermuth, Urs D

2010-12-01

The structures of the anhydrous 1:1 proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with picric acid and 3,5-dinitrosalicylic acid, namely 4-carbamoylpiperidinium 2,4,6-trinitrophenolate, C(6)H(13)N(2)O(+)·C(6)H(2)N(3)O(7)(-), (I), and 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate [two forms of which were found, the monoclinic α-polymorph, (II), and the triclinic β-polymorph, (III)], C(6)H(13)N(2)O(+)·C(7)H(3)N(2)O(7)(-), have been determined at 200 K. All three compounds form hydrogen-bonded structures, viz. one-dimensional in (II), two-dimensional in (I) and three-dimensional in (III). In (I), the cations form centrosymmetric cyclic head-to-tail hydrogen-bonded homodimers [graph set R(2)(2)(14)] through lateral duplex piperidinium-amide N-H...O interactions. These dimers are extended into a two-dimensional network structure through further interactions with phenolate and nitro O-atom acceptors, including a direct symmetric piperidinium-phenol/nitro N-H...O,O cation-anion association [graph set R(1)(2)(6)]. The monoclinic polymorph, (II), has a similar R(1)(2)(6) cation-anion hydrogen-bonding interaction to (I) but with an additional conjoint symmetrical R(1)(2)(4) interaction as well as head-to-tail piperidinium-amide N-H...O,O hydrogen bonds and amide-carboxyl N-H...O hydrogen bonds, giving a network structure which includes large R(4)(3)(20) rings. The hydrogen bonding in the triclinic polymorph, (III), is markedly different from that of monoclinic (II). The asymmetric unit contains two independent cation-anion pairs which associate through cyclic piperidinium-carboxyl N-H...O,O' interactions [graph set R(1)(2)(4)]. The cations also show the zigzag head-to-tail piperidinium-amide N-H...O hydrogen-bonded chain substructures found in (II), but in addition feature amide-nitro and amide-phenolate N-H...O associations. As well, there is a centrosymmetric double-amide N-H...O(carboxyl) bridged bis(cation-anion) ring system [graph set R(4)(2)(8)] in the three-dimensional framework. The structures reported here demonstrate the utility of the isonipecotamide cation as a synthon with previously unrecognized potential for structure assembly applications. Furthermore, the structures of the two polymorphic 3,5-dinitrosalicylic acid salts show an unusual dissimilarity in hydrogen-bonding characteristics, considering that both were obtained from identical solvent systems.

Hierarchical meso/macro-porous carbon fabricated from dual MgO templates for direct electron transfer enzymatic electrodes.

PubMed

Funabashi, Hiroto; Takeuchi, Satoshi; Tsujimura, Seiya

2017-03-23

We designed a three-dimensional (3D) hierarchical pore structure to improve the current production efficiency and stability of direct electron transfer-type biocathodes. The 3D hierarchical electrode structure was fabricated using a MgO-templated porous carbon framework produced from two MgO templates with sizes of 40 and 150 nm. The results revealed that the optimal pore composition for a bilirubin oxidase-catalysed oxygen reduction cathode was a mixture of 33% macropores and 67% mesopores (MgOC 33 ). The macropores improve mass transfer inside the carbon material, and the mesopores improve the electron transfer efficiency of the enzyme by surrounding the enzyme with carbon.

Hierarchical meso/macro-porous carbon fabricated from dual MgO templates for direct electron transfer enzymatic electrodes

NASA Astrophysics Data System (ADS)

Funabashi, Hiroto; Takeuchi, Satoshi; Tsujimura, Seiya

2017-03-01

We designed a three-dimensional (3D) hierarchical pore structure to improve the current production efficiency and stability of direct electron transfer-type biocathodes. The 3D hierarchical electrode structure was fabricated using a MgO-templated porous carbon framework produced from two MgO templates with sizes of 40 and 150 nm. The results revealed that the optimal pore composition for a bilirubin oxidase-catalysed oxygen reduction cathode was a mixture of 33% macropores and 67% mesopores (MgOC33). The macropores improve mass transfer inside the carbon material, and the mesopores improve the electron transfer efficiency of the enzyme by surrounding the enzyme with carbon.

Hysteretic Four-Step Spin Crossover within a Three-Dimensional Porous Hofmann-like Material

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

Clements, John E.; Price, Jason R.; Neville, Suzanne M.

Materials that display multiple stepped spin crossover (SCO) transitions with accompanying hysteresis present the opportunity for ternary, quaternary, and quinary electronic switching and data storage but are rare in existence. Herein, we present the first report of a four-step hysteretic SCO framework. Single-crystal structure analysis of a porous 3D Hofmann-like material showed long-range ordering of spin states: HS, HS 0.67LS 0.33, HS 0.5LS 0.5, HS 0.33LS 0.67, and LS. These detailed structural studies provide insight into how multistep SCO materials can be rationally designed through control of host–host and host–guest interactions.

Plasticity - Theory and finite element applications.

NASA Technical Reports Server (NTRS)

Armen, H., Jr.; Levine, H. S.

1972-01-01

A unified presentation is given of the development and distinctions associated with various incremental solution procedures used to solve the equations governing the nonlinear behavior of structures, and this is discussed within the framework of the finite-element method. Although the primary emphasis here is on material nonlinearities, consideration is also given to geometric nonlinearities acting separately or in combination with nonlinear material behavior. The methods discussed here are applicable to a broad spectrum of structures, ranging from simple beams to general three-dimensional bodies. The finite-element analysis methods for material nonlinearity are general in the sense that any of the available plasticity theories can be incorporated to treat strain hardening or ideally plastic behavior.

Coherent structures and flow topology of transitional separated-reattached flow over two and three dimensional geometrical shapes

NASA Astrophysics Data System (ADS)

Diabil, Hayder Azeez; Li, Xin Kai; Abdalla, Ibrahim Elrayah

2017-09-01

Large-scale organized motions (commonly referred to coherent structures) and flow topology of a transitional separated-reattached flow have been visualised and investigated using flow visualisation techniques. Two geometrical shapes including two-dimensional flat plate with rectangular leading edge and three-dimensional square cylinder are chosen to shed a light on the flow topology and present coherent structures of the flow over these shapes. For both geometries and in the early stage of the transition, two-dimensional Kelvin-Helmholtz rolls are formed downstream of the leading edge. They are observed to be twisting around the square cylinder while they stay flat in the case of the two-dimensional flat plate. For both geometrical shapes, the two-dimensional Kelvin-Helmholtz rolls move downstream of the leading edge and they are subjected to distortion to form three-dimensional hairpin structures. The flow topology in the flat plate is different from that in the square cylinder. For the flat plate, there is a merging process by a pairing of the Kelvin-Helmholtz rolls to form a large structure that breaks down directly into many hairpin structures. For the squire cylinder case, the Kelvin-Helmholtz roll evolves topologically to form a hairpin structure. In the squire cylinder case, the reattachment length is much shorter and a forming of the three-dimensional structures is closer to the leading edge than that in the flat plate case.

A complete-pelvis segmentation framework for image-free total hip arthroplasty (THA): methodology and clinical study.

PubMed

Xie, Weiguo; Franke, Jochen; Chen, Cheng; Grützner, Paul A; Schumann, Steffen; Nolte, Lutz-P; Zheng, Guoyan

2015-06-01

Complete-pelvis segmentation in antero-posterior pelvic radiographs is required to create a patient-specific three-dimensional pelvis model for surgical planning and postoperative assessment in image-free navigation of total hip arthroplasty. A fast and robust framework for accurately segmenting the complete pelvis is presented, consisting of two consecutive modules. In the first module, a three-stage method was developed to delineate the left hemi-pelvis based on statistical appearance and shape models. To handle complex pelvic structures, anatomy-specific information processing techniques were employed. As the input to the second module, the delineated left hemi-pelvis was then reflected about an estimated symmetry line of the radiograph to initialize the right hemi-pelvis segmentation. The right hemi-pelvis was segmented by the same three-stage method, Two experiments conducted on respectively 143 and 40 AP radiographs demonstrated a mean segmentation accuracy of 1.61±0.68 mm. A clinical study to investigate the postoperative assessment of acetabular cup orientations based on the proposed framework revealed an average accuracy of 1.2°±0.9° and 1.6°±1.4° for anteversion and inclination, respectively. Delineation of each radiograph costs less than one minute. Despite further validation needed, the preliminary results implied the underlying clinical applicability of the proposed framework for image-free THA. Copyright © 2014 John Wiley & Sons, Ltd.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

[Computer aided design and rapid manufacturing of removable partial denture frameworks].

PubMed

Han, Jing; Lü, Pei-jun; Wang, Yong

2010-08-01

To introduce a method of digital modeling and fabricating removable partial denture (RPD) frameworks using self-developed software for RPD design and rapid manufacturing system. The three-dimensional data of two partially dentate dental casts were obtained using a three-dimensional crossing section scanner. Self-developed software package for RPD design was used to decide the path of insertion and to design different components of RPD frameworks. The components included occlusal rest, clasp, lingual bar, polymeric retention framework and maxillary major connector. The design procedure for the components was as following: first, determine the outline of the component. Second, build the tissue surface of the component using the scanned data within the outline. Third, preset cross section was used to produce the polished surface. Finally, different RPD components were modeled respectively and connected by minor connectors to form an integrated RPD framework. The finished data were imported into a self-developed selective laser melting (SLM) machine and metal frameworks were fabricated directly. RPD frameworks for the two scanned dental casts were modeled with this self-developed program and metal RPD frameworks were successfully fabricated using SLM method. The finished metal frameworks fit well on the plaster models. The self-developed computer aided design and computer aided manufacture (CAD-CAM) system for RPD design and fabrication has completely independent intellectual property rights. It provides a new method of manufacturing metal RPD frameworks.

Covalent Organic Frameworks as a Platform for Multidimensional Polymerization.

PubMed

Bisbey, Ryan P; Dichtel, William R

2017-06-28

The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems.

Covalent Organic Frameworks as a Platform for Multidimensional Polymerization

PubMed Central

2017-01-01

The simultaneous polymerization and crystallization of monomers featuring directional bonding designs provides covalent organic frameworks (COFs), which are periodic polymer networks with robust covalent bonds arranged in two- or three-dimensional topologies. The range of properties characterized in COFs has rapidly expanded to include those of interest for heterogeneous catalysis, energy storage and photovoltaic devices, and proton-conducting membranes. Yet many of these applications will require materials quality, morphological control, and synthetic efficiency exceeding the capabilities of contemporary synthetic methods. This level of control will emerge from an improved fundamental understanding of COF nucleation and growth processes. More powerful characterization of structure and defects, improved syntheses guided by mechanistic understanding, and accessing diverse isolated forms, ranging from single crystals to thin films to colloidal suspensions, remain important frontier problems. PMID:28691064

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

PubMed

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Applications of three-dimensional (3D) printing for microswimmers and bio-hybrid robotics.

PubMed

Stanton, M M; Trichet-Paredes, C; Sánchez, S

2015-04-07

This article will focus on recent reports that have applied three-dimensional (3D) printing for designing millimeter to micrometer architecture for robotic motility. The utilization of 3D printing has rapidly grown in applications for medical prosthetics and scaffolds for organs and tissue, but more recently has been implemented for designing mobile robotics. With an increase in the demand for devices to perform in fragile and confined biological environments, it is crucial to develop new miniaturized, biocompatible 3D systems. Fabrication of materials at different scales with different properties makes 3D printing an ideal system for creating frameworks for small-scale robotics. 3D printing has been applied for the design of externally powered, artificial microswimmers and studying their locomotive capabilities in different fluids. Printed materials have also been incorporated with motile cells for bio-hybrid robots capable of functioning by cell contraction and swimming. These 3D devices offer new methods of robotic motility for biomedical applications requiring miniature structures. Traditional 3D printing methods, where a structure is fabricated in an additive process from a digital design, and non-traditional 3D printing methods, such as lithography and molding, will be discussed.

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

DOE PAGES

Zhou, Yunlong; Marson, Ryan L.; van Anders, Greg; ...

2016-02-22

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. In this paper, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the aminomore » acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. Finally, the helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.« less

Functionally Graded Metal-Metal Composite Structures

NASA Technical Reports Server (NTRS)

Brice, Craig A. (Inventor)

2017-01-01

Methods and devices are disclosed for creating a multiple alloy composite structure by forming a three-dimensional arrangement of a first alloy composition in which the three-dimensional arrangement has a substantially open and continuous porosity. The three-dimensional arrangement of the first alloy composition is infused with at least a second alloy composition, where the second alloy composition comprises a shape memory alloy. The three-dimensional arrangement is consolidated into a fully dense solid structure, and the original shape of the second alloy composition is set for reversible transformation. Strain is applied to the fully dense solid structure, which is treated with heat so that the shape memory alloy composition becomes memory activated to recover the original shape. An interwoven composite of the first alloy composition and the memory-activated second alloy composition is thereby formed in the multiple alloy composite structure.

Aqueous aerobic oxidation of alkyl arenes and alcohols catalyzed by copper(II) phthalocyanine supported on three-dimensional nitrogen-doped graphene at room temperature.

PubMed

Mahyari, Mojtaba; Laeini, Mohammad Sadegh; Shaabani, Ahmad

2014-07-25

Copper(ii) tetrasulfophthalocyanine supported on three-dimensional nitrogen-doped graphene-based frameworks was synthesized and introduced as a bifunctional catalyst for selective aerobic oxidation of alkyl arenes and alcohols to the corresponding carbonyl compounds. The ease of catalyst separation, high turnover, low catalyst loading and recyclability could potentially render it applicable in industrial setting.

Three-dimensional biofilm structure quantification.

PubMed

Beyenal, Haluk; Donovan, Conrad; Lewandowski, Zbigniew; Harkin, Gary

2004-12-01

Quantitative parameters describing biofilm physical structure have been extracted from three-dimensional confocal laser scanning microscopy images and used to compare biofilm structures, monitor biofilm development, and quantify environmental factors affecting biofilm structure. Researchers have previously used biovolume, volume to surface ratio, roughness coefficient, and mean and maximum thicknesses to compare biofilm structures. The selection of these parameters is dependent on the availability of software to perform calculations. We believe it is necessary to develop more comprehensive parameters to describe heterogeneous biofilm morphology in three dimensions. This research presents parameters describing three-dimensional biofilm heterogeneity, size, and morphology of biomass calculated from confocal laser scanning microscopy images. This study extends previous work which extracted quantitative parameters regarding morphological features from two-dimensional biofilm images to three-dimensional biofilm images. We describe two types of parameters: (1) textural parameters showing microscale heterogeneity of biofilms and (2) volumetric parameters describing size and morphology of biomass. The three-dimensional features presented are average (ADD) and maximum diffusion distances (MDD), fractal dimension, average run lengths (in X, Y and Z directions), aspect ratio, textural entropy, energy and homogeneity. We discuss the meaning of each parameter and present the calculations in detail. The developed algorithms, including automatic thresholding, are implemented in software as MATLAB programs which will be available at site prior to publication of the paper.

ITQ-54: a multi-dimensional extra-large pore zeolite with 20 × 14 × 12-ring channels

DOE PAGES

Jiang, Jiuxing; Yun, Yifeng; Zou, Xiaodong; ...

2015-01-01

A multi-dimensional extra-large pore silicogermanate zeolite, named ITQ-54, has been synthesised by in situ decomposition of the N,N-dicyclohexylisoindolinium cation into the N-cyclohexylisoindolinium cation. Its structure was solved by 3D rotation electron diffraction (RED) from crystals of ca. 1 μm in size. The structure of ITQ-54 contains straight intersecting 20 × 14 × 12-ring channels along the three crystallographic axes and it is one of the few zeolites with extra-large channels in more than one direction. ITQ-54 has a framework density of 11.1 T atoms per 1000 Å 3, which is one of the lowest among the known zeolites. ITQ-54 wasmore » obtained together with GeO 2 as an impurity. A heavy liquid separation method was developed and successfully applied to remove this impurity from the zeolite. ITQ-54 is stable up to 600 °C and exhibits permanent porosity. The structure was further refined using powder X-ray diffraction (PXRD) data for both as-made and calcined samples.« less

Two-stage Framework for a Topology-Based Projection and Visualization of Classified Document Collections

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

Oesterling, Patrick; Scheuermann, Gerik; Teresniak, Sven

During the last decades, electronic textual information has become the world's largest and most important information source available. People have added a variety of daily newspapers, books, scientific and governmental publications, blogs and private messages to this wellspring of endless information and knowledge. Since neither the existing nor the new information can be read in its entirety, computers are used to extract and visualize meaningful or interesting topics and documents from this huge information clutter. In this paper, we extend, improve and combine existing individual approaches into an overall framework that supports topological analysis of high dimensional document point cloudsmore » given by the well-known tf-idf document-term weighting method. We show that traditional distance-based approaches fail in very high dimensional spaces, and we describe an improved two-stage method for topology-based projections from the original high dimensional information space to both two dimensional (2-D) and three dimensional (3-D) visualizations. To show the accuracy and usability of this framework, we compare it to methods introduced recently and apply it to complex document and patent collections.« less

Bioprinting of a mechanically enhanced three-dimensional dual cell-laden construct for osteochondral tissue engineering using a multi-head tissue/organ building system

NASA Astrophysics Data System (ADS)

Shim, Jin-Hyung; Lee, Jung-Seob; Kim, Jong Young; Cho, Dong-Woo

2012-08-01

The aim of this study was to build a mechanically enhanced three-dimensional (3D) bioprinted construct containing two different cell types for osteochondral tissue regeneration. Recently, the production of 3D cell-laden structures using various scaffold-free cell printing technologies has opened up new possibilities. However, ideal 3D complex tissues or organs have not yet been printed because gel-state hydrogels have been used as the principal material and are unable to maintain the desired 3D structure due to their poor mechanical strength. In this study, thermoplastic biomaterial polycaprolactone (PCL), which shows relatively high mechanical properties as compared with hydrogel, was used as a framework for enhancing the mechanical stability of the bioprinted construct. Two different alginate solutions were then infused into the previously prepared framework consisting of PCL to create the 3D construct for osteochondral printing. For this work, a multi-head tissue/organ building system (MtoBS), which was particularly designed to dispense thermoplastic biomaterial and hydrogel having completely different rheology properties, was newly developed and used to bioprint osteochondral tissue. It was confirmed that the line width, position and volume control of PCL and alginate solutions were adjustable in the MtoBS. Most importantly, dual cell-laden 3D constructs consisting of osteoblasts and chondrocytes were successfully fabricated. Further, the separately dispensed osteoblasts and chondrocytes not only retained their initial position and viability, but also proliferated up to 7 days after being dispensed.

One-dimensional, two-dimensional, and three-dimensional photonic crystals fabricated with interferometric techniques on ultrafine-grain silver halide emulsions

NASA Astrophysics Data System (ADS)

Ulibarrena, Manuel; Carretero, Luis; Acebal, Pablo; Madrigal, Roque; Blaya, Salvador; Fimia, Antonio

2004-09-01

Holographic techniques have been used for manufacturing multiple band one-dimensional, two-dimensional, and three-dimensional photonic crystals with different configurations, by multiplexing reflection and transmission setups on a single layer of holographic material. The recording material used for storage is an ultra fine grain silver halide emulsion, with an average grain size around 20 nm. The results are a set of photonic crystals with the one-dimensional, two-dimensional, and three-dimensional index modulation structure consisting of silver halide particles embedded in the gelatin layer of the emulsion. The characterisation of the fabricated photonic crystals by measuring their transmission band structures has been done and compared with theoretical calculations.

Fabrication of 3D nano-structures using reverse imprint lithography

NASA Astrophysics Data System (ADS)

Han, Kang-Soo; Hong, Sung-Hoon; Kim, Kang-In; Cho, Joong-Yeon; Choi, Kyung-woo; Lee, Heon

2013-02-01

In spite of the fact that the fabrication process of three-dimensional nano-structures is complicated and expensive, it can be applied to a range of devices to increase their efficiency and sensitivity. Simple and inexpensive fabrication of three-dimensional nano-structures is necessary. In this study, reverse imprint lithography (RIL) with UV-curable benzylmethacrylate, methacryloxypropyl terminated poly-dimethylsiloxane (M-PDMS) resin and ZnO-nano-particle-dispersed resin was used to fabricate three-dimensional nano-structures. UV-curable resins were placed between a silicon stamp and a PVA transfer template, followed by a UV curing process. Then, the silicon stamp was detached and a 2D pattern layer was transferred to the substrate using diluted UV-curable glue. Consequently, three-dimensional nano-structures were formed by stacking the two-dimensional nano-patterned layers. RIL was applied to a light-emitting diode (LED) to evaluate the optical effects of a nano-patterned layer. As a result, the light extraction of the patterned LED was increased by about 12% compared to an unpatterned LED.

Fabrication of 3D nano-structures using reverse imprint lithography.

PubMed

Han, Kang-Soo; Hong, Sung-Hoon; Kim, Kang-In; Cho, Joong-Yeon; Choi, Kyung-Woo; Lee, Heon

2013-02-01

In spite of the fact that the fabrication process of three-dimensional nano-structures is complicated and expensive, it can be applied to a range of devices to increase their efficiency and sensitivity. Simple and inexpensive fabrication of three-dimensional nano-structures is necessary. In this study, reverse imprint lithography (RIL) with UV-curable benzylmethacrylate, methacryloxypropyl terminated poly-dimethylsiloxane (M-PDMS) resin and ZnO-nano-particle-dispersed resin was used to fabricate three-dimensional nano-structures.UV-curable resins were placed between a silicon stamp and a PVA transfer template, followed by a UV curing process. Then, the silicon stamp was detached and a 2D pattern layer was transferred to the substrate using diluted UV-curable glue. Consequently, three-dimensional nano-structures were formed by stacking the two-dimensional nano-patterned layers. RIL was applied to a light-emitting diode (LED) to evaluate the optical effects of a nano-patterned layer. As a result, the light extraction of the patterned LED was increased by about 12% compared to an unpatterned LED.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

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

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

Stall behavior of a scaled three-dimensional wind turbine blade

NASA Astrophysics Data System (ADS)

Mulleners, Karen; Melius, Matthew; Cal, Raul Bayoan

2014-11-01

The power generation of a wind turbine is influenced by many factors including the unsteady incoming flow characteristics, pitch regulation, and the geometry of the various turbine components. Within the framework of maximizing energy extraction, it is important to understand and tailor the aerodynamics of a wind turbine. In the interest of seeking further understanding into the complex flow over wind turbine blades, a three-dimensional scaled blade model has been designed and manufactured to be dynamically similar to a rotating full-scale NREL 5MW wind turbine blade. A wind tunnel experiment has been carried out in the 2.2 m × 1.8 m cross-section closed loop wind tunnel at DLR in Göttingen by means of time-resolved stereoscopic PIV. An extensive coherent structure analysis of the time-resolved velocity field over the suction side of the blade was performed to study stall characteristics under a geometrically induced pressure gradient. In particular, the radial extent and propagation of stalled flow regions were characterized for various static angles of attack.

A Layered Approach for Robust Spatial Virtual Human Pose Reconstruction Using a Still Image

PubMed Central

Guo, Chengyu; Ruan, Songsong; Liang, Xiaohui; Zhao, Qinping

2016-01-01

Pedestrian detection and human pose estimation are instructive for reconstructing a three-dimensional scenario and for robot navigation, particularly when large amounts of vision data are captured using various data-recording techniques. Using an unrestricted capture scheme, which produces occlusions or breezing, the information describing each part of a human body and the relationship between each part or even different pedestrians must be present in a still image. Using this framework, a multi-layered, spatial, virtual, human pose reconstruction framework is presented in this study to recover any deficient information in planar images. In this framework, a hierarchical parts-based deep model is used to detect body parts by using the available restricted information in a still image and is then combined with spatial Markov random fields to re-estimate the accurate joint positions in the deep network. Then, the planar estimation results are mapped onto a virtual three-dimensional space using multiple constraints to recover any deficient spatial information. The proposed approach can be viewed as a general pre-processing method to guide the generation of continuous, three-dimensional motion data. The experiment results of this study are used to describe the effectiveness and usability of the proposed approach. PMID:26907289

More About The Farley Three-Dimensional Braider

NASA Technical Reports Server (NTRS)

Farley, Gary L.

1993-01-01

Farley three-dimensional braider, undergoing development, is machine for automatic fabrication of three-dimensional braided structures. Incorporates yarns into structure at arbitrary braid angles to produce complicated shape. Braiding surface includes movable braiding segments containing pivot points, along which yarn carriers travel during braiding process. Yarn carrier travels along sequence of pivot points as braiding segments move. Combined motions position yarns for braiding onto preform. Intended for use in making fiber preforms for fiber/matrix composite parts, such as multiblade propellers. Machine also described in "Farley Three-Dimensional Braiding Machine" (LAR-13911).

Syntheses, crystal structures, and properties of four coordination polymers based on mixed multi-N donor and polycarboxylate ligands

NASA Astrophysics Data System (ADS)

Chen, Shui-Sheng; Guo, Xing-Zhe; Zhao, Yue; Li, Wei-Dong

2018-02-01

Four new coordination polymers [Ni2(HL1)2(L1)3(BTC)2]·6H2O (1), [Ni2(L1)3(HBTC)2]·4H2O (2), [Cd2(L2)(BTC)(H2O)3]·2H2O (3) and [Cd2(HL2)(BTCA)] (4) were synthesized by reactions of nickel(II)/ cadmium(II) salts with rigid ligands of 1,4-di(1H-imidazol-4-yl)benzene (L1), 1,3-di(1-imidazolyl)-5-(4H-tetrazol-5-yl)benzene (HL2) and polycarboxylic acids of 1,3,5-benzenetricarboxylic acid (H3BTC), 1,2,4,5-benzenetetracarboxylic acid (H4BTCA), respectively. The structures of the complexes were determined by single crystal X-ray diffraction analysis. The complex 1 is one-dimensional (1D) chain while 2 is a (4, 4)-connected two-dimensional (2D) layered structure with 2D → 2D parallel interpenetration. Complex 3 is a rare tetranodal (3,4)-connected three-dimensional (3D) CrVTiSc architecture with Point (Schläfli) symbol of (4·82)(4·84·10)(42·82·102)(83), and compound 4 has the 2D network with (4,4) topology based on the [Cd2(COO)4] SBUs. The weak interactions such as hydrogen bonds and π···π stacking contribute to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. The UV-vis absorption spectra of 1 - 4 are discussed. Moreover, the photo luminescent properties of 3 and 4 and gas sorption property of 2 have been investigated.

Critical dimensional linewidth calibration using UV microscope and laser interferometry

NASA Astrophysics Data System (ADS)

Li, Qi; Gao, Si-tian; Li, Wei; Lu, Ming-zhen; Zhang, Ming-kai

2013-10-01

In order to calibrate the critical dimensional (CD) uncertainty of lithography masks in semiconductor manufacturing, NIM is building a two dimensional metrological UV microscope which has traceable measurement ability for nanometer linewidths and pitches. The microscope mainly consists of UV light receiving components, piezoelectric ceramics (PZT) driven stage and interferometer calibration framework. In UV light receiving components they include all optical elements on optical path. The UV light originates from Köhler high aperture transmit/reflect illumination sources; then goes through objective lens to UV splitting optical elements; after that, one part of light attains UV camera for large range calibration, the other part of light passes through a three dimensional adjusted pinhole and is collected by PMT for nanoscale scanning. In PZT driven stage, PZT stick actuators with closed loop control are equipped to push/pull a flexural hinge based platform. The platform has a novel designed compound flexural hinges which nest separate X, Y direction moving mechanisms within one layer but avoiding from mutual cross talk, besides this, the hinges also contain leverage structures to amplify moving distance. With these designs, the platform can attain 100 μm displacement ranges as well as 1 nm resolution. In interferometer framework a heterodyne multi-pass interferometer is mounted on the platform, which measures X-Y plane movement and Z axis rotation, through reference mirror mounted on objective lens tube and Zerodur mirror mounted on PZT platform, the displacement is traced back to laser wavelength. When development is finished, the apparatus can offer the capability to calibrate one dimensional linewidths and two dimensional pitches ranging from 200nm to 50μm with expanded uncertainty below 20nm.

The Role of High-Dimensional Diffusive Search, Stabilization, and Frustration in Protein Folding

PubMed Central

Rimratchada, Supreecha; McLeish, Tom C.B.; Radford, Sheena E.; Paci, Emanuele

2014-01-01

Proteins are polymeric molecules with many degrees of conformational freedom whose internal energetic interactions are typically screened to small distances. Therefore, in the high-dimensional conformation space of a protein, the energy landscape is locally relatively flat, in contrast to low-dimensional representations, where, because of the induced entropic contribution to the full free energy, it appears funnel-like. Proteins explore the conformation space by searching these flat subspaces to find a narrow energetic alley that we call a hypergutter and then explore the next, lower-dimensional, subspace. Such a framework provides an effective representation of the energy landscape and folding kinetics that does justice to the essential characteristic of high-dimensionality of the search-space. It also illuminates the important role of nonnative interactions in defining folding pathways. This principle is here illustrated using a coarse-grained model of a family of three-helix bundle proteins whose conformations, once secondary structure has formed, can be defined by six rotational degrees of freedom. Two folding mechanisms are possible, one of which involves an intermediate. The stabilization of intermediate subspaces (or states in low-dimensional projection) in protein folding can either speed up or slow down the folding rate depending on the amount of native and nonnative contacts made in those subspaces. The folding rate increases due to reduced-dimension pathways arising from the mere presence of intermediate states, but decreases if the contacts in the intermediate are very stable and introduce sizeable topological or energetic frustration that needs to be overcome. Remarkably, the hypergutter framework, although depending on just a few physically meaningful parameters, can reproduce all the types of experimentally observed curvature in chevron plots for realizations of this fold. PMID:24739172

Real-time visual tracking of less textured three-dimensional objects on mobile platforms

NASA Astrophysics Data System (ADS)

Seo, Byung-Kuk; Park, Jungsik; Park, Hanhoon; Park, Jong-Il

2012-12-01

Natural feature-based approaches are still challenging for mobile applications (e.g., mobile augmented reality), because they are feasible only in limited environments such as highly textured and planar scenes/objects, and they need powerful mobile hardware for fast and reliable tracking. In many cases where conventional approaches are not effective, three-dimensional (3-D) knowledge of target scenes would be beneficial. We present a well-established framework for real-time visual tracking of less textured 3-D objects on mobile platforms. Our framework is based on model-based tracking that efficiently exploits partially known 3-D scene knowledge such as object models and a background's distinctive geometric or photometric knowledge. Moreover, we elaborate on implementation in order to make it suitable for real-time vision processing on mobile hardware. The performance of the framework is tested and evaluated on recent commercially available smartphones, and its feasibility is shown by real-time demonstrations.

A Conceptual and Psychometric Framework for Distinguishing Categories and Dimensions

ERIC Educational Resources Information Center

De Boeck, Paul; Wilson, Mark; Acton, G. Scott

2005-01-01

An important, sometimes controversial feature of all psychological phenomena is whether they are categorical or dimensional. A conceptual and psychometric framework is described for distinguishing whether the latent structure behind manifest categories (e.g., psychiatric diagnoses, attitude groups, or stages of development) is category-like or…

Interpenetrated Uranyl-Organic Frameworks with bor and pts Topology: Structure, Spectroscopy, and Computation.

PubMed

Liu, Chao; Chen, Fang-Yuan; Tian, Hong-Rui; Ai, Jing; Yang, Weiting; Pan, Qing-Jiang; Sun, Zhong-Ming

2017-11-20

Two novel three-dimensional interpenetrated uranyl-organic frameworks, (NH 4 ) 4 [(UO 2 ) 4 (L 1 ) 3 ]·6H 2 O (1) and [(UO 2 ) 2 (H 2 O) 2 L 2 ]·2H 2 O (2), where L 1 = tetrakis(3-carboxyphenyl)silicon and L 2 = tetrakis(4-carboxyphenyl)silicon, were synthesized by a combination of two isomeric tetrahedral silicon-centered ligands with 3-connected triangular [(UO 2 )(COO) 3 ] - and 4-connected dinuclear [(UO 2 ) 2 (COO) 4 ] units, respectively. Structural analyses indicate that 1 possesses a 2-fold interpenetrating anion bor network, while 2 exhibits a 3-fold interpenetrated 4,4-connected neutral network with pts topology. Both compounds were characterized by thermogravimetric analysis and IR, UV-vis, and photoluminescence spectroscopy. A relativistic density functional theory (DFT) investigation on 10 model compounds of 1 and 2 shows good agreement of the structural parameters, stretching vibrational frequencies, and absorption with experimental results; the time-dependent DFT calculations unravel that low-energy absorption bands originate from ligand-to-uranium charge transfer.

How does symmetry impact the flexibility of proteins?

PubMed

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-02-13

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures-and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body-bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body-bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains.

Synthesis and structure of novel lithium-ion conductor Li7Ge3PS12

NASA Astrophysics Data System (ADS)

Inoue, Yuki; Suzuki, Kota; Matsui, Naoki; Hirayama, Masaaki; Kanno, Ryoji

2017-02-01

The novel lithium-ion conductor Li7Ge3PS12 was synthesized by slow cooling from the ternary Li2S-GeS2-P2S5 system, and was shown to exhibit a cubic argyrodite-type structure. The phase composition was determined by varying the ratio of starting materials; the observed monophasic properties were close to those for the Li7Ge3PS12 composition. The lattice parameter (a =9.80192(3) Å) of Li7Ge3PS12 was slightly smaller than that of Li7PS6 (a =9.993 Å), indicating that substitution of a Li cation by the smaller Ge cation contracted the cubic lattice. In addition, the novel structure consisted of a framework composed of four isolated (Ge/P)S4 tetrahedra. Li+ ions occupied tetrahedral sites within the framework, forming a three-dimensional conduction pathway. Finally, Li7Ge3PS12 exhibited a high ionic conductivity of 1.1×10-4 S cm-1 at 25 °C and an activation energy of 25 kJ mol-1.

3D architecture constructed via the confined growth of MoS2 nanosheets in nanoporous carbon derived from metal-organic frameworks for efficient hydrogen production.

PubMed

Liu, Yun; Zhou, Xiaoli; Ding, Tao; Wang, Chunde; Yang, Qing

2015-11-21

The design and synthesis of robust, high-performance and low-cost three-dimensional (3D) hierarchical structured materials for the electrochemical reduction of water to generate hydrogen is of great significance for practical water splitting applications. In this study, we develop an in situ space-confined method to synthesize an MoS2-based 3D hierarchical structure, in which the MoS2 nanosheets grow in the confined nanopores of metal-organic frameworks (MOFs)-derived 3D carbons as electrocatalysts for efficient hydrogen production. Benefiting from its unique structure, which has more exposed active sites and enhanced conductivity, the as-prepared MoS2/3D nanoporous carbon (3D-NPC) composite exhibits remarkable electrocatalytic activity for the hydrogen evolution reaction (HER) with a small onset overpotential of ∼0.16 V, large cathodic currents, small Tafel slope of 51 mV per decade and good durability. We anticipate that this in situ confined growth provides new insights into the construction of high performance catalysts for energy storage and conversion.

Li0.5Al0.5Mg2(MoO4)3

PubMed Central

Ennajeh, Ines; Zid, Mohamed Faouzi; Driss, Ahmed

2013-01-01

The title compound, lithium/aluminium dimagnesium tetra­kis­[orthomolybdate(VI)], was prepared by a solid-state reaction route. The crystal structure is built up from MgO6 octa­hedra and MoO4 tetra­hedra sharing corners and edges, forming two types of chains running along [100]. These chains are linked into layers parallel to (010) and finally linked by MoO4 tetra­hedra into a three-dimensional framework structure with channels parallel to [001] in which lithium and aluminium cations equally occupy the same position within a distorted trigonal–bipyramidal coordination environment. The title structure is isotypic with LiMgIn(MoO4)3, with the In site becoming an Mg site and the fully occupied Li site a statistically occupied Li/Al site in the title structure. PMID:24426975

Three-dimensional structural analysis using interactive graphics

NASA Technical Reports Server (NTRS)

Biffle, J.; Sumlin, H. A.

1975-01-01

The application of computer interactive graphics to three-dimensional structural analysis was described, with emphasis on the following aspects: (1) structural analysis, and (2) generation and checking of input data and examination of the large volume of output data (stresses, displacements, velocities, accelerations). Handling of three-dimensional input processing with a special MESH3D computer program was explained. Similarly, a special code PLTZ may be used to perform all the needed tasks for output processing from a finite element code. Examples were illustrated.

Interpenetration of a 3D Icosahedral M@Ni12 (M=Al, Ga) Framework with Porphyrin-Reminiscent Boron Layers in MNi9 B8.

PubMed

Zheng, Qiang; Wagner, Frank R; Ormeci, Alim; Prots, Yurii; Burkhardt, Ulrich; Schmidt, Marcus; Schnelle, Walter; Grin, Yuri; Leithe-Jasper, Andreas

2015-11-09

Two ternary borides MNi9 B8 (M=Al, Ga) were synthesized by thermal treatment of mixtures of the elements. Single-crystal X-ray diffraction data reveal AlNi9 B8 and GaNi9 B8 crystallizing in a new type of structure within the space group Cmcm and the lattice parameters a=7.0896(3) Å, b=8.1181(3) Å, c=10.6497(4) Å and a=7.0897(5) Å, b=8.1579(4) Å, c=10.6648(7) Å, respectively. The boron atoms build up two-dimensional layers, which consist of puckered [B16 ] rings with two tailing B atoms, whereas the M atoms reside in distorted vertices-condensed [Ni12 ] icosahedra, which form a three-dimensional framework interpenetrated by boron porphyrin-reminiscent layers. An unusual local arrangement resembling a giant metallo-porphyrin entity is formed by the [B16 ] rings, which, due to their large annular size of approximately 8 Å, chelate four of the twelve icosahedral Ni atoms. An analysis of the chemical bonding by means of the electron localizability approach reveals strong covalent B-B interactions and weak Ni-Ni interactions. Multi-center dative B-Ni interaction occurs between the Al-Ni framework and the boron layers. In agreement with the chemical bonding analysis and band structure calculations, AlNi9 B8 is a Pauli-paramagnetic metal. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Hierarchical MFI Zeolite with a Two-Dimensional Square Mesostructure.

PubMed

Shen, Xuefeng; Mao, Wenting; Ma, Yanhang; Xu, Dongdong; Wu, Peng; Terasaki, Osamu; Han, Lu; Che, Shunai

2018-01-15

A conceptual design and synthesis of ordered mesoporous zeolites is a challenging research subject in material science. Several seminal articles report that one-dimensional (1D) mesostructured lamellar zeolites are possibly directed by sheet-assembly of surfactants, which collapse after removal of intercalated surfactants. However, except for one example of two-dimensional (2D) hexagonal mesoporous zeolite, no other zeolites with ordered 2D or three-dimensional (3D) mesostructures have been reported. An ordered 2D mesoporous zeolite can be templated by a cylindrical assembly unit with specific interactions in the hydrophobic part. A template molecule with azobenzene in the hydrophobic tail and diquaternary ammonium in the hydrophilic head group directs hierarchical MFI zeolite with a 2D square mesostructure. The material has an elongated octahedral morphology, and quaternary, ordered, straight, square channels framed by MFI thin sheets expanded along the a-c planes and joined with 90° rotations. The structural matching between the cylindrical assembly unit and zeolite framework is crucial for mesostructure construction. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stochastic filtering for damage identification through nonlinear structural finite element model updating

NASA Astrophysics Data System (ADS)

Astroza, Rodrigo; Ebrahimian, Hamed; Conte, Joel P.

2015-03-01

This paper describes a novel framework that combines advanced mechanics-based nonlinear (hysteretic) finite element (FE) models and stochastic filtering techniques to estimate unknown time-invariant parameters of nonlinear inelastic material models used in the FE model. Using input-output data recorded during earthquake events, the proposed framework updates the nonlinear FE model of the structure. The updated FE model can be directly used for damage identification and further used for damage prognosis. To update the unknown time-invariant parameters of the FE model, two alternative stochastic filtering methods are used: the extended Kalman filter (EKF) and the unscented Kalman filter (UKF). A three-dimensional, 5-story, 2-by-1 bay reinforced concrete (RC) frame is used to verify the proposed framework. The RC frame is modeled using fiber-section displacement-based beam-column elements with distributed plasticity and is subjected to the ground motion recorded at the Sylmar station during the 1994 Northridge earthquake. The results indicate that the proposed framework accurately estimate the unknown material parameters of the nonlinear FE model. The UKF outperforms the EKF when the relative root-mean-square error of the recorded responses are compared. In addition, the results suggest that the convergence of the estimate of modeling parameters is smoother and faster when the UKF is utilized.

Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system

DOE PAGES

Zheng, Tao; Yang, Zaixing; Gui, Daxiang; ...

2017-05-30

Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. We overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. Furthermore, these compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest voidmore » volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism.« less

Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules.

PubMed

Morphew, Daniel; Shaw, James; Avins, Christopher; Chakrabarti, Dwaipayan

2018-03-27

Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals. We obtain cubic diamond and body-centered cubic crystals via distinct clusters of uniform size and shape, namely, tetrahedra and octahedra, respectively. Such a conceptual design framework has the potential to reliably encode hierarchical self-assembly of colloidal particles into a high level of sophistication. Moreover, the design framework underpins a bottom-up route to cubic diamond colloidal crystals, which have remained elusive despite being much sought after for their attractive photonic applications.

Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system

PubMed Central

Zheng, Tao; Yang, Zaixing; Gui, Daxiang; Liu, Zhiyong; Wang, Xiangxiang; Dai, Xing; Liu, Shengtang; Zhang, Linjuan; Gao, Yang; Chen, Lanhua; Sheng, Daopeng; Wang, Yanlong; Diwu, Juan; Wang, Jianqiang; Zhou, Ruhong; Chai, Zhifang; Albrecht-Schmitt, Thomas E.; Wang, Shuao

2017-01-01

Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. Herein, we overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. These compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest void volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism. PMID:28555656

Overcoming the crystallization and designability issues in the ultrastable zirconium phosphonate framework system

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

Zheng, Tao; Yang, Zaixing; Gui, Daxiang

Metal-organic frameworks (MOFs) based on zirconium phosphonates exhibit superior chemical stability suitable for applications under harsh conditions. These compounds mostly exist as poorly crystallized precipitates, and precise structural information has therefore remained elusive. Furthermore, a zero-dimensional zirconium phosphonate cluster acting as secondary building unit has been lacking, leading to poor designability in this system. We overcome these challenges and obtain single crystals of three zirconium phosphonates that are suitable for structural analysis. Furthermore, these compounds are built by previously unknown isolated zirconium phosphonate clusters and exhibit combined high porosity and ultrastability even in fuming acids. SZ-2 possesses the largest voidmore » volume recorded in zirconium phosphonates and SZ-3 represents the most porous crystalline zirconium phosphonate and the only porous MOF material reported to survive in aqua regia. SZ-2 and SZ-3 can effectively remove uranyl ions from aqueous solutions over a wide pH range, and we have elucidated the removal mechanism.« less

Highly cytocompatible and flexible three-dimensional graphene/polydimethylsiloxane composite for culture and electrochemical detection of L929 fibroblast cells.

PubMed

Waiwijit, Uraiwan; Maturos, Thitima; Pakapongpan, Saithip; Phokharatkul, Ditsayut; Wisitsoraat, Anurat; Tuantranont, Adisorn

2016-08-01

Recently, three-dimensional graphene interconnected network has attracted great interest as a scaffold structure for tissue engineering due to its high biocompatibility, high electrical conductivity, high specific surface area and high porosity. However, free-standing three-dimensional graphene exhibits poor flexibility and stability due to ease of disintegration during processing. In this work, three-dimensional graphene is composited with polydimethylsiloxane to improve the structural flexibility and stability by a new simple two-step process comprising dip coating of polydimethylsiloxane on chemical vapor deposited graphene/Ni foam and wet etching of nickel foam. Structural characterizations confirmed an interconnected three-dimensional multi-layer graphene structure with thin polydimethylsiloxane scaffold. The composite was employed as a substrate for culture of L929 fibroblast cells and its cytocompatibility was evaluated by cell viability (Alamar blue assay), reactive oxygen species production and vinculin immunofluorescence imaging. The result revealed that cell viability on three-dimensional graphene/polydimethylsiloxane composite increased with increasing culture time and was slightly different from a polystyrene substrate (control). Moreover, cells cultured on three-dimensional graphene/polydimethylsiloxane composite generated less ROS than the control at culture times of 3-6 h. The results of immunofluorescence staining demonstrated that fibroblast cells expressed adhesion protein (vinculin) and adhered well on three-dimensional graphene/polydimethylsiloxane surface. Good cell adhesion could be attributed to suitable surface properties of three-dimensional graphene/polydimethylsiloxane with moderate contact angle and small negative zeta potential in culture solution. The results of electrochemical study by cyclic voltammetry showed that an oxidation current signal with no apparent peak was induced by fibroblast cells and the oxidation current at an oxidation potential of +0.9 V increased linearly with increasing cell number. Therefore, the three-dimensional graphene/polydimethylsiloxane composite exhibits high cytocompatibility and can potentially be used as a conductive substrate for cell-based electrochemical sensing. © The Author(s) 2016.

Toward Metal–Organic Framework-Based Solar Cells: Enhancing Directional Exciton Transport by Collapsing Three-Dimensional Film Structures

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

Goswami, Subhadip; Ma, Lin; Martinson, Alex B. F.

Owing to their ability to act as light-harvesting scaffolds, porphyrin-containing metal-organic frameworks (MOFs) are in the forefront of research on the application of highly ordered molecular materials to problems in solar-energy conversion. In this work, solvent-assisted linker exchange (SALE) is performed on a pillared paddlewheel porphyrin containing MOF thin film to collapse a 3D framework to a 2D framework. The change in dimensionality of the framework is confirmed by a decrease in the film thickness, the magnitude of which is in agreement with crystallographic parameters for related bulk materials. Furthermore, NMR spectroscopy performed on the digested sample suggests a similarmore » change in geometry is achieved in bulk MOF samples. The decreased distance between the porphyrin chromophores in the 2D MOF film compared to the 3D film results in enhanced energy transfer through the film. The extent of energy transport was probed by assembling MOF thin film where the outermost layers are palladium porphyrin (P2) units, which act as energy traps and fluorescence quenchers. Steady-state emission spectroscopy together with time-resolved emission spectroscopy indicates that excitons can travel through about 9-11 layers (porphyrin layers) in 2D films, whereas in 3D films energy transfer occurs through no more than about 6-8 layers. The results are difficult to understand if only changes in MOF interlayer spacing are considered but become much more understandable if dipole-dipole coupling distances are considered.« less

Water-Stable In(III)-Based Metal-Organic Frameworks with Rod-Shaped Secondary Building Units: Single-Crystal to Single-Crystal Transformation and Selective Sorption of C2H2 over CO2 and CH4.

PubMed

Guo, Zhen-Ji; Yu, Jiamei; Zhang, Yong-Zheng; Zhang, Jian; Chen, Ya; Wu, Yufeng; Xie, Lin-Hua; Li, Jian-Rong

2017-02-20

Three new water-stable In(III)-based metal-organic frameworks, namely, [In 3 (TTTA) 2 (OH) 3 (H 2 O)]·(DMA) 3 (BUT-70, DMA = N,N-dimethylacetamide), [In 3 (TTTA) 2 (CH 3 O) 3 ] (BUT-70A), and [In 3 (TTTA) 2 (OH) 3 ] (BUT-70B), with rod-shaped secondary building units (SBUs) and an new acrylate-based ligand, (2E,2'E,2″E)-3,3',3″-(2,4,6-trimethylbenzene-1,3,5-triyl)-triacrylate (TTTA 3- ) were obtained and structurally characterized. BUT-70A and -70B were generated in a single-crystal to single-crystal transformation fashion from BUT-70 through guest exchange followed by their removal. The solvents used for guest exchange were methanol and dichloromethane, respectively. Single-crystal structure analyses show that the guest exchange and removal process is accompanied by the substitution of coordinated water molecules of In(III) centers with uncoordinated carboxylate O atoms of TTTA 3- ligands. Moreover, hydroxyl groups bridging two In(III) centers are also replaced by methoxyl groups in the transformation from BUT-70 to -70A. Overall, three metal-organic frameworks (MOFs) are constructed by infinite chains consisting of corner-sharing InO 4 (OR) 2 (R = H or Me) octahedral entities, which are interconnected by TTTA 3- ligands to form three-dimensional frameworks. Unlike most reported MOFs with infinite chains as SBUs, such as well-known MIL-53 and M-MOF-74, which have one-dimensional channels along the chain direction, the BUT-70 series contain two-dimensional intersecting channels. The Brunauer-Emmett-Teller surface area and pore volume of BUT-70A were estimated to be 460 m 2 g -1 and 0.18 cm 3 g -1 , respectively, which are obviously lower than those of BUT-70B (695 m 2 g -1 and 0.29 cm 3 g -1 ). Gas adsorption experiments demonstrated that BUT-70A and -70B are able to selectively adsorb C 2 H 2 over CO 2 and CH 4 . At 1 atm and 298 K, BUT-70A uptakes 3.1 mmol g -1 C 2 H 2 , which is 3.6 times that of the CO 2 uptake and 7.2 times that of the CH 4 uptake. Compared with BUT-70A, BUT-70B presents an even higher C 2 H 2 uptake of 3.9 mmol g -1 at the same conditions, but slightly lower Ideal Adsorbed Solution Theory C 2 H 2 /CO 2 and C 2 H 2 /CH 4 selectivities.

Label-free imaging of the dynamics of cell-to-cell string-like structure bridging in the free-space by low-coherent quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

We succeeded in utilizing our low-coherent quantitative phase microscopy (LC-QPM) to achieve label-free and three-dimensional imaging of string-like structures bridging the free-space between live cells. In past studies, three dimensional morphology of the string-like structures between cells had been investigated by electron microscopies and fluorescence microscopies and these structures were called "membrane nanotubes" or "tunneling nanotubes." However, use of electron microscopy inevitably kills these cells and fluorescence microscopy is itself a potentially invasive method. To achieve noninvasive imaging of live cells, we applied our LC-QPM which is a reflection-type, phase resolved and full-field interference microscope employing a low-coherent light source. LC-QPM is able to visualize the three-dimensional morphology of live cells without labeling by means of low-coherence interferometry. The lateral (diffraction limit) and longitudinal (coherence-length) spatial resolution of LC-QPM were respectively 0.49 and 0.93 micrometers and the repeatability of the phase measurement was 0.02 radians (1.0 nm). We successfully obtained three-dimensional morphology of live cultured epithelial cells (cell type: HeLa, derived from cervix cancer) and were able to clearly observe the individual string-like structures interconnecting the cells. When we performed volumetric imaging, a 80 micrometer by 60 micrometer by 6.5 micrometer volume was scanned every 5.67 seconds and 70 frames of a three-dimensional movie were recorded for a duration of 397 seconds. Moreover, the optical phase images gave us detailed information about the three-dimensional morphology of the string-like structure at sub-wavelength resolution. We believe that our LC-QPM will be a useful tool for the study of three-dimensional morphology of live cells.

Multifunctional nitrogen-doped graphene nanoribbon aerogels for superior lithium storage and cell culture

NASA Astrophysics Data System (ADS)

Liu, Yang; Wang, Xuzhen; Wan, Wubo; Li, Lingli; Dong, Yanfeng; Zhao, Zongbin; Qiu, Jieshan

2016-01-01

Nitrogen-doped graphene nanoribbon aerogels (N-GNRAs) are fabricated through the self-assembly of graphene oxide nanoribbons (GONRs) combined with a thermal annealing process. Amino-groups are grafted to the surface of graphene nanoribbons (GNRs) by an epoxy ring-opening reaction. High nitrogen doping level (7.6 atm% as confirmed by elemental analysis) is achieved during thermal treatment resulting from functionalization and the rich edge structures of GNRs. The three dimensional (3D) N-GNRAs feature a hierarchical porous structure. The quasi-one dimensional (1D) GNRs act as the building blocks for the construction of fishnet-like GNR sheets, which further create 3D frameworks with micrometer-scale pores. The edge effect of GNRs combined with nitrogen doping and porosity give rise to good electrical conductivity, superhydrophilic, highly compressible and low density GNRAs. As a result, a high capacity of 910 mA h g-1 is achieved at a current density of 0.5 A g-1 when they are tested as anode materials for lithium ion batteries. Further cell culture experiments with the GNRAs as human medulloblastoma DAOY cell scaffolds demonstrate their good biocompatibility, inferring potential applications in the biomedical field.Nitrogen-doped graphene nanoribbon aerogels (N-GNRAs) are fabricated through the self-assembly of graphene oxide nanoribbons (GONRs) combined with a thermal annealing process. Amino-groups are grafted to the surface of graphene nanoribbons (GNRs) by an epoxy ring-opening reaction. High nitrogen doping level (7.6 atm% as confirmed by elemental analysis) is achieved during thermal treatment resulting from functionalization and the rich edge structures of GNRs. The three dimensional (3D) N-GNRAs feature a hierarchical porous structure. The quasi-one dimensional (1D) GNRs act as the building blocks for the construction of fishnet-like GNR sheets, which further create 3D frameworks with micrometer-scale pores. The edge effect of GNRs combined with nitrogen doping and porosity give rise to good electrical conductivity, superhydrophilic, highly compressible and low density GNRAs. As a result, a high capacity of 910 mA h g-1 is achieved at a current density of 0.5 A g-1 when they are tested as anode materials for lithium ion batteries. Further cell culture experiments with the GNRAs as human medulloblastoma DAOY cell scaffolds demonstrate their good biocompatibility, inferring potential applications in the biomedical field. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05909g

Fabrication and Structural Characterization of an Ultrathin Film of a Two-Dimensional-Layered Metal-Organic Framework, {Fe(py)2[Ni(CN)4]} (py = pyridine).

PubMed

Sakaida, Shun; Haraguchi, Tomoyuki; Otsubo, Kazuya; Sakata, Osami; Fujiwara, Akihiko; Kitagawa, Hiroshi

2017-07-17

We report the fabrication and characterization of the first example of a tetracyanonickelate-based two-dimensional-layered metal-organic framework, {Fe(py) 2 Ni(CN) 4 } (py = pyridine), thin film. To fabricate a nanometer-sized thin film, we utilized the layer-by-layer method, whereby a substrate was alternately soaked in solutions of the structural components. Surface X-ray studies revealed that the fabricated film was crystalline with well-controlled growth directions both parallel and perpendicular to the substrate. In addition, lattice parameter analysis indicated that the crystal system is found to be close to higher symmetry by being downsized to a thin film.

Freestanding eggshell membrane-based electrodes for high-performance supercapacitors and oxygen evolution reaction

NASA Astrophysics Data System (ADS)

Geng, Jing; Wu, Hao; Al-Enizi, Abdullah M.; Elzatahry, Ahmed A.; Zheng, Gengfeng

2015-08-01

A type of freestanding, light-weight eggshell membrane-based electrode is demonstrated for supercapacitors and for oxygen evolution reaction (OER) catalysis. As a widely available daily waste, eggshell membranes have unique porous three-dimensional grid-like fibrous structures with relatively high surface area and abundant macropores, allowing for effective conjugation of carbon nanotubes and growth of NiCo2O4 nanowire arrays, an effective supercapacitor material and OER catalyst. The three-dimensional fibrous eggshell membrane frameworks with carbon nanotubes offer efficient pathways for charge transport, and the macropores between adjacent fibers are fully accessible for electrolytes and bubble evolution. As a supercapacitor, the eggshell membrane/carbon nanotube/NiCo2O4 electrode shows high specific capacitances at current densities from 1 to 20 A g-1, with excellent capacitance retention (>90%) at 10 A g-1 for over 10 000 cycles. When employed as an OER catalyst, this eggshell membrane-based electrode exhibits an OER onset potential of 1.53 V vs. the reversible hydrogen electrode (RHE), and a stable catalytic current density of 20 mA cm-2 at 1.65 V vs. the RHE.A type of freestanding, light-weight eggshell membrane-based electrode is demonstrated for supercapacitors and for oxygen evolution reaction (OER) catalysis. As a widely available daily waste, eggshell membranes have unique porous three-dimensional grid-like fibrous structures with relatively high surface area and abundant macropores, allowing for effective conjugation of carbon nanotubes and growth of NiCo2O4 nanowire arrays, an effective supercapacitor material and OER catalyst. The three-dimensional fibrous eggshell membrane frameworks with carbon nanotubes offer efficient pathways for charge transport, and the macropores between adjacent fibers are fully accessible for electrolytes and bubble evolution. As a supercapacitor, the eggshell membrane/carbon nanotube/NiCo2O4 electrode shows high specific capacitances at current densities from 1 to 20 A g-1, with excellent capacitance retention (>90%) at 10 A g-1 for over 10 000 cycles. When employed as an OER catalyst, this eggshell membrane-based electrode exhibits an OER onset potential of 1.53 V vs. the reversible hydrogen electrode (RHE), and a stable catalytic current density of 20 mA cm-2 at 1.65 V vs. the RHE. Electronic supplementary information (ESI) available: Supporting figures, with additional SEM images, EDS spectra, N2 sorption isotherms, charge-discharge curves, cycling performance, Ragone plot, Nyquist plots and linear scan voltammogram plots. See DOI: 10.1039/c5nr04603c

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.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming.

PubMed

Abbas, Ahmed; Guo, Xianrong; Jing, Bing-Yi; Gao, Xin

2014-06-01

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on 'slices', which are one-dimensional vectors in three-dimensional spectra that correspond to certain ([Formula: see text]) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Three-dimensional crystal structure of recombinant murine interferon-beta.

PubMed Central

Senda, T; Shimazu, T; Matsuda, S; Kawano, G; Shimizu, H; Nakamura, K T; Mitsui, Y

1992-01-01

The crystal structure of recombinant murine interferon-beta (IFN-beta) has been solved by the multiple isomorphous replacement method and refined to an R-factor of 20.5% against 2.6 A X-ray diffraction data. The structure shows a variant of the alpha-helix bundle with a new chain-folding topology, which seems to represent a basic structural framework of all the IFN-alpha and IFN-beta molecules belonging to the type I family. Functionally important segments of the polypeptide chain, as implied through numerous gene manipulation studies carried out so far, are spatially clustered indicating the binding site(s) to the receptor(s). Comparison of the present structure with those of other alpha-helical cytokine proteins, including porcine growth hormone, interleukin 2 and interferon gamma, indicated either a topological similarity in chain folding or a similar spatial arrangement of the alpha-helices. Images PMID:1505514

Caustic Skeleton & Cosmic Web

NASA Astrophysics Data System (ADS)

Feldbrugge, Job; van de Weygaert, Rien; Hidding, Johan; Feldbrugge, Joost

2018-05-01

We present a general formalism for identifying the caustic structure of a dynamically evolving mass distribution, in an arbitrary dimensional space. The identification of caustics in fluids with Hamiltonian dynamics, viewed in Lagrangian space, corresponds to the classification of singularities in Lagrangian catastrophe theory. On the basis of this formalism we develop a theoretical framework for the dynamics of the formation of the cosmic web, and specifically those aspects that characterize its unique nature: its complex topological connectivity and multiscale spinal structure of sheetlike membranes, elongated filaments and compact cluster nodes. Given the collisionless nature of the gravitationally dominant dark matter component in the universe, the presented formalism entails an accurate description of the spatial organization of matter resulting from the gravitationally driven formation of cosmic structure. The present work represents a significant extension of the work by Arnol'd et al. [1], who classified the caustics that develop in one- and two-dimensional systems that evolve according to the Zel'dovich approximation. His seminal work established the defining role of emerging singularities in the formation of nonlinear structures in the universe. At the transition from the linear to nonlinear structure evolution, the first complex features emerge at locations where different fluid elements cross to establish multistream regions. Involving a complex folding of the 6-D sheetlike phase-space distribution, it manifests itself in the appearance of infinite density caustic features. The classification and characterization of these mass element foldings can be encapsulated in caustic conditions on the eigenvalue and eigenvector fields of the deformation tensor field. In this study we introduce an alternative and transparent proof for Lagrangian catastrophe theory. This facilitates the derivation of the caustic conditions for general Lagrangian fluids, with arbitrary dynamics. Most important in the present context is that it allows us to follow and describe the full three-dimensional geometric and topological complexity of the purely gravitationally evolving nonlinear cosmic matter field. While generic and statistical results can be based on the eigenvalue characteristics, one of our key findings is that of the significance of the eigenvector field of the deformation field for outlining the entire spatial structure of the caustic skeleton emerging from a primordial density field. In this paper we explicitly consider the caustic conditions for the three-dimensional Zel'dovich approximation, extending earlier work on those for one- and two-dimensional fluids towards the full spatial richness of the cosmic web. In an accompanying publication, we apply this towards a full three-dimensional study of caustics in the formation of the cosmic web and evaluate in how far it manages to outline and identify the intricate skeletal features in the corresponding N-body simulations.

Quantifying the effect of hydrogen on dislocation dynamics: A three-dimensional discrete dislocation dynamics framework

NASA Astrophysics Data System (ADS)

Gu, Yejun; El-Awady, Jaafar A.

2018-03-01

We present a new framework to quantify the effect of hydrogen on dislocations using large scale three-dimensional (3D) discrete dislocation dynamics (DDD) simulations. In this model, the first order elastic interaction energy associated with the hydrogen-induced volume change is accounted for. The three-dimensional stress tensor induced by hydrogen concentration, which is in equilibrium with respect to the dislocation stress field, is derived using the Eshelby inclusion model, while the hydrogen bulk diffusion is treated as a continuum process. This newly developed framework is utilized to quantify the effect of different hydrogen concentrations on the dynamics of a glide dislocation in the absence of an applied stress field as well as on the spacing between dislocations in an array of parallel edge dislocations. A shielding effect is observed for materials having a large hydrogen diffusion coefficient, with the shield effect leading to the homogenization of the shrinkage process leading to the glide loop maintaining its circular shape, as well as resulting in a decrease in dislocation separation distances in the array of parallel edge dislocations. On the other hand, for materials having a small hydrogen diffusion coefficient, the high hydrogen concentrations around the edge characters of the dislocations act to pin them. Higher stresses are required to be able to unpin the dislocations from the hydrogen clouds surrounding them. Finally, this new framework can open the door for further large scale studies on the effect of hydrogen on the different aspects of dislocation-mediated plasticity in metals. With minor modifications of the current formulations, the framework can also be extended to account for general inclusion-induced stress field in discrete dislocation dynamics simulations.

Effect of randomness on multi-frequency aeroelastic responses resolved by Unsteady Adaptive Stochastic Finite Elements

NASA Astrophysics Data System (ADS)

Witteveen, Jeroen A. S.; Bijl, Hester

2009-10-01

The Unsteady Adaptive Stochastic Finite Elements (UASFE) method resolves the effect of randomness in numerical simulations of single-mode aeroelastic responses with a constant accuracy in time for a constant number of samples. In this paper, the UASFE framework is extended to multi-frequency responses and continuous structures by employing a wavelet decomposition pre-processing step to decompose the sampled multi-frequency signals into single-frequency components. The effect of the randomness on the multi-frequency response is then obtained by summing the results of the UASFE interpolation at constant phase for the different frequency components. Results for multi-frequency responses and continuous structures show a three orders of magnitude reduction of computational costs compared to crude Monte Carlo simulations in a harmonically forced oscillator, a flutter panel problem, and the three-dimensional transonic AGARD 445.6 wing aeroelastic benchmark subject to random fields and random parameters with various probability distributions.

Poly[di-μ2-chlorido-tri-μ2-terephthalato-tetra­lead(II)

PubMed Central

Yang, Lei; Li, Zhongyue; Li, Guanghua

2011-01-01

The title compound, [Pb4(C8H4O4)3Cl2]n, consists of a three-dimensional inorganic–organic hybrid framework. The asymmetric unit contains two Pb2+ cations, one Cl− anion and one and a half terephthalate anions, the latter being completed by inversion symmetry. The two Pb2+ cations are each surrounded by five O atoms and one Cl atom in the form of irregular polyhedra. The cations are linked by μ2-O and μ2-Cl atoms into binuclear units, which are further extended through Pb—O inter­actions into an undulated inorganic layer parallel to (001). These layers are connected along [001] by the terephthalate groups into a three-dimensional framework. PMID:21754648

Integration of genomic and medical data into a 3D atlas of human anatomy.

PubMed

Turinsky, Andrei L; Fanea, Elena; Trinh, Quang; Dong, Xiaoli; Stromer, Julie N; Shu, Xueling; Wat, Stephen; Hallgrímsson, Benedikt; Hill, Jonathan W; Edwards, Carol; Grosenick, Brenda; Yajima, Masumi; Sensen, Christoph W

2008-01-01

We have developed a framework for the visual integration and exploration of multi-scale biomedical data, which includes anatomical and molecular components. We have also created a Java-based software system that integrates molecular information, such as gene expression data, into a three-dimensional digital atlas of the male adult human anatomy. Our atlas is structured according to the Terminologia Anatomica. The underlying data-indexing mechanism uses open standards and semantic ontology-processing tools to establish the associations between heterogeneous data types. The software system makes an extensive use of virtual reality visualization.

Gain in three-dimensional metamaterials utilizing semiconductor quantum structures

NASA Astrophysics Data System (ADS)

Schwaiger, Stephan; Klingbeil, Matthias; Kerbst, Jochen; Rottler, Andreas; Costa, Ricardo; Koitmäe, Aune; Bröll, Markus; Heyn, Christian; Stark, Yuliya; Heitmann, Detlef; Mendach, Stefan

2011-10-01

We demonstrate gain in a three-dimensional metal/semiconductor metamaterial by the integration of optically active semiconductor quantum structures. The rolling-up of a metallic structure on top of strained semiconductor layers containing a quantum well allows us to achieve a tightly bent superlattice consisting of alternating layers of lossy metallic and amplifying gain material. We show that the transmission through the superlattice can be enhanced by exciting the quantum well optically under both pulsed or continuous wave excitation. This points out that our structures can be used as a starting point for arbitrary three-dimensional metamaterials including gain.

The Structure Lacuna

PubMed Central

Boeyens, Jan C.A.; Levendis, Demetrius C.

2012-01-01

Molecular symmetry is intimately connected with the classical concept of three-dimensional molecular structure. In a non-classical theory of wave-like interaction in four-dimensional space-time, both of these concepts and traditional quantum mechanics lose their operational meaning, unless suitably modified. A required reformulation should emphasize the importance of four-dimensional effects like spin and the symmetry effects of space-time curvature that could lead to a fundamentally different understanding of molecular symmetry and structure in terms of elementary number theory. Isolated single molecules have no characteristic shape and macro-biomolecules only develop robust three-dimensional structure in hydrophobic response to aqueous cellular media. PMID:22942753

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Three-dimensional perspective software for representation of digital imagery data. [Olympic National Park, Washington

NASA Technical Reports Server (NTRS)

Junkin, B. G.

1980-01-01

A generalized three dimensional perspective software capability was developed within the framework of a low cost computer oriented geographically based information system using the Earth Resources Laboratory Applications Software (ELAS) operating subsystem. This perspective software capability, developed primarily to support data display requirements at the NASA/NSTL Earth Resources Laboratory, provides a means of displaying three dimensional feature space object data in two dimensional picture plane coordinates and makes it possible to overlay different types of information on perspective drawings to better understand the relationship of physical features. An example topographic data base is constructed and is used as the basic input to the plotting module. Examples are shown which illustrate oblique viewing angles that convey spatial concepts and relationships represented by the topographic data planes.

[Dimensional structure of the Brazilian version of the Scale of Satisfaction with Interpersonal Processes of General Medical Care].

PubMed

Nascimento, Maria Isabel do; Reichenheim, Michael Eduardo; Monteiro, Gina Torres Rego

2011-12-01

The objective of this study was to reassess the dimensional structure of a Brazilian version of the Scale of Satisfaction with Interpersonal Processes of General Medical Care, proposed originally as a one-dimensional instrument. Strict confirmatory factor analysis (CFA) and exploratory factor analysis modeled within a CFA framework (E/CFA) were used to identify the best model. An initial CFA rejected the one-dimensional structure, while an E/CFA suggested a two-dimensional structure. The latter structure was followed by a new CFA, which showed that the model without cross-loading was the most parsimonious, with adequate fit indices (CFI = 0.982 and TLI = 0.988), except for RMSEA (0.062). Although the model achieved convergent validity, discriminant validity was questionable, with the square-root of the mean variance extracted from dimension 1 estimates falling below the respective factor correlation. According to these results, there is not sufficient evidence to recommend the immediate use of the instrument, and further studies are needed for a more in-depth analysis of the postulated structures.

The crystal structure of the interrupted framework silicate K{sub 9.6}Ca{sub 1.2}Si{sub 12}O{sub 30} determined from laboratory X-ray diffraction data

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

Kahlenberg, V.; Kaindl, R.; Christian-Doppler-Laboratory for Advanced Hard Coatings at the Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, A-6020 Innsbruck

2006-07-15

The crystal structure of a potassium calcium silicate with composition K{sub 9.6}Ca{sub 1.2}Si{sub 12}O{sub 30} (or K{sub 8}CaSi{sub 10}O{sub 25}) has been solved by direct methods aided by distance least squares optimization from laboratory X-ray powder diffraction data. The trigonal compound adopts the non-centrosymmetric space group R3c with the following basic crystallographic data: a=11.13623(5)A, c=21.9890(2)A, V=2361.63(2)A{sup 3}, Z=3, D{sub calc}=2.617gcm{sup -3}. The crystal structure can be classified as an interrupted framework with exclusively Q{sup 3}-units. It can be thought of as being built from layers parallel to (001) containing isolated six-membered tetrahedral rings in UDUDUD conformation. Corner sharing of tetrahedramore » belonging to adjacent sheets results in a tetrahedral framework. The framework density of the structure is 15.2 T-atoms/1000A{sup 3}. The coordination sequences are identical for both silicon atoms in the asymmetric unit: 3-6-11-20-32-46-60-80-102-122. The vertex symbols for the two tetrahedral centers are 10{sub 2}.10{sub 2}.6{sub 1}. Topologically, the structure can be described as an Archimedean three-dimensional 3-connected net. It can be derived from the diamond or cristobalite net by removing 20% of the knots. Charge compensation in the structure is achieved by the incorporation of mono- and divalent M-cations (M: K, Ca). These extra-framework ions are coordinated by six to nine oxygen ligands. Ca/K distributions for the five symmetrically independent M-sites were obtained from a combination of bond distance considerations, site occupancy refinements and the bulk chemical composition. The structural characterization is completed by a detailed Raman spectroscopic study. Furthermore, possible implications of the structural chemistry of interrupted framework silicates for the field of silicate glass research are addressed.« less

Building Background Knowledge through Reading: Rethinking Text Sets

ERIC Educational Resources Information Center

Lupo, Sarah M.; Strong, John Z.; Lewis, William; Walpole, Sharon; McKenna, Michael C.

2018-01-01

To increase reading volume and help students access challenging texts, the authors propose a four-dimensional framework for text sets. The quad text set framework is designed around a target text: a challenging content area text, such as a canonical literary work, research article, or historical primary source document. The three remaining…

New vanadium tellurites: Syntheses, structures, optical properties of noncentrosymmetric VTeO{sub 4}(OH), centrosymmetric Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})

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

Liang, Ming-Li; State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002; Marsh, Matthew

Two new vanadium tellurites, VTeO{sub 4}(OH) (1) and Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2), have been synthesized successfully with the use of hydrothermal reactions. The crystal structures of the two compounds were determined by single-crystal X-ray diffraction. Compound 1 crystallizes in the polar space group Pca2{sub 1} (No. 29) while compound 2 crystallizes in the centrosymmetric space group C2/c (No. 15). The topography of compound 1 reveals a two-dimensional, layered structure comprised of VO{sub 6} octahedral chains and TeO{sub 3}(OH) zig-zag chains. Compound 2, on the contrary, features a three-dimensional [V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})]{sup 4-} anionic framework withmore » Ba{sup 2+} ions filled into the 10-member ring helical tunnels. The [V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})]{sup 4-} anionic network is the first 3D vanadium tellurite framework to be discovered in the alkaline-earth vanadium tellurite system. Powder second harmonic generation (SHG) measurements indicate that compound 1 shows a weak SHG response of about 0.3×KDP (KH{sub 2}PO{sub 4}) under 1064 nm laser radiation. Infrared spectroscopy, elemental analysis, thermal analysis, and dipole moment calculations have also been carried out. - Graphical abstract: VTeO{sub 4}(OH) (1) crystallizes in the noncentrosymmetric space group Pca2{sub 1} (No. 29) while Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2) crystallizes in the centrosymmetric space group C2/c (No. 15). - Highlights: • VTeO{sub 4}(OH) (1) and Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2) have been synthesized successfully with the use of hydrothermal reactions. • VTeO{sub 4}(OH) (1) crystallizes in the noncentrosymmetric space group Pca2{sub 1} and displays a weak SHG response. • VTeO{sub 4}(OH) (1) represents only the fourth SHG-active material found in vanadium tellurite systems. • Ba{sub 2}V{sub 4}O{sub 8}(Te{sub 3}O{sub 10}) (2) exhibits a novel three-dimensional [V{sub 4}O{sub 8}(Te{sub 3}O{sub 10})]{sup 4-} anionic framework.« less

Characterizing College Science Assessments: The Three-Dimensional Learning Assessment Protocol

PubMed Central

Underwood, Sonia M.; Matz, Rebecca L.; Posey, Lynmarie A.; Carmel, Justin H.; Caballero, Marcos D.; Fata-Hartley, Cori L.; Ebert-May, Diane; Jardeleza, Sarah E.; Cooper, Melanie M.

2016-01-01

Many calls to improve science education in college and university settings have focused on improving instructor pedagogy. Meanwhile, science education at the K-12 level is undergoing significant changes as a result of the emphasis on scientific and engineering practices, crosscutting concepts, and disciplinary core ideas. This framework of “three-dimensional learning” is based on the literature about how people learn science and how we can help students put their knowledge to use. Recently, similar changes are underway in higher education by incorporating three-dimensional learning into college science courses. As these transformations move forward, it will become important to assess three-dimensional learning both to align assessments with the learning environment, and to assess the extent of the transformations. In this paper we introduce the Three-Dimensional Learning Assessment Protocol (3D-LAP), which is designed to characterize and support the development of assessment tasks in biology, chemistry, and physics that align with transformation efforts. We describe the development process used by our interdisciplinary team, discuss the validity and reliability of the protocol, and provide evidence that the protocol can distinguish between assessments that have the potential to elicit evidence of three-dimensional learning and those that do not. PMID:27606671

Characterizing College Science Assessments: The Three-Dimensional Learning Assessment Protocol.

PubMed

Laverty, James T; Underwood, Sonia M; Matz, Rebecca L; Posey, Lynmarie A; Carmel, Justin H; Caballero, Marcos D; Fata-Hartley, Cori L; Ebert-May, Diane; Jardeleza, Sarah E; Cooper, Melanie M

2016-01-01

Many calls to improve science education in college and university settings have focused on improving instructor pedagogy. Meanwhile, science education at the K-12 level is undergoing significant changes as a result of the emphasis on scientific and engineering practices, crosscutting concepts, and disciplinary core ideas. This framework of "three-dimensional learning" is based on the literature about how people learn science and how we can help students put their knowledge to use. Recently, similar changes are underway in higher education by incorporating three-dimensional learning into college science courses. As these transformations move forward, it will become important to assess three-dimensional learning both to align assessments with the learning environment, and to assess the extent of the transformations. In this paper we introduce the Three-Dimensional Learning Assessment Protocol (3D-LAP), which is designed to characterize and support the development of assessment tasks in biology, chemistry, and physics that align with transformation efforts. We describe the development process used by our interdisciplinary team, discuss the validity and reliability of the protocol, and provide evidence that the protocol can distinguish between assessments that have the potential to elicit evidence of three-dimensional learning and those that do not.

Synthesis and Structural Studies of Calcium and Magnesium Phosphinate and Phosphonate Compounds

NASA Astrophysics Data System (ADS)

Bampoh, Victoria Naa Kwale

The work presented herein describes synthetic methodologies leading to the design of a wide array of magnesium and calcium based phosphinate and phosphonates with possible applications as bone scaffolding materials or additives to bone cements. The challenge to the chemistry of the alkaline earth phosphonate target compounds includes poor solubility of compounds, and poorly understood details on the control of the metal's coordination environment. Hence, less is known on phosphonate based alkaline earth metal organic frameworks as compared to transition metal phosphonates. Factors governing the challenges in obtaining crystalline, well-defined magnesium and calcium solids lie in the large metal diameters, the absence of energetically available d-orbitals to direct metal geometry, as well as the overall weakness of the metal-ligand bonds. A significant part of this project was concerned with the development of suitable reaction conditions to obtain X-ray quality crystals of the reaction products to allow for structural elucidation of the novel compounds. Various methodologies to aid in crystal growth including hydrothermal methods and gel crystallization were employed. We have used phosphinate and phosphonate ligands with different number of phosphorus oxygen atoms as well as diphosphonates with different linker lengths to determine their effects on the overall structural features. An interesting correlation is observed between the dimensionality of products and the increasing number of donor oxygen atoms in the ligands as we progress from phosphinic acid to the phosphorous acids. As an example, monophosphinate ligand only yielded one-dimensional compounds, whereas the phosphonates crystallize as one and two-dimensional compounds, and the di- and triphosphonate based compounds display two or three-dimensional geometries. This thesis provides a selection of calcium and magnesium compounds with one-dimensional geometry, as represented in a calcium phosphinate to novel two-dimensional sheets of magnesium and pillared calcium phosphonates. The preparation of these novel compounds has led to the establishment of synthetic protocols that allow for the direct preparation of compounds with defined structural features.

Creating physically-based three-dimensional microstructures: Bridging phase-field and crystal plasticity models.

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

Lim, Hojun; Owen, Steven J.; Abdeljawad, Fadi F.

In order to better incorporate microstructures in continuum scale models, we use a novel finite element (FE) meshing technique to generate three-dimensional polycrystalline aggregates from a phase field grain growth model of grain microstructures. The proposed meshing technique creates hexahedral FE meshes that capture smooth interfaces between adjacent grains. Three dimensional realizations of grain microstructures from the phase field model are used in crystal plasticity-finite element (CP-FE) simulations of polycrystalline a -iron. We show that the interface conformal meshes significantly reduce artificial stress localizations in voxelated meshes that exhibit the so-called "wedding cake" interfaces. This framework provides a direct linkmore » between two mesoscale models - phase field and crystal plasticity - and for the first time allows mechanics simulations of polycrystalline materials using three-dimensional hexahedral finite element meshes with realistic topological features.« less

Small-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements.

PubMed

Liebi, Marianne; Georgiadis, Marios; Kohlbrecher, Joachim; Holler, Mirko; Raabe, Jörg; Usov, Ivan; Menzel, Andreas; Schneider, Philipp; Bunk, Oliver; Guizar-Sicairos, Manuel

2018-01-01

Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349-352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.

Controls on coral-ground development along the northern Mesoamerican Reef tract.

PubMed

Rodríguez-Martínez, Rosa E; Jordán-Garza, Adán G; Maldonado, Miguel A; Blanchon, Paul

2011-01-01

Coral-grounds are reef communities that colonize rocky substratum but do not form framework or three-dimensional reef structures. To investigate why, we used video transects and underwater photography to determine the composition, structure and status of a coral-ground community located on the edge of a rocky terrace in front of a tourist park, Xcaret, in the northern Mesoamerican Reef tract, Mexico. The community has a relatively low coral, gorgonian and sponge cover (<10%) and high algal cover (>40%). We recorded 23 species of Scleractinia, 14 species of Gorgonacea and 30 species of Porifera. The coral community is diverse but lacks large coral colonies, being dominated instead by small, sediment-tolerant, and brooding species. In these small colonies, the abundance of potentially lethal interactions and partial mortality is high but decreases when colonies are larger than 40 cm. Such characteristics are consistent with an environment control whereby storm waves periodically remove larger colonies and elevate sediment flux. The community only survives these storm conditions due to its slope-break location, which ensures lack of burial and continued local recruitment. A comparison with similar coral-ground communities in adjacent areas suggests that the narrow width of the rock terrace hinders sediment stabilization, thereby ensuring that communities cannot escape bottom effects and develop into three-dimensional reef structures on geological time scales.

Predicting crystal growth via a unified kinetic three-dimensional partition model

NASA Astrophysics Data System (ADS)

Anderson, Michael W.; Gebbie-Rayet, James T.; Hill, Adam R.; Farida, Nani; Attfield, Martin P.; Cubillas, Pablo; Blatov, Vladislav A.; Proserpio, Davide M.; Akporiaye, Duncan; Arstad, Bjørnar; Gale, Julian D.

2017-04-01

Understanding and predicting crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for more than one hundred years, it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopy. To organize and understand this large amount of new information, new rules for crystal growth need to be developed and tested. However, because of the complexity and variety of different crystal systems, attempts to understand crystal growth in detail have so far relied on developing models that are usually applicable to only one system. Such models cannot be used to achieve the wide scope of understanding that is required to create a unified model across crystal types and crystal structures. Here we describe a general approach to understanding and, in theory, predicting the growth of a wide range of crystal types, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic three-dimensional partition model. This entails dividing the structure into ‘natural tiles’ or Voronoi polyhedra that are metastable and, consequently, temporally persistent. As such, these units are then suitable for re-construction of the crystal via a Monte Carlo algorithm. We demonstrate our approach by predicting the crystal growth of a diverse set of crystal types, including zeolites, metal-organic frameworks, calcite, urea and L-cystine.

Porous Fe2O3 Nanoframeworks Encapsulated within Three-Dimensional Graphene as High-Performance Flexible Anode for Lithium-Ion Battery.

PubMed

Jiang, Tiancai; Bu, Fanxing; Feng, Xiaoxiang; Shakir, Imran; Hao, Guolin; Xu, Yuxi

2017-05-23

Integrating nanoscale porous metal oxides into three-dimensional graphene (3DG) with encapsulated structure is a promising route but remains challenging to develop high-performance electrodes for lithium-ion battery. Herein, we design 3DG/metal organic framework composite by an excessive metal-ion-induced combination and spatially confined Ostwald ripening strategy, which can be transformed into 3DG/Fe 2 O 3 aerogel with porous Fe 2 O 3 nanoframeworks well encapsulated within graphene. The hierarchical structure offers highly interpenetrated porous conductive network and intimate contact between graphene and porous Fe 2 O 3 as well as abundant stress buffer nanospace for effective charge transport and robust structural stability during electrochemical processes. The obtained free-standing 3DG/Fe 2 O 3 aerogel was directly used as highly flexible anode upon mechanical pressing for lithium-ion battery and showed an ultrahigh capacity of 1129 mAh/g at 0.2 A/g after 130 cycles and outstanding cycling stability with a capacity retention of 98% after 1200 cycles at 5 A/g, which is the best results that have been reported so far. This study offers a promising route to greatly enhance the electrochemical properties of metal oxides and provides suggestive insights for developing high-performance electrode materials for electrochemical energy storage.

A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling

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

Lee, Hyun Jung; McDonnell, Kevin T.; Zelenyuk, Alla

2014-03-01

Although the Euclidean distance does well in measuring data distances within high-dimensional clusters, it does poorly when it comes to gauging inter-cluster distances. This significantly impacts the quality of global, low-dimensional space embedding procedures such as the popular multi-dimensional scaling (MDS) where one can often observe non-intuitive layouts. We were inspired by the perceptual processes evoked in the method of parallel coordinates which enables users to visually aggregate the data by the patterns the polylines exhibit across the dimension axes. We call the path of such a polyline its structure and suggest a metric that captures this structure directly inmore » high-dimensional space. This allows us to better gauge the distances of spatially distant data constellations and so achieve data aggregations in MDS plots that are more cognizant of existing high-dimensional structure similarities. Our MDS plots also exhibit similar visual relationships as the method of parallel coordinates which is often used alongside to visualize the high-dimensional data in raw form. We then cast our metric into a bi-scale framework which distinguishes far-distances from near-distances. The coarser scale uses the structural similarity metric to separate data aggregates obtained by prior classification or clustering, while the finer scale employs the appropriate Euclidean distance.« less

OMFIT Tokamak Profile Data Fitting and Physics Analysis

DOE PAGES

Logan, N. C.; Grierson, B. A.; Haskey, S. R.; ...

2018-01-22

Here, One Modeling Framework for Integrated Tasks (OMFIT) has been used to develop a consistent tool for interfacing with, mapping, visualizing, and fitting tokamak profile measurements. OMFIT is used to integrate the many diverse diagnostics on multiple tokamak devices into a regular data structure, consistently applying spatial and temporal treatments to each channel of data. Tokamak data are fundamentally time dependent and are treated so from the start, with front-loaded and logic-based manipulations such as filtering based on the identification of edge-localized modes (ELMs) that commonly scatter data. Fitting is general in its approach, and tailorable in its application inmore » order to address physics constraints and handle the multiple spatial and temporal scales involved. Although community standard one-dimensional fitting is supported, including scale length–fitting and fitting polynomial-exponential blends to capture the H-mode pedestal, OMFITprofiles includes two-dimensional (2-D) fitting using bivariate splines or radial basis functions. These 2-D fits produce regular evolutions in time, removing jitter that has historically been smoothed ad hoc in transport applications. Profiles interface directly with a wide variety of models within the OMFIT framework, providing the inputs for TRANSP, kinetic-EFIT 2-D equilibrium, and GPEC three-dimensional equilibrium calculations. he OMFITprofiles tool’s rapid and comprehensive analysis of dynamic plasma profiles thus provides the critical link between raw tokamak data and simulations necessary for physics understanding.« less

OMFIT Tokamak Profile Data Fitting and Physics Analysis

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

Logan, N. C.; Grierson, B. A.; Haskey, S. R.

Here, One Modeling Framework for Integrated Tasks (OMFIT) has been used to develop a consistent tool for interfacing with, mapping, visualizing, and fitting tokamak profile measurements. OMFIT is used to integrate the many diverse diagnostics on multiple tokamak devices into a regular data structure, consistently applying spatial and temporal treatments to each channel of data. Tokamak data are fundamentally time dependent and are treated so from the start, with front-loaded and logic-based manipulations such as filtering based on the identification of edge-localized modes (ELMs) that commonly scatter data. Fitting is general in its approach, and tailorable in its application inmore » order to address physics constraints and handle the multiple spatial and temporal scales involved. Although community standard one-dimensional fitting is supported, including scale length–fitting and fitting polynomial-exponential blends to capture the H-mode pedestal, OMFITprofiles includes two-dimensional (2-D) fitting using bivariate splines or radial basis functions. These 2-D fits produce regular evolutions in time, removing jitter that has historically been smoothed ad hoc in transport applications. Profiles interface directly with a wide variety of models within the OMFIT framework, providing the inputs for TRANSP, kinetic-EFIT 2-D equilibrium, and GPEC three-dimensional equilibrium calculations. he OMFITprofiles tool’s rapid and comprehensive analysis of dynamic plasma profiles thus provides the critical link between raw tokamak data and simulations necessary for physics understanding.« less

Suitability of a three-dimensional model to measure empathy and its relationship with social and normative adjustment in Spanish adolescents: a cross-sectional study

PubMed Central

Gómez-Ortiz, Olga; Ortega-Ruiz, Rosario; Jolliffe, Darrick; Romera, Eva M.

2017-01-01

Objectives (1) To examine the psychometric properties of the Basic Empathy Scale (BES) with Spanish adolescents, comparing a two and a three-dimensional structure;(2) To analyse the relationship between the three-dimensional empathy and social and normative adjustment in school. Design Transversal and ex post facto retrospective study. Confirmatory factorial analysis, multifactorial invariance analysis and structural equations models were used. Participants 747 students (51.3% girls) from Cordoba, Spain, aged 12–17 years (M=13.8; SD=1.21). Results The original two-dimensional structure was confirmed (cognitive empathy, affective empathy), but a three-dimensional structure showed better psychometric properties, highlighting the good fit found in confirmatory factorial analysis and adequate internal consistent valued, measured with Cronbach’s alpha and McDonald’s omega. Composite reliability and average variance extracted showed better indices for a three-factor model. The research also showed evidence of measurement invariance across gender. All the factors of the final three-dimensional BES model were direct and significantly associated with social and normative adjustment, being most strongly related to cognitive empathy. Conclusions This research supports the advances in neuroscience, developmental psychology and psychopathology through a three-dimensional version of the BES, which represents an improvement in the original two-factorial model. The organisation of empathy in three factors benefits the understanding of social and normative adjustment in adolescents, in which emotional disengagement favours adjusted peer relationships. Psychoeducational interventions aimed at improving the quality of social life in schools should target these components of empathy. PMID:28951400

A polyhedron made of tRNAs.

PubMed

Severcan, Isil; Geary, Cody; Chworos, Arkadiusz; Voss, Neil; Jacovetty, Erica; Jaeger, Luc

2010-09-01

Supramolecular assembly is a powerful strategy used by nature to build nanoscale architectures with predefined sizes and shapes. With synthetic systems, however, numerous challenges remain to be solved before precise control over the synthesis, folding and assembly of rationally designed three-dimensional nano-objects made of RNA can be achieved. Here, using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular three-dimensional particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows the precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs for the construction of thermostable three-dimensional nano-architectures that do not rely on helix bundles or tensegrity. RNA three-dimensional particles could potentially be used as carriers or scaffolds in nanomedicine and synthetic biology.

Modeling and numerical simulations of growth and morphologies of three dimensional aggregated silver films

NASA Astrophysics Data System (ADS)

Davis, L. J.; Boggess, M.; Kodpuak, E.; Deutsch, M.

2012-11-01

We report on a model for the deposition of three dimensional, aggregated nanocrystalline silver films, and an efficient numerical simulation method developed for visualizing such structures. We compare our results to a model system comprising chemically deposited silver films with morphologies ranging from dilute, uniform distributions of nanoparticles to highly porous aggregated networks. Disordered silver films grown in solution on silica substrates are characterized using digital image analysis of high resolution scanning electron micrographs. While the latter technique provides little volume information, plane-projected (two dimensional) island structure and surface coverage may be reliably determined. Three parameters governing film growth are evaluated using these data and used as inputs for the deposition model, greatly reducing computing requirements while still providing direct access to the complete (bulk) structure of the films throughout the growth process. We also show how valuable three dimensional characteristics of the deposited materials can be extracted using the simulated structures.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Helical structures in vertically aligned dust particle chains in a complex plasma

NASA Astrophysics Data System (ADS)

Hyde, Truell W.; Kong, Jie; Matthews, Lorin S.

2013-05-01

Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ2=ω0h/ω0v2 (where ω0h,v are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.85.016406 85, 016406 (2012)].

Theoretical study of platonic crystals with periodically structured N-beam resonators

NASA Astrophysics Data System (ADS)

Gao, Penglin; Climente, Alfonso; Sánchez-Dehesa, José; Wu, Linzhi

2018-03-01

A multiple scattering theory is applied to study the properties of flexural waves propagating in a plate with periodically structured N-beam resonators. Each resonator consists of a circular hole containing an inner disk connected to background plate with N rectangular beams. The Bloch theorem is employed to obtain the band structure of a two-dimensional lattice containing a single resonator per unit cell. Also, a numerical algorithm has been developed to get the transmittance through resonator slabs infinitely long in the direction perpendicular to the incident wave. For the numerical validation, a square lattice of 2-beam resonators has been comprehensively analyzed. Its band structure exhibits several flat bands, indicating the existence of local resonances embedded in the structure. Particularly, the one featured as the fundamental mode of the inner disk opens a bandgap at low frequencies. This mode has been fully described in terms of a simple spring-mass model. As a practical application of the results obtained, a homogenization approach has been employed to design a focusing lens for flexural waves, where the index gradient is obtained by adjusting the orientation of the resonators beams. Numerical experiments performed within the framework of a three-dimensional finite element method have been employed to discuss the accuracy of the models described here.

Moisture-Stable Zn(II) Metal-Organic Framework as a Multifunctional Platform for Highly Efficient CO2 Capture and Nitro Pollutant Vapor Detection.

PubMed

Chen, Di-Ming; Tian, Jia-Yue; Chen, Min; Liu, Chun-Sen; Du, Miao

2016-07-20

A moisture-stable three-dimensional (3D) metal-organic framework (MOF), {(Me2NH2)[Zn2(bpydb)2(ATZ)](DMA)(NMF)2}n (1, where bpydb = 4,4'-(4,4'-bipyridine-2,6-diyl)dibenzoate, ATZ = deprotonated 5-aminotetrazole, DMA = N,N-dimethylacetamide, and NMF = N-methylformamide), with uncoordinated N-donor sites and charged framework skeleton was fabricated. This MOF exhibits interesting structural dynamic upon CO2 sorption at 195 K and high CO2/N2 (127) and CO2/CH4 (131) sorption selectivity at 298 K and 1 bar. Particularly, its CO2/CH4 selectivity is among the highest MOFs for selective CO2 separation. The results of Grand Canonical Monte Carlo (GCMC) simulation indicate that the polar framework contributes to the strong framework-CO2 binding at zero loading, and the tetrazole pillar contributes to the high CO2 uptake capacity at high loading. Furthermore, the solvent-responsive luminescent properties of 1 indicate that it could be utilized as a fluorescent sensor to detect trace amounts of nitrobenzene in both solvent and vapor systems.

Aeroelastic Modeling of a Nozzle Startup Transient

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2014-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a tightly coupled aeroelastic modeling algorithm by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed under the framework of modal analysis. Transient aeroelastic nozzle startup analyses at sea level were performed, and the computed transient nozzle fluid-structure interaction physics presented,

Coherent diffraction imaging: consistency of the assembled three-dimensional distribution.

PubMed

Tegze, Miklós; Bortel, Gábor

2016-07-01

The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.

Mathematical modeling of transformation process of structurally unstable magnetic configurations into structurally stable ones in two-dimensional and three-dimensional geometry

NASA Astrophysics Data System (ADS)

Inovenkov, Igor; Echkina, Eugenia; Ponomarenko, Loubov

Magnetic reconnection is a fundamental process in astrophysical, space and laboratory plasma. In essence, it represents a change of topology of the magnetic field caused by readjustment of the structure of the magnetic field lines. This change leads to release of energy accumulated in the field. We consider transformation process of structurally unstable magnetic configurations into the structurally steady ones from the point of view of the Catastrophe theory. Special attention is paid to modeling of evolution of the structurally unstable three-dimensional magnetic fields.

System for generating two-dimensional masks from a three-dimensional model using topological analysis

DOEpatents

Schiek, Richard [Albuquerque, NM

2006-06-20

A method of generating two-dimensional masks from a three-dimensional model comprises providing a three-dimensional model representing a micro-electro-mechanical structure for manufacture and a description of process mask requirements, reducing the three-dimensional model to a topological description of unique cross sections, and selecting candidate masks from the unique cross sections and the cross section topology. The method further can comprise reconciling the candidate masks based on the process mask requirements description to produce two-dimensional process masks.

Ray tracing a three-dimensional scene using a hierarchical data structure

DOEpatents

Wald, Ingo; Boulos, Solomon; Shirley, Peter

2012-09-04

Ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. One example embodiment is a method for ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. In this example embodiment, the hierarchical data structure includes at least a parent node and a corresponding plurality of child nodes. The method includes a first act of determining that a first active ray in the packet hits the parent node and a second act of descending to each of the plurality of child nodes.

Framework for SEM contour analysis

NASA Astrophysics Data System (ADS)

Schneider, L.; Farys, V.; Serret, E.; Fenouillet-Beranger, C.

2017-03-01

SEM images provide valuable information about patterning capability. Geometrical properties such as Critical Dimension (CD) can be extracted from them and are used to calibrate OPC models, thus making OPC more robust and reliable. However, there is currently a shortage of appropriate metrology tools to inspect complex two-dimensional patterns in the same way as one would work with simple one-dimensional patterns. In this article we present a full framework for the analysis of SEM images. It has been proven to be fast, reliable and robust for every type of structure, and particularly for two-dimensional structures. To achieve this result, several innovative solutions have been developed and will be presented in the following pages. Firstly, we will present a new noise filter which is used to reduce noise on SEM images, followed by an efficient topography identifier, and finally we will describe the use of a topological skeleton as a measurement tool that can extend CD measurements on all kinds of patterns.

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

Microreplication of laser-fabricated surface and three-dimensional structures

NASA Astrophysics Data System (ADS)

Koroleva, Anastasia; Schlie, Sabrina; Fadeeva, Elena; Gittard, Shaun D.; Miller, Philip; Ovsianikov, Aleksandr; Koch, Jürgen; Narayan, Roger J.; Chichkov, Boris N.

2010-12-01

The fabrication of defined surface topographies and three-dimensional structures is a challenging process for various applications, e.g. in photonics and biomedicine. Laser-based technologies provide a promising approach for the production of such structures. The advantages of femtosecond laser ablation and two-photon polymerization for microstructuring are well known. However, these methods cannot be applied to all materials and are limited by their high cost and long production time. In this study, biomedical applications of an indirect rapid prototyping, molding microreplication of laser-fabricated two- and three-dimensional structures are examined. We demonstrate that by this method any laser-generated surface topography as well as three-dimensional structures can be replicated in various materials without losing the original geometry. The replication into multiple copies enables fast and perfect reproducibility of original microstructures for investigations of cell-surface interactions. Compared to unstructured materials, we observe that microstructures have strong influence on morphology and localization of fibroblasts, whereas neuroblastoma cells are not negatively affected.

Bayesian Peak Picking for NMR Spectra

PubMed Central

Cheng, Yichen; Gao, Xin; Liang, Faming

2013-01-01

Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method. PMID:24184964

Dispersion-Assembly Approach to Synthesize Three-Dimensional Graphene/Polymer Composite Aerogel as a Powerful Organic Cathode for Rechargeable Li and Na Batteries.

PubMed

Zhang, Yu; Huang, Yanshan; Yang, Guanhui; Bu, Fanxing; Li, Ke; Shakir, Imran; Xu, Yuxi

2017-05-10

Polymer cathode materials are promising alternatives to inorganic counterparts for both lithium-ion batteries (LIBs) and sodium-ion batteries (SIBs) due to their high theoretical capacity, adjustable molecular structure, and strong adaptability to different counterions in batteries, etc. However, they suffer from poor practical capacity and low rate capability because of their intrinsically poor conductivity. Herein, we report the synthesis of self-assembled graphene/poly(anthraquinonyl sufide) (PAQS) composite aerogel (GPA) with efficient integration of a three-dimensional (3D) graphene framework with electroactive PAQS particles via a novel dispersion-assembly strategy which can be used as a free-standing flexible cathode upon mechanical pressing. The entire GPA cathode can deliver the highest capacity of 156 mAh g -1 at 0.1 C (1 C = 225 mAh g -1 ) with an ultrahigh utilization (94.9%) of PAQS and exhibits an excellent rate performance with 102 mAh g -1 at 20 C in LIBs. Furthermore, the flexible GPA film was also tested as cathode for SIBs and demonstrated a high-rate capability with 72 mAh g -1 at 5 C and an ultralong cycling stability (71.4% capacity retention after 1000 cycles at 0.5 C) which has rarely been achieved before. Such excellent electrochemical performance of GPA as cathode for both LIBs and SIBs could be ascribed to the fast redox kinetics and electron transportation within GPA, resulting from the interconnected conductive framework of graphene and the intimate interaction between graphene and PAQS through an efficient wrapping structure. This approach opens a universal way to develop cathode materials for powerful batteries with different metal-based counter electrodes.

N4H9Cu7S4: a hydrazinium-based salt with a layered Cu7S4- framework.

PubMed

Mitzi, David B

2007-02-05

Crystals of a hydrazinium-based copper(I) sulfide salt, N4H9Cu7S4 (1), have been isolated by an ambient temperature solution-based process. In contrast to previously reported hydrazinium salts of main-group metal chalcogenides, which consist of isolated metal chalcogenide anions, and ACu7S4 (A = NH4+, Rb+, Tl+, K+), which contains a more three-dimensional Cu7S4- framework with partial Cu-site occupancy, the structure of 1 [P21, a = 6.8621(4) A, b = 7.9851(4) A, c = 10.0983(5) A, beta = 99.360(1) degrees , Z = 2] is composed of extended two-dimensional Cu7S4- slabs with full Cu-site occupancy. The Cu7S4- slabs are separated by a mixture of hydrazinium and hydrazine moieties. Thermal decomposition of 1 into copper(I) sulfide proceeds at a significantly lower temperature than that observed for analogous hydrazinium salts of previously considered metal chalcogenides, completing the transition at temperatures as low as 120 degrees C. Solutions of 1 may be used in the solution deposition of a range of Cu-containing chalcogenide films.

In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach

NASA Astrophysics Data System (ADS)

Verlinde, Christophe L. M. J.; Rudenko, Gabrielle; Hol, Wim G. J.

1992-04-01

A modular method for pursuing structure-based inhibitor design in the framework of a design cycle is presented. The approach entails four stages: (1) a design pathway is defined in the three-dimensional structure of a target protein; (2) this pathway is divided into subregions; (3) complementary building blocks, also called fragments, are designed in each subregion; complementarity is defined in terms of shape, hydrophobicity, hydrogen bond properties and electrostatics; and (4) fragments from different subregions are linked into potential lead compounds. Stages (3) and (4) are qualitatively guided by force-field calculations. In addition, the designed fragments serve as entries for retrieving existing compounds from chemical databases. This linked-fragment approach has been applied in the design of potentially selective inhibitors of triosephosphate isomerase from Trypanosoma brucei, the causative agent of sleeping sickness.

Bayesian power spectrum inference with foreground and target contamination treatment

NASA Astrophysics Data System (ADS)

Jasche, J.; Lavaux, G.

2017-10-01

This work presents a joint and self-consistent Bayesian treatment of various foreground and target contaminations when inferring cosmological power spectra and three-dimensional density fields from galaxy redshift surveys. This is achieved by introducing additional block-sampling procedures for unknown coefficients of foreground and target contamination templates to the previously presented ARES framework for Bayesian large-scale structure analyses. As a result, the method infers jointly and fully self-consistently three-dimensional density fields, cosmological power spectra, luminosity-dependent galaxy biases, noise levels of the respective galaxy distributions, and coefficients for a set of a priori specified foreground templates. In addition, this fully Bayesian approach permits detailed quantification of correlated uncertainties amongst all inferred quantities and correctly marginalizes over observational systematic effects. We demonstrate the validity and efficiency of our approach in obtaining unbiased estimates of power spectra via applications to realistic mock galaxy observations that are subject to stellar contamination and dust extinction. While simultaneously accounting for galaxy biases and unknown noise levels, our method reliably and robustly infers three-dimensional density fields and corresponding cosmological power spectra from deep galaxy surveys. Furthermore, our approach correctly accounts for joint and correlated uncertainties between unknown coefficients of foreground templates and the amplitudes of the power spectrum. This effect amounts to correlations and anti-correlations of up to 10 per cent across wide ranges in Fourier space.

Equation of state of the one- and three-dimensional Bose-Bose gases

NASA Astrophysics Data System (ADS)

Chiquillo, Emerson

2018-06-01

We calculate the equation of state of Bose-Bose gases in one and three dimensions in the framework of an effective quantum field theory. The beyond-mean-field approximation at zero temperature and the one-loop finite-temperature results are obtained performing functional integration on a local effective action. The ultraviolet divergent zero-point quantum fluctuations are removed by means of dimensional regularization. We derive the nonlinear Schrödinger equation to describe one- and three-dimensional Bose-Bose mixtures and solve it analytically in the one-dimensional scenario. This equation supports self-trapped brightlike solitonic droplets and self-trapped darklike solitons. At low temperature, we also find that the pressure and the number of particles of symmetric quantum droplets have a nontrivial dependence on the chemical potential and the difference between the intra- and the interspecies coupling constants.

A novel open-framework with non-crossing channels in the uranyl vanadates A(UO 2) 4(VO 4) 3 ( A=Li, Na)

NASA Astrophysics Data System (ADS)

Obbade, S.; Dion, C.; Rivenet, M.; Saadi, M.; Abraham, F.

2004-06-01

A new sodium uranyl vanadate Na(UO 2) 4(VO 4) 3 has been synthesized by solid-state reaction and its structure determined from single-crystal X-ray diffraction data. It crystallizes in the tetragonal symmetry with space group I4 1/ amd and following cell parameters: a=7.2267(4) Å and c=34.079(4) Å, V=1779.8(2) Å 3, Z=4 with ρmes=5.36(3) g/cm 3 and ρcal=5.40(2) g/cm 3. A full-matrix least-squares refinement on the basis of F2 yielded R1=0.028 and w R2=0.056 for 52 parameters with 474 independent reflections with I⩾2 σ( I) collected on a BRUKER AXS diffractometer with Mo Kα radiation and a CCD detector. The crystal structure is characterized by ∞2[(UO 2) 2(VO 4)] sheets parallel to (001) formed by corner-shared UO 6 distorted octahedra and V(2)O 4 tetrahedra, connected by V(1)O 4 tetrahedra to ∞1[UO 5] 4- chains of edge-shared UO 7 pentagonal bipyramids alternately parallel to the a- and b-axis. The resulting three-dimensional framework creates mono-dimensional channels running down the a- and b-axis formed by face-shared oxygen octahedra half occupied by Na. The powder of Li analog compound Li(UO 2) 4(VO 4) 3 has been synthesized by solid-state reaction. The two compounds exhibit high mobility of the alkaline ions within the two-dimensional network of non-intersecting channels.

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

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

Salloum, Maher; Robinson, David B.

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE PAGES

Salloum, Maher; Robinson, David B.

2018-01-30

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

Alkaline earth-based coordination polymers derived from a cyclotriphosphazene-functionalized hexacarboxylate

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

Ling, Yajing; Bai, Dongjie; Feng, Yunlong

Combination of hexakis(4-carboxylatephenoxy)cyclotriphosphazene with alkaline earth ions of increasing ionic radii (Mg{sup 2+}, Ca{sup 2+} and Ba{sup 2+}) under different solvothermal conditions yielded three new coordination polymers, and their crystal structures were determined by single-crystal X-ray diffraction analysis. The magnesium compound displays a three dimensional (3D) network structure constructed from the deprotonated ligand and the secondary building block Mg(COO){sub 4}, which can be rationalized as a (4,6)-connected topological net with the Schläfli symbol of (4{sup 4}·6{sup 2}){sub 3}(4{sup 9}·6{sup 6}){sub 2}. The calcium compound consists of 1D infinite “Ca-O” inorganic chains connected by the deprotonated ligands to from a 3Dmore » framework. The barium compound exhibits a 3D framework in which 1D “Ba-O” inorganic chains are connected together by the deprotonated organic linkers. Due to the semi-rigid nature, the ligand adopts distinctly different conformations in the three compounds. The metal ions’ influence exerted on the final structure of the resulting coordination polymers is also discussed. When the radii of alkaline earth ions increases descending down the group from Mg(II) to Ba(II), the coordination number becomes larger and more versatile: from 6 in the magnesium compound, to 6,7 and 10 in the calcium compound, and to 8 and 9 in the barium compound, thus substantially influencing the resulting final framework structures. Also, the photophysical properties were investigated systematically, revealing that the three compounds are photoluminscent in the solid state at room temperature. This work demonstrates that although the multiplicity of conformation in the hexacarboxylate ligand based on the inorganic scaffold cyclotriphosphazene makes it difficult to predict how this ligand will form extended network, but provides unique opportunities for the formation of diverse inorganic-organic hybrids exhibiting rich structural topologies. - Graphical abstract: Three alkaline earth-based coordination polymers were constructed from a semirigid cyclotriphosphazene-functionalized hexacarboxylate exhibiting different inorganic nodes as well as distinct ligand conformations relying on the metal ions, which presents the first example of such a ligand incorporated into alkaline earth–based coordination polymers. - Highlights: • Three alkaline earth-based coordination polymers were synthesized. • The three compounds exhibit different inorganic nodes and ligand conformations. • The three compounds are photoluminscent in the solid state.« less

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a coupled aeroelastic modeling capability by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed in the framework of modal analysis. Transient aeroelastic nozzle startup analyses of the Block I Space Shuttle Main Engine at sea level were performed. The computed results from the aeroelastic nozzle modeling are presented.

Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

NASA Astrophysics Data System (ADS)

Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei

2015-12-01

Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H2ndc) or 4,4‧-(hydroxymethylene)dibenzoic acid (H2hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd2(2,6-ndc)2(bpp)(DMF)]·2DMF (1) and [Cd3(hmdb)3(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional 'Lucky Clover' shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process.

Confinement and Structural Changes in Vertically Aligned Dust Structures

NASA Astrophysics Data System (ADS)

Hyde, Truell

2013-10-01

In physics, confinement is known to influence collective system behavior. Examples include coulomb crystal variants such as those formed from ions or dust particles (classical), electrons in quantum dots (quantum) and the structural changes observed in vertically aligned dust particle systems formed within a glass box placed on the lower electrode of a Gaseous Electronics Conference (GEC) rf reference cell. Recent experimental studies have expanded the above to include the biological domain by showing that the stability and dynamics of proteins confined through encapsulation and enzyme molecules placed in inorganic cavities such as those found in biosensors are also directly influenced by their confinement. In this paper, the self-assembly and subsequent collective behavior of structures formed from n, charged dust particles interacting with one another and located within a glass box placed on the lower, powered electrode of a GEC rf reference cell is discussed. Self-organized formation of vertically aligned one-dimensional chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from one-dimensional chain structures, through a zigzag transition to a two-dimensional, spindle like structures, and then to various three-dimensional, helical structures exhibiting various symmetries. Stable configurations are shown to be strongly dependent upon system confinement. The critical conditions for structural transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop will be shown to be in good agreement with molecular dynamics simulations.

Three-Dimensionally Hierarchical Graphene Based Aerogel Encapsulated Sulfur as Cathode for Lithium/Sulfur Batteries

PubMed Central

Li, Haipeng; Sun, Liancheng; Wang, Zhuo; Zhang, Yongguang; Tan, Taizhe; Wang, Gongkai

2018-01-01

A simple and effective method was developed to obtain the electrode for lithium/sulfur (Li/S) batteries with high specific capacity and cycling durability via adopting an interconnected sulfur/activated carbon/graphene (reduced graphene oxide) aerogel (S/AC/GA) cathode architecture. The AC/GA composite with a well-defined interconnected conductive network was prepared by a reduction-induced self-assembly process, which allows for obtaining compact and porous structures. During this process, reduced graphene oxide (RGO) was formed, and due to the presence of oxygen-containing functional groups on its surface, it not only improves the electronic conductivity of the cathode but also effectively inhibits the polysulfides dissolution and shuttle. The introduced activated carbon allowed for lateral and vertical connection between individual graphene sheets, completing the formation of a stable three-dimensionally (3D) interconnected graphene framework. Moreover, a high specific surface area and 3D interconnected porous structure efficiently hosts a higher amount of active sulfur material, about 65 wt %. The designed S/AC/GA composite electrodes deliver an initial capacity of 1159 mAh g−1 at 0.1 C and can retain a capacity of 765 mAh g−1 after 100 cycles in potential range from 1 V to 3 V. PMID:29373525

Development of flood routing simulation system of digital Qingjiang based on integrated spatial information technology

NASA Astrophysics Data System (ADS)

Yuan, Yanbin; Zhou, You; Zhu, Yaqiong; Yuan, Xiaohui; Sælthun, N. R.

2007-11-01

Based on digital technology, flood routing simulation system development is an important component of "digital catchment". Taking QingJiang catchment as a pilot case, in-depth analysis on informatization of Qingjiang catchment management being the basis, aiming at catchment data's multi-source, - dimension, -element, -subject, -layer and -class feature, the study brings the design thought and method of "subject-point-source database" (SPSD) to design system structure in order to realize the unified management of catchments data in great quantity. Using the thought of integrated spatial information technology for reference, integrating hierarchical structure development model of digital catchment is established. The model is general framework of the flood routing simulation system analysis, design and realization. In order to satisfy the demands of flood routing three-dimensional simulation system, the object-oriented spatial data model are designed. We can analyze space-time self-adapting relation between flood routing and catchments topography, express grid data of terrain by using non-directed graph, apply breadth first search arithmetic, set up search method for the purpose of dynamically searching stream channel on the basis of simulated three-dimensional terrain. The system prototype is therefore realized. Simulation results have demonstrated that the proposed approach is feasible and effective in the application.

Water-Stable Metal-Organic Framework with Three Hydrogen-Bond Acceptors: Versatile Theoretical and Experimental Insights into Adsorption Ability and Thermo-Hydrolytic Stability.

PubMed

Roztocki, Kornel; Lupa, Magdalena; Sławek, Andrzej; Makowski, Wacław; Senkovska, Irena; Kaskel, Stefan; Matoga, Dariusz

2018-03-19

A new microporous cadmium metal-organic framework was synthesized both mechanochemically and in solution by using a sulfonyl-functionalized dicarboxylate linker and an acylhydrazone colinker. The three-dimensional framework is highly stable upon heating to 300 °C as well as in aqueous solutions at elevated temperatures or acidic conditions. The thermally activated material exhibits steep water vapor uptake at low relative pressures at 298 K and excellent recyclability up to 260 °C as confirmed by both quasi-equilibrated temperature-programmed desorption and adsorption (QE-TPDA) method as well as adsorption isotherm measurements. Reversible isotherms and hysteretic isobars recorded for the desorption-adsorption cycles indicate the maximum uptake of 0.19 g/g (at 298 K, up to p/p 0 = 1) or 0.18 g/g (at 1 bar, within 295-375 K range), respectively. The experimental isosteric heat of adsorption (48.9 kJ/mol) indicates noncoordinative interactions of water molecules with the framework. Exchange of the solvent molecules in the as-made material with water, performed in the single-crystal to single-crystal manner, allows direct comparison of both X-ray crystal structures. The single-crystal X-ray diffraction for the water-loaded framework demonstrates the orientation of water clusters in the framework cavities and reveals their strong hydrogen bonding with sulfonyl, acyl, and carboxylate groups of the two linkers. The grand canonical Monte Carlo (GCMC) simulations of H 2 O adsorption corroborate the experimental findings and reveal preferable locations of guest molecules in the framework voids at various pressures. Additionally, both experimental and GCMC simulation insights into the adsorption of CO 2 (at 195 K) on the activated framework are presented.

Chebyshev polynomial filtered subspace iteration in the discontinuous Galerkin method for large-scale electronic structure calculations

DOE PAGES

Banerjee, Amartya S.; Lin, Lin; Hu, Wei; ...

2016-10-21

The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) canmore » be used to address this issue and push the envelope in large-scale materials simulations in a discontinuous Galerkin framework. We describe how the subspace filtering steps can be performed in an efficient and scalable manner using a two-dimensional parallelization scheme, thanks to the orthogonality of the DG basis set and block-sparse structure of the DG Hamiltonian matrix. The on-the-fly nature of the ALB functions requires additional care in carrying out the subspace iterations. We demonstrate the parallel scalability of the DG-CheFSI approach in calculations of large-scale twodimensional graphene sheets and bulk three-dimensional lithium-ion electrolyte systems. In conclusion, employing 55 296 computational cores, the time per self-consistent field iteration for a sample of the bulk 3D electrolyte containing 8586 atoms is 90 s, and the time for a graphene sheet containing 11 520 atoms is 75 s.« less

Investigation of deformation of elements of three-dimensional reinforced concrete structures located in the soil, interacting with each other through rubber gaskets

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Balafendieva, I. S.; Sachenkov, A. A.; Sekaeva, L. R.

2017-06-01

In work the technique of calculation of elements of three-dimensional reinforced concrete substructures located in a soil, interacting with each other through rubber linings is realized. To describe the interaction of deformable structures with the ground, special “semi-infinite” finite elements are used. A technique has been implemented that allows one to describe the contact interaction of three-dimensional structures by means of a special contact finite element with specific properties. The obtained numerical results are compared with the experimental data, their good agreement is noted.

Resource Limitations, the Demand for Education and Economic Growth--A Macroeconomic View.

ERIC Educational Resources Information Center

Stam, Jerome M.

To develop a theoretical framework for explaining the observed change in demand for human skill and knowledge that occurs with economic growth, a macroeconomic analysis was made of economic variables which are influenced by political, social, and cultural factors. In the three-dimensional framework, total output (Y) of all final goods and services…

The limits of hamiltonian structures in three-dimensional elasticity, shells, and rods

NASA Astrophysics Data System (ADS)

Ge, Z.; Kruse, H. P.; Marsden, J. E.

1996-01-01

This paper uses Hamiltonian structures to study the problem of the limit of three-dimensional (3D) elastic models to shell and rod models. In the case of shells, we show that the Hamiltonian structure for a three-dimensional elastic body converges, in a sense made precise, to that for a shell model described by a one-director Cosserat surface as the thickness goes to zero. We study limiting procedures that give rise to unconstrained as well as constrained Cosserat director models. The case of a rod is also considered and similar convergence results are established, with the limiting model being a geometrically exact director rod model (in the framework developed by Antman, Simo, and coworkers). The resulting model may or may not have constraints, depending on the nature of the constitutive relations and their behavior under the limiting procedure. The closeness of Hamiltonian structures is measured by the closeness of Poisson brackets on certain classes of functions, as well as the Hamiltonians. This provides one way of justifying the dynamic one-director model for shells. Another way of stating the convergence result is that there is an almost-Poisson embedding from the phase space of the shell to the phase space of the 3D elastic body, which implies that, in the sense of Hamiltonian structures, the dynamics of the elastic body is close to that of the shell. The constitutive equations of the 3D model and their behavior as the thickness tends to zero dictates whether the limiting 2D model is a constrained or an unconstrained director model. We apply our theory in the specific case of a 3D Saint Venant-Kirchhoff material and derive the corresponding limiting shell and rod theories. The limiting shell model is an interesting Kirchhoff-like shell model in which the stored energy function is explicitly derived in terms of the shell curvature. For rods, one gets (with an additional inextensibility constraint) a one-director Kirchhoff elastic rod model, which reduces to the well-known Euler elastica if one adds an additional single constraint that the director lines up with the Frenet frame.

Controllable synthesis of single-walled carbon nanotube framework membranes and capsules.

PubMed

Song, Changsik; Kwon, Taeyun; Han, Jae-Hee; Shandell, Mia; Strano, Michael S

2009-12-01

Controlling the morphology of membrane components at the nanometer scale is central to many next-generation technologies in water purification, gas separation, fuel cell, and nanofiltration applications. Toward this end, we report the covalent assembly of single-walled carbon nanotubes (SWNTs) into three-dimensional framework materials with intertube pores controllable by adjusting the size of organic linker molecules. The frameworks are fashioned into multilayer membranes possessing linker spacings from 1.7 to 3.0 nm, and the resulting framework films were characterized, including transport properties. Nanoindentation measurements by atomic force microscopy show that the spring constant of the SWNT framework film (22.6 +/- 1.2 N/m) increased by a factor of 2 from the control value (10.4 +/- 0.1 N/m). The flux ratio comparison in a membrane-permeation experiment showed that larger spacer sizes resulted in larger pore structures. This synthetic method was equally efficient on silica microspheres, which could then be etched to create all-SWNT framework, hollow capsules approximately 5 mum in diameter. These hollow capsules are permeable to organic and inorganic reagents, allowing one to form inorganic nanoparticles, for example, that become entrapped within the capsule. The ability to encapsulate functional nanomaterials inside perm-selective SWNT cages and membranes may find applications in new adsorbents, novel catalysts, and drug delivery vehicles.

Mental Representation and Mental Practice: Experimental Investigation on the Functional Links between Motor Memory and Motor Imagery

PubMed Central

Frank, Cornelia; Land, William M.; Popp, Carmen; Schack, Thomas

2014-01-01

Recent research on mental representation of complex action has revealed distinct differences in the structure of representational frameworks between experts and novices. More recently, research on the development of mental representation structure has elicited functional changes in novices' representations as a result of practice. However, research investigating if and how mental practice adds to this adaptation process is lacking. In the present study, we examined the influence of mental practice (i.e., motor imagery rehearsal) on both putting performance and the development of one's representation of the golf putt during early skill acquisition. Novice golfers (N = 52) practiced the task of golf putting under one of four different practice conditions: mental, physical, mental-physical combined, and no practice. Participants were tested prior to and after a practice phase, as well as after a three day retention interval. Mental representation structures of the putt were measured, using the structural dimensional analysis of mental representation. This method provides psychometric data on the distances and groupings of basic action concepts in long-term memory. Additionally, putting accuracy and putting consistency were measured using two-dimensional error scores of each putt. Findings revealed significant performance improvements over the course of practice together with functional adaptations in mental representation structure. Interestingly, after three days of practice, the mental representations of participants who incorporated mental practice into their practice regime displayed representation structures that were more similar to a functional structure than did participants who did not incorporate mental practice. The findings of the present study suggest that mental practice promotes the cognitive adaptation process during motor learning, leading to more elaborate representations than physical practice only. PMID:24743576

Experimental Investigation of the Unsteady Flow Structures of Two Interacting Pitching Wings

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2015-11-01

Birds, insects and fish propel themselves with unsteady motions of their wings and fins. Many of these animals are also found to fly or swim in three-dimensional flocks and schools. Numerous studies have explored the three-dimensional steady flow interactions and the two-dimensional unsteady flow interactions in collectives. Yet, the characterization of the three-dimensional unsteady interactions remains relatively unexplored. This study aims to characterize the flow structures and interactions between two sinusoidally pitching finite-span wings. The arrangement of the wings varies from a tandem to a bi-plane configuration. The vortex structures for these various arrangements are quantified by using particle image velocimetry. The vortex-wing interactions are also characterized as the synchrony between the wings is modified.

Suitability of a three-dimensional model to measure empathy and its relationship with social and normative adjustment in Spanish adolescents: a cross-sectional study.

PubMed

Herrera-López, Mauricio; Gómez-Ortiz, Olga; Ortega-Ruiz, Rosario; Jolliffe, Darrick; Romera, Eva M

2017-09-25

(1) To examine the psychometric properties of the Basic Empathy Scale (BES) with Spanish adolescents, comparing a two and a three-dimensional structure;(2) To analyse the relationship between the three-dimensional empathy and social and normative adjustment in school. Transversal and ex post facto retrospective study. Confirmatory factorial analysis, multifactorial invariance analysis and structural equations models were used. 747 students (51.3% girls) from Cordoba, Spain, aged 12-17 years (M=13.8; SD=1.21). The original two-dimensional structure was confirmed (cognitive empathy, affective empathy), but a three-dimensional structure showed better psychometric properties, highlighting the good fit found in confirmatory factorial analysis and adequate internal consistent valued, measured with Cronbach's alpha and McDonald's omega. Composite reliability and average variance extracted showed better indices for a three-factor model. The research also showed evidence of measurement invariance across gender. All the factors of the final three-dimensional BES model were direct and significantly associated with social and normative adjustment, being most strongly related to cognitive empathy. This research supports the advances in neuroscience, developmental psychology and psychopathology through a three-dimensional version of the BES, which represents an improvement in the original two-factorial model. The organisation of empathy in three factors benefits the understanding of social and normative adjustment in adolescents, in which emotional disengagement favours adjusted peer relationships. Psychoeducational interventions aimed at improving the quality of social life in schools should target these components of empathy. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Three-Dimensional Bayesian Geostatistical Aquifer Characterization at the Hanford 300 Area using Tracer Test Data

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

Chen, Xingyuan; Murakami, Haruko; Hahn, Melanie S.

2012-06-01

Tracer testing under natural or forced gradient flow holds the potential to provide useful information for characterizing subsurface properties, through monitoring, modeling and interpretation of the tracer plume migration in an aquifer. Non-reactive tracer experiments were conducted at the Hanford 300 Area, along with constant-rate injection tests and electromagnetic borehole flowmeter (EBF) profiling. A Bayesian data assimilation technique, the method of anchored distributions (MAD) [Rubin et al., 2010], was applied to assimilate the experimental tracer test data with the other types of data and to infer the three-dimensional heterogeneous structure of the hydraulic conductivity in the saturated zone of themore » Hanford formation. In this study, the Bayesian prior information on the underlying random hydraulic conductivity field was obtained from previous field characterization efforts using the constant-rate injection tests and the EBF data. The posterior distribution of the conductivity field was obtained by further conditioning the field on the temporal moments of tracer breakthrough curves at various observation wells. MAD was implemented with the massively-parallel three-dimensional flow and transport code PFLOTRAN to cope with the highly transient flow boundary conditions at the site and to meet the computational demands of MAD. A synthetic study proved that the proposed method could effectively invert tracer test data to capture the essential spatial heterogeneity of the three-dimensional hydraulic conductivity field. Application of MAD to actual field data shows that the hydrogeological model, when conditioned on the tracer test data, can reproduce the tracer transport behavior better than the field characterized without the tracer test data. This study successfully demonstrates that MAD can sequentially assimilate multi-scale multi-type field data through a consistent Bayesian framework.« less

Three-dimensional effects on pure tone fan noise due to inflow distortion. [rotor blade noise prediction

NASA Technical Reports Server (NTRS)

Kobayashi, H.

1978-01-01

Two dimensional, quasi three dimensional and three dimensional theories for the prediction of pure tone fan noise due to the interaction of inflow distortion with a subsonic annular blade row were studied with the aid of an unsteady three dimensional lifting surface theory. The effects of compact and noncompact source distributions on pure tone fan noise in an annular cascade were investigated. Numerical results show that the strip theory and quasi three-dimensional theory are reasonably adequate for fan noise prediction. The quasi three-dimensional method is more accurate for acoustic power and model structure prediction with an acoustic power estimation error of about plus or minus 2db.

Enhanced macroboring and depressed calcification drive net dissolution at high-CO2 coral reefs.

PubMed

Enochs, Ian C; Manzello, Derek P; Kolodziej, Graham; Noonan, Sam H C; Valentino, Lauren; Fabricius, Katharina E

2016-11-16

Ocean acidification (OA) impacts the physiology of diverse marine taxa; among them corals that create complex reef framework structures. Biological processes operating on coral reef frameworks remain largely unknown from naturally high-carbon-dioxide (CO 2 ) ecosystems. For the first time, we independently quantified the response of multiple functional groups instrumental in the construction and erosion of these frameworks (accretion, macroboring, microboring, and grazing) along natural OA gradients. We deployed blocks of dead coral skeleton for roughly 2 years at two reefs in Papua New Guinea, each experiencing volcanically enriched CO 2 , and employed high-resolution micro-computed tomography (micro-CT) to create three-dimensional models of changing skeletal structure. OA conditions were correlated with decreased calcification and increased macroboring, primarily by annelids, representing a group of bioeroders not previously known to respond to OA. Incubation of these blocks, using the alkalinity anomaly methodology, revealed a switch from net calcification to net dissolution at a pH of roughly 7.8, within Intergovernmental Panel on Climate Change's (IPCC) predictions for global ocean waters by the end of the century. Together these data represent the first comprehensive experimental study of bioerosion and calcification from a naturally high-CO 2 reef ecosystem, where the processes of accelerated erosion and depressed calcification have combined to alter the permanence of this essential framework habitat. © 2016 The Authors.

Enhanced macroboring and depressed calcification drive net dissolution at high-CO2 coral reefs

PubMed Central

Manzello, Derek P.; Kolodziej, Graham; Noonan, Sam H. C.; Valentino, Lauren; Fabricius, Katharina E.

2016-01-01

Ocean acidification (OA) impacts the physiology of diverse marine taxa; among them corals that create complex reef framework structures. Biological processes operating on coral reef frameworks remain largely unknown from naturally high-carbon-dioxide (CO2) ecosystems. For the first time, we independently quantified the response of multiple functional groups instrumental in the construction and erosion of these frameworks (accretion, macroboring, microboring, and grazing) along natural OA gradients. We deployed blocks of dead coral skeleton for roughly 2 years at two reefs in Papua New Guinea, each experiencing volcanically enriched CO2, and employed high-resolution micro-computed tomography (micro-CT) to create three-dimensional models of changing skeletal structure. OA conditions were correlated with decreased calcification and increased macroboring, primarily by annelids, representing a group of bioeroders not previously known to respond to OA. Incubation of these blocks, using the alkalinity anomaly methodology, revealed a switch from net calcification to net dissolution at a pH of roughly 7.8, within Intergovernmental Panel on Climate Change's (IPCC) predictions for global ocean waters by the end of the century. Together these data represent the first comprehensive experimental study of bioerosion and calcification from a naturally high-CO2 reef ecosystem, where the processes of accelerated erosion and depressed calcification have combined to alter the permanence of this essential framework habitat. PMID:27852802

Synthesis, structure, and luminescent properties of microporous lanthanide metal-organic frameworks with inorganic rod-shaped building units.

PubMed

Guo, Xiaodan; Zhu, Guangshan; Sun, Fuxing; Li, Zhongyue; Zhao, Xiaojun; Li, Xiaotian; Wang, Hanchang; Qiu, Shilun

2006-03-20

A series of microporous lanthanide metal-organic frameworks, Tb3(BDC)(4.5)(DMF)2(H2O)3.(DMF)(H2O) (1) and Ln3(BDC)(4.5)(DMF)2(H2O)3.(DMF)(C2H5OH)(0.5)(H2O)(0.5) [Ln = Dy (2), Ho (3), Er (4)], have been synthesized by the reaction of the lanthanide metal ion (Ln3+) with 1,4-benzenedicarboxylic acid and triethylenetetramine in a mixed solution of N,N'-dimethylformamide (DMF), water, and C(2)H(5)OH. X-ray diffraction analyses reveal that they are extremely similar in structure and crystallized in triclinic space group P. An edge-sharing metallic dimer and 4 metallic monomers assemble with 18 carboxylate groups to form discrete inorganic rod-shaped building units [Ln6(CO2)18], which link to each other through phenyl groups to lead to three-dimensional open frameworks with approximately 4 x 6 A rhombic channels along the [0,-1,1] direction. A water sorption isotherm proves that guest molecules in the framework of complex 1 can be removed to create permanent microporosity and about four water molecules per formula unit can be adsorbed into the micropores. These complexes exhibit blue fluorescence, and complex 1 shows a Tb3+ characteristic emission in the range of 450-650 nm.

Design of composite scaffolds and three-dimensional shape analysis for tissue-engineered ear

PubMed Central

Cervantes, Thomas M.; Bassett, Erik K.; Tseng, Alan; Kimura, Anya; Roscioli, Nick; Randolph, Mark A.; Vacanti, Joseph P.; Hadlock, Theresa A.; Gupta, Rajiv; Pomerantseva, Irina; Sundback, Cathryn A.

2013-01-01

Engineered cartilage is a promising option for auricular reconstruction. We have previously demonstrated that a titanium wire framework within a composite collagen ear-shaped scaffold helped to maintain the gross dimensions of the engineered ear after implantation, resisting the deformation forces encountered during neocartilage maturation and wound healing. The ear geometry was redesigned to achieve a more accurate aesthetic result when implanted subcutaneously in a nude rat model. A non-invasive method was developed to assess size and shape changes of the engineered ear in three dimensions. Computer models of the titanium framework were obtained from CT scans before and after implantation. Several parameters were measured including the overall length, width and depth, the minimum intrahelical distance and overall curvature values for each beam section within the framework. Local curvature values were measured to gain understanding of the bending forces experienced by the framework structure in situ. Length and width changed by less than 2%, whereas the depth decreased by approximately 8% and the minimum intrahelical distance changed by approximately 12%. Overall curvature changes identified regions most susceptible to deformation. Eighty-nine per cent of local curvature measurements experienced a bending moment less than 50 µN-m owing to deformation forces during implantation. These quantitative shape analysis results have identified opportunities to improve shape fidelity of engineered ear constructs. PMID:23904585

Design of composite scaffolds and three-dimensional shape analysis for tissue-engineered ear.

PubMed

Cervantes, Thomas M; Bassett, Erik K; Tseng, Alan; Kimura, Anya; Roscioli, Nick; Randolph, Mark A; Vacanti, Joseph P; Hadlock, Theresa A; Gupta, Rajiv; Pomerantseva, Irina; Sundback, Cathryn A

2013-10-06

Engineered cartilage is a promising option for auricular reconstruction. We have previously demonstrated that a titanium wire framework within a composite collagen ear-shaped scaffold helped to maintain the gross dimensions of the engineered ear after implantation, resisting the deformation forces encountered during neocartilage maturation and wound healing. The ear geometry was redesigned to achieve a more accurate aesthetic result when implanted subcutaneously in a nude rat model. A non-invasive method was developed to assess size and shape changes of the engineered ear in three dimensions. Computer models of the titanium framework were obtained from CT scans before and after implantation. Several parameters were measured including the overall length, width and depth, the minimum intrahelical distance and overall curvature values for each beam section within the framework. Local curvature values were measured to gain understanding of the bending forces experienced by the framework structure in situ. Length and width changed by less than 2%, whereas the depth decreased by approximately 8% and the minimum intrahelical distance changed by approximately 12%. Overall curvature changes identified regions most susceptible to deformation. Eighty-nine per cent of local curvature measurements experienced a bending moment less than 50 µN-m owing to deformation forces during implantation. These quantitative shape analysis results have identified opportunities to improve shape fidelity of engineered ear constructs.

Power-scaling performance of a three-dimensional tritium betavoltaic diode

NASA Astrophysics Data System (ADS)

Liu, Baojun; Chen, Kevin P.; Kherani, Nazir P.; Zukotynski, Stefan

2009-12-01

Three-dimensional diodes fabricated by electrochemical etching are exposed to tritium gas at pressures from 0.05 to 33 atm at room temperature to examine its power scaling performance. It is shown that the three-dimensional microporous structure overcomes the self-absorption limited saturation of beta flux at high tritium pressures. These results are contrasted against the three-dimensional device powered in one instance by tritium absorbed in the near surface region of the three-dimensional microporous network, and in another by a planar scandium tritide foil. These findings suggest that direct tritium occlusion in the near surface of three-dimensional diode can improve the specific power production.

The Reconstruction of Three-Dimensional Morphological and Electrical Paraneters from Two-Dimensional Sections of Neurones

NASA Astrophysics Data System (ADS)

Brawn, A. D.; Wheal, H. V.

1986-07-01

A system is described which can be used to create a three-dimensional model of a neurone from the central nervous system. This model can then be used to obtain quantitative data on the physical and electrical pro, perties of the neurone. Living neurones are either raised in culture, or taken from in vitro preparations of brain tissue and optically sectioned. These two-dimensional sections are digitised, and input to a 68008-based microcomputer. The system reconstructs the three-dimensional structure of the neurone, both geanetrically and electrically. The user can a) View the structure fran any point at any angle b) "Move through" the structure along any given vector c) Nave through" the structure following a neurone process d) Fire the neurone at any point, and "watch" the action potentials propagate e) Vary the parameters of the electrical model of a process element. The system is targeted to a research programme on epilepsy, which makes frequent use of both geometric and electrical neurone modelling. Current techniques which may involve crude histology and two-dimensional drawings have considerable short camings.

Finite element analysis of steady and transiently moving/rolling nonlinear viscoelastic structure. II - Shell and three-dimensional simulations

NASA Technical Reports Server (NTRS)

Kennedy, Ronald; Padovan, Joe

1987-01-01

In a three-part series of papers, a generalized finite element solution strategy is developed to handle traveling load problems in rolling, moving and rotating structure. The main thrust of this section consists of the development of three-dimensional and shell type moving elements. In conjunction with this work, a compatible three-dimensional contact strategy is also developed. Based on these modeling capabilities, extensive analytical and experimental benchmarking is presented. Such testing includes traveling loads in rotating structure as well as low- and high-speed rolling contact involving standing wave-type response behavior. These point to the excellent modeling capabilities of moving element strategies.

Quantum effects and anharmonicity in the H2-Li+-benzene complex: A model for hydrogen storage materials

NASA Astrophysics Data System (ADS)

Kolmann, Stephen J.; D'Arcy, Jordan H.; Jordan, Meredith J. T.

2013-12-01

Quantum and anharmonic effects are investigated in H2-Li+-benzene, a model for hydrogen adsorption in metal-organic frameworks and carbon-based materials. Three- and 8-dimensional quantum diffusion Monte Carlo (QDMC) and rigid-body diffusion Monte Carlo (RBDMC) simulations are performed on potential energy surfaces interpolated from electronic structure calculations at the M05-2X/6-31+G(d,p) and M05-2X/6-311+G(2df,p) levels of theory using a three-dimensional spline or a modified Shepard interpolation. These calculations investigate the intermolecular interactions in this system, with three- and 8-dimensional 0 K H2 binding enthalpy estimates, ΔHbind (0 K), being 16.5 kJ mol-1 and 12.4 kJ mol-1, respectively: 0.1 and 0.6 kJ mol-1 higher than harmonic values. Zero-point energy effects are 35% of the value of ΔHbind (0 K) at M05-2X/6-311+G(2df,p) and cannot be neglected; uncorrected electronic binding energies overestimate ΔHbind (0 K) by at least 6 kJ mol-1. Harmonic intermolecular binding enthalpies can be corrected by treating the H2 "helicopter" and "ferris wheel" rotations as free and hindered rotations, respectively. These simple corrections yield results within 2% of the 8-dimensional anharmonic calculations. Nuclear ground state probability density histograms obtained from the QDMC and RBDMC simulations indicate the H2 molecule is delocalized above the Li+-benzene system at 0 K.

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

Kolmann, Stephen J.; D'Arcy, Jordan H.; Jordan, Meredith J. T., E-mail: m.jordan@chem.usyd.edu.au

Quantum and anharmonic effects are investigated in H{sub 2}-Li{sup +}-benzene, a model for hydrogen adsorption in metal-organic frameworks and carbon-based materials. Three- and 8-dimensional quantum diffusion Monte Carlo (QDMC) and rigid-body diffusion Monte Carlo (RBDMC) simulations are performed on potential energy surfaces interpolated from electronic structure calculations at the M05-2X/6-31+G(d,p) and M05-2X/6-311+G(2df,p) levels of theory using a three-dimensional spline or a modified Shepard interpolation. These calculations investigate the intermolecular interactions in this system, with three- and 8-dimensional 0 K H{sub 2} binding enthalpy estimates, ΔH{sub bind} (0 K), being 16.5 kJ mol{sup −1} and 12.4 kJ mol{sup −1}, respectively: 0.1 and 0.6more » kJ mol{sup −1} higher than harmonic values. Zero-point energy effects are 35% of the value of ΔH{sub bind} (0 K) at M05-2X/6-311+G(2df,p) and cannot be neglected; uncorrected electronic binding energies overestimate ΔH{sub bind} (0 K) by at least 6 kJ mol{sup −1}. Harmonic intermolecular binding enthalpies can be corrected by treating the H{sub 2} “helicopter” and “ferris wheel” rotations as free and hindered rotations, respectively. These simple corrections yield results within 2% of the 8-dimensional anharmonic calculations. Nuclear ground state probability density histograms obtained from the QDMC and RBDMC simulations indicate the H{sub 2} molecule is delocalized above the Li{sup +}-benzene system at 0 K.« less

Structure-Specific Statistical Mapping of White Matter Tracts

PubMed Central

Yushkevich, Paul A.; Zhang, Hui; Simon, Tony; Gee, James C.

2008-01-01

We present a new model-based framework for the statistical analysis of diffusion imaging data associated with specific white matter tracts. The framework takes advantage of the fact that several of the major white matter tracts are thin sheet-like structures that can be effectively modeled by medial representations. The approach involves segmenting major tracts and fitting them with deformable geometric medial models. The medial representation makes it possible to average and combine tensor-based features along directions locally perpendicular to the tracts, thus reducing data dimensionality and accounting for errors in normalization. The framework enables the analysis of individual white matter structures, and provides a range of possibilities for computing statistics and visualizing differences between cohorts. The framework is demonstrated in a study of white matter differences in pediatric chromosome 22q11.2 deletion syndrome. PMID:18407524

Three-Dimensional Printing of a Scalable Molecular Model and Orbital Kit for Organic Chemistry Teaching and Learning

ERIC Educational Resources Information Center

Penny, Matthew R.; Cao, Zi Jing; Patel, Bhaven; dos Santos, Bruno Sil; Asquith, Christopher R. M.; Szulc, Blanka R.; Rao, Zenobia X.; Muwaffak, Zaid; Malkinson, John P.; Hilton, Stephen T.

2017-01-01

Three-dimensional (3D) chemical models are a well-established learning tool used to enhance the understanding of chemical structures by converting two-dimensional paper or screen outputs into realistic three-dimensional objects. While commercial atom model kits are readily available, there is a surprising lack of large molecular and orbital models…

Photoluminescent lead(II) coordination polymers stabilised by bifunctional organoarsonate ligands

NASA Astrophysics Data System (ADS)

Lin, Jian-Di; Onet, Camelia I.; Schmitt, Wolfgang

2015-04-01

Four lead(II) coordination polymers were isolated under hydro(solvo)thermal conditions. The applied synthetic methodology takes advantage of the coordination behaviour of a new bifunctional organoarsonate ligand, 4-(1, 2, 4-triazol-4-yl)phenylarsonic acid (H2TPAA) and involves the variation of lead(II) reactants, metal/ligand mole ratios, and solvents. The constitutional composition of the four lead(II) coordination polymers can be formulated as [Pb2(TPAA)(HTPAA)(NO3)]·6H2O (1), [Pb2(TPAA)(HTPAA)2]·DMF·0.5H2O (DMF = N, N-Dimethylformamide) (2), [Pb2Cl2(TPAA)H2O] (3), and [Pb3Cl(TPAA)(HTPAA)2H2O]Cl (4). The compounds were characterized by single-crystal and powder x-ray diffraction techniques, thermogravimetric analyses, infra-red spectroscopy, and elemental analyses. Single-crystal x-ray diffraction reveals that 1 and 2 represent two-dimensional (2D) layered structures whilst 3 and 4 form three-dimensional (3D) frameworks. The structures of 1, 2, and 4 contain one-dimensional (1D) {PbII/AsO3} substructures, while 3 is composed of 2D {PbII/AsO3} arrays. Besides their interesting topologies, 1-4 all exhibit photoluminescence properties in the solid state at room temperature.

Structure and topology of three-dimensional hydrocarbon polymers.

PubMed

Kondrin, Mikhail V; Lebed, Yulia B; Brazhkin, Vadim V

2016-08-01

A new family of three-dimensional hydrocarbon polymers which are more energetically favorable than benzene is proposed. Although structurally these polymers are closely related to well known diamond and lonsdaleite carbon structures, using topological arguments we demonstrate that they have no known structural analogs. Topological considerations also give some indication of possible methods of synthesis. Taking into account their exceptional optical, structural and mechanical properties these polymers might have interesting applications.

Advances in the Application of High-order Techniques in Simulation of Multi-disciplinary Phenomena

NASA Astrophysics Data System (ADS)

Gaitonde, D. V.; Visbal, M. R.

2003-03-01

This paper describes the development of a comprehensive high-fidelity algorithmic framework to simulate the three-dimensional fields associated with multi-disciplinary physics. A wide range of phenomena is considered, from aero-acoustics and turbulence to electromagnetics, non-linear fluid-structure interactions, and magnetogasdynamics. The scheme depends primarily on "spectral-like," up to sixth-order accurate compact-differencing and up to tenth-order filtering techniques. The tightly coupled procedure suppresses numerical instabilities commonly encountered with high-order methods on non-uniform meshes, near computational boundaries or in the simulation of nonlinear dynamics. Particular emphasis is placed on developing the proper metric evaluation procedures for three-dimensional moving and curvilinear meshes so that the advantages of higher-order schemes are retained in practical calculations. A domain-decomposition strategy based on finite-sized overlap regions and interface boundary treatments enables the development of highly scalable solvers. The utility of the method to simulate problems governed by widely disparate governing equations is demonstrated with several examples encompassing vortex dynamics, wave scattering, electro-fluid plasma interactions, and panel flutter.

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain

PubMed Central

Osechinskiy, Sergey; Kruggel, Frithjof

2011-01-01

Registration of histological images to three-dimensional imaging modalities is an important step in quantitative analysis of brain structure, in architectonic mapping of the brain, and in investigation of the pathology of a brain disease. Reconstruction of histology volume from serial sections is a well-established procedure, but it does not address registration of individual slices from sparse sections, which is the aim of the slice-to-volume approach. This study presents a flexible framework for intensity-based slice-to-volume nonrigid registration algorithms with a geometric transformation deformation field parametrized by various classes of spline functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines. Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain. Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions. For a particular case of histological data, best results are obtained with a TPS three-dimensional (3D) warp, a new unconstrained optimization algorithm (NEWUOA), and a correlation-coefficient-based cost function. PMID:22567290

Three-Dimensional Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between Microscopic Imaging and Mathematical Simulation

PubMed Central

Yu, Zeyun; Holst, Michael J.; Hayashi, Takeharu; Bajaj, Chandrajit L.; Ellisman, Mark H.; McCammon, J. Andrew; Hoshijima, Masahiko

2009-01-01

A general framework of image-based geometric processing is presented to bridge the gap between three-dimensional (3D) imaging that provides structural details of a biological system and mathematical simulation where high-quality surface or volumetric meshes are required. A 3D density map is processed in the order of image pre-processing (contrast enhancement and anisotropic filtering), feature extraction (boundary segmentation and skeletonization), and high-quality and realistic surface (triangular) and volumetric (tetrahedral) mesh generation. While the tool-chain described is applicable to general types of 3D imaging data, the performance is demonstrated specifically on membrane-bound organelles in ventricular myocytes that are imaged and reconstructed with electron microscopic (EM) tomography and two-photon microscopy (T-PM). Of particular interest in this study are two types of membrane-bound Ca2+-handling organelles, namely, transverse tubules (T-tubules) and junctional sarcoplasmic reticulum (jSR), both of which play an important role in regulating the excitation-contraction (E-C) coupling through dynamic Ca2+ mobilization in cardiomyocytes. PMID:18835449

Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation.

PubMed

Yu, Zeyun; Holst, Michael J; Hayashi, Takeharu; Bajaj, Chandrajit L; Ellisman, Mark H; McCammon, J Andrew; Hoshijima, Masahiko

2008-12-01

A general framework of image-based geometric processing is presented to bridge the gap between three-dimensional (3D) imaging that provides structural details of a biological system and mathematical simulation where high-quality surface or volumetric meshes are required. A 3D density map is processed in the order of image pre-processing (contrast enhancement and anisotropic filtering), feature extraction (boundary segmentation and skeletonization), and high-quality and realistic surface (triangular) and volumetric (tetrahedral) mesh generation. While the tool-chain described is applicable to general types of 3D imaging data, the performance is demonstrated specifically on membrane-bound organelles in ventricular myocytes that are imaged and reconstructed with electron microscopic (EM) tomography and two-photon microscopy (T-PM). Of particular interest in this study are two types of membrane-bound Ca(2+)-handling organelles, namely, transverse tubules (T-tubules) and junctional sarcoplasmic reticulum (jSR), both of which play an important role in regulating the excitation-contraction (E-C) coupling through dynamic Ca(2+) mobilization in cardiomyocytes.

Implications and concerns of deep-seated disposal of hydrocarbon exploration produced water using three-dimensional contaminant transport model in Bhit Area, Dadu District of Southern Pakistan.

PubMed

Ahmad, Zulfiqar; Akhter, Gulraiz; Ashraf, Arshad; Fryar, Alan

2010-11-01

A three-dimensional contaminant transport model has been developed to simulate and monitor the migration of disposal of hydrocarbon exploration produced water in Injection well at 2,100 m depth in the Upper Cretaceous Pab sandstone, Bhit area in Dadu district of Southern Pakistan. The regional stratigraphic and structural geological framework of the area, landform characteristics, meteorological parameters, and hydrogeological milieu have been used in the model to generate the initial simulation of steady-state flow condition in the underlying aquifer's layers. The geometry of the shallow and deep-seated characteristics of the geological formations was obtained from the drilling data, electrical resistivity sounding surveys, and geophysical well-logging information. The modeling process comprised of steady-state simulation and transient simulation of the prolific groundwater system of contamination transport after 1, 10, 30 years of injection. The contaminant transport was evaluated from the bottom of the injection well, and its short- and long-term effects were determined on aquifer system lying in varying hydrogeological and geological conditions.

Comparing three-dimensional serial optical coherence tomography histology to MRI imaging in the entire mouse brain

NASA Astrophysics Data System (ADS)

Castonguay, Alexandre; Lefebvre, Joël; Pouliot, Philippe; Lesage, Frédéric

2018-01-01

An automated serial histology setup combining optical coherence tomography (OCT) imaging with vibratome sectioning was used to image eight wild type mouse brains. The datasets resulted in thousands of volumetric tiles resolved at a voxel size of (4.9×4.9×6.5) μm3 stitched back together to give a three-dimensional map of the brain from which a template OCT brain was obtained. To assess deformation caused by tissue sectioning, reconstruction algorithms, and fixation, OCT datasets were compared to both in vivo and ex vivo magnetic resonance imaging (MRI) imaging. The OCT brain template yielded a highly detailed map of the brain structure, with a high contrast in white matter fiber bundles and was highly resemblant to the in vivo MRI template. Brain labeling using the Allen brain framework showed little variation in regional brain volume among imaging modalities with no statistical differences. The high correspondence between the OCT template brain and its in vivo counterpart demonstrates the potential of whole brain histology to validate in vivo imaging.

Low-dimensional quantum magnetism in Cu (NCS) 2: A molecular framework material

NASA Astrophysics Data System (ADS)

Cliffe, Matthew J.; Lee, Jeongjae; Paddison, Joseph A. M.; Schott, Sam; Mukherjee, Paromita; Gaultois, Michael W.; Manuel, Pascal; Sirringhaus, Henning; Dutton, Siân E.; Grey, Clare P.

2018-04-01

Low-dimensional magnetic materials with spin-1/2 moments can host a range of exotic magnetic phenomena due to the intrinsic importance of quantum fluctuations to their behavior. Here, we report the structure, magnetic structure, and magnetic properties of copper ii thiocyanate, Cu(NCS ) 2, a one-dimensional coordination polymer which displays low-dimensional quantum magnetism. Magnetic susceptibility, electron paramagnetic resonance spectroscopy, 13C magic-angle spinning nuclear magnetic resonance spectroscopy, and density functional theory investigations indicate that Cu(NCS ) 2 behaves as a two-dimensional array of weakly coupled antiferromagnetic spin chains [J2=133 (1 ) K , α =J1/J2=0.08 ] . Powder neutron-diffraction measurements confirm that Cu(NCS ) 2 orders as a commensurate antiferromagnet below TN=12 K , with a strongly reduced ordered moment (0.3 μB ) due to quantum fluctuations.

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Introduction of functionality, selection of topology, and enhancement of gas adsorption in multivariate metal-organic framework-177.

PubMed

Zhang, Yue-Biao; Furukawa, Hiroyasu; Ko, Nakeun; Nie, Weixuan; Park, Hye Jeong; Okajima, Satoshi; Cordova, Kyle E; Deng, Hexiang; Kim, Jaheon; Yaghi, Omar M

2015-02-25

Metal-organic framework-177 (MOF-177) is one of the most porous materials whose structure is composed of octahedral Zn4O(-COO)6 and triangular 1,3,5-benzenetribenzoate (BTB) units to make a three-dimensional extended network based on the qom topology. This topology violates a long-standing thesis where highly symmetric building units are expected to yield highly symmetric networks. In the case of octahedron and triangle combinations, MOFs based on pyrite (pyr) and rutile (rtl) nets were expected instead of qom. In this study, we have made 24 MOF-177 structures with different functional groups on the triangular BTB linker, having one or more functionalities. We find that the position of the functional groups on the BTB unit allows the selection for a specific net (qom, pyr, and rtl), and that mixing of functionalities (-H, -NH2, and -C4H4) is an important strategy for the incorporation of a specific functionality (-NO2) into MOF-177 where otherwise incorporation of such functionality would be difficult. Such mixing of functionalities to make multivariate MOF-177 structures leads to enhancement of hydrogen uptake by 25%.

Introduction of Functionality, Selection of Topology, and Enhancement of Gas Adsorption in Multivariate Metal–Organic Framework-177

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

Zhang, Yue-Biao; Furukawa, Hiroyasu; Ko, Nakeun

2015-02-25

Metal–organic framework-177 (MOF-177) is one of the most porous materials whose structure is composed of octahedral Zn 4O(-COO) 6 and triangular 1,3,5-benzenetribenzoate (BTB) units to make a three-dimensional extended network based on the qom topology. This topology violates a long-standing thesis where highly symmetric building units are expected to yield highly symmetric networks. In the case of octahedron and triangle combinations, MOFs based on pyrite (pyr) and rutile (rtl) nets were expected instead of qom. In this study, we have made 24 MOF-177 structures with different functional groups on the triangular BTB linker, having one or more functionalities. We findmore » that the position of the functional groups on the BTB unit allows the selection for a specific net (qom, pyr, and rtl), and that mixing of functionalities (-H, -NH 2, and -C 4H 4) is an important strategy for the incorporation of a specific functionality (-NO 2) into MOF-177 where otherwise incorporation of such functionality would be difficult. Such mixing of functionalities to make multivariate MOF-177 structures leads to enhancement of hydrogen uptake by 25%.« less

Coherent states, quantum gravity, and the Born-Oppenheimer approximation. I. General considerations

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

Stottmeister, Alexander, E-mail: alexander.stottmeister@gravity.fau.de; Thiemann, Thomas, E-mail: thomas.thiemann@gravity.fau.de

2016-06-15

This article, as the first of three, aims at establishing the (time-dependent) Born-Oppenheimer approximation, in the sense of space adiabatic perturbation theory, for quantum systems constructed by techniques of the loop quantum gravity framework, especially the canonical formulation of the latter. The analysis presented here fits into a rather general framework and offers a solution to the problem of applying the usual Born-Oppenheimer ansatz for molecular (or structurally analogous) systems to more general quantum systems (e.g., spin-orbit models) by means of space adiabatic perturbation theory. The proposed solution is applied to a simple, finite dimensional model of interacting spin systems,more » which serves as a non-trivial, minimal model of the aforesaid problem. Furthermore, it is explained how the content of this article and its companion affect the possible extraction of quantum field theory on curved spacetime from loop quantum gravity (including matter fields).« less

Depositional sequence analysis and sedimentologic modeling for improved prediction of Pennsylvanian reservoirs (Annex 1). Annual report, February 1, 1991--January 31, 1992

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

Watney, W.L.

1992-08-01

Interdisciplinary studies of the Upper Pennsylvanian Lansing and Kansas City groups have been undertaken in order to improve the geologic characterization of petroleum reservoirs and to develop a quantitative understanding of the processes responsible for formation of associated depositional sequences. To this end, concepts and methods of sequence stratigraphy are being used to define and interpret the three-dimensional depositional framework of the Kansas City Group. The investigation includes characterization of reservoir rocks in oil fields in western Kansas, description of analog equivalents in near-surface and surface sites in southeastern Kansas, and construction of regional structural and stratigraphic framework to linkmore » the site specific studies. Geologic inverse and simulation models are being developed to integrate quantitative estimates of controls on sedimentation to produce reconstructions of reservoir-bearing strata in an attempt to enhance our ability to predict reservoir characteristics.« less

Depositional sequence analysis and sedimentologic modeling for improved prediction of Pennsylvanian reservoirs (Annex 1)

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

Watney, W.L.

1992-01-01

Interdisciplinary studies of the Upper Pennsylvanian Lansing and Kansas City groups have been undertaken in order to improve the geologic characterization of petroleum reservoirs and to develop a quantitative understanding of the processes responsible for formation of associated depositional sequences. To this end, concepts and methods of sequence stratigraphy are being used to define and interpret the three-dimensional depositional framework of the Kansas City Group. The investigation includes characterization of reservoir rocks in oil fields in western Kansas, description of analog equivalents in near-surface and surface sites in southeastern Kansas, and construction of regional structural and stratigraphic framework to linkmore » the site specific studies. Geologic inverse and simulation models are being developed to integrate quantitative estimates of controls on sedimentation to produce reconstructions of reservoir-bearing strata in an attempt to enhance our ability to predict reservoir characteristics.« less

A T-Cell Receptor Breaks the Rules | Center for Cancer Research

Cancer.gov

Most mature T cells function immunologically when a T-cell receptor (TCR) located on the cell surface encounters and engages its ligand, a major histocompatability complex (MHC), which displays a specific part of a target protein called an antigen. This antigen-presenting complex is assembled from one of the dozen or so MHC molecules that every person inherits from their parents; and the antigen fragment, called a peptide epitope, is excised from one of thousands of possible proteins—originally part of an invading pathogen or a cancer cell—that T cells are capable of identifying and attacking. The framework of an MHC molecule holding a centrally displayed or “presented” peptide is what engages the TCR and triggers T-cell action. This role of MHC molecules presenting antigens to the TCR is a central tenet of immunology, with the fit between a TCR and the MHC framework actually “hardwired” into their three-dimensional structures.

ScMO(BO3) (M = Ca and Cd): new Sc-based oxyborates featuring interesting edge-sharing sandwich-like chains and UV cut-off edges.

PubMed

Ma, Ruru; Xu, Dongdong; Yang, Yun; Su, Xin; Lei, Binghua; Yang, Zhihua; Pan, Shilie

2017-11-07

Two new isostructural rare-earth oxyborates ScMO(BO 3 ) (M = Ca and Cd) with a three-dimensional (3D) cationic framework and parallel arranged [BO 3 ] triangles have been synthesized by the flux method. In the 3D cationic framework, an interesting sandwich-like basic building unit (BBU) is constructed by two [Ca(1)O 4 ] 6- chains and two [Sc(1)O 4 ] 5- chains. ScMO(BO 3 ) melt incongruently, which shows that title compounds can be grown by the flux method. The UV cut-off edges for ScCaO(BO 3 ) and ScCdO(BO 3 ) are 230 and 249 nm, respectively. In addition, the first-principles calculations are performed to gain further insights into the relationship between the microscopic electronic structures and associated optical properties.

Web-Based Geospatial Visualization of GPM Data with CesiumJS

NASA Technical Reports Server (NTRS)

Lammers, Matt

2018-01-01

Advancements in the capabilities of JavaScript frameworks and web browsing technology have made online visualization of large geospatial datasets such as those coming from precipitation satellites viable. These data benefit from being visualized on and above a three-dimensional surface. The open-source JavaScript framework CesiumJS (http://cesiumjs.org), developed by Analytical Graphics, Inc., leverages the WebGL protocol to do just that. This presentation will describe how CesiumJS has been used in three-dimensional visualization products developed as part of the NASA Precipitation Processing System (PPS) STORM data-order website. Existing methods of interacting with Global Precipitation Measurement (GPM) Mission data primarily focus on two-dimensional static images, whether displaying vertical slices or horizontal surface/height-level maps. These methods limit interactivity with the robust three-dimensional data coming from the GPM core satellite. Integrating the data with CesiumJS in a web-based user interface has allowed us to create the following products. We have linked with the data-order interface an on-the-fly visualization tool for any GPM/partner satellite orbit. A version of this tool also focuses on high-impact weather events. It enables viewing of combined radar and microwave-derived precipitation data on mobile devices and in a way that can be embedded into other websites. We also have used CesiumJS to visualize a method of integrating gridded precipitation data with modeled wind speeds that animates over time. Emphasis in the presentation will be placed on how a variety of technical methods were used to create these tools, and how the flexibility of the CesiumJS framework facilitates creative approaches to interact with the data.

Introduction to the special section on mixture modeling in personality assessment.

PubMed

Wright, Aidan G C; Hallquist, Michael N

2014-01-01

Latent variable models offer a conceptual and statistical framework for evaluating the underlying structure of psychological constructs, including personality and psychopathology. Complex structures that combine or compare categorical and dimensional latent variables can be accommodated using mixture modeling approaches, which provide a powerful framework for testing nuanced theories about psychological structure. This special series includes introductory primers on cross-sectional and longitudinal mixture modeling, in addition to empirical examples applying these techniques to real-world data collected in clinical settings. This group of articles is designed to introduce personality assessment scientists and practitioners to a general latent variable framework that we hope will stimulate new research and application of mixture models to the assessment of personality and its pathology.

Three-Dimensional Model of Holographic Formation of Inhomogeneous PPLC Diffraction Structures

NASA Astrophysics Data System (ADS)

Semkin, A. O.; Sharangovich, S. N.

2018-05-01

A three-dimensional theoretical model of holographic formation of inhomogeneous diffraction structures in composite photopolymer - liquid crystal materials is presented considering both the nonlinearity of recording and the amplitude-phase inhomogeneity of the recording light field. Based on the results of numerical simulation, the kinematics of formations of such structures and their spatial profile are investigated.

Bayesian approach for three-dimensional aquifer characterization at the Hanford 300 Area

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

Murakami, Haruko; Chen, X.; Hahn, Melanie S.

2010-10-21

This study presents a stochastic, three-dimensional characterization of a heterogeneous hydraulic conductivity field within DOE's Hanford 300 Area site, Washington, by assimilating large-scale, constant-rate injection test data with small-scale, three-dimensional electromagnetic borehole flowmeter (EBF) measurement data. We first inverted the injection test data to estimate the transmissivity field, using zeroth-order temporal moments of pressure buildup curves. We applied a newly developed Bayesian geostatistical inversion framework, the method of anchored distributions (MAD), to obtain a joint posterior distribution of geostatistical parameters and local log-transmissivities at multiple locations. The unique aspects of MAD that make it suitable for this purpose are itsmore » ability to integrate multi-scale, multi-type data within a Bayesian framework and to compute a nonparametric posterior distribution. After we combined the distribution of transmissivities with depth-discrete relative-conductivity profile from EBF data, we inferred the three-dimensional geostatistical parameters of the log-conductivity field, using the Bayesian model-based geostatistics. Such consistent use of the Bayesian approach throughout the procedure enabled us to systematically incorporate data uncertainty into the final posterior distribution. The method was tested in a synthetic study and validated using the actual data that was not part of the estimation. Results showed broader and skewed posterior distributions of geostatistical parameters except for the mean, which suggests the importance of inferring the entire distribution to quantify the parameter uncertainty.« less

Three-dimensional shape transformations of hydrogel sheets induced by small-scale modulation of internal stresses

NASA Astrophysics Data System (ADS)

Wu, Zi Liang; Moshe, Michael; Greener, Jesse; Therien-Aubin, Heloise; Nie, Zhihong; Sharon, Eran; Kumacheva, Eugenia

2013-03-01

Although Nature has always been a common source of inspiration in the development of artificial materials, only recently has the ability of man-made materials to produce complex three-dimensional (3D) structures from two-dimensional sheets been explored. Here we present a new approach to the self-shaping of soft matter that mimics fibrous plant tissues by exploiting small-scale variations in the internal stresses to form three-dimensional morphologies. We design single-layer hydrogel sheets with chemically distinct, fibre-like regions that exhibit differential shrinkage and elastic moduli under the application of external stimulus. Using a planar-to-helical three-dimensional shape transformation as an example, we explore the relation between the internal architecture of the sheets and their transition to cylindrical and conical helices with specific structural characteristics. The ability to engineer multiple three-dimensional shape transformations determined by small-scale patterns in a hydrogel sheet represents a promising step in the development of programmable soft matter.

A novel 3D framework indium phosphite-oxalate based on a pcu-type topology

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

Zuo, Mengmeng; Zhou, Mingdong; Hu, Dianwen

2016-05-15

A new inorganic–organic hybrid indium phosphite-oxalate, formulated as H[In{sub 5}(HPO{sub 3}){sub 6}(H{sub 2}PO{sub 3}){sub 2}(C{sub 2}O{sub 4}){sub 2}]·(C{sub 4}N{sub 2}H{sub 11}){sub 2}·H{sub 2}O 1 has been hydrothermally synthesized in the presence of piperazine acting as a structure directing agent (SDA). The single crystal X-ray diffraction reveals that compound 1 shows three-dimensional open-framework with intersecting 12-ring channels along the [010] and [001] directions, which is constructed from strictly alternating double 6-ring units (D6Rs), [C{sub 2}O{sub 4}]{sup 2−} groups and [H{sub 2}PO{sub 3}]{sup −} pseudo-pyramids. It is noted that the classical D6R SBU is firstly reported in main metal phosphite/phosphite-oxalate. By regardingmore » D6R as the 6-connected nodes, the inorganic–organic hybrid framework is based on a pcu-type topology. The as-synthesized product was characterized by single-crystal X-ray diffraction, powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis (TGA), ICP-AES and elemental analyses. - Graphical abstract: A 3D open-framework indium phosphite-oxalate has been synthesized under hydrothermal conditions. A classical SBU, D6R, is present in the structure. By regarding D6R as the 6-connected nodes, the inorganic–organic hybrid framework is based on a pcu-type topology. - Highlights: • A new indium phosphite-oxalate based on a pcu-type topology has been synthesized. • A classical SBU, D6R, is present in the structure. • The classical SBU is firstly reported in main metal phosphite/phosphite-oxalate.« less

Multilocality and fusion rules on the generalized structure functions in two-dimensional and three-dimensional Navier-Stokes turbulence.

PubMed

Gkioulekas, Eleftherios

2016-09-01

Using the fusion-rules hypothesis for three-dimensional and two-dimensional Navier-Stokes turbulence, we generalize a previous nonperturbative locality proof to multiple applications of the nonlinear interactions operator on generalized structure functions of velocity differences. We call this generalization of nonperturbative locality to multiple applications of the nonlinear interactions operator "multilocality." The resulting cross terms pose a new challenge requiring a new argument and the introduction of a new fusion rule that takes advantage of rotational symmetry. Our main result is that the fusion-rules hypothesis implies both locality and multilocality in both the IR and UV limits for the downscale energy cascade of three-dimensional Navier-Stokes turbulence and the downscale enstrophy cascade and inverse energy cascade of two-dimensional Navier-Stokes turbulence. We stress that these claims relate to nonperturbative locality of generalized structure functions on all orders and not the term-by-term perturbative locality of diagrammatic theories or closure models that involve only two-point correlation and response functions.

Validating two-dimensional leadership models on three-dimensionally structured fish schools

PubMed Central

Nagy, Máté; Holbrook, Robert I.; Biro, Dora; Burt de Perera, Theresa

2017-01-01

Identifying leader–follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader–follower interactions have often ignored vertical information. This raises the question of whether commonly used two-dimensional leader–follower analyses can be used justifiably on groups that interact in three dimensions. To address this, we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader–follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader–follower relationships in species that move freely in three dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups. PMID:28280582

How does symmetry impact the flexibility of proteins?

PubMed Central

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-01-01

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures—and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body–bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body–bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains. PMID:24379431

Synthesis, structural characterization and high pressure phase transitions of monolithium hydronium sulfate

NASA Astrophysics Data System (ADS)

Banerjee, Debasis; Plonka, Anna M.; Kim, Sun Jin; Xu, Wenqian; Parise, John B.

2013-01-01

A three dimensional lithium hydronium sulfate LiSO4·H3O [1], [space group Pna21a=8.7785(12) Å, b=9.1297(12) Å, c=5.2799(7) Å, V=423.16(10) Å3] was synthesized via solvothermal methods using 1,5-naphthalenedisulfonic acid (1,5-NSA) as the source of sulfate ions. The structure of [1], determined by single crystal X-ray diffraction techniques, consists of corner sharing LiO4 and SO4 tetrahedra, forming an anionic 3-D open framework that is charge balanced by hydronium ions positioned within channels running along [001] and forming strong H-bonding with the framework oxygen atoms. Compound [1] undergoes two reversible phase transitions, involving reorientation of SO42- ions at pressures of approximately 2.5 and 5 GPa at room temperature, as evident from characteristic discontinuous frequency drops in the ν1 mode of the Raman spectra. Additionally, compound [1] forms dense β-lithium sulfate at 300 °C, as evident from temperature dependent powder XRD and combined reversible TGA-DSC experiments.

Synthesis and Structural, Electrical, and Magnetic Properties of New Iron-Aluminum Alluaudite Phases β-Na2Ni2M(PO4)3 (M = Fe and Al).

PubMed

Harbaoui, Douha; Sanad, Moustafa M S; Rossignol, Cécile; Hlil, El Kebir; Amdouni, Noureddine; Obbade, Saïd

2017-11-06

Herein we report the studies of different physical properties (structural, magnetic, thermal, morphologic, electrical, and electrochemical) of two new allotropic β-Na 2 Ni 2 M(PO 4 ) 3 (NNMP) phosphates, with M = Fe and Al. Pure orthorhombic single-phase powders were prepared under air, using an autocombustion synthesis method. They crystallize in the orthorhombic Imma space group with similar unit cell parameters [a = 10.1592(2), b = 13.0321(3), c = 6.4864(2) Å] and [a = 10.3993(1), b = 13.1966(1), c = 6.4955(1) Å] for β-Na 2 Ni 2 M(PO 4 ) 3 (NNAP) and β-Na 2 Ni 2 Fe(PO 4 ) 3 (NNFP), respectively. Crystal structures of both compounds were determined using X-ray powder diffraction and Rietveld method refinements, which indicate the occurrence of Ni 2+ in the 8g site, and of M 3+ in the 4a site of the structure. The structure consists of a three-dimensional anionic framework obtained by the association on MO 6 , NiO 6 , and PO 4 polyhedra, sharing edges and corners. The resulting three-dimensional structure creates monodimensional channels along the [100] and [010] directions formed by face-shared oxygen polyhedra and occupied by Na + cations. This nondisordered cationic distribution is confirmed by a significant change of magnetic properties. Thus, both NNAP and NNFP samples show paramagnetic to ferromagnetic transition at 14 and 19 K, respectively. For the two compounds, thermal stability, electrical conductivity, and electrochemical properties have been also investigated. The intercalation/desintercalation properties of NNMP compounds as positive electrode were tested in sodium-ion batteries. The first cycling curves exhibit a significant polarization for both prepared samples.

A mechanism-based 3D-QSAR approach for classification and prediction of acetylcholinesterase inhibitory potency of organophosphate and carbamate analogs

NASA Astrophysics Data System (ADS)

Lee, Sehan; Barron, Mace G.

2016-04-01

Organophosphate (OP) and carbamate esters can inhibit acetylcholinesterase (AChE) by binding covalently to a serine residue in the enzyme active site, and their inhibitory potency depends largely on affinity for the enzyme and the reactivity of the ester. Despite this understanding, there has been no mechanism-based in silico approach for classification and prediction of the inhibitory potency of ether OPs or carbamates. This prompted us to develop a three dimensional prediction framework for OPs, carbamates, and their analogs. Inhibitory structures of a compound that can form the covalent bond were identified through analysis of docked conformations of the compound and its metabolites. Inhibitory potencies of the selected structures were then predicted using a previously developed three dimensional quantitative structure-active relationship. This approach was validated with a large number of structurally diverse OP and carbamate compounds encompassing widely used insecticides and structural analogs including OP flame retardants and thio- and dithiocarbamate pesticides. The modeling revealed that: (1) in addition to classical OP metabolic activation, the toxicity of carbamate compounds can be dependent on biotransformation, (2) OP and carbamate analogs such as OP flame retardants and thiocarbamate herbicides can act as AChEI, (3) hydrogen bonds at the oxyanion hole is critical for AChE inhibition through the covalent bond, and (4) π-π interaction with Trp86 is necessary for strong inhibition of AChE. Our combined computation approach provided detailed understanding of the mechanism of action of OP and carbamate compounds and may be useful for screening a diversity of chemical structures for AChE inhibitory potency.

Overdenture retaining bar stress distribution: a finite-element analysis.

PubMed

Caetano, Conrado Reinoldes; Mesquita, Marcelo Ferraz; Consani, Rafael Leonardo Xediek; Correr-Sobrinho, Lourenço; Dos Santos, Mateus Bertolini Fernandes

2015-05-01

Evaluate the stress distribution on the peri-implant bone tissue and prosthetic components of bar-clip retaining systems for overdentures presenting different implant inclinations, vertical misfit and framework material. Three-dimensional models of a jaw and an overdenture retained by two implants and a bar-clip attachment were modeled using specific software (SolidWorks 2010). The studied variables were: latero-lateral inclination of one implant (-10°, -5°, 0°, +5°, +10°); vertical misfit on the other implant (50, 100, 200 µm); and framework material (Au type IV, Ag-Pd, Ti cp, Co-Cr). Solid models were imported into mechanical simulation software (ANSYS Workbench 11). All nodes on the bone's external surface were constrained and a displacement was applied to simulate the settling of the framework on the ill-fitted component. Von Mises stress for the prosthetic components and maximum principal stress to the bone tissue were evaluated. The +10° inclination presented the worst biomechanical behavior, promoting the highest stress values on the bar framework and peri-implant bone tissue. The -5° group presented the lowest stress values on the prosthetic components and the lowest stress value on peri-implant bone tissue was observed in -10°. Increased vertical misfit caused an increase on the stress values in all evaluated structures. Stiffer framework materials caused a considerable stress increase in the framework itself, prosthetic screw of the fitted component and peri-implant bone tissue. Inclination of one implant associated with vertical misfit caused a relevant effect on the stress distribution in bar-clip retained overdentures. Different framework materials promoted increased levels of stress in all the evaluated structures.

Synthesis, structural characterization and selectively catalytic properties of metal-organic frameworks with nano-sized channels: A modular design strategy

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

Qiu Lingguang; Gu Lina; Hu Gang

2009-03-15

Modular design method for designing and synthesizing microporous metal-organic frameworks (MOFs) with selective catalytical activity was described. MOFs with both nano-sized channels and potential catalytic activities could be obtained through self-assembly of a framework unit and a catalyst unit. By selecting hexaaquo metal complexes and the ligand BTC (BTC=1,3,5-benzenetricarboxylate) as framework-building blocks and using the metal complex [M(phen){sub 2}(H{sub 2}O){sub 2}]{sup 2+} (phen=1,10-phenanthroline) as a catalyst unit, a series of supramolecular MOFs 1-7 with three-dimensional nano-sized channels, i.e. [M{sup 1}(H{sub 2}O){sub 6}].[M{sup 2}(phen){sub 2}(H{sub 2}O){sub 2}]{sub 2}.2(BTC).xH{sub 2}O (M{sup 1}, M{sup 2}=Co(II), Ni(II), Cu(II), Zn(II), or Mn(II), phen=1,10-phenanthroline, BTC=1,3,5-benzenetricarboxylate, x=22-24),more » were synthesized through self-assembly, and their structures were characterized by IR, elemental analysis, and single-crystal X-ray diffraction. These supramolecular microporous MOFs showed significant size and shape selectivity in the catalyzed oxidation of phenols, which is due to catalytic reactions taking place in the channels of the framework. Design strategy, synthesis, and self-assembly mechanism for the construction of these porous MOFs were discussed. - Grapical abstract: A modular design strategy has been developed to synthesize microporous metal-organic frameworks with potential catalytic activity by self-assembly of the framework-building blocks and the catalyst unit.« less

Engineering the internal surfaces of three-dimensional nanoporous catalysts by surfactant-modified dealloying.

PubMed

Wang, Zhili; Liu, Pan; Han, Jiuhui; Cheng, Chun; Ning, Shoucong; Hirata, Akihiko; Fujita, Takeshi; Chen, Mingwei

2017-10-20

Tuning surface structures by bottom-up synthesis has been demonstrated as an effective strategy to improve the catalytic performances of nanoparticle catalysts. Nevertheless, the surface modification of three-dimensional nanoporous metals, fabricated by a top-down dealloying approach, has not been achieved despite great efforts devoted to improving the catalytic performance of three-dimensional nanoporous catalysts. Here we report a surfactant-modified dealloying method to tailor the surface structure of nanoporous gold for amplified electrocatalysis toward methanol oxidation and oxygen reduction reactions. With the assistance of surfactants, {111} or {100} faceted internal surfaces of nanoporous gold can be realized in a controllable manner by optimizing dealloying conditions. The surface modified nanoporous gold exhibits significantly enhanced electrocatalytic activities in comparison with conventional nanoporous gold. This study paves the way to develop high-performance three-dimensional nanoporous catalysts with a tunable surface structure by top-down dealloying for efficient chemical and electrochemical reactions.

Three new 5-fold interpenetrating diamondoid frameworks constructed by rigid diimidazole and dicarboxylate ligands

NASA Astrophysics Data System (ADS)

Huo, Jianqiang; Yan, Shuai; Li, Haiqiang; Yu, Donghui; Arulsamy, Navamoney

2018-03-01

A series of three-dimensional coordination polymers, namely, [Cd(BIMB)(SCA)]n (1), [M(BIMB)(trans-CHDC)]n (2, M = Cd2+; 3, M = Co2+), where BIMB = 1,4-di(1H-imidazol-1-yl)benzene, SCA2- = succinate dianion, CHDC2- = cyclohexane-1,4-dicarboxylate dianion) are synthesized hydro/solvatothermal methods. The products are characterized by elemental analysis and single-crystal X-ray diffraction data. Both the dianion and BIMB bridge different pairs of the metal ions, the three complexes are polymeric and their three-dimensional topology feature a diamond-like metal-organic framework (MOF). Owing to the length of the two bridging ligands, moderate size voids are formed in the diamondoid networks. However, the voids are filled by mutual interpenetration of four independent equivalent frameworks in a 5-fold interpenetrating architecture, and there is no sufficient void volume available for any guest molecules. The phase purity and thermal stability of the compounds are verified by powder X-ray diffraction (PXRD) and thermogravimetric (TG) data. The solid-state fluorescence spectra for the 3d10 Cd2+ MOF's 1 and 2 reveal significant enhancement in their emission intensities in comparison to the non-metallated BIMB. The enhanced emission is attributed to perturbation of intra-ligand emission states due to Cd2+ coordination.

X-ray diffraction study of Penicillium Vitale catalase in the complex with aminotriazole

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

Borovik, A. A.; Grebenko, A. I.; Melik-Adamyan, V. R., E-mail: mawr@ns.crys.ras.ru

2011-07-15

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.

3-D orbital evolution model of outer asteroid belt

NASA Technical Reports Server (NTRS)

Solovaya, Nina A.; Gerasimov, Igor A.; Pittich, Eduard M.

1992-01-01

The evolution of minor planets in the outer part of the asteroid belt is considered. In the framework of the semi-averaged elliptic restricted three-dimensional three-body model, the boundary of regions of the Hill's stability is found. As was shown in our work, the Jacobian integral exists.

Supporting Three-Dimensional Science Learning: The Role of Curiosity-Driven Classroom Discourse

ERIC Educational Resources Information Center

Johnson, Wendy Renae

2017-01-01

The National Research Council's "Framework for K-12 Science Education" (2011) presents a new vision for science education that calls for the integration of the three dimensions of science learning: science and engineering practices, crosscutting concepts, and disciplinary core ideas. Unlike previous conceptions of science learning that…

A Three-Dimensional Analysis of Black Leadership.

ERIC Educational Resources Information Center

McDaniel, Clyde O., Jr.; Balgopal, Pallassana R.

This book presents an analysis of black leadership from three perspectives: theoretical, historical, and empirical. After deducing the situational-interactional approach as a useful framework, the authors analyze black leadership from 1841 to the present. This period is divided into six time periods, and black leadership and the strategies used by…

Modelling the drying of three-dimensional pulp moulded structures. Part II, Drying data obtained from flat panels using virgin and recycled paper fibre

Treesearch

John F. Hunt; Margit Tamasy-Bano; Heike Nyist

1999-01-01

A three-dimensional structural panel, called FPL Spaceboard, was developed at the USDA Forest Products Laboratory. Spaceboard panels have been formed using a variety of fibrous materials using either a wet- or dry-forming process. Geometrically, the panel departs from the traditional two-dimensional flat panel by integrally forming an array of perpendicular ribs and...

Three-dimensional reconstruction of the fast-start swimming kinematics of densely schooling fish

PubMed Central

Paley, Derek A.

2012-01-01

Information transmission via non-verbal cues such as a fright response can be quantified in a fish school by reconstructing individual fish motion in three dimensions. In this paper, we describe an automated tracking framework to reconstruct the full-body trajectories of densely schooling fish using two-dimensional silhouettes in multiple cameras. We model the shape of each fish as a series of elliptical cross sections along a flexible midline. We estimate the size of each ellipse using an iterated extended Kalman filter. The shape model is used in a model-based tracking framework in which simulated annealing is applied at each step to estimate the midline. Results are presented for eight fish with occlusions. The tracking system is currently being used to investigate fast-start behaviour of schooling fish in response to looming stimuli. PMID:21642367

A multifunctional chemical sensor based on a three-dimensional lanthanide metal-organic framework

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

Du, Pei-Yao; Liao, Sheng-Yun; Gu, Wen, E-mail: guwen68@nankai.edu.cn

2016-12-15

A 3D lanthanide MOF with formula [Sm{sub 2}(abtc){sub 1.5}(H{sub 2}O){sub 3}(DMA)]·H{sub 2}O·DMA (1) has been successfully synthesized via solvothermal method. Luminescence studies reveal that 1 exhibits dual functional detection benzyl alcohol and benzaldehyde among different aromatic molecules. In addition, 1 displays a turn-on luminescence sensing with respect to ethanol among different alcohol molecules, which suggests that 1 is also a promising luminescent probe for high selective sensing of ethanol. - Highlights: • A three-dimensional lanthanide metal-organic framework has been synthesized. • Complex 1 exhibits dual functional detection benzyl alcohol and benzaldehyde among different aromatic molecules. • Complex 1 displays amore » turn-on luminescence sensing with respect to ethanol among different alcohol molecules.« less

BIOMECHANICAL ANALYSIS OF THE STRESSES GENERATED BY DIFFERENT DISOCCLUSION PATTERNS IN AN IMPLANT-SUPPORTED MANDIBULAR COMPLETE DENTURE

PubMed Central

Greco, Gustavo Diniz; Jansen, Wellington Corrêa; Landre, Janis; Seraidarian, Paulo Isaías

2009-01-01

Objectives: This study evaluated by three-dimensional finite element analysis the tensions generated by different disocclusion patterns (canine guide and bilateral balanced occlusion) in an implant-supported mandibular complete denture. Material and Methods: A three-dimensional model of implant-supported mandibular complete denture was fabricated according to the Brånemark protocol. A 5-element 3.75 x 13-mm screw-shape dental implant system was modeled for this study. The implants were located in the intermental foramen region with 3-mm-high prosthetic components joined by a nickel-chromium framework with 12-mm bilateral cantilever covered by acrylic resin and 12 acrylic denture teeth. SolidWorks® software was used before and after processing the simulations. The mechanical properties of the components were inserted in the model and a 15 N load was established in fixed points, in each one of the simulations. Data were collected in the entire nickel-chromium framework. The results were displayed three-dimensionally as color graphic scales. Results: The canine guide generated greater tensions in the region of the first implant, while the bilateral balanced occlusion generated great tensions in the entire metallic framework. The maximum tension found in the simulation of the bilateral balanced occlusion was 3.22 fold higher than the one found in the simulation of the disocclusion in canine guide. Conclusion: The pattern of disocclusion in canine guide is the ideal for implant-supported mandibular complete denture. PMID:19936535

Biomechanical analysis of the stresses generated by different disocclusion patterns in an implant-supported mandibular complete denture.

PubMed

Greco, Gustavo Diniz; Jansen, Wellington Corrêa; Landre Junior, Janis; Seraidarian, Paulo Isaías

2009-01-01

This study evaluated by three-dimensional finite element analysis the tensions generated by different disocclusion patterns (canine guide and bilateral balanced occlusion) in an implant-supported mandibular complete denture. A three-dimensional model of implant-supported mandibular complete denture was fabricated according to the Brånemark protocol. A 5-element 3.75 x 13-mm screw-shape dental implant system was modeled for this study. The implants were located in the inter-mental foramen region with 3-mm-high prosthetic components joined by a nickel-chromium framework with 12-mm bilateral cantilever covered by acrylic resin and 12 acrylic denture teeth. SolidWorks software was used before and after processing the simulations. The mechanical properties of the components were inserted in the model and a 15 N load was established in fixed points, in each one of the simulations. Data were collected in the entire nickel-chromium framework. The results were displayed three-dimensionally as color graphic scales. The canine guide generated greater tensions in the region of the first implant, while the bilateral balanced occlusion generated great tensions in the entire metallic framework. The maximum tension found in the simulation of the bilateral balanced occlusion was 3.22 fold higher than the one found in the simulation of the disocclusion in canine guide. The pattern of disocclusion in canine guide is the ideal for implant-supported mandibular complete denture.

Balancing Newtonian gravity and spin to create localized structures

NASA Astrophysics Data System (ADS)

Bush, Michael; Lindner, John

2015-03-01

Using geometry and Newtonian physics, we design localized structures that do not require electromagnetic or other forces to resist implosion or explosion. In two-dimensional Euclidean space, we find an equilibrium configuration of a rotating ring of massive dust whose inward gravity is the centripetal force that spins it. We find similar solutions in three-dimensional Euclidean and hyperbolic spaces, but only in the limit of vanishing mass. Finally, in three-dimensional Euclidean space, we generalize the two-dimensional result by finding an equilibrium configuration of a spherical shell of massive dust that supports itself against gravitational collapse by spinning isoclinically in four dimensions so its three-dimensional acceleration is everywhere inward. These Newtonian ``atoms'' illuminate classical physics and geometry.

Quality Inspection and Analysis of Three-Dimensional Geographic Information Model Based on Oblique Photogrammetry

NASA Astrophysics Data System (ADS)

Dong, S.; Yan, Q.; Xu, Y.; Bai, J.

2018-04-01

In order to promote the construction of digital geo-spatial framework in China and accelerate the construction of informatization mapping system, three-dimensional geographic information model emerged. The three-dimensional geographic information model based on oblique photogrammetry technology has higher accuracy, shorter period and lower cost than traditional methods, and can more directly reflect the elevation, position and appearance of the features. At this stage, the technology of producing three-dimensional geographic information models based on oblique photogrammetry technology is rapidly developing. The market demand and model results have been emerged in a large amount, and the related quality inspection needs are also getting larger and larger. Through the study of relevant literature, it is found that there are a lot of researches on the basic principles and technical characteristics of this technology, and relatively few studies on quality inspection and analysis. On the basis of summarizing the basic principle and technical characteristics of oblique photogrammetry technology, this paper introduces the inspection contents and inspection methods of three-dimensional geographic information model based on oblique photogrammetry technology. Combined with the actual inspection work, this paper summarizes the quality problems of three-dimensional geographic information model based on oblique photogrammetry technology, analyzes the causes of the problems and puts forward the quality control measures. It provides technical guidance for the quality inspection of three-dimensional geographic information model data products based on oblique photogrammetry technology in China and provides technical support for the vigorous development of three-dimensional geographic information model based on oblique photogrammetry technology.

Three-dimensional graphene-like carbon frameworks as a new electrode material for electrochemical determination of small biomolecules.

PubMed

Deng, Wenfang; Yuan, Xiaoyan; Tan, Yueming; Ma, Ming; Xie, Qingji

2016-11-15

Three-dimensional (3D) graphene-like carbon frameworks (3DGLCFs) were facilely prepared via copyrolysis of polyaniline and nickel nitrate powder, followed by acid etching. The as-prepared 3DGLCFs possess graphene-like network structure, high specific surface area, and high content nitrogen dopant. Because these features enable large electrochemically active surface area, rapid electron transfer, and fast transport of analytes to electrode surface, the 3DGLCFs modified glassy carbon electrode (GCE) shows current response much higher than commercial graphene (CG) modified GCE towards the oxidation of ascorbic acid (AA), dopamine (DA) and uric acid (UA). The anodic peak separations at 3DGLCFs/GCE are 0.23V between AA and DA, 0.13V between DA and UA, and 0.36V between AA and UA. For the simultaneous electrochemical determination of AA, DA and UA using differential pulse voltammetry, the 3DGLCFs/GCE shows linear response ranges of 1.25×10(-5)-4×10(-4)M for AA, 5×10(-8)-1.0×10(-5)M for DA, and 5×10(-8)-1.5×10(-5)M for UA, with low detection limits of 2×10(-6)M for AA, 1×10(-8)M for DA, and 1×10(-8)M for UA. The 3DGLCFs/GCE was also applied for the measurement of human serum, exhibiting satisfactory recoveries. Copyright © 2016 Elsevier B.V. All rights reserved.

Kinetics of intercalation of fluorescent probes in magnesium–aluminium layered double hydroxide within a multiscale reaction–diffusion framework

PubMed Central

Saliba, Daniel

2016-01-01

We report the synthesis of magnesium–aluminium layered double hydroxide (LDH) using a reaction–diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium–aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698034

Kinetics of intercalation of fluorescent probes in magnesium-aluminium layered double hydroxide within a multiscale reaction-diffusion framework

NASA Astrophysics Data System (ADS)

Saliba, Daniel; Al-Ghoul, Mazen

2016-11-01

We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Gold nanocrystals with DNA-directed morphologies.

PubMed

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P; Kwon, Young Jik; Sim, Sang Jun

2016-09-16

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Gold nanocrystals with DNA-directed morphologies

NASA Astrophysics Data System (ADS)

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P.; Kwon, Young Jik; Sim, Sang Jun

2016-09-01

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

The Numerical Simulation of Time Dependent Flow Structures Over a Natural Gravel Surface.

NASA Astrophysics Data System (ADS)

Hardy, R. J.; Lane, S. N.; Ferguson, R. I.; Parsons, D. R.

2004-05-01

Research undertaken over the last few years has demonstrated the importance of the structure of gravel river beds for understanding the interaction between fluid flow and sediment transport processes. This includes the observation of periodic high-speed fluid wedges interconnected by low-speed flow regions. Our understanding of these flows has been enhanced significantly through a series of laboratory experiments and supported by field observations. However, the potential of high resolution three dimensional Computational Fluid Dynamics (CFD) modeling has yet to be fully developed. This is largely the result of the problems of designing numerically stable meshes for use with complex bed topographies and that Reynolds averaged turbulence schemes are applied. This paper develops two novel techniques for dealing with these issues. The first is the development and validation of a method for representing the complex surface topography of gravel-bed rivers in high resolution three-dimensional computational fluid dynamic models. This is based upon a porosity treatment with a regular structured grid and the application of a porosity modification to the mass conservation equation in which: fully blocked cells are assigned a porosity of zero; fully unblocked cells are assigned a porosity of one; and partly blocked cells are assigned a porosity of between 0 and 1, according to the percentage of the cell volume that is blocked. The second is the application of Large Eddy Simulation (LES) which enables time dependent flow structures to be numerically predicted over the complex bed topographies. The regular structured grid with the embedded porosity algorithm maintains a constant grid cell size throughout the domain implying a constant filter scale for the LES simulation. This enables the prediction of coherent structures, repetitive quasi-cyclic large-scale turbulent motions, over the gravel surface which are of a similar magnitude and frequency to those previously observed in both flume and field studies. These structures are formed by topographic forcing within the domain and are scaled with the flow depth. Finally, this provides the numerical framework for the prediction of sediment transport within a time dependent framework. The turbulent motions make a significant contribution to the turbulent shear stress and the pressure fluctuations which significantly affect the forces acting on the bed and potentially control sediment motion.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

Three coordination polymers constructed from 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid: Synthesis, crystal structure and properties

NASA Astrophysics Data System (ADS)

Zhai, Dandan; Sun, Wujuan; Fan, Fei; Liao, Xuzhao; Chen, Sanping; Yang, Xuwu

2017-04-01

Three new coordination polymers, namely, {[Co2(TPA)(μ3-O)3]·0.5DMA}n (1), {[Co(H2TPA)(bibp)(H2O)3]·H2O}n (2) and {[Cd3(TPA)2(phen)4]·4H2O}n (3), (H3TPA = 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid, bibp = 4,4'-bis(imidazolyl)biphenyl, phen = 1,10-phenanthroline and DMA = N,N-dimethylacetamide), have been synthesized under solvothermal conditions and structurally characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction analysis. Polymer 1 exhibits a three-dimensional (3D) structure constructed from 5-connected secondary building units (SBUs) [Co3(μ3-O)] and 3-connected H3TPA ligands. Polymer 2 has a 1D zigzag polymer chain connected by H3TPA and bibp ligands. Polymer 3 features an unusual 3D framework with a (3,4,2)-connected {4; 6;8}{4; 62;83} topology. Moreover, the thermal stabilities of 1-3 and photoluminescence properties of 3 have been investigated. Magnetic susceptibility measurements indicate that polymers 1-2 display antiferromagnetic exchange properties.

Structural diversification and photocatalytic properties of three Cd(II) coordination polymers decorated with different auxiliary ligands

NASA Astrophysics Data System (ADS)

Yin, Wen-Yu; Zhuang, Guo-Yong; Huang, Zuo-Long; Cheng, Hong-Jian; Zhou, Li; Ma, Man-Hong; Wang, Hao; Tang, Xiao-Yan; Ma, Yun-Sheng; Yuan, Rong-Xin

2016-03-01

Three cadmium coordination polymers, [Cd(bismip)]n (1), {[Cd(bismip)(phen)]·H2O}n (2) and {[Cd2(bismip)2(4,4‧-bipy)]·2H2O}n (3) (H2bismip=5-(1H-benzoimidazol-2-ylsulfanylmethyl)-isophthalic acid, phen=1,10-phenanthroline, 4,4‧-bipy=4,4‧-bipyridine) have been prepared under solvothermal conditions. In 1, the [Cd4(bismip)3] units are jointed by bismip ligands to afford a three-dimensional (3D) architecture. Complex 2 exhibits a 3D supramolecular framework based on the interconnection of 1D chains through hydrogen bonding interactions and π-π packing interactions. 3 is a two-fold interpenetrating 3D architecture with a (4·82)(42·84) Schläfli symbol in which 2D layers are interlinked by 4,4‧-bipy ligands. The diverse structures of compounds 1-3 indicate that the auxiliary ligands have significant effects on the final structures. The photoluminescent properties and photocatalytic properties of these coordination polymers in the solid state were also investigated. Remarkably, 3 shows the wide gap semiconductor nature and exhibit excellent photocatalytic performance.

Squeezing the Efimov effect

NASA Astrophysics Data System (ADS)

Sandoval, J. H.; Bellotti, F. F.; Yamashita, M. T.; Frederico, T.; Fedorov, D. V.; Jensen, A. S.; Zinner, N. T.

2018-03-01

The quantum mechanical three-body problem is a source of continuing interest due to its complexity and not least due to the presence of fascinating solvable cases. The prime example is the Efimov effect where infinitely many bound states of identical bosons can arise at the threshold where the two-body problem has zero binding energy. An important aspect of the Efimov effect is the effect of spatial dimensionality; it has been observed in three dimensional systems, yet it is believed to be impossible in two dimensions. Using modern experimental techniques, it is possible to engineer trap geometry and thus address the intricate nature of quantum few-body physics as function of dimensionality. Here we present a framework for studying the three-body problem as one (continuously) changes the dimensionality of the system all the way from three, through two, and down to a single dimension. This is done by considering the Efimov favorable case of a mass-imbalanced system and with an external confinement provided by a typical experimental case with a (deformed) harmonic trap.

Three-dimensional confocal microscopy of the living cornea and ocular lens

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1991-07-01

The three-dimensional reconstruction of the optic zone of the cornea and the ocular crystalline lens has been accomplished using confocal microscopy and volume rendering computer techniques. A laser scanning confocal microscope was used in the reflected light mode to obtain the two-dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with a 488 nm wavelength. The microscope objective was a Leitz X25, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133 three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their 'beaded' cell borders, basal lamina, nerve plexus, nerve fibers, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in- situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers. The three-dimensional data sets of the cornea and the ocular lens were reconstructed in the computer using volume rendering techniques. Stereo pairs were also created of the two- dimensional ocular images for visualization. The stack of two-dimensional images was reconstructed into a three-dimensional object using volume rendering techniques. This demonstration of the three-dimensional visualization of the intact, enucleated eye provides an important step toward quantitative three-dimensional morphometry of the eye. The important aspects of three-dimensional reconstruction are discussed.

Quasi-three-dimensional particle imaging with digital holography.

PubMed

Kemppinen, Osku; Heinson, Yuli; Berg, Matthew

2017-05-01

In this work, approximate three-dimensional structures of microparticles are generated with digital holography using an automated focus method. This is done by stacking a collection of silhouette-like images of a particle reconstructed from a single in-line hologram. The method enables estimation of the particle size in the longitudinal and transverse dimensions. Using the discrete dipole approximation, the method is tested computationally by simulating holograms for a variety of particles and attempting to reconstruct the known three-dimensional structure. It is found that poor longitudinal resolution strongly perturbs the reconstructed structure, yet the method does provide an approximate sense for the structure's longitudinal dimension. The method is then applied to laboratory measurements of holograms of single microparticles and their scattering patterns.

Mapping Sub-Second Structure in Mouse Behavior

PubMed Central

Wiltschko, Alexander B.; Johnson, Matthew J.; Iurilli, Giuliano; Peterson, Ralph E.; Katon, Jesse M.; Pashkovski, Stan L.; Abraira, Victoria E.; Adams, Ryan P.; Datta, Sandeep Robert

2015-01-01

Summary Complex animal behaviors are likely built from simpler modules, but their systematic identification in mammals remains a significant challenge. Here we use depth imaging to show that three-dimensional (3D) mouse pose dynamics are structured at the sub-second timescale. Computational modeling of these fast dynamics effectively describes mouse behavior as a series of reused and stereotyped modules with defined transition probabilities. We demonstrate this combined 3D imaging and machine learning method can be used to unmask potential strategies employed by the brain to adapt to the environment, to capture both predicted and previously-hidden phenotypes caused by genetic or neural manipulations, and to systematically expose the global structure of behavior within an experiment. This work reveals that mouse body language is built from identifiable components and is organized in a predictable fashion; deciphering this language establishes an objective framework for characterizing the influence of environmental cues, genes and neural activity on behavior. PMID:26687221

Crystal structure of (6E,20E)-3,24-di­fluoro-13,14,28,29-tetra­hydro-5H,22H-tetra­benzo[e,j,p,u][1,4,12,15]tetra­oxa­cyclo­docosine-5,22-dione

PubMed Central

Mohamed, Shaaban K.; Akkurt, Mehmet; Hawaiz, Farouq E.; Ayoob, Mzgin M; Hosten, Eric

2017-01-01

The conformation of the title compound, C34H26F2O6, is cone-shaped, partially determined by intra­molecular C—H⋯O short contacts. The benzene rings at the top of the cone are inclined to one another by 73.10 (7)°, while the benzene rings at the bottom of the cone are inclined to one another by 35.49 (8)°. In the crystal, mol­ecules are linked by C—H⋯O and C—H⋯F hydrogen bonds, forming a three-dimensional supra­molecular structure. There are also C—H⋯π contacts present within the framework structure. PMID:28083124

Three-Dimensional, Inelastic Response of Single-Edge Notch Bend Specimens Subjected to Impact Loading

DTIC Science & Technology

1993-08-01

measure the inherent fracture toughness of a material. A thor- ough understanding of the test specimen behavior is a prerequisite to the application of...measured material properties in structural applications . Three- dimensional dynamic analyses are performed for three different specimen configurations...derstanding of the test specimen behavior is a prerequisite to the application of measured ma- terial properties in structural applications . Three

Sulfur-doped porous reduced graphene oxide hollow nanosphere frameworks as metal-free electrocatalysts for oxygen reduction reaction and as supercapacitor electrode materials.

PubMed

Chen, Xi'an; Chen, Xiaohua; Xu, Xin; Yang, Zhi; Liu, Zheng; Zhang, Lijie; Xu, Xiangju; Chen, Ying; Huang, Shaoming

2014-11-21

Chemical doping with foreign atoms is an effective approach to significantly enhance the electrochemical performance of the carbon materials. Herein, sulfur-doped three-dimensional (3D) porous reduced graphene oxide (RGO) hollow nanosphere frameworks (S-PGHS) are fabricated by directly annealing graphene oxide (GO)-encapsulated amino-modified SiO2 nanoparticles with dibenzyl disulfide (DBDS), followed by hydrofluoric acid etching. The XPS and Raman spectra confirmed that sulfur atoms were successfully introduced into the PGHS framework via covalent bonds. The as-prepared S-PGHS has been demonstrated to be an efficient metal-free electrocatalyst for oxygen reduction reaction (ORR) with the activity comparable to that of commercial Pt/C (40%) and much better methanol tolerance and durability, and to be a supercapacitor electrode material with a high specific capacitance of 343 F g(-1), good rate capability and excellent cycling stability in aqueous electrolytes. The impressive performance for ORR and supercapacitors is believed to be due to the synergistic effect caused by sulfur-doping enhancing the electrochemical activity and 3D porous hollow nanosphere framework structures facilitating ion diffusion and electronic transfer.

A structural model for the in vivo human cornea including collagen-swelling interaction

PubMed Central

Cheng, Xi; Petsche, Steven J.; Pinsky, Peter M.

2015-01-01

A structural model of the in vivo cornea, which accounts for tissue swelling behaviour, for the three-dimensional organization of stromal fibres and for collagen-swelling interaction, is proposed. Modelled as a binary electrolyte gel in thermodynamic equilibrium, the stromal electrostatic free energy is based on the mean-field approximation. To account for active endothelial ionic transport in the in vivo cornea, which modulates osmotic pressure and hydration, stromal mobile ions are shown to satisfy a modified Boltzmann distribution. The elasticity of the stromal collagen network is modelled based on three-dimensional collagen orientation probability distributions for every point in the stroma obtained by synthesizing X-ray diffraction data for azimuthal angle distributions and second harmonic-generated image processing for inclination angle distributions. The model is implemented in a finite-element framework and employed to predict free and confined swelling of stroma in an ionic bath. For the in vivo cornea, the model is used to predict corneal swelling due to increasing intraocular pressure (IOP) and is adapted to model swelling in Fuchs' corneal dystrophy. The biomechanical response of the in vivo cornea to a typical LASIK surgery for myopia is analysed, including tissue fluid pressure and swelling responses. The model provides a new interpretation of the corneal active hydration control (pump-leak) mechanism based on osmotic pressure modulation. The results also illustrate the structural necessity of fibre inclination in stabilizing the corneal refractive surface with respect to changes in tissue hydration and IOP. PMID:26156299

Facile Synthesis of Three-Dimensional Sandwiched MnO2@GCs@MnO2 Hybrid Nanostructured Electrode for Electrochemical Capacitors.

PubMed

Jian, Xian; Liu, Shiyu; Gao, Yuqi; Zhang, Wanli; He, Weidong; Mahmood, Asif; M Subramaniyam, Chandrasekar; Wang, Xiaolin; Mahmood, Nasir; Dou, Shi Xue

2017-06-07

Designable control over the morphology and structure of active materials is highly desirable for achieving high-performance devices. Here, we develop a facile microwave-assisted synthesis to decorate MnO 2 nanocrystals on three-dimensional (3D) graphite-like capsules (GCs) to obtain sandwich nanostructures (3D MnO 2 @GCs@MnO 2 ) as electrode materials for electrochemical capacitors (ECs). A templated growth of the 3D GCs was carried out via catalytic chemical vapor deposition and MnO 2 was decorated on the exterior and interior surfaces of the GC walls through microwave irradiation to build an engineered architecture with robust structural and morphological stability. The unique sandwiched architecture has a large interfacial surface area, and allows for rapid electrolyte diffusion through its hollow/open framework and fast electronic motion via the carbon backbone. Furthermore, the tough and rigid nature of GCs provides the necessary structural stability, and the strong synergy between MnO 2 and GCs leads to high electrochemical activity in both neutral (265.1 F/g at 0.5 A/g) and alkaline (390 F/g at 0.5 A/g) electrolytes. The developed hybrid exhibits stable capacitance up to 6000 cycles in 1 M Na 2 SO 4 . The hybrid is a potential candidate for future ECs and the present study opens up an effective avenue to design hybrid materials for various applications.

Automated integration of lidar into the LANDFIRE product suite

Treesearch

Birgit Peterson; Kurtis J. Nelson; Carl Seielstad; Jason Stoker; W. Matt Jolly; Russell Parsons

2015-01-01

Accurate information about three-dimensional canopy structure and wildland fuel across the landscape is necessary for fire behaviour modelling system predictions. Remotely sensed data are invaluable for assessing these canopy characteristics over large areas; lidar data, in particular, are uniquely suited for quantifying three-dimensional canopy structure. Although...

Two-photon polymerization of a three dimensional structure using beams with orbital angular momentum

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

Zhang, Shi-Jie; Li, Yan, E-mail: li@pku.edu.cn; Liu, Zhao-Pei

The focus of a beam with orbital angular momentum exhibits internal structure instead of an elliptical intensity distribution of a Gaussian beam, and the superposition of Gauss-Laguerre beams realized by two-dimensional phase modulation can generate a complex three-dimensional (3D) focus. By taking advantage of the flexibility of this 3D focus tailoring, we have fabricated a 3D microstructure with high resolution by two-photon polymerization with a single exposure. Furthermore, we have polymerized an array of double-helix structures that demonstrates optical chirality.

Three-dimensional nanomagnetism

DOE PAGES

Fernandez-Pacheco, Amalio; Streubel, Robert; Fruchart, Olivier; ...

2017-06-09

Magnetic nanostructures are being developed for use in many aspects of our daily life, spanning areas such as data storage, sensing and biomedicine. Whereas patterned nanomagnets are traditionally two-dimensional planar structures, recent work is expanding nanomagnetism into three dimensions; a move triggered by the advance of unconventional synthesis methods and the discovery of new magnetic effects. In three-dimensional nanomagnets more complex magnetic configurations become possible, many with unprecedented properties. Here we review the creation of these structures and their implications for the emergence of new physics, the development of instrumentation and computational methods, and exploitation in numerous applications.

Reduced basis ANOVA methods for partial differential equations with high-dimensional random inputs

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

Liao, Qifeng, E-mail: liaoqf@shanghaitech.edu.cn; Lin, Guang, E-mail: guanglin@purdue.edu

2016-07-15

In this paper we present a reduced basis ANOVA approach for partial deferential equations (PDEs) with random inputs. The ANOVA method combined with stochastic collocation methods provides model reduction in high-dimensional parameter space through decomposing high-dimensional inputs into unions of low-dimensional inputs. In this work, to further reduce the computational cost, we investigate spatial low-rank structures in the ANOVA-collocation method, and develop efficient spatial model reduction techniques using hierarchically generated reduced bases. We present a general mathematical framework of the methodology, validate its accuracy and demonstrate its efficiency with numerical experiments.

Crystallization, structure and dynamics of the proton-translocating P-type ATPase.

PubMed

Scarborough, G A

2000-01-01

Large single three-dimensional crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase (H(+) P-ATPase) can be grown in polyethylene-glycol-containing solutions optimized for moderate supersaturation of both the protein surfaces and detergent micellar region. Large two-dimensional H(+) P-ATPase crystals also grow on the surface of such mixtures and on carbon films located at such surfaces. Electron crystallographic analysis of the two-dimensional crystals grown on carbon films has recently elucidated the structure of the H(+) P-ATPase at a resolution of 0.8 nm in the membrane plane. The two-dimensional crystals comprise two offset layers of ring-shaped ATPase hexamers with their exocytoplasmic surfaces face to face. Side-to-side interactions between the cytoplasmic regions of the hexamers in each layer can be seen, and an interaction between identical exocytoplasmic loops in opposing hexamer layers holds the two layers together. Detergent rings around the membrane-embedded region of the hexamers are clearly visible, and detergent-detergent interactions between the rings are also apparent. The crystal packing forces thus comprise both protein-protein and detergent-detergent interactions, supporting the validity of the original crystallization strategy. Ten transmembrane helices in each ATPase monomer are well-defined in the structure map. They are all relatively straight, closely packed, moderately tilted at various angles with respect to a plane normal to the membrane surface and average approximately 3.5 nm in length. The transmembrane helix region is connected in at least three places to the larger cytoplasmic region, which comprises several discrete domains separated by relatively wide, deep clefts. Previous work has shown that the H(+) P-ATPase undergoes substantial conformational changes during its catalytic cycle that are not changes in secondary structure. Importantly, the results of hydrogen/deuterium exchange experiments indicate that these conformational changes are probably rigid-body interdomain movements that lead to cleft closure. When interpreted within the framework of established principles of enzyme catalysis, this information on the structure and dynamics of the H(+) P-ATPase molecule provides the basis of a rational model for the sequence of events that occurs as the ATPase proceeds through its transport cycle. The forces that drive the sequence can also be clearly stipulated. However, an understanding of the molecular mechanism of ion transport catalyzed by the H(+) P-ATPase awaits an atomic resolution structure.

Topology of large-scale structure. IV - Topology in two dimensions

NASA Technical Reports Server (NTRS)

Melott, Adrian L.; Cohen, Alexander P.; Hamilton, Andrew J. S.; Gott, J. Richard, III; Weinberg, David H.

1989-01-01

In a recent series of papers, an algorithm was developed for quantitatively measuring the topology of the large-scale structure of the universe and this algorithm was applied to numerical models and to three-dimensional observational data sets. In this paper, it is shown that topological information can be derived from a two-dimensional cross section of a density field, and analytic expressions are given for a Gaussian random field. The application of a two-dimensional numerical algorithm for measuring topology to cross sections of three-dimensional models is demonstrated.

Three-Dimensional Networks of S-Doped Fe/N/C with Hierarchical Porosity for Efficient Oxygen Reduction in Polymer Electrolyte Membrane Fuel Cells.

PubMed

Wu, Yi-Jin; Wang, Yu-Cheng; Wang, Rui-Xiang; Zhang, Peng-Fang; Yang, Xiao-Dong; Yang, Hui-Juan; Li, Jun-Tao; Zhou, Yao; Zhou, Zhi-You; Sun, Shi-Gang

2018-05-02

Reasonable design and synthesis of Fe/N/C-based catalysts is one of the most promising way for developing precious metal-free oxygen reduction reaction (ORR) catalysts in acidic mediums. Herein, we developed a highly active metal-organic framework-derived S-doped Fe/N/C catalyst [S-Fe/Z8/2-aminothiazole (2-AT)] prepared by thermal treatment. The S-Fe/Z8/2-AT catalyst with uniform S-doping possesses a three-dimensional macro-meso-micro hierarchically porous structure. Moreover, the chemical composition and structural features have been well-optimized and characterized for such S-Fe/Z8/2-AT catalysts; and their formation mechanism was also revealed. Significantly, applying the optimal S-Fe/Z8/2-AT catalysts into electrocatalytic test exhibits remarkable ORR catalytic activity with a half-wave potential of 0.82 V (vs reversible hydrogen electrode) and a mass activity of 18.3 A g -1 at 0.8 V in 0.1 M H 2 SO 4 solution; the polymer electrolyte membrane fuel cell test also confirmed their excellent catalytic activity, which gives a maximal power density as high as 800 mW cm -2 at 1 bar. A series of designed experiments disclosed that the favorable structural merits and desirable chemical compositions of S-Fe/Z8/2-AT catalysts are critical factors for efficient electrocatalytic performance. The work provides a new approach to open an avenue for accurately controlling the composition and structure of Fe/N/C catalysts with highly activity for ORR.

A Dynamic Finite Element Analysis of Human Foot Complex in the Sagittal Plane during Level Walking

PubMed Central

Qian, Zhihui; Ren, Lei; Ding, Yun; Hutchinson, John R.; Ren, Luquan

2013-01-01

The objective of this study is to develop a computational framework for investigating the dynamic behavior and the internal loading conditions of the human foot complex during locomotion. A subject-specific dynamic finite element model in the sagittal plane was constructed based on anatomical structures segmented from medical CT scan images. Three-dimensional gait measurements were conducted to support and validate the model. Ankle joint forces and moment derived from gait measurements were used to drive the model. Explicit finite element simulations were conducted, covering the entire stance phase from heel-strike impact to toe-off. The predicted ground reaction forces, center of pressure, foot bone motions and plantar surface pressure showed reasonably good agreement with the gait measurement data over most of the stance phase. The prediction discrepancies can be explained by the assumptions and limitations of the model. Our analysis showed that a dynamic FE simulation can improve the prediction accuracy in the peak plantar pressures at some parts of the foot complex by 10%–33% compared to a quasi-static FE simulation. However, to simplify the costly explicit FE simulation, the proposed model is confined only to the sagittal plane and has a simplified representation of foot structure. The dynamic finite element foot model proposed in this study would provide a useful tool for future extension to a fully muscle-driven dynamic three-dimensional model with detailed representation of all major anatomical structures, in order to investigate the structural dynamics of the human foot musculoskeletal system during normal or even pathological functioning. PMID:24244500

A dynamic finite element analysis of human foot complex in the sagittal plane during level walking.

PubMed

Qian, Zhihui; Ren, Lei; Ding, Yun; Hutchinson, John R; Ren, Luquan

2013-01-01

The objective of this study is to develop a computational framework for investigating the dynamic behavior and the internal loading conditions of the human foot complex during locomotion. A subject-specific dynamic finite element model in the sagittal plane was constructed based on anatomical structures segmented from medical CT scan images. Three-dimensional gait measurements were conducted to support and validate the model. Ankle joint forces and moment derived from gait measurements were used to drive the model. Explicit finite element simulations were conducted, covering the entire stance phase from heel-strike impact to toe-off. The predicted ground reaction forces, center of pressure, foot bone motions and plantar surface pressure showed reasonably good agreement with the gait measurement data over most of the stance phase. The prediction discrepancies can be explained by the assumptions and limitations of the model. Our analysis showed that a dynamic FE simulation can improve the prediction accuracy in the peak plantar pressures at some parts of the foot complex by 10%-33% compared to a quasi-static FE simulation. However, to simplify the costly explicit FE simulation, the proposed model is confined only to the sagittal plane and has a simplified representation of foot structure. The dynamic finite element foot model proposed in this study would provide a useful tool for future extension to a fully muscle-driven dynamic three-dimensional model with detailed representation of all major anatomical structures, in order to investigate the structural dynamics of the human foot musculoskeletal system during normal or even pathological functioning.

A three-dimensional study of the glottal jet

NASA Astrophysics Data System (ADS)

Krebs, F.; Silva, F.; Sciamarella, D.; Artana, G.

2012-05-01

This work builds upon the efforts to characterize the three-dimensional features of the glottal jet during vocal fold vibration. The study uses a Stereoscopic Particle Image Velocimetry setup on a self-oscillating physical model of the vocal folds with a uniform vocal tract. Time averages are documented and analyzed within the framework given by observations reported for jets exiting elongated nozzles. Phase averages are locked to the audio signal and used to obtain a volumetric reconstruction of the jet. From this reconstruction, the intra-cycle dynamics of the jet axis switching is disclosed.

A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel.

PubMed Central

Kurnikova, M G; Coalson, R D; Graf, P; Nitzan, A

1999-01-01

A lattice relaxation algorithm is developed to solve the Poisson-Nernst-Planck (PNP) equations for ion transport through arbitrary three-dimensional volumes. Calculations of systems characterized by simple parallel plate and cylindrical pore geometries are presented in order to calibrate the accuracy of the method. A study of ion transport through gramicidin A dimer is carried out within this PNP framework. Good agreement with experimental measurements is obtained. Strengths and weaknesses of the PNP approach are discussed. PMID:9929470

Hydroelastic behaviour of a structure exposed to an underwater explosion

PubMed Central

Colicchio, G.; Greco, M.; Brocchini, M.; Faltinsen, O. M.

2015-01-01

The hydroelastic interaction between an underwater explosion and an elastic plate is investigated num- erically through a domain-decomposition strategy. The three-dimensional features of the problem require a large computational effort, which is reduced through a weak coupling between a one-dimensional radial blast solver, which resolves the blast evolution far from the boundaries, and a three-dimensional compressible flow solver used where the interactions between the compression wave and the boundaries take place and the flow becomes three-dimensional. The three-dimensional flow solver at the boundaries is directly coupled with a modal structural solver that models the response of the solid boundaries like elastic plates. This enables one to simulate the fluid–structure interaction as a strong coupling, in order to capture hydroelastic effects. The method has been applied to the experimental case of Hung et al. (2005 Int. J. Impact Eng. 31, 151–168 (doi:10.1016/j.ijimpeng.2003.10.039)) with explosion and structure sufficiently far from other boundaries and successfully validated in terms of the evolution of the acceleration induced on the plate. It was also used to investigate the interaction of an underwater explosion with the bottom of a close-by ship modelled as an orthotropic plate. In the application, the acoustic phase of the fluid–structure interaction is examined, highlighting the need of the fluid–structure coupling to capture correctly the possible inception of cavitation. PMID:25512585

DNA Brick Crystals with Prescribed Depth

PubMed Central

Ke, Yonggang; Ong, Luvena L.; Sun, Wei; Song, Jie; Dong, Mingdong; Shih, William M.; Yin, Peng

2014-01-01

We describe a general framework for constructing two-dimensional crystals with prescribed depth and sophisticated three-dimensional features. These crystals may serve as scaffolds for the precise spatial arrangements of functional materials for diverse applications. The crystals are self-assembled from single-stranded DNA components called DNA bricks. We demonstrate the experimental construction of DNA brick crystals that can grow to micron-size in the lateral dimensions with precisely controlled depth up to 80 nanometers. They can be designed to display user-specified sophisticated three-dimensional nanoscale features, such as continuous or discontinuous cavities and channels, and to pack DNA helices at parallel and perpendicular angles relative to the plane of the crystals. PMID:25343605

[The possibility of three-dimensional modeling of the mechanisms of damage formation in the framework of situational expertise].

PubMed

Shakir'yanova, Yu P; Leonov, S V; Pinchuk, P V; Sukhareva, M A

This article was designed to share the experience gained with the three-dimensional modeling for the purpose of situational expertise intended to reconstruct the occurrence circumstances and check up the alternative investigative leads concerning formation of potential injuries to a concrete person. Simulation was performed with the use of the dimensionally scaled model of the place of occurrence as well as the models of the human head and body totally consistent with the anthropometric characteristics of the victim. The results of this work made it possible to reject several potential opportunities for the formation of injuries to the victim and identify the most probable version.

Syntheses, structures and luminescent properties of zero-/two-dimensional Cd(II) and Eu(III) complexes

NASA Astrophysics Data System (ADS)

Fan, Rui-Qing; Wang, Li-Yuan; Wang, Ping; Chen, Hong; Sun, Cun-fa; Yang, Yu-Lin; Su, Qing

2012-12-01

Three metal-organic complexes Cd(HBIDC)(phen)2·4H2O (1), [Cd(BIC)(phen)]n (2) and {[Eu(HBIDC)(H2BIDC)(H2O)]·H2O}n (3) (H3BIDC=benzimidazole-5,6-dicarboxylic acid, H2BIC=benzimidazole-6-carboxylic acid, phen=1,10-phenanthroline) have been synthesized under hydro(solvo)thermal conditions and structurally characterized by elemental analysis, IR spectrum, and single-crystal X-ray diffraction. With similar reaction conditions, reactions of the same ligand with different metal cations selected from different blocks (d-block and f-block) result in different coordination modes of carboxylate groups and final frameworks of complexes 1 and 3. The decarboxylation was observed in complex 2 and resulted in the formation of BIC2- ligand. Complexes 1-3 have intense fluorescent emissions at room temperature in dimethylsulfoxide (DMSO) solution and in the solid-state, which indicate they are potential fluorescence materials. The quantum yields and fluorescence lifetimes of these three complexes were systematically studied.

Generation, Analysis and Characterization of Anisotropic Engineered Meta Materials

NASA Astrophysics Data System (ADS)

Trifale, Ninad T.

A methodology for a systematic generation of highly anisotropic micro-lattice structures was investigated. Multiple algorithms for generation and validation of engineered structures are developed and evaluated. Set of all possible permutations of structures for an 8-node cubic unit cell were considered and the degree of anisotropy of meta-properties in heat transport and mechanical elasticity were evaluated. Feasibility checks were performed to ensure that the generated unit cell network was repeatable and a continuous lattice structure. Four different strategies for generating permutations of the structures are discussed. Analytical models were developed to predict effective thermal, mechanical and permeability characteristics of these cellular structures.Experimentation and numerical modeling techniques were used to validate the models that are developed. A self-consistent mechanical elasticity model was developed which connects the meso-scale properties to stiffness of individual struts. A three dimensional thermal resistance network analogy was used to evaluate the effective thermal conductivity of the structures. The struts were modeled as a network of one dimensional thermal resistive elements and effective conductivity evaluated. Models were validated against numerical simulations and experimental measurements on 3D printed samples. Model was developed to predict effective permeability of these engineered structures based on Darcy's law. Drag coefficients were evaluated for individual connections in transverse and longitudinal directions and an interaction term was calibrated from the experimental data in literature in order to predict permeability. Generic optimization framework coupled to finite element solver is developed for analyzing any application involving use of porous structures. An objective functions were generated structure to address frequently observed trade-off between the stiffness, thermal conductivity, permeability and porosity. Three application were analyzed for potential use of engineered materials. Heat spreader application involving thermal and mechanical constraints, artificial bone grafts application involving mechanical and permeability constraints and structural materials applications involving mechanical, thermal and porosity constraints is analyzed. Recommendations for optimum topologies for specific operating conditions are provided.

Hybrid Dion-Jacobson 2D Lead Iodide Perovskites.

PubMed

Mao, Lingling; Ke, Weijun; Pedesseau, Laurent; Wu, Yilei; Katan, Claudine; Even, Jacky; Wasielewski, Michael R; Stoumpos, Constantinos C; Kanatzidis, Mercouri G

2018-03-14

The three-dimensional hybrid organic-inorganic perovskites have shown huge potential for use in solar cells and other optoelectronic devices. Although these materials are under intense investigation, derivative materials with lower dimensionality are emerging, offering higher tunability of physical properties and new capabilities. Here, we present two new series of hybrid two-dimensional (2D) perovskites that adopt the Dion-Jacobson (DJ) structure type, which are the first complete homologous series reported in halide perovskite chemistry. Lead iodide DJ perovskites adopt a general formula A'A n-1 Pb n I 3 n+1 (A' = 3-(aminomethyl)piperidinium (3AMP) or 4-(aminomethyl)piperidinium (4AMP), A = methylammonium (MA)). These materials have layered structures where the stacking of inorganic layers is unique as they lay exactly on top of another. With a slightly different position of the functional group in the templating cation 3AMP and 4AMP, the as-formed DJ perovskites show different optical properties, with the 3AMP series having smaller band gaps than the 4AMP series. Analysis on the crystal structures and density functional theory (DFT) calculations suggest that the origin of the systematic band gap shift is the strong but indirect influence of the organic cation on the inorganic framework. Fabrication of photovoltaic devices utilizing these materials as light absorbers reveals that (3AMP)(MA) 3 Pb 4 I 13 has the best power conversion efficiency (PCE) of 7.32%, which is much higher than that of the corresponding (4AMP)(MA) 3 Pb 4 I 13 .