Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE PAGES

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei; ...

2017-09-29

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Three-dimensional structure and multistable optical switching of triple-twisted particle-like excitations in anisotropic fluids.

PubMed

Smalyukh, Ivan I; Lansac, Yves; Clark, Noel A; Trivedi, Rahul P

2010-02-01

Control of structures in soft materials with long-range order forms the basis for applications such as displays, liquid-crystal biosensors, tunable lenses, distributed feedback lasers, muscle-like actuators and beam-steering devices. Bistable, tristable and multistable switching of well-defined structures of molecular alignment is of special interest for all of these applications. Here we describe the facile optical creation and multistable switching of localized configurations in the molecular orientation field of a chiral nematic anisotropic fluid. These localized chiro-elastic particle-like excitations--dubbed 'triple-twist torons'--are generated by vortex laser beams and embed the localized three-dimensional (3D) twist into a uniform background. Confocal polarizing microscopy and computer simulations reveal their equilibrium internal structures, manifesting both skyrmion-like and Hopf fibration features. Robust generation of torons at predetermined locations combined with both optical and electrical reversible switching can lead to new ways of multistable structuring of complex photonic architectures in soft materials.

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

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

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

A one-pot gold seed-assisted synthesis of gold/platinum wire nanoassemblies and their enhanced electrocatalytic activity for the oxidation of oxalic acid

NASA Astrophysics Data System (ADS)

Bai, Juan; Fang, Chun-Long; Liu, Zong-Huai; Chen, Yu

2016-01-01

Three-dimensional (3D) noble metal nanoassemblies composed of one-dimensional (1D) nanowires have been attracting much interest due to the unique physical and chemical properties of 1D nanowires as well as the particular interconnected open-pore structure of 3D nanoassemblies. In this work, well-defined Au/Pt wire nanoassemblies were synthesized by using a facile NaBH4 reduction method in the presence of a branched form of polyethyleneimine (PEI). A study of the growth mechanism indicated the morphology of the final product to be highly related to the molecular structure of the polymeric amine. Also, the preferred Pt-on-Pt deposition contributed to the formation of the 1D Pt nanowires. The Au/Pt wire nanoassemblies were functionalized with PEI at the same time that these nanoassemblies were synthesized due to the strong N-Pt bond. The chemically functionalized Au/Pt wire nanoassemblies exhibited better electrocatalytic activity for the electro-oxidation of oxalic acid than did commercial Pt black.Three-dimensional (3D) noble metal nanoassemblies composed of one-dimensional (1D) nanowires have been attracting much interest due to the unique physical and chemical properties of 1D nanowires as well as the particular interconnected open-pore structure of 3D nanoassemblies. In this work, well-defined Au/Pt wire nanoassemblies were synthesized by using a facile NaBH4 reduction method in the presence of a branched form of polyethyleneimine (PEI). A study of the growth mechanism indicated the morphology of the final product to be highly related to the molecular structure of the polymeric amine. Also, the preferred Pt-on-Pt deposition contributed to the formation of the 1D Pt nanowires. The Au/Pt wire nanoassemblies were functionalized with PEI at the same time that these nanoassemblies were synthesized due to the strong N-Pt bond. The chemically functionalized Au/Pt wire nanoassemblies exhibited better electrocatalytic activity for the electro-oxidation of oxalic acid than did commercial Pt black. Electronic supplementary information (ESI) available: Experimental details and additional physical characterization. See DOI: 10.1039/c5nr08150e

Self-assembled three-dimensional hierarchical graphene/polypyrrole nanotube hybrid aerogel and its application for supercapacitors.

PubMed

Ye, Shibing; Feng, Jiachun

2014-06-25

A three-dimensional hierarchical graphene/polypyrrole aerogel (GPA) has been fabricated using graphene oxide (GO) and already synthesized one-dimensional hollow polypyrrole nanotubes (PNTs) as the feedstock. The amphiphilic GO is helpful in effectively promoting the dispersion of well-defined PNTs to result in a stable, homogeneous GO/PNT complex solution, while the PNTs not only provide a large accessible surface area for fast transport of hydrate ions but also act as spacers to prevent the restacking of graphene sheets. By a simple one-step reduction self-assembly process, hierarchically structured, low-density, highly compressible GPAs are easily obtained, which favorably combine the advantages of graphene and PNTs. The supercapacitor electrodes based on such materials exhibit excellent electrochemical performance, including a high specific capacitance up to 253 F g(-1), good rate performance, and outstanding cycle stability. Moreover, this method may be feasible to prepare other graphene-based hybrid aerogels with structure-controllable nanostructures in large scale, thereby holding enormous potential in many application fields.

Extreme Soft Limit Observation of Quantum Hall Effect in a 3-d Semiconductor

NASA Astrophysics Data System (ADS)

Bleiweiss, Michael; Yin, Ming; Amirzadeh, Jafar; Preston, Harry; Datta, Timir

2004-03-01

We report on the evidence for quantum hall effect at 38K and in magnetic fields (B) as low as 1k-Orsted. Our specimens were semiconducting, carbon replica opal (CRO) structures. CRO are three dimensional bulk systems where the carbon is grown by CVD into the porous regions in artificial silica opals. The carbon forms layers on top of the silica spheres as eggshells. The shells are of uneven thickness and are perforated at the contacts points of the opal spheres and form a closed packed, three dimensional crystal structure. Plateaus in inverse R_xy that are conjugated with well-defined Subnikov-deHass modulations in R_xx were observed. The quantum steps that are particularly prominent were the states with fill factors v = p/q (p,q are integers) were the well know fractions, 1/3, 1/2, 3/5, 1 and 5/2. QHE steps indicate that the carriers are localized in two-dimensional regions, which may be due to the extremely large surface to volume ratio associated with replica opal structure. From the B-1 vs v straight line, the effective surface carrier density, ns = 2.2 x 10^14 m-2. To the best of our knowledge, the current work is the first to report fractional quantum hall plateaus in a bulk system.

Resistance and Security Index of Networks: Structural Information Perspective of Network Security

NASA Astrophysics Data System (ADS)

Li, Angsheng; Hu, Qifu; Liu, Jun; Pan, Yicheng

2016-06-01

Recently, Li and Pan defined the metric of the K-dimensional structure entropy of a structured noisy dataset G to be the information that controls the formation of the K-dimensional structure of G that is evolved by the rules, order and laws of G, excluding the random variations that occur in G. Here, we propose the notion of resistance of networks based on the one- and two-dimensional structural information of graphs. Given a graph G, we define the resistance of G, written , as the greatest overall number of bits required to determine the code of the module that is accessible via random walks with stationary distribution in G, from which the random walks cannot escape. We show that the resistance of networks follows the resistance law of networks, that is, for a network G, the resistance of G is , where and are the one- and two-dimensional structure entropies of G, respectively. Based on the resistance law, we define the security index of a network G to be the normalised resistance of G, that is, . We show that the resistance and security index are both well-defined measures for the security of the networks.

Resistance and Security Index of Networks: Structural Information Perspective of Network Security.

PubMed

Li, Angsheng; Hu, Qifu; Liu, Jun; Pan, Yicheng

2016-06-03

Recently, Li and Pan defined the metric of the K-dimensional structure entropy of a structured noisy dataset G to be the information that controls the formation of the K-dimensional structure of G that is evolved by the rules, order and laws of G, excluding the random variations that occur in G. Here, we propose the notion of resistance of networks based on the one- and two-dimensional structural information of graphs. Given a graph G, we define the resistance of G, written , as the greatest overall number of bits required to determine the code of the module that is accessible via random walks with stationary distribution in G, from which the random walks cannot escape. We show that the resistance of networks follows the resistance law of networks, that is, for a network G, the resistance of G is , where and are the one- and two-dimensional structure entropies of G, respectively. Based on the resistance law, we define the security index of a network G to be the normalised resistance of G, that is, . We show that the resistance and security index are both well-defined measures for the security of the networks.

Resistance and Security Index of Networks: Structural Information Perspective of Network Security

PubMed Central

Li, Angsheng; Hu, Qifu; Liu, Jun; Pan, Yicheng

2016-01-01

Recently, Li and Pan defined the metric of the K-dimensional structure entropy of a structured noisy dataset G to be the information that controls the formation of the K-dimensional structure of G that is evolved by the rules, order and laws of G, excluding the random variations that occur in G. Here, we propose the notion of resistance of networks based on the one- and two-dimensional structural information of graphs. Given a graph G, we define the resistance of G, written , as the greatest overall number of bits required to determine the code of the module that is accessible via random walks with stationary distribution in G, from which the random walks cannot escape. We show that the resistance of networks follows the resistance law of networks, that is, for a network G, the resistance of G is , where and are the one- and two-dimensional structure entropies of G, respectively. Based on the resistance law, we define the security index of a network G to be the normalised resistance of G, that is, . We show that the resistance and security index are both well-defined measures for the security of the networks. PMID:27255783

Statistical investigation of avalanches of three-dimensional small-world networks and their boundary and bulk cross-sections

NASA Astrophysics Data System (ADS)

Najafi, M. N.; Dashti-Naserabadi, H.

2018-03-01

In many situations we are interested in the propagation of energy in some portions of a three-dimensional system with dilute long-range links. In this paper, a sandpile model is defined on the three-dimensional small-world network with real dissipative boundaries and the energy propagation is studied in three dimensions as well as the two-dimensional cross-sections. Two types of cross-sections are defined in the system, one in the bulk and another in the system boundary. The motivation of this is to make clear how the statistics of the avalanches in the bulk cross-section tend to the statistics of the dissipative avalanches, defined in the boundaries as the concentration of long-range links (α ) increases. This trend is numerically shown to be a power law in a manner described in the paper. Two regimes of α are considered in this work. For sufficiently small α s the dominant behavior of the system is just like that of the regular BTW, whereas for the intermediate values the behavior is nontrivial with some exponents that are reported in the paper. It is shown that the spatial extent up to which the statistics is similar to the regular BTW model scales with α just like the dissipative BTW model with the dissipation factor (mass in the corresponding ghost model) m2˜α for the three-dimensional system as well as its two-dimensional cross-sections.

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.

Utility of three-dimensional and multiplanar reformatted computed tomography for evaluation of pediatric congenital spine abnormalities.

PubMed

Newton, Peter O; Hahn, Gregory W; Fricka, Kevin B; Wenger, Dennis R

2002-04-15

A retrospective radiographic review of 31 patients with congenital spine abnormalities who underwent conventional radiography and advanced imaging studies was conducted. To analyze the utility of three-dimensional computed tomography with multiplanar reformatted images for congenital spine anomalies, as compared with plain radiographs and axial two-dimensional computed tomography imaging. Conventional radiographic imaging for congenital spine disorders often are difficult to interpret because of the patient's small size, the complexity of the disorder, a deformity not in the plane of the radiographs, superimposed structures, and difficulty in forming a mental three-dimensional image. Multiplanar reformatted and three-dimensional computed tomographic imaging offers many potential advantages for defining congenital spine anomalies including visualization of the deformity in any plane, from any angle, with the overlying structures subtracted. The imaging studies of patients who had undergone a three-dimensional computed tomography for congenital deformities of the spine between 1992 and 1998 were reviewed (31 cases). All plain radiographs and axial two-dimensional computed tomography images performed before the three-dimensional computed tomography were reviewed and the findings documented. This was repeated for the three-dimensional reconstructions and, when available, the multiplanar reformatted images (15 cases). In each case, the utility of the advanced imaging was graded as one of the following: Grade A (substantial new information obtained), Grade B (confirmatory with improved visualization and understanding of the deformity), and Grade C (no added useful information obtained). In 17 of 31 cases, the multiplanar reformatted and three-dimensional images allowed identification of unrecognized malformations. In nine additional cases, the advanced imaging was helpful in better visualizing and understanding previously identified deformities. In five cases, no new information was gained. The standard and curved multiplanar reformatted images were best for defining the occiput-C1-C2 anatomy and the extent of segmentation defects. The curved multiplanar reformatted images were especially helpful in keeping the spine from "coming in" and "going out" of the plane of the image when there was significant spine deformity in the sagittal or coronal plane. The three-dimensional reconstructions proved valuable in defining failures of formation. Advanced computed tomography imaging (three-dimensional computed tomography and curved/standard multiplanar reformatted images) allows better definition of congenital spine anomalies. More than 50% of the cases showed additional abnormalities not appreciated on plain radiographs or axial two-dimensional computed tomography images. Curved multiplanar reformatted images allowed imaging in the coronal and sagittal planes of the entire deformity.

The National Shipbuilding Research Program, Proceedings of the REAPS Technical Symposium Paper No. 6: SPADES System Current Developments

DTIC Science & Technology

1976-06-01

and End-Cuts Program ( PLEC ). A special program to aid in fabrication of complex three-dimensional pipe structures, which is of special interest to...LENGTH AND END-CUTS PROGRAM ( PL E C) PROGRAM DESCRIPTION 1. PROGRAM CAPABILITIES The Pipe Length and End- Cuts ( PLEC ) Development Program allows the...required categories: a. Definition Input This type of input by the ’ PLEC ’ Program can be divided in two is used to define a three-dimensional structure

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-01

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study.

PubMed

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-21

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C 12 E 8 ) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Three Dimensional Modeling of the Attenuation Structure in the Part of the Kumaon Himalaya, India Using Strong Motion Data

NASA Astrophysics Data System (ADS)

Joshi, A.; LAL, S.

2017-12-01

Attenuation property of the medium determines the amplitude of seismic waves at different locations during an earthquake. Attenuation can be defined by the inverse of the parameter known as quality factor `Q' (Knopoff, 1964). It has been observed that the peak ground acceleration in the strong motion accelerogram is associated with arrival of S-waves which is controlled mainly by the shear wave attenuation characteristics of the medium. In the present work attenuation structure is obtained using the modified inversion algorithm given by Joshi et al. (2010). The modified inversion algorithm is designed to provide three dimensional attenuation structure of the region at different frequencies. A strong motion network is installed in the Kumaon Himalaya by the Department of Earth Sciences, Indian Institute of Technology Roorkee under a major research project sponsored by the Ministry of Earth Sciences, Government of India. In this work the detailed three dimensional shear wave quality factor has been determined for the Kumaon Himalaya using strong motion data obtained from this network. In the present work 164 records from 26 events recorded at 15 stations located in an area of 129 km x 62 km has been used. The shear wave attenuation structure for the Kumaon Himalaya has been calculated by dividing the study region into 108 three dimensional rectangular blocks of size 22 km x 11 km x 5 km. The input to the inversion algorithm is the acceleration spectra of S wave identified from each record. A total of 164 spectra from equal number of accelerograms with sampling frequency of .024 Hz is used as an input to the algorithms. A total of 2048 three dimensional attenuation structure is obtained upto frequency of 50 Hz. The obtained structure at various frequencies is compared with the existing geological models in the region and it is seen that the obtained model correlated well with the geological model of the region. References: Joshi, A., Mohanty, M., Bansal, A. R., Dimri, V. P. and Chadha, R. K., 2010, Use of spectral acceleration data for determination of three dimensional attenuation structure in the Pithoragarh region of Kumaon Himalaya, J Seismol., 14, 247-272. Knopoff, L., 1964, Q, Reviews of Geophysics, 2, 625-660.

Three-dimensional hydrogeologic framework model of the Rio Grande transboundary region of New Mexico and Texas, USA, and northern Chihuahua, Mexico

USGS Publications Warehouse

Sweetkind, Donald S.

2017-09-08

As part of a U.S. Geological Survey study in cooperation with the Bureau of Reclamation, a digital three-dimensional hydrogeologic framework model was constructed for the Rio Grande transboundary region of New Mexico and Texas, USA, and northern Chihuahua, Mexico. This model was constructed to define the aquifer system geometry and subsurface lithologic characteristics and distribution for use in a regional numerical hydrologic model. The model includes five hydrostratigraphic units: river channel alluvium, three informal subdivisions of Santa Fe Group basin fill, and an undivided pre-Santa Fe Group bedrock unit. Model input data were compiled from published cross sections, well data, structure contour maps, selected geophysical data, and contiguous compilations of surficial geology and structural features in the study area. These data were used to construct faulted surfaces that represent the upper and lower subsurface hydrostratigraphic unit boundaries. The digital three-dimensional hydrogeologic framework model is constructed through combining faults, the elevation of the tops of each hydrostratigraphic unit, and boundary lines depicting the subsurface extent of each hydrostratigraphic unit. The framework also compiles a digital representation of the distribution of sedimentary facies within each hydrostratigraphic unit. The digital three-dimensional hydrogeologic model reproduces with reasonable accuracy the previously published subsurface hydrogeologic conceptualization of the aquifer system and represents the large-scale geometry of the subsurface aquifers. The model is at a scale and resolution appropriate for use as the foundation for a numerical hydrologic model of the study area.

Three dimensional canonical singularity and five dimensional N = 1 SCFT

NASA Astrophysics Data System (ADS)

Xie, Dan; Yau, Shing-Tung

2017-06-01

We conjecture that every three dimensional canonical singularity defines a five dimensional N = 1 SCFT. Flavor symmetry can be found from singularity structure: non-abelian flavor symmetry is read from the singularity type over one dimensional singular locus. The dimension of Coulomb branch is given by the number of compact crepant divisors from a crepant resolution of singularity. The detailed structure of Coulomb branch is described as follows: a) a chamber of Coulomb branch is described by a crepant resolution, and this chamber is given by its Nef cone and the prepotential is computed from triple intersection numbers; b) Crepant resolution is not unique and different resolutions are related by flops; Nef cones from crepant resolutions form a fan which is claimed to be the full Coulomb branch.

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.

Creation of the reduced-density region by a pulsing optical discharge in the supersonic air flow

NASA Astrophysics Data System (ADS)

Kiseleva, T. A.; Orishich, A. M.; Chirkashenko, V. F.; Yakovlev, V. I.

2016-10-01

As a result of optical and pneumometric measurements is defined the flow shock wave structure that is formed by the optical breakdown, due to focused repetitively pulsed CO2 laser radiation when entering perpendicular to a supersonic (M = 1.36, 1.9) air flow direction. The dynamics of the bow shock formation in front of the energy input area is shown, depending on the frequency of energy impulse sequence. A flow structure is defined in the thermal wake behind pulsing laser plasma as well as wake's length with low thermal heterogeneity. A three-dimensional configuration of the energy area is defined in accordance with pneumometric and optical measuring results. It is shown that Pitot pressure decreases in thermal wake at a substantially constant static pressure, averaged flow parameters weakly depend on the energy impulse's frequency in range of 45-150 kHz.

Ordered three-dimensional interconnected nanoarchitectures in anodic porous alumina

PubMed Central

Martín, Jaime; Martín-González, Marisol; Fernández, Jose Francisco; Caballero-Calero, Olga

2014-01-01

Three-dimensional nanostructures combine properties of nanoscale materials with the advantages of being macro-sized pieces when the time comes to manipulate, measure their properties, or make a device. However, the amount of compounds with the ability to self-organize in ordered three-dimensional nanostructures is limited. Therefore, template-based fabrication strategies become the key approach towards three-dimensional nanostructures. Here we report the simple fabrication of a template based on anodic aluminum oxide, having a well-defined, ordered, tunable, homogeneous 3D nanotubular network in the sub 100 nm range. The three-dimensional templates are then employed to achieve three-dimensional, ordered nanowire-networks in Bi2Te3 and polystyrene. Lastly, we demonstrate the photonic crystal behavior of both the template and the polystyrene three-dimensional nanostructure. Our approach may establish the foundations for future high-throughput, cheap, photonic materials and devices made of simple commodity plastics, metals, and semiconductors. PMID:25342247

Graphene quantum dots-three-dimensional graphene composites for high-performance supercapacitors.

PubMed

Chen, Qing; Hu, Yue; Hu, Chuangang; Cheng, Huhu; Zhang, Zhipan; Shao, Huibo; Qu, Liangti

2014-09-28

Graphene quantum dots (GQDs) have been successfully deposited onto the three-dimensional graphene (3DG) by a benign electrochemical method and the ordered 3DG structure remains intact after the uniform deposition of GQDs. In addition, the capacitive properties of the as-formed GQD-3DG composites are evaluated in symmetrical supercapacitors. It is found that the supercapacitor fabricated from the GQD-3DG composite is highly stable and exhibits a high specific capacitance of 268 F g(-1), representing a more than 90% improvement over that of the supercapacitor made from pure 3DG electrodes (136 F g(-1)). Owing to the convenience of the current method, it can be further used in other well-defined electrode materials, such as carbon nanotubes, carbon aerogels and conjugated polymers to improve the performance of the supercapacitors.

Non-native three-dimensional block copolymer morphologies

DOE PAGES

Rahman, Atikur; Majewski, Pawel W.; Doerk, Gregory; ...

2016-12-22

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials—block copolymer thin films—can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers throughmore » subtle surface topography. As a result, this strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.« less

Non-native three-dimensional block copolymer morphologies

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

Rahman, Atikur; Majewski, Pawel W.; Doerk, Gregory

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials—block copolymer thin films—can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers throughmore » subtle surface topography. As a result, this strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.« less

High-definition polymeric membranes: construction of 3D lithographed channel arrays through control of natural building blocks dynamics.

PubMed

Speranza, Valentina; Trotta, Francesco; Drioli, Enrico; Gugliuzza, Annarosa

2010-02-01

The fabrication of well-defined interfaces is in high demand in many fields of biotechnologies. Here, high-definition membrane-like arrays are developed through the self-assembly of water droplets, which work as natural building blocks for the construction of ordered channels. Solution viscosity together with the dynamics of the water droplets can decide the final formation of three-dimensional well-ordered patterns resembling anodic structures, especially because solvents denser than water are used. Particularly, the polymer solution viscosity is demonstrated to be a powerful tool for control of the mobility of submerged droplets during the microfabrication process. The polymeric patterns are structured at very high levels of organization and exhibit well-established transport-surface property relationships, considered basics for any types of advanced biotechnologies.

3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

PubMed

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

3D structure of eukaryotic flagella/cilia by cryo-electron tomography

PubMed Central

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

PubMed

Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

2015-01-01

Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Spherical shock-wave propagation in three-dimensional granular packings.

PubMed

Xue, Kun; Bai, Chun-Hua

2011-02-01

We investigate numerically the spherical shock-wave propagation in an open dense granular packing perturbed by the sudden expansion of a spherical intruder in the interior of the pack, focusing on the correlation between geometrical fabrics and propagating properties. The measurements of the temporal and spatial variations in a variety of propagating properties define a consistent serrated wave substructure with characteristic length on the orders of particle diameters. Further inspection of particle packing reveals a well-defined particle layering that persists several particle diameters away from the intruder, although its dominant effects are only within one to two diameters. This interface-induced layering not only exactly coincides with the serrated wave profile, but also highlights the competition between two energy transmission mechanisms involving distinct transport speeds. The alternating dominances between these two mechanisms contribute to the nonlinear wave propagation on the particle scale. Moreover, the proliferation of intricate three-dimensional contact force networks suggests the anisotropic stress transmission, which is found to also arise from the localized packing structure in the vicinity of the intruder.

Micrometer-scale fabrication of complex three dimensional lattice + basis structures in silicon

DOE PAGES

Burckel, D. Bruce; Resnick, Paul J.; Finnegan, Patrick S.; ...

2015-01-01

A complementary metal oxide semiconductor (CMOS) compatible version of membrane projection lithography (MPL) for fabrication of micrometer-scale three-dimensional structures is presented. The approach uses all inorganic materials and standard CMOS processing equipment. In a single layer, MPL is capable of creating all 5 2D-Bravais lattices. Furthermore, standard semiconductor processing steps can be used in a layer-by-layer approach to create fully three dimensional structures with any of the 14 3D-Bravais lattices. The unit cell basis is determined by the projection of the membrane pattern, with many degrees of freedom for defining functional inclusions. Here we demonstrate several unique structural motifs, andmore » characterize 2D arrays of unit cells with split ring resonators in a silicon matrix. The structures exhibit strong polarization dependent resonances and, for properly oriented split ring resonators (SRRs), coupling to the magnetic field of a normally incident transverse electromagnetic wave, a response unique to 3D inclusions.« less

Additive manufacturing of collagen scaffolds by three-dimensional plotting of highly viscous dispersions.

PubMed

Lode, Anja; Meyer, Michael; Brüggemeier, Sophie; Paul, Birgit; Baltzer, Hagen; Schröpfer, Michaela; Winkelmann, Claudia; Sonntag, Frank; Gelinsky, Michael

2016-02-27

Additive manufacturing (AM) allows the free form fabrication of three-dimensional (3D) structures with distinct external geometry, fitting into a patient-specific defect, and defined internal pore architecture. However, fabrication of predesigned collagen scaffolds using AM-based technologies is challenging due to the low viscosity of collagen solutions, gels or dispersions commonly used for scaffold preparation. In the present study, we have developed a straightforward method which is based on 3D plotting of a highly viscous, high density collagen dispersion. The swollen state of the collagen fibrils at pH 4 enabled the homogenous extrusion of the material, the deposition of uniform strands and finally the construction of 3D scaffolds. Stabilization of the plotted structures was achieved by freeze-drying and chemical crosslinking with the carbodiimide EDC. The scaffolds exhibited high shape and dimensional fidelity and a hierarchical porosity consisting of macropores generated by strand deposition as well as an interconnected microporosity within the strands as result of the freeze-drying process. Cultivation of human mesenchymal stromal cells on the scaffolds, with and without adipogenic or osteogenic stimulation, revealed their cytocompatibility and potential applicability for adipose and bone tissue engineering.

Graphic kinematics, visual virtual work and elastographics

PubMed Central

Konstantatou, Marina; Athanasopoulos, Georgios; Hannigan, Laura

2017-01-01

In this paper, recent progress in graphic statics is combined with Williot displacement diagrams to create a graphical description of both statics and kinematics for two- and three-dimensional pin-jointed trusses. We begin with reciprocal form and force diagrams. The force diagram is dissected into its component cells which are then translated relative to each other. This defines a displacement diagram which is topologically equivalent to the form diagram (the structure). The various contributions to the overall Virtual Work appear as parallelograms (for two-dimensional trusses) or parallelopipeds (for three-dimensional trusses) that separate the force and the displacement pieces. Structural mechanisms can be identified by translating the force cells such that their shared faces slide across each other without separating. Elastic solutions can be obtained by choosing parallelograms or parallelopipeds of the appropriate aspect ratio. Finally, a new type of ‘elastographic’ diagram—termed a deformed Maxwell–Williot diagram (two-dimensional) or a deformed Rankine–Williot diagram (three-dimensional)—is presented which combines the deflected structure with the forces carried by its members. PMID:28573030

A rudimentary database for three-dimensional objects using structural representation

NASA Technical Reports Server (NTRS)

Sowers, James P.

1987-01-01

A database which enables users to store and share the description of three-dimensional objects in a research environment is presented. The main objective of the design is to make it a compact structure that holds sufficient information to reconstruct the object. The database design is based on an object representation scheme which is information preserving, reasonably efficient, and yet economical in terms of the storage requirement. The determination of the needed data for the reconstruction process is guided by the belief that it is faster to do simple computations to generate needed data/information for construction than to retrieve everything from memory. Some recent techniques of three-dimensional representation that influenced the design of the database are discussed. The schema for the database and the structural definition used to define an object are given. The user manual for the software developed to create and maintain the contents of the database is included.

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…

Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

PubMed Central

Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

2009-01-01

Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

Bimetallic 3D nanostar dimers in ring cavities: recyclable and robust surface-enhanced Raman scattering substrates for signal detection from few molecules.

PubMed

Gopalakrishnan, Anisha; Chirumamilla, Manohar; De Angelis, Francesco; Toma, Andrea; Zaccaria, Remo Proietti; Krahne, Roman

2014-08-26

Top-down fabrication of electron-beam lithography (EBL)-defined metallic nanostructures is a successful route to obtain extremely high electromagnetic field enhancement via plasmonic effects in well-defined regions. To this aim, various geometries have been introduced such as disks, triangles, dimers, rings, self-similar lenses, and more. In particular, metallic dimers are highly efficient for surface-enhanced Raman spectroscopy (SERS), and their decoupling from the substrate in a three-dimensional design has proven to further improve their performance. However, the large fabrication time and cost has hindered EBL-defined structures from playing a role in practical applications. Here we present three-dimensional nanostar dimer devices that can be recycled via maskless metal etching and deposition processes, due to conservation of the nanostructure pattern in the 3D geometry of the underlying Si substrate. Furthermore, our 3D-nanostar-dimer-in-ring structures (3D-NSDiRs) incorporate several advantageous aspects for SERS by enhancing the performance of plasmonic dimers via an external ring cavity, by efficient decoupling from the substrate through an elevated 3D design, and by bimetallic AuAg layers that exploit the increased performance of Ag while maintaining the biocompatibility of Au. We demonstrate SERS detection on rhodamine and adenine at extremely low density up to the limit of few molecules and analyze the field enhancement of the 3D-NSDiRs with respect to the exciting wavelength and metal composition.

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.

Quantum dots in single electron transistors with ultrathin silicon-on-insulator structures

NASA Astrophysics Data System (ADS)

Ihara, S.; Andreev, A.; Williams, D. A.; Kodera, T.; Oda, S.

2015-07-01

We report on fabrication and transport properties of lithographically defined single quantum dots (QDs) in single electron transistors with ultrathin silicon-on-insulator (SOI) substrate. We observed comparatively large charging energy E C ˜ 20 meV derived from the stability diagram at a temperature of 4.2 K. We also carried out three-dimensional calculations of the capacitance matrix and transport properties through the QD for the real structure geometry and found an excellent quantitative agreement with experiment of the calculated main parameters of stability diagram (charging energy, period of Coulomb oscillations, and asymmetry of the diamonds). The obtained results confirm fabrication of well-defined integrated QDs as designed with ultrathin SOI that makes it possible to achieve relatively large QD charging energies, which is useful for stable and high temperature operation of single electron devices.

Regenerable particulate filter

DOEpatents

Stuecker, John N [Albuquerque, NM; Cesarano, III, Joseph; Miller, James E [Albuquerque, NM

2009-05-05

A method of making a three-dimensional lattice structure, such as a filter used to remove particulates from a gas stream, where the physical lattice structure is designed utilizing software simulation from pre-defined mass transfer and flow characteristics and the designed lattice structure is fabricated using a free-form fabrication manufacturing technique, where the periodic lattice structure is comprised of individual geometric elements.

Framework to model neutral particle flux in convex high aspect ratio structures using one-dimensional radiosity

NASA Astrophysics Data System (ADS)

Manstetten, Paul; Filipovic, Lado; Hössinger, Andreas; Weinbub, Josef; Selberherr, Siegfried

2017-02-01

We present a computationally efficient framework to compute the neutral flux in high aspect ratio structures during three-dimensional plasma etching simulations. The framework is based on a one-dimensional radiosity approach and is applicable to simulations of convex rotationally symmetric holes and convex symmetric trenches with a constant cross-section. The framework is intended to replace the full three-dimensional simulation step required to calculate the neutral flux during plasma etching simulations. Especially for high aspect ratio structures, the computational effort, required to perform the full three-dimensional simulation of the neutral flux at the desired spatial resolution, conflicts with practical simulation time constraints. Our results are in agreement with those obtained by three-dimensional Monte Carlo based ray tracing simulations for various aspect ratios and convex geometries. With this framework we present a comprehensive analysis of the influence of the geometrical properties of high aspect ratio structures as well as of the particle sticking probability on the neutral particle flux.

The solution structure of omega-Aga-IVB, a P-type calcium channel antagonist from venom of the funnel web spider, Agelenopsis aperta.

PubMed

Reily, M D; Thanabal, V; Adams, M E

1995-02-01

The 48 amino acid peptides omega-Aga-IVA and omega-Aga-IVB are the first agents known to specifically block P-type calcium channels in mammalian brain, thus complementing the existing suite of pharmacological tools used for characterizing calcium channels. These peptides provide a new set of probes for studies aimed at elucidating the structural basis underlying the subtype specificity of calcium channel antagonists. We used 288 NMR-derived constraints in a protocol combining distance geometry and molecular dynamics employing the program DGII, followed by energy minimization with Discover to derive the three-dimensional structure of omega-Aga-IVB. The toxin consists of a well-defined core region, comprising seven solvent-shielded residues and a well-defined triple-stranded beta-sheet. Four loop regions have average backbone rms deviations between 0.38 and 1.31 A, two of which are well-defined type-II beta-turns. Other structural features include disordered C- and N-termini and several conserved basic amino acids that are clustered on one face of the molecule. The reported structure suggests a possible surface for interaction with the channel. This surface contains amino acids that are identical to those of another known P-type calcium channel antagonist, omega-Aga-IVA, and is rich in basic residues that may have a role in binding to the anionic sites in the extracellular regions of the calcium channel.

High Efficiency Thermoelectric Materials and Devices

NASA Technical Reports Server (NTRS)

Kochergin, Vladimir (Inventor)

2013-01-01

Growth of thermoelectric materials in the form of quantum well super-lattices on three-dimensionally structured substrates provide the means to achieve high conversion efficiency of the thermoelectric module combined with inexpensiveness of fabrication and compatibility with large scale production. Thermoelectric devices utilizing thermoelectric materials in the form of quantum well semiconductor super-lattices grown on three-dimensionally structured substrates provide improved thermoelectric characteristics that can be used for power generation, cooling and other applications..

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Statistical interior properties of globular proteins

NASA Astrophysics Data System (ADS)

Jiang, Zhou-Ting; Zhang, Lin-Xi; Sun, Ting-Ting; Wu, Tai-Quan

2009-10-01

The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters NC and ND are defined to confine the valid residues in detail. The relationship between hydrophobicity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage Pi and sequential residue length Li of a certain protein i are calculated under different conditions. The statistical results show that the average value of Pi as well as Li of all-α proteins has a minimum among these 4 classes of globular proteins, indicating that all-α proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-β proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of β sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.

Dorello's Canal for Laymen: A Lego-Like Presentation.

PubMed

Ezer, Haim; Banerjee, Anirban Deep; Thakur, Jai Deep; Nanda, Anil

2012-06-01

Objective Dorello's canal was first described by Gruber in 1859, and later by Dorello. Vail also described the anatomy of Dorello's canal. In the preceding century, Dorello's canal was clinically important, in understanding sixth nerve palsy and nowadays it is mostly important for skull base surgery. The understanding of the three dimensional anatomy, of this canal is very difficult to understand, and there is no simple explanation for its anatomy and its relationship with adjacent structures. We present a simple, Lego-like, presentation of Dorello's canal, in a stepwise manner. Materials and Methods Dorello's canal was dissected in five formalin-fixed cadaver specimens (10 sides). The craniotomy was performed, while preserving the neural and vascular structures associated with the canal. A 3D model was created, to explain the canal's anatomy. Results Using the petrous pyramid, the sixth nerve, the cavernous sinus, the trigeminal ganglion, the petorclival ligament and the posterior clinoid, the three-dimensional structure of Dorello's canal was defined. This simple representation aids in understanding the three dimensional relationship of Dorello's canal to its neighboring structures. Conclusion Dorello's canal with its three dimensional structure and relationship to its neighboring anatomical structures could be reconstructed using a few anatomical building blocks. This method simplifies the understanding of this complex anatomical structure, and could be used for teaching purposes for aspiring neurosurgeons, and anatomy students.

Dorello's Canal for Laymen: A Lego-Like Presentation

PubMed Central

Ezer, Haim; Banerjee, Anirban Deep; Thakur, Jai Deep; Nanda, Anil

2012-01-01

Objective Dorello's canal was first described by Gruber in 1859, and later by Dorello. Vail also described the anatomy of Dorello's canal. In the preceding century, Dorello's canal was clinically important, in understanding sixth nerve palsy and nowadays it is mostly important for skull base surgery. The understanding of the three dimensional anatomy, of this canal is very difficult to understand, and there is no simple explanation for its anatomy and its relationship with adjacent structures. We present a simple, Lego-like, presentation of Dorello's canal, in a stepwise manner. Materials and Methods Dorello's canal was dissected in five formalin-fixed cadaver specimens (10 sides). The craniotomy was performed, while preserving the neural and vascular structures associated with the canal. A 3D model was created, to explain the canal's anatomy. Results Using the petrous pyramid, the sixth nerve, the cavernous sinus, the trigeminal ganglion, the petorclival ligament and the posterior clinoid, the three-dimensional structure of Dorello's canal was defined. This simple representation aids in understanding the three dimensional relationship of Dorello's canal to its neighboring structures. Conclusion Dorello's canal with its three dimensional structure and relationship to its neighboring anatomical structures could be reconstructed using a few anatomical building blocks. This method simplifies the understanding of this complex anatomical structure, and could be used for teaching purposes for aspiring neurosurgeons, and anatomy students. PMID:23730547

Fabrication of dielectric elastomer stack transducers (DEST) by liquid deposition modeling

NASA Astrophysics Data System (ADS)

Klug, Florian; Solano-Arana, Susana; Mößinger, Holger; Förster-Zügel, Florentine; Schlaak, Helmut F.

2017-04-01

Established fabrication methods for dielectric elastomer stack transducers (DEST) are mostly based on twodimensional thin-film technology. Because of this, DEST are based on simple two-dimensionally structured shapes. For certain applications, like valves or Braille displays, these structures are suited well enough. However, a more flexible fabrication method allows for more complex actuator designs, which would otherwise require extra processing steps. Fabrication methods with the possibility of three-dimensional structuring allow e.g. the integration of electrical connections, cavities, channels, sensor and other structural elements during the fabrication. This opens up new applications, as well as the opportunity for faster prototype production of individually designed DEST for a given application. In this work, a manufacturing system allowing three dimensional structuring is described. It enables the production of multilayer and three-dimensional structured DEST by liquid deposition modelling. The system is based on a custom made dual extruder, connected to a commercial threeaxis positioning system. It allows a computer controlled liquid deposition of two materials. After tuning the manufacturing parameters the production of thin layers with at thickness of less than 50 μm, as well as stacking electrode and dielectric materials is feasible. With this setup a first DEST with dielectric layer thickness less than 50 μm is build successfully and its performance is evaluated.

Three-dimensional recomposition of the absorption field inside a nonbuoyant sooting flame.

PubMed

Legros, Guillaume; Fuentes, Andrés; Ben-Abdallah, Philippe; Baillargeat, Jacques; Joulain, Pierre; Vantelon, Jean-Pierre; Torero, José L

2005-12-15

A remote scanning retrieval method was developed to investigate the soot layer produced by a laminar diffusion flame established over a flat plate burner in microgravity. Experiments were conducted during parabolic flights. This original application of an inverse problem leads to the three-dimensional recomposition by layers of the absorption field inside the flame. This technique provides a well-defined flame length that substitutes for other subjective definitions associated with emissions.

Three-dimensional recomposition of the absorption field inside a nonbuoyant sooting flame

NASA Astrophysics Data System (ADS)

Legros, Guillaume; Fuentes, Andrés; Ben-Abdallah, Philippe; Baillargeat, Jacques; Joulain, Pierre; Vantelon, Jean-Pierre; Torero, José L.

2005-12-01

A remote scanning retrieval method was developed to investigate the soot layer produced by a laminar diffusion flame established over a flat plate burner in microgravity. Experiments were conducted during parabolic flights. This original application of an inverse problem leads to the three-dimensional recomposition by layers of the absorption field inside the flame. This technique provides a well-defined flame length that substitutes for other subjective definitions associated with emissions.

Poly(N-isopropylacrylamide) hydrogel/chitosan scaffold hybrid for three-dimensional stem cell culture and cartilage tissue engineering.

PubMed

Mellati, Amir; Kiamahalleh, Meisam Valizadeh; Madani, S Hadi; Dai, Sheng; Bi, Jingxiu; Jin, Bo; Zhang, Hu

2016-11-01

Providing a controllable and definable three-dimensional (3D) microenvironment for chondrogenic differentiation of mesenchymal stem cells (MSCs) remains a great challenge for cartilage tissue engineering. In this work, poly(N-isopropylacrylamide) (PNIPAAm) polymers with the degrees of polymerization of 100 and 400 (NI100 and NI400) were prepared and the polymer solutions were introduced into the preprepared chitosan porous scaffolds (CS) to form hybrids (CSNI100 and CSNI400, respectively). SEM images indicated that the PNIPAAm gel partially occupied chitosan pores while the interconnected porous structure of chitosan was preserved. MSCs were incorporated within the hybrid and cell proliferation and chondrogenic differentiation were monitored. After 7-day incubation of the cell-laden constructs in a growth medium, the cell viability in CSNI100 and CSNI400 were 54 and 108% higher than that in CS alone, respectively. Glycosaminoglycan and total collagen contents increased 2.6- and 2.5-fold after 28-day culture of cell-laden CSNI400 in the chondrogenic medium. These results suggest that the hybrid structure composed of the chitosan porous scaffold and the well-defined PNIPAAm hydrogel, in particular CSNI400, is suitable for 3D stem cell culture and cartilage tissue engineering. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2764-2774, 2016. © 2016 Wiley Periodicals, Inc.

CCR2 and CCR5 receptor-binding properties of herpesvirus-8 vMIP-II based on sequence analysis and its solution structure.

PubMed

Shao, W; Fernandez, E; Sachpatzidis, A; Wilken, J; Thompson, D A; Schweitzer, B I; Lolis, E

2001-05-01

Human herpesvirus-8 (HHV-8) is the infectious agent responsible for Kaposi's sarcoma and encodes a protein, macrophage inflammatory protein-II (vMIP-II), which shows sequence similarity to the human CC chemokines. vMIP-II has broad receptor specificity that crosses chemokine receptor subfamilies, and inhibits HIV-1 viral entry mediated by numerous chemokine receptors. In this study, the solution structure of chemically synthesized vMIP-II was determined by nuclear magnetic resonance. The protein is a monomer and possesses the chemokine fold consisting of a flexible N-terminus, three antiparallel beta strands, and a C-terminal alpha helix. Except for the N-terminal residues (residues 1-13) and the last two C-terminal residues (residues 73-74), the structure of vMIP-II is well-defined, exhibiting average rmsd of 0.35 and 0.90 A for the backbone heavy atoms and all heavy atoms of residues 14-72, respectively. Taking into account the sequence differences between the various CC chemokines and comparing their three-dimensional structures allows us to implicate residues that influence the quaternary structure and receptor binding and activation of these proteins in solution. The analysis of the sequence and three-dimensional structure of vMIP-II indicates the presence of epitopes involved in binding two receptors CCR2 and CCR5. We propose that vMIP-II was initially specific for CCR5 and acquired receptor-binding properties to CCR2 and other chemokine receptors.

Decoupling Principle Analysis and Development of a Parallel Three-Dimensional Force Sensor

PubMed Central

Zhao, Yanzhi; Jiao, Leihao; Weng, Dacheng; Zhang, Dan; Zheng, Rencheng

2016-01-01

In the development of the multi-dimensional force sensor, dimension coupling is the ubiquitous factor restricting the improvement of the measurement accuracy. To effectively reduce the influence of dimension coupling on the parallel multi-dimensional force sensor, a novel parallel three-dimensional force sensor is proposed using a mechanical decoupling principle, and the influence of the friction on dimension coupling is effectively reduced by making the friction rolling instead of sliding friction. In this paper, the mathematical model is established by combining with the structure model of the parallel three-dimensional force sensor, and the modeling and analysis of mechanical decoupling are carried out. The coupling degree (ε) of the designed sensor is defined and calculated, and the calculation results show that the mechanical decoupling parallel structure of the sensor possesses good decoupling performance. A prototype of the parallel three-dimensional force sensor was developed, and FEM analysis was carried out. The load calibration and data acquisition experiment system are built, and then calibration experiments were done. According to the calibration experiments, the measurement accuracy is less than 2.86% and the coupling accuracy is less than 3.02%. The experimental results show that the sensor system possesses high measuring accuracy, which provides a basis for the applied research of the parallel multi-dimensional force sensor. PMID:27649194

Quantum Monte Carlo study of the transverse-field quantum Ising model on infinite-dimensional structures

NASA Astrophysics Data System (ADS)

Baek, Seung Ki; Um, Jaegon; Yi, Su Do; Kim, Beom Jun

2011-11-01

In a number of classical statistical-physical models, there exists a characteristic dimensionality called the upper critical dimension above which one observes the mean-field critical behavior. Instead of constructing high-dimensional lattices, however, one can also consider infinite-dimensional structures, and the question is whether this mean-field character extends to quantum-mechanical cases as well. We therefore investigate the transverse-field quantum Ising model on the globally coupled network and on the Watts-Strogatz small-world network by means of quantum Monte Carlo simulations and the finite-size scaling analysis. We confirm that both of the structures exhibit critical behavior consistent with the mean-field description. In particular, we show that the existing cumulant method has difficulty in estimating the correct dynamic critical exponent and suggest that an order parameter based on the quantum-mechanical expectation value can be a practically useful numerical observable to determine critical behavior when there is no well-defined dimensionality.

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.

Entangled singularity patterns of photons in Ince-Gauss modes

NASA Astrophysics Data System (ADS)

Krenn, Mario; Fickler, Robert; Huber, Marcus; Lapkiewicz, Radek; Plick, William; Ramelow, Sven; Zeilinger, Anton

2013-01-01

Photons with complex spatial mode structures open up possibilities for new fundamental high-dimensional quantum experiments and for novel quantum information tasks. Here we show entanglement of photons with complex vortex and singularity patterns called Ince-Gauss modes. In these modes, the position and number of singularities vary depending on the mode parameters. We verify two-dimensional and three-dimensional entanglement of Ince-Gauss modes. By measuring one photon and thereby defining its singularity pattern, we nonlocally steer the singularity structure of its entangled partner, while the initial singularity structure of the photons is undefined. In addition we measure an Ince-Gauss specific quantum-correlation function with possible use in future quantum communication protocols.

Large Bone Vertical Augmentation Using a Three-Dimensional Printed TCP/HA Bone Graft: A Pilot Study in Dog Mandible.

PubMed

Carrel, Jean-Pierre; Wiskott, Anselm; Scherrer, Susanne; Durual, Stéphane

2016-12-01

Osteoflux is a three-dimensional printed calcium phosphate porous structure for oral bone augmentation. It is a mechanically stable scaffold with a well-defined interconnectivity and can be readily shaped to conform to the bone bed's morphology. An animal experiment is reported whose aim was to assess the performance and safety of the scaffold in promoting vertical growth of cortical bone in the mandible. Four three-dimensional blocks (10 mm length, 5 mm width, 5 mm height) were affixed to edentulous segments of the dog's mandible and covered by a collagen membrane. During bone bed preparation, particular attention was paid not to create defects 0.5 mm or more so that the real potential of the three-dimensional block in driving vertical bone growth can be assessed. Histomorphometric analyses were performed after 8 weeks. At 8 weeks, the three-dimensional blocks led to substantial vertical bone growth up to 4.5 mm from the bone bed. Between 0 and 1 mm in height, 44% of the surface was filled with new bone, at 1 to 3 mm it was 20% to 35%, 18% at 3 to 4, and ca. 6% beyond 4 mm. New bone was evenly distributed along in mesio-distal direction and formed a new crest contour in harmony with the natural mandibular shape. After two months of healing, the three-dimensional printed blocks conducted new bone growth above its natural bed, up to 4.5 mm in a canine mandibular model. Furthermore, the new bone was evenly distributed in height and density along the block. These results are very promising and need to be further evaluated by a complete powerful study using the same model. © 2016 Wiley Periodicals, Inc.

Automatic blocking for complex three-dimensional configurations

NASA Technical Reports Server (NTRS)

Dannenhoffer, John F., III

1995-01-01

A new blocking technique for complex three-dimensional configurations is described. This new technique is based upon the concept of an abstraction, or squared-up representation, of the configuration and the associated grid. By allowing the user to describe blocking requirements in natural terms (such as 'wrap a grid around this leading edge' or 'make all grid lines emanating from this wall orthogonal to it'), users can quickly generate complex grids around complex configurations, while still maintaining a high level of control where desired. An added advantage of the abstraction concept is that once a blocking is defined for a class of configurations, it can be automatically applied to other configurations of the same class, making the new technique particularly well suited for the parametric variations which typically occur during design processes. Grids have been generated for a variety of real-world, two- and three-dimensional configurations. In all cases, the time required to generate the grid, given just an electronic form of the configuration, was at most a few days. Hence with this new technique, the generation of a block-structured grid is only slightly more expensive than the generation of an unstructured grid for the same configuration.

The helical ventricular myocardial band: global, three-dimensional, functional architecture of the ventricular myocardium.

PubMed

Kocica, Mladen J; Corno, Antonio F; Carreras-Costa, Francesc; Ballester-Rodes, Manel; Moghbel, Mark C; Cueva, Clotario N C; Lackovic, Vesna; Kanjuh, Vladimir I; Torrent-Guasp, Francisco

2006-04-01

We are currently witnessing the advent of new diagnostic tools and therapies for heart diseases, but, without serious scientific consensus on fundamental questions about normal and diseased heart structure and function. During the last decade, three successive, international, multidisciplinary symposia were organized in order to setup fundamental research principles, which would allow us to make a significant step forward in understanding heart structure and function. Helical ventricular myocardial band of Torrent-Guasp is the revolutionary new concept in understanding global, three-dimensional, functional architecture of the ventricular myocardium. This concept defines the principal, cumulative vectors, integrating the tissue architecture (i.e. form) and net forces developed (i.e. function) within the ventricular mass. Here we expose the compendium of Torrent-Guasp's half-century long functional anatomical investigations in the light of ongoing efforts to define the integrative approach, which would lead to new understanding of the ventricular form and function by linking across multiple scales of biological organization, as defined in ongoing Physiome project. Helical ventricular myocardial band of Torrent-Guasp may also, hopefully, allow overcoming some difficulties encountered in contemporary efforts to create a comprehensive mathematical model of the heart.

Beyond the known functions of the CCR4-NOT complex in gene expression regulatory mechanisms: New structural insights to unravel CCR4-NOT mRNA processing machinery.

PubMed

Ukleja, Marta; Valpuesta, José María; Dziembowski, Andrzej; Cuellar, Jorge

2016-10-01

Large protein assemblies are usually the effectors of major cellular processes. The intricate cell homeostasis network is divided into numerous interconnected pathways, each controlled by a set of protein machines. One of these master regulators is the CCR4-NOT complex, which ultimately controls protein expression levels. This multisubunit complex assembles around a scaffold platform, which enables a wide variety of well-studied functions from mRNA synthesis to transcript decay, as well as other tasks still being identified. Solving the structure of the entire CCR4-NOT complex will help to define the distribution of its functions. The recently published three-dimensional reconstruction of the complex, in combination with the known crystal structures of some of the components, has begun to address this. Methodological improvements in structural biology, especially in cryoelectron microscopy, encourage further structural and protein-protein interaction studies, which will advance our comprehension of the gene expression machinery. © 2016 WILEY Periodicals, Inc.

Three-dimensional artificial spin ice in nanostructured Co on an inverse opal-like lattice

NASA Astrophysics Data System (ADS)

Mistonov, A. A.; Grigoryeva, N. A.; Chumakova, A. V.; Eckerlebe, H.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Menzel, D.; Grigoriev, S. V.

2013-06-01

The evolution of the magnetic structure for an inverse opal-like structure under an applied magnetic field is studied by small-angle neutron scattering. The samples were produced by filling the voids of an artificial opal film with Co. It is shown that the local configuration of magnetization is inhomogeneous over the basic element of the inverse opal-like lattice structure (IOLS) but follows its periodicity. Applying the “ice-rule” concept to the structure, we describe the local magnetization of this ferromagnetic three-dimensional lattice. We have developed a model of the remagnetization process predicting the occurrence of an unusual perpendicular component of the magnetization in the IOLS which is defined only by the direction and strength of the applied magnetic field.

Physics of protein folding

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.; Galzitskaya, O. V.

2004-04-01

Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.

Diverse forms of bonding in two-dimensional Si allotropes: Nematic orbitals in the MoS2 structure

NASA Astrophysics Data System (ADS)

Gimbert, Florian; Lee, Chi-Cheng; Friedlein, Rainer; Fleurence, Antoine; Yamada-Takamura, Yukiko; Ozaki, Taisuke

2014-10-01

The interplay of sp2- and sp3-type bonding defines silicon allotropes in two- and three-dimensional forms. A two-dimensional phase bearing structural resemblance to a single MoS2 layer is found to possess a lower total energy than low-buckled silicene and to be stable in terms of its phonon dispersion relations. A set of cigar-shaped nematic orbitals originating from the Si sp2 orbitals realizes bonding with a sixfold coordination of the inner Si atoms of the layer. The identification of these nematic orbitals advocates diverse Si bonding configurations different from those of C atoms.

A new idea for broad band reflector and tunable multichannel filter of one dimensional symmetric photonic crystal with magnetized cold plasma defects

NASA Astrophysics Data System (ADS)

Kumar, Asish; Singh, Prabal P.; Thapa, Khem B.

2018-05-01

The optical properties of one-dimensional periodic structure composed by SiO2 and dielectric (air) layers with asymmetric and symmetric forms studied. The transmittance for symmetric periodic defective structure analyzed by introducing one, two, three layers of magnetized cold plasma (MCP) in one-dimensional periodic structure. We found better result for symmetric defect of three layer of the MCP compare to the other defective structures. On the basis of our calculated results, we proposed a new idea for broadband reflector at lower frequency range as well as the multichannel filter at higher frequency range.

Estimating habitat volume of living resources using three-dimensional circulation and biogeochemical models

NASA Astrophysics Data System (ADS)

Smith, Katharine A.; Schlag, Zachary; North, Elizabeth W.

2018-07-01

Coupled three-dimensional circulation and biogeochemical models predict changes in water properties that can be used to define fish habitat, including physiologically important parameters such as temperature, salinity, and dissolved oxygen. However, methods for calculating the volume of habitat defined by the intersection of multiple water properties are not well established for coupled three-dimensional models. The objectives of this research were to examine multiple methods for calculating habitat volume from three-dimensional model predictions, select the most robust approach, and provide an example application of the technique. Three methods were assessed: the "Step," "Ruled Surface", and "Pentahedron" methods, the latter of which was developed as part of this research. Results indicate that the analytical Pentahedron method is exact, computationally efficient, and preserves continuity in water properties between adjacent grid cells. As an example application, the Pentahedron method was implemented within the Habitat Volume Model (HabVol) using output from a circulation model with an Arakawa C-grid and physiological tolerances of juvenile striped bass (Morone saxatilis). This application demonstrates that the analytical Pentahedron method can be successfully applied to calculate habitat volume using output from coupled three-dimensional circulation and biogeochemical models, and it indicates that the Pentahedron method has wide application to aquatic and marine systems for which these models exist and physiological tolerances of organisms are known.

Solvation structure of the halides from x-ray absorption spectroscopy

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

Antalek, Matthew; Hedman, Britt; Sarangi, Ritimukta, E-mail: ritis@slac.stanford.edu

2016-07-28

Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, andmore » a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (−0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.« less

Fabrication of three-dimensional collagen scaffold using an inverse mould-leaching process.

PubMed

Ahn, SeungHyun; Lee, SuYeon; Cho, Youngseok; Chun, Wook; Kim, GeunHyung

2011-09-01

Natural biopolymers, such as collagen or chitosan, are considered ideal for biomedical scaffolds. However, low processability of the materials has hindered the fabrication of designed pore structures controlled by various solid freeform-fabrication methods. A new technique to fabricate a biomedical three-dimensional collagen scaffold, supplemented with a sacrificial poly(ethylene oxide) mould is proposed. The fabricated collagen scaffold shows a highly porous surface and a three-dimensional structure with high porosity as well as mechanically stable structure. To show its feasibility for biomedical applications, fibroblasts/keratinocytes were co-cultured on the scaffold, and the cell proliferation and cell migration of the scaffold was more favorable than that obtained with a spongy-type collagen scaffold.

Three-Dimensional Self-Assembled Photonic Crystal Waveguide

NASA Astrophysics Data System (ADS)

Baek, Kang-Hyun

Photonic crystals (PCs), two- or three-dimensionally periodic, artificial, and dielectric structures, have a specific forbidden band for electromagnetic waves, referred to as photonic bandgap (PBG). The PBG is analogous to the electronic bandgap in natural crystal structures with periodic atomic arrangement. A well-defined and embedded planar, line, or point defect within the PCs causes a break in its structural periodicity, and introduces a state in the PBG for light localization. It offers various applications in integrated optics and photonics including optical filters, sharp bending light guides and very low threshold lasers. Using nanofabrication processes, PCs of the 2-D slab-type and 3-D layer-by-layer structures have been investigated widely. Alternatively, simple and low-cost self-assembled PCs with full 3-D PBG, inverse opals, have been suggested. A template with face centered cubic closed packed structure, opal, may initially be built by self-assembly of colloidal spheres, and is selectively removed after infiltrating high refractive index materials into the interstitials of spheres. In this dissertation, the optical waveguides utilizing the 3-D self-assembled PCs are discussed. The waveguides were fabricated by microfabrication technology. For high-quality colloidal silica spheres and PCs, reliable synthesis, self-assembly, and characterization techniques were developed. Its theoretical and experimental demonstrations are provided and correlated. They suggest that the self-assembled PCs with PBG are feasible for the applications in integrated optics and photonics.

MISSISSIPPI EMBAYMENT AQUIFER SYSTEM IN MISSISSIPPI: GEOHYDROLOGIC DATA COMPILATION FOR FLOW MODEL SIMULATION.

USGS Publications Warehouse

Arthur, J.K.; Taylor, R.E.

1986-01-01

As part of the Gulf Coast Regional Aquifer System Analysis (GC RASA) study, data from 184 geophysical well logs were used to define the geohydrologic framework of the Mississippi embayment aquifer system in Mississippi for flow model simulation. Five major aquifers of Eocene and Paleocene age were defined within this aquifer system in Mississippi. A computer data storage system was established to assimilate the information obtained from the geophysical logs. Computer programs were developed to manipulate the data to construct geologic sections and structure maps. Data from the storage system will be input to a five-layer, three-dimensional, finite-difference digital computer model that is used to simulate the flow dynamics in the five major aquifers of the Mississippi embayment aquifer system.

Pre-set extrusion bioprinting for multiscale heterogeneous tissue structure fabrication.

PubMed

Kang, Donggu; Ahn, Geunseon; Kim, Donghwan; Kang, Hyun-Wook; Yun, Seokhwan; Yun, Won-Soo; Shim, Jin-Hyung; Jin, Songwan

2018-06-06

Recent advances in three-dimensional bioprinting technology have led to various attempts in fabricating human tissue-like structures. However, current bioprinting technologies have limitations for creating native tissue-like structures. To resolve these issues, we developed a new pre-set extrusion bioprinting technique that can create heterogeneous, multicellular, and multimaterial structures simultaneously. The key to this ability lies in the use of a precursor cartridge that can stably preserve a multimaterial with a pre-defined configuration that can be simply embedded in a syringe-based printer head. The multimaterial can be printed and miniaturized through a micro-nozzle without conspicuous deformation according to the pre-defined configuration of the precursor cartridge. Using this system, we fabricated heterogeneous tissue-like structures such as spinal cords, hepatic lobule, blood vessels, and capillaries. We further obtained a heterogeneous patterned model that embeds HepG2 cells with endothelial cells in a hepatic lobule-like structure. In comparison with homogeneous and heterogeneous cell printing, the heterogeneous patterned model showed a well-organized hepatic lobule structure and higher enzyme activity of CYP3A4. Therefore, this pre-set extrusion bioprinting method could be widely used in the fabrication of a variety of artificial and functional tissues or organs.

Three-dimensional cathodoluminescence characterization of a semipolar GaInN based LED sample

NASA Astrophysics Data System (ADS)

Hocker, Matthias; Maier, Pascal; Tischer, Ingo; Meisch, Tobias; Caliebe, Marian; Scholz, Ferdinand; Mundszinger, Manuel; Kaiser, Ute; Thonke, Klaus

2017-02-01

A semipolar GaInN based light-emitting diode (LED) sample is investigated by three-dimensionally resolved cathodoluminescence (CL) mapping. Similar to conventional depth-resolved CL spectroscopy (DRCLS), the spatial resolution perpendicular to the sample surface is obtained by calibration of the CL data with Monte-Carlo-simulations (MCSs) of the primary electron beam scattering. In addition to conventional MCSs, we take into account semiconductor-specific processes like exciton diffusion and the influence of the band gap energy. With this method, the structure of the LED sample under investigation can be analyzed without additional sample preparation, like cleaving of cross sections. The measurement yields the thickness of the p-type GaN layer, the vertical position of the quantum wells, and a defect analysis of the underlying n-type GaN, including the determination of the free charge carrier density. The layer arrangement reconstructed from the DRCLS data is in good agreement with the nominal parameters defined by the growth conditions.

Boundary acquisition for setup of numerical simulation

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

Diegert, C.

1997-12-31

The author presents a work flow diagram that includes a path that begins with taking experimental measurements, and ends with obtaining insight from results produced by numerical simulation. Two examples illustrate this path: (1) Three-dimensional imaging measurement at micron scale, using X-ray tomography, provides information on the boundaries of irregularly-shaped alumina oxide particles held in an epoxy matrix. A subsequent numerical simulation predicts the electrical field concentrations that would occur in the observed particle configurations. (2) Three-dimensional imaging measurement at meter scale, again using X-ray tomography, provides information on the boundaries fossilized bone fragments in a Parasaurolophus crest recently discoveredmore » in New Mexico. A subsequent numerical simulation predicts acoustic response of the elaborate internal structure of nasal passageways defined by the fossil record. The author must both add value, and must change the format of the three-dimensional imaging measurements before the define the geometric boundary initial conditions for the automatic mesh generation, and subsequent numerical simulation. The author applies a variety of filters and statistical classification algorithms to estimate the extents of the structures relevant to the subsequent numerical simulation, and capture these extents as faceted geometries. The author will describe the particular combination of manual and automatic methods used in the above two examples.« less

Crystal structure of fac-aquatricarbonyl[(S)-valin-ato-κ(2) N,O]-rhenium(I).

PubMed

Piletska, Kseniia O; Domasevitch, Kostiantyn V; Shtemenko, Alexander V

2016-04-01

In the mol-ecule of the title compound, [Re(C5H10NO2)(CO)3(H2O)], the Re(I) atom adopts a distorted octa-hedral coordination sphere defined by one aqua and three carbonyl ligands as well as one amino N and one carboxyl-ate O atom of the chelating valinate anion. The carbonyl ligands are arranged in a fac-configuration around the Re(I) ion. In the crystal, an intricate hydrogen-bonding system under participation of two O-H, two N-H and one C-H donor groups and the carboxyl-ate and carbonyl O atoms as acceptor groups contribute to the formation of a three-dimensional supra-molecular network.

Packaging DNA Origami into Viral Protein Cages.

PubMed

Linko, Veikko; Mikkilä, Joona; Kostiainen, Mauri A

2018-01-01

The DNA origami technique is a widely used method to create customized, complex, spatially well-defined two-dimensional (2D) and three-dimensional (3D) DNA nanostructures. These structures have huge potential to serve as smart drug-delivery vehicles and molecular devices in various nanomedical and biotechnological applications. However, so far only little is known about the behavior of these novel structures in living organisms or in cell culture/tissue models. Moreover, enhancing pharmacokinetic bioavailability and transfection properties of such structures still remains a challenge. One intriguing approach to overcome these issues is to coat DNA origami nanostructures with proteins or lipid membranes. Here, we show how cowpea chlorotic mottle virus (CCMV) capsid proteins (CPs) can be used for coating DNA origami nanostructures. We present a method for disassembling native CCMV particles and isolating the pure CP dimers, which can further bind and encapsulate a rectangular DNA origami shape. Owing to the highly programmable nature of DNA origami, packaging of DNA nanostructures into viral protein cages could find imminent uses in enhanced targeting and cellular delivery of various active nano-objects, such as enzymes and drug molecules.

Three-dimensional evaluation of the facet joints

NASA Astrophysics Data System (ADS)

Folio, Les R.

1990-04-01

Computerized tomography and magnetic resonance imaging nave revolurionalized analysis of vertebral anatomy and pathology. Further advances with 3-dimensional imaging have recently become an important adjunct for diagnosis and treatment in structural abnormalities. Facets are intimately related to their surrounding musculature and malalignment may cause pain directly or indirectly. High resolution 3-dimensional reformations of CT Scans give us new insight on structure and function of facet joints, since their motion and architecture are ever complex. It is well documented in the literature that facet joint biomecnanics is a partial contributor to the myriad at causes of low back The term "facet Joint syndrome" was coined in 1933 by GhorMley.3 The osteopathic lesion complex is well defined by LeRoy and McCole and comparison of roentgenographic findings before and after manipulation has teen described by Long and Lioyd.4,5 since alterations in facet biamechanics are an important aspect of osteopathic manipulative therapy (OT), 3-dimensional hign resolution imaging will prove to be a great asset in osteopathic research. Rotating the spine allows for different viewing perspectives to provide optimal and consistent measurements of the facet joint. Rotations are performed on the X, Y and 7, axis and measurements pre and post-manipulation are performed and compared on matching axis and perspectives. Rotation about the X, Y and Z axis help appreciate the 3-dimensionality of the vertebral column to project to the viewer a feeling that the spine is floating in space before them. This does give the viewer a 3-D understanding of the object however, only at a perspective at a Lime.

Global well-posedness of three-dimensional Navier-Stokes equations with partial viscosity under helical symmetry

NASA Astrophysics Data System (ADS)

Liu, Jitao; Niu, Dongjuan

2017-06-01

In this paper, we investigate the global well-posedness of three-dimensional Navier-Stokes equations with horizontal viscosity under a special symmetric structure: helical symmetry. More precisely, by a revised Ladyzhenskaya-type inequality and utilizing the behavior of helical flows, we prove the global existence and uniqueness of weak and strong solutions to the three-dimensional helical flows. Our result reveals that for the issue of global well-posedness of the viscous helical flows, the horizontal viscosity plays the important role. To some extent, our work can be seen as a generalization of the result by Mahalov et al. (Arch Ration Mech Anal 112(3):193-222, 1990).

Three-dimensionally modulated anisotropic structure for diffractive optical elements created by one-step three-beam polarization holographic photoalignment

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

Kawai, Kotaro, E-mail: s135016@stn.nagaokaut.ac.jp; Sakamoto, Moritsugu; Noda, Kohei

2016-03-28

A diffractive optical element with a three-dimensional liquid crystal (LC) alignment structure for advanced control of polarized beams was fabricated by a highly efficient one-step photoalignment method. This study is of great significance because different two-dimensional continuous and complex alignment patterns can be produced on two alignment films by simultaneously irradiating an empty glass cell composed of two unaligned photocrosslinkable polymer LC films with three-beam polarized interference beam. The polarization azimuth, ellipticity, and rotation direction of the diffracted beams from the resultant LC grating widely varied depending on the two-dimensional diffracted position and the polarization states of the incident beams.more » These polarization diffraction properties are well explained by theoretical analysis based on Jones calculus.« less

A coupled sharp-interface immersed boundary-finite-element method for flow-structure interaction with application to human phonation.

PubMed

Zheng, X; Xue, Q; Mittal, R; Beilamowicz, S

2010-11-01

A new flow-structure interaction method is presented, which couples a sharp-interface immersed boundary method flow solver with a finite-element method based solid dynamics solver. The coupled method provides robust and high-fidelity solution for complex flow-structure interaction (FSI) problems such as those involving three-dimensional flow and viscoelastic solids. The FSI solver is used to simulate flow-induced vibrations of the vocal folds during phonation. Both two- and three-dimensional models have been examined and qualitative, as well as quantitative comparisons, have been made with established results in order to validate the solver. The solver is used to study the onset of phonation in a two-dimensional laryngeal model and the dynamics of the glottal jet in a three-dimensional model and results from these studies are also presented.

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian B.; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2016-03-08

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2017-12-26

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

Microholography of Living Organisms.

ERIC Educational Resources Information Center

Solem, Johndale C.; Baldwin, George C.

1982-01-01

By using intense pulsed coherent x-ray sources it will be possible to obtain magnified three-dimensional images of living elementary biological structures at precisely defined instants. Discussed are sources/geometrics for x-ray holography, x-radiation interactions, factors affecting resolution, recording the hologram, high-intensity holography,…

Factors Influencing Progressive Failure Analysis Predictions for Laminated Composite Structure

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

2008-01-01

Progressive failure material modeling methods used for structural analysis including failure initiation and material degradation are presented. Different failure initiation criteria and material degradation models are described that define progressive failure formulations. These progressive failure formulations are implemented in a user-defined material model for use with a nonlinear finite element analysis tool. The failure initiation criteria include the maximum stress criteria, maximum strain criteria, the Tsai-Wu failure polynomial, and the Hashin criteria. The material degradation model is based on the ply-discounting approach where the local material constitutive coefficients are degraded. Applications and extensions of the progressive failure analysis material model address two-dimensional plate and shell finite elements and three-dimensional solid finite elements. Implementation details are described in the present paper. Parametric studies for laminated composite structures are discussed to illustrate the features of the progressive failure modeling methods that have been implemented and to demonstrate their influence on progressive failure analysis predictions.

[Research progress of three-dimensional digital model for repair and reconstruction of knee joint].

PubMed

Tong, Lu; Li, Yanlin; Hu, Meng

2013-01-01

To review recent advance in the application and research of three-dimensional digital knee model. The recent original articles about three-dimensional digital knee model were extensively reviewed and analyzed. The digital three-dimensional knee model can simulate the knee complex anatomical structure very well. Based on this, there are some developments of new software and techniques, and good clinical results are achieved. With the development of computer techniques and software, the knee repair and reconstruction procedure has been improved, the operation will be more simple and its accuracy will be further improved.

Flexible Volumetric Structure

NASA Technical Reports Server (NTRS)

Cagle, Christopher M. (Inventor); Schlecht, Robin W. (Inventor)

2014-01-01

A flexible volumetric structure has a first spring that defines a three-dimensional volume and includes a serpentine structure elongatable and compressible along a length thereof. A second spring is coupled to at least one outboard edge region of the first spring. The second spring is a sheet-like structure capable of elongation along an in-plane dimension thereof. The second spring is oriented such that its in-plane dimension is aligned with the length of the first spring's serpentine structure.

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)].

Three-dimensional simulations of cumulus congestus clouds on GATE day 261

NASA Technical Reports Server (NTRS)

Simpson, J.; Van Helvoirt, G.; Mccumber, M.

1982-01-01

Schlesinger's (1978) three-dimensional cumulus model is applied to showering congestus clouds on day 261 of GATE. Model results are compared with each other and with observations to analyze the effects of varying shear and altered sounding. Relationships between shear, mesovortices and dynamic entrainment are examined, as well as the model clouds' impact on the environment as a function of shear. The simulations appear to resemble reality in many important aspects. Altostratus layers observed on day 261 are found to be a by-product of convection in three-dimensional shear. Rapid erosion of cloud base to 3.6 km is related to the ambient thermal structure, with wind shear and initial perturbation playing a secondary role. Some of the apparent conflict regarding lateral versus cloud-top entrainment is clarified, as well as some factors governing convective downdraft structure and intensity.

Computer system for definition of the quantitative geometry of musculature from CT images.

PubMed

Daniel, Matej; Iglic, Ales; Kralj-Iglic, Veronika; Konvicková, Svatava

2005-02-01

The computer system for quantitative determination of musculoskeletal geometry from computer tomography (CT) images has been developed. The computer system processes series of CT images to obtain three-dimensional (3D) model of bony structures where the effective muscle fibres can be interactively defined. Presented computer system has flexible modular structure and is suitable also for educational purposes.

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.

Topological study of diverse hydrogen-bonded patterns found in a system of a nickel(II) complex and the sulfate anion.

PubMed

Harvey, Miguel Angel; Suarez, Sebastián; Zolotarev, Pavel N; Proserpio, Davide M; Baggio, Ricardo

2018-03-01

A nickel(II) coordination complex, bis[2,6-bis(1H-benzimidazol-2-yl-κN 3 )pyridine-κN]nickel(II) sulfate, [Ni(C 19 H 13 N 5 ) 2 ]SO 4 or [Ni(H 2 L) 2 ]SO 4 , having four peripheral tetrahedrally oriented N-H donor units, combines with sulfate bridges to create hydrogen-bonded structures of varied dimensionality. The three crystal structures reported herein in the space groups P2 1 2 1 2 1 , I-4 and Pccn are defined solely by strong charge-assisted N-H...O hydrogen bonds and contain disordered guests (water and dimethylformamide) that vary in size, shape and degree of hydrophilicity. Two of the compounds are channelled solids with three-dimensional structures, while the third is one-dimensional in nature. In spite of their differences, all three present a striking resemblance to the previously reported anhydrous relative [Guo et al. (2011). Chin. J. Inorg. Chem. 27, 1517-1520], which is considered as the reference framework from which all three title compounds are derived. The hydrogen-bonded frameworks are described and compared using crystallographic and topological approaches.

Three-dimensional Bragg diffraction in growth-disordered opals

NASA Astrophysics Data System (ADS)

Baryshev, A. V.; Kaplyanskii, Alexander A.; Kosobukin, Vladimir A.; Limonov, M. F.; Samusev, K. B.; Usvyat, D. E.

2003-06-01

After artificial opals as well as opal-based infilled and inverted composites are considered to be promising representatives of photonic crystal materials. Earlier, photonic stop gaps in opals were studied mainly in transmission or specular reflection geometries corresponding to "one-dimensional" Bragg diffraction. On the contrary, this work was aimed at observing the typical patterns of optical Bragg diffraction in which phenomenon opal crystal structure acts as a three-dimensional diffraction grating. Although our experiments were performed for artificial opals possessing unavoidable imperfections a well-pronounced diffraction peaks were observed characteristic of a crystal structure. Each of the diffraction maxima reveals a photonic stop gap in the specified direction, while the spectral width of the peak is a measure of the photonic stop gap width.

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.

Siegert-state expansion for nonstationary systems. IV. Three-dimensional case

NASA Astrophysics Data System (ADS)

Tolstikhin, Oleg I.

2008-03-01

The Siegert-state expansion approach [O. I. Tolstikhin, Phys. Rev. A 73, 062705 (2006)] is extended to the three-dimensional case. Coupled equations defining the time evolution of coefficients in the expansion of the solution to the time-dependent Schrödinger equation in terms of partial-wave Siegert states are derived, and physical observables (probabilities of transitions to discrete states and the momentum distribution of ejected particles) are expressed in terms of these coefficients. The approach is implemented in terms of Siegert pseudostates and illustrated by calculations of the photodetachment of H- by strong high-frequency laser pulses. The present calculations demonstrate that the interference effect in the laser-atom interaction dynamics found recently in the one-dimensional case [K. Toyota , Phys. Rev. A 76, 043418 (2007)] reveals itself in the three-dimensional case as well.

MEAs and 3D nanoelectrodes: electrodeposition as tool for a precisely controlled nanofabrication.

PubMed

Weidlich, Sabrina; Krause, Kay J; Schnitker, Jan; Wolfrum, Bernhard; Offenhäusser, Andreas

2017-01-31

Microelectrode arrays (MEAs) are gaining increasing importance for the investigation of signaling processes between electrogenic cells. However, efficient cell-chip coupling for robust and long-term electrophysiological recording and stimulation still remains a challenge. A possible approach for the improvement of the cell-electrode contact is the utilization of three-dimensional structures. In recent years, various 3D electrode geometries have been developed, but we are still lacking a fabrication approach that enables the formation of different 3D structures on a single chip in a controlled manner. This, however, is needed to enable a direct and reliable comparison of the recording capabilities of the different structures. Here, we present a method for a precisely controlled deposition of nanoelectrodes, enabling the fabrication of multiple, well-defined types of structures on our 64 electrode MEAs towards a rapid-prototyping approach to 3D electrodes.

New faces of porous Prussian blue: interfacial assembly of integrated hetero-structures for sensing applications.

PubMed

Kong, Biao; Selomulya, Cordelia; Zheng, Gengfeng; Zhao, Dongyuan

2015-11-21

Prussian blue (PB), the oldest synthetic coordination compound, is a classic and fascinating transition metal coordination material. Prussian blue is based on a three-dimensional (3-D) cubic polymeric porous network consisting of alternating ferric and ferrous ions, which provides facile assembly as well as precise interaction with active sites at functional interfaces. A fundamental understanding of the assembly mechanism of PB hetero-interfaces is essential to enable the full potential applications of PB crystals, including chemical sensing, catalysis, gas storage, drug delivery and electronic displays. Developing controlled assembly methods towards functionally integrated hetero-interfaces with adjustable sizes and morphology of PB crystals is necessary. A key point in the functional interface and device integration of PB nanocrystals is the fabrication of hetero-interfaces in a well-defined and oriented fashion on given substrates. This review will bring together these key aspects of the hetero-interfaces of PB nanocrystals, ranging from structure and properties, interfacial assembly strategies, to integrated hetero-structures for diverse sensing.

Revised Geometric Measure of Entanglement in Infinite Dimensional Multipartite Quantum Systems

NASA Astrophysics Data System (ADS)

Wang, Yinzhu; Wang, Danxia; Huang, Li

2018-05-01

In Cao and Wang (J. Phys.: Math. Theor. 40, 3507-3542, 2007), the revised geometric measure of entanglement (RGME) for states in finite dimensional bipartite quantum systems was proposed. Furthermore, in Cao and Wang (Commun. Theor. Phys. 51(4), 613-620, 2009), the authors obtained the revised geometry measure of entanglement for multipartite states including three-qubit GHZ state, W state, and the generalized Smolin state in the presence of noise and the two-mode squeezed thermal state, and defined the Gaussian geometric entanglement measure. In this paper, we generalize the RGME to infinite dimensional multipartite quantum systems, and prove that this measure satisfies some necessary properties as a well-defined entanglement measure, including monotonicity under local operations and classical communications.

Ion current in a magnetic neutral region - Generation of an incipient magnetopause

NASA Technical Reports Server (NTRS)

Whipple, E. C.; Silevitch, M. B.

1982-01-01

The current contributed by ions trapped in the vicinity of a magnetic X line is calculated. The three dimensional configuration of the neutral region is found to be critical in determining the current in that the escape mechanism and trapping times depend on the three-dimensional aspects. A trapping criterion is defined. In the neutral region the ions can gain substantial kinetic energy, and the current will change the X line configuration in such a way that there will be a positive feedback effect, rapidly forming an extended magnetopauselike structure for even very small incident plasma densities.

The geometry of structural equilibrium

PubMed Central

2017-01-01

Building on a long tradition from Maxwell, Rankine, Klein and others, this paper puts forward a geometrical description of structural equilibrium which contains a procedure for the graphic analysis of stress resultants within general three-dimensional frames. The method is a natural generalization of Rankine’s reciprocal diagrams for three-dimensional trusses. The vertices and edges of dual abstract 4-polytopes are embedded within dual four-dimensional vector spaces, wherein the oriented area of generalized polygons give all six components (axial and shear forces with torsion and bending moments) of the stress resultants. The relevant quantities may be readily calculated using four-dimensional Clifford algebra. As well as giving access to frame analysis and design, the description resolves a number of long-standing problems with the incompleteness of Rankine’s description of three-dimensional trusses. Examples are given of how the procedure may be applied to structures of engineering interest, including an outline of a two-stage procedure for addressing the equilibrium of loaded gridshell rooves. PMID:28405361

Structural diversity of supercoiled DNA

PubMed Central

Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

2015-01-01

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function. PMID:26455586

Structural diversity of supercoiled DNA

NASA Astrophysics Data System (ADS)

Irobalieva, Rossitza N.; Fogg, Jonathan M.; Catanese, Daniel J.; Sutthibutpong, Thana; Chen, Muyuan; Barker, Anna K.; Ludtke, Steven J.; Harris, Sarah A.; Schmid, Michael F.; Chiu, Wah; Zechiedrich, Lynn

2015-10-01

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

Binary Colloidal Alloy Test-5: Three-Dimensional Melt

NASA Technical Reports Server (NTRS)

Yodh, Arjun G.

2008-01-01

Binary Colloidal Alloy Test - 5: Three-Dimensional Melt (BCAT-5-3DMelt) photographs initially randomized colloidal samples in microgravity to determine their resulting structure over time. BCAT-5-3D-Melt will allow the scientists to capture the kinetics (evolution) of their samples, as well as the final equilibrium state of each sample. BCAT-5-3D-Melt will look at the mechanisms of melting using three-dimensional temperature sensitive colloidal crystals. Results will help scientists develop fundamental physics concepts previously shadowed by the effects of gravity.

Farley Three-Dimensional-Braiding Machine

NASA Technical Reports Server (NTRS)

Farley, Gary L.

1991-01-01

Process and device known as Farley three-dimensional-braiding machine conceived to fabricate dry continuous fiber-reinforced preforms of complex three-dimensional shapes for subsequent processing into composite structures. Robotic fiber supply dispenses yarn as it traverses braiding surface. Combines many attributes of weaving and braiding processes with other attributes and capabilities. Other applications include decorative cloths, rugs, and other domestic textiles. Concept could lead to large variety of fiber layups and to entirely new products as well as new fiber-reinforcing applications.

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.

Implementing quantum Ricci curvature

NASA Astrophysics Data System (ADS)

Klitgaard, N.; Loll, R.

2018-05-01

Quantum Ricci curvature has been introduced recently as a new, geometric observable characterizing the curvature properties of metric spaces, without the need for a smooth structure. Besides coordinate invariance, its key features are scalability, computability, and robustness. We demonstrate that these properties continue to hold in the context of nonperturbative quantum gravity, by evaluating the quantum Ricci curvature numerically in two-dimensional Euclidean quantum gravity, defined in terms of dynamical triangulations. Despite the well-known, highly nonclassical properties of the underlying quantum geometry, its Ricci curvature can be matched well to that of a five-dimensional round sphere.

Overview of aerothermodynamic loads definition study

NASA Technical Reports Server (NTRS)

Gaugler, Raymond E.

1991-01-01

The objective of the Aerothermodynamic Loads Definition Study is to develop methods of accurately predicting the operating environment in advanced Earth-to-Orbit (ETO) propulsion systems, such as the Space Shuttle Main Engine (SSME) powerhead. Development of time averaged and time dependent three dimensional viscous computer codes as well as experimental verification and engine diagnostic testing are considered to be essential in achieving that objective. Time-averaged, nonsteady, and transient operating loads must all be well defined in order to accurately predict powerhead life. Described here is work in unsteady heat flow analysis, improved modeling of preburner flow, turbulence modeling for turbomachinery, computation of three dimensional flow with heat transfer, and unsteady viscous multi-blade row turbine analysis.

The Infinitesimal Moduli Space of Heterotic G 2 Systems

NASA Astrophysics Data System (ADS)

de la Ossa, Xenia; Larfors, Magdalena; Svanes, Eirik E.

2018-06-01

Heterotic string compactifications on integrable G 2 structure manifolds Y with instanton bundles {(V,A), (TY,\\tilde{θ})} yield supersymmetric three-dimensional vacua that are of interest in physics. In this paper, we define a covariant exterior derivative D and show that it is equivalent to a heterotic G 2 system encoding the geometry of the heterotic string compactifications. This operator D acts on a bundle Q}=T^*Y \\oplus End(V) \\oplus End(TY)} and satisfies a nilpotency condition \\check{{D^2=0} , for an appropriate projection of D. Furthermore, we determine the infinitesimal moduli space of these systems and show that it corresponds to the finite-dimensional cohomology group H^1_{D}(Q). We comment on the similarities and differences of our result with Atiyah's well-known analysis of deformations of holomorphic vector bundles over complex manifolds. Our analysis leads to results that are of relevance to all orders in the {α'} expansion.

Synthesis and Characterization of Three Dimensional Nanostructures Based on Interconnected Carbon Nanomaterials

NASA Astrophysics Data System (ADS)

Koizumi, Ryota

This thesis addresses various types of synthetic methods for novel three dimensional nanomaterials and nanostructures based on interconnected carbon nanomaterials using solution chemistry and chemical vapor deposition (CVD) methods. Carbon nanotube (CNT) spheres with porous and scaffold structures consisting of interconnected CNTs were synthesized by solution chemistry followed by freeze-drying, which have high elasticity under nano-indentation tests. This allows the CNT spheres to be potentially applied to mechanical dampers. CNTs were also grown on two dimensional materials--such as reduced graphene oxide (rGO) and hexagonal boron nitride (h-BN)--by CVD methods, which are chemically interconnected. CNTs on rGO and h-BN interconnected structures performed well as electrodes for supercapacitors. Furthermore, unique interconnected flake structures of alpha-phase molybdenum carbide were developed by a CVD method. The molybdenum carbide can be used for a catalyst of hydrogen evolution reaction activity as well as an electrode for supercapacitors.

Nanocrystals with linear and branched topology

DOEpatents

Alivisatos, A. Paul; Milliron, Delia; Manna, Liberato; Hughes, Steven M.

2007-12-04

Disclosed herein are nanostructures comprising distinct dots and rods coupled through potential barriers of tuneable height and width, and arranged in three dimensional space at well defined angles and distances. Such control allows investigation of potential applications ranging from quantum information processing to artificial photosynthesis.

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

PubMed Central

Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

2013-01-01

Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210

Fast computational methods for predicting protein structure from primary amino acid sequence

DOEpatents

Agarwal, Pratul Kumar [Knoxville, TN

2011-07-19

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Large three-dimensional photonic crystals based on monocrystalline liquid crystal blue phases.

PubMed

Chen, Chun-Wei; Hou, Chien-Tsung; Li, Cheng-Chang; Jau, Hung-Chang; Wang, Chun-Ta; Hong, Ching-Lang; Guo, Duan-Yi; Wang, Cheng-Yu; Chiang, Sheng-Ping; Bunning, Timothy J; Khoo, Iam-Choon; Lin, Tsung-Hsien

2017-09-28

Although there have been intense efforts to fabricate large three-dimensional photonic crystals in order to realize their full potential, the technologies developed so far are still beset with various material processing and cost issues. Conventional top-down fabrications are costly and time-consuming, whereas natural self-assembly and bottom-up fabrications often result in high defect density and limited dimensions. Here we report the fabrication of extraordinarily large monocrystalline photonic crystals by controlling the self-assembly processes which occur in unique phases of liquid crystals that exhibit three-dimensional photonic-crystalline properties called liquid-crystal blue phases. In particular, we have developed a gradient-temperature technique that enables three-dimensional photonic crystals to grow to lateral dimensions of ~1 cm (~30,000 of unit cells) and thickness of ~100 μm (~ 300 unit cells). These giant single crystals exhibit extraordinarily sharp photonic bandgaps with high reflectivity, long-range periodicity in all dimensions and well-defined lattice orientation.Conventional fabrication approaches for large-size three-dimensional photonic crystals are problematic. By properly controlling the self-assembly processes, the authors report the fabrication of monocrystalline blue phase liquid crystals that exhibit three-dimensional photonic-crystalline properties.

Crystal structure of fac-[2-(4-methyl-5-phenyl-pyridin-2-yl)phenyl-κ2C1,N]bis-[2-(pyridin-2-yl)phenyl-κ2C1,N]iridium(III).

PubMed

Lee, Chi-Heon; Moon, Suk-Hee; Park, Ki-Min; Kang, Youngjin

2016-12-01

In the title compound, [Ir(C 11 H 8 N) 2 (C 18 H 14 N)], the Ir III ion adopts a distorted octa-hedral coordination environment defined by three C , N -chelating ligands, one stemming from a 2-(4-phenyl-5-methyl-pyridin-2-yl)phenyl ligand and two from 2-(pyridin-2-yl)phenyl ligands, arranged in a facial manner. The Ir III ion lies almost in the equatorial plane [deviation = 0.0069 (15) Å]. In the crystal, inter-molecular π-π stacking inter-actions, as well as inter-molecular C-H⋯π inter-actions, are present, leading to a three-dimensional network.

User-Defined Material Model for Progressive Failure Analysis

NASA Technical Reports Server (NTRS)

Knight, Norman F. Jr.; Reeder, James R. (Technical Monitor)

2006-01-01

An overview of different types of composite material system architectures and a brief review of progressive failure material modeling methods used for structural analysis including failure initiation and material degradation are presented. Different failure initiation criteria and material degradation models are described that define progressive failure formulations. These progressive failure formulations are implemented in a user-defined material model (or UMAT) for use with the ABAQUS/Standard1 nonlinear finite element analysis tool. The failure initiation criteria include the maximum stress criteria, maximum strain criteria, the Tsai-Wu failure polynomial, and the Hashin criteria. The material degradation model is based on the ply-discounting approach where the local material constitutive coefficients are degraded. Applications and extensions of the progressive failure analysis material model address two-dimensional plate and shell finite elements and three-dimensional solid finite elements. Implementation details and use of the UMAT subroutine are described in the present paper. Parametric studies for composite structures are discussed to illustrate the features of the progressive failure modeling methods that have been implemented.

Effects of three-dimensional velocity structure on the seismicity of the 1984 Morgan Hill, California, aftershock sequence

USGS Publications Warehouse

Michael, A.J.

1988-01-01

A three-dimensional velocity model for the area surrounding the 24 April 1984 Morgan Hill earthquake has been developed by simultaneously inverting local earthquake and refraction arrival-time data. This velocity model corresponds well to the surface geology of the region, predominantly showing a low-velocity region associated with the sedimentary sequence to the south-west of the Madrone Springs fault. The focal mechanisms were also determined for 946 earthquakes using both the one-dimensional and three-dimensional earth models. Both earth models yield similar focal mechanisms for these earthquakes. -from Author

Development of Seismic Isolation Systems Using Periodic Materials

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

Yan, Yiqun; Mo, Yi-Lung; Menq, Farn-Yuh

Advanced fast nuclear power plants and small modular fast reactors are composed of thin-walled structures such as pipes; as a result, they do not have sufficient inherent strength to resist seismic loads. Seismic isolation, therefore, is an effective solution for mitigating earthquake hazards for these types of structures. Base isolation, on which numerous studies have been conducted, is a well-defined structure protection system against earthquakes. In conventional isolators, such as high-damping rubber bearings, lead-rubber bearings, and friction pendulum bearings, large relative displacements occur between upper structures and foundations. Only isolation in a horizontal direction is provided; these features are notmore » desirable for the piping systems. The concept of periodic materials, based on the theory of solid-state physics, can be applied to earthquake engineering. The periodic material is a material that possesses distinct characteristics that prevent waves with certain frequencies from being transmitted through it; therefore, this material can be used in structural foundations to block unwanted seismic waves with certain frequencies. The frequency band of periodic material that can filter out waves is called the band gap, and the structural foundation made of periodic material is referred to as the periodic foundation. The design of a nuclear power plant, therefore, can be unified around the desirable feature of a periodic foundation, while the continuous maintenance of the structure is not needed. In this research project, three different types of periodic foundations were studied: one-dimensional, two-dimensional, and three-dimensional. The basic theories of periodic foundations are introduced first to find the band gaps; then the finite element methods are used, to perform parametric analysis, and obtain attenuation zones; finally, experimental programs are conducted, and the test data are analyzed to verify the theory. This procedure shows that the periodic foundation is a promising and effective way to mitigate structural damage caused by earthquake excitation.« less

Programmable growth of branched silicon nanowires using a focused ion beam.

PubMed

Jun, Kimin; Jacobson, Joseph M

2010-08-11

Although significant progress has been made in being able to spatially define the position of material layers in vapor-liquid-solid (VLS) grown nanowires, less work has been carried out in deterministically defining the positions of nanowire branching points to facilitate more complicated structures beyond simple 1D wires. Work to date has focused on the growth of randomly branched nanowire structures. Here we develop a means for programmably designating nanowire branching points by means of focused ion beam-defined VLS catalytic points. This technique is repeatable without losing fidelity allowing multiple rounds of branching point definition followed by branch growth resulting in complex structures. The single crystal nature of this approach allows us to describe resulting structures with linear combinations of base vectors in three-dimensional (3D) space. Finally, by etching the resulting 3D defined wire structures branched nanotubes were fabricated with interconnected nanochannels inside. We believe that the techniques developed here should comprise a useful tool for extending linear VLS nanowire growth to generalized 3D wire structures.

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

PubMed Central

2010-01-01

Background In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. Results Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. Discussion The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction. PMID:20550657

Compact 3D photonic crystals sensing platform with 45 degree angle polished fibers

NASA Astrophysics Data System (ADS)

Guo, Yuqing; Chen, Lu; Zhu, Jiali; Ni, Haibin; Xia, Wei; Wang, Ming

2017-07-01

Three dimensional photonic crystals are a kind of promising sensing materials in biology and chemistry. A compact structure, consists of planner colloidal crystals and 45 degree angle polished fiber, is proposed as a platform for accurate, fast, reliable three dimensional photonic crystals sensing in practice. This structure show advantages in compact size for integration and it is ease for large scale manufacture. Reflectivity of the 45 degree angle polished surface with and without a layer of Ag film are simulated by FDTD simulation. Refractive index sensing properties as well as mode distribution of this structure consists of both polystyrene opal and silica inverse opal film is investigated, and an experimental demonstration of silica inverse opal film is performed, which shows a sensitivity of 733 nm/RIU. Different kinds of three dimensional photonic crystals can also be applied in this structure for particular purpose.

Heuristic problems in defining the three-dimensional arrangement of the ventricular myocytes.

PubMed

Anderson, Robert H; Ho, Siew Yen; Sanchez-Quintana, Damian; Redmann, Klaus; Lunkenheimer, Paul P

2006-06-01

There is lack of consensus concerning the three-dimensional arrangement of the myocytes within the ventricular muscle masses. Bioengineers are seeking to model the structure of the heart. Although the success of such models depends on the accuracy of the anatomic evidence, most of them have been based on concepts that are far from anatomical reality, which ignore many significant previous accounts of anatomy presented over the past 400 years. During the 19th century, Pettigrew emphasized that the heart was built on the basis of a modified blood vessel rather than in the form of skeletal muscles. This fact was reemphasized by Lev and Simkins as well as Grant in the 20th century, but the caveats listed by these authors have been ignored by proponents of two current concepts, which state either that the myocardium is arranged in the form of a "unique myocardial band," or that the walls of the ventricles are sequestrated in uniform fashion by laminar sheets of fibrous tissue extending from epicardium to endocardium. These two concepts are themselves incompatible and are further at variance with the majority of anatomic studies, which have emphasized the regional heterogeneity to be found in the three-dimensional packing of the myocytes within a supporting matrix of fibrous tissue. We reemphasize the significance of this three-dimensional muscular mesh, showing how the presence of intruding aggregates of myocytes extending in oblique transmural fashion also contends against the notion that all myocytes are orientated with their long axes parallel to the epicardial and enodcardial surfaces.

Importance of preoperative imaging with 64-row three-dimensional multidetector computed tomography for safer video-assisted thoracic surgery in lung cancer.

PubMed

Akiba, Tadashi; Marushima, Hideki; Harada, Junta; Kobayashi, Susumu; Morikawa, Toshiaki

2009-01-01

Video-assisted thoracic surgery (VATS) has recently been adopted for complicated anatomical lung resections. During these thoracoscopic procedures, surgeons view the operative field on a two-dimensional (2-D) video monitor and cannot palpate the organ directly, thus frequently encountering anatomical difficulties. This study aimed to estimate the usefulness of preoperative three-dimensional (3-D) imaging of thoracic organs. We compared the preoperative 64-row three-dimensional multidetector computed tomography (3DMDCT) findings of lung cancer-affected thoracic organs to the operative findings. In comparison to the operative findings, the branches of pulmonary arteries, veins, and bronchi were well defined in the 3D-MDCT images of 27 patients. 3D-MDCT imaging is useful for preoperatively understanding the individual thoracic anatomy in lung cancer surgery. This modality can therefore contribute to safer anatomical pulmonary operations, especially in VATS.

An implicit solution of the three-dimensional Navier-Stokes equations for an airfoil spanning a wind tunnel. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Moitra, A.

1982-01-01

An implicit finite-difference algorithm is developed for the numerical solution of the incompressible three dimensional Navier-Stokes equations in the non-conservative primitive-variable formulation. The flow field about an airfoil spanning a wind-tunnel is computed. The coordinate system is generated by an extension of the two dimensional body-fitted coordinate generation techniques of Thompson, as well as that of Sorenson, into three dimensions. Two dimensional grids are stacked along a spanwise coordinate defined by a simple analytical function. A Poisson pressure equation for advancing the pressure in time is arrived at by performing a divergence operation on the momentum equations. The pressure at each time-step is calculated on the assumption that continuity be unconditionally satisfied. An eddy viscosity coefficient, computed according to the algebraic turbulence formulation of Baldwin and Lomax, simulates the effects of turbulence.

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.

Interactive computer aided technology, evolution in the design/manufacturing process

NASA Technical Reports Server (NTRS)

English, C. H.

1975-01-01

A powerful computer-operated three dimensional graphic system and associated auxiliary computer equipment used in advanced design, production design, and manufacturing was described. This system has made these activities more productive than when using older and more conventional methods to design and build aerospace vehicles. With the use of this graphic system, designers are now able to define parts using a wide variety of geometric entities, define parts as fully surface 3-dimensional models as well as "wire-frame" models. Once geometrically defined, the designer is able to take section cuts of the surfaced model and automatically determine all of the section properties of the planar cut, lightpen detect all of the surface patches and automatically determine the volume and weight of the part. Further, his designs are defined mathematically at a degree of accuracy never before achievable.

Recent progress in DNA origami technology.

PubMed

Endo, Masayuki; Sugiyama, Hiroshi

2011-06-01

DNA origami is an emerging technology for designing defined two-dimensional DNA nanostructures. In this review, we focus on and describe several types of DNA origami-related studies, as follows: (1) programmed DNA origami assembly, (2) DNA origami-templated molecular assembly, (3) design and construction of various three-dimensional DNA origami structures, (4) programmed functionalization of DNA origami and combination with top-down nanotechnology, (5) single molecular observation on a designed DNA origami, and (6) DNA nanomachines working on a DNA origami. © 2011 by John Wiley & Sons, Inc.

Structure and Uncoating of Immature Adenovirus

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

Perez-Berna, A.J.; Mangel, W.; Marabini, R.

2009-09-18

Maturation via proteolytic processing is a common trait in the viral world and is often accompanied by large conformational changes and rearrangements in the capsid. The adenovirus protease has been shown to play a dual role in the viral infectious cycle: (a) in maturation, as viral assembly starts with precursors to several of the structural proteins but ends with proteolytically processed versions in the mature virion, and (b) in entry, because protease-impaired viruses have difficulties in endosome escape and uncoating. Indeed, viruses that have not undergone proteolytic processing are not infectious. We studied the three-dimensional structure of immature adenovirus particlesmore » as represented by the adenovirus type 2 thermosensitive mutant ts1 grown under non-permissive conditions and compared it with the mature capsid. Our three-dimensional electron microscopy maps at subnanometer resolution indicate that adenovirus maturation does not involve large-scale conformational changes in the capsid. Difference maps reveal the locations of unprocessed peptides pIIIa and pVI and help define their role in capsid assembly and maturation. An intriguing difference appears in the core, indicating a more compact organization and increased stability of the immature cores. We have further investigated these properties by in vitro disassembly assays. Fluorescence and electron microscopy experiments reveal differences in the stability and uncoating of immature viruses, both at the capsid and core levels, as well as disassembly intermediates not previously imaged.« less

Aspects of three-dimensional strain at the margin of the extensional orogen, Virgin River depression area, Nevada, Utah, and Arizona

USGS Publications Warehouse

Anderson, R.E.; Barnhard, T.P.

1993-01-01

The Virgin River depression and surrounding mountains are Neogene features that are partly contiguous with the little-strained rocks of the structural transition to the Colorado Plateau province. This contiguity makes the area ideally suited for evaluating the sense, magnitude, and kinematics of Neogene deformation. Analysis along the strain boundary shows that, compared to the adjacent little-strained area, large-magnitude vertical deformation greatly exceeds extensional deformation and that significant amounts of lateral displacement approximately parallel the province boundary. Isostatic rebound following tectonic denudation is an unlikely direct cause of the strong vertical structural relief adjacent to the strain boundary. Instead, the observed structures are first-order features defining a three-dimensional strain field produced by approximately east-west extension, vertical structural attenuation, and extension-normal shortening. All major structural elements of the strain-boundary strain field are also found in the adjacent Basin and Range. -from Authors

The underlying structure of diagnostic systems of schizophrenia: a comprehensive polydiagnostic approach.

PubMed

Peralta, Victor; Cuesta, Manuel J

2005-11-15

The objective was to ascertain the underlying factor structure of alternative definitions of schizophrenia, and to examine the distribution of schizophrenia-related variables against the resulting factor solution. Twenty-three diagnostic schemes of schizophrenia were applied to 660 patients presenting with psychotic symptoms regardless of the specific diagnosis of psychotic disorder. Factor analysis of the 23 diagnostic schemes yielded three interpretable factors explaining 58% of the variance, the first factor (general schizophrenia factor) accounting for most of the variance (36%). On the basis of the general schizophrenia factor score, the sample was divided in quintile groups representing 5 levels of schizophrenia definition (absent, doubtful, very broad, broad and narrow) and the distribution of a number of schizophrenia-related variables was examined across the groups. This grouping procedure was used for examining the comparative validity of alternative levels of categorically defined schizophrenia and an ordinal (i.e. dimensional) definition. Overall, schizophrenia-related variables displayed a dose-response relationship with level of schizophrenia definition. Logistic regression analyses revealed that the dimensional definition explained more variance in the schizophrenia-related variables than the alternative levels for defining schizophrenia categorically. These results are consistent with a unitary and dimensional construct of schizophrenia with no clear "points of rarity" at its boundaries, thus supporting the continuum hypothesis of the psychotic illness.

Depth-tunable three-dimensional display with interactive light field control

NASA Astrophysics Data System (ADS)

Xie, Songlin; Wang, Peng; Sang, Xinzhu; Li, Chenyu; Dou, Wenhua; Xiao, Liquan

2016-07-01

A software-defined depth-tunable three-dimensional (3D) display with interactive 3D depth control is presented. With the proposed post-processing system, the disparity of the multi-view media can be freely adjusted. Benefiting from a wealth of information inherently contains in dense multi-view images captured with parallel arrangement camera array, the 3D light field is built and the light field structure is controlled to adjust the disparity without additional acquired depth information since the light field structure itself contains depth information. A statistical analysis based on the least square is carried out to extract the depth information inherently exists in the light field structure and the accurate depth information can be used to re-parameterize light fields for the autostereoscopic display, and a smooth motion parallax can be guaranteed. Experimental results show that the system is convenient and effective to adjust the 3D scene performance in the 3D display.

Gravitational instantons admit hyper-Kähler structure

NASA Astrophysics Data System (ADS)

Aliev, A. N.; Nutku, Y.

1999-01-01

We construct the explicit form of three almost-complex structures that a Riemannian manifold with self-dual curvature admits and show that their Nijenhuis tensors vanish so that they are integrable. This proves that gravitational instantons with self-dual curvature admit hyper-Kähler structure. In order to arrive at the three vector-valued 1-forms defining almost-complex structure, we give a spinor description of real four-dimensional Riemannian manifolds with Euclidean signature in terms of two independent sets of two-component spinors. This is a version of the original Newman-Penrose formalism that is appropriate to the discussion of the mathematical, as well as physical properties of gravitational instantons. We shall build on the work of Goldblatt who first developed an NP formalism for gravitational instantons but we shall adopt it to differential forms in the NP basis to make the formalism much more compact. We shall show that the spin coefficients, connection 1-form, curvature 2-form, Ricci and Bianchi identities, as well as the Maxwell equations naturally split up into their self-dual and anti-self-dual parts corresponding to the two independent spin frames. We shall give the complex dyad as well as the spinor formulation of the almost-complex structures and show that they reappear under the guise of a triad basis for the Petrov classification of gravitational instantons. Completing the work of Salamon on hyper-Kähler structure, we show that the vanishing of the Nijenhuis tensor for all three almost-complex structures depends on the choice of a self-dual gauge for the connection which is guaranteed by virtue of the fact that the curvature 2-form is self-dual for gravitational instantons.

Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

PubMed Central

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized. PMID:24688696

Conformational sampling in template-free protein loop structure modeling: an overview.

PubMed

Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

Three-Dimensional Properties of Coronal Mass Ejections from STEREO/SECCHI Observations

NASA Astrophysics Data System (ADS)

Bosman, E.; Bothmer, V.; Nisticò, G.; Vourlidas, A.; Howard, R. A.; Davies, J. A.

2012-11-01

We identify 565 coronal mass ejections (CMEs) between January 2007 and December 2010 in observations from the twin STEREO/SECCHI/COR2 coronagraphs aboard the STEREO mission. Our list is in full agreement with the corresponding SOHO/LASCO CME Catalog (http://cdaw.gsfc.nasa.gov/CME_list/) for events with angular widths of 45∘ and up. The monthly event rates behave similarly to sunspot rates showing a three- to fourfold rise between September 2009 and March 2010. We select 51 events with well-defined white-light structure and model them as three-dimensional (3D) flux ropes using a forward-modeling technique developed by Thernisien, Howard and Vourlidas (Astrophys. J. 652, 763 - 773, 2006). We derive their 3D properties and identify their source regions. We find that the majority of the CME flux ropes (82 %) lie within 30∘ of the solar equator. Also, 82 % of the events are displaced from their source region, to a lower latitude, by 25∘ or less. These findings provide strong support for the deflection of CMEs towards the solar equator reported in earlier observations, e.g. by Cremades and Bothmer ( Astron. Astrophys. 422, 307 - 322, 2004).

Towards three-dimensional optical metamaterials

NASA Astrophysics Data System (ADS)

Tanaka, Takuo; Ishikawa, Atsushi

2017-12-01

Metamaterials have opened up the possibility of unprecedented and fascinating concepts and applications in optics and photonics. Examples include negative refraction, perfect lenses, cloaking, perfect absorbers, and so on. Since these metamaterials are man-made materials composed of sub-wavelength structures, their development strongly depends on the advancement of micro- and nano-fabrication technologies. In particular, the realization of three-dimensional metamaterials is one of the big challenges in this research field. In this review, we describe recent progress in the fabrication technologies for three-dimensional metamaterials, as well as proposed applications.

The three-dimensional structure of swirl-switching in bent pipe flow

DOE PAGES

Hufnagel, Lorenz; Canton, Jacopo; Örlü, Ramis; ...

2017-11-27

Swirl-switching is a low-frequency oscillatory phenomenon which affects the Dean vortices in bent pipes and may cause fatigue in piping systems. Despite thirty years worth of research, the mechanism that causes these oscillations and the frequencies that characterise them remain unclear. In this paper, we show that a three-dimensional wave-like structure is responsible for the low-frequency switching of the dominant Dean vortex. The present study, performed via direct numerical simulation, focuses on the turbulent flow through amore » $$90^{\\circ }$$pipe bend preceded and followed by straight pipe segments. A pipe with curvature 0.3 (defined as ratio between pipe radius and bend radius) is studied for a bulk Reynolds number $$Re=11\\,700$$, corresponding to a friction Reynolds number $$Re_{\\unicode[STIX]{x1D70F}}\\approx 360$$. Synthetic turbulence is generated at the inflow section and used instead of the classical recycling method in order to avoid the interference between recycling and swirl-switching frequencies. The flow field is analysed by three-dimensional proper orthogonal decomposition (POD) which for the first time allows the identification of the source of swirl-switching: a wave-like structure that originates in the pipe bend. Contrary to some previous studies, the flow in the upstream pipe does not show any direct influence on the swirl-switching modes. Finally, our analysis further shows that a three-dimensional characterisation of the modes is crucial to understand the mechanism, and that reconstructions based on two-dimensional POD modes are incomplete.« less

The three-dimensional structure of swirl-switching in bent pipe flow

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

Hufnagel, Lorenz; Canton, Jacopo; Örlü, Ramis

Swirl-switching is a low-frequency oscillatory phenomenon which affects the Dean vortices in bent pipes and may cause fatigue in piping systems. Despite thirty years worth of research, the mechanism that causes these oscillations and the frequencies that characterise them remain unclear. In this paper, we show that a three-dimensional wave-like structure is responsible for the low-frequency switching of the dominant Dean vortex. The present study, performed via direct numerical simulation, focuses on the turbulent flow through amore » $$90^{\\circ }$$pipe bend preceded and followed by straight pipe segments. A pipe with curvature 0.3 (defined as ratio between pipe radius and bend radius) is studied for a bulk Reynolds number $$Re=11\\,700$$, corresponding to a friction Reynolds number $$Re_{\\unicode[STIX]{x1D70F}}\\approx 360$$. Synthetic turbulence is generated at the inflow section and used instead of the classical recycling method in order to avoid the interference between recycling and swirl-switching frequencies. The flow field is analysed by three-dimensional proper orthogonal decomposition (POD) which for the first time allows the identification of the source of swirl-switching: a wave-like structure that originates in the pipe bend. Contrary to some previous studies, the flow in the upstream pipe does not show any direct influence on the swirl-switching modes. Finally, our analysis further shows that a three-dimensional characterisation of the modes is crucial to understand the mechanism, and that reconstructions based on two-dimensional POD modes are incomplete.« less

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

Solution of the Burnett equations for hypersonic flows near the continuum limit

NASA Technical Reports Server (NTRS)

Imlay, Scott T.

1992-01-01

The INCA code, a three-dimensional Navier-Stokes code for analysis of hypersonic flowfields, was modified to analyze the lower reaches of the continuum transition regime, where the Navier-Stokes equations become inaccurate and Monte Carlo methods become too computationally expensive. The two-dimensional Burnett equations and the three-dimensional rotational energy transport equation were added to the code and one- and two-dimensional calculations were performed. For the structure of normal shock waves, the Burnett equations give consistently better results than Navier-Stokes equations and compare reasonably well with Monte Carlo methods. For two-dimensional flow of Nitrogen past a circular cylinder the Burnett equations predict the total drag reasonably well. Care must be taken, however, not to exceed the range of validity of the Burnett equations.

A computer program for the calculation of the flow field in supersonic mixed-compression inlets at angle of attack using the three-dimensional method of characteristics with discrete shock wave fitting

NASA Technical Reports Server (NTRS)

Vadyak, J.; Hoffman, J. D.; Bishop, A. R.

1978-01-01

The calculation procedure is based on the method of characteristics for steady three-dimensional flow. The bow shock wave and the internal shock wave system were computed using a discrete shock wave fitting procedure. The general structure of the computer program is discussed, and a brief description of each subroutine is given. All program input parameters are defined, and a brief discussion on interpretation of the output is provided. A number of sample cases, complete with data deck listings, are presented.

Atomically thin two-dimensional organic-inorganic hybrid perovskites

NASA Astrophysics Data System (ADS)

Dou, Letian; Wong, Andrew B.; Yu, Yi; Lai, Minliang; Kornienko, Nikolay; Eaton, Samuel W.; Fu, Anthony; Bischak, Connor G.; Ma, Jie; Ding, Tina; Ginsberg, Naomi S.; Wang, Lin-Wang; Alivisatos, A. Paul; Yang, Peidong

2015-09-01

Organic-inorganic hybrid perovskites, which have proved to be promising semiconductor materials for photovoltaic applications, have been made into atomically thin two-dimensional (2D) sheets. We report the solution-phase growth of single- and few-unit-cell-thick single-crystalline 2D hybrid perovskites of (C4H9NH3)2PbBr4 with well-defined square shape and large size. In contrast to other 2D materials, the hybrid perovskite sheets exhibit an unusual structural relaxation, and this structural change leads to a band gap shift as compared to the bulk crystal. The high-quality 2D crystals exhibit efficient photoluminescence, and color tuning could be achieved by changing sheet thickness as well as composition via the synthesis of related materials.

Two and three dimensional grid generation by an algebraic homotopy procedure

NASA Technical Reports Server (NTRS)

Moitra, Anutosh

1990-01-01

An algebraic method for generating two- and three-dimensional grid systems for aerospace vehicles is presented. The method is based on algebraic procedures derived from homotopic relations for blending between inner and outer boundaries of any given configuration. Stable properties of homotopic maps have been exploited to provide near-orthogonality and specified constant spacing at the inner boundary. The method has been successfully applied to analytically generated blended wing-body configurations as well as discretely defined geometries such as the High-Speed Civil Transport Aircraft. Grid examples representative of the capabilities of the method are presented.

[Worker's Health Surveillance

PubMed

Machado

1997-01-01

This paper is part of a broader discussion on the need for more in-depth study of workers' health surveillance practices, which are most often developed empirically, without well-defined theoretical or technical foundations. The paper presents a concept of surveillance in workers' health as a fulcrum for actions in the relationship between the work process and health. It emphasizes the exposure-based perspective involved in the epidemiological approach. Risk situations and effects are placed in spatial and technological context. The model provides an interdisciplinary approach with a technological, social, and epidemiological basis in a three-dimensional structure. A matrix for planning actions in workers' health surveillance is also presented, focusing on the connections between effects, risks, territory, and activities.

Three-dimensional lithospheric electrical structure of Southern Granulite Terrain, India and its tectonic implications

NASA Astrophysics Data System (ADS)

Patro, Prasanta K.; Sarma, S. V. S.; Naganjaneyulu, K.

2014-01-01

crustal as well as the upper mantle lithospheric electrical structure of the Southern Granulite Terrain (SGT) is evaluated, using the magnetotelluric (MT) data from two parallel traverses: one is an 500 km long N-S trending traverse across SGT and another a 200 km long traverse. Data space Occam 3-D inversion was used to invert the MT data. The electrical characterization of lithospheric structure in SGT shows basically a highly resistive (several thousands of Ohm meters) upper crustal layer overlying a moderately resistive (a few hundred Ohm meters) lower crustal layer which in turn is underlain by the upper mantle lithosphere whose resistivity shows significant changes along the traverse. The highly resistive upper crustal layer is interspersed with four major conductive features with three of them cutting across the crustal column, bringing out a well-defined crustal block structure in SGT with individual highly resistive blocks showing correspondence to the geologically demarcated Salem, Madurai, and Trivandrum blocks. The 3-D model also brought out a well-defined major crustal conductor located in the northern half of the Madurai block. The electrical characteristics of this south dipping conductor and its close spatial correlation with two of the major structural elements, viz., Karur-Oddanchatram-Kodaikanal Shear Zone and Karur-Kamban-Painavu-Trichur Shear Zone, suggest that this conductive feature is closely linked to the subduction-collision tectonic processes in the SGT, and it is inferred that the Archean Dharwar craton/neoproterozoic SGT terrain boundary lies south of the Palghat-Cauvery shear zone. The results also showed that the Achankovil shear zone is characterized by a well-defined north dipping conductive feature. The resistive block adjoining this conductor on the southern side, representing the Trivandrum block, is shown to be downthrown along this north dipping crustal conductor relative to the Madurai block, suggesting a northward movement of Trivandrum block colliding against the Madurai block. The lithospheric upper mantle electrical structure of the SGT up to a depth of 100 km may be broadly divided into two distinctly different segments, viz., northern and southern segments. The northern lithospheric segment, over a major part, is characterized by a thick resistive upper mantle, while the southern one is characterized by a dominantly conductive medium suggesting a relatively thinned lithosphere in the southern segment.

Creating "hotels" for cells by electrospinning honeycomb-like polymeric structures.

PubMed

Liang, T; Mahalingam, S; Edirisinghe, M

2013-10-01

It is well established that three-dimensional honeycomb-like nanofibrous structures enhance cell activity. In this work, we report that electrospun polymer nanofibres self-assemble into three-dimensional honeycomb-like structures. The underlying mechanism is studied by varying the polymer solution concentration, collecting substrates and working distance. The polymer solution concentration has a significant effect on the size of the electrospun nanofibres. The collection substrate and working distance affect the electric field strength, the evaporation of solvent and the discharging of nanofibres and consequently these two had a significant influence on the self-assembly of nanofibres. © 2013.

Dimensionality reduction of collective motion by principal manifolds

NASA Astrophysics Data System (ADS)

Gajamannage, Kelum; Butail, Sachit; Porfiri, Maurizio; Bollt, Erik M.

2015-01-01

While the existence of low-dimensional embedding manifolds has been shown in patterns of collective motion, the current battery of nonlinear dimensionality reduction methods is not amenable to the analysis of such manifolds. This is mainly due to the necessary spectral decomposition step, which limits control over the mapping from the original high-dimensional space to the embedding space. Here, we propose an alternative approach that demands a two-dimensional embedding which topologically summarizes the high-dimensional data. In this sense, our approach is closely related to the construction of one-dimensional principal curves that minimize orthogonal error to data points subject to smoothness constraints. Specifically, we construct a two-dimensional principal manifold directly in the high-dimensional space using cubic smoothing splines, and define the embedding coordinates in terms of geodesic distances. Thus, the mapping from the high-dimensional data to the manifold is defined in terms of local coordinates. Through representative examples, we show that compared to existing nonlinear dimensionality reduction methods, the principal manifold retains the original structure even in noisy and sparse datasets. The principal manifold finding algorithm is applied to configurations obtained from a dynamical system of multiple agents simulating a complex maneuver called predator mobbing, and the resulting two-dimensional embedding is compared with that of a well-established nonlinear dimensionality reduction method.

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 model of the hydrostratigraphy and structure of the area in and around the U.S. Army-Camp Stanley Storage Activity Area, northern Bexar County, Texas

USGS Publications Warehouse

Pantea, Michael P.; Blome, Charles D.; Clark, Allan K.

2014-01-01

A three-dimensional model of the Camp Stanley Storage Activity area defines and illustrates the surface and subsurface hydrostratigraphic architecture of the military base and adjacent areas to the south and west using EarthVision software. The Camp Stanley model contains 11 hydrostratigraphic units in descending order: 1 model layer representing the Edwards aquifer; 1 model layer representing the upper Trinity aquifer; 6 model layers representing the informal hydrostratigraphic units that make up the upper part of the middle Trinity aquifer; and 3 model layers representing each, the Bexar, Cow Creek, and the top of the Hammett of the lower part of the middle Trinity aquifer. The Camp Stanley three-dimensional model includes 14 fault structures that generally trend northeast/southwest. The top of Hammett hydrostratigraphic unit was used to propagate and validate all fault structures and to confirm most of the drill-hole data. Differences between modeled and previously mapped surface geology reflect interpretation of fault relations at depth, fault relations to hydrostratigraphic contacts, and surface digital elevation model simplification to fit the scale of the model. In addition, changes based on recently obtained drill-hole data and field reconnaissance done during the construction of the model. The three-dimensional modeling process revealed previously undetected horst and graben structures in the northeastern and southern parts of the study area. This is atypical, as most faults in the area are en echelon that step down southeasterly to the Gulf Coast. The graben structures may increase the potential for controlling or altering local groundwater flow.

Enhanced Impact Resistance of Three-Dimensional-Printed Parts with Structured Filaments.

PubMed

Peng, Fang; Zhao, Zhiyang; Xia, Xuhui; Cakmak, Miko; Vogt, Bryan D

2018-05-09

Net-shape manufacture of customizable objects through three-dimensional (3D) printing offers tremendous promise for personalization to improve the fit, performance, and comfort associated with devices and tools used in our daily lives. However, the application of 3D printing in structural objects has been limited by their poor mechanical performance that manifests from the layer-by-layer process by which the part is produced. Here, this interfacial weakness is overcome using a structured, core-shell polymer filament where a polycarbonate (PC) core solidifies quickly to define the shape, whereas an olefin ionomer shell contains functionality (crystallinity and ionic) that strengthen the interface between the printed layers. This structured filament leads to improved dimensional accuracy and impact resistance in comparison to the individual components. The impact resistance from structured filaments containing 45 vol % shell can exceed 800 J/m. The origins of this improved impact resistance are probed using X-ray microcomputed tomography. Energy is dissipated by delamination of the shell from PC near the crack tip, whereas PC remains intact to provide stability to the part after impact. This structured filament provides tremendous improvements in the critical properties for manufacture and represents a major leap forward in the impact properties obtainable for 3D-printed parts.

HARPA: A versatile three-dimensional Hamiltonian ray-tracing program for acoustic waves in the atmosphere above irregular terrain

NASA Astrophysics Data System (ADS)

Jones, R. M.; Riley, J. P.; Georges, T. M.

1986-08-01

The modular FORTRAN 77 computer program traces the three-dimensional paths of acoustic rays through continuous model atmospheres by numerically integrating Hamilton's equations (a differential expression of Fermat's principle). The user specifies an atmospheric model by writing closed-form formulas for its three-dimensional wind and temperature (or sound speed) distribution, and by defining the height of the reflecting terrain vs. geographic latitude and longitude. Some general-purpose models are provided, or users can readily design their own. In addition to computing the geometry of each raypath, HARPA can calculate pulse travel time, phase time, Doppler shift (if the medium varies in time), absorption, and geometrical path length. The program prints a step-by-step account of a ray's progress. The 410-page documentation describes the ray-tracing equations and the structure of the program, and provides complete instructions, illustrated by a sample case.

The factorial validity of the Maslach Burnout Inventory-Student Survey in China.

PubMed

Hu, Qiao; Schaufeli, Wilmar B

2009-10-01

The dimensional structure of the Maslach Burnout Inventory-Student Survey (MBI-SS) was investigated using data collected from three samples of Chinese students in two high schools, a university, and a nursing school, respectively (total N = 1,499; 36% males, 64% females; M age 19.0 yr., SD = 1.3). Single group Confirmatory Factor Analyses corroborated the hypothesized three-factor model for the composite sample as well as for the three independent samples. Subsequent multigroup analyses revealed that the three-dimensional structure of the MBI-SS is partially invariant across three samples. It is concluded that the MBI-SS can be used to assess burnout in Chinese students.

Slip as the basic mechanism for formation of deformation relief structural elements

NASA Astrophysics Data System (ADS)

Lychagin, D. V.; Alfyorova, E. A.

2017-07-01

The experimental results of investigation of the nickel single crystal surface morphology after compression deformation are presented. The quasi-periodic character of the deformation profile, common for shear deformation of different types of relief structural elements, is found. It is demonstrated that the morphological manifestation of these structural elements is determined by local shear systems along octahedral planes. The regularities of the deformation structure in these regions defining the material extrusion and intrusion regions and the specific features of disorientation accumulation are established. If reorientation of local regions takes part in the relief element formation, along with octahedral slip, much stronger growth of the surface area is observed. The possibility of application of two-dimensional and three-dimensional surface roughness parameters for description of deformation relief is considered.

Programmable resistive-switch nanowire transistor logic circuits.

PubMed

Shim, Wooyoung; Yao, Jun; Lieber, Charles M

2014-09-10

Programmable logic arrays (PLA) constitute a promising architecture for developing increasingly complex and functional circuits through nanocomputers from nanoscale building blocks. Here we report a novel one-dimensional PLA element that incorporates resistive switch gate structures on a semiconductor nanowire and show that multiple elements can be integrated to realize functional PLAs. In our PLA element, the gate coupling to the nanowire transistor can be modulated by the memory state of the resistive switch to yield programmable active (transistor) or inactive (resistor) states within a well-defined logic window. Multiple PLA nanowire elements were integrated and programmed to yield a working 2-to-4 demultiplexer with long-term retention. The well-defined, controllable logic window and long-term retention of our new one-dimensional PLA element provide a promising route for building increasingly complex circuits with nanoscale building blocks.

Application of two-dimensional NMR spectroscopy and molecular dynamics simulations to the conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of Streptococcus group A.

PubMed

Kreis, U C; Varma, V; Pinto, B M

1995-06-01

This paper describes the use of a protocol for conformational analysis of oligosaccharide structures related to the cell-wall polysaccharide of Streptococcus group A. The polysaccharide features a branched structure with an L-rhamnopyranose (Rhap) backbone consisting of alternating alpha-(1-->2) and alpha-(1-->3) links and D-N-acetylglucosamine (GlcpNAc) residues beta-(1-->3)-connected to alternating rhamnose rings: [formula: see text] Oligomers consisting of three to six residues have been synthesized and nuclear magnetic resonance (NMR) assignments have been made. The protocol for conformational analysis of the solution structure of these oligosaccharides involves experimental and theoretical methods. Two-dimensional NMR spectroscopy methods (TOCSY, ROESY and NOESY) are utilized to obtain chemical shift data and proton-proton distances. These distances are used as constraints in 100 ps molecular dynamics simulations in water using QUANTA and CHARMm. In addition, the dynamics simulations are performed without constraints. ROE build-up curves are computed from the averaged structures of the molecular dynamics simulations using the CROSREL program and compared with the experimental curves. Thus, a refinement of the initial structure may be obtained. The alpha-(1-->2) and the beta-(1-->3) links are unambiguously defined by the observed ROE cross peaks between the A-B',A'-B and C-B,C'-B' residues, respectively. The branch-point of the trisaccharide CBA' is conformationally well-defined. Assignment of the conformation of the B-A linkage (alpha-(1-->3)) was problematic due to TOCSY relay, but could be solved by NOESY and T-ROESY techniques. A conformational model for the polysaccharide is proposed.

Coulomb double helical structure

NASA Astrophysics Data System (ADS)

Kamimura, Tetsuo; Ishihara, Osamu

2012-01-01

Structures of Coulomb clusters formed by dust particles in a plasma are studied by numerical simulation. Our study reveals the presence of various types of self-organized structures of a cluster confined in a prolate spheroidal electrostatic potential. The stable configurations depend on a prolateness parameter for the confining potential as well as on the number of dust particles in a cluster. One-dimensional string, two-dimensional zigzag structure and three-dimensional double helical structure are found as a result of the transition controlled by the prolateness parameter. The formation of stable double helical structures resulted from the transition associated with the instability of angular perturbations on double strings. Analytical perturbation study supports the findings of numerical simulations.

Excitation basis for (3+1)d topological phases

NASA Astrophysics Data System (ADS)

Delcamp, Clement

2017-12-01

We consider an exactly solvable model in 3+1 dimensions, based on a finite group, which is a natural generalization of Kitaev's quantum double model. The corresponding lattice Hamiltonian yields excitations located at torus-boundaries. By cutting open the three-torus, we obtain a manifold bounded by two tori which supports states satisfying a higher-dimensional version of Ocneanu's tube algebra. This defines an algebraic structure extending the Drinfel'd double. Its irreducible representations, labeled by two fluxes and one charge, characterize the torus-excitations. The tensor product of such representations is introduced in order to construct a basis for (3+1)d gauge models which relies upon the fusion of the defect excitations. This basis is defined on manifolds of the form Σ × S_1 , with Σ a two-dimensional Riemann surface. As such, our construction is closely related to dimensional reduction from (3+1)d to (2+1)d topological orders.

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.

Magnesiothermic conversion of the silica-mineralizing golden algae Mallomonas caudata and Synura petersenii to elemental silicon with high geometric precision

PubMed Central

Petrack, Janina; Jost, Steffen; Boenigk, Jens

2014-01-01

Summary Chrysophyceae, also known as golden algae, contain characteristic, three-dimensional biomineralized silica structures. Their chemical composition and microscopic structure was studied. By high-temperature conversion of the skeleton of Mallomonas caudata and Synura petersenii into elementary silicon by magnesium vapour, nanostructured defined replicates were produced which were clearly seen after removal of the formed magnesium oxide with acid. PMID:24991491

Honeycomb-like PLGA- b-PEG Structure Creation with T-Junction Microdroplets.

PubMed

Gultekinoglu, Merve; Jiang, Xinyue; Bayram, Cem; Ulubayram, Kezban; Edirisinghe, Mohan

2018-06-04

Amphiphilic block copolymers are widely used in science owing to their versatile properties. In this study, amphiphilic block copolymer poly(lactic- co-glycolic acid)- block-poly(ethylene glycol) (PLGA- b-PEG) was used to create microdroplets in a T-junction microfluidic device with a well-defined geometry. To compare interfacial characteristics of microdroplets, dichloromethane (DCM) and chloroform were used to prepare PLGA- b-PEG solution as an oil phase. In the T-junction device, water and oil phases were manipulated at variable flow rates from 50 to 300 μL/min by increments of 50 μL/min. Fabricated microdroplets were directly collected on a glass slide. After a drying period, porous two-dimensional and three-dimensional structures were obtained as honeycomb-like structure. Pore sizes were increased according to increased water/oil flow rate for both DCM and chloroform solutions. Also, it was shown that increasing polymer concentration decreased the pore size of honeycomb-like structures at a constant water/oil flow rate (50:50 μL/min). Additionally, PLGA- b-PEG nanoparticles were also obtained on the struts of honeycomb-like structures according to the water solubility, volatility, and viscosity properties of oil phases, by the aid of Marangoni flow. The resulting structures have a great potential to be used in biomedical applications, especially in drug delivery-related studies, with nanoparticle forming ability and cellular responses in different surface morphologies.

β-connectin studies by small-angle x-ray scattering and single-molecule force spectroscopy by atomic force microscopy

NASA Astrophysics Data System (ADS)

Marchetti, S.; Sbrana, F.; Toscano, A.; Fratini, E.; Carlà, M.; Vassalli, M.; Tiribilli, B.; Pacini, A.; Gambi, C. M. C.

2011-05-01

The three-dimensional structure and the mechanical properties of a β-connectin fragment from human cardiac muscle, belonging to the I band, from I27 to I34, were investigated by small-angle x-ray scattering (SAXS) and single-molecule force spectroscopy (SMFS). This molecule presents an entropic elasticity behavior, associated to globular domain unfolding, that has been widely studied in the last 10 years. In addition, atomic force microscopy based SMFS experiments suggest that this molecule has an additional elastic regime, for low forces, probably associated to tertiary structure remodeling. From a structural point of view, this behavior is a mark of the fact that the eight domains in the I27-I34 fragment are not independent and they organize in solution, assuming a well-defined three-dimensional structure. This hypothesis has been confirmed by SAXS scattering, both on a diluted and a concentrated sample. Two different models were used to fit the SAXS curves: one assuming a globular shape and one corresponding to an elongated conformation, both coupled with a Coulomb repulsion potential to take into account the protein-protein interaction. Due to the predominance of the structure factor, the effective shape of the protein in solution could not be clearly disclosed. By performing SMFS by atomic force microscopy, mechanical unfolding properties were investigated. Typical sawtooth profiles were obtained and the rupture force of each unfolding domain was estimated. By fitting a wormlike chain model to each peak of the sawtooth profile, the entropic elasticity of octamer was described.

Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation.

PubMed

Ozgur, Beytullah; Sayar, Mehmet

2016-10-06

Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.

Effects of pictorially-defined surfaces on visual search.

PubMed

Morita, Hiromi; Kumada, Takatsune

2003-08-01

Three experiments of visual search for a cube (for a square pillar in Experiment 3) with an odd conjunction of orientation of faces and color (a cube with a red top face and a green right face among cubes with a green top face and a red right face, for example) showed that the search is made more efficient by arranging cubes (or square pillars) so that their top faces lie in a horizontal surface defined by pictorial cues. This effect shows the same asymmetry as that of the surface defined by the disparity cue did [Perception and Psychophysics, 62 (2000) 540], implying that the effect is independent of the three-dimensional cue and the global surface structure influences the control of attention during the search.

A three-dimensional model of co-rotating streams in the solar wind. 2: Hydrodynamic streams

NASA Technical Reports Server (NTRS)

Pizzo, V. J.

1979-01-01

Theoretical aspects of corotating solar wind dynamics on a global scale are explored by means of numerical simulations executed with a nonlinear, inviscid, adiabatic, single-fluid, three-dimensional (3-D) hydrodynamic formulation. A simple, hypothetical 3-D stream structure is defined on a source surface located at 35 solar radius and carefully documents its evolution to 1 AU under the influence of solar rotation. By manipulating the structure of this prototype configuration at the source surface, it is possible to elucidate the factors most strongly affecting stream evolution: (1) the intrinsic correlations among density, temperature, and velocity existing near the source; (2) the amplitude of the stream; (3) the longitudinal breadth of the stream; (4) the latitudinal breadth of the stream; and (5) the heliographic latitude of the centroid of the stream.

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

Special Issue: NextGen Materials for 3D Printing.

PubMed

Chua, Chee Kai; Yeong, Wai Yee; An, Jia

2018-04-04

Only a handful of materials are well-established in three-dimensional (3D) printing and well-accepted in industrial manufacturing applications. However, recent advances in 3D printable materials have shown potential for enabling numerous novel applications in the future. This special issue, consisting of 2 reviews and 10 research articles, intends to explore the possible materials that could define next-generation 3D printing.

Assessment of variations in taxonomic diversity, forest structure, and aboveground biomass using remote sensing along an altitudinal gradient in tropical montane forest of Costa Rica

NASA Astrophysics Data System (ADS)

Robinson, C. M.; Saatchi, S. S.; Clark, D.; Fricker, G. A.; Wolf, J.; Gillespie, T. W.; Rovzar, C. M.; Andelman, S.

2012-12-01

This research sought to understand how alpha and beta diversity of plants vary and relate to the three-dimensional vegetation structure and aboveground biomass along environmental gradients in the tropical montane forests of Braulio Carrillo National Park in Costa Rica. There is growing evidence that ecosystem structure plays an important role in defining patterns of species diversity and along with abiotic factors (climate and edaphic) control the phenotypic and functional variations across landscapes. It is well documented that strong subdivisions at local and regional scales are found mainly on geologic or climate gradients. These general determinants of biodiversity are best demonstrated in regions with natural gradients such as tropical montane forests. Altitudinal gradients provide a landscape scale changes through variations in topography, climate, and edaphic conditions on which we tested several theoretical and biological hypotheses regarding drivers of biodiversity. The study was performed by using forest inventory and botanical data from nine 1-ha plots ranging from 100 m to 2800 m above sea level and remote sensing data from airborne lidar and radar sensors to quantify variations in forest structure. In this study we report on the effectiveness of relating patterns of tree taxonomic alpha diversity to three-dimensional structure of a tropical montane forest using lidar and radar observations of forest structure and biomass. We assessed alpha and beta diversity at the species, genus, and family levels utilizing datasets provided by the Terrestrial Ecology Assessment and Monitoring (TEAM) Network. Through the comparison to active remote sensing imagery, our results show that there is a strong relationship between forest 3D-structure, and alpha and beta diversity controlled by variations in abiotic factors along the altitudinal gradient. Using spatial analysis with the aid of remote sensing data, we find distinct patterns along the environmental gradients defining species turnover and changes in functional diversity. The study will provide novel approaches to use detailed spatial information from remote sensing data to study relations between functional and taxonomic dimensions of diversity.

Isothermal crystallization of poly(3-hydroxybutyrate) studied by terahertz two-dimensional correlation spectroscopy

NASA Astrophysics Data System (ADS)

Hoshina, Hiromichi; Ishii, Shinya; Morisawa, Yusuke; Sato, Harumi; Noda, Isao; Ozaki, Yukihiro; Otani, Chiko

2012-01-01

The isothermal crystallization of poly(3-hydroxybutylate) (PHB) was studied by monitoring the temporal evolution of terahertz absorption spectra in conjunction with spectral analysis using two-dimensional correlation spectroscopy. Correlation between the absorption peaks and the sequential order of the changes in spectral intensity extracted from synchronous and asynchronous plots indicated that crystallization of PHB at 90 °C is a two step process, in which C-H...O=C hydrogen bonds are initially formed before well-defined crystal structures are established.

Dynamical ion transfer between coupled Coulomb crystals in a double-well potential.

PubMed

Klumpp, Andrea; Zampetaki, Alexandra; Schmelcher, Peter

2017-09-01

We investigate the nonequilibrium dynamics of coupled Coulomb crystals of different sizes trapped in a double well potential. The dynamics is induced by an instantaneous quench of the potential barrier separating the two crystals. Due to the intra- and intercrystal Coulomb interactions and the asymmetric population of the potential wells, we observe a complex reordering of ions within the two crystals as well as ion transfer processes from one well to the other. The study and analysis of the latter processes constitutes the main focus of this work. In particular, we examine the dependence of the observed ion transfers on the quench amplitude performing an analysis for different crystalline configurations ranging from one-dimensional ion chains via two-dimensional zigzag chains and ring structures to three-dimensional spherical structures. Such an analysis provides us with the means to extract the general principles governing the ion transfer dynamics and we gain some insight on the structural disorder caused by the quench of the barrier height.

Building bridges between cellular and molecular structural biology.

PubMed

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

2017-07-06

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Three-body problem in d-dimensional space: Ground state, (quasi)-exact-solvability

NASA Astrophysics Data System (ADS)

Turbiner, Alexander V.; Miller, Willard; Escobar-Ruiz, M. A.

2018-02-01

As a straightforward generalization and extension of our previous paper [A. V. Turbiner et al., "Three-body problem in 3D space: Ground state, (quasi)-exact-solvability," J. Phys. A: Math. Theor. 50, 215201 (2017)], we study the aspects of the quantum and classical dynamics of a 3-body system with equal masses, each body with d degrees of freedom, with interaction depending only on mutual (relative) distances. The study is restricted to solutions in the space of relative motion which are functions of mutual (relative) distances only. It is shown that the ground state (and some other states) in the quantum case and the planar trajectories (which are in the interaction plane) in the classical case are of this type. The quantum (and classical) Hamiltonian for which these states are eigenfunctions is derived. It corresponds to a three-dimensional quantum particle moving in a curved space with special d-dimension-independent metric in a certain d-dependent singular potential, while at d = 1, it elegantly degenerates to a two-dimensional particle moving in flat space. It admits a description in terms of pure geometrical characteristics of the interaction triangle which is defined by the three relative distances. The kinetic energy of the system is d-independent; it has a hidden sl(4, R) Lie (Poisson) algebra structure, alternatively, the hidden algebra h(3) typical for the H3 Calogero model as in the d = 3 case. We find an exactly solvable three-body S3-permutationally invariant, generalized harmonic oscillator-type potential as well as a quasi-exactly solvable three-body sextic polynomial type potential with singular terms. For both models, an extra first order integral exists. For d = 1, the whole family of 3-body (two-dimensional) Calogero-Moser-Sutherland systems as well as the Tremblay-Turbiner-Winternitz model is reproduced. It is shown that a straightforward generalization of the 3-body (rational) Calogero model to d > 1 leads to two primitive quasi-exactly solvable problems. The extension to the case of non-equal masses is straightforward and is briefly discussed.

Quantification of the Spatial Organization of the Nuclear Lamina as a Tool for Cell Classification

PubMed Central

Righolt, Christiaan H.; Zatreanu, Diana A.; Raz, Vered

2013-01-01

The nuclear lamina is the structural scaffold of the nuclear envelope that plays multiple regulatory roles in chromatin organization and gene expression as well as a structural role in nuclear stability. The lamina proteins, also referred to as lamins, determine nuclear lamina organization and define the nuclear shape and the structural integrity of the cell nucleus. In addition, lamins are connected with both nuclear and cytoplasmic structures forming a dynamic cellular structure whose shape changes upon external and internal signals. When bound to the nuclear lamina, the lamins are mobile, have an impact on the nuclear envelop structure, and may induce changes in their regulatory functions. Changes in the nuclear lamina shape cause changes in cellular functions. A quantitative description of these structural changes could provide an unbiased description of changes in cellular function. In this review, we describe how changes in the nuclear lamina can be measured from three-dimensional images of lamins at the nuclear envelope, and we discuss how structural changes of the nuclear lamina can be used for cell classification. PMID:27335676

Quantification of the Spatial Organization of the Nuclear Lamina as a Tool for Cell Classification.

PubMed

Righolt, Christiaan H; Zatreanu, Diana A; Raz, Vered

2013-01-01

The nuclear lamina is the structural scaffold of the nuclear envelope that plays multiple regulatory roles in chromatin organization and gene expression as well as a structural role in nuclear stability. The lamina proteins, also referred to as lamins, determine nuclear lamina organization and define the nuclear shape and the structural integrity of the cell nucleus. In addition, lamins are connected with both nuclear and cytoplasmic structures forming a dynamic cellular structure whose shape changes upon external and internal signals. When bound to the nuclear lamina, the lamins are mobile, have an impact on the nuclear envelop structure, and may induce changes in their regulatory functions. Changes in the nuclear lamina shape cause changes in cellular functions. A quantitative description of these structural changes could provide an unbiased description of changes in cellular function. In this review, we describe how changes in the nuclear lamina can be measured from three-dimensional images of lamins at the nuclear envelope, and we discuss how structural changes of the nuclear lamina can be used for cell classification.

Geometric phase of mixed states for three-level open systems

NASA Astrophysics Data System (ADS)

Jiang, Yanyan; Ji, Y. H.; Xu, Hualan; Hu, Li-Yun; Wang, Z. S.; Chen, Z. Q.; Guo, L. P.

2010-12-01

Geometric phase of mixed state for three-level open system is defined by establishing in connecting density matrix with nonunit vector ray in a three-dimensional complex Hilbert space. Because the geometric phase depends only on the smooth curve on this space, it is formulated entirely in terms of geometric structures. Under the limiting of pure state, our approach is in agreement with the Berry phase, Pantcharatnam phase, and Aharonov and Anandan phase. We find that, furthermore, the Berry phase of mixed state correlated to population inversions of three-level open system.

Velocity distribution of fragments of catastrophic impacts

NASA Technical Reports Server (NTRS)

Takagi, Yasuhiko; Kato, Manabu; Mizutani, Hitoshi

1992-01-01

Three dimensional velocities of fragments produced by laboratory impact experiments were measured for basalts and pyrophyllites. The velocity distribution of fragments obtained shows that the velocity range of the major fragments is rather narrow, at most within a factor of 3 and that no clear dependence of velocity on the fragment mass is observed. The NonDimensional Impact Stress (NDIS) defined by Mizutani et al. (1990) is found to be an appropriate scaling parameter to describe the overall fragment velocity as well as the antipodal velocity.

Self-organization of a self-assembled supramolecular rectangle, square, and three-dimensional cage on Au111 surfaces.

PubMed

Yuan, Qun-Hui; Wan, Li-Jun; Jude, Hershel; Stang, Peter J

2005-11-23

The structure and conformation of three self-assembled supramolecular species, a rectangle, a square, and a three-dimensional cage, on Au111 surfaces were investigated by scanning tunneling microscopy. These supramolecular assemblies adsorb on Au111 surfaces and self-organize to form highly ordered adlayers with distinct conformations that are consistent with their chemical structures. The faces of the supramolecular rectangle and square lie flat on the surface, preserving their rectangle and square conformations, respectively. The three-dimensional cage also forms well-ordered adlayers on the gold surface, forming regular molecular rows of assemblies. When the rectangle and cage were mixed together, the assemblies separated into individual domains, and no mixed adlayers were observed. These results provide direct evidence of the noncrystalline solid-state structures of these assemblies and information about how they self-organize on Au111 surfaces, which is of importance in the potential manufacturing of functional nanostructures and devices.

Directed assembly of bio-inspired hierarchical materials with controlled nanofibrillar architectures

NASA Astrophysics Data System (ADS)

Tseng, Peter; Napier, Bradley; Zhao, Siwei; Mitropoulos, Alexander N.; Applegate, Matthew B.; Marelli, Benedetto; Kaplan, David L.; Omenetto, Fiorenzo G.

2017-05-01

In natural systems, directed self-assembly of structural proteins produces complex, hierarchical materials that exhibit a unique combination of mechanical, chemical and transport properties. This controlled process covers dimensions ranging from the nano- to the macroscale. Such materials are desirable to synthesize integrated and adaptive materials and systems. We describe a bio-inspired process to generate hierarchically defined structures with multiscale morphology by using regenerated silk fibroin. The combination of protein self-assembly and microscale mechanical constraints is used to form oriented, porous nanofibrillar networks within predesigned macroscopic structures. This approach allows us to predefine the mechanical and physical properties of these materials, achieved by the definition of gradients in nano- to macroscale order. We fabricate centimetre-scale material geometries including anchors, cables, lattices and webs, as well as functional materials with structure-dependent strength and anisotropic thermal transport. Finally, multiple three-dimensional geometries and doped nanofibrillar constructs are presented to illustrate the facile integration of synthetic and natural additives to form functional, interactive, hierarchical networks.

A system of three-dimensional complex variables

NASA Technical Reports Server (NTRS)

Martin, E. Dale

1986-01-01

Some results of a new theory of multidimensional complex variables are reported, including analytic functions of a three-dimensional (3-D) complex variable. Three-dimensional complex numbers are defined, including vector properties and rules of multiplication. The necessary conditions for a function of a 3-D variable to be analytic are given and shown to be analogous to the 2-D Cauchy-Riemann equations. A simple example also demonstrates the analogy between the newly defined 3-D complex velocity and 3-D complex potential and the corresponding ordinary complex velocity and complex potential in two dimensions.

Development of an unstructured solution adaptive method for the quasi-three-dimensional Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Yi-Tsann

1993-01-01

A general solution adaptive scheme-based on a remeshing technique is developed for solving the two-dimensional and quasi-three-dimensional Euler and Favre-averaged Navier-Stokes equations. The numerical scheme is formulated on an unstructured triangular mesh utilizing an edge-based pointer system which defines the edge connectivity of the mesh structure. Jameson's four-stage hybrid Runge-Kutta scheme is used to march the solution in time. The convergence rate is enhanced through the use of local time stepping and implicit residual averaging. As the solution evolves, the mesh is regenerated adaptively using flow field information. Mesh adaptation parameters are evaluated such that an estimated local numerical error is equally distributed over the whole domain. For inviscid flows, the present approach generates a complete unstructured triangular mesh using the advancing front method. For turbulent flows, the approach combines a local highly stretched structured triangular mesh in the boundary layer region with an unstructured mesh in the remaining regions to efficiently resolve the important flow features. One-equation and two-equation turbulence models are incorporated into the present unstructured approach. Results are presented for a wide range of flow problems including two-dimensional multi-element airfoils, two-dimensional cascades, and quasi-three-dimensional cascades. This approach is shown to gain flow resolution in the refined regions while achieving a great reduction in the computational effort and storage requirements since solution points are not wasted in regions where they are not required.

Development of an unstructured solution adaptive method for the quasi-three-dimensional Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Yi-Tsann; Usab, William J., Jr.

1993-01-01

A general solution adaptive scheme based on a remeshing technique is developed for solving the two-dimensional and quasi-three-dimensional Euler and Favre-averaged Navier-Stokes equations. The numerical scheme is formulated on an unstructured triangular mesh utilizing an edge-based pointer system which defines the edge connectivity of the mesh structure. Jameson's four-stage hybrid Runge-Kutta scheme is used to march the solution in time. The convergence rate is enhanced through the use of local time stepping and implicit residual averaging. As the solution evolves, the mesh is regenerated adaptively using flow field information. Mesh adaptation parameters are evaluated such that an estimated local numerical error is equally distributed over the whole domain. For inviscid flows, the present approach generates a complete unstructured triangular mesh using the advancing front method. For turbulent flows, the approach combines a local highly stretched structured triangular mesh in the boundary layer region with an unstructured mesh in the remaining regions to efficiently resolve the important flow features. One-equation and two-equation turbulence models are incorporated into the present unstructured approach. Results are presented for a wide range of flow problems including two-dimensional multi-element airfoils, two-dimensional cascades, and quasi-three-dimensional cascades. This approach is shown to gain flow resolution in the refined regions while achieving a great reduction in the computational effort and storage requirements since solution points are not wasted in regions where they are not required.

Atomically thin two-dimensional organic-inorganic hybrid perovskites.

PubMed

Dou, Letian; Wong, Andrew B; Yu, Yi; Lai, Minliang; Kornienko, Nikolay; Eaton, Samuel W; Fu, Anthony; Bischak, Connor G; Ma, Jie; Ding, Tina; Ginsberg, Naomi S; Wang, Lin-Wang; Alivisatos, A Paul; Yang, Peidong

2015-09-25

Organic-inorganic hybrid perovskites, which have proved to be promising semiconductor materials for photovoltaic applications, have been made into atomically thin two-dimensional (2D) sheets. We report the solution-phase growth of single- and few-unit-cell-thick single-crystalline 2D hybrid perovskites of (C4H9NH3)2PbBr4 with well-defined square shape and large size. In contrast to other 2D materials, the hybrid perovskite sheets exhibit an unusual structural relaxation, and this structural change leads to a band gap shift as compared to the bulk crystal. The high-quality 2D crystals exhibit efficient photoluminescence, and color tuning could be achieved by changing sheet thickness as well as composition via the synthesis of related materials. Copyright © 2015, American Association for the Advancement of Science.

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

PubMed

Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

2016-11-01

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs. © 2016 Federation of European Biochemical Societies.

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.

Characterization of Viscoelastic Materials Through an Active Mixer by Direct-Ink Writing

NASA Astrophysics Data System (ADS)

Drake, Eric

The goal of this thesis is two-fold: First, to determine mixing effectiveness of an active mixer attachment to a three-dimensional (3D) printer by characterizing actively-mixed, three-dimensionally printed silicone elastomers. Second, to understand mechanical properties of a printed lattice structure with varying geometry and composition. Ober et al defines mixing effectiveness as a measureable quantity characterized by two key variables: (i) a dimensionless impeller parameter (O ) that depends on mixer geometry as well as Peclet number (Pe) and (ii) a coefficient of variation (COV) that describes the mixer effectiveness based upon image intensity. The first objective utilizes tungsten tracer particles distributed throughout a batch of Dow Corning SE1700 (two parts silicone) - ink "A". Ink "B" is made from pure SE1700. Using the in-site active mixer, both ink "A" and "B" coalesce to form a hybrid ink just before extrusion. Two samples of varying mixer speeds and composition ratios are printed and analyzed by microcomputed tomography (MicroCT). A continuous stirred tank reactor (CSTR) model is applied to better understand mixing behavior. Results are then compared with computer models to verify the hypothesis. Data suggests good mixing for the sample with higher impeller speed. A Radial Distrubtion Function (RDF) macro is used to provide further qualitative analysis of mixing efficiency. The second objective of this thesis utilized three-dimensionally printed samples of varying geometry and composition to ascertain mechanical properties. Samples were printed using SE1700 provided by Lawrence Livermore National Laboratory with a face-centered tetragonal (FCT) structure. Hardness testing is conducted using a Shore OO durometer guided by a computer-controlled, three-axis translation stage to provide precise movements. Data is collected across an 'x-y' plane of the specimen. To explain the data, a simply supported beam model is applied to a single unit cell which yields basic structural behavior per cell. Characterizing the sample as a whole requires a more rigorous approach and non-trivial complexities due to varying geometries and compositions exist. The data demonstrates a uniform change in hardness as a function of position. Additionally, the data indicates periodicities in the lattice structure.

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell

DOE PAGES

Yeager, Ashley N.; Weber, Peter K.; Kraft, Mary L.

2016-01-08

Metabolic stable isotope incorporation and secondary ion mass spectrometry(SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the 18O-cholesterol and 15N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of 18O-cholesterol and 15N-sphingolipid enrichment that seem to be separate subcellular compartments. Furthermore, the low levels of nitrogen-containing secondary ions detected at the 18O-enriched regions suggest that these 18O-cholesterol-rich structures may be lipiddroplets, which have a core consisting of cholesterol esters and triacylglycerides.

Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell

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

Yeager, Ashley N.; Weber, Peter K.; Kraft, Mary L.

Metabolic stable isotope incorporation and secondary ion mass spectrometry(SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the 18O-cholesterol and 15N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of 18O-cholesterol and 15N-sphingolipid enrichment that seem to be separate subcellular compartments. Furthermore, the low levels of nitrogen-containing secondary ions detected at the 18O-enriched regions suggest that these 18O-cholesterol-rich structures may be lipiddroplets, which have a core consisting of cholesterol esters and triacylglycerides.

An efficient three-dimensional Poisson solver for SIMD high-performance-computing architectures

NASA Technical Reports Server (NTRS)

Cohl, H.

1994-01-01

We present an algorithm that solves the three-dimensional Poisson equation on a cylindrical grid. The technique uses a finite-difference scheme with operator splitting. This splitting maps the banded structure of the operator matrix into a two-dimensional set of tridiagonal matrices, which are then solved in parallel. Our algorithm couples FFT techniques with the well-known ADI (Alternating Direction Implicit) method for solving Elliptic PDE's, and the implementation is extremely well suited for a massively parallel environment like the SIMD architecture of the MasPar MP-1. Due to the highly recursive nature of our problem, we believe that our method is highly efficient, as it avoids excessive interprocessor communication.

Brief report: Assessing dispositional optimism in adolescence--factor structure and concurrent validity of the Life Orientation Test--Revised.

PubMed

Monzani, Dario; Steca, Patrizia; Greco, Andrea

2014-02-01

Dispositional optimism is an individual difference promoting psychosocial adjustment and well-being during adolescence. Dispositional optimism was originally defined as a one-dimensional construct; however, empirical evidence suggests two correlated factors in the Life Orientation Test - Revised (LOT-R). The main aim of the study was to evaluate the dimensionality of the LOT-R. This study is the first attempt to identify the best factor structure, comparing congeneric, two correlated-factor, and two orthogonal-factor models in a sample of adolescents. Concurrent validity was also assessed. The results demonstrated the superior fit of the two orthogonal-factor model thus reconciling the one-dimensional definition of dispositional optimism with the bi-dimensionality of the LOT-R. Moreover, the results of correlational analyses proved the concurrent validity of this self-report measure: optimism is moderately related to indices of psychosocial adjustment and well-being. Thus, the LOT-R is a useful, valid, and reliable self-report measure to properly assess optimism in adolescence. Copyright © 2013 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

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.

Sustainable use of marine resources: cultivation of sponges.

PubMed

Brümmer, F; Nickel, M

2003-01-01

Among all metazoan phyla, sponges are known to produce the largest number of bioactive compounds, some of them metabolites with human therapeutic value. Therefore, an increasing interest in basic cell biology research up to biochemical engineering can be observed aiming at the production of sponge metabolites under completely controlled conditions. One major obstacle is the limited availability of larger quantities of defined sponge material--the so-called supply problem. In this chapter, different approaches used so far for producing sponge biomass by in situ aquaculture as well as some significant progress in the maintenance of sponges in aquaria are reviewed. These approaches are mainly based on old methods for producing commercial bath sponges as well as on experience in maintaining sponges in public aquaria and on the usage of artificial substrates for a natural-like colonization structure. In recent years, great efforts have been made to set up in vitro culture systems for the cultivation of sponge cells. One of the major advantages of cell cultures is the possibility to control and manipulate the cultivation conditions depending on the sponge species and the target metabolite. Up to now, monolayer cultures of dissociated sponge cells have been shown in a few cases to produce the desired product. However, to date, no continuously growing sponge cell line has been established. Organotypic culture systems, which maintain or mimic the natural tissue structure, have been developed in recent years and demonstrate a promising way towards the biotechnology of sponges. Successful attempts to produce sponge metabolites using the three-dimensional growing primmorphs are given. The use of sponge fragments, another three-dimensional approach, has reappeared and has also been successfully used as an in vitro approach as well as for the biotechnological production of boreal sponge tissue.

Induced formation and maturation of acetylcholine receptor clusters in a defined 3D bio-artificial muscle.

PubMed

Wang, Lin; Shansky, Janet; Vandenburgh, Herman

2013-12-01

Dysfunction of the neuromuscular junction is involved in a wide range of muscular diseases. The development of neuromuscular junction through which skeletal muscle is innervated requires the functional modulation of acetylcholine receptor (AchR) clustering on myofibers. However, studies on AchR clustering in vitro are mostly done on monolayer muscle cell culture, which lacks a three-dimensional (3D) structure, a prominent limitation of the two-dimensional (2D) system. To enable a better understanding on the structure-function correlation underlying skeletal muscle innervation, a muscle system with a well-defined geometry mimicking the in vivo muscular setting is needed. Here, we report a 3D bio-artificial muscle (BAM) bioengineered from green fluorescent protein-transduced C3H murine myoblasts as a novel in vitro tissue-based model for muscle innervation studies. Our cell biological and molecular analysis showed that this BAM is structurally similar to in vivo muscle tissue and can reach the perinatal differentiation stage, higher than does 2D culture. Effective clustering and morphological maturation of AchRs on BAMs induced by agrin and laminin indicate the functional activity and plasticity of this BAM system toward innervation. Taken together, our results show that the BAM provides a favorable 3D environment that at least partially recapitulates real physiological skeletal muscle with regard to innervation. With a convenience of fabrication and manipulation, this 3D in vitro system offers a novel model for studying mechanisms underlying skeletal muscle innervation and testing therapeutic strategies for relevant nervous and muscular diseases.

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.

Microscopy and Chemical Inversing Techniques to Determine the Photonic Crystal Structure of Iridescent Beetle Scales in the Cerambycidae Family

NASA Astrophysics Data System (ADS)

Richey, Lauren; Gardner, John; Standing, Michael; Jorgensen, Matthew; Bartl, Michael

2010-10-01

Photonic crystals (PCs) are periodic structures that manipulate electromagnetic waves by defining allowed and forbidden frequency bands known as photonic band gaps. Despite production of PC structures operating at infrared wavelengths, visible counterparts are difficult to fabricate because periodicities must satisfy the diffraction criteria. As part of an ongoing search for naturally occurring PCs [1], a three-dimensional array of nanoscopic spheres in the iridescent scales of the Cerambycidae insects A. elegans and G. celestis has been found. Such arrays are similar to opal gemstones and self-assembled colloidal spheres which can be chemically inverted to create a lattice-like PC. Through a chemical replication process [2], scanning electron microscopy analysis, sequential focused ion beam slicing and three-dimensional modeling, we analyzed the structural arrangement of the nanoscopic spheres. The study of naturally occurring structures and their inversing techniques into PCs allows for diversity in optical PC fabrication. [1] J.W. Galusha et al., Phys. Rev. E 77 (2008) 050904. [2] J.W. Galusha et al., J. Mater. Chem. 20 (2010) 1277.

Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders.

PubMed

Yun, Yifeng; Zou, Xiaodong; Hovmöller, Sven; Wan, Wei

2015-03-01

Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

Topics in Two-Dimensional Quantum Gravity and Chern-Simons Gauge Theories

NASA Astrophysics Data System (ADS)

Zemba, Guillermo Raul

A series of studies in two and three dimensional theories is presented. The two dimensional problems are considered in the framework of String Theory. The first one determines the region of integration in the space of inequivalent tori of a tadpole diagram in Closed String Field Theory, using the naive Witten three-string vertex. It is shown that every surface is counted an infinite number of times and the source of this behavior is identified. The second study analyzes the behavior of the discrete matrix model of two dimensional gravity without matter using a mathematically well-defined construction, confirming several conjectures and partial results from the literature. The studies in three dimensions are based on Chern Simons pure gauge theory. The first one deals with the projection of the theory onto a two-dimensional surface of constant time, whereas the second analyzes the large N behavior of the SU(N) theory and makes evident a duality symmetry between the only two parameters of the theory. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253 -1690.).

Automated aberration correction of arbitrary laser modes in high numerical aperture systems.

PubMed

Hering, Julian; Waller, Erik H; Von Freymann, Georg

2016-12-12

Controlling the point-spread-function in three-dimensional laser lithography is crucial for fabricating structures with highest definition and resolution. In contrast to microscopy, aberrations have to be physically corrected prior to writing, to create well defined doughnut modes, bottlebeams or multi foci modes. We report on a modified Gerchberg-Saxton algorithm for spatial-light-modulator based automated aberration compensation to optimize arbitrary laser-modes in a high numerical aperture system. Using circularly polarized light for the measurement and first-guess initial conditions for amplitude and phase of the pupil function our scalar approach outperforms recent algorithms with vectorial corrections. Besides laser lithography also applications like optical tweezers and microscopy might benefit from the method presented.

Synthesis of spiro quasi[1]catenanes and quasi[1]rotaxanes via a templated backfolding strategy

PubMed Central

Steemers, Luuk; Wanner, Martin J.; Lutz, Martin; Hiemstra, Henk; van Maarseveen, Jan H.

2017-01-01

Due to their well-defined three-dimensional geometry, spiro compounds are widely utilized in drug research. From the central tetrahedral carbon atom, besides the regular structure, an inverted spiro connectivity may be envisioned. Here we disclose the synthesis of this molecule class that we have coined quasi[1]catenanes. Next to their fascinating and aesthetic shape, the higher compactness as compared to regular spiro bicycles is noteworthy. To enable synthetic access to compact entangled multimacrocyclic molecules, we have developed a new strategy. The key element is a template, which is covalently connected to the linear precursors, and spatially directs the sterically congested backfolding macrocyclizations that are required to give quasi[1]catenanes. Similarly, quasi[1]rotaxanes are made. PMID:28541349

Phosphoinositide 3-kinase (PI3K(p110alpha)) directly regulates key components of the Z-disc and cardiac structure.

PubMed

Waardenberg, Ashley J; Bernardo, Bianca C; Ng, Dominic C H; Shepherd, Peter R; Cemerlang, Nelly; Sbroggiò, Mauro; Wells, Christine A; Dalrymple, Brian P; Brancaccio, Mara; Lin, Ruby C Y; McMullen, Julie R

2011-09-02

Maintenance of cardiac structure and Z-disc signaling are key factors responsible for protecting the heart in a setting of stress, but how these processes are regulated is not well defined. We recently demonstrated that PI3K(p110α) protects the heart against myocardial infarction. The aim of this study was to determine whether PI3K(p110α) directly regulates components of the Z-disc and cardiac structure. To address this question, a unique three-dimensional virtual muscle model was applied to gene expression data from transgenic mice with increased or decreased PI3K(p110α) activity under basal conditions (sham) and in a setting of myocardial infarction to display the location of structural proteins. Key findings from this analysis were then validated experimentally. The three-dimensional virtual muscle model visually highlighted reciprocally regulated transcripts associated with PI3K activation that encoded key components of the Z-disc and costamere, including melusin. Studies were performed to assess whether PI3K and melusin interact in the heart. Here, we identify a novel melusin-PI3K interaction that generates lipid kinase activity. The direct impact of PI3K(p110α) on myocyte structure was assessed by treating neonatal rat ventricular myocytes with PI3K(p110α) inhibitors and examining the myofiber morphology of hearts from PI3K transgenic mice. Results demonstrate that PI3K is critical for myofiber maturation and Z-disc alignment. In summary, PI3K regulates the expression of genes essential for cardiac structure and Z-disc signaling, interacts with melusin, and is critical for Z-disc alignment.

Phosphoinositide 3-Kinase (PI3K(p110α)) Directly Regulates Key Components of the Z-disc and Cardiac Structure*

PubMed Central

Waardenberg, Ashley J.; Bernardo, Bianca C.; Ng, Dominic C. H.; Shepherd, Peter R.; Cemerlang, Nelly; Sbroggiò, Mauro; Wells, Christine A.; Dalrymple, Brian P.; Brancaccio, Mara; Lin, Ruby C. Y.; McMullen, Julie R.

2011-01-01

Maintenance of cardiac structure and Z-disc signaling are key factors responsible for protecting the heart in a setting of stress, but how these processes are regulated is not well defined. We recently demonstrated that PI3K(p110α) protects the heart against myocardial infarction. The aim of this study was to determine whether PI3K(p110α) directly regulates components of the Z-disc and cardiac structure. To address this question, a unique three-dimensional virtual muscle model was applied to gene expression data from transgenic mice with increased or decreased PI3K(p110α) activity under basal conditions (sham) and in a setting of myocardial infarction to display the location of structural proteins. Key findings from this analysis were then validated experimentally. The three-dimensional virtual muscle model visually highlighted reciprocally regulated transcripts associated with PI3K activation that encoded key components of the Z-disc and costamere, including melusin. Studies were performed to assess whether PI3K and melusin interact in the heart. Here, we identify a novel melusin-PI3K interaction that generates lipid kinase activity. The direct impact of PI3K(p110α) on myocyte structure was assessed by treating neonatal rat ventricular myocytes with PI3K(p110α) inhibitors and examining the myofiber morphology of hearts from PI3K transgenic mice. Results demonstrate that PI3K is critical for myofiber maturation and Z-disc alignment. In summary, PI3K regulates the expression of genes essential for cardiac structure and Z-disc signaling, interacts with melusin, and is critical for Z-disc alignment. PMID:21757757

The Restorative Role of Apology in Resolving Medical Disputes: Lessons From Chinese Legal Culture.

PubMed

Lin, Nuannuan

2015-12-01

This article is the first exploration of the Chinese notion of apology from a comparative legal perspective. By reviewing the significance of apology in the context of Chinese culture, the article presents a three-dimensional structure of apology that, in contrast to the understanding the research community now has, defines acknowledgement of fault, admission of responsibility, and offer of reparation as three essential elements of an apology. It is the combination of these three elements that enables apology to serve as a form of reparation. The article further places the three-dimensional apology in the context of the Chinese concept of "the relations of humanity," arguing that an apology accompanying admission of fault and responsibility may help to restore the harmony of relations and, by so doing, resolve medical disputes positively.

Special Issue: NextGen Materials for 3D Printing

PubMed Central

Yeong, Wai Yee

2018-01-01

Only a handful of materials are well-established in three-dimensional (3D) printing and well-accepted in industrial manufacturing applications. However, recent advances in 3D printable materials have shown potential for enabling numerous novel applications in the future. This special issue, consisting of 2 reviews and 10 research articles, intends to explore the possible materials that could define next-generation 3D printing. PMID:29617311

A simple method for in vivo measurement of implant rod three-dimensional geometry during scoliosis surgery.

PubMed

Salmingo, Remel A; Tadano, Shigeru; Fujisaki, Kazuhiro; Abe, Yuichiro; Ito, Manabu

2012-05-01

Scoliosis is defined as a spinal pathology characterized as a three-dimensional deformity of the spine combined with vertebral rotation. Treatment for severe scoliosis is achieved when the scoliotic spine is surgically corrected and fixed using implanted rods and screws. Several studies performed biomechanical modeling and corrective forces measurements of scoliosis correction. These studies were able to predict the clinical outcome and measured the corrective forces acting on screws, however, they were not able to measure the intraoperative three-dimensional geometry of the spinal rod. In effect, the results of biomechanical modeling might not be so realistic and the corrective forces during the surgical correction procedure were intra-operatively difficult to measure. Projective geometry has been shown to be successful in the reconstruction of a three-dimensional structure using a series of images obtained from different views. In this study, we propose a new method to measure the three-dimensional geometry of an implant rod using two cameras. The reconstruction method requires only a few parameters, the included angle θ between the two cameras, the actual length of the rod in mm, and the location of points for curve fitting. The implant rod utilized in spine surgery was used to evaluate the accuracy of the current method. The three-dimensional geometry of the rod was measured from the image obtained by a scanner and compared to the proposed method using two cameras. The mean error in the reconstruction measurements ranged from 0.32 to 0.45 mm. The method presented here demonstrated the possibility of intra-operatively measuring the three-dimensional geometry of spinal rod. The proposed method could be used in surgical procedures to better understand the biomechanics of scoliosis correction through real-time measurement of three-dimensional implant rod geometry in vivo.

Cost-effective MEMS piezoresistive cantilever-based sensor fabrication for gait movement analysis

NASA Astrophysics Data System (ADS)

Saadon, Salem; Anuar, A. F. M.; Wahab, Yufridin

2017-03-01

The conventional photolithography of crystalline silicon technique is limited to two-dimensional and structure scaling. It's also requiring a lot of time and chemical involves for the whole process. These problems can be overcome by using laser micromachining technique, that capable to produce three-dimensional structure and simultaneously avoiding the photo mask needs. In this paper, we reported on the RapidX-250 Excimer laser micromachining with 248 nm KrF to create in-time mask design and assisting in the fabrication process of piezo-resistive micro cantilever structures. Firstly, laser micromachining parameters have been investigated in order to fabricate the acceleration sensor to analyzing human gait movement. Preliminary result shows that the fabricated sensor able to define the movement difference of human motion regarding the electrical characteristic of piezo-resistor.

Three-dimensional spectral-spatial EPR imaging of free radicals in the heart: a technique for imaging tissue metabolism and oxygenation.

PubMed Central

Kuppusamy, P; Chzhan, M; Vij, K; Shteynbuk, M; Lefer, D J; Giannella, E; Zweier, J L

1994-01-01

It has been hypothesized that free radical metabolism and oxygenation in living organs and tissues such as the heart may vary over the spatially defined tissue structure. In an effort to study these spatially defined differences, we have developed electron paramagnetic resonance imaging instrumentation enabling the performance of three-dimensional spectral-spatial images of free radicals infused into the heart and large vessels. Using this instrumentation, high-quality three-dimensional spectral-spatial images of isolated perfused rat hearts and rabbit aortas are obtained. In the isolated aorta, it is shown that spatially and spectrally accurate images of the vessel lumen and wall could be obtained in this living vascular tissue. In the isolated rat heart, imaging experiments were performed to determine the kinetics of radical clearance at different spatial locations within the heart during myocardial ischemia. The kinetic data show the existence of regional and transmural differences in myocardial free radical clearance. It is further demonstrated that EPR imaging can be used to noninvasively measure spatially localized oxygen concentrations in the heart. Thus, the technique of spectral-spatial EPR imaging is shown to be a powerful tool in providing spatial information regarding the free radical distribution, metabolism, and tissue oxygenation in living biological organs and tissues. Images PMID:8159757

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

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.

Iterative optimizing quantization method for reconstructing three-dimensional images from a limited number of views

DOEpatents

Lee, Heung-Rae

1997-01-01

A three-dimensional image reconstruction method comprises treating the object of interest as a group of elements with a size that is determined by the resolution of the projection data, e.g., as determined by the size of each pixel. One of the projections is used as a reference projection. A fictitious object is arbitrarily defined that is constrained by such reference projection. The method modifies the known structure of the fictitious object by comparing and optimizing its four projections to those of the unknown structure of the real object and continues to iterate until the optimization is limited by the residual sum of background noise. The method is composed of several sub-processes that acquire four projections from the real data and the fictitious object: generate an arbitrary distribution to define the fictitious object, optimize the four projections, generate a new distribution for the fictitious object, and enhance the reconstructed image. The sub-process for the acquisition of the four projections from the input real data is simply the function of acquiring the four projections from the data of the transmitted intensity. The transmitted intensity represents the density distribution, that is, the distribution of absorption coefficients through the object.

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

NASA Technical Reports Server (NTRS)

Kim, S. H.; Sussman, J. L.; Suddath, F. L.; Quigley, G. J.; Mcpherson, A.; Wang, A. H. J.; Seeman, N. C.; Rich, A.

1974-01-01

Results of an analysis and interpretation of a 3-A electron density map of yeast phenylalanine transfer RNA. Some earlier detailed assignments of nucleotide residues to electron density peaks are found to be in error, even though the overall tracing of the backbone conformation of yeast phenylalanine transfer RNA was generally correct. A new, more comprehensive interpretation is made which makes it possible to define the tertiary interactions in the molecule. The new interpretation makes it possible to visualize a number of tertiary interactions which not only explain the structural role of most of the bases which are constant in transfer RNAs, but also makes it possible to understand in a direct and simple fashion the chemical modification data on transfer RNA. In addition, this pattern of tertiary interactions provides a basis for understanding the general three-dimensional folding of all transfer RNA molecules.

Development of a μO-Conotoxin Analogue with Improved Lipid Membrane Interactions and Potency for the Analgesic Sodium Channel NaV1.8*

PubMed Central

Deuis, Jennifer R.; Dekan, Zoltan; Inserra, Marco C.; Lee, Tzong-Hsien; Aguilar, Marie-Isabel; Craik, David J.; Lewis, Richard J.; Alewood, Paul F.; Mobli, Mehdi; Schroeder, Christina I.; Henriques, Sónia Troeira; Vetter, Irina

2016-01-01

The μO-conotoxins MrVIA, MrVIB, and MfVIA inhibit the voltage-gated sodium channel NaV1.8, a well described target for the treatment of pain; however, little is known about the residues or structural elements that define this activity. In this study, we determined the three-dimensional structure of MfVIA, examined its membrane binding properties, performed alanine-scanning mutagenesis, and identified residues important for its activity at human NaV1.8. A second round of mutations resulted in (E5K,E8K)MfVIA, a double mutant with greater positive surface charge and greater affinity for lipid membranes compared with MfVIA. This analogue had increased potency at NaV1.8 and was analgesic in the mouse formalin assay. PMID:27026701

A Particle-in-cell scheme of the RFQ in the SSC-Linac

NASA Astrophysics Data System (ADS)

Xiao, Chen; He, Yuan; Lu, Yuan-Rong; Yuri, Batygin; Yin, Ling; Wang, Zhi-Jun; Yuan, You-Jin; Liu, Yong; Chang, Wei; Du, Xiao-Nan; Wang, Zhi; Xia, Jia-Wen

2010-11-01

A 52 MHz Radio Frequency Quadrupole (RFQ) linear accelerator (linac) is designed to serve as an initial structure for the SSC-Linac system (injector into Separated Sector Cyclotron). The designed injection and output energy are 3.5 keV/u and 143 keV/u, respectively. The beam dynamics in this RFQ have been studied using a three-dimensional Particle-In-Cell (PIC) code BEAMPATH. Simulation results show that this RFQ structure is characterized by stable values of beam transmission efficiency (at least 95%) for both zero-current mode and the space charge dominated regime. The beam accelerated in the RFQ has good quality in both transverse and longitudinal directions, and could easily be accepted by Drift Tube Linac (DTL). The effect of the vane error and that of the space charge on the beam parameters have been studied as well to define the engineering tolerance for RFQ vane machining and alignment.

Synthesis of nanostructured bio-related materials by hybridization of synthetic polymers with polysaccharides or saccharide residues.

PubMed

Kaneko, Yoshiro; Kadokawa, Jun-Ichi

2006-01-01

In the first part of this review, we describe the synthesis of nanostructured hybrid materials composed of polysaccharides and synthetic polymers. Amylose-synthetic polymer inclusion complexes were synthesized by amylose-forming polymerization using phosphorylase enzyme in the presence of synthetic polymers such as polyethers and polyesters. Alginate-polymethacrylate hybrid materials were prepared by free-radical polymerization of cationic methacrylate in the presence of sodium alginate. These methods allow the simultaneous control of the nanostructure with polymerization, giving well-defined hybrid materials. In the second part of this review, we describe the synthesis of novel glycopolymers with rigid structures. Polyaniline-based glycopolymers were synthesized by means of oxidative polymerization of N-glycosylaniline. Polysiloxane-based glycopolymers were prepared by means of introduction of sugar-lactone to the rodlike polysiloxane. These glycopolymers had regular higher-ordered structures due to their rigid polymer backbones, resulting in control of the three-dimensional array of sugar-residues.

Three-dimensional baroclinic instability of a Hadley cell for small Richardson number

NASA Technical Reports Server (NTRS)

Antar, B. N.; Fowlis, W. W.

1983-01-01

For the case of a baroclinic flow whose Richardson number, Ri, is of order unity, a three-dimensional linear stability analysis is conducted on the basis of a model for a thin, horizontal, rotating fluid layer which is subjected to horizontal and vertical temperature gradients. The Hadley cell basic state and stability analysis are both based on the Navier-Stokes and energy equations, and perturbations possessing zonal, meridional, and vertical structures are considered. An attempt is made to extend the previous theoretical work on three-dimensional baroclinic instability for small Ri to a more realistic model involving the Prandtl and Ekman numbers, as well as to finite growth rates and a wider range of the zonal wavenumber. In general, it is found that the symmetric modes of maximum growth are not purely symmetric, but have a weak zonal structure.

Advanced Reservoir Characterization and Development through High-Resolution 3C3D Seismic and Horizontal Drilling: Eva South Marrow Sand Unit, Texas County, Oklahoma

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

Wheeler,David M.; Miller, William A.; Wilson, Travis C.

2002-03-11

The Eva South Morrow Sand Unit is located in western Texas County, Oklahoma. The field produces from an upper Morrow sandstone, termed the Eva sandstone, deposited in a transgressive valley-fill sequence. The field is defined as a combination structural stratigraphic trap; the reservoir lies in a convex up -dip bend in the valley and is truncated on the west side by the Teepee Creek fault. Although the field has been a successful waterflood since 1993, reservoir heterogeneity and compartmentalization has impeded overall sweep efficiency. A 4.25 square mile high-resolution, three component three-dimensional (3C3D) seismic survey was acquired in order tomore » improve reservoir characterization and pinpoint the optimal location of a new horizontal producing well, the ESU 13-H.« less

Maxwell Strata and Cut Locus in the Sub-Riemannian Problem on the Engel Group

NASA Astrophysics Data System (ADS)

Ardentov, Andrei A.; Sachkov, Yuri L.

2017-12-01

We consider the nilpotent left-invariant sub-Riemannian structure on the Engel group. This structure gives a fundamental local approximation of a generic rank 2 sub-Riemannian structure on a 4-manifold near a generic point (in particular, of the kinematic models of a car with a trailer). On the other hand, this is the simplest sub-Riemannian structure of step three. We describe the global structure of the cut locus (the set of points where geodesics lose their global optimality), the Maxwell set (the set of points that admit more than one minimizer), and the intersection of the cut locus with the caustic (the set of conjugate points along all geodesics). The group of symmetries of the cut locus is described: it is generated by a one-parameter group of dilations R+ and a discrete group of reflections Z2 × Z2 × Z2. The cut locus admits a stratification with 6 three-dimensional strata, 12 two-dimensional strata, and 2 one-dimensional strata. Three-dimensional strata of the cut locus are Maxwell strata of multiplicity 2 (for each point there are 2 minimizers). Two-dimensional strata of the cut locus consist of conjugate points. Finally, one-dimensional strata are Maxwell strata of infinite multiplicity, they consist of conjugate points as well. Projections of sub-Riemannian geodesics to the 2-dimensional plane of the distribution are Euler elasticae. For each point of the cut locus, we describe the Euler elasticae corresponding to minimizers coming to this point. Finally, we describe the structure of the optimal synthesis, i. e., the set of minimizers for each terminal point in the Engel group.

Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: A small-angle x-ray scattering study

DOE PAGES

Zhang, Honghu; Liu, Xunpei; Feng, Shuren; ...

2015-02-10

In this study, magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence ofmore » hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core–corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures.« less

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

Uzun, Suzan; Ilavsky, Jan; Padua, Graciela Wild

Zein, a protein of corn, has an amphiphilic molecule capable of self-assembly into distinctly different structures. In this work, ultra-small-angle X-ray scattering (USAXS) was applied to investigate the formation of self-assembled zein structures in binary solvent systems of ethanol and water. Our study included observing structural changes due to aging. Three hierarchical structures were identified in zein-solvent systems, molecular zein 2D films, believed to be formed by zein rods assembled first into one-dimensional fibers and then into two-dimensional films, and 3D spherical aggregates. Aging did not change the size or shape of primary units, but promoted their self-assembly into intermediatemore » 2D structures and shaped 3D structures into well19 defined spheres. We found that the rheological parameters, consistency index (K) and behavior index (n), storage and loss moduli (G’ and G”) were also measured. K and n, changed markedly with aging, from nearly Newtonian low consistency fresh samples to highly viscous pseudoplastic aged samples. G’ and G” increased with aging for all samples reflecting increased interactions among zein self-assembled structures. Furthermore, viscoelastic parameters indicated that zein dispersions formed gels upon aging. It was observed that USAX reported on molecular scale self-assembly processes, while rheological measurements reported on the macroscale interaction between self-assembled particles. Raman spectra suggested that α-helix to β-sheet transformations prompted zein self-assembly, which influenced the size and morphology of molecular assemblies and ultimately the rheological properties of zein dispersions.« less

Growing Three-Dimensional Corneal Tissue in a Bioreactor

NASA Technical Reports Server (NTRS)

Spaulding, Glen F.; Goodwin, Thomas J.; Aten, Laurie; Prewett, Tacey; Fitzgerald, Wendy S.; OConnor, Kim; Caldwell, Delmar; Francis, Karen M.

2003-01-01

Spheroids of corneal tissue about 5 mm in diameter have been grown in a bioreactor from an in vitro culture of primary rabbit corneal cells to illustrate the production of optic cells from aggregates and tissue. In comparison with corneal tissues previously grown in vitro by other techniques, this tissue approximates intact corneal tissue more closely in both size and structure. This novel three-dimensional tissue can be used to model cell structures and functions in normal and abnormal corneas. Efforts continue to refine the present in vitro method into one for producing human corneal tissue to overcome the chronic shortage of donors for corneal transplants: The method would be used to prepare corneal tissues, either from in vitro cultures of a patient s own cells or from a well-defined culture from another human donor known to be healthy. As explained in several articles in prior issues of NASA Tech Briefs, generally cylindrical horizontal rotating bioreactors have been developed to provide nutrient-solution environments conducive to the 30 NASA Tech Briefs, October 2003 growth of delicate animal cells, with gentle, low-shear flow conditions that keep the cells in suspension without damaging them. The horizontal rotating bioreactor used in this method, denoted by the acronym "HARV," was described in "High-Aspect-Ratio Rotating Cell-Culture Vessel" (MSC-21662), NASA Tech Briefs, Vol. 16, No. 5 (May, 1992), page 150.

Peptide-directed self-assembly of hydrogels

PubMed Central

Kopeček, Jindřich; Yang, Jiyuan

2009-01-01

This review focuses on the self-assembly of macromolecules mediated by the biorecognition of peptide/protein domains. Structures forming α-helices and β-sheets have been used to mediate self-assembly into hydrogels of peptides, reactive copolymers and peptide motifs, block copolymers, and graft copolymers. Structural factors governing the self-assembly of these molecules into precisely defined three-dimensional structures (hydrogels) are reviewed. The incorporation of peptide motifs into hybrid systems, composed of synthetic and natural macromolecules, enhances design opportunities for new biomaterials when compared to individual components. PMID:18952513

Self-diffusion in a stochastically heated two-dimensional dusty plasma

NASA Astrophysics Data System (ADS)

Sheridan, T. E.

2016-09-01

Diffusion in a two-dimensional dusty plasma liquid (i.e., a Yukawa liquid) is studied experimentally. The dusty plasma liquid is heated stochastically by a surrounding three-dimensional toroidal dusty plasma gas which acts as a thermal reservoir. The measured dust velocity distribution functions are isotropic Maxwellians, giving a well-defined kinetic temperature. The mean-square displacement for dust particles is found to increase linearly with time, indicating normal diffusion. The measured diffusion coefficients increase approximately linearly with temperature. The effective collision rate is dominated by collective dust-dust interactions rather than neutral gas drag, and is comparable to the dusty-plasma frequency.

Astigmatism inducing the degenerate effect in nearly hemispherical cavities: generation of three-dimensional structured light

NASA Astrophysics Data System (ADS)

Tung, J. C.; Hsieh, Y. H.; Liang, H. C.; Su, K. W.; Huang, K. F.; Chen, Y. F.

2017-04-01

We originally perform an analytical form to explore the influence of the astigmatism on the degenerate effect in nearly hemispherical cavities. The frequency spectrum near hemispherical cavities clearly reveals that not only the difference of cavity lengths between each degeneracies but also frequency gaps have significant difference from non-hemispherical cavities. We further thoroughly demonstrate the laser experiment under the condition of nearly hemispherical cavities to confirm the theoretical exploration that the transverse topology of three-dimensional (3D) structured light in the degenerate cavities is well localized on the Lissajous curves.

Direct correlations of structural and optical properties of three-dimensional GaN/InGaN core/shell micro-light emitting diodes

NASA Astrophysics Data System (ADS)

Sadat Mohajerani, Matin; Müller, Marcus; Hartmann, Jana; Zhou, Hao; Wehmann, Hergo-H.; Veit, Peter; Bertram, Frank; Christen, Jürgen; Waag, Andreas

2016-05-01

Three-dimensional (3D) InGaN/GaN quantum-well (QW) core-shell light emitting diodes (LEDs) are a promising candidate for the future solid state lighting. In this contribution, we study direct correlations of structural and optical properties of the core-shell LEDs using highly spatially-resolved cathodoluminescence spectroscopy (CL) in combination with scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM). Temperature-dependent resonant photoluminescence (PL) spectroscopy has been performed to understand recombination mechanisms and to estimate the internal quantum efficiency (IQE).

Three-dimensional vortex wake structure of flapping wings in hovering flight.

PubMed

Cheng, Bo; Roll, Jesse; Liu, Yun; Troolin, Daniel R; Deng, Xinyan

2014-02-06

Flapping wings continuously create and send vortices into their wake, while imparting downward momentum into the surrounding fluid. However, experimental studies concerning the details of the three-dimensional vorticity distribution and evolution in the far wake are limited. In this study, the three-dimensional vortex wake structure in both the near and far field of a dynamically scaled flapping wing was investigated experimentally, using volumetric three-component velocimetry. A single wing, with shape and kinematics similar to those of a fruitfly, was examined. The overall result of the wing action is to create an integrated vortex structure consisting of a tip vortex (TV), trailing-edge shear layer (TESL) and leading-edge vortex. The TESL rolls up into a root vortex (RV) as it is shed from the wing, and together with the TV, contracts radially and stretches tangentially in the downstream wake. The downwash is distributed in an arc-shaped region enclosed by the stretched tangential vorticity of the TVs and the RVs. A closed vortex ring structure is not observed in the current study owing to the lack of well-established starting and stopping vortex structures that smoothly connect the TV and RV. An evaluation of the vorticity transport equation shows that both the TV and the RV undergo vortex stretching while convecting downwards: a three-dimensional phenomenon in rotating flows. It also confirms that convection and secondary tilting and stretching effects dominate the evolution of vorticity.

Engineered peptide-based nanobiomaterials for electrochemical cell chip.

PubMed

Kafi, Md Abdul; Cho, Hyeon-Yeol; Choi, Jeong-Woo

2016-01-01

Biomaterials having cell adhesion ability are considered to be integral part of a cell chip. A number of researches have been carried out to search for a suitable material for effective immobilization of cell on substrate. Engineered ECM materials or their components like collagen, Poly-l-Lysine (PLL), Arg-Gly-Asp (RGD) peptide have been extensively used for mammalian cell adhesion and proliferation with the aim of tissue regeneration or cell based sensing application. This review focuses on the various approaches for two- and three-dimensionally patterned nanostructures of a short peptide i.e. RGD peptide on chip surfaces together with their effects on cell behaviors and electrochemical measurements. Most of the study concluded with positive remarks on the well-oriented engineered RGD peptide over their homogenous thin film. The engineered RGD peptide not only influences cell adhesion, spreading and proliferation but also their periodic nano-arrays directly influence electrochemical measurements of the chips. The electrochemical signals found to be enhanced when RGD peptides were used in well-defined two-dimensional nano-arrays. The topographic alteration of three-dimensional structure of engineered RGD peptide was reported to be suitably contacted with the integrin receptors of cellular membrane which results indicated the enhanced cell-electrode adhesion and efficient electron exchange phenomenon. This enhanced electrochemical signal increases the sensitivity of the chip against the target analytes. Therefore, development of engineered cellular recognizable peptides and its 3D topological design for fabrication of cell chip will provide the synergetic effect on bio-affinity, sensitivity and accuracy for the in situ real-time monitoring of analytes.

Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome.

PubMed

Boudaoud, Imène; Fournier, Éric; Baguette, Audrey; Vallée, Maxime; Lamaze, Fabien C; Droit, Arnaud; Bilodeau, Steve

2017-09-01

Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS. Copyright © 2017 by the Genetics Society of America.

Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

PubMed

Sergeyev, Ivan; Moyna, Guillermo

2005-05-02

A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

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 improved panel method for the solution of three-dimensional leading edge vortex flows Volume 2: User's guide and programmer's document

NASA Technical Reports Server (NTRS)

Tinoco, E. N.; Lu, P.; Johnson, F. T.

1980-01-01

A computer program developed for solving the subsonic, three dimensional flow over wing-body configurations with leading edge vortex separation is presented. Instructions are given for the proper set up and input of a problem into the computer code. Program input formats and output are described, as well as the overlay structure of the program. The program is written in FORTRAN.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

PubMed Central

Lee, Dongwook; Seo, Jiwon

2014-01-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance. PMID:25492227

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

NASA Astrophysics Data System (ADS)

Lee, Dongwook; Seo, Jiwon

2014-12-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors.

PubMed

Lee, Dongwook; Seo, Jiwon

2014-12-10

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Accessibility of selenomethionine proteins by total chemical synthesis: structural studies of human herpesvirus-8 MIP-II.

PubMed

Shao, W; Fernandez, E; Wilken, J; Thompson, D A; Siani, M A; West, J; Lolis, E; Schweitzer, B I

1998-12-11

The determination of high resolution three-dimensional structures by X-ray crystallography or nuclear magnetic resonance (NMR) is a time-consuming process. Here we describe an approach to circumvent the cloning and expression of a recombinant protein as well as screening for heavy atom derivatives. The selenomethionine-modified chemokine macrophage inflammatory protein-II (MIP-II) from human herpesvirus-8 has been produced by total chemical synthesis, crystallized, and characterized by NMR. The protein has a secondary structure typical of other chemokines and forms a monomer in solution. These results indicate that total chemical synthesis can be used to accelerate the determination of three-dimensional structures of new proteins identified in genome programs.

Reconstitution of a Patterned Neural Tube from Single Mouse Embryonic Stem Cells.

PubMed

Ishihara, Keisuke; Ranga, Adrian; Lutolf, Matthias P; Tanaka, Elly M; Meinhardt, Andrea

2017-01-01

The recapitulation of tissue development and patterning in three-dimensional (3D) culture is an important dimension of stem cell research. Here, we describe a 3D culture protocol in which single mouse ES cells embedded in Matrigel under neural induction conditions clonally form a lumen containing, oval-shaped epithelial structure within 3 days. By Day 7 an apicobasally polarized neuroepithelium with uniformly dorsal cell identity forms. Treatment with retinoic acid at Day 2 results in posteriorization and self-organization of dorsal-ventral neural tube patterning. Neural tube organoid growth is also supported by pure laminin gels as well as poly(ethylene glycol) (PEG)-based artificial extracellular matrix hydrogels, which can be fine-tuned for key microenvironment characteristics. The rapid generation of a simple, patterned tissue in well-defined culture conditions makes the neural tube organoid a tractable model for studying neural stem cell self-organization.

Personalization of structural PDB files.

PubMed

Woźniak, Tomasz; Adamiak, Ryszard W

2013-01-01

PDB format is most commonly applied by various programs to define three-dimensional structure of biomolecules. However, the programs often use different versions of the format. Thus far, no comprehensive solution for unifying the PDB formats has been developed. Here we present an open-source, Python-based tool called PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one's own PDB versions. PDBinout is freely available under the LGPL licence at http://pdbinout.ibch.poznan.pl.

Processing Cones: A Computational Structure for Image Analysis.

DTIC Science & Technology

1981-12-01

image analysis applications, referred to as a processing cone, is described and sample algorithms are presented. A fundamental characteristic of the structure is its hierarchical organization into two-dimensional arrays of decreasing resolution. In this architecture, a protypical function is defined on a local window of data and applied uniformly to all windows in a parallel manner. Three basic modes of processing are supported in the cone: reduction operations (upward processing), horizontal operations (processing at a single level) and projection operations (downward

Apparatus for electrohydrodynamically assembling patterned colloidal structures

NASA Technical Reports Server (NTRS)

Trau, Mathias (Inventor); Aksay, Ilhan A. (Inventor); Saville, Dudley A. (Inventor)

2000-01-01

A method apparatus is provided for electrophoretically depositing particles onto an electrode, and electrohydrodynamically assembling the particles into crystalline structures. Specifically, the present method and apparatus creates a current flowing through a solution to cause identically charged electrophoretically deposited colloidal particles to attract each other over very large distances (<5 particle diameters) on the surface of electrodes to form two-dimensional colloidal crystals. The attractive force can be created with both DC and AC fields and can modulated by adjusting either the field strength or frequency of the current. Modulating this lateral attraction between the particles causes the reversible formation of two-dimensional fluid and crystalline colloidal states on the electrode surface. Further manipulation allows for the formation of two or three-dimensional colloidal crystals, as well as more complex designed structures. Once the required structures are formed, these three-dimension colloidal crystals can be permanently frozen or glued by controlled coagulation induced by to the applied field to form a stable crystalline structure.

Method for electrohydrodynamically assembling patterned colloidal structures

NASA Technical Reports Server (NTRS)

Trau, Mathias (Inventor); Aksay, Ilhan A. (Inventor); Saville, Dudley A. (Inventor)

1999-01-01

A method apparatus is provided for electrophoretically depositing particles onto an electrode, and electrohydrodynamically assembling the particles into crystalline structures. Specifically, the present method and apparatus creates a current flowing through a solution to cause identically charged electrophoretically deposited colloidal particles to attract each other over very large distances (<5 particle diameters) on the surface of electrodes to form two-dimensional colloidal crystals. The attractive force can be created with both DC and AC fields and can modulated by adjusting either the field strength or frequency of the current. Modulating this lateral attraction between the particles causes the reversible formation of two-dimensional fluid and crystalline colloidal states on the electrode surface. Further manipulation allows for the formation of two or three-dimensional colloidal crystals, as well as more complex designed structures. Once the required structures are formed, these three-dimension colloidal crystals can be permanently frozen or glued by controlled coagulation induced by to the applied field to form a stable crystalline structure.

Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21

PubMed Central

Wang, Yuefeng; Fisher, John C.; Mathew, Rose; Ou, Li; Otieno, Steve; Sublett, Jack; Xiao, Limin; Chen, Jianhan; Roussel, Martine F.; Kriwacki, Richard W.

2011-01-01

Traditionally, well-defined three-dimensional structure was thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently exhibit “binding diversity” by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and herein report that the cyclin-dependent kinase (Cdk) inhibitor, p21Cip1, adaptively binds to and inhibits the various Cdk/cyclin complexes that regulate eukaryotic cell division. Based on results from NMR spectroscopy, and biochemical and cellular assays, we show that structural adaptability of a helical sub-domain within p21 termed LH enables two other sub-domains termed D1 and D2 to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk/cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes. PMID:21358637

[Three-dimensional genome organization: a lesson from the Polycomb-Group proteins].

PubMed

Bantignies, Frédéric

2013-01-01

As more and more genomes are being explored and annotated, important features of three-dimensional (3D) genome organization are just being uncovered. In the light of what we know about Polycomb group (PcG) proteins, we will present the latest findings on this topic. The PcG proteins are well-conserved chromatin factors that repress transcription of numerous target genes. They bind the genome at specific sites, forming chromatin domains of associated histone modifications as well as higher-order chromatin structures. These 3D chromatin structures involve the interactions between PcG-bound regulatory regions at short- and long-range distances, and may significantly contribute to PcG function. Recent high throughput "Chromosome Conformation Capture" (3C) analyses have revealed many other higher order structures along the chromatin fiber, partitioning the genomes into well demarcated topological domains. This revealed an unprecedented link between linear epigenetic domains and chromosome architecture, which might be intimately connected to genome function. © Société de Biologie, 2013.

Role of upper-level wind shear on the structure and maintenance of derecho-producing convective systems

NASA Astrophysics Data System (ADS)

Coniglio, Michael Charles

Common large-scale environments associated with the development of derecho-producing convective systems from a large number of events are identified using statistical clustering of the 500-mb geopotential heights as guidance. The majority of the events (72%) fall into three main patterns that include a well-defined upstream trough (40%), a ridge (20%), and a zonal, low-amplitude flow (12%), which is defined as an additional warm-season pattern that is not identified in past studies of derecho environments. Through an analysis of proximity soundings, discrepancies are found in both low-level and deep-tropospheric shear parameters between observations and the shear profiles considered favorable for strong, long-lived convective systems in idealized simulations. To explore the role of upper-level shear in derecho environments, a set of two-dimensional simulations of density currents within a dry, neutrally stable environment are used to examine the ability of a cold pool to lift environmental air within a vertically sheared flow. The results confirm that the addition of upper-level shear to a wind profile with weak to moderate low-level shear increases the vertical displacement of low-level parcels despite a decrease in the vertical velocity along the cold pool interface, as suggested by previous studies. Parcels that are elevated above the surface (1-2 km) overturn and are responsible for the deep lifting in the deep-shear environments. This deep overturning caused by the upper-level shear helps to maintain the tilt of the convective systems in more complex two-dimensional and three dimensional simulations. The overturning also is shown to greatly increase the size of the convective systems in the three-dimensional simulations by facilitating the initiation and maintenance of convective cells along the cold pool. When combined with estimates of the cold pool motion and the storm-relative hodograph, these results may best be used for the prediction of the demise of strong, linear mesoscale convective systems (MCSs) and may provide a conceptual model for the persistence of strong MCSs above a surface nocturnal inversion in situations that are not forced by a low-level jet.

MESH2D Grid generator design and use

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

Flach, G. P.

Mesh2d is a Fortran90 program originally designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). x-coordinates depending only on index i implies strictly vertical x-grid lines, whereas the y-grid lines can undulate. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations. Since the original development effort, Mesh2d has been extended to more general two-dimensional structured grids of the form [x(i,j),(i,j)].

A new model to simulate the elastic properties of mineralized collagen fibril.

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

Yuan, F.; Stock, S.R.; Haeffner, D.R.

Bone, because of its hierarchical composite structure, exhibits an excellent combination of stiffness and toughness, which is due substantially to the structural order and deformation at the smaller length scales. Here, we focus on the mineralized collagen fibril, consisting of hydroxyapatite plates with nanometric dimensions aligned within a protein matrix, and emphasize the relationship between the structure and elastic properties of a mineralized collagen fibril. We create two- and three-dimensional representative volume elements to represent the structure of the fibril and evaluate the importance of the parameters defining its structure and properties of the constituent mineral and collagen phase. Elasticmore » stiffnesses are calculated by the finite element method and compared with experimental data obtained by synchrotron X-ray diffraction. The computational results match the experimental data well, and provide insight into the role of the phases and morphology on the elastic deformation characteristics. Also, the effects of water, imperfections in the mineral phase and mineral content outside the mineralized collagen fibril upon its elastic properties are discussed.« less

A new model to simulate the elastic properties of mineralized collagen fibril

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

Yuan, F.; Stock, S.R.; Haeffner, D.R.

Bone, because of its hierarchical composite structure, exhibits an excellent combination of stiffness and toughness, which is due substantially to the structural order and deformation at the smaller length scales. Here, we focus on the mineralized collagen fibril, consisting of hydroxyapatite plates with nanometric dimensions aligned within a protein matrix, and emphasize the relationship between the structure and elastic properties of a mineralized collagen fibril. We create two- and three-dimensional representative volume elements to represent the structure of the fibril and evaluate the importance of the parameters defining its structure and properties of the constituent mineral and collagen phase. Elasticmore » stiffnesses are calculated by the finite element method and compared with experimental data obtained by synchrotron X-ray diffraction. The computational results match the experimental data well, and provide insight into the role of the phases and morphology on the elastic deformation characteristics. Also, the effects of water, imperfections in the mineral phase and mineral content outside the mineralized collagen fibril upon its elastic properties are discussed.« less

Visualization of Two Dimensional to Three Dimensional Transformations--Exploration through Technology

ERIC Educational Resources Information Center

Costa, G. B.; Gorak, M.; Melendez, B. S.

2006-01-01

A small class of functions is described that easily lend themselves to two-dimensional and three-dimensional visualizations at the basic calculus level. The intended audience is those educators involved in the instruction of elementary calculus. This note is an educational piece that begins with the question: "What happens if a function defined on…

Existence of three-dimensional ideal-magnetohydrodynamic equilibria with current sheets

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

Loizu, J.; Princeton Plasma Physics Laboratory, PO Box 451, Princeton, New Jersey 08543; Hudson, S. R.

2015-09-15

We consider the linear and nonlinear ideal plasma response to a boundary perturbation in a screw pinch. We demonstrate that three-dimensional, ideal-MHD equilibria with continuously nested flux-surfaces and with discontinuous rotational-transform across the resonant rational-surfaces are well defined and can be computed both perturbatively and using fully nonlinear equilibrium calculations. This rescues the possibility of constructing MHD equilibria with current sheets and continuous, smooth pressure profiles. The results predict that, even if the plasma acts as a perfectly conducting fluid, a resonant magnetic perturbation can penetrate all the way into the center of a tokamak without being shielded at themore » resonant surface.« less

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.

Role of Precambrian compositions and fabrics in the development of foreland structures, southern Front Range, Colorado

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

Chase, R.B.

1985-01-01

The Front Range terminates to the south as three basement-cored uplifts located north and west of the Canon City embayment. Precambrian units consist of foliated and non-foliated granitic rocks, augen gneiss, interlayered schist and gneiss, amphibolite, quartzite, and pegmatite. Precambrian deformations include at least three phases of folding, two phases of crenulation cleavage development, and local mylonitization. Metamorphic conditions reached those of cordierite-sillimanite grade. Paleozoic and Mesozoic sediments surround and overlap the exposed uplifts to form south-plunging arches. Excellent three-dimensional exposure of structural relationships between Precambrian rocks and overlying Phanerozoic sediments is present. Deformation styles in the sedimentary cover aremore » strongly influenced by underlying Precambrian lithologies and structural orientations. Where the crystalline units are granitic, with steeply-dipping foliation or no directional fabric, uplifts are bounded by high angle faults. Some such faults show evidence of repeated movements and reversals dating back to Precambrian time. The boundary between mechanical basement and suprastructure is clearly not defined as the base of the sedimentary section. Balanced cross-sections constructed through the southern Front Range must include contemporaneous flexural folds and thrusts in Precambrian schistose and gneissic rocks as well as in Phanerozoic sedimentary layers.« less

Unsteady Performance of Finite-Span Pitching Propulsors in Mixtures of Side-by-Side and In-Line Arrangements

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2016-11-01

Birds, insects, and fish propel themselves by flapping their wings or oscillating their fins in unsteady motions. Many of these animals fly or swim in groups or collectives, typically described as flocks, swarms and schools. The three-dimensional steady flow interactions and the two dimensional unsteady flow interactions that occur in collectives are well characterized. However, the interactions that occur among three-dimensional unsteady propulsors remain relatively unexplored. The aim of the current study is to measure the forces acting on and the energetics of two finite-span pitching wings. The wings are arranged in mixtures of canonical in-line and side-by-side configurations while the phase delay between the pitching wings is varied. The thrust force, fluid-mediated interaction force between the wings and the propulsive efficiency are quantified. The three-dimensional interaction mechanisms are compared and contrasted with previously examined two-dimensional mechanisms. Stereoscopic particle image velocimetry is employed to characterize the three-dimensional flow structures along the span of the pitching wings.

Structural Analysis of Composite Flywheels: an Integrated NDE and FEM Approach

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George; Trudell, Jeffrey

2001-01-01

A structural assessment by integrating finite-element methods (FEM) and a nondestructive evaluation (NDE) of two flywheel rotor assemblies is presented. Composite rotor A is pancake-like with a solid hub design, and composite rotor B is cylindrical with a hollow hub design. Detailed analyses under combined centrifugal and interference-fit loading are performed. Two- and three-dimensional stress analyses and two-dimensional fracture mechanics analyses are conducted. A comparison of the structural analysis results obtained with those extracted via NDE findings is reported. Contact effects due to press-fit conditions are evaluated. Stress results generated from the finite-element analyses were corroborated with the analytical solution. Cracks due to rotational loading up to 48,000 rpm for rotor A and 34,000 rpm for rotor B were successfully imaged with NDE and predicted with FEM and fracture mechanics analyses. A procedure that extends current structural analysis to a life prediction tool is also defined.

Modeling the structural, dynamical, and magnetic properties of liquid Al1-xMnx ( x=0.14 , 0.2, and 0.4): A first-principles investigation

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2007-07-01

We report the results of first-principles molecular dynamics simulations of liquid Al1-xMnx alloys at three different compositions. The local structure as defined by the Bhatia-Thornton partial structure factors is found to display significant changes at x=0.4 . In addition, a structural analysis using three-dimensional pair-analysis techniques evidences a fivefold symmetry around x=0.14 , in agreement with the experimental quasicrystal-forming range, and an increasing complexity of the Frank-Kasper polytetrahedral symmetry around Mn atoms at x=0.4 . We also examine the time evolution of the configurations at the three compositions in terms of the mean-square displacements and self-diffusion coefficients. Finally, we show a strong interplay between the structural changes and the evolution of the magnetic properties of the Mn atoms as a function of composition.

Echocardiography in the Era of Multimodality Cardiovascular Imaging

PubMed Central

Shah, Benoy Nalin

2013-01-01

Echocardiography remains the most frequently performed cardiac imaging investigation and is an invaluable tool for detailed and accurate evaluation of cardiac structure and function. Echocardiography, nuclear cardiology, cardiac magnetic resonance imaging, and cardiovascular-computed tomography comprise the subspeciality of cardiovascular imaging, and these techniques are often used together for a multimodality, comprehensive assessment of a number of cardiac diseases. This paper provides the general cardiologist and physician with an overview of state-of-the-art modern echocardiography, summarising established indications as well as highlighting advances in stress echocardiography, three-dimensional echocardiography, deformation imaging, and contrast echocardiography. Strengths and limitations of echocardiography are discussed as well as the growing role of real-time three-dimensional echocardiography in the guidance of structural heart interventions in the cardiac catheter laboratory. PMID:23878804

Technical aspects of virtual liver resection planning.

PubMed

Glombitza, G; Lamadé, W; Demiris, A M; Göpfert, M R; Mayer, A; Bahner, M L; Meinzer, H P; Richter, G; Lehnert, T; Herfarth, C

1998-01-01

Operability of a liver tumor is depending on its three dimensional relation to the intrahepatic vascular trees which define autonomously functioning liver (sub-)segments. Precise operation planning is complicated by anatomic variability, distortion of the vascular trees by the tumor or preceding liver resections. Because of the missing possibility to track the deformation of the liver during the operation an integration of the resection planning system into an intra-operative navigation system is not feasible. So the main task of an operation planning system in this domain is a quantifiable patient selection by exact prediction of post-operative liver function and a quantifiable resection proposal. The system quantifies the organ structures and resection volumes by means of absolute and relative values. It defines resection planes depending on security margins and the vascular trees and presents the data in visualized form as a 3D movie. The new 3D operation planning system offers quantifiable liver resection proposals based on individualized liver anatomy. The results are visualized in digital movies as well as in quantitative reports.

Three-dimensional analysis of tubular permanent magnet machines

NASA Astrophysics Data System (ADS)

Chai, J.; Wang, J.; Howe, D.

2006-04-01

This paper presents results from a three-dimensional finite element analysis of a tubular permanent magnet machine, and quantifies the influence of the laminated modules from which the stator core is assembled on the flux linkage and thrust force capability as well as on the self- and mutual inductances. The three-dimensional finite element (FE) model accounts for the nonlinear, anisotropic magnetization characteristic of the laminated stator structure, and for the voids which exist between the laminated modules. Predicted results are compared with those deduced from an axisymmetric FE model. It is shown that the emf and thrust force deduced from the three-dimensional model are significantly lower than those which are predicted from an axisymmetric field analysis, primarily as a consequence of the teeth and yoke being more highly saturated due to the presence of the voids in the laminated stator core.

Three-dimensional magnetic induction model of an octagonal edge-defined film-fed growth system

NASA Astrophysics Data System (ADS)

Rajendran, S.; Holmes, K.; Menna, A.

1994-03-01

Silicon wafers for the photovoltaic industry are produced by growing thin octagonal tubes by the edge-defined film-fed growth (EFG) process. The thermal origin of the wafer thickness variations was studied with a three-dimensional (3D) magnetic induction model. The implementation of the computer code and the significance of the computed results for improving the thickness uniformity are discussed.

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...

Spontaneous formation of three-dimensionally ordered Bi-rich nanostructures within GaAs1-x Bi x /GaAs quantum wells

NASA Astrophysics Data System (ADS)

Luna, E.; Wu, M.; Hanke, M.; Puustinen, J.; Guina, M.; Trampert, A.

2016-08-01

In this work, we report on the spontaneous formation of ordered arrays of nanometer-sized Bi-rich structures due to lateral composition modulations in Ga(As,Bi)/GaAs quantum wells grown by molecular beam epitaxy. The overall microstructure and chemical distribution is investigated using transmission electron microscopy. The information is complemented by synchrotron x-ray grazing incidence diffraction, which provides insight into the in-plane arrangement. Due to the vertical inheritance of the lateral modulation, the Bi-rich nanostructures eventually shape into a three-dimensional assembly. Whereas the Bi-rich nanostructures are created via two-dimensional phase separation at the growing surface, our results suggest that the process is assisted by Bi segregation which is demonstrated to be strong and more complex than expected, implying both lateral and vertical (surface segregation) mass transport. As demonstrated here, the inherent thermodynamic miscibility gap of Ga(As,Bi) alloys can be exploited to create highly uniform Bi-rich units embedded in a quantum confinement structure.

The three-dimensional shape of serrations at barn owl wings: towards a typical natural serration as a role model for biomimetic applications

PubMed Central

Bachmann, Thomas; Wagner, Hermann

2011-01-01

Barn owl feathers at the leading edge of the wing are equipped with comb-like structures termed serrations on their outer vanes. Each serration is formed by one barb ending that separates and bends upwards. This structure is considered to play a role in air-flow control and noise reduction during flight. Hence, it has considerable potential for engineering applications, particularly in the aviation industry. Several publications have reported possible functions of serrations at artificial airfoils. However, only crude approximations of natural serrations have so far been investigated. We refer to these attempts as zero-order approximations of serrations. It was the goal of this study to present a quantitative three-dimensional characterization of natural serrations as first-order approximations (mean values) and second-order approximations (listed differences depending on the position of the serration along the leading edge). Confocal laser scanning microscopy was used for a three-dimensional reconstruction and investigation with high spatial resolution. Each serration was defined by its length, profile geometry and curvature. Furthermore, the orientation of the serrations at the leading edge was characterized by the inclination angle, the tilt angle and the separation distance of neighboring serrations. These data are discussed with respect to possible applications of serration-like structures for noise suppression and air-flow control. PMID:21507001

Bio-inspired configurable multiscale extracellular matrix-like structures for functional alignment and guided orientation of cells.

PubMed

Bae, Won-Gyu; Kim, Jangho; Choung, Yun-Hoon; Chung, Yesol; Suh, Kahp Y; Pang, Changhyun; Chung, Jong Hoon; Jeong, Hoon Eui

2015-11-01

Inspired by the hierarchically organized protein fibers in extracellular matrix (ECM) as well as the physiological importance of multiscale topography, we developed a simple but robust method for the design and manipulation of precisely controllable multiscale hierarchical structures using capillary force lithography in combination with an original wrinkling technique. In this study, based on our proposed fabrication technology, we approached a conceptual platform that can mimic the hierarchically multiscale topographical and orientation cues of the ECM for controlling cell structure and function. We patterned the polyurethane acrylate-based nanotopography with various orientations on the microgrooves, which could provide multiscale topography signals of ECM to control single and multicellular morphology and orientation with precision. Using our platforms, we found that the structures and orientations of fibroblast cells were greatly influenced by the nanotopography, rather than the microtopography. We also proposed a new approach that enables the generation of native ECM having nanofibers in specific three-dimensional (3D) configurations by culturing fibroblast cells on the multiscale substrata. We suggest that our methodology could be used as efficient strategies for the design and manipulation of various functional platforms, including well-defined 3D tissue structures for advanced regenerative medicine applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Self assembling proteins

DOEpatents

Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

2004-06-29

Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

Polymeric nanofibrous substrates stimulate pluripotent stem cells to form three-dimensional multilayered patty-like spheroids in feeder-free culture and maintain their pluripotency.

PubMed

Alamein, Mohammad A; Wolvetang, Ernst J; Ovchinnikov, Dmitry A; Stephens, Sebastien; Sanders, Katherine; Warnke, Patrick H

2015-09-01

Expansion of pluripotent stem cells in defined media devoid of animal-derived feeder cells to generate multilayered three-dimensional (3D) bulk preparations or spheroids, rather than two-dimensional (2D) monolayers, is advantageous for many regenerative, biological or disease-modelling studies. Here we show that electrospun polymer matrices comprised of nanofibres that mimic the architecture of the natural fibrous extracellular matrix allow for feeder-free expansion of pluripotent human induced pluripotent stem cells (IPSCs) and human embryonic stem cells (HESCs) into multilayered 3D 'patty-like' spheroid structures in defined xeno-free culture medium. The observation that IPSCs and HESCs readily revert to 2D growth in the absence of the synthetic nanofibre membranes suggests that this 3D expansion behaviour is mediated by the physical microenvironment and artificial niche provided by the nanofibres only. Importantly, we could show that such 3D growth as patties maintained the pluripotency of cells as long as they were kept on nanofibres. The generation of complex multilayered 3D structures consisting of only pluripotent cells on biodegradable nanofibre matrices of the desired shape and size will enable both industrial-scale expansion and intricate organ-tissue engineering applications with human pluripotent stem cells, where simultaneous coupling of differentiation pathways of all germ layers from one stem cell source may be required for organ formation. Copyright © 2014 John Wiley & Sons, Ltd.

Study on prestressed concrete reactor vessel structures. II-5: Crack analysis by three dimensional finite elements method of 1/20 multicavity type PCRV subjected to internal pressure

NASA Technical Reports Server (NTRS)

1978-01-01

A three-dimensional finite elements analysis is reported of the nonlinear behavior of PCRV subjected to internal pressure by comparing calculated results with test results. As the first stage, an analysis considering the nonlinearity of cracking in concrete was attempted. As a result, it is found possible to make an analysis up to three times the design pressure (50 kg/sqcm), and calculated results agree well with test results.

Color Algebras

NASA Technical Reports Server (NTRS)

Mulligan, Jeffrey B.

2017-01-01

A color algebra refers to a system for computing sums and products of colors, analogous to additive and subtractive color mixtures. We would like it to match the well-defined algebra of spectral functions describing lights and surface reflectances, but an exact correspondence is impossible after the spectra have been projected to a three-dimensional color space, because of metamerism physically different spectra can produce the same color sensation. Metameric spectra are interchangeable for the purposes of addition, but not multiplication, so any color algebra is necessarily an approximation to physical reality. Nevertheless, because the majority of naturally-occurring spectra are well-behaved (e.g., continuous and slowly-varying), color algebras can be formulated that are largely accurate and agree well with human intuition. Here we explore the family of algebras that result from associating each color with a member of a three-dimensional manifold of spectra. This association can be used to construct a color product, defined as the color of the spectrum of the wavelength-wise product of the spectra associated with the two input colors. The choice of the spectral manifold determines the behavior of the resulting system, and certain special subspaces allow computational efficiencies. The resulting systems can be used to improve computer graphic rendering techniques, and to model various perceptual phenomena such as color constancy.

Quantitative analysis of eyes and other optical systems in linear optics.

PubMed

Harris, William F; Evans, Tanya; van Gool, Radboud D

2017-05-01

To show that 14-dimensional spaces of augmented point P and angle Q characteristics, matrices obtained from the ray transference, are suitable for quantitative analysis although only the latter define an inner-product space and only on it can one define distances and angles. The paper examines the nature of the spaces and their relationships to other spaces including symmetric dioptric power space. The paper makes use of linear optics, a three-dimensional generalization of Gaussian optics. Symmetric 2 × 2 dioptric power matrices F define a three-dimensional inner-product space which provides a sound basis for quantitative analysis (calculation of changes, arithmetic means, etc.) of refractive errors and thin systems. For general systems the optical character is defined by the dimensionally-heterogeneous 4 × 4 symplectic matrix S, the transference, or if explicit allowance is made for heterocentricity, the 5 × 5 augmented symplectic matrix T. Ordinary quantitative analysis cannot be performed on them because matrices of neither of these types constitute vector spaces. Suitable transformations have been proposed but because the transforms are dimensionally heterogeneous the spaces are not naturally inner-product spaces. The paper obtains 14-dimensional spaces of augmented point P and angle Q characteristics. The 14-dimensional space defined by the augmented angle characteristics Q is dimensionally homogenous and an inner-product space. A 10-dimensional subspace of the space of augmented point characteristics P is also an inner-product space. The spaces are suitable for quantitative analysis of the optical character of eyes and many other systems. Distances and angles can be defined in the inner-product spaces. The optical systems may have multiple separated astigmatic and decentred refracting elements. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

Variable dimensionality in the uranium fluoride/2-methyl-piperazine system: Synthesis and structures of UFO-5, -6, and -7; Zero-, one-, and two-dimensional materials with unprecedented topologies

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

Francis, R.J.; Halasyamani, P.S.; Bee, J.S.

Recently, low temperature (T < 300 C) hydrothermal reactions of inorganic precursors in the presence of organic cations have proven highly productive for the synthesis of novel solid-state materials. Interest in these materials is driven by the astonishingly diverse range of structures produced, as well as by their many potential materials chemistry applications. This report describes the high yield, phase pure hydrothermal syntheses of three new uranium fluoride phases with unprecedented structure types. Through the systematic control of the synthesis conditions the authors have successfully controlled the architecture and dimensionality of the phase formed and selectively synthesized novel zero-, one-,more » and two-dimensional materials.« less

Generation of a three-dimensional ultrastructural model of human respiratory cilia.

PubMed

Burgoyne, Thomas; Dixon, Mellisa; Luther, Pradeep; Hogg, Claire; Shoemark, Amelia

2012-12-01

The ultrastructures of cilia and flagella are highly similar and well conserved through evolution. Consequently, Chlamydomonas is commonly used as a model organism for the study of human respiratory cilia. Since detailed models of Chlamydomonas axonemes were generated using cryoelectron tomography, disparities among some of the ultrastructural features have become apparent when compared with human cilia. Extrapolating information on human disease from the Chlamydomonas model may lead to discrepancies in translational research. This study aimed to establish the first three-dimensional ultrastructural model of human cilia. Tomograms of transverse sections (n = 6) and longitudinal sections (n = 9) of human nasal respiratory cilia were generated from three healthy volunteers. Key features of the cilium were resolved using subatomic averaging, and were measured. For validation of the method, a model of the well characterized structure of Chlamydomonas reinhardtii was simultaneously generated. Data were combined to create a fully quantified three-dimensional reconstruction of human nasal respiratory cilia. We highlight key differences in the axonemal sheath, microtubular doublets, radial spokes, and dynein arms between the two structures. We show a decreased axial periodicity of the radial spokes, inner dynein arms, and central pair protrusions in the human model. We propose that this first human model will provide a basis for research into the function and structure of human respiratory cilia in health and in disease.

Motivated Proteins: A web application for studying small three-dimensional protein motifs

PubMed Central

Leader, David P; Milner-White, E James

2009-01-01

Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema. PMID:19210785

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.

Variation analysis of the severe acute respiratory syndrome coronavirus putative non-structural protein 2 gene and construction of three-dimensional model.

PubMed

Lu, Jia-hai; Zhang, Ding-mei; Wang, Guo-ling; Guo, Zhong-min; Zhang, Chuan-hai; Tan, Bing-yan; Ouyang, Li-ping; Lin, Li; Liu, Yi-min; Chen, Wei-qing; Ling, Wen-hua; Yu, Xin-bing; Zhong, Nan-shan

2005-05-05

The rapid transmission and high mortality rate made severe acute respiratory syndrome (SARS) a global threat for which no efficacious therapy is available now. Without sufficient knowledge about the SARS coronavirus (SARS-CoV), it is impossible to define the candidate for the anti-SARS targets. The putative non-structural protein 2 (nsp2) (3CL(pro), following the nomenclature by Gao et al, also known as nsp5 in Snidjer et al) of SARS-CoV plays an important role in viral transcription and replication, and is an attractive target for anti-SARS drug development, so we carried on this study to have an insight into putative polymerase nsp2 of SARS-CoV Guangdong (GD) strain. The SARS-CoV strain was isolated from a SARS patient in Guangdong, China, and cultured in Vero E6 cells. The nsp2 gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and cloned into eukaryotic expression vector pCI-neo (pCI-neo/nsp2). Then the recombinant eukaryotic expression vector pCI-neo/nsp2 was transfected into COS-7 cells using lipofectin reagent to express the nsp2 protein. The expressive protein of SARS-CoV nsp2 was analyzed by 7% sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). The nucleotide sequence and protein sequence of GD nsp2 were compared with that of other SARS-CoV strains by nucleotide-nucleotide basic local alignment search tool (BLASTN) and protein-protein basic local alignment search tool (BLASTP) to investigate its variance trend during the transmission. The secondary structure of GD strain and that of other strains were predicted by Garnier-Osguthorpe-Robson (GOR) Secondary Structure Prediction. Three-dimensional-PSSM Protein Fold Recognition (Threading) Server was employed to construct the three-dimensional model of the nsp2 protein. The putative polymerase nsp2 gene of GD strain was amplified by RT-PCR. The eukaryotic expression vector (pCI-neo/nsp2) was constructed and expressed the protein in COS-7 cells successfully. The result of sequencing and sequence comparison with other SARS-CoV strains showed that nsp2 gene was relatively conservative during the transmission and total five base sites mutated in about 100 strains investigated, three of which in the early and middle phases caused synonymous mutation, and another two base sites variation in the late phase resulted in the amino acid substitutions and secondary structure changes. The three-dimensional structure of the nsp2 protein was successfully constructed. The results suggest that polymerase nsp2 is relatively stable during the phase of epidemic. The amino acid and secondary structure change may be important for viral infection. The fact that majority of single nucleotide variations (SNVs) are predicted to cause synonymous, as well as the result of low mutation rate of nsp2 gene in the epidemic variations, indicates that the nsp2 is conservative and could be a target for anti-SARS drugs. The three-dimensional structure result indicates that the nsp2 protein of GD strain is high homologous with 3CL(pro) of SARS-CoV urbani strain, 3CL(pro) of transmissible gastroenteritis virus and 3CL(pro) of human coronavirus 229E strain, which further suggests that nsp2 protein of GD strain possesses the activity of 3CL(pro).

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

PubMed Central

2010-01-01

Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. Conclusions RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field. PMID:20459631

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

PubMed

Popenda, Mariusz; Szachniuk, Marta; Blazewicz, Marek; Wasik, Szymon; Burke, Edmund K; Blazewicz, Jacek; Adamiak, Ryszard W

2010-05-06

Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.

DNA origami nanopillars as standards for three-dimensional superresolution microscopy.

PubMed

Schmied, Jürgen J; Forthmann, Carsten; Pibiri, Enrico; Lalkens, Birka; Nickels, Philipp; Liedl, Tim; Tinnefeld, Philip

2013-02-13

Nanopillars are promising nanostructures composed of various materials that bring new functionalities for applications ranging from photovoltaics to analytics. We developed DNA nanopillars with a height of 220 nm and a diameter of ~14 nm using the DNA origami technique. Modifying the base of the nanopillars with biotins allowed selective, upright, and rigid immobilization on solid substrates. With the help of site-selective dye labels, we visualized the structure and determined the orientation of the nanopillars by three-dimensional fluorescence superresolution microscopy. Because of their rigidity and nanometer-precise addressability, DNA origami nanopillars qualify as scaffold for the assembly of plasmonic devices as well as for three-dimensional superresolution standards.

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

An efficient closed-form solution for acoustic emission source location in three-dimensional structures

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

Li, Xibing; Dong, Longjun, E-mail: csudlj@163.com; Australian Centre for Geomechanics, The University of Western Australia, Crawley, 6009

This paper presents an efficient closed-form solution (ECS) for acoustic emission(AE) source location in three-dimensional structures using time difference of arrival (TDOA) measurements from N receivers, N ≥ 6. The nonlinear location equations of TDOA are simplified to linear equations. The unique analytical solution of AE sources for unknown velocity system is obtained by solving the linear equations. The proposed ECS method successfully solved the problems of location errors resulting from measured deviations of velocity as well as the existence and multiplicity of solutions induced by calculations of square roots in existed close-form methods.

Illustration as a way to explain the complex structures of foraminifera. The scientific drawing of Lukas Hottinger. In memoriam (1933-2011)

NASA Astrophysics Data System (ADS)

Leria, M.; Ferrandez, C.; Ruiz-Ortega, M.

2012-12-01

Scientific illustration is a fundamental tool for transmitting scientific knowledge because it allows to define aspects that cannot be appreciated just by text description, or by means of photography. This study is based on the collection of illustrations created by the paleontologist Lukas Hottinger (1933-2011) during his extensive career. Hottinger studied, described and illustrated foraminifera for more than fifty years. The use of illustration is essential for studying, describing and clasifying these marine microfossils. Foraminifera are a constituent of marine sedimentary rocks; the study of their internal anatomy often is made from thin sections of rocks, a destructive technique which provides only two dimensional sections. The internal three-dimensional morphology of a species must be interpreted and reconstructed from numerous random two-dimensional sections. New technologies, such as SEM or more recently X-ray Microtomography provided progressively better images of the internal structure but this information, while useful, is still insufficient to explain with simplicity and efficacy what an illustration of a synthetic 3D model shows at a glance. This study is based on a review of 78 publications by Lukas Hottinger on foraminiferal inner structure. In addition, up to 150 illustrations by Hottinger were analyzed, as well as other works written by his colleagues during the same years (1956-2009). Hottinger's work includes several reference papers on the structure and systematics of different groups of larger foraminifera in which his three dimensional models play a fundamental role in synthesizing and making understandable the complexity of these shells. Illustrations of 3D models were particularly selected because of their conceptual complexity. They do not represent a view of the foraminiferal structure that can be observe directly, but a synthetic abstraction constructed from the observation and interpretation of many random two-dimensional sections of diverse individuals. We also analyzed the evolution of the method and techniques of representation through the different papers, coming to the conclusion that they changed according to the printing methods and the current technology (e.g. computer drawing software), but the basic concept of drawings has not been highly modified. The preliminary results demonstrate that illustrations are a necessary and fundamental element in the study of foraminiferal structure, and that it is beneficial for the scientist to have a good knowledge of the various skills involved in drawing and illustration, in order to better disseminate the results of his research with clarity and make complexity comprehensible.

Three-dimensional Biomimetic Technology: Novel Biorubber Creates Defined Micro- and Macro-scale Architectures in Collagen Hydrogels

PubMed Central

Rodriguez-Rivera, Veronica; Weidner, John W.; Yost, Michael J.

2016-01-01

Tissue scaffolds play a crucial role in the tissue regeneration process. The ideal scaffold must fulfill several requirements such as having proper composition, targeted modulus, and well-defined architectural features. Biomaterials that recapitulate the intrinsic architecture of in vivo tissue are vital for studying diseases as well as to facilitate the regeneration of lost and malformed soft tissue. A novel biofabrication technique was developed which combines state of the art imaging, three-dimensional (3D) printing, and selective enzymatic activity to create a new generation of biomaterials for research and clinical application. The developed material, Bovine Serum Albumin rubber, is reaction injected into a mold that upholds specific geometrical features. This sacrificial material allows the adequate transfer of architectural features to a natural scaffold material. The prototype consists of a 3D collagen scaffold with 4 and 3 mm channels that represent a branched architecture. This paper emphasizes the use of this biofabrication technique for the generation of natural constructs. This protocol utilizes a computer-aided software (CAD) to manufacture a solid mold which will be reaction injected with BSA rubber followed by the enzymatic digestion of the rubber, leaving its architectural features within the scaffold material. PMID:26967145

Three-dimensional Biomimetic Technology: Novel Biorubber Creates Defined Micro- and Macro-scale Architectures in Collagen Hydrogels.

PubMed

Rodriguez-Rivera, Veronica; Weidner, John W; Yost, Michael J

2016-02-12

Tissue scaffolds play a crucial role in the tissue regeneration process. The ideal scaffold must fulfill several requirements such as having proper composition, targeted modulus, and well-defined architectural features. Biomaterials that recapitulate the intrinsic architecture of in vivo tissue are vital for studying diseases as well as to facilitate the regeneration of lost and malformed soft tissue. A novel biofabrication technique was developed which combines state of the art imaging, three-dimensional (3D) printing, and selective enzymatic activity to create a new generation of biomaterials for research and clinical application. The developed material, Bovine Serum Albumin rubber, is reaction injected into a mold that upholds specific geometrical features. This sacrificial material allows the adequate transfer of architectural features to a natural scaffold material. The prototype consists of a 3D collagen scaffold with 4 and 3 mm channels that represent a branched architecture. This paper emphasizes the use of this biofabrication technique for the generation of natural constructs. This protocol utilizes a computer-aided software (CAD) to manufacture a solid mold which will be reaction injected with BSA rubber followed by the enzymatic digestion of the rubber, leaving its architectural features within the scaffold material.

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.

Aerostructural Shape and Topology Optimization of Aircraft Wings

NASA Astrophysics Data System (ADS)

James, Kai

A series of novel algorithms for performing aerostructural shape and topology optimization are introduced and applied to the design of aircraft wings. An isoparametric level set method is developed for performing topology optimization of wings and other non-rectangular structures that must be modeled using a non-uniform, body-fitted mesh. The shape sensitivities are mapped to computational space using the transformation defined by the Jacobian of the isoparametric finite elements. The mapped sensitivities are then passed to the Hamilton-Jacobi equation, which is solved on a uniform Cartesian grid. The method is derived for several objective functions including mass, compliance, and global von Mises stress. The results are compared with SIMP results for several two-dimensional benchmark problems. The method is also demonstrated on a three-dimensional wingbox structure subject to fixed loading. It is shown that the isoparametric level set method is competitive with the SIMP method in terms of the final objective value as well as computation time. In a separate problem, the SIMP formulation is used to optimize the structural topology of a wingbox as part of a larger MDO framework. Here, topology optimization is combined with aerodynamic shape optimization, using a monolithic MDO architecture that includes aerostructural coupling. The aerodynamic loads are modeled using a three-dimensional panel method, and the structural analysis makes use of linear, isoparametric, hexahedral elements. The aerodynamic shape is parameterized via a set of twist variables representing the jig twist angle at equally spaced locations along the span of the wing. The sensitivities are determined analytically using a coupled adjoint method. The wing is optimized for minimum drag subject to a compliance constraint taken from a 2 g maneuver condition. The results from the MDO algorithm are compared with those of a sequential optimization procedure in order to quantify the benefits of the MDO approach. While the sequentially optimized wing exhibits a nearly-elliptical lift distribution, the MDO design seeks to push a greater portion of the load toward the root, thus reducing the structural deflection, and allowing for a lighter structure. By exploiting this trade-off, the MDO design achieves a 42% lower drag than the sequential result.

Lobe-cleft instability in the buoyant gravity current generated by estuarine outflow

NASA Astrophysics Data System (ADS)

Horner-Devine, Alexander R.; Chickadel, C. Chris

2017-05-01

Gravity currents represent a broad class of geophysical flows including turbidity currents, powder avalanches, pyroclastic flows, sea breeze fronts, haboobs, and river plumes. A defining feature in many gravity currents is the formation of three-dimensional lobes and clefts along the front and researchers have sought to understand these ubiquitous geophysical structures for decades. The prevailing explanation is based largely on early laboratory and numerical model experiments at much smaller scales, which concluded that lobes and clefts are generated due to hydrostatic instability exclusively in currents propagating over a nonslip boundary. Recent studies suggest that frontal dynamics change as the flow scale increases, but no measurements have been made that sufficiently resolve the flow structure in full-scale geophysical flows. Here we use thermal infrared and acoustic imaging of a river plume to reveal the three-dimensional structure of lobes and clefts formed in a geophysical gravity current front. The observed lobes and clefts are generated at the front in the absence of a nonslip boundary, contradicting the prevailing explanation. The observed flow structure is consistent with an alternative formation mechanism, which predicts that the lobe scale is inherited from subsurface vortex structures.

Leaving the structural ivory tower, assisted by interactive 3D PDF.

PubMed

Kumar, Pravin; Ziegler, Alexander; Grahn, Alexander; Hee, Chee Seng; Ziegler, Andreas

2010-08-01

The ability to embed interactive three-dimensional (3D) models into electronic publications in portable document format (PDF) greatly enhances the accessibility of molecular structures. Here, we report advances in this procedure and discuss what is needed to develop this format into a truly useful tool for the structural biology community as well as for readers who are less well trained in molecular visualization. Copyright 2010 Elsevier Ltd. All rights reserved.

Life is three-dimensional, and it begins with molecules.

PubMed

Bourne, Philip E

2017-03-01

The iconic image of the DNA double helix embodies the central role that three-dimensional structures play in understanding biological processes, which, in turn, impact health and well-being. Here, that role is explored through the eyes of one scientist, who has been lucky enough to have over 150 talented people pass through his laboratory. Each contributed to that understanding. What follows is a small fraction of their story, with an emphasis on basic research outcomes of importance to society at large.

Three-dimensional visualization and characterization of bone structure using reconstructed in-vitro μCT images: A pilot study for bone microarchitecture analysis

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

Latief, Fourier Dzar Eljabbar, E-mail: fourier@fi.itb.ac.id; Dewi, Dyah Ekashanti Octorina; Shari, Mohd Aliff Bin Mohd

Micro Computed Tomography (μCT) has been largely used to perform micrometer scale imaging of specimens, bone biopsies and small animals for the study of porous or cavity-containing objects. One of its favored applications is for assessing structural properties of bone. In this research, we perform a pilot study to visualize and characterize bone structure of a chicken bone thigh, as well as to delineate its cortical and trabecular bone regions. We utilize an In-Vitro μCT scanner Skyscan 1173 to acquire a three dimensional image data of a chicken bone thigh. The thigh was scanned using X-ray voltage of 45 kVmore » and current of 150 μA. The reconstructed images have spatial resolution of 142.50 μm/pixel. Using image processing and analysis e.i segmentation by thresholding the gray values (which represent the pseudo density) and binarizing the images, we were able to visualize each part of the bone, i.e., the cortical and trabecular regions. Total volume of the bone is 4663.63 mm{sup 3}, and the surface area of the bone is 7913.42 mm{sup 2}. The volume of the cortical is approximately 1988.62 mm{sup 3} which is nearly 42.64% of the total bone volume. This pilot study has confirmed that the μCT is capable of quantifying 3D bone structural properties and defining its regions separately. For further development, these results can be improved for understanding the pathophysiology of bone abnormality, testing the efficacy of pharmaceutical intervention, or estimating bone biomechanical properties.« less

Three-dimensional Model of Human Platelet Integrin αIIbβ3 in Solution Obtained by Small Angle Neutron Scattering*

PubMed Central

Nogales, Aurora; García, Carolina; Pérez, Javier; Callow, Phil; Ezquerra, Tiberio A.; González-Rodríguez, José

2010-01-01

Integrin αIIbβ3 is the major membrane protein and adhesion receptor at the surface of blood platelets, which after activation plays a key role in platelet plug formation in hemostasis and thrombosis. Small angle neutron scattering (SANS) and shape reconstruction algorithms allowed formation of a low resolution three-dimensional model of whole αIIbβ3 in Ca2+/detergent solutions. Model projections after 90° rotation along its long axis show an elongated and “arched” form (135°) not observed before and a “handgun” form. This 20-nm-long structure is well defined, despite αIIbβ3 multidomain nature and expected segmental flexibility, with the largest region at the top, followed by two narrower and smaller regions at the bottom. Docking of this SANS envelope into the high resolution structure of αIIbβ3, reconstructed from crystallographic and NMR data, shows that the solution structure is less constrained, allows tentative assignment of the disposition of the αIIb and β3 subunits and their domains within the model, and points out the structural analogies and differences of the SANS model with the crystallographic models of the recombinant ectodomains of αIIbβ3 and αVβ3 and with the cryo-electron microscopy model of whole αIIbβ3. The ectodomain is in the bent configuration at the top of the model, where αIIb and β3 occupy the concave and convex sides, respectively, at the arched projection, with their bent knees at its apex. It follows the narrower transmembrane region and the cytoplasmic domains at the bottom end. αIIbβ3 aggregated in Mn2+/detergent solutions, which impeded to get its SANS model. PMID:19897481

Three-dimensional benchmark for variable-density flow and transport simulation: matching semi-analytic stability modes for steady unstable convection in an inclined porous box

USGS Publications Warehouse

Voss, Clifford I.; Simmons, Craig T.; Robinson, Neville I.

2010-01-01

This benchmark for three-dimensional (3D) numerical simulators of variable-density groundwater flow and solute or energy transport consists of matching simulation results with the semi-analytical solution for the transition from one steady-state convective mode to another in a porous box. Previous experimental and analytical studies of natural convective flow in an inclined porous layer have shown that there are a variety of convective modes possible depending on system parameters, geometry and inclination. In particular, there is a well-defined transition from the helicoidal mode consisting of downslope longitudinal rolls superimposed upon an upslope unicellular roll to a mode consisting of purely an upslope unicellular roll. Three-dimensional benchmarks for variable-density simulators are currently (2009) lacking and comparison of simulation results with this transition locus provides an unambiguous means to test the ability of such simulators to represent steady-state unstable 3D variable-density physics.

Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization

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

Chennubhotla, Chakra; Castro, Jason

2013-01-01

In contrast to most other sensory modalities, the basic perceptual dimensions of olfaction remain un- clear. Here, we use non-negative matrix factorization (NMF) - a dimensionality reduction technique - to uncover structure in a panel of odor profiles, with each odor defined as a point in multi-dimensional descriptor space. The properties of NMF are favorable for the analysis of such lexical and perceptual data, and lead to a high-dimensional account of odor space. We further provide evidence that odor di- mensions apply categorically. That is, odor space is not occupied homogenously, but rather in a discrete and intrinsically clustered manner.more » We discuss the potential implications of these results for the neural coding of odors, as well as for developing classifiers on larger datasets that may be useful for predicting perceptual qualities from chemical structures.« less

Iterative optimizing quantization method for reconstructing three-dimensional images from a limited number of views

DOEpatents

Lee, H.R.

1997-11-18

A three-dimensional image reconstruction method comprises treating the object of interest as a group of elements with a size that is determined by the resolution of the projection data, e.g., as determined by the size of each pixel. One of the projections is used as a reference projection. A fictitious object is arbitrarily defined that is constrained by such reference projection. The method modifies the known structure of the fictitious object by comparing and optimizing its four projections to those of the unknown structure of the real object and continues to iterate until the optimization is limited by the residual sum of background noise. The method is composed of several sub-processes that acquire four projections from the real data and the fictitious object: generate an arbitrary distribution to define the fictitious object, optimize the four projections, generate a new distribution for the fictitious object, and enhance the reconstructed image. The sub-process for the acquisition of the four projections from the input real data is simply the function of acquiring the four projections from the data of the transmitted intensity. The transmitted intensity represents the density distribution, that is, the distribution of absorption coefficients through the object. 5 figs.

Solvothermal Synthesis of Three-Dimensional Hierarchical CuS Microspheres from a Cu-Based Ionic Liquid Precursor for High-Performance Asymmetric Supercapacitors.

PubMed

Zhang, Jing; Feng, Huijie; Yang, Jiaqin; Qin, Qing; Fan, Hongmin; Wei, Caiying; Zheng, Wenjun

2015-10-07

It is meaningful to exploit copper sulfide materials with desired structure as well as potential application due to their cheapness and low toxicity. A low-temperature and facile solvothermal method for preparing three-dimensional (3D) hierarchical covellite (CuS) microspheres from an ionic liquid precursor [Bmim]2Cu2Cl6 (Bmim = 1-butyl-3-methylimidazolium) is reported. The formation of CuS nanostructures was achieved by decomposition of intermediate complex Cu(Tu)3Cl (thiourea = Tu), which produced CuS microspheres with diameters of 2.5-4 μm assembled by nanosheets with thicknesses of 10-15 nm. The ionic liquid, as an "all-in-one" medium, played a key role for the fabrication and self-assembly of CuS nanosheets. The alkylimidazolium rings ([Bmim](+)) were found to adsorb onto the (001) facets of CuS crystals, which inhibited the crystal growth along the [001] direction, while the alkyl chain had influence on the assembly of CuS nanosheets. The CuS microspheres showed enhanced electrochemical performance and high stability for the application in supercapacitors due to intriguing structural design and large specific surface area. When this well-defined CuS electrode was assembled into an asymmetric supercapacitor (ASC) with an activated carbon (AC) electrode, the CuS//AC-ASC demonstrated good cycle performance (∼88% capacitance after 4000 cycles) and high energy density (15.06 W h kg(-1) at a power density of 392.9 W kg(-1)). This work provides new insights into the use of copper sulfide electrode materials for asymmetric supercapacitors and other electrochemical devices.

Characterization of zein assemblies by ultra-small-angle X-ray scattering

DOE PAGES

Uzun, Suzan; Ilavsky, Jan; Padua, Graciela Wild

2017-03-23

Zein, a protein of corn, has an amphiphilic molecule capable of self-assembly into distinctly different structures. In this work, ultra-small-angle X-ray scattering (USAXS) was applied to investigate the formation of self-assembled zein structures in binary solvent systems of ethanol and water. Our study included observing structural changes due to aging. Three hierarchical structures were identified in zein-solvent systems, molecular zein 2D films, believed to be formed by zein rods assembled first into one-dimensional fibers and then into two-dimensional films, and 3D spherical aggregates. Aging did not change the size or shape of primary units, but promoted their self-assembly into intermediatemore » 2D structures and shaped 3D structures into well19 defined spheres. We found that the rheological parameters, consistency index (K) and behavior index (n), storage and loss moduli (G’ and G”) were also measured. K and n, changed markedly with aging, from nearly Newtonian low consistency fresh samples to highly viscous pseudoplastic aged samples. G’ and G” increased with aging for all samples reflecting increased interactions among zein self-assembled structures. Furthermore, viscoelastic parameters indicated that zein dispersions formed gels upon aging. It was observed that USAX reported on molecular scale self-assembly processes, while rheological measurements reported on the macroscale interaction between self-assembled particles. Raman spectra suggested that α-helix to β-sheet transformations prompted zein self-assembly, which influenced the size and morphology of molecular assemblies and ultimately the rheological properties of zein dispersions.« less

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.

Accurate complex scaling of three dimensional numerical potentials

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

Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan

2013-05-28

The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scalingmore » of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.« less

Three-Dimensional Topographic Surface Changes in Response to Compartmental Volumization of the Medial Cheek: Defining a Malar Augmentation Zone.

PubMed

Stern, Carrie S; Schreiber, Jillian E; Surek, Chris C; Garfein, Evan S; Jelks, Elizabeth B; Jelks, Glenn W; Tepper, Oren M

2016-05-01

Given the widespread use of facial fillers and recent identification of distinct facial fat compartments, a better understanding of three-dimensional surface changes in response to volume augmentation is needed. Advances in three-dimensional imaging technology now afford an opportunity to elucidate these morphologic changes for the first time. A cadaver study was undertaken in which volumization of the deep medial cheek compartment was performed at intervals up to 4 cc (n = 4). Three-dimensional photographs were taken after each injection to analyze the topographic surface changes, which the authors define as the "augmentation zone." Perimeter, diameter, and projection were studied. The arcus marginalis of the inferior orbit consistently represented a fixed boundary of the augmentation zone, and additional cadavers underwent similar volumization following surgical release of this portion of the arcus marginalis (n = 4). Repeated three-dimensional computer analysis was performed comparing the augmentation zone with and without arcus marginalis release. Volumization of the deep medial cheek led to unique topographic changes of the malar region defined by distinct boundaries. Interestingly, the cephalic border of the augmentation zone was consistently noted to be at the level of the arcus marginalis in all specimens. When surgical release of the arcus marginalis was performed, the cephalic border of the augmentation zone was no longer restricted. Using advances in three-dimensional photography and computer analysis, the authors demonstrate characteristic surface anatomy changes in response to volume augmentation of facial compartments. This novel concept of the augmentation zone can be applied to volumization of other distinct facial regions. Therapeutic, V.

Three-dimensional atomic force microscopy mapping at the solid-liquid interface with fast and flexible data acquisition

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

Söngen, Hagen, E-mail: soengen@uni-mainz.de; Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz; Nalbach, Martin

2016-06-15

We present the implementation of a three-dimensional mapping routine for probing solid-liquid interfaces using frequency modulation atomic force microscopy. Our implementation enables fast and flexible data acquisition of up to 20 channels simultaneously. The acquired data can be directly synchronized with commercial atomic force microscope controllers, making our routine easily extendable for related techniques that require additional data channels, e.g., Kelvin probe force microscopy. Moreover, the closest approach of the tip to the sample is limited by a user-defined threshold, providing the possibility to prevent potential damage to the tip. The performance of our setup is demonstrated by visualizing themore » hydration structure above the calcite (10.4) surface in water.« less

Neural Integration of Information Specifying Human Structure from Form, Motion, and Depth

PubMed Central

Jackson, Stuart; Blake, Randolph

2010-01-01

Recent computational models of biological motion perception operate on ambiguous two-dimensional representations of the body (e.g., snapshots, posture templates) and contain no explicit means for disambiguating the three-dimensional orientation of a perceived human figure. Are there neural mechanisms in the visual system that represent a moving human figure’s orientation in three dimensions? To isolate and characterize the neural mechanisms mediating perception of biological motion, we used an adaptation paradigm together with bistable point-light (PL) animations whose perceived direction of heading fluctuates over time. After exposure to a PL walker with a particular stereoscopically defined heading direction, observers experienced a consistent aftereffect: a bistable PL walker, which could be perceived in the adapted orientation or reversed in depth, was perceived predominantly reversed in depth. A phase-scrambled adaptor produced no aftereffect, yet when adapting and test walkers differed in size or appeared on opposite sides of fixation aftereffects did occur. Thus, this heading direction aftereffect cannot be explained by local, disparity-specific motion adaptation, and the properties of scale and position invariance imply higher-level origins of neural adaptation. Nor is disparity essential for producing adaptation: when suspended on top of a stereoscopically defined, rotating globe, a context-disambiguated “globetrotter” was sufficient to bias the bistable walker’s direction, as were full-body adaptors. In sum, these results imply that the neural signals supporting biomotion perception integrate information on the form, motion, and three-dimensional depth orientation of the moving human figure. Models of biomotion perception should incorporate mechanisms to disambiguate depth ambiguities in two-dimensional body representations. PMID:20089892

The alphabet of intrinsic disorder

PubMed Central

Theillet, Francois-Xavier; Kalmar, Lajos; Tompa, Peter; Han, Kyou-Hoon; Selenko, Philipp; Dunker, A. Keith; Daughdrill, Gary W.; Uversky, Vladimir N

2013-01-01

A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting. PMID:28516008

A one-dimensional ice structure built from pentagons

NASA Astrophysics Data System (ADS)

Carrasco, Javier; Michaelides, Angelos

2010-03-01

Heterogeneous nucleation of water plays a key role in fields as diverse as atmospheric chemistry, astrophysics, and biology. Ice nucleation on metal surfaces offers an opportunity to watch this process unfold, providing a molecular-scale description at a well-defined, planar interface. We discuss a density-functional theory study on a metal surface specifically designed to understand such phenomena. Together with our colleges at the University of Liverpool, we found that the nanometer wide water-ice chains experimentally observed to nucleate and grow on Cu(110) are built from a face sharing arrangement of water pentagons [1]. The novel one-dimensional pentagon structure maximizes the water-metal bonding whilst simultaneously maintaining a strong hydrogen bonding network. These results reveal an unanticipated structural adaptability of water-ice films, demonstrating that the presence of the substrate can be sufficient to favor non-conventional structural units. [4pt] [1] J. Carrasco et al., Nature Mater. 8, 427 (2009).

The University Münster Model Surgery System for Orthognathic Surgery. Part II -- KD-MMS.

PubMed

Ehmer, Ulrike; Joos, Ulrich; Ziebura, Thomas; Flieger, Stefanie; Wiechmann, Dirk

2013-01-04

Model surgery is an integral part of the planning procedure in orthognathic surgery. Most concepts comprise cutting the dental cast off its socket. The standardized spacer plates of the KD-MMS provide for a non-destructive, reversible and reproducible means of maxillary and/or mandibular plaster cast separation. In the course of development of the system various articulator types were evaluated with regard to their capability to provide a means of realizing the concepts comprised of the KD-MMS. Special attention was dedicated to the ability to perform three-dimensional displacements without cutting of plaster casts. Various utilities were developed to facilitate maxillary displacement in accordance to the planning. Objectives of this development comprised the ability to implement the values established in the course of two-dimensional ceph planning. The system - KD-MMS comprises a set of hardware components as well as a defined procedure. Essential hardware components are red spacer and blue mounting plates. The blue mounting plates replace the standard yellow SAM mounting elements. The red spacers provide for a defined leeway of 8 mm for three-dimensional movements. The non-destructive approach of the KD-MMS makes it possible to conduct different model surgeries with the same plaster casts as well as to restore the initial, pre-surgical situation at any time. Thereby, surgical protocol generation and gnathologic splint construction are facilitated. The KD-MMS hardware components in conjunction with the defined procedures are capable of increasing efficiency and accuracy of model surgery and splint construction. In cases where different surgical approaches need to be evaluated in the course of model surgery, a significant reduction of chair time may be achieved.

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

NASA Astrophysics Data System (ADS)

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron; Zhu, Allen; Jungmann, Ralf; Bellot, Gaetan; Ke, Yonggang; Yin, Peng

2017-12-01

Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands. Even larger DNA origami structures are possible, but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock. This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success. Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1-1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.

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.

Integrated NDE and FEM characterization of composite rotors

NASA Astrophysics Data System (ADS)

Abdul-Aziz, Ali; Baaklini, George Y.; Trudell, Jeffrey J.

2001-08-01

A structural assessment by integrating finite-element methods (FEM) and a nondestructive evaluation (NDE) of two flywheel rotor assemblies is presented. Composite rotor A is pancake like with a solid hub design, and composite rotor B is cylindrical with a hollow hub design. Detailed analyses under combined centrifugal and interference-fit loading are performed. Two- and three-dimensional stress analyses and two-dimensional fracture mechanics analyses are conducted. A comparison of the structural analysis results obtained with those extracted via NDE findings is reported. Contact effects due to press-fit conditions are evaluated. Stress results generated from the finite-element analyses were corroborated with the analytical solution. Cracks due to rotational loading up to 48 000 rpm for rotor A and 34 000 rpm for rotor B were successfully imaged with NDE and predicted with FEM and fracture mechanics analyses. A procedure that extends current structural analysis to a life prediction tool is also defined.

An Integrated NDE and FEM Characterization of Composite Rotors

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Baaklini, George Y.; Trudell, Jeffrey J.

2000-01-01

A structural assessment by integrating finite-element methods (FEM) and a nondestructive evaluation (NDE) of two flywheel rotor assemblies is presented. Composite rotor A is pancake like with a solid hub design, and composite rotor B is cylindrical with a hollow hub design. Detailed analyses under combined centrifugal and interference-fit loading are performed. Two- and three-dimensional stress analyses and two-dimensional fracture mechanics analyses are conducted. A comparison of the structural analysis results obtained with those extracted via NDE findings is reported. Contact effects due to press-fit conditions are evaluated. Stress results generated from the finite-element analyses were corroborated with the analytical solution. Cracks due to rotational loading up to 49 000 rpm for rotor A and 34 000 rpm for rotor B were successfully imaged with NDE and predicted with FEM and fracture mechanics analyses. A procedure that extends current structural analysis to a life prediction tool is also defined.

One-dimensional gravity in infinite point distributions.

PubMed

Gabrielli, A; Joyce, M; Sicard, F

2009-10-01

The dynamics of infinite asymptotically uniform distributions of purely self-gravitating particles in one spatial dimension provides a simple and interesting toy model for the analogous three dimensional problem treated in cosmology. In this paper we focus on a limitation of such models as they have been treated so far in the literature: the force, as it has been specified, is well defined in infinite point distributions only if there is a centre of symmetry (i.e., the definition requires explicitly the breaking of statistical translational invariance). The problem arises because naive background subtraction (due to expansion, or by "Jeans swindle" for the static case), applied as in three dimensions, leaves an unregulated contribution to the force due to surface mass fluctuations. Following a discussion by Kiessling of the Jeans swindle in three dimensions, we show that the problem may be resolved by defining the force in infinite point distributions as the limit of an exponentially screened pair interaction. We show explicitly that this prescription gives a well defined (finite) force acting on particles in a class of perturbed infinite lattices, which are the point processes relevant to cosmological N -body simulations. For identical particles the dynamics of the simplest toy model (without expansion) is equivalent to that of an infinite set of points with inverted harmonic oscillator potentials which bounce elastically when they collide. We discuss and compare with previous results in the literature and present new results for the specific case of this simplest (static) model starting from "shuffled lattice" initial conditions. These show qualitative properties of the evolution (notably its "self-similarity") like those in the analogous simulations in three dimensions, which in turn resemble those in the expanding universe.

Three-dimensional micro/nano-scale structure fabricated by combination of non-volatile polymerizable RTIL and FIB irradiation

PubMed Central

Kuwabata, Susumu; Minamimoto, Hiro; Inoue, Kosuke; Imanishi, Akihito; Hosoya, Ken; Uyama, Hiroshi; Torimoto, Tsukasa; Tsuda, Tetsuya; Seki, Shu

2014-01-01

Room-temperature ionic liquid (RTIL) has been widely investigated as a nonvolatile solvent as well as a unique liquid material because of its interesting features, e.g., negligible vapor pressure and high thermal stability. Here we report that a non-volatile polymerizable RTIL is a useful starting material for the fabrication of micro/nano-scale polymer structures with a focused-ion-beam (FIB) system operated under high-vacuum condition. Gallium-ion beam irradiation to the polymerizable 1-allyl-3-ethylimidazolium bis((trifluoromethane)sulfonyl)amide RTIL layer spread on a Si wafer induced a polymerization reaction without difficulty. What is interesting to note is that we have succeeded in provoking the polymerization reaction anywhere on the Si wafer substrate by using FIB irradiation with a raster scanning mode. By this finding, two- and three-dimensional micro/nano-scale polymer structure fabrications were possible at the resolution of 500,000 dpi. Even intricate three-dimensional micro/nano-figures with overhang and hollow moieties could be constructed at the resolution of approximately 100 nm. PMID:24430465

A three-dimensional construction of the active site (region 507-749) of human neutral endopeptidase (EC.3.4.24.11).

PubMed

Tiraboschi, G; Jullian, N; Thery, V; Antonczak, S; Fournie-Zaluski, M C; Roques, B P

1999-02-01

A three-dimensional model of the 507-749 region of neutral endopeptidase-24.11 (NEP; E.C.3.4.24.11) was constructed integrating the results of secondary structure predictions and sequence homologies with the bacterial endopeptidase thermolysin. Additional data were extracted from the structure of two other metalloproteases, astacin and stromelysin. The resulting model accounts for the main biological properties of NEP and has been used to describe the environment close to the zinc atom defining the catalytic site. The analysis of several thiol inhibitors, complexed in the model active site, revealed the presence of a large hydrophobic pocket at the S1' subsite level. This is supported by the nature of the constitutive amino acids. The computed energies of bound inhibitors correspond with the relative affinities of the stereoisomers of benzofused macrocycle derivatives of thiorphan. The model could be used to facilitate the design of new NEP inhibitors, as illustrated in the paper.

Maxillary reaction patterns identified by three-dimensional analysis of casts from infants with unilateral cleft lip and palate.

PubMed

Neuschulz, J; Schaefer, I; Scheer, M; Christ, H; Braumann, B

2013-07-01

In order to visualize and quantify the direction and extent of morphological upper-jaw changes in infants with unilateral cleft lip and palate (UCLP) during early orthodontic treatment, a three-dimensional method of cast analysis for routine application was developed. In the present investigation, this method was used to identify reaction patterns associated with specific cleft forms. The study included a cast series reflecting the upper-jaw situations of 46 infants with complete (n=27) or incomplete (n=19) UCLP during week 1 and months 3, 6, and 12 of life. Three-dimensional datasets were acquired and visualized with scanning software (DigiModel®; OrthoProof, The Netherlands). Following interactive identification of landmarks on the digitized surface relief, a defined set of representative linear parameters were three-dimensionally measured. At the same time, the three-dimensional surfaces of one patient series were superimposed based on a defined reference plane. Morphometric differences were statistically analyzed. Thanks to the user-friendly software, all landmarks could be identified quickly and reproducibly, thus, allowing for simultaneous three-dimensional measurement of all defined parameters. The measured values revealed that significant morphometric differences were present in all three planes of space between the two patient groups. Patients with complete UCLP underwent significantly larger reductions in cleft width (p<0.001), and sagittal growth in the complete UCLP group exceeded sagittal growth in the incomplete UCLP group by almost 50% within the first year of life. Based on patients with incomplete versus complete UCLP, different reaction patterns were identified that depended not on apparent severities of malformation but on cleft forms.

An intermediate-scale model for thermal hydrology in low-relief permafrost-affected landscapes

DOE PAGES

Jan, Ahmad; Coon, Ethan T.; Painter, Scott L.; ...

2017-07-10

Integrated surface/subsurface models for simulating the thermal hydrology of permafrost-affected regions in a warming climate have recently become available, but computational demands of those new process-rich simu- lation tools have thus far limited their applications to one-dimensional or small two-dimensional simulations. We present a mixed-dimensional model structure for efficiently simulating surface/subsurface thermal hydrology in low-relief permafrost regions at watershed scales. The approach replaces a full three-dimensional system with a two-dimensional overland thermal hydrology system and a family of one-dimensional vertical columns, where each column represents a fully coupled surface/subsurface thermal hydrology system without lateral flow. The system is then operatormore » split, sequentially updating the overland flow system without sources and the one-dimensional columns without lateral flows. We show that the app- roach is highly scalable, supports subcycling of different processes, and compares well with the corresponding fully three-dimensional representation at significantly less computational cost. Those advances enable recently developed representations of freezing soil physics to be coupled with thermal overland flow and surface energy balance at scales of 100s of meters. Furthermore developed and demonstrated for permafrost thermal hydrology, the mixed-dimensional model structure is applicable to integrated surface/subsurface thermal hydrology in general.« less

Right-Handed Helical Foldamers Consisting of De Novo d -AApeptides

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

Teng, Peng; Ma, Ning; Cerrato, Darrell Cole

New types of foldamer scaffolds are formidably challenging to design and synthesize, yet highly desirable as structural mimics of peptides/proteins with a wide repertoire of functions. In particular, the development of peptidomimetic helical foldamers holds promise for new biomaterials, catalysts, and drug molecules. Unnatural l-sulfono-γ-AApeptides were recently developed and shown to have potential applications in both biomedical and material sciences. However, d-sulfono-γ-AApeptides, the enantiomers of l-sulfono-γ-AApeptides, have never been studied due to the lack of high-resolution three-dimensional structures to guide structure-based design. Herein, we report the first synthesis and X-ray crystal structures of a series of 2:1 l-amino acid/d-sulfono-γ-AApeptide hybridmore » foldamers, and elucidate their folded conformation at the atomic level. Single-crystal X-ray crystallography indicates that this class of oligomers folds into well-defined right-handed helices with unique helical parameters. The helical structures were consistent with data obtained from solution 2D NMR, CD studies, and molecular dynamics simulations. Our findings are expected to inspire the structure-based design of this type of unique folding biopolymers for biomaterials and biomedical applications.« less

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.

Improving Mixed Variable Optimization of Computational and Model Parameters Using Multiple Surrogate Functions

DTIC Science & Technology

2008-03-01

multiplicative corrections as well as space mapping transformations for models defined over a lower dimensional space. A corrected surrogate model for the...correction functions used in [72]. If the low fidelity model g(x̃) is defined over a lower dimensional space then a space mapping transformation is...required. As defined in [21, 72], space mapping is a method of mapping between models of different dimensionality or fidelity. Let P denote the space

Electronic structure, charge transfer, and intrinsic luminescence of gadolinium oxide nanoparticles: Experiment and theory

NASA Astrophysics Data System (ADS)

Zatsepin, D. A.; Boukhvalov, D. W.; Zatsepin, A. F.; Kuznetsova, Yu. A.; Mashkovtsev, M. A.; Rychkov, V. N.; Shur, V. Ya.; Esin, A. A.; Kurmaev, E. Z.

2018-04-01

The cubic (c) and monoclinic (m) polymorphs of Gd2O3 were studied using the combined analysis of several materials science techniques - X-ray diffraction (XRD), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and photoluminescence (PL) spectroscopy. Density functional theory (DFT) based calculations for the samples under study were performed as well. The cubic phase of gadolinium oxide (c-Gd2O3) synthesized using a precipitation method exhibits spheroidal-like nanoclusters with well-defined edges assembled from primary nanoparticles with an average size of 50 nm, whereas the monoclinic phase of gadolinium oxide (m-Gd2O3) deposited using explosive pyrolysis has a denser structure compared with natural gadolinia. This phase also has a structure composed of three-dimensional complex agglomerates without clear-edged boundaries that are ∼21 nm in size plus a cubic phase admixture of only 2 at.% composed of primary edge-boundary nanoparticles ∼15 nm in size. These atomic features appear in the electronic structure as different defects ([Gd…Osbnd OH] and [Gd…Osbnd O]) and have dissimilar contributions to the charge-transfer processes among the appropriate electronic states with ambiguous contributions in the Gd 5р - O 2s core-like levels in the valence band structures. The origin of [Gd…Osbnd OH] defects found by XPS was well-supported by PL analysis. The electronic and atomic structures of the synthesized gadolinias calculated using DFT were compared and discussed on the basis of the well-known joint OKT-van der Laan model, and good agreement was established.

Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

PubMed Central

Pietilä, Maija K.; Laurinmäki, Pasi; Russell, Daniel A.; Ko, Ching-Chung; Jacobs-Sera, Deborah; Butcher, Sarah J.

2013-01-01

Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice. PMID:23283946

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

PubMed Central

Baker, T. S.; Olson, N. H.; Fuller, S. D.

1999-01-01

Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969

Method to planarize three-dimensional structures to enable conformal electrodes

DOEpatents

Nikolic, Rebecca J; Conway, Adam M; Graff, Robert T; Reinhardt, Catherine; Voss, Lars F; Shao, Qinghui

2012-11-20

Methods for fabricating three-dimensional PIN structures having conformal electrodes are provided, as well as the structures themselves. The structures include a first layer and an array of pillars with cavity regions between the pillars. A first end of each pillar is in contact with the first layer. A segment is formed on the second end of each pillar. The cavity regions are filled with a fill material, which may be a functional material such as a neutron sensitive material. The fill material covers each segment. A portion of the fill material is etched back to produce an exposed portion of the segment. A first electrode is deposited onto the fill material and each exposed segment, thereby forming a conductive layer that provides a common contact to each the exposed segment. A second electrode is deposited onto the first layer.

Magnetic diagnostics for equilibrium reconstructions in the presence of nonaxisymmetric eddy current distributions in tokamaks (invited).

PubMed

Berzak, L; Jones, A D; Kaita, R; Kozub, T; Logan, N; Majeski, R; Menard, J; Zakharov, L

2010-10-01

The lithium tokamak experiment (LTX) is a modest-sized spherical tokamak (R(0)=0.4 m and a=0.26 m) designed to investigate the low-recycling lithium wall operating regime for magnetically confined plasmas. LTX will reach this regime through a lithium-coated shell internal to the vacuum vessel, conformal to the plasma last-closed-flux surface, and heated to 300-400 °C. This structure is highly conductive and not axisymmetric. The three-dimensional nature of the shell causes the eddy currents and magnetic fields to be three-dimensional as well. In order to analyze the plasma equilibrium in the presence of three-dimensional eddy currents, an extensive array of unique magnetic diagnostics has been implemented. Sensors are designed to survive high temperatures and incidental contact with lithium and provide data on toroidal asymmetries as well as full coverage of the poloidal cross-section. The magnetic array has been utilized to determine the effects of nonaxisymmetric eddy currents and to model the start-up phase of LTX. Measurements from the magnetic array, coupled with two-dimensional field component modeling, have allowed a suitable field null and initial plasma current to be produced. For full magnetic reconstructions, a three-dimensional electromagnetic model of the vacuum vessel and shell is under development.

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives.

PubMed

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q (2) values of 0.753 and 0.770, and r (2) values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2'-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure-property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature.

Open Sim and Sloodle Integration for Preservice Foreign Language Teachers' Continuing Professional Development: A Comparative Analysis of Learning Effectiveness Using the Community of Inquiry Model

ERIC Educational Resources Information Center

Pellas, Nikolaos; Boumpa, Anna

2016-01-01

A considerable interest in using three-dimensional multi-user virtual worlds for different educational disciplines has been widely observed. Despite the potential benefits of this technology, many questions still remain open, as far as the design of appropriate activities in well-defined instructional design frameworks and their effectiveness on…

Mesenchymal Stem Cells Sense Three Dimensional Type I Collagen through Discoidin Domain Receptor 1.

PubMed

Lund, A W; Stegemann, J P; Plopper, G E

2009-01-01

The extracellular matrix provides structural and organizational cues for tissue development and defines and maintains cellular phenotype during cell fate determination. Multipotent mesenchymal stem cells use this matrix to tightly regulate the balance between their differentiation potential and self-renewal in the native niche. When understood, the mechanisms that govern cell-matrix crosstalk during differentiation will allow for efficient engineering of natural and synthetic matrices to specifically direct and maintain stem cell phenotype. This work identifies the discoidin domain receptor 1 (DDR1), a collagen activated receptor tyrosine kinase, as a potential link through which stem cells sense and respond to the 3D organization of their extracellular matrix microenvironment. DDR1 is dependent upon both the structure and proteolytic state of its collagen ligand and is specifically expressed and localized in three dimensional type I collagen culture. Inhibition of DDR1 expression results in decreased osteogenic potential, increased cell spreading, stress fiber formation and ERK1/2 phosphorylation. Additionally, loss of DDR1 activity alters the cell-mediated organization of the naïve type I collagen matrix. Taken together, these results demonstrate a role for DDR1 in the stem cell response to and interaction with three dimensional type I collagen. Dynamic changes in cell shape in 3D culture and the tuning of the local ECM microstructure, directs crosstalk between DDR1 and two dimensional mechanisms of osteogenesis that can alter their traditional roles.

A nitrogen-doped 3D hierarchical carbon/sulfur composite for advanced lithium sulfur batteries

NASA Astrophysics Data System (ADS)

Liu, Xiaoyan; Huang, Wenlong; Wang, Dongdong; Tian, Jianhua; Shan, Zhongqiang

2017-07-01

Hybrid nanostructures containing one-dimensional (1D) carbon nanotubes (CNTs) and three-dimensional (3D) mesoporous carbon sphere have many promising applications due to their unique physical chemical properties. In this study, a novel 3D hierarchical carbon material (MCCNT) composed of mesoporous carbon sphere core and nitrogen rich CNTs shell is successfully prepared via an aerosol spray and subsequent chemical vapor deposition (CVD) processes. Owning to its well defined porous structure and favorable conductive framework, MCCNT is used as a potential sulfur host in lithium sulfur batteries through a classic melt-diffusion method. When cycled at a current density of 0.2 C (1 C = 1675 mA h g-1), it delivers an initial capacity as high as 1438.7 mAh g-1. Even if the current density increase to 1 C, the specific capacity still remain up to 534.6 mAh g-1 after 300 cycles. The enhanced electrochemical performance can be attributed to the hybrid structure of MCCNT, in which, the porous core works as a host to confine sulfur and accommodate volume expansion and the external CNTs provide excellent electron and ion conductive frame work. Furthermore, the in-situ doped nitrogen on the surface of CNTs enables effective trapping of lithium polysulfides, leading to a much-improved cycling performance.

Lax representations for matrix short pulse equations

NASA Astrophysics Data System (ADS)

Popowicz, Z.

2017-10-01

The Lax representation for different matrix generalizations of Short Pulse Equations (SPEs) is considered. The four-dimensional Lax representations of four-component Matsuno, Feng, and Dimakis-Müller-Hoissen-Matsuno equations are obtained. The four-component Feng system is defined by generalization of the two-dimensional Lax representation to the four-component case. This system reduces to the original Feng equation, to the two-component Matsuno equation, or to the Yao-Zang equation. The three-component version of the Feng equation is presented. The four-component version of the Matsuno equation with its Lax representation is given. This equation reduces the new two-component Feng system. The two-component Dimakis-Müller-Hoissen-Matsuno equations are generalized to the four-parameter family of the four-component SPE. The bi-Hamiltonian structure of this generalization, for special values of parameters, is defined. This four-component SPE in special cases reduces to the new two-component SPE.

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.

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.

Self-assembly of knots and links

NASA Astrophysics Data System (ADS)

Orlandini, Enzo; Polles, Guido; Marenduzzo, Davide; Micheletti, Cristian

2017-03-01

Guiding the self-assembly of identical building blocks towards complex three-dimensional structures with a set of desired properties is a major goal in material science, chemistry and physics. A particularly challenging problem, especially explored in synthetic chemistry, is that of self-assembling closed structures with a target topology starting by simple geometrical templates. Here we overview and revisit recent advancements, based on stochastic simulations, where the geometry of rigid helical templates with functionalised sticky ends has been designed for self-assembling efficiently and reproducibly into a wide range of three-dimensional closed structures. Notably, these include non trivial topologies of links and knots, including the 819 knot that we had predicted to be highly encodable and that has only recently been obtained experimentally. By appropriately tuning the parameters that define the template shape, we show that, for fixed concentration of templates, the assembly process can be directed towards the formation of specific knotted and linked structures such as the trefoils, pentafoil knots, Hopf and Solomon links. More exotic and unexpected knots and links are also found. Our results should be relevant to the design of new protocols that can both increase and broaden the population of synthetise molecular knots and catenanes.

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.

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…

Two-Dimensional Stoichiometric Boron Oxides as a Versatile Platform for Electronic Structure Engineering.

PubMed

Zhang, Ruiqi; Li, Zhenyu; Yang, Jinlong

2017-09-21

Oxides of two-dimensional (2D) atomic crystals have been widely studied due to their unique properties. In most 2D oxides, oxygen acts as a functional group, which makes it difficult to control the degree of oxidation. Because borophene is an electron-deficient system, it is expected that oxygen will be intrinsically incorporated into the basal plane of borophene, forming stoichiometric 2D boron oxide (BO) structures. By using first-principles global optimization, we systematically explore structures and properties of 2D BO systems with well-defined degrees of oxidation. Stable B-O-B and OB 3 tetrahedron structure motifs are identified in these structures. Interesting properties, such as strong linear dichroism, Dirac node-line (DNL) semimetallicity, and negative differential resistance, have been predicted for these systems. Our results demonstrate that 2D BO represents a versatile platform for electronic structure engineering via tuning the stoichiometric degree of oxidation, which leads to various technological applications.

Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction.

PubMed

Dukowic-Schulze, Stefanie; Liu, Chang; Chen, Changbin

2018-01-01

DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.

Micro-Mirrors for Nanoscale Three-Dimensional Microscopy

PubMed Central

Seale, Kevin; Janetopoulos, Chris; Wikswo, John

2013-01-01

A research-grade optical microscope is capable of resolving fine structures in two-dimensional images. However, three-dimensional resolution, or the ability of the microscope to distinguish between objects lying above or below the focal plane from in-focus objects, is not nearly as good as in-plane resolution. In this issue of ACS Nano, McMahon et al. report the use of mirrored pyramidal wells with a conventional microscope for rapid, 3D localization and tracking of nanoparticles. Mirrors have been used in microscopy before, but recent work with MPWs is unique because it enables the rapid determination of the x-, y-, and z-position of freely diffusing nanoparticles and cellular nanostructures with unprecedented speed and spatial accuracy. As inexpensive tools for 3D visualization, mirrored pyramidal wells may prove to be invaluable aids in nanotechnology and engineering of nanomaterials. PMID:19309167

A New Approach to Galaxy Morphology. I. Analysis of the Sloan Digital Sky Survey Early Data Release

NASA Astrophysics Data System (ADS)

Abraham, Roberto G.; van den Bergh, Sidney; Nair, Preethi

2003-05-01

In this paper we present a new statistic for quantifying galaxy morphology based on measurements of the Gini coefficient of galaxy light distributions. This statistic is easy to measure and is commonly used in econometrics to measure how wealth is distributed in human populations. When applied to galaxy images, the Gini coefficient provides a quantitative measure of the inequality with which a galaxy's light is distributed among its constituent pixels. We measure the Gini coefficient of local galaxies in the Early Data Release of the Sloan Digital Sky Survey and demonstrate that this quantity is closely correlated with measurements of central concentration, but with significant scatter. This scatter is almost entirely due to variations in the mean surface brightness of galaxies. By exploring the distribution of galaxies in the three-dimensional parameter space defined by the Gini coefficient, central concentration, and mean surface brightness, we show that all nearby galaxies lie on a well-defined two-dimensional surface (a slightly warped plane) embedded within a three-dimensional parameter space. By associating each galaxy sample with the equation of this plane, we can encode the morphological composition of the entire SDSS g*-band sample using the following three numbers: {22.451, 5.366, 7.010}. The i*-band sample is encoded as {22.149, 5.373, and 7.627}.

Structural consequences of metallothionein dimerization: solution structure of the isolated Cd4-alpha-domain and comparison with the holoprotein dimer.

PubMed

Ejnik, John W; Muñoz, Amalia; DeRose, Eugene; Shaw, C Frank; Petering, David H

2003-07-22

The NMR determination of the structure of Cd(7)-metallothionein was done previously using a relatively large protein concentration that favors dimer formation. The reactivity of the protein is also affected under this condition. To examine the influence of protein concentration on metallothionein conformation, the isolated Cd(4)-alpha-domain was prepared from rabbit metallothionein-2 (MT 2), and its three-dimensional structure was determined by heteronuclear, (1)H-(111)Cd, and homonuclear, (1)H-(1)H NMR, correlation experiments. The three-dimensional structure was refined using distance and angle constraints derived from these two-dimensional NMR data sets and a distance geometry/simulated annealing protocol. The backbone superposition of the alpha-domain from rabbit holoprotein Cd(7)-MT 2 and the isolated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A. Nevertheless, the conformations of the two Cd-thiolate clusters were distinctly different at two of the cadmium centers. In addition, solvent access to the sulfhydryl ligands of the isolated Cd(4)-alpha cluster was 130% larger due to this small change in cluster geometry. To probe whether these differences were an artifact of the structure calculation, the Cd(4)-alpha-domain structure in rabbit Cd(7)-MT 2 was redetermined, using the previously defined set of NOEs and the present calculation protocol. All calculations employed the same ionic radius for Cd(2+) and same cadmium-thiolate bond distance. The newly calculated structure matched the original with an RMSD of 1.24 A. It is hypothesized that differences in the two alpha-domain structures result from a perturbation of the holoprotein structure because of head-to-tail dimerization under the conditions of the NMR experiments.

Bottom-up Design of Three-Dimensional Carbon-Honeycomb with Superb Specific Strength and High Thermal Conductivity.

PubMed

Pang, Zhenqian; Gu, Xiaokun; Wei, Yujie; Yang, Ronggui; Dresselhaus, Mildred S

2017-01-11

Low-dimensional carbon allotropes, from fullerenes, carbon nanotubes, to graphene, have been broadly explored due to their outstanding and special properties. However, there exist significant challenges in retaining such properties of basic building blocks when scaling them up to three-dimensional materials and structures for many technological applications. Here we show theoretically the atomistic structure of a stable three-dimensional carbon honeycomb (C-honeycomb) structure with superb mechanical and thermal properties. A combination of sp 2 bonding in the wall and sp 3 bonding in the triple junction of C-honeycomb is the key to retain the stability of C-honeycomb. The specific strength could be the best in structural carbon materials, and this strength remains at a high level but tunable with different cell sizes. C-honeycomb is also found to have a very high thermal conductivity, for example, >100 W/mK along the axis of the hexagonal cell with a density only ∼0.4 g/cm 3 . Because of the low density and high thermal conductivity, the specific thermal conductivity of C-honeycombs is larger than most engineering materials, including metals and high thermal conductivity semiconductors, as well as lightweight CNT arrays and graphene-based nanocomposites. Such high specific strength, high thermal conductivity, and anomalous Poisson's effect in C-honeycomb render it appealing for the use in various engineering practices.

Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging

DOE PAGES

Ishikawa, Ryo; Lupini, Andrew R.; Hinuma, Yoyo; ...

2014-11-26

To completely understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us tomore » measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation.« less

Investigating the Role of Surface Materials and Three Dimensional Architecture on In Vitro Differentiation of Porcine Monocyte-Derived Dendritic Cells

PubMed Central

Hartmann, Sofie Bruun; Mohanty, Soumyaranjan; Skovgaard, Kerstin; Brogaard, Louise; Flagstad, Frederikke Bjergvang; Emnéus, Jenny; Wolff, Anders; Summerfield, Artur; Jungersen, Gregers

2016-01-01

In vitro generation of dendritic-like cells through differentiation of peripheral blood monocytes is typically done using two-dimensional polystyrene culture plates. In the process of optimising cell culture techniques, engineers have developed fluidic micro-devises usually manufactured in materials other than polystyrene and applying three-dimensional structures more similar to the in vivo environment. Polydimethylsiloxane (PDMS) is an often used polymer for lab-on-a-chip devices but not much is known about the effect of changing the culture surface material from polystyrene to PDMS. In the present study the differentiation of porcine monocytes to monocyte-derived dendritic cells (moDCs) was investigated using CD172apos pig blood monocytes stimulated with GM-CSF and IL-4. Monocytes were cultured on surfaces made of two- and three-dimensional polystyrene as well as two- and three-dimensional PDMS and carbonised three-dimensional PDMS. Cells cultured conventionally (on two-dimensional polystyrene) differentiated into moDCs as expected. Interestingly, gene expression of a wide range of cytokines, chemokines, and pattern recognition receptors was influenced by culture surface material and architecture. Distinct clustering of cells, based on similar expression patterns of 46 genes of interest, was seen for cells isolated from two- and three-dimensional polystyrene as well as two- and three-dimensional PDMS. Changing the material from polystyrene to PDMS resulted in cells with expression patterns usually associated with macrophage expression (upregulation of CD163 and downregulation of CD1a, FLT3, LAMP3 and BATF3). However, this was purely based on gene expression level, and no functional assays were included in this study which would be necessary in order to classify the cells as being macrophages. When changing to three-dimensional culture the cells became increasingly activated in terms of IL6, IL8, IL10 and CCR5 gene expression. Further stimulation with LPS resulted in a slight increase in the expression of maturation markers (SLA-DRB1, CD86 and CD40) as well as cytokines (IL6, IL8, IL10 and IL23A) but the influence of the surfaces was unchanged. These findings highlights future challenges of combining and comparing data generated from microfluidic cell culture-devices made using alternative materials to data generated using conventional polystyrene plates used by most laboratories today. PMID:27362493

Investigating the Role of Surface Materials and Three Dimensional Architecture on In Vitro Differentiation of Porcine Monocyte-Derived Dendritic Cells.

PubMed

Hartmann, Sofie Bruun; Mohanty, Soumyaranjan; Skovgaard, Kerstin; Brogaard, Louise; Flagstad, Frederikke Bjergvang; Emnéus, Jenny; Wolff, Anders; Summerfield, Artur; Jungersen, Gregers

2016-01-01

In vitro generation of dendritic-like cells through differentiation of peripheral blood monocytes is typically done using two-dimensional polystyrene culture plates. In the process of optimising cell culture techniques, engineers have developed fluidic micro-devises usually manufactured in materials other than polystyrene and applying three-dimensional structures more similar to the in vivo environment. Polydimethylsiloxane (PDMS) is an often used polymer for lab-on-a-chip devices but not much is known about the effect of changing the culture surface material from polystyrene to PDMS. In the present study the differentiation of porcine monocytes to monocyte-derived dendritic cells (moDCs) was investigated using CD172apos pig blood monocytes stimulated with GM-CSF and IL-4. Monocytes were cultured on surfaces made of two- and three-dimensional polystyrene as well as two- and three-dimensional PDMS and carbonised three-dimensional PDMS. Cells cultured conventionally (on two-dimensional polystyrene) differentiated into moDCs as expected. Interestingly, gene expression of a wide range of cytokines, chemokines, and pattern recognition receptors was influenced by culture surface material and architecture. Distinct clustering of cells, based on similar expression patterns of 46 genes of interest, was seen for cells isolated from two- and three-dimensional polystyrene as well as two- and three-dimensional PDMS. Changing the material from polystyrene to PDMS resulted in cells with expression patterns usually associated with macrophage expression (upregulation of CD163 and downregulation of CD1a, FLT3, LAMP3 and BATF3). However, this was purely based on gene expression level, and no functional assays were included in this study which would be necessary in order to classify the cells as being macrophages. When changing to three-dimensional culture the cells became increasingly activated in terms of IL6, IL8, IL10 and CCR5 gene expression. Further stimulation with LPS resulted in a slight increase in the expression of maturation markers (SLA-DRB1, CD86 and CD40) as well as cytokines (IL6, IL8, IL10 and IL23A) but the influence of the surfaces was unchanged. These findings highlights future challenges of combining and comparing data generated from microfluidic cell culture-devices made using alternative materials to data generated using conventional polystyrene plates used by most laboratories today.

An Example of Body-Centered Cubic Crystal Structure: The Atomium in Brussels as an Educative Tool for Introductory Materials Chemistry

ERIC Educational Resources Information Center

Pinto, Gabriel

2012-01-01

When students are introduced to the ways in which atoms are arranged in crystal structures, transposing the textbook illustrations into three-dimensional structures is difficult for some of them. To facilitate this transition, this article describes an approach to the study of the structure of solids through a well-known monument, the Atomium in…

Production of Human Pluripotent Stem Cell Therapeutics Under Defined Xeno-free Conditions: Progress and Challenges

PubMed Central

Fan, Yongjia; Wu, Jincheng; Ashok, Preeti; Hsiung, Michael; Tzanakakis, Emmanuel S.

2014-01-01

Recent advances on human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) have brought us closer to the realization of their clinical potential. Nonetheless, tissue engineering and regenerative medicine applications will require the generation of hPSC products well beyond the laboratory scale. This also mandates the production of hPSC therapeutics in fully-defined, xeno-free systems and in a reproducible manner. Toward this goal, we summarize current developments in defined media free of animal-derived components for hPSC culture. Bioinspired and synthetic extracellular matrices for the attachment growth and differentiation of hPSCs are also reviewed. Given that most progress in xeno-free medium and substrate development has been demonstrated in two-dimensional rather than three dimensional culture systems, translation from the former to the latter poses unique difficulties. These challenges are discussed in the context of cultivation platforms of hPSCs as aggregates, on microcarriers or after encapsulation in biocompatible scaffolds. PMID:25077810

Production of human pluripotent stem cell therapeutics under defined xeno-free conditions: progress and challenges.

PubMed

Fan, Yongjia; Wu, Jincheng; Ashok, Preeti; Hsiung, Michael; Tzanakakis, Emmanuel S

2015-02-01

Recent advances on human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) have brought us closer to the realization of their clinical potential. Nonetheless, tissue engineering and regenerative medicine applications will require the generation of hPSC products well beyond the laboratory scale. This also mandates the production of hPSC therapeutics in fully-defined, xeno-free systems and in a reproducible manner. Toward this goal, we summarize current developments in defined media free of animal-derived components for hPSC culture. Bioinspired and synthetic extracellular matrices for the attachment, growth and differentiation of hPSCs are also reviewed. Given that most progress in xeno-free medium and substrate development has been demonstrated in two-dimensional rather than three dimensional culture systems, translation from the former to the latter poses unique difficulties. These challenges are discussed in the context of cultivation platforms of hPSCs as aggregates, on microcarriers or after encapsulation in biocompatible scaffolds.

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.

Spatial patterns in the effects of fire on savanna vegetation three-dimensional structure.

PubMed

Levick, Shaun R; Asner, Gregory P; Smit, Izak P J

2012-12-01

Spatial variability in the effects of fire on savanna vegetation structure is seldom considered in ecology, despite the inherent heterogeneity of savanna landscapes. Much has been learned about the effects of fire on vegetation structure from long-term field experiments, but these are often of limited spatial extent and do not encompass different hillslope catena elements. We mapped vegetation three-dimensional (3-D) structure over 21 000 ha in nine savanna landscapes (six on granite, three on basalt), each with contrasting long-term fire histories (higher and lower fire frequency), as defined from a combination of satellite imagery and 67 years of management records. Higher fire frequency areas contained less woody canopy cover than their lower fire frequency counterparts in all landscapes, and woody cover reduction increased linearly with increasing difference in fire frequency (r2 = 0.58, P = 0.004). Vegetation height displayed a more heterogeneous response to difference in fire frequency, with taller canopies present in the higher fire frequency areas of the wetter sites. Vegetation 3-D structural differences between areas of higher and lower fire frequency differed between geological substrates and varied spatially across hillslopes. Fire had the greatest relative impact on vegetation structure on nutrient-rich basalt substrates, and it imparted different structural responses upon vegetation in upland, midslope, and lowland topographic positions. These results highlight the complexity of fire vegetation relationships in savanna systems, and they suggest that underlying landscape heterogeneity needs more explicit incorporation into fire management policies.

Three-dimensional solution structure of lactoferricin B, an antimicrobial peptide derived from bovine lactoferrin.

PubMed

Hwang, P M; Zhou, N; Shan, X; Arrowsmith, C H; Vogel, H J

1998-03-24

The solution structure of bovine lactoferricin (LfcinB) has been determined using 2D 1H NMR spectroscopy. LfcinB is a 25-residue antimicrobial peptide released by pepsin cleavage of lactoferrin, an 80 kDa iron-binding glycoprotein with many immunologically important functions. The NMR structure of LfcinB reveals a somewhat distorted antiparallel beta-sheet. This contrasts with the X-ray structure of bovine lactoferrin, in which residues 1-13 (of LfcinB) form an alpha-helix. Hence, this region of lactoferricin B appears able to adopt a helical or sheetlike conformation, similar to what has been proposed for the amyloidogenic prion proteins and Alzheimer's beta-peptides. LfcinB has an extended hydrophobic surface comprised of residues Phe1, Cys3, Trp6, Trp8, Pro16, Ile18, and Cys20. The side chains of these residues are well-defined in the NMR structure. Many hydrophilic and positively charged residues surround the hydrophobic surface, giving LfcinB an amphipathic character. LfcinB bears numerous similarities to a vast number of cationic peptides which exert their antimicrobial activities through membrane disruption. The structures of many of these peptides have been well characterized, and models of their membrane-permeabilizing mechanisms have been proposed. The NMR solution structure of LfcinB may be more relevant to membrane interaction than that suggested by the X-ray structure of intact lactoferrin. Based on the solution structure, it is now possible to propose potential mechanisms for the antimicrobial action of LfcinB.

Atomic Layer Deposition of Pd Nanoparticles on TiO₂ Nanotubes for Ethanol Electrooxidation: Synthesis and Electrochemical Properties.

PubMed

Assaud, Loïc; Brazeau, Nicolas; Barr, Maïssa K S; Hanbücken, Margrit; Ntais, Spyridon; Baranova, Elena A; Santinacci, Lionel

2015-11-11

Palladium nanoparticles are grown on TiO2 nanotubes by atomic layer deposition (ALD), and the resulting three-dimensional nanostructured catalysts are studied for ethanol electrooxidation in alkaline media. The morphology, the crystal structure, and the chemical composition of the Pd particles are fully characterized using scanning and transmission electron microscopies, X-ray diffraction, and X-ray photoelectron spectroscopy. The characterization revealed that the deposition proceeds onto the entire surface of the TiO2 nanotubes leading to the formation of well-defined and highly dispersed Pd nanoparticles. The electrooxidation of ethanol on Pd clusters deposited on TiO2 nanotubes shows not only a direct correlation between the catalytic activity and the particle size but also a steep increase of the response due to the enhancement of the metal-support interaction when the crystal structure of the TiO2 nanotubes is modified by annealing at 450 °C in air.

Artificial two-dimensional polar metal at room temperature.

PubMed

Cao, Yanwei; Wang, Zhen; Park, Se Young; Yuan, Yakun; Liu, Xiaoran; Nikitin, Sergey M; Akamatsu, Hirofumi; Kareev, M; Middey, S; Meyers, D; Thompson, P; Ryan, P J; Shafer, Padraic; N'Diaye, A; Arenholz, E; Gopalan, Venkatraman; Zhu, Yimei; Rabe, Karin M; Chakhalian, J

2018-04-18

Polar metals, commonly defined by the coexistence of polar crystal structure and metallicity, are thought to be scarce because the long-range electrostatic fields favoring the polar structure are expected to be fully screened by the conduction electrons of a metal. Moreover, reducing from three to two dimensions, it remains an open question whether a polar metal can exist. Here we report on the realization of a room temperature two-dimensional polar metal of the B-site type in tri-color (tri-layer) superlattices BaTiO 3 /SrTiO 3 /LaTiO 3 . A combination of atomic resolution scanning transmission electron microscopy with electron energy-loss spectroscopy, optical second harmonic generation, electrical transport, and first-principles calculations have revealed the microscopic mechanisms of periodic electric polarization, charge distribution, and orbital symmetry. Our results provide a route to creating all-oxide artificial non-centrosymmetric quasi-two-dimensional metals with exotic quantum states including coexisting ferroelectric, ferromagnetic, and superconducting phases.

Artificial two-dimensional polar metal at room temperature

DOE PAGES

Cao, Yanwei; Wang, Zhen; Park, Se Young; ...

2018-04-18

Polar metals, commonly defined by the coexistence of polar crystal structure and metallicity, are thought to be scarce because the long-range electrostatic fields favoring the polar structure are expected to be fully screened by the conduction electrons of a metal. Moreover, reducing from three to two dimensions, it remains an open question whether a polar metal can exist. Here we report on the realization of a room temperature two-dimensional polar metal of the B-site type in tri-color (tri-layer) superlattices BaTiO 3/SrTiO 3/LaTiO 3. A combination of atomic resolution scanning transmission electron microscopy with electron energy-loss spectroscopy, optical second harmonic generation,more » electrical transport, and first-principles calculations have revealed the microscopic mechanisms of periodic electric polarization, charge distribution, and orbital symmetry. Lastly, our results provide a route to creating all-oxide artificial non-centrosymmetric quasi-two-dimensional metals with exotic quantum states including coexisting ferroelectric, ferromagnetic, and superconducting phases.« less

Artificial two-dimensional polar metal at room temperature

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

Cao, Yanwei; Wang, Zhen; Park, Se Young

Polar metals, commonly defined by the coexistence of polar crystal structure and metallicity, are thought to be scarce because the long-range electrostatic fields favoring the polar structure are expected to be fully screened by the conduction electrons of a metal. Moreover, reducing from three to two dimensions, it remains an open question whether a polar metal can exist. Here we report on the realization of a room temperature two-dimensional polar metal of the B-site type in tri-color (tri-layer) superlattices BaTiO 3/SrTiO 3/LaTiO 3. A combination of atomic resolution scanning transmission electron microscopy with electron energy-loss spectroscopy, optical second harmonic generation,more » electrical transport, and first-principles calculations have revealed the microscopic mechanisms of periodic electric polarization, charge distribution, and orbital symmetry. Lastly, our results provide a route to creating all-oxide artificial non-centrosymmetric quasi-two-dimensional metals with exotic quantum states including coexisting ferroelectric, ferromagnetic, and superconducting phases.« less

Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways.

PubMed

Bhatia, Dhiraj; Arumugam, Senthil; Nasilowski, Michel; Joshi, Himanshu; Wunder, Christian; Chambon, Valérie; Prakash, Ved; Grazon, Chloé; Nadal, Brice; Maiti, Prabal K; Johannes, Ludger; Dubertret, Benoit; Krishnan, Yamuna

2016-12-01

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Modularity and three-dimensional isostructurality of novel synthons in sulfonamide–lactam cocrystals

PubMed Central

Bolla, Geetha; Mittapalli, Sudhir; Nangia, Ashwini

2015-01-01

The design of novel supramolecular synthons for functional groups relevant to drugs is an essential prerequisite for applying crystal engineering in the development of novel pharmaceutical cocrystals. It has been convincingly shown over the past decade that molecular level control and modulation can influence the physicochemical properties of drug cocrystals. Whereas considerable advances have been reported on the design of cocrystals for carboxylic acids and carboxamide functional groups, the sulfonamide group, which is a cornerstone of sulfa drugs, is relatively unexplored for reproducible heterosynthon-directed crystal engineering. The occurrence of synthons and isostructurality in sulfonamide–lactam cocrystals (SO2NH2⋯CONH hydrogen bonding) is analyzed to define a strategy for amide-type GRAS (generally recognized as safe) coformers with sulfonamides. Three types of supramolecular synthons are identified for the N—H donor of sulfonamide hydrogen bonding to the C=O acceptor of amide. Synthon 1: catemer synthon C 2 1(4) chain motif, synthon 2: dimer–cyclic ring synthon R 2 2(8)R 4 2(8) motifs, and synthon 3: dimer–catemer synthon of R 2 2(8)C 1 1(4)D notation. These heterosynthons of the cocrystals observed in this study are compared with the N—H⋯O dimer R 2 2(8) ring and C(4) chain motifs of the individual sulfonamide structures. The X-ray crystal structures of sulfonamide–lactam cocrystals exhibit interesting isostructurality trends with the same synthon being present. One-dimensional, two-dimensional and three-dimensional isostructurality in crystal structures is associated with isosynthons and due to their recurrence, novel heterosynthons for sulfonamide cocrystals are added to the crystal engineer’s toolkit. With the predominance of sulfa drugs in medicine, these new synthons provide rational strategies for the design of binary and potentially ternary cocrystals of sulfonamides. PMID:26175899

Modularity and three-dimensional isostructurality of novel synthons in sulfonamide-lactam cocrystals.

PubMed

Bolla, Geetha; Mittapalli, Sudhir; Nangia, Ashwini

2015-07-01

The design of novel supramolecular synthons for functional groups relevant to drugs is an essential prerequisite for applying crystal engineering in the development of novel pharmaceutical cocrystals. It has been convincingly shown over the past decade that molecular level control and modulation can influence the physicochemical properties of drug cocrystals. Whereas considerable advances have been reported on the design of cocrystals for carboxylic acids and carboxamide functional groups, the sulfonamide group, which is a cornerstone of sulfa drugs, is relatively unexplored for reproducible heterosynthon-directed crystal engineering. The occurrence of synthons and isostructurality in sulfonamide-lactam cocrystals (SO2NH2⋯CONH hydrogen bonding) is analyzed to define a strategy for amide-type GRAS (generally recognized as safe) coformers with sulfonamides. Three types of supramolecular synthons are identified for the N-H donor of sulfonamide hydrogen bonding to the C=O acceptor of amide. Synthon 1: catemer synthon C 2 (1)(4) chain motif, synthon 2: dimer-cyclic ring synthon R 2 (2)(8)R 4 (2)(8) motifs, and synthon 3: dimer-catemer synthon of R 2 (2)(8)C 1 (1)(4)D notation. These heterosynthons of the cocrystals observed in this study are compared with the N-H⋯O dimer R 2 (2)(8) ring and C(4) chain motifs of the individual sulfonamide structures. The X-ray crystal structures of sulfonamide-lactam cocrystals exhibit interesting isostructurality trends with the same synthon being present. One-dimensional, two-dimensional and three-dimensional isostructurality in crystal structures is associated with isosynthons and due to their recurrence, novel heterosynthons for sulfonamide cocrystals are added to the crystal engineer's toolkit. With the predominance of sulfa drugs in medicine, these new synthons provide rational strategies for the design of binary and potentially ternary cocrystals of sulfonamides.

Real-time three-dimensional ultrasound-assisted axillary plexus block defines soft tissue planes.

PubMed

Clendenen, Steven R; Riutort, Kevin; Ladlie, Beth L; Robards, Christopher; Franco, Carlo D; Greengrass, Roy A

2009-04-01

Two-dimensional (2D) ultrasound is commonly used for regional block of the axillary brachial plexus. In this technical case report, we described a real-time three-dimensional (3D) ultrasound-guided axillary block. The difference between 2D and 3D ultrasound is similar to the difference between plain radiograph and computer tomography. Unlike 2D ultrasound that captures a planar image, 3D ultrasound technology acquires a 3D volume of information that enables multiple planes of view by manipulating the image without movement of the ultrasound probe. Observation of the brachial plexus in cross-section demonstrated distinct linear hyperechoic tissue structures (loose connective tissue) that initially inhibited the flow of the local anesthesia. After completion of the injection, we were able to visualize the influence of arterial pulsation on the spread of the local anesthesia. Possible advantages of this novel technology over current 2D methods are wider image volume and the capability to manipulate the planes of the image without moving the probe.

A three-dimensional modelling of the layered structure of comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Penasa, L.; Massironi, M.; Naletto, G.; Simioni, E.; Ferrari, S.; Pajola, M.; Lucchetti, A.; Preusker, F.; Scholten, F.; Jorda, L.; Gaskell, R.; Ferri, F.; Marzari, F.; Davidsson, B.; Mottola, S.; Sierks, H.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Koschny, D.; Rickman, H.; Keller, H. U.; Agarwal, J.; A'Hearn, M. F.; Barucci, M. A.; Bertaux, J. L.; Bertini, I.; Cremonese, G.; Da Deppo, V.; Debei, S.; De Cecco, M.; Deller, J.; Feller, C.; Fornasier, S.; Frattin, E.; Fulle, M.; Groussin, O.; Gutierrez, P. J.; Güttler, C.; Hofmann, M.; Hviid, S. F.; Ip, W. H.; Knollenberg, J.; Kramm, J. R.; Kührt, E.; Küppers, M.; La Forgia, F.; Lara, L. M.; Lazzarin, M.; Lee, J.-C.; Lopez Moreno, J. J.; Oklay, N.; Shi, X.; Thomas, N.; Tubiana, C.; Vincent, J. B.

2017-07-01

We provide a three-dimensional model of the inner layered structure of comet 67P based on the hypothesis of an extended layering independently wrapping each lobe. A large set of terrace orientations was collected on the latest shape model and then used as a proxy for the local orientation of the surfaces of discontinuity which defines the layers. We modelled the terraces as a family of concentric ellipsoidal shells with fixed axis ratios, producing a model that is completely defined by just eight free parameters. Each lobe of 67P has been modelled independently, and the two sets of parameters have been estimated by means of non-linear optimization of the measured terrace orientations. The proposed model is able to predict the orientation of terraces, the elongation of cliffs, the linear traces observed in the Wosret and Hathor regions and the peculiar alignment of boulder-like features which has been observed in the Hapi region, which appears to be related to the inner layering of the big lobe. Our analysis allowed us to identify a plane of junction between the two lobes, further confirming the independent nature of the lobes. Our layering models differ from the best-fitting topographic ellipsoids of the surface, demonstrating that the terraces are aligned to an internal structure of discontinuities, which is unevenly exposed on the surface, suggesting a complex history of localized material removal from the nucleus.

Toward defining deep brain stimulation targets in MNI space: A subcortical atlas based on multimodal MRI, histology and structural connectivity.

PubMed

Ewert, Siobhan; Plettig, Philip; Li, Ningfei; Chakravarty, M Mallar; Collins, D Louis; Herrington, Todd M; Kühn, Andrea A; Horn, Andreas

2018-04-15

Three-dimensional atlases of subcortical brain structures are valuable tools to reference anatomy in neuroscience and neurology. For instance, they can be used to study the position and shape of the three most common deep brain stimulation (DBS) targets, the subthalamic nucleus (STN), internal part of the pallidum (GPi) and ventral intermediate nucleus of the thalamus (VIM) in spatial relationship to DBS electrodes. Here, we present a composite atlas based on manual segmentations of a multimodal high resolution brain template, histology and structural connectivity. In a first step, four key structures were defined on the template itself using a combination of multispectral image analysis and manual segmentation. Second, these structures were used as anchor points to coregister a detailed histological atlas into standard space. Results show that this approach significantly improved coregistration accuracy over previously published methods. Finally, a sub-segmentation of STN and GPi into functional zones was achieved based on structural connectivity. The result is a composite atlas that defines key nuclei on the template itself, fills the gaps between them using histology and further subdivides them using structural connectivity. We show that the atlas can be used to segment DBS targets in single subjects, yielding more accurate results compared to priorly published atlases. The atlas will be made publicly available and constitutes a resource to study DBS electrode localizations in combination with modern neuroimaging methods. Copyright © 2017 Elsevier Inc. All rights reserved.

Predicting residue-wise contact orders in proteins by support vector regression.

PubMed

Song, Jiangning; Burrage, Kevin

2006-10-03

The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography

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

Segal-Peretz, Tamar; Winterstein, Jonathan; Doxastakis, Manolis

Understanding and controlling the three-dimensional structure of block copolymer (BCP) thin films is critical for utilizing these materials for sub-20 nm nanopatterning in semiconductor devices, as well as in membranes and solar cell applications. Combining an atomic layer deposition (ALD) based technique for enhancing the contrast of BCPs in transmission electron microscopy (TEM) together with scanning TEM (STEM) tomography reveals and characterizes the three-dimensional structures of poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films with great clarity. Sequential infiltration synthesis (SIS), a block-selective technique for growing inorganic materials in BCPs films in ALD, and an emerging tool for enhancing the etch contrast ofmore » BCPs, was harnessed to significantly enhance the high-angle scattering from the polar domains of BCP films in the TEM. The power of combining SIS and STEM tomography for three dimensional (3D) characterization of BCPs films was demonstrated with the following cases: self-assembled cylindrical, lamellar, and spherical PS-PMMA thin films. In all cases, STEM tomography has revealed 3D structures that were hidden underneath the surface, including: 1) the 3D structure of defects in cylindrical and lamellar phases, 2) non-perpendicular 3D surface of grain boundaries in the cylindrical phase, and 3) the 3D arrangement of spheres in body centered cubic (BCC) and hexagonal closed pack (HCP) morphologies in the spherical phase. The 3D data of the spherical morphologies was compared to coarse-grained simulations and assisted in validating the simulations’ parameters. STEM tomography of SIS-treated BCP films enables the characterization of the exact structure used for pattern transfer, and can lead to better understating of the physics which is utilized in BCP lithography.« less

Modelling Behaviour of a Carbon Epoxy Composite Exposed to Fire: Part I-Characterisation of Thermophysical Properties.

PubMed

Tranchard, Pauline; Samyn, Fabienne; Duquesne, Sophie; Estèbe, Bruno; Bourbigot, Serge

2017-05-04

Thermophysical properties of a carbon-reinforced epoxy composite laminate (T700/M21 composite for aircraft structures) were evaluated using different innovative characterisation methods. Thermogravimetric Analysis (TGA), Simultaneous Thermal analysis (STA), Laser Flash analysis (LFA), and Fourier Transform Infrared (FTIR) analysis were used for measuring the thermal decomposition, the specific heat capacity, the anisotropic thermal conductivity of the composite, the heats of decomposition and the specific heat capacity of released gases. It permits to get input data to feed a three-dimensional (3D) model given the temperature profile and the mass loss obtained during well-defined fire scenarios (model presented in Part II of this paper). The measurements were optimised to get accurate data. The data also permit to create a public database on an aeronautical carbon fibre/epoxy composite for fire safety engineering.

Potential, velocity, and density fields from redshift-distance samples: Application - Cosmography within 6000 kilometers per second

NASA Technical Reports Server (NTRS)

Bertschinger, Edmund; Dekel, Avishai; Faber, Sandra M.; Dressler, Alan; Burstein, David

1990-01-01

A potential flow reconstruction algorithm has been applied to the real universe to reconstruct the three-dimensional potential, velocity, and mass density fields smoothed on large scales. The results are shown as maps of these fields, revealing the three-dimensional structure within 6000 km/s distance from the Local Group. The dominant structure is an extended deep potential well in the Hydra-Centaurus region, stretching across the Galactic plane toward Pavo, broadly confirming the Great Attractor (GA) model of Lynden-Bell et al. (1988). The Local Supercluster appears to be an extended ridge on the near flank of the GA, proceeding through the Virgo Southern Extension to the Virgo and Ursa Major clusters. The Virgo cluster and the Local Group are both falling toward the bottom of the GA potential well with peculiar velocities of 658 + or - 121 km/s and 565 + or - 125 km/s, respectively.

Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications.

PubMed

Kübel, Christian; Voigt, Andreas; Schoenmakers, Remco; Otten, Max; Su, David; Lee, Tan-Chen; Carlsson, Anna; Bradley, John

2005-10-01

Electron tomography is a well-established technique for three-dimensional structure determination of (almost) amorphous specimens in life sciences applications. With the recent advances in nanotechnology and the semiconductor industry, there is also an increasing need for high-resolution three-dimensional (3D) structural information in physical sciences. In this article, we evaluate the capabilities and limitations of transmission electron microscopy (TEM) and high-angle-annular-dark-field scanning transmission electron microscopy (HAADF-STEM) tomography for the 3D structural characterization of partially crystalline to highly crystalline materials. Our analysis of catalysts, a hydrogen storage material, and different semiconductor devices shows that features with a diameter as small as 1-2 nm can be resolved in three dimensions by electron tomography. For partially crystalline materials with small single crystalline domains, bright-field TEM tomography provides reliable 3D structural information. HAADF-STEM tomography is more versatile and can also be used for high-resolution 3D imaging of highly crystalline materials such as semiconductor devices.

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

Driscoll, P.C.; Gronenborn, A.M.; Beress, L.

The three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata has been determined on the basis of 489 interproton and 24 hydrogen-bonding distance restraints supplemented by 23 {phi} backbone and 21 {sub {chi}1} side-chain torsion angle restraints derived from nuclear magnetic resonance (NMR) measurements. A total of 42 structures is calculated by a hybrid metric matrix distance geometry-dynamical simulated annealing approach. Both the backbone and side-chain atom positions are well defined. The average atomic rms difference between the 42 individual SA structures and the mean structure obtained by averaging their coordinates is 0.67more » {plus minus} 0.12 {angstrom} for the backbone atoms and 0.90 {plus minus} 0.17 {angstrom} for all atoms. The core of the protein is formed by a triple-stranded antiparallel {beta}-sheet composed of residues 14-16 (strand 1), 30-34 (strand 2), and 37-41 (strand 3) with an additional mini-antiparallel {beta}-sheet at the N-terminus (residues 6-9). The first and second strands of the triple-stranded antiparallel {beta}-sheet are connected by a long exposed loop. A number of side-chain interactions are discussed in light of the structure.« less

Generation of three-dimensional body-fitted grids by solving hyperbolic partial differential equations

NASA Technical Reports Server (NTRS)

Steger, Joseph L.

1989-01-01

Hyperbolic grid generation procedures are described which have been used in external flow simulations about complex configurations. For many practical applications a single well-ordered (i.e., structured) grid can be used to mesh an entire configuration, in other problems, composite or unstructured grid procedures are needed. Although the hyperbolic partial differential equation grid generation procedure has mainly been utilized to generate structured grids, an extension of the procedure to semiunstructured grids is briefly described. Extensions of the methodology are also described using two-dimensional equations.

Generation of three-dimensional body-fitted grids by solving hyperbolic and parabolic partial differential equations

NASA Technical Reports Server (NTRS)

Steger, Joseph L.

1989-01-01

Hyperbolic grid generation procedures are described which have been used in external flow simulations about complex configurations. For many practical applications a single well-ordered (i.e., structured) grid can be used to mesh an entire configuration, in other problems, composite or unstructured grid procedures are needed. Although the hyperbolic partial differential equation grid generation procedure has mainly been utilized to generate structured grids, extension of the procedure to semiunstructured grids is briefly described. Extensions of the methodology are also described using two-dimensional equations.

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.

Stereo Science Results at Solar Minimum

NASA Technical Reports Server (NTRS)

Christian, Eric R.; Kaiser, Michael L.; Kucera Therese A.; St. Cyr, O. C.; van Driel-Gesztelyi, Lidia; Mandrini, Cristina H.

2009-01-01

The magnetic fields that drive solar activity are complex and inherently three-dimensional structures. Twisted flux ropes, magnetic reconnection and the initiation of solar storms, as well as space weather propagation through the heliosphere, are just a few of the topics that cannot properly be observed or modeled in only two dimensions. Examination of this three-dimensional complex has been hampered by the fact that solar remote sensing observations have occurred only from the Earth-Sun line, and in situ observations, while available from a greater variety of locations, have been sparse throughout the heliosphere.

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.

Silica bioreplication preserves three-dimensional spheroid structures of human pluripotent stem cells and HepG2 cells

DOE PAGES

Lou, Yan-Ru; Kanninen, Liisa; Kaehr, Bryan; ...

2015-09-01

Three-dimensional (3D) cell cultures produce more in vivo-like multicellular structures such as spheroids that cannot be obtained in two-dimensional (2D) cell cultures. Thus, they are increasingly employed as models for cancer and drug research, as well as tissue engineering. It has proven challenging to stabilize spheroid architectures for detailed morphological examination. Here we overcome this issue using a silica bioreplication (SBR) process employed on spheroids formed from human pluripotent stem cells (hPSCs) and hepatocellular carcinoma HepG2 cells cultured in the nanofibrillar cellulose (NFC) hydrogel. The cells in the spheroids are more round and tightly interacting with each other than thosemore » in 2D cultures, and they develop microvilli-like structures on the cell membranes as seen in 2D cultures. Furthermore, SBR preserves extracellular matrix-like materials and cellular proteins. In conclusion, these findings provide the first evidence of intact hPSC spheroid architectures and similar fine structures to 2D-cultured cells, providing a pathway to enable our understanding of morphogenesis in 3D cultures.« less

Silica bioreplication preserves three-dimensional spheroid structures of human pluripotent stem cells and HepG2 cells

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

Lou, Yan-Ru; Kanninen, Liisa; Kaehr, Bryan

Three-dimensional (3D) cell cultures produce more in vivo-like multicellular structures such as spheroids that cannot be obtained in two-dimensional (2D) cell cultures. Thus, they are increasingly employed as models for cancer and drug research, as well as tissue engineering. It has proven challenging to stabilize spheroid architectures for detailed morphological examination. Here we overcome this issue using a silica bioreplication (SBR) process employed on spheroids formed from human pluripotent stem cells (hPSCs) and hepatocellular carcinoma HepG2 cells cultured in the nanofibrillar cellulose (NFC) hydrogel. The cells in the spheroids are more round and tightly interacting with each other than thosemore » in 2D cultures, and they develop microvilli-like structures on the cell membranes as seen in 2D cultures. Furthermore, SBR preserves extracellular matrix-like materials and cellular proteins. In conclusion, these findings provide the first evidence of intact hPSC spheroid architectures and similar fine structures to 2D-cultured cells, providing a pathway to enable our understanding of morphogenesis in 3D cultures.« less

Silica bioreplication preserves three-dimensional spheroid structures of human pluripotent stem cells and HepG2 cells.

PubMed

Lou, Yan-Ru; Kanninen, Liisa; Kaehr, Bryan; Townson, Jason L; Niklander, Johanna; Harjumäki, Riina; Jeffrey Brinker, C; Yliperttula, Marjo

2015-09-01

Three-dimensional (3D) cell cultures produce more in vivo-like multicellular structures such as spheroids that cannot be obtained in two-dimensional (2D) cell cultures. Thus, they are increasingly employed as models for cancer and drug research, as well as tissue engineering. It has proven challenging to stabilize spheroid architectures for detailed morphological examination. Here we overcome this issue using a silica bioreplication (SBR) process employed on spheroids formed from human pluripotent stem cells (hPSCs) and hepatocellular carcinoma HepG2 cells cultured in the nanofibrillar cellulose (NFC) hydrogel. The cells in the spheroids are more round and tightly interacting with each other than those in 2D cultures, and they develop microvilli-like structures on the cell membranes as seen in 2D cultures. Furthermore, SBR preserves extracellular matrix-like materials and cellular proteins. These findings provide the first evidence of intact hPSC spheroid architectures and similar fine structures to 2D-cultured cells, providing a pathway to enable our understanding of morphogenesis in 3D cultures.

Development of a direct three-dimensional biomicrofabrication concept based on electrospraying a custom made siloxane sol.

PubMed

Sullivan, Alice C; Jayasinghe, Suwan N

2007-07-19

We demonstrate here the discovery of a unique and direct three-dimensional biomicrofabrication concept possessing the ability to revolutionize the jet-based fabrication arena. Previous work carried out on similar jet-based approaches have been successful in fabricating only vertical wallpillar-structures by the controlled deposition of stacked droplets. However, these advanced jet-techniques have not been able to directly fabricate self-supporting archeslinks (without molds or reaction methods) between adjacent structures (walls or pillars). Our work reported here gives birth to a unique type of jet determined by high intensity electric fields, which is derived from a specially formulated siloxane sol. The sol studied here has been chosen for its attractive properties (such as an excellent cross-linking nature as well as the ability to polymerize via polycondensation on deposition to its biocompatability), which promotes direct forming of biostructures with nanometer (<50 nm) sized droplets in three dimensions. We foresee that this direct three-dimensional biomicrofabrication jet technique coupled with a variety of formulated sols having focused and enhanced functionality will be explored throughout the physical and life sciences.

Evidence for coexisting magnetic order in frustrated three-dimensional honeycomb iridates Li2IrO3

NASA Astrophysics Data System (ADS)

Breznay, Nicholas; Ruiz, Alejandro; Frano, Alex; Analytis, James

The search for unconventional magnetism has found a fertile hunting ground in 5d iridium oxide (iridate) materials. The competition between coulomb, spin-orbit, and crystal field energy scales in honeycomb iridates leads to a quantum magnetic system with localized spin-1/2 moments communicating through spin-anisotropic Kitaev exchange interactions. Although early and ongoing work has focused on layered two-dimensional honeycomb compounds such as Na2IrO3 and a 4d analog, RuCl3, recently discovered polytypes of Li2IrO3 take on three-dimensional honeycomb structures. Bulk thermodynamic studies, as well as recent resonant x-ray diffraction and absorption spectroscopy experiments, have uncovered a rich phase diagram for these three-dimensional honeycomb iridates. Low temperature incommensurate and commensurate magnetic orders can be stabilized by tuning the applied magnetic field, displaying a delicate coexistence that signals highly frustrated magnetism.

From tissue to silicon to plastic: three-dimensional printing in comparative anatomy and physiology

PubMed Central

Lauridsen, Henrik; Hansen, Kasper; Nørgård, Mathias Ørum; Wang, Tobias; Pedersen, Michael

2016-01-01

Comparative anatomy and physiology are disciplines related to structures and mechanisms in three-dimensional (3D) space. For the past centuries, scientific reports in these fields have relied on written descriptions and two-dimensional (2D) illustrations, but in recent years 3D virtual modelling has entered the scene. However, comprehending complex anatomical structures is hampered by reproduction on flat inherently 2D screens. One way to circumvent this problem is in the production of 3D-printed scale models. We have applied computed tomography and magnetic resonance imaging to produce digital models of animal anatomy well suited to be printed on low-cost 3D printers. In this communication, we report how to apply such technology in comparative anatomy and physiology to aid discovery, description, comprehension and communication, and we seek to inspire fellow researchers in these fields to embrace this emerging technology. PMID:27069653

Two-dimensional protein crystals (S-layers): fundamentals and applications.

PubMed

Sleytr, U B; Sára, M; Messner, P; Pum, D

1994-10-01

Two-dimensional crystalline surface layers (S-layers) composed of protein or glycoprotein subunits are one of the most commonly observed prokaryotic cell envelope structures. Isolated S-layer subunits are endowed with the ability to assemble into monomolecular arrays in suspension, on surfaces or interfaces by an entropy-driven process. S-layer lattices are isoporous structures with functional groups located on the surface in an identical position and orientation. These characteristic features have already led to applications of S-layers as (1) ultrafiltration membranes with well-defined molecular weight cut-offs and excellent antifouling characteristics, (2) immobilization matrices for functional molecules as required for affinity and enzyme membranes, affinity microcarriers and biosensors, (3) conjugate vaccines, (4) carriers for Langmuir-Blodgett films and reconstituted biological membranes, and (5) patterning elements in molecular nanotechnology.

A coarse-grained Monte Carlo approach to diffusion processes in metallic nanoparticles

NASA Astrophysics Data System (ADS)

Hauser, Andreas W.; Schnedlitz, Martin; Ernst, Wolfgang E.

2017-06-01

A kinetic Monte Carlo approach on a coarse-grained lattice is developed for the simulation of surface diffusion processes of Ni, Pd and Au structures with diameters in the range of a few nanometers. Intensity information obtained via standard two-dimensional transmission electron microscopy imaging techniques is used to create three-dimensional structure models as input for a cellular automaton. A series of update rules based on reaction kinetics is defined to allow for a stepwise evolution in time with the aim to simulate surface diffusion phenomena such as Rayleigh breakup and surface wetting. The material flow, in our case represented by the hopping of discrete portions of metal on a given grid, is driven by the attempt to minimize the surface energy, which can be achieved by maximizing the number of filled neighbor cells.

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.

Structures with three dimensional nanofences comprising single crystal segments

DOEpatents

Goyal, Amit; Wee, Sung-Hun

2013-08-27

An article includes a substrate having a surface and a nanofence supported by the surface. The nanofence includes a multiplicity of primary nanorods and branch nanorods, each of the primary nanorods being attached to said substrate, and each of the branch nanorods being attached to a primary nanorods and/or another branch nanorod. The primary and branch nanorods are arranged in a three-dimensional, interconnected, interpenetrating, grid-like network defining interstices within the nanofence. The article further includes an enveloping layer supported by the nanofence, disposed in the interstices, and forming a coating on the primary and branch nanorods. The enveloping layer has a different composition from that of the nanofence and includes a radial p-n single junction solar cell photovoltaic material and/or a radial p-n multiple junction solar cell photovoltaic material.

Well-dispersed LiFePO4 nanoparticles anchored on a three-dimensional graphene aerogel as high-performance positive electrode materials for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Tian, Xiaohui; Zhou, Yingke; Tu, Xiaofeng; Zhang, Zhongtang; Du, Guodong

2017-02-01

A three-dimensional graphene aerogel supporting LiFePO4 nanoparticles (LFP/GA) has been synthesized by a hydrothermal process. The morphology and microstructure of LFP/GA were investigated by X-ray diffraction, scanning electron microscopy, transmission electron microscopy and thermal gravimetric analysis. The electrochemical properties were evaluated by constant-current charge/discharge tests, cyclic voltammetry and electrochemical impedance spectroscopy. Well-distributed LFP nanoparticles are anchored on both sides of graphene and then assemble into a highly porous three-dimensional aerogel architecture. Conductive graphene networks provide abundant paths to facilitate the transfer of electrons, while the aerogel structures offer plenty of interconnected open pores for the storage of electrolyte to enable the fast supply of Li ions. The LFP and graphene aerogel composites present superior specific capacity, rate capability and cycling performance in comparison to the pristine LFP or LFP supported on graphene sheets and are thus promising for lithium-ion battery applications.

Natural Strain

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1997-01-01

Logarithmic strain is the preferred measure of strain used by materials scientists, who typically refer to it as the "true strain." It was Nadai who gave it the name "natural strain," which seems more appropriate. This strain measure was proposed by Ludwik for the one-dimensional extension of a rod with length l. It was defined via the integral of dl/l to which Ludwik gave the name "effective specific strain." Today, it is after Hencky, who extended Ludwik's measure to three-dimensional analysis by defining logarithmic strains for the three principal directions.

Structure of the Espanola Basin, Rio Grande Rift, New Mexico, from SAGE seismic and gravity data

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

Ferguson, J.F.; Baldridge, W.S.; Braile, L.W.

1995-04-01

Seismic and gravity data, acquired by the SAGE program over the past twelve years, are used to define the geometry of the Espanola basin and the extent of pre-Tertiary sedimentary rocks. The Paleozoic and Mesozoic units have been thinned and removed during Laramide uplift in an area now obscured by the younger rift basin. The Espanola basin is generally a shallow, asymmetric transitional structure between deeper, better developed basins to the northeast and southwest. The gravity data indicate the presence of three narrow, but deep, structural lows arrayed along the Embudo/Pajarito fault system. These sub-basins seem to be younger thanmore » the faults on the basin margins. This apparent focussing of deformation in the later history of the basin may be a response to changes in regional stress or more local accommodation of the rift extension. Future work is planned to develop seismic data over one of these sub-basins, the Velarde graben, and to better define the gravity map in order to facilitate three-dimensional modeling.« less

Plasmonic photonic crystals realized through DNA-programmable assembly

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

Park, Daniel J.; Zhang, Chuan; Ku, Jessie C.

Three-dimensional dielectric photonic crystals have well-established enhanced light-matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed withmore » backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry-Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (~102) over the visible and near-infrared spectrum.« less

Plasmonic photonic crystals realized through DNA-programmable assembly

DOE PAGES

Park, Daniel J.; Zhang, Chuan; Ku, Jessie C.; ...

2014-12-29

Three-dimensional dielectric photonic crystals have well-established enhanced light-matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed withmore » backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry-Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (~102) over the visible and near-infrared spectrum.« less

Plasmonic photonic crystals realized through DNA-programmable assembly

PubMed Central

Park, Daniel J.; Zhang, Chuan; Ku, Jessie C.; Zhou, Yu; Schatz, George C.; Mirkin, Chad A.

2015-01-01

Three-dimensional dielectric photonic crystals have well-established enhanced light–matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed with backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry–Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (∼102) over the visible and near-infrared spectrum. PMID:25548175

Plasmonic photonic crystals realized through DNA-programmable assembly.

PubMed

Park, Daniel J; Zhang, Chuan; Ku, Jessie C; Zhou, Yu; Schatz, George C; Mirkin, Chad A

2015-01-27

Three-dimensional dielectric photonic crystals have well-established enhanced light-matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed with backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry-Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (∼10(2)) over the visible and near-infrared spectrum.

Pair distribution function study and mechanical behavior of as-cast and structurally relaxed Zr-based bulk metallic glasses

NASA Astrophysics Data System (ADS)

Fan, Cang; Liaw, P. K.; Wilson, T. W.; Choo, H.; Gao, Y. F.; Liu, C. T.; Proffen, Th.; Richardson, J. W.

2006-12-01

Contrary to reported results on structural relaxation inducing brittleness in amorphous alloys, the authors found that structural relaxation actually caused an increase in the strength of Zr55Cu35Al10 bulk metallic glass (BMG) without changing the plasticity. Three dimensional models were rebuilt for the as-cast and structurally relaxed BMGs by reverse Monte Carlo (RMC) simulations based on the pair distribution function (PDF) measured by neutron scattering. Only a small portion of the atom pairs was found to change to more dense packing. The concept of free volume was defined based on the PDF and RMC studies, and the mechanism of mechanical behavior was discussed.

Lithographically defined porous Ni-carbon nanocomposite supercapacitors.

PubMed

Xiao, Xiaoyin; Beechem, Thomas; Wheeler, David R; Burckel, D Bruce; Polsky, Ronen

2014-03-07

Ni was deposited onto lithographically-defined conductive three dimensional carbon networks to form asymmetric pseudo-capacitive electrodes. A real capacity of above 500 mF cm(-2), or specific capacitance of ∼2100 F g(-1) near the theoretical value, has been achieved. After a rapid thermal annealing process, amorphous carbon was partially converted into multilayer graphene depending on the annealing temperature and time duration. These annealed Ni-graphene composite structures exhibit enhanced charge transport kinetics relative to un-annealed Ni-carbon scaffolds indicated by a reduction in peak separation from 0.84 V to 0.29 V at a scan rate of 1000 mV s(-1).

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.

Changes in luminescence emission induced by proton irradiation: InGaAs/GaAs quantum wells and quantum dots

NASA Technical Reports Server (NTRS)

Leon, R.; Swift, G. M.; Magness, B.; Taylor, W. A.; Tang, Y. S.; Wang, K. L.; Dowd, P.; Zhang, Y. H.

2000-01-01

The photoluminescence emission from InGaAs/GaAs quantum-well and quantum-dot (QD) structures are compared after controlled irradiation with 1.5 MeV proton fluxes. Results presented here show a significant enhancement in radiation tolerance with three-dimensional quantum confinement.

Three Dimensional Flow and Pressure Patterns in a Single Pocket of a Hydrostatic Journal Bearing

NASA Technical Reports Server (NTRS)

Braun, M. Jack; Dzodzo, Milorad B.

1996-01-01

The flow in a hydrostatic pocket is described by a mathematical model that uses the three dimensional Navier-Stokes equations written in terms of the primary variables, u, v, w, and p. Using a conservative formulation, a finite volume multi-block method is applied through a collocated, body fitted grid. The flow is simulated in a shallow pocket with a depth/length ratio of 0.02. The flow structures obtained and described by the authors in their previous two dimensional models are made visible in their three dimensional aspect for the Couette flow. It has been found that the flow regimes formed central and secondary vortical cells with three dimensional corkscrew-like structures that lead the fluid on an outward bound path in the axial direction of the pocket. The position of the central vortical cell center is at the exit region of the capillary restrictor feedline. It has also been determined that a fluid turn around zone occupies all the upstream space between the floor of the pocket and the runner, thus preventing any flow exit through the upstream port. The corresponding pressure distribution under the shaft presented as well. It was clearly established that for the Couette dominated case the pressure varies significantly in the pocket in the circumferential direction, while its variation is less pronounced axially.

Three-dimensional structure of the Upper Scorpius association with the Gaia first data release

NASA Astrophysics Data System (ADS)

Galli, Phillip A. B.; Joncour, Isabelle; Moraux, Estelle

2018-06-01

Using new proper motion data from recently published catalogues, we revisit the membership of previously identified members of the Upper Scorpius association. We confirmed 750 of them as cluster members based on the convergent point method, compute their kinematic parallaxes, and combined them with Gaia parallaxes to investigate the 3D structure and geometry of the association using a robust covariance method. We find a mean distance of 146 ± 3 ± 6 pc and show that the morphology of the association defined by the brightest (and most massive) stars yields a prolate ellipsoid with dimensions of 74 × 38 × 32 pc3, while the faintest cluster members define a more elongated structure with dimensions of 98 × 24 × 18 pc3. We suggest that the different properties of both populations are an imprint of the star formation history in this region.

Hamiltonian structure of three-dimensional gravity in Vielbein formalism

NASA Astrophysics Data System (ADS)

Hajihashemi, Mahdi; Shirzad, Ahmad

2018-01-01

Considering Chern-Simons like gravity theories in three dimensions as first order systems, we analyze the Hamiltonian structure of three theories Topological massive gravity, New massive gravity, and Zwei-Dreibein Gravity. We show that these systems demonstrate a new feature of the constrained systems in which a new kind of constraints emerge due to factorization of determinant of the matrix of Poisson brackets of constraints. We find the desired number of degrees of freedom as well as the generating functional of local Lorentz transformations and diffeomorphism through canonical structure of the system. We also compare the Hamiltonian structure of linearized version of the considered models with the original ones.

Topological magnetoelectric pump in three dimensions

NASA Astrophysics Data System (ADS)

Fukui, Takahiro; Fujiwara, Takanori

2017-11-01

We study the topological pump for a lattice fermion model mainly in three spatial dimensions. We first calculate the U(1) current density for the Dirac model defined in continuous space-time to review the known results as well as to introduce some technical details convenient for the calculations of the lattice model. We next investigate the U(1) current density for a lattice fermion model, a variant of the Wilson-Dirac model. The model we introduce is defined on a lattice in space but in continuous time, which is suited for the study of the topological pump. For such a model, we derive the conserved U(1) current density and calculate it directly for the (1 +1 )-dimensional system as well as (3 +1 )-dimensional system in the limit of the small lattice constant. We find that the current includes a nontrivial lattice effect characterized by the Chern number, and therefore the pumped particle number is quantized by the topological reason. Finally, we study the topological temporal pump in 3 +1 dimensions by numerical calculations. We discuss the relationship between the second Chern number and the first Chern number, the bulk-edge correspondence, and the generalized Streda formula which enables us to compute the second Chern number using the spectral asymmetry.

Fast determination of three-dimensional fibril orientation of type-I collagen via macroscopic chirality

NASA Astrophysics Data System (ADS)

Zhuo, Guan-Yu; Chen, Mei-Yu; Yeh, Chao-Yuan; Guo, Chin-Lin; Kao, Fu-Jen

2017-01-01

Polarization-resolved second harmonic generation (SHG) microscopy is appealing for studying structural proteins and well-organized biophotonic nanostructures, due to its highly sensitized structural specificity. In recent years, it has been used to investigate the chiroptical effect, particularly SHG circular dichroism (SHG-CD) in biological tissues. Although SHG-CD attributed to macromolecular structures has been demonstrated, the corresponding quantitative analysis and interpretation on how SHG correlates with second-order susceptibility χ(2) under circularly polarized excitations remains unclear. In this study, we demonstrate a method based on macroscopic chirality to elucidate the correlation between SHG-CD and the orientation angle of the molecular structure. By exploiting this approach, three-dimensional (3D) molecular orientation of type-I collagen is revealed with only two cross polarized SHG images (i.e., interactions of left and right circular polarizations) without acquiring an image stack of varying polarization.

Adaptive optics and the eye (super resolution OCT).

PubMed

Miller, D T; Kocaoglu, O P; Wang, Q; Lee, S

2011-03-01

The combination of adaptive optics (AO) and optical coherence tomography (OCT) was first reported 8 years ago and has undergone tremendous technological advances since then. The technical benefits of adding AO to OCT (increased lateral resolution, smaller speckle, and enhanced sensitivity) increase the imaging capability of OCT in ways that make it well suited for three-dimensional (3D) cellular imaging in the retina. Today, AO-OCT systems provide ultrahigh 3D resolution (3 × 3 × 3 μm³) and ultrahigh speed (up to an order of magnitude faster than commercial OCT). AO-OCT systems have been used to capture volume images of retinal structures, previously only visible with histology, and are being used for studying clinical conditions. Here, we present representative examples of cellular structures that can be visualized with AO-OCT. We overview three studies from our laboratory that used ultrahigh-resolution AO-OCT to measure the cross-sectional profiles of individual bundles in the retinal nerve fiber layer; the diameters of foveal capillaries that define the terminal rim of the foveal avascular zone; and the spacing and length of individual cone photoreceptor outer segments as close as 0.5° from the fovea center.

A three-dimensional collagen-fiber network model of the extracellular matrix for the simulation of the mechanical behaviors and micro structures.

PubMed

Dong, Shoubin; Huang, Zetao; Tang, Liqun; Zhang, Xiaoyang; Zhang, Yongrou; Jiang, Yi

2017-07-01

The extracellular matrix (ECM) provides structural and biochemical support to cells and tissues, which is a critical factor for modulating cell dynamic behavior and intercellular communication. In order to further understand the mechanisms of the interactive relationship between cell and the ECM, we developed a three-dimensional (3D) collagen-fiber network model to simulate the micro structure and mechanical behaviors of the ECM and studied the stress-strain relationship as well as the deformation of the ECM under tension. In the model, the collagen-fiber network consists of abundant random distributed collagen fibers and some crosslinks, in which each fiber is modeled as an elastic beam and a crosslink is modeled as a linear spring with tensile limit, it means crosslinks will fail while the tensile forces exceed the limit of spring. With the given parameters of the beam and the spring, the simulated tensile stress-strain relation of the ECM highly matches the experimental results including damaged and failed behaviors. Moreover, by applying the maximal inscribed sphere method, we measured the size distribution of pores in the fiber network and learned the variation of the distribution with deformation. We also defined the alignment of the collagen-fibers to depict the orientation of fibers in the ECM quantitatively. By the study of changes of the alignment and the damaged crosslinks against the tensile strain, this paper reveals the comprehensive mechanisms of four stages of 'toe', 'linear', 'damage' and 'failure' in the tensile stress-strain relation of the ECM which can provide further insight in the study of cell-ECM interaction.

Dynamical Coupling of Intrinsically Disordered Proteins and Their Hydration Water: Comparison with Folded Soluble and Membrane Proteins

PubMed Central

Gallat, F.-X.; Laganowsky, A.; Wood, K.; Gabel, F.; van Eijck, L.; Wuttke, J.; Moulin, M.; Härtlein, M.; Eisenberg, D.; Colletier, J.-P.; Zaccai, G.; Weik, M.

2012-01-01

Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context. PMID:22828339

Full Disk Image of the Sun, March 26, 2007 Anaglyph

NASA Image and Video Library

2007-04-27

NASA Solar TErrestrial RElations Observatory STEREO satellites have provided the first three-dimensional images of the Sun. The structure of the corona shows well in this image. 3D glasses are necessary to view this image.

On the n-symplectic structure of faithful irreducible representations

NASA Astrophysics Data System (ADS)

Norris, L. K.

2017-04-01

Each faithful irreducible representation of an N-dimensional vector space V1 on an n-dimensional vector space V2 is shown to define a unique irreducible n-symplectic structure on the product manifold V1×V2 . The basic details of the associated Poisson algebra are developed for the special case N = n2, and 2n-dimensional symplectic submanifolds are shown to exist.

Mouse fetal whole intestine culture system for ex vivo manipulation of signaling pathways and three-dimensional live imaging of villus development.

PubMed

Walton, Katherine D; Kolterud, Asa

2014-09-04

Most morphogenetic processes in the fetal intestine have been inferred from thin sections of fixed tissues, providing snapshots of changes over developmental stages. Three-dimensional information from thin serial sections can be challenging to interpret because of the difficulty of reconstructing serial sections perfectly and maintaining proper orientation of the tissue over serial sections. Recent findings by Grosse et al., 2011 highlight the importance of three- dimensional information in understanding morphogenesis of the developing villi of the intestine(1). Three-dimensional reconstruction of singly labeled intestinal cells demonstrated that the majority of the intestinal epithelial cells contact both the apical and basal surfaces. Furthermore, three-dimensional reconstruction of the actin cytoskeleton at the apical surface of the epithelium demonstrated that the intestinal lumen is continuous and that secondary lumens are an artifact of sectioning. Those two points, along with the demonstration of interkinetic nuclear migration in the intestinal epithelium, defined the developing intestinal epithelium as a pseudostratified epithelium and not stratified as previously thought(1). The ability to observe the epithelium three-dimensionally was seminal to demonstrating this point and redefining epithelial morphogenesis in the fetal intestine. With the evolution of multi-photon imaging technology and three-dimensional reconstruction software, the ability to visualize intact, developing organs is rapidly improving. Two-photon excitation allows less damaging penetration deeper into tissues with high resolution. Two-photon imaging and 3D reconstruction of the whole fetal mouse intestines in Walton et al., 2012 helped to define the pattern of villus outgrowth(2). Here we describe a whole organ culture system that allows ex vivo development of villi and extensions of that culture system to allow the intestines to be three-dimensionally imaged during their development.

Protein-directed assembly of arbitrary three-dimensional nanoporous silica architectures.

PubMed

Khripin, Constantine Y; Pristinski, Denis; Dunphy, Darren R; Brinker, C Jeffrey; Kaehr, Bryan

2011-02-22

Through precise control of nanoscale building blocks, such as proteins and polyamines, silica condensing microorganisms are able to create intricate mineral structures displaying hierarchical features from nano- to millimeter-length scales. The creation of artificial structures of similar characteristics is facilitated through biomimetic approaches, for instance, by first creating a bioscaffold comprised of silica condensing moieties which, in turn, govern silica deposition into three-dimensional (3D) structures. In this work, we demonstrate a protein-directed approach to template silica into true arbitrary 3D architectures by employing cross-linked protein hydrogels to controllably direct silica condensation. Protein hydrogels are fabricated using multiphoton lithography, which enables user-defined control over template features in three dimensions. Silica deposition, under acidic conditions, proceeds throughout protein hydrogel templates via flocculation of silica nanoparticles by protein molecules, as indicated by dynamic light scattering (DLS) and time-dependent measurements of elastic modulus. Following silica deposition, the protein template can be removed using mild thermal processing yielding high surface area (625 m(2)/g) porous silica replicas that do not undergo significant volume change compared to the starting template. We demonstrate the capabilities of this approach to create bioinspired silica microstructures displaying hierarchical features over broad length scales and the infiltration/functionalization capabilities of the nanoporous silica matrix by laser printing a 3D gold image within a 3D silica matrix. This work provides a foundation to potentially understand and mimic biogenic silica condensation under the constraints of user-defined biotemplates and further should enable a wide range of complex inorganic architectures to be explored using silica transformational chemistries, for instance silica to silicon, as demonstrated herein.

Defining an essence of structure determining residue contacts in proteins.

PubMed

Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-12-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the fields of structure prediction, empirical potentials and docking.

Defining an Essence of Structure Determining Residue Contacts in Proteins

PubMed Central

Sathyapriya, R.; Duarte, Jose M.; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-01-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this “structural essence” has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts—such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed “cone-peeling” that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 Å Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This “structural essence” opens new avenues in the fields of structure prediction, empirical potentials and docking. PMID:19997489

Quasi-one-dimensional density of states in a single quantum ring.

PubMed

Kim, Heedae; Lee, Woojin; Park, Seongho; Kyhm, Kwangseuk; Je, Koochul; Taylor, Robert A; Nogues, Gilles; Dang, Le Si; Song, Jin Dong

2017-01-05

Generally confinement size is considered to determine the dimensionality of nanostructures. While the exciton Bohr radius is used as a criterion to define either weak or strong confinement in optical experiments, the binding energy of confined excitons is difficult to measure experimentally. One alternative is to use the temperature dependence of the radiative recombination time, which has been employed previously in quantum wells and quantum wires. A one-dimensional loop structure is often assumed to model quantum rings, but this approximation ceases to be valid when the rim width becomes comparable to the ring radius. We have evaluated the density of states in a single quantum ring by measuring the temperature dependence of the radiative recombination of excitons, where the photoluminescence decay time as a function of temperature was calibrated by using the low temperature integrated intensity and linewidth. We conclude that the quasi-continuous finely-spaced levels arising from the rotation energy give rise to a quasi-one-dimensional density of states, as long as the confined exciton is allowed to rotate around the opening of the anisotropic ring structure, which has a finite rim width.

Three-dimensional focus of attention for iterative cone-beam micro-CT reconstruction

NASA Astrophysics Data System (ADS)

Benson, T. M.; Gregor, J.

2006-09-01

Three-dimensional iterative reconstruction of high-resolution, circular orbit cone-beam x-ray CT data is often considered impractical due to the demand for vast amounts of computer cycles and associated memory. In this paper, we show that the computational burden can be reduced by limiting the reconstruction to a small, well-defined portion of the image volume. We first discuss using the support region defined by the set of voxels covered by all of the projection views. We then present a data-driven preprocessing technique called focus of attention that heuristically separates both image and projection data into object and background before reconstruction, thereby further reducing the reconstruction region of interest. We present experimental results for both methods based on mouse data and a parallelized implementation of the SIRT algorithm. The computational savings associated with the support region are substantial. However, the results for focus of attention are even more impressive in that only about one quarter of the computer cycles and memory are needed compared with reconstruction of the entire image volume. The image quality is not compromised by either method.

Fabrication of freestanding, microperforated membranes and their applications in microfluidics

PubMed Central

Zheng, Yizhe; Dai, Wen; Ryan, Declan; Wu, Hongkai

2010-01-01

This manuscript describes a convenient method for the fabrication of freestanding, microperforated membranes in photocurable polymers using only one step of photolithography. We used photosensitive prepolymers to make the membranes and photolithography to define the micropatterns. We demonstrated the fabrication of single- and multilayer microperforated membranes in SU-8 photoresist and Norland Optical Adhesive prepolymer. These membranes can be used to pattern surfaces in various materials and to fabricate complex three-dimensional microfluidic channel structures. PMID:21045933

Generation of animation sequences of three dimensional models

NASA Technical Reports Server (NTRS)

Poi, Sharon (Inventor); Bell, Brad N. (Inventor)

1990-01-01

The invention is directed toward a method and apparatus for generating an animated sequence through the movement of three-dimensional graphical models. A plurality of pre-defined graphical models are stored and manipulated in response to interactive commands or by means of a pre-defined command file. The models may be combined as part of a hierarchical structure to represent physical systems without need to create a separate model which represents the combined system. System motion is simulated through the introduction of translation, rotation and scaling parameters upon a model within the system. The motion is then transmitted down through the system hierarchy of models in accordance with hierarchical definitions and joint movement limitations. The present invention also calls for a method of editing hierarchical structure in response to interactive commands or a command file such that a model may be included, deleted, copied or moved within multiple system model hierarchies. The present invention also calls for the definition of multiple viewpoints or cameras which may exist as part of a system hierarchy or as an independent camera. The simulated movement of the models and systems is graphically displayed on a monitor and a frame is recorded by means of a video controller. Multiple movement and hierarchy manipulations are then recorded as a sequence of frames which may be played back as an animation sequence on a video cassette recorder.

Structure formation in organic thin films observed in real time by energy dispersive near-edge x-ray absorption fine-structure spectroscopy

NASA Astrophysics Data System (ADS)

Scholz, M.; Sauer, C.; Wiessner, M.; Nguyen, N.; Schöll, A.; Reinert, F.

2013-08-01

We study the structure formation of 1,4,5,8-naphthalene-tetracarboxylicacid-dianhydride (NTCDA) multilayer films on Ag(111) surfaces by energy dispersive near-edge x-ray absorption fine-structure spectroscopy (NEXAFS) and photoelectron spectroscopy. The time resolution of seconds of the method allows us to identify several sub-processes, which occur during the post-growth three-dimensional structural ordering, as well as their characteristic time scales. After deposition at low temperature the NTCDA molecules are preferentially flat lying and the films exhibit no long-range order. Upon annealing the molecules flip into an upright orientation followed by an aggregation in a transient phase which exists for several minutes. Finally, three-dimensional islands are established with bulk-crystalline structure involving substantial mass transport on the surface and morphological roughening. By applying the Kolmogorov-Johnson-Mehl-Avrami model the activation energies of the temperature-driven sub-processes can be derived from the time evolution of the NEXAFS signal.

VizieR Online Data Catalog: Outliers and similarity in APOGEE (Reis+, 2018)

NASA Astrophysics Data System (ADS)

Reis, I.; Poznanski, D.; Baron, D.; Zasowski, G.; Shahaf, S.

2017-11-01

t-SNE is a dimensionality reduction algorithm that is particularly well suited for the visualization of high-dimensional datasets. We use t-SNE to visualize our distance matrix. A-priori, these distances could define a space with almost as many dimensions as objects, i.e., tens of thousand of dimensions. Obviously, since many stars are quite similar, and their spectra are defined by a few physical parameters, the minimal spanning space might be smaller. By using t-SNE we can examine the structure of our sample projected into 2D. We use our distance matrix as input to the t-SNE algorithm and in return get a 2D map of the objects in our dataset. For each star in a sample of 183232 APOGEE stars, the APOGEE IDs of the 99 stars with most similar spectra (according to the method described in paper), ordered by similarity. (3 data files).

Compression-recovery model of absorptive glass mat (AGM) separator guided by X-ray micro-computed tomography analysis

NASA Astrophysics Data System (ADS)

Kameswara Rao, P. V.; Rawal, Amit; Kumar, Vijay; Rajput, Krishn Gopal

2017-10-01

Absorptive glass mat (AGM) separators play a key role in enhancing the cycle life of the valve regulated lead acid (VRLA) batteries by maintaining the elastic characteristics under a defined level of compression force with the plates of the electrodes. Inevitably, there are inherent challenges to maintain the required level of compression characteristics of AGM separators during the charge and discharge of the battery. Herein, we report a three-dimensional (3D) analytical model for predicting the compression-recovery behavior of AGM separators by formulating a direct relationship with the constituent fiber and structural parameters. The analytical model of compression-recovery behavior of AGM separators has successfully included the fiber slippage criterion and internal friction losses. The presented work uses, for the first time, 3D data of fiber orientation from X-ray micro-computed tomography, for predicting the compression-recovery behavior of AGM separators. A comparison has been made between the theoretical and experimental results of compression-recovery behavior of AGM samples with defined fiber orientation characteristics. In general, the theory agreed reasonably well with the experimental results of AGM samples in both dry and wet states. Through theoretical modeling, fiber volume fraction was established as one of the key structural parameters that modulates the compression hysteresis of an AGM separator.

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.

PubMed

Krissinel, E; Henrick, K

2004-12-01

The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign.

In situ synchrotron X-ray diffraction study on epitaxial-growth dynamics of III–V semiconductors

NASA Astrophysics Data System (ADS)

Takahasi, Masamitu

2018-05-01

The application of in situ synchrotron X-ray diffraction (XRD) to the molecular-beam epitaxial (MBE) growth of III–V semiconductors is overviewed along with backgrounds of the diffraction theory and instrumentation. X-rays are sensitive not only to the surface of growing films but also to buried interfacial structures because of their large penetration depth. Moreover, a spatial coherence length up to µm order makes X-rays widely applicable to the characterization of low-dimensional structures, such as quantum dots and wires. In situ XRD studies during growth were performed using an X-ray diffractometer, which was combined with an MBE chamber. X-ray reciprocal space mapping at a speed matching a typical growth rate was achieved using intense X-rays available from a synchrotron light source and an area detector. The importance of measuring the three-dimensional distribution of XRD intensity in a reciprocal space map is demonstrated for the MBE growth of two-, one-, and zero-dimensional structures. A large amount of information about the growth process of two-dimensional InGaAs/GaAs(001) epitaxial films has been provided by three-dimensional X-ray reciprocal mappings, including the anisotropic strain relaxation, the compositional inhomogeneity, and the evolution of surface and interfacial roughness. For one-dimensional GaAs nanowires grown in a Au-catalyzed vapor-liquid–solid mode, the relationship between the diameter of the nanowires and the formation of polytypes has been suggested on the basis of in situ XRD measurements. In situ three-dimensional X-ray reciprocal space mapping is also shown to be useful for determining the lateral and vertical sizes of self-assembled InAs/GaAs(001) quantum dots as well as their internal strain distributions during growth.

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.

Evaluation and operationalization of a novel forest detrainment modeling approach for computational snow avalanche simulation

NASA Astrophysics Data System (ADS)

Teich, M.; Feistl, T.; Fischer, J.; Bartelt, P.; Bebi, P.; Christen, M.; Grêt-Regamey, A.

2013-12-01

Two-dimensional avalanche simulation software operating in three-dimensional terrain are widely used for hazard zoning and engineering to predict runout distances and impact pressures of snow avalanche events. Mountain forests are an effective biological protection measure; however, the protective capacity of forests to decelerate or even to stop avalanches that start within forested areas or directly above the treeline is seldom considered in this context. In particular, runout distances of small- to medium-scale avalanches are strongly influenced by the structural conditions of forests in the avalanche path. This varying decelerating effect has rarely been addressed or implemented in avalanche simulation. We present an evaluation and operationalization of a novel forest detrainment modeling approach implemented in the avalanche simulation software RAMMS. The new approach accounts for the effect of forests in the avalanche path by detraining mass, which leads to a deceleration and runout shortening of avalanches. The extracted avalanche mass caught behind trees stops immediately and, therefore, is instantly subtracted from the flow and the momentum of the stopped mass is removed from the total momentum of the avalanche flow. This relationship is parameterized by the empirical detrainment coefficient K [Pa] which accounts for the braking power of different forest types per unit area. To define K dependent on specific forest characteristics, we simulated 40 well-documented small- to medium-scale avalanches which released in and ran through forests with varying K-values. Comparing two-dimensional simulation results with one-dimensional field observations for a high number of avalanche events and simulations manually is however time consuming and rather subjective. In order to process simulation results in a comprehensive and standardized way, we used a recently developed automatic evaluation and comparison method defining runout distances based on a pressure-based runout indicator in an avalanche path dependent coordinate system. Analyzing and comparing observed and simulated runout distances statistically revealed values for K suitable to simulate the combined influence of four forest characteristics on avalanche runout: forest type, crown coverage, vertical structure and surface roughness, e.g. values for K were higher for dense spruce and mixed spruce-beech forests compared to open larch forests at the upper treeline. Considering forest structural conditions within avalanche simulation will improve current applications for avalanche simulation tools in mountain forest and natural hazard management considerably. Furthermore, we show that an objective and standardized evaluation of two-dimensional simulation results is essential for a successful evaluation and further calibration of avalanche models in general.

A three-dimensional neural spheroid model for capillary-like network formation.

PubMed

Boutin, Molly E; Kramer, Liana L; Livi, Liane L; Brown, Tyler; Moore, Christopher; Hoffman-Kim, Diane

2018-04-01

In vitro three-dimensional neural spheroid models have an in vivo-like cell density, and have the potential to reduce animal usage and increase experimental throughput. The aim of this study was to establish a spheroid model to study the formation of capillary-like networks in a three-dimensional environment that incorporates both neuronal and glial cell types, and does not require exogenous vasculogenic growth factors. We created self-assembled, scaffold-free cellular spheroids using primary-derived postnatal rodent cortex as a cell source. The interactions between relevant neural cell types, basement membrane proteins, and endothelial cells were characterized by immunohistochemistry. Transmission electron microscopy was used to determine if endothelial network structures had lumens. Endothelial cells within cortical spheroids assembled into capillary-like networks with lumens. Networks were surrounded by basement membrane proteins, including laminin, fibronectin and collagen IV, as well as key neurovascular cell types. Existing in vitro models of the cortical neurovascular environment study monolayers of endothelial cells, either on transwell inserts or coating cellular spheroids. These models are not well suited to study vasculogenesis, a process hallmarked by endothelial cell cord formation and subsequent lumenization. The neural spheroid is a new model to study the formation of endothelial cell capillary-like structures in vitro within a high cell density three-dimensional environment that contains both neuronal and glial populations. This model can be applied to investigate vascular assembly in healthy or disease states, such as stroke, traumatic brain injury, or neurodegenerative disorders. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Three-Dimensional Reconstruction and Solar Energy Potential Estimation of Buildings

NASA Astrophysics Data System (ADS)

Chen, Y.; Li, M.; Cheng, L.; Xu, H.; Li, S.; Liu, X.

2017-12-01

In the context of the construction of low-carbon cities, green cities and eco-cities, the ability of the airborne and mobile LiDAR should be explored in urban renewable energy research. As the main landscape in urban environment, buildings have large regular envelopes could receive a huge amount of solar radiation. In this study, a relatively complete calculation scheme about building roof and façade solar utilization potential is proposed, using building three-dimensional geometric feature information. For measuring the city-level building solar irradiance, the precise three-dimensional building roof and façade models should be first reconstructed from the airborne and mobile LiDAR, respectively. In order to obtaining the precise geometric structure of building facades from the mobile LiDAR data, a new method for structure detection and the three-dimensional reconstruction of building façades from mobile LiDAR data is proposed. The method consists of three steps: the preprocessing of façade points, the detection of façade structure, the restoration and reconstruction of building façade. As a result, the reconstruction method can effectively deal with missing areas caused by occlusion, viewpoint limitation, and uneven point density, as well as realizing the highly complete 3D reconstruction of a building façade. Furthermore, the window areas can be excluded for more accurate estimation of solar utilization potential. After then, the solar energy utilization potential of global building roofs and facades is estimate by using the solar irradiance model, which combine the analysis of the building shade and sky diffuse, based on the analysis of the geometrical structure of buildings.

Abiological origin of described stromatolites older than 3.2 Ga

NASA Technical Reports Server (NTRS)

Lowe, D. R.

1994-01-01

The three well-documented occurrences of three-dimensional stromatolites older than 3.2 Ga meet most criteria for biogenicity except the presence of fossil bacteria. However, they also show features more consistent with nonbiological origins. Small conical structures in the Strelley Pool chert in the upper part of the Warrawoona Group (3.5-3.2 Ga), Western Australia, lack the structure typical of stromatolites and probably formed mainly through evaporitc precipitation. A domal structure from the North Pole chert, Warrawoona Group, formed by soft-sediment deformation or originally flat layers. Laminated chert containing domal and pseudocolumnar structures in the Onverwacht Group (3.5-3.3 Ga), Barberton Greenstone Belt, South Africa, extends downward into veins and cavities, where it formed through inorganic precipitation. Although bacterial communities were widespread on Earth prior to 3.2 Ga, these particular three-dimensional structures are probably abiotic in origin and do not provide information on the paleobiology or paleoecology of early organisms. The paucity of Archean stromatolites older than 3.2 Ga probably reflects the paucity of known and possibly extant carbonate deposits of this age.

DYNAMICS OF TURBULENT CONVECTION AND CONVECTIVE OVERSHOOT IN A MODERATE-MASS STAR

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

Kitiashvili, I. N.; Mansour, N. N.; Wray, A. A.

We present results of realistic three-dimensional (3D) radiative hydrodynamic simulations of the outer layers of a moderate-mass star (1.47 M {sub ⊙}), including the full convection zone, the overshoot region, and the top layers of the radiative zone. The simulation results show that the surface granulation has a broad range of scales, from 2 to 12 Mm, and that large granules are organized in well-defined clusters, consisting of several granules. Comparison of the mean structure profiles from 3D simulations with the corresponding one-dimensional (1D) standard stellar model shows an increase of the stellar radius by ∼800 km, as well as significantmore » changes in the thermodynamic structure and turbulent properties of the ionization zones. Convective downdrafts in the intergranular lanes between granulation clusters reach speeds of more than 20 km s{sup −1}, penetrate through the whole convection zone, hit the radiative zone, and form an 8 Mm thick overshoot layer. Contrary to semi-empirical overshooting models, our results show that the 3D dynamic overshoot region consists of two layers: a nearly adiabatic extension of the convection zone and a deeper layer of enhanced subadiabatic stratification. This layer is formed because of heating caused by the braking of the overshooting convective plumes. This effect has to be taken into account in stellar modeling and the interpretation of asteroseismology data. In particular, we demonstrate that the deviations of the mean structure of the 3D model from the 1D standard model of the same mass and composition are qualitatively similar to the deviations for the Sun found by helioseismology.« less

Cross-National Invariance of Attention-Deficit/Hyperactivity Disorder Factors in Japanese and U.S. University Students

ERIC Educational Resources Information Center

Davis, J. Mark; Cheung, Shu Fai; Takahashi, Tomone; Shinoda, Haruo; Lindstrom, William A.

2011-01-01

Prior research with children generally supports the two-dimensional structure of Attention-Deficit/Hyperactivity Disorder (ADHD; inattentive and hyperactive/impulsive factors) of the DSM-IV-TR as well as invariance of the two-factor structure across nations and cultures. Research with adults supports either a two-factor or three-factor structure…

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…

Self-assembly of heterogeneous supramolecular structures with uniaxial anisotropy.

PubMed

Ruiz-Osés, M; Gonzalez-Lakunza, N; Silanes, I; Gourdon, A; Arnau, A; Ortega, J E

2006-12-28

Uniaxial anisotropy in two-dimensional self-assembled supramolecular structures is achieved by the coadsorption of two different linear molecules with complementary amine and imide functionalization. The two-dimensional monolayer is defined by a one-dimensional stack of binary chains, which can be forced to line up along steps in vicinal surfaces. The competing driving forces in the self-organization process are discussed in light of the structures observed during single molecule adsorption and coadsorption on flat and vicinal surfaces and the corresponding theoretical calculations.

Seismic reflection images of the accretionary wedge of Costa Rica

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

Shipley, T.H.; Stoffa, P.L.; McIntosh, K.

The large-scale structure of modern accretionary wedges is known almost entirely from seismic reflection investigations using single or grids of two-dimensional profiles. The authors will report on the first three-dimensional seismic reflection data volume collected of a wedge. This data set covers a 9-km-wide {times} 22-km-long {times} 6-km-thick volume of the accretionary wedge just arcward of the Middle America Trench off Costa Rica. The three-dimensional processing has improved the imaging ability of the multichannel data, and the data volume allows mapping of structures from a few hundred meters to kilometers in size. These data illustrate the relationships between the basement,more » the wedge shape, and overlying slope sedimentary deposits. Reflections from within the wedge define the gross structural features and tectonic processes active along this particular convergent margin. So far, the analysis shows that the subdued basement relief (horst and graben structures seldom have relief of more than a few hundred meters off Costa Rica) does affect the larger scale through going structural features within the wedge. The distribution of mud volcanoes and amplitude anomalies associated with the large-scale wedge structures suggests that efficient fluid migration paths may extend from the top of the downgoing slab at the shelf edge out into the lower and middle slope region at a distance of 50-100 km. Offscraping of the uppermost (about 45 m) sediment occurs within 4 km of the trench, creating a small pile of sediments near the trench lower slope. Underplating of parts of the 400-m-thick subducted sedimentary section begins at a very shallow structural level, 4-10 km arcward of the trench. Volumetrically, the most important accretionary process is underplating.« less

A web service system supporting three-dimensional post-processing of medical images based on WADO protocol.

PubMed

He, Longjun; Xu, Lang; Ming, Xing; Liu, Qian

2015-02-01

Three-dimensional post-processing operations on the volume data generated by a series of CT or MR images had important significance on image reading and diagnosis. As a part of the DIOCM standard, WADO service defined how to access DICOM objects on the Web, but it didn't involve three-dimensional post-processing operations on the series images. This paper analyzed the technical features of three-dimensional post-processing operations on the volume data, and then designed and implemented a web service system for three-dimensional post-processing operations of medical images based on the WADO protocol. In order to improve the scalability of the proposed system, the business tasks and calculation operations were separated into two modules. As results, it was proved that the proposed system could support three-dimensional post-processing service of medical images for multiple clients at the same moment, which met the demand of accessing three-dimensional post-processing operations on the volume data on the web.

Cyclotron resonance of dirac fermions in InAs/GaSb/InAs quantum wells

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

Krishtopenko, S. S.; Ikonnikov, A. V., E-mail: antikon@ipmras.ru; Maremyanin, K. V.

2017-01-15

The band structure of three-layer symmetric InAs/GaSb/InAs quantum wells confined between AlSb barriers is analyzed theoretically. It is shown that, depending on the thicknesses of the InAs and GaSb layers, a normal band structure, a gapless state with a Dirac cone at the center of the Brillouin zone, or inverted band structure (two-dimensional topological insulator) can be realized in this system. Measurements of the cyclotron resonance in structures with gapless band spectra carried out for different electron concentrations confirm the existence of massless Dirac fermions in InAs/GaSb/InAs quantum wells.

Tracking the Magnetization Evolution in γ-Fe2O3 / Metallic Fe Core-Shell Nanoparticle Variants

NASA Astrophysics Data System (ADS)

Kons, C.; Nemati, Z.; Srikanth, H.; Phan, M.-H.; Krycka, K.; Borchers, J.; Keavney, D.; Arena, D. A.

Iron-core magnetic nanoparticles (MNPs) with oxide shells exhibit varying magnetic properties due to the different ordering temperatures of the core and shell spins, as well as the coupling across the metal/oxide interface. While spin coupling across two dimensional interfaces has been well explored, less is known about three dimensional interfaces such as those presented in the MNPs. In this work, MNPs were synthesized with a bcc Fe core and γ-Fe2O3 shell and placed in an oxygen rich environment to encourage the transition from cores shell (CS) to core void shell (CVS) to hollow (H) structures. Static magnetic measurements (MvT) and AC magnetometry were performed to explore the magnetic behavior of the various synthesized structures. To further understand the nature of the spin coupling in the MNPs, TEM and conventional magnetometry as well as variable-temperature small angle neutron scattering (SANS), x-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism (XMCD) spectroscopy were performed. Modeling of the x-ray spectra and SANS data will enable us to develop a cohesive picture of spin coupling, freezing and frustration along the three-dimensional metal / oxide interface. Supported by Department of Energy award #DE-FG02-07ER46438; NSF Award #DMR-1508249.

Feedback-Based, System-Level Properties of Vertebrate-Microbial Interactions

PubMed Central

Rivas, Ariel L.; Jankowski, Mark D.; Piccinini, Renata; Leitner, Gabriel; Schwarz, Daniel; Anderson, Kevin L.; Fair, Jeanne M.; Hoogesteijn, Almira L.; Wolter, Wilfried; Chaffer, Marcelo; Blum, Shlomo; Were, Tom; Konah, Stephen N.; Kempaiah, Prakash; Ong’echa, John M.; Diesterbeck, Ulrike S.; Pilla, Rachel; Czerny, Claus-Peter; Hittner, James B.; Hyman, James M.; Perkins, Douglas J.

2013-01-01

Background Improved characterization of infectious disease dynamics is required. To that end, three-dimensional (3D) data analysis of feedback-like processes may be considered. Methods To detect infectious disease data patterns, a systems biology (SB) and evolutionary biology (EB) approach was evaluated, which utilizes leukocyte data structures designed to diminish data variability and enhance discrimination. Using data collected from one avian and two mammalian (human and bovine) species infected with viral, parasite, or bacterial agents (both sensitive and resistant to antimicrobials), four data structures were explored: (i) counts or percentages of a single leukocyte type, such as lymphocytes, neutrophils, or macrophages (the classic approach), and three levels of the SB/EB approach, which assessed (ii) 2D, (iii) 3D, and (iv) multi-dimensional (rotating 3D) host-microbial interactions. Results In all studies, no classic data structure discriminated disease-positive (D+, or observations in which a microbe was isolated) from disease-negative (D–, or microbial-negative) groups: D+ and D– data distributions overlapped. In contrast, multi-dimensional analysis of indicators designed to possess desirable features, such as a single line of observations, displayed a continuous, circular data structure, whose abrupt inflections facilitated partitioning into subsets statistically significantly different from one another. In all studies, the 3D, SB/EB approach distinguished three (steady, positive, and negative) feedback phases, in which D– data characterized the steady state phase, and D+ data were found in the positive and negative phases. In humans, spatial patterns revealed false-negative observations and three malaria-positive data classes. In both humans and bovines, methicillin-resistant Staphylococcus aureus (MRSA) infections were discriminated from non-MRSA infections. Conclusions More information can be extracted, from the same data, provided that data are structured, their 3D relationships are considered, and well-conserved (feedback-like) functions are estimated. Patterns emerging from such structures may distinguish well-conserved from recently developed host-microbial interactions. Applications include diagnosis, error detection, and modeling. PMID:23437039

Feedback-based, system-level properties of vertebrate-microbial interactions.

PubMed

Rivas, Ariel L; Jankowski, Mark D; Piccinini, Renata; Leitner, Gabriel; Schwarz, Daniel; Anderson, Kevin L; Fair, Jeanne M; Hoogesteijn, Almira L; Wolter, Wilfried; Chaffer, Marcelo; Blum, Shlomo; Were, Tom; Konah, Stephen N; Kempaiah, Prakash; Ong'echa, John M; Diesterbeck, Ulrike S; Pilla, Rachel; Czerny, Claus-Peter; Hittner, James B; Hyman, James M; Perkins, Douglas J

2013-01-01

Improved characterization of infectious disease dynamics is required. To that end, three-dimensional (3D) data analysis of feedback-like processes may be considered. To detect infectious disease data patterns, a systems biology (SB) and evolutionary biology (EB) approach was evaluated, which utilizes leukocyte data structures designed to diminish data variability and enhance discrimination. Using data collected from one avian and two mammalian (human and bovine) species infected with viral, parasite, or bacterial agents (both sensitive and resistant to antimicrobials), four data structures were explored: (i) counts or percentages of a single leukocyte type, such as lymphocytes, neutrophils, or macrophages (the classic approach), and three levels of the SB/EB approach, which assessed (ii) 2D, (iii) 3D, and (iv) multi-dimensional (rotating 3D) host-microbial interactions. In all studies, no classic data structure discriminated disease-positive (D+, or observations in which a microbe was isolated) from disease-negative (D-, or microbial-negative) groups: D+ and D- data distributions overlapped. In contrast, multi-dimensional analysis of indicators designed to possess desirable features, such as a single line of observations, displayed a continuous, circular data structure, whose abrupt inflections facilitated partitioning into subsets statistically significantly different from one another. In all studies, the 3D, SB/EB approach distinguished three (steady, positive, and negative) feedback phases, in which D- data characterized the steady state phase, and D+ data were found in the positive and negative phases. In humans, spatial patterns revealed false-negative observations and three malaria-positive data classes. In both humans and bovines, methicillin-resistant Staphylococcus aureus (MRSA) infections were discriminated from non-MRSA infections. More information can be extracted, from the same data, provided that data are structured, their 3D relationships are considered, and well-conserved (feedback-like) functions are estimated. Patterns emerging from such structures may distinguish well-conserved from recently developed host-microbial interactions. Applications include diagnosis, error detection, and modeling.

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

Avoidant/Restrictive Food Intake Disorder: a Three-Dimensional Model of Neurobiology with Implications for Etiology and Treatment.

PubMed

Thomas, Jennifer J; Lawson, Elizabeth A; Micali, Nadia; Misra, Madhusmita; Deckersbach, Thilo; Eddy, Kamryn T

2017-08-01

DSM-5 defined avoidant/restrictive food intake disorder (ARFID) as a failure to meet nutritional needs leading to low weight, nutritional deficiency, dependence on supplemental feedings, and/or psychosocial impairment. We summarize what is known about ARFID and introduce a three-dimensional model to inform research. Because ARFID prevalence, risk factors, and maintaining mechanisms are not known, prevailing treatment approaches are based on clinical experience rather than data. Furthermore, most ARFID research has focused on children, rather than adolescents or adults. We hypothesize a three-dimensional model wherein neurobiological abnormalities in sensory perception, homeostatic appetite, and negative valence systems underlie the three primary ARFID presentations of sensory sensitivity, lack of interest in eating, and fear of aversive consequences, respectively. Now that ARFID has been defined, studies investigating risk factors, prevalence, and pathophysiology are needed. Our model suggests testable hypotheses about etiology and highlights cognitive-behavioral therapy as one possible treatment.

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.

Adinkra (in)equivalence from Coxeter group representations: A case study

NASA Astrophysics Data System (ADS)

Chappell, Isaac; Gates, S. James; Hübsch, T.

2014-02-01

Using a MathematicaTM code, we present a straightforward numerical analysis of the 384-dimensional solution space of signed permutation 4×4 matrices, which in sets of four, provide representations of the 𝒢ℛ(4, 4) algebra, closely related to the 𝒩 = 1 (simple) supersymmetry algebra in four-dimensional space-time. Following after ideas discussed in previous papers about automorphisms and classification of adinkras and corresponding supermultiplets, we make a new and alternative proposal to use equivalence classes of the (unsigned) permutation group S4 to define distinct representations of higher-dimensional spin bundles within the context of adinkras. For this purpose, the definition of a dual operator akin to the well-known Hodge star is found to partition the space of these 𝒢ℛ(4, 4) representations into three suggestive classes.

Attenuation Tomography Based on Strong Motion Data: Case Study of Central Honshu Region, Japan

NASA Astrophysics Data System (ADS)

Kumar, Parveen; Joshi, A.; Verma, O. P.

2013-12-01

Three-dimensional frequency dependent S-wave quality factor (Qβ(f)) value for the central Honshu region of Japan has been determined in this paper using an algorithm based on inversion of strong motion data. The method of inversion for determination of three-dimensional attenuation coefficients is proposed by H ashida and S himazaki (J Phys Earth. 32, 299-316, 1984) and has been used and modified by J oshi (Curr Sci. 90, 581-585, 2006; Nat Hazards. 43, 129-146, 2007) and J oshi et al. (J. Seismol. 14, 247-272, 2010). Twenty-one earthquakes digitally recorded on strong motion stations of Kik-net network have been used in this work. The magnitude of these earthquake ranges from 3.1 to 4.2 and depth ranging from 5 to 20 km, respectively. The borehole data having high signal to noise ratio and minimum site effect is used in the present work. The attenuation structure is determined by dividing the entire area into twenty-five three-dimensional blocks of uniform thickness having different frequency-dependent shear wave quality factor. Shear wave quality factor values have been determined at frequencies of 2.5, 7.0 and 10 Hz from record in a rectangular grid defined by 35.4°N to 36.4°N and 137.2°E to 138.2°E. The obtained attenuation structure is compared with the available geological features in the region and comparison shows that the obtained structure is capable of resolving important tectonic features present in the area. The proposed attenuation structure is compared with the probabilistic seismic hazard map of the region and shows that it bears some remarkable similarity in the patterns seen in seismic hazard map.

A spectral-Tchebychev solution for three-dimensional dynamics of curved beams under mixed boundary conditions

NASA Astrophysics Data System (ADS)

Bediz, Bekir; Aksoy, Serdar

2018-01-01

This paper presents the application of the spectral-Tchebychev (ST) technique for solution of three-dimensional dynamics of curved beams/structures having variable and arbitrary cross-section under mixed boundary conditions. To accurately capture the vibrational behavior of curved structures, a three-dimensional (3D) solution approach is required since these structures generally exhibit coupled motions. In this study, the integral boundary value problem (IBVP) governing the dynamics of the curved structures is found using extended Hamilton's principle where the strain energy is expressed using 3D linear elasticity equation. To solve the IBVP numerically, the 3D spectral Tchebychev (3D-ST) approach is used. To evaluate the integral and derivative operations defined by the IBVP and to render the complex geometry into an equivalent straight beam with rectangular cross-section, a series of coordinate transformations are applied. To validate and assess the performance of the presented solution approach, two case studies are performed: (i) curved beam with rectangular cross-section, (ii) curved and pretwisted beam with airfoil cross-section. In both cases, the results (natural frequencies and mode shapes) are also found using a finite element (FE) solution approach. It is shown that the difference in predicted natural frequencies are less than 1%, and the mode shapes are in excellent agreement based on the modal assurance criteria (MAC) analyses; however, the presented spectral-Tchebychev solution approach significantly reduces the computational burden. Therefore, it can be concluded that the presented solution approach can capture the 3D vibrational behavior of curved beams as accurately as an FE solution, but for a fraction of the computational cost.

Protein Engineering Approaches in the Post-Genomic Era.

PubMed

Singh, Raushan K; Lee, Jung-Kul; Selvaraj, Chandrabose; Singh, Ranjitha; Li, Jinglin; Kim, Sang-Yong; Kalia, Vipin C

2018-01-01

Proteins are one of the most multifaceted macromolecules in living systems. Proteins have evolved to function under physiological conditions and, therefore, are not usually tolerant of harsh experimental and environmental conditions. The growing use of proteins in industrial processes as a greener alternative to chemical catalysts often demands constant innovation to improve their performance. Protein engineering aims to design new proteins or modify the sequence of a protein to create proteins with new or desirable functions. With the emergence of structural and functional genomics, protein engineering has been invigorated in the post-genomic era. The three-dimensional structures of proteins with known functions facilitate protein engineering approaches to design variants with desired properties. There are three major approaches of protein engineering research, namely, directed evolution, rational design, and de novo design. Rational design is an effective method of protein engineering when the threedimensional structure and mechanism of the protein is well known. In contrast, directed evolution does not require extensive information and a three-dimensional structure of the protein of interest. Instead, it involves random mutagenesis and selection to screen enzymes with desired properties. De novo design uses computational protein design algorithms to tailor synthetic proteins by using the three-dimensional structures of natural proteins and their folding rules. The present review highlights and summarizes recent protein engineering approaches, and their challenges and limitations in the post-genomic era. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Modeling Three-Dimensional Flow in Confined Aquifers by Superposition of Both Two- and Three-Dimensional Analytic Functions

NASA Astrophysics Data System (ADS)

Haitjema, Henk M.

1985-10-01

A technique is presented to incorporate three-dimensional flow in a Dupuit-Forchheimer model. The method is based on superposition of approximate analytic solutions to both two- and three-dimensional flow features in a confined aquifer of infinite extent. Three-dimensional solutions are used in the domain of interest, while farfield conditions are represented by two-dimensional solutions. Approximate three- dimensional solutions have been derived for a partially penetrating well and a shallow creek. Each of these solutions satisfies the condition that no flow occurs across the confining layers of the aquifer. Because of this condition, the flow at some distance of a three-dimensional feature becomes nearly horizontal. Consequently, remotely from a three-dimensional feature, its three-dimensional solution is replaced by a corresponding two-dimensional one. The latter solution is trivial as compared to its three-dimensional counterpart, and its use greatly enhances the computational efficiency of the model. As an example, the flow is modeled between a partially penetrating well and a shallow creek that occur in a regional aquifer system.

Multiple brain atlas database and atlas-based neuroimaging system.

PubMed

Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

1997-01-01

For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

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.

Microfluidic 3D cell culture: potential application for tissue-based bioassays

PubMed Central

Li, XiuJun (James); Valadez, Alejandra V.; Zuo, Peng; Nie, Zhihong

2014-01-01

Current fundamental investigations of human biology and the development of therapeutic drugs, commonly rely on two-dimensional (2D) monolayer cell culture systems. However, 2D cell culture systems do not accurately recapitulate the structure, function, physiology of living tissues, as well as highly complex and dynamic three-dimensional (3D) environments in vivo. The microfluidic technology can provide micro-scale complex structures and well-controlled parameters to mimic the in vivo environment of cells. The combination of microfluidic technology with 3D cell culture offers great potential for in vivo-like tissue-based applications, such as the emerging organ-on-a-chip system. This article will review recent advances in microfluidic technology for 3D cell culture and their biological applications. PMID:22793034

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".

Three dimensional cross-correlation dynamic light scattering by non-ergodic turbid media.

PubMed

Haro-Pérez, C; Ojeda-Mendoza, G J; Rojas-Ochoa, L F

2011-06-28

We investigate dynamic light scattering by non-ergodic turbid media with an adapted version of the method proposed by Pusey and van Megen [Physica A 157, 705 (1989)]. Our formulation follows the derivation of the original method by extending it to the three dimensional cross-correlation scheme (3DDLS). The main finding is an expression to obtain the dynamic structure factor from light scattering that takes into account the system turbidity and the peculiarities of the 3D geometry. From 3DDLS measurements in well-controlled solid-like systems of different turbidity, we confirm that our results can be interpreted reasonably well by the theoretical approach described here. Good agreement is found with earlier reported results on similar systems.

High-Dimensional Intrinsic Interpolation Using Gaussian Process Regression and Diffusion Maps

DOE PAGES

Thimmisetty, Charanraj A.; Ghanem, Roger G.; White, Joshua A.; ...

2017-10-10

This article considers the challenging task of estimating geologic properties of interest using a suite of proxy measurements. The current work recast this task as a manifold learning problem. In this process, this article introduces a novel regression procedure for intrinsic variables constrained onto a manifold embedded in an ambient space. The procedure is meant to sharpen high-dimensional interpolation by inferring non-linear correlations from the data being interpolated. The proposed approach augments manifold learning procedures with a Gaussian process regression. It first identifies, using diffusion maps, a low-dimensional manifold embedded in an ambient high-dimensional space associated with the data. Itmore » relies on the diffusion distance associated with this construction to define a distance function with which the data model is equipped. This distance metric function is then used to compute the correlation structure of a Gaussian process that describes the statistical dependence of quantities of interest in the high-dimensional ambient space. The proposed method is applicable to arbitrarily high-dimensional data sets. Here, it is applied to subsurface characterization using a suite of well log measurements. The predictions obtained in original, principal component, and diffusion space are compared using both qualitative and quantitative metrics. Considerable improvement in the prediction of the geological structural properties is observed with the proposed method.« less

High-Dimensional Intrinsic Interpolation Using Gaussian Process Regression and Diffusion Maps

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

Thimmisetty, Charanraj A.; Ghanem, Roger G.; White, Joshua A.

This article considers the challenging task of estimating geologic properties of interest using a suite of proxy measurements. The current work recast this task as a manifold learning problem. In this process, this article introduces a novel regression procedure for intrinsic variables constrained onto a manifold embedded in an ambient space. The procedure is meant to sharpen high-dimensional interpolation by inferring non-linear correlations from the data being interpolated. The proposed approach augments manifold learning procedures with a Gaussian process regression. It first identifies, using diffusion maps, a low-dimensional manifold embedded in an ambient high-dimensional space associated with the data. Itmore » relies on the diffusion distance associated with this construction to define a distance function with which the data model is equipped. This distance metric function is then used to compute the correlation structure of a Gaussian process that describes the statistical dependence of quantities of interest in the high-dimensional ambient space. The proposed method is applicable to arbitrarily high-dimensional data sets. Here, it is applied to subsurface characterization using a suite of well log measurements. The predictions obtained in original, principal component, and diffusion space are compared using both qualitative and quantitative metrics. Considerable improvement in the prediction of the geological structural properties is observed with the proposed method.« less

Modeling the three-dimensional structure of macroscopic magma transport systems: Application to Kilauea volcano, Hawaii

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

Ryan, M.P.; Koyanagi, R.Y.; Fiske, R.S.

1981-08-10

We report the results of modeling the three-dimensional internal structure of Kilauea's magmatic passageways. The approach uses a clear plexiglass model containing equally-spaced levels upon which well-located seismic hypocenters are plotted. Application of constraining geologic and geophysical criteria to this distributed volume of earthquakes permits the interpretation of seismic structures produced by fracturing in response to locally high fluid pressures. Four magma transport and storage structures produce have been identified within and beneath Kilauea: (1) Primary conduit. The conduit transporting magma into Kilauea's summit storage reservoir rises from the model base (14.6 km) to 6.5 km depth level. It ismore » a zone of intense fracturing and inferred intrusion, whose horizontal sections are elliptical in planform. Over its height, the average major axis of component horizontal section is 3.3 km, with an average minor axis of 1.7 km. This yields an aspect ratio of xi = 0.52. At the 14.6 km level, the strike of the major axis is N67 /sup 0/E. During passage from the upper mantle through the oceanic crust, this axis rotates in a right-handed sense, until the strike is N41 /sup 0/W at the 6.5 km level. (2) Magma chamber complex floor. The interval from 6.5 to 5.7 km, immediately over the primary conduit, is aseismic. This suggests differentially high fluid-to-rock ratios, and relatively weak pathways for further vertical transport into higher levels of the storage complex, as well as lateral leakage eastward into the Mauna Ulu staging area: for later vertical ascent beneath the upper east rift zone. Seismicity within the immediately subjacent rocks that form the top of the primary conduit (at 6.5 km) suggests that this inferred magma-rich horizon forms the effective floor of the summit storage complex. (3) Magma chamber crown. Intense seismicity over the 1.1--1.9 km depth interval defines an elliptical region in plan view.« less

Synthesis and identification of three-dimensional faces from image(s) and three-dimensional generic models

NASA Astrophysics Data System (ADS)

Liu, Zexi; Cohen, Fernand

2017-11-01

We describe an approach for synthesizing a three-dimensional (3-D) face structure from an image or images of a human face taken at a priori unknown poses using gender and ethnicity specific 3-D generic models. The synthesis process starts with a generic model, which is personalized as images of the person become available using preselected landmark points that are tessellated to form a high-resolution triangular mesh. From a single image, two of the three coordinates of the model are reconstructed in accordance with the given image of the person, while the third coordinate is sampled from the generic model, and the appearance is made in accordance with the image. With multiple images, all coordinates and appearance are reconstructed in accordance with the observed images. This method allows for accurate pose estimation as well as face identification in 3-D rendering of a difficult two-dimensional (2-D) face recognition problem into a much simpler 3-D surface matching problem. The estimation of the unknown pose is achieved using the Levenberg-Marquardt optimization process. Encouraging experimental results are obtained in a controlled environment with high-resolution images under a good illumination condition, as well as for images taken in an uncontrolled environment under arbitrary illumination with low-resolution cameras.

Three-dimensional (3D) printing of mouse primary hepatocytes to generate 3D hepatic structure.

PubMed

Kim, Yohan; Kang, Kyojin; Jeong, Jaemin; Paik, Seung Sam; Kim, Ji Sook; Park, Su A; Kim, Wan Doo; Park, Jisun; Choi, Dongho

2017-02-01

The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6-8 weeks old mice by a 2-step collagenase method. Samples of 4 × 10 7 hepatocytes with 80%-90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin , HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers.

Three-dimensional image contrast using biospeckle

NASA Astrophysics Data System (ADS)

Godinho, Robson Pierangeli; Braga, Roberto A., Jr.

2010-09-01

The biospeckle laser (BSL) has been applied in many areas of knowledge and a variety of approaches has been presented to address the best results in biological and non-biological samples, in fast or slow activities, or else in defined flow of materials or in random activities. The methodologies accounted in the literature consider the apparatus used in the image assembling and the way the collected data is processed. The image processing steps presents in turn a variety of procedures with first or second order statistics analysis, and as well with different sizes of data collected. One way to access the biospeckle in defined flow, such as in capillary blood flow in alive animals, was the adoption of the image contrast technique which uses only one image from the illuminated sample. That approach presents some problems related to the resolution of the image, which is reduced during the image contrast processing. In order to help the visualization of the low resolution image formed by the contrast technique, this work presents the three-dimensional procedure as a reliable alternative to enhance the final image. The work based on a parallel processing, with the generation of a virtual map of amplitudes, and maintaining the quasi-online characteristic of the contrast technique. Therefore, it was possible to generate in the same display the observed material, the image contrast result and in addiction the three-dimensional image with adjustable options of rotation. The platform also offers to the user the possibility to access the 3D image offline.

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.

Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins.

PubMed

Neumann, Sindy; Hartmann, Holger; Martin-Galiano, Antonio J; Fuchs, Angelika; Frishman, Dmitrij

2012-03-01

Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/. Copyright © 2011 Wiley Periodicals, Inc.

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.

Linear Static Behavior of Damaged Laminated Composite Plates and Shells

PubMed Central

2017-01-01

A mathematical scheme is proposed here to model a damaged mechanical configuration for laminated and sandwich structures. In particular, two kinds of functions defined in the reference domain of plates and shells are introduced to weaken their mechanical properties in terms of engineering constants: a two-dimensional Gaussian function and an ellipse shaped function. By varying the geometric parameters of these distributions, several damaged configurations are analyzed and investigated through a set of parametric studies. The effect of a progressive damage is studied in terms of displacement profiles and through-the-thickness variations of stress, strain, and displacement components. To this end, a posteriori recovery procedure based on the three-dimensional equilibrium equations for shell structures in orthogonal curvilinear coordinates is introduced. The theoretical framework for the two-dimensional shell model is based on a unified formulation able to study and compare several Higher-order Shear Deformation Theories (HSDTs), including Murakami’s function for the so-called zig-zag effect. Thus, various higher-order models are used and compared also to investigate the differences which can arise from the choice of the order of the kinematic expansion. Their ability to deal with several damaged configurations is analyzed as well. The paper can be placed also in the field of numerical analysis, since the solution to the static problem at issue is achieved by means of the Generalized Differential Quadrature (GDQ) method, whose accuracy and stability are proven by a set of convergence analyses and by the comparison with the results obtained through a commercial finite element software. PMID:28773170

Fragmentary and incidental behaviour of columns, slabs and crystals

PubMed Central

Whiteley, Walter

2014-01-01

Between the study of small finite frameworks and infinite incidentally periodic frameworks, we find the real materials which are large, but finite, fragments that fit into the infinite periodic frameworks. To understand these materials, we seek insights from both (i) their analysis as large frameworks with associated geometric and combinatorial properties (including the geometric repetitions) and (ii) embedding them into appropriate infinite periodic structures with motions that may break the periodic structure. A review of real materials identifies a number of examples with a local appearance of ‘unit cells’ which repeat under isometries but perhaps in unusual forms. These examples also refocus attention on several new classes of infinite ‘periodic’ frameworks: (i) columns—three-dimensional structures generated with one repeating isometry and (ii) slabs—three-dimensional structures with two independent repeating translations. With this larger vision of structures to be studied, we find some patterns and partial results that suggest new conjectures as well as many additional open questions. These invite a search for new examples and additional theorems. PMID:24379423

Highly conducting divalent Mg{sup 2+} cation solid electrolytes with well-ordered three-dimensional network structure

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

Tamura, Shinji; Yamane, Megumi; Hoshino, Yasunori

2016-03-15

A three-dimensionally well-ordered NASICON-type Mg{sup 2+} cation conductor, (Mg{sub x}Hf{sub 1−x}){sub 4/(4−2x)}Nb(PO{sub 4}){sub 3}, was firstly developed by partial substitution of lower valent Mg{sup 2+} cation onto the Hf{sup 4+} sites in a HfNb(PO{sub 4}){sub 3} solid to realize high Mg{sup 2+} cation conductivity even at moderate temperatures. Due to the formation of well-ordered NASICON-type structure, both the high Mg{sup 2+} cation conductivity below 450 °C and the low activation energy for Mg{sup 2+} cation migration was successfully realized for the (Mg{sub 0.1}Hf{sub 0.9}){sub 4/3.8}Nb(PO{sub 4}){sub 3} solid. Pure Mg{sup 2+} cation conduction in the NASICON-type (Mg{sub 0.1}Hf{sub 0.9}){sub 4/3.8}Nb(PO{submore » 4}){sub 3} solid was directly and quantitatively demonstrated by means of two kinds of dc electrolysis. - Graphical abstract: Image of the Mg{sup 2+} cation conduction in NASICON-type (Mg{sub 0.1}Hf{sub 0.9}){sub 4/3.8}Nb(PO{sub 4}){sub 3} and its Mg{sup 2+} conductivity. - Highlights: • We develop a three-dimensionally well-ordered NASICON-type Mg{sup 2+} cation conductor. • A high magnesium cation conductivity is realized even at moderate temperatures. • Divalent magnesium cation conduction is demonstrated directly and quantitatively.« less

Identifying three-dimensional nested groundwater flow systems in a Tóthian basin

NASA Astrophysics Data System (ADS)

Wang, Xu-Sheng; Wan, Li; Jiang, Xiao-Wei; Li, Hailong; Zhou, Yangxiao; Wang, Junzhi; Ji, Xiaohui

2017-10-01

Nested groundwater flow systems have been revealed in Tóth's theory as the structural property of basin-scale groundwater circulation but were only well known with two-dimensional (2D) profile models. The method of searching special streamlines across stagnation points for partitioning flow systems, which has been successfully applied in the 2D models, has never been implemented for three-dimensional (3D) Tóthian basins because of the difficulty in solving the dual stream functions. Alternatively, a new method is developed to investigate 3D nested groundwater flow systems without determination of stagnation points. Connective indices are defined to quantify the connection between individual recharge and discharge zones along streamlines. Groundwater circulation cells (GWCCs) are identified according to the distribution of the connective indices and then grouped into local, intermediate and regional flow systems. This method requires existing solution of the flow velocity vector and is implemented via particle tracking technique. It is applied in a hypothetical 3D Tóthian basin with an analytical solution of the flow field and in a real-world basin with a numerical modeling approach. Different spatial patterns of flow systems compared to 2D profile models are found. The outcrops boundaries of GWCCs on water table may significantly deviate from and are not parallel to the nearby water table divides. Topological network is proposed to represent the linked recharge-discharge zones through closed and open GWCCs. Sensitivity analysis indicates that the development of GWCCs depends on the basin geometry, hydraulic parameters and water table shape.

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.

Structural diversity: a multi-dimensional approach to assess recreational services in urban parks.

PubMed

Voigt, Annette; Kabisch, Nadja; Wurster, Daniel; Haase, Dagmar; Breuste, Jürgen

2014-05-01

Urban green spaces provide important recreational services for urban residents. In general, when park visitors enjoy "the green," they are in actuality appreciating a mix of biotic, abiotic, and man-made park infrastructure elements and qualities. We argue that these three dimensions of structural diversity have an influence on how people use and value urban parks. We present a straightforward approach for assessing urban parks that combines multi-dimensional landscape mapping and questionnaire surveys. We discuss the method as well the results from its application to differently sized parks in Berlin and Salzburg.

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.

A model-based approach to predict muscle synergies using optimization: application to feedback control

PubMed Central

Sharif Razavian, Reza; Mehrabi, Naser; McPhee, John

2015-01-01

This paper presents a new model-based method to define muscle synergies. Unlike the conventional factorization approach, which extracts synergies from electromyographic data, the proposed method employs a biomechanical model and formally defines the synergies as the solution of an optimal control problem. As a result, the number of required synergies is directly related to the dimensions of the operational space. The estimated synergies are posture-dependent, which correlate well with the results of standard factorization methods. Two examples are used to showcase this method: a two-dimensional forearm model, and a three-dimensional driver arm model. It has been shown here that the synergies need to be task-specific (i.e., they are defined for the specific operational spaces: the elbow angle and the steering wheel angle in the two systems). This functional definition of synergies results in a low-dimensional control space, in which every force in the operational space is accurately created by a unique combination of synergies. As such, there is no need for extra criteria (e.g., minimizing effort) in the process of motion control. This approach is motivated by the need for fast and bio-plausible feedback control of musculoskeletal systems, and can have important implications in engineering, motor control, and biomechanics. PMID:26500530

Propagation Diagnostic Simulations Using High-Resolution Equatorial Plasma Bubble Simulations

NASA Astrophysics Data System (ADS)

Rino, C. L.; Carrano, C. S.; Yokoyama, T.

2017-12-01

In a recent paper, under review, equatorial-plasma-bubble (EPB) simulations were used to conduct a comparative analysis of the EPB spectra characteristics with high-resolution in-situ measurements from the C/NOFS satellite. EPB realizations sampled in planes perpendicular to magnetic field lines provided well-defined EPB structure at altitudes penetrating both high and low-density regions. The average C/NOFS structure in highly disturbed regions showed nearly identical two-component inverse-power-law spectral characteristics as the measured EPB structure. This paper describes the results of PWE simulations using the same two-dimensional cross-field EPB realizations. New Irregularity Parameter Estimation (IPE) diagnostics, which are based on two-dimensional equivalent-phase-screen theory [A theory of scintillation for two-component power law irregularity spectra: Overview and numerical results, by Charles Carrano and Charles Rino, DOI: 10.1002/2015RS005903], have been successfully applied to extract two-component inverse-power-law parameters from measured intensity spectra. The EPB simulations [Low and Midlatitude Ionospheric Plasma DensityIrregularities and Their Effects on Geomagnetic Field, by Tatsuhiro Yokoyama and Claudia Stolle, DOI 10.1007/s11214-016-0295-7] have sufficient resolution to populate the structure scales (tens of km to hundreds of meters) that cause strong scintillation at GPS frequencies. The simulations provide an ideal geometry whereby the ramifications of varying structure along the propagation path can be investigated. It is well known path-integrated one-dimensional spectra increase the one-dimensional index by one. The relation requires decorrelation along the propagation path. Correlated structure would be interpreted as stochastic total-electron-content (TEC). The simulations are performed with unmodified structure. Because the EPB structure is confined to the central region of the sample planes, edge effects are minimized. Consequently, the propagated signal phase can be comparted to path-integrated phase for evaluating TEC extraction. Only the frequency dependence of phase scintillation distinguishes phase scintillation. The simulations allow scale-dependent exploration of remote-sensing diagnostics.

Fast Two-Dimensional Bubble Analysis of Biopolymer Filamentous Networks Pore Size from Confocal Microscopy Thin Data Stacks

PubMed Central

Molteni, Matteo; Magatti, Davide; Cardinali, Barbara; Rocco, Mattia; Ferri, Fabio

2013-01-01

The average pore size ξ0 of filamentous networks assembled from biological macromolecules is one of the most important physical parameters affecting their biological functions. Modern optical methods, such as confocal microscopy, can noninvasively image such networks, but extracting a quantitative estimate of ξ0 is a nontrivial task. We present here a fast and simple method based on a two-dimensional bubble approach, which works by analyzing one by one the (thresholded) images of a series of three-dimensional thin data stacks. No skeletonization or reconstruction of the full geometry of the entire network is required. The method was validated by using many isotropic in silico generated networks of different structures, morphologies, and concentrations. For each type of network, the method provides accurate estimates (a few percent) of the average and the standard deviation of the three-dimensional distribution of the pore sizes, defined as the diameters of the largest spheres that can be fit into the pore zones of the entire gel volume. When applied to the analysis of real confocal microscopy images taken on fibrin gels, the method provides an estimate of ξ0 consistent with results from elastic light scattering data. PMID:23473499

Three-dimensional bio-printing.

PubMed

Gu, Qi; Hao, Jie; Lu, YangJie; Wang, Liu; Wallace, Gordon G; Zhou, Qi

2015-05-01

Three-dimensional (3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.

Three dimensional computed tomography lung modeling is useful in simulation and navigation of lung cancer surgery.

PubMed

Ikeda, Norihiko; Yoshimura, Akinobu; Hagiwara, Masaru; Akata, Soichi; Saji, Hisashi

2013-01-01

The number of minimally invasive operations, such as video-assisted thoracoscopic surgery (VATS) lobectomy or segmentectomy, has enormously increased in recent years. These operations require extreme knowledge of the anatomy of pulmonary vessels and bronchi in each patient, and surgeons must carefully dissect the branches of pulmonary vessels during operation. Thus, foreknowledge of the anatomy of each patient would greatly contribute to the safety and accuracy of the operation. The development of multi-detector computed tomography (MDCT) has promoted three dimensional (3D) images of lung structures. It is possible to see the vascular and bronchial structures from the view of the operator; therefore, it is employed for preoperative simulation as well as navigation during operation. Due to advances in software, even small vessels can be accurately imaged, which is useful in performing segmentectomy. Surgical simulation and navigation systems based on high quality 3D lung modeling, including vascular and bronchial structures, can be used routinely to enhance the safety operation, education of junior staff, as well as providing a greater sense of security to the operators.

A computer program for the calculation of the flow field including boundary layer effects for mixed-compression inlets at angle of attack

NASA Technical Reports Server (NTRS)

Vadyak, J.; Hoffman, J. D.

1982-01-01

A computer program was developed which is capable of calculating the flow field in the supersonic portion of a mixed compression aircraft inlet operating at angle of attack. The supersonic core flow is computed using a second-order three dimensional method-of-characteristics algorithm. The bow shock and the internal shock train are treated discretely using a three dimensional shock fitting procedure. The boundary layer flows are computed using a second-order implicit finite difference method. The shock wave-boundary layer interaction is computed using an integral formulation. The general structure of the computer program is discussed, and a brief description of each subroutine is given. All program input parameters are defined, and a brief discussion on interpretation of the output is provided. A number of sample cases, complete with data listings, are provided.

Short peptides self-assemble to produce catalytic amyloids

NASA Astrophysics Data System (ADS)

Rufo, Caroline M.; Moroz, Yurii S.; Moroz, Olesia V.; Stöhr, Jan; Smith, Tyler A.; Hu, Xiaozhen; Degrado, William F.; Korendovych, Ivan V.

2014-04-01

Enzymes fold into unique three-dimensional structures, which underlie their remarkable catalytic properties. The requirement to adopt a stable, folded conformation is likely to contribute to their relatively large size (>10,000 Da). However, much shorter peptides can achieve well-defined conformations through the formation of amyloid fibrils. To test whether short amyloid-forming peptides might in fact be capable of enzyme-like catalysis, we designed a series of seven-residue peptides that act as Zn2+-dependent esterases. Zn2+ helps stabilize the fibril formation, while also acting as a cofactor to catalyse acyl ester hydrolysis. These results indicate that prion-like fibrils are able to not only catalyse their own formation, but they can also catalyse chemical reactions. Thus, they might have served as intermediates in the evolution of modern-day enzymes. These results also have implications for the design of self-assembling nanostructured catalysts including ones containing a variety of biological and non-biological metal ions.

Modelling Behaviour of a Carbon Epoxy Composite Exposed to Fire: Part I—Characterisation of Thermophysical Properties

PubMed Central

Tranchard, Pauline; Samyn, Fabienne; Duquesne, Sophie; Estèbe, Bruno; Bourbigot, Serge

2017-01-01

Thermophysical properties of a carbon-reinforced epoxy composite laminate (T700/M21 composite for aircraft structures) were evaluated using different innovative characterisation methods. Thermogravimetric Analysis (TGA), Simultaneous Thermal analysis (STA), Laser Flash analysis (LFA), and Fourier Transform Infrared (FTIR) analysis were used for measuring the thermal decomposition, the specific heat capacity, the anisotropic thermal conductivity of the composite, the heats of decomposition and the specific heat capacity of released gases. It permits to get input data to feed a three-dimensional (3D) model given the temperature profile and the mass loss obtained during well-defined fire scenarios (model presented in Part II of this paper). The measurements were optimised to get accurate data. The data also permit to create a public database on an aeronautical carbon fibre/epoxy composite for fire safety engineering. PMID:28772854

Electronic properties of two inequivalent surfaces in MoTe2 studied by quasi-particle interference

NASA Astrophysics Data System (ADS)

Iaia, Davide; Shichao, Yan; Madhavan, Vidya

MoTe2 has received renewed interest due to its topological properties. At a temperature below 250 K, MoTe2 is a type II Weyl semimetal hosting three-dimensional (3D) linearly dispersing states with well defined chirality. Nodes in this 3D dispersion are called Weyl points. Weyl points of opposite chirality are expected to be connected by topologically protected Fermi arcs. In this talk we discuss low temperature scanning tunneling microscopy studies of the electronic structure of MoTe2. The electronic properties are studied using quasi-particle interference technique which allows us to resolve Fermi arcs features and to clearly distinguish between two inequivalent MoTe2 surfaces. Our results provide important contributions to further our understanding of the electronic properties of this new and exotic class of materials. National Science Foundation (NSF).

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

PubMed

Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

2015-01-01

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

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).

Computerized mappings of the cerebral cortex: a multiresolution flattening method and a surface-based coordinate system

NASA Technical Reports Server (NTRS)

Drury, H. A.; Van Essen, D. C.; Anderson, C. H.; Lee, C. W.; Coogan, T. A.; Lewis, J. W.

1996-01-01

We present a new method for generating two-dimensional maps of the cerebral cortex. Our computerized, two-stage flattening method takes as its input any well-defined representation of a surface within the three-dimensional cortex. The first stage rapidly converts this surface to a topologically correct two-dimensional map, without regard for the amount of distortion introduced. The second stage reduces distortions using a multiresolution strategy that makes gross shape changes on a coarsely sampled map and further shape refinements on progressively finer resolution maps. We demonstrate the utility of this approach by creating flat maps of the entire cerebral cortex in the macaque monkey and by displaying various types of experimental data on such maps. We also introduce a surface-based coordinate system that has advantages over conventional stereotaxic coordinates and is relevant to studies of cortical organization in humans as well as non-human primates. Together, these methods provide an improved basis for quantitative studies of individual variability in cortical organization.

Unsupervised machine learning account of magnetic transitions in the Hubbard model

NASA Astrophysics Data System (ADS)

Ch'ng, Kelvin; Vazquez, Nick; Khatami, Ehsan

2018-01-01

We employ several unsupervised machine learning techniques, including autoencoders, random trees embedding, and t -distributed stochastic neighboring ensemble (t -SNE), to reduce the dimensionality of, and therefore classify, raw (auxiliary) spin configurations generated, through Monte Carlo simulations of small clusters, for the Ising and Fermi-Hubbard models at finite temperatures. Results from a convolutional autoencoder for the three-dimensional Ising model can be shown to produce the magnetization and the susceptibility as a function of temperature with a high degree of accuracy. Quantum fluctuations distort this picture and prevent us from making such connections between the output of the autoencoder and physical observables for the Hubbard model. However, we are able to define an indicator based on the output of the t -SNE algorithm that shows a near perfect agreement with the antiferromagnetic structure factor of the model in two and three spatial dimensions in the weak-coupling regime. t -SNE also predicts a transition to the canted antiferromagnetic phase for the three-dimensional model when a strong magnetic field is present. We show that these techniques cannot be expected to work away from half filling when the "sign problem" in quantum Monte Carlo simulations is present.

Euclidean scalar field theory in the bilocal approximation

NASA Astrophysics Data System (ADS)

Nagy, S.; Polonyi, J.; Steib, I.

2018-04-01

The blocking step of the renormalization group method is usually carried out by restricting it to fluctuations and to local blocked action. The tree-level, bilocal saddle point contribution to the blocking, defined by the infinitesimal decrease of the sharp cutoff in momentum space, is followed within the three dimensional Euclidean ϕ6 model in this work. The phase structure is changed, new phases and relevant operators are found, and certain universality classes are restricted by the bilocal saddle point.

Verification and Validation Plan for Three-Dimensional Probability of Incapacitation Methodology for Masonry Structures (3DPIMMS)

DTIC Science & Technology

2011-01-01

all panels of a test were recorded, it was reduced into text format and then input into the code. B. Current Development The capabilities...due to fragmentation. Any or all of these models can be activated for a particular lethality assessment. Incapacitation criteria of different times...defined for all fragments represented in the file. Only the fragment material density needs to be set by the user. 3DPIMMS accounts for some statistical

Three-dimensional photography for the evaluation of facial profiles in obstructive sleep apnoea.

PubMed

Lin, Shih-Wei; Sutherland, Kate; Liao, Yu-Fang; Cistulli, Peter A; Chuang, Li-Pang; Chou, Yu-Ting; Chang, Chih-Hao; Lee, Chung-Shu; Li, Li-Fu; Chen, Ning-Hung

2018-06-01

Craniofacial structure is an important determinant of obstructive sleep apnoea (OSA) syndrome risk. Three-dimensional stereo-photogrammetry (3dMD) is a novel technique which allows quantification of the craniofacial profile. This study compares the facial images of OSA patients captured by 3dMD to three-dimensional computed tomography (3-D CT) and two-dimensional (2-D) digital photogrammetry. Measurements were correlated with indices of OSA severity. Thirty-eight patients diagnosed with OSA were included, and digital photogrammetry, 3dMD and 3-D CT were performed. Distances, areas, angles and volumes from the images captured by three methods were analysed. Almost all measurements captured by 3dMD showed strong agreement with 3-D CT measurements. Results from 2-D digital photogrammetry showed poor agreement with 3-D CT. Mandibular width, neck perimeter size and maxillary volume measurements correlated well with the severity of OSA using all three imaging methods. Mandibular length, facial width, binocular width, neck width, cranial base triangle area, cranial base area 1 and middle cranial fossa volume correlated well with OSA severity using 3dMD and 3-D CT, but not with 2-D digital photogrammetry. 3dMD provided accurate craniofacial measurements of OSA patients, which were highly concordant with those obtained by CT, while avoiding the radiation associated with CT. © 2018 Asian Pacific Society of Respirology.

Three-dimensional assembly structure of anatase TiO2 hollow microspheres with enhanced photocatalytic performance

NASA Astrophysics Data System (ADS)

Tang, Yihao; Zhan, Shuai; Wang, Li; Zhang, Bin; Ding, Minghui

The pure anatase TiO2 hollow microspheres are synthesized by a one-step template-free hydrothermal route. By defining temperature and time limits, we produce TiO2 hollow microspheres with a fluoride-mediated self-transformation. The surface morphology of TiO2 hollow microspheres was studied by SEM. The hollow microspheres have diameters of about 800 nm and are remarkably uniform. The UV-light photocatalytic activity and the stability/multifunction of TiO2 hollow microspheres structure were evaluated by photocatalytic degradation of methylene blue and photocatalytic hydrogen evolution. The excellent photocatalytic activity is attributed to large specific surface area, more active sites, unique hollow structures, and improved light scattering.

A Conceptual Three-Dimensional Model for Evaluating Community-Based Substance Abuse Prevention Programs.

ERIC Educational Resources Information Center

Albers, Eric C.; Santangelo, Linda K.; McKinlay, George; Cavote, Steve; Rock, Stephen L.; Evans, William

2002-01-01

Presents a three-dimensional model for conceptualizing existing prevention programs, defining and measuring effects of prevention programs, and making a connection between those programmatic effects, and the interests of the funder. This paper describes the methodology and its use for promoting the efficiency and effectiveness of substance abuse…

Three-dimensional plasmonic chiral tetramers assembled by DNA origami.

PubMed

Shen, Xibo; Asenjo-Garcia, Ana; Liu, Qing; Jiang, Qiao; García de Abajo, F Javier; Liu, Na; Ding, Baoquan

2013-05-08

Molecular chemistry offers a unique toolkit to draw inspiration for the design of artificial metamolecules. For a long time, optical circular dichroism has been exclusively the terrain of natural chiral molecules, which exhibit optical activity mainly in the UV spectral range, thus greatly hindering their significance for a broad range of applications. Here we demonstrate that circular dichroism can be generated with artificial plasmonic chiral nanostructures composed of the minimum number of spherical gold nanoparticles required for three-dimensional (3D) chirality. We utilize a rigid addressable DNA origami template to precisely organize four nominally identical gold nanoparticles into a three-dimensional asymmetric tetramer. Because of the chiral structural symmetry and the strong plasmonic resonant coupling between the gold nanoparticles, the 3D plasmonic assemblies undergo different interactions with left and right circularly polarized light, leading to pronounced circular dichroism. Our experimental results agree well with theoretical predictions. The simplicity of our structure geometry and, most importantly, the concept of resorting on biology to produce artificial photonic functionalities open a new pathway to designing smart artificial plasmonic nanostructures for large-scale production of optically active metamaterials.

HR Del REMNANT ANATOMY USING TWO-DIMENSIONAL SPECTRAL DATA AND THREE-DIMENSIONAL PHOTOIONIZATION SHELL MODELS

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

Moraes, Manoel; Diaz, Marcos

2009-12-15

The HR Del nova remnant was observed with the IFU-GMOS at Gemini North. The spatially resolved spectral data cube was used in the kinematic, morphological, and abundance analysis of the ejecta. The line maps show a very clumpy shell with two main symmetric structures. The first one is the outer part of the shell seen in H{alpha}, which forms two rings projected in the sky plane. These ring structures correspond to a closed hourglass shape, first proposed by Harman and O'Brien. The equatorial emission enhancement is caused by the superimposed hourglass structures in the line of sight. The second structuremore » seen only in the [O III] and [N II] maps is located along the polar directions inside the hourglass structure. Abundance gradients between the polar caps and equatorial region were not found. However, the outer part of the shell seems to be less abundant in oxygen and nitrogen than the inner regions. Detailed 2.5-dimensional photoionization modeling of the three-dimensional shell was performed using the mass distribution inferred from the observations and the presence of mass clumps. The resulting model grids are used to constrain the physical properties of the shell as well as the central ionizing source. A sequence of three-dimensional clumpy models including a disk-shaped ionization source is able to reproduce the ionization gradients between polar and equatorial regions of the shell. Differences between shell axial ratios in different lines can also be explained by aspherical illumination. A total shell mass of 9 x 10{sup -4} M {sub sun} is derived from these models. We estimate that 50%-70% of the shell mass is contained in neutral clumps with density contrast up to a factor of 30.« less

Structure of the Tucson Basin, Arizona from gravity and aeromagnetic data

USGS Publications Warehouse

Rystrom, Victoria Louise

2003-01-01

Interpretation of gravity and high-resolution aeromagnetic data reveal the three-dimensional geometry of the Tuscson Basin, Arizona and the lithology of its basement. Limited drill hole and seismic data indicate that the maximum depth to the crystalline basement is approximately 3600 meters and that the sedimentary sequences in the upper ~2000 m of the basin were deposited during the most recent extensional episode that commenced about 13 Ma. The negative density contrasts between these upper Neogene and Quaternary sedimentary sequences and the adjacent country rock produce a Bouguer residual gravity low, whose steep gradients clearly define the lateral extent of the upper ~2000m of the basin. The aeromagnetic maps show large positive anomalies associated with deeply buried, late Cretaceous-early Tertiary and mid-Tertiary igneous rocks at and below the surface of the basin. These magnetic anomalies provide insight into the older (>13 Ma) and deeper structures of the basin. Simultaneous 2.5-dimensional modeling of both gravity and magnetic anomalies constrained by geologic and seismic data delineates the thickness of the basin and the dips of the buried faults that bound the basin. This geologic-based forward modeling approach to using geophysical data is shown to result in more information about the geologic and tectonic history of the basin as well as more accurate depth to basement determinations than using generalized geophysical inversion techniques.

The diffusive boundary layer of sediments: oxygen microgradients over a microbial mat

NASA Technical Reports Server (NTRS)

Jorgensen, B. B.; Des Marais, D. J.

1990-01-01

Oxygen microelectrodes were used to analyze the distribution of the diffusive boundary layer (DBL) at the sediment-water interface in relation to surface topography and flow velocity. The sediment, collected from saline ponds, was covered by a microbial mat that had high oxygen consumption rate and well-defined surface structure. Diffusion through the DBL constituted an important rate limitation to the oxygen uptake of the sediment. The mean effective DBL thickness decreased from 0.59 to 0.16 mm as the flow velocity of the overlying water was increased from 0.3 to 7.7 cm s-1 (measured 1 cm above the mat). The oxygen uptake rate concurrently increased from 3.9 to 9.4 nmol cm-2 min-1. The effects of surface roughness and topography on the thickness and distribution of the DBL were studied by three-dimensional mapping of the sediment-water interface and the upper DBL boundary at 0.1-mm spatial resolution. The DBL boundary followed mat structures that had characteristic dimensions > 1/2 DBL thickness but the DBL had a dampened relief relative to the mat. The effective surface area of the sediment-water interface and of the upper DBL boundary were 31 and 14% larger, respectively, than a flat plane. Surface topography thereby increased the oxygen flux across the sediment-water interface by 49% relative to a one-dimensional diffusion flux calculated from the vertical oxygen microgradients.

Microelectrodes with Three-Dimensional Structures for Improved Neural Interfacing

DTIC Science & Technology

2001-10-25

highly xible bio-interfaces [2]. Polyimides combine excellent ectrical and mechanical characteristics with biocompatibility ], and are well known in...excellent biocompatibility , polyimide -based electrodes promise for fabrication of long-term implants for the use in prostheses. The flexible structures...R. R. Richardson, J. A. Miller, and W. M. Reichert, " Polyimides as Biomaterials - Preliminary Biocompatibility Testing," Biomaterials, vol. 14, pp

Non-stationary Drainage Flows and Cold Pools in Gentle Terrain

NASA Astrophysics Data System (ADS)

Mahrt, L.

2015-12-01

Previous studies have concentrated on organized topography with well-defined slopes or valleys in an effort to understand the flow dynamics. However, most of the Earth's land surface consists of gentle terrain that is quasi three dimensional. Different scenarios are briefly classified. A network of measurements are analyzed to examine shallow cold pools and drainage flow down the valley which develop for weak ambient wind and relatively clear skies. However, transient modes constantly modulate or intermittently eliminate the cold pool, which makes extraction and analysis of the horizontal structure of the cold pool difficult with traditional analysis methods. Singular value decomposition successfully isolates the effects of large-scale flow from local down-valley cold air drainage within the cold pool in spite of the intermittent nature of this local flow. The traditional concept of a cold pool must be generalized to include cold pool intermittency, complex variation of temperature related to some three-dimensionality and a diffuse cold pool top. Different types of cold pools are classified in terms of the stratification and gradient of potential temperature along the slope. The strength of the cold pool is related to a forcing temperature scale proportional to the net radiative cooling divided by the wind speed above the valley. The scatter is large partly due to nonstationarity of the marginal cold pool in this shallow valley

Seismic-geodynamic constraints on three-dimensional structure, vertical flow, and heat transfer in the mantle

USGS Publications Warehouse

Forte, A.M.; Woodward, R.L.

1997-01-01

Joint inversions of seismic and geodynamic data are carried out in which we simultaneously constrain global-scale seismic heterogeneity in the mantle as well as the amplitude of vertical mantle flow across the 670 km seismic discontinuity. These inversions reveal the existence of a family of three-dimensional (3-D) mantle models that satisfy the data while at the same time yielding predictions of layered mantle flow. The new 3-D mantle models we obtain demonstrate that the buoyancy forces due to the undulations of the 670 km phase-change boundary strongly inhibit the vertical flow between the upper and lower mantle. The strong stabilizing effect of the 670 km topography also has an important impact on the predicted dynamic topography of the Earth's solid surface and on the surface gravity anomalies. The new 3-D models that predict strongly or partially layered mantle flow provide essentially identical fits to the global seismic data as previous models that have, until now, predicted only whole-mantle flow. The convective vertical transport of heat across the mantle predicted on the basis of the new 3-D models shows that the heat flow is a minimum at 1000 km depth. This suggests the presence at this depth of a globally defined horizon across which the pattern of lateral heterogeneity changes rapidly. Copyright 1997 by the American Geophysical Union.

Mechanotransduction mechanisms in growing spherically structured tissues

NASA Astrophysics Data System (ADS)

Littlejohns, Euan; Dunlop, Carina M.

2018-04-01

There is increasing experimental interest in mechanotransduction in multi-cellular tissues as opposed to single cells. This is driven by a growing awareness of the importance of physiologically relevant three-dimensional culture and of cell–cell and cell–gel interactions in directing growth and development. The paradigm biophysical technique for investigating tissue level mechanobiology in this context is to grow model tissues in artificial gels with well-defined mechanical properties. These studies often indicate that the stiffness of the encapsulating gel can significantly alter cellular behaviours. We demonstrate here potential mechanisms linking tissue growth with stiffness-mediated mechanotransduction. We show how tissue growth in gel systems generates points at which there is a significant qualitative change in the cellular stress and strain experienced. We show analytically how these potential switching points depend on the mechanical properties of the constraining gel and predict when they will occur. Significantly, we identify distinct mechanisms that act separately in each of the stress and strain fields at different times. These observations suggest growth as a potential physical mechanism coupling gel stiffness with cellular mechanotransduction in three-dimensional tissues. We additionally show that non-proliferating areas, in the case that the constraining gel is soft compared with the tissue, will expand and contract passively as a result of growth. Central compartment size is thus seen to not be a reliable indicator on its own for growth initiation or active behaviour.

Three dimensional macroporous architectures and aerogels built of carbon nanotubes and/or graphene: synthesis and applications.

PubMed

Nardecchia, Stefania; Carriazo, Daniel; Ferrer, M Luisa; Gutiérrez, María C; del Monte, Francisco

2013-01-21

Carbon nanotubes and graphene are some of the most intensively explored carbon allotropes in materials science. This interest mainly resides in their unique properties with electrical conductivities as high as 10(4) S cm(-1), thermal conductivities as high as 5000 W m(-1) K and superior mechanical properties with elastic moduli on the order of 1 TPa for both of them. The possibility to translate the individual properties of these monodimensional (e.g. carbon nanotubes) and bidimensional (e.g. graphene) building units into two-dimensional free-standing thick and thin films has paved the way for using these allotropes in a number of applications (including photocatalysis, electrochemistry, electronics and optoelectronics, among others) as well as for the preparation of biological and chemical sensors. More recently and while recognizing the tremendous interest of these two-dimensional structures, researchers are noticing that the performance of certain devices can experience a significant enhancement by the use of three-dimensional architectures and/or aerogels because of the increase of active material per projected area. This is obviously the case as long as the nanometre-sized building units remain accessible so that the concept of hierarchical three-dimensional organization is critical to guarantee the mass transport and, as consequence, performance enhancement. Thus, this review aims to describe the different synthetic processes used for preparation of these three-dimensional architectures and/or aerogels containing either any or both allotropes, and the different fields of application in which the particular structure of these materials provided a significant enhancement in the efficacy as compared to their two-dimensional analogues or even opened the path to novel applications. The unprecedented compilation of information from both CNT- and graphene-based three-dimensional architectures and/or aerogels in a single revision is also of interest because it allows a straightforward comparison between the particular features provided by each allotrope.

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.

A computer program for fitting smooth surfaces to three-dimensional aircraft configurations

NASA Technical Reports Server (NTRS)

Craidon, C. B.; Smith, R. E., Jr.

1975-01-01

A computer program developed to fit smooth surfaces to the component parts of three-dimensional aircraft configurations was described. The resulting equation definition of an aircraft numerical model is useful in obtaining continuous two-dimensional cross section plots in arbitrarily defined planes, local tangents, enriched surface plots and other pertinent geometric information; the geometry organization used as input to the program has become known as the Harris Wave Drag Geometry.

A new dipolar potential for numerical simulations of polar fluids on the 4D hypersphere

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

Caillol, Jean-Michel, E-mail: Jean-Michel.Caillol@th.u-psud.fr; Trulsson, Martin, E-mail: martin.trulsson@lptms.u-psud.fr

2014-09-28

We present a new method for Monte Carlo or Molecular Dynamics numerical simulations of three-dimensional polar fluids. The simulation cell is defined to be the surface of the northern hemisphere of a four-dimensional (hyper)sphere. The point dipoles are constrained to remain tangent to the sphere and their interactions are derived from the basic laws of electrostatics in this geometry. The dipole-dipole potential has two singularities which correspond to the following boundary conditions: when a dipole leaves the northern hemisphere at some point of the equator, it reappears at the antipodal point bearing the same dipole moment. We derive all themore » formal expressions needed to obtain the thermodynamic and structural properties of a polar liquid at thermal equilibrium in actual numerical simulation. We notably establish the expression of the static dielectric constant of the fluid as well as the behavior of the pair correlation at large distances. We report and discuss the results of extensive numerical Monte Carlo simulations for two reference states of a fluid of dipolar hard spheres and compare these results with previous methods with a special emphasis on finite size effects.« less

A new dipolar potential for numerical simulations of polar fluids on the 4D hypersphere

NASA Astrophysics Data System (ADS)

Caillol, Jean-Michel; Trulsson, Martin

2014-09-01

We present a new method for Monte Carlo or Molecular Dynamics numerical simulations of three-dimensional polar fluids. The simulation cell is defined to be the surface of the northern hemisphere of a four-dimensional (hyper)sphere. The point dipoles are constrained to remain tangent to the sphere and their interactions are derived from the basic laws of electrostatics in this geometry. The dipole-dipole potential has two singularities which correspond to the following boundary conditions: when a dipole leaves the northern hemisphere at some point of the equator, it reappears at the antipodal point bearing the same dipole moment. We derive all the formal expressions needed to obtain the thermodynamic and structural properties of a polar liquid at thermal equilibrium in actual numerical simulation. We notably establish the expression of the static dielectric constant of the fluid as well as the behavior of the pair correlation at large distances. We report and discuss the results of extensive numerical Monte Carlo simulations for two reference states of a fluid of dipolar hard spheres and compare these results with previous methods with a special emphasis on finite size effects.

Development of a direct three-dimensional biomicrofabrication concept based on electrospraying a custom made siloxane sol

PubMed Central

Sullivan, Alice C.; Jayasinghe, Suwan N.

2007-01-01

We demonstrate here the discovery of a unique and direct three-dimensional biomicrofabrication concept possessing the ability to revolutionize the jet-based fabrication arena. Previous work carried out on similar jet-based approaches have been successful in fabricating only vertical wall∕pillar-structures by the controlled deposition of stacked droplets. However, these advanced jet-techniques have not been able to directly fabricate self-supporting arches∕links (without molds or reaction methods) between adjacent structures (walls or pillars). Our work reported here gives birth to a unique type of jet determined by high intensity electric fields, which is derived from a specially formulated siloxane sol. The sol studied here has been chosen for its attractive properties (such as an excellent cross-linking nature as well as the ability to polymerize via polycondensation on deposition to its biocompatability), which promotes direct forming of biostructures with nanometer (<50 nm) sized droplets in three dimensions. We foresee that this direct three-dimensional biomicrofabrication jet technique coupled with a variety of formulated sols having focused and enhanced functionality will be explored throughout the physical and life sciences. PMID:19693359

Sonic morphology: Aesthetic dimensional auditory spatial awareness

NASA Astrophysics Data System (ADS)

Whitehouse, Martha M.

The sound and ceramic sculpture installation, " Skirting the Edge: Experiences in Sound & Form," is an integration of art and science demonstrating the concept of sonic morphology. "Sonic morphology" is herein defined as aesthetic three-dimensional auditory spatial awareness. The exhibition explicates my empirical phenomenal observations that sound has a three-dimensional form. Composed of ceramic sculptures that allude to different social and physical situations, coupled with sound compositions that enhance and create a three-dimensional auditory and visual aesthetic experience (see accompanying DVD), the exhibition supports the research question, "What is the relationship between sound and form?" Precisely how people aurally experience three-dimensional space involves an integration of spatial properties, auditory perception, individual history, and cultural mores. People also utilize environmental sound events as a guide in social situations and in remembering their personal history, as well as a guide in moving through space. Aesthetically, sound affects the fascination, meaning, and attention one has within a particular space. Sonic morphology brings art forms such as a movie, video, sound composition, and musical performance into the cognitive scope by generating meaning from the link between the visual and auditory senses. This research examined sonic morphology as an extension of musique concrete, sound as object, originating in Pierre Schaeffer's work in the 1940s. Pointing, as John Cage did, to the corporeal three-dimensional experience of "all sound," I composed works that took their total form only through the perceiver-participant's participation in the exhibition. While contemporary artist Alvin Lucier creates artworks that draw attention to making sound visible, "Skirting the Edge" engages the perceiver-participant visually and aurally, leading to recognition of sonic morphology.

Structured light optical microscopy for three-dimensional reconstruction of technical surfaces

NASA Astrophysics Data System (ADS)

Kettel, Johannes; Reinecke, Holger; Müller, Claas

2016-04-01

In microsystems technology quality control of micro structured surfaces with different surface properties is playing an ever more important role. The process of quality control incorporates three-dimensional (3D) reconstruction of specularand diffusive reflecting technical surfaces. Due to the demand on high measurement accuracy and data acquisition rates, structured light optical microscopy has become a valuable solution to solve this problem providing high vertical and lateral resolution. However, 3D reconstruction of specular reflecting technical surfaces still remains a challenge to optical measurement principles. In this paper we present a measurement principle based on structured light optical microscopy which enables 3D reconstruction of specular- and diffusive reflecting technical surfaces. It is realized using two light paths of a stereo microscope equipped with different magnification levels. The right optical path of the stereo microscope is used to project structured light onto the object surface. The left optical path is used to capture the structured illuminated object surface with a camera. Structured light patterns are generated by a Digital Light Processing (DLP) device in combination with a high power Light Emitting Diode (LED). Structured light patterns are realized as a matrix of discrete light spots to illuminate defined areas on the object surface. The introduced measurement principle is based on multiple and parallel processed point measurements. Analysis of the measured Point Spread Function (PSF) by pattern recognition and model fitting algorithms enables the precise calculation of 3D coordinates. Using exemplary technical surfaces we demonstrate the successful application of our measurement principle.

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.

Transport of phase space densities through tetrahedral meshes using discrete flow mapping

NASA Astrophysics Data System (ADS)

Bajars, Janis; Chappell, David J.; Søndergaard, Niels; Tanner, Gregor

2017-01-01

Discrete flow mapping was recently introduced as an efficient ray based method determining wave energy distributions in complex built up structures. Wave energy densities are transported along ray trajectories through polygonal mesh elements using a finite dimensional approximation of a ray transfer operator. In this way the method can be viewed as a smoothed ray tracing method defined over meshed surfaces. Many applications require the resolution of wave energy distributions in three-dimensional domains, such as in room acoustics, underwater acoustics and for electromagnetic cavity problems. In this work we extend discrete flow mapping to three-dimensional domains by propagating wave energy densities through tetrahedral meshes. The geometric simplicity of the tetrahedral mesh elements is utilised to efficiently compute the ray transfer operator using a mixture of analytic and spectrally accurate numerical integration. The important issue of how to choose a suitable basis approximation in phase space whilst maintaining a reasonable computational cost is addressed via low order local approximations on tetrahedral faces in the position coordinate and high order orthogonal polynomial expansions in momentum space.

Hydrophobic core malleability of a de novo designed three-helix bundle protein.

PubMed

Walsh, S T; Sukharev, V I; Betz, S F; Vekshin, N L; DeGrado, W F

2001-01-12

De novo protein design provides a tool for testing the principles that stabilize the structures of proteins. Recently, we described the design and structure determination of alpha(3)D, a three-helix bundle protein with a well-packed hydrophobic core. Here, we test the malleability and adaptability of this protein's structure by mutating a small, Ala residue (A60) in its core to larger, hydrophobic side-chains, Leu and Ile. Such changes introduce strain into the structures of natural proteins, and therefore generally destabilize the native state. By contrast, these mutations were slightly stabilizing ( approximately 1.5 kcal mol(-1)) to the tertiary structure of alpha(3)D. The value of DeltaC(p) for unfolding of these mutants was not greatly affected relative to wild-type, indicating that the change in solvent accessibility for unfolding was similar. However, two-dimensional heteronuclear single quantum coherence spectra indicate that the protein adjusts to the introduction of steric bulk in different ways. A60L-alpha(3)D showed serious erosion in the dispersion of both the amide backbone as well as the side-chain methyl chemical shifts. By contrast, A60I-alpha(3)D showed excellent dispersion of the backbone resonances, and selective changes in dispersion of the aliphatic side-chains proximal to the site of mutation. Together, these data suggest that alpha(3)D, although folded into a unique three-dimensional structure, is nevertheless more malleable and flexible than most natural, native proteins. Copyright 2001 Academic Press.