Science.gov

Sample records for 3d magnetic structure

  1. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

    The study of solar coronal structures and, in particular prominences, is a key part of understanding the highly complex physical mechanisms occurring in the Sun's atmosphere. Solar prominences are important in their own right and some of the most puzzling questions in solar theory have arisen through their study. For example, how do they form and how is their mass continuously replenished? How can the magnetic field provide their continuous support against gravity over time periods of several months? How can such cool, dense material exist in thermal equilibrium in the surrounding coronal environment? Why do they erupt? A study of their structure and that of the surrounding medium is important in determining the nature of the coronal plasma and magnetic field. Also, prominences are closely associated with other key phenomena such as coronal mass ejections and eruptive solar flares which occur as a prominence loses equilibrium and rises from the solar surface. Our current understanding of these fascinating structures is extremely limited and we know very little about their basic global structure. In fact, recent prominence observations have caused our basic paradigms to be challenged (Priest, 1996) and so we must set up new models in order to gain even a fundamental understanding. Prominences are highly nonlinear, three-dimensional structures. Large feet (or barbs) reach out from the main body of a prominence and reach down to the photosphere where the dense material continuously drains away. These provide a real clue to the three-dimensional nature of the coronal field and its relation to the photospheric field. It is important, therefore, to make stereographic observations of prominences in order to gain a basic understanding of their essentially three-dimensional nature and attempt to formulate new paradigms for their structure and evolution. There is no doubt that the study of prominences in three dimensions is a crucial exercise if we are to develop a better

  2. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-07

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

  3. Cross modality registration of video and magnetic tracker data for 3D appearance and structure modeling

    NASA Astrophysics Data System (ADS)

    Sargent, Dusty; Chen, Chao-I.; Wang, Yuan-Fang

    2010-02-01

    The paper reports a fully-automated, cross-modality sensor data registration scheme between video and magnetic tracker data. This registration scheme is intended for use in computerized imaging systems to model the appearance, structure, and dimension of human anatomy in three dimensions (3D) from endoscopic videos, particularly colonoscopic videos, for cancer research and clinical practices. The proposed cross-modality calibration procedure operates this way: Before a colonoscopic procedure, the surgeon inserts a magnetic tracker into the working channel of the endoscope or otherwise fixes the tracker's position on the scope. The surgeon then maneuvers the scope-tracker assembly to view a checkerboard calibration pattern from a few different viewpoints for a few seconds. The calibration procedure is then completed, and the relative pose (translation and rotation) between the reference frames of the magnetic tracker and the scope is determined. During the colonoscopic procedure, the readings from the magnetic tracker are used to automatically deduce the pose (both position and orientation) of the scope's reference frame over time, without complicated image analysis. Knowing the scope movement over time then allows us to infer the 3D appearance and structure of the organs and tissues in the scene. While there are other well-established mechanisms for inferring the movement of the camera (scope) from images, they are often sensitive to mistakes in image analysis, error accumulation, and structure deformation. The proposed method using a magnetic tracker to establish the camera motion parameters thus provides a robust and efficient alternative for 3D model construction. Furthermore, the calibration procedure does not require special training nor use expensive calibration equipment (except for a camera calibration pattern-a checkerboard pattern-that can be printed on any laser or inkjet printer).

  4. Properties of the prominence magnetic field and plasma distributions as obtained from 3D whole-prominence fine structure modeling

    NASA Astrophysics Data System (ADS)

    Gunár, S.; Mackay, D. H.

    2016-07-01

    Aims: We analyze distributions of the magnetic field strength and prominence plasma (temperature, pressure, plasma β, and mass) using the 3D whole-prominence fine structure model. Methods: The model combines a 3D magnetic field configuration of an entire prominence, obtained from non-linear force-free field simulations, with a detailed semi-empirically derived description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Results: We show that in the modeled prominence, the variations of the magnetic field strength and its orientation are insignificant on scales comparable to the smallest dimensions of the observed prominence fine structures. We also show the ability of the 3D whole-prominence fine structure model to reveal the distribution of the prominence plasma with respect to its temperature within the prominence volume. This provides new insights into the composition of the prominence-corona transition region. We further demonstrate that the values of the plasma β are small throughout the majority of the modeled prominences when realistic photospheric magnetic flux distributions and prominence plasma parameters are assumed. While this is generally true, we also find that in the region with the deepest magnetic dips, the plasma β may increase towards unity. Finally, we show that the mass of the modeled prominence plasma is in good agreement with the mass of observed non-eruptive prominences.

  5. Electronic structure and local magnetism of 3d-5d impurity substituted CeFe2

    NASA Astrophysics Data System (ADS)

    Das, Rakesh; Das, G. P.; Srivastava, S. K.

    2016-04-01

    We present here a systematic first-principles study of electronic structure and local magnetic properties of Ce[Fe0.75M0.25]2 compounds, where M is a 3d, 4d or 5d transition or post-transition element, using the generalized gradient approximation of the density functional theory. The d-f band hybridizations existing in CeFe2 get modified by the impurity M in an orderly manner across a period for each impurity series: the hybridization is strongest for the Mn group impurity in the period and gets diminished on either side of it. The weakening of the d-f hybridization strength is also associated with a relative localization of the Ce 4f states with respect to the delocalized 4f states in CeFe2. The above effects are most prominent for 3d impurity series, while for 4d and 5d impurities, the hybridizations and relocalizations are relatively weak due primarily to the relatively extended nature of 4d and 5d wavefunctions. The Ce local moment is found to decrease from the CeFe2 value in proportion to the strength of relocalization, thus following almost the same orderly trend as obeyed by the d-f hybridization. Further, depending on the way the spin-up and spin-down densities of states of an impurity shift relative to the Fermi energy, the impurity local moments are highest for Mn or Fe group, reduce on either side, become zero for Ni to Ga, and are small but negative for V and Ti. The Ce hyperfine field is found to follow the M local moment in a linear fashion, and vice-versa.

  6. Magnetic Properties of 3D Printed Toroids

    NASA Astrophysics Data System (ADS)

    Bollig, Lindsey; Otto, Austin; Hilpisch, Peter; Mowry, Greg; Nelson-Cheeseman, Brittany; Renewable Energy; Alternatives Lab (REAL) Team

    Transformers are ubiquitous in electronics today. Although toroidal geometries perform most efficiently, transformers are traditionally made with rectangular cross-sections due to the lower manufacturing costs. Additive manufacturing techniques (3D printing) can easily achieve toroidal geometries by building up a part through a series of 2D layers. To get strong magnetic properties in a 3D printed transformer, a composite filament is used containing Fe dispersed in a polymer matrix. How the resulting 3D printed toroid responds to a magnetic field depends on two structural factors of the printed 2D layers: fill factor (planar density) and fill pattern. In this work, we investigate how the fill factor and fill pattern affect the magnetic properties of 3D printed toroids. The magnetic properties of the printed toroids are measured by a custom circuit that produces a hysteresis loop for each toroid. Toroids with various fill factors and fill patterns are compared to determine how these two factors can affect the magnetic field the toroid can produce. These 3D printed toroids can be used for numerous applications in order to increase the efficiency of transformers by making it possible for manufacturers to make a toroidal geometry.

  7. Crystal, magnetic and electronic structures of 3d-5d ordered double perovskite Ba2CoReO6

    NASA Astrophysics Data System (ADS)

    Musa Saad H.-E., M.; Rammeh, N.

    2016-12-01

    A comprehensive study on crystal, magnetic and electronic structures of ordered double perovskite Ba2CoReO6 was carried out using X-ray powder diffraction (XRD) and superconducting quantum interference device (SQUID). Also, the density functional theory (DFT) calculations were performed by full potential linear muffin-tin orbital (FP-LMTO) method within the localized spin density approximation (LSDA+U) and generalized gradient approximation (GGA+U). At room temperature, the crystal structure of Ba2CoReO6 is face-centered cubic, space group Fm 3 bar m , containing an almost completely ordered arrangement of CoO6-ReO6 octahedra. Magnetic structure showed an antiferromagnetic (AF) behavior below TN=41 K. The magnetic and electronic structures are consistent with the electronic configurations Co2+(3d7)-Re6+(5d1) having a total spin magnetic moment of about 2.0 μB/f.u. DFT electronic structures predicted half-metallic yields from 3d-t2g↓ and 5d-t2g↓ through O2-.

  8. A series of novel lanthanide carboxyphosphonates with a 3D framework structure: synthesis, structure, and luminescent and magnetic properties.

    PubMed

    Chen, Kai; Dong, Da-Peng; Sun, Zhen-Gang; Jiao, Cheng-Qi; Li, Chao; Wang, Cheng-Lin; Zhu, Yan-Yu; Zhao, Yan; Zhu, Jiang; Sun, Shou-Hui; Zheng, Ming-Jing; Tian, Hui; Chu, Wei

    2012-08-28

    By introduction of 1,4-benzenedicarboxylic acid as the second organic ligand, a series of novel lanthanide carboxyphosphonates with a 3D framework structure, namely, [Ln(3)(H(2)L)(HL)(2)(bdc)(2)(H(2)O)]·7H(2)O (Ln = La (1), Ce (2), Pr (3), Nd (4), Sm (5), Eu (6), Gd (7), Tb (8); H(3)L = H(2)O(3)PCH(2)NC(5)H(9)COOH; H(2)bdc = HOOCC(6)H(4)COOH) have been synthesized under hydrothermal conditions. Compounds are isostructural and feature a 3D framework in which Ln(III) polyhedra are interconnected by bridging {CPO(3)} tetrahedra into 2D inorganic layers parallel to the ab plane. The organic groups of H(2)L(-) are grafted on the two sides of the layer. These layers are further cross-linked by the bdc(2-) ligands from one layer to the Ln atoms from the other into a pillared-layered architecture with one-dimensional channel system along the a axis. The thermal stability of compounds has been investigated. Luminescent properties of compounds , and the magnetic properties of compound have also been studied.

  9. Structural, electronic and magnetic properties of 3d metal trioxide clusters-doped monolayer graphene: A first-principles study

    NASA Astrophysics Data System (ADS)

    Rafique, Muhammad; Shuai, Yong; Tan, He-Ping; Hassan, Muhammad

    2017-03-01

    We present first-principles density-functional calculations for the structural, electronic and magnetic properties of monolayer graphene doped with 3d (Ti, V, Cr, Fe, Co, Mn and Ni) metal trioxide TMO3 halogen clusters. In this paper we used two approaches for 3d metal trioxide clusters (i) TMO3 halogen cluster was embedded in monolayer graphene substituting four carbon (C) atoms (ii) three C atoms were substituted by three oxygen (O) atoms in one graphene ring and TM atom was adsorbed at the hollow site of O atoms substituted graphene ring. All the impurities were tightly bonded in the graphene ring. In first case of TMO3 doped graphene layer, the bond length between Csbnd O atom was reduced and bond length between TM-O atom was increased. In case of Cr, Fe, Co and Ni atoms substitution in between the O atoms, leads to Fermi level shifting to conduction band thereby causing the Dirac cone to move into valence band, however a band gap appears at high symmetric K-point. In case of TiO3 and VO3 substitution, system exhibits semiconductor properties. Interestingly, TiO3-substituted system shows dilute magnetic semiconductor behavior with 2.00 μB magnetic moment. On the other hand, the substitution of CoO3, CrO3, FeO3 and MnO3 induced 1.015 μB, 2.347 μB, 2.084 μB and 3.584 μB magnetic moment, respectively. In second case of O atoms doped in graphene and TM atoms adsorbed at the hollow site, the O atom bulges out of graphene plane and bond length between TM-O atom is increased. After TM atoms adsorption at the O substituted graphene ring the Fermi level (EF) shifts into conduction band. In case of Cr and Ni adsorption, system displays indirect band gap semiconductor properties with 0.0 μB magnetic moment. Co adsorption exhibits dilute magnetic semiconductor behavior producing 0.916 μB magnetic moment. Fe, Mn, Ti and V adsorption introduces band gap at high symmetric K-point also inducing 1.54 μB, 0.9909 μB, 1.912 μB, and 0.98 μB magnetic moments, respectively

  10. Interpretation of gravity and magnetic data with geological constraints for 3D structure of the Thuringian Basin, Germany

    NASA Astrophysics Data System (ADS)

    Prutkin, Ilya; Vajda, Peter; Jahr, Thomas; Bleibinhaus, Florian; Novák, Pavel; Tenzer, Robert

    2017-01-01

    We apply a novel method for the separation of potential field sources and their 3D inversion at the regional study area of Thuringian Basin in central Germany. The gravity and magnetic data are separated into long, medium and short wavelengths and then inverted separately. The main goal is to study uniqueness of the solution and its stability in all numerical steps of the interpretation process and to demonstrate, how geological constraints can diminish the degree of non-uniqueness by the interpretation of the gravity and magnetic anomalies. Our numerical experiments with medium wavelengths reveal that if we explain negative anomalies with the topography of near-surface layers, the obtained solution is not supported by borehole data. These negative anomalies are thus explained by restricted bodies (granitic intrusions) at the depths from 4 down to 10 km. These bodies are located above a density interface with topography at the depth of approximately 10 km. The 3D inversion of magnetic data (at short wavelengths) allows investigating a detailed structure of the upper boundary of the crystalline basement: two uplifts in the depths between 2.0 and 0.7 km are found. By using the residual negative anomalies we further study the salt tectonics, showing that the geometry of a salt pillow with a thickness of approximately 200 m closely agrees with borehole data.

  11. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  12. Internal structure and volcanic hazard potential of Mt Tongariro, New Zealand, from 3D gravity and magnetic models

    NASA Astrophysics Data System (ADS)

    Miller, Craig A.; Williams-Jones, Glyn

    2016-06-01

    A new 3D geophysical model of the Mt Tongariro Volcanic Massif (TgVM), New Zealand, provides a high resolution view of the volcano's internal structure and hydrothermal system, from which we derive implications for volcanic hazards. Geologically constrained 3D inversions of potential field data provides a greater level of insight into the volcanic structure than is possible from unconstrained models. A complex region of gravity highs and lows (± 6 mGal) is set within a broader, ~ 20 mGal gravity low. A magnetic high (1300 nT) is associated with Mt Ngauruhoe, while a substantial, thick, demagnetised area occurs to the north, coincident with a gravity low and interpreted as representing the hydrothermal system. The hydrothermal system is constrained to the west by major faults, interpreted as an impermeable barrier to fluid migration and extends to basement depth. These faults are considered low probability areas for future eruption sites, as there is little to indicate they have acted as magmatic pathways. Where the hydrothermal system coincides with steep topographic slopes, an increased likelihood of landslides is present and the newly delineated hydrothermal system maps the area most likely to have phreatic eruptions. Such eruptions, while small on a global scale, are important hazards at the TgVM as it is a popular hiking area with hundreds of visitors per day in close proximity to eruption sites. The model shows that the volume of volcanic material erupted over the lifespan of the TgVM is five to six times greater than previous estimates, suggesting a higher rate of magma supply, in line with global rates of andesite production. We suggest that our model of physical property distribution can be used to provide constraints for other models of dynamic geophysical processes occurring at the TgVM.

  13. Uranyl and uranyl-3d block cation complexes with 1,3-adamantanedicarboxylate: crystal structures, luminescence, and magnetic properties.

    PubMed

    Thuéry, Pierre; Rivière, Eric; Harrowfield, Jack

    2015-03-16

    The reaction of 1,3-adamantanedicarboxylic acid (LH2) with uranyl nitrate under solvo-hydrothermal conditions, either alone or in the presence of additional metal cations (Co(2+), Ni(2+), or Cu(2+)) gives a series of nine complexes displaying a wide range of architectures. While [UO2(L)(H2O)]·1.25CH3CN (1) and [UO2(L)(DMF)] (2) are one-dimensional (1D) species analogous to that previously known, [H2NMe2]2[(UO2)2(L)3]·1.5H2O (3), which includes dimethylammonium counterions generated in situ, is a three-dimensional (3D) framework, and [UO2(L)(NMP)] (4) (NMP = N-methyl-2-pyrrolidone) is a braid-shaped 1D polymer. When 3d block metal ions are present and bound to 2,2'-bipyridine (bipy) coligands, their role is reduced to that of decorating species attached to uranyl-containing 1D polymers, as in [UO2M(L)2(bipy)2]·0.5H2O with M = Co (5) or Ni (6), and [(UO2)2Cu2(L)3(NO3)2(bipy)2]·0.5H2O (9), or of counterions, as in [Ni(bipy)3][(UO2)4(O)2(L)3]·3H2O (7), in which a two-dimensional (2D) assembly is built from tetranuclear uranyl-containing building units. In contrast, the heterometallic 3D framework [UO2Cu(L)2] (8) can be isolated in the absence of bipy. The emission spectra measured in the solid state display the usual uranyl vibronic fine structure, with various degrees of resolution and quenching, except for that of complex 7, which shows emission from the nickel(II) centers. The magnetic properties of complexes 5, 6, 8, and 9 were investigated, showing, in particular, the presence of zero-field splitting effects in 6 and weak antiferromagnetic interactions in 9.

  14. 3D structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Dougherty, William M.; Goodwin, Paul C.

    2011-03-01

    Three-dimensional structured illumination microscopy achieves double the lateral and axial resolution of wide-field microscopy, using conventional fluorescent dyes, proteins and sample preparation techniques. A three-dimensional interference-fringe pattern excites the fluorescence, filling in the "missing cone" of the wide field optical transfer function, thereby enabling axial (z) discrimination. The pattern acts as a spatial carrier frequency that mixes with the higher spatial frequency components of the image, which usually succumb to the diffraction limit. The fluorescence image encodes the high frequency content as a down-mixed, moiré-like pattern. A series of images is required, wherein the 3D pattern is shifted and rotated, providing down-mixed data for a system of linear equations. Super-resolution is obtained by solving these equations. The speed with which the image series can be obtained can be a problem for the microscopy of living cells. Challenges include pattern-switching speeds, optical efficiency, wavefront quality and fringe contrast, fringe pitch optimization, and polarization issues. We will review some recent developments in 3D-SIM hardware with the goal of super-resolved z-stacks of motile cells.

  15. 3-D magnetic field calculations for wiggglers using MAGNUS-3D

    SciTech Connect

    Pissanetzky, S.; Tompkins, P.

    1988-01-01

    The recent but steady trend toward increased magnetic and geometric complexity in the design of wigglers and undulators, of which tapered wigglers, hybrid structures, laced electromagnetic wigglers, magnetic cladding, twisters and magic structures are examples, has caused a need for reliable 3-D computer models and a better understanding of the behavior of magnetic systems in three dimensions. The capabilities of the MAGNUS-3D Group of Programs are ideally suited to solve this class of problems and provide insight into 3-D effects. MAGNUS-3D can solve any problem of Magnetostatics involving permanent magnets, linear or nonlinear ferromagnetic materials and electric conductors of any shape in space. The magnetic properties of permanent magnets are described by the complete nonlinear demagnetization curve as provided by the manufacturer, or, at the user's choice, by a simpler approximation involving the coercive force, the residual induction and the direction of magnetization. The ferromagnetic materials are described by a magnetization table and an accurate interpolation relation. An internal library with properties of common industrial steels is available. The conductors are independent of the mesh and are described in terms of conductor elements from an internal library.

  16. Analyses of Magnetic Structures of Active Region 11117 Evolution using a 3D Data-Driven Magnetohydrodynamic Model

    NASA Astrophysics Data System (ADS)

    Wu, Shi; Jiang, Chaowei; Feng, Xueshang

    We use the photospheric vector magnetograms obtained by Helioseismic and Magnetic Image (HMI) on-board the Solar Dynamic Observatory (SDO) as the boundary conditions for a Data-Driven CESE-MHD model (Jiang et al. 2012) to investigate the physical characteristics and evolution of magnetic field configurations in the corona before and after a solar eruptive event. Specifically, the evolution of AR11117 characteristics such as length of magnetic shear along the neutral line, current helicity, magnetic free energy and the energy flux across the photosphere due to flux emergence and surface flow are presented. The computed 3D magnetic field configuration are compared with AIA (Atmosphere Image Assembly) which shows remarkable resemblance. A topological analyses reveals that the small flare is correlated with a bald patch (BP, where the magnetic field is tangent to the photosphere), suggesting that the energy release of the flare is caused by magnetic reconnection associated with the BP separatrices. The total magnetic flux and energy keep increasing slightly in spite of flare, while the computed magnetic free energy drops during the flare by 10 (30) ergs which is adequate in providing the energy budget of a minor C-class confined flare as observed. Jiang, Chaowei, Xueshang, Feng, S. T Wu and Qiang Hu, Ap. J., 759:85, 2012 Nov 10

  17. Seven 3d-4f coordination polymers of macrocyclic oxamide with polycarboxylates: Syntheses, crystal structures and magnetic properties

    NASA Astrophysics Data System (ADS)

    Xin, Na; Sun, Ya-Qiu; Zheng, Yan-Feng; Xu, Yan-Yan; Gao, Dong-Zhao; Zhang, Guo-Ying

    2016-11-01

    Seven new 3d-4f heterometallic coordination polymers, [Ln(CuL)2(Hbtca)(btca)(H2O)]·2H2O (Ln = TbIII1, PrIII2, SmIII3, EuIII4, YbIII5), [Nd(NiL)(nip)(Rnip)]·0·25H2O·0.25CH3OH (R= 0.6CH3, 0.4H) 6 and [Nd2(NiL)(nip)3(H2O)]·2H2O 7(CuL or NiL, H2L = 2, 3-dioxo-5, 6, 14, 15-dibenzo-1, 4, 8, 12-tetraazacyclo-pentadeca-7, 13-dien; H2btca = benzotriazole-5-carboxylic acid; H2nip = 5-nitroisophthalic acid) have been synthesized by a solvothermal method and characterized by single-crystal X-ray diffraction. Complexes 1-5 exhibit a double-strand meso-helical chain structures formed by [LnIIICuII2] units via the oxamide and benzotriazole-5-carboxylate bridges, while complex 6 exhibits a four-strand meso-helical chain formed by NdNi unit via the oxamide and 5-nitroisophthalate bridges. Complex 7 consists of a 2D layer framework formed by four-strand meso-helical chain via the nip2- bridges. Moreover, the magnetic properties of them were investigated, and the best-fit analysis of χMT versus T show that the anisotropic contribution of Ln(III) ions (arising from the spin-orbit coupling or the crystal field perturbation) dominates (weak exchange limit) in these complexes(for 3, λ = 214.6 cm-1, zj' = -0.33 cm-1, gav = 1.94; for 5, Δ = 6.98 cm-1, zj' = 1.53 cm-1, gav = 1.85).

  18. Reconstruction of 3D Coronal Magnetic Structures from THEMIS/MTR and Hinode/SOT Vector Maps

    NASA Astrophysics Data System (ADS)

    Schmieder, B.; Guo, Y.; Aulanier, G.; Démoulin, P.; Török, T.; Bommier, V.; Wiegelmann, T.; Gosain, S.

    2012-08-01

    Coordinated campaigns using THEMIS, Hinode, and other instruments have allowed us to study the magnetic fields of faculae, filaments, and active regions. In a first case, we modelled the 3D magnetic field in a flaring active region with a nonlinear force-free field extrapolation, using magnetic vectors observed by THEMIS/MTR as boundary condition. In order to construct a consistent bottom boundary for the model, we first removed the 180 degree ambiguity of the transverse fields and minimized the force and torque in the observed vector fields. We found a twisted magnetic flux rope, well aligned with the polarity inversion line and a part of an Hα filament, and located where a large flare is initiated about two hours later. In a second case, Hinode/SOT allowed us to detect fine flux concentrations in faculae, while MTR provided us with magnetic information at different levels in the atmosphere. The polarimetry analysis of the MTR and SOT data gave consistent results, using both UNNOFIT and MELANIE inversion codes.

  19. 3D print of polymer bonded rare-earth magnets, and 3D magnetic field scanning with an end-user 3D printer

    NASA Astrophysics Data System (ADS)

    Huber, C.; Abert, C.; Bruckner, F.; Groenefeld, M.; Muthsam, O.; Schuschnigg, S.; Sirak, K.; Thanhoffer, R.; Teliban, I.; Vogler, C.; Windl, R.; Suess, D.

    2016-10-01

    3D print is a recently developed technique, for single-unit production, and for structures that have been impossible to build previously. The current work presents a method to 3D print polymer bonded isotropic hard magnets with a low-cost, end-user 3D printer. Commercially available isotropic NdFeB powder inside a PA11 matrix is characterized, and prepared for the printing process. An example of a printed magnet with a complex shape that was designed to generate a specific stray field is presented, and compared with finite element simulation solving the macroscopic Maxwell equations. For magnetic characterization, and comparing 3D printed structures with injection molded parts, hysteresis measurements are performed. To measure the stray field outside the magnet, the printer is upgraded to a 3D magnetic flux density measurement system. To skip an elaborate adjusting of the sensor, a simulation is used to calibrate the angles, sensitivity, and the offset of the sensor. With this setup, a measurement resolution of 0.05 mm along the z-axes is achievable. The effectiveness of our calibration method is shown. With our setup, we are able to print polymer bonded magnetic systems with the freedom of having a specific complex shape with locally tailored magnetic properties. The 3D scanning setup is easy to mount, and with our calibration method we are able to get accurate measuring results of the stray field.

  20. Structure and magnetism of a binuclear Cu(II) pyrophosphate: transition to a 3D magnetic behaviour studied by single crystal EPR.

    PubMed

    Sartoris, Rosana P; Nascimento, Otaciro R; Santana, Ricardo C; Perec, Mireille; Baggio, Ricardo F; Calvo, Rafael

    2015-03-14

    A binuclear Cu(II) compound [Cu2(bpa)2(P2O7)(H2O)2]·2.5H2O, 1, (bpa = 2,2'-bipyridylamine), with pairs of Cu(II) ions bridged by one pyrophosphate tetra-anion, was synthesized and crystallized. Its triclinic structure was determined by single-crystal X-ray diffraction. Electron paramagnetic resonance (EPR) spectra of single crystal samples of 1 were recorded for a fixed orientation of the magnetic field (B0) as a function of temperature (T) between 4.7 and 293 K, and at T = 4.7, 50 and 293 K, as a function of the orientation of B0. Below ∼8 K, the spectra are assigned to two types of mononuclear crystal defects hyperfine-coupled to one copper and two nitrogen nuclei. The g-matrices and hyperfine couplings at these T provide information about the structures of these defects. Above 10 K, the spectrum is dominated by the response of the bulk binuclear Cu(II) material, showing hyperfine interactions with two copper nuclei, collapsing to a single peak above 18 K when the units are magnetically connected, and the magnetic behaviour becomes 3D. We attribute the results above 10 K to the interplay of an AFM intrabinuclear exchange interaction J0 = -28(3) cm(-1) (defined as Hex = -J0S1·S2), and three orders of magnitude weaker exchange coupling with average magnitude |J1| ≥ 0.022 cm(-1) between Cu(II) ions in neighbouring binuclear units. The interplays between structure, exchange couplings, magnetic dimension and spin dynamics in the binuclear compound are discussed. A previously unreported situation, where the structure of the spectra arising from the anisotropic spin-spin interaction term (D) within the binuclear unit is averaged out, but the forbidden half field transition is not, is observed and explained.

  1. A series of rare earth complexes with novel non-interpenetrating 3D networks: synthesis, structures, magnetic and optical properties.

    PubMed

    Wei, Xiao-Hua; Yang, Lin-Yan; Liao, Sheng-Yun; Zhang, Ming; Tian, Jin-Lei; Du, Pei-Yao; Gu, Wen; Liu, Xin

    2014-04-21

    A series of metal-organic framework {Ln(BCPBA)(H2O)}n {Ln = Nd (1), Sm (2), Eu (3), Tb (4), Dy (5)}; {[Ln(BCPBA)(H2O)](H2O)}n {Ln = Pr (6), Gd (7)} have been synthesized through the hydrothermal synthesis method. These compounds possess non-interpenetrating 3D networks with 10.1438 Å× 17.9149 Å rhombic channels along the [001] direction. The results of temperature-dependent magnetic susceptibility measurements indicate that compounds 4 and 7 exhibit Ln(III)Ln(III) antiferromagnetic interactions, while compound 5 exhibits Ln(III)Ln(III) ferromagnetic interactions. Frequency dependent out-of-phase signals were observed in alternating current (ac) magnetic susceptibility measurements which indicate that they have slow magnetic relaxation characteristics. The luminescent properties of 1, 2, 3, 4, and 5 are also discussed. Due to the good match between the lowest triplet state of the ligand and the resonant energy level of the lanthanide ion, compound 4 has longer fluorescence lifetime (τ1 = 400.0000 ms, τ2 = 1143.469 ms) and higher quantum yield (Φ = 42%) compared with other compounds.

  2. In vivo application of 3D-line skeleton graph analysis (LSGA) technique with high-resolution magnetic resonance imaging of trabecular bone structure.

    PubMed

    Pothuaud, Laurent; Newitt, David C; Lu, Ying; MacDonald, Brian; Majumdar, Sharmila

    2004-05-01

    Over the last several years magnetic resonance (MR) imaging has emerged as a means of measuring in vivo 3D trabecular bone structure. In particular, MR based diagnosis could be used to complement standard bone mineral density (BMD) methods for assessing osteoporosis and evaluating longitudinal changes. The aim of this study was to demonstrate the feasibility of using the 3D-LSGA technique for the evaluation of trabecular bone structure of high-resolution MR images, particularly for assessing longitudinal changes, in vivo. First, the reproducibility of topological 3D-LSGA based measurements was evaluated in a set of seven volunteers, and coefficients of variations ranged from 3.5% to 6%. Second, high-resolution MR images of the radius in 30 postmenopausal women from a placebo controlled drug study (Idoxifene), divided into placebo ( n=9) and treated ( n=21) groups, were obtained at baseline (BL) and after 1 year of treatment (follow-up, FU). In addition, dual X-ray absorptiometry (DXA) measures of BMD were obtained in the distal radius. Standard morphological measurements based on the mean intercept length (MIL) technique as well as 3D-LSGA based measurements were applied to the 3D MR images. Significant changes from BL to FU were detected, in the treated group, using the topological 3D-LSGA based measurements, morphological measures of volume of connected trabeculae and App Tb.N from MIL analysis. The duration of the study was short, and the number of patients remaining in the study was small, hence these results cannot be interpreted with regard to a true therapeutic response. Furthermore, the site (wrist) and the drug (idoxifene) are not optimal for follow-up study. However, this paper demonstrated the feasibility of using 3D-LSGA based evaluation coupled with in vivo high-resolution MR imaging as a complementary approach for the monitoring of trabecular bone changes in individual subjects.

  3. Multifractal analysis of white matter structural changes on 3D magnetic resonance imaging between normal aging and early Alzheimer’s disease

    NASA Astrophysics Data System (ADS)

    Ni, Huang-Jing; Zhou, Lu-Ping; Zeng, Peng; Huang, Xiao-Lin; Liu, Hong-Xing; Ning, Xin-Bao

    2015-07-01

    Applications of multifractal analysis to white matter structure changes on magnetic resonance imaging (MRI) have recently received increasing attentions. Although some progresses have been made, there is no evident study on applying multifractal analysis to evaluate the white matter structural changes on MRI for Alzheimer’s disease (AD) research. In this paper, to explore multifractal analysis of white matter structural changes on 3D MRI volumes between normal aging and early AD, we not only extend the traditional box-counting multifractal analysis (BCMA) into the 3D case, but also propose a modified integer ratio based BCMA (IRBCMA) algorithm to compensate for the rigid division rule in BCMA. We verify multifractal characteristics in 3D white matter MRI volumes. In addition to the previously well studied multifractal feature, Δα, we also demonstrated Δf as an alternative and effective multifractal feature to distinguish NC from AD subjects. Both Δα and Δf are found to have strong positive correlation with the clinical MMSE scores with statistical significance. Moreover, the proposed IRBCMA can be an alternative and more accurate algorithm for 3D volume analysis. Our findings highlight the potential usefulness of multifractal analysis, which may contribute to clarify some aspects of the etiology of AD through detection of structural changes in white matter. Project supported by the National Natural Science Foundation of China (Grant No. 61271079), the Vice Chancellor Research Grant in University of Wollongong, and the Priority Academic Program Development of Jiangsu Higher Education Institutions, China.

  4. Jovian Plasmas Torus Interaction with Europa. Plasma Wake Structure and Effect of Inductive Magnetic Field: 3D Hybrid Kinetic Simulation

    NASA Technical Reports Server (NTRS)

    Lipatov, A. S.; Cooper, J F.; Paterson, W. R.; Sittler, E. C., Jr.; Hartle, R. E.; Simpson, David G.

    2013-01-01

    The hybrid kinetic model supports comprehensive simulation of the interaction between different spatial and energetic elements of the Europa moon-magnetosphere system with respect to a variable upstream magnetic field and flux or density distributions of plasma and energetic ions, electrons, and neutral atoms. This capability is critical for improving the interpretation of the existing Europa flyby measurements from the Galileo Orbiter mission, and for planning flyby and orbital measurements (including the surface and atmospheric compositions) for future missions. The simulations are based on recent models of the atmosphere of Europa (Cassidy et al., 2007; Shematovich et al., 2005). In contrast to previous approaches with MHD simulations, the hybrid model allows us to fully take into account the finite gyroradius effect and electron pressure, and to correctly estimate the ion velocity distribution and the fluxes along the magnetic field (assuming an initial Maxwellian velocity distribution for upstream background ions). Photoionization, electron-impact ionization, charge exchange and collisions between the ions and neutrals are also included in our model. We consider the models with Oþ þ and Sþ þ background plasma, and various betas for background ions and electrons, and pickup electrons. The majority of O2 atmosphere is thermal with an extended non-thermal population (Cassidy et al., 2007). In this paper, we discuss two tasks: (1) the plasma wake structure dependence on the parameters of the upstream plasma and Europa's atmosphere (model I, cases (a) and (b) with a homogeneous Jovian magnetosphere field, an inductive magnetic dipole and high oceanic shell conductivity); and (2) estimation of the possible effect of an induced magnetic field arising from oceanic shell conductivity. This effect was estimated based on the difference between the observed and modeled magnetic fields (model II, case (c) with an inhomogeneous Jovian magnetosphere field, an inductive

  5. 3D structural cartography based on magnetic and gravity data inversion - Case of South-West Algeria

    NASA Astrophysics Data System (ADS)

    Hichem, Boubekri; Mohamed, Hamoudi; Abderrahmane, Bendaoud; Ivan, Priezzhev; Karim, Allek

    2015-12-01

    This article presents the results of 3D aeromagnetic and gravity data inversion across the West African Craton (WAC) in South West Algeria. Although the used data have different origins and resolutions, the performed manual and automatic interpretation for each dataset shows a good correlation with some earlier geological studies of the region, major structural aspects of the locality, as well as other new structural features. Many curved faults parallel to the suture zone indicate the presence of terranes or the metacratonization of the WAC and a related fault network of great importance with NE-SW and NW-SE directions. The mega shear zones from north to south, which are visible at the surface in the Hoggar, are also observed along the Saharan Platform. The fact that these faults are observed since the Cambro-Ordovician in all crust (including the Saharan Basins) indicates that this area, which is situated on the border of the WAC, remained active during the entire period of time.

  6. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  7. Protocol for volumetric segmentation of medial temporal structures using high-resolution 3-D magnetic resonance imaging.

    PubMed

    Bonilha, Leonardo; Kobayashi, Eliane; Cendes, Fernando; Min Li, Li

    2004-06-01

    Quantitative analysis of brain structures in normal subjects and in different neurological conditions can be carried out in vivo through magnetic resonance imaging (MRI) volumetric studies. The use of high-resolution MRI combined with image post-processing that allows simultaneous multiplanar view may facilitate volumetric segmentation of temporal lobe structures. We define a protocol for volumetric studies of medial temporal lobe structures using high-resolution MR images and we studied 30 healthy subjects (19 women; mean age, 33 years; age range, 21-55 years). Images underwent field non-homogeneity correction and linear stereotaxic transformation into a standard space. Structures of interest comprised temporopolar, entorhinal, perirhinal, parahippocampal cortices, hippocampus, and the amygdala. Segmentation was carried out with multiplanar assessment. There was no statistically significant left/right-sided asymmetry concerning any structure analyzed. Neither gender nor age influenced the volumes obtained. The coefficient of repeatability showed no significant difference of intra- and interobserver measurements. Imaging post-processing and simultaneous multiplanar view of high-resolution MRI facilitates volumetric assessment of the medial portion of the temporal lobe with strict adherence to anatomic landmarks. This protocol shows no significant inter- and intraobserver variations and thus is reliable for longitudinal studies.

  8. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

    We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.

  9. A series of 3D metal organic frameworks based on [24-MC-6] metallacrown clusters: structure, magnetic and luminescence properties.

    PubMed

    Wang, Kai; Zou, Hua-Hong; Chen, Zi-Lu; Zhang, Zhong; Sun, Wei-Yin; Liang, Fu-Pei

    2014-09-14

    Four isostructural metal organic frameworks (MOFs), namely [Co6(HipO)6]·6H2O (1), [Mn6(HipO)6]·6H2O (2), [Cd6(HipO)6]·6H2O (3) and [Zn6(HipO)6]·7H2O (4) (H3ipO = 2-hydroxyisophthalic acid), were synthesized and structurally characterized. They have a 3D (4,6)-connected framework based on [24-MC-6] metallacrown clusters ([24-MC-6]-based MOFs). The arrangements of the 24-MC-6 metallacrown SBUs show a regular change indicated by the orientation of their symmetry axes, resulting in a special dense packing mode different from other [24-MC-6]-based MOFs. The analysis of SQUID measurements reveal that compound 1 displays the dominant antiferromagnetic exchanges in 300-10 K between the adjacent Co(II) ions and a ferromagnetic-like behavior at lower temperatures, whereas compound 2 shows an antiferromagnetic interaction between the adjacent Mn(II) ions. Compound 1 exhibits a magnetocaloric effect (MCE) with the resulting entropy change (-ΔS(m)) of 15.20 J kg(-1) K(-1) for ΔH = 50 kG at 6 K, which is the highest value among the cobalt-based MOFs with MCE reported so far. The luminescence properties of compounds 3 and 4 were studied, both of them exhibit photoluminescence in the solid state at room temperature which can be ascribed to intraligand π→π* transitions.

  10. A new 3D Co(II)–organic framework with acylamide-containing tetracarboxylate ligand: Solvothermal synthesis, crystal structure, gas adsorption and magnetic property

    SciTech Connect

    Zhang, Qingfu Zhang, Haina; Geng, Aijing; Wang, Suna; Zhang, Chong

    2014-04-01

    A new cobalt(II)–organic framework, [Co{sub 2}(L)(py){sub 2}(DMSO)]{sub n}• 0.5nDMF• 2nDMSO (1) [H{sub 4}L=5,5'-((naphthalene-2,6-dicarbonyl)bis(azanediyl))diisophthalic acid, py=pyridine, DMSO=dimethyl sulfoxide, DMF=N,N-dimethylformamide], has been solvothermally synthesized and characterized by elemental analysis, IR, TGA, PXRD and single-crystal X-ray crystallography. The structural analysis reveals that complex 1 is a 3D framework built from nanosized acylamide-containing tetracarboxylate ligands (L{sup 4−}) and dinuclear [Co{sub 2}(CO{sub 2}){sub 4}] secondary building units (SBUs), exhibiting a uninodal (4,4)-connected crb topology with the Schläfli symbol of (4• 6{sup 5}). The desolvated complex (1a) displays higher adsorption capability for CO{sub 2} than N{sub 2}, which may be due to the relatively strong binding affinity between the CO{sub 2} molecules and acylamide groups in the framework. The magnetic investigation shows that the dominant antiferromagnetic interaction is observed in complex 1. - Graphical abstract: A new 3D Co(II)–organic framework with nanosized acylamide-containing tetracarboxylate ligand was solvothermally synthesized and structurally characterized, its thermal stability, gas adsorption and magnetic property were studied. - Highlights: • A new 3D Co(II)–organic framework with nanosized acylamide-containing tetracarboxylate ligand has been solvothermally synthesized and characterized. • Complex 1 exhibits a uninodal (4,4)-connected crb topology. • The thermal stability, gas adsorption and magnetic property were studied.

  11. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

    Three dimensional (3D) micro-scale structures attached to a silicon substrate have various applications in microelectronics. However, formation of 3D structures using conventional micro-fabrication techniques are not efficient and require precise control of processing parameters. Self assembly is a method for creating 3D structures that takes advantage of surface area minimization phenomena. Solder based self assembly (SBSA), the subject of this dissertation, uses solder as a facilitator in the formation of 3D structures from 2D patterns. Etching a sacrificial layer underneath a portion of the 2D pattern allows the solder reflow step to pull those areas out of the substrate plane resulting in a folded 3D structure. Initial studies using the SBSA method demonstrated low yields in the formation of five different polyhedra. The failures in folding were primarily attributed to nonuniform solder deposition on the underlying metal pads. The dip soldering method was analyzed and subsequently refined. A modified dip soldering process provided improved yield among the polyhedra. Solder bridging referred as joining of solder deposited on different metal patterns in an entity influenced the folding mechanism. In general, design parameters such as small gap-spacings and thick metal pads were found to favor solder bridging for all patterns studied. Two types of soldering: face and edge soldering were analyzed. Face soldering refers to the application of solder on the entire metal face. Edge soldering indicates application of solder only on the edges of the metal face. Mechanical grinding showed that face soldered SBSA structures were void free and robust in nature. In addition, the face soldered 3D structures provide a consistent heat resistant solder standoff height that serve as attachments in the integration of dissimilar electronic technologies. Face soldered 3D structures were developed on the underlying conducting channel to determine the thermo-electric reliability of

  12. Infrared-induced variation of the magnetic properties of a magnetoplasmonic film with a 3D sub-micron periodic triangular roof-type antireflection structure.

    PubMed

    Tian, Junlong; Zhang, Wang; Huang, Yiqiao; Liu, Qinglei; Wang, Yuhua; Zhang, Zhijian; Zhang, Di

    2015-01-26

    A carbon-matrix nickel composite magnetoplasmonic film with a 3D sub-micron periodic triangular roof-type antireflection structure (SPTAS) was fabricated via a simple and promising method that combines chemosynthesis with biomimetic techniques. The Troides helena (Linnaeus) forewing (T_FW) was chosen as the biomimetic template. The carbon-matrix Ni wing fabricated via electroless Ni deposition for 6 h (CNMF_6h) exhibits enhanced infrared absorption. Over a wavelength range (888-2500 nm), the enhancement of the infrared absorption of CNMF_6h is up to 1.85 times compared with the T_FW. Furthermore, infrared excitation induces a photothermal effect that results in variation in the magnetic properties of the carbon-matrix Ni wing. The magnetic properties were also confirmed using atomic force microscopy (AFM) and magnetic force microscopy (MFM). The good correlation between the AFM and MFM images demonstrates that the surface of the SPTAS of CNMF_6h exhibits strong magnetic properties. The infrared induced photothermal effect that results in magnetic variation is promising for use in the design of novel magnetoplasmonic films with potential applications in infrared information recording and heat-assisted magnetic recording.

  13. Infrared-induced variation of the magnetic properties of a magnetoplasmonic film with a 3D sub-micron periodic triangular roof-type antireflection structure

    NASA Astrophysics Data System (ADS)

    Tian, Junlong; Zhang, Wang; Huang, Yiqiao; Liu, Qinglei; Wang, Yuhua; Zhang, Zhijian; Zhang, Di

    2015-01-01

    A carbon-matrix nickel composite magnetoplasmonic film with a 3D sub-micron periodic triangular roof-type antireflection structure (SPTAS) was fabricated via a simple and promising method that combines chemosynthesis with biomimetic techniques. The Troides helena (Linnaeus) forewing (T_FW) was chosen as the biomimetic template. The carbon-matrix Ni wing fabricated via electroless Ni deposition for 6 h (CNMF_6h) exhibits enhanced infrared absorption. Over a wavelength range (888-2500 nm), the enhancement of the infrared absorption of CNMF_6h is up to 1.85 times compared with the T_FW. Furthermore, infrared excitation induces a photothermal effect that results in variation in the magnetic properties of the carbon-matrix Ni wing. The magnetic properties were also confirmed using atomic force microscopy (AFM) and magnetic force microscopy (MFM). The good correlation between the AFM and MFM images demonstrates that the surface of the SPTAS of CNMF_6h exhibits strong magnetic properties. The infrared induced photothermal effect that results in magnetic variation is promising for use in the design of novel magnetoplasmonic films with potential applications in infrared information recording and heat-assisted magnetic recording.

  14. Infrared-induced variation of the magnetic properties of a magnetoplasmonic film with a 3D sub-micron periodic triangular roof-type antireflection structure

    PubMed Central

    Tian, Junlong; Zhang, Wang; Huang, Yiqiao; Liu, Qinglei; Wang, Yuhua; Zhang, Zhijian; Zhang, Di

    2015-01-01

    A carbon-matrix nickel composite magnetoplasmonic film with a 3D sub-micron periodic triangular roof-type antireflection structure (SPTAS) was fabricated via a simple and promising method that combines chemosynthesis with biomimetic techniques. The Troides helena (Linnaeus) forewing (T_FW) was chosen as the biomimetic template. The carbon-matrix Ni wing fabricated via electroless Ni deposition for 6 h (CNMF_6h) exhibits enhanced infrared absorption. Over a wavelength range (888–2500 nm), the enhancement of the infrared absorption of CNMF_6h is up to 1.85 times compared with the T_FW. Furthermore, infrared excitation induces a photothermal effect that results in variation in the magnetic properties of the carbon-matrix Ni wing. The magnetic properties were also confirmed using atomic force microscopy (AFM) and magnetic force microscopy (MFM). The good correlation between the AFM and MFM images demonstrates that the surface of the SPTAS of CNMF_6h exhibits strong magnetic properties. The infrared induced photothermal effect that results in magnetic variation is promising for use in the design of novel magnetoplasmonic films with potential applications in infrared information recording and heat-assisted magnetic recording. PMID:25620787

  15. Note: 3D printed spheroid for uniform magnetic field generation

    NASA Astrophysics Data System (ADS)

    Öztürk, Y.; Aktaş, B.

    2016-10-01

    This article is focused on a novel and practical production method for a uniform magnetic field generator. The method involves building of a surface coil template using a desktop 3D printer and winding of a conducting wire onto the structure using surface grooves as a guide. Groove pattern was based on the parametric spheroidal helical coil formula. The coil was driven by a current source and the magnetic field inside was measured using a Hall probe placed into the holes on the printed structure. The measurements are found to be in good agreement with our finite element analysis results and indicate a fairly uniform field inside.

  16. A 3D oxalate-based network as a precursor for the CoMn₂O₄ spinel: synthesis and structural and magnetic studies.

    PubMed

    Habjanič, Jelena; Jurić, Marijana; Popović, Jasminka; Molčanov, Krešimir; Pajić, Damir

    2014-09-15

    A novel heterometallic oxalate-based compound of the formula {[Co(bpy)3][Mn2(C2O4)3]·H2O}n (1; bpy = 2,2'-bipyridine) was synthesized and characterized by elemental analysis, IR spectroscopy, single-crystal X-ray diffraction (XRD), and magnetization measurement. The molecular structure of 1 is made of a three-dimensional (3D) anionic network, [Mn2(C2O4)3]n(2n-), and tris-chelated cations [Co(bpy)3](2+) occupying the vacancies of the framework. Splitting between the zero-field-cooled (ZFC) and field-cooled (FC) branches of susceptibility below the small peak at 13 K indicates magnetic ordering. Compound 1 was used as a single-source precursor for the formation of the mixed-metal oxide CoMn2O4. This conversion via thermal decomposition was explored by thermal analysis (TGA and DTA), IR spectroscopy, powder XRD, and magnetic susceptibility measurement. From refined structural parameters, it could be seen that the spinel obtained by the thermal treatment of 1 at 800 °C is characterized by the inversion parameter δ = 21%, and therefore the structural formula at room temperature can be written as (tet)[Co(0.79)Mn(0.21)](oct)[Co(0.105)Mn(0.895)]2O4. The temperature dependence of magnetization for CoMn2O4 points to at least three magnetic phases: the ferrimagnetic state is observed below 83 K, and up to 180 K blocking of the magnetic moments of nanocrystallites of 31 nm appears, transforming to paramagnetic-like behavior above 180 K. Microstructural characterization of the CoMn2O4 sample was carried out by means of XRD line-broadening analysis.

  17. 3D Magnetic inversion and remanence: solving the problem

    NASA Astrophysics Data System (ADS)

    Thomson, V.; Morris, W.

    2003-04-01

    3D inversion of surface magnetic data is a common processing technique when used in mineral exploration. The major drawback of most 3D inversion algorithms is that they assume that the surface magnetic anomaly is produced by induced magnetization and that there are no remanent magnetization or demagnetization effects present. This has a significant impact when modeling magnetic data that has remanent magnetization. The magnetic anomaly produced by a dipping subsurface body will be identical for a consistent relationship between the dip of the body and the dip of the magnetic vector, regardless of the actual dip of the magnetic body. For example, in the case where a subsurface body is dipping, such as a dipping dike, the dip estimated by the inversion routine will be correct only if induced magnetization is present. This has serious implications for mineral exploration. A solution to the remanence problem is to model the surface magnetic anomaly using a constrained 2D approach rather than 3D. Using a priori information on dip and strike length of a source body, it is possible to approximate the remanence direction and intensity. The 2D solutions can then be rendered into a 3D imaging package to create a model in 3D. A case study was performed on a mafic-ultramafic layered igneous intrusion located in Big Trout Lake, northwestern Ontario, Canada. Large layered igneous intrusions are known to have significant remanence. Like many other layered igneous intrusions such as the Bushveld Complex in South Africa, the Big Trout Lake Complex is highly prospective for Platinum Group Elements (PGEs). Intruded during Archean time, the Big Trout Lake Complex has been subsequently folded and faulted to near vertical. As a consequence of limited surface exposures, knowledge of layering within the pluton and the extent of deformation of the pluton is very limited. Newly acquired high-resolution aeromagnetic data shows a strongly mineralized horizon within the intrusion that

  18. Magnetism in a graphene-4 f -3 d hybrid system

    NASA Astrophysics Data System (ADS)

    Huttmann, Felix; Klar, David; Atodiresei, Nicolae; Schmitz-Antoniak, Carolin; Smekhova, Alevtina; Martínez-Galera, Antonio J.; Caciuc, Vasile; Bihlmayer, Gustav; Blügel, Stefan; Michely, Thomas; Wende, Heiko

    2017-02-01

    We create an interface of graphene with a metallic and magnetic support that leaves its electronic structure largely intact. This is achieved by exposing epitaxial graphene on ferromagnetic thin films of Co and Ni to vapor of the rare earth metal Eu at elevated temperatures, resulting in the intercalation of an Eu monolayer in between graphene and its substrate. The system is atomically well defined, with the Eu monolayer forming a (√{3 }×√{3 }) R 30∘ superstructure with respect to the graphene lattice. Thereby, we avoid the strong hybridization with the (Ni,Co) substrate 3 d states that otherwise drastically modify the electronic structure of graphene. This picture is suggested by our x-ray absorption spectroscopy measurements which show that after Eu intercalation the empty 2 p states of C atoms resemble more the ones measured for graphite in contrast to graphene directly bound to 3 d ferromagnetic substrates. We use x-ray magnetic circular dichroism at the Co and Ni L2 ,3 and Eu M4 ,5 as an element-specific probe to investigate magnetism in these systems. An antiferromagnetic coupling between Eu and Co/Ni moments is found, which is so strong that a magnetic moment of the Eu layer can be detected at room temperature. Density functional theory calculations confirm the antiferromagnetic coupling and provide an atomic insight into the magnetic coupling mechanism.

  19. Structure and magnetic properties of electrodeposited, ferromagnetic, group 3-d element films grown onto GaAs (011) substrate

    NASA Astrophysics Data System (ADS)

    Scheck, C.; Evans, P.; Schad, R.; Zangari, G.

    2003-05-01

    Ni, Co, and iron-rich FeNi films were grown onto n-GaAs (011) substrates using electrodeposition from metal sulfate solutions, at room temperature, with a current density of 3.5 mA/cm2 at a pH of 2.5. The structure of Ni film is found to be fcc with a (111) preferred orientation, whereas Co films show a mixed fcc and hcp structure that is confirmed by x-ray diffraction and transmission electron microscopy data. The structure of iron-rich (>90%) FeNi films remains unclear at the moment. The films show a well-defined, in-plane, uniaxial anisotropy with the easy axis along the [011] GaAs direction for Ni, and [011¯] GaAs direction for Co and FeNi films (i.e., anisotropy rotated by 90° compared to Ni). Co films maintain their anisotropy even for large thicknesses (>250 nm) and so does Ni (up to 90 nm). Surprisingly, thin Ni films exhibit a larger HK value (950 Oe) than what would be expected from a purely crystalline anisotropy. This effect is ascribed to internal stresses in the as-deposited films.

  20. Imaging a 3D geological structure from HEM, airborne magnetic and ground ERT data in Kalat-e-Reshm area, Iran

    NASA Astrophysics Data System (ADS)

    Shirzaditabar, Farzad; Bastani, Mehrdad; Oskooi, Behrooz

    2011-11-01

    A set of geophysical data collected in an area in Iran are analyzed to check the validity of a geological map that was prepared in connection to a mineral prospecting project and also to image the spatial electrical resistivity distribution. The data set includes helicopter electromagnetic (HEM), airborne magnetic and ground electrical resistivity measurement. Occam approach was used to invert the HEM data to model the resistivity using a layered earth model with fixed thicknesses. The algorithm is based on a nonlinear inverse problem in a least-squares sense. The algorithm was tested on a part of an HEM dataset acquired with a DIGHEM helicopter EM system at Kalat-e-Reshm, Semnan in Iran. The area contains a resistive porphyry andesite that is covered by Eocene sedimentary units. The results are shown as resistivity sections and maps confirming the existence of an arc like resistive structure in the survey area. The resistive andesite seems to be thicker than it is indicated in the geological maps. The results are compared with the reduced to the pole (RTP) airborne magnetic anomaly field data as well as with two ground resistivity profiles. We found reasonable correlations between the HEM 1D resistivity models and 2D models from electrical resistivity tomography (ERT) inversions. A 3D visualization of the 1D models along all flight lines provided a useful tool for the study of spatial variations of the resistivity structure in the investigation area.

  1. 3D Structures of Responsive Nanocompartmentalized Microgels.

    PubMed

    Gelissen, Arjan P H; Oppermann, Alex; Caumanns, Tobias; Hebbeker, Pascal; Turnhoff, Sarah K; Tiwari, Rahul; Eisold, Sabine; Simon, Ulrich; Lu, Yan; Mayer, Joachim; Richtering, Walter; Walther, Andreas; Wöll, Dominik

    2016-11-09

    Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.

  2. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen.

  3. Global magnetosphere-like 3D structure formation in kinetics by hot magnetized plasma flow characterized by shape of the particle distribution function

    NASA Astrophysics Data System (ADS)

    Gubchenko, Vladimir

    The task was to provide an analytical elementary magnetosphere-like model in kinetics for verification of the 3D EM PIC codes created for space/aerospace and HED plasmas applications. Kinetic approach versus cold MHD approach takes into account different behavior in the EM fields of resonant and non resonant particles in the velocity phase space, which appears via shape characteristics of the particle velocity distribution function (PVDF) and via the spatial dispersion effect forming the collisionless dissipation in the EM fields. The external flow is a hot collisionless plasma characterized by the particle velocity distribution function (PVDF) with different shapes: Maxwellian, kappa, etc. The flow is in a “hot regime”: it can be supersonic but its velocity remains less the thermal velocity of the electrons. The “internal” part of the magnetosphere formed by trapped particles is the prescribed 3D stationary magnetization considered as a spherical “quasiparticle” with internal magnetodipole and toroidal moments represented as a broadband EM driver. We obtain after the linearization of Vlasov/Maxwell equations a self-consistent 3D large scale kinetic solution of the classic problem. Namely, we: model the “outer” part of the magnetosphere formed by external hot plasma flow of the flyby particles. Solution of the Vlasov equation expressed via a tensor of dielectric permittivity of nonmagnetized and magnetized flowing plasma. Here, we obtain the direct kinetic dissipative effect of the magnetotail formation and the opposite diamagnetic effect of the magnetosphere “dipolization”. We get MHD wave cone in flow magnetized by external guiding magnetic (GM) field. Magnetosphere in our consideration is a 3D dissipative “wave” package structure of the skinned EM fields formed by the “waves” excited at frequency bands where we obtain negative values and singularities (resonances) of squared EM refractive index of the cold plasma. The hot regime

  4. Transformation from a 2D stacked layer to 3D interpenetrated framework by changing the spacer functionality: synthesis, structure, adsorption, and magnetic properties.

    PubMed

    Maji, Tapas Kumar; Ohba, Masaaki; Kitagawa, Susumu

    2005-12-12

    Two novel coordination polymers of Cu(II), viz. [Cu(bipy)(1,4-napdc)(H2O)2]n and {[Cu(bpe)1.5(1,4-napdc)](H2O)}n (bipy=4,4'-bipyridine; bpe=1,2-bis(4-pyridyl)ethane; 1,4-napdc2-=1,4-naphthalenedicarboxylate), have been synthesized and structurally characterized by changing only the pillar motifs. Both the compounds crystallize by slow evaporation from the ammoniacal solution of the as-synthesized solid. Framework 1 crystallizes in monoclinic crystal system, space group P2/n (No. 13), with a=11.028(19) A, b=11.16(3) A, c=7.678(13) A, beta=103.30(5) degrees, and Z=2. Framework 2 crystallizes in triclinic system, space group, P (No. 2), a=10.613(4) A, b=10.828(10) A, c=13.333(9) A, alpha=85.25(9) degrees, beta=82.59(6) degrees, gamma=60.37(5) degrees, and Z=2. The structure determination reveals that has a 2D network based on rectangular grids, where each Cu(II) is in 4+2 coordination mode. The 2D networks stacked in a staggered manner through the pi-pi interaction to form a 3D supramolecular network. In the case of, a {Cu(bpe)1.5}n ladder connected by 1,4-napdc2- results a 2D cuboidal bilayer network and each bilayer network is interlocked by two adjacent identical network (upper and lower) forming 3-fold interpenetrated 3D framework with small channel along the c-axis, which accommodates two water molecules. The TGA and XRPD measurements reveal that both the frameworks are stable after dehydration. Adsorption measurements (N2, CO2, and different solvents, like H2O, MeOH, etc.) were carried out for both frameworks. Framework shows type-II sorption profile with N2 in contrast to H2O and MeOH, which are chemisorbed in the framework. In case of, only H2O molecules can diffuse into the micropore, whereas N2, CO2, and MeOH cannot be adsorbed, as corroborated by the smaller channel aperture. The low-temperature (300-2 K) magnetic measurement of and reveals that both are weakly antiferromagnetically coupled (J=-1.85 cm-1, g=2.02; J=-0.153 cm-1, g=2.07), which is correlated

  5. Preliminary investigations on 3D PIC simulation of DPHC structure using NEPTUNE3D code

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Wang, Qiang

    2016-10-01

    Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) structure was chosen to perform a series of fully 3D PIC simulations using NEPTUNE3D codes, massive data ( 200GB) could be acquired and solved in less than 5 hours. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated by comparisons between output magnetic field profiles with or without electron emission. PIC simulation results showed three stages of current transforming process with election emission in DPHC structure, the maximum ( 20%) current loss was 437kA at 15ns, while only 0.46% 0.48% was lost when driving current reached its peak. DPHC structure proved valuable functions during energy transform process in PTS facility, and NEPTUNE3D provided tools to explore this sophisticated physics. Project supported by the National Natural Science Foundation of China, Grant No. 11571293, 11505172.

  6. Synthesis, structure and magnetic properties of low dimensional spin systems in the 3d transition metal oxides and superconductivity in magnesium borate

    NASA Astrophysics Data System (ADS)

    Rogado, Nyrissa S.

    The major part of this thesis deals with the synthesis and magnetic characterization of low dimensional spin systems in the 3d transition metal oxides. Such systems are of interest due to the simplicity of their structures, allowing theoretical modeling of their electronic and magnetic behavior. Exotic properties are also often encountered. Studies involving layered magnetic materials based on triangle lattices, in particular, have resulted in many observations of unusual low temperature spin dynamics, and have presented new challenges for the theoretical understanding of magnetic systems. The magnetic properties of some compounds exhibiting these triangle-based lattices are described here in detail. BaNi2V2O8 is a spin-1 antiferromagnet on a honeycomb net. Susceptibility chi(T), specific heat C(T), and neutron diffraction measurements on this compound reveal the onset of antiferromagnetic (AFM) long-range ordering (LRO) close to 50 K. Diffuse diffraction peaks that are characteristic of two-dimensional (2D) short-range order are also observed up to 100 K. chi(T) of Ba(Ni1-xMgx)2V 2O8 shows the gradual disappearance of LRO with doping. Ni3V2O8, Co3V2O 8, and beta-Cu3V2O8 have spin-1, spin-3/2, and spin-1/2 magnetic lattices that are a new anisotropic variant of the Kagome net, wherein edge-sharing MO6 octahedra form the rises and rungs of a "Kagome staircase". The anisotropy largely relieves the geometric frustration, but results in rich magnetic behavior. Characterization of the magnetization of polycrystalline samples of Ni 3V2O8 and Co3V2O8 reveals that the compounds are ferrimagnetic in character. C(T) show four distinct magnetic phase transitions below 9 K for Ni3V2O 8 and two below 11 K for Co3V2O8. In the case of beta-Cu3V2O8, chi(T) and C(T) show the onset of short-range ordering at approximately 75 K, and a magnetic phase transition with the characteristics of antiferromagnetism at around 29 K. The second part of this thesis describes the bulk synthesis of

  7. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  8. Designing bioinspired composite reinforcement architectures via 3D magnetic printing

    NASA Astrophysics Data System (ADS)

    Martin, Joshua J.; Fiore, Brad E.; Erb, Randall M.

    2015-10-01

    Discontinuous fibre composites represent a class of materials that are strong, lightweight and have remarkable fracture toughness. These advantages partially explain the abundance and variety of discontinuous fibre composites that have evolved in the natural world. Many natural structures out-perform the conventional synthetic counterparts due, in part, to the more elaborate reinforcement architectures that occur in natural composites. Here we present an additive manufacturing approach that combines real-time colloidal assembly with existing additive manufacturing technologies to create highly programmable discontinuous fibre composites. This technology, termed as `3D magnetic printing', has enabled us to recreate complex bioinspired reinforcement architectures that deliver enhanced material performance compared with monolithic structures. Further, we demonstrate that we can now design and evolve elaborate reinforcement architectures that are not found in nature, demonstrating a high level of possible customization in discontinuous fibre composites with arbitrary geometries.

  9. Designing bioinspired composite reinforcement architectures via 3D magnetic printing

    PubMed Central

    Martin, Joshua J.; Fiore, Brad E.; Erb, Randall M.

    2015-01-01

    Discontinuous fibre composites represent a class of materials that are strong, lightweight and have remarkable fracture toughness. These advantages partially explain the abundance and variety of discontinuous fibre composites that have evolved in the natural world. Many natural structures out-perform the conventional synthetic counterparts due, in part, to the more elaborate reinforcement architectures that occur in natural composites. Here we present an additive manufacturing approach that combines real-time colloidal assembly with existing additive manufacturing technologies to create highly programmable discontinuous fibre composites. This technology, termed as ‘3D magnetic printing', has enabled us to recreate complex bioinspired reinforcement architectures that deliver enhanced material performance compared with monolithic structures. Further, we demonstrate that we can now design and evolve elaborate reinforcement architectures that are not found in nature, demonstrating a high level of possible customization in discontinuous fibre composites with arbitrary geometries. PMID:26494282

  10. Discovering Structural Regularity in 3D Geometry

    PubMed Central

    Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.

    2010-01-01

    We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292

  11. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations.

  12. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

    González-Torre, Iván; Losada, Juan Carlos; Falconer, Ruth; Hapca, Simona; Tarquis, Ana M.

    2015-04-01

    Soil structure may be defined as the spatial arrangement of soil particles, aggregates and pores. The geometry of each one of these elements, as well as their spatial arrangement, has a great influence on the transport of fluids and solutes through the soil. Fractal/Multifractal methods have been increasingly applied to quantify soil structure thanks to the advances in computer technology (Tarquis et al., 2003). There is no doubt that computed tomography (CT) has provided an alternative for observing intact soil structure. These CT techniques reduce the physical impact to sampling, providing three-dimensional (3D) information and allowing rapid scanning to study sample dynamics in near real-time (Houston et al., 2013a). However, several authors have dedicated attention to the appropriate pore-solid CT threshold (Elliot and Heck, 2007; Houston et al., 2013b) and the better method to estimate the multifractal parameters (Grau et al., 2006; Tarquis et al., 2009). The aim of the present study is to evaluate the effect of the algorithm applied in the multifractal method (box counting and box gliding) and the cube size on the calculation of generalized fractal dimensions (Dq) in grey images without applying any threshold. To this end, soil samples were extracted from different areas plowed with three tools (moldboard, chissel and plow). Soil samples for each of the tillage treatment were packed into polypropylene cylinders of 8 cm diameter and 10 cm high. These were imaged using an mSIMCT at 155keV and 25 mA. An aluminium filter (0.25 mm) was applied to reduce beam hardening and later several corrections where applied during reconstruction. References Elliot, T.R. and Heck, R.J. 2007. A comparison of 2D and 3D thresholding of CT imagery. Can. J. Soil Sci., 87(4), 405-412. Grau, J, Médez, V.; Tarquis, A.M., Saa, A. and Díaz, M.C.. 2006. Comparison of gliding box and box-counting methods in soil image analysis. Geoderma, 134, 349-359. González-Torres, Iván. Theory and

  13. Multimaterial magnetically assisted 3D printing of composite materials

    PubMed Central

    Kokkinis, Dimitri; Schaffner, Manuel; Studart, André R.

    2015-01-01

    3D printing has become commonplace for the manufacturing of objects with unusual geometries. Recent developments that enabled printing of multiple materials indicate that the technology can potentially offer a much wider design space beyond unusual shaping. Here we show that a new dimension in this design space can be exploited through the control of the orientation of anisotropic particles used as building blocks during a direct ink-writing process. Particle orientation control is demonstrated by applying low magnetic fields on deposited inks pre-loaded with magnetized stiff platelets. Multimaterial dispensers and a two-component mixing unit provide additional control over the local composition of the printed material. The five-dimensional design space covered by the proposed multimaterial magnetically assisted 3D printing platform (MM-3D printing) opens the way towards the manufacturing of functional heterogeneous materials with exquisite microstructural features thus far only accessible by biological materials grown in nature. PMID:26494528

  14. Multimaterial magnetically assisted 3D printing of composite materials

    NASA Astrophysics Data System (ADS)

    Kokkinis, Dimitri; Schaffner, Manuel; Studart, André R.

    2015-10-01

    3D printing has become commonplace for the manufacturing of objects with unusual geometries. Recent developments that enabled printing of multiple materials indicate that the technology can potentially offer a much wider design space beyond unusual shaping. Here we show that a new dimension in this design space can be exploited through the control of the orientation of anisotropic particles used as building blocks during a direct ink-writing process. Particle orientation control is demonstrated by applying low magnetic fields on deposited inks pre-loaded with magnetized stiff platelets. Multimaterial dispensers and a two-component mixing unit provide additional control over the local composition of the printed material. The five-dimensional design space covered by the proposed multimaterial magnetically assisted 3D printing platform (MM-3D printing) opens the way towards the manufacturing of functional heterogeneous materials with exquisite microstructural features thus far only accessible by biological materials grown in nature.

  15. Free-Standing Magnetic Nanopillars for 3D Nanomagnet Logic

    PubMed Central

    2014-01-01

    Nanomagnet logic (NML) is a relatively new computation technology that uses arrays of shape-controlled nanomagnets to enable digital processing. Currently, conventional resist-based lithographic processes limit the design of NML circuitry to planar nanostructures with homogeneous thicknesses. Here, we demonstrate the focused electron beam induced deposition of Fe-based nanomaterial for magnetic in-plane nanowires and out-of-plane nanopillars. Three-dimensional (3D) NML was achieved based on the magnetic coupling between nanowires and nanopillars in a 3D array. Additionally, the same Fe-based nanomaterial was used to produce tilt-corrected high-aspect-ratio probes for the accurate magnetic force microscopy (MFM) analysis of the fabricated 3D NML gate arrays. The interpretation of the MFM measurements was supported by magnetic simulations using the Object Oriented MicroMagnetic Framework. Introducing vertical out-of-plane nanopillars not only increases the packing density of 3D NML but also introduces an extra magnetic degree of freedom, offering a new approach to input/output and processing functionalities in nanomagnetic computing. PMID:25296008

  16. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-01-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  17. Microfabricating 3D Structures by Laser Origami

    DTIC Science & Technology

    2011-11-09

    technique generates 3D microstructures by controlled out-of- plane folding of 2D patterns through a variety of laser-based digital fabrication...processes. Digital microfabrication techniques such as laser direct-write (LDW) offer a viable alternative for generating 3D self-folding designs. These...folding at the microscale where manual or mechanized actuation of the smaller struc- tures is not practical. LDW techniques allow micromachining and

  18. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  19. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa.

  20. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-07-08

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.

  1. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

    Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-01-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  2. Self-assembled 3D heterometallic Cu(II)/Fe(II) coordination polymers with octahedral net skeletons: structural features, molecular magnetism, thermal and oxidation catalytic properties.

    PubMed

    Karabach, Yauhen Y; Guedes da Silva, M Fátima C; Kopylovich, Maximilian N; Gil-Hernández, Beatriz; Sanchiz, Joaquin; Kirillov, Alexander M; Pombeiro, Armando J L

    2010-12-06

    The new three-dimensional (3D) heterometallic Cu(II)/Fe(II) coordination polymers [Cu(6)(H(2)tea)(6)Fe(CN)(6)](n)(NO(3))(2n)·6nH(2)O (1) and [Cu(6)(Hmdea)(6)Fe(CN)(6)](n)(NO(3))(2n)·7nH(2)O (2) have been easily generated by aqueous-medium self-assembly reactions of copper(II) nitrate with triethanolamine or N-methyldiethanolamine (H(3)tea or H(2)mdea, respectively), in the presence of potassium ferricyanide and sodium hydroxide. They have been isolated as air-stable crystalline solids and fully characterized including by single-crystal X-ray diffraction analyses. The latter reveal the formation of 3D metal-organic frameworks that are constructed from the [Cu(2)(μ-H(2)tea)(2)](2+) or [Cu(2)(μ-Hmdea)(2)](2+) nodes and the octahedral [Fe(CN)(6)](4-) linkers, featuring regular (1) or distorted (2) octahedral net skeletons. Upon dehydration, both compounds show reversible escape and binding processes toward water or methanol molecules. Magnetic susceptibility measurements of 1 and 2 reveal strong antiferromagnetic [J = -199(1) cm(-1)] or strong ferromagnetic [J = +153(1) cm(-1)] couplings between the copper(II) ions through the μ-O-alkoxo atoms in 1 or 2, respectively. The differences in magnetic behavior are explained in terms of the dependence of the magnetic coupling constant on the Cu-O-Cu bridging angle. Compounds 1 and 2 also act as efficient catalyst precursors for the mild oxidation of cyclohexane by aqueous hydrogen peroxide to cyclohexanol and cyclohexanone (homogeneous catalytic system), leading to maximum total yields (based on cyclohexane) and turnover numbers (TONs) up to about 22% and 470, respectively.

  3. Magnetism In 3d Transition Metals at High Pressures

    SciTech Connect

    Iota, V

    2006-02-09

    This research project examined the changes in electronic and magnetic properties of transition metals and oxides under applied pressures, focusing on complex relationship between magnetism and phase stability in these correlated electron systems. As part of this LDRD project, we developed new measurement techniques and adapted synchrotron-based electronic and magnetic measurements for use in the diamond anvil cell. We have performed state-of-the-art X-ray spectroscopy experiments at the dedicated high-pressure beamline HP-CAT (Sector 16 Advanced Photon Source, Argonne National Laboratory), maintained in collaboration with of University of Nevada, Las Vegas and Geophysical Laboratory of The Carnegie Institution of Washington. Using these advanced measurements, we determined the evolution of the magnetic order in the ferromagnetic 3d transition metals (Fe, Co and Ni) under pressure, and found that at high densities, 3d band broadening results in diminished long range magnetic coupling. Our experiments have allowed us to paint a unified picture of the effects of pressure on the evolution of magnetic spin in 3d electron systems. The technical and scientific advances made during this LDRD project have been reported at a number of scientific meetings and conferences, and have been submitted for publication in technical journals. Both the technical advances and the physical understanding of correlated systems derived from this LDRD are being applied to research on the 4f and 5f electron systems under pressure.

  4. Three-dimensional (3D) printing of mouse primary hepatocytes to generate 3D hepatic structure

    PubMed Central

    Kim, Yohan; Kang, Kyojin; Jeong, Jaemin; Paik, Seung Sam; Kim, Ji Sook; Park, Su A; Kim, Wan Doo; Park, Jisun

    2017-01-01

    Purpose 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. Methods 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 × 107 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. Results 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. Conclusion 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. PMID:28203553

  5. Voltage controlled magnetism in 3d transitional metals

    NASA Astrophysics Data System (ADS)

    Wang, Weigang

    2015-03-01

    Despite having attracted much attention in multiferroic materials and diluted magnetic semiconductors, the impact of an electric field on the magnetic properties remains largely unknown in 3d transitional ferromagnets (FMs) until recent years. A great deal of effort has been focused on the voltage-controlled magnetic anisotropy (VCMA) effect where the modulation of anisotropy field is understood by the change of electron density among different d orbitals of FMs in the presence of an electric field. Here we demonstrate another approach to alter the magnetism by electrically controlling the oxidation state of the 3d FM at the FM/oxide interface. The thin FM film sandwiched between a heavy metal layer and a gate oxide can be reversibly changed from an optimally-oxidized state with a strong perpendicular magnetic anisotropy to a metallic state with an in-plane magnetic anisotropy, or to a fully-oxidized state with nearly zero magnetization, depending on the polarity and time duration of the applied electric fields. This is a voltage controlled magnetism (VCM) effect, where both the saturation magnetization and anisotropy field of the 3d FM layer can be simultaneously controlled by voltage in a non-volatile fashion. We will also discuss the impact of this VCM effect on magnetic tunnel junctions and spin Hall switching experiments. This work, in collaboration with C. Bi, Y.H. Liu, T. Newhouse-Illige, M. Xu, M. Rosales, J.W. Freeland, O. Mryasov, S. Zhang, and S.G.E. te Velthuis, was supported in part by NSF (ECCS-1310338) and by C-SPIN, one of six centers of STARnet, a Semiconductor Research Corporation program, sponsored by MARCO and DARPA.

  6. Direct-write 3D printing of NdFeB bonded magnets

    DOE PAGES

    Compton, Brett Gibson; Kemp, James William; Novikov, Timofei V.; ...

    2016-08-17

    We report a method to fabricate Nd-Fe-B bonded magnets of complex shape via extrusion-based additive manufacturing (AM), also known as 3D-printing. We have successfully formulated a 3D-printable epoxy-based ink for direct-write AM with anisotropic MQA NdFeB magnet particles that can be deposited at room temperature. The new feedstocks contain up to 40 vol.% MQA anisotropic Nd-Fe-B magnet particles, and they are shown to remain uniformly dispersed in the thermoset matrix throughout the deposition process. Ring, bar, and horseshoe-type 3D magnet structures were printed and cured in air at 100°C without degrading the magnetic properties. Lastly, this study provides a newmore » pathway for fabricating Nd-Fe-B bonded magnets with complex geometry at low temperature, and presents new opportunities for fabricating multifunctional hybrid structures and devices.« less

  7. Direct-write 3D printing of NdFeB bonded magnets

    SciTech Connect

    Compton, Brett Gibson; Kemp, James William; Novikov, Timofei V.; Pack, Robert Cody; Nlebedim, Cajetan I.; Duty, Chad Edward; Rios, Orlando; Paranthaman, M. Parans

    2016-08-17

    We report a method to fabricate Nd-Fe-B bonded magnets of complex shape via extrusion-based additive manufacturing (AM), also known as 3D-printing. We have successfully formulated a 3D-printable epoxy-based ink for direct-write AM with anisotropic MQA NdFeB magnet particles that can be deposited at room temperature. The new feedstocks contain up to 40 vol.% MQA anisotropic Nd-Fe-B magnet particles, and they are shown to remain uniformly dispersed in the thermoset matrix throughout the deposition process. Ring, bar, and horseshoe-type 3D magnet structures were printed and cured in air at 100°C without degrading the magnetic properties. Lastly, this study provides a new pathway for fabricating Nd-Fe-B bonded magnets with complex geometry at low temperature, and presents new opportunities for fabricating multifunctional hybrid structures and devices.

  8. RNA Structure: Advances and Assessment of 3D Structure Prediction.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

    Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  9. Switchable field-tuned control of magnetic domain wall pinning along Co microwires by 3D e-beam lithographed structures

    NASA Astrophysics Data System (ADS)

    Blanco-Roldán, C.; Quirós, C.; Rodriguez-Rodriguez, G.; Vélez, M.; Martín, J. I.; Alameda, J. M.

    2016-02-01

    Three-dimensional magnetic circuits composed of Co microwires crossed by elevated Co bridges have been patterned on Si substrate by e-beam lithography and lift-off process. The lithographic procedure includes a double resist procedure that optimizes the shape of the bridge, so that 200 nm air gaps can be routinely achieved in between the wire and bridge elements. Microwire magnetization reversal processes have been analyzed by magneto-optical Kerr effect microscopy with different remanent bridge configurations. When the Co bridge is magnetized along the in-plane direction parallel to the wire axis, its stray field induces a marked pinning effect on domain wall propagation along the wire below it, even without being in contact. Changing the sign of the remanent state of the bridge, domain wall pinning can be selected to occur in either the ascending or descending branches of the wire hysteresis loop. Thus, these wire-bridge 3D circuits provide a simple system for tunable domain wall pinning controllable through the pre-recorded bridge remanent state.

  10. Positional isomeric tunable two Co(II) 6-connected 3-D frameworks with pentanuclear to binuclear units: structures, ion-exchange and magnetic properties.

    PubMed

    Han, Min-Le; Duan, Ya-Ping; Li, Dong-Sheng; Wang, Hai-Bin; Zhao, Jun; Wang, Yao-Yu

    2014-11-07

    Two new Co(II) based metal-organic frameworks, namely {[Co5(μ3-OH)2(m-pda)3(bix)4]·2ClO4}n (1) and {[Co2(p-pda)2(bix)2(H2O)]·H2O}n (2), were prepared by hydrothermal reactions of Co(II) salt with two isomeric dicarboxyl tectons 1,3-phenylenediacetic acid (m-pda) and 1,4-phenylenediacetic acid (p-pda), along with 1,3-bis(imidazol-L-ylmethyl)benzene (bix). Both complexes 1 and 2 have been characterized by elemental analysis, IR spectroscopy, single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). 1 shows a 6-connected 3-D pcu cationic framework with pentanuclear [Co5(μ3-OH)2(COO)6(bix)2](2+) units, while 2 exhibits a 6-connected 3-D msw net based on [Co2(μ2-H2O)(COO)2](2+) clusters. The results indicate that the different dispositions of the carboxylic groups of dicarboxylates have an important effect on the overall coordination frameworks. Perchlorate anions in 1 can be partly exchanged by thiocyanate and azide anions, however they are unavailable to nitrate anions. Magnetic susceptibility measurements indicate that both 1 and 2 show weak antiferromagnetic interactions between the adjacent Co(II) ions.

  11. Kinetic shielding of magnetic islands in 3-D equilibria

    NASA Astrophysics Data System (ADS)

    Hegna, C. C.

    2010-11-01

    Kinetic theory is employed to calculate corrections to analytic predictions of saturated magnetic islands due to pressure gradients in 3-D magnetic configurations. The theory calculates the dominant trapped particle response to 3-D field induced net bounce averaged radial drifts. The associated kinetic response describes plasma currents that flow within magnetic surfaces. In general, these currents have a component that resonates with the helical angle of the magnetic island and affect saturated island sizes through the parallel currents generated to satisfy quasineutrality. The resulting kinetic response generally opposes the effects of singular Pfirsch-Schlüter currents that arise at the rational surfaces of general 3-D MHD equilibria. Accounting for both the MHD and kinetic responses, self-consistent magnetic island widths are calculated using Ampere's law. The kinetic effect is largest at lowest collisionality suggesting high-β stellarators are more resilient to retaining flux surface integrity at high-temperatures than predictions from conventional MHD based theory would imply.

  12. Effect of temperature on magnetization reversal characteristics of ferromagnetic 3 d metal layers within exchange-coupled FeMn-based structures

    NASA Astrophysics Data System (ADS)

    Vas'kovskiy, V. O.; Adanakova, O. A.; Gorkovenko, A. N.; Lepalovskij, V. N.; Svalov, A. V.; Stepanova, E. A.

    2015-12-01

    Multilayer films Fe20Ni80/FeMn/FM (with FM = Ni, Fe11Ni89, Fe20Ni80, Co30Ni70, Fe, Co) have been prepared and their structure has been estimated. Their hysteretic properties and interlayer coupling parameters have been studied in a temperature range of 5-350 K. Regularities of the magnetization reversal of ferromagnetic layers under magnetic exchange-bias conditions have been interpreted.

  13. 3-D Display Of Magnetic Resonance Imaging Of The Spine

    NASA Astrophysics Data System (ADS)

    Nelson, Alan C.; Kim, Yongmin; Haralick, Robert M.; Anderson, Paul A.; Johnson, Roger H.; DeSoto, Larry A.

    1988-06-01

    The original data is produced through standard magnetic resonance imaging (MRI) procedures with a surface coil applied to the lower back of a normal human subject. The 3-D spine image data consists of twenty-six contiguous slices with 256 x 256 pixels per slice. Two methods for visualization of the 3-D spine are explored. One method utilizes a verifocal mirror system which creates a true 3-D virtual picture of the object. Another method uses a standard high resolution monitor to simultaneously show the three orthogonal sections which intersect at any user-selected point within the object volume. We discuss the application of these systems in assessment of low back pain.

  14. 3-D, Impulsive Magnetic Reconnection in a Laboratory Plasma (Invited)

    NASA Astrophysics Data System (ADS)

    Dorfman, S. E.; Ji, H.; Yamada, M.; Yoo, J.; Myers, C. E.; Roytershteyn, V.; Daughton, W. S.; Jara-Almonte, J.

    2013-12-01

    Magnetic reconnection is a fundamental plasma process involving the efficient conversion of magnetic field energy to plasma kinetic energy through changing field line topology. In many space and astrophysical systems, including the solar surface and the Earth's magnetotail, reconnection is not only fast, but also impulsive; in other words, a slow buildup phase is followed by a comparatively quick release of magnetic energy. An important question in the literature is if these examples of impulsive reconnection can be described by a two-dimensional model with no variation in the out-of-plane direction or if impulsive reconnection is fundamentally three-dimensional. Events observed on the Magnetic Reconnection Experiment (MRX) are characterized by large local gradients in the third direction and cannot be explained by 2-D models [1]. Detailed measurements show that the ejection of flux rope structures from the current sheet plays a key role in these events. By contrast, even though electromagnetic fluctuations in the lower hybrid frequency range are also observed concurrently with the impulsive behavior, they are not the key physics responsible. Furthermore, an important discrepancy in the layer width and force balance between the collisionless regime of MRX and kinetic simulations [2-4] persists when the fluctuations are small or absent, implying that they are not the cause of the wider electron layers observed in the experiment [5]. These wider layers may instead be due to the formation of flux ropes with a wide range of sizes; consistent with this hypothesis, flux rope signatures are observed down to the smallest scales resolved by the diagnostics. Finally, a qualitative, 3-D, two-fluid model is proposed to explain the observed disruptions. Many of the features observed in MRX including current disruptions [6], flux ropes [7], and electromagnetic fluctuations [8] have analogues in space observations. Thus, further detailed comparisons may enhance our understanding

  15. Quantitative 3D structured illumination microscopy of nuclear structures.

    PubMed

    Kraus, Felix; Miron, Ezequiel; Demmerle, Justin; Chitiashvili, Tsotne; Budco, Alexei; Alle, Quentin; Matsuda, Atsushi; Leonhardt, Heinrich; Schermelleh, Lothar; Markaki, Yolanda

    2017-05-01

    3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.

  16. Particle acceleration at 3D reconnecting magnetic separators

    NASA Astrophysics Data System (ADS)

    Threlfall, James; Neukirch, Thomas; Parnell, Clare; Stevenson, Julie

    2015-04-01

    We present results of test particle orbit calculations in three different environments which model separator reconnection in three dimensions. The test particle (electron and proton) orbits are calculated using the relativistic guiding centre approximation. We investigate test particle orbits in a time-dependent (analytical) electro-magnetic field configuration [detailed in Threlfall et al. (A&A, in press); arXiv:1410.6465]. These results are also compared with orbits based upon large-scale 3D MHD simulations of both a single reconnecting magnetic separator and an observationally driven 3D model of a solar active region which contains several topological features of interest, including separators. We discuss how the test-particle orbits and the energy gain depend on the initial conditions, and how observations (for example, of solar flares) may be used to constrain model parameters.

  17. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.

  18. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  19. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  20. Supramolecular 3d-4f single-molecule magnet architectures.

    PubMed

    Schmitz, Sebastian; van Leusen, Jan; Izarova, Natalya V; Lan, Yanhua; Wernsdorfer, Wolfgang; Kögerler, Paul; Monakhov, Kirill Yu

    2016-10-18

    The nanosized self-assemblies {[{Ln(III)}{H2O⊂CrLn}]2(H2O)} (Ln = Dy, 1 and Tb, 2) based on new 3d-4f mixed-metal coordination topologies are formed via extensive intramolecular hydrogen bonding that is directed by enclosed water molecules. Compounds 1 and 2 show single-molecule magnet characteristics manifested by hysteresis loops up to 1.6 K (Ueff = 8.3 cm(-1)) and 1 K (Ueff = 3.4 cm(-1)), respectively.

  1. Magnetically Defined Qubits on 3D Topological Insulators

    NASA Astrophysics Data System (ADS)

    Ferreira, Gerson J.; Loss, Daniel

    2013-09-01

    We explore potentials that break time-reversal symmetry to confine the surface states of 3D topological insulators into quantum wires and quantum dots. A magnetic domain wall on a ferromagnet insulator cap layer provides interfacial states predicted to show the quantum anomalous Hall effect (QAHE). Here, we show that confinement can also occur at magnetic domain heterostructures, with states extended in the inner domain, as well as interfacial QAHE states at the surrounding domain walls. The proposed geometry allows the isolation of the wire and dot from spurious circumventing surface states. For the quantum dots, we find that highly spin-polarized quantized QAHE states at the dot edge constitute a promising candidate for quantum computing qubits.

  2. Magnetically Defined Qubits on 3D Topological Insulators

    NASA Astrophysics Data System (ADS)

    Ferreira, Gerson J.; Loss, Daniel

    2014-03-01

    We explore potentials that break time-reversal symmetry to confine the surface states of 3D topological insulators into quantum wires and quantum dots. A magnetic domain wall on a ferromagnet insulator cap layer provides interfacial states predicted to show the quantum anomalous Hall effect. Here, we show that confinement can also occur at magnetic domain heterostructures, with states extended in the inner domain, as well as interfacial QAHE states at the surrounding domain walls. The proposed geometry allows the isolation of the wire and dot from spurious circumventing surface states. For the quantum dots, we find that highly spin-polarized quantized QAHE states at the dot edge constitute a promising candidate for quantum computing qubits. See [Ferreira and Loss, Phys. Rev. Lett. 111, 106802 (2013)]. We explore potentials that break time-reversal symmetry to confine the surface states of 3D topological insulators into quantum wires and quantum dots. A magnetic domain wall on a ferromagnet insulator cap layer provides interfacial states predicted to show the quantum anomalous Hall effect. Here, we show that confinement can also occur at magnetic domain heterostructures, with states extended in the inner domain, as well as interfacial QAHE states at the surrounding domain walls. The proposed geometry allows the isolation of the wire and dot from spurious circumventing surface states. For the quantum dots, we find that highly spin-polarized quantized QAHE states at the dot edge constitute a promising candidate for quantum computing qubits. See [Ferreira and Loss, Phys. Rev. Lett. 111, 106802 (2013)]. We acknowledge support from the Swiss NSF, NCCR Nanoscience, NCCR QSIT, and the Brazillian Research Support Center Initiative (NAP Q-NANO) from Pró-Reitoria de Pesquisa (PRP/USP).

  3. Observation of a 3D Magnetic Null Point

    NASA Astrophysics Data System (ADS)

    Romano, P.; Falco, M.; Guglielmino, S. L.; Murabito, M.

    2017-03-01

    We describe high-resolution observations of a GOES B-class flare characterized by a circular ribbon at the chromospheric level, corresponding to the network at the photospheric level. We interpret the flare as a consequence of a magnetic reconnection event that occurred at a three-dimensional (3D) coronal null point located above the supergranular cell. The potential field extrapolation of the photospheric magnetic field indicates that the circular chromospheric ribbon is cospatial with the fan footpoints, while the ribbons of the inner and outer spines look like compact kernels. We found new interesting observational aspects that need to be explained by models: (1) a loop corresponding to the outer spine became brighter a few minutes before the onset of the flare; (2) the circular ribbon was formed by several adjacent compact kernels characterized by a size of 1″–2″ (3) the kernels with a stronger intensity emission were located at the outer footpoint of the darker filaments, departing radially from the center of the supergranular cell; (4) these kernels started to brighten sequentially in clockwise direction; and (5) the site of the 3D null point and the shape of the outer spine were detected by RHESSI in the low-energy channel between 6.0 and 12.0 keV. Taking into account all these features and the length scales of the magnetic systems involved in the event, we argue that the low intensity of the flare may be ascribed to the low amount of magnetic flux and to its symmetric configuration.

  4. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

    When Rutherford, Geiger and Marsden discovered the atomic nucleus in 1909 in Manchester, they at the same time also laid the foundations for the most successful method to study the structure of nuclei and nucleons. They found a point-like scattering centre inside the atom and identified it with the atomic nucleus and the theoretical description of this process has been known as Rutherford scattering ever since. The deviation between the theoretical description for a point-like scattering centre and experimental data has since been used to reveal information about the structure of the nucleus as well as the nucleon. There has been a continuous development from Hofstadters experiments in the 1950s, over the SLAC experiments in the 60s and 70s to the the HERA experiments at DESY and the experimental programme at Jeffersonlab. In this paper I am presenting the most recent results in Deeply Virtual Compton Scattering from the Hermes experiment at DESY, taken with a high density unpolarised target and a recoil detector in 2006/7.

  5. 3D Animations for Exploring Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

    Over the last few years many intuitive pictures have been developed for the interpretation of electron hadron scattering experiments, such as a mechanism for transverse single-spin asymmetries in semi-inclusive deep-inelastic scattering experiments. While Dr. Burkardt's pictures have been helpful for many researchers in the field, they are still difficult to visualize for broader audiences since they rely mostly on 2-dimensional static images. In order to make more accessible for a broader audience what can be learned from Jefferson Lab experiments, we have started to work on developing 3-dimensional animations for these processes. The goal is to enable the viewer to repeatedly look at the same microscopic mechanism for a specific reaction, with the viewpoint of the observer changing. This should help an audience that is not so familiar with these reactions to better understand what can be learned from various experiments at Jefferson Lab aimed at exploring the nucleon structure. Jefferson Lab Minority/Female Undergraduate Research Assistantship.

  6. 3D fibre deposition and stereolithography techniques for the design of multifunctional nanocomposite magnetic scaffolds.

    PubMed

    De Santis, Roberto; D'Amora, Ugo; Russo, Teresa; Ronca, Alfredo; Gloria, Antonio; Ambrosio, Luigi

    2015-10-01

    Magnetic nanocomposite scaffolds based on poly(ε-caprolactone) and poly(ethylene glycol) were fabricated by 3D fibre deposition modelling (FDM) and stereolithography techniques. In addition, hybrid coaxial and bilayer magnetic scaffolds were produced by combining such techniques. The aim of the current research was to analyse some structural and functional features of 3D magnetic scaffolds obtained by the 3D fibre deposition technique and by stereolithography as well as features of multimaterial scaffolds in the form of coaxial and bilayer structures obtained by the proper integration of such methods. The compressive mechanical behaviour of these scaffolds was investigated in a wet environment at 37 °C, and the morphological features were analysed through scanning electron microscopy (SEM) and X-ray micro-computed tomography. The capability of a magnetic scaffold to absorb magnetic nanoparticles (MNPs) in water solution was also assessed. confocal laser scanning microscopy was used to assess the in vitro biological behaviour of human mesenchymal stem cells (hMSCs) seeded on 3D structures. Results showed that a wide range of mechanical properties, covering those spanning hard and soft tissues, can be obtained by 3D FDM and stereolithography techniques. 3D virtual reconstruction and SEM showed the precision with which the scaffolds were fabricated, and a good-quality interface between poly(ε-caprolactone) and poly(ethylene glycol) based scaffolds was observed for bilayer and coaxial scaffolds. Magnetised scaffolds are capable of absorbing water solution of MNPs, and a preliminary information on cell adhesion and spreading of hMSCs was obtained without the application of an external magnetic field.

  7. Lithologic identification & mapping test based on 3D inversion of magnetic and gravity

    NASA Astrophysics Data System (ADS)

    Yan, Jiayong; Lv, Qingtian; Qi, Guang; Zhao, Jinhua; Zhang, Yongqian

    2016-04-01

    Though lithologic identification & mapping to achieve ore concentration district transparent within 5km depth is the main way to realize deep fine structures study, to explore deep mineral resources and to reveal metallogenic regularity of large-scale ore district . Owing to the wide covered area, high sampling density and mature three-dimensional inversion algorithm of gravity and magnetic data, so gravity and magnetic inversion become the most likely way to achieve three-dimensional lithologic mapping at the present stage. In this paper, we take Lu-zong(Lujiang county to Zongyang county in Anhui province ,east China) ore district as a case, we proposed lithologic mapping flow based 3D inversion of gravity magnetic and then carry out the lithologic mapping test. Lithologic identification & mapping flow is as follows: 1. Analysis relations between lithology and density and magnetic susceptibility by cross plot. 2.Extracting appropriate residual anomalies from high-precision Bourger gravity and aeromagnetic. 3.Use same mesh, do 3D magnetic and gravity inversion respectively under prior information constrained, and then invert susceptibility and density 3D model. 4. According setp1, construct logical topology operations between density 3D model and susceptibility. 5.Use the logical operations, identify lithogies cell by cell in 3D mesh, and then get 3D lithological model. According this flow, we obtained three-dimensional distribution of five main type lithologies in the Lu-Zong ore district within 5km depth. The result of lithologic mapping not only showed that the shallow characteristics and surface geological mapping are basically Coincide,more importantly ,it reveals the deeper lithologic changes.The lithlogical model make up the insufficient of surface geological mapping. The lithologic mapping test results in Lu-Zong ore concentration district showed that lithological mapping using 3D inversion of gravity and magnetic is a effective method to reveal the

  8. Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data

    NASA Astrophysics Data System (ADS)

    Strait, E. J.; King, J. D.; Hanson, J. M.; Logan, N. C.

    2016-11-01

    An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ˜10-3 to 10-5 of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

  9. Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data.

    PubMed

    Strait, E J; King, J D; Hanson, J M; Logan, N C

    2016-11-01

    An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ∼10(-3) to 10(-5) of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

  10. Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data

    DOE PAGES

    Strait, E. J.; King, J. D.; Hanson, J. M.; ...

    2016-08-11

    An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ~10-3 to 10-5 of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Lastly, applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

  11. Two-dimensional 3d-4f heterometallic coordination polymers: syntheses, crystal structures, and magnetic properties of six new Co(II)-Ln(III) compounds.

    PubMed

    Díaz-Gallifa, Pau; Fabelo, Oscar; Pasán, Jorge; Cañadillas-Delgado, Laura; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

    2014-06-16

    Six new heterometallic cobalt(II)-lanthanide(III) complexes of formulas [Ln(bta)(H2O)2]2[Co(H2O)6]·10H2O [Ln = Nd(III) (1) and Eu(III) (2)] and [Ln2Co(bta)2(H2O)8]n·6nH2O [Ln = Eu(III) (3), Sm(III) (4), Gd(III) (5), and Tb(III) (6)] (H4bta = 1,2,4,5-benzenetretracaboxylic acid) have been synthesized and characterized via single-crystal X-ray diffraction. 1 and 2 are isostructural compounds with a structure composed of anionic layers of [Ln(bta)(H2O)2]n(n-) sandwiching mononuclear [Co(H2O)6](2+) cations plus crystallization water molecules, which are interlinked by electrostatic forces and hydrogen bonds, leading to a supramolecular three-dimensional network. 3-6 are also isostructural compounds, and their structure consists of neutral layers of formula [Ln2Co(bta)2(H2O)8]n and crystallization water molecules, which are connected through hydrogen bonds to afford a supramolecular three-dimensional network. Heterometallic chains formed by the regular alternation of two nine-coordinate lanthanide(III) polyhedra [Ln(III)O9] and one compressed cobalt(II) octahedron [Co(II)O6] along the crystallographic c-axis are cross-linked by bta ligands within each layer of 3-6. Magnetic susceptibility measurements on polycrystalline samples for 3-6 have been carried out in the temperature range of 2.0-300 K. The magnetic behavior of these types of Ln(III)-Co(II) complexes, which have been modeled by using matrix dagonalization techniques, reveals the lack of magnetic coupling for 3 and 4, and the occurrence of weak antiferromagnetic interactions within the Gd(III)-Gd(III) (5) and Tb(III)-Tb(III) (6) dinuclear units through the exchange pathway provided by the double oxo(carboxylate) and double syn-syn carboxylate bridges.

  12. MagicFinger: 3D Magnetic Fingerprints for Indoor Location

    PubMed Central

    Carrillo, Daniel; Moreno, Victoria; Úbeda, Benito; Skarmeta, Antonio F.

    2015-01-01

    Given the indispensable role of mobile phones in everyday life, phone-centric sensing systems are ideal candidates for ubiquitous observation purposes. This paper presents a novel approach for mobile phone-centric observation applied to indoor location. The approach involves a location fingerprinting methodology that takes advantage of the presence of magnetic field anomalies inside buildings. Unlike existing work on the subject, which uses the intensity of magnetic field for fingerprinting, our approach uses all three components of the measured magnetic field vectors to improve accuracy. By using adequate soft computing techniques, it is possible to adequately balance the constraints of common solutions. The resulting system does not rely on any infrastructure devices and therefore is easy to manage and deploy. The proposed system consists of two phases: the offline phase and the online phase. In the offline phase, magnetic field measurements are taken throughout the building, and 3D maps are generated. Then, during the online phase, the user's location is estimated through the best estimator for each zone of the building. Experimental evaluations carried out in two different buildings confirm the satisfactory performance of indoor location based on magnetic field vectors. These evaluations provided an error of (11.34 m, 4.78 m) in the (x, y) components of the estimated positions in the first building where the experiments were carried out, with a standard deviation of (3.41 m, 4.68 m); and in the second building, an error of (4 m, 2.98 m) with a deviation of (2.64 m, 2.33 m). PMID:26184230

  13. Synthesis of 3D Model of a Magnetic Field-Influenced Body from a Single Image

    NASA Technical Reports Server (NTRS)

    Wang, Cuilan; Newman, Timothy; Gallagher, Dennis

    2006-01-01

    A method for recovery of a 3D model of a cloud-like structure that is in motion and deforming but approximately governed by magnetic field properties is described. The method allows recovery of the model from a single intensity image in which the structure's silhouette can be observed. The method exploits envelope theory and a magnetic field model. Given one intensity image and the segmented silhouette in the image, the method proceeds without human intervention to produce the 3D model. In addition to allowing 3D model synthesis, the method's capability to yield a very compact description offers further utility. Application of the method to several real-world images is demonstrated.

  14. Unsupervised fuzzy segmentation of 3D magnetic resonance brain images

    NASA Astrophysics Data System (ADS)

    Velthuizen, Robert P.; Hall, Lawrence O.; Clarke, Laurence P.; Bensaid, Amine M.; Arrington, J. A.; Silbiger, Martin L.

    1993-07-01

    Unsupervised fuzzy methods are proposed for segmentation of 3D Magnetic Resonance images of the brain. Fuzzy c-means (FCM) has shown promising results for segmentation of single slices. FCM has been investigated for volume segmentations, both by combining results of single slices and by segmenting the full volume. Different strategies and initializations have been tried. In particular, two approaches have been used: (1) a method by which, iteratively, the furthest sample is split off to form a new cluster center, and (2) the traditional FCM in which the membership grade matrix is initialized in some way. Results have been compared with volume segmentations by k-means and with two supervised methods, k-nearest neighbors and region growing. Results of individual segmentations are presented as well as comparisons on the application of the different methods to a number of tumor patient data sets.

  15. 3-D visualization of geologic structures and processes

    NASA Astrophysics Data System (ADS)

    Pflug, R.; Klein, H.; Ramshorn, Ch.; Genter, M.; Stärk, A.

    Interactive 3-D computer graphics techniques are used to visualize geologic structures and simulated geologic processes. Geometric models that serve as input to 3-D viewing programs are generated from contour maps, from serial sections, or directly from simulation program output. Choice of viewing parameters strongly affects the perception of irregular surfaces. An interactive 3-D rendering program and its graphical user interface provide visualization tools for structural geology, seismic interpretation, and visual post-processing of simulations. Dynamic display of transient ground-water simulations and sedimentary process simulations can visualize processes developing through time.

  16. Experimental Studies on the 3D Macro- and Microphysics of Magnetic Reconnection

    NASA Astrophysics Data System (ADS)

    Jara-Almonte, J.; Ji, H.; Yamada, M.; Yoo, J.; Fox, W. R., II

    2015-12-01

    Magnetic reconnection has been extensively studied in 2D geometries for many decades and considerable progress has been made in understating 2D reconnection physics, yet in real plasmas reconnection is fundamentally 3D in nature. Only recently has it become possible to study 3D reconnection using simulations, however some initial results have suggested that the inclusion of 3D effects does not strongly affect the basic properties of reconnection (e.g. reconnection rate or particle acceleration). Yet on the other hand, previous experiments, without direct 3D measurements, have implied that 3D effects could be important even in a quasi-2D system. Here we experimentally study both the (1) macro- and (2) microphysics of 3D reconnection in order to directly test the importance of 3D effects in a quasi-2D experiment. Using fully simultaneous 3D measurements, it is shown that during highly driven reconnection the macroscopic structure of the current sheet can become strongly 3D despite an essentially 2D upstream region. The correlation length along the current sheet is measured to be far shorter than suggested by kinetic simulations. Results from new experiments with stronger reconnection drive and diagnostics designed to estimate the 3D reconnection rate will be discussed. With regards to (2), the 3D microphysics, new diagnostics capable of measuring fluctuations at frequencies up to the electron cyclotron frequency (~ 300 MHz) have been developed and have identified the presence of very high frequency waves (~ 100 MHz) during asymmetric reconnection, localized to the low-density side. The detailed properties of these waves, including the measured power spectra and dispersion relation, will be discussed and compared with both previous satellite observations of high-frequency waves as well as with theoretical predictions on the generation of whistler waves during reconnection.

  17. Finding Organized Structures in 3-D LADAR Data

    DTIC Science & Technology

    2004-12-01

    work exists also on how to extract planar and linear objects from scattered 3-D point clouds , see for example [5], [6]. Methods were even proposed to...of structure detection and segmentation from 3-D point clouds collected from a single sensor location or integrated from multiple locations. In [2...primitives to point clouds are difficult to use practically for large data sets containing multiple complex structures, in opposition to multiple planar

  18. Evaluation of 3D Printer Accuracy in Producing Fractal Structure.

    PubMed

    Kikegawa, Kana; Takamatsu, Kyuuichirou; Kawakami, Masaru; Furukawa, Hidemitsu; Mayama, Hiroyuki; Nonomura, Yoshimune

    2017-01-01

    Hierarchical structures, also known as fractal structures, exhibit advantageous material properties, such as water- and oil-repellency as well as other useful optical characteristics, owing to its self-similarity. Various methods have been developed for producing hierarchical geometrical structures. Recently, fractal structures have been manufactured using a 3D printing technique that involves computer-aided design data. In this study, we confirmed the accuracy of geometrical structures when Koch curve-like fractal structures with zero to three generations were printed using a 3D printer. The fractal dimension was analyzed using a box-counting method. This analysis indicated that the fractal dimension of the third generation hierarchical structure was approximately the same as that of the ideal Koch curve. These findings demonstrate that the design and production of fractal structures can be controlled using a 3D printer. Although the interior angle deviated from the ideal value, the side length could be precisely controlled.

  19. Direct-Write 3D Nanoprinting of Plasmonic Structures

    DOE PAGES

    Winkler, Robert; Schmidt, Franz-Philipp; Karl-Franzens Univ.; ...

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, puremore » gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.« less

  20. Direct-Write 3D Nanoprinting of Plasmonic Structures.

    PubMed

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D; Lewis, Brett B; Kothleitner, Gerald; Rack, Philip D; Plank, Harald

    2017-03-08

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. While several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. In this study, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. By that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  1. Direct-Write 3D Nanoprinting of Plasmonic Structures

    SciTech Connect

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D.; Lewis, Brett B.; Kothleitner, Gerald; Rack, Philip D.; Plank, Harald

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  2. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  3. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

    Coronal Mass Ejections (CMEs) represent one of the most powerful energy release phenomena in the entire solar system and are a major driver of space weather. Prior to 2006, our observational access to CMEs was limited to single viewpoint remote sensing observations in the inner/outer corona, and in-situ observations further away, e.g. at 1 AU. Taking all these factors together, turned out to be a major obstacle in our understanding and characterizing of the 3D structure and evolution of CMEs. The situation improved dramatically with the availability of multi-viewpoint imaging observations of CMEs, all way through from the Sun to 1 AU, from the STEREO mission since 2006, combined with observations from other missions (SOHO, Hinode, SDO, IRIS). With this talk we will discuss several key recent results in CME science resulting from the analysis of multi-viewpoint observations. This includes: (1) shape and structure; (2) kinematics and energetics; (3) trajectories, deflections and rotations; (4) arrival times and velocities at 1 AU; (5) magnetic field structure; (6) relationships with coronal and interplanetary shocks and solar energetic particles. The implications of these results in terms of CME theories and models will be also addressed. We will conclude with a discussion of important open issues in our understanding of CMEs and how these could be addressed with upcoming (Solar Orbiter, Solar Probe Plus) and under-study missions (e.g., L5).

  4. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  5. 3D Geological Model of Nihe ore deposit Constrained by Gravity and Magnetic Modeling

    NASA Astrophysics Data System (ADS)

    Qi, Guang; Yan, Jiayong; Lv, Qingtan; Zhao, Jinhua

    2016-04-01

    We present a case study on using integrated geologic model in mineral exploration at depth. Nihe ore deposit in Anhui Province, is deep hidden ore deposit which was discovered in recent years, this finding is the major driving force of deep mineral exploration work in Luzong. Building 3D elaborate geological model has the important significance for prospecting to deep or surround in this area, and can help us better understand the metallogenic law and ore-controlling regularity. A 3D geological model, extending a depth from +200m to -1500m in Nihe ore deposit, has been compiled from surface geological map, cross-section, borehole logs and amounts of geological inference. And then the 3D geological models have been given physical property parameter for calculating the potential field. Modelling the potential response is proposed as means of evaluating the viability of the 3D geological models, and the evidence of making small changes to the uncertain parts of the original 3D geological models. It is expected that the final models not only reproduce supplied prior geological knowledge, but also explain the observed geophysical data. The workflow used to develop the 3D geologic model in this study includes the three major steps, as follows: (1) Determine the basic information of Model: Defining the 3D limits of the model area, the basic geological and structural unit, and the tectonic contact relations and the sedimentary sequences between these units. (2) 3D model construction: Firstly, a series of 2D geological cross sections over the model area are built by using all kinds of prior information, including surface geology, borehole data, seismic sections, and local geologists' knowledge and intuition. Lastly, we put these sections into a 3D environment according to their profile locations to build a 3D model by using geostatistics method. (3) 3D gravity and magnetic modeling: we calculate the potential field responses of the 3D model, and compare the predicted and

  6. Toward mobile 3D visualization for structural biologists.

    PubMed

    Tanramluk, Duangrudee; Akavipat, Ruj; Charoensawan, Varodom

    2013-12-01

    Technological advances in crystallography have led to the ever-rapidly increasing number of biomolecular structures deposited in public repertoires. This undoubtedly shifts the bottleneck of structural biology research from obtaining high-quality structures to data analysis and interpretation. The recently available glasses-free autostereoscopic laptop offers an unprecedented opportunity to visualize and study 3D structures using a much more affordable, and for the first time, portable device. Together with a gamepad re-programmed for 3D structure controlling, we describe how the gaming technologies can deliver the output 3D images for high-quality viewing, comparable to that of a passive stereoscopic system, and can give the user more control and flexibility than the conventional controlling setup using only a mouse and a keyboard.

  7. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  8. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

    Campbell, Leckey Cara A/; Miler, Corey A.; Hinders, Mark K.

    2011-01-01

    Structural health monitoring (SHM) for the detection of damage in aerospace materials is an important area of research at NASA. Ultrasonic guided Lamb waves are a promising SHM damage detection technique since the waves can propagate long distances. For complicated flaw geometries experimental signals can be difficult to interpret. High performance computing can now handle full 3-dimensional (3D) simulations of elastic wave propagation in materials. We have developed and implemented parallel 3D elastodynamic finite integration technique (3D EFIT) code to investigate ultrasound scattering from flaws in materials. EFIT results have been compared to experimental data and the simulations provide unique insight into details of the wave behavior. This type of insight is useful for developing optimized experimental SHM techniques. 3D EFIT can also be expanded to model wave propagation and scattering in anisotropic composite materials.

  9. Proposed traceable structural resolution protocols for 3D imaging systems

    NASA Astrophysics Data System (ADS)

    MacKinnon, David; Beraldin, J.-Angelo; Cournoyer, Luc; Carrier, Benjamin; Blais, François

    2009-08-01

    A protocol for determining structural resolution using a potentially-traceable reference material is proposed. Where possible, terminology was selected to conform to those published in ISO JCGM 200:2008 (VIM) and ASTM E 2544-08 documents. The concepts of resolvability and edge width are introduced to more completely describe the ability of an optical non-contact 3D imaging system to resolve small features. A distinction is made between 3D range cameras, that obtain spatial data from the total field of view at once, and 3D range scanners, that accumulate spatial data for the total field of view over time. The protocol is presented through the evaluation of a 3D laser line range scanner.

  10. Analysis of a 3-D system function measured for magnetic particle imaging.

    PubMed

    Rahmer, Jürgen; Weizenecker, Jürgen; Gleich, Bernhard; Borgert, Jörn

    2012-06-01

    Magnetic particle imaging (MPI) is a new tomographic imaging approach that can quantitatively map magnetic nanoparticle distributions in vivo. It is capable of volumetric real-time imaging at particle concentrations low enough to enable clinical applications. For image reconstruction in 3-D MPI, a system function (SF) is used, which describes the relation between the acquired MPI signal and the spatial origin of the signal. The SF depends on the instrumental configuration, the applied field sequence, and the magnetic particle characteristics. Its properties reflect the quality of the spatial encoding process. This work presents a detailed analysis of a measured SF to give experimental evidence that 3-D MPI encodes information using a set of 3-D spatial patterns or basis functions that is stored in the SF. This resembles filling 3-D k-space in magnetic resonance imaging, but is faster since all information is gathered simultaneously over a broad acquisition bandwidth. A frequency domain analysis shows that the finest structures that can be encoded with the presented SF are as small as 0.6 mm. SF simulations are performed to demonstrate that larger particle cores extend the set of basis functions towards higher resolution and that the experimentally observed spatial patterns require the existence of particles with core sizes of about 30 nm in the calibration sample. A simple formula is presented that qualitatively describes the basis functions to be expected at a certain frequency.

  11. Bifurcation to 3D helical magnetic equilibrium in an axisymmetric toroidal device.

    PubMed

    Bergerson, W F; Auriemma, F; Chapman, B E; Ding, W X; Zanca, P; Brower, D L; Innocente, P; Lin, L; Lorenzini, R; Martines, E; Momo, B; Sarff, J S; Terranova, D

    2011-12-16

    We report the first direct measurement of the internal magnetic field structure associated with a 3D helical equilibrium generated spontaneously in the core of an axisymmetric toroidal plasma containment device. Magnetohydrodynamic equilibrium bifurcation occurs in a reversed-field pinch when the innermost resonant magnetic perturbation grows to a large amplitude, reaching up to 8% of the mean field strength. Magnetic topology evolution is determined by measuring the Faraday effect, revealing that, as the perturbation grows, toroidal symmetry is broken and a helical equilibrium is established.

  12. CH5M3D: an HTML5 program for creating 3D molecular structures

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  13. Combined registration of 3D tibia and femur implant models in 3D magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Englmeier, Karl-Hans; Siebert, Markus; von Eisenhart-Rothe, Ruediger; Graichen, Heiko

    2008-03-01

    The most frequent reasons for revision of total knee arthroplasty are loosening and abnormal axial alignment leading to an unphysiological kinematic of the knee implant. To get an idea about the postoperative kinematic of the implant, it is essential to determine the position and orientation of the tibial and femoral prosthesis. Therefore we developed a registration method for fitting 3D CAD-models of knee joint prostheses into an 3D MR image. This rigid registration is the basis for a quantitative analysis of the kinematics of knee implants. Firstly the surface data of the prostheses models are converted into a voxel representation; a recursive algorithm determines all boundary voxels of the original triangular surface data. Secondly an initial preconfiguration of the implants by the user is still necessary for the following step: The user has to perform a rough preconfiguration of both remaining prostheses models, so that the fine matching process gets a reasonable starting point. After that an automated gradient-based fine matching process determines the best absolute position and orientation: This iterative process changes all 6 parameters (3 rotational- and 3 translational parameters) of a model by a minimal amount until a maximum value of the matching function is reached. To examine the spread of the final solutions of the registration, the interobserver variability was measured in a group of testers. This variability, calculated by the relative standard deviation, improved from about 50% (pure manual registration) to 0.5% (rough manual preconfiguration and subsequent fine registration with the automatic fine matching process).

  14. Exact spectra of strong coulomb correlations of 3-D 2-e harmonic dots in magnetic field

    NASA Astrophysics Data System (ADS)

    Aggarwal, Priyanka; Sharma, Shivalika; Kaur, Harsimran; Singh, Sunny; Hazra, Ram Kuntal

    2017-01-01

    Applications of 3-D 2-e systems have proliferated very fast due to technological advancements in wide range of phenomena from atomic landscape to mesoscopic scale. The unusual properties of atomic/mesoscopic systems are the results of interplaying charge interactions among different bound states. The non-trivial e-e correlations in electrically and/or magnetically confined systems improvise wealth of intriguing challenges at fundamental level due to lack of exact solution of Schrödinger equations. For the first time, a novel methodology of exactly finite summed coulomb correlations invented by us is so handy that even usual programmable calculator can be used to examine the electronic structures of 3-D 2-e harmonic dots in perpendicular magnetic field (symmetric gauge). Statistics of electronic levels, heat capacity measurements and magnetization (T∼1 K) are also investigated in brief to probe the degree of disorderedness.

  15. Analysis and measurement of the 3D magnetic field in a rotating magnetic field driven FRC

    NASA Astrophysics Data System (ADS)

    Velas, K. M.; Milroy, R. D.

    2012-10-01

    A translatable three-axis probe was installed on TCSU shortly before its shutdown. The probe has 90 windings that simultaneously measure Br, Bθ, and Bz at 30 radial positions. Positioning the probe at multiple axial positions and taking multiple repeatable shots allows for a full r-z map of the magnetic field. Probe measurements are used to calculate the end-shorting torque and the rotating magnetic field (RMF) torque. The torque applied to the plasma is the RMF torque reduced by the shorting torque. An estimate of the plasma resistivity is made based on the steady state balance between the applied torque and the resistive torque. The steady state data from applying a 10 kHz low pass filter used in conjunction with data at the RMF frequency yields a map of the full 3D rotating field structure. Data from even- and odd-parity experiments will be presented. The NIMROD code has been adapted to simulate the TCSU experiment using boundary conditions adjusted to match both even- and odd-parity experimental conditions. A comparison of the n=0 components of the calculated fields to the 3-axis probe measurements shows agreement in the magnetic field structure of the FRC as well as in the jet region.

  16. Automated 3D structure composition for large RNAs

    PubMed Central

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

    2012-01-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

  17. Automated 3D structure composition for large RNAs.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W

    2012-08-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

  18. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

    Gong, Xingting; Cho, Yigil; Castle, Toen; Sussman, Daniel; Kamien, Randall

    2015-03-01

    The purpose of this talk is to explore how one can create 3D structures from 2D materials through the art of kirigami. Kirigami expands upon origami by allowing not only folds, but also cuts, into materials. If we take an incompressible material such as paper and remove a hole from it, the paper will buckle into the third dimension once that hole is sealed in order to relieve strain. Thus, orienting cuts and folds in certain places throughout a sheet of paper can influence its ``pop-up,'' 3D structure. To narrow down the inverse design problem, we confined ourselves to making only one kind of cut (which we call the ``5-7 cut'') on a honeycomb grid, and we show how this single cut can give rise to arbitrarily complex three dimensional structures. A simple set of rules exists: (a) one 5-7 cut divides the material into 2 sections which can choose to pop-up or down independently of each other, (b) rows of uniform cuts must pop up or down in unison, giving (nearly) arbitrary 2D structure, and (c) the 5-7 cuts can be arranged in various ways to create 6 basic pop-up ``modes,'' which can then be arranged to give (nearly) arbitrary 3D structure. These simple rules allow a framework for designing targeted 3D structure from an initial 2D sheet of material. This work was supported by NSF EFRI-ODISSEI Grant EFRI 13-31583.

  19. Coherent structures in 3D viscous time-periodic flow

    NASA Astrophysics Data System (ADS)

    Znaien, J. G.; Speetjens, M. F. M.; Trieling, R. R.; Clercx, H. J. H.

    2010-11-01

    Periodically driven laminar flows occur in many industrial processes from food-mixing devices to micro-mixer in lab-on-a-chip systems. The present study is motivated by better understanding fundamental transport phenomena in three-dimensional viscous time-periodic flows. Both numerical simulation and three-dimensional Particle Tracking Velocimetry measurements are performed to investigate the 3D advection of a passive scalar in a lid-driven cylindrical cavity flow. The flow is forced by a time-periodic in-plane motion of one endwall via a given forcing protocol. We concentrate on the formation and interaction of coherent structures due to fluid inertia, which play an important role in 3D mixing by geometrically determining the tracer transport. The disintegration of these structures by fluid inertia reflects an essentially 3D route to chaos. Data from tracking experiments of small particles will be compared with predictions from numerical simulations on transport of passive tracers.

  20. GPU-accelerated denoising of 3D magnetic resonance images

    SciTech Connect

    Howison, Mark; Wes Bethel, E.

    2014-05-29

    The raw computational power of GPU accelerators enables fast denoising of 3D MR images using bilateral filtering, anisotropic diffusion, and non-local means. In practice, applying these filtering operations requires setting multiple parameters. This study was designed to provide better guidance to practitioners for choosing the most appropriate parameters by answering two questions: what parameters yield the best denoising results in practice? And what tuning is necessary to achieve optimal performance on a modern GPU? To answer the first question, we use two different metrics, mean squared error (MSE) and mean structural similarity (MSSIM), to compare denoising quality against a reference image. Surprisingly, the best improvement in structural similarity with the bilateral filter is achieved with a small stencil size that lies within the range of real-time execution on an NVIDIA Tesla M2050 GPU. Moreover, inappropriate choices for parameters, especially scaling parameters, can yield very poor denoising performance. To answer the second question, we perform an autotuning study to empirically determine optimal memory tiling on the GPU. The variation in these results suggests that such tuning is an essential step in achieving real-time performance. These results have important implications for the real-time application of denoising to MR images in clinical settings that require fast turn-around times.

  1. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

    Additive manufacturing or 3D printing techniques are being vigorously investigated as a replacement to the traditional and conventional methods in fabrication to bring forth cost and time effective approaches. Introduction of 3D printing has led to printing micro and nanoscale structures including tissues and organelles, bioelectric sensors and devices, artificial bones and transplants, microfluidic devices, batteries and various other biomaterials. Various microfabrication processes have been developed to fabricate micro components and assemblies at lab scale. 3D Fabrication processes that can accommodate the functional and geometrical requirements to realize complicated structures are becoming feasible through advances in additive manufacturing. This advancement could lead to simpler development mechanisms of novel components and devices exhibiting complex features. For instance, development of microstructure electrodes that can penetrate the epidermis of the skin to collect the bio potential signal may prove very effective than the electrodes that measure signal from the skin's surface. The micro and nanostructures will have to possess extraordinary material and mechanical properties for its dexterity in the applications. A substantial amount of research being pursued on stretchable and flexible devices based on PDMA, textiles, and organic electronics. Despite the numerous advantages these substrates and techniques could solely offer, 3D printing enables a multi-dimensional approach towards finer and complex applications. This review emphasizes the use of 3D printing to fabricate micro and nanostructures for that can be applied for human healthcare.

  2. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

    PubMed Central

    Rahrig, Ryan R.; Petrov, Anton I.; Leontis, Neocles B.; Zirbel, Craig L.

    2013-01-01

    The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  3. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

  4. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  5. Reconstructing the Vulcano Island evolution from 3D modeling of magnetic signatures

    NASA Astrophysics Data System (ADS)

    Napoli, Rosalba; Currenti, Gilda

    2016-06-01

    High-resolution ground and marine magnetic data are exploited for a detailed definition of a 3D model of the Vulcano Island volcanic complex. The resulting 3D magnetic imaging, obtained by 3-D inverse modeling technique, has delivered useful constraints both to reconstruct the Vulcano Island evolution and to be used as input data for volcanic hazard assessment models. Our results constrained the depth and geometry of the main geo-structural features revealing more subsurface volcanic structures than exposed ones and allowing to elucidate the relationships between them. The recognition of two different magnetization sectors, approximatively coincident with the structural depressions of Piano caldera, in the southern half of the island, and La Fossa caldera at the north, suggests a complex structural and volcanic evolution. Magnetic highs identified across the southern half of the island reflect the main crystallized feeding systems, intrusions and buried vents, whose NNW-SSE preferential alignment highlights the role of the NNW-SSE Tindari-Letojanni regional system from the initial activity of the submarine edifice, to the more recent activity of the Vulcano complex. The low magnetization area, in the middle part of the island may result from hydrothermally altered rocks. Their presence not only in the central part of the volcano edifice but also in other peripheral areas, is a sign of a more diffuse historical hydrothermal activity than in present days. Moreover, the high magnetization heterogeneity within the upper flanks of La Fossa cone edifice is an imprint of a composite distribution of unaltered and altered rocks with different mechanical properties, which poses in this area a high risk level for failure processes especially during volcanic or hydrothermal crisis.

  6. RNA and protein 3D structure modeling: similarities and differences.

    PubMed

    Rother, Kristian; Rother, Magdalena; Boniecki, Michał; Puton, Tomasz; Bujnicki, Janusz M

    2011-09-01

    In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed "protein-like" modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using "protein-like" methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

  7. Strategies to reconstruct 3D Coffea arabica L. plant structure.

    PubMed

    Matsunaga, Fabio Takeshi; Tosti, Jonas Barbosa; Androcioli-Filho, Armando; Brancher, Jacques Duílio; Costes, Evelyne; Rakocevic, Miroslava

    2016-01-01

    Accurate model of structural elements is necessary to model the foliage and fruit distributions in cultivated plants, both of them being key parameters for yield prediction. However, the level of details in architectural data collection could vary, simplifying the data collection when plants get older and because of the high time cost required. In the present study, we aimed at reconstructing and analyzing plant structure, berry distributions and yield in Coffea arabica (Arabica coffee), by using both detailed or partial morphological information and probabilistic functions. Different datasets of coffee plant architectures were available with different levels of detail depending on the tree age. Three scales of decomposition-plant, axes and metamers were used reconstruct the plant architectures. CoffePlant3D, a software which integrates a series of mathematical, computational and statistical methods organized in three newly developed modules, AmostraCafe3D, VirtualCafe3D and Cafe3D, was developed to accurately reconstruct coffee plants in 3D, whatever the level of details available. The number of metamers of the 2nd order axes was shown to be linearly proportional to that of the orthotropic trunk, and the number of berries per metamer was modeled as a Gaussian function within a specific zone along the plagiotropic axes. This ratio of metamer emission rhythm between the orthotropic trunk and plagiotropic axes represents the pillar of botanical events in the C. arabica development and was central in our modeling approach, especially to reconstruct missing data. The methodology proposed for reconstructing coffee plants under the CoffePlant3D was satisfactorily validated across dataset available and could be performed for any other Arabica coffee variety.

  8. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Fang, Nicholas X.; Boyce, Mary C.

    2014-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the complex instability and wrinkling pattern arising in 3D structured composites and the effect of the buckling pattern on the overall structural response. The 3D structured composites consisted of stiffer plates supported by soft matrix on both sides. Compression beyond the critical strain led to complex buckling patterns in the initially straight plates. The motivation of our work is to elaborate the formation of a system of prescribed periodic scatterers (metamaterials) due to buckling, and their effect to interfere wave propagation through the metamaterial structures. Such metamaterials made from elastomers enable large reversible deformation and, as a result, significant changes of the wave propagation properties. We developed analytical and finite element models to capture various aspects of the instability mechanism. Mechanical experiments were designed to further explore the modeling results. The ability to actively alter the 3D composite structure can enable on-demand tunability of many different functions, such as active control of wave propagation to create band-gaps and waveguides.

  9. Structured Light-Based 3D Reconstruction System for Plants.

    PubMed

    Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima

    2015-07-29

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance.

  10. Structured Light-Based 3D Reconstruction System for Plants

    PubMed Central

    Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  11. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

    Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.

    2016-02-01

    This paper shows the first application of in situ manipulation of discontinuous fibrous structure mid-print, within a 3D printed polymeric composite architecture. Currently, rapid prototyping methods (fused filament fabrication, stereolithography) are gaining increasing popularity within the engineering commnity to build structural components. Unfortunately, the full potential of these components is limited by the mechanical properties of the materials used. The aim of this study is to create and demonstrate a novel method to instantaneously orient micro-scale glass fibres within a selectively cured photocurable resin system, using ultrasonic forces to align the fibres in the desired 3D architecture. To achieve this we have mounted a switchable, focused laser module on the carriage of a three-axis 3D printing stage, above an in-house ultrasonic alignment rig containing a mixture of photocurable resin and discontinuous 14 μm diameter glass fibre reinforcement(50 μm length). In our study, a suitable print speed of 20 mm s-1 was used, which is comparable to conventional additive layer techniques. We show the ability to construct in-plane orthogonally aligned sections printed side by side, where the precise orientation of the configurations is controlled by switching the ultrasonic standing wave profile mid-print. This approach permits the realisation of complex fibrous architectures within a 3D printed landscape. The versatile nature of the ultrasonic manipulation technique also permits a wide range of particle types (diameters, aspect ratios and functions) and architectures (in-plane, and out-plane) to be patterned, leading to the creation of a new generation of fibrous reinforced composites for 3D printing.

  12. Joint inversions of two VTEM surveys using quasi-3D TDEM and 3D magnetic inversion algorithms

    NASA Astrophysics Data System (ADS)

    Kaminski, Vlad; Di Massa, Domenico; Viezzoli, Andrea

    2016-05-01

    In the current paper, we present results of a joint quasi-three-dimensional (quasi-3D) inversion of two versatile time domain electromagnetic (VTEM) datasets, as well as a joint 3D inversion of associated aeromagnetic datasets, from two surveys flown six years apart from one another (2007 and 2013) over a volcanogenic massive sulphide gold (VMS-Au) prospect in northern Ontario, Canada. The time domain electromagnetic (TDEM) data were inverted jointly using the spatially constrained inversion (SCI) approach. In order to increase the coherency in the model space, a calibration parameter was added. This was followed by a joint inversion of the total magnetic intensity (TMI) data extracted from the two surveys. The results of the inversions have been studied and matched with the known geology, adding some new valuable information to the ongoing mineral exploration initiative.

  13. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

    Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

  14. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  15. Cancer3D: understanding cancer mutations through protein structures.

    PubMed

    Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution.

  16. The 3D lightweight structural characteristics of the beetle forewing.

    PubMed

    Chen, Jinxiang; Tuo, Wanyong; Guo, Zhensheng; Yan, Lili

    2017-02-01

    The present paper renewedly expounds upon the characteristics of the 3D lightweight structure of beetle forewings and notes that two biomimetic structures (models) that have appeared in recent years do not comply with these characteristics based on a comparison of the structures of the biological prototypes. The first model features transverse tubules based on observations of circular holes in cross-sectional figures of the Cybister forewing. The second is a biomimetic spherical cavity model with hollow trabeculae that reportedly exhibits superior mechanical properties because its structures are most similar to the biological prototype. Finally, a false biomimetic proposition that the mechanical properties of biomimetic structures with "fiber winding" patterns are superior to those of structures constructed of pure "epoxy" is also noted. Hopefully, the present study can serve to improve the state of research on biomimetic applications of beetle forewing structures.

  17. Dynactin 3D structure: implications for assembly and dynein binding.

    PubMed

    Imai, Hiroshi; Narita, Akihiro; Maéda, Yuichiro; Schroer, Trina A

    2014-09-23

    The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification.

  18. Magnetic reconnection in 3D magnetosphere models: magnetic separators and open flux production

    NASA Astrophysics Data System (ADS)

    Glocer, A.; Dorelli, J.; Toth, G.; Komar, C. M.; Cassak, P.

    2014-12-01

    There are multiple competing definitions of magnetic reconnection in 3D (e.g., Hesse and Schindler [1988], Lau and Finn [1990], and Boozer [2002]). In this work we focus on separator reconnection. A magnetic separator can be understood as the 3D analogue of a 2D x line with a guide field, and is defined by the line corresponding to the intersection of the separatrix surfaces associated with the magnetic nulls. A separator in the magnetosphere represents the intersection of four distinct magnetic topologies: solar wind, closed, open connected to the northern hemisphere, and open connected to the southern hemisphere. The integral of the parallel electric field along the separator defines the rate of open flux production, and is one measure of the reconnection rate. We present three methods for locating magnetic separators and apply them to 3D resistive MHD simulations of the Earth's magnetosphere using the BATS-R-US code. The techniques for finding separators and determining the reconnection rate are insensitive to IMF clock angle and can in principle be applied to any magnetospheric model. The present work examines cases of high and low resistivity, for two clock angles. We also examine the separator during Flux Transfer Events (FTEs) and Kelvin-Helmholtz instability.

  19. Optimization of a Hybrid Magnetic Bearing for a Magnetically Levitated Blood Pump via 3-D FEA

    PubMed Central

    Cheng, Shanbao; Olles, Mark W.; Burger, Aaron F.; Day, Steven W.

    2011-01-01

    In order to improve the performance of a magnetically levitated (maglev) axial flow blood pump, three-dimensional (3-D) finite element analysis (FEA) was used to optimize the design of a hybrid magnetic bearing (HMB). Radial, axial, and current stiffness of multiple design variations of the HMB were calculated using a 3-D FEA package and verified by experimental results. As compared with the original design, the optimized HMB had twice the axial stiffness with the resulting increase of negative radial stiffness partially compensated for by increased current stiffness. Accordingly, the performance of the maglev axial flow blood pump with the optimized HMBs was improved: the maximum pump speed was increased from 6000 rpm to 9000 rpm (50%). The radial, axial and current stiffness of the HMB was found to be linear at nominal operational position from both 3-D FEA and empirical measurements. Stiffness values determined by FEA and empirical measurements agreed well with one another. The magnetic flux density distribution and flux loop of the HMB were also visualized via 3-D FEA which confirms the designers’ initial assumption about the function of this HMB. PMID:22065892

  20. Optimization of a Hybrid Magnetic Bearing for a Magnetically Levitated Blood Pump via 3-D FEA.

    PubMed

    Cheng, Shanbao; Olles, Mark W; Burger, Aaron F; Day, Steven W

    2011-10-01

    In order to improve the performance of a magnetically levitated (maglev) axial flow blood pump, three-dimensional (3-D) finite element analysis (FEA) was used to optimize the design of a hybrid magnetic bearing (HMB). Radial, axial, and current stiffness of multiple design variations of the HMB were calculated using a 3-D FEA package and verified by experimental results. As compared with the original design, the optimized HMB had twice the axial stiffness with the resulting increase of negative radial stiffness partially compensated for by increased current stiffness. Accordingly, the performance of the maglev axial flow blood pump with the optimized HMBs was improved: the maximum pump speed was increased from 6000 rpm to 9000 rpm (50%). The radial, axial and current stiffness of the HMB was found to be linear at nominal operational position from both 3-D FEA and empirical measurements. Stiffness values determined by FEA and empirical measurements agreed well with one another. The magnetic flux density distribution and flux loop of the HMB were also visualized via 3-D FEA which confirms the designers' initial assumption about the function of this HMB.

  1. Edge structure preserving 3D image denoising by local surface approximation.

    PubMed

    Qiu, Peihua; Mukherjee, Partha Sarathi

    2012-08-01

    In various applications, including magnetic resonance imaging (MRI) and functional MRI (fMRI), 3D images are becoming increasingly popular. To improve the reliability of subsequent image analyses, 3D image denoising is often a necessary preprocessing step, which is the focus of the current paper. In the literature, most existing image denoising procedures are for 2D images. Their direct extensions to 3D cases generally cannot handle 3D images efficiently because the structure of a typical 3D image is substantially more complicated than that of a typical 2D image. For instance, edge locations are surfaces in 3D cases which would be much more challenging to handle compared to edge curves in 2D cases. We propose a novel 3D image denoising procedure in this paper, based on local approximation of the edge surfaces using a set of surface templates. An important property of this method is that it can preserve edges and major edge structures (e.g., intersections of two edge surfaces and pointed corners). Numerical studies show that it works well in various applications.

  2. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  3. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe

    2007-09-01

    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  4. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

    A new image matching technique is described. It is implemented as an object-independent hierarchical structural juxtaposition algorithm based on an alphabet of simple object-independent contour structural elements. The structural matching applied implements an optimized method of walking through a truncated tree of all possible juxtapositions of two sets of structural elements. The algorithm was initially developed for dealing with 2D images such as the aerospace photographs, and it turned out to be sufficiently robust and reliable for matching successfully the pictures of natural landscapes taken in differing seasons from differing aspect angles by differing sensors (the visible optical, IR, and SAR pictures, as well as the depth maps and geographical vector-type maps). At present (in the reported version), the algorithm is enhanced based on additional use of information on third spatial coordinates of observed points of object surfaces. Thus, it is now capable of matching the images of 3D scenes in the tasks of automatic navigation of extremely low flying unmanned vehicles or autonomous terrestrial robots. The basic principles of 3D structural description and matching of images are described, and the examples of image matching are presented.

  5. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  6. An endoscopic 3D scanner based on structured light.

    PubMed

    Schmalz, Christoph; Forster, Frank; Schick, Anton; Angelopoulou, Elli

    2012-07-01

    We present a new endoscopic 3D scanning system based on Single Shot Structured Light. The proposed design makes it possible to build an extremely small scanner. The sensor head contains a catadioptric camera and a pattern projection unit. The paper describes the working principle and calibration procedure of the sensor. The prototype sensor head has a diameter of only 3.6mm and a length of 14mm. It is mounted on a flexible shaft. The scanner is designed for tubular cavities and has a cylindrical working volume of about 30mm length and 30mm diameter. It acquires 3D video at 30 frames per second and typically generates approximately 5000 3D points per frame. By design, the resolution varies over the working volume, but is generally better than 200μm. A prototype scanner has been built and is evaluated in experiments with phantoms and biological samples. The recorded average error on a known test object was 92μm.

  7. 3-D Attenuation Structure around the SAFOD site, Parkfield, California

    NASA Astrophysics Data System (ADS)

    Harrington, N. L.; Thurber, C. H.; Zhang, H.; Roecker, S.

    2006-12-01

    We are developing models of the 3-D attenuation structure, both Qp and Qs, for a region about 15 km square centered on SAFOD. We are analyzing local earthquake data collected in 2001 and 2002 from the UW/RPI PASO array, the UC-Berkeley HRSN, and USGS seismic network stations around Parkfield. We determine the P- or S-wave t* values for an individual local earthquake for each of the observing stations by fitting observed spectra using a joint inversion for a common corner frequency, low-frequency amplitude, and t*. Within our initial data set, we examine 575 events recorded at up to 111 stations and obtain over 19000 P- wave t* values. We use these t* values in simul2000 and tomoDD to perform the inversion to obtain a 3-D, frequency-independent Qp model of the attenuation structure, using an existing 3-D Vp model and associated event locations. We will use this same procedure to obtain the Qs structure. In our preliminary Qp structure results, we observe a high Qp feature (about 250) at 0-8 km depth on the southwest side of the fault. We associate this feature with the high density, high velocity Salinian basement rocks. We also see a moderate Qp feature (about 150) in the fault zone that encompasses the hypocenters of our events. On the northeast side of the fault, we observe Qp values generally increasing with depth, from 125 at the surface to 200 at 8 km. We will present our final Qp and Qs models, identify major features within the two, and discuss how these features relate to the findings of other geophysical studies in the area (seismic velocity, electrical resistivity, anisotropy). We will discuss how these features relate to the nature of the crust in that area, including the local geology, presence of fluids, fracturing, etc.

  8. Effects of 3D Toroidally Asymmetric Magnetic Field on Tokamak Magnetic Surfaces

    NASA Astrophysics Data System (ADS)

    Lao, L. L.

    2005-10-01

    The effects of 3D error magnetic field on magnetic surfaces are investigated using the DIII-D internal coils (I-Coils). Slowly rotating n=1 traveling waves at 5 Hz and various amplitudes were applied to systematically perturb the edge surfaces by programming the I-Coil currents. The vertical separatrix location difference between EFIT magnetic reconstructions that assumes toroidal symmetry and Thomson scattering Te measurements responds in phase to the applied perturbed field. The oscillation amplitudes increase with the strength of the applied field but are much smaller than those expected from the applied field alone. The results indicate that plasma response is important. Various plasma response models based on results from the MHD codes MARS and GATO are being developed and compared to the experimental observations. To more accurately evaluate the effects of magnetic measurement errors, a new form of the magnetic uncertainty matrix is also being implemented into EFIT. Details will be presented.

  9. DIII-D Equilibrium Reconstructions with New 3D Magnetic Probes

    NASA Astrophysics Data System (ADS)

    Lao, Lang; Strait, E. J.; Ferraro, N. M.; Ferron, J. R.; King, J. D.; Lee, X.; Meneghini, O.; Turnbull, A. D.; Huang, Y.; Qian, J. G.; Wingen, A.

    2015-11-01

    DIII-D equilibrium reconstructions with the recently installed new 3D magnetic diagnostic are presented. In addition to providing information to allow more accurate 2D reconstructions, the new 3D probes also provide useful information to guide computation of 3D perturbed equilibria. A new more comprehensive magnetic compensation has been implemented. Algorithms are being developed to allow EFIT to reconstruct 3D perturbed equilibria making use of the new 3D probes and plasma responses from 3D MHD codes such as GATO and M3D-C1. To improve the computation efficiency, all inactive probes in one of the toroidal planes in EFIT have been replaced with new probes from other planes. Other 3D efforts include testing of 3D reconstructions using V3FIT and a new 3D variational moment equilibrium code VMOM3D. Other EFIT developments include a GPU EFIT version and new safety factor and MSE-LS constraints. The accuracy and limitation of the new probes for 3D reconstructions will be discussed. Supported by US DOE under DE-FC02-04ER54698 and DE-FG02-95ER54309.

  10. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

  11. Water linked 3D coordination polymers: Syntheses, structures and applications

    NASA Astrophysics Data System (ADS)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

    Three new coordination polymers (CPs) based on Cd and Pb, [Cd(OBA)(μ-H2O)(H2O)]n1, [Pb(OBA)(μ-H2O)]n2 [where OBA=4,4'-Oxybis(benzoate)] and [Pb(SDBA)(H2O)]n.1/4DMF 3 (SDBA=4,4'-Sulfonyldibenzoate), have been synthesized and characterized. The single crystal structural studies reveal that CPs 1 and 2 have three dimensional structure. A water molecule bridges two metal centres which appears to the responsible for the dimensionality increase from 2D to 3D. Compound 3 has a supramolecular 3D structure involving water molecule and hydrogen bonds. A structural transformation is observed when 3 was heated at 100 °C or kept in methanol, forming [Pb(SDBA)]n4. Compound 4 is used as supporting matrix for palladium nanoparticles, PdNPs@4. The PdNPs@4 exhibits good catalytic activity toward the reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) in the presence of NaBH4 at room temperature. Luminescence studies revealed that all CPs could be an effective sensor for nitroaromatic explosives.

  12. Fast 3D fluid registration of brain magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Leporé, Natasha; Chou, Yi-Yu; Lopez, Oscar L.; Aizenstein, Howard J.; Becker, James T.; Toga, Arthur W.; Thompson, Paul M.

    2008-03-01

    Fluid registration is widely used in medical imaging to track anatomical changes, to correct image distortions, and to integrate multi-modality data. Fluid mappings guarantee that the template image deforms smoothly into the target, without tearing or folding, even when large deformations are required for accurate matching. Here we implemented an intensity-based fluid registration algorithm, accelerated by using a filter designed by Bro-Nielsen and Gramkow. We validated the algorithm on 2D and 3D geometric phantoms using the mean square difference between the final registered image and target as a measure of the accuracy of the registration. In tests on phantom images with different levels of overlap, varying amounts of Gaussian noise, and different intensity gradients, the fluid method outperformed a more commonly used elastic registration method, both in terms of accuracy and in avoiding topological errors during deformation. We also studied the effect of varying the viscosity coefficients in the viscous fluid equation, to optimize registration accuracy. Finally, we applied the fluid registration algorithm to a dataset of 2D binary corpus callosum images and 3D volumetric brain MRIs from 14 healthy individuals to assess its accuracy and robustness.

  13. Contiguous 3 d and 4 f Magnetism: Strongly Correlated 3 d Electrons in YbFe2Al10

    NASA Astrophysics Data System (ADS)

    Khuntia, P.; Peratheepan, P.; Strydom, A. M.; Utsumi, Y.; Ko, K.-T.; Tsuei, K.-D.; Tjeng, L. H.; Steglich, F.; Baenitz, M.

    2014-11-01

    We present magnetization, specific heat, and Al 27 NMR investigations on YbFe2Al10 over a wide range in temperature and magnetic field. The magnetic susceptibility at low temperatures is strongly enhanced at weak magnetic fields, accompanied by a ln (T0/T ) divergence of the low-T specific heat coefficient in zero field, which indicates a ground state of correlated electrons. From our hard-x-ray photoemission spectroscopy study, the Yb valence at 50 K is evaluated to be 2.38. The system displays valence fluctuating behavior in the low to intermediate temperature range, whereas above 400 K, Yb3 + carries a full and stable moment, and Fe carries a moment of about 3.1 μB. The enhanced value of the Sommerfeld-Wilson ratio and the dynamic scaling of the spin-lattice relaxation rate divided by T [(1 /T1T ) 27 ] with static susceptibility suggests admixed ferromagnetic correlations. (1 /T1T ) 27 simultaneously tracks the valence fluctuations from the 4 f Yb ions in the high temperature range and field dependent antiferromagnetic correlations among partially Kondo screened Fe 3 d moments at low temperature; the latter evolve out of an Yb 4 f admixed conduction band.

  14. A 3D Current Loop Model of Magnetic Clouds

    NASA Astrophysics Data System (ADS)

    Chen, James

    1992-05-01

    A magnetohydrodynamic (MHD) model is developed to study magnetic clouds (Burlaga et al. 1981). In this model, magnetic clouds observed near 1 AU are treated as a consequence of eruptive solar current loops. It is shown that current loops intially in MHD equilibrium can be triggered to rise rapidly, propelling material of up to 10(16) g at up to ~ 1000 km s(-1) and dissipating ~ 10(32) erg of magnetic energy in tens of minutes. The initial rise profile is consistent with observed height-time profiles of erupting filaments (Kahler et al. 1988). Two triggering mechanisms for eruption are suggested: (1)subphotospheric energy storage and trigger and (2) in situ (coronal) energy storage and trigger. In the former, eruption occurs as a result of changes in the subphotospheric magnetic topology and subsequent relaxation to a new equilibrium. In the latter, the current loop can evolve to exceed a local maximum in the magnetic potential associated with the ambient magnetic fields. The former scenario leads to more energetic and longer-lasting eruption than the latter. Burlaga, L. F., Sittler, E., Mariani, F., and Schwenn, R. 1981, J. Geophys. Res., 86, 6673. Kahler, S. W., Moore, R. L., Kane, S. R., and Zirin, H. 1988, Ap. J., 328, 824.

  15. 3D stochastic joint inversion of gravity and magnetic data

    NASA Astrophysics Data System (ADS)

    Shamsipour, Pejman; Marcotte, Denis; Chouteau, Michel

    2012-04-01

    A novel stochastic joint inversion method based on cokriging is applied to estimate density and magnetic susceptibility distributions from gravity and total magnetic field data. The method fully integrates the physical relations between density-gravity, on one hand, and magnetic susceptibility-total magnetic field, on the other hand. As a consequence, when the data are considered noise-free, the responses from the inverted density and susceptibility data exactly reproduce the observed data. The required density and magnetic susceptibility auto- and cross covariance are assumed to follow a linear model of coregionalization (LCM). The parameters of the LCM are estimated from v-v plot fitting of the gravity and total magnetic experimental covariances. The model is tested on two synthetic cases and one real data set, the Perseverance mine (Quebec, Canada). Joint inversions are compared to separate inversions. The joint inversions better recover the known models in the synthetic cases. With the real data set, better definition and location of the mineralized lenses are achieved by joint inversion.

  16. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  17. Effect of Resonant Magnetic Perturbations on 3D equilibria in the MST RFP

    NASA Astrophysics Data System (ADS)

    Munaretto, Stefano

    2015-11-01

    The orientation of 3D, stellarator-like equilibria in the MST RFP can now be controlled with application of an m = 1 RMP. This has led to greatly improved diagnosis, revealing enhancements in both the central electron temperature and density. Coupled to a recent advance in the V3FIT code, reconstructions of the 3D equilibria have also been dramatically improved. The RMP also inhibits the generation of high-energy >20 keV electrons that is otherwise common with the 3D state. This state occurs when the normally broad spectrum of core-resonant m = 1 tearing modes condenses, with the innermost resonant mode growing to large amplitude, reaching ~ 8% of the axisymmetric field strength. This occurs in plasmas of sufficiently large Lundquist number ~ IpTe3/2, and the duration of the state is maximized with zero applied Bt (infinite toroidal beta). As the dominant mode grows, eddy current in MST's conducting shell slows the mode's rotation. This leads to locking of the 3D structure, but with an orientation that varies randomly shot to shot, making diagnosis difficult. An m = 1 RMP can now be applied with an array of saddle coils at the vertical insulated cut in the shell. With an amplitude br/B ~ 10% and a tailored temporal waveform, the RMP can force the 3D structure into any desired orientation relative to MST's diagnostics. A recent advance in V3FIT allows calculation of the substantial helical image current flowing in MST's shell, which has in turn allowed self-consistent utilization of both external and internal (Faraday rotation) measurements of the magnetic field. The ORBIT code predicts reduced stochasticity and improved confinement of high-energy electrons within the 3D structure. The suppression of these electrons by the m = 1 RMP may reflect a change to the central magnetic topology. The generation of these electrons is unaffected by non-resonant perturbations, such as m = 3. Supported by the US DOE.

  18. A symmetric, triply interlaced 3-D anionic MOF that exhibits both magnetic order and SMM behaviour.

    PubMed

    Campo, J; Falvello, L R; Forcén-Vázquez, E; Sáenz de Pipaón, C; Palacio, F; Tomás, M

    2016-11-14

    A newly prepared 3-D polymer of cobalt citrate cubanes bridged by high-spin Co(ii) centres displays both single-molecule magnet (SMM) behaviour and magnetic ordering. Triple interpenetration of the 3-D diamondoid polymers yields a crystalline solid with channels that host cations and free water molecules, with the SMM behaviour of the Co4O4 cores preserved. The octahedrally coordinated Co(ii) bridges are implicated in the onset of magnetic order at an experimentally accessible temperature.

  19. Analysis of the 3D magnetic field and its errors for undulators with iron poles

    SciTech Connect

    Ingold, G.; Bahrdt, J.; Gaupp, A.

    1995-12-31

    The attainable field strength and field quality, such as the optical phase error, the electron beam displacement within the undulator and higher order multipoles of the magnetic field, are discussed. These issues are critical to the design and construction of short period undulators for use in short wavelength FEL or for operation in third generation light sources. We discuss two approaches: (i) For superferric undulators the construction of a full length device would rely on the optimum sorting of precision machined undulator segments. Magnetic data on segments with 20 periods (period length 8.80mm) will be presented. (ii) For hybrid undulators the sorting has to be done on individual poles and magnets. For this approach typical error sources such as machining tolerances, magnetization errors of the permanent magnet material and assembly errors are modeled in 3D and compared to induced errors on an existing hybrid undulator segment. In case of undulators having a full length of hundred periods at least five times as many individual parts have to be characterized. This should be done automatically where both the mechanical and magnetic data before and after the assembly of the magnetic structure are recorded in one step. A CNC programmable measuring device suitable for this task will shortly be presented.

  20. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  1. A Magnetic Diagnostic Code for 3D Fusion Equilibria

    SciTech Connect

    Samuel A. Lazerson, S. Sakakibara and Y. Suzuki

    2013-03-12

    A synthetic magnetic diagnostics code for fusion equilibria is presented. This code calculates the response of various magnetic diagnostics to the equilibria produced by the VMEC and PIES codes. This allows for treatment of equilibria with both good nested flux surfaces and those with stochastic regions. DIAGNO v2.0 builds upon previous codes through the implementation of a virtual casing principle. The code is validated against a vacuum shot on the Large Helical Device (LHD) where the vertical field was ramped. As an exercise of the code, the diagnostic response for various equilibria are calculated on the LHD.

  2. Structural analysis of tropical cyclone using INSAT-3D observations

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

    The continuous observations from visible and thermal infrared (TIR) channels of geostationary satellites are highly useful for obtaining the features associated with the shape and dynamics of cloud structures within the tropical cyclones (TCs). As TC develops from an unstructured cloud cluster and intensifies, the cloud structures become more axisymmetric around the centre of the TC. To better understand the structure of TC during different stages of its evolution i.e. from its cyclogenesis to maturity and dissipation, the continuous satellite observations plays a key role. The high spatial and temporal resolution observations from geostationary satellites are very useful in order to analyze the cloud organization during the cyclogenesis. The gradient of the brightness temperatures measures the level of symmetry of each structure, which characterizes the degree of cloud organization of the TC. In the present work, the structural analysis of TC during its life period using the observations from Indian geostationary satellite INSAT-3D has been discussed. The visible and TIR observations from INSAT-3D satellite were used to fix the center position of the cyclone which is an input for the cyclone track and intensity prediction models. This data is also used to estimate the intensity of cyclone in the advanced Dvorak technique (ADT), and in the estimation of radius of maximum winds (Rmax) of TC which is an essential input parameter for the prediction of storm surge associated to the cyclones. The different patterns of cloud structure during the intensification stage, eye-wall formation and dissipation have been discussed. The early identification of these features helps in predicting the rapid intensification of TC which in turn improves the intensity predictions.

  3. Protein 3D structure computed from evolutionary sequence variation.

    PubMed

    Marks, Debora S; Colwell, Lucy J; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures

  4. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  5. 3D Printing of Hierarchical Silk Fibroin Structures.

    PubMed

    Sommer, Marianne R; Schaffner, Manuel; Carnelli, Davide; Studart, André R

    2016-12-21

    Like many other natural materials, silk is hierarchically structured from the amino acid level up to the cocoon or spider web macroscopic structures. Despite being used industrially in a number of applications, hierarchically structured silk fibroin objects with a similar degree of architectural control as in natural structures have not been produced yet due to limitations in fabrication processes. In a combined top-down and bottom-up approach, we exploit the freedom in macroscopic design offered by 3D printing and the template-guided assembly of ink building blocks at the meso- and nanolevel to fabricate hierarchical silk porous materials with unprecedented structural control. Pores with tunable sizes in the range 40-350 μm are generated by adding sacrificial organic microparticles as templates to a silk fibroin-based ink. Commercially available wax particles or monodisperse polycaprolactone made by microfluidics can be used as microparticle templates. Since closed pores are generated after template removal, an ultrasonication treatment can optionally be used to achieve open porosity. Such pore templating particles can be further modified with nanoparticles to create a hierarchical template that results in porous structures with a defined nanotopography on the pore walls. The hierarchically porous silk structures obtained with this processing technique can potentially be utilized in various application fields from structural materials to thermal insulation to tissue engineering scaffolds.

  6. Diagnosis and control of 3D elastic mechanical structures

    NASA Astrophysics Data System (ADS)

    Krajcin, Idriz; Soeffker, Dirk

    2005-05-01

    In this paper, a model-based approach for fault detection and vibration control of flexible structures is proposed and applied to 3D-structures. Faults like cracks or impacts acting on a flexible structure are considered as unknown inputs acting on the structure. The Proportional-Integral-Observer (PI-Observer) is used to estimate the system states as well as unknown inputs acting on a system. Also the effects of structural changes are understood as external effects (related to the unchanged structure) and are considered as fictitious external forces or moments. The paper deals with the design of the PI-Observer for practical applications when measurement noise and model uncertainties are present and shows its performance in experimental results. As examples, impacts acting upon a one side clamped elastic beam and on a thin plate structure are estimated using displacement or strain measurements. To control the vibration of the flexible plate, two piezoelectric patches bonded on the structure are used as actuators. The control algorithm introduced in this contribution contains a state feedback control and additionally a disturbance rejection. The disturbances are estimated using the PI-Observer. Experimental results show the performance and the robustness properties of the control strategy for the vibration control of a very thin plate.

  7. 3D and 4D magnetic susceptibility tomography based on complex MR images

    DOEpatents

    Chen, Zikuan; Calhoun, Vince D

    2014-11-11

    Magnetic susceptibility is the physical property for T2*-weighted magnetic resonance imaging (T2*MRI). The invention relates to methods for reconstructing an internal distribution (3D map) of magnetic susceptibility values, .chi. (x,y,z), of an object, from 3D T2*MRI phase images, by using Computed Inverse Magnetic Resonance Imaging (CIMRI) tomography. The CIMRI technique solves the inverse problem of the 3D convolution by executing a 3D Total Variation (TV) regularized iterative convolution scheme, using a split Bregman iteration algorithm. The reconstruction of .chi. (x,y,z) can be designed for low-pass, band-pass, and high-pass features by using a convolution kernel that is modified from the standard dipole kernel. Multiple reconstructions can be implemented in parallel, and averaging the reconstructions can suppress noise. 4D dynamic magnetic susceptibility tomography can be implemented by reconstructing a 3D susceptibility volume from a 3D phase volume by performing 3D CIMRI magnetic susceptibility tomography at each snapshot time.

  8. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

    Clancy, Neil T.; Lin, Jianyu; Arya, Shobhit; Hanna, George B.; Elson, Daniel S.

    2015-03-01

    Intraoperative feedback on tissue function, such as blood volume and oxygenation would be useful to the surgeon in cases where current clinical practice relies on subjective measures, such as identification of ischaemic bowel or tissue viability during anastomosis formation. Also, tissue surface profiling may be used to detect and identify certain pathologies, as well as diagnosing aspects of tissue health such as gut motility. In this paper a dual modality laparoscopic system is presented that combines multispectral reflectance and 3D surface imaging. White light illumination from a xenon source is detected by a laparoscope-mounted fast filter wheel camera to assemble a multispectral image (MSI) cube. Surface shape is then calculated using a spectrally-encoded structured light (SL) pattern detected by the same camera and triangulated using an active stereo technique. Images of porcine small bowel were acquired during open surgery. Tissue reflectance spectra were acquired and blood volume was calculated at each spatial pixel across the bowel wall and mesentery. SL features were segmented and identified using a `normalised cut' algoritm and the colour vector of each spot. Using the 3D geometry defined by the camera coordinate system the multispectral data could be overlaid onto the surface mesh. Dual MSI and SL imaging has the potential to provide augmented views to the surgeon supplying diagnostic information related to blood supply health and organ function. Future work on this system will include filter optimisation to reduce noise in tissue optical property measurement, and minimise spot identification errors in the SL pattern.

  9. Tuning the Origin of Magnetic Relaxation by Substituting the 3d or Rare-Earth Ions into Three Isostructural Cyano-Bridged 3d-4f Heterodinuclear Compounds.

    PubMed

    Zhang, Yan; Guo, Zhen; Xie, Shuang; Li, Hui-Li; Zhu, Wen-Hua; Liu, Li; Dong, Xun-Qing; He, Wei-Xun; Ren, Jin-Chao; Liu, Ling-Zhi; Powell, Annie K

    2015-11-02

    Three isostructural cyano-bridged 3d-4f compounds, [YFe(CN)6(hep)2(H2O)4] (1), [DyFe(CN)6(hep)2(H2O)4] (2), and [DyCo(CN)6(hep)2(H2O)4] (3), were successfully assembled by site-targeted substitution of the 3d or rare-earth ions. All compounds have been structurally characterized to display slightly distorted pentagonal-bipyramidal local coordination geometry around the rare-earth ions. Magnetic analyses revealed negligible magnetic coupling in compound 1, antiferromagnetic intradimer interaction in 2, and weak ferromagnetic coupling through dipolar-dipolar interaction in 3. Under an applied direct-current (dc) field, 1 (Hdc = 2.5 kOe, τ0 = 1.3 × 10(-7) s, and Ueff/kB = 23 K) and 3 (Hdc = 2.0 kOe, τ0 = 7.1 × 10(-11) s, and Ueff/kB = 63 K) respectively indicated magnetic relaxation behavior based on a single [Fe(III)]LS ion and a Dy(III) ion; nevertheless, 2 (Hdc = 2.0 kOe, τ0 = 9.7 × 10(-8) s, and Ueff/kB = 23 K) appeared to be a single-molecule magnet based on a cyano-bridged DyFe dimer. Compound 1, which can be regarded as a single-ion magnet of the [Fe(III)]LS ion linked to a diamagnetic Y(III) ion in a cyano-bridged heterodimer, represents one of the rarely investigated examples based on a single Fe(III) ion explored in magnetic relaxation behavior. It demonstrated that the introduction of intradimer magnetic interaction of 2 through a cyano bridge between Dy(III) and [Fe(III)]LS ions negatively affects the energy barrier and χ″(T) peak temperature compared to 3.

  10. 3-D joint inversion of the magnetotelluric phase tensor and vertical magnetic transfer functions

    NASA Astrophysics Data System (ADS)

    Tietze, Kristina; Ritter, Oliver; Egbert, Gary D.

    2015-11-01

    With advancing computational resources, 3-D inversion techniques have become feasible in recent years and are now a more widely used tool for magnetotelluric (MT) data interpretation. Galvanic distortion caused by small-scale near-surface inhomogeneities remains an obstacle for 3-D MT inversion which so far has experienced little attention. If not considered properly, the effect on 3-D inversion can be immense and result in erroneous subsurface models and interpretations. To tackle the problem we implemented inversion of the distortion-free phase tensor into the ModEM inversion package. The dimensionless phase tensor components describe only variations of the conductivity structure. When inverting these data, particular care has to be taken of the conductivity structure in the a priori model, which provides the reference frame when transferring the information from phase tensors into absolute conductivity values. Our results obtained with synthetic data show that phase tensor inversion can recover the regional conductivity structure in presence of galvanic distortion if the a priori model provides a reasonable assumption for the regional resistivity average. Joint inversion of phase tensor data and vertical magnetic transfer functions improves recovery of the absolute resistivity structure and is less dependent on the prior model. We also used phase tensor inversion for a data set of more than 250 MT sites from the central San Andreas fault, California, where a number of sites showed significant galvanic distortion. We find the regional structure of the phase tensor inversion results compatible with previously obtained models from impedance inversion. In the vicinity of distorted sites, phase tensor inversion models exhibit more homogeneous/smoother conductivity structures.

  11. Statistical Flux Tube Properties of 3D Magnetic Carpet Fields

    NASA Astrophysics Data System (ADS)

    Close, R. M.; Parnell, C. E.; Mackay, D. H.; Priest, E. R.

    2003-02-01

    The quiet-Sun photosphere consists of numerous magnetic flux fragments of both polarities that evolve with granular and supergranular flow fields. These concentrations give rise to a web of intermingled magnetic flux tubes which characterise the coronal magnetic field. Here, the nature of these flux tubes is studied. The photosphere is taken to be the source plane and each photospheric fragment is represented by a series of point sources. By analysing the potential field produced by these sources, it is found that the distribution of flux tube lengths obtained by (i) integrating forward from positive sources and (ii) tracing back from negative sources is highly dependent on the total flux imbalance within the region of interest. It is established that the relation between the footpoint separation of a flux tube and its height cannot be assumed to be linear. Where there is a significant imbalance of flux within a region, it is found that fragments of the dominant polarity will have noticeably more connections, on average, than the minority polarity fragments. Despite this difference, the flux from a single fragment of either polarity is typically divided such that (i) 60-70% connects to one opposite-polarity fragment, (ii) 25-30% goes to a further 1 to 2 opposite-polarity fragments, and (iii) any remaining flux may connect to as many as another 50 or more other opposite-polarity fragments. This is true regardless of any flux imbalance within the region. It is found that fragments connect preferentially to their nearest neighbours, with, on average, around 60-70% of flux closing down within 10 Mm of a typical fragment. Only 50% of the flux in a quiet region extends higher than 2.5 Mm above the solar surface and 5-10% extends higher than 25 Mm. The fragments that contribute to the field above this height cover a range of sizes, with even the smallest of fragments contributing to the field at heights of over 50 Mm.

  12. POISs3: A 3D poisson smoother of structured grids

    NASA Astrophysics Data System (ADS)

    Lehtimaeki, R.

    Flow solvers based on solving Navier-Stokes or Euler equations generally need a computational grid to represent the domain of the flow. A structured computational grid can be efficiently produced by algebraic methods like transfinite interpolation. Unfortunately, algebraic methods propagate all kinds of unsmoothness of the boundary into the field. Unsmoothness of the grid, in turn, can result in inaccuracy in the flow solver. In the present work a 3D elliptic grid smoother was developed. The smoother is based on solving three Poisson equations, one for each curvilinear direction. The Poisson equations formed in the physical region are first transformed to the computational (rectilinear) region. The resulting equations form a system of three coupled elliptic quasi-linear partial differential equations in the computational domain. A short review of the Poisson method is presented. The regularity of a grid cell is studied and a skewness value is developed.

  13. Online reconstruction of 3D magnetic particle imaging data

    NASA Astrophysics Data System (ADS)

    Knopp, T.; Hofmann, M.

    2016-06-01

    Magnetic particle imaging is a quantitative functional imaging technique that allows imaging of the spatial distribution of super-paramagnetic iron oxide particles at high temporal resolution. The raw data acquisition can be performed at frame rates of more than 40 volumes s-1. However, to date image reconstruction is performed in an offline step and thus no direct feedback is available during the experiment. Considering potential interventional applications such direct feedback would be mandatory. In this work, an online reconstruction framework is implemented that allows direct visualization of the particle distribution on the screen of the acquisition computer with a latency of about 2 s. The reconstruction process is adaptive and performs block-averaging in order to optimize the signal quality for a given amount of reconstruction time.

  14. 3D Magnetic Measurements of Kink and Locked Modes in DIII-D

    NASA Astrophysics Data System (ADS)

    King, J. D.; Strait, E. J.; Hanson, J. M.; Paz-Soldan, C.; Logan, N. C.; Lanctot, M. J.; Shiraki, D.

    2013-10-01

    The DIII-D magnetics diagnostic has been greatly expanded to fully characterize non-axisymmetric ``3D'' fields. Five poloidal locations now recover n <= 3 , while new HFS arrays provide poloidal spectral resolution of 7.4 cm. Initial measurements suggest externally driven kink structures deviate from MARS-F and IPEC models. These variations extend to the ideal regime, where toroidal agreement is observed. The plasma response to an n = 3 RMP increases monotonically as beta increases and q95 decreases, contrary to predictions of a screening to kink valley. Finally, the temporal evolution of the 3D eigenstructure of a slowly rotating (5 Hz) quasi-static, born locked, tearing mode provides the first evidence of an appreciable n = 2 error field, and an estimate of the phase for future correction. This new 3D capability will be used to understand and optimize control of RWMs, NTV torque, ELMs, and error field correction to extend stable tokamak operation. Work supported in part by the US Department of Energy under DE-AC05-00OR22725, DE-FC02-04ER54698, DE-FG02-95ER54309, DE-AC02-09CH11466, DE-FG02-04ER54761 and DE-AC52-07NA27344.

  15. 3D In Vitro Model for Breast Cancer Research Using Magnetic Levitation and Bioprinting Method.

    PubMed

    Leonard, Fransisca; Godin, Biana

    2016-01-01

    Tumor microenvironment composition and architecture are known as a major factor in orchestrating the tumor growth and its response to various therapies. In this context, in vivo studies are necessary to evaluate the responses. However, while tumor cells can be of human origin, tumor microenvironment in the in vivo models is host-based. On the other hand, in vitro studies in a flat monoculture of tumor cells (the most frequently used in vitro tumor model) are unable to recapitulate the complexity of tumor microenvironment. Three-dimensional (3D) in vitro cell cultures of tumor cells have been proven to be an important experimental tool in understanding mechanisms of tumor growth, response to therapeutics, and transport of nutrients/drugs. We have recently described a novel tool to create 3D co-cultures of tumor cells and cells in the tumor microenvironment. Our method utilizes magnetic manipulation/levitation of the specific ratios of tumor cells and cells in the tumor microenvironment (from human or animal origin) aiding in the formation of tumor spheres with defined cellular composition and density, as quickly as within 24 h. This chapter describes the experimental protocols developed to model the 3D structure of the cancer environment using the above method.

  16. 3D in vitro model for breast cancer research using magnetic levitation and bioprinting method

    PubMed Central

    Leonard, Fransisca; Godin, Biana

    2016-01-01

    Summary Tumor microenvironment composition and architecture are known as a major factor in orchestrating the tumor growth and its response to various therapies. In this context, in vivo studies are necessary to evaluate the responses. However, while tumor cells can be of human origin, tumor microenvironment in the in vivo models is host-based. On the other hand, in vitro studies in a flat monoculture of tumor cells (the most frequently used in vitro tumor model) are unable to recapitulate the complexity of tumor microenvironment. Three-dimensional (3D) in vitro cell cultures of tumor cells have been proven to be an important experimental tool in understanding mechanisms of tumor growth, response to therapeutics and transport of nutrients/drugs. We have recently described a novel tool to create 3D co-cultures of tumor cells and cells in the tumor microenvironment. Our method utilizes magnetic manipulation/levitation of the specific ratios of tumor cells and cells in the tumor microenvironment (from human or animal origin) aiding in the formation of tumor spheres with defined cellular composition and density, as quickly as within 24 hours. This chapter describes the experimental protocols developed to model the 3D structure of the cancer environment using the above method. PMID:26820961

  17. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-15

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  18. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  19. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  20. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  1. 2D and 3D ordered arrays of Co magnetic nanowires

    NASA Astrophysics Data System (ADS)

    Garcia, J.; Prida, V. M.; Vega, V.; Rosa, W. O.; Caballero-Flores, R.; Iglesias, L.; Hernando, B.

    2015-06-01

    Cobalt nanowire arrays spatially distributed in 2D and 3D arrangements have been performed by pulsed electrodeposition into the pores of planar and cylindrical nanoporous anodic alumina membranes, respectively. Morphological characterization points out the good filling factor reached by electroplated Co nanowires in both kinds of alumina membranes exhibiting hexagonally self-ordered porous structures. Co nanowires grown in both kinds of alumina templates exhibit the same crystalline phases. DC magnetometry and First Order Reversal Curve (FORC) analysis were carried out in order to determine the overall magnetic behavior for both nanowire array geometries. It is found that when the Co nanowires of two kinds of arrays are perpendicularly magnetized, both hysteresis loops are identical, suggesting that neither the intrinsic magnetic behavior of the nanowires nor the collective one depend on the arrays geometry. FORC analysis performed along the radial direction of the Co nanowire arrays embedded in the cylindrical alumina template reveals that the contribution of each nanowire to the magnetization reversal process involves its specific orientation with respect to the applied field direction. Furthermore, the comparison between the magnetic properties for both kinds of Co nanowire arrays allows discussing about the effect of the cylindrical geometry of the template on the magnetostatic interaction among nanowires.

  2. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

    Beaussier, Stephane; Gerya, Taras; Burg, Jean-Pierre

    2016-04-01

    Many orogenies display along-strike variations in their orogenic wedge geometry. For instance, the Alps is an example of lateral changes in the subducting lithosphere polarity. High resolution tomography has shown that the southeast dipping European lithosphere is separated from the northeast dipping Adriatic lithosphere by a narrow transition zone at about the "Judicarian" line (Kissling et al. 2006). The formation of such 3D variations remains conjectural. We investigate the conditions that can spontaneously induce such lithospheric structures, and intend to identify the main parameters controlling their formation and geometry. Using the 3D thermo-mechanical code, I3ELVIS (Gerya and Yuen 2007) we modelled a Wilson cycle starting from a continental lithosphere in an extensional setting resulting in continental breakup and oceanic spreading. At a later stage, divergence is gradually reversed to convergence, which induce subduction of the oceanic lithosphere formed during oceanic spreading. In this model, all lateral and longitudinal structures of the lithospheres are generated self-consistently, and are consequences of the initial continental structure, tectono-magmatic inheritance, and material rheology. Our numerical simulations point out the control of rheological parameters defining the brittle/plastic yielding conditions for the lithosphere. Formation of several opposing domains of opposing subduction polarity is facilitated by wide and weak oceanic lithospheres. Furthermore, contrasts of strength between the continental and oceanic lithosphere, as well as the angle between the plate suture and the shortening direction have a second order effect on the lateral geometry of the subduction zone. In our numerical experiments systematic lateral changes in the subduction lithosphere polarity during subduction initiation form spontaneously suggesting intrinsic physical origin of this phenomenon. Further studies are necessary to understand why this feature, observed

  3. 3-D explosions: a meditation on rotation (and magnetic fields)

    NASA Astrophysics Data System (ADS)

    Wheeler, J. C.

    This is the text of an introduction to a workshop on asymmetric explosions held in Austin in June, 2003. The great progress in supernova research over thirty-odd years is briefly reviewed. The context in which the meeting was called is then summarized. The theoretical success of the intrinsically multidimensional delayed detonation paradigm in explaining the nature of Type Ia supernovae coupled with new techniques of observations in the near IR and with spectropolarimetry promise great advances in understanding binary progenitors, the explosion physics, and the ever more accurate application to cosmology. Spectropolarimetry has also revealed the strongly asymmetric nature of core collapse and given valuable perspectives on the supernova - gamma-ray burst connection. The capability of the magneto-rotational instability to rapidly create strong toroidal magnetic fields in the core collapse ambiance is outlined. This physics may be the precursor to driving MHD jets that play a role in asymmetric supernovae. Welcome to the brave new world of three-dimensional explosions!

  4. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  5. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

    In the 3D printing technology, the research for using various materials has been performing. In this research work, 3D printable high viscous materials are suggested as one of the solutions for problems in the traditional 3D printing technology. First, Cu-Ag coreshell was synthesized as a functional material. In terms of the reaction rate, reaction rate limiting step was defined as a fundamental research, and then prepared Cu-Ag coreshell was printed and analyzed. Second, the high viscous Cu paste was prepared and then metal 3D printed structure was fabricated by using new printing method. In the synthesis of Cu-Ag coreshell, different sizes of Cu particle, 2μm and 100nm were used, and when 2μm Cu was applied, the reaction rate was limited by film diffusion control. However, when 100nm Cu was applied, reaction rate was controlled by CuO film and the rate of the reaction, which includes removing CuO film in the solution, is limited by chemical reaction control. The shape of Cu-Ag particle is spherical in the 2μm Cu condition and dendrite shape in the 100nm Cu condition respectively. The conductivity of Cu-Ag coreshell paste increased as increasing content of coreshell particle in the paste and sintering temperature. In order to print high viscous metal paste, the high viscous Cu paste was printed by using screw extruder, and the viscosity of Cu paste was measured as a fundamental research. As increasing wt.% of Cu in the paste, the viscosity also increased. In addition, the shrinkage factor was reduced by increasing wt.% of Cu in the paste. An optimized printing condition for the high viscous material was obtained, and by using this condition, 3D metal structure was fabricated. The final product was heat treated and polished. Through these processes, a fine quality of metal 3D structure was printed.

  6. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

    Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.

    2015-09-01

    Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.

  7. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  8. Improved hybrid optimization algorithm for 3D protein structure prediction.

    PubMed

    Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

  9. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

    Gritto, Roland; O'Connell, Daniel; Elobaid Elnaiem, Ali; Mohamed, Fathelrahman; Sadooni, Fadhil

    2016-04-01

    The Middle-East has seen a recent boom in construction including the planning and development of complete new sub-sections of metropolitan areas. Before planning and construction can commence, however, the development areas need to be investigated to determine their suitability for the planned project. Subsurface parameters such as the type of material (soil/rock), thickness of top soil or rock layers, depth and elastic parameters of basement, for example, comprise important information needed before a decision concerning the suitability of the site for construction can be made. A similar problem arises in environmental impact studies, when subsurface parameters are needed to assess the geological heterogeneity of the subsurface. Environmental impact studies are typically required for each construction project, particularly for the scale of the aforementioned building boom in the Middle East. The current study was conducted in Qatar at the location of a future highway interchange to evaluate a suite of 3D seismic techniques in their effectiveness to interrogate the subsurface for the presence of karst-like collapse structures. The survey comprised an area of approximately 10,000 m2 and consisted of 550 source- and 192 receiver locations. The seismic source was an accelerated weight drop while the geophones consisted of 3-component 10 Hz velocity sensors. At present, we analyzed over 100,000 P-wave phase arrivals and performed high-resolution 3-D tomographic imaging of the shallow subsurface. Furthermore, dispersion analysis of recorded surface waves will be performed to obtain S-wave velocity profiles of the subsurface. Both results, in conjunction with density estimates, will be utilized to determine the elastic moduli of the subsurface rock layers.

  10. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins.

    PubMed

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function.

  11. The 3D Attenuation Structure of Deception Island (Antarctica)

    NASA Astrophysics Data System (ADS)

    Prudencio, J.; De Siena, L.; Ibáñez, J. M.; Del Pezzo, E.; García-Yeguas, A.; Díaz-Moreno, A.

    2015-05-01

    The seismic and volcanological structure of Deception Island (Antarctica) is an intense focus topic in Volcano Geophysics. The interpretations given by scientists on the origin, nature, and location of the structures buried under the island strongly diverge. We present a high-resolution 3D P-wave attenuation tomography model obtained by using the coda normalization method on 20,293 high-quality waveforms produced by active sources. The checkerboard and synthetic anomaly tests guarantee the reproduction of the input anomalies under the island down to a depth of 4 km. The results, once compared with our current knowledge on the geological, geochemical, and geophysical structure of the region, depict Deception as a piecemeal caldera structure coming out of the Bransfield Trough. High-attenuation anomalies contouring the northeastern emerged caldera rim correlate with the locations of sediments. In our interpretation, the main attenuation contrast, which appears under the collapsed southeastern caldera rim, is related to the deeper feeding systems. A unique P-wave high-attenuation spherical-like anomaly in the inner bay extends between depths of 1 and 3 km. The northern contour of the anomaly coincides with the calderic rim both at 1 and 2 km, while smaller anomalies connect it with deeper structures below 3 km, dipping toward the Bransfield Trough. In our interpretation, the large upper anomaly is caused by a high-temperature shallow (1-3 km deep) geothermal system, located beneath the sediment-filled bay in the collapsed blocks and heated by smaller, deeper contributions of molten materials (magma) rising from southeast.

  12. Anatomical delineation of congenital heart disease using 3D magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Adams Bornemeier, Renee; Fellows, Kenneth E.; Fogel, Mark A.; Weinberg, Paul M.

    1994-05-01

    Anatomic delineation of the heart and great vessels is a necessity when managing children with congenital heart disease. Spatial orientation of the vessels and chambers in the heart and the heart itself may be quite abnormal. Though magnetic resonance imaging provides a noninvasive means for determining the anatomy, the intricate interrelationships between many structures are difficult to conceptualize from a 2-D format. Taking the 2-D images and using a volumetric analysis package allows for a 3-D replica of the heart to be created. This model can then be used to view the anatomy and spatial arrangement of the cardiac structures. This information may be utilized by the physicians to assist in the clinical management of these children.

  13. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

    Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.

    2012-01-01

    Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045

  14. Pack Aluminization Synthesis of Superalloy 3D Woven and 3D Braided Structures

    NASA Astrophysics Data System (ADS)

    Erdeniz, Dinc; Levinson, Amanda J.; Sharp, Keith W.; Rowenhorst, David J.; Fonda, Richard W.; Dunand, David C.

    2015-01-01

    Micro-architectured, precipitation-strengthened structures were created in a new process combining weaving, gas-phase alloying, diffusion, and precipitation. First, high-ductility Ni-20 wt pct Cr wires with 202 μm diameter were braided, or non-crimp orthogonal woven, into three-dimensional structures. Second, these structures were vapor-phase alloyed with Al at 1273 K (1000 °C) by pack cementation, creating uniform NiAl coatings on the wires when using a retort. Also, solid-state bonding was achieved at wire intersections, where two wires were sufficiently close to each other, as determined via optical and X-ray tomographic microscopy. Third, the NiAl-coated wires were fully homogenized and aged to form γ' precipitates distributed in a γ matrix phase, the same microstructure providing strength in nickel-based superalloys. The resulting structures—consisting of wires (i) woven in a controlled three-dimensional architecture, (ii) bonded at contact points and (iii) strengthened by γ' precipitates—are expected to show high strength at ambient and elevated temperatures, low density, and high permeability which is useful for active cooling.

  15. Band like Electronic Structures in Square Hollow Quantum Dots by 3D-MHFKS Calculation

    NASA Astrophysics Data System (ADS)

    Takizawa, Tokihiro; Okada, Hoshihito; Matsuse, Takehiro

    To find novel aspects of the electronic structures in quantum dots (QD) from a view point of spatial broken symmetry, 3-dimensional-mesh Hartree-Fock-Kohn-Sham (3D-MHFKS) calculations1 are applied to the interacting electron system of electron number N in a symmetry broken hollow QD. For the case of a square hollow quantum dot confined in square hard wall (HW) potential (SSHQD), the magnetic (B) field dependence of the obtained single particle energy levels and chemical potentials in B-N diagram are shown to have a band like electronic structures over the wide B-field range up to 20T. To clarify the origin of the band like electronic structures in SSHQD, 3D-MHFKS calculations are also applied for the mixed symmetry QD's with a circular hollow in square HW potential (SCHQD) and with a square hollow in circular HW potential (CSHQD).

  16. On the magnetotransport of 3D systems in quantizing magnetic field

    NASA Astrophysics Data System (ADS)

    Cheremisin, M. V.

    2014-12-01

    The resistivity components of 3D electron gas placed in quantizing magnetic field are calculated taking into account the correction caused by combined action of the Peltier and Seebeck thermoelectric effects. The longitudinal, transverse and the Hall magnetoresistivities exhibit familiar 1/B-period oscillations being universal functions of magnetic field and temperature.

  17. New Era in 3-D Modeling of Convection and Magnetic Dynamos in Stellar Envelopes and Cores

    NASA Astrophysics Data System (ADS)

    Toomre, J.; Augustson, K. C.; Brown, B. P.; Browning, M. K.; Brun, A. S.; Featherstone, N. A.; Miesch, M. S.

    2012-09-01

    The recent advances in asteroseismology and spectropolarimetry are beginning to provide estimates of differential rotation and magnetic structures for a range of F and G-type stars possessing convective envelopes, and in A-type stars with convective cores. It is essential to complement such observational work with theoretical studies based on 3-D simulations of highly turbulent convection coupled to rotation, shear and magnetic fields in full spherical geometries. We have so employed the anelastic spherical harmonic (ASH) code, which deals with compressible magnetohydrodynamics (MHD) in spherical shells, to examine the manner in which the global-scale convection can establish differential rotation and meridional circulations under current solar rotation rates, and these make good contact with helioseismic findings. For younger G stars rotating 3 to 5 times faster than the current Sun, the convection establishes ever stronger angular velocity contrasts between their fast equators and slow poles, and these are accompanied by prominent latitudinal temperature contrasts as well. Turning to MHD simulation of magnetic dynamo action within these younger G stars, the resulting magnetism involves wreaths of strong toroidal magnetic fields (up to 50 to 100 kG strengths) in the bulk of the convection zone, typically of opposite polarity in the northern and southern hemispheres. These fields can persist for long intervals despite being pummeled by the fast convective downflows, but they can also exhibit field reversals and cycles. Turning to shallower convective envelopes in the more luminous F-type stars that range in mass from 1.2 to 1.4 solar masses and for various rotation rates, we find that the convection can again establish solar-like differential rotation profiles with a fast equator and slow poles, but the opposite is achieved at the slower rotation rates. The F stars are also capable of building strong magnetic fields, often as wreaths, through dynamo action. We also

  18. GMC Collisions as Triggers of Star Formation. II. 3D Turbulent, Magnetized Simulations

    NASA Astrophysics Data System (ADS)

    Wu, Benjamin; Tan, Jonathan C.; Nakamura, Fumitaka; Van Loo, Sven; Christie, Duncan; Collins, David

    2017-02-01

    We investigate giant molecular cloud collisions and their ability to induce gravitational instability and thus star formation. This mechanism may be a major driver of star formation activity in galactic disks. We carry out a series of 3D, magnetohydrodynamics (MHD), adaptive mesh refinement simulations to study how cloud collisions trigger formation of dense filaments and clumps. Heating and cooling functions are implemented based on photo-dissociation region models that span the atomic-to-molecular transition and can return detailed diagnostic information. The clouds are initialized with supersonic turbulence and a range of magnetic field strengths and orientations. Collisions at various velocities and impact parameters are investigated. Comparing and contrasting colliding and non-colliding cases, we characterize morphologies of dense gas, magnetic field structure, cloud kinematic signatures, and cloud dynamics. We present key observational diagnostics of cloud collisions, especially: relative orientations between magnetic fields and density structures, like filaments; 13CO(J = 2-1), 13CO(J = 3-2), and 12CO(J = 8-7) integrated intensity maps and spectra; and cloud virial parameters. We compare these results to observed Galactic clouds.

  19. Focused shape models for hip joint segmentation in 3D magnetic resonance images.

    PubMed

    Chandra, Shekhar S; Xia, Ying; Engstrom, Craig; Crozier, Stuart; Schwarz, Raphael; Fripp, Jurgen

    2014-04-01

    Deformable models incorporating shape priors have proved to be a successful approach in segmenting anatomical regions and specific structures in medical images. This paper introduces weighted shape priors for deformable models in the context of 3D magnetic resonance (MR) image segmentation of the bony elements of the human hip joint. The fully automated approach allows the focusing of the shape model energy to a priori selected anatomical structures or regions of clinical interest by preferentially ordering the shape representation (or eigen-modes) within this type of model to the highly weighted areas. This focused shape model improves accuracy of the shape constraints in those regions compared to standard approaches. The proposed method achieved femoral head and acetabular bone segmentation mean absolute surface distance errors of 0.55±0.18mm and 0.75±0.20mm respectively in 35 3D unilateral MR datasets from 25 subjects acquired at 3T with different limited field of views for individual bony components of the hip joint.

  20. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

    Tarquis, A. M.; Gonzalez-Nieto, P. L.; Bird, N. R. A.

    2012-04-01

    Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice-Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.

  1. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

    Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.

  2. 3D-xy critical properties of YBa2Cu4O8 and magnetic-field-induced 3D to 1D crossover

    NASA Astrophysics Data System (ADS)

    Weyeneth, S.; Schneider, T.; Bukowski, Z.; Karpinski, J.; Keller, H.

    2008-08-01

    We present reversible magnetization data of a YBa2Cu4O8 single crystal and analyze the evidence for 3D-xy critical behavior and a magnetic-field-induced 3D to 1D crossover. Remarkable consistency with these phenomena is observed in agreement with a magnetic-field-induced finite size effect, whereupon the correlation length transverse to the applied magnetic field cannot grow beyond the limiting magnetic length scale LH = (Φ0/(aH))1/2. By applying the appropriate scaling form we obtain the zero-field critical temperature, the 3D to 1D crossover, the vortex melting line and the universal ratios of the related scaling variables. Accordingly there is no continuous phase transition in the (H,T) plane along the Hc2 lines as predicted by the mean-field treatment.

  3. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

    Wang, Jian; Zhao, Yunjie; Zhu, Chunyan; Xiao, Yi

    2015-01-01

    Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models. PMID:25712091

  4. 3D Magnetic Induction Maps of Nanoscale Materials Revealed by Electron Holographic Tomography

    PubMed Central

    2015-01-01

    The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing. Here, we demonstrate the quantitative 3D reconstruction of the dominant axial component of the magnetic induction and electrostatic potential within a cobalt nanowire (NW) of 100 nm in diameter with spatial resolution below 10 nm by applying electron holographic tomography. The tomogram was obtained using a dedicated TEM sample holder for acquisition, in combination with advanced alignment and tomographic reconstruction routines. The powerful approach presented here is widely applicable to a broad range of 3D magnetic nanostructures and may trigger the progress of novel spintronic nonplanar nanodevices. PMID:27182110

  5. Magnetic Dissipation in Asymmetric Strong Guide 3D Simulations: Examples of Magnetic Diffusion and Reconnection

    NASA Astrophysics Data System (ADS)

    Scudder, J. D.; Karimabadi, H.; Daughton, W. S.

    2013-12-01

    Interpretations of 2D simulations of magnetic reconnection are greatly simplified by using the flux function, usually the out of plane component of the vector potential. This theoretical device is no longer available when simulations are analyzed in 3-D. We illustrate the results of determining the locale rates of flux slippage in simulations by a technique based on Maxwell's equations. The technique recovers the usual results obtained for the flux function in 2D simulations, but remains viable in 3D simulations where there is no flux function. The method has also been successfully tested for full PIC simulations where reconnection is geometrically forbiddden. While such layers possess measurable flux slippages (diffusion) their level is not as strong as recorded in known 2D PIC reconnection sites using the same methodology. This approach will be used to explore the spatial incidence and strength of flux slippages across a 3D, asymmetric, strong guide field run discussed previously in the literature. Regions of diffusive behavior are illustrated where LHDI has been previously identified out on the separatrices, while much stronger flux slippages, typical of the X-regions of 2D simulations, are shown to occur elsewhere throughout the simulation. These results suggest that reconnection requires sufficiently vigorous flux slippage to be self sustaining, while non-zero flux slippage can and does occur without being at the reconnection site. A cross check of this approach is provided by the mixing ratio of tagged simulation particles of known spatial origin discussed by Daughton et al., 2013 (this meeting); they provide an integral measure of flux slippage up to the present point in the simulation. We will discuss the correlations between our Maxwell based flux slippage rates and the inferred rates of change of this mixing ratio (as recorded in the local fluid frame).

  6. Tuning the electronic and magnetic properties of borophene by 3d transition-metal atom adsorption

    NASA Astrophysics Data System (ADS)

    Li, J. Y.; Lv, H. Y.; Lu, W. J.; Shao, D. F.; Xiao, R. C.; Sun, Y. P.

    2016-12-01

    The electronic and magnetic properties of borophene functionalized by 3d transition metal (TM) atom adsorption are investigated by using first-principles calculations. The results show that the 3d TM atoms can be adsorbed on borophene with high binding energies ranging between 5.9 and 8.3 eV. Interestingly, the originally nonmagnetic borophene tends to be ferromagnetic when Ti, V, Cr, Mn, and Fe atoms are adsorbed, and the magnetic moments are dominated by the TM atoms. The origin of the ferromagnetism is discussed based on the Stoner criterion. Our results indicate that the magnetic properties of borophene can be effectively tuned through the adsorption of 3d TM atoms, which could have promising applications in spintronics and nanoelectronics.

  7. Microscopic magnetic nature of K2NiF4-type 3d transition metal oxides

    NASA Astrophysics Data System (ADS)

    Sugiyama, J.; Nozaki, H.; Umegaki, I.; Higemoto, W.; Ansaldo, E. J.; Brewer, J. H.; Sakurai, H.; Kao, T.-H.; Yang, H.-D.; Månsson, M.

    2014-12-01

    In order to elucidate the magnetic nature of K2NiF4-type 3d transition metal oxides, we have measured μ+SR spectra for Sr2VO4, LaSrVO4, and Sr2CrO4 using powder samples. ZF- and wTF-μ+SR measurements propose that Sr2VO4 enters into the static antiferromagnetic (AF) order phase below 8 K. In addition, TF-μ+SR measurements evidence that the transition at 105 K is not magnetic but structural and/or electronic in origin. For LaSrVO4, static long-range order has not been observed down to 20 K, while, as T decreases from 145 K, wTF asymmetry starts to decrease below 60 K, suggesting the appearance and evolution of localized magnetic moments below 60 K. For Sr2CrO4, by contrast, both ZF- and wTF-μ+SR have confirmed the presence of antiferromagnetic order below 117 K, as predicted in the χ(T) curve.

  8. Multilevel-3D bit patterned magnetic media with 8 signal levels per nanocolumn.

    PubMed

    Amos, Nissim; Butler, John; Lee, Beomseop; Shachar, Meir H; Hu, Bing; Tian, Yuan; Hong, Jeongmin; Garcia, Davil; Ikkawi, Rabee M; Haddon, Robert C; Litvinov, Dmitri; Khizroev, Sakhrat

    2012-01-01

    This letter presents an experimental study that shows that a 3(rd) physical dimension may be used to further increase information packing density in magnetic storage devices. We demonstrate the feasibility of at least quadrupling the magnetic states of magnetic-based data storage devices by recording and reading information from nanopillars with three magnetically-decoupled layers. Magneto-optical Kerr effect microscopy and magnetic force microscopy analysis show that both continuous (thin film) and patterned triple-stack magnetic media can generate eight magnetically-stable states. This is in comparison to only two states in conventional magnetic recording. Our work further reveals that ferromagnetic interaction between magnetic layers can be reduced by combining Co/Pt and Co/Pd multilayers media. Finally, we are showing for the first time an MFM image of multilevel-3D bit patterned media with 8 discrete signal levels.

  9. Microfluidic Fabrication of Bio-Inspired Microfibers with Controllable Magnetic Spindle-Knots for 3D Assembly and Water Collection.

    PubMed

    He, Xiao-Heng; Wang, Wei; Liu, Ying-Mei; Jiang, Ming-Yue; Wu, Fang; Deng, Ke; Liu, Zhuang; Ju, Xiao-Jie; Xie, Rui; Chu, Liang-Yin

    2015-08-12

    A simple and flexible approach is developed for controllable fabrication of spider-silk-like microfibers with tunable magnetic spindle-knots from biocompatible calcium alginate for controlled 3D assembly and water collection. Liquid jet templates with volatile oil drops containing magnetic Fe3O4 nanoparticles are generated from microfluidics for fabricating spider-silk-like microfibers. The structure of jet templates can be precisely adjusted by simply changing the flow rates to tailor the structures of the resultant spider-silk-like microfibers. The microfibers can be well manipulated by external magnetic fields for controllably moving, and patterning and assembling into different 2D and 3D structures. Moreover, the dehydrated spider-silk-like microfibers, with magnetic spindle-knots for collecting water drops, can be controllably assembled into spider-web-like structures for excellent water collection. These spider-silk-like microfibers are promising as functional building blocks for engineering complex 3D scaffolds for water collection, cell culture, and tissue engineering.

  10. 3D Kinetic Simulation of Plasma Jet Penetration in Magnetic Field

    NASA Astrophysics Data System (ADS)

    Galkin, Sergei A.; Bogatu, I. N.; Kim, J. S.

    2009-11-01

    A high velocity plasmoid penetration through a magnetic barrier is a problem of a great experimental and theoretical interest. Our LSP PIC code 3D fully kinetic numerical simulations of high density (10^16 cm-3) high velocity (30-140 km/sec) plasma jet/bullet, penetrating through the transversal magnetic field, demonstrate three different regimes: reflection by field, penetration by magnetic field expulsion and penetration by magnetic self-polarization. The behavior depends on plasma jet parameters and its composition: hydrogen, carbon (A=12) and C60-fullerene (A=720) plasmas were investigated. The 3D simulation of two plasmoid head-on injections along uniform magnetic field lines is analyzed. Mini rail plasma gun (accelerator) modeling is also presented and discussed.

  11. DIRECT DETECTION OF THE HELICAL MAGNETIC FIELD GEOMETRY FROM 3D RECONSTRUCTION OF PROMINENCE KNOT TRAJECTORIES

    SciTech Connect

    Zapiór, Maciej; Martinez-Gómez, David

    2016-02-01

    Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1–3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 10{sup 9} A.

  12. 3D effects of edge magnetic field configuration on divertor/scrape-off layer transport and optimization possibilities for a future reactor

    NASA Astrophysics Data System (ADS)

    Kobayashi, M.; Xu, Y.; Ida, K.; Corre, Y.; Feng, Y.; Schmitz, O.; Frerichs, H.; Tabares, F. L.; Evans, T. E.; Coenen, J. W.; Liang, Y.; Bader, A.; Itoh, K.; Yamada, H.; Ghendrih, Ph.; Ciraolo, G.; Tafalla, D.; Lopez-Fraguas, A.; Guo, H. Y.; Cui, Z. Y.; Reiter, D.; Asakura, N.; Wenzel, U.; Morita, S.; Ohno, N.; Peterson, B. J.; Masuzaki, S.

    2015-10-01

    This paper assesses the three-dimensional (3D) effects of the edge magnetic field structure on divertor/scrape-off layer transport, based on an inter-machine comparison of experimental data and on the recent progress of 3D edge transport simulation. The 3D effects are elucidated as a consequence of competition between transports parallel (\\parallel ) and perpendicular (\\bot ) to the magnetic field, in open field lines cut by divertor plates, or in magnetic islands. The competition has strong impacts on divertor functions, such as determination of the divertor density regime, impurity screening and detachment control. The effects of magnetic perturbation on the edge electric field and turbulent transport are also discussed. Parameterization to measure the 3D effects on the edge transport is attempted for the individual divertor functions. Based on the suggested key parameters, an operation domain of the 3D divertor configuration is discussed for future devices.

  13. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING. II. PROMINENCE EVOLUTION

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-10-20

    We use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing position of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.

  14. Cation Exchange in Dynamic 3D Porous Magnets: Improvement of the Physical Properties.

    PubMed

    Grancha, Thais; Acosta, Alvaro; Cano, Joan; Ferrando-Soria, Jesús; Seoane, Beatriz; Gascon, Jorge; Pasán, Jorge; Armentano, Donatella; Pardo, Emilio

    2015-11-16

    We report two novel three-dimensional porous coordination polymers (PCPs) of formulas Li4{Mn4[Cu2(Me3mpba)2]3}·68H2O (2) and K4{Mn4[Cu2(Me3mpba)2]3}·69H2O (3) obtained-via alkali cation exchange in a single-crystal to single-crystal process-from the earlier reported anionic manganese(II)-copper(II) PCP of formula Na4{Mn4[Cu2(Me3mpba)2]3}·60H2O (1) [Me3mpba(4-) = N,N'-2,4,6-trimethyl-1,3-phenylenebis(oxamate)]. This postsynthetic process succeeds where the direct synthesis in solution from the corresponding building blocks fails and affords significantly more robust PCPs with enhanced magnetic properties [long-range 3D magnetic ordering temperatures for the dehydrated phases (1'-3') of 2.0 (1'), 12.0 (2'), and 20.0 K (3')]. Changes in the adsorptive properties upon postsynthetic exchange suggest that the nature, electrostatic properties, mobility, and location of the cations within the framework are crucial for the enhanced structural stability. Overall, these results further confirm the potential of postsynthetic methods (including cation exchange) to obtain PCPs with novel or enhanced physical properties while maintaining unaltered their open-framework structures.

  15. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

    Andreasen, Arne; Drewes, Asbjorn M.; Assentoft, Joergen E.

    1992-06-01

    In the study of the rabbit hippocampal region, images of 430 serial sections were aligned by a `parameter-shift' algorithm. The resulting 3-D matrix represents a fixed and stained but `whole' rabbit brain. From this virtual object the slice procedure, displacement, and re- alignment could be computer simulated and the artifacts associated with these procedures estimated.

  16. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

    How graphics postprocessing techniques are currently used to examine the results of 3-D nonlinear analyses, some new techniques which take advantage of recent technology, and how these results relate to both the finite element model and its geometric parent are reviewed.

  17. Synthesis, characterization, magnetic and electrochemical properties of a new 3D hexa-copper-substituted germanotungstate

    SciTech Connect

    Li, Yanzhou; Luo, Jie; Zhang, Yanting; Zhao, Junwei; Chen, Lijuan; Ma, Pengtao; Niu, Jingyang

    2013-09-15

    An inorganic–organic hybrid hexa-copper-substituted germanotungstate Na{sub 2}[Cu(dap){sub 2}]{sub 2}[Cu(dap){sub 2}] ([Cu{sub 6}(H{sub 2}O){sub 2}(dap){sub 2}][B-α-GeW{sub 9}O{sub 34}]{sub 2})·4H{sub 2}O (1) (dap=1,2-diaminopropane) has been hydrothermally prepared and characterized by elemental analyses, inductively coupled plasma atomic emission spectrometry (ICP–AES) analyses, IR spectra, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA) and single-crystal X-ray diffraction. 1 displays the six-connected 3D network with the long topological (O′Keefe) vertex symbol is 4·4·6{sub 4}·4·4·4·4·6{sub 4}·4·4·4·6{sub 4}·4·4·4 and the short vertex (Schläfli) symbol of 4{sup 12}6{sup 3}. Magnetic measurements indicate that there are the overall ferromagnetic exchange interactions in the belt-like hexa-Cu{sup II} cluster in 1. Furthermore, the electrochemical behavior and electrocatalysis of 1 modified carbon paste electrode (1-CPE) have been studied. The reductions of nitrite, bromate and hydrogen peroxide are principally mediated by the W{sup VI}-based wave. - Graphical abstract: A hexa-Cu{sup II} sandwiched germanotungstate has been synthesized and structurally characterized. The magnetic, solid-state electrochemical and electrocatalytic properties have been investigated. Display Omitted - Highlights: • Transition-metal substituted polyoxometalates. • Hexa-copper-substituted germanotungstate. • Six-connected 3D network. • Electrocatalytic reduction of nitrite, bromate and hydrogen peroxide.

  18. Simulation of bootstrap current in 2D and 3D ideal magnetic fields in tokamaks

    NASA Astrophysics Data System (ADS)

    Raghunathan, M.; Graves, J. P.; Cooper, W. A.; Pedro, M.; Sauter, O.

    2016-09-01

    We aim to simulate the bootstrap current for a MAST-like spherical tokamak using two approaches for magnetic equilibria including externally caused 3D effects such as resonant magnetic perturbations (RMPs), the effect of toroidal ripple, and intrinsic 3D effects such as non-resonant internal kink modes. The first approach relies on known neoclassical coefficients in ideal MHD equilibria, using the Sauter (Sauter et al 1999 Phys. Plasmas 6 2834) expression valid for all collisionalities in axisymmetry, and the second approach being the quasi-analytic Shaing-Callen (Shaing and Callen 1983 Phys. Fluids 26 3315) model in the collisionless regime for 3D. Using the ideal free-boundary magnetohydrodynamic code VMEC, we compute the flux-surface averaged bootstrap current density, with the Sauter and Shaing-Callen expressions for 2D and 3D ideal MHD equilibria including an edge pressure barrier with the application of resonant magnetic perturbations, and equilibria possessing a saturated non-resonant 1/1 internal kink mode with a weak internal pressure barrier. We compare the applicability of the self-consistent iterative model on the 3D applications and discuss the limitations and advantages of each bootstrap current model for each type of equilibrium.

  19. 3D Seismic and Magnetic characterization of the Borax Lake Hydrothermal System in the Alvord Desert, southeastern Oregon.

    NASA Astrophysics Data System (ADS)

    Hess, S.; Bradford, J.; Lyle, M.; Routh, P.; Liberty, L.; Donaldson, P.

    2004-05-01

    As part of an interdisciplinary project aiming to study the link between the physical characteristics of hydrothermal systems and biota that occupy those systems, we are conducting a detailed geophysical characterization of an active hydrothermal system. The Borax Lake Hydrothermal System (BLHS), consisting of Borax Lake and the surrounding hot springs. BLHS is located near the center of the Alvord Basin in southeastern Oregon. The Alvord Basin is a north-south trending graben in the Northern Great Basin bounded by the Steens Mountains to the west and the Trout Creek Mountains to the east. We conducted a 2D seismic survey to characterize the geologic structure of the basin, a high-resolution 3D seismic survey to characterize the geologic structure of the BLHS, and a high-resolution 3D magnetic survey to characterize any lineaments in the bedrock that might control fluid flow in the BLHS. Previous results from the 2D seismic survey show a mid-basin basement high aligned approximately with the hot springs. In this study we present the results from the high-resolution 3D seismic and magnetic survey of the BLHS. We acquired the 3D seismic data using an SKS rifle and 240 channel recording system. The seismic survey covers approximately 90,000 sq. m with a maximum inline offset aperture of 225 m, crossline aperture of 75 m, and 360 degree azimuthal coverage. The coincidental magnetic survey was collected using a Geometrics 858G cesium vapor magnetometer. We designed both surveys to span nearly 100 active hydrothermal springs, including an approximately 50 m stepover in the trend of the surface expression of the hot springs. After preliminary processing, the 3D seismic data show continuous reflections up to 300 ms (~ 480 m). The initial interpretation of features seen in the 3D data cube include: normal faults dipping to the east and west, near-surface disturbances that are consistent with the trend of the hot springs, and significant near surface velocity anomalies

  20. Magnetic and Magnetoresistive Properties of 3D Interconnected NiCo Nanowire Networks

    NASA Astrophysics Data System (ADS)

    da Câmara Santa Clara Gomes, Tristan; De La Torre Medina, Joaquín; Lemaitre, Matthieu; Piraux, Luc

    2016-10-01

    Track-etched polymer membranes with crossed nanochannels have been revealed to be most suitable as templates to produce large surface area and mechanically stable 3D interconnected nanowire (NW) networks by electrodeposition. Geometrically controlled NW superstructures made of NiCo ferromagnetic alloys exhibit appealing magnetoresistive properties. The combination of exact alloy compositions with the spatial arrangement of NWs in the 3D network is decisive to obtain specific magnetic and magneto-transport behavior. A proposed simple model based on topological aspects of the 3D NW networks is used to accurately determine the anisotropic magnetoresistance ratios. Despite of their complex topology, the microstructure of Co-rich NiCo NW networks display mixed fcc-hcp phases with the c-axis of the hcp phase oriented perpendicular to their axis. These interconnected NW networks have high potential as reliable and stable magnetic field sensors.

  1. Ballooning Stability Of Tokamak Pedestals In The Presence Of Applied 3D Magnetic Perturbations

    NASA Astrophysics Data System (ADS)

    Cote, T. B.; Hegna, C. C.; Willensdorfer, M.; Strumberger, E.; Suttrop, W.; Zohm, H.

    2016-10-01

    Applied 3d magnetic perturbations can destabilize ideal mhd ballooning modes in tokamak pedestals. In this work, we describe techniques for studying infinite-n ballooning stability of 3d equilibria deduced from vmec calculations. Full magnetic profiles from vmec are used to construct local equilibria for flux surfaces in and around the edge pedestal region. These local equilibrium calculations are coupled with ideal ballooning stability analysis to determine stability of the system for given rmp configurations. This theoretical development is motivated by recent asdex-u experiments, where toroidally localized high-n mhd activity is observed in the presence of applied 3d fields. We will attempt to explain these observations. Supported by US DOE under Grant No. DE-FG02-86ER53218.

  2. Real-time structured light intraoral 3D measurement pipeline

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

    Computer aided design and manufacturing (CAD/CAM) is increasingly becoming a standard feature and service provided to patients in dentist offices and denture manufacturing laboratories. Although the quality of the tools and data has slowly improved in the last years, due to various surface measurement challenges, practical, accurate, invivo, real-time 3D high quality data acquisition and processing still needs improving. Advances in GPU computational power have allowed for achieving near real-time 3D intraoral in-vivo scanning of patient's teeth. We explore in this paper, from a real-time perspective, a hardware-software-GPU solution that addresses all the requirements mentioned before. Moreover we exemplify and quantify the hard and soft deadlines required by such a system and illustrate how they are supported in our implementation.

  3. 3-D Localization Method for a Magnetically Actuated Soft Capsule Endoscope and Its Applications

    PubMed Central

    Yim, Sehyuk; Sitti, Metin

    2014-01-01

    In this paper, we present a 3-D localization method for a magnetically actuated soft capsule endoscope (MASCE). The proposed localization scheme consists of three steps. First, MASCE is oriented to be coaxially aligned with an external permanent magnet (EPM). Second, MASCE is axially contracted by the enhanced magnetic attraction of the approaching EPM. Third, MASCE recovers its initial shape by the retracting EPM as the magnetic attraction weakens. The combination of the estimated direction in the coaxial alignment step and the estimated distance in the shape deformation (recovery) step provides the position of MASCE in 3-D. It is experimentally shown that the proposed localization method could provide 2.0–3.7 mm of distance error in 3-D. This study also introduces two new applications of the proposed localization method. First, based on the trace of contact points between the MASCE and the surface of the stomach, the 3-D geometrical model of a synthetic stomach was reconstructed. Next, the relative tissue compliance at each local contact point in the stomach was characterized by measuring the local tissue deformation at each point due to the preloading force. Finally, the characterized relative tissue compliance parameter was mapped onto the geometrical model of the stomach toward future use in disease diagnosis. PMID:25383064

  4. Extensions of 1d Bgk Electron Solitary Wave Solutions To 3d Magnetized and Unmagnetized Plasmas

    NASA Astrophysics Data System (ADS)

    Chen, Li-Jen; Parks, George K.

    This paper will compare the key results for BGK electron solitary waves in 3D mag- netized and unmagnetized plasmas. For 3D magnetized plasmas with highly magnetic field-aligned electrons, our results predict that the parallel widths of the solitary waves can be smaller than one Debye length, the solitary waves can be large scale features of the magnetosphere, and the parallel width-amplitude relation has a dependence on the perpendicular size. We can thus obtain an estimate on the typical perpendicular size of the observed solitary waves assuming a series of consecutive solitary waves are in the same flux tude with a particular perpendicular span. In 3D unmagnetized plasma systems such as the neutral sheet and magnetic reconnection sites, our theory indi- cates that although mathematical solutions can be constructed as the time-stationary solutions for the nonlinear Vlasov-Poisson equations, there does not exist a param- eter range for the solutions to be physical. We conclude that single-humped solitary potential pulses cannot be self-consistently supported by charged particles in 3D un- magnetized plasmas.

  5. Effect of magnetism on the solubility of 3 d elements in BCC iron: Results of first-principle investigations

    NASA Astrophysics Data System (ADS)

    Gorbatov, O. I.; Okatov, S. V.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.

    2013-08-01

    The methods of quantum-mechanical simulation have been used to study alloys of bcc iron with 3 d transition metals in the ferromagnetic and paramagnetic states. It has been shown that the main factor that determines the solubility of the 3 d elements is their electronic structure. The energy of the solution, mixing, and effective interatomic interactions vary regularly depending on the position of the element in the Periodic Table and on the magnetic state of the matrix. In some cases, depending on the magnetic state, changes in these quantities lead to the violation of the Hume-Rothery rules that determine the solubility of substitutional elements in alloys. The results obtained help us to understand the microscopic mechanisms that determine the solubility of alloying elements and their effect on the phase stability and structural state of steels.

  6. Experimental onset threshold and magnetic pressure pileup for 3D Sweet-Parker reconnection

    SciTech Connect

    Intrator, Thomas P; Sun, Xuan; Lapenta, Giovanni; Furno, Ivo

    2008-01-01

    In space, astrophysical and laboratory plasmas, magnetic reconnect ion converts magnetic into particle energy during unsteady, explosive events. The abrupt onset and cessation has been a long standing puzzle. We show the first three-dimensional (3D) laboratory example of onset and stagnation of Sweet-Parker type magnetic reconnection between magnetized and parallel current (flux) ropes driven by magnetohydrodynamic (MHD) attraction and 3D instability. Mutually attracting flux ropes advect and merge oppositely directed magnetic fields. Magnetic flux is annihilated, but reaches soon a threshold where magnetic flux and pressure pile up, and reconnection magnetic topology appears. This occurs when inflow speeds exceed the SweetParker speed v{sub SP} = v{sub A} / S{sup 1/2}, where v{sub A} is the Alfven speed and S is the Lundquist number for the reconnection layer, as magnetic flux arrives faster than flux annihilation can process it. Finally piled up fields generate MHD reaction forces that stall the inflow and the reconnection process.

  7. 3D Electromagnetic Particle-in-Cell simulations of the solar wind interaction with lunar magnetic anomalies

    NASA Astrophysics Data System (ADS)

    Deca, J.; Lapenta, G.; Divin, A. V.; Lembege, B.; Markidis, S.

    2013-12-01

    Unlike the Earth and Mercury, our Moon has no global magnetic field and is therefore not shielded from the impinging solar wind by a magnetosphere. However, lunar magnetic field measurements made by the Apollo missions provided direct evidence that the Moon has regions of small-scale crustal magnetic fields, ranging up to a few 100km in scale size with surface magnetic field strengths up to hundreds of nanoTeslas. More recently, the Lunar Prospector spacecraft has provided high-resolution observations allowing to construct magnetic field maps of the entire Moon, confirming the earlier results from Apollo, but also showing that the lunar plasma environment is much richer than earlier believed. Typically the small-scale magnetic fields are non-dipolar and rather tiny compared to the lunar radius and mainly clustered on the far side of the moon. Using iPic3D we present the first 3D fully kinetic and electromagnetic Particle-in-Cell simulations of the solar wind interaction with lunar magnetic anomalies. We study the behaviour of a dipole model with variable surface magnetic field strength under changing solar wind conditions and confirm that lunar crustal magnetic fields may indeed be strong enough to stand off the solar wind and form a mini-magnetosphere, as suggested by MHD and hybrid simulations and spacecraft observations. 3D-PIC simulations reveal to be very helpful to analyze the diversion/braking of the particle flux and the characteristics of the resulting particles accumulation. The particle flux to the surface is significantly reduced at the magnetic anomaly, surrounded by a region of enhanced density due to the magnetic mirror effect. Second, the ability of iPic3D to resolve all plasma components (heavy ions, protons and electrons) allows to discuss in detail the electron physics leading to the highly non-adiabatic interactions expected as well as the implications for solar wind shielding of the lunar surface, depending on the scale size (solar wind protons

  8. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

  9. Development of the Improving Process for the 3D Printed Structure

    NASA Astrophysics Data System (ADS)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  10. Development of the Improving Process for the 3D Printed Structure

    PubMed Central

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics. PMID:28054558

  11. Development of the Improving Process for the 3D Printed Structure.

    PubMed

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

  12. 3-D MHD modeling and stability analysis of jet and spheromak plasmas launched into a magnetized plasma

    NASA Astrophysics Data System (ADS)

    Fisher, Dustin; Zhang, Yue; Wallace, Ben; Gilmore, Mark; Manchester, Ward; Arge, C. Nick

    2016-10-01

    The Plasma Bubble Expansion Experiment (PBEX) at the University of New Mexico uses a coaxial plasma gun to launch jet and spheromak magnetic plasma configurations into the Helicon-Cathode (HelCat) plasma device. Plasma structures launched from the gun drag frozen-in magnetic flux into the background magnetic field of the chamber providing a rich set of dynamics to study magnetic turbulence, force-free magnetic spheromaks, and shocks. Preliminary modeling is presented using the highly-developed 3-D, MHD, BATS-R-US code developed at the University of Michigan. BATS-R-US employs an adaptive mesh refinement grid that enables the capture and resolution of shock structures and current sheets, and is particularly suited to model the parameter regime under investigation. CCD images and magnetic field data from the experiment suggest the stabilization of an m =1 kink mode trailing a plasma jet launched into a background magnetic field. Results from a linear stability code investigating the effect of shear-flow as a cause of this stabilization from magnetic tension forces on the jet will be presented. Initial analyses of a possible magnetic Rayleigh Taylor instability seen at the interface between launched spheromaks and their entraining background magnetic field will also be presented. Work supported by the Army Research Office Award No. W911NF1510480.

  13. The ITER 3D Magnetic Diagnostic Response to Applied n=3 and n=4 RMP's

    SciTech Connect

    Lazerson, S A

    2014-09-01

    The ITER magnetic diagnostic response to applied n=3 and n=4 RMPs has been calculated for the 15MA scenario. The VMEC code was utilized to calculate free boundary 3D ideal MHD equilibria, where the non-stellarator symmetric terms were included in the calculation. This allows an assessment to be made of the possible boundary displacements due to RMP application in ITER. As the VMEC code assumes a continuous set of nested flux surface, the possibility of island and stochastic region formation is ignored. At the start of the current at-top (L-Mode) application of n = 4 RMP's indicates approximately 1 cm peak-to-peak displacements on the low field side of the plasma while later in the shot (H-mode) perturbations as large as 3 cm are present. Forward modeling of the ITER magnetic diagnostics indicates significant non-axisymmetric plasma response, exceeding 10% the axisymmetric signal in many of the flux loops. Magnetic field probes seem to indicate a greater robustness to 3D effects but still indicate large sensitivities to 3D effects in a number of sensors. Forward modeling of the diagnostics response to 3D equilibria allows assessment of diagnostics design and control scenarios.

  14. Nonthermal Particle Acceleration in 3D Relativistic Magnetic Reconnection in Pair Plasma

    NASA Astrophysics Data System (ADS)

    Uzdensky, Dmitri; Werner, Gregory; Zhdankin, Vladimir

    2016-10-01

    Magnetic reconnection is a fundamental plasma process that converts magnetic energy into particle kinetic energy. ``Relativistic'' reconnection is of interest in astrophysical contexts because it can accelerate particles to relativistic energies high enough for synchrotron (or inverse Compton) emission to explain observed high-energy radiation. After several 2D particle-in-cell (PIC) simulations of reconnection in pair plasmas demonstrated power-law electron-energy spectra extending to high energies, a few 3D simulations surprisingly confirmed the robustness of nonthermal particle acceleration, despite fundamental differences, such as the development of the relativistic drift-kink instability (RDKI) in 3D. We present a comprehensive PIC study of 3D relativistic pair-plasma reconnection characterizing the effect of the third dimension. We investigate how reconnection dynamics and particle acceleration depend on guide magnetic field Bz and on the simulation box length Lz in the third dimension. We find that, while the RDKI does indeed grow in 3D reconnection, it does not inhibit particle acceleration, even in the absence of guide field. This work was funded by NSF, DOE, and NASA.

  15. Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

  16. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    PubMed Central

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-01-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials. PMID:27897209

  17. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    NASA Astrophysics Data System (ADS)

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

  18. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties.

    PubMed

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-29

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80-250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

  19. 4D Magnetic Resonance Velocimetry in a 3D printed brain aneurysm

    NASA Astrophysics Data System (ADS)

    Amili, Omid; Schiavazzi, Daniele; Coletti, Filippo

    2016-11-01

    Cerebral aneurysms are of great clinical importance. It is believed that hemodynamics play a critical role in the development, growth, and rupture of brain arteries with such condition. The flow structure in the aneurysm sac is complex, unsteady, and three-dimensional. Therefore the time-resolved measurement of the three-dimensional three-component velocity field is crucial to predict the clinical outcome. In this study magnetic resonance velocimetry is used to assess the fluid dynamics inside a 3D printed model of a giant intracranial aneurysm. We reach sub-millimeter resolution while resolving sixteen instances within the cardiac cycle. The physiological flow waveform is imposed using an in-house built pump in a flow circuit where the cardiovascular impedance is matched. The flow evolution over time is reconstructed in detail. The complex flow structure is characterized by vortical and helical motions that reside in the aneurysm for most part of the cycle. The 4D pressured distribution is also reconstructed from the velocity field. The present case study was used in a previous CFD challenge, therefore these results may provide useful experimental comparison for simulations performed by other research groups.

  20. Anisotropic heat transport in integrable and chaotic 3-D magnetic fields

    SciTech Connect

    Del-Castillo-Negrete, Diego B; Blazevski, D.; Chacon, Luis

    2012-01-01

    A study of anisotropic heat transport in 3-D chaotic magnetic fields is presented. The approach is based on the recently proposed Lagrangian-Green s function (LG) method in Ref. [1] that allows an efficient and accurate integration of the parallel transport equation applicable to general magnetic fields with local or non-local parallel flux closures. We focus on reversed shear magnetic field configurations known to exhibit separatrix reconnection and shearless transport barriers. The role of reconnection and magnetic field line chaos on temperature transport is studied. Numerical results are presented on the anomalous relaxation of radial temperature gradients in the presence of shearless Cantori partial barri- ers. Also, numerical evidence of non-local effective radial temperature transport in chaotic fields is presented. Going beyond purely parallel transport, the LG method is generalized to include finite perpendicular diffusivity, and the problem of temperature flattening inside a magnetic island is studied.

  1. Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations

    PubMed Central

    Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2010-01-01

    Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D. PMID:20700534

  2. Synthesis, structure and properties of a 3D acentric coordination polymer with noninterpenetrated (10,3)-d topology

    NASA Astrophysics Data System (ADS)

    Lun, Huijie; Li, Xuefei; Wang, Xiao; Li, Haiyan; Li, Yamin; Bai, Yan

    2017-01-01

    A new coordination polymer, {[Mn(HPIDC)(H2O)]·2H2O}n (1) (H3PIDC = 2-(pyridin-4-yl)-1H-imidazole-4,5-dicarboxylic acid), has been obtained by hydrothermal method and structurally characterized by X-ray single crystal diffraction, elemental analysis and thermogravimetric analysis (TGA). X-ray single crystal diffraction reveals that compound 1 crystallizing in acentric Pna21 space group, exhibits an ultimate racemic three-dimension framework with rare noninterpenetrated (10,3)-d (or utp) topology due to the alternate array of left- and right-handed helixes. Moreover, compound 1 also features ferroelectric, nonlinear optical (NLO) and antiferromagnetic behaviors.

  3. Genome3D: exploiting structure to help users understand their sequences

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Oates, Matt E.; Punta, Marco; Rackham, Owen J.L.; Stahlhacke, Jonathan; Sternberg, Michael J.E.; Velankar, Sameer; Orengo, Christine

    2015-01-01

    Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models. PMID:25348407

  4. Magnetic and Electronic Phase Diagram of Sr2VFeAsO3-d

    NASA Astrophysics Data System (ADS)

    Tojo, Yujiro; Shibuya, Taizo; Nakamura, Tetsuro; Shoji, Koichiro; Matoba, Masanori; Yasui, Shintaro; Itoh, Mitsuru; Kitao, Shinji; Seto, Makoto; Kamihara, Yoichi; Research Grants From Keio Univ. Collaboration; Msl Collaborative Research Project Collaboration; Joint Usage in Krri Collaboration

    2014-03-01

    Ae2MFePnO3 (so-called 21113 systems) with perovskite-type layers such as Ae2MO3, where Ae denotes alkaline earth metals, M does Sc, Ti, Cr, V and other transition metal atoms and Pn does As and P shows superconductivity at T <46 K. Sr2VFeAsO3-d is a representative compound in 21113 systems. [Zhu et al, Phys. Rev. B (2009); Ogino et al, Supercond. Sci. Technol. (2009); Ogino et al, Supercond. Sci. Technol. (2009)] Although the oxygen deficiency (d) as a function of Tc is still controversial in Sr2VFeAsO3-d, many samples have been reported as superconductors with Tc = 24-37 K. In this study, a polycrystalline Sr2VFeAsO3-d (d = ~ 0.1- 0.6) were prepared by a solid state reaction using an alumina tube in a sealed silica tube. DC electrical resistivity was measured by a four-probe technique. Magnetization measurements were performed on a superconducting quantum interference device. 57Fe Mossbauer spectra were obtained using conventional equipment. The electronic and magnetic phase diagram of Sr2VFeAsO3-d is elucidated.

  5. Histo-anatomic 3D printing of dental structures.

    PubMed

    Schweiger, J; Beuer, F; Stimmelmayr, M; Edelhoff, D; Magne, P; Güth, J F

    2016-11-04

    The creation of dental restorations with natural appearance and biomechanics represents a major challenge for the restorative team. The manufacturing-process of high-aesthetic restorations from tooth-coloured restorative materials is currently dominated by manual manufacturing procedures and the outcome is highly dependent on the knowledge and skills of the performing dental technician. On the other hand, due to the simplicity of the manufacturing process, CAD/CAM restorations from different material classes gain more and more acceptance in the daily routine. Multi-layered restorations show significant aesthetic advantages versus monolithic ones, but are difficult to fabricate using digital technologies. The key element for the successful automated digital fabrication of aesthetic anterior restorations seems to be the form of the individual dentine core as defined by dentine enamel junction (DEJ) covered by a more transparent layer of material imitating the enamel layer to create the outer enamel surface (OES). This article describes the possibilities and technologies available for so-called '4D-printing'. It introduces the digital manufacturing process of multilayered anterior teeth using 3D multipart printing, taking the example of manufacturing replicas of extracted intact natural teeth.

  6. 3-D Modeling of Magnetic Fields for the Lithium Tokamak eXperiment

    NASA Astrophysics Data System (ADS)

    Logan, N.; Berzak, L.; Kaita, R.; Majeski, R.; Menard, J.; Zakharov, L.

    2010-11-01

    The Lithium Tokamak eXperiment (LTX) is designed to investigate low-recycling operating regimes by surrounding 85% of the last closed flux surface with liquid lithium evaporated onto a copper and stainless steel shell conformal to the plasma. Fields generated by currents in this conducting shell have significant effects on magnetic configurations. To understand these effects, the commercially available code Aether [http://www.fieldp.com] is used to simulate time varying magnetic fields in a 3-D model of LTX. The model is built using LTX CAD files and divided into a regular mesh for computing the evolution of coupled electromagnetic vector quantities through time and space. Applicable boundary conditions and symmetries are analyzed. Comparisons with measured data, results from a 2-D code, and results from a 3-D code designed specifically for LTX demonstrate the possible benefits and limitations of using this commercial code.

  7. 3D position estimation using a single coil and two magnetic field sensors.

    PubMed

    Tadayon, P; Staude, G; Felderhoff, T

    2015-01-01

    This paper presents an algorithm which enables the estimation of relative 3D position of a sensor module with two magnetic sensors with respect to a magnetic field source using a single transmitting coil. Starting with the description of the ambiguity problem caused by using a single coil, a system concept comprising two sensors having a fixed spatial relation to each other is introduced which enables the unique determination of the sensors' position in 3D space. For this purpose, an iterative two-step algorithm is presented: In a first step, the data of one sensor is used to limit the number of possible position solutions. In a second step, the spatial relation between the sensors is used to determine the correct sensor position.

  8. A high-throughput in vitro ring assay for vasoactivity using magnetic 3D bioprinting

    PubMed Central

    Tseng, Hubert; Gage, Jacob A.; Haisler, William L.; Neeley, Shane K.; Shen, Tsaiwei; Hebel, Chris; Barthlow, Herbert G.; Wagoner, Matthew; Souza, Glauco R.

    2016-01-01

    Vasoactive liabilities are typically assayed using wire myography, which is limited by its high cost and low throughput. To meet the demand for higher throughput in vitro alternatives, this study introduces a magnetic 3D bioprinting-based vasoactivity assay. The principle behind this assay is the magnetic printing of vascular smooth muscle cells into 3D rings that functionally represent blood vessel segments, whose contraction can be altered by vasodilators and vasoconstrictors. A cost-effective imaging modality employing a mobile device is used to capture contraction with high throughput. The goal of this study was to validate ring contraction as a measure of vasoactivity, using a small panel of known vasoactive drugs. In vitro responses of the rings matched outcomes predicted by in vivo pharmacology, and were supported by immunohistochemistry. Altogether, this ring assay robustly models vasoactivity, which could meet the need for higher throughput in vitro alternatives. PMID:27477945

  9. Simulation of the 3-D Evolution of Electron Scale Magnetic Reconnection - Motivated by Laboratory Experiments Predictions for MMS

    NASA Astrophysics Data System (ADS)

    Buechner, J.; Jain, N.; Sharma, A.

    2013-12-01

    The four s/c of the Magnetospheric Multiscale (MMS) mission, to be launched in 2014, will use the Earth's magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes. One of them is magnetic reconnection, an essentially multi-scale process. While laboratory experiments and past theoretical investigations have shown that important processes necessary to understand magnetic reconnection take place at electron scales the MMS mission for the first time will be able to resolve these scales by in space observations. For the measurement strategy of MMS it is important to make specific predictions of the behavior of current sheets with a thickness of the order of the electron skin depth which play an important role in the evolution of collisionless magnetic reconnection. Since these processes are highly nonlinear and non-local numerical simulation is needed to specify the current sheet evolution. Here we present new results about the nonlinear evolution of electron-scale current sheets starting from the linear stage and using 3-D electron-magnetohydrodynamic (EMHD) simulations. The growth rates of the simulated instabilities compared well with the growth rates obtained from linear theory. Mechanisms and conditions of the formation of flux ropes and of current filamentation will be discussed in comparison with the results of fully kinetic simulations. In 3D the X- and O-point configurations of the magnetic field formed in reconnection planes alternate along the out-of-reconnection-plane direction with the wavelength of the unstable mode. In the presence of multiple reconnection sites, the out-of-plane magnetic field can develop nested structure of quadrupoles in reconnection planes, similar to the 2-D case, but now with variations in the out-of-plane direction. The structures of the electron flow and magnetic field in 3-D simulations will be compared with those in 2-D simulations to discriminate the essentially 3D features. We also discuss

  10. Semiautomatic approaches to account for 3-D distortion of the electric field from local, near-surface structures in 3-D resistivity inversions of 3-D regional magnetotelluric data

    USGS Publications Warehouse

    Rodriguez, Brian D.

    2017-03-31

    This report summarizes the results of three-dimensional (3-D) resistivity inversion simulations that were performed to account for local 3-D distortion of the electric field in the presence of 3-D regional structure, without any a priori information on the actual 3-D distribution of the known subsurface geology. The methodology used a 3-D geologic model to create a 3-D resistivity forward (“known”) model that depicted the subsurface resistivity structure expected for the input geologic configuration. The calculated magnetotelluric response of the modeled resistivity structure was assumed to represent observed magnetotelluric data and was subsequently used as input into a 3-D resistivity inverse model that used an iterative 3-D algorithm to estimate 3-D distortions without any a priori geologic information. A publicly available inversion code, WSINV3DMT, was used for all of the simulated inversions, initially using the default parameters, and subsequently using adjusted inversion parameters. A semiautomatic approach of accounting for the static shift using various selections of the highest frequencies and initial models was also tested. The resulting 3-D resistivity inversion simulation was compared to the “known” model and the results evaluated. The inversion approach that produced the lowest misfit to the various local 3-D distortions was an inversion that employed an initial model volume resistivity that was nearest to the maximum resistivities in the near-surface layer.

  11. Air-structured optical fiber drawn from a 3D-printed preform.

    PubMed

    Cook, Kevin; Canning, John; Leon-Saval, Sergio; Reid, Zane; Hossain, Md Arafat; Comatti, Jade-Edouard; Luo, Yanhua; Peng, Gang-Ding

    2015-09-01

    A structured optical fiber is drawn from a 3D-printed structured preform. Preforms containing a single ring of holes around the core are fabricated using filament made from a modified butadiene polymer. More broadly, 3D printers capable of processing soft glasses, silica, and other materials are likely to come on line in the not-so-distant future. 3D printing of optical preforms signals a new milestone in optical fiber manufacture.

  12. 3D low-beta magnetized plasma equilibria from external shaping

    NASA Astrophysics Data System (ADS)

    Hassam, A.; Tenbarge, J.; Landreman, M.; Dorland, W.; Sengupta, W.

    2016-10-01

    A 3D nonlinear dissipative MHD code is in development to allow relaxation to low-beta MHD equilibrium inside a shaped 3D conducting boundary with prescribed conserved axial magnetic flux and no external current. Formation of magnetic islands is expected. Heat sources would be eventually introduced to allow the possibility of non-stationary convection depending on the stability properties of the accessible MHD equilibria. The initial development will be done using the code UMHD. The initial emphasis will be on recovering expected physics in simpler 3D geometries. A primary objective is to minimize numerical boundary noise. In particular, codes which specify the normal magnetic field B.n on bounding surfaces are prone to noise generation. We plan to shape the boundary to conform to the desired field shape so that B.n is zero on the boundary. Non-orthogonal coordinates will be chosen to effect this. We will test noise reduction within the tangential field approach. Results obtained to date support this conjecture. Initial results from simple 2D code equilibria have been verified against analytic solution of equilibria in weak shaping. Initial results also recover the expected features of the Hahm- Kulsrud island formation solution. Work supported by US DOE.

  13. Using "click-e-bricks" to make 3D elastomeric structures.

    PubMed

    Morin, Stephen A; Shevchenko, Yanina; Lessing, Joshua; Kwok, Sen Wai; Shepherd, Robert F; Stokes, Adam A; Whitesides, George M

    2014-09-10

    Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.

  14. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.

  15. 3D Design, Contruction, and Field Analysis of CIS Main Dipole Magnets

    NASA Astrophysics Data System (ADS)

    Berg, G. P. A.; Fox, W.; Friesel, D. L.; Rinckel, T.

    1997-05-01

    The lattice for CIS ( Cooler Injection Synchroton ) requires four laminated 90^circ main dipole magnets with bending radius ρ = 1.273 m, EFL = 2 m, and an edge angle of 12^circ. Optimum Cooler injection and injection in the planned 15 GeV LISS ring requires operation up to about 1.75 T. Initial operation of 1 Hz, with later upgrade to 5 Hz is planned. We will present 2D and 3D field calculations used to optimize the shape of laminations and endpacks of the magnet. Endpacks are designed to determine edge angle and to compensate hexapole components, in particular above 1.4 T where saturation becomes significant. The large dipole curvature required a new type of dipole construction. Each magnet consists of wedge shaped blocks fabricated from stamped lamination of cold rolled low carbon iron. B-stage (dry) epopy was used for bonding and insulation. The end blocks are machined to include the calculated 3D shape of the endpacks. All four magnets were mapped in the field range from 0.3 T - 1.8 T. Comparison of calculations and data in terms of B(I) curves, EFL, edge angle, and hexapole component as function of field excitation will be presented. The constructed magnets are well within expected specifications.

  16. SAFAS: Unifying Form and Structure through Interactive 3D Simulation

    ERIC Educational Resources Information Center

    Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.

    2015-01-01

    There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…

  17. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

    We review the observational evidences concerning the three-dimensional structure of the Galactic bulge. Although the inner few kpc of our Galaxy are normally referred to as the bulge, all the observations demonstrate that this region is dominated by a bar, i.e., the bulge is a bar. The bar has a boxy/peanut (X-shaped) structure in its outer regions, while it seems to become less and less elongated in its innermost region. A thinner and longer structure departing from the main bar has also been found, although the observational evidences that support the scenario of two separate structures has been recently challenged. Metal-poor stars ([Fe/H] ≲ -0.5 dex) trace a different structure, and also have different kinematics.

  18. Magnetic engineering in 3d transition metals on phosphorene by strain

    NASA Astrophysics Data System (ADS)

    Cai, Xiaolin; Niu, Chunyao; Wang, Jianjun; Yu, Weiyang; Ren, XiaoYan; Zhu, Zhili

    2017-04-01

    Using first-principles density functional theory (DFT) calculations, we systematically investigate the strain effects on the adsorption energies, magnetic ordering and electronic properties of 3d transition metal (TM) atoms (from Sc to Co) adsorbed on phosphorene (P). We find that the adsorption energy of TM can be enhanced by compressive strain whereas weakened by tensile strain. Our results show that strain plays a decisive role in the magnetic moments as well as the magnetic coupling states of TM adatoms. Importantly, the transitions from antiferromagnetic (AFM) state to ferromagnetic (FM) state or to another different AFM ordering can be induced by strain effect. In addition, we observe the semiconductor to metal or half-metal transitions in some TM@P systems by applying strain. Our findings shed a new light on precisely engineering the magnetic properties and electronic properties of the TM@P systems, which will have great potential applications in spin electronics and other related fields.

  19. A 3-D Magnetic Analysis of a Linear Alternator For a Stirling Power System

    NASA Technical Reports Server (NTRS)

    Geng, Steven M.; Schwarze, Gene E.; Niedra, Janis M.

    2000-01-01

    The NASA Glenn Research Center and the Department of Energy (DOE) are developing advanced radioisotope Stirling convertors, under contract with Stirling Technology Company (STC), for space applications. Of critical importance to the successful development of the Stirling convertor for space power applications is the development of a lightweight and highly efficient linear alternator. This paper presents a 3-D finite element method (FEM) approach for evaluating Stirling convertor linear alternators. Preliminary correlations with open-circuit voltage measurements provide an encouraging level of confidence in the model. Spatial plots of magnetic field strength (H) are presented in the region of the exciting permanent magnets. These plots identify regions of high H, where at elevated temperature and under electrical load, the potential to alter the magnetic moment of the magnets exists. This implies the need for further testing and analysis.

  20. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  1. The 3D structures of VDAC represent a native conformation

    PubMed Central

    Hiller, Sebastian; Abramson, Jeff; Mannella, Carmen; Wagner, Gerhard; Zeth, Kornelius

    2010-01-01

    The most abundant protein of the mitochondrial outer membrane is the voltage-dependent anion channel (VDAC), which facilitates the exchange of ions and molecules between mitochondria and cytosol and is regulated by interactions with other proteins and small molecules. VDAC has been extensively studied for more than three decades, and last year three independent investigations revealed a structure of VDAC-1 exhibiting 19 transmembrane β-strands, constituting a unique structural class of β-barrel membrane proteins. Here, we provide a historical perspective on VDAC research and give an overview of the experimental design used to obtain these structures. Furthermore, we validate the protein refolding approach and summarize biochemical and biophysical evidence that links the 19-stranded structure to the native form of VDAC. PMID:20708406

  2. MUFOLD: A new solution for protein 3D structure prediction.

    PubMed

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-04-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Calpha or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 A, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8.

  3. Quantitative 3D magnetic resonance elastography: Comparison with dynamic mechanical analysis

    PubMed Central

    Rossman, Phillip J.; Arani, Arvin; Lake, David S.; Glaser, Kevin J.; Trzasko, Joshua D.; Manduca, Armando; McGee, Kiaran P.; Ehman, Richard L.; Araoz, Philip A.

    2016-01-01

    Purpose Magnetic resonance elastography (MRE) is a rapidly growing noninvasive imaging technique for measuring tissue mechanical properties in vivo. Previous studies have compared two‐dimensional MRE measurements with material properties from dynamic mechanical analysis (DMA) devices that were limited in frequency range. Advanced DMA technology now allows broad frequency range testing, and three‐dimensional (3D) MRE is increasingly common. The purpose of this study was to compare 3D MRE stiffness measurements with those of DMA over a wide range of frequencies and shear stiffnesses. Methods 3D MRE and DMA were performed on eight different polyvinyl chloride samples over 20–205 Hz with stiffness between 3 and 23 kPa. Driving frequencies were chosen to create 1.1, 2.2, 3.3, 4.4, 5.5, and 6.6 effective wavelengths across the diameter of the cylindrical phantoms. Wave images were analyzed using direct inversion and local frequency estimation algorithm with the curl operator and compared with DMA measurements at each corresponding frequency. Samples with sufficient spatial resolution and with an octahedral shear strain signal‐to‐noise ratio > 3 were compared. Results Consistency between the two techniques was measured with the intraclass correlation coefficient (ICC) and was excellent with an overall ICC of 0.99. Conclusions 3D MRE and DMA showed excellent consistency over a wide range of frequencies and stiffnesses. Magn Reson Med 77:1184–1192, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. PMID:27016276

  4. Structured light imaging system for structural and optical characterization of 3D tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Liu, Songde; Smith, Zach; Xu, Ronald X.

    2016-10-01

    There is a pressing need for a phantom standard to calibrate medical optical devices. However, 3D printing of tissue-simulating phantom standard is challenged by lacking of appropriate methods to characterize and reproduce surface topography and optical properties accurately. We have developed a structured light imaging system to characterize surface topography and optical properties (absorption coefficient and reduced scattering coefficient) of 3D tissue-simulating phantoms. The system consisted of a hyperspectral light source, a digital light projector (DLP), a CMOS camera, two polarizers, a rotational stage, a translation stage, a motion controller, and a personal computer. Tissue-simulating phantoms with different structural and optical properties were characterized by the proposed imaging system and validated by a standard integrating sphere system. The experimental results showed that the proposed system was able to achieve pixel-level optical properties with a percentage error of less than 11% for absorption coefficient and less than 7% for reduced scattering coefficient for phantoms without surface curvature. In the meanwhile, 3D topographic profile of the phantom can be effectively reconstructed with an accuracy of less than 1% deviation error. Our study demonstrated that the proposed structured light imaging system has the potential to characterize structural profile and optical properties of 3D tissue-simulating phantoms.

  5. Subtractive 3D Printing of Optically Active Diamond Structures

    NASA Astrophysics Data System (ADS)

    Martin, Aiden A.; Toth, Milos; Aharonovich, Igor

    2014-05-01

    Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

  6. Study on embedding fiber Bragg grating sensor into the 3D printing structure for health monitoring

    NASA Astrophysics Data System (ADS)

    Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

    2016-10-01

    3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

  7. Evaluation of Gastric Volumes: Comparison of 3-D Ultrasound and Magnetic Resonance Imaging.

    PubMed

    Buisman, Wijnand J; Mauritz, Femke A; Westerhuis, Wouter E; Gilja, Odd Helge; van der Zee, David C; van Herwaarden-Lindeboom, Maud Y A

    2016-07-01

    To investigate gastric accommodation, accurate measurements of gastric volumes are necessary. An excellent technique to measure gastric volumes is dynamic magnetic resonance imaging (MRI). Unfortunately, dynamic MRI is expensive and not always available. A new 3-D ultrasound (US) method using a matrix transducer was developed to measure gastric volumes. In this prospective study, 14 healthy volunteers underwent a dynamic MRI and a 3-D US. Gastric volumes were calculated with intra-gastric liquid content and total gastric volume. Mean postprandial liquid gastric content was 397 ± 96.5 mL. Mean volume difference was 1.0 mL with limits of agreement of -8.9 to 10.9 mL. When gastric air was taken into account, mean total gastric volume was 540 ± 115.4 mL SD. Mean volume difference was 2.3 mL with limits of agreement of -21.1 to 26.4 mL. The matrix 3-D US showed excellent agreement with dynamic MRI. Therefore matrix 3-D US is a reliable alternative to measure gastric volumes.

  8. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

    A pipeline, implemented within the Insight Segmentation and Registration Toolkit (ITK) and The Visualization Toolkit (VTK) framework, to delineate each nucleus and to profile morphometric and colony organization. At an abstract level, our approach is an extension of a previously developed method for monolayer call structure models.

  9. Steady state reconnection at a single 3D magnetic null point

    NASA Astrophysics Data System (ADS)

    Galsgaard, K.; Pontin, D. I.

    2011-05-01

    Aims: We systematically stress a rotationally symmetric 3D magnetic null point by advecting the opposite footpoints of the spine axis in opposite directions. This stress eventually concentrates in the vicinity of the null point, thereby forming a local current sheet through which magnetic reconnection takes place. The aim is to look for a steady state evolution of the current sheet dynamics, which may provide scaling relations for various characteristic parameters of the system. Methods: The evolution is followed by solving numerically the non-ideal MHD equations in a Cartesian domain. The null point is embedded in an initially constant density and temperature plasma. Results: It is shown that a quasi-steady reconnection process can be set up at a 3D null by continuous shear driving. It appears that a true steady state is unlikely to be realised because the current layer tends to grow until it is restricted by the geometry of the computational domain and the imposed driving profile. However, ratios between characteristic quantities clearly settle after some time to stable values, so that the evolution is quasi-steady. The experiments show a number of scaling relations, but they do not provide a clear consensus for extending to lower magnetic resistivity or faster driving velocities. More investigations are needed to fully clarify the properties of current sheets at magnetic null points.

  10. Magnetospheric Magnetic Reconnection with Southward IMF by a 3D EMPM Simulation

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Yan, X. Y.; Cai, D. S.; Lembege, B.

    2004-01-01

    We report our new simulation results on magnetospheric magnetic reconnection with southward IMF using a 3D EMPM model, with greater resolution and more particles using the parallelized 3D HPF TRISTAN code on VPP5000 supercomputer. Main parameters used in the new simulation are: domain size is 215 x 145 x 145, grid size = 0.5 Earth radius, initial particle number is 16 per cell, the IMF is southward. Arrival of southward IMF will cause reconnection in the magnetopause, thus allowing particles to enter into the inner magnetosphere. Sunward and tailward high particle flow are observed by satellites, and these phenomena are also observed in the simulation near the neutral line (X line) of the near-Earth magnetotail. This high particle flow goes along with the reconnected island. The magnetic reconnection process contributes to direct plasma entry between the magnetosheath to the inner magnetosphere and plasma sheet, in which the entry process eats the magnetosheath plasma to plasma sheet temperatures. We investigate magnetic, electric fields, density, and current during this magnetic reconnection with southward IMF. Further investigation with this simulation will provide insight into unsolved problems, such as the triggering of storms and substorms, and the storm-substorm relationship. New results will be presented at the meeting.

  11. Breast Density Analysis with Automated Whole-Breast Ultrasound: Comparison with 3-D Magnetic Resonance Imaging.

    PubMed

    Chen, Jeon-Hor; Lee, Yan-Wei; Chan, Si-Wa; Yeh, Dah-Cherng; Chang, Ruey-Feng

    2016-05-01

    In this study, a semi-automatic breast segmentation method was proposed on the basis of the rib shadow to extract breast regions from 3-D automated whole-breast ultrasound (ABUS) images. The density results were correlated with breast density values acquired with 3-D magnetic resonance imaging (MRI). MRI images of 46 breasts were collected from 23 women without a history of breast disease. Each subject also underwent ABUS. We used Otsu's thresholding method on ABUS images to obtain local rib shadow information, which was combined with the global rib shadow information (extracted from all slice projections) and integrated with the anatomy's breast tissue structure to determine the chest wall line. The fuzzy C-means classifier was used to extract the fibroglandular tissues from the acquired images. Whole-breast volume (WBV) and breast percentage density (BPD) were calculated in both modalities. Linear regression was used to compute the correlation of density results between the two modalities. The consistency of density measurement was also analyzed on the basis of intra- and inter-operator variation. There was a high correlation of density results between MRI and ABUS (R(2) = 0.798 for WBV, R(2) = 0.825 for PBD). The mean WBV from ABUS images was slightly smaller than the mean WBV from MR images (MRI: 342.24 ± 128.08 cm(3), ABUS: 325.47 ± 136.16 cm(3), p < 0.05). In addition, the BPD calculated from MR images was smaller than the BPD from ABUS images (MRI: 24.71 ± 15.16%, ABUS: 28.90 ± 17.73%, p < 0.05). The intra-operator and inter-operator variant analysis results indicated that there was no statistically significant difference in breast density measurement variation between the two modalities. Our results revealed a high correlation in WBV and BPD between MRI and ABUS. Our study suggests that ABUS provides breast density information useful in the assessment of breast health.

  12. An approach to 3D magnetic field calculation using numerical and differential algebra methods

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.; Brady, V.O.

    1992-07-17

    Motivated by the need for new means for specification and determination of 3D fields that are produced by electromagnetic lens elements in the region interior to coil windings and seeking to obtain techniques that will be convenient for accurate conductor placement and dynamical study of particle motion, we have conveniently gene the representation of a 2D magnetic field to 3D. We have shown that the 3 dimensioal magnetic field components of a multipole magnet in the curl-fire divergence-fire region near the axis r=0 can be derived from one dimensional functions A{sub n}(z) and their derivatives (part 1). In the region interior to coil windings of accelerator magnets the three spatial components of magnet fields can be expressed in terms of harmonic components'' proportional to functions sin (n{theta}) or cos (n{theta}) of the azimuthal angle. The r,z dependence of any such component can then be expressed in terms of powers of r times functions A{sub n}(z) and their derivatives. For twodimensional configurations B{sub z} of course is identically zero, the derivatives of A{sub n}(z) vanish, and the harmonic components of the transverse field then acquire a simple proportionality B{sub r,n} {proportional to} r{sup n-1} sin (n{theta}),B{sub {theta},n} {proportional to} r{sup n-1} cos (n{theta}), whereas in a 3-D configuration the more complex nature of the field gives rise to additional so-called psuedomultipole'' components as judged by additional powers of r required in the development of the field. Computation of the 3-D magnetic field arising at a sequence of field points, as a direct result of a specified current configuration or coil geometry, can be calculated explicitly through use of the Biot-Savart law and from such data the coefficients can then be derived for a general development of the type indicated above. We indicate, discuss, and illustrate two means by which this development may be performed.

  13. Effects of magnetic ripple on 3D equilibrium and alpha particle confinement in the European DEMO

    NASA Astrophysics Data System (ADS)

    Pfefferlé, D.; Cooper, W. A.; Fasoli, A.; Graves, J. P.

    2016-11-01

    An assessment of alpha particle confinement is performed in the European DEMO reference design. 3D MHD equilibria with nested flux-surfaces and single magnetic axis are obtained with the VMEC free-boundary code, thereby including the plasma response to the magnetic ripple created by the finite number of TF coils. Populations of fusion alphas that are consistent with the equilibrium profiles are evolved until slowing-down with the VENUS-LEVIS orbit code in the guiding-centre approximation. Fast ion losses through the last-closed flux-surface are numerically evaluated with two ripple models: (1) using the 3D equilibrium and (2) algebraically adding the non-axisymmetric ripple perturbation to the 2D equilibrium. By virtue of the small ripple field and its non-resonant nature, both models quantitatively agree. Differences are however noted in the toroidal location of particles losses on the last-closed flux-surface, which in the first case is 3D and in the second not. Superbanana transport, i.e. ripple-well trapping and separatrix crossing, is expected to be the dominant loss mechanism, the strongest effect on alphas being between 100-200 KeV. Above this, stochastic ripple diffusion is responsible for a rather weak loss rate, as the stochastisation threshold is observed numerically to be higher than analytic estimates. The level of ripple in the current 18 TF coil design of the European DEMO is not found to be detrimental to fusion alpha confinement.

  14. ProSAT+: visualizing sequence annotations on 3D structure.

    PubMed

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org.

  15. 3D spin-flop transition in enhanced 2D layered structure single crystalline TlCo2Se2

    NASA Astrophysics Data System (ADS)

    Jin, Z.; Xia, Z.-C.; Wei, M.; Yang, J.-H.; Chen, B.; Huang, S.; Shang, C.; Wu, H.; Zhang, X.-X.; Huang, J.-W.; Ouyang, Z.-W.

    2016-10-01

    The enhanced 2D layered structure single crystalline TlCo2Se2 has been successfully fabricated, which exhibits field-induced 3D spin-flop phase transitions. In the case of the magnetic field parallel to the c-axis (B//c), the applied magnetic field induces the evolution of the noncollinear helical magnetic coupling into a ferromagnetic (FM) state with all the magnetization of the Co ion parallel to the c-axis. A striking variation of the field-induced strain within the ab-plane is noticed in the magnetic field region of 20-30 T. In the case of the magnetic field perpendicular to the c-axis (B  ⊥  c), the inter-layer helical antiferromagnetic (AFM) coupling may transform to an initial canted AFM coupling, and then part of it transforms to an intermediate metamagnetic phase with the alignment of two-up-one-down Co magnetic moments and finally to an ultimate FM coupling in higher magnetic fields. The robust noncollinear AFM magnetic coupling is completely destroyed above 30 T. In combination with the measurements of magnetization, magnetoresistance and field-induced strain, a complete magnetic phase diagram of the TlCo2Se2 single crystal has been depicted, demonstrating complex magnetic structures even though the crystal geometry itself gives no indication of the magnetic frustration.

  16. Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures

    DTIC Science & Technology

    2015-11-17

    fabricated using 3D printer . The fill factor decreases radially outwards and the voids are visible in the unit cells as you approach the periphery of the...with thin walls) [29]. Figure 6: Examples of lenses fabricated with AM (a) GRIN lens fabricated using 3D printer . The fill factor decreases...AFRL-RW-EG-TP-2015-002 Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures Jeffery W. Allen Monica S. Allen Brett

  17. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

    Roddy, P. A.; Huang, C. Y.; Lyke, J.; Baur, J.; Durstock, M.; MacDonald, E.

    2013-12-01

    Three-dimensional printing, more formally Additive Manufacturing (AM), is being explored by groups worldwide for use in space missions, but we recognize the amazing potential of this emerging technology to produce space weather environmental sensors at costs commensurate with declining research budgets. We present here a plan to go substantially beyond the novelty stage of this technology by developing a foundation for using AM in high-assurance space system missions. Our two-pronged approach involves (1) a disciplined investigation of material properties and reliability (electrical, mechanical, radiation) of AM and (2) the extension of this knowledge to make complex structures that can exploit the advantages of AM. We address the design, manufacture, and optimization of multifunctional space structures using multi-physics design methods, integrated computational models, and AM. Integrated multifunctional structures have significant advantage in flexibility, size, weight, and power in comparison to formally attached elements, but their design and fabrication can be complex. The complexity and range in element shape, processing method, material properties and vehicle integration make this an ideal problem to advance the current state of the art methods for multiphysics mechanism design and strengthening AM processing science.

  18. Code System for Analysis of 3-D Reinforced Concrete Structures.

    SciTech Connect

    ANDERSON, C. A.

    1999-11-22

    Version 00 NONSAP-C is a finite element program for determining the static and dynamic response of three-dimensional reinforced concrete structures. Long-term, or creep, behavior of concrete structures can also be analyzed. Nonlinear constitutive relations for concrete under short-term loads are incorporated in two time-independent models, a variable-modulus approach with orthotropic behavior induced in the concrete due to the development of different tangent moduli in different directions and an elastic-plastic model in which the concrete is assumed to be a continuous, isotropic, and linearly elastic-plastic strain-hardening-fracture material. A viscoelastic constitutive model for long-term thermal creep of concrete is included. Three-dimensional finite elements available in NONSAP-C include a truss element, a multinode tendon element for prestressed and post tensioned concrete structures, an elastic-plastic membrane element to represent the behavior of cavity liners, and a general isoparametric element with a variable number of nodes for analysis of solids and thick shells.

  19. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  20. An orientation measurement method based on Hall-effect sensors for permanent magnet spherical actuators with 3D magnet array.

    PubMed

    Yan, Liang; Zhu, Bo; Jiao, Zongxia; Chen, Chin-Yin; Chen, I-Ming

    2014-10-24

    An orientation measurement method based on Hall-effect sensors is proposed for permanent magnet (PM) spherical actuators with three-dimensional (3D) magnet array. As there is no contact between the measurement system and the rotor, this method could effectively avoid friction torque and additional inertial moment existing in conventional approaches. Curved surface fitting method based on exponential approximation is proposed to formulate the magnetic field distribution in 3D space. The comparison with conventional modeling method shows that it helps to improve the model accuracy. The Hall-effect sensors are distributed around the rotor with PM poles to detect the flux density at different points, and thus the rotor orientation can be computed from the measured results and analytical models. Experiments have been conducted on the developed research prototype of the spherical actuator to validate the accuracy of the analytical equations relating the rotor orientation and the value of magnetic flux density. The experimental results show that the proposed method can measure the rotor orientation precisely, and the measurement accuracy could be improved by the novel 3D magnet array. The study result could be used for real-time motion control of PM spherical actuators.

  1. Structural 3d Monitoring Using a New Sinusoidal Fitting Adjustment

    NASA Astrophysics Data System (ADS)

    Detchev, I.; Habib, A.; Lichti, D.; El-Badry, M.

    2016-06-01

    Digital photogrammetric systems combined with image processing techniques have been used for structural monitoring purposes for more than a decade. For applications requiring sub-millimetre level precision, the use of off-the-shelf DSLR cameras is a suitable choice, especially when the low cost of the involved sensors is a priority. The disadvantage in the use of entry level DSLRs is that there is a trade-off between frame rate and burst rate - a high frame rate is either not available or it cannot be sustained long enough. This problem must be overcome when monitoring a structural element undergoing a dynamic test, where a range of loads are cycled through multiple times a second. In order to estimate deflections during such a scenario, this paper proposes a new least-squares adjustment for sinusoidal fitting. The new technique is capable of processing multiple back-to-back bursts of data within the same adjustment, which synthetically increases the de-facto temporal resolution of the system. The paper describes a beam deformation test done in a structures laboratory. The experimental results were assessed in terms of both their precision and accuracy. The new method increased the effective sampling frequency three-fold, which improved the standard deviations of the estimated parameters with up to two orders of magnitude. A residual RMSE as low as 30 μm was attained, and likewise the RMSE of the computed amplitudes between the photogrammetric system and the control laser transducers was as small as 34 μm.

  2. Small-angle scattering and 3D structure interpretation.

    PubMed

    Trewhella, Jill

    2016-10-01

    This review focuses on advances in the application of solution small-angle scattering (SAS) in structural analysis of biomolecules and the complexes they form. Examples highlighted illustrate the unique contribution of SAS, using both X-rays and neutrons, in hybrid or integrative modelling methods. The increased information content when neutron scattering with contrast variation is used is a particular focus. Finally, progress toward an agreed reporting framework, the development of open data and model archives, and the importance of these initiatives is covered.

  3. Structural and property studies on metal-organic compounds with 3-D supramolecular network

    NASA Astrophysics Data System (ADS)

    Zhang, Qi-Ying; Ma, Ke-Fang; Xiao, Hong-Ping; Li, Xin-Hua; Shi, Qian

    2014-07-01

    Two carboxylato-bridged allomeric compounds, {[Cu2(dbsa)2(hmt) (H2O)4]1/2·2H2O}n (1), {[Ni(dbsa)(H2O)2]1/2[Ni(dbsa)(hmt)(H2O)2]1/2·2H2O}n (2) (H2dbsa=meso-2,3-dibromosuccinic acid, hmt=hexamethylenetetramine) have been synthesized and characterized by X-ray structral analyses. The metal ions have two kinds of coordination fashion in one unit, and bridged by carboxylate and hmt ligands along with weak interactions existing in the solid structure, forming a 3-D supramolecular network. Variable-temperature magnetic property studies reveal the existence of antiferromagnetic interactions in 1 and 2 with g=2.2, J1=-3.5 cm-1, J2=-2.8 cm-1 for 1, and g=2.1, J=-3.5 cm-1 for 2.

  4. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  5. 3D nano-structures for laser nano-manipulation

    PubMed Central

    Seniutinas, Gediminas; Gervinskas, Gediminas; Brasselet, Etienne; Juodkazis, Saulius

    2013-01-01

    Summary The resputtering of gold films from nano-holes defined in a sacrificial PMMA mask, which was made by electron beam lithography, was carried out with a dry plasma etching tool in order to form well-like structures with a high aspect ratio (height/width ≈ 3–4) at the rims of the nano-holes. The extraordinary transmission through the patterns of such nano-wells was investigated experimentally and numerically. By doing numerical simulations of 50-nm and 100-nm diameter polystyrene beads in water and air, we show the potential of such patterns for self-induced back-action (SIBA) trapping. The best trapping conditions were found to be a trapping force of 2 pN/W/μm2 (numerical result) exerted on a 50-nm diameter bead in water. The simulations were based on the analytical Lorentz force model. PMID:24062979

  6. 3D mapping of neuronal migration in the embryonic mouse brain with magnetic resonance microimaging.

    PubMed

    Deans, Abby E; Wadghiri, Youssef Zaim; Aristizábal, Orlando; Turnbull, Daniel H

    2015-07-01

    A prominent feature of the developing mammalian brain is the widespread migration of neural progenitor (NP) cells during embryogenesis. A striking example is provided by NP cells born in the ventral forebrain of mid-gestation stage mice, which subsequently migrate long distances to their final positions in the cortex and olfactory bulb. Previous studies have used two-dimensional histological methods, making it difficult to analyze three-dimensional (3D) migration patterns. Unlike histology, magnetic resonance microimaging (micro-MRI) is a non-destructive, quantitative and inherently 3D imaging method for analyzing mouse embryos. To allow mapping of migrating NP cells with micro-MRI, cells were labeled in situ in the medial (MGE) and lateral (LGE) ganglionic eminences, using targeted in utero ultrasound-guided injection of micron-sized particles of iron-oxide (MPIO). Ex vivo micro-MRI and histology were then performed 5-6days after injection, demonstrating that the MPIO had magnetically labeled the migrating NP populations, which enabled 3D visualization and automated segmentation of the labeled cells. This approach was used to analyze the distinct patterns of migration from the MGE and LGE, and to construct rostral-caudal migration maps from each progenitor region. Furthermore, abnormal migratory phenotypes were observed in Nkx2.1(-/-) embryos, most notably a significant increase in cortical neurons derived from the Nkx2.1(-/-) LGE. Taken together, these results demonstrate that MPIO labeling and micro-MRI provide an efficient and powerful approach for analyzing 3D cell migration patterns in the normal and mutant mouse embryonic brain.

  7. 3-D Structure of Sunspots using Imaging Spectroscopy

    NASA Technical Reports Server (NTRS)

    Balasubramaniam, K. S.; Gary, G. Allen; Reardon, K.

    2006-01-01

    We use the Interferometric BIdimensional Spectrometer (IBIS) of the INAF/Arcetri Astrophysical Observatory and installed at the National Solar Observatory (NSO) Dunn Solar Telescope, to understand the structure of sunspots. Using the spectral lines FeI 6301.5 A, FeII 7224.4 A, and CaII 8542.6 A, we examine the spectroscopic variation of sunspot penumbral and umbral structures at the heights of formation of these lines. These high resolution observations were acquired on 2004 July 30-31, of active region NOAA 10654, using the high order NSO adaptive optics system. We map the spatio-temporal variation of Doppler signatures in these spectral lines, from the photosphere to the chromosphere. From a 70-minute temporal average of individual 32-second cadence Doppler observations we find that the averaged velocities decrease with height, about 3.5 times larger in the deeper photosphere (FeII 7224.4 A; height-of-formation approx. 50 km) than in the upper photosphere FeI 6301.5 A; height-of-formation approx. 350 km), There is a remarkable coherence of Doppler signals over the height difference of 300 km. From a high-speed animation of the Doppler sequence we find evidence for what appears to be ejection of high speed gas concentrations from edges of penumbral filaments into the surrounding granular photosphere. The Evershed flow persists a few arcseconds beyond the traditionally demarcated penumbra-granulation boundary. We present these and other results and discuss the implications of these measurements for sunspot models.

  8. Fabrication of 2D and 3D photonic structures using laser lithography

    NASA Astrophysics Data System (ADS)

    Gaso, P.; Jandura, D.; Pudis, D.

    2016-12-01

    In this paper we demonstrate possibilities of three-dimensional (3D) printing technology based on two photon polymerization. We used three-dimensional dip-in direct-laser-writing (DLW) optical lithography to fabricate 2D and 3D optical structures for optoelectronics and for optical sensing applications. DLW lithography allows us use a non conventional way how to couple light into the waveguide structure. We prepared ring resonator and we investigated its transmission spectral characteristic. We present 3D inverse opal structure from its design to printing and scanning electron microscope (SEM) imaging. Finally, SEM images of some prepared photonic crystal structures were performed.

  9. Treatment envelope evaluation in transcranial magnetic resonance-guided focused ultrasound utilizing 3D MR thermometry

    PubMed Central

    2014-01-01

    Background Current clinical targets for transcranial magnetic resonance-guided focused ultrasound (tcMRgFUS) are all located close to the geometric center of the skull convexity, which minimizes challenges related to focusing the ultrasound through the skull bone. Non-central targets will have to be reached to treat a wider variety of neurological disorders and solid tumors. Treatment envelope studies utilizing two-dimensional (2D) magnetic resonance (MR) thermometry have previously been performed to determine the regions in which therapeutic levels of FUS can currently be delivered. Since 2D MR thermometry was used, very limited information about unintended heating in near-field tissue/bone interfaces could be deduced. Methods In this paper, we present a proof-of-concept treatment envelope study with three-dimensional (3D) MR thermometry monitoring of FUS heatings performed in a phantom and a lamb model. While the moderate-sized transducer used was not designed for transcranial geometries, the 3D temperature maps enable monitoring of the entire sonication field of view, including both the focal spot and near-field tissue/bone interfaces, for full characterization of all heating that may occur. 3D MR thermometry is achieved by a combination of k-space subsampling and a previously described temporally constrained reconstruction method. Results We present two different types of treatment envelopes. The first is based only on the focal spot heating—the type that can be derived from 2D MR thermometry. The second type is based on the relative near-field heating and is calculated as the ratio between the focal spot heating and the near-field heating. This utilizes the full 3D MR thermometry data achieved in this study. Conclusions It is shown that 3D MR thermometry can be used to improve the safety assessment in treatment envelope evaluations. Using a non-optimal transducer, it is shown that some regions where therapeutic levels of FUS can be delivered, as suggested by

  10. Stress Recovery and Error Estimation for 3-D Shell Structures

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

    The C1-continuous stress fields obtained from finite element analyses are in general lower- order accurate than are the corresponding displacement fields. Much effort has focussed on increasing their accuracy and/or their continuity, both for improved stress prediction and especially error estimation. A previous project developed a penalized, discrete least squares variational procedure that increases the accuracy and continuity of the stress field. The variational problem is solved by a post-processing, 'finite-element-type' analysis to recover a smooth, more accurate, C1-continuous stress field given the 'raw' finite element stresses. This analysis has been named the SEA/PDLS. The recovered stress field can be used in a posteriori error estimators, such as the Zienkiewicz-Zhu error estimator or equilibrium error estimators. The procedure was well-developed for the two-dimensional (plane) case involving low-order finite elements. It has been demonstrated that, if optimal finite element stresses are used for the post-processing, the recovered stress field is globally superconvergent. Extension of this work to three dimensional solids is straightforward. Attachment: Stress recovery and error estimation for shell structure (abstract only). A 4-node, shear-deformable flat shell element developed via explicit Kirchhoff constraints (abstract only). A novel four-node quadrilateral smoothing element for stress enhancement and error estimation (abstract only).

  11. One-, Two-, and Three-Dimensional Heterospin Complexes Consisting of 4-(N-tert-Butyloxylamino)pyridine (4NOpy), Dicyanamide Ion (DCA), and 3d Metal Ions: Crystal Structures and Magnetic Properties of [M(II)(4NOpy)x(DCA)y(CH3CN)z]n (M = Mn, Co, Ni, Cu, Zn).

    PubMed

    Ogawa, Hiraku; Mori, Koya; Murashima, Kensuke; Karasawa, Satoru; Koga, Noboru

    2016-01-19

    Solutions of 3d metal ion salts, M(NO3)2, 4-(N-tert-butyloxylamino)pyridine (4NOpy), and dicyanamide (DCA) in CH3CN were mixed to afford single crystals of the polymeric complexes [M(II)(4NOpy)x(DCA)y(CH3CN)z]n (M(II) = Mn (1), Co (2), Ni (3), Cu (4a and 4b), Zn (5)). X-ray crystallography revealed that the crystal structures are a three-dimensional (3-D) network for 1, 2-D networks for 2, 3, 4a, and 5, and a 1-D chain for 4b. Crystals of 2, 3, 4a, and 5 contained CH3CN molecules as crystal solvents, which were readily desorbed in the ambient atmosphere. After desorption of the CH3CN molecules, the crystal structures of 2 and 3 were confirmed to be slightly shrunk without destruction of the crystal lattice. Crystals of 2, 3, 4a, and 5 after desorption of crystal solvents were used for investigations of the magnetic properties. Complex 1 showed antiferromagnetic interactions to form a ferrimagnetic chain and exhibited the magnetic behavior of a 2-D (or 3-D) spin-canted antiferromagnet with TN = 12 K. Complex 2 containing anisotropic Co(II) ions also showed the behavior of a 1-D (or 2-D) spin-canted antiferromagnet with TN = 6 K. In 3, 4a, and 4b, the aminoxyl of 4NOpy ferromagnetically interacted with the metal ion with coupling constants of JM-NO/kB = 45, 45, and 43 K, respectively. In 5, the magnetic couplings between the aminoxyls in 4NOpy through the diamagnetic Zn(II) ion were weakly antiferromagntic (JNO-NO = -1.2 K). DCA might be a weak antiferromagnetic connector for the metal chains.

  12. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J. ); Jones, G.L. )

    1996-01-01

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  13. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  14. A 3-D fluorescence imaging system incorporating structured illumination technology

    NASA Astrophysics Data System (ADS)

    Antos, L.; Emord, P.; Luquette, B.; McGee, B.; Nguyen, D.; Phipps, A.; Phillips, D.; Helguera, M.

    2010-02-01

    A currently available 2-D high-resolution, optical molecular imaging system was modified by the addition of a structured illumination source, OptigridTM, to investigate the feasibility of providing depth resolution along the optical axis. The modification involved the insertion of the OptigridTM and a lens in the path between the light source and the image plane, as well as control and signal processing software. Projection of the OptigridTM onto the imaging surface at an angle, was resolved applying the Scheimpflug principle. The illumination system implements modulation of the light source and provides a framework for capturing depth resolved mages. The system is capable of in-focus projection of the OptigridTM at different spatial frequencies, and supports the use of different lenses. A calibration process was developed for the system to achieve consistent phase shifts of the OptigridTM. Post-processing extracted depth information using depth modulation analysis using a phantom block with fluorescent sheets at different depths. An important aspect of this effort was that it was carried out by a multidisciplinary team of engineering and science students as part of a capstone senior design program. The disciplines represented are mechanical engineering, electrical engineering and imaging science. The project was sponsored by a financial grant from New York State with equipment support from two industrial concerns. The students were provided with a basic imaging concept and charged with developing, implementing, testing and validating a feasible proof-of-concept prototype system that was returned to the originator of the concept for further evaluation and characterization.

  15. The 3D velocity structure beneath Iceland: Identifying melt pathways

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

    The integration of various seismic datasets, recorded by the broadband HOTSPOT network deployed across Iceland, provides one of the highest resolution studies of the crust and mantle structure associated with a plume-ridge system. The mantle P- and S-velocity models (ICEMAN), derived from teleseismic body-wave and surface wave analysis, show a vertical, cylindrical low velocity anomaly ˜200 km in diameter extending from ˜400 km, the maximum depth of resolution, up to ˜200 km above which low velocity material is present beneath all of Iceland. The maximum P- and S-velocity anomalies of -2% and -4% respectively are found beneath the northwestern edge of Vatnajokull. The crustal S-velocity model (ICECRTb) is constrained by local surface waves, refraction experiments and receiver functions, and shows significant variation in crustal thickness. The thinnest, ˜15 km, crust is found around coastal regions, the thickest crust is beneath northwestern Vatnajokull where it reaches a thickness of 45 km. Within this thick crustal root is a vertical low velocity anomaly connecting the core of the mantle anomaly to horizontal low velocity regions that extend along the western and eastern volcanic zones but not the northern volcanic zone. These crustal low velocity zones are interpreted as regions through which melt is fed from the mantle to shallow magma chambers beneath the rift zones, where crustal formation occurs. The pipework between the core of the mantle anomaly and the southern rift zones is responsible for ˜30 km thick crust. Its absence to the north results in relatively thin, ˜20 km thick, crust.

  16. Electrodeposition-based 3D Printing of Metallic Microarchitectures with Controlled Internal Structures.

    PubMed

    Seol, Seung Kwon; Kim, Daeho; Lee, Sanghyeon; Kim, Jung Hyun; Chang, Won Suk; Kim, Ji Tae

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions.

  17. Four 3D "brick-wall"-like metal-organic frameworks with a flexible ligand of (S,S,R,R)-1,2,3,4-cyclopentanetetracarboxylic acid: crystal structures, luminescent and magnetic properties.

    PubMed

    Cui, Lin; Luan, Xin-Jun; Zhang, Cui-Ping; Kang, Yi-Fan; Zhang, Wen-Tao; Wang, Yao-Yu; Shi, Qi-Zhen

    2013-02-07

    To investigate the conformation of cyclopentanetetracarboxylic acid, four new "brick-wall"-like metal-organic frameworks have been synthesized from hydrothermal reactions with different metal salts, (S,S,R,R)-1,2,3,4-cyclopentanetetracarboxylic acid (H(4)cptc) and auxiliary N-donor ligands, namely, Cu(2)(S,S,R,R-cptc)(bpe)(H(2)O)(2)·2H(2)O (1), Co(2)(S,S,R,R-cptc)(bpe)(0.5)(H(2)O)(2)·2H(2)O (2), Cd(4)(S,S,R,R-cptc)(2)(bpa)(2)(H(2)O)(5)·2H(2)O (3) and Co(2)(S,S,R,R-cptc)(bpy)(0.5)(H(2)O)(2)·2(H(2)O) (4) (bpe = 4-(2-(pyridine-4-yl)vinyl)pyridine, bpa = 4-(2-(pyridine-4-yl)ethyl)pyridine, bpy = 4-(pyridine-4-yl)pyridine). The complexes were further characterized by single-crystal X-ray diffraction, power X-ray diffraction, FT-IR spectra, fluorescent measurements and variable-temperature magnetic susceptibility measurements. The results of the structural investigations show that 1 is a charming (3,3,4)-trinodal architecture, 3 is an interesting trinodal (3,4,5)-connected architecture, and 2 and 4 are isostructural, which are both (4,5)-connected networks. In addition, the magnetic measurements indicate that 2 and 4 show weak antiferromagnetic interactions, and the fluorescent measurement shows the strong solid-state fluorescent emission at room temperature for 3.

  18. Searching protein 3-D structures for optimal structure alignment using intelligent algorithms and data structures.

    PubMed

    Novosád, Tomáš; Snášel, Václav; Abraham, Ajith; Yang, Jack Y

    2010-11-01

    In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.

  19. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets.

  20. 3D linear inversion of magnetic susceptibility data acquired by frequency domain EMI

    NASA Astrophysics Data System (ADS)

    Thiesson, J.; Tabbagh, A.; Simon, F.-X.; Dabas, M.

    2017-01-01

    Low induction number EMI instruments are able to simultaneously measure a soil's apparent magnetic susceptibility and electrical conductivity. This family of dual measurement instruments is highly useful for the analysis of soils and archeological sites. However, the electromagnetic properties of soils are found to vary over considerably different ranges: whereas their electrical conductivity varies from ≤ 0.1 to ≥ 100 mS/m, their relative magnetic permeability remains within a very small range, between 1.0001 and 1.01 SI. Consequently, although apparent conductivity measurements need to be inverted using non-linear processes, the variations of the apparent magnetic susceptibility can be approximated through the use of linear processes, as in the case of the magnetic prospection technique. Our proposed 3D inversion algorithm starts from apparent susceptibility data sets, acquired using different instruments over a given area. A reference vertical profile is defined by considering the mode of the vertical distributions of both the electrical resistivity and of the magnetic susceptibility. At each point of the mapped area, the reference vertical profile response is subtracted to obtain the apparent susceptibility variation dataset. A 2D horizontal Fourier transform is applied to these variation datasets and to the dipole (impulse) response of each instrument, a (vertical) 1D inversion is performed at each point in the spectral domain, and finally the resulting dataset is inverse transformed to restore the apparent 3D susceptibility variations. It has been shown that when applied to synthetic results, this method is able to correct the apparent deformations of a buried object resulting from the geometry of the instrument, and to restore reliable quantitative susceptibility contrasts. It also allows the thin layer solution, similar to that used in magnetic prospection, to be implemented. When applied to field data it initially delivers a level of contrast

  1. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

  2. Structure of the Rambler Rhyolite, Baie Verte Peninsula, Newfoundland: Inversions using UBC-GIF Grav3D and Mag3D

    NASA Astrophysics Data System (ADS)

    Spicer, B.; Morris, B.; Ugalde, H.

    2011-09-01

    Hosted within the Pacquet Harbour Group (PHG) on the Baie Verte Peninsula of north-central Newfoundland, the Rambler rhyolite is a 487 Ma unit of felsic tuffs, flows and subvolcanic intrusive rocks. The PHG has been affected by multiple phases of deformation with the youngest D4 deformation event producing broad northeast plunging upright cross folds in the Rambler rhyolite. Fold culminations on the upper bounding surface of the rhyolite host Cu +/- Au volcanogenic massive sulfide deposits (e.g. Rambler and Ming mines). Geophysical inversions of recently acquired high resolution gravity and magnetic data have been implemented to determine the extent of the fold axis (dome) at depth. To direct the outcome of the inversion process towards a more geologically reasonable solution this study outlines a procedure which permits the inclusion of known geological and geophysical constraints into the input (reference) model for inversion using the MAG3D and GRAV3D algorithms provided by the University of British Columbia Geophysical Inversion Facility. Reference model constraints included surficial geological contacts as defined by aeromagnetic data, and subsurface distribution of physical property variations from a series of drill-hole logs. The output (computed) model images the surface of the rhyolite dome as dipping roughly 40° to the northeast as a series of voxels with density values ranging from 2.71 to 2.75 g/cm3. While previously published ore deposit models parallel this structure in the near surface, results from these inversions suggest deeper exploration may be favorable. Magnetic inversion modeling has not provided any insight into dome morphology however it outlines the distribution of gabbroic dykes surrounding the dome.

  3. Sawtooth mitigation in 3D MHD tokamak modelling with applied magnetic perturbations

    NASA Astrophysics Data System (ADS)

    Bonfiglio, D.; Veranda, M.; Cappello, S.; Chacón, L.; Escande, D. F.

    2017-01-01

    The effect of magnetic perturbations (MPs) on the sawtoothing dynamics of the internal kink mode in the tokamak is discussed in the framework of nonlinear 3D MHD modelling. Numerical simulations are performed with the pixie3d code (Chacón 2008 Phys. Plasmas 15 056103) based on a D-shaped configuration in toroidal geometry. MPs are applied as produced by two sets of coils distributed along the toroidal direction, one set located above and the other set below the outboard midplane, like in experimental devices such as DIII-D and ASDEX Upgrade. The capability of n  =  1 MPs to affect quasi-periodic sawteeth is shown to depend on the toroidal phase difference Δ φ between the perturbations produced by the two sets of coils. In particular, sawtooth mitigation is obtained for the Δ φ =π phasing, whereas no significant effect is observed for Δ φ =0 . Numerical findings are explained by the interplay between different poloidal harmonics in the spectrum of applied MPs, and appear to be consistent with experiments performed in the DIII-D device. Sawtooth mitigation and stimulation of self-organized helical states by applied MPs have been previously demonstrated in both circular tokamak and reversed-field pinch (RFP) experiments in the RFX-mod device, and in related 3D MHD modelling.

  4. 3D kinematics of the tarsal joints from magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Hirsch, Bruce E.; Udupa, Jayaram K.; Okereke, Enyi; Hillstrom, Howard J.; Siegler, Sorin; Ringleb, Stacie I.; Imhauser, Carl W.

    2001-09-01

    We have developed a method for analyzing motion at skeletal joints based on the 3D reconstruction of magnetic resonance (MR) image data. Since the information about each voxel in MR images includes its location in the scanner, it follows that information is available for each organ whose 3D surface is computed from a series of MR slices. In addition, there is information on the shape and orientation of each organ, and the contact areas of adjacent bones. By collecting image data in different positions we can calculate the motion of the individual bones. We have used this method to study human foot bones, in order to understand normal and abnormal foot function. It has been used to evaluate patients with tarsal coalitions, various forms of pes planus, ankle sprains, and several other conditions. A newly described feature of this system is the ability to visualize the contact area at a joint, as determined by the region of minimum distance. The display of contact area helps understand abnormal joint function. Also, the use of 3D imaging reveals motions in joints which cannot otherwise be visualized, such as the subtalar joint, for more accurate diagnosis of joint injury.

  5. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    NASA Astrophysics Data System (ADS)

    Babu, Sabarish; Liao, Pao-Chuan; Shin, Min C.; Tsap, Leonid V.

    2006-12-01

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  6. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  7. Fast ion transport during applied 3D magnetic perturbations on DIII-D

    DOE PAGES

    Van Zeeland, Michael A.; Ferraro, N. M.; Grierson, Brian A.; ...

    2015-06-26

    In this paper, measurements show fast ion losses correlated with applied three-dimensional (3D) fields in a variety of plasmas ranging from L-mode to resonant magnetic perturbation (RMP) edge localized mode (ELM) suppressed H-mode discharges. In DIII-D L-mode discharges with a slowly rotatingmore » $n=2$ magnetic perturbation, scintillator detector loss signals synchronized with the applied fields are observed to decay within one poloidal transit time after beam turn-off indicating they arise predominantly from prompt loss orbits. Full orbit following using M3D-C1 calculations of the perturbed fields and kinetic profiles reproduce many features of the measured losses and points to the importance of the applied 3D field phase with respect to the beam injection location in determining the overall impact on prompt beam ion loss. Modeling of these results includes a self-consistent calculation of the 3D perturbed beam ion birth profiles and scrape-off-layer ionization, a factor found to be essential to reproducing the experimental measurements. Extension of the simulations to full slowing down timescales, including fueling and the effects of drag and pitch angle scattering, show the applied $n=3$ RMPs in ELM suppressed H-mode plasmas can induce a significant loss of energetic particles from the core. With the applied $n=3$ fields, up to 8.4% of the injected beam power is predicted to be lost, compared to 2.7% with axisymmetric fields only. These fast ions, originating from minor radii $$\\rho >0.7$$ , are predicted to be primarily passing particles lost to the divertor region, consistent with wide field-of-view infrared periscope measurements of wall heating in $n=3$ RMP ELM suppressed plasmas. Edge fast ion $${{\\text{D}}_{\\alpha}}$$ (FIDA) measurements also confirm a large change in edge fast ion profile due to the $n=3$ fields, where the effect was isolated by using short 50 ms RMP-off periods during which ELM suppression was maintained yet the fast ion profile

  8. Fast ion transport during applied 3D magnetic perturbations on DIII-D

    SciTech Connect

    Van Zeeland, Michael A.; Ferraro, N. M.; Grierson, Brian A.; Heidbrink, W. W.; Kramer, G. J.; Lasnier, C. J.; Pace, David C.; Allen, Steve L.; Chen, X.; Evans, T. E.; García-Muñoz, M.; Hanson, J. M.; Lanctot, M. J.; Lao, L. L.; Meyer, W. H.; Moyer, R. A.; Nazikian, R.; Orlov, D. M.; Paz-Soldan, C.; Wingen, A.

    2015-06-26

    In this paper, measurements show fast ion losses correlated with applied three-dimensional (3D) fields in a variety of plasmas ranging from L-mode to resonant magnetic perturbation (RMP) edge localized mode (ELM) suppressed H-mode discharges. In DIII-D L-mode discharges with a slowly rotating $n=2$ magnetic perturbation, scintillator detector loss signals synchronized with the applied fields are observed to decay within one poloidal transit time after beam turn-off indicating they arise predominantly from prompt loss orbits. Full orbit following using M3D-C1 calculations of the perturbed fields and kinetic profiles reproduce many features of the measured losses and points to the importance of the applied 3D field phase with respect to the beam injection location in determining the overall impact on prompt beam ion loss. Modeling of these results includes a self-consistent calculation of the 3D perturbed beam ion birth profiles and scrape-off-layer ionization, a factor found to be essential to reproducing the experimental measurements. Extension of the simulations to full slowing down timescales, including fueling and the effects of drag and pitch angle scattering, show the applied $n=3$ RMPs in ELM suppressed H-mode plasmas can induce a significant loss of energetic particles from the core. With the applied $n=3$ fields, up to 8.4% of the injected beam power is predicted to be lost, compared to 2.7% with axisymmetric fields only. These fast ions, originating from minor radii $\\rho >0.7$ , are predicted to be primarily passing particles lost to the divertor region, consistent with wide field-of-view infrared periscope measurements of wall heating in $n=3$ RMP ELM suppressed plasmas. Edge fast ion ${{\\text{D}}_{\\alpha}}$ (FIDA) measurements also confirm a large change in edge fast ion profile due to the $n=3$ fields, where the effect was isolated by using short 50 ms RMP-off periods during which ELM suppression was maintained yet the fast ion profile was allowed

  9. A 3D MOF constructed from dysprosium(III) oxalate and capping ligands: ferromagnetic coupling and field-induced two-step magnetic relaxation.

    PubMed

    Liu, Cai-Ming; Zhang, De-Qing; Zhu, Dao-Ben

    2016-04-04

    A novel 3D MOF based on dysprosium(iii) oxalate and 1,10-phenanthroline (phen), {[Dy(C2O4)1.5phen]·0.5H2O}n (1), has been hydrothermally synthesized. The Dy(3+) ion acts as a typical Y-shaped node, linking to each other to generate an interesting 3D topology structure. Complex 1 is the first 3D DyMOF displaying both ferromagnetic coupling and field-induced two-step magnetic relaxation.

  10. Magnetic Damping of g-Jitter Driven Flows: 3-D Calculations

    NASA Technical Reports Server (NTRS)

    Shang, D. Y.; Li, B. Q.; deGroh, H. C.

    1997-01-01

    A 3-D numerical model is developed to represent the oscillating natural convection induced in a cylindrical cavity filled with Ga-doped germanium with and without the presence of an external magnetic field. The model is developed based on the penalty-finite element solution of the equations describing the transport of momentum, heat and solutal element as well as the electromagnetic field distribution in the melt pool. Automatic time step control is applied to help speed up the calculations. Numerical simulations are conducted to study the convection and magnetic damping effects as a function of frequency, directions and amplitudes of g-jitter and also the direction and magnitudes of the applied magnetic fields. The results show that the g-jitter driven flow is time dependent and exhibits a complex recirculating convection pattern in three dimensions and that an applied magnetic field can be employed to suppress this deleterious convective flow and both magnitude and orientation of the applied field are important in magnetic damping of the g-jitter induced convective flows.

  11. Heat Transfer Affected by Transverse Magnetic Field using 3D Modeling of Arc Plasma

    NASA Astrophysics Data System (ADS)

    Maeda, Yoshifumi; Tanaka, Tatsuro; Yamamoto, Shinji; Iwao, Toru

    2016-10-01

    Gas shielded metal arc welding is used to join the various metal because this is the high quality joining technology. Thus, this welding is used for a welding of large buildings such as bridges and LNG tanks. However, the welding defect caused by the heat transfer decrement may occur with increasing the wind velocity. This is because that the convection loss increases because the arc deflects to leeward side with increasing the wind velocity. In order to prevent from the arc deflection, it is used that the transverse magnetic field is applied to the arc. However, the arc deflection occurs with increasing the transverse magnetic field excessively. The energy balance of the arc is changed with increasing the convection loss caused by the arc deflection, and the heat transfer to the anode decreases. Therefore, the analysis including the arc and anode is necessary to elucidate the heat transfer to the anode. In this paper, the heat transfer affected by the transverse magnetic field using 3D modeling of the arc plasma is elucidated. The heat transfer to the anode is calculated by using the EMTF(electromagnetic thermal fluid) simulation with increasing the transverse magnetic field. As a result, the heat transfer decreased with increasing the transverse magnetic field.

  12. Calculating Pressure-Driven Current Near Magnetic Islands for 3D MHD Equilibria

    NASA Astrophysics Data System (ADS)

    Radhakrishnan, Dhanush; Reiman, Allan

    2016-10-01

    In general, 3D MHD equilibria in toroidal plasmas do not result in nested pressure surfaces. Instead, islands and chaotic regions appear in the equilibrium. Near small magnetic islands, the pressure varies within the flux surfaces, which has a significant effect on the pressure-driven current, introducing singularities. Previously, the MHD equilibrium current near a magnetic island was calculated, including the effect of ``stellarator symmetry,'' wherein the singular components of the pressure-driven current vanish [A. H. Reiman, Phys. Plasmas 23, 072502 (2016)]. Here we first solve for pressure in a cylindrical plasma from the heat diffusion equation, after adding a helical perturbation. We then numerically calculate the corresponding Pfirsch-Schluter current. At the small island limit, we compare the pressure-driven current with the previously calculated solution, and far from the island, we recover the solution for nested flux surfaces. Lastly, we compute the current for a toroidal plasma for symmetric and non-symmetric geometries.

  13. Study of the internal magnetic field of Mercury through 3D hybrid simulations

    NASA Astrophysics Data System (ADS)

    Leclercq, Ludivine; Marcel Chanteur, Gerard; Modolo, Ronan; Leblanc, Francois; Schmidt, Carl; Langlais, Benoît; Thebault, Erwan

    2016-10-01

    In 1974, Mariner 10 discovered the intrinsic magnetic field of Mercury which interacts with the solar wind, leading to the formation of a magnetosphere. In spite of the recent MESSENGER observations, this magnetosphere remains quite unknown, especially in the Southern hemisphere. In order to improve our understanding of the Hermean magnetosphere, and to prepare the Bepi-Colombo mission (ESA/JAXA), we simulated the magnetized environment of Mercury using the model named LatHyS (LATMOS Hybrid Simulation). LatHyS is a 3D parallel multi-species hybrid code which has been applied to Mars, Titan and Ganymede, which has recently be improved by the implementation of a multi-grid method allowing to refine the spatial resolution near the planetary object (40 km in the case of Mercury). In order to investigate the Hermean environment, several hybrid simulations have been performed considering different internal field models, and results are compared with MESSENGER observations.

  14. Laser direct writing 3D structures for microfluidic channels: flow meter and mixer

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Lang; Liu, Yi-Jui; Lin, Zheng-Da; Wu, Bo-Long; Lee, Yi-Hsiung; Shin, Chow-Shing; Baldeck, Patrice L.

    2015-03-01

    The 3D laser direct-writing technology is aimed at the modeling of arbitrary three-dimensional (3D) complex microstructures by scanning a laser-focusing point along predetermined trajectories. Through the perspective technique, the details of designed 3D structures can be properly fabricated in a microchannel. This study introduces a direct reading flow meter and a 3D passive mixer fabricated by laser direct writing for microfluidic applications. The flow meter consists of two rod-shaped springs, a pillar, an anchor, and a wedge-shaped indicator, installed inside a microfluidic channel. The indicator is deflected by the flowing fluid while restrained by the spring to establish an equilibrium indication according to the flow rate. The measurement is readily carried out by optical microscopy observation. The 3D passive Archimedes-screw-shaped mixer is designed to disturb the laminar flow 3D direction for enhancing the mixing efficiency. The simulation results indicate that the screw provides 3D disturbance of streamlines in the microchannel. The mixing demonstration for fluids flowing in the micrchannel approximately agrees with the simulation result. Thanks to the advantage of the laser direct writing technology, this study performs the ingenious applications of 3D structures for microchannels.

  15. Fluorescence in situ hybridization applications for super-resolution 3D structured illumination microscopy.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Cremer, Marion; Schermelleh, Lothar

    2013-01-01

    Fluorescence in situ hybridization on three-dimensionally preserved cells (3D-FISH) is an efficient tool to analyze the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level. 3D reconstructions from serial optical sections obtained by confocal laser scanning microscopy (CLSM) have long been considered the gold standard for 3D-FISH analyses. Recent super-resolution techniques circumvent the diffraction-limit of optical resolution and have defined a new state-of-the-art in bioimaging. Three-dimensional structured illumination microscopy (3D-SIM) represents one of these technologies. Notably, 3D-SIM renders an eightfold improved volumetric resolution over conventional imaging, and allows the simultaneous visualization of differently labeled target structures. These features make this approach highly attractive for the analysis of spatial relations and substructures of nuclear targets that escape detection by conventional light microscopy. Here, we focus on the application of 3D-SIM for the visualization of subnuclear 3D-FISH preparations. In comparison with conventional fluorescence microscopy, the quality of 3D-SIM data is dependent to a much greater extent on the optimal sample preparation, labeling and acquisition conditions. We describe typical problems encountered with super-resolution imaging of in situ hybridizations in mammalian tissue culture cells and provide optimized DNA-/(RNA)-FISH protocols including combinations with immunofluorescence staining (Immuno-FISH) and DNA replication labeling using click chemistry.

  16. Effects of 2D and 3D Error Fields on the SAS Divertor Magnetic Topology

    NASA Astrophysics Data System (ADS)

    Trevisan, G. L.; Lao, L. L.; Strait, E. J.; Guo, H. Y.; Wu, W.; Evans, T. E.

    2016-10-01

    The successful design of plasma-facing components in fusion experiments is of paramount importance in both the operation of future reactors and in the modification of operating machines. Indeed, the Small Angle Slot (SAS) divertor concept, proposed for application on the DIII-D experiment, combines a small incident angle at the plasma strike point with a progressively opening slot, so as to better control heat flux and erosion in high-performance tokamak plasmas. Uncertainty quantification of the error fields expected around the striking point provides additional useful information in both the design and the modeling phases of the new divertor, in part due to the particular geometric requirement of the striking flux surfaces. The presented work involves both 2D and 3D magnetic error field analysis on the SAS strike point carried out using the EFIT code for 2D equilibrium reconstruction, V3POST for vacuum 3D computations and the OMFIT integrated modeling framework for data analysis. An uncertainty in the magnetic probes' signals is found to propagate non-linearly as an uncertainty in the striking point and angle, which can be quantified through statistical analysis to yield robust estimates. Work supported by contracts DE-FG02-95ER54309 and DE-FC02-04ER54698.

  17. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

    A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

  18. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets. PMID:28358834

  19. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.

  20. A 3D acquisition system combination of structured-light scanning and shape from silhouette

    NASA Astrophysics Data System (ADS)

    Sun, Changku; Tao, Li; Wang, Peng; He, Li

    2006-05-01

    A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  1. Effect of 3d doping on the electronic structure of BaFe2As2

    SciTech Connect

    McLeod, John A.; Buling, A.; Green, R.J.; Boyko, T.D.; Skorikov, N.A.; Kurmaev, E.Z.; Neumann, M.; Finkelstein, L.D.; Ni, Ni; Thaler, Alexander; Budko, Serguei L.; Canfield, Paul; Moewes, A.

    2012-04-25

    The electronic structure of BaFe2As2 doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d10 shell. These findings help shed light on why superconductivity can occur in BaFe2As2 doped with Co and Ni but not Cu.

  2. Particle energization in 3D magnetic reconnection of relativistic pair plasmas

    SciTech Connect

    Liu Wei; Yin Lin; Albright, B. J.; Bowers, K. J.; Liang, Edison P.; Li Hui

    2011-05-15

    We present large scale 3D particle-in-cell simulations to examine particle energization in magnetic reconnection of relativistic electron-positron (pair) plasmas. The initial configuration is set up as a relativistic Harris equilibrium without a guide field. These simulations are large enough to accommodate a sufficient number of tearing and kink modes. Contrary to the non-relativistic limit, the linear tearing instability is faster than the linear kink instability, at least in our specific parameters. We find that the magnetic energy dissipation is first facilitated by the tearing instability and followed by the secondary kink instability. Particles are mostly energized inside the magnetic islands during the tearing stage due to the spatially varying electric fields produced by the outflows from reconnection. Secondary kink instability leads to additional particle acceleration. Accelerated particles are, however, observed to be thermalized quickly. The large amplitude of the vertical magnetic field resulting from the tearing modes by the secondary kink modes further help thermalizing the non-thermal particles generated from the secondary kink instability. Implications of these results for astrophysics are briefly discussed.

  3. Perineal body anatomy in living women: 3-D analysis using thin-slice magnetic resonance imaging

    PubMed Central

    Larson, Kindra A.; Yousuf, Aisha; Lewicky-Gaupp, Christina; Fenner, Dee E.; DeLancey, John O.L.

    2012-01-01

    Objective To describe a framework for visualizing the perineal body's complex anatomy using thin-slice MR imaging. Study Design Two mm-thick MR images were acquired in 11 women with normal pelvic support and no incontinence/prolapse symptoms. Anatomic structures were analyzed in axial, sagittal and coronal slices. 3-D models were generated from these images. Results Three distinct perineal body regions are visible on MRI: (1) a superficial region at the level of the vestibular bulb, (2) a mid region at the proximal end of the superficial transverse perineal muscle, and (3) a deep region at the level of the midurethra and puborectalis muscle. Structures are best visualized on axial scans while cranio-caudal relationships are appreciated on sagittal scans. The 3-D model further clarifies inter-relationships. Conclusion Advances in MR technology allow visualization of perineal body anatomy in living women and development of 3D models which enhance our understanding of its three different regions: superficial, mid and deep. PMID:21055513

  4. Deformable registration of 3D vessel structures to a single projection image

    NASA Astrophysics Data System (ADS)

    Zikic, Darko; Groher, Martin; Khamene, Ali; Navab, Nassir

    2008-03-01

    Alignment of angiographic preoperative 3D scans to intraoperative 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene. Our approach addresses the inherent ill-posedness of the problem by incorporating a priori knowledge about the vessel structures into the formulation. We minimize the distance between the 2D points and corresponding projected 3D points together with regularization terms encoding the properties of length preservation of vessel structures and smoothness of deformation. We demonstrate the performance and accuracy of the proposed method by quantitative tests on synthetic examples as well as real angiographic scenes.

  5. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    SciTech Connect

    Babu, S; Liao, P; Shin, M C; Tsap, L V

    2004-04-28

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell and its state. Chromosome analysis is significant in the detection of deceases and in monitoring environmental gene mutations. The algorithm incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  6. Contribution of 3D inversion of Electrical Resistivity Tomography data applied to volcanic structures

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2016-04-01

    The electrical resistivity tomography (ERT) method, initially developed for environmental and engineering exploration, is now commonly used for geological structures imaging. Such structures can present complex characteristics that conventional 2D inversion processes cannot perfectly integrate. Here we present a new 3D inversion algorithm named EResI, firstly developed for levee investigation, and presently applied to the study of a complex lava dome (the Puy de Dôme volcano, France). EResI algorithm is based on a conventional regularized Gauss-Newton inversion scheme and a 3D non-structured discretization of the model (double grid method based on tetrahedrons). This discretization allows to accurately model the topography of investigated structure (without a mesh deformation procedure) and also permits a precise location of the electrodes. Moreover, we demonstrate that a complete 3D unstructured discretization limits the number of inversion cells and is better adapted to the resolution capacity of tomography than a structured discretization. This study shows that a 3D inversion with a non-structured parametrization has some advantages compared to classical 2D inversions. The first advantage comes from the fact that a 2D inversion leads to artefacts due to 3D effects (3D topography, 3D internal resistivity). The second advantage comes from the fact that the capacity to experimentally align electrodes along an axis (for 2D surveys) depends on the constrains on the field (topography...). In this case, a 2D assumption induced by 2.5D inversion software prevents its capacity to model electrodes outside this axis leading to artefacts in the inversion result. The last limitation comes from the use of mesh deformation techniques used to accurately model the topography in 2D softwares. This technique used for structured discretization (Res2dinv) is prohibed for strong topography (>60 %) and leads to a small computational errors. A wide geophysical survey was carried out

  7. Inductively Driven, 3D Liner Compression of a Magnetized Plasma to Megabar Energy Densities

    SciTech Connect

    Slough, John

    2015-02-01

    modules. The additional energy and switching capability proposed will thus provide for optimal utilization of the liner energy. The following tasks were outlined for the three year effort: (1) Design and assemble the foil liner compression test structure and chamber including the compression bank and test foils [Year 1]. (2) Perform foil liner compression experiments and obtain performance data over a range on liner dimensions and bank parameters [Year 2]. (3) Carry out compression experiments of the FRC plasma to Megagauss fields and measure key fusion parameters [Year 3]. (4) Develop numerical codes and analyze experimental results, and determine the physics and scaling for future work [Year 1-3]. The principle task of the project was to design and assemble the foil liner FRC formation chamber, the full compression test structure and chamber including the compression bank. This task was completed successfully. The second task was to test foils in the test facility constructed in year one and characterize the performance obtained from liner compression. These experimental measurements were then compared with analytical predictions, and numerical code results. The liner testing was completed and compared with both the analytical results as well as the code work performed with the 3D structural dynamics package of ANSYS Metaphysics®. This code is capable of modeling the dynamic behavior of materials well into the non-linear regime (e.g. a bullet hit plate glass). The liner dynamic behavior was found to be remarkably close to that predicted by the 3D structural dynamics results. Incorporating a code that can also include the magnetics and plasma physics has also made significant progress at the UW. The remaining test bed construction and assembly task is was completed, and the FRC formation and merging experiments were carried out as planned. The liner compression of the FRC to Megagauss fields was not performed due to not obtaining a sufficiently long lived FRC during the

  8. 3D structure and dynamics of prominences in IRIS-Hinode collaborative observations

    NASA Astrophysics Data System (ADS)

    Okamoto, J.; De Pontieu, B.; Tarbell, T. D.; Title, A. M.

    2013-12-01

    A new solar physics satellite, Interface Region Imaging Spectrograph (IRIS), was launched on June 27, 2013. IRIS obtains UV spectra and images with high spatial resolution (0.33 arcsec) and high time cadence (1 sec / slit) of the chromosphere and transition region of the Sun. The chromosphere is located between the photosphere and the corona. Recently, the Hinode satellite has revealed that the chromosphere is highly active and suggested that it is a very important region in terms of energy deposit and transfer for coronal heating and solar wind acceleration. However, we cannot have further chromospheric information by Hinode because the Hinode Solar Optical Telescope has only a filtergraph for chromospheric observations. Now we have IRIS. IRIS performs spectroscopic observations to get the missing physical quantities of the dynamic chromosphere. Moreover, IRIS and Hinode is the most powerful collaboration to understand chromospheric activities. Hinode observes extremely high-cadence (1.6 sec) and high-spatial (0.2 arcsec) 2-D images, while IRIS measures line-of-sight velocity and Doppler width of fine structures with temperature dependence. This combination provides information about 3-D structures and dynamic phenomena of chromospheric features. Here we focus on prominence observations performed by IRIS and Hinode, and introduce the initial results of prominence dynamics and magnetic structures such as helical configurations, propagating waves and their damping mechanisms, and formation processes.

  9. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    PubMed

    Brigo, Laura; Urciuolo, Anna; Giulitti, Stefano; Giustina, Gioia Della; Tromayer, Maximilian; Liska, Robert; Elvassore, Nicola; Brusatin, Giovanna

    2017-03-25

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5 µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures.

  10. Modification of magnetic anisotropy through 3d-4f coupling in La0.75Pr0.25Co2P2

    NASA Astrophysics Data System (ADS)

    Kovnir, Kirill; Thompson, Corey M.; Garlea, V. Ovidiu; Haskel, Daniel; Polyanskii, Anatolii A.; Zhou, Haidong; Shatruk, Michael

    2013-09-01

    Magnetic behavior of La0.75Pr0.25Co2P2 was investigated by a combination of magnetic measurements, magneto-optical imaging, neutron diffraction, and x-ray absorption spectroscopy, including x-ray magnetic circular dichroism. The material crystallizes in the ThCr2Si2 structure type and exhibits three consecutive magnetic phase transitions. At 167 K, the Co magnetic moments order ferromagnetically in the ab plane of the tetragonal crystal structure. At 66 K, a ferromagnetic ordering of Pr(4f) moments parallel to the c axis causes a rotation of the Co(3d) moments towards the c axis in the direction opposite to the Pr moments, thus forming a noncollinear ferrimagnetically ordered structure and switching the direction of the total magnetization from the ab plane to the c axis. The third magnetic transition observed at 35 K is likely associated with the establishment of the collinear ferrimagnetic order along the c axis.

  11. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

    PubMed Central

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

    2017-01-01

    Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation

  12. Interpretation of Magnetic Anomalies in Salihli (Turkey) Geothermal Area Using 3-D Inversion and Edge Detection Techniques

    NASA Astrophysics Data System (ADS)

    Timur, Emre

    2016-04-01

    There are numerous geophysical methods used to investigate geothermal areas. The major purpose of this magnetic survey is to locate the boudaries of active hydrothermal system in the South of Gediz Graben in Salihli (Manisa/Turkey). The presence of the hydrothermal system had already been inferred from surface evidence of hydrothermal activity and drillings. Firstly, 3-D prismatic models were theoretically investigated and edge detection methods were utilized with an iterative inversion method to define the boundaries and the parameters of the structure. In the first step of the application, it was necessary to convert the total field anomaly into a pseudo-gravity anomaly map. Then the geometric boudaries of the structures were determined by applying a MATLAB based software with 3 different edge detection algorithms. The exact location of the structures were obtained by using these boundary coordinates as initial geometric parameters in the inversion process. In addition to these methods, reduction to pole and horizontal gradient methods were applied to the data to achieve more information about the location and shape of the possible reservoir. As a result, the edge detection methods were found to be successful, both in the field and as theoretical data sets for delineating the boundaries of the possible geothermal reservoir structure. The depth of the geothermal reservoir was determined as 2,4 km from 3-D inversion and 2,1 km from power spectrum methods.

  13. A unique 2D → 3D polycatenation cobalt(II)-based molecule magnet showing coexistence of paramagnetism and canted antiferromagnetism.

    PubMed

    Xu, Bo; Lin, Xi; He, Zhangzhen; Lin, Zujin; Cao, Rong

    2011-04-07

    A novel entangled architecture [Co(1.5)(bpmp)(Hcda)(cda)(H(2)O)] (1) based on 4(4)-sql subunits, showing an interesting 2D → 3D inclined polycatenation structure feature, is reported. Magnetic investigation shows that compound 1 exhibits coexistence of paramagnetism and canted antiferromagnetism with Tc of 48 K.

  14. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  15. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  16. 3D Equilibrium Reconstruction with Improved Magnetic Diagnostics on the Compact Toroidal Hybrid

    NASA Astrophysics Data System (ADS)

    Ma, Xinxing; Hanson, James D.; Hartwell, Gregory J.; Knowlton, Stephen F.; Maurer, David A.

    2013-10-01

    Equilibrium reconstructions using the three-dimensional V3FIT code [ 1 ] have been performed for low density (low β) current carrying plasmas on the Compact Toroidal Hybrid (CTH), a torsatron in which the magnetic configuration can be strongly modified by an ohmically-driven plasma current. These reconstructions use 50 external magnetic diagnostic measurements, including segmented and full Rogowski coils, saddle loops, poloidal and radial magnetic pickup coils. Time dependent 3D reconstructions document the evolution of the plasma cross section and current profile, with calculated value of βθ much less than the plasma internal inductance, li. Reconstructions typically show the plasma to move outward in major radius and become less elongated in poloidal cross section with increasing plasma current. In plasmas with low vacuum transform (ιvac ~ 0 . 04), the plasma current profile peaks with li above 0 . 84 when the total transform is 1 / 2 , which typically leads disruption. With values of ιvac >= 0 . 1 , li remains low (~ 0 . 7), and the discharges no longer disrupt. This work is supported by the USDoE under grant DE-FG02-00ER54610.

  17. Quiescence of magnetic braking and control of 3D non-resonance in KSTAR

    NASA Astrophysics Data System (ADS)

    Park, J.-K.; in, Y.; Jeon, Y. M.; Logan, N. C.; Wang, Z. R.; Menard, J. E.; Kim, J. H.; Ko, W. H.; Kstar Team

    2016-10-01

    Magnetic braking using non-axisymmetric (3D) field is a promising tool to control rotation in tokamaks and thereby micro-to-macro instabilities. Ideally magnetic braking should induce only neoclassical momentum transport, without provoking resonant instabilities or unnecessary perturbations in particle or heat transport. Indeed in KSTAR, it was shown that the 3 rows of internal coils could be used to generate highly non-resonant n =1 with backward-helicity field distribution, called -90 phasing, and to change rotation without any perturbations to other transport channels. Recent KSTAR experiments, however, have also shown that the broad-wavelength field distribution, called 0 phasing, is rather more quiescent whereas -90 phasing can be highly degrading especially in high q95 plasmas. IPEC and NTV modeling are consistent with both observations, and further provide the optimal point in coil phasing and amplitude space. Additional experiments and comparisons with modeling all imply the sensitivity of plasma response to remnant resonant field, and thus importance of non-resonance control, to accomplish quiescent magnetic braking. This work was supported by DOE Contract DE-AC02-09CH11466.

  18. Denoising of 3D magnetic resonance images by using higher-order singular value decomposition.

    PubMed

    Zhang, Xinyuan; Xu, Zhongbiao; Jia, Nan; Yang, Wei; Feng, Qianjin; Chen, Wufan; Feng, Yanqiu

    2015-01-01

    The denoising of magnetic resonance (MR) images is important to improve the inspection quality and reliability of quantitative image analysis. Nonlocal filters by exploiting similarity and/or sparseness among patches or cubes achieve excellent performance in denoising MR images. Recently, higher-order singular value decomposition (HOSVD) has been demonstrated to be a simple and effective method for exploiting redundancy in the 3D stack of similar patches during denoising 2D natural image. This work aims to investigate the application and improvement of HOSVD to denoising MR volume data. The wiener-augmented HOSVD method achieves comparable performance to that of BM4D. For further improvement, we propose to augment the standard HOSVD stage by a second recursive stage, which is a repeated HOSVD filtering of the weighted summation of the residual and denoised image in the first stage. The appropriate weights have been investigated by experiments with different image types and noise levels. Experimental results over synthetic and real 3D MR data demonstrate that the proposed method outperforms current state-of-the-art denoising methods.

  19. Integration of 3D 1H-magnetic resonance spectroscopy data into neuronavigation systems for tumor biopsies

    NASA Astrophysics Data System (ADS)

    Kanberoglu, Berkay; Moore, Nina Z.; Frakes, David; Karam, Lina J.; Debbins, Josef P.; Preul, Mark C.

    2013-03-01

    Many important applications in clinical medicine can benefit from the fusion of spectroscopy data with anatomical images. For example, the correlation of metabolite profiles with specific regions of interest in anatomical tumor images can be useful in characterizing and treating heterogeneous tumors that appear structurally homogeneous. Such applications can build on the correlation of data from in-vivo Proton Magnetic Resonance Spectroscopy Imaging (1HMRSI) with data from genetic and ex-vivo Nuclear Magnetic Resonance spectroscopy. To establish that correlation, tissue samples must be neurosurgically extracted from specifically identified locations with high accuracy. Toward that end, this paper presents new neuronavigation technology that enhances current clinical capabilities in the context of neurosurgical planning and execution. The proposed methods improve upon the current state-of-the-art in neuronavigation through the use of detailed three dimensional (3D) 1H-MRSI data. MRSI spectra are processed and analyzed, and specific voxels are selected based on their chemical contents. 3D neuronavigation overlays are then generated and applied to anatomical image data in the operating room. Without such technology, neurosurgeons must rely on memory and other qualitative resources alone for guidance in accessing specific MRSI-identified voxels. In contrast, MRSI-based overlays provide quantitative visual cues and location information during neurosurgery. The proposed methods enable a progressive new form of online MRSI-guided neuronavigation that we demonstrate in this study through phantom validation and clinical application.

  20. A 3-D Puzzle Approach to Building Protein-DNA Structures.

    PubMed

    Hinton, Deborah M

    2017-02-02

    Despite recent advances in structural analysis, it is still challenging to obtain a high resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3-D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

  1. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated.

  2. 3D and 4D atlas system of living human body structure.

    PubMed

    Suzuki, N; Takatsu, A; Hattori, A; Ezumi, T; Oda, S; Yanai, T; Tominaga, H

    1998-01-01

    A reference system for accessing anatomical information from a complete 3D structure of the whole body "living human", including 4D cardiac dynamics, was reconstructed with 3D and 4D data sets obtained from normal volunteers. With this system, we were able to produce a human atlas in which sectional images can be accessed from any part of the human body interactively by real-time image generation.

  3. Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

    PubMed

    Weisenburger, Siegfried; Boening, Daniel; Schomburg, Benjamin; Giller, Karin; Becker, Stefan; Griesinger, Christian; Sandoghdar, Vahid

    2017-02-01

    We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

  4. Linear-time protein 3-D structure searching with insertions and deletions

    PubMed Central

    2010-01-01

    Background Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era. Results We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (i.e., insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels k is bounded by a constant. Our algorithm solves the above problem for a query of size m and a database of size N in average-case O(N) time, whereas the time complexity of the previously best algorithm was O(Nmk+1). Conclusions Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. PMID:20047663

  5. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  6. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  7. 3D modeling inversion calculation of magnetic data using iterative reweighted least squares at the Lau basin, Southwest Pacific

    NASA Astrophysics Data System (ADS)

    Choi, S.; Kim, C.; Kim, H. R.; Park, C.; Park, H. Y.

    2015-12-01

    We performed the marine magnetic and the bathymetry survey in the Lau basin for finding the submarine hydrothermal deposits in October 2009. We acquired magnetic and bathymetry datasets by using Overhouser Proton Magnetometer SeaSPY(Marine Magnetics Co.) and Multi-Beam Echo Sounder EM120(Kongsberg Co.). We conducted the data processing to obtain detailed seabed topography, magnetic anomaly and reduction to the pole(RTP). The Lau basin is one of the youngest back-arc basins in the Southwest Pacific. This region was a lot of hydrothermal activities and hydrothermal deposits. In particular, Tofua Arc(TA) in the Lau basin consists of various and complex stratovolcanos(from Massoth et al., 2007).), We calculated the magnetic susceptibility distribution of the TA19-1 seamount(longitude:176°23.5'W, latitude: 22°42.5'W)area using the RTP data by 3-D magnetic inversion from Jung's previous study(2013). Based on 2D 'compact gravity inversion' by Last & Kubik(1983), we expend it to the 3D algorithm using iterative reweighted least squares method with some weight matrices. The used weight matrices are two types: 1) the minimum gradient support(MGS) that controls the spatial distribution of the solution from Porniaguine and Zhdanov(1999); 2) the depth weight that are used according to the shape of subsurface structures. From the modeling, we derived the appropriate scale factor for the use of depth weight and setting magnetic susceptibility. Furthermore, we have to enter a very small error value to control the computation of the singular point of the inversion model that was able to be easily calculated for modeling. In addition, we applied separately weighted value for the correct shape and depth of the magnetic source. We selected the best results model by change to converge of RMS. Compared between the final modeled result and RTP values in this study, they are generally similar to the each other. But the input values and the modeled values have slightly little difference

  8. Band structure and spin texture of Bi2Se3 3 d ferromagnetic metal interface

    NASA Astrophysics Data System (ADS)

    Zhang, Jia; Velev, Julian P.; Dang, Xiaoqian; Tsymbal, Evgeny Y.

    2016-07-01

    The spin-helical surface states in a three-dimensional topological insulator (TI), such as Bi2Se3 , are predicted to have superior efficiency in converting charge current into spin polarization. This property is said to be responsible for the giant spin-orbit torques observed in ferromagnetic metal/TI structures. In this work, using first-principles and model tight-binding calculations, we investigate the interface between the topological insulator Bi2Se3 and 3 d -transition ferromagnetic metals Ni and Co. We find that the difference in the work functions of the topological insulator and the ferromagnetic metals shift the topological surface states down about 0.5 eV below the Fermi energy where the hybridization of these surface states with the metal bands destroys their helical spin structure. The band alignment of Bi2Se3 and Ni (Co) places the Fermi energy far in the conduction band of bulk Bi2Se3 , where the spin of the carriers is aligned with the magnetization in the metal. Our results indicate that the topological surface states are unlikely to be responsible for the huge spin-orbit torque effect observed experimentally in these systems.

  9. 3D Characterization of the Magnetic Signature of a Medium Sized Impact Crater at Odessa, TX

    NASA Astrophysics Data System (ADS)

    Robinson, A.; Soule, D.; Everett, M.; Rodman, T.; Mangue Ndong, M.; Pereira, A.; Platt, P.; Trahan, A.

    2008-12-01

    Meteorite impacts are a common occurrence throughout Earth's geologic history. Many of the surface expressions of large ancient impacts have been subsequently erased by weathering and erosion processes. The study of preserved meteorite impacts is necessary to better understand this natural hazard which has been increasingly linked to rapid climate change and mass extinctions. The 60 ka Odessa meteorite crater located in Ector Co. Texas, is unique because it is not only well-preserved, but also has been the subject of extensive geologic examination. Geologic mapping and numeric models indicate that the crater was caused by a relatively small oblique impactor. The crater rim is remarkably well exposed. Much of the ejecta blanket is present, although deeply eroded. There has been considerable site disturbance due to drilling, shaft excavation, trenching, construction of a museum, trails, and the oil/gas activity in surrounding fields. Two previous geophysical investigations have shown that our data clearly corresponds to large-scale thrust deformation. With this in mind we have performed 3D high resolution magnetic gradiometer surveys that will allow us to quantify and characterize the magnetic signature of small to medium impacts. We will tie this data set to a 3D photorealistic outcrop image provided by laser scanning with coarser-scale, below-ground geophysical information. Our geophysical imagery provides a useful constraint on numerical simulations of the impact and its immediate regional-scale environmental effects. This information can be used to identify impact sites whose surface expression has been erased by natural erosional processes, allowing for improved frequency estimates and improved geo-hazard assessment.

  10. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  11. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  12. Gene3D: structural assignments for the biologist and bioinformaticist alike

    PubMed Central

    Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.

    2003-01-01

    The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH. PMID:12520054

  13. The Donegal Sign Tree: A Local Legend Confirmed with Holographic Radar and 3-D Magnetics

    NASA Astrophysics Data System (ADS)

    Bechtel, T.; Cassidy, M.; Inagaki, M.; Windsor, C.; Capineri, L.; Falorni, P.; Bulleti, A.; Valentini, S.; Borgioli, G.; Ivashov, S.; Zhuravlev, A.; Razewig, V.; Vasiliev, I.; Bechtel, E.

    2009-05-01

    A tree at a crossroad in Historic Donegal, PA (founded 1722) bears unusual burls. Two are similar in size, and lie on opposite sides of the trunk at a height of six feet. Locals say that the tree engulfed an old road sign, and the geometry of the burls gives this appearance. However, the trunk between these two burls bears no welt where it sealed after swallowing the sign. In addition, there are other burls farther up the tree, which are not consistent with engulfed signs. Although the locals all know the legend of the swallowed sign, none ever actually saw the sign; not even an octogenarian who has lived at the crossroad his entire life, and recalls the tree as a child just as it is today. In order to test the veracity of the legend, this study performed subsurface imaging of the tree using holographic subsurface radar (Rascan), and 3-D measurements of the magnetic field about the tree using cesium vapor sensors. The Rascan system used is a continuous wave subsurface radar that operates at 5 discrete frequencies between 1.5 and 2.0 GHz. Reflections from subsurface objects are recorded as the phase difference pattern between an internal reference signal, and the reflected signal. Thus, it is a microwave analogy for optical holography. Rascan records reflections with two receiving antennae - parallel and perpendicular to the transmitter - so a single set of scans provides ten images; five frequencies at two polarizations. This ensures that an object at arbitrary depth will produce a strong phase difference in one of the images. As a consequence, elongate objects that are angled from the plane of scanning (e.g. a dipping sheet) produce "zebra stripes" of contrast values that vary cyclically with depth. The presence of stripes, and their relative positions in the different frequency images (the movement of which has been dubbed the "zebra shift") is useful for determining the relative depth of different portions of a dipping planar, or curved subsurface object. Rascan

  14. Polyethylenimine-interlayered core-shell-satellite 3D magnetic microspheres as versatile SERS substrates

    NASA Astrophysics Data System (ADS)

    Wang, Chongwen; Li, Ping; Wang, Junfeng; Rong, Zhen; Pang, Yuanfeng; Xu, Jiawen; Dong, Peitao; Xiao, Rui; Wang, Shengqi

    2015-11-01

    Precise fabrication of subtle nanogaps amid individual nanoparticles or between adjacent ones to obtain the highest SERS enhancement is still a challenge. Here, we reported a novel approach for fabricating core-shell-satellite 3D magnetic microspheres (CSSM), that easily form a porous 1.5 nm PEI interlayer to accommodate molecules and create sufficient hotspots between the inner Fe3O4@Ag core and outer assembled Au@Ag satellites. Experiments and finite-difference time-domain (FDTD) simulation demonstrated that the enhancement factor (EF) was about 2.03 × 108 and 6.25 × 106, respectively. In addition, the micro-scale magnetic core endowed the CSSM with a superior magnetic nature, which enabled easy separation and further enhanced Raman signals due to enrichment of targeted analytes and abundant interparticle hotspots created by magnetism-induced aggregation. Our results further demonstrated that the CSSM is expected to be a versatile SERS substrate, which has been verified by the detection of the adsorbed pesticide thiram and the non-adsorbed pesticide paraquat with a detection limit as low as 5 × 10-12 M and 1 × 10-10 M, respectively. The novel CSSM can overcome the long-standing limitations of SERS for the trace characterization of various analytes in different solutions and promises to transform SERS into a practical analytical technique.Precise fabrication of subtle nanogaps amid individual nanoparticles or between adjacent ones to obtain the highest SERS enhancement is still a challenge. Here, we reported a novel approach for fabricating core-shell-satellite 3D magnetic microspheres (CSSM), that easily form a porous 1.5 nm PEI interlayer to accommodate molecules and create sufficient hotspots between the inner Fe3O4@Ag core and outer assembled Au@Ag satellites. Experiments and finite-difference time-domain (FDTD) simulation demonstrated that the enhancement factor (EF) was about 2.03 × 108 and 6.25 × 106, respectively. In addition, the micro

  15. Relativistic MHD simulations of core-collapse GRB jets: 3D instabilities and magnetic dissipation

    NASA Astrophysics Data System (ADS)

    Bromberg, Omer; Tchekhovskoy, Alexander

    2016-02-01

    Relativistic jets are associated with extreme astrophysical phenomena, like the core collapse of massive stars in gamma-ray bursts (GRBs) and the accretion on to supermassive black holes in active galactic nuclei. It is generally accepted that these jets are powered electromagnetically, by the magnetized rotation of a central compact object (black hole or neutron star). However, how the jets produce the observed emission and survive the propagation for many orders of magnitude in distance without being disrupted by current-driven instabilities is the subject of active debate. We carry out time-dependent 3D relativistic magnetohydrodynamic (MHD) simulations of relativistic, Poynting-flux-dominated jets. The jets are launched self-consistently by the rotation of a strongly magnetized central object. This determines the natural degree of azimuthal magnetic field winding, a crucial factor that controls jet stability. We find that the jets are susceptible to two types of instability: (i) a global, external kink mode that grows on long time-scales. It bodily twists the jet, reducing its propagation velocity. We show analytically that in flat density profiles, like the ones associated with galactic cores, the external mode grows and may stall the jet. In the steep profiles of stellar envelopes the external kink weakens as the jet propagates outward. (ii) a local, internal kink mode that grows over short time-scales and causes small-angle magnetic reconnection and conversion of about half of the jet electromagnetic energy flux into heat. We suggest that internal kink instability is the main dissipation mechanism responsible for powering GRB prompt emission.

  16. 3D-printing and mechanics of bio-inspired articulated and multi-material structures.

    PubMed

    Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

    2016-12-21

    3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic.

  17. Lithographically-generated 3D lamella layers and their structural color.

    PubMed

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-28

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ∼ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  18. Lithographically-generated 3D lamella layers and their structural color

    NASA Astrophysics Data System (ADS)

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-01

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ~ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  19. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

    Nugraha, Andri Dian; Syahputra, Ahmad; Fatkhan,; Sule, Rachmat

    2013-09-09

    We conducted delay time tomography to determine 3-D seismic velocity structures (Vp, Vs, and Vp/Vs ratio) using micro-seismic events in the geothermal field. The P-and S-wave arrival times of these micro-seismic events have been used as input for the tomographic inversion. Our preliminary seismic velocity results show that the subsurface condition of geothermal field can be fairly delineated the characteristic of reservoir. We then extended our understanding of the subsurface physical properties through determining of attenuation structures (Qp, Qs, and Qs/Qp ratio) using micro-seismic waveform. We combined seismic velocities and attenuation structures to get much better interpretation of the reservoir characteristic. Our preliminary attanuation structures results show reservoir characterization can be more clearly by using the 3-D attenuation model of Qp, Qs, and Qs/Qp ratio combined with 3-D seismic velocity model of Vp, Vs, and Vp/Vs ratio.

  20. 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.

  1. System for conveyor belt part picking using structured light and 3D pose estimation

    NASA Astrophysics Data System (ADS)

    Thielemann, J.; Skotheim, Ø.; Nygaard, J. O.; Vollset, T.

    2009-01-01

    Automatic picking of parts is an important challenge to solve within factory automation, because it can remove tedious manual work and save labor costs. One such application involves parts that arrive with random position and orientation on a conveyor belt. The parts should be picked off the conveyor belt and placed systematically into bins. We describe a system that consists of a structured light instrument for capturing 3D data and robust methods for aligning an input 3D template with a 3D image of the scene. The method uses general and robust pre-processing steps based on geometric primitives that allow the well-known Iterative Closest Point algorithm to converge quickly and robustly to the correct solution. The method has been demonstrated for localization of car parts with random position and orientation. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  2. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

    3D printing is a form of additive manufacturing whereby the building up of layers of material creates objects. The selective laser sintering process (SLS) uses a laser beam to sinter powdered material to create objects. This paper builds upon previous research into 3D printed textile based material exploring the use of SLS using nylon powder to create flexible weft knitted structures. The results show the potential to print flexible textile based structures that exhibit the properties of traditional knitted textile structures along with the mechanical properties of the material used, whilst describing the challenges regarding fineness of printing resolution. The conclusion highlights the potential future development and application of such pieces.

  3. Definition of subsurface stratigraphy, structure and rock properties from 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Hart, Bruce S.

    1999-10-01

    This paper summarizes how three-dimensional (3-D) seismic technology is being used, primarily in the petroleum industry, to define subsurface structure, stratigraphy and rock properties. A 3-D seismic data volume: (a) provides a more accurate image of the subsurface than can be obtained with 2-D seismic methods; (b) is continuous, and so has a much greater spatial sampling than is obtained with 2-D seismic or other subsurface data (e.g., wells); and (c) can be viewed and interpreted interactively from a variety of perspectives, thus enhancing the interpreter's ability to generate an accurate description of subsurface features of interest. Seismic interpretation was once the almost exclusive realm of geophysicists, however, most 3-D seismic interpretation today is conducted by multidisciplinary teams that integrate geophysical, geological, petrophysical and engineering data and concepts into the 3-D seismic interpretation. These factors, plus proper survey design, help to increase the chances of success of a 3-D seismic interpretation project. Although there are cases where the technology is not appropriate or cannot be applied (for economic reasons or otherwise), the general success of 3-D seismic has led it to become a mainstay of the petroleum industry. The approach and technology, first developed in that industry, have potential applications in other applied and fundamental earth science disciplines, including mining, environmental geology, structural geology and stratigraphy.

  4. A remark on the Beale-Kato-Majda criterion for the 3D MHD equations with zero magnetic diffusivity

    NASA Astrophysics Data System (ADS)

    Gala, Sadek; Ragusa, Maria Alessandra

    2016-06-01

    In this work, we show that a smooth solution of the 3D MHD equations with zero magnetic diffusivity in the whole space ℝ3 breaks down if and only if a certain norm of the magnetic field blows up at the same time.

  5. Ce 5d and Fe 3d magnetic profiles in CeH2/Fe multilayers probed by XRMS

    NASA Astrophysics Data System (ADS)

    Jaouen, N.; Tonnerre, J. M.; Raoux, D.; Ortega, L.; Bontempi, E.; Münzenberg, M.; Felsch, W.; Suzuki, M.; Maruyama, H.; Dürr, H. A.; Dudzik, E.; van der Laan, G.

    The element and electronic shell specificities of X-ray resonant magnetic scattering have been used to investigate the magnetization of Ce 5d and Fe 3d states in [CeH2(19.6 Å)/Fe(25.4 Å)]*38 a multilayer. We show that the measurement of the magnetic contribution to the intensities reflected at low angles at the Ce L2 and Fe L2,3 edges allows us to investigate the profile of the Ce 5d and Fe 3d magnetic polarization. The Fe 3d polarization is found to be uniform across the Fe layer and the Ce 5d polarization appears to be restricted close to the interface with Fe.

  6. Three-dimensional two-fluid investigation of 3D-localized magnetic reconnection and its relation to whistler waves

    NASA Astrophysics Data System (ADS)

    Yoon, Young Dae; Bellan, Paul M.

    2016-10-01

    A full three-dimensional computer code was developed in order to simulate a 3D-localized magnetic reconnection. We assume an incompressible two-fluid regime where the ions are stationary, and electron inertia and Hall effects are present. We solve a single dimensionless differential equation for perturbed magnetic fields with arbitrary background fields. The code has successfully reproduced both experimental and analytic solutions to resonance and Gendrin mode whistler waves in a uniform background field. The code was then modified to model 3D-localized magnetic reconnection as a 3D-localized perturbation on a hyperbolic-tangent background field. Three-dimensional properties that are asymmetric in the out-of-plane direction have been observed. These properties pertained to magnetic field lines, electron currents and their convection. Helicity and energy have also been examined, as well as the addition of a guide field.

  7. Accretion to magnetized stars through the Rayleigh-Taylor instability: global 3D simulations

    NASA Astrophysics Data System (ADS)

    Kulkarni, A. K.; Romanova, M. M.

    2008-05-01

    We present results of 3D simulations of magnetohydrodynamics (MHD) instabilities at the accretion disc-magnetosphere boundary. The instability is Rayleigh-Taylor, and develops for a fairly broad range of accretion rates and stellar rotation rates and magnetic fields. It manifests itself in the form of tall, thin tongues of plasma that penetrate the magnetosphere in the equatorial plane. The shape and number of the tongues changes with time on the inner disc dynamical time-scale. In contrast with funnel flows, which deposit matter mainly in the polar region, the tongues deposit matter much closer to the stellar equator. The instability appears for relatively small misalignment angles, Θ <~ 30°, between the star's rotation and magnetic axes, and is associated with higher accretion rates. The hotspots and light curves during accretion through instability are generally much more chaotic than during stable accretion. The unstable state of accretion has possible implications for quasi-periodic oscillations and intermittent pulsations from accreting systems, as well as planet migration.

  8. Local and Global 3-D Effects in the Magnetic Reconnection Experiment (MRX)

    NASA Astrophysics Data System (ADS)

    Dorfman, S.; Ji, H.; Yamada, M.; Oz, E.; Yoo, J.; Daughton, W.; Roytershteyn, V.

    2009-11-01

    One of the key open questions in Magnetic Reconnection is the nature of the mechanism that governs the reconnection rate in real astrophysical and laboratory systems. Comparisons between fully kinetic 2-D simulations of the Magnetic Reconnection Experiment (MRX) and experimental data show that the 2-D, collisionless expression for the electric field due to particle dynamics [1] does not match MRX data; related to this is a factor of 3-5 discrepancy in the layer width [2,3]. Adding collisions to the simulation leads to a broadening of the layer, but the level of collisionality present in MRX may not be high enough to resolve the discrepancy. Ongoing research on MRX explores the role of fluctuations and 3-D effects in the force balance. Significant toroidal asymmetries have been found, manifested by regions of high inductive electric field moving in the electron flow direction within the layer. Electromagnetic fluctuations in the lower hybrid frequency range [4] tend to occur in discharges with high local currents and a rapid local reconnection rate. The precise relation of these phenomena to fast reconnection is actively being investigated. [1] M. Hesse, et al., Phys. Plasmas, 6:1781 (1999). [2] Y. Ren, et al., Phys. Plasmas 15, 082113 (2008). [3] S. Dorfman, et al., Phys. Plasmas 15, 102107 (2008). [4] H. Ji, et al., Phys.Rev.Lett. 92 (2004) 115001. Supported by NDSEG, DOE, NASA, and NSF.

  9. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

    McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; de Esch, Iwan J P; Lusher, Scott J; Leurs, Rob; Ridder, Lars; Kooistra, Albert J; Ritschel, Tina; de Graaf, Chris

    2017-02-27

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

  10. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation.

  11. Novel scanning electron microscopy methods for analyzing the 3D structure of the Golgi apparatus.

    PubMed

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

  12. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  13. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  14. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand-strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases.

  15. Single crystalline cylindrical nanowires – toward dense 3D arrays of magnetic vortices

    PubMed Central

    Ivanov, Yurii P.; Chuvilin, Andrey; Vivas, Laura G.; Kosel, Jurgen; Chubykalo-Fesenko, Oksana; Vázquez, Manuel

    2016-01-01

    Magnetic vortex-based media have recently been proposed for several applications of nanotechnology; however, because lithography is typically used for their preparation, their low-cost, large-scale fabrication is a challenge. One solution may be to use arrays of densely packed cobalt nanowires that have been efficiently fabricated by electrodeposition. In this work, we present this type of nanoscale magnetic structures that can hold multiple stable magnetic vortex domains at remanence with different chiralities. The stable vortex state is observed in arrays of monocrystalline cobalt nanowires with diameters as small as 45 nm and lengths longer than 200 nm with vanishing magnetic cross talk between closely packed neighboring wires in the array. Lorentz microscopy, electron holography and magnetic force microscopy, supported by micromagnetic simulations, show that the structure of the vortex state can be adjusted by varying the aspect ratio of the nanowires. The data we present here introduce a route toward the concept of 3-dimensional vortex-based magnetic memories. PMID:27030143

  16. Single crystalline cylindrical nanowires – toward dense 3D arrays of magnetic vortices

    NASA Astrophysics Data System (ADS)

    Ivanov, Yurii P.; Chuvilin, Andrey; Vivas, Laura G.; Kosel, Jurgen; Chubykalo-Fesenko, Oksana; Vázquez, Manuel

    2016-03-01

    Magnetic vortex-based media have recently been proposed for several applications of nanotechnology; however, because lithography is typically used for their preparation, their low-cost, large-scale fabrication is a challenge. One solution may be to use arrays of densely packed cobalt nanowires that have been efficiently fabricated by electrodeposition. In this work, we present this type of nanoscale magnetic structures that can hold multiple stable magnetic vortex domains at remanence with different chiralities. The stable vortex state is observed in arrays of monocrystalline cobalt nanowires with diameters as small as 45 nm and lengths longer than 200 nm with vanishing magnetic cross talk between closely packed neighboring wires in the array. Lorentz microscopy, electron holography and magnetic force microscopy, supported by micromagnetic simulations, show that the structure of the vortex state can be adjusted by varying the aspect ratio of the nanowires. The data we present here introduce a route toward the concept of 3-dimensional vortex-based magnetic memories.

  17. Remote magnetic actuation of micrometric probes for in situ 3D mapping of bacterial biofilm physical properties.

    PubMed

    Galy, Olivier; Zrelli, Kais; Latour-Lambert, Patricia; Kirwan, Lyndsey; Henry, Nelly

    2014-05-02

    Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development - maintenance or eradication - depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer's point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures.

  18. Remote Magnetic Actuation of Micrometric Probes for in situ 3D Mapping of Bacterial Biofilm Physical Properties

    PubMed Central

    Galy, Olivier; Zrelli, Kais; Latour-Lambert, Patricia; Kirwan, Lyndsey; Henry, Nelly

    2014-01-01

    Bacterial adhesion and growth on interfaces lead to the formation of three-dimensional heterogeneous structures so-called biofilms. The cells dwelling in these structures are held together by physical interactions mediated by a network of extracellular polymeric substances. Bacterial biofilms impact many human activities and the understanding of their properties is crucial for a better control of their development — maintenance or eradication — depending on their adverse or beneficial outcome. This paper describes a novel methodology aiming to measure in situ the local physical properties of the biofilm that had been, until now, examined only from a macroscopic and homogeneous material perspective. The experiment described here involves introducing magnetic particles into a growing biofilm to seed local probes that can be remotely actuated without disturbing the structural properties of the biofilm. Dedicated magnetic tweezers were developed to exert a defined force on each particle embedded in the biofilm. The setup is mounted on the stage of a microscope to enable the recording of time-lapse images of the particle-pulling period. The particle trajectories are then extracted from the pulling sequence and the local viscoelastic parameters are derived from each particle displacement curve, thereby providing the 3D-spatial distribution of the parameters. Gaining insights into the biofilm mechanical profile is essential from an engineer's point of view for biofilm control purposes but also from a fundamental perspective to clarify the relationship between the architectural properties and the specific biology of these structures. PMID:24837001

  19. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  20. Structure-From-Motion in 3D Space Using 2D Lidars

    PubMed Central

    Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

    2017-01-01

    This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

  1. Synthesis, structure determination and 3D molecular modeling of some novel manganese(II) complexes

    NASA Astrophysics Data System (ADS)

    Hari Kumaran Nair, M. L.; Lalitha, K. P.

    2013-06-01

    Some novel manganese(II) complexes with the ligand (z)-4-((2-hydroxy-4-methoxyphenyl)diazenyl)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one, MPAAP, 3-methoxy phenol azoantipyrine, L1, having the formulae [Mn(L1)2(X)2], [Mn(L1)2(Y)2], where X = Cl- / Br-; Y = NCS- were synthesized and characterized by elemental analysis, molar conductance and magnetic susceptibility measurements, spectral (IR, UV-Visible, EPR, FAB mass) studies, thermogravimetric analysis, powder XRD and cyclic voltammetric studies and by SEM image. An octahedral structure is tentatively proposed for the complexes with respect to the above studies. The [Mn(L1)2(Y)2] was subjected to γ-ray irradiation and the internal changes accompanied were evaluated. The energy minimized configuration of the complex [Mn(L1)2(Y)2] was made with CHEM Bio 3D Ultra 11.0 and the respective parameters are computed. The ligand and its complex [Mn(L1)2(Y)2] were screened for their possible antimicrobial activities.

  2. 3-D RPIC Simulations of Relativistic Jets: Particle Acceleration, Magnetic Field Generation, and Emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Mizuno, Y.; Hardee, P.; Hededal, C. B.; Fishman, G. J.

    2006-01-01

    Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets into ambient plasmas show that acceleration occurs in relativistic shocks. The Weibel instability created in shocks is responsible for particle acceleration, and generation and amplification of highly inhomogeneous, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection in relativistic jets. The "jitter" radiation from deflected electrons has different properties than the synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understand the complex time evolution and spectral structure in relativistic jets and gamma-ray bursts. We will present recent PIC simulations which show particle acceleration and magnetic field generation. We will also calculate associated self-consistent emission from relativistic shocks.

  3. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  4. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  5. Enhanced genome annotation using structural profiles in the program 3D-PSSM.

    PubMed

    Kelley, L A; MacCallum, R M; Sternberg, M J

    2000-06-02

    A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm

  6. Relevance of 3D magnetic resonance imaging sequences in diagnosing basal subarachnoid neurocysticercosis.

    PubMed

    Carrillo Mezo, Roger; Lara García, Javier; Arroyo, Mariana; Fleury, Agnès

    2015-12-01

    Imagenological diagnosis of subarachnoid neurocysticercosis is usually difficult when classical magnetic resonance imaging (MRI) sequences are used. The purpose of this study was to evaluate the advantages of 3D MRI sequences (Fast Imaging Employing Steady-state Acquisition (FIESTA) and Spoiled Gradient Recalled Echo (SPGR)) with respect to classical sequences (Fluid Attenuation Inversion Recovery (FLAIR) and T1) in visualizing Taenia solium cyst in these locations. Forty-seven T. solium cysts located in the basal cisterns of the subarachnoid space were diagnosed in eighteen Mexican patients. A pre-treatment MRI was performed on all patients, and all four sequences (FIESTA, FLAIR, T1 SPGR, and T2) were evaluated independently by two neuroradiologists. The sensitivity of each sequence to detect the parasite membrane and scolex was evaluated, along with its capacity to detect differences in signal intensity between cerebrospinal fluid (CSF) and cysts. FIESTA sequences allowed the visualization of cyst membrane in 87.2% of the parasites evaluated, FLAIR in 38.3%, SPGR in 23.4%, and T2 in 17.0%. The superiority of FIESTA sequences over the other three imaging methods was statistically significant (P<0.001). Scolices were detected by FIESTA twice as much as the other sequences did, although this difference was not significant (P>0.05). Differences in signal intensity between CSF and parasite cysts were significant in FIESTA (P<0.0001), SPGR (P<0.0001), and FLAIR (P=0.005) sequences. For the first time, the usefulness of 3D MRI sequences to diagnose T. solium cysts located in the basal cisterns of the subarachnoid space was demonstrated. The routine use of these sequences could favor an earlier diagnosis and greatly improve the prognosis of patients affected by this severe form of the disease.

  7. Influence of Jahn-Teller Cu2+ (3d9) ion on structural and magnetic properties of Al-Cr co-substituted CuFe2O4

    NASA Astrophysics Data System (ADS)

    Tanna, A. R.; Trivedi, U. N.; Chhantbar, M. C.; Joshi, H. H.

    2013-11-01

    Four specimens of two compositions of the spinel oxide system CuAlxCrxFe2-2xO4 with x = 0.2 and 0.6 have been synthesized by double sintering ceramic technique with different thermal history i.e. quenched and slow-cooled. X-ray diffractometry has confirmed that tetragonal distortion is present in slow-cooled sample, while it is absent in quenched sample. The lower value of saturation moment compared to Neel's moment for each composition is explained by invoking random canting of spins model. Hyperfine interaction parameters: nuclear hyperfine field, quadrupole splitting (shifts), isomer shift and Fe3+ ion distribution are deduced through computer simulation of Mössbauer spectra. 57Fe Mössbauer spectra recorded at room temperature show the effect of magnetic dilution of inter-sublattice ( A- B) interaction (frustration) more in case of quenched-sample compared to slow-cooled one. FTIR spectra also corroborate the influence of Jahn-Teller (J-T) distortion of octahedral void arising due to larger Cu2+ ion occupancy at octahedral sites. The force constants are also estimated from FTIR spectra.

  8. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  9. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  10. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  11. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  12. Simulation approach of atomic layer deposition in large 3D structures

    NASA Astrophysics Data System (ADS)

    Schwille, Matthias C.; Barth, Jonas; Schössler, Timo; Schön, Florian; Bartha, Johann W.; Oettel, Martin

    2017-04-01

    We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.

  13. Magnetic field induced controllable self-assembly of maghemite nanocrystals: From 3D arrays to 1D nanochains

    NASA Astrophysics Data System (ADS)

    Tang, Yan; Chen, Qianwang; Chen, Rongsheng

    2015-08-01

    A hydrothermal process has been used to synthesize walnut-like maghemite superstructures which can be further self-assembled in a controllable manner into ordered three-dimensional (3D) architectures and one-dimensional (1D) nanochains in the presence of different external magnetic field. The assembly behavior of the maghemite nanoparticles isclosely related to the van der Waals interactions and external-field-induced magnetic dipole interactions. The magnetic properties of these nanostructures are also investigated.

  14. Computational methods for constructing protein structure models from 3D electron microscopy maps.

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.

  15. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  16. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

    PubMed

    Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

    2016-07-08

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.

  17. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

    Heller, L.; Vokoun, D.; Šittner, P.; Finckh, H.

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

  18. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  19. Structure, stability, and evolution of 3D Rossby vortices in protoplanetary disks

    NASA Astrophysics Data System (ADS)

    Richard, S.; Barge, P.; Le Dizès, S.

    2013-11-01

    Context. Large-scale persistent vortices could play a key role in the evolution of protoplanetary disks, particularly in the dead zone where no turbulence associated with a magnetic field is expected. These vortices are known to form easily in 2D disks via the Rossby wave or the baroclinic instability. In three dimensions, however, their formation and stability is a complex problem and still a matter of debate. Aims: We study the formation of vortices by the Rossby wave instability in a stratified inviscid disk and describe their 3D structure, stability, and long-term evolution. Methods: Numerical simulations were performed using a fully compressible hydrodynamical code based on a second-order finite volume method. We assumed a perfect-gas law and a non-homentropic adiabatic flow. Results: The Rossby wave instability is found to proceed in 3D in a similar way as in 2D. Vortices produced by the instability look like columns of vorticity in the whole disk thickness; the weak vertical motions are related to the weak inclination of the vortex axis that appears during the development of the RWI. Vortices with aspect ratios higher than 6 are unaffected by the elliptical instability. They relax into a quasi-steady columnar structure that survives hundreds of rotations while slowly migrating inward toward the star at a rate that reduces with the vortex aspect ratio. Vortices with a lower aspect ratio are by contrast affected by the elliptic instability. Short aspect ratio vortices (χ < 4) are completely destroyed in a few orbital periods. Vortices with an intermediate aspect ratio (4 < χ < 6) are partially destroyed by the elliptical instability in a region away from the midplane where the disk stratification is sufficiently strong. Conclusions: Elongated Rossby vortices can survive many orbital periods in protoplanetary disks in the form of vorticity columns. They could play a significant role in the evolution of the gas and the gathering of solid particles to form

  20. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  1. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  2. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  3. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation.

  4. Protein-protein interaction networks studies and importance of 3D structure knowledge.

    PubMed

    Lu, Hui-Chun; Fornili, Arianna; Fraternali, Franca

    2013-12-01

    Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.

  5. Voxel-coding method for quantification of vascular structure from 3D images

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Shahrokni, Ali; Zoroofi, Reza A.

    2001-05-01

    This paper presents an image processing method for information extraction from 3D images of vasculature. It automates the study of vascular structures by extracting quantitative information such as skeleton, length, diameter, and vessel-to- tissue ratio for different vessels as well as their branches. Furthermore, it generates 3D visualization of vessels based on desired anatomical characteristics such as vessel diameter or 3D connectivity. Steps of the proposed approach are as follows. (1) Preprocessing, in which intensity adjustment, optimal thresholding, and median filtering are done. (2) 3D thinning, in which medial axis and skeleton of the vessels are found. (3) Branch labeling, in which different branches are identified and each voxel is assigned to the corresponding branch. (4) Quantitation, in which length of each branch is estimated, based on the number of voxels assigned to it, and its diameter is calculated using the medial axis direction. (5) Visualization, in which vascular structure is shown in 3D, using color coding and surface rendering methods. We have tested and evaluated the proposed algorithms using simulated images of multi-branch vessels and real confocal microscopic images of the vessels in rat brains. Experimental results illustrate performance of the methods and usefulness of the results for medical image analysis applications.

  6. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  7. 3D PIC Simulations of Collisionless Shocks at Lunar Magnetic Anomalies and Their Role in Forming Lunar Swirls

    NASA Astrophysics Data System (ADS)

    Bamford, R. A.; Alves, E. P.; Cruz, F.; Kellett, B. J.; Fonseca, R. A.; Silva, L. O.; Trines, R. M. G. M.; Halekas, J. S.; Kramer, G.; Harnett, E.; Cairns, R. A.; Bingham, R.

    2016-10-01

    Investigation of the lunar crustal magnetic anomalies offers a comprehensive long-term data set of observations of small-scale magnetic fields and their interaction with the solar wind. In this paper a review of the observations of lunar mini-magnetospheres is compared quantifiably with theoretical kinetic-scale plasma physics and 3D particle-in-cell simulations. The aim of this paper is to provide a complete picture of all the aspects of the phenomena and to show how the observations from all the different and international missions interrelate. The analysis shows that the simulations are consistent with the formation of miniature (smaller than the ion Larmor orbit) collisionless shocks and miniature magnetospheric cavities, which has not been demonstrated previously. The simulations reproduce the finesse and form of the differential proton patterns that are believed to be responsible for the creation of both the “lunar swirls” and “dark lanes.” Using a mature plasma physics code like OSIRIS allows us, for the first time, to make a side-by-side comparison between model and space observations. This is shown for all of the key plasma parameters observed to date by spacecraft, including the spectral imaging data of the lunar swirls. The analysis of miniature magnetic structures offers insight into multi-scale mechanisms and kinetic-scale aspects of planetary magnetospheres.

  8. 3D modelling of an aero-gravity and -magnetic survey as an first exploration step in a frontier basin

    NASA Astrophysics Data System (ADS)

    Köther, Nils; Eckard, Marcel; Götze, Hans-Jürgen

    2010-05-01

    The West African Taoudeni basin covers a desert area of about 1.8 million km² and is one of the last frontier basins worldwide. Here Wintershall Holding AG holds acreage of about 68000 km². During 2005-2007 geological surveys and an aero-gravity and -magnetic survey were conducted in this area. The potential field modelling should contribute first insight about the subsurface to plan an economic seismic survey. 2D models lead to poor results. 2008 the results of an internship (NK) were 3D subsurface models, which were enhanced during the following diploma thesis (Köther, 2009). Complex igneous rocks and sparsely distributed constraints lead to an ambiguous interpretation. Therefore, several simple 3D models were compiled with the in-house software IGMAS+, which base on geological ideas of the underground and fit well the measured data. These basic models allow a geophysical evaluation of different geological theories about the subsurface. Also, for a thorough interpretation field transformations (Euler, Curvature, and Derivatives) were calculated. These results led to new constraints for further interpretation of the basin structures and therefore they are important contributions for future exploration e.g. the planning of seismic surveys.

  9. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  10. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  11. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  12. Ising-like chain magnetism, Arrhenius magnetic relaxation, and case against 3D magnetic ordering in β-manganese phthalocyanine (C32H16MnN8)

    NASA Astrophysics Data System (ADS)

    Wang, Zhengjun; Seehra, Mohindar S.

    2016-04-01

    Previous magnetic studies in the organic semiconductor β-manganese phthalocyanine (β-MnPc) have reported it to be a canted ferromagnet below T C  ≈  8.6 K. However, the recent result of the lack of a λ-type anomaly in the specific heat versus temperature data near the quoted T C has questioned the presence of long-range 3-dimensional (3D) magnetic ordering in this system. In this paper, detailed measurements and analysis of the temperature (2 K-300 K) and magnetic field (up to 90 kOe) dependence of the dc and ac magnetic susceptibilities in a powder sample of β-MnPc leads us to conclude that 3D long-range magnetic ordering is absent in this material. This is supported by the Arrott plots and the lack of a peak in the ac susceptibilities, χ‧ and χ″, near the quoted T C. Instead, the system can be best described as an Ising-like chain magnet with Arrhenius relaxation of the magnetization governed by an intra-layer ferromagnetic exchange constant J/k B  =  2.6 K and the single ion anisotropy energy parameter |D|/k B  =  8.3 K. The absence of 3D long range order is consistent with the measured \\mid D\\mid   >  J.

  13. Effect of rosiglitazone on progression of atherosclerosis: insights using 3D carotid cardiovascular magnetic resonance

    PubMed Central

    Varghese, Anitha; Yee, Michael S; Chan, Cheuk F; Crowe, Lindsey A; Keenan, Niall G; Johnston, Desmond G; Pennell, Dudley J

    2009-01-01

    Background There is recent evidence suggesting that rosiglitazone increases death from cardiovascular causes. We investigated the direct effect of this drug on atheroma using 3D carotid cardiovascular magnetic resonance. Results A randomized, placebo-controlled, double-blind study was performed to evaluate the effect of rosiglitazone treatment on carotid atherosclerosis in subjects with type 2 diabetes and coexisting vascular disease or hypertension. The primary endpoint of the study was the change from baseline to 52 weeks of carotid arterial wall volume, reflecting plaque burden, as measured by carotid cardiovascular magnetic resonance. Rosiglitazone or placebo was allocated to 28 and 29 patients respectively. Patients were managed to have equivalent glycemic control over the study period, but in fact the rosiglitazone group lowered their HbA1c by 0.88% relative to placebo (P < 0.001). Most patients received a statin or fibrate as lipid control medication (rosiglitazone 78%, controls 83%). Data are presented as mean ± SD. At baseline, the carotid arterial wall volume in the placebo group was 1146 ± 550 mm3 and in the rosiglitazone group was 1354 ± 532 mm3. After 52 weeks, the respective volumes were 1134 ± 523 mm3 and 1348 ± 531 mm3. These changes (-12.1 mm3 and -5.7 mm3 in the placebo and rosiglitazone groups, respectively) were not statistically significant between groups (P = 0.57). Conclusion Treatment with rosiglitazone over 1 year had no effect on progression of carotid atheroma in patients with type 2 diabetes mellitus compared to placebo. PMID:19635160

  14. Connecting Global Measures of 3D Magnetic Reconnection to Local Kinetic Physics

    SciTech Connect

    Daughton, William Scott

    2015-07-16

    After giving the motivation for the work, slides present the topic under the following headings: Description of LAPD experiment; Actual simulation setup; Simple kinetic theory of ined-tied tearing; Diagnostics to characterizing 3D reconnection; Example #1 - short-tied system; and Example #2 - long line-tied system. Colorful simulations are shown for quasipotential vs field line exponentiation, field line integrated Ohms Law, and correlation with agyrotopy & energy conversion for example #1; and evolution of current density for largest case, field exponentiation vs quasi-potential, and time evolution of magnetic field lines for example #2. To satisfy line-tied boundary conditions, there is need for superposition of oblique modes--the simple two-mode approximation works surprisingly well. For force-free layers with bg >1, the fastest growing periodic modes are oblique with kxλ ~0.5. This implies a minimum length of Ly > 2πλbg. There are strong correlations between σ → Ξ → A0e (observable with spacecraft). Electron pressure tensor is the dominant non-ideal term.

  15. Craniosynostosis: prenatal diagnosis by 2D/3D ultrasound, magnetic resonance imaging and computed tomography.

    PubMed

    Helfer, Talita Micheletti; Peixoto, Alberto Borges; Tonni, Gabriele; Araujo Júnior, Edward

    2016-09-01

    Craniosynostosis is defined as the process of premature fusion of one or more of the cranial sutures. It is a common condition that occurs in about 1 to 2,000 live births. Craniosynostosis may be classified in primary or secondary. It is also classified as nonsyndromic or syndromic. According to suture commitment, craniosynostosis may affect a single suture or multiple sutures. There is a wide range of syndromes involving craniosynostosis and the most common are Apert, Pffeifer, Crouzon, Shaethre-Chotzen and Muenke syndromes. The underlying etiology of nonsyndromic craniosynostosis is unknown. Mutations in the fibroblast growth factor (FGF) signalling pathway play a crucial role in the etiology of craniosynostosis syndromes. Prenatal ultrasound`s detection rate of craniosynostosis is low. Nowadays, different methods can be applied for prenatal diagnosis of craniosynostosis, such as two-dimensional (2D) and three-dimensional (3D) ultrasound, magnetic resonance imaging (MRI), computed tomography (CT) scan and, finally, molecular diagnosis. The presence of craniosynostosis may affect the birthing process. Fetuses with craniosynostosis also have higher rates of perinatal complications. In order to avoid the risks of untreated craniosynostosis, children are usually treated surgically soon after postnatal diagnosis.

  16. Synthesis, characterization, magnetic and electrochemical properties of a new 3D hexa-copper-substituted germanotungstate

    NASA Astrophysics Data System (ADS)

    Li, Yanzhou; Luo, Jie; Zhang, Yanting; Zhao, Junwei; Chen, Lijuan; Ma, Pengtao; Niu, Jingyang

    2013-09-01

    An inorganic-organic hybrid hexa-copper-substituted germanotungstate Na2[Cu(dap)2]2[Cu(dap)2] {[Cu6(H2O)2(dap)2][B-α-GeW9O34]2}·4H2O (1) (dap=1,2-diaminopropane) has been hydrothermally prepared and characterized by elemental analyses, inductively coupled plasma atomic emission spectrometry (ICP-AES) analyses, IR spectra, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA) and single-crystal X-ray diffraction. 1 displays the six-connected 3D network with the long topological (O'Keefe) vertex symbol is 4·4·64·4·4·4·4·64·4·4·4·64·4·4·4 and the short vertex (Schläfli) symbol of 41263. Magnetic measurements indicate that there are the overall ferromagnetic exchange interactions in the belt-like hexa-CuII cluster in 1. Furthermore, the electrochemical behavior and electrocatalysis of 1 modified carbon paste electrode (1-CPE) have been studied. The reductions of nitrite, bromate and hydrogen peroxide are principally mediated by the WVI-based wave.

  17. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  18. Graphene originated 3D structures grown on the assembled nickel particles

    NASA Astrophysics Data System (ADS)

    Paronyan, Tereza; Harutyunyan, Avetik; Honda Research Institute USA Inc. Team

    2013-03-01

    Recently, the fabrication of various morphologies of graphene originated structures became very important due to the perspective of wide range of new applications. Particularly, free standing 3D structured graphene foams could be imperative in energy related areas . Here, we present the new approach of the CVD growth of 3D graphene network by using primarily sintered Ni particle's (~40 μm size) assembles as a template-catalyst via decomposition of low rate of CH4 at 1100° C based on synthesis method described earlier. SEM and Raman spectra analysis revealed the formation of graphene structure containing a single up to few layers grown on the sintered metal particles served as a catalyst-template. After etching the metal frame without using any support polymer, 3D free-standing graphene microporous structure was formed demonstrating high BET surface area. Two probe measurements of frame resistance were ~2-8 Ω. Our approach allows controllable tune the pore size and thereby the surface area of 3D graphene network through the variation of the template-catalyst particles size.

  19. Observation of Magnetic Reconnection at a 3D Null Point Associated with a Solar Eruption

    NASA Astrophysics Data System (ADS)

    Sun, J. Q.; Zhang, J.; Yang, K.; Cheng, X.; Ding, M. D.

    2016-10-01

    Magnetic null has long been recognized as a special structure serving as a preferential site for magnetic reconnection (MR). However, the direct observational study of MR at null-points is largely lacking. Here, we show the observations of MR around a magnetic null associated with an eruption that resulted in an M1.7 flare and a coronal mass ejection. The Geostationary Operational Environmental Satellites X-ray profile of the flare exhibited two peaks at ∼02:23 UT and ∼02:40 UT on 2012 November 8, respectively. Based on the imaging observations, we find that the first and also primary X-ray peak was originated from MR in the current sheet (CS) underneath the erupting magnetic flux rope (MFR). On the other hand, the second and also weaker X-ray peak was caused by MR around a null point located above the pre-eruption MFR. The interaction of the null point and the erupting MFR can be described as a two-step process. During the first step, the erupting and fast expanding MFR passed through the null point, resulting in a significant displacement of the magnetic field surrounding the null. During the second step, the displaced magnetic field started to move back, resulting in a converging inflow and subsequently the MR around the null. The null-point reconnection is a different process from the current sheet reconnection in this flare; the latter is the cause of the main peak of the flare, while the former is the cause of the secondary peak of the flare and the conspicuous high-lying cusp structure.

  20. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  1. 3D hybrid simulations of the plasma penetration across a magnetic field

    NASA Astrophysics Data System (ADS)

    Omelchenko, Yuri

    2016-10-01

    The expansion of hot dense plasmas across ambient magnetic fields in physical systems with spatial scales comparable to the ion gyro and inertial lengths is of great interest to space physics and fusion. This work presents results from recent three-dimensional hybrid simulations (kinetic ions, fluid electrons) of experiments at the LAPD and Nevada Terawatt Facility where short-pulse lasers are used to ablate solid targets to produce plasmas that expand across external magnetic fields. The first simulation recreates flutelike density striations observed at the leading edge of the carbon plasma and predicts an early destruction of the magnetic cavity in agreement with experimental evidence. In the second simulation the plasma contains protons and carbon ions produced during the ablation of a polyethylene target. A mechanism is demonstrated that allows protons to penetrate the magnetic field in the form of a collimated flow while the carbon ion component forms a supporting magnetic structure. The role of ion kinetic and Hall effects in creating an electric field responsible for plasma transport is discussed and results are compared to experimental data. The hybrid simulations are performed with a massively parallel hybrid code, HYPERS that advances fields and particles asynchronously on time scales determined by local physical and geometric properties. Supported by US DOE Award DE-SC0012345.

  2. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  3. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  4. Studies of the 3D Structure of the Nucleon at Jlab

    SciTech Connect

    Avakian, Harut

    2016-07-01

    Studies of the 3D structure of the nucleon encoded in Transverse Momentum Dependent distribution and fragmentation functions of partons and Generalized Parton Distributions are among the key objectives of the JLab 12 GeV upgrade and the Electron Ion Collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  5. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  6. Measurements of the 3D boundary distortion due to external n=2 magnetic perturbations in comparison to ideal MHD

    NASA Astrophysics Data System (ADS)

    Willensdorfer, Matthias; Suttrop, Wolfgang; Strumberger, Erika; Zohm, Hartmut; Orain, Francois; Kirk, Andrew; Ryan, David; ASDEX Upgrade Team Team

    2016-10-01

    Best ELM mitigation/suppression at DIII-D and AUG are achieved by external magnetic perturbation (MP) fields, when the applied poloidal mode spectrum is aligned with the mode (kink) at the edge that is most strongly amplified by the plasma. This kink mode causes a 3D displacement of the plasma boundary, which is characterized at AUG using data from toroidally localized high resolution diagnostics and rigid rotating MP-fields with different applied poloidal mode spectra. Various profile and imaging diagnostics, e.g. electron cyclotron emission (ECE), are used to determine the amplitude, the penetration and the poloidal mode structure of the displacement around the outer midplane. The displacement around the X-point/plasma top, which is related to ELM mitigation, is measured using a new steerable ECE and SOFT X-ray. These measurements are compared to MHD codes like JOREK, MARS-F and VMEC. As predicted by MHD, the measured amplitudes clearly exceed the vacuum field calculations. The displacement measured by imaging ECE indicates a resonant response, although the calculated magnetic structure of this edge kink peaks at poloidal mode numbers larger than the resonant components.

  7. Plasma response measurements of external magnetic perturbations using electron cyclotron emission and comparisons to 3D ideal MHD equilibrium

    NASA Astrophysics Data System (ADS)

    Willensdorfer, M.; Denk, S. S.; Strumberger, E.; Suttrop, W.; Vanovac, B.; Brida, D.; Cavedon, M.; Classen, I.; Dunne, M.; Fietz, S.; Fischer, R.; Kirk, A.; Laggner, F. M.; Liu, Y. Q.; Odstrčil, T.; Ryan, D. A.; Viezzer, E.; Zohm, H.; Luhmann, I. C.; The ASDEX Upgrade Team; The EUROfusion MST1 Team

    2016-11-01

    The plasma response from an external n  =  2 magnetic perturbation field in ASDEX Upgrade has been measured using mainly electron cyclotron emission (ECE) diagnostics and a rigid rotating field. To interpret ECE and ECE-imaging (ECE-I) measurements accurately, forward modeling of the radiation transport has been combined with ray tracing. The measured data is compared to synthetic ECE data generated from a 3D ideal magnetohydrodynamics (MHD) equilibrium calculated by VMEC. The measured amplitudes of the helical displacement around the outboard midplane are in reasonable agreement with the one from the synthetic VMEC diagnostics. Both exceed the predictions from the vacuum field calculations and indicate the presence of a kink response at the edge, which amplifies the perturbation. VMEC and MARS-F have been used to calculate the properties of this kink mode. The poloidal mode structure of the magnetic perturbation of this kink mode at the edge peaks at poloidal mode numbers larger than the resonant components |m|>|nq| , whereas the poloidal mode structure of its displacement is almost resonant |m|≈ |nq| . This is expected from ideal MHD in the proximity of rational surfaces. The displacement measured by ECE-I confirms this resonant response.

  8. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-08-09

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

  9. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  10. Recursive estimation of 3D motion and surface structure from local affine flow parameters.

    PubMed

    Calway, Andrew

    2005-04-01

    A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

  11. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  12. 3D electrical structure of porphyry copper deposit: A case study of Shaxi copper deposit

    NASA Astrophysics Data System (ADS)

    Chen, Xiang-Bin; Lü, Qing-Tian; Yan, Jia-Yong

    2012-06-01

    Located in Lu-Zong ore concentration area, middle-lower Yangtze metallogenic belt, ShaXi porphyry copper deposit is a typical hydrothermal deposit. To investigate the distribution of deep ore bodies and spatial characteristics of host structures, an AMT survey was conducted in mining area. Eighteen pseudo-2D resistivity sections were constructed through careful processing and inversion. These sections clearly show resistivity difference between the Silurian sandstones formation and quartz diorite porphyry and this porphyry copper formation was controlled by the highly resistive anticlines. Using 3D block Kriging interpolation method and 3D visualization techniques, we constructed a detailed 3D resistivity model of quartz diorite porphyry which shows the shape and spatial distribution of deep ore bodies. This case study can serve as a good example for future ore prospecting in and around this mining area.

  13. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  14. 3D printed low-loss THz waveguide based on Kagome photonic crystal structure.

    PubMed

    Yang, Jing; Zhao, Jiayu; Gong, Cheng; Tian, Haolin; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-10-03

    A low-loss hollow core terahertz waveguide based on Kagome photonic crystal structure has been designed and fabricated by 3D printing. The 3D printed waveguide has been characterized by using THz time-domain spectroscopy. The results demonstrate that the obtained waveguide features average power propagation loss of 0.02 cm-1 for 0.2-1.0 THz (the minimum is about 0.002 cm-1 at 0.75 THz). More interesting, it could be simply mechanically spliced without any additional alignment, while maintaining the excellent performance. The 3D printing technique will be a promising solution to fabricate Kagome THz waveguide with well controllable characteristics and low cost.

  15. Human Sinoatrial Node Structure: 3D Microanatomy of Sinoatrial Conduction Pathways

    PubMed Central

    Csepe, Thomas A.; Zhao, Jichao; Hansen, Brian J.; Li, Ning; Sul, Lidiya V.; Lim, Praise; Wang, Yufeng; Simonetti, Orlando P.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul ML.; Fedorov, Vadim V.

    2016-01-01

    Introduction Despite a century of extensive study on the human sinoatrial node (SAN), the structure-to-function features of specialized SAN conduction pathways (SACP) are still unknown and debated. We report a new method for direct analysis of the SAN microstructure in optically-mapped human hearts with and without clinical history of SAN dysfunction. Methods Two explanted donor human hearts were coronary-perfused and optically-mapped. Structural analyses of histological sections parallel to epicardium (~13-21μm intervals) were integrated with optical maps to create 3D computational reconstructions of the SAN complex. High-resolution fiber fields were obtained using 3D Eigen-analysis of the structure tensor, and used to analyze SACP microstructure with a fiber-tracking approach. Results Optical mapping revealed normal SAN activation of the atria through a lateral SACP proximal to the crista terminalis in Heart #1 but persistent SAN exit block in diseased Heart #2. 3D structural analysis displayed a functionally-observed SAN border composed of fibrosis, fat, and/or discontinuous fibers between SAN and atria, which was only crossed by several branching myofiber tracts in SACP regions. Computational 3D fiber-tracking revealed that myofiber tracts of SACPs created continuous connections between SAN #1 and atria, but in SAN #2, SACP region myofiber tracts were discontinuous due to fibrosis and fat. Conclusions We developed a new integrative functional, structural and computational approach that allowed for the resolution of the specialized 3D microstructure of human SACPs for the first time. Application of this integrated approach will shed new light on the role of the specialized SAN microanatomy in maintaining sinus rhythm. PMID:26743207

  16. A review of 3D first-pass, whole-heart, myocardial perfusion cardiovascular magnetic resonance.

    PubMed

    Fair, Merlin J; Gatehouse, Peter D; DiBella, Edward V R; Firmin, David N

    2015-08-01

    A comprehensive review is undertaken of the methods available for 3D whole-heart first-pass perfusion (FPP) and their application to date, with particular focus on possible acceleration techniques. Following a summary of the parameters typically desired of 3D FPP methods, the review explains the mechanisms of key acceleration techniques and their potential use in FPP for attaining 3D acquisitions. The mechanisms include rapid sequences, non-Cartesian k-space trajectories, reduced k-space acquisitions, parallel imaging reconstructions and compressed sensing. An attempt is made to explain, rather than simply state, the varying methods with the hope that it will give an appreciation of the different components making up a 3D FPP protocol. Basic estimates demonstrating the required total acceleration factors in typical 3D FPP cases are included, providing context for the extent that each acceleration method can contribute to the required imaging speed, as well as potential limitations in present 3D FPP literature. Although many 3D FPP methods are too early in development for the type of clinical trials required to show any clear benefit over current 2D FPP methods, the review includes the small but growing quantity of clinical research work already using 3D FPP, alongside the more technical work. Broader challenges concerning FPP such as quantitative analysis are not covered, but challenges with particular impact on 3D FPP methods, particularly with regards to motion effects, are discussed along with anticipated future work in the field.

  17. Synthesis and Application of Novel 3D Magnetic Chlorogenic Acid Imprinted Polymers Based on a Graphene-Carbon Nanotube Composite.

    PubMed

    Yan, Liang; Yin, Yuli; Lv, Piaopiao; Zhang, Zhaohui; Wang, Jing; Long, Fang

    2016-04-20

    A novel three-dimensional (3D) magnetic chlorogenic acid (CGA) imprinted polymer (MMIP) was prepared with novel carbon hybrid nanocomposite as the carrier, chlorogenic acid as the template molecule, and methacrylic acid as the functional monomer. The 3D MMIPs were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis, vibrating sample magnetometer, and UV spectrometry in detail. The results showed that the imprinted layer was attached successfully on the surface of a 3D magnetic carbon hybrid nanocomposite. The adsorption performance of the 3D MMIPs was investigated, and the results showed that the 3D MMIPs exhibited high adsorption capacity and fast adsorption rate toward CGA with a maximum adsorption capacity of 10.88 mg g(-1). The extraction conditions involving washing solvent, the pH of eluent solvent, elution volume, and desorption time were also investigated in detail. Combined with high-performance liquid chromatography, the 3D MMIPs have been applied to successfully extract CGA from Eucommia leaf extract samples.

  18. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    PubMed

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2016-12-26

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

  19. Advancement of 31P Magnetic Resonance Spectroscopy Using GRAPPA Reconstruction on a 3D Volume

    NASA Astrophysics Data System (ADS)

    Clevenger, Tony

    The overall objective of this research is to improve currently available metabolic imaging techniques for clinical use in monitoring and predicting treatment response to radiation therapy in liver cancer. Liver metabolism correlates with inflammatory and neoplastic liver diseases, which alter the intracellular concentration of phosphorus- 31 (31P) metabolites [1]. It is assumed that such metabolic changes occur prior to physical changes of the tissue. Therefore, information on regional changes of 31P metabolites in the liver, obtained by Magnetic Resonance Spectroscopic Imaging (MRSI) [1,2], can help in diagnosis and follow-up of various liver diseases. Specifically, there appears to be an immediate need of this technology for both the assessment of tumor response in patients with Hepatocellular Carcinoma (HCC) treated with Stereotactic Body Radiation Therapy (SBRT) [3--5], as well as assessment of radiation toxicity, which can result in worsening liver dysfunction [6]. Pilot data from our lab has shown that 31P MRSI has the potential to identify treatment response five months sooner than conventional methods [7], and to assess the biological response of liver tissue to radiation 24 hours post radiation therapy [8]. While this data is very promising, commonly occurring drawbacks for 31P MRSI are patient discomfort due to long scan times and prone positioning within the scanner, as well as reduced data quality due to patient motion and respiration. To further advance the full potential of 31P MRSI as a clinical diagnostic tool in the management of liver cancer, this PhD research project had the following aims: I) Reduce the long acquisition time of 3D 31P MRS by formulating and imple- menting an appropriate GRAPPA undersampling scheme and reconstruction on a clinical MRI scanner II) Testing and quantitative validation of GRAPPA reconstruction on 3D 31P MRSI on developmental phantoms and healthy volunteers At completion, this work should considerably advance 31P MRSI

  20. Toward the automatic quantification of in utero brain development in 3D structural MRI: A review.

    PubMed

    Benkarim, Oualid M; Sanroma, Gerard; Zimmer, Veronika A; Muñoz-Moreno, Emma; Hahner, Nadine; Eixarch, Elisenda; Camara, Oscar; González Ballester, Miguel Angel; Piella, Gemma

    2017-02-14

    Investigating the human brain in utero is important for researchers and clinicians seeking to understand early neurodevelopmental processes. With the advent of fast magnetic resonance imaging (MRI) techniques and the development of motion correction algorithms to obtain high-quality 3D images of the fetal brain, it is now possible to gain more insight into the ongoing maturational processes in the brain. In this article, we present a review of the major building blocks of the pipeline toward performing quantitative analysis of in vivo MRI of the developing brain and its potential applications in clinical settings. The review focuses on T1- and T2-weighted modalities, and covers state of the art methodologies involved in each step of the pipeline, in particular, 3D volume reconstruction, spatio-temporal modeling of the developing brain, segmentation, quantification techniques, and clinical applications. Hum Brain Mapp, 2017. © 2017 Wiley Periodicals, Inc.

  1. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

  2. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  3. Cryo-EM structure of a 3D DNA-origami object

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

  4. Parametric estimation of 3D tubular structures for diffuse optical tomography.

    PubMed

    Larusson, Fridrik; Anderson, Pamela G; Rosenberg, Elizabeth; Kilmer, Misha E; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L

    2013-02-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction.

  5. The Deep Structure and 3D Thermo-geodynamics of the Caucasus by Geophysical Data.

    NASA Astrophysics Data System (ADS)

    Chelidze, T.; Gugunava, G.; Gamkrelidze, N.; Mindeli, P.; Kiria, J.; Ghonghadze, S.; Janovskaya, O.

    2012-04-01

    allows the construction of three-dimensional non-stationary geothermal and thermo-elastic models of the Caucasus and the Black and the Caspian seas water areas proposed by the authors of this paper. Paleo-reconstruction schemes of development of sedimentary cover of the Caucasus (Sholpo, 1978) and the Black sea area (Kasmin at al. 2000) and a lot of other data regarding the Caspian sea area have been used for the construction of three-dimensional non-stationary models of investigated region. Numerical modeling of thermal and thermo-elastic processes allows revealing the temporal distribution of a number of thermo-geodynamic events including the formation of some deep faults and active seismic zones. The above preliminary results on 3D structure and temperature fields in Caucasus were compared to recent publication on 3D crust structure and thermal model of Western and Central Europe (Tesauro, Kaban, and Cloetingh, 2010) and quite satisfactory agreement with our results was found for matching areas (North Turley, Black Sea, Crimea) of considered regions.

  6. Magnetic multilayer structure

    DOEpatents

    Herget, Philipp; O'Sullivan, Eugene J.; Romankiw, Lubomyr T.; Wang, Naigang; Webb, Bucknell C.

    2017-03-21

    A mechanism is provided for an integrated laminated magnetic device. A substrate and a multilayer stack structure form the device. The multilayer stack structure includes alternating magnetic layers and diode structures formed on the substrate. Each magnetic layer in the multilayer stack structure is separated from another magnetic layer in the multilayer stack structure by a diode structure.

  7. Magnetic multilayer structure

    SciTech Connect

    Herget, Philipp; O'Sullivan, Eugene J.; Romankiw, Lubomyr T.; Wang, Naigang; Webb, Bucknell C.

    2016-07-05

    A mechanism is provided for an integrated laminated magnetic device. A substrate and a multilayer stack structure form the device. The multilayer stack structure includes alternating magnetic layers and diode structures formed on the substrate. Each magnetic layer in the multilayer stack structure is separated from another magnetic layer in the multilayer stack structure by a diode structure.

  8. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

  9. ConvNet-Based Localization of Anatomical Structures in 3D Medical Images.

    PubMed

    de Vos, Bob; Wolterink, Jelmer; de Jong, Pim; Leiner, Tim; Viergever, Max; Isgum, Ivana

    2017-02-23

    Localization of anatomical structures is a prerequisite for many tasks in medical image analysis. We propose a method for automatic localization of one or more anatomical structures in 3D medical images through detection of their presence in 2D image slices using a convolutional neural network (ConvNet). A single ConvNet is trained to detect presence of the anatomical structure of interest in axial, coronal, and sagittal slices extracted from a 3D image. To allow the ConvNet to analyze slices of different sizes, spatial pyramid pooling is applied. After detection, 3D bounding boxes are created by combining the output of the ConvNet in all slices. In the experiments 200 chest CT, 100 cardiac CT angiography (CTA), and 100 abdomen CT scans were used. The heart, ascending aorta, aortic arch, and descending aorta were localized in chest CT scans, the left cardiac ventricle in cardiac CTA scans, and the liver in abdomen CT scans. Localization was evaluated using the distances between automatically and manually defined reference bounding box centroids and walls. The best results were achieved in localization of structures with clearly defined boundaries (e.g. aortic arch) and the worst when the structure boundary was not clearly visible (e.g. liver). The method was more robust and accurate in localization multiple structures.

  10. ORBXYZ: a 3D single-particle orbit code for following charged-particle trajectories in equilibrium magnetic fields

    SciTech Connect

    Anderson, D.V.; Cohen, R.H.; Ferguson, J.R.; Johnston, B.M.; Sharp, C.B.; Willmann, P.A.

    1981-06-30

    The single particle orbit code, TIBRO, has been modified extensively to improve the interpolation methods used and to allow use of vector potential fields in the simulation of charged particle orbits on a 3D domain. A 3D cubic B-spline algorithm is used to generate spline coefficients used in the interpolation. Smooth and accurate field representations are obtained. When vector potential fields are used, the 3D cubic spline interpolation formula analytically generates the magnetic field used to push the particles. This field has del.BETA = 0 to computer roundoff. When magnetic induction is used the interpolation allows del.BETA does not equal 0, which can lead to significant nonphysical results. Presently the code assumes quadrupole symmetry, but this is not an essential feature of the code and could be easily removed for other applications. Many details pertaining to this code are given on microfiche accompanying this report.

  11. ORBXYZ: A 3D single-particle orbit code for following charged particle trajectories in equilibrium magnetic fields

    NASA Astrophysics Data System (ADS)

    Anderson, D. V.; Cohen, R. H.; Ferguson, J. R.; Johnston, B. M.; Sharp, C. B.; Willmann, P. A.

    1981-06-01

    The single particle orbit code, TIBRO, was modified extensively to improve the interpolation methods used and to allow use of vector potential fields in the simulation of charged particle orbits on a 3D domain. A 3D cubic B-spline algorithm is used to generate spline coefficients used in the interpolation. Smooth and accurate field representations are obtained. When vector potential fields are used, the 3D cubic spline interpolation formula analytically generates the magnetic field used to push the particles. This field has del.BETA = 0 to computer roundoff. When magnetic induction is used the interpolation allows del.BETA does not equal 0, which can lead to significant nonphysical results. Presently the code assumes quadrupole symmetry, but this is not an essential feature of the code and could be easily removed for other applications.

  12. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    NASA Astrophysics Data System (ADS)

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; zur Loye, Hans-Conrad

    2012-11-01

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi2O2(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P21 (a=9.6479(9) Å, b=4.2349(4) Å, c=11.9615(11) Å, β=109.587(1)°), which contains Bi2O2 chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi4Na4(1R3S-cam)8(EtOH)3.1(H2O)3.4 (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P21 (a=19.0855(7) Å, b=13.7706(5) Å, c=19.2429(7) Å, β=90.701(1)°) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi3+, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer.

  13. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

  14. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  15. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  16. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  17. Pipeline inwall 3D measurement system based on the cross structured light

    NASA Astrophysics Data System (ADS)

    Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

    2014-01-01

    In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

  18. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.