Three-dimensional flow and turbulence structure in electrostatic precipitator
DEFF Research Database (Denmark)
Ullum, Thorvald Uhrskov; Larsen, Poul Scheel; Özcan, Oktay
2002-01-01
and bulk velocity U0 on secondary flows and turbulence levels and structures due to the action of the three-dimensional electrostatic field on the charged gas. At constant bulk velocity (U0 = 1 m/s) and current density (Jm = 0.4 mA/m2), secondary flows in the form of rolls of axial vorticity with swirl...
Araujo, Vitor; Viana, Marcelo
2010-01-01
In this book, the authors present the elements of a general theory for flows on three-dimensional compact boundaryless manifolds, encompassing flows with equilibria accumulated by regular orbits. The book aims to provide a global perspective of this theory and make it easier for the reader to digest the growing literature on this subject. This is not the first book on the subject of dynamical systems, but there are distinct aspects which together make this book unique. Firstly, this book treats mostly continuous time dynamical systems, instead of its discrete counterpart, exhaustively treated
Three-dimensional investigation of the two-phase flow structure in a bubbly pipe flow
International Nuclear Information System (INIS)
Schmidl, W.; Hassan, Y.A.; Ortiz-Villafuerte, J.
1996-01-01
Particle image velocimetry (PIV) is a nonintrusive measurement technique that can be used to study the structure of various fluid flows. PIV is used to measure the time-varying, full-field velocity data of a particle-seeded flow field within either a two-dimensional plane or three-dimensional volume. PIV is a very efficient measurement technique since it can obtain both qualitative and quantitative spatial information about the flow field being studied. The quantitative spatial velocity information can be further processed into information of flow parameters such as vorticity and turbulence over extended areas. The objective of this study was to apply recent advances and improvements in the PIV flow measurement technique to the full-field, nonintrusive analysis of a three-dimensional, two-phase fluid flow system in such a manner that both components of the two-phase system could be experimentally quantified
Bradbrook, Kathryn Frances
1999-01-01
This thesis investigates controls on and the nature of three-dimensional flow structures at river channel confluences. Previous work has shown that junction angle is an important control on the flow patterns at channel junctions since it affects the degree of curvature of flow from each tributary and sets up secondary circulation cells similar to those in meander bends. Recent work has highlighted the common occurrence of, and importance of, bed discordance at river confluences due to a signi...
Three-dimensional investigation of the two-phase flow structure in a bubbly pipe flow
International Nuclear Information System (INIS)
Hassan, Y.A.; Schmidl, W.D.; Ortiz-Villafuerte, J.
1997-01-01
Particle Image Velocimetry (PIV) is a non-intrusive measurement technique, which can be used to study the structure of various fluid flows. PIV is used to measure the time varying full field velocity data of a particle-seeded flow field within either a two-dimensional plane or three-dimensional volume. PIV is a very efficient measurement technique since it can obtain both qualitative and quantitative spatial information about the flow field being studied. This information can be further processed into information such as vorticity and pathlines. Other flow measurement techniques (Laser Doppler Velocimetry, Hot Wire Anemometry, etc...) only provide quantitative information at a single point. PIV can be used to study turbulence structures if a sufficient amount of data can be acquired and analyzed, and it can also be extended to study two-phase flows if both phases can be distinguished. In this study, the flow structure around a bubble rising in a pipe filled with water was studied in three-dimensions. The velocity of the rising bubble and the velocity field of the surrounding water was measured. Then the turbulence intensities and Reynolds stresses were calculated from the experimental data. (author)
PIV measurements in a microfluidic 3D-sheathing structure with three-dimensional flow behaviour
DEFF Research Database (Denmark)
Klank, Henning; Goranovic, Goran; Kutter, Jörg Peter
2002-01-01
. The structures are often of complex geometry and include strongly three-dimensional flow behaviour, which poses a challenge for the micro particle image velocimetry (micro-PIV) technique. The flow in a microfluidic 3D-sheathing structure has been measured throughout the volume using micro-PIV. In addition......, a stereoscopic principle was applied to obtain all three velocity components, showing the feasibility of obtaining full volume mapping (x, y, z, U, V, W) from micro-PIV measurements. The results are compared with computational fluid dynamics (CFD) simulations....
Measuring three-dimensional flow structures in the conductive airways using 3D-PTV
Janke, Thomas; Schwarze, Rüdiger; Bauer, Katrin
2017-10-01
Detailed information about flow patterns and mass transport in the conductive airways is of crucial interest to improve ventilation strategies as well as targeted drug delivery. Despite a vast number of flow studies in this field, there is still a dearth in experimental data of three-dimensional flow patterns, in particular for the validation of numerical results. Therefore, oscillating flow within a realistic model of the upper human conductive airways is studied here experimentally. The investigated range of Reynolds numbers is Re = 250-2000 and the Womersley number is varied between α = 1.9-5.1, whereby physiological flow at rest conditions is included. In employing the three-dimensional particle tracking velocimetry measurement technique, we can directly visualize airway specific flow structures as well as examine Lagrangian trajectory statistics, which has not been covered to date. The systematic variation of characteristic flow parameters in combination with the advanced visualization technique sheds new light on the mechanisms of evolving flow patterns. By determining Lagrangian properties such as pathline curvature and torsion, we find that both strongly depend on the Reynolds number. Moreover, the probability density function of the curvature reveals a unique shape for certain flow regions and resembles a turbulent like behavior at the small scales.
Emergence of three-dimensional flow structures in shock boundary layer interactions
Gs, Sidharth; Dwivedi, Anubhav; Nichols, Joseph; Jovanovic, Mihailo; Candler, Graham
2017-11-01
Experiments and computations point to the emergence of three-dimensional (3D) flow structures in laminar shock boundary layer interactions in various configurations. We examine a Mach 5 flow over a double compression ramp and reveal the presence of a bifurcation from a steady 2D to a steady 3D flow state. This is done by varying the relative angle of the two ramps which increases the interaction strength. We employ global linear stability analysis and direct numerical simulation to characterize this bifurcation and demonstrate that global instability induces 3D flow structures. We use the direct and adjoint linear equations to further investigate the origin of this instability and examine the influence of uncertainty (including the effect of geometric irregularities in the ramp and free-stream disturbances in wind tunnel) on this bifurcation. This work was supported by Office of Naval Research through Grant Number N00014-15-1-2522.
PIV measurements in a microfluidic 3D-sheathing structure with three-dimensional flow behaviour
DEFF Research Database (Denmark)
Klank, Henning; Goranovic, Goran; Kutter, Jörg Peter
2002-01-01
. The structures are often of complex geometry and include strongly three-dimensional flow behaviour, which poses a challenge for the micro particle image velocimetry (micro-PIV) technique. The flow in a microfluidic 3D-sheathing structure has been measured throughout the volume using micro-PIV. In addition......The design and production time for complex microfluidic systems is considerable, often up to several months. It is therefore important to be able to understand and predict the flow phenomena prior to design and fabrication of the microdevice in order to save costly fabrication resources......, a stereoscopic principle was applied to obtain all three velocity components, showing the feasibility of obtaining full volume mapping (x, y, z, U, V, W) from micro-PIV measurements. The results are compared with computational fluid dynamics (CFD) simulations....
Three-dimensional flow structure measurements behind a queue of studied model vehicles
International Nuclear Information System (INIS)
Huang, J.F.; Chan, T.L.; Zhou, Y.
2009-01-01
The three-dimensional flow structures of a queue of studied model vehicles (i.e., one-, two- and three-vehicle cases) were investigated comprehensively in a closed-circuit wind tunnel using particle image velocimetry (PIV) for the typical urban vehicle speeds (i.e., 10, 30 and 50 km/h). In this three-dimensional vehicle wake, a pair of longitudinal vortices is characterized by counter-rotating and moving downstream at relatively low velocity than their surrounding flow. The flow structures of multiple studied model vehicles are dominated by the wake generated from the last studied model vehicle but the preceding studied model vehicle(s) also has/have some minor effects. Cross-sectional turbulence distribution is non-uniform in the far-wake region for all studied cases. The lowest turbulence occurs at the center part of the vehicle wake while high turbulence occurs at its two sides. As such, it may lead to considerable underestimation in turbulence magnitude if the measurement is only taken along the centerline of the vehicle wake.
Viscoelastic polymer flows and elastic turbulence in three-dimensional porous structures.
Mitchell, Jonathan; Lyons, Kyle; Howe, Andrew M; Clarke, Andrew
2016-01-14
Viscoelastic polymer solutions flowing through reservoir rocks have been found to improve oil displacement efficiency when the aqueous-phase shear-rate exceeds a critical value. A possible mechanism for this enhanced recovery is elastic turbulence that causes breakup and mobilization of trapped oil ganglia. Here, we apply nuclear magnetic resonance (NMR) pulsed field gradient (PFG) diffusion measurements in a novel way to detect increased motion of disconnected oil ganglia. The data are acquired directly from a three-dimensional (3D) opaque porous structure (sandstone) when viscoelastic fluctuations are expected to be present in the continuous phase. The measured increase in motion of trapped ganglia provides unequivocal evidence of fluctuations in the flowing phase in a fully complex 3D system. This work provides direct evidence of elastic turbulence in a realistic reservoir rock - a measurement that cannot be readily achieved by conventional laboratory methods. We support the NMR data with optical microscopy studies of fluctuating ganglia in simple two-dimensional (2D) microfluidic networks, with consistent apparent rheological behaviour of the aqueous phase, to provide conclusive evidence of elastic turbulence in the 3D structure and hence validate the proposed flow-fluctuation mechanism for enhanced oil recovery.
Leaving flatland: Diagnostics for Lagrangian coherent structures in three-dimensional flows
Sulman, Mohamed H. M.; Huntley, Helga S.; Lipphardt, B. L.; Kirwan, A. D.
2013-09-01
Finite-time Lyapunov exponents (FTLE) are often used to identify Lagrangian Coherent Structures (LCS). Most applications are confined to flows on two-dimensional (2D) surfaces where the LCS are characterized as curves. The extension to three-dimensional (3D) flows, whose LCS are 2D structures embedded in a 3D volume, is theoretically straightforward. However, in geophysical flows at regional scales, full prognostic computation of the evolving 3D velocity field is not computationally feasible. The vertical or diabatic velocity, then, is either ignored or estimated as a diagnostic quantity with questionable accuracy. Even in cases with reliable 3D velocities, it may prove advantageous to minimize the computational burden by calculating trajectories from velocities on carefully chosen surfaces only. When reliable 3D velocity information is unavailable or one velocity component is explicitly ignored, a reduced FTLE form to approximate 2D LCS surfaces in a 3D volume is necessary. The accuracy of two reduced FTLE formulations is assessed here using the ABC flow and a 3D quadrupole flow as test models. One is the standard approach of knitting together FTLE patterns obtained on adjacent surfaces. The other is a new approximation accounting for the dispersion due to vertical (u,v) shear. The results are compared with those obtained from the full 3D velocity field. We introduce two diagnostic quantities to identify situations when a fully 3D computation is required for an accurate determination of the 2D LCS. For the ABC flow, we found the full 3D calculation to be necessary unless the vertical (u,v) shear is sufficiently small. However, both methods compare favorably with the 3D calculation for the quadrupole model scaled to typical open ocean conditions.
Three dimensional flow structures and turbulence distribution in an urban environment
Monnier, Bruno
Understanding and controlling the dispersion of pollutants and contaminants in urban areas has become a major focus recently. Field measurements, numerical studies, and wind tunnel experiments have increased in number. Specifically, there is a growing need for a spatio-temporal description of such complex flow fields under well-controlled conditions, typically obtained in wind tunnel experiments. The reduced scale model of interest is a 4 by 3 array of cuboid blocks in an experimentally modeled, neutrally stratified, atmospheric boundary-layer. The use of Stereoscopic Particle Image Velocimetry (SPIV) allows for a three-dimensional description of this urban flow. A large amount of SPIV data is collected upstream and in each middle street of the urban environment allowing for a study of the flow evolution from street to street. Valuable information about the flow structures are presented along with the mechanisms responsible for contaminant transport and dispersion. The effects of small incidence angles of the incoming flow with respect to the urban array and the effects of streamwise spacing between streets on the flow characteristics are investigated. A major observation from this work is that a strong channeling effect is observed for incidence angles as small as 4.5° and is found to be comparable in strength to that observed in other investigations for much larger angles. A coupling between this channeling effect and the structures responsible for contaminant transport is revealed. An innovative method using sparse measurements to estimate the continuous temporal evolution of the dominant structures in the flow is investigated. Proper Orthogonal Decomposition is used to obtain a reduced-order representation (ROR) of the flow field. Sparse velocity measurements within the domain serve as input to measurement models that provide an estimation of the ROR of the velocity field. This ROR of the flow field could be regarded as the first that provides a temporal
Three-dimensional structure of clumpy outflow from supercritical accretion flow onto black holes
Kobayashi, Hiroshi; Ohsuga, Ken; Takahashi, Hiroyuki R.; Kawashima, Tomohisa; Asahina, Yuta; Takeuchi, Shun; Mineshige, Shin
2018-02-01
We perform global three-dimensional (3D) radiation-hydrodynamic (RHD) simulations of outflow from supercritical accretion flow around a 10 M⊙ black hole. We only solve the outflow part, starting from the axisymmetric 2D simulation data in a nearly steady state but with small perturbations in a sinusoidal form being added in the azimuthal direction. The mass accretion rate onto the black hole is ˜102LE/c2 in the underlying 2D simulation data, and the outflow rate is ˜10 LE/c2 (with LE and c being the Eddington luminosity and speed of light, respectively). We first confirm the emergence of clumpy outflow, which was discovered by the 2D RHD simulations, above the photosphere located at a few hundreds of Schwarzschild radii (rS) from the central black hole. As prominent 3D features we find that the clumps have the shape of a torn sheet, rather than a cut string, and that they are rotating around the central black hole with a sub-Keplerian velocity at a distance of ˜103 rS from the center. The typical clump size is ˜30 rS or less in the radial direction, and is more elongated in the angular directions, ˜ hundreds of rS at most. The sheet separation ranges from 50 to 150 rS. We expect stochastic time variations when clumps pass across the line of the sight of a distant observer. Variation timescales are estimated to be several seconds for a black hole with mass of ten to several tens of M⊙, in rough agreement with the observations of some ultra-luminous X-ray sources.
International Nuclear Information System (INIS)
Yoon, Sang Youl; Kim, Kyung Chun
2003-01-01
The three-dimensional spatial structures of impeller flow created by a six bladed Rushton turbine have identified based on the volumetric velocity information from multi-plane stereoscopic PIV measurements. A total of 10 planes with 2 mm space and a 50 mm by 64 mm size of the field of view were targeted. To reduce the depth of focus, we adopted an angle offset configuration which satisfied the Scheimpflug condition. The distortion compensation procedure was utilized during the in situ calibration. Phase-locked instantaneous data were ensemble averaged and interpolated in order to obtain mean 3-D, volumetric velocity fields on a 60 degree sector of a cylindrical ring volume enclosing the turbine blade. Using the equi-vorticity surface rendering, the spatial structure of the trailing vortices was clearly demonstrated. Detail flow characteristics of the radial jet reported in previous studies of mixer flows were easily identified
International Nuclear Information System (INIS)
Bettencourt, João H; López, Cristóbal; Hernández-García, Emilio
2013-01-01
In this paper, we use the finite-size Lyapunov exponent (FSLE) to characterize Lagrangian coherent structures in three-dimensional (3D) turbulent flows. Lagrangian coherent structures act as the organizers of transport in fluid flows and are crucial to understand their stirring and mixing properties. Generalized maxima (ridges) of the FSLE fields are used to locate these coherent structures. 3D FSLE fields are calculated in two phenomenologically distinct turbulent flows: a wall-bounded flow (channel flow) and a regional oceanic flow obtained by the numerical solution of the primitive equations where two-dimensional (2D) turbulence dominates. In the channel flow, autocorrelations of the FSLE field show that the structure is substantially different from the near wall to the mid-channel region and relates well to the more widely studied Eulerian coherent structure of the turbulent channel flow. The ridges of the FSLE field have complex shapes due to the 3D character of the turbulent fluctuations. In the oceanic flow, strong horizontal stirring is present and the flow regime is similar to that of 2D turbulence where the domain is populated by coherent eddies that interact strongly. This in turn results in the presence of high FSLE lines throughout the domain leading to strong non-local mixing. The ridges of the FSLE field are quasi-vertical surfaces, indicating that the horizontal dynamics dominates the flow. Indeed, due to rotation and stratification, vertical motions in the ocean are much less intense than horizontal ones. This suppression is absent in the channel flow, as the 3D character of the FSLE ridges shows. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Lyapunov analysis: from dynamical systems theory to applications’. (paper)
Experimental investigation of three-dimensional flow structures in annular swirling jets
Percin, M.; Vanierschot, M.; Van Oudheusden, B.W.
2015-01-01
Annular jet flows are of practical interest in view of their occurrence in many industrial applications in the context of bluff-body combustors [1]. They feature different complex flow characteristics despite their simple geometry: a central recirculation zone (CRZ) as a result of flow separation
Clark, Heather
Blunt trailing edge airfoils offer structural and aerodynamic advantages in modern wind turbine and aircraft applications. However, penalties are introduced concurrently by vortex shedding at separation. In particular, the adverse effects of increased drag and unsteady loading motivate the development of a control strategy for the blunt trailing edge wake. Closed-loop control is pursued for its potentially greater effectiveness and efficiency, relative to open-loop forcing. Toward this aim, the thesis addresses the need for estimation of the state from limited measurements. The wake of a blunt trailing edge body is investigated experimentally through simultaneous measurements of velocity and the spanwise distribution of fluctuating surface pressure. Passive forcing is implemented with an array of vortex generators that are arranged according to the characteristic wavelength of the dominant small-scale instability. The guiding considerations for the analysis and discussion are physical characterization and the development of estimation strategies based on surface pressure. Joint examination of the measured variables through reduced-order modelling, wavelet analysis, and conditional averaging yields insight regarding the unsteady, three-dimensional nature of the flow. The investigation of forcing is focused upon the influence of the perturbation on the surface pressure and the performance of estimation models in the modified wake. It is found that low-frequency amplitude modulation of the pressure results from variation of both the magnitude of velocity fluctuations and the vortex formation length. The forcing regularizes the shedding in time and space, as evidenced by the attenuated modulation and enhanced spanwise coherence of the amplitude and phase. Examination of this behaviour confirms the connection between amplitude modulation and vortex dislocations in bluff body wakes. Several properties of the estimation approaches hold in general. It is shown that the
Two-dimensional turbulence in three-dimensional flows
Xia, H.; Francois, N.
2017-11-01
This paper presents a review of experiments performed in three-dimensional flows that show behaviour associated with two-dimensional turbulence. Experiments reveal the presence of the inverse energy cascade in two different systems, namely, flows in thick fluid layers driven electromagnetically and the Faraday wave driven flows. In thick fluid layers, large-scale coherent structures can shear off the vertical eddies and reinforce the planarity of the flow. Such structures are either self-generated or externally imposed. In the Faraday wave driven flows, a seemingly three-dimensional flow is shown to be actually two-dimensional when it is averaged over several Faraday wave periods. In this system, a coupling between the wave motion and 2D hydrodynamic turbulence is uncovered.
Forte, A.M.; Woodward, R.L.
1997-01-01
Joint inversions of seismic and geodynamic data are carried out in which we simultaneously constrain global-scale seismic heterogeneity in the mantle as well as the amplitude of vertical mantle flow across the 670 km seismic discontinuity. These inversions reveal the existence of a family of three-dimensional (3-D) mantle models that satisfy the data while at the same time yielding predictions of layered mantle flow. The new 3-D mantle models we obtain demonstrate that the buoyancy forces due to the undulations of the 670 km phase-change boundary strongly inhibit the vertical flow between the upper and lower mantle. The strong stabilizing effect of the 670 km topography also has an important impact on the predicted dynamic topography of the Earth's solid surface and on the surface gravity anomalies. The new 3-D models that predict strongly or partially layered mantle flow provide essentially identical fits to the global seismic data as previous models that have, until now, predicted only whole-mantle flow. The convective vertical transport of heat across the mantle predicted on the basis of the new 3-D models shows that the heat flow is a minimum at 1000 km depth. This suggests the presence at this depth of a globally defined horizon across which the pattern of lateral heterogeneity changes rapidly. Copyright 1997 by the American Geophysical Union.
Computational study of three-dimensional wake structure
International Nuclear Information System (INIS)
Himeno, R.; Shirayama, S.; Kamo, K.; Kuwahara, K.
1986-01-01
Three-dimensional wake structure is studied by numerically solving the incompressible Navier-Stokes equations. Results are visualized by a three-dimensional color graphic system. It was found that a pair of vortex tubes separated from a body plays the most important role in the wake. Near the body vortex tubes are rather stable, however, they gradually become unsteady as they flow down
Vocal Fold Pathologies and Three-Dimensional Flow Separation Phenomena
Apostoli, Adam G.; Weiland, Kelley S.; Plesniak, Michael W.
2013-11-01
Polyps and nodules are two different pathologies, which are geometric abnormalities that form on the medial surface of the vocal folds, and have been shown to significantly disrupt a person's ability to communicate. Although the mechanism by which the vocal folds self-oscillate and the three-dimensional nature of the glottal jet has been studied, the effect of irregularities caused by pathologies is not fully understood. Examining the formation and evolution of vortical structures created by a geometric protuberance is important, not only for understanding the aerodynamic forces exerted by these structures on the vocal folds, but also in the treatment of the above-mentioned pathological conditions. Using a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, the present investigation considers three-dimensional flow separation induced by a model vocal fold polyp. Building on previous work using skin friction line visualization, both the velocity flow field and wall pressure measurements around the model polyp are presented and compared. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).
A method for fabricating a three-dimensional carbon structure
DEFF Research Database (Denmark)
2017-01-01
A method for fabricating a three-dimensional carbon structure (4) is disclosed. A mould (1) defining a three-dimensional shape is provided, and natural protein containing fibres are packed in the mould (1) at a predetermined packing density. The packed natural protein containing fibre structure (3......) undergoes pyrolysis, either while still in the mould (1) or after having been removed from the mould (1). Thereby a three-dimensional porous and electrically conducting carbon structure (4) having a three-dimensional shape defined by the three-dimensional shape of the mould (1) and a porosity defined...
Pittman, J. L.; Giles, G. L.
1986-01-01
An iterative procedure for the static aeroelastic design of a flexible wing at supersonic speeds has been developed. The procedure combines a nonlinear, full-potential solver (NCOREL) with an equivalent plate structural analysis method. The NCOREL method yields significantly improved aerodynamic estimates compared to linear theory. The equivalent plate structural analysis method demonstrates an order of magnitude reduction in computer memory and execution time compared to finite-element methods. A highly swept wing is analyzed at high lift using this aeroelastic procedure. The results indicate that the wing deforms favorably due to aerodynamic loading and, consequently, that the inviscid drag levels do not vary at the required lift coefficient although the angle of attack varies significantly. A sensitivity analysis of the type required for optimization studies was also performed with the aeroelastic design procedure.
Singularities at rims in three-dimensional fluid flow
Driesen, C.H.; Kuerten, Johannes G.M.
1999-01-01
Asymptotic solutions are presented for Stokes flow near circular rims in three-dimensional geometries. Using nonstandard toroidal coordinates, asymptotic analytical expressions are derived for different corner angles. In comparison to the two-dimensional case, an extra critical corner angle value is
Turbulent Flows Over Three-Dimensional Shark Skin
Boomsma, Aaron; Wen, Li; Lauder, George; Sotiropoulos, Fotis
2012-11-01
Shark skin is covered with thousands of small tooth-like structures called denticles. It has long been hypothesized that denticles act as riblets do in a turbulent boundary layer and help reduce friction drag and enhance shark swimming efficiency. We employ the Curvilinear Immersed Boundary (CURVIB) method (Ge and Sotiropoulos, J. Comp. Physics, 2008) to carry out high-resolution large eddy simulations of turbulent flow past a series of anatomically realistic shark denticles mounted on a flat plate. The denticle shapes used in our simulations were obtained by scanning Mako Short Fin shark skin with micro-CT. The computed results are analyzed to elucidate the three-dimensional structure of the flow past the denticles and identify possible drag reduction mechanics. Drag measurements obtained in a laboratory flume for various denticle spacings and arrangements are also reported and analyzed in tandem with the LES results to explore similarities between shark skin and engineered riblets. Computational Resources were provided by the University of Minnesota Supercomputing Institute.
Analysis and visualization of complex unsteady three-dimensional flows
Van Dalsem, William R.; Buning, Pieter G.; Dougherty, F. Carroll; Smith, Merritt H.
1989-01-01
Flow field animation is the natural choice as a tool in the analysis of the numerical simulations of complex unsteady three-dimensional flows. The PLOT4D extension of the widely used PLOT3D code to allow the interactive animation of a broad range of flow variables was developed and is presented. To allow direct comparison with unsteady experimental smoke and dye flow visualization, the code STREAKER was developed to produce time accurate streaklines. Considerations regarding the development of PLOT4D and STREAKER, and example results are presented.
Magnetic structure of two- and three-dimensional supramolecular compounds
Energy Technology Data Exchange (ETDEWEB)
Decurtins, S.; Schmalle, H.W.; Pellaux, R. [Zurich Univ. (Switzerland); Fischer, P.; Fauth, F. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Ouladdiaf, B. [Institut Max von Laue - Paul Langevin, 75 - Paris (France)
1997-09-01
Supramolecular chiral networks of oxalato-bridged transition metals show either two- or three-dimensional structural features. The magnetic structures of such compounds have been investigated by means of elastic neutron powder diffraction. (author) 2 figs., 2 refs.
Three-dimensional structures of laccases.
Hakulinen, N; Rouvinen, J
2015-03-01
Laccases are phenol oxidases that belong to the family of multi-copper oxidases and the superfamily of cupredoxins. A number of potential industrial applications for laccases have led to intensive structure-function studies and an increased amount of crystal structures has been solved. The objective of this review is to summarize and analyze available crystal structures of laccases. The experimental crystallographic data are now easily available from the websites and electron density maps can be used for the interpretation of the structural models. The crystal structures can give valuable insights into the functional mechanisms and may serve as the basis for the development of laccases for industrial applications.
Analysis and validation of carbohydrate three-dimensional structures
International Nuclear Information System (INIS)
Lütteke, Thomas
2009-01-01
The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures
Discretization model for nonlinear dynamic analysis of three dimensional structures
International Nuclear Information System (INIS)
Hayashi, Y.
1982-12-01
A discretization model for nonlinear dynamic analysis of three dimensional structures is presented. The discretization is achieved through a three dimensional spring-mass system and the dynamic response obtained by direct integration of the equations of motion using central diferences. First the viability of the model is verified through the analysis of homogeneous linear structures and then its performance in the analysis of structures subjected to impulsive or impact loads, taking into account both geometrical and physical nonlinearities is evaluated. (Author) [pt
New "sandwich" structures conformed from three dimensional
Directory of Open Access Journals (Sweden)
Alba, Juan J.
1996-03-01
Full Text Available Poor interlaminar properties as well as poor-skin-to-core adhesion properties are very often the common existing problems we find when designing with "sandwich" structures. A new type of 3D-fabric "sandwich" structure is being developed in order to avoid these problems. Although the manufacturing process is very simple, a very complex "sandwich" structure is obtained as a result of the complexity of the 3D-fabric used. This 3D-fabric is a 3D woven glass fabric produced on velvet weaving machines with glass yarns. It is an integrally woven "sandwich" laminate for all kinds of composite products. The strength of the vertical fibers makes, that also after impregnation with a resin matrix, the "sandwich" structure is maintained. The result is a laminate with high strength and stiffness and low weight. On each side of this "sandwich" laminate additional reinforcement materials can be laminated and a synthetic foam can be injected in the hollow structure. This will allow to establish the mechanical properties of a finished product.
Las pobres propiedades, tanto interlaminares como de adhesión entre piel y núcleo, constituyen uno de los grandes problemas cuando se diseñan estructuras utilizando paneles tipo "sandwich". Un nuevo tipo de panel "sandwich", configurado a partir de tejidos tridimensionales, está siendo desarrollado en la actualidad con el objetivo de eliminar esos problemas. Aunque el proceso de fabricación es muy simple, el panel "sandwich" obtenido es de estructura compleja, como resultado de la complejidad del tejido tridimensional utilizado. Este tejido tridimensional (3D es un tejido de fibra de vidrio producido en máquinas de tejer especializadas. La resistencia de las fibras verticales hace que, después de la impregnación con una resina, se mantenga la configuración tipo "sandwich". El resultado es un laminado de alta resistencia, gran rigidez y bajo peso. Sobre cada uno de los lados del panel "sandwich" se pueden
Three-dimensional flow measurements in a tesla turbine rotor
Fuchs, Thomas; Schosser, Constantin; Hain, Rainer; Kaehler, Christian
2015-11-01
Tesla turbines are fluid mechanical devices converting flow energy into rotation energy by two physical effects: friction and adhesion. The advantages of the tesla turbine are its simple and robust design, as well as its scalability, which makes it suitable for custom power supply solutions, and renewable energy applications. To this day, there is a lack of experimental data to validate theoretical studies, and CFD simulations of these turbines. This work presents a comprehensive analysis of the flow through a tesla turbine rotor gap, with a gap height of only 0.5 mm, by means of three-dimensional Particle Tracking Velocimetry (3D-PTV). For laminar flows, the experimental results match the theory very well, since the measured flow profiles show the predicted second order parabolic shape in radial direction and a fourth order behavior in circumferential direction. In addition to these laminar measurements, turbulent flows at higher mass flow rates were investigated.
Three Dimensional Cancellous Bone Structure in Hypoparathyroidism
Rubin, Mishaela R.; Dempster, David W.; Kohler, Thomas; Stauber, Martin; Zhou, Hua; Shane, Elizabeth; Nickolas, Thomas; Stein, Emily; Sliney, James; Silverberg, Shonni J.; Bilezikian, John P.; Müller, Ralph
2009-01-01
By conventional 2-dimensional histomorphometric analysis, we have shown that cancellous bone architecture is markedly altered in hypoparathyroidism. We have now extended these observations to a 3-dimensional analysis using microcomputed tomography. Percutaneous iliac crest bone biopsies were analyzed by high-resolution microcomputed tomography from the following 25 subjects with hypoparathyroidism: 5 postmenopausal women, 13 premenopausal women and 7 men. Thirteen living premenopausal healthy controls and 12 cadaver subjects without bone disease served as matched controls. Hypoparathyroid subjects had significantly greater bone surface density (BS/TV: 5.74 ± 4.7 vs. 3.73 ± 1.01 mm2/mm3 [mean ± SD]; p=0.04), trabecular thickness (Tb.Th: 0.25 ± 0.19 vs. 0.17 ± 0.04 mm; p=0.04), trabecular number (Tb.N: 2.99 ± 3.4 vs. 1.62 ± 0.39 mm−1; p=0.05) and connectivity density (Conn.D: 16.63 ± 18.7 vs. 8.39 ± 5.8 mm3; p=0.04) in comparison to matched controls. When an additional 8 hypoparathyorid (total n= 33) and 24 cadaver (total cadaver n= 36) subjects were added to the groups for an unmatched analysis, hypoparathyroid subjects had significantly greater cancellous bone volume (BV/TV: 26.98 ± 10 vs. 15.39 ± 4%; phypoparathyroid subjects, as assessed by microcomputed tomography, were highly correlated with those assessed by conventional histomorphometry. We conclude that cancellous bone in hypoparathyroidism is abnormal, suggesting that parathyroid hormone is required to maintain normal trabecular structure. The effect of these structural changes on bone strength remains to be determined. PMID:19782782
Three-dimensional flows in a transonic compressor rotor
Reid, Lonnie; Celestina, Mark L.; Dewitt, Kenneth; Keith, Theo
1991-01-01
This study involves an experimental and numerical investigation of the three-dimensional flows in a transonic compressor rotor. A variety of data which could be used, in a complementary fashion, to validate/calibrate the computational fluid dynamics turbomachinery code and improve understanding of the flow physics, were acquired. Detailed radial survey data which consisted of total pressure, total temperature, static pressure and flow angle were obtained at stations upstream and downstream of the rotor blade. Detailed velocity and turbulence profiles were obtained upstream of the rotor and used as the upstream boundary conditions for the numerical analysis. Calibrated flush-mounted hot film probes were used to measure wall shear stress on the hub and casing walls upstream of the rotor. The blade-to-blade shear-stress angle distributions were obtained at two axial locations on the rotor casing, using flush-mounted hot film probes. A numerical analysis conducted using a three-dimensional Navier-Stokes code was compared with the experimental results.
Three-dimensional Reciprocal Structures: Morphology, Concepts, Generative Rules
DEFF Research Database (Denmark)
Parigi, Dario; Pugnale, Alberto
2012-01-01
This paper present seven different three dimensional structures based on the principle of structural reciprocity with superimposition joint and standardized un-notched elements. Such typology could be regarded as being intrinsically three-dimensional because elements sit one of the top of the oth......, causing every configuration to develop naturally out-of the plane. The structures presented here were developed and built by the students of the Master of Science in “Architectural Design” during a two week long workshop organized at Aalborg University in the fall semester 2011....
Lagrangian chaos in three- dimensional steady buoyancy-driven flows
Contreras, Sebastian; Speetjens, Michel; Clercx, Herman
2016-11-01
Natural convection plays a key role in fluid dynamics owing to its ubiquitous presence in nature and industry. Buoyancy-driven flows are prototypical systems in the study of thermal instabilities and pattern formation. The differentially heated cavity problem has been widely studied for the investigation of buoyancy-induced oscillatory flow. However, far less attention has been devoted to the three-dimensional Lagrangian transport properties in such flows. This study seeks to address this by investigating Lagrangian transport in the steady flow inside a cubic cavity differentially-heated from the side. The theoretical and numerical analysis expands on previously reported similarities between the current flow and lid-driven flows. The Lagrangian dynamics are controlled by the Péclet number (Pe) and the Prandtl number (Pr). Pe controls the behaviour qualitatively in that growing Pe progressively perturbs the integable state (Pe =0), thus paving the way to chaotic dynamics. Pr plays an entirely quantitative role in that Pr1 amplifies and diminishes, respectively, the perturbative effect of non-zero Pe. S.C. acknowledges financial support from Consejo Nacional de Ciencia y Tecnología (CONACYT).
Three-dimensional structure of heat shock protein 90 from ...
Indian Academy of Sciences (India)
Madhu Sudhan
2007-04-02
Apr 2, 2007 ... Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory ... role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length .... PfHsp90 and for the development of small-molecule targets.
Self-organization in three-dimensional compressible magnetohydrodynamic flow
International Nuclear Information System (INIS)
Horiuchi, Ritoku; Sato, Tetsuya.
1987-07-01
A three-dimensional self-organization process of a compressible dissipative plasma with a velocity-magnetic field correlation is investigated in detail by means of a variational method and a magnetohydrodynamic simulation. There are two types of relaxation, i.e., fast relaxation in which the cross helicity is not conserved, and slow relaxation in which the cross helicity is approximately conserved. In the slow relaxation case the cross helicity consists of two components with opposite sign which have almost the same amplitude in the large wavenumber region. In both cases the system approaches a high correlation state, dependent on the initial condition. These results are consistent with an observational data of the solar wind. Selective dissipation of magnetic energy, normal cascade of magnetic energy spectrum and inverse cascade of magnetic helicity spectrum are observed for the sub-Alfvenic flow case as was previously observed for the zero flow case. When the flow velocity is super-Alfvenic, the relaxation process is significantly altered from the zero flow case. (author)
Three dimensional Lagrangian structures in the Antarctic Polar Vortex.
Mancho, Ana M.; Garcia-Garrido, Victor J.; Curbelo, Jezabel; Niang, Coumba; Mechoso, Carlos R.; Wiggins, Stephen
2017-04-01
Dynamical systems theory has supported the description of transport processes in fluid dynamics. For understanding trajectory patterns in chaotic advection the geometrical approach by Poincaré seeks for spatial structures that separate regions corresponding to qualitatively different types of trajectories. These structures have been referred to as Lagrangian Coherent Structures (LCS), which typically in geophysical flows are well described under the approach of incompressible 2D flows. Different tools have been used to visualize LCS. In this presentation we use Lagrangian Descriptors [1,2,3,4] (function M) for visualizing 3D Lagrangian structures in the atmosphere, in particular in the Antarctic Polar Vortex. The function M is computed in a fully 3D incompressible flow obtained from data provided by the European Centre for Medium-Range Weather Forecast and it is represented in 2D surfaces. We discuss the findings during the final warming that took place in the spring of 1979 [5]. This research is supported by MINECO grant MTM2014-56392-R. Support is acknowledged also from CSIC grant COOPB20265, U.S. NSF grant AGS-1245069 and ONR grant No. N00014- 01-1-0769. C. Niang acknowledges Fundacion Mujeres por Africa and ICMAT Severo Ochoa project SEV-2011-0087 for financial support. [1] C. Mendoza, A. M. Mancho. The hidden geometry of ocean flows. Physical Review Letters 105 (2010), 3, 038501-1-038501-4. [2] A. M. Mancho, S. Wiggins, J. Curbelo, C. Mendoza. Lagrangian Descriptors: A Method for Revealing Phase Space Structures of General Time Dependent Dynamical Systems. Communications in Nonlinear Science and Numerical Simulation. 18 (2013) 3530-3557. [3] C. Lopesino, F. Balibrea-Iniesta, S. Wiggins and A. M. Mancho. Lagrangian descriptors for two dimensional, area preserving autonomous and nonautonomous maps. Communications in Nonlinear Science and Numerical Simulations, 27 (2015) (1-3), 40-51. [4] C. Lopesino, F. Balibrea-Iniesta, V. J. García-Garrido, S. Wiggins, and A
Large Eddy Simulation of turbulent flow fields over three- dimensional alluvial dunes
Hardy, R. J.; Parsons, D. R.; Best, J.; Reesink, A. J. H.; Ockelford, A.
2016-12-01
Flow over fluvial dunes has been extensively studied and there is general understanding of the nature of the flow field over two dimensional dunes under equilibrium flow conditions. However, fluvial systems typically experience unsteady flow and therefore the sediment-water interface is constantly reorganizing to form complex three-dimensional morphologies (ripples, dunes and bar forms). Here we report on a numerical experiment which predicts flow over three dimensional dunes using Large Eddy Simulation (LES). Bed topography generated through flume experiments, where fine sand was water worked under a range of unsteady hydraulic conditions to generate quasi-equilibrium three dimensional bed forms, was measured with terrestrial LiDAR to create digital elevation models. This topography was then incorporated into a LES model, with a wall-adapting local eddy-viscosity turbulence model, through a Mass Flux Scaling algorithm, to generate three dimensional, high resolution space time prediction of flow over naturally formed dunes. The numerically predicted flows were analysed by standard Reynolds decomposition approaches, Eulerian and Lagrangian coherent flow structure identification methods and proper orthogonal decomposition. The results show that superimposed bed forms can cause changes in the nature of the classical separated flow regions and turbulence field. In particular, the number of locations where vortices are shed increase which causes coalescence of vortices. This increases the rate of transfer of turbulent kinetic energy into smaller scales. This has significant implications for the time dependent prediction of shear stress and as such for sediment transport dynamics which are required for an improved process understanding of three-dimensional bed form adjustment.
Three-dimensional P velocity structure in Beijing area
Yu, Xiang-Wei; Chen, Yun-Tai; Wang, Pei-De
2003-01-01
A detail three-dimensional P wave velocity structure of Beijing, Tianjin and Tangshan area (BTT area) was determined by inverting local earthquake data. In total 16 048 P wave first arrival times from 16048 shallow and mid-depth crustal earthquakes, which occurred in and around the BTT area from 1992 to 1999 were used. The first arrival times are recorded by Northern China United Telemetry Seismic Network and Yanqing-Huailai Digital Seismic Network. Hypocentral parameters of 1 132 earthquakes with magnitude M L=1.7 6.2 and the three-dimensional P wave velocity structure were obtained simultaneously. The inversion result reveals the complicated lateral heterogeneity of P wave velocity structure around BTT area. The tomographic images obtained are also found to explain other seismological observations well.
The Three Dimensional Structure and Dynamics of Magnetotail Reconnection
Walker, Raymond; Lapenta, Giovanni; Liang, Haoming; El Alaoui, Mostafa; Berchem, Jean; Goldstein, Melvyn
2017-04-01
Magnetic reconnection is a fundamental process by which magnetic energy is dissipated and converted into particle energy. In the next few months the Magnetosphere Multi-Scale Mission (MMS) will provide high resolution observations of reconnection and its consequences in the magnetotail. Of high priority will be observations of the electron diffusion region (EDR) where the actual process of reconnection is thought to occur. In preparation for the MMS observations we have investigated tail reconnection in a realistic magnetospheric configuration by using a new approach that combines a global magnetohydrodynamic simulation of the solar wind, magnetosphere and ionosphere system with a large scale (30X12X12RE) implicit particle-in-cell (iPic3D) simulation (see Lapenta et al., 2016 Geophys. Res. Lett. 43, 515-524, doi:10.1002/2015GL066689 for a discussion of the technique). In particular we have investigated the three dimensional structure and dynamics of tail reconnection during a substorm on February 15, 2008. We found that just earthward of the reconnection site the tail becomes highly structured in the Y direction in the GSM coordinate system. The structures result from an instability associated with strong shear flows in the Y direction within the current sheet. In particular we found that the work done by the magnetic field J•E in the electron frame alternated between positive and negative although the net J•E was positive. We used several methods for identifying the EDR (non-gyrotropy, slippage, the non-ideal terms in OHM's law as well as J•E) and found that all gave false positive results in some regions of the tail. However all of the approaches gave positive results in some of the small structures with J•E positive. These putative EDRs extended ( 2di, >1di, 1di) in the X, Y and Z directions.
The importance of three dimensional dune morphology on the time dependent flow field
Hardy, Richard; Parsons, Dan; Reesink, Arnold; Best, Jim
2017-04-01
The flow field over dunes has been extensively studied and there is general understanding of the nature of the flow over dunes formed over two dimensional dunes under equilibrium flow conditions. This model is typically used to explain flow fields over all dunes fields. However, fluvial systems typically experience unsteady flow and therefore the sediment-water interface is constantly reorganizing to form complex three-dimensional morphologies (ripples, dunes and bar forms). Here we investigate how flow over natural three dimensional dunes differs from the accepted model of flow of two dimensional dunes. A series of experiments were undertaken in a flume where fine sand was water worked under a range of unsteady hydraulic conditions to generate quasi-equilibrium three dimensional bed forms. On four occasions, the flume was drained and the bed topography measured with terrestrial LiDAR to create digital elevation models (DEM). Here to demonstrate the approach we choose the DEM with the greatest topographic variation and apply a new Large Eddy Simulation model with an wall-adapting local eddy-viscosity (WALE) turbulence model and a non-linear higher-order numerical differencing scheme. This provided a three dimensional time dependent prediction of the flow field over the static three-dimensional dune morphology at millimeter and hertz scale resolution. The numerically predicted flows were analyzed by standard Reynolds decomposition approaches and Eulerian and Lagrangian coherent flow structure identification methods. The results show that the superimposed bed forms can cause changes in the nature of the classical separated flow regions, in particularly the number of locations where vortices are shed and the points of flow reattachment. Coalescence of vortices generated downstream and can be seen to move to the free surface and form kolk signatures. These structures also correlate in space and time showing a clear flow morphology feedback. The modified flow field
Three-dimensional simulation of viscous-flow agglomerate sintering.
Kirchhof, M J; Schmid, H -J; Peukert, W
2009-08-01
The viscous-flow sintering of different agglomerate particle morphologies is studied by three-dimensional computer simulations based on the concept of fractional volume of fluid. For a fundamental understanding of particle sintering characteristics, the neck growth kinetics in agglomerate chains and in doublets consisting of differently sized primary particles is investigated. Results show that different sintering contacts in agglomerates even during the first stages are not completely independent from each other, even though differences are small. The neck growth kinetics of differently sized primary particles is determined by the smaller one up to a size difference by a factor of approximately 2, whereas for larger size differences, the kinetics becomes faster. In particular, the agglomerate sintering kinetics is investigated for particle chains of different lengths and for different particle morphologies each having ten primary particles and nine initial sintering contacts. For agglomerate chains, the kinetics approximately can be normalized by using the radius of the fully coalesced sphere. In general, different agglomerate morphologies show equal kinetics during the first sintering stages, whereas during advanced stages, compact morphologies show significantly faster sintering progress than more open morphologies. Hence, the overall kinetics cannot be described by simply using constant morphology correction factors such as fractal dimension or mean coordination number which are used in common sintering models. However, for the first stages of viscous-flow agglomerate sintering, which are the most important for many particle processes, a sintering equation is presented. Although we use agglomerates consisting of spherical primary particles, our methodology can be applied to other aggregate geometries as well.
Three Dimensional Flow and Pressure Patterns in a Single Pocket of a Hydrostatic Journal Bearing
Braun, M. Jack; Dzodzo, Milorad B.
1996-01-01
The flow in a hydrostatic pocket is described by a mathematical model that uses the three dimensional Navier-Stokes equations written in terms of the primary variables, u, v, w, and p. Using a conservative formulation, a finite volume multi-block method is applied through a collocated, body fitted grid. The flow is simulated in a shallow pocket with a depth/length ratio of 0.02. The flow structures obtained and described by the authors in their previous two dimensional models are made visible in their three dimensional aspect for the Couette flow. It has been found that the flow regimes formed central and secondary vortical cells with three dimensional corkscrew-like structures that lead the fluid on an outward bound path in the axial direction of the pocket. The position of the central vortical cell center is at the exit region of the capillary restrictor feedline. It has also been determined that a fluid turn around zone occupies all the upstream space between the floor of the pocket and the runner, thus preventing any flow exit through the upstream port. The corresponding pressure distribution under the shaft presented as well. It was clearly established that for the Couette dominated case the pressure varies significantly in the pocket in the circumferential direction, while its variation is less pronounced axially.
Three-dimensional hypersonic rarefied flow calculations using direct simulation Monte Carlo method
Celenligil, M. Cevdet; Moss, James N.
1993-01-01
A summary of three-dimensional simulations on the hypersonic rarefied flows in an effort to understand the highly nonequilibrium flows about space vehicles entering the Earth's atmosphere for a realistic estimation of the aerothermal loads is presented. Calculations are performed using the direct simulation Monte Carlo method with a five-species reacting gas model, which accounts for rotational and vibrational internal energies. Results are obtained for the external flows about various bodies in the transitional flow regime. For the cases considered, convective heating, flowfield structure and overall aerodynamic coefficients are presented and comparisons are made with the available experimental data. The agreement between the calculated and measured results are very good.
Phonon band structures of the three dimensional latticed pentamode metamaterials
Directory of Open Access Journals (Sweden)
Guan Wang
2017-02-01
Full Text Available The artificially designed three-dimensional (3D pentamode metamaterials have such an extraordinary characteristic that the solid materials behave like liquids. Meanwhile, the ideal structure of the pentamode metamaterials arranges in the same way as that of the diamond crystals. In the present research, we regard three types of pentamode metamaterials derived from the 3D crystal lattices as research objects. The phonon band structures of the candidate pentamode structures are calculated by using the finite element method (FEM. We illustrate the relation between the ratio of the bulk modulus B and the shear modulus G of different combinations of D and d. Finally, we find out the relationship between the phonon band structure and the structure parameters. It is useful for generating the phonon band structure and controlling elastic wave propagation.
The three-dimensional crystal structure of cholera toxin
Energy Technology Data Exchange (ETDEWEB)
Zhang, Rong-Guang; Westbrook, M.L.; Nance, S.; Spangler, B.D. [Argonne National Lab., IL (United States); Scott, D.L. [Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry; Westbrook, E.M. [Northwestern Univ., Evanston, IL (United States)
1996-02-01
The clinical manifestations of cholera are largely attributable to the actions of a secreted hexameric AB{sub 5} enterotoxin (choleragen). We have solved the three-dimensional structure of choleragen at 2.5 {Angstrom} resolution and compared the refined coordinates with those of choleragenoid (isolated B pentamer) and the heat-labile enterotoxin from Escherichia coli (LT). The crystalline coordinates provide a detailed view of the stereochemistry implicated in binding to GM1 gangliosides and in carrying out ADP-ribosylation. The A2 chain of choleragen, in contrast to that of LT, is a nearly continuous {alpha}-helix with an interpretable carboxyl tail.
Modeling flow and shear stress fields over unsteady three dimensional dunes
Hardy, Richard; Parsons, Dan; Ashworth, Phil; Reesink, Arjan; Best, Jim
2014-05-01
The flow field over dunes has been extensively measured in laboratory conditions and there is general understanding on the nature of the flow over dunes formed under equilibrium flow conditions. This has allowed an understanding of bed shear stress to be derived and the development of morpho-dynamic models. However, fluvial systems typically experience unsteady flow and therefore the sediment-water interface is constantly responding and reorganizing to these unsteady flows and stresses, over a range of both spatial and temporal scales. This is primarily through the adjustment of bed forms (including ripples, dunes and bar forms) which then subsequently alter the flow field. This paper investigates, through the application of a numerical model, the influence of these roughness elements on the overall flow and bed shear stress. A series of physical experiments were undertaken in a flume, 16m long and 2m wide, where a fine sand (D50 of 239µm) was water worked under a range of unsteady hydraulic conditions to generate a series of quasi-equilibrium three dimensional bed forms. During the experiments flow was measured with acoustic Doppler velocimeters, (aDv's). On four occasions the flume was drained and the bed topography measured with terrestrial LiDAR to create digital elevation models. This data provide the necessary boundary conditions and validation data for a numerical three dimensional flow model. The prediction of flow over the four static beds demonstrates the spatial distribution of shear stress and the potential sediment transport paths between the dune crests. These appear to be associated with coherent flow structures formed by localized shear flow. These flow predictions are currently being used to develop a fully three dimensional morphodynamic model to further understand dune dynamics under unsteady flow conditions.
Three-dimensional periodic dielectric structures having photonic Dirac points
Bravo-Abad, Jorge; Joannopoulos, John D.; Soljacic, Marin
2015-06-02
The dielectric, three-dimensional photonic materials disclosed herein feature Dirac-like dispersion in quasi-two-dimensional systems. Embodiments include a face-centered cubic (fcc) structure formed by alternating layers of dielectric rods and dielectric slabs patterned with holes on respective triangular lattices. This fcc structure also includes a defect layer, which may comprise either dielectric rods or a dielectric slab with patterned with holes. This defect layer introduces Dirac cone dispersion into the fcc structure's photonic band structure. Examples of these fcc structures enable enhancement of the spontaneous emission coupling efficiency (the .beta.-factor) over large areas, contrary to the conventional wisdom that the .beta.-factor degrades as the system's size increases. These results enable large-area, low-threshold lasers; single-photon sources; quantum information processing devices; and energy harvesting systems.
Three-dimensional structural characterization of nonwoven fabrics.
Venu, Lalith B Suragani; Shim, Eunkyoung; Anantharamaiah, Nagendra; Pourdeyhimi, Behnam
2012-12-01
Nonwoven materials are found in a gamut of critical applications. This is partly due to the fact that these structures can be produced at high speed and engineered to deliver unique functionality at low cost. The behavior of these materials is highly dependent on alignment of fibers within the structure. The ability to characterize and also to control the structure is important, but very challenging due to the complex nature of the structures. Thus, to date, focus has been placed mainly on two-dimensional analysis techniques for describing the behavior of nonwovens. This article demonstrates the utility of three-dimensional (3D) digital volumetric imaging technique for visualizing and characterizing a complex 3D class of nonwoven structures produced by hydroentanglement.
Three-dimensional structure of the γ-secretase complex
International Nuclear Information System (INIS)
Ogura, Toshihiko; Mio, Kazuhiro; Hayashi, Ikuo; Miyashita, Hiroyuki; Fukuda, Rie; Kopan, Raphael; Kodama, Tatsuhiko; Hamakubo, Takao; Iwastubo, Takeshi; Tomita, Taisuke; Sato, Chikara
2006-01-01
γ-Secretase belongs to an atypical class of aspartic proteases that hydrolyzes peptide bonds within the transmembrane domain of substrates, including amyloid-β precursor protein and Notch. γ-Secretase is comprised of presenilin, nicastrin, APH-1, and PEN-2 which form a large multimeric membrane protein complex, the three-dimensional structure of which is unknown. To gain insight into the structure of this complex enzyme, we purified functional γ-secretase complex reconstituted in Sf9 cells and analyzed it using negative stain electron microscopy and 3D reconstruction techniques. Analysis of 2341 negatively stained particle images resulted in the three-dimensional representation of γ-secretase at a resolution of 48 A. The structure occupies a volume of 560 x 320 x 240 A and resembles a flat heart comprised of two oppositely faced, dimpled domains. A low density space containing multiple pores resides between the domains. Some of the dimples in the putative transmembrane region may house the catalytic site. The large dimensions are consistent with the observation that γ-secretase activity resides within a high molecular weight complex
Three-dimensional protein structure prediction: Methods and computational strategies.
Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C
2014-10-12
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.
Three-dimensional photonic band gaps in woven structures
Tsai Ya Chih; Pendry, J B
1998-01-01
In this paper, we studied the photonic properties of dielectric fibres woven into three-dimensional (3D) structures. Such fibres can be fabricated on the micrometre scale, and hence the gaps are in the far-infrared to the infrared regime. The vector-wave transfer matrix method is applied to evaluate the photonic band structures. We have also employed the constant-frequency dispersion surface scheme to investigate the development of a full band gap. Such a 3D absolute gap is observed in a rectangular lattice, but at a fairly large dielectric constant for the fibres. Ways to improve on this have been suggested. Our study indicates that woven structures are promising materials for realizing the 3D photonic insulator in the infrared regime. (author)
Gresse, Marceau; Vandemeulebrouck, Jean; Byrdina, Svetlana; Chiodini, Giovanni; Revil, André; Johnson, Timothy C.; Ricci, Tullio; Vilardo, Giuseppe; Mangiacapra, Annarita; Lebourg, Thomas; Grangeon, Jacques; Bascou, Pascale; Metral, Laurent
2017-11-01
The Solfatara volcano is the main degassing area of the Campi Flegrei caldera, characterized by 60 years of unrest. Assessing such renewal activity is a challenging task because hydrothermal interactions with magmatic gases remain poorly understood. In this study, we decipher the complex structure of the shallow Solfatara hydrothermal system by performing the first 3-D, high-resolution, electrical resistivity tomography of the volcano. The 3-D resistivity model was obtained from the inversion of 43,432 resistance measurements performed on an area of 0.68 km2. The proposed interpretation of the multiphase hydrothermal structures is based on the resistivity model, a high-resolution infrared surface temperature image, and 1,136 soil CO2 flux measurements. In addition, we realized 27 soil cation exchange capacity and pH measurements demonstrating a negligible contribution of surface conductivity to the shallow bulk electrical conductivity. Hence, we show that the resistivity changes are mainly controlled by fluid content and temperature. The high-resolution tomograms identify for the first time the structure of the gas-dominated reservoir at 60 m depth that feeds the Bocca Grande fumarole through a 10 m thick channel. In addition, the resistivity model reveals a channel-like conductive structure where the liquid produced by steam condensation around the main fumaroles flows down to the Fangaia area within a buried fault. The model delineates the emplacement of the main geological structures: Mount Olibano, Solfatara cryptodome, and tephra deposits. It also reveals the anatomy of the hydrothermal system, especially two liquid-dominated plumes, the Fangaia mud pool and the Pisciarelli fumarole, respectively.
Three-dimensional structure of brain tissue at submicrometer resolution
Energy Technology Data Exchange (ETDEWEB)
Saiga, Rino; Mizutani, Ryuta, E-mail: ryuta@tokai-u.jp [Department of Applied Biochemistry, Tokai University, Hiratsuka, Kanagawa 259-1292 (Japan); Inomoto, Chie; Takekoshi, Susumu; Nakamura, Naoya; Tsuboi, Akio; Osawa, Motoki [Tokai University School of Medicine, Isehara, Kanagawa 259-1193 (Japan); Arai, Makoto; Oshima, Kenichi; Itokawa, Masanari [Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506 (Japan); Uesugi, Kentaro; Takeuchi, Akihisa; Terada, Yasuko; Suzuki, Yoshio [Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), Sayo, Hyogo 679-5198 (Japan)
2016-01-28
Biological objects are composed of submicrometer structures such as cells and organelles that are essential for their functions. Here, we report on three-dimensional X-ray visualization of cells and organelles at resolutions up to 100 nm by imaging microtomography (micro-CT) equipped with Fresnel zone plate optics. Human cerebral tissue, fruit fly cephalic ganglia, and Escherichia coli bacteria labeled with high atomic-number elements were embedded in epoxy resin and subjected to X-ray microtomography at the BL37XU and BL47XU beamlines of the SPring-8 synchrotron radiation facility. The obtained results indicated that soft tissue structures can be visualized with the imaging microtomography.
Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data.
Xiao, Guanghua; Wang, Xinlei; Khodursky, Arkady B
2011-03-01
Recent genomic studies have shown that significant chromosomal spatial correlation exists in gene expression of many organisms. Interestingly, coexpression has been observed among genes separated by a fixed interval in specific regions of a chromosome chain, which is likely caused by three-dimensional (3D) chromosome folding structures. Modeling such spatial correlation explicitly may lead to essential understandings of 3D chromosome structures and their roles in transcriptional regulation. In this paper, we explore chromosomal spatial correlation induced by 3D chromosome structures, and propose a hierarchical Bayesian method based on helical structures to formally model and incorporate the correlation into the analysis of gene expression microarray data. It is the first study to quantify and infer 3D chromosome structures in vivo using expression microarrays. Simulation studies show computing feasibility of the proposed method and that, under the assumption of helical chromosome structures, it can lead to precise estimation of structural parameters and gene expression levels. Real data applications demonstrate an intriguing biological phenomenon that functionally associated genes, which are far apart along the chromosome chain, are brought into physical proximity by chromosomal folding in 3D space to facilitate their coexpression. It leads to important biological insight into relationship between chromosome structure and function.
Three-dimensional solution structure of Acanthamoeba profilin-I
1993-01-01
We have determined a medium resolution three-dimensional solution structure of Acanthamoeba profilin-I by multidimensional nuclear magnetic resonance spectroscopy. This 13-kD actin binding protein consists of a five stranded antiparallel beta sheet flanked by NH2- and COOH-terminal helices on one face and by a third helix and a two stranded beta sheet on the other face. Data from actin-profilin cross- linking experiments and the localization of conserved residues between profilins in different phyla indicate that actin binding occurs on the molecular face occupied by the terminal helices. The other face of the molecule contains the residues that differ between Acanthamoeba profilins-I and II and may be important in determining the difference in polyphosphoinositide binding between these isoforms. This suggests that lipids and actin bind to different faces of the molecule. PMID:8397216
Three-dimensional structure determination from a single view.
Raines, Kevin S; Salha, Sara; Sandberg, Richard L; Jiang, Huaidong; Rodríguez, Jose A; Fahimian, Benjamin P; Kapteyn, Henry C; Du, Jincheng; Miao, Jianwei
2010-01-14
The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution, and a single poliovirus at 2-3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.
Yang, Ren; Feeback, Daniel L.; Wang, Wan-Jun
2005-01-01
This paper details a novel three-dimensional (3D) hydro-focusing micro cell sorter for micro flow cytometry applications. The unit was microfabricated by means of SU-8 3D lithography. The 3D microstructure for coaxial sheathing was designed, microfabricated, and tested. Three-dimensional hydrofocusing capability was demonstrated with an experiment to sort labeled tanned sheep erythrocytes (red blood cells). This polymer hydro-focusing microstructure is easily microfabricated and integrated with other polymer microfluidic structures. Keywords: SU-8, three-dimensional hydro-focusing, microfluidic, microchannel, cytometer
Micromagnetic studies of three-dimensional pyramidal shell structures
International Nuclear Information System (INIS)
Knittel, A; Franchin, M; Fischbacher, T; Fangohr, H; Nasirpouri, F; Bending, S J
2010-01-01
We present a systematic numerical analysis of the magnetic properties of pyramidal-shaped core-shell structures in a size range below 400 nm. These are three-dimensional structures consisting of a ferromagnetic shell which is grown on top of a non-magnetic core. The standard micromagnetic model without the magnetocrystalline anisotropy term is used to describe the properties of the shell. We vary the thickness of the shell between the limiting cases of an ultra-thin shell and a conventional pyramid and delineate different stable magnetic configurations. We find different kinds of single-domain states, which predominantly occur at smaller system sizes. In analogy to equivalent states in thin square films we term these onion, flower, C and S states. At larger system sizes, we also observe two types of vortex states, which we refer to as symmetric and asymmetric vortex states. For a classification of the observed states, we derive a phase diagram that specifies the magnetic ground state as a function of structure size and shell thickness. The transitions between different ground states can be understood qualitatively. We address the issue of metastability by investigating the stability of all occurring configurations for different shell thicknesses. For selected geometries and directions hysteresis measurements are analysed and discussed. We observe that the magnetic behaviour changes distinctively in the limit of ultra-thin shells. The study has been motivated by the recent progress made in the growth of faceted core-shell structures.
RICHTER, DAVID
2010-03-29
The results from a numerical investigation of inertial viscoelastic flow past a circular cylinder are presented which illustrate the significant effect that dilute concentrations of polymer additives have on complex flows. In particular, effects of polymer extensibility are studied as well as the role of viscoelasticity during three-dimensional cylinder wake transition. Simulations at two distinct Reynolds numbers (Re = 100 and Re = 300) revealed dramatic differences based on the choice of the polymer extensibility (L2 in the FENE-P model), as well as a stabilizing tendency of viscoelasticity. For the Re = 100 case, attention was focused on the effects of increasing polymer extensibility, which included a lengthening of the recirculation region immediately behind the cylinder and a sharp increase in average drag when compared to both the low extensibility and Newtonian cases. For Re = 300, a suppression of the three-dimensional Newtonian mode B instability was observed. This effect is more pronounced for higher polymer extensibilities where all three-dimensional structure is eliminated, and mechanisms for this stabilization are described in the context of roll-up instability inhibition in a viscoelastic shear layer. © 2010 Cambridge University Press.
Visualization of three dimensional earth fissures in geological structure
Directory of Open Access Journals (Sweden)
L. Zhu
2015-11-01
Full Text Available This paper proposes a new method for visualizing the earth fissures of geological structure in three dimensional (3-D domains on the basis of the seismic data and features information of earth fissures. The seismic data were interpreted for obtaining the stratagraphic data with various lithological information and the depth of the earth fissures. The spatial distribution of the ground fissures including the dip, strike and width were digitalized on an ArcGIS platform. Firstly, the 3-D geological structure was rebuilt using the Generalized Tri-Prism (GTP method which is a real solid method for displaying geological structures. The GTP method can reflect the inner material of the strata and can simulate complicated geological structures such as faults and stratagraphic pinch outs. The upper and lower surfaces of each stratum consist of Triangle Irregular Networks (TIN. The inner solid between the two surfaces are a series of triangular prisms. Secondly, since the width of the ground fissure gradually decreases with depth, multiple edge lines of the earth fissures on the bottom stratum surface are deduced on the basis of the fissure characteristics. Then, the model of the earth fissures consisting of a series of triangular pyramids can be constructed using these points and the edge lines. A cutting operation was carried out on the 3-D geological structure using this ground fissures model. If the surfaces of the ground fissures model intersects with the GTPs in the geological structure model, new GTPs were generated within the local regions. During this process, the topological relations between TIN, triangular prism and lines were reconstructed so that the visualization of ground fissures in the geological structure model is realized. This method can facilitate the mechanism for studying fissures and avoid the gaps between the fissure solid and the geological structure to accurately reflect their 3-D characteristics.
Swarming in viscous fluids: Three-dimensional patterns in swimmer- and force-induced flows
Chuang, Yao-Li; Chou, Tom; D'Orsogna, Maria R.
2016-04-01
We derive a three-dimensional theory of self-propelled particle swarming in a viscous fluid environment. Our model predicts emergent collective behavior that depends critically on fluid opacity, mechanism of self-propulsion, and type of particle-particle interaction. In "clear fluids" swimmers have full knowledge of their surroundings and can adjust their velocities with respect to the lab frame, while in "opaque fluids" they control their velocities only in relation to the local fluid flow. We also show that "social" interactions that affect only a particle's propensity to swim towards or away from neighbors induces a flow field that is qualitatively different from the long-ranged flow fields generated by direct "physical" interactions. The latter can be short-ranged but lead to much longer-ranged fluid-mediated hydrodynamic forces, effectively amplifying the range over which particles interact. These different fluid flows conspire to profoundly affect swarm morphology, kinetically stabilizing or destabilizing swarm configurations that would arise in the absence of fluid. Depending upon the overall interaction potential, the mechanism of swimming ( e.g., pushers or pullers), and the degree of fluid opaqueness, we discover a number of new collective three-dimensional patterns including flocks with prolate or oblate shapes, recirculating pelotonlike structures, and jetlike fluid flows that entrain particles mediating their escape from the center of mill-like structures. Our results reveal how the interplay among general physical elements influence fluid-mediated interactions and the self-organization, mobility, and stability of new three-dimensional swarms and suggest how they might be used to kinetically control their collective behavior.
Three-dimensional analysis of anisotropic spatially reinforced structures
Bogdanovich, Alexander E.
1993-01-01
The material-adaptive three-dimensional analysis of inhomogeneous structures based on the meso-volume concept and application of deficient spline functions for displacement approximations is proposed. The general methodology is demonstrated on the example of a brick-type mosaic parallelepiped arbitrarily composed of anisotropic meso-volumes. A partition of each meso-volume into sub-elements, application of deficient spline functions for a local approximation of displacements and, finally, the use of the variational principle allows one to obtain displacements, strains, and stresses at anypoint within the structural part. All of the necessary external and internal boundary conditions (including the conditions of continuity of transverse stresses at interfaces between adjacent meso-volumes) can be satisfied with requisite accuracy by increasing the density of the sub-element mesh. The application of the methodology to textile composite materials is described. Several numerical examples for woven and braided rectangular composite plates and stiffened panels under transverse bending are considered. Some typical effects of stress concentrations due to the material inhomogeneities are demonstrated.
Three-Dimensional Flow Separation Induced by a Model Vocal Fold Polyp
Stewart, Kelley C.; Erath, Byron D.; Plesniak, Michael W.
2012-11-01
The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. A recent in-vitro investigation of a model polyp in a driven vocal fold apparatus demonstrated that such a geometric abnormality considerably disrupts the glottal jet behavior and that this flow field adjustment was a likely reason for the severe degradation of the vocal quality in patients. Understanding of the formation and propagation of vortical structures from a geometric protuberance, and their subsequent impact on the aerodynamic loadings that drive vocal fold dynamic, is a critical component in advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp. Unsteady three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).
Quasi-Three-Dimensional Analysis Of Turbine Flow
Hsu, Wayne W.
1988-01-01
Computer program reduces computer time and treats multiple elements. Improved design-analysis program for turbomachinery applied to multiple turbine elements simultaneously. Enables continuous and coherent analyses rather than previous piece-meal analyses of flow fields. Effects of upstream elements on downstream flow taken into account automatically.
Three-Dimensional parton structure of light nuclei
Scopetta, Sergio; Del Dotto, Alessio; Kaptari, Leonid; Pace, Emanuele; Rinaldi, Matteo; Salmè, Giovanni
2018-03-01
Two promising directions beyond inclusive deep inelastic scattering experiments, aimed at unveiling the three dimensional structure of the bound nucleon, are reviewed, considering in particular the 3He nuclear target. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative part is encoded in generalized parton distributions. In this way, the distribution of partons in the transverse plane can be obtained. As an example of a deep exclusive process, coherent deeply virtual Compton scattering off 3He nuclei, important to access the neutron generalized parton distributions (GPDs), will be discussed. In Impulse Approximation (IA), the sum of the two leading twist, quark helicity conserving GPDs of 3He, H and E, at low momentum transfer, turns out to be dominated by the neutron contribution. Besides, a technique, able to take into account the nuclear effects included in the Impulse Approximation analysis, has been developed. The spin dependent GPD \\tilde H of 3He is also found to be largely dominated, at low momentum transfer, by the neutron contribution. The knowledge of the GPDs H,E and \\tilde H of 3He is relevant for the planning of coherent DVCS off 3He measurements. Semi-inclusive deep inelastic scattering processes access the momentum space 3D structure parameterized through transverse momentum dependent parton distributions. A distorted spin-dependent spectral function has been recently introduced for 3He, in a non-relativistic framework, to take care of the final state interaction between the observed pion and the remnant in semi-inclusive deep inelastic electron scattering off transversely polarized 3He. The calculation of the Sivers and Collins single spin asymmetries for 3He, and a straightforward procedure to effectively take into account nuclear dynamics and final state interactions, will be reviewed. The Light-front dynamics generalization of the analysis is also addressed.
A three-dimensional autonomous nonlinear dynamical system modelling equatorial ocean flows
Ionescu-Kruse, Delia
2018-04-01
We investigate a nonlinear three-dimensional model for equatorial flows, finding exact solutions that capture the most relevant geophysical features: depth-dependent currents, poleward or equatorial surface drift and a vertical mixture of upward and downward motions.
Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase
Energy Technology Data Exchange (ETDEWEB)
Kamat, S.S.; Swaminathan, S.; Bagaria, A.; Kumaran, D.; Holmes-Hampton, G. P.; Fan, H.; Sali, A.; Sauder, J. M.; Burley, S. K.; Lindahl, P. A.; Raushel, F. M.
2011-03-22
Adenine deaminase (ADE) catalyzes the conversion of adenine to hypoxanthine and ammonia. The enzyme isolated from Escherichia coli using standard expression conditions was low for the deamination of adenine (k{sub cat} = 2.0 s{sup -1}; k{sub cat}/K{sub m} = 2.5 x 10{sup 3} M{sup -1} s{sup -1}). However, when iron was sequestered with a metal chelator and the growth medium was supplemented with Mn{sup 2+} prior to induction, the purified enzyme was substantially more active for the deamination of adenine with kcat and kcat/Km values of 200 s{sup -1} and 5 x 10{sup 5} M{sup -1} s{sup -1}, respectively. The apoenzyme was prepared and reconstituted with Fe{sup 2+}, Zn{sup 2+}, or Mn{sup 2+}. In each case, two enzyme equivalents of metal were necessary for reconstitution of the deaminase activity. This work provides the first example of any member of the deaminase subfamily of the amidohydrolase superfamily to utilize a binuclear metal center for the catalysis of a deamination reaction. [Fe{sup II}/Fe{sup II}]-ADE was oxidized to [Fe{sup III}/Fe{sup III}]-ADE with ferricyanide with inactivation of the deaminase activity. Reducing [Fe{sup III}/Fe{sup III}]-ADE with dithionite restored the deaminase activity, and thus, the diferrous form of the enzyme is essential for catalytic activity. No evidence of spin coupling between metal ions was evident by electron paramagnetic resonance or Moessbauer spectroscopy. The three-dimensional structure of adenine deaminase from Agrobacterium tumefaciens (Atu4426) was determined by X-ray crystallography at 2.2 {angstrom} resolution, and adenine was modeled into the active site on the basis of homology to other members of the amidohydrolase superfamily. On the basis of the model of the adenine-ADE complex and subsequent mutagenesis experiments, the roles for each of the highly conserved residues were proposed. Solvent isotope effects, pH-rate profiles, and solvent viscosity were utilized to propose a chemical reaction mechanism and the
Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase
Energy Technology Data Exchange (ETDEWEB)
S Kamat; A Bagaria; D Kumaran; G Holmes-Hampton; H Fan; A Sali; J Sauder; S Burley; P Lindahl; et. al.
2011-12-31
Adenine deaminase (ADE) catalyzes the conversion of adenine to hypoxanthine and ammonia. The enzyme isolated from Escherichia coli using standard expression conditions was low for the deamination of adenine (k{sub cat} = 2.0 s{sup -1}; k{sub cat}/K{sub m} = 2.5 x 10{sup 3} M{sup -1} s{sup -1}). However, when iron was sequestered with a metal chelator and the growth medium was supplemented with Mn{sup 2+} prior to induction, the purified enzyme was substantially more active for the deamination of adenine with k{sub cat} and k{sub cat}/K{sub m} values of 200 s{sup -1} and 5 x 10{sup 5} M{sup -1} s{sup -1}, respectively. The apoenzyme was prepared and reconstituted with Fe{sup 2+}, Zn{sup 2+}, or Mn{sup 2+}. In each case, two enzyme equivalents of metal were necessary for reconstitution of the deaminase activity. This work provides the first example of any member of the deaminase subfamily of the amidohydrolase superfamily to utilize a binuclear metal center for the catalysis of a deamination reaction. [Fe{sup II}/Fe{sup II}]-ADE was oxidized to [Fe{sup III}/Fe{sup III}]-ADE with ferricyanide with inactivation of the deaminase activity. Reducing [Fe{sup III}/Fe{sup III}]-ADE with dithionite restored the deaminase activity, and thus, the diferrous form of the enzyme is essential for catalytic activity. No evidence of spin coupling between metal ions was evident by electron paramagnetic resonance or Moessbauer spectroscopy. The three-dimensional structure of adenine deaminase from Agrobacterium tumefaciens (Atu4426) was determined by X-ray crystallography at 2.2 {angstrom} resolution, and adenine was modeled into the active site on the basis of homology to other members of the amidohydrolase superfamily. On the basis of the model of the adenine-ADE complex and subsequent mutagenesis experiments, the roles for each of the highly conserved residues were proposed. Solvent isotope effects, pH-rate profiles, and solvent viscosity were utilized to propose a chemical reaction
Numerical Calculation of the Three-Dimensional Swirling Flow Inside the Centrifugal Pump Volutes
Directory of Open Access Journals (Sweden)
E. Cezmi Nursen
2003-01-01
Full Text Available The flow inside the volute of a centrifugal pump is threedimensional and, depending upon the position of the inlet relative to the cross-section center line, a single or double swirling flow occurs. The purpose of this study was the calculation of the three-dimensional swirling flow inside the centrifugal pump volute.
Three-dimensional attached viscous flow basic principles and theoretical foundations
Hirschel, Ernst Heinrich; Kordulla, Wilhelm
2014-01-01
Viscous flow is usually treated in the frame of boundary-layer theory and as a two-dimensional flow. At best, books on boundary layers provide the describing equations for three-dimensional boundary layers, and solutions only for certain special cases. This book presents the basic principles and theoretical foundations of three-dimensional attached viscous flows as they apply to aircraft of all kinds. Though the primary flight speed range is that of civil air transport vehicles, flows past other flying vehicles up to hypersonic speeds are also considered. Emphasis is put on general three-dimensional attached viscous flows and not on three-dimensional boundary layers, as this wider scope is necessary in view of the theoretical and practical problems that have to be overcome in practice. The specific topics covered include weak, strong, and global interaction; the locality principle; properties of three-dimensional viscous flows; thermal surface effects; characteristic properties; wall compatibility con...
International Nuclear Information System (INIS)
Moritaka, Toseo; Kuramitsu, Yasuhiro; Sakawa, Youichi; Yamaura, Yuta; Ishikawa, Taishi; Takabe, Hideaki; Morita, Taichi
2016-01-01
Collisionless shocks mediated by Weibel instability are attracting attention for their relevance to experimental demonstrations of astrophysical shocks in high-intensity laser facilities. The three dimensional structure of Weibel-mediated shocks is investigated through a fully kinetic particle-in-cell simulation. The structures obtained are characterized by the following features: (i) helical magnetic field lines elongated in the direction upstream of the shock region, (ii) high and low density filaments inside the helical field lines. These structures originate from the interaction between counter-streaming plasma flow and magnetic vortexes caused by Weibel instability, and potentially affect the shock formation mechanism. (paper)
Three-dimensional vortex wake structure of flapping wings in hovering flight.
Cheng, Bo; Roll, Jesse; Liu, Yun; Troolin, Daniel R; Deng, Xinyan
2014-02-06
Flapping wings continuously create and send vortices into their wake, while imparting downward momentum into the surrounding fluid. However, experimental studies concerning the details of the three-dimensional vorticity distribution and evolution in the far wake are limited. In this study, the three-dimensional vortex wake structure in both the near and far field of a dynamically scaled flapping wing was investigated experimentally, using volumetric three-component velocimetry. A single wing, with shape and kinematics similar to those of a fruitfly, was examined. The overall result of the wing action is to create an integrated vortex structure consisting of a tip vortex (TV), trailing-edge shear layer (TESL) and leading-edge vortex. The TESL rolls up into a root vortex (RV) as it is shed from the wing, and together with the TV, contracts radially and stretches tangentially in the downstream wake. The downwash is distributed in an arc-shaped region enclosed by the stretched tangential vorticity of the TVs and the RVs. A closed vortex ring structure is not observed in the current study owing to the lack of well-established starting and stopping vortex structures that smoothly connect the TV and RV. An evaluation of the vorticity transport equation shows that both the TV and the RV undergo vortex stretching while convecting downwards: a three-dimensional phenomenon in rotating flows. It also confirms that convection and secondary tilting and stretching effects dominate the evolution of vorticity.
Lagrangian transport in a class of three-dimensional buoyancy-driven flows
Contreras, Sebastian; Speetjens, Michel; Clercx, Herman
2017-11-01
The study concerns the Lagrangian dynamics of three-dimensional (3D) buoyancy-driven cavity flows under steady and laminar conditions due to a global temperature gradient imposed via an opposite hot and cold sidewall. This serves as archetypal configuration for natural-convection flows in which gravity is perpendicular to the global temperature gradient. Limited insight into the Lagrangian properties of this class of flows motivates this study. The 3D Lagrangian dynamics are investigated in terms of the generic structure of the Lagrangian flow topology that is described in terms of the Grashof number (Gr) and the Prandtl number (Pr). Gr is the principal control parameter for the flow topology: vanishing Gr yields a state of closed streamlines (integrable state); increasing Gr causes the formation of toroidal coherent structures embedded in chaotic streamlines governed by Hamiltonian mechanisms. Fluid inertia prevails for ``smaller'' Gr. A buoyancy-induced bifurcation of the flow topology occurs for ``larger'' Gr and underlies the emergence of ``secondary rolls'' and secondary tori for ``larger'' Pr. Stagnation points and corresponding manifold interactions are key to the dynamics. S.C. acknowledges financial support from Consejo Nacional de Ciencia y Tecnología (CONACYT).
Reynolds number effects on three-dimensional flow control over a square cylinder
Malekzadeh, S.; Mirzaee, I.; Pourmahmoud, N.
2018-04-01
In this article, the effects of Reynolds number on three-dimensional flow over a square cylinder with flow control are discussed at moderate Reynolds numbers, i.e. Re W = 200–1000 (based on the width of the square cylinder and the inlet flow velocity). The flow is controlled by a thin vertical plate placed upstream of the cylinder. The vorticity structures at different Reynolds numbers, turbulent kinetic energy, Reynolds stresses, and mean and fluctuating fluid forces on the square cylinder in the presence of the control plate are investigated in order to determine the characteristics of the transient flow regime at the wake region behind the square cylinder. The results show that the transitional process of the flow regime from laminar to turbulent in the wake region behind the square cylinder at Re W = 300–600 causes the pulsation phenomena to happen in the instantaneous lift signals of the square cylinder, and both of spanwise instability modes of A and B, as well as the dislocation phenomena are presented in the wake region behind the cylinder. It is also found that the mean and fluctuating fluid forces of the square cylinder in the presence of the control plate decrease in comparison to the single square cylinder, except for the rms drag coefficient at Re W = 300.
Richardson, S. I. Heath; Baggaley, A. W.; Hill, N. A.
2018-02-01
We study the effects of imposed three-dimensional flows on the trajectories and mixing of gyrotactic swimming microorganisms and identify phenomena not seen in flows restricted to two dimensions. Through numerical simulation of Taylor-Green and Arnold-Beltrami-Childress (ABC) flows, we explore the role that the flow and the cell shape play in determining the long-term configuration of the cells' trajectories, which often take the form of multiple sinuous and helical "plumelike" structures, even in the chaotic ABC flow. This gyrotactic suppression of Lagrangian chaos persists even in the presence of random noise. Analytical solutions for a number of cases reveal the how plumes form and the nature of the competition between torques acting on individual cells. Furthermore, studies of Lyapunov exponents reveal that, as the ratio of cell swimming speed relative to the flow speed increases from zero, the initial chaotic trajectories are first suppressed and then give way to a second unexpected window of chaotic trajectories at speeds greater than unity, before suppression of chaos at high relative swimming speeds.
Manufacturing of Three-dimensional Micro Structure Using Proton Beam
Energy Technology Data Exchange (ETDEWEB)
Lee, Suonggyu; Kwon, Wontae [Seoul University, Seoul (Korea, Republic of)
2015-04-15
The diameter of a proton beam emanating from the MC-50 cyclotron is about 2?3 mm with Gaussian distribution. This widely irradiated proton beam is not suitable for semiconductor etching, precise positioning, and micromachining, which require a small spot. In this study, a beam cutting method using a microhole is proposed as an economical alternative. We produced a microhole with aspect ratio, average diameter, and thickness of 428, 21 μm, and 9 mm, respectively, for cutting the proton beam. By using this high-aspect-ratio microhole, we conducted machinability tests on microstructures with sizes of tens of μm. Additionally, the results of simulation using GEANT4 and those of the actual experiment were compared and analyzed. The outcome confirmed the possibility of implementing a micro process technology for the fabrication of three-dimensional microstructures of 20 micron units using the MC-50 cyclotron with the microhole.
Visualization of Three-Dimensional Nephron Structure With Microcomputed Tomography
International Nuclear Information System (INIS)
Bentley, M.; Jorgensen, S.; Lerman, L.; Ritman, E.; Romero, J.
2007-01-01
The three-dimensional architecture of nephrons in situ and their interrelationship with other nephrons are difficult to visualize by microscopic methods. The present study uses microcomputed X-ray tomography (micro-CT) to visualize intact nephrons in situ. Rat kidneys were perfusion-fixed with buffered formalin and their vasculature was subsequently perfused with radiopaque silicone. Cortical tissue was stained en bloc with osmium tetroxide, embedded in plastic, scanned, and reconstructed at voxel resolutions of 6, 2, and 1 μm. At 6 μm resolution, large blood vessels and glomeruli could be visualized but nephrons and their lumens were small and difficult to visualize. Optimal images were obtained using a synchrotron radiation source at 2 μm resolution where nephron components could be identified, correlated with histological sections, and traced. Proximal tubules had large diameters and opaque walls, whereas distal tubules, connecting tubules, and collecting ducts had smaller diameters and less opaque walls. Blood vessels could be distinguished from nephrons by the luminal presence of radiopaque silicone. Proximal tubules were three times longer than distal tubules. Proximal and distal tubules were tightly coiled in the outer cortex but were loosely coiled in the middle and inner cortex. The connecting tubules had the narrowest diameters of the tubules and converged to form arcades that paralleled the radial vessels as they extended to the outer cortex. These results illustrate a potential use of micro-CT to obtain three-dimensional information about nephron architecture and nephron interrelationships, which could be useful in evaluating experimental tubular hypertrophy, atrophy, and necrosis
Three-dimensional Cascaded Lattice Boltzmann Model for Thermal Convective Flows
Hajabdollahi, Farzaneh; Premnath, Kannan
2017-11-01
Fluid motion driven by thermal effects, such as due to buoyancy in differentially heated enclosures arise in several natural and industrial settings, whose understanding can be achieved via numerical simulations. Lattice Boltzmann (LB) methods are efficient kinetic computational approaches for coupled flow physics problems. In this study, we develop three-dimensional (3D) LB models based on central moments and multiple relaxation times for D3Q7 and D3Q15 lattices to solve the energy transport equations in a double distribution function approach. Their collision operators lead to a cascaded structure involving higher order terms resulting in improved stability. This is coupled to a central moment based LB flow solver with source terms. The new 3D cascaded LB models for the convective flows are first validated for natural convection of air driven thermally on two vertically opposite faces in a cubic cavity at different Rayleigh numbers against prior numerical and experimental data, which show good quantitative agreement. Then, the detailed structure of the 3D flow and thermal fields and the heat transfer rates at different Rayleigh numbers are analyzed and interpreted.
Kinoshita, Haruyuki; Kaneda, Shohei; Fujii, Teruo; Oshima, Marie
2007-03-01
This paper presents a micro-flow diagnostic technique, 'high-speed confocal micro-particle image velocimetry (PIV)', and its application to the internal flow measurement of a droplet passing through a microchannel. A confocal micro-PIV system has been successfully constructed wherein a high-speed confocal scanner is combined with the conventional micro-PIV technique. The confocal micro-PIV system enables us to obtain a sequence of sharp and high-contrast cross-sectional particle images at 2000 frames s(-1). This study investigates the confocal depth, which is a significant parameter to determine the out-of-plane measurement resolution in confocal micro-PIV. Using the present confocal micro-PIV system, we can measure velocity distributions of micro-flows in a 228 microm x 171 microm region with a confocal depth of 1.88 microm. We also propose a three-dimensional velocity measurement method based on the confocal micro-PIV and the equation of continuity. This method enables us to measure three velocity components in a three-dimensional domain of micro flows. The confocal micro-PIV system is applied to the internal flow measurement of a droplet. We have measured three-dimensional distributions of three-component velocities of a droplet traveling in a 100 microm (width) x 58 microm (depth) channel. A volumetric velocity distribution inside a droplet is obtained by the confocal micro-PIV and the three-dimensional flow structure inside the droplet is investigated. The measurement results suggest that a three-dimensional and complex circulating flow is formed inside the droplet.
Three-Dimensional Numerical Analysis of LOX/Kerosene Engine Exhaust Plume Flow Field Characteristics
Directory of Open Access Journals (Sweden)
Hong-hua Cai
2017-01-01
Full Text Available Aiming at calculating and studying the flow field characteristics of engine exhaust plume and comparative analyzing the effects of different chemical reaction mechanisms on the engine exhaust plume flow field characteristics, a method considering fully the combustion state influence is put forward, which is applied to exhaust plume flow field calculation of multinozzle engine. On this basis, a three-dimensional numerical analysis of the effects of different chemical reaction mechanisms on LOX/kerosene engine exhaust plume flow field characteristics was carried out. It is found that multistep chemical reaction can accurately describe the combustion process in the LOX/kerosene engine, the average chamber pressure from the calculation is 4.63% greater than that of the test, and the average chamber temperature from the calculation is 3.34% greater than that from the thermodynamic calculation. The exhaust plumes of single nozzle and double nozzle calculated using the global chemical reaction are longer than those using the multistep chemical reaction; the highest temperature and the highest velocity on the plume axis calculated using the former are greater than that using the latter. The important influence of chemical reaction mechanism must be considered in the study of the fixing structure of double nozzle engine on the rocket body.
Measurements of the three-dimensional oscillatory flow in a double bifurcation
Nemes, Andras; Jalal, Sahar; van de Moortele, Tristan; Coletti, Filippo
2015-11-01
Above a certain ventilation frequency, the unsteady nature of the respiratory flow becomes apparent, and inhalation and exhalation cannot be approximated as quasi-stationary processes. This is especially important in the upper and central airways, where length and velocity scales are the largest, making inertia and acceleration effects dominant over viscous dissipation. We experimentally investigate the primary features of the oscillatory flow through a symmetric double bifurcation which models the self-similar branching of the human bronchial tree. We consider a range of Reynolds and Womersley numbers relevant to physiological conditions between the trachea and the lobar bronchi. Three-component, three-dimensional velocity fields are acquired at multiple phases within the ventilation cycle using magnetic resonance imaging (MRI), and are complemented with instantaneous two-dimensional fields obtained by particle image velocimetry (PIV). The phase-averaged volumetric data provide a description of the rich flow topology, characterizing the main secondary flow structures and their spatio-temporal evolution. The instantaneous measurements reveal some of the dynamics of the laminar-to-turbulent transition in the bifurcations, and its aperiodicity throughout the respiratory cycle.
Flow transitions in three-dimensional double-diffusive fingering convection in a porous cavity
Sezai, I.
2002-08-01
In the present study the existence of multiple three-dimensional double-diffusive flow patterns in a horizontal rectangular porous cavity of a square cross-section, having horizontal aspect ratios Ax = Ay = 2 is investigated numerically. Opposing vertical gradients of temperature and concentration are applied between the two horizontal walls of the cavity, where the solute gradient is destabilizing against a stabilizing temperature gradient. All vertical walls are considered to be impermeable and adiabatic. The Brinkman and Forchheimer terms are included in the momentum equations where the convective terms are retained. The effect of the buoyancy ratio, N, thermal Rayleigh number, RaT and Lewis number, Le, on the formation of multiple flow patterns is investigated over a wide range of parameters. Altogether 36 symmetric flow structures have been identified when each of the parameters N, RaT, and Le is varied independently, keeping the others as constants. The results of the calculations are presented in terms of the average Sherwood number curves consisting of different solution branches, where transitions between the branches are indicated. The flow patterns are classified according to their symmetry properties and the type of symmetries broken or preserved are identified during the bifurcation processes.
Pasta, Salvatore; Gentile, Giovanni; Raffa, Giuseppe M; Scardulla, Francesco; Bellavia, Diego; Luca, Angelo; Pilato, Michele; Scardulla, Cesare
2017-09-01
Bicuspid aortic valve (BAV)-associated ascending aneurysmal aortopathy (namely "bicuspid aortopathy") is a heterogeneous disease making surgeon predictions particularly challenging. Computational flow analysis can be used to evaluate the BAV-related hemodynamic disturbances, which likely lead to aneurysm enlargement and progression. However, the anatomic reconstruction process is time consuming so that predicting hemodynamic and structural evolution by computational modeling is unfeasible in routine clinical practice. The aim of the study was to design and develop a parametric program for three-dimensional (3D) representations of aneurysmal aorta and different BAV phenotypes starting from several measures derived by computed-tomography angiography (CTA). Assuming that wall shear stress (WSS) has an important implication on bicuspid aortopathy, computational flow analyses were then performed to estimate how different would such an important parameter be, if a parametric aortic geometry was used as compared to standard geometric reconstructions obtained by CTA scans. Morphologic parameters here documented can be used to rapidly model the aorta and any phenotypes of BAV. t-test and Bland-Altman plot demonstrated that WSS obtained by flow analysis of parametric aortic geometries was in good agreement with that obtained from the flow analysis of CTA-related geometries. The proposed program offers a rapid and automated tool for 3D anatomic representations of bicuspid aortopathy with promising application in routine clinical practice by reducing the amount of time for anatomic reconstructions. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.
Magnetic field effect on a three-dimensional mixed convective flow ...
African Journals Online (AJOL)
An analytical solution to the problem of the MHD free and forced convection three dimensional flow of an incompressible viscous electrically conducting fluid with mass transfer along a vertical porous plate with transverse sinusoidal suction velocity is presented. A uniform magnetic field is assumed to be applied transversely ...
Experimental investigation of three-dimensional flow instabilities in a rotating lid-driven cavity
DEFF Research Database (Denmark)
Sørensen, Jens Nørkær; Naumov, I.; Mikkelsen, Robert Flemming
2006-01-01
liquid. For the first time the onset of three-dimensionality and transition are analysed by combining the high spatial resolution of Particle Image Velocimetry (PIV) and the temporal accuracy of Laser Doppler Anemometry (LDA). A detailed mapping of the transition from steady and axisymmetric flow...
Miao, Sha; Hendrickson, Kelli; Liu, Yuming
2017-12-01
This work presents a Fully-Coupled Immersed Flow (FCIF) solver for the three-dimensional simulation of fluid-fluid interaction by coupling two distinct flow solvers using an Immersed Boundary (IB) method. The FCIF solver captures dynamic interactions between two fluids with disparate flow properties, while retaining the desirable simplicity of non-boundary-conforming grids. For illustration, we couple an IB-based unsteady Reynolds Averaged Navier Stokes (uRANS) simulator with a depth-integrated (long-wave) solver for the application of slug development with turbulent gas and laminar liquid. We perform a series of validations including turbulent/laminar flows over prescribed wavy boundaries and freely-evolving viscous fluids. These confirm the effectiveness and accuracy of both one-way and two-way coupling in the FCIF solver. Finally, we present a simulation example of the evolution from a stratified turbulent/laminar flow through the initiation of a slug that nearly bridges the channel. The results show both the interfacial wave dynamics excited by the turbulent gas forcing and the influence of the liquid on the gas turbulence. These results demonstrate that the FCIF solver effectively captures the essential physics of gas-liquid interaction and can serve as a useful tool for the mechanistic study of slug generation in two-phase gas/liquid flows in channels and pipes.
Three Dimensional Flow and Pressure Patterns in a Hydrostatic Journal Bearing
Braun, M. Jack; Dzodzo, Milorad B.
1996-01-01
The flow in a hydrostatic journal bearing (HJB) is described by a mathematical model that uses the three dimensional non-orthogonal form of the Navier-Stokes equations. Using the u, v, w, and p, as primary variables, a conservative formulation, finite volume multi-block method is applied through a collocated, body fitted grid. The HJB has four shallow pockets with a depth/length ratio of 0.067. This paper represents a natural extension to the two and three dimensional studies undertaken prior to this project.
On a modified form of navier-stokes equations for three-dimensional flows.
Venetis, J
2015-01-01
A rephrased form of Navier-Stokes equations is performed for incompressible, three-dimensional, unsteady flows according to Eulerian formalism for the fluid motion. In particular, we propose a geometrical method for the elimination of the nonlinear terms of these fundamental equations, which are expressed in true vector form, and finally arrive at an equivalent system of three semilinear first order PDEs, which hold for a three-dimensional rectangular Cartesian coordinate system. Next, we present the related variational formulation of these modified equations as well as a general type of weak solutions which mainly concern Sobolev spaces.
Three-dimensional flow past a fixed or freely vibrating cylinder in the early turbulent regime
Gsell, Simon; Bourguet, Rémi; Braza, Marianna
2018-01-01
The three-dimensional structure of the flow downstream of a circular cylinder, either fixed or subjected to vortex-induced vibrations, is investigated by means of numerical simulation, at Reynolds number 3900, based on the cylinder diameter and current velocity. The flow exhibits pronounced fluctuations distributed along the span in all studied cases. Qualitatively, it is characterized by spanwise undulations of the shear layers separating from the body and the development of vortices elongated in the plane normal to its axis (planar vortices). A quantitative analysis of crossflow vorticity fluctuations in the spanwise direction reveals a peak of fluctuation amplitude in the near region (i.e., area of formation of the spanwise wake vortices) and opposite trends of the spanwise wavelength in the shear layer and wake regions; the wavelength tends to decrease as a function of the streamwise distance in the shear layers down to a minimum value close to 0.5 body diameters and then slowly increases further in the wake. The spanwise structure of the flow is differently altered in these two regions, once the cylinder vibrates. In the shear layer region, body motion is associated with an enhancement of planar vortex formation. The amplification of vorticity spanwise fluctuations in this region is accompanied by a reduction of the spanwise wavelength; it is found to decrease as a function of the instantaneous Reynolds number based on the instantaneous flow velocity seen by the moving body, following the global trend of the wavelength versus Reynolds number previously reported for fixed cylinders. In the wake region, the flow spanwise structure is essentially unaltered compared to the fixed body case, in spite of the major distortions of the streamwise and crossflow length scales.
Energy distribution of structure-borne sound in three-dimensional structures
DEFF Research Database (Denmark)
Hugin, Claus Thomas
1996-01-01
This report deals with the prediction of energy distribution of structure-borne sound in three-dimensional structures consisting of coupled thin rectangular plates. The frequency range addressed is the medium frequency range, which is characterised by having so few modes that a traditional...
THREE-DIMENSIONAL SIMULATION OF FLOW AT AN OPEN-CHANNEL CONFLUENCE WITH TURBULENCE MODELS
Dinh Thanh, Mung; Kimura, Ichiro; Shimizu, Yasuyuki
Open-channel confluence flows are common in natural river systems as well as in environmental and hydraulic engineering, such as in river engineering. Often, these flows are three-dimensional and complex,while numerical studies fully describing confluence flow are still few. This paper presents the results of investigation of confluence flow using a three-dimensional numerical model with the linear and nonlinear k-ε models. To treat the dynamic boundary condition at the free surface, non-hydrostatic pressure is included in the present model. The model is validated using the experimental data available. Adequacy of the present model with two turbulence models above is indicated based on the result analysis. The nonlinear model is indicated as the more advantageous one than the linear one.
Subramanian, S. V.; Bozzola, R.; Povinelli, L. A.
1986-01-01
The performance of a three dimensional computer code developed for predicting the flowfield in stationary and rotating turbomachinery blade rows is described in this study. The four stage Runge-Kutta numerical integration scheme is used for solving the governing flow equations and yields solution to the full, three dimensional, unsteady Euler equations in cylindrical coordinates. This method is fully explicit and uses the finite volume, time marching procedure. In order to demonstrate the accuracy and efficiency of the code, steady solutions were obtained for several cascade geometries under widely varying flow conditions. Computed flowfield results are presented for a fully subsonic turbine stator and a low aspect ratio, transonic compressor rotor blade under maximum flow and peak efficiency design conditions. Comparisons with Laser Anemometer measurements and other numerical predictions are also provided to illustrate that the present method predicts important flow features with good accuracy and can be used for cost effective aerodynamic design studies.
K. V. Pagalthivarthi; R. J. Visintainer
2013-01-01
Multi-size particulate dense slurry flow through three-dimensional rectangular channel is modeled using penalty finite elements with 8-noded hexahedral elements. The methodology previously developed for two-dimensional channel is extended. The computed eddy viscosity of the pure carrier flow is modified to account for the presence of solid particles. Predictions from Spalart-Almaras and k-ε turbulence models are compared to show consistency of trends in results. Results are also found to comp...
Three-dimensional power Doppler sonography: imaging and quantifying blood flow and vascularization.
Pairleitner, H; Steiner, H; Hasenoehrl, G; Staudach, A
1999-08-01
To assess the feasibility of imaging low-velocity blood flow in adnexal masses by transvaginal three-dimensional power Doppler sonography, to analyze three-dimensional power Doppler sonography data sets with a new computer-assisted method and to test the reproducibility of the technique. A commercially available 5-MHz Combison 530 ultrasound system was used to perform three-dimensional power Doppler sonography transvaginally. A cube (= volume of interest) was defined enclosing the vessels of the cyst and the Cartesian characteristics were stored on a hard disk. This cube was analyzed using specially designed software. Five indices representing vascularization (the vascularization index (VI) or blood flow (the flow index (FI)) or both (the vascularization-flow index (VFI)) were calculated. The intraobserver repeatability of cube definition and scan repetition was assessed using Hartley's test for homogeneous variances. Interobserver agreement was assessed by the Pearson correlation coefficient. Imaging of vessels with low-velocity blood flow by three-dimensional power Doppler sonography and cube definition was possible in all adnexal massed studied. In some cases even induced non-vascular flow related to endometriosis was detected. The calculated F value with intraobserver repeated Cartesian file-saving ranged from 0 to 18.8, with intraobserver scan repetition from 4.74 to 24.8 for VI, FI 1, FI 2 and VFI 1; for VFI 2 the calculated F value was 64. The interobserver correlation coefficient ranged between 0.83 and 0.92 for VI, FI 1, FI 2 and VFI 1; for VFI 2 the correlation coefficient was less than 0.75. Vessels with low-velocity blood flow can be imaged using three-dimensional power Doppler sonography. Induced non-vascular flow was detected in endometriotic cyst fluid. Three-dimensional power Doppler sonography combined with the cube method gave reproducible information for all indices except VFI 2. These indices might prove to be a new predictor in all fields of
A finite area scheme for shallow granular flows on three-dimensional surfaces
Rauter, Matthias
2017-04-01
Shallow granular flow models have become a popular tool for the estimation of natural hazards, such as landslides, debris flows and avalanches. The shallowness of the flow allows to reduce the three-dimensional governing equations to a quasi two-dimensional system. Three-dimensional flow fields are replaced by their depth-integrated two-dimensional counterparts, which yields a robust and fast method [1]. A solution for a simple shallow granular flow model, based on the so-called finite area method [3] is presented. The finite area method is an adaption of the finite volume method [4] to two-dimensional curved surfaces in three-dimensional space. This method handles the three dimensional basal topography in a simple way, making the model suitable for arbitrary (but mildly curved) topography, such as natural terrain. Furthermore, the implementation into the open source software OpenFOAM [4] is shown. OpenFOAM is a popular computational fluid dynamics application, designed so that the top-level code mimics the mathematical governing equations. This makes the code easy to read and extendable to more sophisticated models. Finally, some hints on how to get started with the code and how to extend the basic model will be given. I gratefully acknowledge the financial support by the OEAW project "beyond dense flow avalanches". Savage, S. B. & Hutter, K. 1989 The motion of a finite mass of granular material down a rough incline. Journal of Fluid Mechanics 199, 177-215. Ferziger, J. & Peric, M. 2002 Computational methods for fluid dynamics, 3rd edn. Springer. Tukovic, Z. & Jasak, H. 2012 A moving mesh finite volume interface tracking method for surface tension dominated interfacial fluid flow. Computers & fluids 55, 70-84. Weller, H. G., Tabor, G., Jasak, H. & Fureby, C. 1998 A tensorial approach to computational continuum mechanics using object-oriented techniques. Computers in physics 12(6), 620-631.
Energy Technology Data Exchange (ETDEWEB)
Shehzad, S.A., E-mail: ali_qau70@yahoo.com [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan); Abdullah, Z. [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan); Alsaedi, A. [Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Faculty of Science, King Abdulaziz University, P. O. Box 80257, Jeddah 21589 (Saudi Arabia); Abbasi, F.M. [Department of Mathematics, Comsats Institute of Information Technology, Islamabad 44000 (Pakistan); Hayat, T. [Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Faculty of Science, King Abdulaziz University, P. O. Box 80257, Jeddah 21589 (Saudi Arabia); Department of Mathematics, Quaid-I-Azam University 45320, Islamabad 44000 (Pakistan)
2016-01-01
This research work addresses the three-dimensional hydromagnetic flow of Jeffrey fluid with nanoparticles. Flow is generated by a bidirectional stretching surface. The effects of thermal radiation and internal heat generation are encountered in energy expressions. More realistic convective boundary conditions at the surface are employed instead of constant surface temperature and mass species conditions. Boundary layer assumptions lead to the governing non-linear mathematical model. Resulting equations through momentum, energy and mass species are made dimensionless using suitable variables. The solution expressions of dimensionless velocities, temperature and nanoparticle concentration have been computed for the convergent series solutions. The impacts of interesting parameters on the dimensionless quantities are displayed and interpreted. The values of physical quantities are computed and analyzed. - Highlights: • Three-dimensional hydromagnetic flow of Jeffrey nanofluid is considered. • Brownian motion and thermophoresis effects are encountered. • Heat transfer analysis is performed with thermal radiation. • Results are plotted and visualized.
Impact of magnetic field in three-dimensional flow of Sisko nanofluid with convective condition
Energy Technology Data Exchange (ETDEWEB)
Hayat, T. [Department of Mathematics, Quaid-I-Azam University, Islamabad 44000 (Pakistan); Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589 (Saudi Arabia); Muhammad, Taseer, E-mail: taseer_qau@yahoo.com [Department of Mathematics, Quaid-I-Azam University, Islamabad 44000 (Pakistan); Ahmad, B. [Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589 (Saudi Arabia); Shehzad, S.A. [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan)
2016-09-01
This communication addresses the magnetohydrodynamic (MHD) three dimensional flow of Sisko nanofluid bounded by a surface stretched bidirectionally. Nanofluid model includes the Brownian motion and thermophoresis. Heat transfer through convective condition is discussed. Developed condition with the zero nanoparticles mass flux at the surface is implemented. The governing problems subject to boundary layer approximations are computed for the convergent series solutions. Effects of interesting flow parameters on the temperature and nanoparticles concentration distributions are studied and discussed. Skin friction coefficients and the local Nusselt number are computed and analyzed. - Highlights: • Three-dimensional flow of Sisko nanofluid is modeled. • Uniform applied magnetic field is adopted. • Brownian motion and thermophoresis effects are accounted. • Heat transfer convective condition is utilized. • Recently constructed condition with zero nanoparticles mass flux is implemented.
Three-Dimensional Cellular Structures Enhanced By Shape Memory Alloys
Nathal, Michael V.; Krause, David L.; Wilmoth, Nathan G.; Bednarcyk, Brett A.; Baker, Eric H.
2014-01-01
This research effort explored lightweight structural concepts married with advanced smart materials to achieve a wide variety of benefits in airframe and engine components. Lattice block structures were cast from an aerospace structural titanium alloy Ti-6Al-4V and a NiTi shape memory alloy (SMA), and preliminary properties have been measured. A finite element-based modeling approach that can rapidly and accurately capture the deformation response of lattice architectures was developed. The Ti-6-4 and SMA material behavior was calibrated via experimental tests of ligaments machined from the lattice. Benchmark testing of complete lattice structures verified the main aspects of the model as well as demonstrated the advantages of the lattice structure. Shape memory behavior of a sample machined from a lattice block was also demonstrated.
International Nuclear Information System (INIS)
Wong, C.N.C.; Cheng, S.K.; Todreas, N.E.
1982-01-01
This report provides the HEATRAN user with programming and input information. HEATRAN is a computer program which is written to analyze the transient three dimensional single phase incompressible fluid flow and heat transfer problem. In this report, the programming information is given first. This information includes details concerning the code and structure. The description of the required input variables is presented next. Following the input description, the sample problems are described and HEATRAN's results are presented
The Three-Dimensional Structural Basis of Type II Hyperprolinemia
Energy Technology Data Exchange (ETDEWEB)
Srivastava, Dhiraj; Singh, Ranjan K.; Moxley, Michael A.; Henzl, Michael T.; Becker, Donald F.; Tanner, John J. (UNL); (UMC)
2012-08-31
Type II hyperprolinemia is an autosomal recessive disorder caused by a deficiency in {Delta}{sup 1}-pyrroline-5-carboxylate dehydrogenase (P5CDH; also known as ALDH4A1), the aldehyde dehydrogenase that catalyzes the oxidation of glutamate semialdehyde to glutamate. Here, we report the first structure of human P5CDH (HsP5CDH) and investigate the impact of the hyperprolinemia-associated mutation of Ser352 to Leu on the structure and catalytic properties of the enzyme. The 2. 5-{angstrom}-resolution crystal structure of HsP5CDH was determined using experimental phasing. Structures of the mutant enzymes S352A (2.4 {angstrom}) and S352L (2.85 {angstrom}) were determined to elucidate the structural consequences of altering Ser352. Structures of the 93% identical mouse P5CDH complexed with sulfate ion (1.3 {angstrom} resolution), glutamate (1.5 {angstrom}), and NAD{sup +} (1.5 {angstrom}) were determined to obtain high-resolution views of the active site. Together, the structures show that Ser352 occupies a hydrophilic pocket and is connected via water-mediated hydrogen bonds to catalytic Cys348. Mutation of Ser352 to Leu is shown to abolish catalytic activity and eliminate NAD{sup +} binding. Analysis of the S352A mutant shows that these functional defects are caused by the introduction of the nonpolar Leu352 side chain rather than the removal of the Ser352 hydroxyl. The S352L structure shows that the mutation induces a dramatic 8-{angstrom} rearrangement of the catalytic loop. Because of this conformational change, Ser349 is not positioned to interact with the aldehyde substrate, conserved Glu447 is no longer poised to bind NAD{sup +}, and Cys348 faces the wrong direction for nucleophilic attack. These structural alterations render the enzyme inactive.
Three-dimensional hierarchical structures for fog harvesting.
Andrews, H G; Eccles, E A; Schofield, W C E; Badyal, J P S
2011-04-05
Conventional fog-harvesting mechanisms are effectively pseudo-2D surface phenomena in terms of water droplet-plant interactions. In the case of the Cotula fallax plant, a unique hierarchical 3D arrangement formed by its leaves and the fine hairs covering them has been found to underpin the collection and retention of water droplets on the foliage for extended periods of time. The mechanisms of water capture and release as a function of the surface 3D structure and chemistry have been identified. Of particular note is that water is retained throughout the entirety of the plant and held within the foliage itself (rather than in localized regions). Individual plant hairs form matlike structures capable of supporting water droplets; these hairs wrap around water droplets in a 3D fashion to secure them via a fine nanoscale groove structure that prevents them from easily falling to the ground.
Evaluation of Three Dimensional Underground Structure at SAFOD Project
International Nuclear Information System (INIS)
Malin, Peter
2014-01-01
In the SAFOD project, the imaging of the fault zone was implemented using data acquired by a pilot hole array of a vertical depth of 2 km and then a main hole was drilled using these data. The trajectory of the main hole below vertical depth of 1.5 km was angled toward/through the fault zone up to a vertical depth of 3 km. An sensor array was located in the hole. As a result, the hypocenter locations of small earthquakes within the fault zone were determined with high accuracy (location error within 10 meters) and the location of the fault zone was able to be identified with high accuracy. Using this data, high resolution underground structure around the San Andreas fault zone was obtained. It was reported that this underground structure revealed the deep structure of the San Andreas Fault at the Parkfield site as well as the branch fault. (author)
Guide to Three Dimensional Structure and Motion Factorization
Wang, Guanghui
2011-01-01
The problem of structure and motion recovery from image sequences is an important theme in computer vision. Considerable progress has been made in this field during the past two decades, resulting in successful applications in robot navigation, augmented reality, industrial inspection, medical image analysis, and digital entertainment, among other areas. However, many of these methods work only for rigid objects and static scenes. The study of non-rigid structure from motion is not only of academic significance, but also has important practical applications in real-world, nonrigid or dynamic s
Quantized fluctuational electrodynamics for three-dimensional plasmonic structures
DEFF Research Database (Denmark)
Partanen, Mikko; Häyrynen, Teppo; Tulkki, Jukka
2017-01-01
We recently introduced a quantized fluctuational electrodynamics (QFED) formalism that provides a physically insightful definition of an effective position-dependent photon-number operator and the associated ladder operators. However, this far the formalism has been applicable only for the normal...... incidence of the electromagnetic field in planar structures. In this work, we overcome the main limitation of the one-dimensional QFED formalism by extending the model to three dimensions, allowing us to use the QFED method to study, e.g., plasmonic structures. To demonstrate the benefits of the developed...
From three-dimensional GPCR structure to rational ligand discovery
Kooistra, A.J.; Leurs, R.; de Esch, I.J.P.; de Graaf, C.
2014-01-01
This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding
Structurally Efficient Three-dimensional Metamaterials with Controllable Thermal Expansion
Xu, Hang; Pasini, Damiano
2016-01-01
The coefficient of thermal expansion (CTE) of architected materials, as opposed to that of conventional solids, can be tuned to zero by intentionally altering the geometry of their structural layout. Existing material architectures, however, achieve CTE tunability only with a sacrifice in structural efficiency, i.e. a drop in both their stiffness to mass ratio and strength to mass ratio. In this work, we elucidate how to resolve the trade-off between CTE tunability and structural efficiency and present a lightweight bi-material architecture that not only is stiffer and stronger than other 3D architected materials, but also has a highly tunable CTE. Via a combination of physical experiments on 3D fabricated prototypes and numeric simulations, we demonstrate how two distinct mechanisms of thermal expansion appearing in a tetrahedron, can be exploited in an Octet lattice to generate a large range of CTE values, including negative, zero, or positive, with no loss in structural efficiency. The novelty and simplicity of the proposed design as well as the ease in fabrication, make this bi-material architecture well-suited for a wide range of applications, including satellite antennas, space optical systems, precision instruments, thermal actuators, and MEMS. PMID:27721437
Three-dimensional structure of Rubella virus factories
International Nuclear Information System (INIS)
Fontana, Juan; Lopez-Iglesias, Carmen; Tzeng, Wen-Ping; Frey, Teryl K.; Fernandez, Jose J.; Risco, Cristina
2010-01-01
Viral factories are complex structures in the infected cell where viruses compartmentalize their life cycle. Rubella virus (RUBV) assembles factories by recruitment of rough endoplasmic reticulum (RER), mitochondria and Golgi around modified lysosomes known as cytopathic vacuoles or CPVs. These organelles contain active replication complexes that transfer replicated RNA to assembly sites in Golgi membranes. We have studied the structure of RUBV factory in three dimensions by electron tomography and freeze-fracture. CPVs contain stacked membranes, rigid sheets, small vesicles and large vacuoles. These membranes are interconnected and in communication with the endocytic pathway since they incorporate endocytosed BSA-gold. RER and CPVs are coupled through protein bridges and closely apposed membranes. Golgi vesicles attach to the CPVs but no tight contacts with mitochondria were detected. Immunogold labelling confirmed that the mitochondrial protein p32 is an abundant component around and inside CPVs where it could play important roles in factory activities.
Computational Study of Colloidal Droplet Interactions with Three Dimensional Structures
2015-05-18
create a novel multiphysics model that enables the prediction of colloidal droplet interactions with complex porous structures; (b) advance the...diameter and penetration depth. (2) A model for the transport and deposition of nanoparticles in the porous matrix during droplet sorption was...process. The main research goals of this proposal are to (a) create a novel multiphysics model that enables the prediction of colloidal droplet
Three-dimensional modeling of diesel engine intake flow, combustion and emissions-II
Energy Technology Data Exchange (ETDEWEB)
Reitz, R.D.; Rutland, C.J.
1993-09-01
A three-dimensional computer code, KIVA, is being modified to include state-of-the-art submodels for diesel engine flow and combustion. Improved and/or new submodels which have already been implemented and previously reported are: Wall heat transfer with unsteadiness and compressibility, laminar-turbulent characteristic time combustion with unburned HC and Zeldo`vich NO{sub x}, and spray/wall impingement with rebounding and sliding drops. Progress on the implementation of improved spray drop drag and drop breakup models, the formulation and testing of a multistep kinetics ignition model and preliminary soot modeling results are described in this report. In addition, the use of a block structured version of KIVA to model the intake flow process is described. A grid generation scheme has been developed for modeling realistic (complex) engine geometries, and computations have been made of intake flow in the ports and combustion chamber of a two-intake-valve engine. The research also involves the use of the code to assess the effects of subprocesses on diesel engine performance. The accuracy of the predictions is being tested by comparisons with engine experiments. To date, comparisons have been made with measured engine cylinder pressure, temperature and heat flux data, and the model results are in good agreement with the experiments. Work is in progress that will allow validation of in-cylinder flow and soot formation predictions. An engine test facility is described that is being used to provide the needed validation data. Test results have been obtained showing the effect of injection rate and split injections on engine performance and emissions.
Large Eddy Simulations of the Flow in a Three-Dimensional Ventilated Room
DEFF Research Database (Denmark)
Davidson, Lars; Nielsen, Peter V.
We have done Large Eddy Simulations (LES) of the flow in a three-dimensional ventilated room. A finite volume method is used with a collocated grid arrangement. The momentum equations are solved with an explicit method using central differencing for all terms. The pressure is obtained from a Pois...... a Poisson equation, which is solved with a conjugate gradient method. For the discretization in time we use the Adam-Bashfourth scheme, which is second-order accurate.......We have done Large Eddy Simulations (LES) of the flow in a three-dimensional ventilated room. A finite volume method is used with a collocated grid arrangement. The momentum equations are solved with an explicit method using central differencing for all terms. The pressure is obtained from...
Thermally induced rarefied gas flow in a three-dimensional enclosure with square cross-section
Zhu, Lianhua; Yang, Xiaofan; Guo, Zhaoli
2017-12-01
Rarefied gas flow in a three-dimensional enclosure induced by nonuniform temperature distribution is numerically investigated. The enclosure has a square channel-like geometry with alternatively heated closed ends and lateral walls with a linear temperature distribution. A recently proposed implicit discrete velocity method with a memory reduction technique is used to numerically simulate the problem based on the nonlinear Shakhov kinetic equation. The Knudsen number dependencies of the vortices pattern, slip velocity at the planar walls and edges, and heat transfer are investigated. The influences of the temperature ratio imposed at the ends of the enclosure and the geometric aspect ratio are also evaluated. The overall flow pattern shows similarities with those observed in two-dimensional configurations in literature. However, features due to the three-dimensionality are observed with vortices that are not identified in previous studies on similar two-dimensional enclosures at high Knudsen and small aspect ratios.
Three-Dimensional Mapping of Air Flow at an Urban Canyon Intersection
Carpentieri, Matteo; Robins, Alan G.; Baldi, Sandro
2009-11-01
In this experimental work both qualitative (flow visualisation) and quantitative (laser Doppler anemometry) methods were applied in a wind tunnel in order to describe the complex three-dimensional flow field in a real environment (a street canyon intersection). The main aim was an examination of the mean flow, turbulence and flow pathlines characterising a complex three-dimensional urban location. The experiments highlighted the complexity of the observed flows, particularly in the upwind region of the intersection. In this complex and realistic situation some details of the upwind flow, such as the presence of two tall towers, play an important role in defining the flow field within the intersection, particularly at roof level. This effect is likely to have a strong influence on the mass exchange mechanism between the canopy flow and the air aloft, and therefore the distribution of pollutants. This strong interaction between the flows inside and outside the urban canopy is currently neglected in most state-of-the-art local scale dispersion models.
Three-Dimensional Structure and Catalytic Mechanism of Cytosine Deaminase
Energy Technology Data Exchange (ETDEWEB)
R Hall; A Fedorov; C Xu; E Fedorov; S Almo; F Raushel
2011-12-31
Cytosine deaminase (CDA) from E. coli is a member of the amidohydrolase superfamily. The structure of the zinc-activated enzyme was determined in the presence of phosphonocytosine, a mimic of the tetrahedral reaction intermediate. This compound inhibits the deamination of cytosine with a K{sub i} of 52 nM. The zinc- and iron-containing enzymes were characterized to determine the effect of the divalent cations on activation of the hydrolytic water. Fe-CDA loses activity at low pH with a kinetic pKa of 6.0, and Zn-CDA has a kinetic pKa of 7.3. Mutation of Gln-156 decreased the catalytic activity by more than 5 orders of magnitude, supporting its role in substrate binding. Mutation of Glu-217, Asp-313, and His-246 significantly decreased catalytic activity supporting the role of these three residues in activation of the hydrolytic water molecule and facilitation of proton transfer reactions. A library of potential substrates was used to probe the structural determinants responsible for catalytic activity. CDA was able to catalyze the deamination of isocytosine and the hydrolysis of 3-oxauracil. Large inverse solvent isotope effects were obtained on k{sub cat} and k{sub cat}/K{sub m}, consistent with the formation of a low-barrier hydrogen bond during the conversion of cytosine to uracil. A chemical mechanism for substrate deamination by CDA was proposed.
Three dimensional PNS solutions of hypersonic internal flows with equilibrium chemistry
Liou, May-Fun
1989-01-01
An implicit procedure for solving parabolized Navier-Stokes equations under the assumption of a general equation of state for a gas in chemical equilibrium is given. A general and consistent approach for the evaluation of Jacobian matrices in the implicit operator avoids the use of unnecessary auxiliary quantities and approximations, and leads to a simple expression. Applications to two- and three-dimensional flow problems show efficiency in computer time and economy in storage.
Three-dimensional shallow velocity structure beneath Taal Volcano, Philippines
You, Shuei-Huei; Konstantinou, Konstantinos I.; Gung, Yuancheng; Lin, Cheng-Horng
2017-11-01
Based on its numerous historical explosive eruptions and high potential hazards to nearby population of millions, Taal Volcano is one of the most dangerous "Decade Volcanoes" in the world. To provide better investigation on local seismicity and seismic structure beneath Taal Volcano, we deployed a temporary seismic network consisting of eight stations from March 2008 to March 2010. In the preliminary data processing stage, three periods showing linear time-drifting of internal clock were clearly identified from noise-derived empirical Green's functions. The time-drifting errors were corrected prior to further data analyses. By using VELEST, 2274 local earthquakes were manually picked and located. Two major earthquake groups are noticed, with one lying beneath the western shore of Taal Lake showing a linear feature, and the other spreading around the eastern flank of Taal Volcano Island at shallower depths. We performed seismic tomography to image the 3D structure beneath Taal Volcano using the LOTOS algorithm. Some interesting features are revealed from the tomographic results, including a solidified magma conduit below the northwestern corner of Taal Volcano Island, indicated by high Vp, Vs, and low Vp/Vs ratio, and a large potential hydrothermal reservoir beneath the center of Taal Volcano Island, suggested by low Vs and high Vp/Vs ratio. Furthermore, combining earthquake distributions and tomographic images, we suggest potential existence of a hydrothermal reservoir beneath the southwestern corner of Taal Lake, and a fluid conduit extending to the northwest. These seismic features have never been proposed in previous studies, implying that new hydrothermal activity might be formed in places away from the historical craters on Taal Volcano Island.
Nadeem, S.; Abbas, Nadeem; Khan, A. U.
2018-03-01
The characteristics of three-dimensional stagnation point flow of Hybrid nanofluid past a circular cylinder are explored. The fluid flow is entertained in the presence/absence of thermal slip effects. The flow model is controlled through the partial differential equations. Since these equations are highly non-linear in character. So for the order reduction a suitable set of transformation is used. The reduced system is solved by using shooting method. The obtained results are offered through graphs and tables. It is noticed that the heat transfer rate is high in Hybrid nanofluid as compared to nanofluid. The present work is validated by developing comprising with existing literature.
Three-dimensional fluid flow phenomena in the blade end wall corner region
Hazarika, B. K.; Raj, R.; Boldman, D. R.
1986-01-01
Flow visualization, static and total pressure measurements, and mean velocity profile measurements with a single-sensor inclined hot wire probe, are used in a study of three-dimensional flow at a turbine blade end wall corner region for six critical axial stations along the blade chord. Three vortices are identified: (1) a horseshoe vortex near the leading edge; (2) a corner eddy between the horseshoe vortex and the corner; and (3) a vortex at the rear portion of the corner due to the corner eddy's secondary flow. Attention is given to the relative size and rate-of-spread of the vortices in the streamwise direction.
The influence of three dimensional dunes on river flows and fluxes
Hardy, R. J.; Parsons, D. R.; Ockelford, A.; Ashworth, P. J.; Reesink, A.; Best, J.
2015-12-01
Fluvial systems in large river basins experience temporal variations in flow discharge, which creates unsteady changes in the flow field and sediment fluxes. The sediment-water interface responds and organizes to these changes over a wide range of spatial and temporal scales, primarily through adjustment of a variety of bed roughness elements. These roughness elements are the key component of overall flow resistance and the magnitude of their form drag significantly influences river stage levels for given discharge and determines the state and functioning of river systems and sediment fluxes. Here we present three dimensional numerically predicted flow results to demonstrate the importance of complex morphology on flow and sediment fluxes. Model boundary conditions and validation data were taken from two sources. Initially, they were collected from a field campaign on a 1.5 by 0.3 km stretch of the Mississippi near Alton, Illinois. Secondly, a series of flume experiments were undertaken that applied unsteady hydraulic conditions to generate a series of quasi-equilibrium three dimensional bed forms, which were scaled on the data collected in the field. The numerical flow results show that superimposed bed forms can cause changes in the nature of the classical separated flow region in particularly the number of locations where vortices are shed and the point of flow reattachment, which may be important for sediment flux dynamics during bed form adjustment.
Wu, Chung-Hua
1993-01-01
This report represents a general theory applicable to axial, radial, and mixed flow turbomachines operating at subsonic and supersonic speeds with a finite number of blades of finite thickness. References reflect the evolution of computational methods used, from the inception of the theory in the 50's to the high-speed computer era of the 90's. Two kinds of relative stream surfaces, S(sub 1) and S(sub 2), are introduced for the purpose of obtaining a three-dimensional flow solution through the combination of two-dimensional flow solutions. Nonorthogonal curvilinear coordinates are used for the governing equations. Methods of computing transonic flow along S(sub 1) and S(sub 2) stream surfaces are given for special cases as well as for fully three-dimensional transonic flows. Procedures pertaining to the direct solutions and inverse solutions are presented. Information on shock wave locations and shapes needed for computations are discussed. Experimental data from a Deutsche Forschungs- und Versuchsanstalt fur Luft- und Raumfahrt e.V. (DFVLR) rotor and from a Chinese Academy of Sciences (CAS) transonic compressor rotor are compared with the computed flow properties.
Experimental investigation of three-dimensional flow instabilities in a rotating lid-driven cavity
DEFF Research Database (Denmark)
Sørensen, Jens Nørkær; Naumov, I.; Mikkelsen, Robert Flemming
2006-01-01
The flow between a rotating lid and a stationary cylinder is studied experimentally. The flow is governed by two parameters: The ratio of container height to disk radius, h, and the Reynolds number, Re, based on the disk angular velocity, cylinder radius and kinematic viscosity of the working...... stability analysis of Gelfgat et al. [J. Fluid. Mech. 438, (2001)]. In most cases the measured onset of three-dimensionality is in good agreement with the numerical results and disagreements can be explained by bifurcations not accounted for by the stability analysis....
Directory of Open Access Journals (Sweden)
K. V. Pagalthivarthi
2013-03-01
Full Text Available Multi-size particulate dense slurry flow through three-dimensional rectangular channel is modeled using penalty finite elements with 8-noded hexahedral elements. The methodology previously developed for two-dimensional channel is extended. The computed eddy viscosity of the pure carrier flow is modified to account for the presence of solid particles. Predictions from Spalart-Almaras and k-ε turbulence models are compared to show consistency of trends in results. Results are also found to compare well with experimental results from the literature.
Three-dimensional visualization of myocardial motion and blood flow with cine-MR images
International Nuclear Information System (INIS)
Oshiro, Osamu; Matani, Ayumu; Chihara, Kunihiro; Mikami, Taisei; Kitabatake, Akira.
1997-01-01
This paper describes a three-dimensional (3D) reconstruction and presentation method to visualize myocardial motion and blood flow in a heart using cine-MR (magnetic resonance) images. Firstly, the region of myocardium and blood were segmented with certain threshold gray values. Secondly, some slices were interpolated linearly to reconstruct a 3D static image. Finally, a 3D dynamic image was presented with displaying the 3D static images sequentially. The experimental results indicate that this method enables to visualize not only normal but also abnormal blood flow in cine-mode. (author)
Wavelet-based regularization of the Galerkin truncated three-dimensional incompressible Euler flows.
Farge, Marie; Okamoto, Naoya; Schneider, Kai; Yoshimatsu, Katsunori
2017-12-01
We present numerical simulations of the three-dimensional Galerkin truncated incompressible Euler equations that we integrate in time while regularizing the solution by applying a wavelet-based denoising. For this, at each time step, the vorticity field is decomposed into wavelet coefficients, which are split into strong and weak coefficients, before reconstructing them in physical space to obtain the corresponding coherent and incoherent vorticities. Both components are multiscale and orthogonal to each other. Then, by using the Biot-Savart kernel, one obtains the coherent and incoherent velocities. Advancing the coherent flow in time, while filtering out the noiselike incoherent flow, models turbulent dissipation and corresponds to an adaptive regularization. To track the flow evolution in both space and scale, a safety zone is added in wavelet coefficient space to the coherent wavelet coefficients. It is shown that the coherent flow indeed exhibits an intermittent nonlinear dynamics and a k^{-5/3} energy spectrum, where k is the wave number, characteristic of three-dimensional homogeneous isotropic turbulence. Finally, we compare the dynamical and statistical properties of Euler flows subjected to four kinds of regularizations: dissipative (Navier-Stokes), hyperdissipative (iterated Laplacian), dispersive (Euler-Voigt), and wavelet-based regularizations.
Three-dimensional structure of a pre-catalytic human spliceosomal complex B.
Boehringer, Daniel; Makarov, Evgeny M; Sander, Bjoern; Makarova, Olga V; Kastner, Berthold; Lührmann, Reinhard; Stark, Holger
2004-05-01
Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have immunoaffinity-purified human spliceosomes (designated B Delta U1) at a stage after U4/U6.U5 tri-snRNP integration but before activation, and have determined the three-dimensional structure of B Delta U1 by single-particle electron cryomicroscopy at a resolution of approximately 40 A. The overall size of the complex is about 370 x 270 x 170 A. The three-dimensional structure features a roughly triangular body linked to a head domain in variable orientations. The body is very similar in size and shape to the isolated U4/U6.U5 tri-snRNP. This provides initial insight into the structural organization of complex B.
Three dimensional computations of the flow around a LM19 rotor
Energy Technology Data Exchange (ETDEWEB)
Hambraeus, T. [FFA, Bromma (Sweden)
1997-12-31
To achieve insight in the flow phenomenon occurring in wind power engineering modeling of the flow through the basic governing equations, Navier-Stokes and Euler, can be a great complement to experiments and other computational methods such as the BEM (Blade Element Momentum). Navier-Stokes methods is regularly used in prediction of air-foil flows but then mostly under attached flow conditions. One of the main differences between air-foil computations for aircraft industry and computations for wind turbine applications is that the former is not very interested in separated flow while for the latter case this is part of the operating conditions. It has been noted that separated flow poses problems since the most popular turbulence models such as Baldwin-Lomax and the {kappa}-{epsilon} model seems to over estimate the amount of turbulent viscosity produced and thus suppressing the separation. The work with finding better turbulence models is presently an area with large amount of research offering improved models. However, in the present report only the two mentioned turbulence models have been used. The present report shows computational results obtained with the Navier-Stokes solver EU-RANUS. First the results from a two-dimensional verification cases are shown to verify that the solver produces results comparable with other solvers. The flow computed is attached flow and slightly separated flow over the so called Profile-A. Secondly three dimensional computations of the flow over a full three dimensional rotor at attached and stalled conditions is shown. The computed results are compared with measured power data from field experiments. (EG)
Xu, C.; Luo, Z.; Sun, R.; Li, Q.
2017-12-01
The Tibetan Plateau, the largest and highest plateau on Earth, was uplifted, shorten and thicken by the collision and continuous convergence of the Indian and Eurasian plates since 50 million years ago, the Eocene epoch. Fine three-dimensional crustal structure of the Tibetan Plateau is helpful in understanding the tectonic development. At present, the ordinary method used for revealing crustal structure is seismic method, which is inhibited by poor seismic station coverage, especially in the central and western plateau primarily due to the rugged terrain. Fortunately, with the implementation of satellite gravity missions, gravity field models have demonstrated unprecedented global-scale accuracy and spatial resolution, which can subsequently be employed to study the crustal structure of the entire Tibetan Plateau. This study inverts three-dimensional crustal density and Moho topography of the Tibetan Plateau from gravity data using multi-scale gravity analysis. The inverted results are in agreement with those provided by the previous works. Besides, they can reveal rich tectonic development of the Tibetan Plateau: (1) The low-density channel flow can be observed from the inverted crustal density; (2) The Moho depth in the west is deeper than that in the east, and the deepest Moho, which is approximately 77 km, is located beneath the western Qiangtang Block; (3) The Moho fold, the directions of which are in agreement with the results of surface movement velocities estimated from Global Positioning System, exists clearly on the Moho topography.This study is supported by the National Natural Science Foundation of China (Grant No. 41504015), the China Postdoctoral Science Foundation (Grant No. 2015M572146), and the Surveying and Mapping Basic Research Programme of the National Administration of Surveying, Mapping and Geoinformation (Grant No. 15-01-08).
International Nuclear Information System (INIS)
Taggart, K.A.; Liles, D.R.
1977-08-01
The development of the TRAC computer code for analysis of LOCAs in light-water reactors involves the use of a three-dimensional (r-theta-z), two-fluid hydrodynamics model to describe the two-phase flow of steam and water through the reactor vessel. One of the major problems involved in interpreting results from this code is the presentation of three-dimensional flow patterns. The purpose of the report is to present a partial solution to this data display problem. A first version of a code which produces three-dimensional movies of flow in the reactor vessel has been written and debugged. This code (POST) is used as a postprocessor in conjunction with a stand alone three-dimensional two-phase hydrodynamics code (CYLTF) which is a test bed for the three-dimensional algorithms to be used in TRAC
A three-dimensional viscous/potential flow interaction analysis method for multi-element wings
Dvorak, F. A.; Woodward, F. A.; Maskew, B.
1977-01-01
An analysis method and computer program were developed for the calculation of the viscosity dependent aerodynamic characteristics of multi-element, finite wings in incompressible flow. A fully-three dimensional potential flow program is used to determine the inviscid pressure distribution about the configuration. The potential flow program uses surface source and vortex singularities to represent the inviscid flow. The method is capable of analysing configurations having at most one slat, a main element, and two slotted flaps. Configurations are limited to full span slats or flaps. The configuration wake is allowed to relax as a force free wake, although roll up is not allowed at this time. Once the inviscid pressure distribution is calculated, a series of boundary layer computations are made along streamwise strips.
Three-dimensional rotating flow of carbon nanotubes with Darcy-Forchheimer porous medium.
Directory of Open Access Journals (Sweden)
Tasawar Hayat
Full Text Available Here we are concerned with the Darcy-Forchheimer three-dimensional flow of carbon nanotubes in a rotating frame. Flow is generated by stretching of the surface. Xue model is adopted for nanofluid transport mechanism. Results for single wall carbon nanotubes (SWCNTs and multi wall carbon nanotubes are achieved and compared. Flow saturating porous space obeys Darcy-Forchheimer expression. Boundary layer approximations are invoked to simplify governing partial differential system. Optimal homotopy analysis method (OHAM is utilized for solutions of governing model. The optimal values of auxiliary parameters are computed. Plots have been displayed in order to analyze how the velocities and temperature fields get affected by various flow parameters. Skin-friction coefficients and local Nusselt number are presented through numerical data for both SWCNTs and MWCNTs. Moreover the skin-friction coefficients and local Nusselt number are enhanced for larger values of nanoparticles volume fraction.
Three-dimensional rotating flow of carbon nanotubes with Darcy-Forchheimer porous medium.
Hayat, Tasawar; Haider, Farwa; Muhammad, Taseer; Alsaedi, Ahmed
2017-01-01
Here we are concerned with the Darcy-Forchheimer three-dimensional flow of carbon nanotubes in a rotating frame. Flow is generated by stretching of the surface. Xue model is adopted for nanofluid transport mechanism. Results for single wall carbon nanotubes (SWCNTs) and multi wall carbon nanotubes are achieved and compared. Flow saturating porous space obeys Darcy-Forchheimer expression. Boundary layer approximations are invoked to simplify governing partial differential system. Optimal homotopy analysis method (OHAM) is utilized for solutions of governing model. The optimal values of auxiliary parameters are computed. Plots have been displayed in order to analyze how the velocities and temperature fields get affected by various flow parameters. Skin-friction coefficients and local Nusselt number are presented through numerical data for both SWCNTs and MWCNTs. Moreover the skin-friction coefficients and local Nusselt number are enhanced for larger values of nanoparticles volume fraction.
Ray tracing a three-dimensional scene using a hierarchical data structure
Wald, Ingo; Boulos, Solomon; Shirley, Peter
2012-09-04
Ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. One example embodiment is a method for ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. In this example embodiment, the hierarchical data structure includes at least a parent node and a corresponding plurality of child nodes. The method includes a first act of determining that a first active ray in the packet hits the parent node and a second act of descending to each of the plurality of child nodes.
An implicit three-dimensional Navier-Stokes solver for compressible flow
International Nuclear Information System (INIS)
Yoon, Seokkwan; Kwak, Dochan.
1991-01-01
A three-dimensional numerical method based on the lower-upper symmetric-Gauss-Seidel implicit scheme in conjunction with the flux-limited dissipation model is developed for solving the compressible Navier-Stokes equations. A new computer code which is based on this method requires only 9 microsec per grid-point per iteration on a single processor of a Cray YMP computer and executes at the sustained rate of 170 MFLOPS. A reduction of 4 orders of magnitude in the residual for a high Reynolds number flow using 230 K grid points is obtained in 24 minutes. The computational results compare well with available experimental data. 39 refs
Calculation of three-dimensional fluid flow with multiple free surfaces
International Nuclear Information System (INIS)
Vander Vorst, M.J.; Chan, R.K.C.
1978-01-01
This paper presents a method for computing incompressible fluid flows with multiple free surfaces which are not restricted in their orientation. The method is presented in the context of the three-dimensional flow in a Mark I reactor pressure suppression system immediately following a postulated loss of coolant accident. The assumption of potential flow is made. The numerical method is a mixed Eulerian-Lagrangian formulation with the interior treated as Eulerian and the free surfaces as Lagrangian. The accuracy of solution hinges on the careful treatment of two important aspects. First, the Laplace equation for the potential is solved at interior points of the Eulerian finite difference mesh using a three-dimensional ''irregular star'' so that boundary conditions can be imposed at the exact position of the free surface. Second, the Lagrangian free surfaces are composed of triangular elements, upon each vertex of which is applied the fully nonlinear Bernoulli equation. One result of these calculations is the transient load on the suppression vessel during the vent clearing and bubble formation events of a loss of coolant accident
Stabilisation of a three-dimensional boundary layer by base-flow manipulation using plasma actuators
International Nuclear Information System (INIS)
Dörr, P C; Kloker, M J
2015-01-01
The applicability of dielectric barrier discharge plasma actuators for controlling the crossflow-vortex-induced laminar breakdown in a three-dimensional swept-wing-type boundary-layer flow is investigated using direct numerical simulation. Similar to the classical application of suction at the wall the aim is to modify the quasi two-dimensional base flow and to weaken primary crossflow (CF) instability, mainly due to a reduction of the basic CF. Not only localised volumetric forcing by plasma actuators but also CF counter-blowing and spots with a moving wall are investigated to identify effective fundamental mechanisms. It is found that counter blowing always results in partial blockage of the flow and eventually increased CF velocity, whereas moving-wall spots can slightly reduce the CF and the amplitude of crossflow vortices. Using discrete volumetric forcing a significant attenuation even of finite-amplitude crossflow vortices and thus a distinct transition delay is achieved. (paper)
Energy Technology Data Exchange (ETDEWEB)
Rauf, A., E-mail: raufamar@ciitsahiwal.edu.pk [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan); Siddiq, M.K. [Centre for Advanced Studies in Pure and Applied Mathematics, Department of Mathematics, Bahauddin Zakariya University, Multan 63000 (Pakistan); Abbasi, F.M. [Department of Mathematics, Comsats Institute of Information Technology, Islamabad 44000 (Pakistan); Meraj, M.A. [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan); Ashraf, M. [Centre for Advanced Studies in Pure and Applied Mathematics, Department of Mathematics, Bahauddin Zakariya University, Multan 63000 (Pakistan); Shehzad, S.A. [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan)
2016-10-15
The present work deals with the steady laminar three-dimensional mixed convective magnetohydrodynamic (MHD) boundary layer flow of Casson nanofluid over a bidirectional stretching surface. A uniform magnetic field is applied normal to the flow direction. Similarity variables are implemented to convert the non-linear partial differential equations into ordinary ones. Convective boundary conditions are utilized at surface of the sheet. A numerical technique of Runge–Kutta–Fehlberg (RFK45) is used to obtain the results of velocity, temperature and concentration fields. The physical dimensionless parameters are discussed through tables and graphs. - Highlights: • Mixed convective boundary layer flow of Casson nanofluid is taken into account. • Impact of magnetic field is examined. • Convective heat and mass conditions are imposed. • Numerical solutions are presented and discussed.
Mao, Xiaole; Nawaz, Ahmad Ahsan; Lin, Sz-Chin Steven; Lapsley, Michael Ian; Zhao, Yanhui; McCoy, J Philip; El-Deiry, Wafik S; Huang, Tony Jun
2012-06-01
In this work, we demonstrate an integrated, single-layer, miniature flow cytometry device that is capable of multi-parametric particle analysis. The device integrates both particle focusing and detection components on-chip, including a "microfluidic drifting" based three-dimensional (3D) hydrodynamic focusing component and a series of optical fibers integrated into the microfluidic architecture to facilitate on-chip detection. With this design, multiple optical signals (i.e., forward scatter, side scatter, and fluorescence) from individual particles can be simultaneously detected. Experimental results indicate that the performance of our flow cytometry chip is comparable to its bulky, expensive desktop counterpart. The integration of on-chip 3D particle focusing with on-chip multi-parametric optical detection in a single-layer, mass-producible microfluidic device presents a major step towards low-cost flow cytometry chips for point-of-care clinical diagnostics.
Numerical method for three dimensional steady-state two-phase flow calculations
International Nuclear Information System (INIS)
Raymond, P.; Toumi, I.
1992-01-01
This paper presents the numerical scheme which was developed for the FLICA-4 computer code to calculate three dimensional steady state two phase flows. This computer code is devoted to steady state and transient thermal hydraulics analysis of nuclear reactor cores 1,3 . The first section briefly describes the FLICA-4 flow modelling. Then in order to introduce the numerical method for steady state computations, some details are given about the implicit numerical scheme based upon an approximate Riemann solver which was developed for calculation of flow transients. The third section deals with the numerical method for steady state computations, which is derived from this previous general scheme and its optimization. We give some numerical results for steady state calculations and comparisons on required CPU time and memory for various meshing and linear system solvers
DEFF Research Database (Denmark)
Sørensen, Jens Nørkær; Gelfgat, A. Yu; Naumov, I. V.
2009-01-01
for each mode. The onset of three-dimensional flow behavior is measured by combining the high spatial resolution of particle image velocimetry and the temporal accuracy of laser Doppler anemometry. The results are compared to the numerical stability analysis. The measured onset of three dimensionality......The three-dimensional axisymmetry-breaking instability of axisymmetric flow between a rotating lid and a stationary cylinder is analyzed both numerically and experimentally for the case of tall cylinders with the height/radius aspect ratio between 3.3 and 5.5. A complete stability diagram...... for the primary three-dimensional instability is obtained experimentally and computed numerically. The instability sets in due to different three-dimensional disturbance modes that are characterized by different azimuthal wavenumbers. The critical Reynolds numbers and associated frequencies are identified...
Urhahne, Detlef; Nick, Sabine; Schanze, Sascha
2009-08-01
In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer’s generative theory of multimedia learning. Simulations might lead to a decrease in cognitive load and thus support active learning. In our studies, the learning effectiveness of three-dimensional simulations was compared to two-dimensional illustrations by use of different versions of a computer programme concerning the modifications of carbon. The first and third study with freshman students of chemistry and biochemistry show that no more knowledge was acquired when participants learnt with three-dimensional simulations than with two-dimensional figures. In the second study with 16-year old secondary school students, use of simulations facilitated the acquisition of conceptual knowledge. It was concluded that three-dimensional simulations are more effective for younger students who lack the experience of learning with different visual representation formats in chemistry. In all three studies, a significant relationship between spatial ability and conceptual knowledge about the modifications of carbon was detected.
A three-dimensional view of the thermal structure in a super-penumbral canopy
Energy Technology Data Exchange (ETDEWEB)
Beck, C. [National Solar Observatory (NSO), 3010 Coronal Loop, Sunspot, NM 88349 (United States); Choudhary, D. P. [Department of Physics and Astronomy, California State University, Northridge (CSUN), CA 91330-8268 (United States); Rezaei, R., E-mail: cbeck@nso.edu [Kiepenheuer Institut für Sonnenphysik (KIS), Schöneckstrasse 6, D-79104 Freiburg (Germany)
2014-06-20
We investigate the three-dimensional (3D) thermal topology in a super-penumbral canopy of an active region (AR). We derive temperature stratifications in the AR by an inversion of the Ca II IR line at 854.2 nm, assuming local thermal equilibrium. We find that about half of the radially oriented fibrils in the super-penumbral canopy form short, low-lying (h < 1 Mm) loops in the 3D temperature cube. These closed loops connect from bright grains in or close to the penumbra to the photosphere a few Mms away from the sunspot. The other half of the fibrils monotonically rise with distance from the sunspot. Many of the fibrils show a central dark core and two lateral brightenings in line-core intensity images. The corresponding velocity image shows fibrils that are as wide as the fibrils seen in intensity without a lateral substructure. Additionally, we study a feature from a different class of structures without prominent mass flows. Its 3D topology is formed by two parallel, closed loops that connect patches of opposite polarity. We present evidence that the inverse Evershed flow into the sunspot in the lower chromosphere is the consequence of siphon flows along short loops that connect photospheric foot points. The dark-cored structure of the chromospheric fibrils cannot have a convective origin because of their location above regular granulation. The dark core most likely results from an opacity difference between the central axis and the lateral edges caused by the significant flow speed along the fibrils.
International Nuclear Information System (INIS)
Rao, S.I.; Dimiduk, D.M.; Parthasarathy, T.A.; Uchic, M.D.; Tang, M.; Woodward, C.
2008-01-01
Recent experimental studies have revealed that micrometer-scale face-centered cubic (fcc) crystals show strong strengthening effects, even at high initial dislocation densities. We use large-scale three-dimensional discrete dislocation simulations (DDS) to explicitly model the deformation behavior of fcc Ni microcrystals in the size range of 0.5-20 μm. This study shows that two size-sensitive athermal hardening processes, beyond forest hardening, are sufficient to develop the dimensional scaling of the flow stress, stochastic stress variation, flow intermittency and high initial strain-hardening rates, similar to experimental observations for various materials. One mechanism, source-truncation hardening, is especially potent in micrometer-scale volumes. A second mechanism, termed exhaustion hardening, results from a breakdown of the mean-field conditions for forest hardening in small volumes, thus biasing the statistics of ordinary dislocation processes
Unsteady three-dimensional flow of Casson–Carreau fluids past a stretching surface
Directory of Open Access Journals (Sweden)
C.S.K. Raju
2016-06-01
Full Text Available In this study, we investigated the effects of nonlinear thermal radiation and non-uniform heat source/sink in unsteady three-dimensional flow of Carreau and Casson fluids past a stretching surface in the presence of homogeneous–heterogeneous reactions. The transformed governing equations are solved numerically using Runge–Kutta based shooting technique. We obtained good accuracy of the present results by comparing with the already published literature. The influence of dimensionless governing parameters on velocity, temperature and concentration profiles along with the friction factors, local Nusselt and Sherwood numbers is discussed and presented graphically. We presented dual solutions for flow, heat and mass transfer in Carreau and Casson fluids. It is found that the heat and mass transfer rate in Casson fluid is significantly high while compared with the Carreau fluid.
Hayat, Tasawar; Ayub, Tayyaba; Muhammad, Taseer; Alsaedi, Ahmed
Here three dimensional (3D) flow of second grade fluid has been studied in the presence of Cattaneo-Christov double diffusion and heterogeneous-homogeneous reactions. Flow is bounded by a bidirectional linear stretchable surface. Generalized versions of Fourier's and Fick's law through Cattaneo-Christov double diffusion are employed. Equal diffusion coefficients are considered for both autocatalyst and reactants. The conversion of partial differential system to nonlinear ordinary differential system has been done by employing appropriate transformations. The obtained nonlinear systems have been solved through the optimal homotopy analysis method (OHAM). Graphs have been displayed in order to examine how the velocities, temperature and concentration fields are affected by various pertinent parameters. Moreover the skin friction coefficients and heat and mass transfer rates have been computed and analyzed.
User's manual for three-dimensional analysis of propeller flow fields
Chaussee, D. S.; Kutler, P.
1983-01-01
A detailed operating manual is presented for the prop-fan computer code (in addition to supporting programs) recently developed by Kutler, Chaussee, Sorenson, and Pulliam while at the NASA'S Ames Research Center. This code solves the inviscid Euler equations using an implicit numerical procedure developed by Beam and Warming of Ames. A description of the underlying theory, numerical techniques, and boundary conditions with equations, formulas, and methods for the mesh generation program (MGP), three dimensional prop-fan flow field program (3DPFP), and data reduction program (DRP) is provided, together with complete operating instructions. In addition, a programmer's manual is also provided to assist the user interested in modifying the codes. Included in the programmer's manual for each program is a description of the input and output variables, flow charts, program listings, sample input and output data, and operating hints.
Advanced numerical methods for three dimensional two-phase flow calculations
Energy Technology Data Exchange (ETDEWEB)
Toumi, I. [Laboratoire d`Etudes Thermiques des Reacteurs, Gif sur Yvette (France); Caruge, D. [Institut de Protection et de Surete Nucleaire, Fontenay aux Roses (France)
1997-07-01
This paper is devoted to new numerical methods developed for both one and three dimensional two-phase flow calculations. These methods are finite volume numerical methods and are based on the use of Approximate Riemann Solvers concepts to define convective fluxes versus mean cell quantities. The first part of the paper presents the numerical method for a one dimensional hyperbolic two-fluid model including differential terms as added mass and interface pressure. This numerical solution scheme makes use of the Riemann problem solution to define backward and forward differencing to approximate spatial derivatives. The construction of this approximate Riemann solver uses an extension of Roe`s method that has been successfully used to solve gas dynamic equations. As far as the two-fluid model is hyperbolic, this numerical method seems very efficient for the numerical solution of two-phase flow problems. The scheme was applied both to shock tube problems and to standard tests for two-fluid computer codes. The second part describes the numerical method in the three dimensional case. The authors discuss also some improvements performed to obtain a fully implicit solution method that provides fast running steady state calculations. Such a scheme is not implemented in a thermal-hydraulic computer code devoted to 3-D steady-state and transient computations. Some results obtained for Pressurised Water Reactors concerning upper plenum calculations and a steady state flow in the core with rod bow effect evaluation are presented. In practice these new numerical methods have proved to be stable on non staggered grids and capable of generating accurate non oscillating solutions for two-phase flow calculations.
Parallel Simulation of Three-Dimensional Free Surface Fluid Flow Problems
International Nuclear Information System (INIS)
BAER, THOMAS A.; SACKINGER, PHILIP A.; SUBIA, SAMUEL R.
1999-01-01
Simulation of viscous three-dimensional fluid flow typically involves a large number of unknowns. When free surfaces are included, the number of unknowns increases dramatically. Consequently, this class of problem is an obvious application of parallel high performance computing. We describe parallel computation of viscous, incompressible, free surface, Newtonian fluid flow problems that include dynamic contact fines. The Galerkin finite element method was used to discretize the fully-coupled governing conservation equations and a ''pseudo-solid'' mesh mapping approach was used to determine the shape of the free surface. In this approach, the finite element mesh is allowed to deform to satisfy quasi-static solid mechanics equations subject to geometric or kinematic constraints on the boundaries. As a result, nodal displacements must be included in the set of unknowns. Other issues discussed are the proper constraints appearing along the dynamic contact line in three dimensions. Issues affecting efficient parallel simulations include problem decomposition to equally distribute computational work among a SPMD computer and determination of robust, scalable preconditioners for the distributed matrix systems that must be solved. Solution continuation strategies important for serial simulations have an enhanced relevance in a parallel coquting environment due to the difficulty of solving large scale systems. Parallel computations will be demonstrated on an example taken from the coating flow industry: flow in the vicinity of a slot coater edge. This is a three dimensional free surface problem possessing a contact line that advances at the web speed in one region but transitions to static behavior in another region. As such, a significant fraction of the computational time is devoted to processing boundary data. Discussion focuses on parallel speed ups for fixed problem size, a class of problems of immediate practical importance
DNA Structure and Stability Tutorial: Interactive animations of the DNA three-dimensional structure
Directory of Open Access Journals (Sweden)
Larissa Assis Barony Valadares Fonseca
2017-10-01
Full Text Available The tutorial "DNA Structure and Stability" was developed articulating Ausubel's Theory of Meaningful Learning and Mayer's Multimedia principles, in order to favor the DNA structure significant learning through the guided and gradual exploration of the DNA three-dimensional structure interactive animations. In this sense, conceptual units with auxiliary medias have been established, such as texts, diagrams and tables, which assist in the explanation of animations. Several chemical and biochemical concepts are explained in order to favor understanding of DNA as a biopolymer determined by its intra/intermolecular chemical interactions that consequently establish the structure/stability relationships and structure/biological activity. In this way, was developed an interactive tutorial that can be used in several teaching and learning situations in order to favor the construction of knowledge by the learner.
Controlled Ag electroless deposition in bulk structures with complex three-dimensional profiles
DEFF Research Database (Denmark)
Malureanu, Radu; Zalkovskij, Maksim; Andryieuski, Andrei
2010-01-01
In this work we show the possibility of controlled deposition of a nanometer-sized silver layer on three-dimensional 3D structures. The deposition takes place in liquid environment, allowing for an easy and fast processing with intrinsically isotropic characteristics. The obtained layers...
DEFF Research Database (Denmark)
Yoon, Gil Ho; Joung, Young Soo; Kim, Yoon Young
2005-01-01
The topology design optimization of “three-dimensional geometrically-nonlinear” continuum structures is still a difficult problem not only because of its problem size but also the occurrence of unstable continuum finite elements during the design optimization. To overcome this difficulty, the ele...
Boekema, Egbert J.; Heel, Marin G. van; Bruggen, Ernst F.J. van
1984-01-01
We have studied the structure of bovine heart mitochondrial NADH:ubiquinone (Q) oxidoreductase (EC 1.6.99.3) by image analysis of electron micrographs. A three-dimensional reconstruction was calculated from a tilt-series of a two-dimensional crystal of the molecule. Our interpretation of the
Selective SiO2 etching in three dimensional structures using parylene-C as mask
Veltkamp, Henk-Willem; Zhao, Yiyuan; de Boer, Meint J.; Wiegerink, Remco J.; Lötters, Joost Conrad
2017-01-01
This abstract describes an application of an easy and straightforward method for selective SiO2 etching in three dimensional structures, which is developed by our group. The application in this abstract is the protection of the buried-oxide (BOX) layer of a silicon-on-insulator (SOI) wafer against
Krabbenborg, B.H.; Krabbenborg, B.H.; Bosma, A.; de Graaff, H.C.; de Graaff, H.C.; Mouthaan, A.J.
1996-01-01
In this paper, a method is proposed for extraction of coupled networks from layout information for simulation of electrothermal device behavior. The networks represent a three-dimensional (3-D) device structure with circuit elements. The electrical and thermal characteristics of this circuit
Multi-GPU three dimensional Stokes solver for simulating glacier flow
Licul, Aleksandar; Herman, Frédéric; Podladchikov, Yuri; Räss, Ludovic; Omlin, Samuel
2016-04-01
Here we present how we have recently developed a three-dimensional Stokes solver on the GPUs and apply it to a glacier flow. We numerically solve the Stokes momentum balance equations together with the incompressibility equation, while also taking into account strong nonlinearities for ice rheology. We have developed a fully three-dimensional numerical MATLAB application based on an iterative finite difference scheme with preconditioning of residuals. Differential equations are discretized on a regular staggered grid. We have ported it to C-CUDA to run it on GPU's in parallel, using MPI. We demonstrate the accuracy and efficiency of our developed model by manufactured analytical solution test for three-dimensional Stokes ice sheet models (Leng et al.,2013) and by comparison with other well-established ice sheet models on diagnostic ISMIP-HOM benchmark experiments (Pattyn et al., 2008). The results show that our developed model is capable to accurately and efficiently solve Stokes system of equations in a variety of different test scenarios, while preserving good parallel efficiency on up to 80 GPU's. For example, in 3D test scenarios with 250000 grid points our solver converges in around 3 minutes for single precision computations and around 10 minutes for double precision computations. We have also optimized the developed code to efficiently run on our newly acquired state-of-the-art GPU cluster octopus. This allows us to solve our problem on more than 20 million grid points, by just increasing the number of GPU used, while keeping the computation time the same. In future work we will apply our solver to real world applications and implement the free surface evolution capabilities. REFERENCES Leng,W.,Ju,L.,Gunzburger,M. & Price,S., 2013. Manufactured solutions and the verification of three-dimensional stokes ice-sheet models. Cryosphere 7,19-29. Pattyn, F., Perichon, L., Aschwanden, A., Breuer, B., de Smedt, B., Gagliardini, O., Gudmundsson,G.H., Hindmarsh, R
Software Package \\Nesvetay-3D" for modeling three-dimensional flows of monatomic rarefied gas
Directory of Open Access Journals (Sweden)
V. A. Titarev
2014-01-01
Full Text Available Analysis of three-dimensional rarefied gas flowsin microdevices (micropipes, micropumps etc and over re-entry vehicles requires development of methods of computational modelling. One of such methods is the direct numerical solution of the Boltzmann kinetic equation for the velocity distribution function with either exact or approximate (model collision integral. At present, for flows of monatomic rarefied gas the Shakhov model kinetic equation, also called S-model, has gained wide-spread use. The equation can be regarded as a model equation of the incomplete thirdorder approximation. Despite its relative simplicity, the S-model is still a complicated integrodifferential equation of high dimension. The numerical solution of such an equation requires high-accuracy parallel methods.The present work is a review of recent results concerning the development and application of three-dimensional computer package Nesvetay-3D intended for modelling of rarefied gas flows. The package solves Boltzmann kinetic equation with the BGK (Krook and Shakhov model collision integrals using the discrete velocity approach. Calculations are carried out in non-dimensional variables. A finite integration domain and a mesh are introduced in the molecular velocity space. Next, the kinetic equation is re-written as a system of kinetic equations for each of the discrete velocities. The system is solved using an implicit finite-volume method of Godunov type. The steady-state solution is computed by a time marching method. High order of spatial accuracy is achieved by using a piece-wise linear representation of the distribution function in each spatial cell. In general, the coefficients of such an approximation are found using the least-square method. Arbitrary unstructured meshes in the physical space can be used in calculations, which allow considering flows over objects of general geometrical shape. Conservative property of the method with respect to the model collision
Directory of Open Access Journals (Sweden)
Jean-Paul Kone
2017-03-01
Full Text Available A review of published three-dimensional, computational fluid dynamics models for proton exchange membrane fuel cells that accounts for multiphase flow is presented. The models can be categorized as models for transport phenomena, geometry or operating condition effects, and thermal effects. The influences of heat and water management on the fuel cell performance have been repeatedly addressed, and these still remain two central issues in proton exchange membrane fuel cell technology. The strengths and weaknesses of the models, the modelling assumptions, and the model validation are discussed. The salient numerical features of the models are examined, and an overview of the most commonly used computational fluid dynamic codes for the numerical modelling of proton exchange membrane fuel cells is given. Comprehensive three-dimensional multiphase flow computational fluid dynamic models accounting for the major transport phenomena inside a complete cell have been developed. However, it has been noted that more research is required to develop models that include among other things, the detailed composition and structure of the catalyst layers, the effects of water droplets movement in the gas flow channels, the consideration of phase change in both the anode and the cathode sides of the fuel cell, and dissolved water transport.
Jayendiran, R; Nour, B M; Ruimi, A
2018-02-01
Aortic dissection (AD) is a serious medical condition characterized by a tear in the intima, the inner layer of the aortic walls. In such occurrence, blood is being diverted to the media (middle) layer and may result in patient death if not quickly attended. In the case where the diseased portion of the aorta needs to be replaced, one common surgical technique is to use a graft made of Dacron, a synthetic fabric. We investigate the response of a composite human aortic segment-Dacron graft structure subjected to blood flow using the three-dimensional fluid-structure-interaction (FSI) capability in Abaqus. We obtain stress and strain profiles in each of the three layers of the aortic walls as well as in the Dacron graft. Results are compared when elastic and hyperelastic models are used and when isotropy vs. anisotropy is assumed. The more complex case (hyperelastic-anisotropy) is represented by the Holzapfel-Gasser-Ogden (HGO) model which also accounts for the orientation of the fibers present in the tissues. The fluid flow is taken as Newtonian, incompressible, pulsatile and turbulent. The simulation show that for all the cases, the von Mises stress distribution at aorta-Dacron interface is well below the ultimate strength of the aorta. No significant change in radial displacement at the interface of the two materials due to blood flow is observed. Computation cost is also addressed and results show that the hyperelastic-anisotropic model takes about three times longer to run than the elastic isotropic case. Trade-off between accuracy and computational cost has to be weighted. Copyright © 2017 Elsevier Ltd. All rights reserved.
Tellez Alvarez, Jackson David; Redondo, Jose Manuel; Sanchez, Jesu Mary
2016-04-01
fresh water in order to form density interfaces. The Reynolds number can be reduced adding Glicerine the set of dimensionless parameters define different conditions of both numeric and small scale laboratory applied often in modeling environmental flows. Fields of velocity, density and their gradients are computed using advanced visualization [8 9]. Visualizations are performed by PIV, Particle tracking and shadowgraph. When convective heating and cooling takes place the patterns depend on the parameter space region of the initial conditions We also map the different transitions between two and three dimensional convection in an enclosure with several complex driven flows. The size of the water tank is of 0.2 x 0.2 x 0.1 m and the heat sources or sinks can be regulated both in power and sign [2-4]. The thermal convective driven flows are generated by Seebeck and Peltier effects in 4 wall extended positions of 0.05 x 0.05 cm each. The parameter range of convective cell array varies strongly with the Topology of the boundary conditions. At present side heat fluxes are considered and estimated as a function of Rayleigh, Peclet and Nusselt numbers, [4-6] The evolution of the mixing fronts are compared and the topological characteristics of the merging of plumes and jets in different configurations presenting detailed comparison of the evolution of RM and RT, Jets and Plumes in overall mixing. The relation between structure functions, fractal analysis and spectral analysis can be very useful to determine the evolution of scales. Experimental and numerical results on the advance of a mixing or non-mixing front occurring at a density interface due to body forces [12] can be compared with the convective fronts. The evolution of the turbulent mixing layer and its complex configuration is studied taking into account the dependence on the initial modes at the early stages, Self-similar information [13]. Spectral and Fractal analysis on the images seems very useful in order to
Development of Three-Dimensional Dental Scanning Apparatus Using Structured Illumination
Ahn, Jae Sung; Park, Anjin; Kim, Ju Wan; Lee, Byeong Ha; Eom, Joo Beom
2017-01-01
We demonstrated a three-dimensional (3D) dental scanning apparatus based on structured illumination. A liquid lens was used for tuning focus and a piezomotor stage was used for the shift of structured light. A simple algorithm, which detects intensity modulation, was used to perform optical sectioning with structured illumination. We reconstructed a 3D point cloud, which represents the 3D coordinates of the digitized surface of a dental gypsum cast by piling up sectioned images. We performed ...
McBride, D.; Cross, M.; Croft, N.; Bennett, C.; Gebhardt, J.
2006-03-01
A computational procedure is presented for solving complex variably saturated flows in porous media, that may easily be implemented into existing conventional finite-volume-based computational fluid dynamics codes, so that their functionality might be geared upon to readily enable the modelling of a complex suite of interacting fluid, thermal and chemical reaction process physics. This procedure has been integrated within a multi-physics finite volume unstructured mesh framework, allowing arbitrarily complex three-dimensional geometries to be modelled. The model is particularly targeted at ore heap-leaching processes, which encounter complex flow problems, such as infiltration into dry soil, drainage, perched water tables and flow through heterogeneous materials, but is equally applicable to any process involving flow through porous media, such as in environmental recovery processes. The computational procedure is based on the mixed form of the classical Richards equation, employing an adaptive transformed mixed algorithm that is numerically robust and significantly reduces compute (or CPU) time. The computational procedure is accurate (compares well with other methods and analytical data), comprehensive (representing any kind of porous flow model), and is computationally efficient. As such, this procedure provides a suitable basis for the implementation of large-scale industrial heap-leach models.
Suzuki, Yoshiyuki
2004-12-01
Detection of natural selection operating at the amino acid sequence level is important in the study of molecular evolution. Single-site analysis and one-dimensional window analysis can be used to detect selection when the biological functions of amino acid sites are unknown. Single-site analysis is useful when selection operates more or less constantly over evolutionary time, but less so when selection operates temporarily. One-dimensional window analysis is more sensitive than single-site analysis when the functions of amino acid sites in close proximity in the linear sequence are similar, although this is not always the case. Here I present a three-dimensional window analysis method for detecting selection given the three-dimensional structure of the protein of interest. In the three-dimensional structure, the window is defined as the sphere centered on the alpha-carbon of an amino acid site. The window size is the radius of the sphere. The sites whose alpha-carbons are included in the window are grouped for the neutrality test. The window is moved within the three-dimensional structure by sequentially moving the central site along the primary amino acid sequence. To detect positive selection, it may also be useful to group the surface-exposed sites in the window separately. Three-dimensional window analysis appears not only to be more sensitive than single-site analysis and one-dimensional window analysis but also to provide similar specificity for inferring positive selection in the analyses of the hemagglutinin and neuraminidase genes of human influenza A viruses. This method, however, may fail to detect selection when it operates only on a particular site, in which case single-site analysis may be preferred, although a large number of sequences is required.
Three dimensional boundary layer flow of a viscoelastic nanofluid with Soret and Dufour effects
Directory of Open Access Journals (Sweden)
M. Ramzan
2016-03-01
Full Text Available The present research focuses on the three-dimensional flow of viscoelastic fluid in the presence of Soret and Dufour effects. Effects of thermophoresis and Brownian motion are taken into account. Appropriate similarity transformations lead to nonlinear ordinary differential equations. Solution expressions of velocity, temperature and nanoparticle concentration are computed via homotopy analysis method (HAM. Convergence of obtained solutions is analyzed graphically and numerically. Results are plotted and analyzed for the dimensionless velocities, temperature and nanoparticle concentration. Values of local Nusselt and Sherwood numbers are examined through tabular form. It is observed that Temperature field is enhanced for the larger Brownian motion parameter and an increase in Dufour number gives rise to the temperature and thermal boundary layer thickness.
Free convection nanofluid flow in the stagnation-point region of a three-dimensional body.
Farooq, Umer; Xu, Hang
2014-01-01
Analytical results are presented for a steady three-dimensional free convection flow in the stagnation point region over a general curved isothermal surface placed in a nanofluid. The momentum equations in x- and y-directions, energy balance equation, and nanoparticle concentration equation are reduced to a set of four fully coupled nonlinear differential equations under appropriate similarity transformations. The well known technique optimal homotopy analysis method (OHAM) is used to obtain the exact solution explicitly, whose convergence is then checked in detail. Besides, the effects of the physical parameters, such as the Lewis number, the Brownian motion parameter, the thermophoresis parameter, and the buoyancy ratio on the profiles of velocities, temperature, and concentration, are studied and discussed. Furthermore the local skin friction coefficients in x- and y-directions, the local Nusselt number, and the local Sherwood number are examined for various values of the physical parameters.
International Nuclear Information System (INIS)
Graf, U.
1986-01-01
A combination of several numerical methods is used to construct a procedure for effective calculation of complex three-dimensional fluid flow problems. The split coefficient matrix (SCM) method is used so that the differenced equations of the hyperbolic system do not disturb correct signal propagation. The semi-discretisation of the equations of the SCM method is done with the asymmetric, separated region, weighted residual (ASWR) method to give accurate solutions on a relatively coarse mesh. For the resulting system of ordinary differential equations, a general-purpose ordinary differential equation solver is used in conjunction with a method of fractional steps for an economic solution of the large system of linear equations. (orig.) [de
Mixing in three-dimensional turbulent flow near the river confluence
Lyubimova, T.; Lepikhin, A.; Konovalov, V.; Parshakova, Ya.; Tiunov, A.
2012-04-01
Main source of potable water for Perm city having about one million inhabitants is Chusovaya water intake located in the immediate vicinity of the confluence of Chusovaya and Sylva rivers. These rivers are similar in water content but significantly different in hydrochemical regime: the water of Sylva river is characterized by high hardness and the hardness of Chusovaya river is much lower. Since the hardness is an important indicator of water quality, there arises the goal to organize the water intake in such a way that water was characterized by minimal hardness. The solution to this problem in the discussed case is complicated due to the fact that the water intake is located in the zone of hydraulic backwater of the Kama hydroelectric power station and the hydrodynamic regime in this zone depends not only on the cumulative effect of hydrological regimes of Chusovaya and Sylva rivers but also on the filling level of the Kama water reservoir and on the reset mode on the Kama hydroelectric power station. From the viewpoint of ensuring the standard water quality, the dynamics of water hardness in the considered rivers and its dependence on the water flow rates is of the fundamental importance. This is especially significant for low flow rates typical for winter seasons. For large flow velocities and small differences in mineralization, one could expect sufficient homogeneity of water composition in depth due to intense vertical mixing. And in winter season, at low flow velocities and significant differences in mineralization, considerable vertical inhomogeneity of water composition may arise. Experimental measurements show that, in winter low flow season, specific electric conductivity and, consequently, mineralization and hardness of the water near the bottom several times larger than their values near the surface. To study the formation of vertical stratification in different conditions, numerical simulation of mixing in three-dimensional turbulent flows for the
Finite analytic numerical method for three-dimensional fluid flow in heterogeneous porous media
Wang, Yan-Feng; Liu, Zhi-Feng; Wang, Xiao-Hong
2014-12-01
Understanding fluid flows in heterogeneous porous media is fundamental to applied geosciences. The wide connectivity variations in the natural aquifer or oil reservoirs make the equivalent permeability have strong spatial variations. When performing the simulations for subsurface flows, the permeabilities may have strong discontinuities across the interfaces between different grid cells. Utilizing the traditional numerical schemes to simulate flows in strong heterogeneous media, the refinement ratio for the grid cell needs to increase dramatically to get an accurate result. Recently, we proposed a finite analytic numerical scheme to solve the two-dimensional fluid flows in heterogeneous porous media. With only 2 × 2 or 3 × 3 subdivisions, this scheme can provide rather accurate solutions. In this paper, we develop the finite analytic numerical method for solving the three-dimensional fluid flows in heterogeneous porous media. For the rectangular grid system, it is generally proposed that the pressure gradient in a plane normal to the edge joining different permeability regions will tend to infinite as approaching the edge according to a typical power-law solution and the tangential derivate of the pressure along the edge must be of limited value due to the pressure continuity. Consequently, the three-dimensional flow will reduce to the two-dimensional one in the neighborhood around each edge. Such quasi-two-dimensional behavior is then applied to construct a finite analytic numerical scheme. Numerical examples show that the proposed scheme can provide rather accurate solutions with only 2 × 2 × 2 or 3 × 3 × 3 subdivisions and the convergent speed is independent of the permeability heterogeneity. Due to its high calculation efficiency, the proposed scheme is utilized to test the well known LLM (Landau, Lifshitz and Matheron) conjecture, which provides keq /kG = exp (1/6σlnk2) for the isotropic log-normal porous medium. The numerical results do not
Three-dimensional detonation cellular structures in rectangular ducts using an improved CESE scheme
Shen, Yang
2016-11-01
The three-dimensional premixed H2-O2 detonation propagation in rectangular ducts is simulated using an in-house parallel detonation code based on the second-order space–time conservation element and solution element (CE/SE) scheme. The simulation reproduces three typical cellular structures by setting appropriate cross-sectional size and initial perturbation in square tubes. As the cross-sectional size decreases, critical cellular structures transforming the rectangular or diagonal mode into the spinning mode are obtained and discussed in the perspective of phase variation as well as decreasing of triple point lines. Furthermore, multiple cellular structures are observed through examples with typical aspect ratios. Utilizing the visualization of detailed three-dimensional structures, their formation mechanism is further analyzed.
Directory of Open Access Journals (Sweden)
Dilovan S. Cati
2017-05-01
Full Text Available The complete molecules of the title compounds, N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (I, 3,6-dimethyl-N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C20H20N6O2 (II, and N2,N5-bis(pyridin-4-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (III, are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each molecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7° in (I, 75.83 (8° in (II and by 82.71 (6° in (III. In the crystal of (I, molecules are linked by N—H...N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (II, molecules are also linked by N—H...N hydrogen bonds, forming layers lying parallel to the (10-1 plane. As in (I, the layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (III, molecules are again linked by N—H...N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π–π interactions [intercentroid distance = 3.739 (1 Å]. The sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. Compound (I crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008, 11, 1–4]. The molecular structures of the two polymorphs are compared.
Effective Rheology of Two-Phase Flow in Three-Dimensional Porous Media: Experiment and Simulation.
Sinha, Santanu; Bender, Andrew T; Danczyk, Matthew; Keepseagle, Kayla; Prather, Cody A; Bray, Joshua M; Thrane, Linn W; Seymour, Joseph D; Codd, Sarah L; Hansen, Alex
2017-01-01
We present an experimental and numerical study of immiscible two-phase flow of Newtonian fluids in three-dimensional (3D) porous media to find the relationship between the volumetric flow rate ( Q ) and the total pressure difference ([Formula: see text]) in the steady state. We show that in the regime where capillary forces compete with the viscous forces, the distribution of capillary barriers at the interfaces effectively creates a yield threshold ([Formula: see text]), making the fluids reminiscent of a Bingham viscoplastic fluid in the porous medium. In this regime, Q depends quadratically on an excess pressure drop ([Formula: see text]). While increasing the flow rate, there is a transition, beyond which the overall flow is Newtonian and the relationship is linear. In our experiments, we build a model porous medium using a column of glass beads transporting two fluids, deionized water and air. For the numerical study, reconstructed 3D pore networks from real core samples are considered and the transport of wetting and non-wetting fluids through the network is modeled by tracking the fluid interfaces with time. We find agreement between our numerical and experimental results. Our results match with the mean-field results reported earlier.
Conservation of the three-dimensional structure in non-homologous or unrelated proteins
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Sousounis Konstantinos
2012-08-01
Full Text Available Abstract In this review, we examine examples of conservation of protein structural motifs in unrelated or non-homologous proteins. For this, we have selected three DNA-binding motifs: the histone fold, the helix-turn-helix motif, and the zinc finger, as well as the globin-like fold. We show that indeed similar structures exist in unrelated proteins, strengthening the concept that three-dimensional conservation might be more important than the primary amino acid sequence.
Three-dimensional pore structure and ion conductivity of porous ceramic diaphragms
Wiedenmann, Daniel; Keller, Lukas; Holzer, Lorenz; Stojadinović, Jelena; Münch, Beat; Suarez, Laura; Fumey, Benjamin; Hagendorfer, Harald; Brönnimann, Rolf; Modregger, Peter; Gorbar, Michal; Vogt, Ulrich F.; Züttel, Andreas; Mantia, Fabio La; Wepf, Roger
2013-01-01
The ion conductivity of two series of porous ceramic diaphragms impregnated with caustic potash was investigated by electrochemical impedance spectroscopy. To understand the impact of the pore structure on ion conductivity, the three-dimensional (3-D) pore geometry of the diaphragms was characterized with synchrotron x-ray absorption tomography. Ion migration was calculated based on an extended pore structure model, which includes the electrolyte conductivity and geometric pore parameters, fo...
A Three-Dimensional Enormous Surface Area Aluminum Microneedle Array with Nanoporous Structure
Chen, Po Chun; Hsieh, Sheng Jen; Chen, Chien Chon; Zou, Jun
2013-01-01
We proposed fabricating an aluminum microneedle array with a nanochannel structure on the surface by combining micromachining, electrolyte polishing, and anodization methods. The microneedle array provides a three-dimensional (3D) structure that possesses several hundred times more surface area than a traditional nanochannel template. Therefore, the microneedle array can potentially be used in many technology applications. This 3D microneedle array device can not only be used for painless inj...
Energy Technology Data Exchange (ETDEWEB)
Aizenberg, Joanna; Burgess, Ian; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko
2017-12-26
A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.
Optical Fiber/Nanowire Hybrid Structures for Efficient Three-Dimensional Dye-Sensitized Solar Cells
Weintraub, Benjamin
2009-11-09
Wired up: The energy conversion efficiency of three-dimensional dye-sensitized solar cells (DSSCs) in a hybrid structure that integrates optical fibers and nanowire arrays is greater than that of a two-dimensional device. Internal axial illumination enhances the energy conversion efficiency of a rectangular fiber-based hybrid structure (see picture) by a factor of up to six compared to light illumination normal to the fiber axis from outside the device.
Gyger, Cyrill; Cattin, Roger; Hasler, Pascal W.; Maloca, Peter
2014-07-01
Optical coherence tomography (OCT) is a high-resolution noninvasive technology used in medical imaging for the spatial visualization of biological tissue. Due to its coherent nature, OCT suffers from speckle noise, which significantly degrades the information content of resulting scans. We introduce a new filtering method for three-dimensional OCT images, inspired by film grain removal techniques. By matching structural relatedness along all dimensions, the algorithm builds up vector paths for every voxel in the image volume representing its structural neighborhood. Then, by considering the information redundancy along these paths, our filter is able to reduce speckle noise significantly while simultaneously preserving structural information. This filter exceeds some common three-dimensional denoising algorithms used for OCT images, both in visual rendering quality and in measurable noise reduction. The noise-reduced results allow for improvement in subsequent processing steps, such as image segmentation.
Energy Technology Data Exchange (ETDEWEB)
Salah, Anis Bousbia; Vlassenbroeck, Jacques [Bel V - Subsidiary of the Belgian Federal Agency for Nuclear Contro, Brussels (Belize)
2017-04-15
Coolant mixing under natural circulation flow regime constitutes a key parameter that may play a role in the course of an accidental transient in a nuclear pressurized water reactor. This issue has motivated some experimental investigations carried out within the OECD/NEA PKL projects. The aim was to assess the coolant mixing phenomenon in the reactor pressure vessel downcomer and the core lower plenum under several asymmetric steady and unsteady flow conditions, and to provide experimental data for code validations. Former studies addressed the mixing phenomenon using, on the one hand, one-dimensional computational approaches with cross flows that are not fully validated under transient conditions and, on the other hand, expensive computational fluid dynamic tools that are not always justified for large-scale macroscopic phenomena. In the current framework, an unsteady coolant mixing experiment carried out in the Rossendorf coolant mixing test facility is simulated using the three-dimensional porous media capabilities of the thermal–hydraulic system CATHARE code. The current study allows highlighting the current capabilities of these codes and their suitability for reproducing the main phenomena occurring during asymmetric transient natural circulation mixing conditions.
Numerical three-dimensional turbulent flow analysis trough a pump-turbine in the turbine modes
International Nuclear Information System (INIS)
Cvetkovski, Zlatko; Popovski, Predrag; Markov, Zoran; Lipej, Andrej
2004-01-01
During the design of a new or rehabilitated hydraulic machines, prediction of the performances is one of the most important step in development procedure. However, for re-design of old machines, a fast and reliable flow analyses tool is necessary for allocation of the 'bed geometry' condition. This work describes new computational approaches for modern re-design of a radial type single stage pump-turbine. A pump-turbine with specific speed ns = 89 was calculated, as an example of the applicability of this methodology. The simulation of three-dimensional turbulent flow through a Pump-Turbine impeller at turbine mode, as a part of the complete pump-turbine calculation [3] during the re-design procedure is presented. Four operational regimes were calculated based on the Computational Fluid Dynamics - CFD Methodology (Navier-Stokes equations and the k-e turbulent model). The mesh discretization, boundary conditions and calculated results are presented and the)) shall be useful for development, optimisation, refurbishment or rehabilitation projects, because the impeller behaviour can be a major criterion for increasing the performances of the Pump-Turbines. The complete flow field consists of spiral case, a channel between stator vanes, a channel between guide vanes, a channel between rotor vanes and complete draft tube. Two step calculations are applied. In the first step, calculation was performed for the spiral case and the stator. Second step of the calculations was performed for cascade, rotor and draft tube. (Author)
Directory of Open Access Journals (Sweden)
M. Ali Abbas
2016-03-01
Full Text Available In this present analysis, three dimensional peristaltic flow of hyperbolic tangent fluid in a non-uniform channel has been investigated. We have considered that the pressure is uniform over the whole cross section and the interial effects have been neglected. For this purpose we consider laminar flow under the assumptions of long wavelength (λ→∞ and creeping flow (Re→0 approximations. The attained highly nonlinear equations are solved with the help of Homotopy perturbation method. The influence of various physical parameters of interest is demonstrated graphically for wall tension, mass characterization, damping nature of the wall, wall rigidity, wall elastance, aspect ratio and the Weissenberg number. In this present investigation we found that the magnitude of the velocity is maximum in the center of the channel whereas it is minimum near the walls. Stream lines are also drawn to discuss the trapping mechanism for all the physical parameters. Comparison has also been presented between Newtonian and non-Newtonian fluid.
Directory of Open Access Journals (Sweden)
Qihua Zhang
Full Text Available Abstract To describe flow-induced fiber orientation, the Fokker-Planck equation is widely applied in the processing of composites and fiber suspensions. The analytical solution only exists when the Péclet number is infinite. So developing a numerical method covering a full range of Péclet number is of great significance. To accurately solve the Fokker-Planck equation, a numerical scheme based on the finite volume method is developed. Using spherical symmetry, the boundary is discretized and formulated into a cyclic tridiagonal matrix which is further solved by the CTDMA algorithm. To examine its validity, benchmark tests over a wide range of Péclet number are performed in a simple shear flow. For Pe=∞, the results agree well with the analytical solutions. For the other Pe numbers, the results are compared to results available in the literature. The tests show that this algorithm is accurate, stable, and globally conservative. Furthermore, this algorithm can be extended and used to predict the three-dimensional orientation distribution of complex suspension flows.
Computational strategies for three-dimensional flow simulations on distributed computer systems
Sankar, Lakshmi N.; Weed, Richard A.
1995-01-01
This research effort is directed towards an examination of issues involved in porting large computational fluid dynamics codes in use within the industry to a distributed computing environment. This effort addresses strategies for implementing the distributed computing in a device independent fashion and load balancing. A flow solver called TEAM presently in use at Lockheed Aeronautical Systems Company was acquired to start this effort. The following tasks were completed: (1) The TEAM code was ported to a number of distributed computing platforms including a cluster of HP workstations located in the School of Aerospace Engineering at Georgia Tech; a cluster of DEC Alpha Workstations in the Graphics visualization lab located at Georgia Tech; a cluster of SGI workstations located at NASA Ames Research Center; and an IBM SP-2 system located at NASA ARC. (2) A number of communication strategies were implemented. Specifically, the manager-worker strategy and the worker-worker strategy were tested. (3) A variety of load balancing strategies were investigated. Specifically, the static load balancing, task queue balancing and the Crutchfield algorithm were coded and evaluated. (4) The classical explicit Runge-Kutta scheme in the TEAM solver was replaced with an LU implicit scheme. And (5) the implicit TEAM-PVM solver was extensively validated through studies of unsteady transonic flow over an F-5 wing, undergoing combined bending and torsional motion. These investigations are documented in extensive detail in the dissertation, 'Computational Strategies for Three-Dimensional Flow Simulations on Distributed Computing Systems', enclosed as an appendix.
A three-dimensional model for thermal analysis in a vanadium flow battery
International Nuclear Information System (INIS)
Zheng, Qiong; Zhang, Huamin; Xing, Feng; Ma, Xiangkun; Li, Xianfeng; Ning, Guiling
2014-01-01
Highlights: • A three-dimensional model for thermal analysis in a VFB has been developed. • A quasi-static thermal behavior and temperature spatial distribution were showed. • Ohmic heat gets vital in heat generation if applied current density is large enough. • A lower porosity or a faster flow shows a more uniform temperature distribution. • The model shows good prospect in heat and temperature management for a VFB. - Abstract: A three-dimensional model for thermal analysis has been developed to gain a better understanding of thermal behavior in a vanadium flow battery (VFB). The model is based on a comprehensive description of mass, momentum, charge and energy transport and conservation, combining with a global kinetic model for reactions involving all vanadium species. The emphasis in this paper is placed on the heat losses inside a cell. A quasi-static behavior of temperature and the temperature spatial distribution were characterized via the thermal model. The simulations also indicate that the heat generation exhibits a strong dependence on the applied current density. The reaction rate and the over potential rise with an increased applied current density, resulting in the electrochemical reaction heat rises proportionally and the activation heat rises at a parabolic rate. Based on the Ohm’s law, the ohmic heat rises at a parabolic rate when the applied current density increases. As a result, the determining heat source varies when the applied current density changes. While the relative contribution of the three types of heat is dependent on the cell materials and cell geometry, the regularities of heat losses can also be attained via the model. In addition, the electrochemical reaction heat and activation heat have a lack of sensitivity to the porosity and flow rate, whereas an obvious increase of ohmic heat has been observed with the rise of the porosity. A lower porosity or a faster flow shows a better uniformity of temperature distribution in
Statistics of highly heterogeneous flow fields confined to three-dimensional random porous media
Jin, C.; Langston, P. A.; Pavlovskaya, G. E.; Hall, M. R.; Rigby, S. P.
2016-01-01
We present a strong relationship between the microstructural characteristics of, and the fluid velocity fields confined to, three-dimensional random porous materials. The relationship is revealed through simultaneously extracting correlation functions Ru u(r ) of the spatial (Eulerian) velocity fields and microstructural two-point correlation functions S2(r ) of the random porous heterogeneous materials. This demonstrates that the effective physical transport properties depend on the characteristics of complex pore structure owing to the relationship between Ru u(r ) and S2(r ) revealed in this study. Further, the mean excess plot was used to investigate the right tail of the streamwise velocity component that was found to obey light-tail distributions. Based on the mean excess plot, a generalized Pareto distribution can be used to approximate the positive streamwise velocity distribution.
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.
Cruz, José Almeida; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M; Chen, Shi-Jie; Cao, Song; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V; Flores, Samuel Coulbourn; Huang, Lili; Lavender, Christopher A; Lisi, Véronique; Major, François; Mikolajczak, Katarzyna; Patel, Dinshaw J; Philips, Anna; Puton, Tomasz; Santalucia, John; Sijenyi, Fredrick; Hermann, Thomas; Rother, Kristian; Rother, Magdalena; Serganov, Alexander; Skorupski, Marcin; Soltysinski, Tomasz; Sripakdeevong, Parin; Tuszynska, Irina; Weeks, Kevin M; Waldsich, Christina; Wildauer, Michael; Leontis, Neocles B; Westhof, Eric
2012-04-01
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.
Three-dimensional simulation of a solid-liquid flow by the DEM-SPH method
Sun, Xiaosong; Sakai, Mikio; Yamada, Yoshinori
2013-09-01
In this paper, we describe a new Lagrangian-Lagrangian algorithm, which is referred to be the DEM-SPH method, for solid-liquid flows involving free surfaces. The DEM solid phase and the SPH liquid phase are coupled using the local averaging technique described by Lagrangian approaches, where both the continuity equation and the interaction force, i.e. drag force, are connected with the local mean voidage. Conservative forms of momentum transformation are derived for the DEM-SPH interaction via a variational approach. By introducing a correction to the SPH approximation with explicit inclusion of boundary information, arbitrary boundaries can be modeled without any extra wall particles, where the boundary is used commonly for both DEM and SPH phases. We deploy level-set distance functions to efficiently construct and evaluate this boundary model. To examine the validity of the present method, we perform three-dimensional simulations of a dynamic flow in a solid-liquid dam break and a quasi-steady flow in a rotating cylindrical tank; and we conduct validation experiments to justify the simulation results. In the dam-break problem, positions of wave fronts during the collapse are computed and compared with experimental measurements; for the circulating tank, some macroscopic aspects of the steady flow, e.g. the shape, dimension and velocity profile of the solid bed, are obtained for validation data. In both cases, the simulation results are in good agreement with those of the experiment. Consequently, the DEM-SPH method is proved to be adequate in modeling solid-liquid flows through this study.
International Nuclear Information System (INIS)
Morisada, Y.; Fujii, H.; Kawahito, Y.; Nakata, K.; Tanaka, M.
2011-01-01
Material flow during friction stir welding is crucial to obtaining sound joints. However, this phenomenon is still not fully understood despite many investigations and numerous models. In this study, the material flow is three-dimensionally visualized by X-ray radiography using a tiny spherical tungsten tracer. The movement of the tracer during the friction stir welding is observed by two pairs of X-ray transmission real-time imaging systems. The three-dimensional material flow is obtained by following the locus of the tracer.
Three-dimensional instabilities for the flow around a heaving foil
Sun, Liping; Deng, Jian; Shao, Xueming
2018-01-01
This paper investigates the three-dimensional instabilities of the flow past a periodically heaving airfoil. By comparison with a pitching foil [Deng et al., Phys. Rev. E 92, 063013 (2015), 10.1103/PhysRevE.92.063013], here we present distinctive characteristics for the heaving foil, particulary regarding its Floquet modes. By increasing the frequency (Sr), or equivalently decreasing the amplitude (AD) along the marginal stability curve in the (Sr ,AD ) phase space, the critical Floquet mode emerges sequentially as A, quasiperiodic (QP), and B. It is interesting to note that both modes A and B are synchronous with the base flow, in contrast to the quasiperiodic mode QP. To further investigate the instability across the marginal curve, we fix the frequency at Sr =0.187 , of which the critical Floquet mode is located in the synchronous regime, while varying AD around the critical point. We find that the dominant mode switches from mode A to mode B, while mode QP never becomes critical as we increase AD. We note that mode S, a subharmonic mode, can also be unstable, which, however, is not physically realizable, because the magnitude of its Floquet multiplier is always smaller than that of mode B. We have also studied the influence of various Reynolds numbers at the same critical point on the marginal stability curve, with the results resembling that by varying the amplitude AD.
Three-dimensional features of GAM zonal flows in the HL-2A tokamak
International Nuclear Information System (INIS)
Yan, L.W.; Cheng, J.; Hong, W.Y.; Zhao, K.J.; Lan, T.; Dong, J.Q.; Liu, A.D.; Yu, C.X.; Yu, D.L.; Qian, J.; Huang, Y.; Yang, Q.W.; Ding, X.T.; Liu, Y.; Pan, C.H.
2007-01-01
A novel design of the three-step Langmuir probe (TSLP) array has been developed to investigate the zonal flow (ZF) physics in the HL-2A tokamak. Three TSLP arrays are applied to measure the three-dimensional (3D) features of ZFs. They are separated by 65 mm in the poloidal and 800 mm in the toroidal directions, respectively. The 3D properties of the geodesic acoustic mode (GAM) ZFs are presented. The poloidal and toroidal modes of the radial electric fields of the GAM perturbations are simultaneously determined in the HL-2A tokamak for the first time. The modes have narrow radial wave numbers (k r ρ i = 0.03-0.07) and short radial scale lengths (2.4-4.2 cm). High coherence of both the GAM and the ambient turbulence separated by toroidal 22.5 0 along a magnetic field line is observed, which contrasts with the high coherence of the GAM and the low coherence of the ambient turbulence apart from the field line. The nonlinear three wave coupling between the turbulent fluctuations and the ZFs is a plausible mechanism for flow generation. The skewness and kurtosis spectra of the probability distribution function of the potential perturbations are contrasted with the corresponding bicoherence for the first time, which support the three wave coupling mechanism
Hayat, Tasawar; Ashraf, Muhammad Bilal; Alsulami, Hamed H; Alhuthali, Muhammad Shahab
2014-01-01
The objective of present research is to examine the thermal radiation effect in three-dimensional mixed convection flow of viscoelastic fluid. The boundary layer analysis has been discussed for flow by an exponentially stretching surface with convective conditions. The resulting partial differential equations are reduced into a system of nonlinear ordinary differential equations using appropriate transformations. The series solutions are developed through a modern technique known as the homotopy analysis method. The convergent expressions of velocity components and temperature are derived. The solutions obtained are dependent on seven sundry parameters including the viscoelastic parameter, mixed convection parameter, ratio parameter, temperature exponent, Prandtl number, Biot number and radiation parameter. A systematic study is performed to analyze the impacts of these influential parameters on the velocity and temperature, the skin friction coefficients and the local Nusselt number. It is observed that mixed convection parameter in momentum and thermal boundary layers has opposite role. Thermal boundary layer is found to decrease when ratio parameter, Prandtl number and temperature exponent are increased. Local Nusselt number is increasing function of viscoelastic parameter and Biot number. Radiation parameter on the Nusselt number has opposite effects when compared with viscoelastic parameter.
An Incompressible Three-Dimensional Multiphase Particle-in-Cell Model for Dense Particle Flows
Snider, D. M.
2001-07-01
A three-dimensional, incompressible, multiphase particle-in-cell method is presented for dense particle flows. The numerical technique solves the governing equations of the fluid phase using a continuum model and those of the particle phase using a Lagrangian model. Difficulties associated with calculating interparticle interactions for dense particle flows with volume fractions above 5% have been eliminated by mapping particle properties to an Eulerian grid and then mapping back computed stress tensors to particle positions. A subgrid particle, normal stress model for discrete particles which is robust and eliminates the need for an implicit calculation of the particle normal stress on the grid is presented. Interpolation operators and their properties are defined which provide compact support, are conservative, and provide fast solution for a large particle population. The solution scheme allows for distributions of types, sizes, and density of particles, with no numerical diffusion from the Lagrangian particle calculations. Particles are implicitly coupled to the fluid phase, and the fluid momentum and pressure equations are implicitly solved, which gives a robust solution.
Three-dimensional density and compressible magnetic structure in solar wind turbulence
Roberts, Owen W.; Narita, Yasuhito; Escoubet, C.-Philippe
2018-03-01
The three-dimensional structure of both compressible and incompressible components of turbulence is investigated at proton characteristic scales in the solar wind. Measurements of the three-dimensional structure are typically difficult, since the majority of measurements are performed by a single spacecraft. However, the Cluster mission consisting of four spacecraft in a tetrahedral formation allows for a fully three-dimensional investigation of turbulence. Incompressible turbulence is investigated by using the three vector components of the magnetic field. Meanwhile compressible turbulence is investigated by considering the magnitude of the magnetic field as a proxy for the compressible fluctuations and electron density data deduced from spacecraft potential. Application of the multi-point signal resonator technique to intervals of fast and slow wind shows that both compressible and incompressible turbulence are anisotropic with respect to the mean magnetic field direction P⟂ ≫ P∥ and are sensitive to the value of the plasma beta (β; ratio of thermal to magnetic pressure) and the wind type. Moreover, the incompressible fluctuations of the fast and slow solar wind are revealed to be different with enhancements along the background magnetic field direction present in the fast wind intervals. The differences in the fast and slow wind and the implications for the presence of different wave modes in the plasma are discussed.
Three-dimensional magnetization structures revealed with X-ray vector nanotomography
Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Gliga, Sebastian; Holler, Mirko; Raabe, Jörg; Heyderman, Laura J.
2017-07-01
In soft ferromagnetic materials, the smoothly varying magnetization leads to the formation of fundamental patterns such as domains, vortices and domain walls. These have been studied extensively in thin films of thicknesses up to around 200 nanometres, in which the magnetization is accessible with current transmission imaging methods that make use of electrons or soft X-rays. In thicker samples, however, in which the magnetization structure varies throughout the thickness and is intrinsically three dimensional, determining the complex magnetic structure directly still represents a challenge. We have developed hard-X-ray vector nanotomography with which to determine the three-dimensional magnetic configuration at the nanoscale within micrometre-sized samples. We imaged the structure of the magnetization within a soft magnetic pillar of diameter 5 micrometres with a spatial resolution of 100 nanometres and, within the bulk, observed a complex magnetic configuration that consists of vortices and antivortices that form cross-tie walls and vortex walls along intersecting planes. At the intersections of these structures, magnetic singularities—Bloch points—occur. These were predicted more than fifty years ago but have so far not been directly observed. Here we image the three-dimensional magnetic structure in the vicinity of the Bloch points, which until now has been accessible only through micromagnetic simulations, and identify two possible magnetization configurations: a circulating magnetization structure and a twisted state that appears to correspond to an ‘anti-Bloch point’. Our imaging method enables the nanoscale study of topological magnetic structures in systems with sizes of the order of tens of micrometres. Knowledge of internal nanomagnetic textures is critical for understanding macroscopic magnetic properties and for designing bulk magnets for technological applications.
International Nuclear Information System (INIS)
Klein, S A; Moran, J L; Posner, J D; Frakes, D H
2012-01-01
We present a diagnostic platform for measuring three-dimensional three-component (3D3C) velocity fields in microscopic volumes. The imaging system uses high-speed Nipkow spinning disk confocal microscopy. Confocal microscopy provides optical sectioning using pinhole spatial filtering which rejects light originating from out-of-focus objects. The system accomplishes volumetric scanning by rapid translation of the high numerical aperture objective using a piezo objective positioner. The motion of fluorescent microspheres is quantified using 3D3C super resolution particle-imaging velocimetry with instantaneous spatial resolutions of the order of 5 µm or less in all three dimensions. We examine 3D3C flow in a PDMS microchannel with an expanding section at 3D acquisition rates of 30 Hz, and find strong agreement with a computational model. Equations from the PIV and PTV literature adapted for a scanning objective provide estimates of maximum measurable velocity. The technique allows for isosurface visualization of 3D particle motion and robust high spatial resolution velocity measurements without requiring a calibration step or reconstruction algorithms. (paper)
Xiang, G.; Wang, C.; Teng, H.; Jiang, Z.
2018-03-01
This study explores the three-dimensional (3D) wave configurations induced by 3D asymmetrical intersecting compression wedges in supersonic and hypersonic inviscid flows. By using the "spatial dimension reduction" approach, the problem of 3D steady shock/shock interaction is converted to that of the interaction of two moving shock waves in the characteristic two-dimensional (2D) plane. Shock polar theory is used to analyze the shock configurations in asymmetrical situations. The results show that various shock configurations exist in 3D asymmetrical shock wave interactions, including regular interaction, transitioned regular interaction, single Mach interaction, inverse single Mach interaction, transitional double Mach interaction, weak shock interaction, and weak single Mach interaction. All of the above 3D steady shock/shock interactions have their corresponding 2D moving shock/shock interaction configurations. Numerical simulations are performed by solving the 3D inviscid Euler equations with the non-oscillatory, non-free parameters, dissipative (NND) numerical scheme, and good agreement with the theoretical analysis is obtained. Furthermore, the comparison of results show that the concept of the "virtual wall" in shock dynamics theory is helpful for understanding the mechanism of two-dimensional shock/shock interactions.
Pore-scale simulation of fluid flow and solute dispersion in three-dimensional porous media
Icardi, Matteo
2014-07-31
In the present work fluid flow and solute transport through porous media are described by solving the governing equations at the pore scale with finite-volume discretization. Instead of solving the simplified Stokes equation (very often employed in this context) the full Navier-Stokes equation is used here. The realistic three-dimensional porous medium is created in this work by packing together, with standard ballistic physics, irregular and polydisperse objects. Emphasis is placed on numerical issues related to mesh generation and spatial discretization, which play an important role in determining the final accuracy of the finite-volume scheme and are often overlooked. The simulations performed are then analyzed in terms of velocity distributions and dispersion rates in a wider range of operating conditions, when compared with other works carried out by solving the Stokes equation. Results show that dispersion within the analyzed porous medium is adequately described by classical power laws obtained by analytic homogenization. Eventually the validity of Fickian diffusion to treat dispersion in porous media is also assessed. © 2014 American Physical Society.
Three dimensional cerebral blood flow in patients with idiopathic Parkinson's disease
International Nuclear Information System (INIS)
Hata, Takashi
1987-01-01
Three dimensional local cerebral blood flow values were measured in 28 patients with idiopathic Parkinson's disease without dementia and 17 control subjects, by means of xenon enhanced CT method using low concentration cold xenon and autoradiographic strategy. The results demonstrated that local cerebral perfusion in the patients with Parkinson's disease decreased with close correlations with aging and severity of the clinical symptoms and signs. Stepwise multiregression analysis revealed that mean CBF values and 1-CBF values through thalamus and white matter decreased primarily depending on aging and degree of brain atrophy, whereas 1-CBF values through basal ganglia decreased depending on severity of disease. The spatial distributions of 1-CBF were maintained normally and symmetrically even in the severely affected cases or in those with hemiparkinsonism, therefore hyperfrontalities were well preserved in all of the patients. Acute intravenous administration of L-DOPA gave rise to a diffuse increase in 1-CBF only in the patients and the increment was more prominent in patients severely affected than in those mildly affected. It was concluded that reduction of 1-CBF in the basal ganglia and cortex may be attributed to hypometabolism in the mesostriatal and mesocortical dopaminergic system. (author)
Chung, Woo-Young; Choi, Byoung-Joo; Lim, Seong-Hoon; Matsuo, Yoshiki; Lennon, Ryan J; Gulati, Rajiv; Sandhu, Gurpreet S; Holmes, David R; Rihal, Charanjit S; Lerman, Amir
2015-06-01
Conventional coronary angiography (CAG) has limitations in evaluating lesions producing ischemia. Three dimensional quantitative coronary angiography (3D-QCA) shows reconstructed images of CAG using computer based algorithm, the Cardio-op B system (Paieon Medical, Rosh Ha'ayin, Israel). The aim of this study was to evaluate whether 3D-QCA can reliably predict ischemia assessed by myocardial fractional flow reserve (FFR) < 0.80. 3D-QCA images were reconstructed from CAG which also were evaluated with FFR to assess ischemia. Minimal luminal diameter (MLD), percent diameter stenosis (%DS), minimal luminal area (MLA), and percent area stenosis (%AS) were obtained. The results of 3D-QCA and FFR were compared. A total of 266 patients was enrolled for the present study. FFR for all lesions ranged from 0.57 to 1.00 (0.85 ± 0.09). Measurement of MLD, %DS, MLA, and %AS all were significantly correlated with FFR (r = 0.569, 0609, 0.569, 0.670, respectively, all P < 0.001). In lesions with MLA < 4.0 mm(2), %AS of more than 65.5% had a 80% sensitivity and a 83% specificity to predict FFR < 0.80 (area under curve, AUC was 0.878). 3D-QCA can reliably predict coronary lesions producing ischemia and may be used to guide therapeutic approach for coronary artery disease.
Wu, J.; Shu, C.
2010-07-01
The recently proposed boundary condition-enforced immersed boundary-lattice Boltzmann method (IB-LBM) [14] is improved in this work to simulate three-dimensional incompressible viscous flows. In the conventional IB-LBM, the restoring force is pre-calculated, and the non-slip boundary condition is not enforced as compared to body-fitted solvers. As a result, there is a flow penetration to the solid boundary. This drawback was removed by the new version of IB-LBM [14], in which the restoring force is considered as unknown and is determined in such a way that the non-slip boundary condition is enforced. Since Eulerian points are also defined inside the solid boundary, the computational domain is usually regular and the Cartesian mesh is used. On the other hand, to well capture the boundary layer and in the meantime, to save the computational effort, we often use non-uniform mesh in IB-LBM applications. In our previous two-dimensional simulations [14], the Taylor series expansion and least squares-based lattice Boltzmann method (TLLBM) was used on the non-uniform Cartesian mesh to get the flow field. The final expression of TLLBM is an algebraic formulation with some weighting coefficients. These coefficients could be computed in advance and stored for the following computations. However, this way may become impractical for 3D cases as the memory requirement often exceeds the machine capacity. The other way is to calculate the coefficients at every time step. As a result, extra time is consumed significantly. To overcome this drawback, in this study, we propose a more efficient approach to solve lattice Boltzmann equation on the non-uniform Cartesian mesh. As compared to TLLBM, the proposed approach needs much less computational time and virtual storage. Its good accuracy and efficiency are well demonstrated by its application to simulate the 3D lid-driven cubic cavity flow. To valid the combination of proposed approach with the new version of IBM [14] for 3D flows
Resolution of the three dimensional structure of components of the glomerular filtration barrier.
Arkill, Kenton P; Qvortrup, Klaus; Starborg, Tobias; Mantell, Judith M; Knupp, Carlo; Michel, C Charles; Harper, Steve J; Salmon, Andy H J; Squire, John M; Bates, Dave O; Neal, Chris R
2014-02-01
The human glomerulus is the primary filtration unit of the kidney, and contains the Glomerular Filtration Barrier (GFB). The GFB had been thought to comprise 3 layers - the endothelium, the basement membrane and the podocyte foot processes. However, recent studies have suggested that at least two additional layers contribute to the function of the GFB, the endothelial glycocalyx on the vascular side, and the sub-podocyte space on the urinary side. To investigate the structure of these additional layers is difficult as it requires three-dimensional reconstruction of delicate sub-microscopic (glomerular volume). Secondly, Focused Ion Beam milling Scanning Electron Microscopy (FIB-SEM) was used to image a filtration region (48 μm3 volume). Lastly Transmission Electron Tomography (Tom-TEM) was performed on a 0.3 μm3 volume to identify the fine structure of the glycocalyx. Tom-TEM clearly showed 20 nm fibre spacing in the glycocalyx, within a limited field of view. FIB-SEM demonstrated, in a far greater field of view, how the glycocalyx structure related to fenestrations and the filtration slits, though without the resolution of TomTEM. SBF-SEM was able to determine the extent of the sub-podocyte space and glycocalyx coverage, without additional heavy metal staining. Neither SBF- nor FIB-SEM suffered the anisotropic shrinkage under the electron beam that is seen with Tom-TEM. These images demonstrate that the three dimensional structure of the GFB can be imaged, and investigated from the whole glomerulus to the fine structure of the glycocalyx using three dimensional electron microscopy techniques. This should allow the identification of structural features regulating physiology, and their disruption in pathological states, aiding the understanding of kidney disease.
Bíscaro, Helton H; Nunes, Fátima L S; Dos Santos Oliveira, Jéssica; Pereira, Gustavo R
2016-10-01
Data structures have been explored for several domains of computer applications in order to ensure efficiency in the data store and retrieval. However, data structures can present different behavior depending on applications that they are being used. Three-dimensional interactive environments offered by techniques of Virtual Reality require operations of loading and manipulating objects in real time, where realism and response time are two important requirements. Efficient representation of geometrical models plays an important part so that the simulation may become real. In this paper, we present the implementation and the comparison of two topologically efficient data structures - Compact Half-Edge and Mate-Face - for the representation of objects for three-dimensional interactive environments. The structures have been tested at different conditions of processors and RAM memories. The results show that both these structures can be used in an efficient manner. Mate-Face structure has shown itself to be more efficient for the manipulation of neighborhood relationships and the Compact Half-Edge was more efficient for loading of the geometric models. We also evaluated the data structures embedded in applications of biopsy simulation using virtual reality, considering a deformation simulation method applied in virtual human organs. The results showed that their use allows the building of applications considering objects with high resolutions (number of vertices), without significant impact in the time spent in the simulation. Therefore, their use contributes for the construction of more realistic simulators. Copyright © 2016 Elsevier Inc. All rights reserved.
Insulin as a model to teach three-dimensional structure of proteins
Directory of Open Access Journals (Sweden)
João Batista Teixeira da Rocha
2018-02-01
Proteins are the most ubiquitous macromolecules found in the living cells and have innumerous physiological functions. Therefore, it is fundamental to build a solid knowledge about the proteins three dimensional structure to better understand the living state. The hierarchical structure of proteins is usually studied in the undergraduate discipline of Biochemistry. Here we described pedagogical interventions designed to increase the preservice teacher chemistry students’ knowledge about protein structure. The activities were made using alternative and cheap materials to encourage the application of these simple methodologies by the future teachers in the secondary school. From the primary structure of insulin chains, students had to construct a three-dimensional structure of insulin. After the activities, the students highlighted an improvement of their previous knowledge about proteins structure. The construction of a tridimensional model together with other activities seems to be an efficient way to promote the learning about the structure of proteins to undergraduate students. The methodology used was inexpensiveness and simple and it can be used both in the university and in the high-school.
Generation of a Three-Dimensional Kidney Structure from Pluripotent Stem Cells.
Yoshimura, Yasuhiro; Taguchi, Atsuhiro; Nishinakamura, Ryuichi
2017-01-01
The kidney is a vital organ that has an important role in the maintenance of homeostasis by fluid volume regulation and waste product excretion. This role cannot be performed without the three-dimensional (3D) structure of the kidney. Therefore, it is important to generate the 3D structure of the kidney when inducing functional kidney tissue or the whole organ from pluripotent stem cells. In this chapter, we describe the detailed methods to induce kidney progenitor cells from pluripotent stem cells, which are based on embryological development. We also provide a method to generate 3D kidney tissue with vascularized glomeruli upon transplantation.
Three-dimensional dielectric photonic crystal structures for laser-driven acceleration
Directory of Open Access Journals (Sweden)
Benjamin M. Cowan
2008-01-01
Full Text Available We present the design and simulation of a three-dimensional photonic crystal waveguide for linear laser-driven acceleration in vacuum. The structure confines a synchronous speed-of-light accelerating mode in both transverse dimensions. We report the properties of this mode, including sustainable gradient and optical-to-beam efficiency. We present a novel method for confining a particle beam using optical fields as focusing elements. This technique, combined with careful structure design, is shown to have a large dynamic aperture and minimal emittance growth, even over millions of optical wavelengths.
Three-Dimensional CFD Modeling of Transport Phenomena in a Cross-Flow Anode-Supported Planar SOFC
Directory of Open Access Journals (Sweden)
Zhonggang Zhang
2013-12-01
Full Text Available In this study, a three-dimensional computational fluid dynamics (CFD model is developed for an anode-supported planar SOFC from the Chinese Academy of Science Ningbo Institute of Material Technology and Engineering (NIMTE. The simulation results of the developed model are in good agreement with the experimental data obtained under the same conditions. With the simulation results, the distribution of temperature, flow velocity and the gas concentrations through the cell components and gas channels is presented and discussed. Potential and current density distributions in the cell and overall fuel utilization are also presented. It is also found that the temperature gradients exist along the length of the cell, and the maximum value of the temperature for the cross-flow is at the outlet region of the cell. The distribution of the current density is uneven, and the maximum current density is located at the interfaces between the channels, ribs and the electrodes, the maximum current density result in a large over-potential and heat source in the electrodes, which is harmful to the overall performance and working lifespan of the fuel cells. A new type of flow structure should be developed to make the current flow be more evenly distributed and promote most of the TPB areas to take part in the electrochemical reactions.
Tung, J. C.; Hsieh, Y. H.; Liang, H. C.; Su, K. W.; Huang, K. F.; Chen, Y. F.
2017-04-01
We originally perform an analytical form to explore the influence of the astigmatism on the degenerate effect in nearly hemispherical cavities. The frequency spectrum near hemispherical cavities clearly reveals that not only the difference of cavity lengths between each degeneracies but also frequency gaps have significant difference from non-hemispherical cavities. We further thoroughly demonstrate the laser experiment under the condition of nearly hemispherical cavities to confirm the theoretical exploration that the transverse topology of three-dimensional (3D) structured light in the degenerate cavities is well localized on the Lissajous curves.
Directory of Open Access Journals (Sweden)
Xibing Li
2014-02-01
Full Text Available This paper presents an efficient closed-form solution (ECS for acoustic emission(AE source location in three-dimensional structures using time difference of arrival (TDOA measurements from N receivers, N ≥ 6. The nonlinear location equations of TDOA are simplified to linear equations. The unique analytical solution of AE sources for unknown velocity system is obtained by solving the linear equations. The proposed ECS method successfully solved the problems of location errors resulting from measured deviations of velocity as well as the existence and multiplicity of solutions induced by calculations of square roots in existed close-form methods.
Three dimensional flow field at confluent fixed-bed open channels
Schleiss, Anton; De Cesare, Giovanni; Franca, Mário J.; Pfister, Michael; Birjukova, Olga; Guillén Ludeña, Sebastián; Alegria, Francisco; Cardoso, Antonio H.
2014-01-01
River confluences are known for their marked 3D patterns and, due to the complexity of local flow features and bed morphology, they require particular consideration. Although there are studies on the flow structure in junctions of two streams, amore detailed description of the flow patterns is still required. The objective of this work is to contribute to such description at river confluence for concordant bed, where both main and tributary channel beds have the same elevation. For that purpo...
Electronic transport on the spatial structure of the protein: Three-dimensional lattice model
International Nuclear Information System (INIS)
Sarmento, R.G.; Frazão, N.F.; Macedo-Filho, A.
2017-01-01
Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.
Electronic transport on the spatial structure of the protein: Three-dimensional lattice model
Energy Technology Data Exchange (ETDEWEB)
Sarmento, R.G. [Departamento de Ciências Biológicas, Universidade Federal do Piauí, 64800-000 Floriano, PI (Brazil); Frazão, N.F. [Centro de Educação e Saúde, Universidade Federal de Campina Grande, 581750-000 Cuité, PB (Brazil); Macedo-Filho, A., E-mail: amfilho@gmail.com [Campus Prof. Antonio Geovanne Alves de Sousa, Universidade Estadual do Piauí, 64260-000 Piripiri, PI (Brazil)
2017-01-30
Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.
VanderWal, D.J.; Goffart, D.; Klomp, E.M.; Hoogstraten, H.W; Janssen, L.P.B.M.
Three-dimensional flow simulations of kneading elements in an intermeshing corotating twin-screw extruder are performed by solving the Navier Stokes equations with a finite element package, Sepran. Instead of using the whole geometry of the 8-shaped barrel a simplified geometry is used, representing
Wal, D.J. van der; Goffart, D.; Klomp, E.M.; Hoogstraten, H.W.; Janssen, L.P.B.M.
1996-01-01
Three-dimensional flow simulations of kneading elements in an intermeshing corotating twin-screw extruder are performed by solving the Navier Stokes equations with a finite element package, Sepran. Instead of using the whole geometry of the 8-shaped barrel a simplified geometry is used, representing
International Nuclear Information System (INIS)
Song, P P; Wei, M S; Shi, L; Ma, C C
2013-01-01
Three-dimensional numerical simulations of a scroll expander were performed with dynamic mesh technology. R245fa was selected as the working fluid in the simulations. The PISO algorithm was applied to solve the governing equations with RNG k-ε turbulent model. The distribution and variation of three-dimensional flow field inside the scroll expander were obtained. The research indicates that the flow field is nonuniform and asymmetrical distributions exist inside the expander. Vortex flows also exist in some working chambers. Dynamic clearance leakage flows and inlet orifice throttling have great effects on the flow field distribution. Transient output torque and the mass flux have periodic fluctuations during the working cycles
Sikarwar, Nidhi
multiple experiments or numerical simulations. Alternatively an inverse design method can be used. An adjoint optimization method can be used to achieve the optimum blowing rate. It is shown that the method works for both geometry optimization and active control of the flow in order to deflect the flow in desirable ways. An adjoint optimization method is described. It is used to determine the blowing distribution in the diverging section of a convergent-divergent nozzle that gives a desired pressure distribution in the nozzle. Both the direct and adjoint problems and their associated boundary conditions are developed. The adjoint method is used to determine the blowing distribution required to minimize the shock strength in the nozzle to achieve a known target pressure and to achieve close to an ideally expanded flow pressure. A multi-block structured solver is developed to calculate the flow solution and associated adjoint variables. Two and three-dimensional calculations are performed for internal and external of the nozzle domains. A two step MacCormack scheme based on predictor- corrector technique is was used for some calculations. The four and five stage Runge-Kutta schemes are also used to artificially march in time. A modified Runge-Kutta scheme is used to accelerate the convergence to a steady state. Second order artificial dissipation has been added to stabilize the calculations. The steepest decent method has been used for the optimization of the blowing velocity after the gradients of the cost function with respect to the blowing velocity are calculated using adjoint method. Several examples are given of the optimization of blowing using the adjoint method.
Use of three-dimensional parameters in the analysis of crystal structures under compression
DEFF Research Database (Denmark)
Balic Zunic, Tonci
2007-01-01
Volume-related parameters of atomic coordinations are an important tool for the analysis of structural changes. Unlike usual tables of bond distances and angles they directly depict three-dimensional properties of coordination polyhedra, and in many instances give more profound structural...... data through use of a procrystal model. For non-regular coordination polyhedra a determination of the point with the minimum variation of distances to the vertices (the centroid of coordination) is a necessary prerequisite for a calculation of the volume-related parameters. The three parameters...... of the coordination polyhedra of cations and the voids that separate them. Analysis of individual compressional characteristics of structural components gives clues for the strong and weak parts of structures under high pressures and paths for structural transformations. The expected behaviour of distortion...
Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution
Energy Technology Data Exchange (ETDEWEB)
Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Abramchik, Yu. A., E-mail: ugama@yandex.ru [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Zhukhlistova, N. E., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Muravieva, T. I.; Esipov, R. S. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)
2016-03-15
Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment of the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB-ID: 4RJ2).
An `H'-shape three-dimensional meta-material used in honeycomb structure absorbing material
Huang, Daqing; Kang, Feiyu; Zhou, Zhuohui; Cheng, Hongfei; Ding, Heyan
2015-03-01
An `H'-shape three-dimensional meta-material structure which loaded on the sidewall of honeycomb structure absorbing material was designed and fabricated in this project. The simulation results demonstrated a super-wide absorption band below -10 dB between 2.3 and 18 GHz, which expanded 7 GHz compared with the absorber without meta-material. The relative impedance curve was analyzed, which showed that the meta-material has little impact on the impedance-matching characteristics of the honeycomb structure absorbing material. We further studied the distribution of both electronic field energy and magnetic field energy. The former one indicated that the low-frequency absorption peaks could easily be moved by adjusting the parameters of the parallel-plate capacitors which generate electric resonance, and the latter one illustrated that the three-dimensional meta-material could generate magnetic resonance between units which would not exist in two-dimensional meta-material. Then we verified the simulation results through experiment which display a similar absorbing curve. The differences between simulation results and experiment results were caused by the addition substrate of the meta-material, which could not be eliminated in this experiment. However, it still implied that we can obtain a meta-material absorber that has a super-wide absorbing band if we can put the meta-material on the sidewall of the honeycomb without attachments.
Three-dimensionality of the bulk electronic structure in WTe2
Wu, Yun; Jo, Na Hyun; Mou, Daixiang; Huang, Lunan; Bud'ko, S. L.; Canfield, P. C.; Kaminski, Adam
2017-05-01
We use temperature- and field-dependent resistivity measurements (Shubnikov-de Haas quantum oscillations) and ultrahigh-resolution, tunable, vacuum ultraviolet laser-based angle-resolved photoemission spectroscopy (ARPES) to study the three-dimensionality (3D) of the bulk electronic structure in WTe 2 , a type II Weyl semimetal. The bulk Fermi surface (FS) consists of two pairs of electron pockets and two pairs of hole pockets along the X -Γ -X direction as detected by using an incident photon energy of 6.7 eV, which is consistent with the previously reported data. However, if using an incident photon energy of 6.36 eV, another pair of tiny electron pockets is detected on both sides of the Γ point, which is in agreement with the small quantum oscillation frequency peak observed in the magnetoresistance. Therefore, the bulk, 3D FS consists of three pairs of electron pockets and two pairs of hole pockets in total. With the ability of fine tuning the incident photon energy, we demonstrate the strong three-dimensionality of the bulk electronic structure in WTe 2 . The combination of resistivity and ARPES measurements reveals the complete, and consistent, picture of the bulk electronic structure of this material.
Optical chracterization and lasing in three-dimensional opal-structures
Directory of Open Access Journals (Sweden)
Yoshiaki eNishijima
2015-06-01
Full Text Available The lasing properties of dye-permeated opal pyramidal structures are compared with the lasing properties of opal films. The opal-structures studied were made by sedimentation of micro-spheres and by sol-gel inversion of the direct-opals. Forced-sedimentation by centrifugation inside wet-etched pyramidal pits on silicon surfaces was used to improve the structural quality of the direct-opal structures. Single crystalline pyramids with the base length of ∼ 100 µm were formed by centrifuged sedimentation. The lasing of dyes in the well-ordered crystalline and poly-crystalline structures showed a distinct multi-modal spectrum. Gain via a distributed feedback was responsible for the lasing since the photonic band gap was negligible in a low refractive index contrast medium; the indices of silica and ethylene glycol are 1.46 and 1.42, respectively. A disordered lasing spectrum was observed from opal films with structural defects and multi-domain regions. The three dimensional structural quality of the structures was assessed by in situ optical diffraction and confocal fluorescence. A correlation between the lasing spectrum and the three-dimensional structural quality was established. Lasing threshold of a sulforhodamine dye in a silica opal was controlled via Förster mechanism by addition of a donor rhodamine 6G dye. The lasing spectrum had a well-ordered modal structure which was spectrally stable at different excitation powers. The sharp lasing threshold characterized by a spontaneous emission coupling ratio β ' 10−2 was obtained.
Energy Technology Data Exchange (ETDEWEB)
Speetjens, M. F. M.; Demissie, E. A. [Department of Mechanical Engineering, Energy Technology Laboratory, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Metcalfe, G. [Commonwealth Scientific and Industrial Research Organisation (CSIRO), VIC 3190 Melbourne (Australia); Clercx, H. J. H. [Department of Applied Physics, Fluid Dynamics Laboratory, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands)
2014-11-15
Laminar mixing by the inline-mixing principle is a key to many industrial fluids-engineering systems of size extending from micrometers to meters. However, insight into fundamental transport phenomena particularly under the realistic conditions of three-dimensionality (3D) and fluid inertia remains limited. This study addresses these issues for inline mixers with cylindrical geometries and adopts the Rotated Arc Mixer (RAM) as a representative system. Transport is investigated from a Lagrangian perspective by identifying and examining coherent structures that form in the 3D streamline portrait. 3D effects and fluid inertia introduce three key features that are not found in simplified configurations: transition zones between consecutive mixing cells of the inline-mixing flow; local upstream flow (in certain parameter regimes); transition/inertia-induced breaking of symmetries in the Lagrangian equations of motion (causing topological changes in coherent structures). Topological considerations strongly suggest that there nonetheless always exists a net throughflow region between inlet and outlet of the inline-mixing flow that is strictly separated from possible internal regions. The Lagrangian dynamics in this region admits representation by a 2D time-periodic Hamiltonian system. This establishes one fundamental kinematic structure for the present class of inline-mixing flows and implies universal behavior in that all states follow from the Hamiltonian breakdown of one common integrable state. A so-called period-doubling bifurcation is the only way to eliminate transport barriers originating from this state and thus is a necessary (yet not sufficient) condition for global chaos. Important in a practical context is that a common simplification in literature, i.e., cell-wise fully-developed Stokes flow (“2.5D approach”), retains these fundamental kinematic properties and deviates from the generic 3D inertial case only in a quantitative sense. This substantiates its
International Nuclear Information System (INIS)
Speetjens, M. F. M.; Demissie, E. A.; Metcalfe, G.; Clercx, H. J. H.
2014-01-01
Laminar mixing by the inline-mixing principle is a key to many industrial fluids-engineering systems of size extending from micrometers to meters. However, insight into fundamental transport phenomena particularly under the realistic conditions of three-dimensionality (3D) and fluid inertia remains limited. This study addresses these issues for inline mixers with cylindrical geometries and adopts the Rotated Arc Mixer (RAM) as a representative system. Transport is investigated from a Lagrangian perspective by identifying and examining coherent structures that form in the 3D streamline portrait. 3D effects and fluid inertia introduce three key features that are not found in simplified configurations: transition zones between consecutive mixing cells of the inline-mixing flow; local upstream flow (in certain parameter regimes); transition/inertia-induced breaking of symmetries in the Lagrangian equations of motion (causing topological changes in coherent structures). Topological considerations strongly suggest that there nonetheless always exists a net throughflow region between inlet and outlet of the inline-mixing flow that is strictly separated from possible internal regions. The Lagrangian dynamics in this region admits representation by a 2D time-periodic Hamiltonian system. This establishes one fundamental kinematic structure for the present class of inline-mixing flows and implies universal behavior in that all states follow from the Hamiltonian breakdown of one common integrable state. A so-called period-doubling bifurcation is the only way to eliminate transport barriers originating from this state and thus is a necessary (yet not sufficient) condition for global chaos. Important in a practical context is that a common simplification in literature, i.e., cell-wise fully-developed Stokes flow (“2.5D approach”), retains these fundamental kinematic properties and deviates from the generic 3D inertial case only in a quantitative sense. This substantiates its
Approximation and stability of three-dimensional natural convection flows in a porous medium
International Nuclear Information System (INIS)
Janotto, Marie-Laurence
1991-01-01
The equations of the three-dimensional natural convection in a porous medium within a differentially heated horizontal walls cavity are solved by a pseudo-spectral method. First we will present the evolution of the two main modes according to two models of convection. A few asymptotic properties connected to the small and large eddies are set up and numerically validated. A new approximate inertial manifold is then proposed. The numerical scheme used is an exponential fitting algorithm the convergence of which is proved. We will present the physical mechanism at the origin of the un-stationary three-dimensional convection at high Rayleigh numbers. (author) [fr
TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.
Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng
2014-01-01
The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. © The Author(s) 2014. Published by Oxford University Press.
Wu, Yuxiang; Sui, Tao; Cao, Xiaojian; Lv, Xiaohua; Zeng, Shaoqun; Sun, Peng
2011-05-01
Peripheral nerve injury repair is one of the most challenging problems in neurosurgery, partially due to lack of knowledge of three-dimensional (3-D) fine structure and organization of peripheral nerves. In this paper, we explored the structures of nerve fibers in ventral and dorsal nerves with a laser scanning confocal microscopy. Thick tissue staining results suggested that nerve fibers have a different 3-D structure in ventral and dorsal nerves, and reconstruction from serial sectioning images showed that in ventral nerves the nerve fibers travel in a winding form, while in dorsal nerves, the nerve fibers form in a parallel cable pattern. These structural differences could help surgeons to differentiate ventral and dorsal nerves in peripheral nerve injury repair, and also facilitate scientists to get a deeper understanding about nerve fiber organization.
Three-dimensional on-chip continuous-flow polymerase chain reaction employing a single heater.
Wu, Wenming; Lee, Nae Yoon
2011-06-01
Multi-step temperature control in a polymerase chain reaction (PCR) is a limiting factor in device miniaturization and portability. In this study, we propose the fabrication of a three-dimensional (3D) microdevice employing a single heater to minimize temperature control required for an on-chip continuous-flow PCR as well as the overall footprint by stacking the device in multi-layers. Two poly(dimethylsiloxane) (PDMS) layers with differing thicknesses are vertically stacked with their microchannel-engraved sides facing down. Through-holes are made in the thicker PDMS layer, which is sandwiched between a glass substrate at the bottom and the thinner PDMS layer at the top. In this way, a fluidic conduit is realized in a 3D configuration. The assembled 3D microdevice is then placed onto a heater glass-side down. The interface of the two PDMS layers displays a relatively lower temperature than that of the PDMS and glass layers due to the low thermal conductivity of the PDMS and its physical distance from the heater. The denaturation temperature can be controlled by adjusting the temperature of the heater, while the annealing/extension temperature can be controlled automatically by molding the thicker bottom PDMS layer into the appropriate thickness calculated using a numerical derivation proposed in this study. In this way, a cumbersome temperature measurement step is eliminated. DNA amplification was successfully carried out using the proposed 3D fluidic microdevice, and the intensity of the resulting amplicon was comparable to that obtained using a thermal cycler. This novel concept of adopting a single heating source greatly simplifies the temperature control issue present in an on-chip continuous-flow PCR. It also allows the use of a commercialized hot plate as a potential heat source, paving the way for device miniaturization and portability in a highly cost-effective manner. In this study, a simple and facile technique to make arrays of through-holes for the
International Nuclear Information System (INIS)
De Marchis, M.; Napoli, E.
2012-01-01
Highlights: ► 3D irregular rough surfaces produce higher effects than those observed over 2D. ► Effective slope is a geometrical parameter representative of the roughness effects. ► 3D rough surfaces enhance the turbulence isotropization. ► 2D and 3D irregular roughness partially support the wall similarity. ► Irregular rough surfaces shear some features with regular rough walls. - Abstract: Wall-resolved Large Eddy Simulation of fully developed turbulent channel flows over two different rough surfaces is performed to investigate on the effects of irregular 2D and 3D roughness on the turbulence. The two geometries are obtained through the superimposition of sinusoidal functions having random amplitudes and different wave lengths. In the 2D configuration the irregular shape in the longitudinal direction is replicated in the transverse one, while in the 3D case the sinusoidal functions are generated both in streamwise and spanwise directions. Both channel walls are roughened in such a way as to obtain surfaces with statistically equivalent roughness height, but different shapes. In order to compare the turbulence properties over the two rough walls and to analyse the differences with a smooth wall, the simulations are performed at the same Reynolds number Re τ = 395. The same mean roughness height h = 0.05δ (δ the half channel height) is used for the rough walls. The roughness function obtained with the 3D roughness is larger than in the 2D case, although the two walls share the same mean height. Thus, the considered irregular 3D roughness is more effective in reducing the flow velocity with respect to the 2D roughness, coherently with the literature results that identified a clear dependence of the roughness function on the effective slope (see ), higher in the generated 3D rough wall. The analysis of higher-order statistics shows that the effects of the roughness, independently on its two- or three-dimensional shape, are mainly confined in the inner
Caster, Amanda H; Kahn, Richard A
2012-10-01
The use of fluorescence microscopy is central to cell biology in general, and essential to many fields (e.g., membrane traffic) that rely upon it to identify cellular locations of molecules under study and the extent to which they co-localize with others. Rigorous localization or co-localization data require quantitative image analyses that can vary widely between fields and laboratories. While most published data use two-dimensional images, there is an increasing appreciation for the advantages of collecting three-dimensional data sets. These include the ability to evaluate the entire cell and avoidance of focal plane bias. This is particularly important when imaging and quantifying changes in organelles with irregular borders and which vary in appearance between cells in a population, e.g., the Golgi. We describe a method developed for quantifying changes in signal intensity of one protein within any three-dimensional structure, defined by the presence of a different marker. We use as examples of this method the quantification of adaptor recruitment to transmembrane protein cargos at the Golgi though it can be directly applied to any site in the cell. Together, these advantages facilitate rigorous statistical testing of differences between conditions, despite variations in organelle structure, and we believe that this method of quantification of fluorescence data can be productively applied to a wide array of experimental questions.
Preservation of three-dimensional spatial structure in the gut microbiome.
Directory of Open Access Journals (Sweden)
Yuko Hasegawa
Full Text Available Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA and 4', 6-diamidino-2-phenylindole (DAPI. Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA or with Carnoy's fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.
International Nuclear Information System (INIS)
Billaux, D.; Long, J.C.S.; Peterson, J.E. Jr.
1990-03-01
A model for channelized flow in three-dimensional, random networks of fractures has been developed. In this model, the fractures are disc-shaped discontinuities in an impermeable matrix. Within each fracture, flow occurs only in a network of random channels. The channels in each fracture can be generated independently with random distributions of length, conductivity, and orientation in the fracture plane. Boundary conditions are specified on the sides of a ''flow region,'' and at the intersections of the channels with interior ''holes'' specified by the user to simulate boreholes or drifts. This code is part of a set of programs used to generate two-dimensional or three-dimensional random fracture networks, plot them, compute flow through them and analyze the results. 8 refs., 13 figs
Three-dimensional multi-relaxation-time lattice Boltzmann front-tracking method for two-phase flow
International Nuclear Information System (INIS)
Xie Hai-Qiong; Zeng Zhong; Zhang Liang-Qi
2016-01-01
We developed a three-dimensional multi-relaxation-time lattice Boltzmann method for incompressible and immiscible two-phase flow by coupling with a front-tracking technique. The flow field was simulated by using an Eulerian grid, an adaptive unstructured triangular Lagrangian grid was applied to track explicitly the motion of the two-fluid interface, and an indicator function was introduced to update accurately the fluid properties. The surface tension was computed directly on a triangular Lagrangian grid, and then the surface tension was distributed to the background Eulerian grid. Three benchmarks of two-phase flow, including the Laplace law for a stationary drop, the oscillation of a three-dimensional ellipsoidal drop, and the drop deformation in a shear flow, were simulated to validate the present model. (paper)
Energy Technology Data Exchange (ETDEWEB)
Jang, Jer-Huan [Department of Mechanical Engineering, Northern Taiwan Institute of Science and Technology, Beitou, Taipei 11202 (China); Yan, Wei-Mon; Li, Hung-Yi; Tsai, Wei-Che [Department of Mechatronic Engineering, Huafan University, Shih-Ting, Taipei 22305 (China)
2008-01-15
In this paper, a three-dimensional numerical model of the proton exchange membrane fuel cells (PEMFCs) with conventional flow field designs (parallel flow field, Z-type flow field, and serpentine flow field) has been established to investigate the performance and transport phenomena in the PEMFCs. The influences of the flow field designs on the fuel utilization, the water removal, and the cell performance of the PEMFC are studied. The distributions of velocity, oxygen mass fraction, current density, liquid water, and pressure with the convention flow fields are presented. For the conventional flow fields, the cell performance can be enhanced by adding the corner number, increasing the flow channel length, and decreasing the flow channel number. The cell performance of the serpentine flow field is the best, followed by the Z-type flow field and then the parallel flow field. (author)
Roszelle, Breigh N.; Deutsch, Steven; Manning, Keefe B.
2010-01-01
In order to aid the ongoing concern of limited organ availability for pediatric heart transplants, Penn State has continued development of a pulsatile Pediatric Ventricular Assist Device (PVAD). Initial studies of the PVAD observed an increase in thrombus formation due to differences in flow field physics when compared to adult sized devices, which included a higher degree of three-dimensionality. This unique flow field brings into question the use of 2D planar particle image velocimetry (PIV...
Takagi, Kenta; Omote, Masanori; Kawasaki, Akira
2010-03-01
The orderly build-up of monosized microspheres with sizes of hundreds of micrometres enabled us to develop three-dimensional (3D) photonic crystal devices for terahertz electromagnetic waves. We designed and manufactured an original 3D particle assembly system capable of fabricating arbitrary periodic structures from these spherical particles. This method employs a pick-and-place assembling approach with robotic manipulation and interparticle laser microwelding in order to incorporate a contrivance for highly accurate arraying: an operation that compensates the size deviation of raw monosized particles. Pre-examination of particles of various materials revealed that interparticle laser welding must be achieved with local melting by suppressing heat diffusion from the welding area. By optimizing the assembly conditions, we succeeded in fabricating an accurate periodic structure with a diamond lattice from 400 µm polyethylene composite particles. This structure demonstrated a photonic bandgap in the terahertz frequency range.
Three-dimensional P-wave velocity structure of Mt. Etna, Italy
Villasenor, A.; Benz, H.M.; Filippi, L.; De Luca, G.; Scarpa, R.; Patane, G.; Vinciguerra, S.
1998-01-01
The three-dimensional P-wave velocity structure of Mt. Etna is determined to depths of 15 km by tomographic inversion of first arrival times from local earthquakes recorded by a network of 29 permanent and temporary seismographs. Results show a near-vertical low-velocity zone that extends from beneath the central craters to a depth of 10 km. This low-velocity region is coincident with a band of steeply-dipping seismicity, suggesting a magmatic conduit that feeds the summit eruptions. The most prominent structure is an approximately 8-km-diameter high-velocity body located between 2 and 12 km depth below the southeast flank of the volcano. This high-velocity body is interpreted as a remnant mafic intrusion that is an important structural feature influencing both volcanism and east flank slope stability and faulting.
Lidke, Diane S; Lidke, Keith A
2012-06-01
A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.
Ishikawa, Atsushi; Kato, Taiki; Takeyasu, Nobuyuki; Fujimori, Kazuhiro; Tsuruta, Kenji
2017-10-01
A technique of selective electroless plating onto PLA-ABS (Polylactic Acid-Acrylonitrile Butadiene Styrene) composite structures fabricated by three-dimensional (3D) printing is demonstrated to construct 3D microwave metamaterials. The reducing activity of the PLA surface is selectively enhanced by the chemical modification involving Sn2+ in a simple wet process, thereby forming a highly conductive Ag-plated membrane only onto the PLA surface. The fabricated metamaterial composed of Ag-plated PLA and non-plated ABS parts is characterized experimentally and numerically to demonstrate the important bi-anisotropic microwave responses arising from the 3D nature of metallodielectric structures. Our approach based on a simple wet chemical process allows for the creation of highly complex 3D metal-insulator structures, thus paving the way toward the sophisticated microwave applications of the 3D printing technology.
Akparov, V. Kh.; Timofeev, V. I.; Kuranova, I. P.
2011-07-01
Crystals of recombinant carboxypeptidase T (CPT) from Thermoactinomyces vulgaris were grown in a capillary by the counterdiffusion method in the absence of calcium ions. The three-dimensional structure of CPT was solved at 1.69-Å resolution using the X-ray diffraction data collected from the crystals of the enzyme on the SPring-8 synchrotron radiation facility and was then refined to Rfact = 16.903% and Rfree = 18.165%. The coordinates of the refined model were deposited in the Protein Data Bank (PDB ID: 3QNV). A comparison of this structure with the structure of wild-type CPT containing bound calcium ions, which was determined earlier, revealed a number of conformational changes both in the calcium-binding sites and the enzyme active site. Based on the results of this comparison, the possible factors responsible for the difference in the catalytic activity of the two forms of the enzyme are considered.
International Nuclear Information System (INIS)
Takagi, Kenta; Omote, Masanori; Kawasaki, Akira
2010-01-01
The orderly build-up of monosized microspheres with sizes of hundreds of micrometres enabled us to develop three-dimensional (3D) photonic crystal devices for terahertz electromagnetic waves. We designed and manufactured an original 3D particle assembly system capable of fabricating arbitrary periodic structures from these spherical particles. This method employs a pick-and-place assembling approach with robotic manipulation and interparticle laser microwelding in order to incorporate a contrivance for highly accurate arraying: an operation that compensates the size deviation of raw monosized particles. Pre-examination of particles of various materials revealed that interparticle laser welding must be achieved with local melting by suppressing heat diffusion from the welding area. By optimizing the assembly conditions, we succeeded in fabricating an accurate periodic structure with a diamond lattice from 400 µm polyethylene composite particles. This structure demonstrated a photonic bandgap in the terahertz frequency range.
In Vivo Three-Dimensional Velocity Vector Imaging and Volumetric Flow Rate Measurements
DEFF Research Database (Denmark)
Pihl, Michael Johannes; Stuart, Matthias Bo; Tomov, Borislav Gueorguiev
2013-01-01
The three-dimensional (3-D) Transverse Oscillation (TO) method is used to obtain 3-D velocity vector estimates in two orthogonal planes. The method is suitable for a real-time implementation. Data are acquired using a Vermon 3.0 MHz 32x32 element 2-D phased array and the experimental ultrasound s...
Montessori, A; Falcucci, G; Prestininzi, P; La Rocca, M; Succi, S
2014-05-01
We investigate the accuracy and performance of the regularized version of the single-relaxation-time lattice Boltzmann equation for the case of two- and three-dimensional lid-driven cavities. The regularized version is shown to provide a significant gain in stability over the standard single-relaxation time, at a moderate computational overhead.
Fiegel, Henning C; Havers, Joerg; Kneser, Ulrich; Smith, Molly K; Moeller, Tim; Kluth, Dietrich; Mooney, David J; Rogiers, Xavier; Kaufmann, Peter M
2004-01-01
Maintenance of liver-specific function of hepatocytes in culture is still difficult. Improved culture conditions may enhance the cell growth and function of cultured cells. We investigated the effect of three-dimensional culture under flow conditions, and the influence of surface modifications in hepatocyte cultures. Hepatocytes were harvested from Lewis rats. Cells were cultured on three-dimensional polymeric poly-lactic-co-glycolic acid (PLGA) matrices in static culture, or in a pulsatile flow-bioreactor system. Different surface modifications of matrices were investigated: coating with collagen I, collagen IV, laminin, or fibronectin; or uncoated matrix. Hepatocyte numbers, DNA content, and albumin secretion rate were assessed over the observation period. Culture under flow condition significantly enhanced cell numbers. An additional improvement of this effect was observed, when matrix coating was used. Cellular function also showed a significant increase (4- to 5-fold) under flow conditions when compared with static culture. Our data showed that culture under flow conditions improves cell number, and strongly enhances cellular function. Matrix modification by coating with extracellular matrix showed overall an additive stimulatory effect. Our conclusion is that combining three-dimensional culture under flow conditions and using matrix modification significantly improves culture conditions and is therefore attractive for the development of successful culture systems for hepatocytes.
Three-Dimensional Unsteady Flow Elicited by Finite Wings and Complex Configurations.
1987-01-01
flow. Anemometric measurements added quantitative magnitudes and spatial verification to the visualized flow structures. The experiments were designed... anemometric measurements were taken at each span location and chordwise at 0.00c(leading edge), 0.17c, 0.33c, 0.50c, 0.67c, 0.83c and 1.00c. " An X...The hot wire recorded the absolute velocity of the flow field during the cyclic motion history of the three wings. The anemometric measurements were
Directory of Open Access Journals (Sweden)
Zamaliev Farit Sakhapovich
2012-12-01
steel-concrete slabs limits their use in the construction of residential housing. This article describes the composition, geometry, reinforcement, and anchors to enable the use of concrete slabs and steel beams. The article contains photographs that illustrate the load distribution model. Methods of testing of fiber strains of concrete slabs and steel profiles, deflections of beams, shear stresses in the layers of the "steel-to-concrete" contact area that may involve slab cracking are analyzed. Dynamics of fiber deformations of concrete slabs, steel beams, and layers of the "steel-to-concrete" contact areas, deflection development patterns, initial cracking and crack development to destruction are analyzed. The author also describes the fracture behavior of the floor model. Results of experimental studies of the three-dimensional overlapping of structural elements are compared to the test data of individual composite beams. Peculiarities of the stress-strain state of composite steel and concrete slabs, graphs of strains and stresses developing in sections of middle and external steel-and-concrete beams, deflection graphs depending on the loading intensity are provided. The findings of the experimental studies of the three-dimensional performance of composite steel-and-concrete slabs are provided, as well.
Three-dimensional coating and rimming flow: a ring of fluid on a rotating horizontal cylinder
Leslie, G. A.
2013-01-29
The steady three-dimensional flow of a thin, slowly varying ring of Newtonian fluid on either the outside or the inside of a uniformly rotating large horizontal cylinder is investigated. Specifically, we study \\'full-ring\\' solutions, corresponding to a ring of continuous, finite and non-zero thickness that extends all of the way around the cylinder. In particular, it is found that there is a critical solution corresponding to either a critical load above which no full-ring solution exists (if the rotation speed is prescribed) or a critical rotation speed below which no full-ring solution exists (if the load is prescribed). We describe the behaviour of the critical solution and, in particular, show that the critical flux, the critical load, the critical semi-width and the critical ring profile are all increasing functions of the rotation speed. In the limit of small rotation speed, the critical flux is small and the critical ring is narrow and thin, leading to a small critical load. In the limit of large rotation speed, the critical flux is large and the critical ring is wide on the upper half of the cylinder and thick on the lower half of the cylinder, leading to a large critical load. We also describe the behaviour of the non-critical full-ring solution and, in particular, show that the semi-width and the ring profile are increasing functions of the load but, in general, non-monotonic functions of the rotation speed. In the limit of large rotation speed, the ring approaches a limiting non-uniform shape, whereas in the limit of small load, the ring is narrow and thin with a uniform parabolic profile. Finally, we show that, while for most values of the rotation speed and the load the azimuthal velocity is in the same direction as the rotation of the cylinder, there is a region of parameter space close to the critical solution for sufficiently small rotation speed in which backflow occurs in a small region on the upward-moving side of the cylinder. © 2013
Directory of Open Access Journals (Sweden)
Zhi-jian Wang
2013-01-01
Full Text Available The three-dimensional flow physical model of any stage of the 20BZ4 multistage centrifugal pump is built which includes inlet region, impeller flow region, guide-vane flow region and exit region. The three-dimensional unsteady turbulent flow numerical model is created based on Navier-Stoke solver and standard k-ε turbulent equations. The method of multireference frame (MRF and SIMPLE algorithm are used to simulate the flow in multistage centrifugal pump based on FLUENT software. The distributions of relative velocity, absolute velocity, static pressure, and total pressure in guide vanes and impellers under design condition are analyzed. The simulation results show that the flow in impeller is mostly uniform, without eddy, backflow, and separation flow, and jet-wake phenomenon appears only along individual blades. There is secondary flow at blade end and exit of guide vane. Due to the different blade numbers of guide vane and impeller, the total pressure distribution is asymmetric. This paper also simulates the flow under different working conditions to predict the hydraulic performances of centrifugal pump and external characteristics including flow-lift, flow-shaft power, and flow-efficiency are attained. The simulation results are compared with the experimental results, and because of the mechanical losses and volume loss ignored, there is a little difference between them.
Scherbaum, Frank
1990-08-01
The estimation of Q values and/or source corner frequencies fc from single-station narrow-band recordings of microearthquake spectra is a strongly nonunique problem. This is due to the fact that the spectra can be equally well fitted with low-Q/high-fc or a high-Q/low-fc spectral models. Here, a method is proposed to constrain this ambiguity by inverting a set of microearthquake spectra for a three-dimensional Q model structure and model source parameters seismic moment (Mo ) and corner frequency (fc ) simultaneously. The inversion of whole path Q can be stated as a linear problem in the attenuation operator t* and solved using a tomographic reconstruction of the three-dimensional Q structure. This Q structure is then used as a "geometrical constraint" for a nonlinear Marquardt-Levenberg inversion of Mo and fc and a new Q value. The first step of the method consists of interactively fitting the observed microearthquake spectra by spectral models consisting of a source spectrum with an assumed high-frequency decay, a single-layer resonance filter to account for local site effects, and additional "whole path attenuation" along the ray path. From the obtained Q values, a three-dimensional Q model is calculated using a tomographic reconstruction technique (SIRT). The individual Q values along each ray path are then used as Q starting values for a nonlinear iterative Marquardt-Levenberg inversion of Mo and fc and a "new" Q value. Subsequently, the "new" Q values are used to reconstruct the next Q model which again provides starting values for the "next" nonlinear inversion of Mo, fc, and Q. This process is repeated until the "goodness of fit measure" indicates no further improvement of the results. The method has been tested on a set of approximately 2800 P wave spectra (0.9 effects close to the surface shows that site effects may cause a corruption of the resulting Q model at shallow depths. For the given data set and depths below 3-5 km, the method is believed to be
Directory of Open Access Journals (Sweden)
Xuejiao Jin
2018-01-01
Full Text Available Positive-sense (+ RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+ RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D imaging technologies, such as electron tomography (ET and focused ion beam-scanning electron microscopy (FIB-SEM, has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.
Jin, Xuejiao; Cao, Xiuling; Wang, Xueting; Jiang, Jun; Wan, Juan; Laliberté, Jean-François; Zhang, Yongliang
2018-01-01
Positive-sense (+) RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+) RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D) imaging technologies, such as electron tomography (ET) and focused ion beam-scanning electron microscopy (FIB-SEM), has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.
A Three-Dimensional Enormous Surface Area Aluminum Microneedle Array with Nanoporous Structure
Directory of Open Access Journals (Sweden)
Po Chun Chen
2013-01-01
Full Text Available We proposed fabricating an aluminum microneedle array with a nanochannel structure on the surface by combining micromachining, electrolyte polishing, and anodization methods. The microneedle array provides a three-dimensional (3D structure that possesses several hundred times more surface area than a traditional nanochannel template. Therefore, the microneedle array can potentially be used in many technology applications. This 3D microneedle array device can not only be used for painless injection or extraction, but also for storage, highly sensitive detection, drug delivery, and microelectrodes. From the calculation we made, the microneedle array not only increases surface area, but also enlarges the capacity of the device. Therefore, the microneedle array can further be used on many detecting, storing, or drug delivering applications.
A Three-Dimensional Enormous Surface Area Aluminum Microneedle Array with Nanoporous Structure
International Nuclear Information System (INIS)
Chen, P.Ch.; Zou, J.; Hsieh, Sh.J.; Chen, Ch.Ch.
2013-01-01
We proposed fabricating an aluminum micro needle array with a nano channel structure on the surface by combining micromachining, electrolyte polishing, and anodization methods. The micro needle array provides a three-dimensional (3D) structure that possesses several hundred times more surface area than a traditional nano channel template. Therefore, the micro needle array can potentially be used in many technology applications. This 3D micro needle array device can not only be used for painless injection or extraction, but also for storage, highly sensitive detection, drug delivery, and microelectrodes. From the calculation we made, the micro needle array not only increases surface area, but also enlarges the capacity of the device. Therefore, the micro needle array can further be used on many detecting, storing, or drug delivering applications.
Kasoju, Aruna; Narasu, M Lakshmi; Muvva, Charuvaka; Subbarao, Bathula Vv
2012-01-01
Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.
Magnetic field effect in three-dimensional flow of an Oldroyd-B nanofluid over a radiative surface
Energy Technology Data Exchange (ETDEWEB)
Shehzad, S.A., E-mail: ali_qau70@yahoo.com [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan); Abdullah, Z. [Department of Mathematics, Comsats Institute of Information Technology, Sahiwal 57000 (Pakistan); Abbasi, F.M. [Department of Mathematics, Comsats Institute of Information Technology, Islamabad 44000 (Pakistan); Hayat, T. [Department of Mathematics, Quaid-I-Azam University 45320, Islamabad 44000 (Pakistan); Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Faculty of Science, King Abdulaziz University, P. O. Box 80257, Jeddah 21589 (Saudi Arabia); Alsaedi, A. [Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Faculty of Science, King Abdulaziz University, P. O. Box 80257, Jeddah 21589 (Saudi Arabia)
2016-02-01
This article investigates the convective heat and mass conditions in three-dimensional flow of an Oldroyd-B nanofluid. The stretched flow is electrically conducting in the presence of an applied magnetic field. Thermal radiation effects are accounted in the energy equation. The governing nonlinear problems are computed for the convergent approximate solutions. Influences of different parameters on the dimensionless temperature and nanoparticle concentration fields are shown and examined. Quantities of physical interest namely local Nusselt and Sherwood numbers are computed and analyzed numerically. Comparison in a limiting case is made with the previous published result and an excellent agreement is noted. - Highlights: • Impact of magnetic field in three-dimensional flow is investigated. • Thermal radiation effects are accounted in the energy equation. • Convective type conditions of temperature and concentration are imposed. • The governing nonlinear problems are computed for the convergent approximate solutions. • Influences of different parameters are shown and examined.
Impact of genetic variation on three dimensional structure and function of proteins.
Directory of Open Access Journals (Sweden)
Roshni Bhattacharya
Full Text Available The Protein Data Bank (PDB; http://wwpdb.org was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D structures of biological macromolecules (proteins, DNA, RNA, all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation.
Romero-Brey, Inés; Merz, Andreas; Chiramel, Abhilash; Lee, Ji-Young; Chlanda, Petr; Haselman, Uta; Santarella-Mellwig, Rachel; Habermann, Anja; Hoppe, Simone; Kallis, Stephanie; Walther, Paul; Antony, Claude; Krijnse-Locker, Jacomine; Bartenschlager, Ralf
2012-01-01
All positive strand RNA viruses are known to replicate their genomes in close association with intracellular membranes. In case of the hepatitis C virus (HCV), a member of the family Flaviviridae, infected cells contain accumulations of vesicles forming a membranous web (MW) that is thought to be the site of viral RNA replication. However, little is known about the biogenesis and three-dimensional structure of the MW. In this study we used a combination of immunofluorescence- and electron microscopy (EM)-based methods to analyze the membranous structures induced by HCV in infected cells. We found that the MW is derived primarily from the endoplasmic reticulum (ER) and contains markers of rough ER as well as markers of early and late endosomes, COP vesicles, mitochondria and lipid droplets (LDs). The main constituents of the MW are single and double membrane vesicles (DMVs). The latter predominate and the kinetic of their appearance correlates with kinetics of viral RNA replication. DMVs are induced primarily by NS5A whereas NS4B induces single membrane vesicles arguing that MW formation requires the concerted action of several HCV replicase proteins. Three-dimensional reconstructions identify DMVs as protrusions from the ER membrane into the cytosol, frequently connected to the ER membrane via a neck-like structure. In addition, late in infection multi-membrane vesicles become evident, presumably as a result of a stress-induced reaction. Thus, the morphology of the membranous rearrangements induced in HCV-infected cells resemble those of the unrelated picorna-, corona- and arteriviruses, but are clearly distinct from those of the closely related flaviviruses. These results reveal unexpected similarities between HCV and distantly related positive-strand RNA viruses presumably reflecting similarities in cellular pathways exploited by these viruses to establish their membranous replication factories.
International Nuclear Information System (INIS)
Kulak, R.F.; Belytschko, T.B.
1975-09-01
The formulation of a finite-element procedure for the implicit transient and static analysis of plate/shell type structures in three-dimensional space is described. The triangular plate/shell element can sustain both membrane and bending stresses. Both geometric and material nonlinearities can be treated, and an elastic-plastic material law has been incorporated. The formulation permits the element to undergo arbitrarily large rotations and translations; but, in its present form it is restricted to small strains. The discretized equations of motion are obtained by a stiffness method. An implicit integration algorithm based on trapezoidal integration formulas is used to integrate the discretized equations of motion in time. To ensure numerical stability, an iterative solution procedure with equilibrium checks is used
Production of three-dimensional structures of PHB using selective laser sintering
International Nuclear Information System (INIS)
Pereira, Tatiana F.; Costa, Marysilvia F.; Thire, Rossana M.S.M.; Oliveira, Marcelo F.; Maia, Izaque A.; Silva, Jorge V.L.
2011-01-01
Selective Laser Sintering (SLS) is a technology of layer-by-layer fabrication of three-dimensional physical models directly from their computational design. The poly(3-hydroxybutyrate) (PHB) is a microbial, biodegradable and semicrystalline polyester. The objective of this work was to produce PHB parts, evaluating the reuse of material in the production of the new parts. Images of SEM of part surface showed the formation of neck that indicates sintering between PHB particles during processing. Analysis of NMR and DSC of the reused polymer showed no changes in the chemical structure and thermal properties of PHB. The parts produced from virgin and reused PHB showed no significant difference in their thermal properties. This could suggest that the reuse of raw material did not influence the process reproducibility. (author)
Directory of Open Access Journals (Sweden)
Lucas Eduardo Ritacco
2013-01-01
Full Text Available Structural bone allograft has been used in bone defect reconstruction during the last fifty years with acceptable results. However, allograft selection methods were based on 2-dimensional templates using X-rays. Thanks to preoperative planning platforms, three-dimensional (3D CT-derived bone models were used to define size and shape comparison between host and donor. The purpose of this study was to describe the workflow of this virtual technique in order to explain how to choose the best allograft using a virtual bone bank system. We measured all bones in a 3D virtual environment determining the best match. The use of a virtual bone bank system has allowed optimizing the allograft selection in a bone bank, providing more information to the surgeons before surgery. In conclusion, 3D preoperative planning in a virtual environment for allograft selection is an important and helpful tool in order to achieve a good match between host and donor.
Gauge structure, anomalies and mass generation in a three dimensional thirring model
International Nuclear Information System (INIS)
Gomes, M.; Mendes, R.S.; Ribeiro, R.F.; Silva, A.J. da.
1990-05-01
We consider a three dimensional model of spinor fields with a Thirring like, quadrilinear self interaction. Using either two or four component Dirac spinors, we prove that the 1/N expansion for the model is renormalizable if a gauge structure to select physical quantities is introduced. For certain values of the coupling the leading 1/N approximation exihibits bound state poles. Dynamical breaking of parity or chiral symmetry is shown to occur as a cooperative effect of different orders of 1/N, if N is smaller than the critical value N c = 128 / x 2 D' , where D is two or four depending on wether the fermion field has two or four components. (author) [pt
Son, Geunsoo; Kim, Dongsu; Kim, YoungDo; Lyu, Siwan; Kim, Seojun
2017-04-01
concentration by using acoustic backscatter. Cross-sectional ADCP measurements in a confluence were collected with high spatial resolution in order to analyze the details of spatial distribution in the perspective of the three-dimensional mixing patterns of flow and sediment, where backscatters (or SNR) measured from ADCPs were used to track sediment mixing assuming that it could be a surrogate to estimate the suspended sediment concentration. Raw backscatter data were corrected by considering the beam spreading and absorption by water. Also, an optical Laser diffraction instrument (LISST) was used to verify the method of acoustic backscatter and to collect the particle size distribution of main stream and tributary. In addition, image-based spatial distributions of sediment mixture in the confluence were monitored in various flow conditions by using an unmanned aerial vehicle (UAV), which were compared with the spatial distribution of acoustic backscatter. As results, we found that when acoustic backscatter and flow measurements by ADCPs were well processed, they could be proper indicators to identify the spatial patterns of the three-dimensional mixing process between two rivers.
Suzuki, Kohei; Omori, Takesi; Kajishima, Takeo
2014-11-01
Although the advantage of using arbitrarily-shaped polyhedral meshes for the industrial flow applications is clear, their employment to two-phase flows is rather limited due to the poor prediction accuracy of the existing numerical methods on such meshes. We present a numerical method based on VOF (Volume of Fluid) method which works on arbitrarily-shaped three-dimensional polyhedral meshes with little volume/shape error for the interface advection and with little curvature estimation error. To make the implementation in three-dimensional geometry feasible, we extend THINC (Tangent of Hyperbola Interface Capturing) method for polyhedral meshes which does not require laborious geometric arithmetics. In the oral presentation we will also show that the combination of RDF (Reconstructed Distance Function) algorithm and the carefully selected discretization procedure gives good performance in the interface curvature estimation.
Directory of Open Access Journals (Sweden)
Khansa Rubab
Full Text Available This letter investigates the MHD three-dimensional flow of upper-convected Maxwell (UCM fluid over a bi-directional stretching surface by considering the Cattaneo-Christov heat flux model. This model has tendency to capture the characteristics of thermal relaxation time. The governing partial differential equations even after employing the boundary layer approximations are non linear. Accurate analytic solutions for velocity and temperature distributions are computed through well-known homotopy analysis method (HAM. It is noticed that velocity decreases and temperature rises when stronger magnetic field strength is accounted. Penetration depth of temperature is a decreasing function of thermal relaxation time. The analysis for classical Fourier heat conduction law can be obtained as a special case of the present work. To our knowledge, the Cattaneo-Christov heat flux model law for three-dimensional viscoelastic flow problem is just introduced here.
Rubab, Khansa; Mustafa, M
2016-01-01
This letter investigates the MHD three-dimensional flow of upper-convected Maxwell (UCM) fluid over a bi-directional stretching surface by considering the Cattaneo-Christov heat flux model. This model has tendency to capture the characteristics of thermal relaxation time. The governing partial differential equations even after employing the boundary layer approximations are non linear. Accurate analytic solutions for velocity and temperature distributions are computed through well-known homotopy analysis method (HAM). It is noticed that velocity decreases and temperature rises when stronger magnetic field strength is accounted. Penetration depth of temperature is a decreasing function of thermal relaxation time. The analysis for classical Fourier heat conduction law can be obtained as a special case of the present work. To our knowledge, the Cattaneo-Christov heat flux model law for three-dimensional viscoelastic flow problem is just introduced here.
Spatial patterns in the effects of fire on savanna vegetation three-dimensional structure.
Levick, Shaun R; Asner, Gregory P; Smit, Izak P J
2012-12-01
Spatial variability in the effects of fire on savanna vegetation structure is seldom considered in ecology, despite the inherent heterogeneity of savanna landscapes. Much has been learned about the effects of fire on vegetation structure from long-term field experiments, but these are often of limited spatial extent and do not encompass different hillslope catena elements. We mapped vegetation three-dimensional (3-D) structure over 21 000 ha in nine savanna landscapes (six on granite, three on basalt), each with contrasting long-term fire histories (higher and lower fire frequency), as defined from a combination of satellite imagery and 67 years of management records. Higher fire frequency areas contained less woody canopy cover than their lower fire frequency counterparts in all landscapes, and woody cover reduction increased linearly with increasing difference in fire frequency (r2 = 0.58, P = 0.004). Vegetation height displayed a more heterogeneous response to difference in fire frequency, with taller canopies present in the higher fire frequency areas of the wetter sites. Vegetation 3-D structural differences between areas of higher and lower fire frequency differed between geological substrates and varied spatially across hillslopes. Fire had the greatest relative impact on vegetation structure on nutrient-rich basalt substrates, and it imparted different structural responses upon vegetation in upland, midslope, and lowland topographic positions. These results highlight the complexity of fire vegetation relationships in savanna systems, and they suggest that underlying landscape heterogeneity needs more explicit incorporation into fire management policies.
Directory of Open Access Journals (Sweden)
Saeed Dinarvand
2012-01-01
Full Text Available The steady three-dimensional flow of condensation or spraying on inclined spinning disk is studied analytically. The governing nonlinear equations and their associated boundary conditions are transformed into the system of nonlinear ordinary differential equations. The series solution of the problem is obtained by utilizing the homotopy perturbation method (HPM. The velocity and temperature profiles are shown and the influence of Prandtl number on the heat transfer and Nusselt number is discussed in detail. The validity of our solutions is verified by the numerical results. Unlike free surface flows on an incline, this through flow is highly affected by the spray rate and the rotation of the disk.
Chu, H K; Huan, Z; Mills, J K; Yang, J; Sun, D
2015-02-07
Cell manipulation is imperative to the areas of cellular biology and tissue engineering, providing them a useful tool for patterning cells into cellular patterns for different analyses and applications. This paper presents a novel approach to perform three-dimensional (3D) cell manipulation and patterning with a multi-layer engineered scaffold. This scaffold structure employed dielectrophoresis as the non-contact mechanism to manipulate cells in the 3D domain. Through establishing electric fields via this multi-layer structure, the cells in the medium became polarized and were attracted towards the interior part of the structure, forming 3D cellular patterns. Experiments were conducted to evaluate the manipulation and the patterning processes with the proposed structure. Results show that with the presence of a voltage input, this multi-layer structure was capable of manipulating different types of biological cells examined through dielectrophoresis, enabling automatic cell patterning in the time-scale of minutes. The effects of the voltage input on the resultant cellular pattern were examined and discussed. Viability test was performed after the patterning operation and the results confirmed that majority of the cells remained viable. After 7 days of culture, 3D cellular patterns were observed through SEM. The results suggest that this scaffold and its automated dielectrophoresis-based patterning mechanism can be used to construct artificial tissues for various tissue engineering applications.
Karpov, D; Liu, Z; Rolo, T Dos Santos; Harder, R; Balachandran, P V; Xue, D; Lookman, T; Fohtung, E
2017-08-17
Topological defects of spontaneous polarization are extensively studied as templates for unique physical phenomena and in the design of reconfigurable electronic devices. Experimental investigations of the complex topologies of polarization have been limited to surface phenomena, which has restricted the probing of the dynamic volumetric domain morphology in operando. Here, we utilize Bragg coherent diffractive imaging of a single BaTiO 3 nanoparticle in a composite polymer/ferroelectric capacitor to study the behavior of a three-dimensional vortex formed due to competing interactions involving ferroelectric domains. Our investigation of the structural phase transitions under the influence of an external electric field shows a mobile vortex core exhibiting a reversible hysteretic transformation path. We also study the toroidal moment of the vortex under the action of the field. Our results open avenues for the study of the structure and evolution of polar vortices and other topological structures in operando in functional materials under cross field configurations.Imaging of topological states of matter such as vortex configurations has generally been limited to 2D surface effects. Here Karpov et al. study the volumetric structure and dynamics of a vortex core mediated by electric-field induced structural phase transition in a ferroelectric BaTiO 3 nanoparticle.
Quasiconservation laws for compressible three-dimensional Navier-Stokes flow.
Gibbon, J D; Holm, D D
2012-10-01
We formulate the quasi-Lagrangian fluid transport dynamics of mass density ρ and the projection q=ω·∇ρ of the vorticity ω onto the density gradient, as determined by the three-dimensional compressible Navier-Stokes equations for an ideal gas, although the results apply for an arbitrary equation of state. It turns out that the quasi-Lagrangian transport of q cannot cross a level set of ρ. That is, in this formulation, level sets of ρ (isopycnals) are impermeable to the transport of the projection q.
Oba, Yoshiyuki; De Messemaeker, Joke; Tyrovouzi, Anna Maria; Miyamori, Yuichi; De Vos, Joeri; Wang, Teng; Beyer, Gerald; Beyne, Eric; De Wolf, Ingrid; Croes, Kristof
2015-05-01
Electromigration failure locations in three-dimensional (3D) interconnect structures with high-aspect-ratio through silicon vias, (TSVs, Φ5 × 50 µm2) connected to 40-µm-pitch CuSn solder joints have been identified using test structures which were designed to avoid failures in the back-end-of-line (BEOL). The resistance of the structures with the TSV and bump connections showed a continuous increase until failure. For the structures without a bump connection, where only TSV and re-distributed line (RDL) were the electrically connected, the resistance remained constant prior to the final failure. From cross-sectional analyses after the test, the failure locations were identified at the TSV bottom or at the bump bottom. The location of void formation was changed by applied current direction. The flux divergence generated by the barrier metal and the reservoir effect plays a crucial role in the void formation, and each failure mode is considered to have a different impact on the reliability performance.
KNApSAcK-3D: a three-dimensional structure database of plant metabolites.
Nakamura, Kensuke; Shimura, Naoki; Otabe, Yuuki; Hirai-Morita, Aki; Nakamura, Yukiko; Ono, Naoaki; Ul-Amin, Md Altaf; Kanaya, Shigehiko
2013-02-01
Studies on plant metabolites have attracted significant attention in recent years. Over the past 8 years, we have constructed a unique metabolite database, called KNApSAcK, that contains information on the relationships between metabolites and their expressing organism(s). In the present paper, we introduce KNApSAcK-3D, which contains the three-dimensional (3D) structures of all of the metabolic compounds included in the original KNApSAcK database. The 3D structure for each compound was optimized using the Merck Molecular Force Field (MMFF94), and a multiobjective genetic algorithm was used to search extensively for possible conformations and locate the global minimum. The resulting set of structures may be used for docking studies to identify new and potentially unexpected binding sites for target proteins. The 3D structures may also be utilized for more qualitative studies, such as the estimation of biological activities using 3D-QSAR. The database can be accessed via a link from the KNApSAcK Family website (http://kanaya.naist.jp/KNApSAcK_Family/) or directory at http://kanaya.naist.jp/knapsack3d/.
Growth mechanism of InGaN nanodots on three-dimensional GaN structures
Energy Technology Data Exchange (ETDEWEB)
Park, Donghwy; Min, Daehong; Nam, Okhyun [Department of Nano-Optical Engineering, Convergence Center for Advanced Nano-Semiconductor (CANS), Korea Polytechnic University (KPU), Siheung-si, Gyeonggi-do (Korea, Republic of)
2017-07-15
In this study, we investigated the growth mechanism of indium gallium nitride (InGaN) nanodots (NDs) and an InGaN layer, which were simultaneously formed on a three-dimensional (3D) gallium nitride (GaN) structure, having (0001) polar, (11-22) semi-polar, and (11-20) nonpolar facets. We observed the difference in the morphological and compositional properties of the InGaN structures. From the high resolution transmission electron microscopy (HR-TEM) images, it can be seen that the InGaN NDs were formed only on the polar and nonpolar facets, whereas an InGaN layer was formed on the semi-polar facet. The indium composition variation in all the InGaN structures was observed using scanning transmission electron microscopy (STEM) and the energy dispersive X-ray spectroscopy (EDS). The different growth mechanism can be explained by two reasons: (i) The difference in the diffusivities of indium and gallium adatoms at each facet of 3D GaN structure; and (ii) the difference in the kinetic Wulff plots of polar, semi-polar, and nonpolar GaN planes. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Potentially of using vertical and three dimensional isolation systems in nuclear structures
Energy Technology Data Exchange (ETDEWEB)
Zhou, Zhiuang [Research Institute of Structural Engineering and Disaster Reduction, Tongji University, Shanghai (China); Wong, Jenna [Lawrence Berkeley National Laboratories, Berkeley (United States); Mahin, Stephen [University of California, Berkeley (United States)
2016-10-15
Although the horizontal component of an earthquake response can be significantly reduced through the use of conventional seismic isolators, the vertical component of excitation is still transmitted directly into the structure. Records from instrumented structures, and some recent tests and analyses have actually seen increases in vertical responses in base isolated structures under the combined effects of horizontal and vertical ground motions. This issue becomes a great concern to facilities such as a Nuclear Power Plants (NPP), with specialized equipment and machinery that is not only expensive, but critical to safe operation. As such, there is considerable interest worldwide in vertical and three-dimensional (3D) isolation systems. This paper examines several vertical and 3D isolation systems that have been proposed and their potential application to modern nuclear facilities. In particular, a series of case study analyses of a modern NPP model are performed to examine the benefits and challenges associated with 3D isolation compared with horizontal isolation. It was found that compared with the general horizontal isolators, isolators that have vertical frequencies of no more than 3 Hz can effectively reduce the vertical in-structure responses for the studied NPP model. Among the studied cases, the case that has a vertical isolation frequency of 3 Hz is the one that can keep the horizontal period of the isolators as the first period while having the most flexible vertical isolator properties. When the vertical frequency of isolators reduces to 1 Hz, the rocking effect is obvious and rocking restraining devices are necessary.
Three dimensional simulation of giant magneto-impedance effect in thin film structures
Li, Bodong
2011-04-04
In this paper, a three dimensional model for the giant magneto-impedance (GMI) effect in thin film structures is developed using the finite element method(FEM) with a GMI permeability model embedded. One-layer, three-layer, and five-layer thin film structures are simulated. The GMI effect and the sensitivity are calculated as a function of the external magnetic field, driving frequency, and the thickness of the magnetic layers. The results show that the five-layer structure has the best performance, which is in accordance with experimental results. The GMI ratio and the sensitivity first improve with the increasing thickness of the magnetic layer but reach saturation at a certain value of the thickness. In a five-layer structure,saturation of the GMI effect becomes effective at about 3 μm thickness of the magnetic layers, where a GMI ratio of 1125% was obtained, with a corresponding sensitivity of 0.37%/A/m (29.6%/Oe).
Three-dimensional Nanowire Structures for Ultra-Fast Separation of DNA, Protein and RNA Molecules
Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu
2015-01-01
Separation and analysis of biomolecules represent crucial processes for biological and biomedical engineering development; however, separation resolution and speed for biomolecules analysis still require improvements. To achieve separation and analysis of biomolecules in a short time, the use of highly-ordered nanostructures fabricated by top-down or bottom-up approaches have been proposed. Here, we reported on the use of three-dimensional (3D) nanowire structures embedded in microchannels fabricated by a bottom-up approach for ultrafast separation of small biomolecules, such as DNA, protein, and RNA molecules. The 3D nanowire structures could analyze a mixture of DNA molecules (50–1000 bp) within 50 s, a mixture of protein molecules (20–340 kDa) within 5 s, and a mixture of RNA molecules (100–1000 bases) within 25 s. And, we could observe the electrophoretic mobility difference of biomolecules as a function of molecular size in the 3D nanowire structures. Since the present methodology allows users to control the pore size of sieving materials by varying the number of cycles for nanowire growth, the 3D nanowire structures have a good potential for use as alternatives for other sieving materials. PMID:26073192
Morphology and Three-Dimensional Inhalation Flow in Human Airways in Healthy and Diseased Subjects
Van de Moortele, Tristan
We investigate experimentally the relation between anatomical structure and respiratory function in healthy and diseased airways. Computed Tomography (CT) scans of human lungs are analyzed from the data base of a large multi-institution clinical study on Chronic Obstructive Pulmonary Disease (COPD). Through segmentation, the 3D volumes of the airways are determined at total lung capacity. A geometric analysis provides data on the morphometry of the airways, including the length and diameter of branches, the child-to-parent diameter ratio, and branching angles. While several geometric parameters are confirmed to match past studies for healthy subjects, previously unreported trends are reported on the length of branches. Specifically, in most dichotomous airway bifurcation, the branch of smaller diameter tends to be significantly longer than the one of larger diameter. Additionally, the branch diameter tends to be smaller in diseased airways than in healthy airways up to the 7th generation of bronchial branching. 3D fractal analysis is also performed on the airway volume. Fractal dimensions of 1.89 and 1.83 are found for healthy non-smokers and declining COPD subjects, respectively, furthering the belief that COPD (and lung disease in general) significantly affects the morphometry of the airways already in early stages of the disease. To investigate the inspiratory flow, 3D flow models of the airways are generated using Computer Aided Design (CAD) software and 3D printed. Using Magnetic Resonance Velocimetry (MRV), 3-component 3D flow fields are acquired for steady inhalation at Reynolds number Re 2000 defined at the trachea. Analysis of the flow data reveals that diseased subjects may experience greater secondary flow strength in their conducting airways, especially in deeper generations.
Trapnell, Dorset W; Hamrick, J L; Nason, John D
2004-05-01
Epiphytic plants occupy three-dimensional space, which allows more individuals to be closely clustered spatially than is possible for populations occupying two dimensions. The unique characteristics of epiphytes can act in concert to influence the fine-scale genetic structure of their populations which can, in turn, influence mating patterns and other population phenomena. Three large populations of Laelia rubescens (Orchidaceae) in the Costa Rican seasonal dry forest were sampled at two levels of intensity to determine: (i) whether individual clusters contain more than one genotype, and (ii) the spatial distribution and fine-scale genetic structure of genotypes within populations. Samples were assayed for their multilocus allozyme genotypes and spatial autocorrelation analyses were performed. High levels of genetic diversity, high genotypic diversity and low among-population variation were found. In the larger clusters, multiple genets per cluster were common with discrete clusters containing up to nine genotypes. Spatial autocorrelation analyses indicated significant positive genetic structure at distances of
Three-dimensional glue detection and evaluation based on linear structured light
Xiao, Zhitao; Yang, Ruipeng; Geng, Lei; Liu, Yanbei
2018-01-01
During the online glue detection of body in white (BIW), the purpose of traditional glue detection based on machine vision is the localization and segmentation of glue, which is dissatisfactory for estimating the uniformity of glue with complex shape. A three-dimensional glue detection method based on the linear structured light and the movement parameters of robot is proposed. Firstly, the linear structured light and epipolar constraint algorithm are used for sign matching of binocular vision. Then, hand-eye relationship between robot and binocular camera is utilized to unified coordinate system. Finally, a structured light stripe extraction method is proposed to extract the sub-pixel coordinates of the light strip center. Experiments results demonstrate that the propose method can estimate the shape of glue accurately. For three kinds of glue with complex shape and uneven illumination, our method can detect the positions of blemishes. The absolute error of measurement is less than 1.04mm and the relative error is less than 10% respectively, which is suitable for online glue detection in BIW.
Stereo-vision three-dimensional reconstruction of curvilinear structures imaged with a TEM.
Oveisi, Emad; Letouzey, Antoine; De Zanet, Sandro; Lucas, Guillaume; Cantoni, Marco; Fua, Pascal; Hébert, Cécile
2018-01-01
Deriving accurate three-dimensional (3-D) structural information of materials at the nanometre level is often crucial for understanding their properties. Tomography in transmission electron microscopy (TEM) is a powerful technique that provides such information. It is however demanding and sometimes inapplicable, as it requires the acquisition of multiple images within a large tilt arc and hence prolonged exposure to electrons. In some cases, prior knowledge about the structure can tremendously simplify the 3-D reconstruction if incorporated adequately. Here, a novel algorithm is presented that is able to produce a full 3-D reconstruction of curvilinear structures from stereo pair of TEM images acquired within a small tilt range that spans from only a few to tens of degrees. Reliability of the algorithm is demonstrated through reconstruction of a model 3-D object from its simulated projections, and is compared with that of conventional tomography. This method is experimentally demonstrated for the 3-D visualization of dislocation arrangements in a deformed metallic micro-pillar. Copyright © 2017. Published by Elsevier B.V.
Three-dimensional structure and evolution of an asymmetric pull-apart basin
Sagy, Amir; Hamiel, Yariv
2017-07-01
The structure of a 250-m-long asymmetrical pull-apart basin developed in carbonate rocks at the Galilee heights, Israel, is herein analyzed. The reconstruction of the basin geometry is based on detailed mapping and LiDAR measurements of fault scarps. The architecture of faults is then used as a boundary condition for calculating the stress pattern in the vicinity of the basin, using a dislocation model. The basin is found to be an asymmetrical V-shaped structure bordered by two longitudinal oblique right-lateral strike-slip faults. The strike of one of the faults is bent at the eastern edge of the basin, generating a transverse boundary fault which joins the second boundary fault orthogonally. The overall lateral displacement is smaller than the basin length, and no transverse or diagonal fault is observed in the western end of the basin. The deformation around the basin is mostly displayed by fractures. Yet, folds and fault branches are observed near the tips of the boundary faults and near kink points of fault segments. Stress analysis obtained by the three-dimensional model is in general agreement with the orientation of fractures and location of high deformation regions in and around the basin. Based on our observations, we present a conceptual model which demonstrates the development of asymmetric basins in releasing bends and sheds light on the structures of similar large pull-apart basins.
Feinberg, Adam
We demonstrate the additive manufacturing of complex three-dimensional (3D) structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels (FRESH), enables 3D printing of hydrated materials with an elastic modulus less than 500 kPa including alginate, collagen, hyaluronic acid and fibrin. A range of crosslinking mechanisms can be used depending on the polymer being printed, including ionic, enzymatic, pH, thermal and light based approaches. CAD models of 3D optical, computed tomography, and magnetic resonance imaging data can be 3D printed at a resolution of 100 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains are mechanically robust and recreate complex 3D internal and external anatomical architectures. Recent advances have improved the resolution and broadened the range of materials that can be FRESH 3D printed. This work was supported in part by the NIH Director's New Innovator Award (DP2HL117750) and the NSF CAREER Award (1454248).
Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure.
Yu, Xiaxia; Weber, Irene T; Harrison, Robert W
2014-01-01
Drug resistance has become a severe challenge for treatment of HIV infections. Mutations accumulate in the HIV genome and make certain drugs ineffective. Prediction of resistance from genotype data is a valuable guide in choice of drugs for effective therapy. In order to improve the computational prediction of resistance from genotype data we have developed a unified encoding of the protein sequence and three-dimensional protein structure of the drug target for classification and regression analysis. The method was tested on genotype-resistance data for mutants of HIV protease and reverse transcriptase. Our graph based sequence-structure approach gives high accuracy with a new sparse dictionary classification method, as well as support vector machine and artificial neural networks classifiers. Cross-validated regression analysis with the sparse dictionary gave excellent correlation between predicted and observed resistance. The approach of encoding the protein structure and sequence as a 210-dimensional vector, based on Delaunay triangulation, has promise as an accurate method for predicting resistance from sequence for drugs inhibiting HIV protease and reverse transcriptase.
Lemos, Raquel; Santana, Isabel; Caetano, Gina; Bernardino, Inês; Morais, Ricardo; Farivar, Reza; Castelo-Branco, Miguel
2016-08-01
Mild cognitive impairment (MCI) has been associated with a high risk of conversion to Alzheimer's dementia. In addition to memory complaints, impairments in the visuospatial domain have been reported in this condition. We have previously shown that deficits in perceiving structure-from-motion (SFM) objects are reflected in functional reorganization of brain activity within the visual ventral stream. Here we aimed to identify structural correlates of psychophysical complex face and object recognition performance in amnestic MCI patients (n=30 vs. n=25 controls). This study was, therefore, motivated by evidence from recent studies showing that a combination of visual information across dorsal and ventral visual streams may be needed for the perception of three-dimensional (3D) SFM objects. In our experimental paradigm, participants had to discriminate 3D SFM shapes (faces and objects) from 3D SFM meaningless (scrambled) shapes. Morphometric analysis established neuroanatomical evidence for impairment in MCI as demonstrated by smaller hippocampal volumes. We found association between cortical thickness and face recognition performance, comprising the occipital lobe and visual ventral stream fusiform regions (overlapping the known location of face fusiform area) in the right hemisphere, in MCI. We conclude that impairment of 3D visual integration exists at the MCI stage involving also the visual ventral stream and contributing to face recognition deficits. The specificity of such observed structure-function correlation for faces suggests a special role of this processing pathway in health and disease. (JINS, 2016, 22, 744-754).
Three-dimensional printing of shape memory hydrogels with internal structure for drug delivery.
Wang, Yongzhou; Miao, Ying; Zhang, Jieling; Wu, Jian Ping; Kirk, Thomas Brett; Xu, Jiake; Ma, Dong; Xue, Wei
2018-03-01
Hydrogels with shape memory behavior and internal structure have wide applications in fields ranging from tissue engineering and medical instruments to drug delivery; however, creating the hydrogels has proven to be extremely challenging. This study presents a three-dimensional (3D) printing technology to fabricate the shape memory hydrogels with internal structure (SMHs) by combining sodium alginate (alginate) and pluronic F127 diacrylate macromer (F127DA). SMHs were constituted by a dual network structure. One is a stable network which is formed by F127DA photo-crosslinking; the other one is a reversible network which is formed by Ca 2+ cross-linked alginate. SMHs recovery ratio was 98.15% in 10min after Ca 2+ was removed in the Na 2 CO 3 solution, and the elastic modulus remains essentially stable after the shape memory cycle. It showed that the drug releasing rate is more rapid compared with traditional drug-loaded hydrogels in in vitro experiments. The viability of 3T3 fibroblasts remained intact which revealed its excellent biocompatibility. Therefore, SMHs have a huge prospect for application in drug carriers and tissue engineering scaffold. Copyright © 2017 Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Bernard, J.P.; Haekkinen, J.; Sarkomaa, P.
1997-01-01
A number of numerical studies on three-dimensional flows in reactor vessels of nuclear power plants have been carried out recently. The main reason for this is the phenomenon of inherent boron dilution. These studies have been done for Loviisa nuclear power plant as well. This presentation focuses on the three dimensional modeling of Loviisa's lower plenum with the commercial CFX code. The investigations particularly deal with the modeling of the two perforated plates located at the bottom and just below the core of the vessel. The perforated plates can be modeled as porous media in the CFX code. The model has been validated against available experimental data. Velocity profiles around the plates, the pressure drop through the plates, and the simulation of mixing factors have been investigated specifically. (author)
International Nuclear Information System (INIS)
Kawai, Yoshinori; Hatae, Tanenori
1990-01-01
Computer-aided three-dimensional models of the helical structure within an apical tubule (AT) of several absorbing epithelia (kidney proximal tubule, visceral yolk sac, and ductuli efferentes) were constructed using ray-tracing graphics software to further understand the highly ordered structural configuration. Our previous electron microscopic studies using thin-section technique have first revealed the helical structure within the AT fixed in situ with a mixture of formaldehyde, glutaraldehyde, and osmium tetroxide. In the present study, we construct a computer-aided three-dimensional model of the helical structure in the AT to explain quantitative data obtained by the electron microscopy. The model could well explain several aspects of electron microscopical images and enables us to understand more clearly the three-dimensional configuration of the unique structure associated with the AT. (author)
International Nuclear Information System (INIS)
Kuwabara, Y.; Ogiwara, Y.; Suzuki, T.; Tsuchiya, H.; Nakayama, M.
1981-01-01
It is generally recognized that the earthquake response of a structure can be significantly affected by the dynamic interaction between the structure and the surrounding soil. Dynamic soil-structure interaction effects are usually analyzed by using a lumped mass model or a finite element model. In the lumped mass model, the soil is represented by springs and dashpots based on the half-space elastic theory. Each model has its advantages and limitations. The Three Dimensional Thin Layered Element Theory has been developed by Dr. Hiroshi Tajimi based on the combined results of the abovementioned lumped mass model and finite element model. The main characteristic of this theory is that, in consideration and can be applied in the analysis of many problems in soil-structure interaction, such as those involving radiation damping, embedded structures, and multi-layered soil deposits. This paper describes test results on a small scale model used to prove the validity of the computer program based on the Thin Layered Element Theory. As a numerical example, the response analysis of a PWR nuclear power plant is carried out using this program. The vibration test model is simplified and the scale is 1/750 for line. The soil layer of the model is made of congealed gelatine. The test soil layer is 80 cm long, 35 cm wide and 10 cm thick. The super structure is a one mass model made of metal sheet spring and solid mass metal. As fixed inputs, sinusoidal waves (10, 20 gal level) are used. The displacements of the top and base of the super structure, and the accelerations and the displacements of the shaking table are measured. The main parameter of the test is the shear wave velocity of the soil layer. (orig./RW)
Three-dimensional structure of olefinic thermoplastic elastomer blends using electron tomography
Sengupta, P.; Noordermeer, Jacobus W.M.
2005-01-01
The present communication reports the first use of electron tomography in reconstructing the three-dimensional morphology in thermoplastic elastomer blends. The blends investigated were dynamically vulcanized blends of ethylene-propylene-diene (EPDM) rubber/poly(propylene)/oil and
Reconstruction of Mammary Gland Structure Using Three-Dimensional Computer-Based Microscopy
National Research Council Canada - National Science Library
de
2003-01-01
During the administrative funding period of this grant we have developed a system that permits three-dimensional reconstruction of entire the entire murine ductal epithelium from physical tissue sections...
Reconstruction of Mammary Gland Structure Using Three-Dimensional Computer-Based Microscopy
National Research Council Canada - National Science Library
De Solorzano, Carlos O
2004-01-01
During the administrative funding period of this grant we have developed a system that permits three-dimensional reconstruction of entire the entire murine ductal epithelium from physical tissue sections...
Investigation of three-dimensional turbulent structures in the torsatron TJ-K
Energy Technology Data Exchange (ETDEWEB)
Mahdizadeh, N.
2007-02-14
In this work, for the first time, the three-dimensional nature of drift waves has been verified experimentally inside the confinement region of the toroidal plasma in TJ-K. The perpendicular dynamics of turbulence has been studied with the focus on the poloidal wavenumber spectra and the scaling of the turbulent structure with the drift scale. To this end, a 64 tip Langmuir probe array has been used, which is poloidally positioned on a flux surface. For the first time, the parallel dynamics of turbulence has been investigated in the core of a toroidally confined plasma. In contrast to previous experiments, multi-probe measurements were carried out to get simultaneous information on the shape and the propagation direction of the turbulent structures. The results for the parallel wave number and the parallel propagation velocity have been compared with results from the simulation code GEM3. It is demonstrated that the propagation in the direction parallel to the magnetic field is affected by Alfven dynamics. Together, these results strongly confirm previous investigations, which have demonstrated the importance of drift-wave turbulence in TJ-K and therefore also in fusion edge plasma. (orig.)
Modeling and numerical analysis of a three-dimensional shape memory alloy shell structure
Zhao, Pengtao; Qiu, Jinhao; Ji, Hongli; Wang, Mingyi; Nie, Rui
2012-04-01
In this paper, modeling and numerical analysis of a three dimensional shell structure made of shape memory alloy (SMA) are introduced. As a new smart material, SMA material has been applied in many fields due to two significant macroscopic phenomena which are called the shape memory effect (SME) and pseudoelasticity. The material of SMA exhibits two-way shape memory effect (TWSME) after undergoing especial heat treatment and thermo-mechanical training. This work investigates the numerical simulation and application of the SMA component: SMA strip, which has been pre-curved in the room temperature. The component is expected to extend upon heating and shorten on cooling along the curve. Hence the shape memory effect can be used to change the shape of the structure. The return mapping algorithm of the 3-D SMA thermomechanical constitutive equations based on Boyd-Lagoudas model is used in the finite element analysis to describe the material features of the SMA. In this paper, the ABAQUS finite element program has been utilized with a user material subroutine (UMAT) which is written in the FORTRAN code for the modeling of the SMA strip. The SMA component which has a certain initial transformation strain can emerge considerable deflection during the reverse phase transformation inducing by the temperature.
Effects of lens extirpation with anterior vitrectomy on vitreous three-dimensional mesh structure
Directory of Open Access Journals (Sweden)
Yan Zhao
2017-06-01
Full Text Available AIM: To investigate the changes in vitreous gel structure after lens extirpation combined with anterior vitrectomy in rabbit eyes. METHODS: Twenty-eight chinchilla rabbits were divided into three groups. The control group (Group I included 16 eyes from eight rabbits who did not receive any treatment. Group II included 20 eyes from 10 rabbits that underwent lens aspiration only. Group III included 20 eyes from 10 rabbits that underwent lens aspiration combined with posterior capsulotomy and anterior vitrectomy. Eyes were harvested on the 30th and 60th day postoperatively, respectively. Changes in vitreous gel stretch length due to gravity and the rate of vitreous liquefaction were observed. The collagen content in the vitreous body was examined using the L-hydroxyproline test. Electronic microscopic images were obtained from each eyeball. RESULTS: On both the 30th and 60th day postoperatively, the vitreous gel length of group III was significantly shorter than group I and group II (P<0.05, while the rate of liquefaction of the vitreous body in group III was significantly higher than group I and group II (P<0.05. The collagen content in group III was also higher than that in group I and group II (P<0.05. CONCLUSION: Loss of vitreous gel mass is more likely to occur in the eyes of rabbits receiving anterior vitrectomy. Lensectomy combined with anterior vitrectomy may damage the stable three-dimensional mesh structure of collagen, which could aggravate vitreous gel liquefaction.
Three-dimensional bioprinting is not only about cell-laden structures
Directory of Open Access Journals (Sweden)
Hong-Bo Zhang
2016-08-01
Full Text Available In this review, we focused on a few obstacles that hinder three-dimensional (3D bioprinting process in tissue engineering. One of the obstacles is the bioinks used to deliver cells. Hydrogels are the most widely used bioink materials; however, they are mechanically weak in nature and cannot meet the requirements for supporting structures, especially when the tissues, such as cartilage, require extracellular matrix to be mechanically strong. Secondly and more importantly, tissue regeneration is not only about building all the components in a way that mimics the structures of living tissues, but also about how to make the constructs function normally in the long term. One of the key issues is sufficient nutrient and oxygen supply to the engineered living constructs. The other is to coordinate the interplays between cells, bioactive agents and extracellular matrix in a natural way. This article reviews the approaches to improve the mechanical strength of hydrogels and their suitability for 3D bioprinting; moreover, the key issues of multiple cell lines coprinting with multiple growth factors, vascularization within engineered living constructs etc. were also reviewed.
Li, Guanghui; Wei, Jianhua; Wang, Xi; Wu, Guofeng; Ma, Dandan; Wang, Bo; Liu, Yanpu; Feng, Xinghua
2013-08-01
Cleft lip in the presence or absence of a cleft palate is a major public health problem. However, few studies have been published concerning the soft-tissue morphology of cleft lip infants. Currently, obtaining reliable three-dimensional (3D) surface models of infants remains a challenge. The aim of this study was to investigate a new way of capturing 3D images of cleft lip infants using a structured light scanning system. In addition, the accuracy and precision of the acquired facial 3D data were validated and compared with direct measurements. Ten unilateral cleft lip patients were enrolled in the study. Briefly, 3D facial images of the patients were acquired using a 3D scanner device before and after the surgery. Fourteen items were measured by direct anthropometry and 3D image software. The accuracy and precision of the 3D system were assessed by comparative analysis. The anthropometric data obtained using the 3D method were in agreement with the direct anthropometry measurements. All data calculated by the software were 'highly reliable' or 'reliable', as defined in the literature. The localisation of four landmarks was not consistent in repeated experiments of inter-observer reliability in preoperative images (P0.05). The structured light scanning system is proven to be a non-invasive, accurate and precise method in cleft lip anthropometry. Copyright © 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.
Investigation of three-dimensional turbulent structures in the torsatron TJ-K
International Nuclear Information System (INIS)
Mahdizadeh, N.
2007-01-01
In this work, for the first time, the three-dimensional nature of drift waves has been verified experimentally inside the confinement region of the toroidal plasma in TJ-K. The perpendicular dynamics of turbulence has been studied with the focus on the poloidal wavenumber spectra and the scaling of the turbulent structure with the drift scale. To this end, a 64 tip Langmuir probe array has been used, which is poloidally positioned on a flux surface. For the first time, the parallel dynamics of turbulence has been investigated in the core of a toroidally confined plasma. In contrast to previous experiments, multi-probe measurements were carried out to get simultaneous information on the shape and the propagation direction of the turbulent structures. The results for the parallel wave number and the parallel propagation velocity have been compared with results from the simulation code GEM3. It is demonstrated that the propagation in the direction parallel to the magnetic field is affected by Alfven dynamics. Together, these results strongly confirm previous investigations, which have demonstrated the importance of drift-wave turbulence in TJ-K and therefore also in fusion edge plasma. (orig.)
Fully three-dimensional analysis of high-speed train-track-soil-structure dynamic interaction
Galvín, P.; Romero, A.; Domínguez, J.
2010-11-01
In this paper, a general and fully three dimensional multi-body-finite element-boundary element model, formulated in the time domain to predict vibrations due to train passage at the vehicle, the track and the free field, is presented. The vehicle is modelled as a multi-body system and, therefore, the quasi-static and the dynamic excitation mechanisms due to train passage can be considered. The track is modelled using finite elements. The soil is considered as a homogeneous half-space by the boundary element method. This methodology could be used to take into account local soil discontinuities, underground constructions such as underpasses, and coupling with nearby structures that break the uniformity of the geometry along the track line. The nonlinear behaviour of the structures could be also considered. In the present paper, in order to test the model, vibrations induced by high-speed train passage are evaluated for a ballasted track. The quasi-static and dynamic load components are studied and the influence of the suspended mass on the vertical loads is analyzed. The numerical model is validated by comparison with experimental records from two HST lines. Finally, the dynamic behaviour of a transition zone between a ballast track and a slab track is analyzed and the obtained results from the proposed model are compared with those obtained from a model with invariant geometry with respect to the track direction.
Three-Dimensional Electronic Structure of the Type-II Weyl Semimetal WTe_{2}.
Di Sante, Domenico; Das, Pranab Kumar; Bigi, C; Ergönenc, Z; Gürtler, N; Krieger, J A; Schmitt, T; Ali, M N; Rossi, G; Thomale, R; Franchini, C; Picozzi, S; Fujii, J; Strocov, V N; Sangiovanni, G; Vobornik, I; Cava, R J; Panaccione, G
2017-07-14
By combining bulk sensitive soft-x-ray angular-resolved photoemission spectroscopy and first-principles calculations we explored the bulk electron states of WTe_{2}, a candidate type-II Weyl semimetal featuring a large nonsaturating magnetoresistance. Despite the layered geometry suggesting a two-dimensional electronic structure, we directly observe a three-dimensional electronic dispersion. We report a band dispersion in the reciprocal direction perpendicular to the layers, implying that electrons can also travel coherently when crossing from one layer to the other. The measured Fermi surface is characterized by two well-separated electron and hole pockets at either side of the Γ point, differently from previous more surface sensitive angle-resolved photoemission spectroscopy experiments that additionally found a pronounced quasiparticle weight at the zone center. Moreover, we observe a significant sensitivity of the bulk electronic structure of WTe_{2} around the Fermi level to electronic correlations and renormalizations due to self-energy effects, previously neglected in first-principles descriptions.
Kulkarni, Santosh S; Newman, Amy Hauck; Houlihan, William J
2002-09-12
A three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a series of mazindol analogues using the comparative molecular field analysis (CoMFA) method with their corresponding binding affinities for the displacement of [(3)H]WIN 35 428 from rat caudate putamen tissue. The cross-validated CoMFA models were derived from a training set of 50 compounds, and the predictive ability of the resulting CoMFA models was evaluated against a test set of 21 compounds. A set of alignment rules was derived to superimpose these compounds onto a template structure, mazindol (1). These CoMFA models yielded significant cross-validated r(2)(cv) values. Inclusion of additional descriptors did not improve the significance of the CoMFA models; thus, steric and electrostatic fields are the relevant descriptors for these compounds. The best QSAR model was selected on the basis of the predictive ability of the activity on the external test set of compounds. The analysis of coefficient contour maps provided further insight into the binding interactions of mazindol analogues with the DAT. The aromatic rings C and D are involved in hydrophobic interactions in which ring D may bind in a large hydrophobic groove. The relative orientation of these two rings is also important for high binding affinity to the DAT.
Langer, P.; Sepahvand, K.; Guist, C.; Bär, J.; Peplow, A.; Marburg, S.
2018-03-01
The simulation model which examines the dynamic behavior of real structures needs to address the impact of uncertainty in both geometry and material parameters. This article investigates three-dimensional finite element models for structural dynamics problems with respect to both model and parameter uncertainties. The parameter uncertainties are determined via laboratory measurements on several beam-like samples. The parameters are then considered as random variables to the finite element model for exploring the uncertainty effects on the quality of the model outputs, i.e. natural frequencies. The accuracy of the output predictions from the model is compared with the experimental results. To this end, the non-contact experimental modal analysis is conducted to identify the natural frequency of the samples. The results show a good agreement compared with experimental data. Furthermore, it is demonstrated that geometrical uncertainties have more influence on the natural frequencies compared to material parameters and material uncertainties are about two times higher than geometrical uncertainties. This gives valuable insights for improving the finite element model due to various parameter ranges required in a modeling process involving uncertainty.
Energy Technology Data Exchange (ETDEWEB)
Rocha, B.A.M.; Bezerra, M.J.B.; Bezerra, G.A.; Alencar, K.L.L.; Nascimento, K.S.; Naganao, C.S.; Sampaio, A.H.; Cavada, B.S. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil); Delatorre, P. [Universidade Federal da Paraiba (UFPB), Joao Pessoa, PB (Brazil); Rodrigues, N.V.; Pires, A.F.; Assreuy, A.M.S. [Universidade Estadual do Ceara (UECE), Fortaleza, CE (Brazil); Marins, J.L. [Universidade Federal de Pelotas (UFPel), Pelotas, RS (Brazil)
2012-07-01
Full text: Lectins are a structural heterogeneous group of proteins possessing at least one non-catalytic domain that binds reversibly to a specific mono or oligosaccharide. Diocleinae lectins exhibit glucose/mannose monosaccharide binding specificity and studies of their chemical and physicochemical properties revealed a high degree of identity in their amino acid sequences and three dimensional structures. This study investigated structural/functional relationships between lectins obtained from Dioclea violacea (DVL) and Dioclea rostrata (DRL). The purified lectin (DVL) was solubilized in 20 mM Tris-HCl pH 7.6 with 5 mM CaCl{sub 2} and MnCl{sub 2} buffer and incubated during one hour before the crystallization experiments with the ligand X-Man (5-bromo-4-chloro-3-indolyl-{alpha}-D-mannose) at 3 mM. Crystals of DVL grew in condition 33 of Crystal Screen I (4M Sodium formate) and belong to the orthorhombic space group I222. The structure of DVL at 2.6 resolution was obtained by molecular replacement using the coordinates of DRL (PDB code 2ZBJ), after the last refinement the structure presented R factor of 0.23 and R free of 0.27. The crystal structures reveal differences between them and could be related to relaxant activity. The conformation of residues HIS51, HIS131 and GLU205 and others positioned at CRD lead to different lectin binding activities. In fact, the pocket in DVL is small and deep and promotes weak interaction with carbohydrates, while DRL pocket is large and shallow, allowing strong interaction between CRD and sugars. This can explain why DVL and DRL elicited different degrees of aorta relaxation showing maximal effects of 43 % and 96 %, respectively. (author)
Wang, Kai-Tong; Xing, Yanxia; Cheung, King Tai; Wang, Jian; Pan, Hui; Zhao, Hong-Kang
2017-10-01
We numerically study the focusing effect induced by a single p–n junction in three-dimensional topological insulators (3D TIs). It is found that, for either surface states or bulk states of 3D TIs, the corresponding electrons injected from the n/p region can be perfectly focused at the symmetric position in the p/n region. These results suggest that the focusing effect is a general phenomenon in materials which can be described by massless or massive Dirac equations. We also find that the focusing effect is robust against moderate random disorders. In the presence of external magnetic fields, the focusing effect remains good, but the position of the focus point oscillates periodically due to the finite size effect.
DEFF Research Database (Denmark)
Christensen, I T; Jørgensen, Flemming Steen; Svensson, L A
1993-01-01
Three-dimensional structures of the enzyme phospholipase A2 (PLA2) from human pancreas and from human synovial fluid were constructed by model building based on high-resolution X-ray crystallographic structures and homology considerations. The structure of the human pancreatic PLA2 was based...
Energy Technology Data Exchange (ETDEWEB)
Hu, Rui
2017-09-03
Mixing, thermal-stratification, and mass transport phenomena in large pools or enclosures play major roles for the safety of reactor systems. Depending on the fidelity requirement and computational resources, various modeling methods, from the 0-D perfect mixing model to 3-D Computational Fluid Dynamics (CFD) models, are available. Each is associated with its own advantages and shortcomings. It is very desirable to develop an advanced and efficient thermal mixing and stratification modeling capability embedded in a modern system analysis code to improve the accuracy of reactor safety analyses and to reduce modeling uncertainties. An advanced system analysis tool, SAM, is being developed at Argonne National Laboratory for advanced non-LWR reactor safety analysis. While SAM is being developed as a system-level modeling and simulation tool, a reduced-order three-dimensional module is under development to model the multi-dimensional flow and thermal mixing and stratification in large enclosures of reactor systems. This paper provides an overview of the three-dimensional finite element flow model in SAM, including the governing equations, stabilization scheme, and solution methods. Additionally, several verification and validation tests are presented, including lid-driven cavity flow, natural convection inside a cavity, laminar flow in a channel of parallel plates. Based on the comparisons with the analytical solutions and experimental results, it is demonstrated that the developed 3-D fluid model can perform very well for a wide range of flow problems.
Rasskazov, Andrey; Chertovskih, Roman; Zheligovsky, Vladislav
2018-04-01
We introduce six families of three-dimensional space-periodic steady solenoidal flows, whose kinetic helicity density is zero at any point. Four families are analytically defined. Flows in four families have zero helicity spectrum. Sample flows from five families are used to demonstrate numerically that neither zero kinetic helicity density nor zero helicity spectrum prohibit generation of large-scale magnetic field by the two most prominent dynamo mechanisms: the magnetic α -effect and negative eddy diffusivity. Our computations also attest that such flows often generate small-scale field for sufficiently small magnetic molecular diffusivity. These findings indicate that kinetic helicity and helicity spectrum are not the quantities controlling the dynamo properties of a flow regardless of whether scale separation is present or not.
Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM.
Oi, Takao; Enomoto, Sakiko; Nakao, Tomoyo; Arai, Shigeo; Yamane, Koji; Taniguchi, Mitsutaka
2017-07-01
Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction. Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software. The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other. Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll
Non-Linear Three Dimensional Finite Elements for Composite Concrete Structures
Directory of Open Access Journals (Sweden)
O. Kohnehpooshi
Full Text Available Abstract The current investigation focused on the development of effective and suitable modelling of reinforced concrete component with and without strengthening. The modelling includes physical and constitutive models. New interface elements have been developed, while modified constitutive law have been applied and new computational algorithm is utilised. The new elements are the Truss-link element to model the interaction between concrete and reinforcement bars, the interface element between two plate bending elements and the interface element to represent the interfacial behaviour between FRP, steel plates and concrete. Nonlinear finite-element (FE codes were developed with pre-processing. The programme was written using FORTRAN language. The accuracy and efficiency of the finite element programme were achieved by analyzing several examples from the literature. The application of the 3D FE code was further enhanced by carrying out the numerical analysis of the three dimensional finite element analysis of FRP strengthened RC beams, as well as the 3D non-linear finite element analysis of girder bridge. Acceptable distributions of slip, deflection, stresses in the concrete and FRP plate have also been found. These results show that the new elements are effective and appropriate to be used for structural component modelling.
International Nuclear Information System (INIS)
Miki, K.
1979-01-01
The core elements of an LMFBR are bowed due to radial gradients of both temperature and neutron flux in the core. Since all hexagonal elements are multiply supported by adjacent elements or the restraint system, restraint forces and bending stresses are induced. In turn, these forces and stresses are relaxed by irradiation enhanced creep of the material. The analysis of the core bowing behavior requires a three-dimensional consideration of the mechanical interactions among the core elements, because the core consists of different kinds of elements and of fuel assemblies with various burnup histories. A new computational code BEACON has been developed for analyzing the bowing behavior of an LMFBR's core in three dimensions. To evaluate mechanical interactions among core elements, the code uses the analytical method of the earlier SHADOW code. BEACON analyzes the mechanical interactions in three directions, which form angles of 60 0 with one another. BEACON is applied to the 60 0 sector of a typical LMFBR's core for analyzing the bowing history during one equilibrium cycle. 120 core elements are treated, assuming the boundary condition of rotational symmetry. The application confirms that the code can be an effective tool for parametric studies as well as for detailed structural analysis of LMFBR's core. (orig.)
Three-dimensional structure of the two-peptide bacteriocin plantaricin JK.
Rogne, Per; Haugen, Christofer; Fimland, Gunnar; Nissen-Meyer, Jon; Kristiansen, Per Eugen
2009-09-01
The three-dimensional structures of the two peptides, PlnJ and PlnK, that constitutes the two-peptide bacteriocin plantaricin JK have been solved in water/TFE and water/DPC-micellar solutions using nuclear magnetic resonance (NMR) spectroscopy. PlnJ, a 25 residue peptide, has an N-terminal amphiphilic alpha-helix between Trp-3 and Tyr-15. The 32 residues long PlnK forms a central amphiphilic alpha-helix between Gly-9 and Leu-24. Measurements of the effect on anti-microbial activity of single glycine replacements in PlnJ and PlnK show that Gly-13 and Gly-17 in both peptides are very sensitive, giving more than a 100-fold reduction in activity when large residues replace glycine. In variants where other glycine residues, Gly-20 in PlnJ and Gly-7, Gly-9, Gly-24 and Gly-25 in PlnK, were replaced, the activity was reduced less than 10-fold. It is proposed that the detrimental effect on activity when exchanging Gly-13 and Gly-17 in PlnJ and PlnK is a result of reduced ability of the two peptides to interact through the GxxxG-motifs constituting Gly-13 and Gly-17.
Altimetric signal and three-dimensional structure of the sea in the Channel of Sicily
Nardelli, Bruno Buongiorno; Santoleri, Rosalia; Iudicone, Daniele; Zoffoli, Simona; Marullo, Salvatore
1999-09-01
The 1996 Altimeter/Synoptic Mesoscale Plancton Experiment (ALT/SYMPLEX) was specifically designed to perform in situ measurements simultaneous with the passage of TOPEX/POSEIDON (T/P) and ERS 2 over selected tracks in the central and eastern Sicily Channel. This experiment made it possible to have, for the first time, a validation of altimetry with in situ data over the Mediterranean, where weak dynamics results in a modest sea elevation, rarely exceeding 10 cm. Historical infrared and altimetric satellite data were first analyzed in order to study the variability of the circulation in the area. The comparative and integrative analysis of simultaneous satellite data and in situ measurements permitted investigation of the relation between the altimeter-derived surface topography and the three-dimensional structure of the sea. The Pearson correlation coefficients between altimeter data and dynamic heights along track resulted to be 0.72-0.89 (T/P) and 0.88 (ERS 2) when using conventional repeat track analysis. For T/P, a correlation value of 0.87 was found for time differences computed basing on a collinear analysis technique. This analysis also led to the identification of a strong barotropic component of the velocity field located near the Sicilian continental shelf, where it is responsible for approximately 60% of the signal.
International Nuclear Information System (INIS)
Kim, Yeon Joon; Kim, Woo Youn
2015-01-01
We present a powerful method for the conversion of molecular structures from atomic connectivity to bond orders to three-dimensional (3D) geometries. There are a number of bond orders and 3D geometries corresponding to a given atomic connectivity. To uniquely determine an energetically more favorable one among them, we use general chemical rules without invoking any empirical parameter, which makes our method valid for any organic molecule. Specifically, we first assign a proper bond order to each atomic pair in the atomic connectivity so as to maximize their sum and the result is converted to a SMILES notation using graph theory. The corresponding 3D geometry is then obtained using force field or ab initio calculations. This method successfully reproduced the bond order matrices and 3D geometries of 10 000 molecules randomly sampled from the PubChem database with high success rates of near 100% except a few exceptional cases. As an application, we demonstrate that it can be used to search for molecular isomers efficiently
Three-dimensional structure of the bacterial protein-translocation complex SecYEG.
Breyton, Cécile; Haase, Winfried; Rapoport, Tom A; Kühlbrandt, Werner; Collinson, Ian
2002-08-08
Transport and membrane integration of polypeptides is carried out by specific protein complexes in the membranes of all living cells. The Sec transport path provides an essential and ubiquitous route for protein translocation. In the bacterial cytoplasmic membrane, the channel is formed by oligomers of a heterotrimeric membrane protein complex consisting of subunits SecY, SecE and SecG. In the endoplasmic reticulum membrane, the channel is formed from the related Sec61 complex. Here we report the structure of the Escherichia coli SecYEG assembly at an in-plane resolution of 8 A. The three-dimensional map, calculated from two-dimensional SecYEG crystals, reveals a sandwich of two membranes interacting through the extensive cytoplasmic domains. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. In the centre of the dimer we observe a 16 x 25 A cavity closed on the periplasmic side by two highly tilted transmembrane helices. This may represent the closed state of the protein-conducting channel.
Structural dynamic modeling for rotating blades using three dimensional finite elements
Energy Technology Data Exchange (ETDEWEB)
Kee, Young Jung; Shin, Sang Joon [Seoul National University, Seoul (Korea, Republic of)
2015-04-15
A precise analysis model was developed in this paper to investigate the dynamic characteristics of rotating composite blades. An eighteen-node solid-shell finite element was used to model the blade structures. This study is focused on geometrically nonlinear problems, because the material is assumed linear elastic. Incremental total Lagrangian approach was adopted to allow estimations on arbitrarily large rotations and displacements. The equations of motion for the finite element model were derived by using Hamilton's principle, and the resulting nonlinear equilibrium equations were solved by applying Newton-Raphson method combined with load control. A modified stress-strain relation was adopted to avoid the transverse shear locking problem, and fairly reliable results were obtained with no sign of locking phenomenon. The obtained numerical results were compared to several benchmark problems, and the results show a good correlation with the experimental data and other finite element analysis results. The vibration characteristics of shell- and beam-type blades were investigated. For shell-type blades, the dynamic characteristics may be significantly influenced by blade curvature, pre-twist, and geometric nonlinearity. For beam-type blades, one-dimensional beam and three-dimensional solid models offer comparable predictions for the straight and large aspect ratio blade. As blade aspect ratio decreases, considerable differences appear in the bending and torsion modes. The tip sweep angle tends to decrease the flap bending frequencies, but the torsion frequency increases with the tip sweep angle.
Structural dynamic modeling for rotating blades using three dimensional finite elements
International Nuclear Information System (INIS)
Kee, Young Jung; Shin, Sang Joon
2015-01-01
A precise analysis model was developed in this paper to investigate the dynamic characteristics of rotating composite blades. An eighteen-node solid-shell finite element was used to model the blade structures. This study is focused on geometrically nonlinear problems, because the material is assumed linear elastic. Incremental total Lagrangian approach was adopted to allow estimations on arbitrarily large rotations and displacements. The equations of motion for the finite element model were derived by using Hamilton's principle, and the resulting nonlinear equilibrium equations were solved by applying Newton-Raphson method combined with load control. A modified stress-strain relation was adopted to avoid the transverse shear locking problem, and fairly reliable results were obtained with no sign of locking phenomenon. The obtained numerical results were compared to several benchmark problems, and the results show a good correlation with the experimental data and other finite element analysis results. The vibration characteristics of shell- and beam-type blades were investigated. For shell-type blades, the dynamic characteristics may be significantly influenced by blade curvature, pre-twist, and geometric nonlinearity. For beam-type blades, one-dimensional beam and three-dimensional solid models offer comparable predictions for the straight and large aspect ratio blade. As blade aspect ratio decreases, considerable differences appear in the bending and torsion modes. The tip sweep angle tends to decrease the flap bending frequencies, but the torsion frequency increases with the tip sweep angle.
A low-profile three-dimensional neural probe array using a silicon lead transfer structure
Cheng, Ming-Yuan; Je, Minkyu; Tan, Kwan Ling; Lim Tan, Ee; Lim, Ruiqi; Yao, Lei; Li, Peng; Park, Woo-Tae; Phua, Eric Jian Rong; Lip Gan, Chee; Yu, Aibin
2013-09-01
This paper presents a microassembly method for low-profile three-dimensional probe arrays for neural prosthesis and neuroscience applications. A silicon (Si) lead transfer structure, Si interposer, is employed to form electrical connections between two orthogonal planes—the two dimensional probes and the dummy application-specific integrated circuit (ASIC) chip. In order to hold the probe array and facilitate the alignment of probes during assembly, a Si platform is designed to have through-substrate slots for the insertion of probes and cavities for holding the Si interposers. The electrical interconnections between the probes and the dummy ASIC chip are formed by solder reflow, resulting in greatly improved throughput in the proposed assembly method. Moreover, since the backbone of the probe can be embedded inside the cavity of the Si platform, the profile of the probe array above the cortical surface can be controlled within 750 µm. This low-profile allows the probe array not to touch the skull after it is implanted on the brain. The impedance of the assembled probe is also measured and discussed.
Three-dimensional structural representation of the sleep-wake adaptability.
Putilov, Arcady A
2016-01-01
Various characteristics of the sleep-wake cycle can determine the success or failure of individual adjustment to certain temporal conditions of the today's society. However, it remains to be explored how many such characteristics can be self-assessed and how they are inter-related one to another. The aim of the present report was to apply a three-dimensional structural representation of the sleep-wake adaptability in the form of "rugby cake" (scalene or triaxial ellipsoid) to explain the results of analysis of the pattern of correlations of the responses to the initial 320-item list of a new inventory with scores on the six scales designed for multidimensional self-assessment of the sleep-wake adaptability (Morning and Evening Lateness, Anytime and Nighttime Sleepability, and Anytime and Daytime Wakeability). The results obtained for sample consisting of 149 respondents were confirmed by the results of similar analysis of earlier collected responses of 139 respondents to the same list of 320 items and responses of 1213 respondents to the 72 items of one of the earlier established questionnaire tools. Empirical evidence was provided in support of the model-driven prediction of the possibility to identify items linked to as many as 36 narrow (6 core and 30 mixed) adaptabilities of the sleep-wake cycle. The results enabled the selection of 168 items for self-assessment of all these adaptabilities predicted by the rugby cake model.
Yang, W.; Kobayashi, H.; Kondoh, A.
2016-12-01
Three-dimensional (3-D) Monte Carlo (MC)-based radiative transfer (RT) models can simulate highly detailed forest environments, and have produced simulations that agree well with observations; thus, they are routinely used for benchmarking in intercomparisons of RT models. However, MC-based RT models have not been widely applied to the development of inversion algorithms for generating global remote sensing products of forests, due mainly to the difficulties in obtaining realistic forest structures for a variety of forest biomes. In this study, we developed a Forest Structure Dynamics Model (FSDM) to facilitate the application of MC-based RT models to global forests. In this model, the tree architectures are determined based on allometric equations, and the tree locations within a study domain are determined by statistical distributions. The performance of the FSDM was evaluated using field measurements of forest landscapes at two sites located at Järvselja, Estonia and the Poker Flat Research Range (PFRR), USA, respectively. The bidirectional reflectance factor (BRF) for the two study sites was simulated by an MC-based RT model, based on the measured forest stands and modeled stands from the FSDM. A comparison of the results demonstrated that the simulated BRF based on the measured forest stands agreed well with the simulated BRF based on the modeled stands from the FSDM for the two study sites. The applicability of the FSDM to a leaf area index (LAI) retrieval algorithm was also verified using simulations from the MC-based RT model. The results indicate that the FSDM can provide reasonable forest structures to drive 3-D canopy RT models, with no loss of simulation accuracy. When combined with several existing field data sets and satellite products, the FSDM can be used to generate a typical stand structure database for global forest biomes.
Potentiality of Using Vertical and Three-Dimensional Isolation Systems in Nuclear Structures
Directory of Open Access Journals (Sweden)
Zhiguang Zhou
2016-10-01
Full Text Available Although the horizontal component of an earthquake response can be significantly reduced through the use of conventional seismic isolators, the vertical component of excitation is still transmitted directly into the structure. Records from instrumented structures, and some recent tests and analyses have actually seen increases in vertical responses in base isolated structures under the combined effects of horizontal and vertical ground motions. This issue becomes a great concern to facilities such as a Nuclear Power Plants (NPP, with specialized equipment and machinery that is not only expensive, but critical to safe operation. As such, there is considerable interest worldwide in vertical and three-dimensional (3D isolation systems. This paper examines several vertical and 3D isolation systems that have been proposed and their potential application to modern nuclear facilities. In particular, a series of case study analyses of a modern NPP model are performed to examine the benefits and challenges associated with 3D isolation compared with horizontal isolation. It was found that compared with the general horizontal isolators, isolators that have vertical frequencies of no more than 3 Hz can effectively reduce the vertical in-structure responses for the studied NPP model. Among the studied cases, the case that has a vertical isolation frequency of 3 Hz is the one that can keep the horizontal period of the isolators as the first period while having the most flexible vertical isolator properties. When the vertical frequency of isolators reduces to 1 Hz, the rocking effect is obvious and rocking restraining devices are necessary.
Versatile morphometric analysis and visualization of the three-dimensional structure of neurons.
Aguiar, Paulo; Sousa, Mafalda; Szucs, Peter
2013-10-01
The computational properties of a neuron are intimately related to its morphology. However, unlike electrophysiological properties, it is not straightforward to collapse the complexity of the three-dimensional (3D) structure into a small set of measurements accurately describing the structural properties. This strong limitation leads to the fact that many studies involving morphology related questions often rely solely on empirical analysis and qualitative description. It is possible however to acquire hierarchical lists of positions and diameters of points describing the spatial structure of the neuron. While there is a number of both commercially and freely available solutions to import and analyze this data, few are extendable in the sense of providing the possibility to define novel morphometric measurements in an easy to use programming environment. Fewer are capable of performing morphometric analysis where the output is defined over the topology of the neuron, which naturally requires powerful visualization tools. The computer application presented here, Py3DN, is an open-source solution providing novel tools to analyze and visualize 3D data collected with the widely used Neurolucida (MBF) system. It allows the construction of mathematical representations of neuronal topology, detailed visualization and the possibility to define non-standard morphometric analysis on the neuronal structures. Above all, it provides a flexible and extendable environment where new types of analyses can be easily set up allowing a high degree of freedom to formulate and test new hypotheses. The application was developed in Python and uses Blender (open-source software) to produce detailed 3D data representations.
Yun, Keon-Young
For the computation of hypersonic flowfields about space vehicles in low earth orbits, where the local Knudsen numbers (Kn) lie in continuum-transition regime, a set of extended three-dimensional hydrodynamic equations are required which are more accurate than the Navier-Stokes equations and computationally more efficient than the Direct Simulation Monte Carlo (DSMC) computations in this regime. In this thesis, the three-dimensional augmented Burnett equations are derived from the Chapman-Enskog expansion of the Boltzmann equation to O(Kn 2) and adding the augmented terms (linear third-order super Burnett terms with coefficients determined from linearized stability analysis to ensure stability of the augmented Burnett equations to small wavelength disturbances). The three-dimensional augmented Burnett equations are applied to compute the three-dimensional hypersonic blunt body flows for various range of Knudsen numbers and Mach numbers. An explicit time-stepping scheme with Steger-Warming flux vector splitting is employed to discretize the convective flux terms. Stress and heat flux terms are central differenced. For the wall boundary conditions, the first-order Maxwell-Smoluchowski slip boundary conditions are employed. The computational results are compared with the Navier-Stokes solutions, the existing augmented Burnett solutions of Zhong, and the available DSMC results. The comparisons show that the difference between the Navier-Stokes and the augmented Burnett solutions is very small at Knudsen numbers less than 0.01; the difference becomes significant as the Knudsen number increases. The comparisons also show that the augmented Burnett solutions are much closer to the DSMC results in the continuum-transition regime than the Navier-Stokes calculations.
Kurt, Melike; Moored, Keith
2018-04-19
We present experiments that examine the modes of interaction, the collective performance and the role of three-dimensionality in two pitching propulsors in an in-line arrangement. Both two-dimensional foils and three-dimensional rectangular wings of $AR = 2$ are examined. \\kwm{In contrast to previous work, two interaction modes distinguished as the coherent and branched wake modes are not observed to be directly linked to the propulsive efficiency, although they are linked to peak thrust performance and minimum power consumption as previously described \\cite[]{boschitsch2014propulsive}.} \\kwm{In fact, in closely-spaced propulsors peak propulsive efficiency of the follower occurs near its minimum power and this condition \\kwm{ reveals a} branched wake mode. Alternatively, for propulsors spaced far apart peak propulsive efficiency of the follower occurs near its peak thrust and this condition \\kwm{reveals a} coherent wake mode.} By examining the collective performance, it is discovered that there is an optimal spacing between the propulsors to maximize the collective efficiency. For two-dimensional foils the optimal spacing of $X^* = 0.75$ and the synchrony of $\\phi = 2\\pi /3$ leads to a collective efficiency and thrust enhancement of 50\\% and 32\\%, respectively, as compared to two isolated foils. In comparison, for $AR = 2$ wings the optimal spacing of $X^* = 0.25$ and the synchrony of $\\phi = 7\\pi /6$ leads to a collective efficiency and thrust enhancement of 30\\% and 22\\%, respectively. In addition, at the optimal conditions the collective lateral force coefficients in both the two- and three-dimensional cases are negligible, while operating off these conditions can lead to non-negligible lateral forces. Finally, the peak efficiency of the collective and the follower are shown to have opposite trends with increasing spacing in two- and three-dimensional flows. This is correlated to the breakdown of the impinging vortex on the follower wing in three
Three-dimensional structure of wind turbine wakes as measured by scanning lidar
Bodini, Nicola; Zardi, Dino; Lundquist, Julie K.
2017-08-01
The lower wind speeds and increased turbulence that are characteristic of turbine wakes have considerable consequences on large wind farms: turbines located downwind generate less power and experience increased turbulent loads. The structures of wakes and their downwind impacts are sensitive to wind speed and atmospheric variability. Wake characterization can provide important insights for turbine layout optimization in view of decreasing the cost of wind energy. The CWEX-13 field campaign, which took place between June and September 2013 in a wind farm in Iowa, was designed to explore the interaction of multiple wakes in a range of atmospheric stability conditions. Based on lidar wind measurements, we extend, present, and apply a quantitative algorithm to assess wake parameters such as the velocity deficits, the size of the wake boundaries, and the location of the wake centerlines. We focus on wakes from a row of four turbines at the leading edge of the wind farm to explore variations between wakes from the edge of the row (outer wakes) and those from turbines in the center of the row (inner wakes). Using multiple horizontal scans at different elevations, a three-dimensional structure of wakes from the row of turbines can be created. Wakes erode very quickly during unstable conditions and can in fact be detected primarily in stable conditions in the conditions measured here. During stable conditions, important differences emerge between the wakes of inner turbines and the wakes of outer turbines. Further, the strong wind veer associated with stable conditions results in a stretching of the wake structures, and this stretching manifests differently for inner and outer wakes. These insights can be incorporated into low-order wake models for wind farm layout optimization or for wind power forecasting.
Hayat, Tasawar; Aziz, Arsalan; Muhammad, Taseer; Alsaedi, Ahmed
2017-09-01
The present study elaborates three-dimensional flow of Williamson nanoliquid over a nonlinear stretchable surface. Fluid flow obeys Darcy–Forchheimer porous medium. A bidirectional nonlinear stretching surface generates the flow. Convective surface condition of heat transfer is taken into consideration. Further the zero nanoparticles mass flux condition is imposed at the boundary. Effects of thermophoresis and Brownian diffusion are considered. Assumption of boundary layer has been employed in the problem formulation. Convergent series solutions for the nonlinear governing system are established through the optimal homotopy analysis method (OHAM). Graphs have been sketched in order to analyze that how the velocity, temperature and concentration distributions are affected by distinct emerging flow parameters. Skin friction coefficients and local Nusselt number are also computed and discussed.
Takenaka, N; Fujii, T; Mizubata, M; Yoshii, K
1999-01-01
Three-dimensional void fraction distribution of air-water two-phase flow in a 4x4 rod-bundle near a spacer was visualized by fast neutron radiography using a CT method. One-dimensional cross sectional averaged void fraction distribution was also calculated. The behaviors of low void fraction (thick water) two-phase flow in the rod bundle around the spacer were clearly visualized. It was shown that the void fraction distributions were visualized with a quality similar to those by thermal neutron radiography for low void fraction two-phase flow which is difficult to visualize by thermal neutron radiography. It is concluded that the fast neutron radiography is efficiently applicable to two-phase flow studies.
Directory of Open Access Journals (Sweden)
Castejón, L.
1997-12-01
Full Text Available Sandwich-type structures have proved to be alternatives of great success for several fields of application, and specially in the building sector. This is due to their outstanding properties of .specific rigidity and strength against bending loads and other range of advantages like fatigue and impact resistance, attainment of flat and smooth surfaces, high electric and thermal insulation, design versatility and some others. However, traditional sandwich structures present problems like their tendency towards delamination, stress concentrations in bores or screwed Joints, and pre resistance. These problems are alleviated thanks to the use of new sandwich structures built using three dimensional structures of advanced composite materials, maintaining the present advantages for more traditional sandwich structures. At this rate, these new structures can be applied in several areas where conventional sandwich structures used to be like walls, partitions, floor and ceiling structures, domes, vaults and dwellings, but with greater success.
Las estructuras tipo sándwich han demostrado ser alternativas de gran éxito para diversos campos de aplicación y, en concreto, en el sector de la construcción, listo es gracias a sus excelentes propiedades de rigidez y resistencia específica frente a cargas de flexión y otra larga lista de ventajas, a la que pertenecen, por ejemplo, su buena resistencia a fatiga, resistencia al impacto, obtención de superficies lisas y suaves, elevado aislamiento térmico y eléctrico, versatilidad de diseño y otras. Sin embargo, las estructuras sándwich, tradicionales presentan una problemática consistente en su tendencia a la delaminación, concentraciones de tensiones ¿aparecidas ante la existencia de agujeros o uniones atornilladas y resistencia al fuego. Estos problemas son pifiados gracias a la aplicación de estructuras novedosas tipo sándwich, construidas a partir de tejidos tridimensionales de materiales
Three-dimensional calculation of the flow in the cold plenum of the Fast Breeder Reactor 1500 MW
International Nuclear Information System (INIS)
Chabard, J.P.; Daubert, O.; Gregoire, J.P.; Hemmerich, P.
1987-01-01
To solve thermalhydraulics problems which are rising for example on the various parts of nuclear reactors, several departments of the Direction des Etudes et Recherches are developing the N3S code, three-dimensional code using the finite element method. First, this paper presents the basic equations (Navies-Stokes with turbulence modelling and coupled with the thermal equation) and well suited algorithms to solve them. The industrial adequacy of the code is clearly demonstrated through the application to the computation of the flow in the cold plenum of the Fast Breeder Reactor 1500 MW on a mesh of about 20000 velocity nodes [fr
Olsen, Aaron M; Westneat, Mark W
2016-12-01
Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing
Three-dimensional structure and stoichiometry of Helmintosporium victoriae190S totivirus
International Nuclear Information System (INIS)
Caston, Jose R.; Luque, Daniel; Trus, Benes L.; Rivas, German; Alfonso, Carlos; Gonzalez, Jose M.; Carrascosa, Jose L.; Annamalai, Padmanaban; Ghabrial, Said A.
2006-01-01
Most double-stranded RNA viruses have a characteristic capsid consisting of 60 asymmetric coat protein dimers in a so-called T = 2 organization, a feature probably related to their unique life cycle. These capsids organize the replicative complex(es) that is actively involved in genome transcription and replication. Available structural data indicate that their RNA-dependent RNA polymerase (RDRP) is packaged as an integral capsid component, either as a replicative complex at the pentameric vertex (as in reovirus capsids) or as a fusion protein with the coat protein (as in some totivirus). In contrast with members of the family Reoviridae, there are two well-established capsid arrangements for dsRNA fungal viruses, exemplified by the totiviruses L-A and UmV and the chrysovirus PcV. Whereas L-A and UmV have a canonical T = 2 capsid, the PcV capsid is based on a T = 1 lattice composed of 60 capsid proteins. We used cryo-electron microscopy combined with three-dimensional reconstruction techniques and hydrodynamic analysis to determine the structure at 13.8 A resolution of Helminthosporium victoriae 190S virus (Hv190SV), a totivirus isolated from a filamentous fungus. The Hv190SV capsid has a smooth surface and is based on a T = 2 lattice with 60 equivalent dimers. Unlike the RDRP of some other totiviruses, which are expressed as a capsid protein-RDRP fusion protein, the Hv190SV RDRP is incorporated into the capsid as a separate, nonfused protein, free or non-covalently associated to the capsid interior
Directory of Open Access Journals (Sweden)
Tasawar Hayat
Full Text Available Here three dimensional (3D flow of second grade fluid has been studied in the presence of CattaneoâChristov double diffusion and heterogeneous-homogeneous reactions. Flow is bounded by a bidirectional linear stretchable surface. Generalized versions of Fourierâs and Fickâs law through CattaneoâChristov double diffusion are employed. Equal diffusion coefficients are considered for both autocatalyst and reactants. The conversion of partial differential system to nonlinear ordinary differential system has been done by employing appropriate transformations. The obtained nonlinear systems have been solved through the optimal homotopy analysis method (OHAM. Graphs have been displayed in order to examine how the velocities, temperature and concentration fields are affected by various pertinent parameters. Moreover the skin friction coefficients and heat and mass transfer rates have been computed and analyzed. Keywords: Three-dimensional flow, Second grade fluid, CattaneoâChristov double diffusion, Homogenous-heterogeneous reactions, OHAM
Impact of data resolution on three-dimensional structure inference methods.
Park, Jincheol; Lin, Shili
2016-02-06
Assays that are capable of detecting genome-wide chromatin interactions have produced massive amount of data and led to great understanding of the chromosomal three-dimensional (3D) structure. As technology becomes more sophisticated, higher-and-higher resolution data are being produced, going from the initial 1 Megabases (Mb) resolution to the current 10 Kilobases (Kb) or even 1 Kb resolution. The availability of genome-wide interaction data necessitates development of analytical methods to recover the underlying 3D spatial chromatin structure, but challenges abound. Most of the methods were proposed for analyzing data at low resolution (1 Mb). Their behaviors are thus unknown for higher resolution data. For such data, one of the key features is the high proportion of "0" contact counts among all available data, in other words, the excess of zeros. To address the issue of excess of zeros, in this paper, we propose a truncated Random effect EXpression (tREX) method that can handle data at various resolutions. We then assess the performance of tREX and a number of leading existing methods for recovering the underlying chromatin 3D structure. This was accomplished by creating in-silico data to mimic multiple levels of resolution and submit the methods to a "stress test". Finally, we applied tREX and the comparison methods to a Hi-C dataset for which FISH measurements are available to evaluate estimation accuracy. The proposed tREX method achieves consistently good performance in all 30 simulated settings considered. It is not only robust to resolution level and underlying parameters, but also insensitive to model misspecification. This conclusion is based on observations made in terms of 3D structure estimation accuracy and preservation of topologically associated domains. Application of the methods to the human lymphoblastoid cell line data on chromosomes 14 and 22 further substantiates the superior performance of tREX: the constructed 3D structure from tREX is
Mao, Xiaole; Nawaz, Ahmad Ahsan; Lin, Sz-Chin Steven; Lapsley, Michael Ian; Zhao, Yanhui; McCoy, J. Philip; El-Deiry, Wafik S.; Huang, Tony Jun
2012-01-01
In this work, we demonstrate an integrated, single-layer, miniature flow cytometry device that is capable of multi-parametric particle analysis. The device integrates both particle focusing and detection components on-chip, including a “microfluidic drifting” based three-dimensional (3D) hydrodynamic focusing component and a series of optical fibers integrated into the microfluidic architecture to facilitate on-chip detection. With this design, multiple optical signals (i.e., forward scatter, side scatter, and fluorescence) from individual particles can be simultaneously detected. Experimental results indicate that the performance of our flow cytometry chip is comparable to its bulky, expensive desktop counterpart. The integration of on-chip 3D particle focusing with on-chip multi-parametric optical detection in a single-layer, mass-producible microfluidic device presents a major step towards low-cost flow cytometry chips for point-of-care clinical diagnostics. PMID:22567082
Energy Technology Data Exchange (ETDEWEB)
Kirtley, K.R.
1988-10-01
A new coupled parabolic-marching method was developed to solve the three-dimensional incompressible Navier-Stokes equation for turbulent turbomachinery flows. Earlier space-marching methods were analyzed to determine their global stability during multiple passes of the computational domain. The methods were found to be unconditionally unstable even when an extra equation for the pressure, namely the Poisson equation for the pressure, was used between passes of the domain. Relaxation of one constraint during the solution process was found to be necessary for the successful calculation of a complex flow.Thus, the method of pseudocompressibility was introduced into the partially parabolized Navier-Stokes equation to relax the mass flow constraint during a forward-marching integration as well as globally stable during successive passes of the domain. With consistent discretization, the new method was found to be convergent.
He, Liping; Lu, Gang; Chen, Dachuan; Li, Wenjun; Lu, Chunsheng
2017-07-01
This paper investigates the three-dimensional (3D) injection molding flow of short fiber-reinforced polymer composites using a smoothed particle hydrodynamics (SPH) simulation method. The polymer melt was modeled as a power law fluid and the fibers were considered as rigid cylindrical bodies. The filling details and fiber orientation in the injection-molding process were studied. The results indicated that the SPH method could effectively predict the order of filling, fiber accumulation, and heterogeneous distribution of fibers. The SPH simulation also showed that fibers were mainly aligned to the flow direction in the skin layer and inclined to the flow direction in the core layer. Additionally, the fiber-orientation state in the simulation was quantitatively analyzed and found to be consistent with the results calculated by conventional tensor methods.
Three-dimensional P velocity structure of the crust and upper mantle under Beijing region
Energy Technology Data Exchange (ETDEWEB)
Quan, A.; Liu, F.; Sun, Y.
1980-04-01
By use of the teleseismic P arrival times at 15 stations of the Beijing network for 120 events distributed over various azimuths, we studied the three-dimensional P velocity structure under the Beijing region. In calculating the theoretic travel time, we adopted the source parameters given in BISC, and used the J-B model as the standard model of earth. On inversion, we adopted singular value decomposition as a generalized inversion package, which can be used for solving very large over-determined systems of equations Gm = t without resorting to normal equations G/sup T/Gm = G/sup T/t. The results are that within the crust and upper mantle under the Beijing region there are clear lateral differences. In the results obtained by use of data from 1972 to 1975, it can be seen that there are three different zones of P-velocity. In the southeast Beijing region, P velocity is lower than that of the normal model by 10 to 14% within the crust, and by 8 to 9% within the upper mantle. The northwest Beijing region is a higher-velocity zone, within which the average P-velocity is faster than that of the normal model by about 9%. It disappears after entering into the upper mantle. The central part of this region is a normal zone. On the surface, the distribution of these P velocity variations corresponds approximately to the distribution of the over-burden. But in the deeper region, the distribution of velocity variation agrees with the distribution of seismicity. It is interesting to note that the hypocenters of several major earthquakes in this region, e.g., the Sanhe-Pinggu earthquake (1679, M = 8), the Shacheng earthquake (1730, M = 6-3/4) and the Tangshan earthquake (1976, M = 7.8), are all located very close to this boundary of these P-velocity variation zones.
Neal, Rebekah A.; Jean, Aurélie; Park, Hyoungshin; Wu, Patrick B.; Hsiao, James; Engelmayr, George C.; Langer, Robert
2013-01-01
Tissue-engineered constructs, at the interface of material science, biology, engineering, and medicine, have the capacity to improve outcomes for cardiac patients by providing living cells and degradable biomaterials that can regenerate the native myocardium. With an ultimate goal of both delivering cells and providing mechanical support to the healing heart, we designed three-dimensional (3D) elastomeric scaffolds with (1) stiffnesses and anisotropy mimicking explanted myocardial specimens as predicted by finite-element (FE) modeling, (2) systematically varied combinations of rectangular pore pattern, pore aspect ratio, and strut width, and (3) structural features approaching tissue scale. Based on predicted mechanical properties, three scaffold designs were selected from eight candidates for fabrication from poly(glycerol sebacate) by micromolding from silicon wafers. Large 20×20 mm scaffolds with high aspect ratio features (5:1 strut height:strut width) were reproducibly cast, cured, and demolded at a relatively high throughput. Empirically measured mechanical properties demonstrated that scaffolds were cardiac mimetic and validated FE model predictions. Two-layered scaffolds providing fully interconnected pore networks were fabricated by layer-by-layer assembly. C2C12 myoblasts cultured on one-layered scaffolds exhibited specific patterns of cell elongation and interconnectivity that appeared to be guided by the scaffold pore pattern. Neonatal rat heart cells cultured on two-layered scaffolds for 1 week were contractile, both spontaneously and in response to electrical stimulation, and expressed sarcomeric α-actinin, a cardiac biomarker. This work not only demonstrated several scaffold designs that promoted functional assembly of rat heart cells, but also provided the foundation for further computational and empirical investigations of 3D elastomeric scaffolds for cardiac tissue engineering. PMID:23190320
Fluid-structure interaction of three-dimensional magnetic artificial cilia
Khaderi, S. N.; Onck, P. R.
2012-01-01
A numerical model is developed to analyse the interaction of artificial cilia with the surrounding fluid in a three-dimensional setting in the limit of vanishing fluid inertia forces. The cilia are modelled using finite shell elements and the fluid is modelled using a boundary element approach. The
International Nuclear Information System (INIS)
Costa, Gustavo Koury
2004-11-01
Although incompressible fluid flows can be regarded as a particular case of a general problem, numerical methods and the mathematical formulation aimed to solve compressible and incompressible flows have their own peculiarities, in such a way, that it is generally not possible to attain both regimes with a single approach. In this work, we start from a typically compressible formulation, slightly modified to make use of pressure variables and, through augmenting the stabilising parameters, we end up with a simplified model which is able to deal with a wide range of flow regimes, from supersonic to low speed gas flows. The resulting methodology is flexible enough to allow for the simulation of liquid flows as well. Examples using conservative and pressure variables are shown and the results are compared to those published in the literature, in order to validate the method. (author)
Directory of Open Access Journals (Sweden)
Doroshenko Sergey Aleksandrovich
2012-10-01
Full Text Available The authors discuss wind loads applied to a set of two buildings. The wind load is simulated with the help of the wind tunnel. In the Russian Federation, special attention is driven to the aerodynamics of high-rise buildings and structures. According to the Russian norms, identification of aerodynamic coefficients for high-rise buildings, as well as the influence of adjacent buildings and structures, is performed on the basis of models of structures exposed to wind impacts simulated in the wind tunnel. This article deals with the results of the wind tunnel test of buildings. The simulation was carried out with the involvement of a model of two twenty-three storied buildings. The experiment was held in a wind tunnel of the closed type at in the Institute of Mechanics of Moscow State University. Data were compared at the zero speed before and after the experiment. LabView software was used to process the output data. Graphs and tables were developed in the Microsoft Excel package. GoogleSketchUp software was used as a visualization tool. The three-dimensional flow formed in the wind tunnel can't be adequately described by solving the two-dimensional problem. The aerodynamic experiment technique is used to analyze the results for eighteen angles of the wind attack.
Three-dimensional neuroimaging
International Nuclear Information System (INIS)
Toga, A.W.
1990-01-01
This book reports on new neuroimaging technologies that are revolutionizing the study of the brain be enabling investigators to visualize its structure and entire pattern of functional activity in three dimensions. The book provides a theoretical and practical explanation of the new science of creating three-dimensional computer images of the brain. The coverage includes a review of the technology and methodology of neuroimaging, the instrumentation and procedures, issues of quantification, analytic protocols, and descriptions of neuroimaging systems. Examples are given to illustrate the use of three-dimensional enuroimaging to quantitate spatial measurements, perform analysis of autoradiographic and histological studies, and study the relationship between brain structure and function
Energy Technology Data Exchange (ETDEWEB)
Carrington, David Bradley [Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Monayem, A. K. M. [Univ. of New Mexico, Albuquerque, NM (United States); Mazumder, H. [Univ. of New Mexico, Albuquerque, NM (United States); Heinrich, Juan C. [Univ. of New Mexico, Albuquerque, NM (United States)
2015-03-05
A three-dimensional finite element method for the numerical simulations of fluid flow in domains containing moving rigid objects or boundaries is developed. The method falls into the general category of Arbitrary Lagrangian Eulerian methods; it is based on a fixed mesh that is locally adapted in the immediate vicinity of the moving interfaces and reverts to its original shape once the moving interfaces go past the elements. The moving interfaces are defined by separate sets of marker points so that the global mesh is independent of interface movement and the possibility of mesh entanglement is eliminated. The results is a fully robust formulation capable of calculating on domains of complex geometry with moving boundaries or devises that can also have a complex geometry without danger of the mesh becoming unsuitable due to its continuous deformation thus eliminating the need for repeated re-meshing and interpolation. Moreover, the boundary conditions on the interfaces are imposed exactly. This work is intended to support the internal combustion engines simulator KIVA developed at Los Alamos National Laboratories. The model's capabilities are illustrated through application to incompressible flows in different geometrical settings that show the robustness and flexibility of the technique to perform simulations involving moving boundaries in a three-dimensional domain.
Mushtaq, Ammar; Mustafa, Meraj; Hayat, Tasawar; Alsaedi, Ahmed
2014-12-01
The steady laminar three-dimensional magnetohydrodynamic (MHD) boundary layer flow and heat transfer over a stretching sheet is investigated. The sheet is linearly stretched in two lateral directions. Heat transfer analysis is performed by utilizing a nonlinear radiative heat flux in Rosseland approximation for thermal radiation. Two different wall conditions, namely (i) constant wall temperature and (ii) prescribed surface temperature are considered. The developed nonlinear boundary value problems (BVPs) are solved numerically through fifth-order Runge-Kutta method using a shooting technique. To ascertain the accuracy of results the solutions are also computed by using built in function bvp4c of MATLAB. The behaviours of interesting parameters are carefully analyzed through graphs for velocity and temperature distributions. The dimensionless expressions of wall shear stress and heat transfer rate at the sheet are evaluated and discussed. It is seen that a point of inflection of the temperature function exists for sufficiently large values of wall to ambient temperature ratio. The solutions are in excellent agreement with the previous studies in a limiting sense. To our knowledge, the novel idea of nonlinear thermal radiation in three-dimensional flow is just introduced here.
Simulation of three-dimensional viscous flow within a multistage turbine
Adamczyk, John J.; Celestina, Mark L.; Beach, Tim A.; Barnett, Mark
1989-01-01
This work outlines a procedure for simulating the flow field within multistage turbomachinery which includes the effects of unsteadiness, compressibility, and viscosity. The associated modeling equations are the average passage equation system which governs the time-averaged flow field within a typical passage of a blade row embedded within a multistage configuration. The results from a simulation of a low aspect ratio stage and a one-half turbine will be presented and compared with experimental measurements. It will be shown that the secondary flow field generated by the rotor causes the aerodynamic performance of the downstream vane to be significantly different from that of an isolated blade row.
Three dimensional numerical simulation for air flow field in melt blowing
Xie, Sheng; Han, Wanli; Jiang, Guojun
2017-10-01
Melt blowing is one-step approach for producing microfibrous nonwovens. In this study, the characteristics of air flow field in different die melt blowing were studied. CFD simulation analysis was adopted to complete the air flow field simulation. The characteristics of the air flow fields in different die melt blowing were revealed and compared. Meanwhile, the fiber paths in these two melt-blowing processes are recorded with a high-speed camera. The fiber path profiles, especially the whipping, are obtained and presented.
Pulse-Like Rupture Induced by Three-Dimensional Fault Zone Flower Structures
Pelties, Christian
2014-07-04
© 2014, Springer Basel. Faults are often embedded in low-velocity fault zones (LVFZ) caused by material damage. Previous 2D dynamic rupture simulations (Huang and Ampuero, 2011; Huang et al., 2014) showed that if the wave velocity contrast between the LVFZ and the country rock is strong enough, ruptures can behave as pulses, i.e. with local slip duration (rise time) much shorter than whole rupture duration. Local slip arrest (healing) is generated by waves reflected from the LVFZ–country rock interface. This effect is robust against a wide range of fault zone widths, absence of frictional healing, variation of initial stress conditions, attenuation, and off-fault plasticity. These numerical studies covered two-dimensional problems with fault-parallel fault zone structures. Here, we extend previous work to 3D and geometries that are more typical of natural fault zones, including complexities such as flower structures with depth-dependent velocity and thickness, and limited fault zone depth extent. This investigation requires high resolution and flexible mesh generation, which are enabled here by the high-order accurate arbitrary high-order derivatives discontinuous Galerkin method with an unstructured tetrahedral element discretization (Peltieset al., 2012). We show that the healing mechanism induced by waves reflected in the LVFZ also operates efficiently in such three-dimensional fault zone structures and that, in addition, a new healing mechanism is induced by unloading waves generated when the rupture reaches the surface. The first mechanism leads to very short rise time controlled by the LVFZ width to wave speed ratio. The second mechanism leads to generally longer, depth-increasing rise times, is also conditioned by the existence of an LVFZ, and persists at some depth below the bottom of the LVFZ. Our simulations show that the generation of slip pulses by these two mechanisms is robust to the depth extent of the LVFZ and to the position of the hypocenter
Akutsu, Toshinosuke; Matsumoto, Akira
2010-12-01
The current design of the bileaflet valve, the leaflets of which open outside first, differs significantly from the natural valve whose leaflets open center first. This difference generates a completely different flow field in the bileaflet valve compared to that in the natural heart valve. In a previous study, it was demonstrated that the valve design greatly affects the aortic flow field as well as the circulatory flow inside sinuses of Valsalva, using saline solution as a working fluid. A limited discussion on the turbulence flow field that could be generated by the valve was provided. In this continuation of that study, therefore, a dynamic PIV study was conducted to analyze the influence of the heart valve design on the aortic flow field, and particularly on the turbulent profile. This study also aimed to determine the influence of the viscosity of the testing fluid. Three bileaflet prostheses-the St. Jude Medical (SJM), the On-X, and the MIRA valves-were tested under pulsatile flow conditions. Flow through the central orifice of the SJM valve was slower than that through the newer designs. The newer designs tend to show strong flow through all orifices. The On-X valve generates simple jet-type flow while the MIRA valve with circumferentially curved leaflets generates a strong but three-dimensionally diffuse flow, resulting in a more complex flow field downstream of the aortic valve with higher turbulence. A 180° orientation that is more popular clinically seems to provide a less diffuse flow than a 90° orientation. The effect of increasing the viscosity was found to be an increase in the flow velocity through the central orifice and a more organized flow field for all of the valves tested.
International Nuclear Information System (INIS)
Hua, T.Q.; Walker, J.S.; Picologlou, B.F.; Reed, C.B.
1988-07-01
Magnetohydrodynamic flows of liquid metals in rectangular ducts with thin conducting walls in the presence of strong nonuniform transverse magnetic fields are examined. The interaction parameter and Hartmann number are assumed to be large, whereas the magnetic Reynolds number is assumed to be small. Under these assumptions, viscous and inertial effects are confined in very thin boundary layers adjacent to the walls. A significant fraction of the fluid flow is concentrated in the boundary layers adjacent to the side walls which are parallel to the magnetic field. This paper describes the analysis and numerical methods for obtaining 3-D solutions for flow parameters outside these layers, without solving explicitly for the layers themselves. Numerical solutions are presented for cases which are relevant to the flows of liquid metals in fusion reactor blankets. Experimental results obtained from the ALEX experiments at Argonne National Laboratory are used to validate the numerical code. In general, the agreement is excellent. 5 refs., 14 figs
Three-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (3DFATMIC) Model
This model simulates subsurface flow, fate and transport of contaminants that are undergoing chemical or biological transformations. The model is applicable to transient conditions in both saturated and unsaturated zones.
Directory of Open Access Journals (Sweden)
A.M. Rashad
2017-04-01
Full Text Available The present study explores the impact of anistropic slip on transient three dimensional MHD flow of Cobalt-kerosene ferrofluid over an inclined radiate stretching surface. The governing partial differential equations for this study are solved by the Thomas algorithm with finite-difference type. The impacts of several significant parameters on flow and heat transfer characteristics are exhibited graphically. The conclusion is revealed that the local Nusselt number is significantly promoted due to influence of thermal radiation whereas diminished with elevating the solid volume fraction, magnet parameter and slip factors. Further, the skin friction coefficients visualizes a considerable enhancement with boosting the magnet and radiation parameters, but a prominent reduction is recorded by elevating the solid volume fraction and slip factors.
Directory of Open Access Journals (Sweden)
Alexandr Kоshev
2014-12-01
Full Text Available The mathematical model of electrochemical processes distribution within the three-dimensional flow-through electrode for the system Fe(III/Fe(II/Fe is described in this paper, considering also the electrochemical reactions of hydrogen and molecular oxygen reduction. Possible dynamic changes in the parameters of electrode, electrolyte and the process are taken into account in the mathematical model, such as electro-conductivity of electrode material, electrolyte flow rate, material porosity and specific electrode surface, concentrations of electro-active substances and other characteristics within the local volume of electrode. Electrode and process characteristics are treated as time and coordinate functions within the electrode volume. The results of calculations and experimental studies of iron electro-reduction are given, the analysis of the numerical modeling is provided.
Hathaway, Michael D.; Chriss, Randall M.; Strazisar, Anthony J.; Wood, Jerry R.
1995-01-01
A laser anemometer system was used to provide detailed surveys of the three-dimensional velocity field within the NASA low-speed centrifugal impeller operating with a vaneless diffuser. Both laser anemometer and aerodynamic performance data were acquired at the design flow rate and at a lower flow rate. Floor path coordinates, detailed blade geometry, and pneumatic probe survey results are presented in tabular form. The laser anemometer data are presented in the form of pitchwise distributions of axial, radial, and relative tangential velocity on blade-to-blade stream surfaces at 5-percent-of-span increments, starting at 95-percent-of-span from the hub. The laser anemometer data are also presented as contour and wire-frame plots of throughflow velocity and vector plots of secondary velocities at all measurement stations through the impeller.
Study of Flow Deformation around Wind-Vane Mounted Three-Dimensional Hot-Wire Probes
DEFF Research Database (Denmark)
Rømer Rasmussen, K.; Larsen, Søren Ejling; Jørgensen, F. E.
1981-01-01
Open wind tunnel tests on several different sensor systems consisting of triaxial hot-wire probes mounted on wind vanes (DISA and Riso vanes) have shown that flow deformation around the hot-wire sensor introduces errors in the measured velocity components. Though changes in the horizontal...... components proved to be negligible, flow deformation resulted in an overestimation of the vertical component from 1.1 to 1.5, depending on the direction of the vertical component. Turbulence and mean value data were adjusted by use of a linear correction derived from the wind tunnel tests. Wind vane...... construction must strike a compromise between minor flow disturbance and sufficient probe support. The final version of the DISA vane resulted in an acceptable vertical correction of about 10%....
Numerical simulation analysis of three dimensional flow field in the lower plenum of CNP1000
International Nuclear Information System (INIS)
Liu Changwen; Jiang Xiaohua; Chen Weihong
2004-01-01
China National Nuclear Corporation (CNNC) proposed the CNP1000 design for Chinese market, which is a 1000MWe class nuclear power plant with three loops, in order to meet the electric power requirements of China and to fit the Chinese nuclear power development plan. This design, in which the number of fuel assembly is reasonably increased to 177 to lower the linear power density, has the characteristics of high safety and better economy. Comparing with the typical three-loop 1000MWe class nuclear power plant with 157 fuel assemblies, the reactor internals has been redesigned due to increasing of core diameter. NPIC has performed the hydraulic simulation test in order to validate the reactor internals design and analyze the reactor hydraulic characteristics. The aims of this paper are to analyze the effect of the new reactor internals design on the reactor thermal-hydraulic characteristics, particularly the flow distribution of the lower plenum and the core inlet flow distribution. The hydraulic tests were usually used to investigate the flow-rate distribution and flow resistance in the core. But the experimental periods were so long and the experiments were too expensive, especially for optimizing schemes. Along with the development of computer, computational fluid dynamics (CFD) became one kind of powerful means for research and engineering design. The flow distribution and pressure drop of the lower core plate can be obtained by numerical simulation of the 3-D flow field in the lower plenum. Through the comparison with the experiment data, not only the reactor internals design can be validated, but also the thermal hydraulic characteristics of the flow in the reactor vessel can be analyzed in detail. Computational fluid dynamics is the combination of neoteric hydrodynamics, numerical mathematics and computer science. It is a fringe subject with powerful vitality. CFD uses computer and discretization method to simulate the practical hydrodynamic problem. There are
Mu, Xiang-Qi; Savarino, Stephen J; Bullitt, Esther
2008-02-22
To survive the harsh environment of a churning intestinal tract, bacteria attach to the host epithelium via thin fibers called pili (or fimbriae). Enterotoxigenic Escherichia coli bacteria expressing colonization factor antigen I (CFA/I) pili and related pili are the most common known bacterial cause of diarrheal disease, including traveler's diarrhea. CFA/I pili, assembled via the alternate chaperone pathway, are essential for binding and colonization of the small bowel by these pathogenic bacteria. Herein, we elucidate unique structural features of CFA/I pili that appear to optimize their function as bacterial tethers in the intestinal tract. Using transmission electron microscopy of negatively stained samples in combination with iterative three-dimensional helical reconstruction methods for image processing, we determined the structure of the CFA/I pilus filament. Our results indicate that strong end-to-end protein interactions and weak interactions between the coils of a sturdy spring-like helix provide the combination of strength, stability, and flexibility required to sustain bacterial adhesion and incite intestinal disease. We propose that CFA/I pili behave like a spring to maintain attachment to the gut lining during vortex mixing and downward flow of the intestinal contents, thereby persisting long enough for these bacteria to colonize the host epithelium and cause enteric disease.
Directory of Open Access Journals (Sweden)
Wei Fan
2016-01-01
Full Text Available Transmission loss (TL is often used to evaluate the acoustic attenuation performance of a silencer. In this work, a three-dimensional (3D finite element method (FEM is employed to calculate the TL of some representative silencers, namely, circular expansion chamber silencer and straight-through perforated pipe silencer. In order to account for the effect of mean flow that exists inside the silencer, the 3D FEM is used in conjunction with the Computational Fluid Dynamics (CFD simulation of the flow field. More concretely, the 3D mean flow field is computed by firstly using CFD, and then the obtained mean flow data are imported to an acoustic solution undertaken using FEM. The data transfer between the two steps is accomplished by mesh mapping. The results presented demonstrate good agreement between present TL predictions and previously published experimental and numerical works. Also, the details of the flow inside the silencers may be studied. Furthermore, the effect of mean flow velocity on acoustic attenuation performance of the silencers is investigated. It is concluded that for the studied silencers, in general, increasing flow velocity increases the TL and decreases the resonance peaks.
International Nuclear Information System (INIS)
Kumamaru, Hiroshige
2003-01-01
A three-dimensional numerical calculation has been performed on liquid-metal magnetohydrodynamic (MHD) flow through a rectangular channel in the outlet region of the magnetic field, including a region downstream the magnetic field section. The continuity equation, the momentum equation and the induction equation have been solved numerically by the finite difference method. Along the flow axis (i.e. the channel axis), the pressure decreases rapidly as a fully-developed MHD flow, drops more rapidly in the magnetic-field outlet-region, and finally decreases slowly as a normal non-MHD flow. The pressure recovery that was observed in the magnetic-field inlet-region does not appear in the magnetic-field outlet-region. The total pressure drop through the magnetic-field outlet-region is larger than that through the magnetic-field inlet-region. The flow velocity distribution also changes gradually from a flat profile of a fully-developed MHD flow to a parabolic profile of a non-MHD laminar flow. (author)
Shear-induced particle migration in one-, two-, and three-dimensional flows
Gao, C.; Gilchrist, J. F.
2008-02-01
We investigate the segregation resulting from the competition between advection and shear-induced migration of suspensions in steady open flows. Herringbone channels form a concentration profile deviating from the particle focusing found in straight channels. Transients can result from a buckling instability during the onset of migration when particle-depleted fluid is injected into particle-rich fluid. In chaotic flows, the better mixing found at low bulk volume fraction is not seen at higher bulk volume fraction. Thus, the ability of static mixers to reduce the effects of shear-induced migration is significantly limited.
A comparison of upwind schemes for computation of three-dimensional hypersonic real-gas flows
Gerbsch, R. A.; Agarwal, R. K.
1992-01-01
The method of Suresh and Liou (1992) is extended, and the resulting explicit noniterative upwind finite-volume algorithm is applied to the integration of 3D parabolized Navier-Stokes equations to model 3D hypersonic real-gas flowfields. The solver is second-order accurate in the marching direction and employs flux-limiters to make the algorithm second-order accurate, with total variation diminishing in the cross-flow direction. The algorithm is used to compute hypersonic flow over a yawed cone and over the Ames All-Body Hypersonic Vehicle. The solutions obtained agree well with other computational results and with experimental data.
Ryan, Kevin J.; Coletti, Filippo; Elkins, Christopher J.; Dabiri, John O.; Eaton, John K.
2016-03-01
Three-dimensional, three-component mean velocity fields have been measured around and downstream of a scale model vertical axis wind turbine (VAWT) operated at tip speed ratios (TSRs) of 1.25 and 2.5, in addition to a non-rotating case. The five-bladed turbine model has an aspect ratio (height/diameter) of 1 and is operated in a water tunnel at a Reynolds number based on turbine diameter of 11,600. Velocity fields are acquired using magnetic resonance velocimetry (MRV) at an isotropic resolution of 1/50 of the turbine diameter. Mean flow reversal is observed immediately behind the turbine for cases with rotation. The turbine wake is highly three-dimensional and asymmetric throughout the investigated region, which extends up to 7 diameters downstream. A vortex pair, generated at the upwind-turning side of the turbine, plays a dominant role in wake dynamics by entraining faster fluid from the freestream and aiding in wake recovery. The higher TSR case shows a larger region of reverse flow and greater asymmetry in the near wake of the turbine, but faster wake recovery due to the increase in vortex pair strength with increasing TSR. The present measurement technique also provides detailed information about flow in the vicinity of the turbine blades and within the turbine rotor. The details of the flow field around VAWTs and in their wakes can inform the design of high-density VAWT wind farms, where wake interaction between turbines is a principal consideration.
Thoughts on the chimera method of simulation of three-dimensional viscous flow
Steger, Joseph L.
1991-01-01
The chimera overset grid is reviewed and discussed relative to other procedures for simulating flow about complex configurations. It is argued that while more refinement of the technique is needed, current schemes are competitive to unstructured grid schemes and should ultimately prove more useful.
Development of a Three-Dimensional Unstructured Euler Solver for High-Speed Flows
Directory of Open Access Journals (Sweden)
Tudorel Petronel AFILIPOAE
2015-12-01
Full Text Available This paper addresses the solution of the compressible Euler equations on hexahedral meshes for supersonic and hypersonic flows. Spatial discretization is accomplished by a cell-centered finite-volume formulation which employs two different upwind schemes for the computation of convective fluxes. Second-order solutions are attained through a linear state reconstruction technique that yields highly resolved flows in smooth regions while providing a sharp and clean resolution of shocks. The solution gradients required for the higher-order spatial discretization are estimated by a least-square method while Venkatakrishnan limiter is employed to preserve monotonicity and avoid oscillations in the presence of shocks. Furthermore, solutions are advanced in time by an explicit third-order Runge-Kutta scheme and convergence to steady state is accelerated using implicit residual smoothing. Flow around a circular arc in a channel and flow past a circular cylinder are studied and results are presented for various Mach numbers together with comparisons to theoretical and experimental data where possible.
Three-dimensional flow and load characteristics of flexible revolving wings at low Reynolds number
van de Meerendonk, R.; Perçin, M.; van Oudheusden, B.W.
2016-01-01
This study explores the flow field and fluid-dynamic loads generated by revolving low-aspect-ratio flat plate wings undergoing a revolving motion starting from rest. Three wings with different degree of chordwise flexural stiffness (i.e., rigid, moderate flexibility and high flexibility) have been
The Three-Dimensional Velocity Distribution of Wide Gap Taylor-Couette Flow Modelled by CFD
Directory of Open Access Journals (Sweden)
David Shina Adebayo
2016-01-01
Full Text Available A numerical investigation is conducted for the flow between two concentric cylinders with a wide gap, relevant to bearing chamber applications. This wide gap configuration has received comparatively less attention than narrow gap journal bearing type geometries. The flow in the gap between an inner rotating cylinder and an outer stationary cylinder has been modelled as an incompressible flow using an implicit finite volume RANS scheme with the realisable k-ε model. The model flow is above the critical Taylor number at which axisymmetric counterrotating Taylor vortices are formed. The tangential velocity profiles at all axial locations are different from typical journal bearing applications, where the velocity profiles are quasilinear. The predicted results led to two significant findings of impact in rotating machinery operations. Firstly, the axial variation of the tangential velocity gradient induces an axially varying shear stress, resulting in local bands of enhanced work input to the working fluid. This is likely to cause unwanted heat transfer on the surface in high torque turbomachinery applications. Secondly, the radial inflow at the axial end-wall boundaries is likely to promote the transport of debris to the junction between the end-collar and the rotating cylinder, causing the build-up of fouling in the seal.
A three-dimensional dynamical model for channeled lava flow with nonlinear rheology
Filippucci, Marilena; Tallarico, Andrea; Dragoni, Michele
2010-05-01
Recent laboratory studies on the rheology of lava samples from different volcanic areas have highlighted that the apparent viscosity depends on a power of the strain rate. Several authors agree in attributing this dependence to the crystal content of the sample and to temperature. Starting from these results, in this paper we studied the effect of a power law rheology on a gravity-driven lava flow. The equation of motion is nonlinear in the diffusion term, and an analytical solution does not seem to be possible. The finite-volume method has been applied to solve numerically the equation governing the fully developed laminar flow of a power law non-Newtonian fluid in an inclined rectangular channel. The convergence, the stability, and the order of approximation were tested for the Newtonian rheology case, comparing the numerical solution with the available analytical solution. Results indicate that the assumption on the rheology, whether linear or nonlinear, strongly affects the velocity and/or the thickness of the lava channel both for channels with fixed geometry and for channels with constant flow rate. Results on channels with fixed geometry are confirmed by some simulations for real lava channels. Finally, the study of the Reynolds number indicates that gravity-driven lava channel flows are always in laminar regime, except for strongly nonlinear pseudoplastic fluids with low fluid consistency and at high slopes.
Mao, X.; Prommer, H.; Barry, D.A.; Langevin, C.D.; Panteleit, B.; Li, L.
2006-01-01
PHWAT is a new model that couples a geochemical reaction model (PHREEQC-2) with a density-dependent groundwater flow and solute transport model (SEAWAT) using the split-operator approach. PHWAT was developed to simulate multi-component reactive transport in variable density groundwater flow. Fluid density in PHWAT depends not on only the concentration of a single species as in SEAWAT, but also the concentrations of other dissolved chemicals that can be subject to reactive processes. Simulation results of PHWAT and PHREEQC-2 were compared in their predictions of effluent concentration from a column experiment. Both models produced identical results, showing that PHWAT has correctly coupled the sub-packages. PHWAT was then applied to the simulation of a tank experiment in which seawater intrusion was accompanied by cation exchange. The density dependence of the intrusion and the snow-plough effect in the breakthrough curves were reflected in the model simulations, which were in good agreement with the measured breakthrough data. Comparison simulations that, in turn, excluded density effects and reactions allowed us to quantify the marked effect of ignoring these processes. Next, we explored numerical issues involved in the practical application of PHWAT using the example of a dense plume flowing into a tank containing fresh water. It was shown that PHWAT could model physically unstable flow and that numerical instabilities were suppressed. Physical instability developed in the model in accordance with the increase of the modified Rayleigh number for density-dependent flow, in agreement with previous research. ?? 2004 Elsevier Ltd. All rights reserved.
Cereser, Alberto; Strobl, Markus; Hall, Stephen; Steuwer, Axel; Kiyanagi, Ryoji; Tremsin, Anton; Knudsen, Erik Bergbäck; Shinohara, Takenao; Willendrup, Peter; Fanta, Alice Bastos da Silva; Iyengar, Srinivasan; Larsen, Peter Mahler; Hanashima, Takayasu; Moyoshi, Taketo; Kadletz, Peter M.
2017-01-01
The physical properties of polycrystalline materials depend on their microstructure, which is the nano- to centimeter scale arrangement of phases and defects in their interior. Such microstructure depends on the shape, crystallographic phase and orientation, and interfacing of the grains constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional ne...
Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors
Oprea, Tudor I.; García, Angel E.
1996-06-01
Inhibition of aromatase, a cytochrome P450 that converts androgens to estrogens, is relevant in the therapeutic control of breast cancer. We investigate this inhibition using a three-dimensional quantitative structure-activity relationship (3D QSAR) method known as Comparative Molecular Field Analysis, CoMFA [Cramer III, R.D. et al., J. Am. Chem. Soc., 110 (1988) 5959]. We analyzed the data for 50 steroid inhibitors [Numazawa, M. et al., J. Med. Chem., 37 (1994) 2198, and references cited therein] assayed against androstenedione on human placental microsomes. An initial CoMFA resulted in a three-component model for log(1/Ki), with an explained variance r2 of 0.885, and a cross-validated q2 of 0.673. Chemometric studies were performed using GOLPE [Baroni, M. et al., Quant. Struct.-Act. Relatsh., 12 (1993) 9]. The CoMFA/GOLPE model is discussed in terms of robustness, predictivity, explanatory power and simplicity. After randomized exclusion of 25 or 10 compounds (repeated 25 times), the q2 for one component was 0.62 and 0.61, respectively, while r2 was 0.674. We demonstrate that the predictive r2 based on the mean activity (Ym) of the training set is misleading, while the test set Ym-based predictive r2 index gives a more accurate estimate of external predictivity. Using CoMFA, the observed differences in aromatase inhibition among C6-substituted steroids are rationalized at the atomic level. The CoMFA fields are consistent with known, potent inhibitors of aromatase, not included in the model. When positioned in the same alignment, these compounds have distinct features that overlap with the steric and electrostatic fields obtained in the CoMFA model. The presence of two hydrophobic binding pockets near the aromatase active site is discussed: a steric bulk tolerant one, common for C4, C6-alpha and C7-alpha substitutents, and a smaller one at the C6-beta region.
Three-dimensional measurement of the laminar flow field inside a static mixer
Speetjens, Michel; Jilisen, Rene; Bloemen, Paul
2011-11-01
Static mixers are widely used in industry for laminar mixing of viscous fluids as e.g. polymers and food stuffs. Moreover, given the similarities in flow regime, static mixers often serve as model for compact mixers for process intensification and even for micro-mixers. This practical relevance has motivated a host of studies on the mixing characteristics of static mixers and their small-scale counterparts. However, these studies are primarily theoretical and numerical. Experimental studies, in contrast, are relatively rare and typically restricted to local 2D flow characteristics or integral quantities (pressure drop, residence-time distributions). The current study concerns 3D measurements on the laminar flow field inside a static mixer using 3D Particle-Tracking Velocimetry (3D-PTV) Key challenges to the 3D-PTV image-processing procedure are the optical distortion and degradation of the particle imagery due to light refraction and reflection caused by the cylindrical boundary and the internal elements. Ways to tackle these challenges are discussed and first successful 3D measurements in an actual industrial static mixer are presented.
Algabri, Y. A.; Rookkapan, S.; Chatpun, S.
2017-09-01
An abdominal aortic aneurysm (AAA) is considered a deadly cardiovascular disease that defined as a focal dilation of blood artery. The healthy aorta size is between 15 and 24 mm based on gender, bodyweight, and age. When the diameter increased to 30 mm or more, the rupture can occur if it is kept growing or untreated. Moreover, the proximal angular neck of aneurysm is categorized as a significant morphological feature with prime harmful effects on endovascular aneurysm repair (EVAR). Flow pattern in pathological vessel can influence the vascular intervention. The aim of this study is to investigate the blood flow behaviours in angular neck abdominal aortic aneurysm with simulated geometry based on patient’s information using computational fluid dynamics (CFD). The 3D angular neck AAA models have been designed by using SolidWorks Software. Consequently, CFD tools are used for simulating these 3D models of angular neck AAA in ANSYS FLUENT Software. Eventually, based on the results, we summarized that the CFD techniques have shown high performance in explaining and investigating the flow patterns for angular neck abdominal aortic aneurysm.
Campbell, C. L.; Wood, K.; Brown, C. T. A.; Moseley, H.
2016-07-01
We explore the effects of three dimensional (3D) tumour structures on depth dependent fluence rates, photodynamic doses (PDD) and fluorescence images through Monte Carlo radiation transfer modelling of photodynamic therapy. The aim with this work was to compare the commonly used uniform tumour densities with non-uniform densities to determine the importance of including 3D models in theoretical investigations. It was found that fractal 3D models resulted in deeper penetration on average of therapeutic radiation and higher PDD. An increase in effective treatment depth of 1 mm was observed for one of the investigated fractal structures, when comparing to the equivalent smooth model. Wide field fluorescence images were simulated, revealing information about the relationship between tumour structure and the appearance of the fluorescence intensity. Our models indicate that the 3D tumour structure strongly affects the spatial distribution of therapeutic light, the PDD and the wide field appearance of surface fluorescence images.
Saaid, Hicham; Segers, Patrick; Novara, Matteo; Claessens, Tom; Verdonck, Pascal
2018-03-01
The characterization of flow patterns in the left ventricle may help the development and interpretation of flow-based parameters of cardiac function and (patho-)physiology. Yet, in vivo visualization of highly dynamic three-dimensional flow patterns in an opaque and moving chamber is a challenging task. This has been shown in several recent multidisciplinary studies where in vivo imaging methods are often complemented by in silico solutions, or by in vitro methods. Because of its distinctive features, particle image velocimetry (PIV) has been extensively used to investigate flow dynamics in the cardiovascular field. However, full volumetric PIV data in a dynamically changing geometry such as the left ventricle remain extremely scarce, which justifies the present study. An investigation of the left ventricle flow making use of a customized cardiovascular simulator is presented; a multiplane scanning-stereoscopic PIV setup is used, which allows for the measurement of independent planes across the measurement volume. Due to the accuracy in traversing the illumination and imaging systems, the present setup allows to reconstruct the flow in a 3D volume performing only one single calibration. The effects of the orientation of a prosthetic mitral valve in anatomical and anti-anatomical configurations have been investigated during the diastolic filling time. The measurement is performed in a phase-locked manner; the mean velocity components are presented together with the vorticity and turbulent kinetic energy maps. The reconstructed 3D flow structures downstream the bileaflet mitral valve are shown, which provides additional insight of the highly three-dimensional flow.
Breburda, C. S.; Griffin, B. P.; Pu, M.; Rodriguez, L.; Cosgrove, D. M. 3rd; Thomas, J. D.
1998-01-01
OBJECTIVES: We sought to validate direct planimetry of mitral regurgitant orifice area from three-dimensional echocardiographic reconstructions. BACKGROUND: Regurgitant orifice area (ROA) is an important measure of the severity of mitral regurgitation (MR) that up to now has been calculated from hemodynamic data rather than measured directly. We hypothesized that improved spatial resolution of the mitral valve (MV) with three-dimensional (3D) echo might allow accurate planimetry of ROA. METHODS: We reconstructed the MV using 3D echo with 3 degrees rotational acquisitions (TomTec) using a transesophageal (TEE) multiplane probe in 15 patients undergoing MV repair (age 59 +/- 11 years). One observer reconstructed the prolapsing mitral leaflet in a left atrial plane parallel to the ROA and planimetered the two-dimensional (2D) projection of the maximal ROA. A second observer, blinded to the results of the first, calculated maximal ROA using the proximal convergence method defined as maximal flow rate (2pi(r2)va, where r is the radius of a color alias contour with velocity va) divided by regurgitant peak velocity (obtained by continuous wave [CW] Doppler) and corrected as necessary for proximal flow constraint. RESULTS: Maximal ROA was 0.79 +/- 0.39 (mean +/- SD) cm2 by 3D and 0.86 +/- 0.42 cm2 by proximal convergence (p = NS). Maximal ROA by 3D echo (y) was highly correlated with the corresponding flow measurement (x) (y = 0.87x + 0.03, r = 0.95, p proximal convergence measurements.
International Nuclear Information System (INIS)
Lee, Wu Sang; Kim, Dae Hyun; Min, Jae Hong; Chung Jin Taek
2007-01-01
Endwall losses contribute significantly to the overall losses in modern turbomachinery, especially when aerodynamic airfoil load and pressure ratio are increased. Hence, reducing the extend and intensity of the secondary flow structures helps to enhance overall efficiency. From the large range of viable approaches, a promising combination positioning and height of endwall contouring was chosen. The objective of this study is to document the three-dimensional flow in a turbine cascade in terms of streamwise vorticity, total pressure loss distribution and static pressure distribution on the endwall and blade surface and to propose an appropriate positioning and height of the endwall contouring which show best secondary, overall loss reduction among the simulated endwall. The flow through the gas turbine were numerically analyzed using three dimensional Navier-Stroke equations with a commercial CFD code ANSYS CFX-10. The result shows that the overall loss is reduced near the flat endwall rather than contoured endwall, and the case of contoured endwall installed at 30% from leading edge with height of 25% for span showed best performance
Lattice Boltzmann simulations of leukocyte rolling and deformation in a three-dimensional shear flow
Luo, Ye; Qi, Dewei; He, Guowei
2013-11-01
Lattice Boltzmann simulation is used to simulate the motion of a leukocyte in fluid. The cell membrane is built by lattice spring model. The interaction between the fluid flow and the solid surface is treated by immersed boundary method. Stochastic Monte Carlo method is used to deal with receptor/ligand interaction. It is shown that the model can correctly predict the characteristic ``stop-and-g'' motion of rolling leukocytes. Effects of cell deformation, shear rates, bonding force, microvilli distribution on rolling are studied and compared with experiments.
Kobayashi, Y.; Towhata, I.
2005-01-01
Since the design policy of countermeasures to liquefaction is currently prevention of liquefaction, conventional liquefaction analysis aims to predict the possibility of liquefaction at a target site. However, quantitative prediction of ground flow by liquefaction has been studied for new design policy that allows the deformation of liquefied ground if it is not critical. This paper presents a method for prediction of the ground deformation related liquefaction by viscous fluid model. Furthermore, the mitigation effect of a sheet pile wall is assessed by modeling a sheet pile wall as an elastic beam.
The three-dimensional flow in the chamber of a gas centrifuge with an installed obstacle
International Nuclear Information System (INIS)
Elsholz, E.
1977-01-01
The flow-field in a very fast rotating chamber under the presence of a stationarily installed obstacle is calculated numerically from the complete set of Navier-Stokes-equations. A special differential approximation applied, provides stable and non-oscillating solutions even within the region of very small Ekman-numbers. This type of approximation will be derived and its advantages are discussed. Finally, a numerical result is presented which includes strong radial density gradients and shows very clearly the compressible effects as well as the mechanism of vortex shedding generated by the obstacle. (orig.) [de
Three dimensional radiative flow of magnetite-nanofluid with homogeneous-heterogeneous reactions
Hayat, Tasawar; Rashid, Madiha; Alsaedi, Ahmed
2018-03-01
Present communication deals with the effects of homogeneous-heterogeneous reactions in flow of nanofluid by non-linear stretching sheet. Water based nanofluid containing magnetite nanoparticles is considered. Non-linear radiation and non-uniform heat sink/source effects are examined. Non-linear differential systems are computed by Optimal homotopy analysis method (OHAM). Convergent solutions of nonlinear systems are established. The optimal data of auxiliary variables is obtained. Impact of several non-dimensional parameters for velocity components, temperature and concentration fields are examined. Graphs are plotted for analysis of surface drag force and heat transfer rate.
Time-domain Green's Function Method for three-dimensional nonlinear subsonic flows
Tseng, K.; Morino, L.
1978-01-01
The Green's Function Method for linearized 3D unsteady potential flow (embedded in the computer code SOUSSA P) is extended to include the time-domain analysis as well as the nonlinear term retained in the transonic small disturbance equation. The differential-delay equations in time, as obtained by applying the Green's Function Method (in a generalized sense) and the finite-element technique to the transonic equation, are solved directly in the time domain. Comparisons are made with both linearized frequency-domain calculations and existing nonlinear results.
Three-Dimensional Interactions and Vortical Flows with Emphasis on High Speeds
1980-07-01
Rainbird (1968b). 24 Overall Viscous Flow Field - With the introduction of fast computers, such as the CDC 7600, a moi ’r less complete picture of the...1M)e) (b) TURBULENT: u.-" 200 ftfm~; RD - 2 x 106, R6 -0.4 x 106! ( FAST AND HOXEY lft) S5 Fig. 34 Skin-friction lines on surfaces about protuberance...isuliatin n crclarcoe a hgh eltiv icidnc, a2,wit trbuen layes (ainird t a. 166) LIA4o -- "o Fi. 7 ildt sr facealo visualization on cirular~s cuofne of
Directory of Open Access Journals (Sweden)
Yogo Takada
2013-01-01
Full Text Available A fish robot with image sensors is useful to research for underwater creatures such as fish. However, the propulsion velocity of a fish robot is very slow compared with live fish. It is necessary to swim at a speed several times faster than the speed of the current robots for various usages. Therefore, we are searching for the method of making the robot swim fast. The simulation before making the robot is important. We have made the computational simulation program of three-dimensional fluid-structure analysis. The flow around the caudal fin can be examined by analyzing the fin as an elastic body. We compared the results of numerical analysis with the results of PIV measurement. Both were agreed well. Because the performance of a fish robot with two joints is better than that of a fish robot with one joint, we searched for an excellent fin for the fish robot with two joints by using CFD. We confirmed that the swimming performance of a fish robot becomes very good when the caudal fin is rigid except for the root of the fin which is comparatively flexible.
Three-dimensional spatial structures of solar wind turbulence from 10 000-km to 100-km scales
Directory of Open Access Journals (Sweden)
Y. Narita
2011-10-01
Full Text Available Using the four Cluster spacecraft, we have determined the three-dimensional wave-vector spectra of fluctuating magnetic fields in the solar wind. Three different solar wind intervals of Cluster data are investigated for this purpose, representing three different spatial scales: 10 000 km, 1000 km, and 100 km. The spectra are determined using the wave telescope technique (k-filtering technique without assuming the validity of Taylor's frozen-in-flow hypothesis nor are any assumptions made as to the symmetry properties of the fluctuations. We find that the spectra are anisotropic on all the three scales and the power is extended primarily in the directions perpendicular to the mean magnetic field, as might be expected of two-dimensional turbulence, however, the analyzed fluctuations are not axisymmetric. The lack of axisymmetry invalidates some earlier techniques using single spacecraft observations that were used to estimate the percentage of magnetic energy residing in quasi-two-dimensional power. However, the dominance of two-dimensional turbulence is consistent with the relatively long mean free paths of cosmic rays in observed in the heliosphere. On the other hand, the spectra also exhibit secondary extended structures oblique from the mean magnetic field direction. We discuss possible origins of anisotropy and asymmetry of solar wind turbulence spectra.
International Nuclear Information System (INIS)
Bentaleb, Y.; Leschziner, M.A.
2013-01-01
Highlights: • We study a spatially-evolving three-dimensional boundary layer. • We impose a streamwise-varying spanwise-homogeneous pressure gradient. • A collateral flow is formed close to the wall, and this is investigated alongside the skewed upper part of the boundary layer. • A wide range of flow-physical properties have been studied. -- Abstract: A spatially-evolving three-dimensional boundary layer, subjected to a streamwise-varying spanwise-homogeneous pressure gradient, equivalent to a body force, is investigated by way of direct numerical simulation. The pressure gradient, prescribed to change its sign half-way along the boundary layer, provokes strong skewing of the velocity vector, with a layer of nearly collateral flow forming close to the wall up to the position of maximum spanwise velocity. A wide range of flow-physical properties have been studied, with particular emphasis on the near-wall layer, including second-moments, major budget contributions and wall-normal two-point correlations of velocity fluctuations and their angles, relative to wall-shear fluctuations. The results illustrate the complexity caused by skewing, including a damping in turbulent mixing and a significant lag between strains and stresses. The study has been undertaken in the context of efforts to develop and test novel hybrid LES–RANS schemes for non-equilibrium near-wall flows, with an emphasis on three-dimensional near-wall straining. Fundamental flow-physical issues aside, the data derived should be of particular relevance to a priori studies of second-moment RANS closure and the development and validation of RANS-type near-wall approximations implemented in LES schemes for high-Reynolds-number complex flows
Parametric analysis of three dimensional flow models applied to tidal energy sites in Scotland
Rahman, Anas; Venugopal, Vengatesan
2017-04-01
This paper presents a detailed parametric analysis on various input parameters of two different numerical models, namely Telemac3D and Delft3D, used for the simulation of tidal current flow at potential tidal energy sites in the Pentland Firth in Scotland. The motivation behind this work is to investigate the influence of the input parameters on the above 3D models, as the majority of past research has mainly focused on using the 2D depth-averaged flow models for this region. An extended description of the models setup, along with the utilised parameters is provided. The International Hydrographic Organisation (IHO) tidal gauges and Acoustic Doppler and Current Profiler (ADCP) measurements are used in calibrating model output to ensure the robustness of the models. Extensive parametric study on the impact of varying drag coefficients, roughness formulae and turbulence models has been investigated and reported. The results indicate that both Telemac3D and Delft3D models are able to produce excellent comparison against measured data; however, with Delft3D, the model parameters which provided higher correlation with the measured data, are found to be different from those reported in the previous literature, which could be attributed to the choice of boundary conditions and the mesh size.
International Nuclear Information System (INIS)
Li Ying; Zhou Wenxia; Zhang Jige; Wang Dezhong
2009-01-01
In order to achieve the level of self-design and domestic manufacture of the reactor coolant pump (nuclear main pump), the software FLUENT was used to simulate the three-dimensional flow through full passage of one nuclear main pump basing on RNG κ-ε turbulence model and SIMPLE algorithm. The distribution of pressure and velocity of the flow in the impeller's surface was analyzed in different working conditions. Moreover, the performance of the pump was predicted based on the simulation results. The results show that the distributions of pressure and velocity are reasonable in both the working and back face of the blade in the steady working condition. The pressure of the flow is increased from the inlet to the outlet of the pump, and shows the maximal value in the impeller region. Comparatively satisfactory efficiency and head value were obtained in the condition of the pump design. The shaft power of the nuclear main pump is gradually increased with the increase of the flow flux. These results are helpful in understanding the change of the internal flow field in the nuclear main pump, which is of some importance for the pre-exploration and theoretical research on the domestic manufacture of the nuclear main pump. (authors)
Roszelle, Breigh N; Deutsch, Steven; Manning, Keefe B
2010-02-01
In order to aid the ongoing concern of limited organ availability for pediatric heart transplants, Penn State has continued development of a pulsatile Pediatric Ventricular Assist Device (PVAD). Initial studies of the PVAD observed an increase in thrombus formation due to differences in flow field physics when compared to adult sized devices, which included a higher degree of three-dimensionality. This unique flow field brings into question the use of 2D planar particle image velocimetry (PIV) as a flow visualization technique, however the small size and high curvature of the PVAD make other tools such as stereoscopic PIV impractical. In order to test the reliability of the 2D results, we perform a pseudo-3D PIV study using planes both parallel and normal to the diaphragm employing a mock circulatory loop containing a viscoelastic fluid that mimics 40% hematocrit blood. We find that while the third component of velocity is extremely helpful to a physical understanding of the flow, particularly of the diastolic jet and the development of a desired rotational pattern, the flow data taken parallel to the diaphragm is sufficient to describe the wall shear rates, a critical aspect to the study of thrombosis and design of such pumps.
Energy Technology Data Exchange (ETDEWEB)
Dickson, M.R.; Downing, K.H.; Wu, W.H.; Glaeser, R.M.
1986-09-01
The three-dimensional structure of the protein which forms the S layer of Aquaspirilium serpens strain VHA has been determined by electron microscopy. Structures have been reconstructed to a resolution of about 1.6 nm for single-layered specimens and about 4 nm for two-layered specimens. The structure, which has hexagonal symmetry, consists of a core in the shape of a cup, with six projections arising from the rim of the cup to join adjacent subunits at the threefold symmetry axes. The model is consistent with edge views of the S layer which have been obtained in this and other work. It is now clear from this work and from three-dimensional reconstructions of other bacterial S layers that a wide diversity exists in the morphology of surface layers.
Dickson, M R; Downing, K H; Wu, W H; Glaeser, R M
1986-09-01
The three-dimensional structure of the protein which forms the S layer of Aquaspirillum serpens strain VHA has been determined by electron microscopy. Structures have been reconstructed to a resolution of about 1.6 nm for single-layered specimens and about 4 nm for two-layered specimens. The structure, which has hexagonal symmetry, consists of a core in the shape of a cup, with six projections arising from the rim of the cup to join adjacent subunits at the threefold symmetry axes. The model is consistent with edge views of the S layer which have been obtained in this and other work. It is now clear from this work and from three-dimensional reconstructions of other bacterial S layers that a wide diversity exists in the morphology of surface layers.
International Nuclear Information System (INIS)
Pandey, Pradeep; Nayak, A.K.; Vijayan, P.K.
2014-01-01
Three dimensional flow patterns appearing in geometries such as curved pipes and T-channel junctions have important applications and are attractive for research. Unlike the flow in a straight tube, fluid motion in a curved tube is not parallel to the axis of bend, owing to the presence of centrifugal effects. It is characterized by a secondary flow in a cross-sectional plane normal to the main flow. Consequently, secondary flow separation near the inner wall is observed in the developing region. The strength of the secondary flow is greatly influenced by the curvature ratio and in turn, a non-dimensional parameter called the Dean Number. Secondary flow increases flow resistance, resulting in a larger pressure drop along the bend. The location of the maximum axial velocity gets shifted towards the outer wall. Flow in a T-channel junction is also a configuration of great significance. The simulations of the present work show that flow at low Reynolds numbers (Re ≤ 115) is steady and symmetric. For low Reynolds numbers, flow in the downstream channel remains highly segregated about the centerline. The appearance of vortices in the T-channel junction does little to redistribute concentration when flow remains symmetric. With increasing Reynolds number, transition takes place towards asymmetric flow. The incoming flow field gets redistributed at the center-plane and the dividing streamline becomes increasingly distorted. The flow field is characterized by thin elongated fluid interfaces across which momentum diffusion takes place. Flow at higher Reynolds numbers (Re ≥ 250) becomes unsteady in which unstable stagnation stream traces move periodically leftward and rightward at top and bottom walls. Trajectories of mass-less particles show greater dwelling in the junction as compared to those of finite mass particle. The numerical simulation is carried out in the present work using ANUPRAVAHA, a general purpose CFD solver developed at IIT Kanpur in collaboration with
Fully three-dimensional analysis of high-speed traintracksoil-structure dynamic interaction
Galvín, Pedro; Romero Ordoñez, Antonio; Domínguez Abascal, José
2010-01-01
In this paper, a general and fully three dimensional multi-body-finite element-boundary element model, formulated in the time domain to predict vibrations due to train passage at the vehicle, the track and the free field, is presented. The vehicle is modelled as a multi-body system and, therefore, the quasi-static and the dynamic excitation mechanisms due to train passage can be considered. The track is modelled using finite elements. The soil is considered as a homogeneous half-space by the ...
Three-dimensional Investigations of Wave Overtopping on Rubble Mound Structures
DEFF Research Database (Denmark)
Andersen, Thomas Lykke; Burcharth, Hans F.
2009-01-01
To study the influence of wave obliquity and directional spreading on wave overtopping of rubble mound breakwaters a total of 736 three-dimensional model tests were carried out at Aalborg University. The results of these tests are presented and analysed in this paper yielding a new empirical...... reduction factor to describe the influence of wave obliquity and directional spreading on the average wave overtopping discharges. The study shows that perpendicularly incident, long-crested waves result in conservative values of the overtopping discharge for the tested cross-section....
Multigrid methods for flow transition in three-dimensional boundary layers with surface roughness
Liu, Chaoqun; Liu, Zhining; Mccormick, Steve
1993-01-01
The efficient multilevel adaptive method has been successfully applied to perform direct numerical simulations (DNS) of flow transition in 3-D channels and 3-D boundary layers with 2-D and 3-D isolated and distributed roughness in a curvilinear coordinate system. A fourth-order finite difference technique on stretched and staggered grids, a fully-implicit time marching scheme, a semi-coarsening multigrid method associated with line distributive relaxation scheme, and an improved outflow boundary-condition treatment, which needs only a very short buffer domain to damp all order-one wave reflections, are developed. These approaches make the multigrid DNS code very accurate and efficient. This allows us not only to be able to do spatial DNS for the 3-D channel and flat plate at low computational costs, but also to do spatial DNS for transition in the 3-D boundary layer with 3-D single and multiple roughness elements, which would have extremely high computational costs with conventional methods. Numerical results show good agreement with the linear stability theory, the secondary instability theory, and a number of laboratory experiments. The contribution of isolated and distributed roughness to transition is analyzed.
Three-dimensional modeling of flow through fractured tuff at Fran Ridge
International Nuclear Information System (INIS)
Eaton, R.R.; Ho, C.K.; Glass, R.J.; Nicholl, M.J.; Arnold, B.W.
1996-01-01
Numerical studies have been made of an infiltration experiment at Fran Ridge using the TOUGH2 code to aid in the selection of computational models for performance assessment. The exercise investigates the capabilities of TOUGH2 to model transient flows through highly fractured tuff and provides a possible means of calibration. Two distinctly different conceptual models were used in the TOUGH2 code, the dual permeability model and the equivalent continuum model. The infiltration test modeled involved the infiltration of dyed ponded water for 36 minutes. The 205 gallon filtration of water observed in the experiment was subsequently modeled using measured Fran Ridge fracture frequencies, and a specified fracture aperture of 285 μm. The dual permeability formulation predicted considerable infiltration along the fracture network, which was in agreement with the experimental observations. As expected, minimal fracture penetration of the infiltrating water was calculated using the equivalent continuum model, thus demonstrating that this model is not appropriate for modeling the highly transient experiment. It is therefore recommended that the dual permeability model be given priority when computing high-flux infiltration for use in performance assessment studies
Three-dimensional modeling of flow through fractured tuff at Fran Ridge
International Nuclear Information System (INIS)
Eaton, R.R.; Ho, C.K.; Glass, RJ.; Nicholl, M.J.; Arnold, B.W.
1996-09-01
Numerical studies have been made of an infiltration experiment at Fran Ridge using the TOUGH2 code to aid in the selection of computational models for performance assessment. The exercise investigates the capabilities of TOUGH2 to model transient flows through highly fractured tuff and provides a possible means of calibration. Two distinctly different conceptual models were used in the TOUGH2 code, the dual permeability model and the equivalent continuum model. The infiltration test modeled involved the infiltration of dyed ponded water for 36 minutes. The 205 gallon infiltration of water observed in the experiment was subsequently modeled using measured Fran Ridge fracture frequencies, and a specified fracture aperture of 285 microm. The dual permeability formulation predicted considerable infiltration along the fracture network, which was in agreement with the experimental observations. As expected, al fracture penetration of the infiltrating water was calculated using the equivalent continuum model, thus demonstrating that this model is not appropriate for modeling the highly transient experiment. It is therefore recommended that the dual permeability model be given priority when computing high-flux infiltration for use in performance assessment studies
Energy Technology Data Exchange (ETDEWEB)
Mimouni, N.; Chikh, S.; Rahli, O. [Laboratoire LTPMP, Fac GMGP, USTHB, BP 32, Alia, Bab Ezzouar, Algiers (Algeria); Bennacer, R., E-mail: Rachid.Bennacer@ens-cachan.fr [LMT-ENS Cachan, 61 av. du président Wilson F-94235 Cachan Cedex (France)
2014-07-15
Two-dimensional (2D) and three-dimensional (3D) numerical simulations of double diffusion natural convection in an elongated enclosure filled with a binary fluid saturating a porous medium are carried out in the present work. The Boussinesq approximation is made in the formulation of the problem, and Neumann boundary conditions for temperature and concentration are adopted, respectively, on vertical and horizontal walls of the cavity. The used numerical method is based on the control volume approach, with the third order quadratic upstream interpolation scheme in approximating the advection terms. A semi implicit method algorithm is used to handle the velocity-pressure coupling. To avoid the excessively high computer time inherent to the solution of 3D natural convection problems, full approximation storage with full multigrid method is used to solve the problem. A wide range of the controlling parameters (Rayleigh-Darcy number Ra, lateral aspect ratio Ay, Lewis number Le, and the buoyancy ration N) is investigated. We clearly show that increasing the depth of the cavity (i.e., the lateral aspect ratio) has an important effect on the flow patterns. The 2D perfect parallel flows obtained for small lateral aspect ratio are drastically destabilized by increasing the cavity lateral dimension. This yields a 3D fluid motion with a much more complex flow pattern and the usually considered 2D parallel flow model cannot be applied.
Cati, Dilovan S; Stoeckli-Evans, Helen
2017-05-01
The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.
Retrograde flow in the dural sinuses detected by three-dimensional time-of-flight MR angiography
International Nuclear Information System (INIS)
Uchino, Akira; Nomiyama, Keita; Takase, Yukinori; Nakazono, Takahiko; Tominaga, Yukiko; Imaizumi, Takeshi; Kudo, Sho
2007-01-01
Retrograde flow in the left dural sinuses is sometimes detected by three-dimensional time-of-flight (3D-TOF) magnetic resonance (MR) angiography. The purpose of this study was to evaluate the incidence of this phenomenon and its characteristic features on 3D-TOF MR angiograms. We retrospectively reviewed cranial MR angiography images of 1,078 patients examined at our institution. All images were obtained by the 3D-TOF technique with one of two 1.5-T scanners. Maximum intensity projection (MIP) images in the horizontal rotation view were displayed stereoscopically. We reviewed the source images, inferosuperior MIP images, and horizontal MIP images and identified retrograde flow in the dural sinuses. We found retrograde flow in the dural sinuses of 67 patients on the source images from 3D-TOF MR angiography; the incidence was 6.2%. In 47 of the 67 patients, retrograde flow was identified in the left inferior petrosal sinus, in 13, it was seen in the left sigmoid sinus, and in 6, it was seen in the left inferior petrosal and left sigmoid sinuses. The remaining patient had retrograde flow in the left inferior petrosal and left and right sigmoid sinuses. The mean age of the patients with retrograde flow was slightly greater than that of the patients without this phenomenon (70 years vs 63 years). Retrograde flow in the dural sinuses frequently occurs on the left side in middle-aged and elderly patients during 3D-TOF MR angiography performed with the patient in the supine position. This phenomenon should not be misdiagnosed as a dural arteriovenous fistula. (orig.)
Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.
2010-01-01
A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…
Jusoh, R.; Nazar, R.; Pop, I.
2018-03-01
A reformulation of the three-dimensional flow of a nanofluid by employing Buongiorno's model is presented. A new boundary condition is implemented in this study with the assumption of nanoparticle mass flux at the surface is zero. This condition is practically more realistic since the nanoparticle fraction at the boundary is latently controlled. This study is devoted to investigate the impact of the velocity slip and suction to the flow and heat transfer characteristics of nanofluid. The governing partial differential equations corresponding to the momentum, energy, and concentration are reduced to the ordinary differential equations by utilizing the appropriate transformation. Numerical solutions of the ordinary differential equations are obtained by using the built-in bvp4c function in Matlab. Graphical illustrations displaying the physical influence of the several nanofluid parameters on the flow velocity, temperature, and nanoparticle volume fraction profiles, as well as the skin friction coefficient and the local Nusselt number are provided. The present study discovers the existence of dual solutions at a certain range of parameters. Surprisingly, both of the solutions merge at the stretching sheet indicating that the presence of the velocity slip affects the skin friction coefficients. Stability analysis is carried out to determine the stability and reliability of the solutions. It is found that the first solution is stable while the second solution is not stable.
Prasad, Dipak; Divito, Nicholas; Byers, Matthew; White, William; Benson, Michael; van Poppel, Bret; Elkins, Christopher; Containment Dispersion Team
2017-11-01
The dispersion of a scalar contaminant through an urban environment is complex to simulate and current modeling techniques lack detailed validation data necessary to assess accuracy. This work provides a detailed data set for Computational Fluid Dynamic simulations as well as an analysis of fluid flow and contaminant dispersion across two incident angles, 0 and 45 degrees from the freestream, across an array of cubical buildings, with one building in the center column three times as tall. The contaminant is injected from the base behind the tall building. Magnetic resonance imaging techniques are used to collect three-dimensional, time-averaged, three-component velocity and concentration field data. The flow is conducted in a water channel at a fully turbulent condition. The 0 degree case shows symmetrical velocity flow around each building with counter-rotating vortices immediately behind the tall building. Scalar contaminant dispersion in this array shows a rapid draw of higher concentration fluid up the back of the tall building, which is advected downstream. The 45 degree array shows similar patterns with vortices covering a larger area in the wake of the tall building. Analysis of the streamlines around the tall building indicate more `mechanical' dispersion due to the lateral spreading of the streamlines. These experiments should help improve prediction performance.
Directory of Open Access Journals (Sweden)
Yan Zhu
2016-05-01
Full Text Available Due to the high nonlinearity of the three-dimensional (3-D unsaturated-saturated water flow equation, using a fully 3-D numerical model is computationally expensive for large scale applications. A new unsaturated-saturated water flow model is developed in this paper based on the vertical/horizontal splitting (VHS concept to split the 3-D unsaturated-saturated Richards’ equation into a two-dimensional (2-D horizontal equation and a one-dimensional (1-D vertical equation. The horizontal plane of average head gradient in the triangular prism element is derived to split the 3-D equation into the 2-D equation. The lateral flow in the horizontal plane of average head gradient represented by the 2-D equation is then calculated by the water balance method. The 1-D vertical equation is discretized by the finite difference method. The two equations are solved simultaneously by coupling them into a unified nonlinear system with a single matrix. Three synthetic cases are used to evaluate the developed model code by comparing the modeling results with those of Hydrus1D, SWMS2D and FEFLOW. We further apply the model to regional-scale modeling to simulate groundwater table fluctuations for assessing the model applicability in complex conditions. The proposed modeling method is found to be accurate with respect to measurements.
Directory of Open Access Journals (Sweden)
Song-Gui Chen
2016-01-01
Full Text Available This paper presents a three-dimensional (3D parallel multiple-relaxation-time lattice Boltzmann model (MRT-LBM for Bingham plastics which overcomes numerical instabilities in the simulation of non-Newtonian fluids for the Bhatnagar–Gross–Krook (BGK model. The MRT-LBM and several related mathematical models are briefly described. Papanastasiou’s modified model is incorporated for better numerical stability. The impact of the relaxation parameters of the model is studied in detail. The MRT-LBM is then validated through a benchmark problem: a 3D steady Poiseuille flow. The results from the numerical simulations are consistent with those derived analytically which indicates that the MRT-LBM effectively simulates Bingham fluids but with better stability. A parallel MRT-LBM framework is introduced, and the parallel efficiency is tested through a simple case. The MRT-LBM is shown to be appropriate for parallel implementation and to have high efficiency. Finally, a Bingham fluid flowing past a square-based prism with a fixed sphere is simulated. It is found the drag coefficient is a function of both Reynolds number (Re and Bingham number (Bn. These results reveal the flow behavior of Bingham plastics.
A simple three-dimensional-focusing, continuous-flow mixer for the study of fast protein dynamics.
Burke, Kelly S; Parul, Dzmitry; Reddish, Michael J; Dyer, R Brian
2013-08-07
We present a simple, yet flexible microfluidic mixer with a demonstrated mixing time as short as 80 μs that is widely accessible because it is made of commercially available parts. To simplify the study of fast protein dynamics, we have developed an inexpensive continuous-flow microfluidic mixer, requiring no specialized equipment or techniques. The mixer uses three-dimensional, hydrodynamic focusing of a protein sample stream by a surrounding sheath solution to achieve rapid diffusional mixing between the sample and sheath. Mixing initiates the reaction of interest. Reactions can be spatially observed by fluorescence or absorbance spectroscopy. We characterized the pixel-to-time calibration and diffusional mixing experimentally. We achieved a mixing time as short as 80 μs. We studied the kinetics of horse apomyoglobin (apoMb) unfolding from the intermediate (I) state to its completely unfolded (U) state, induced by a pH jump from the initial pH of 4.5 in the sample stream to a final pH of 2.0 in the sheath solution. The reaction time was probed using the fluorescence of 1-anilinonaphthalene-8-sulfonate (1,8-ANS) bound to the folded protein. We observed unfolding of apoMb within 760 μs, without populating additional intermediate states under these conditions. We also studied the reaction kinetics of the conversion of pyruvate to lactate catalyzed by lactate dehydrogenase using the intrinsic tryptophan emission of the enzyme. We observe sub-millisecond kinetics that we attribute to Michaelis complex formation and loop domain closure. These results demonstrate the utility of the three-dimensional focusing mixer for biophysical studies of protein dynamics.
Three Dimensional Structure of the Mars North Polar Basal Unit from MARSIS data
Frigeri, A.; Orosei, R.; Cartacci, M.; Cicchetti, A.; Mitri, G.; Giuppi, S.; Noschese, R.; Picardi, G.; Plaut, J.
2012-04-01
Mars Advanced Radar for Subsurface and Ionospheric Sounding (MARSIS) is an orbital subsurface sounder aboard ESA's Mars Express spacecraft . It transmits a low-frequency radar pulse that is capable of penetrating below the surface, and is reflected by subsurface dielectric discontinuities. MARSIS has been used to probe both the south and the north polar caps of Mars, revealing their thickness and structure. We report on the results of a campaign of observations of the north polar ice cap of Mars that took place between May and December 2011 in uniquely favorable conditions and produced data of unprecedented quality. The focus of this work is the so-called Basal Unit, a dark, ice-rich, complexely layered geologic unit lying stratigraphically between the polar layered deposits and the Vastitas Borealis Formation, and extending beneath most of Planum Boreum and Olympia Planitia. The objective of this work is the to study the full three dimensional structure of the Northern Polar Deposit and in particular of the Basal Unit (BU). It was recently found that the BU consists of two markedly different units, called the Rupes Tenuis unit and the Planum Boreum cavi unit. The Rupes Tenuis unit appears to be older, horizontally layered, and lacking erosional contacts. It has been thus interpreted as the result of precipitation and cold-trapping of dust-laden volatiles. The Planum Boreum cavi unit displays cross-bedding, indicating dune accumulation. Bright layers within it are interpreted as being made of ice-cemented dust, while dark layers should consist of weathered basalt fines. It seems likely that, in places, the Planum Boreum cavi unit rests directly on the Vastitas Borealis, without the Rupes Tenuis unit in between. Because the two units in the BU have formed much earlier than the north polar layered deposits, and at some interval from each other, they bear evidence of past climatic conditions that were very different from present, so that they "could potentially be a
DEFF Research Database (Denmark)
Cereser, Alberto; Strobl, Markus; Hall, Stephen A.
2017-01-01
constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional neutron diffraction (ToF 3DND). Compared to existing analogous X-ray diffraction techniques, ToF 3DND......-of-flight neutron beamline. The technique was developed and tested with data collected at the Materials and Life Science Experimental Facility of the Japan Proton Accelerator Complex (J-PARC) for an iron sample. We successfully reconstructed the shape of 108 grains and developed an indexing procedure....... The reconstruction algorithms have been validated by reconstructing two stacked Co-Ni-Ga single crystals, and by comparison with a grain map obtained by post-mortem electron backscatter diffraction (EBSD)....
Designing spatial correlation of quantum dots: towards self-assembled three-dimensional structures
International Nuclear Information System (INIS)
Bortoleto, J R R; Zelcovit, J G; Gutierrez, H R; Bettini, J; Cotta, M A
2008-01-01
Buried two-dimensional arrays of InP dots were used as a template for the lateral ordering of self-assembled quantum dots. The template strain field can laterally organize compressive (InAs) as well as tensile (GaP) self-assembled nanostructures in a highly ordered square lattice. High-resolution transmission electron microscopy measurements show that the InAs dots are vertically correlated to the InP template, while the GaP dots are vertically anti-correlated, nucleating in the position between two buried InP dots. Finite InP dot size effects are observed to originate InAs clustering but do not affect GaP dot nucleation. The possibility of bilayer formation with different vertical correlations suggests a new path for obtaining three-dimensional pseudocrystals
DEFF Research Database (Denmark)
Terrence Brooks, Patrick; Rasmussen, Mikkel Aabech; Hyttel, Poul
2016-01-01
Objective: The present study aimed at establishing a method for production of a three-dimensional (3D) human neural tissue derived from induced pluripotent stem cells (iPSCs) and analyzing the outcome by a combination of tissue ultrastructure and expression of neural markers. Methods: A two......-step cell culture procedure was implemented by subjecting human iPSCs to a 3D scaffoldbased neural differentiation protocol. First, neural fate-inducing small molecules were used to create a neuroepithelial monolayer. Second, the monolayer was trypsinized into single cells and seeded into a porous...... polystyrene scaffold and further cultured to produce a 3D neural tissue. The neural tissue was characterized by a combination of immunohistochemistry and transmission electron microscopy (TEM). Results: iPSCs developed into a 3D neural tissue expressing markers for neural progenitor cells, early neural...
Energy Technology Data Exchange (ETDEWEB)
Geloni, Gianluca; Ilinski, Petr; Saldin, Evgeni; Schneidmiller, Evgeni; Yurkov, Mikhail
2009-05-15
We describe a novel technique to characterize ultrashort electron bunches in Xray Free-Electron Lasers. Namely, we propose to use coherent Optical Transition Radiation to measure three-dimensional (3D) electron density distributions. Our method relies on the combination of two known diagnostics setups, an Optical Replica Synthesizer (ORS) and an Optical Transition Radiation (OTR) imager. Electron bunches are modulated at optical wavelengths in the ORS setup.When these electron bunches pass through a metal foil target, coherent radiation pulses of tens MW power are generated. It is thereafter possible to exploit advantages of coherent imaging techniques, such as direct imaging, diffractive imaging, Fourier holography and their combinations. The proposed method opens up the possibility of real-time, wavelength-limited, single-shot 3D imaging of an ultrashort electron bunch. (orig.)
Wei, Wenbo; Zhang, Letian; Jin, Sheng; Ye, Gaofeng; Jing, Jianen; Dong, Hao; Xie, Chengliang; Yin, Yaotian
2017-04-01
The on-going continent-continent collision between the Indian and Eurasian plates since 55 Ma has created the spectacular topography of the Tibetan plateau. However, many first order questions remain to be answered as to the mechanisms behind this young orogenic process. Under the auspices of the SinoProbe Project, a three dimensional (3-D) Magnetotelluric (MT) array have been deployed on the Tibetan Plateau from 2010 to 2013 to better understand this orogeny. By the end of 2013, 1099 MT stations have been completed, including 102 combined broadband MT (BBMT) and long period MT (LMT) stations. In this study, MT data of these 102 combined stations have been used to investigate the deep lithospheric electrical structure of the Tibetan Plateau. MT impedances within the period range of 10 - 50000 s were extracted to be used for 3-D inversions with the ModEM code using the standard NLCG algorithm. The resulting lithospheric electrical structure of the Tibetan Plateau shows a distinct pattern of strong variation not only vertically, but also horizontally. Conductors are found to be widespread in the middle to lower crust. But their geometries are quite complex, and not obviously consistent with the hypothesis of continuous eastward channel flow. Instead, most crustal conductors in central and southern Tibet display a pattern of N-S extension. In the depth range of the upper mantle, two more conductive regions can be identified in the southern Qiangtang Terrane and in the central Lhasa Terrane. Resistor associated with the underthrust Inidan plate can be traced beneath the Bangong-Nujiang suture in western Tibet, but only beneath the central Lhasa terrane in central Tibet. * This work was jointly supported by the grants from Project SinoProbe-01 and National Natural Science Foundation of China (41404060).
Fuller, Patrick O; Higham, Timothy E; Clark, Andrew J
2011-04-01
Differences in habitat use are often correlated with differences in morphology and behavior, while animals in similar habitats often exhibit similarities in form and function. However, this has not been tested extensively among lizards, especially geckos. Most studies of gecko locomotion have focused on the ability to adhere to surfaces. However, there are several species of geckos that have either secondarily lost adhesive capabilities or simply lack the capability. We quantified the three-dimensional locomotor kinematics for two desert-dwelling padless geckos, Teratoscincus scincus and Eublepharis macularius, on a level trackway over a range of speeds. Our results indicate that T. scincus landed with a high relative hip height of 48.7 ± 2.4% of total limb length at footfall, while E. macularius exhibited hip heights averaging only 36.0 ± 1.8% of total limb length for footfall. The three-dimensional knee angle of T. scincus averaged 120.6 ± 3.9° at footfall, while E. macularius averaged only 101.6 ± 1.8° at footfall. In addition, the femur of E. macularius was elevated to a much greater extent (i.e., was closer to being perpendicular to the long axis of the body) than that of T. scincus and every other lizard that has been studied, suggesting they move with a "hyper-sprawled" posture. Both of these gecko species live in deserts, but T. scincus is psammophilic while E. macularius inhabits a rocky, more densely vegetated environment. Benefits of the more upright posture of T. scincus on open sandy habitat may include a greater field of view and more efficient locomotion. The more sprawled posture of E. macularius may lower its center of gravity and aid in balance while climbing on rocks or shrubs. Copyright © 2011 Elsevier GmbH. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
W. Steven Holbrook
2004-11-11
This report contains a summary of work conducted and results produced under the auspices of award DE-FC26-00NT40921, ''DOE Three-Dimensional Structure and Physical Properties of a Methane Hydrate Deposit and Gas Reservoir, Blake Ridge.'' This award supported acquisition, processing, and interpretation of two- and three-dimensional seismic reflection data over a large methane hydrate reservoir on the Blake Ridge, offshore South Carolina. The work supported by this project has led to important new conclusions regarding (1) the use of seismic reflection data to directly detect methane hydrate, (2) the migration and possible escape of free gas through the hydrate stability zone, and (3) the mechanical controls on the maximum thickness of the free gas zone and gas escape.
Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A
2010-01-01
A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.
International Nuclear Information System (INIS)
Czarnecki, J.B.; Faunt, C.C.; Gable, C.W.; Zyvoloski, G.A.
1996-01-01
Development of a preliminary three-dimensional model of the saturated zone at Yucca Mountain, the potential location for a high-level nuclear waste repository, is presented. The development of the model advances the technology of interfacing: (1)complex three-dimensional hydrogeologic framework modeling; (2) fully three-dimensional, unstructured, finite-element mesh generation; and (3) groundwater flow, heat, and transport simulation. The three-dimensional hydrogeologic framework model is developed using maps, cross sections, and well data. The framework model data are used to feed an automated mesh generator, designed to discretize irregular three-dimensional solids,a nd to assign materials properties from the hydrogeologic framework model to the tetrahedral elements. The mesh generator facilitated the addition of nodes to the finite-element mesh which correspond to the exact three-dimensional position of the potentiometric surface based on water-levels from wells. A ground water flow and heat simulator is run with the resulting finite- element mesh, within a parameter-estimation program. The application of the parameter-estimation program is designed to provide optimal values of permeability and specified fluxes over the model domain to minimize the residual between observed and simulated water levels
Dinarvand, S.; Hosseini, R.; Tamim, H.; Damangir, E.; Pop, I.
2015-07-01
An unsteady three-dimensional stagnation-point flow of a nanofluid past a circular cylinder with sinusoidal radius variation is investigated numerically. By introducing new similarity transformations for the velocity, temperature, and nanoparticle volume fraction, the basic equations governing the flow and heat and mass transfer are reduced to highly nonlinear ordinary differential equations. The resulting nonlinear system is solved numerically by the fourth-order Runge-Kutta method with the shooting technique. The thermophoresis and Brownian motion effects occur in the transport equations. The velocity, temperature, and nanoparticle concentration profiles are analyzed with respect to the involved parameters of interest, namely, unsteadiness parameter, Brownian motion parameter, thermophoresis parameter, Prandtl number, and Lewis number. Numerical values of the friction coefficient, diffusion mass flux, and heat flux are computed. It is found that the friction coefficient and heat transfer rate increase with increasing unsteadiness parameter (the highest heat transfer rate at the surface occurs if the thermophoresis and Brownian motion effects are absent) and decrease with increasing both thermophoresis and Brownian motion parameters. The present results are found to be in good agreement with previously published results.
International Nuclear Information System (INIS)
Smith, Brian L.
2007-01-01
The paper describes Computational Fluid Dynamics (CFD) calculations undertaken in support of analyses of three-dimensional flows that take place in the drywell volumes of advanced boiling water reactors with passive decay-heat removal systems. Data for comparison are taken from the 1/40th-scale European Simplified Boiling Water Reactor (ESBWR) mock-up facility PANDA under conditions of symmetric steam injection and asymmetric outflow. Steady-state simulations for pure steam conditions illustrate how the separate flow streams mix to ensure balanced outflow conditions to the condenser units. A transient calculation has also been performed to examine how air, assumed to be released from solution in the PANDA boiler, would ultimately accumulate in the separate condenser units. Results provide a possible explanation for the rundown in performance of one of the condensers, behaviour which was repeatedly observed in some of the earlier PANDA tests. The work also provides more general insights on how trace amounts of non-condensable gases may accumulate in passive cooling equipment
Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.
2011-01-01
Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…
Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.
2011-01-01
Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…
Hansen, Arthur G.
1958-01-01
Analysis is presented on the possible similarity solutions of the three-dimensional, laminar, incompressible, boundary-layer equations referred to orthogonal, curvilinear coordinate systems. Requirements of the existence of similarity solutions are obtained for the following: flow over developable surface and flow over non-developable surfaces with proportional mainstream velocity components.
Three-dimensional metamaterials
Burckel, David Bruce [Albuquerque, NM
2012-06-12
A fabrication method is capable of creating canonical metamaterial structures arrayed in a three-dimensional geometry. The method uses a membrane suspended over a cavity with predefined pattern as a directional evaporation mask. Metallic and/or dielectric material can be evaporated at high vacuum through the patterned membrane to deposit resonator structures on the interior walls of the cavity, thereby providing a unit cell of micron-scale dimension. The method can produce volumetric metamaterial structures comprising layers of such unit cells of resonator structures.
The band structures of three-dimensional nonlinear plasma photonic crystals
Zhang, Hai-Feng
2018-01-01
In this paper, the properties of the photonic band gaps (PBGs) for three-dimensional (3D) nonlinear plasma photonic crystals (PPCs) are theoretically investigated by the plane wave expansion method, whose equations for calculations also are deduced. The configuration of 3D nonlinear PPCs is the Kerr nonlinear dielectric spheres (Kerr effect is considered) inserted in the plasma background with simple-cubic lattices. The inserted dielectric spheres are Kerr nonlinear dielectrics whose relative permittivities are the functions of the external light intensity. Three different Kerr nonlinear dielectrics are considered, which can be expressed as the functions of space coordinates. The influences of the parameters for the Kerr nonlinear dielectrics on the PBGs also are discussed. The calculated results demonstrate that the locations, bandwidths and number of PBGs can be manipulated with the different Kerr nonlinear dielectrics. Compared with the conventional 3D dielectric PCs and PPCs with simple-cubic lattices, the more PBGs or larger PBG can be achieved in the 3D nonlinear PPCs. Those results provide a new way to design the novel devices based on the PPCs.
The band structures of three-dimensional nonlinear plasma photonic crystals
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Hai-Feng Zhang
2018-01-01
Full Text Available In this paper, the properties of the photonic band gaps (PBGs for three-dimensional (3D nonlinear plasma photonic crystals (PPCs are theoretically investigated by the plane wave expansion method, whose equations for calculations also are deduced. The configuration of 3D nonlinear PPCs is the Kerr nonlinear dielectric spheres (Kerr effect is considered inserted in the plasma background with simple-cubic lattices. The inserted dielectric spheres are Kerr nonlinear dielectrics whose relative permittivities are the functions of the external light intensity. Three different Kerr nonlinear dielectrics are considered, which can be expressed as the functions of space coordinates. The influences of the parameters for the Kerr nonlinear dielectrics on the PBGs also are discussed. The calculated results demonstrate that the locations, bandwidths and number of PBGs can be manipulated with the different Kerr nonlinear dielectrics. Compared with the conventional 3D dielectric PCs and PPCs with simple-cubic lattices, the more PBGs or larger PBG can be achieved in the 3D nonlinear PPCs. Those results provide a new way to design the novel devices based on the PPCs.
Cereser, Alberto; Strobl, Markus; Hall, Stephen A; Steuwer, Axel; Kiyanagi, Ryoji; Tremsin, Anton S; Knudsen, Erik B; Shinohara, Takenao; Willendrup, Peter K; da Silva Fanta, Alice Bastos; Iyengar, Srinivasan; Larsen, Peter M; Hanashima, Takayasu; Moyoshi, Taketo; Kadletz, Peter M; Krooß, Philipp; Niendorf, Thomas; Sales, Morten; Schmahl, Wolfgang W; Schmidt, Søren
2017-08-25
The physical properties of polycrystalline materials depend on their microstructure, which is the nano- to centimeter scale arrangement of phases and defects in their interior. Such microstructure depends on the shape, crystallographic phase and orientation, and interfacing of the grains constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional neutron diffraction (ToF 3DND). Compared to existing analogous X-ray diffraction techniques, ToF 3DND enables studies of samples that can be both larger in size and made of heavier elements. Moreover, ToF 3DND facilitates the use of complicated sample environments. The basic ToF 3DND setup, utilizing an imaging detector with high spatial and temporal resolution, can easily be implemented at a time-of-flight neutron beamline. The technique was developed and tested with data collected at the Materials and Life Science Experimental Facility of the Japan Proton Accelerator Complex (J-PARC) for an iron sample. We successfully reconstructed the shape of 108 grains and developed an indexing procedure. The reconstruction algorithms have been validated by reconstructing two stacked Co-Ni-Ga single crystals, and by comparison with a grain map obtained by post-mortem electron backscatter diffraction (EBSD).
Application of equivalent elastic methods in three-dimensional finite element structural analysis
International Nuclear Information System (INIS)
Jones, D.P.; Gordon, J.L.; Hutula, D.N.; Holliday, J.E.; Jandrasits, W.G.
1998-02-01
This paper describes use of equivalent solid (EQS) modeling to obtain efficient solutions to perforated material problems using three-dimensional finite element analysis (3D-FEA) programs. It is shown that the accuracy of EQS methods in 3D-FEA depends on providing sufficient equivalent elastic properties to allow the EQS material to respond according to the elastic symmetry of the pattern. Peak stresses and ligament stresses are calculated from the EQS stresses by an appropriate 3D-FEA submodel approach. The method is demonstrated on the problem of a transversely pressurized simply supported plate with a central divider lane separating two perforated regions with circular penetrations arranged in a square pattern. A 3D-FEA solution for a model that incorporates each penetration explicitly is used for comparison with results from an EQS solution for the plate. Results for deflection and stresses from the EQS solution are within 3% of results from the explicit 3D-FE model. A solution to the sample problem is also provided using the procedures in the ASME B and PV Code. The ASME B and PV Code formulas for plate deflection were shown to overestimate the stiffening effects of the divider lane and the outer stiffening ring
Three dimensional analysis of turbulent steam jets in enclosed structures: a CFD approach
International Nuclear Information System (INIS)
Ishii, M.; NguyenLe, Q.
1999-01-01
This paper compares the three-dimensional numerical simulation with the experimental data of a steam blowdown event in a light water reactor containment building. The temperature and pressure data of a steam blowdown event was measured at the Purdue University Multi-Dimensional Integrated Test Assembly (PUMA), a scaled model of the General Electric simplified Boiling Water Reactor. A three step approach was used to analyze the steam jet behavior. First, a 1-Dimensional, system level RELAP5/Mod3.2 model of the steam blowdown event was created and the results used to set the initial conditions for the PUMA blowdown experiments. Second, 2-Dimensional CFD models of the discharged steam jets were computed using PHOENICS, a commercially available CFD package. Finally, 3-Dimensional model of the PUMA drywell was created with the boundary conditions based on experimental measurements. The results of the 1-D and 2-D models were reported in the previous meeting. This paper discusses in detail the formulation and the results of the 3-Dimensional PHOENICS model of the PUMA drywell. It is found that the 3-D CFD solutions compared extremely well with the measured data
Kriebel, Andreas; Rumman, Muhammad; Scheld, Miriam; Hodde, Dorothee; Brook, Gary; Mey, Jörg
2014-02-01
Peripheral nerve injuries can be surgically repaired by suturing the transected nerve stumps or, in case of larger lesions, by the transplantation of an autologous nerve graft. To avoid donor site morbidity, the development of artificial implants is desired. Clinically, hollow conduits have been used for this purpose but are inferior to the autograft because they lack internal guidance cues for Schwann cells and regenerating axons. In this article, we describe the design of a three-dimensional (3D) scaffold consisting of parallel fibers embedded in a collagen matrix. For this purpose, an electrospinning device was developed to produce and manipulate a 3D array of aligned poly(ɛ-caprolactone) (PCL) microfibers. This fiber array was then incorporated into biodegradable PCL tubes to serve as artificial nerve bridges. Using primary cultures of embryonic chicken dorsal root ganglia, we show that PCL microfibers in the 3D matrix of our composite scaffold guide the direction of Schwann cell migration and axonal growth. Copyright © 2013 Wiley Periodicals, Inc.
A compact structured light based otoscope for three dimensional imaging of the tympanic membrane
Das, Anshuman J.; Estrada, Julio C.; Ge, Zhifei; Dolcetti, Sara; Chen, Deborah; Raskar, Ramesh
2015-02-01
Three dimensional (3D) imaging of the tympanic membrane (TM) has been carried out using a traditional otoscope equipped with a high-definition webcam, a portable projector and a telecentric optical system. The device allows us to project fringe patterns on the TM and the magnified image is processed using phase shifting algorithms to arrive at a 3D description of the TM. Obtaining a 3D image of the TM can aid in the diagnosis of ear infections such as otitis media with effusion, which is essentially fluid build-up in the middle ear. The high resolution of this device makes it possible examine a computer generated 3D profile for abnormalities in the shape of the eardrum. This adds an additional dimension to the image that can be obtained from a traditional otoscope by allowing visualization of the TM from different perspectives. In this paper, we present the design and construction of this device and details of the imaging processing for recovering the 3D profile of the subject under test. The design of the otoscope is similar to that of the traditional device making it ergonomically compatible and easy to adopt in clinical practice.
Three-dimensional structure of P3HT assemblies in organic solvents revealed by cryo-TEM.
Wirix, Maarten J M; Bomans, Paul H H; Friedrich, Heiner; Sommerdijk, Nico A J M; de With, Gijsbertus
2014-01-01
Poly(3-hexylthiophene) (P3HT) assemblies in vitrified organic solvents were visualized at nanometer scale resolution by cryo-transmission electron microscopy, low dose electron diffraction, and cryo-tomography revealing a three-dimensional lamellar structure formed by the stacking of the conjugated backbones of P3HT with a distance of 1.7 nm and increased order in the bulk of the nanowire. This combination of techniques reveals local structures in dispersion and the condensed state that play a crucial role in the performance of organic electronic devices.
Segal-Peretz, Tamar; Winterstein, Jonathan; Doxastakis, Manolis; Ramírez-Hernández, Abelardo; Biswas, Mahua; Ren, Jiaxing; Suh, Hyo Seon; Darling, Seth B; Liddle, J Alexander; Elam, Jeffrey W; de Pablo, Juan J; Zaluzec, Nestor J; Nealey, Paul F
2015-05-26
Understanding and controlling the three-dimensional structure of block copolymer (BCP) thin films is critical for utilizing these materials for sub-20 nm nanopatterning in semiconductor devices, as well as in membranes and solar cell applications. Combining an atomic layer deposition (ALD)-based technique for enhancing the contrast of BCPs in transmission electron microscopy (TEM) together with scanning TEM (STEM) tomography reveals and characterizes the three-dimensional structures of poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films with great clarity. Sequential infiltration synthesis (SIS), a block-selective technique for growing inorganic materials in BCPs films in an ALD tool and an emerging technique for enhancing the etch contrast of BCPs, was harnessed to significantly enhance the high-angle scattering from the polar domains of BCP films in the TEM. The power of combining SIS and STEM tomography for three-dimensional (3D) characterization of BCP films was demonstrated with the following cases: self-assembled cylindrical, lamellar, and spherical PS-b-PMMA thin films. In all cases, STEM tomography has revealed 3D structures that were hidden underneath the surface, including (1) the 3D structure of defects in cylindrical and lamellar phases, (2) the nonperpendicular 3D surface of grain boundaries in the cylindrical phase, and (3) the 3D arrangement of spheres in body-centered-cubic (BCC) and hexagonal-closed-pack (HCP) morphologies in the spherical phase. The 3D data of the spherical morphologies was compared to coarse-grained simulations and assisted in validating the simulations' parameters. STEM tomography of SIS-treated BCP films enables the characterization of the exact structure used for pattern transfer and can lead to a better understating of the physics that is utilized in BCP lithography.
Salama, Amgad
2013-09-01
In this work the problem of flow in three-dimensional, axisymmetric, heterogeneous porous medium domain is investigated numerically. For this system, it is natural to use cylindrical coordinate system, which is useful in describing phenomena that have some rotational symmetry about the longitudinal axis. This can happen in porous media, for example, in the vicinity of production/injection wells. The basic feature of this system is the fact that the flux component (volume flow rate per unit area) in the radial direction is changing because of the continuous change of the area. In this case, variables change rapidly closer to the axis of symmetry and this requires the mesh to be denser. In this work, we generalize a methodology that allows coarser mesh to be used and yet yields accurate results. This method is based on constructing local analytical solution in each cell in the radial direction and moves the derivatives in the other directions to the source term. A new expression for the harmonic mean of the hydraulic conductivity in the radial direction is developed. Apparently, this approach conforms to the analytical solution for uni-directional flows in radial direction in homogeneous porous media. For the case when the porous medium is heterogeneous or the boundary conditions is more complex, comparing with the mesh-independent solution, this approach requires only coarser mesh to arrive at this solution while the traditional methods require more denser mesh. Comparisons for different hydraulic conductivity scenarios and boundary conditions have also been introduced. © 2013 Elsevier B.V.
Directory of Open Access Journals (Sweden)
Yifeng Yun
2015-03-01
Full Text Available Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED data collection, namely automated diffraction tomography (ADT and rotation electron diffraction (RED, have been developed. Compared with X-ray diffraction (XRD and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional
On the calculation of dynamic and heat loads on a three-dimensional body in a hypersonic flow
Bocharov, A. N.; Bityurin, V. A.; Evstigneev, N. M.; Fortov, V. E.; Golovin, N. N.; Petrovskiy, V. P.; Ryabkov, O. I.; Teplyakov, I. O.; Shustov, A. A.; Solomonov, Yu S.
2018-01-01
We consider a three-dimensional body in a hypersonic flow at zero angle of attack. Our aim is to estimate heat and aerodynamic loads on specific body elements. We are considering a previously developed code to solve coupled heat- and mass-transfer problem. The change of the surface shape is taken into account by formation of the iterative process for the wall material ablation. The solution is conducted on the multi-graphics-processing-unit (multi-GPU) cluster. Five Mach number points are considered, namely for M = 20-28. For each point we estimate body shape after surface ablation, heat loads on the surface and aerodynamic loads on the whole body and its elements. The latter is done using Gauss-type quadrature on the surface of the body. The comparison of the results for different Mach numbers is performed. We also estimate the efficiency of the Navier-Stokes code on multi-GPU and central processing unit architecture for the coupled heat and mass transfer problem.
Befus, K. M.; Kroeger, K. D.; Smith, C. G.; Swarzenski, P. W.
2017-12-01
Fresh groundwater discharge to coastal environments contribute to the physical and chemical conditions of coastal waters. At regional scales, groundwater fluxes remain poorly constrained, representing uncertainty in both water and chemical budgets that have implications for downstream ecosystem health and for how human activities alter coastal hydrologic processes. Coastal groundwater discharges remain widely unconstrained due to the interconnectedness of highly heterogeneous hydrogeologic frameworks and hydrologic conditions. We use regional-scale, three-dimensional groundwater flow models with the best available hydrostratigraphic framework data to calculate the magnitude of groundwater discharging from coastal aquifers to coastal waterbodies along the eastern U.S. In addition, we constrain the inland areas that contribute to coastal groundwater discharges using particle tracking. We find that 27 km3/yr of groundwater enters coastal waters of the eastern U.S. and Gulf of Mexico and was over 175,000 km2. The contributing areas to coastal groundwater discharge extended kilometers inland and often were supplied by recharge occurring tens of kilometers inland. These results suggest that coastal groundwater discharges rely on larger contributing areas and potentially transport more dissolved constituents than previously calculated, which are important factors for constraining the role of groundwater in coastal chemical budgets and its impacts on coastal ecosystems.
A three-dimensional two-phase flow model for a liquid-fed direct methanol fuel cell
Ge, Jiabin; Liu, Hongtan
A three-dimensional, two-phase, multi-component model has been developed for a liquid-fed DMFC. The modeling domain consists of the membrane, two catalyst layers, two diffusion layers, and two channels. Both liquid and gas phases are considered in the entire anode, including the channel, the diffusion layer and the catalyst layer; while at the cathode, two phases are considered in the gas diffusion layer and the catalyst layer but only single gas phase is considered in the channels. For electrochemical kinetics, the Tafel equation incorporating the effects of two phases is used at both the cathode and anode sides. At the anode side the presence of gas phase reduces the active catalyst areas, while at the cathode side the presence of liquid water reduces the active catalyst areas. The mixed potential effects due to methanol crossover are also included in the model. The results from the two-phase flow mode fit the experimental results better than those from the single-phase model. The modeling results show that the single-phase models over-predict methanol crossover. The modeling results also show that the porosity of the anode diffusion layer plays an important role in the DMFC performance. With low diffusion layer porosity, the produced carbon dioxide cannot be removed effectively from the catalyst layer, thus reducing the active catalyst area as well as blocking methanol from reaching the reaction zone. A similar effect exits in the cathode for the liquid water.
Xu, Hang; Fan, Tao; You, Xiang Cheng
2012-09-01
The steady, three dimensional mixed convection flow of a Cu-water nanofluid past a stretching sheet is investigated. The homogenous model is adopted to simplify the physical problem. With a set of similarity transformations, the governing equations are reduced to a set of ordinary differential equations, which are then solved by means of the homotopy analysis method (HAM). The novel HAM technique for the choice of the convergent control auxiliary parameters ħ and optimal parameters of the initial guesses, as well as the new approach of the computational errors are introduced. with the help of these novel methods, the highly accurate analytical approximations are obtained for both the velocity and the temperature profiles. Besides, the effects of the nanoparticle volume fraction φ on the local skin friction and the local Nusselt number are presented and discussed. It is found that the nanofluid can improve on the heat transfer characteristics to a large extent. As far as we know, this problem has not been considered before and the results are new and original.
Khan, Waqar Azeem; Khan, Masood; Malik, Rabia
2014-01-01
This article addresses the steady three-dimensional flow of an Oldroyd-B nanofluid over a bidirectional stretching surface with heat generation/absorption effects. Suitable similarity transformations are employed to reduce the governing partial differential equations into coupled nonlinear ordinary differential equations. These nonlinear ordinary differential equations are then solved analytically by using the homotpy analysis method (HAM). Graphically results are presented and discussed for various parameters, namely, Deborah numbers β1 and β2, heat generation/absorption parameter λ, Prandtl parameter Pr, Brownian motion parameters Nb, thermophoresis parameter Nt and Lewis number Le. We have seen that the increasing values of the Brownian motion parameter Nt and thermophoresis parameter Nt leads to an increase in the temperature field and thermal boundary layer thickness while the opposite behavior is observed for concentration field and concentration boundary layer thickness. To see the validity of the present work, the numerical results are compared with the analytical solutions obtained by Homotopy analysis method and noted an excellent agreement for the limiting cases.
Directory of Open Access Journals (Sweden)
Ahmadreza Baghaie
Full Text Available Scanning Electron Microscope (SEM as one of the major research and industrial equipment for imaging of micro-scale samples and surfaces has gained extensive attention from its emerge. However, the acquired micrographs still remain two-dimensional (2D. In the current work a novel and highly accurate approach is proposed to recover the hidden third-dimension by use of multi-view image acquisition of the microscopic samples combined with pre/post-processing steps including sparse feature-based stereo rectification, nonlocal-based optical flow estimation for dense matching and finally depth estimation. Employing the proposed approach, three-dimensional (3D reconstructions of highly complex microscopic samples were achieved to facilitate the interpretation of topology and geometry of surface/shape attributes of the samples. As a byproduct of the proposed approach, high-definition 3D printed models of the samples can be generated as a tangible means of physical understanding. Extensive comparisons with the state-of-the-art reveal the strength and superiority of the proposed method in uncovering the details of the highly complex microscopic samples.
Lu, Yuzhen; Lu, Renfu
2017-05-01
Three-dimensional (3-D) shape information is valuable for fruit quality evaluation. This study was aimed at developing phase analysis techniques for reconstruction of the 3-D surface of fruit from the pattern images acquired by a structuredillumination reflectance imaging (SIRI) system. Phase-shifted sinusoidal patterns, distorted by the fruit geometry, were acquired and processed through phase demodulation, phase unwrapping and other post-processing procedures to obtain phase difference maps relative to the phase of a reference plane. The phase maps were then transformed into height profiles and 3-D shapes in a world coordinate system based on phase-to-height and in-plane calibrations. A reference plane-based approach, coupled with the curve fitting technique using polynomials of order 3 or higher, was utilized for phase-to-height calibrations, which achieved superior accuracies with the root-mean-squared errors (RMSEs) of 0.027- 0.033 mm for a height measurement range of 0-91 mm. The 3rd-order polynomial curve fitting technique was further tested on two reference blocks with known heights, resulting in relative errors of 3.75% and 4.16%. In-plane calibrations were performed by solving a linear system formed by a number of control points in a calibration object, which yielded a RMSE of 0.311 mm. Tests of the calibrated system for reconstructing the surface of apple samples showed that surface concavities (i.e., stem/calyx regions) could be easily discriminated from bruises from the phase difference maps, reconstructed height profiles and the 3-D shape of apples. This study has laid a foundation for using SIRI for 3-D shape measurement, and thus expanded the capability of the technique for quality evaluation of horticultural products. Further research is needed to utilize the phase analysis techniques for stem/calyx detection of apples, and optimize the phase demodulation and unwrapping algorithms for faster and more reliable detection.
Schor, Alisha R.; Buie, Cullen R.
2016-10-01
In this work, we demonstrate a microfluidic particle sorter consisting of three-dimensional, conducting microposts. Our sorter uses dielectrophoresis (DEP) to sort high- and low-lipid phenotypes of the yeast Yarrowia lipolytica. Y. lipolytica is one of the many microorganisms being explored as a hydrocarbon source for biodiesel, Omega-3 additives, and other products derived from fatty acids. A rapid, non-destructive, lipid-based sorting tool would accelerate the commercialization of these products. Our device consists of an array of 105, 25 μm wide gold microposts that span the height of a 15 μm channel. This array generates an electric field in a microfluidic device that is uniform through the channel height, but has a custom-shaped non-uniformity in the horizontal directions. This is crucial in order to achieve continuous sorting using DEP, as it ensures all cells are exposed to the same conditions throughout the channel height. By using very low currents (100 μA), we are able to electroplate these post arrays in fewer than 15 min. This is an order of magnitude improvement over previous reports of electroplated microstructures. With an applied signal of 250 MHz, 2.6 V pp in our device, we separate a heterogeneous population with a purity of 97.8% in the low-lipid stream and 71.4% in the high-lipid stream. The high-lipid stream purity can be improved by adjusting the spacing of the array. This unique protocol for the rapid fabrication of 3D microstructures has enabled the creation of a non-invasive sorting tool for genetically engineered, lipid-producing organisms. The ability to screen organisms based on lipid content will alleviate one of the major bottlenecks in commercialization of microbial biofuels.
Lardeau, Sylvain; Ferrari, Simone; Rossi, Lionel
2008-12-01
Three-dimensional (3D) direct numerical simulations of a flow driven by multiscale electromagnetic forcing are performed in order to reproduce with maximum accuracy the quasi-two-dimensional (2D) flow generated by the same multiscale forcing in the laboratory. The method presented is based on a 3D description of the flow and the electromagnetic forcing. Very good agreements between our simulations and the experiments are found both on velocity and acceleration field, this last comparison being, to our knowledge, done for the first time. Such agreement requires that both experiments and simulations are carefully performed and, more importantly, that the underlying simplification to model the experiments and the multiscale electromagnetic forcing do not introduce significant errors. The results presented in this paper differ significantly from previous 2D direct numerical simulation in which a classical linear Rayleigh friction modeling term was used to mimic the effect of the wall-normal friction. Indeed, purely 2D simulations are found to underestimate the Reynolds number and, due to the dominance of nonhomogeneous bottom friction, lead to the wrong physical mechanism. For the range of conditions presented in this paper, the Reynolds number, defined by the ratio between acceleration and viscous terms, remains the order of unity, and the Hartmann number, defined by the ratio between electromagnetic force terms and viscous terms, is about 2. The main conclusion is that 3D simulations are required to model the (3D) electromagnetic forces and the wall-normal shear. Indeed, even if the flow is quasi-2D in terms of energy, a full 3D approach is required to simulate these shallow layer flows driven by multiscale electromagnetic forcing. In the range of forcing intensity investigated in this paper, these multiscale flows remain quasi-2D, with negligible energy in the wall-normal velocity component. It is also shown that the driving terms are the electromagnetic forcing and
Lazarowitz, Reuven; Naim, Raphael
2014-01-01
The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular…
Three-dimensional fluid mechanics of particulate two-phase flows in U-bend and helical conduits
Tiwari, Prashant; Antal, Steven P.; Podowski, Michael Z.
2006-04-01
The results of numerous studies performed to date have shown that the performance of various hydraulic systems can be significantly improved by using curved conduit geometries instead of straight tubes. In particular, the formation of Dean vortices, which enhance the development of centrifugal instabilities, has been identified as a factor behind reducing the near-wall concentration buildup in particulate flow devices (e.g., in membrane filtration modules). Still, several issues regarding the effect of conduit curvature on local multidimensional phenomena governing fluid flow still remain open. A related issue is concerned with the impact that conduit geometry makes on the concentration distribution of a dispersed phase in two-phase flows in general, and in particulate flows (solid/liquid or solid/gas suspensions) in particular. It turns out that only very limited efforts have been made in the past to understand the fluid mechanics of such flows via advanced computer simulations. The purpose of this paper is to present the results of full three-dimensional (3D) theoretical and numerical analyses of single- and two-phase dilute particle/liquid flows in U-bend and helical curved conduits. The numerical analysis is based on computational fluid dynamics (CFD) simulations performed using a state-of-the-art multiphase flow computer code, NPHASE. The major issues discussed in the first part of the paper are concerned with the effect of curved/coiled geometry on the evolution of flow field and the associated wall shear. It has been demonstrated that the primary curvature (a common factor for both the U-bend and helix geometries) may cause a substantial asymmetry in the radial distribution of the main flow velocity. This, in turn, leads to a significant, albeit highly nonuniform, increase in the wall shear stress. Specifically, the wall shear around the outer half of tube circumference may become twice the corresponding value for a straight tube, and gradually decrease to
Jamieson, E. C.; Rennie, C. D.; Townsend, R. D.
2009-05-01
Stream barbs (a type of submerged groyne or spur dike) are low-profile linear rock structures that prevent the erosion of stream banks by redirecting high velocity flow away from the bank. Stream barbs are becoming a popular method for stream bank protection as they can be built at a relatively low cost and provide added ecological benefit. The design and construction of stream barbs in Sawmill Creek, a small urban stream in the city of Ottawa, Canada, will serve as a demonstration project for the use of barbs as a bank stabilization technique that will contribute to the rehabilitation of urban creeks while reducing erosion threats to property and infrastructure. As well as providing bank protection, these structures promote vegetated stream banks, create resting pools and scour holes for fish habitat, and increase bio-diversity for aquatic species. Despite these benefits, stream barbs are not a common means of stream bank protection in Canada, due largely to a lack of suitable design guidelines. The overall goal of stream habitat restoration in incising channel systems should be to accelerate natural processes of channel equilibrium recovery, riparian re-vegetation, and stream-floodplain interaction. Incorporating stream barbs, instead of traditional bank protection measures, attempts to achieve these goals. A three-dimensional numerical model: 'Simulation in Intakes with Multiblock option' (SSIIM), was used to model the effects of placing a series of stream barbs along an unstable section of Sawmill Creek. The average bankfull depth, width, and discharge of the creek are 1.2 m, 7.5 m, and 9 m3/s respectively. The model was used to assess various design alternatives for a series of seven stream barbs at two consecutive channel bends requiring stabilization measures along their outer banks. Design criteria were principally based on the reduction of velocity, shear stress and subsequent erosion at the outside bank of each bend, and on the relocation of a new thalweg
Kordilla, Jannes; Noffz, Torsten; Dentz, Marco; Geyer, Tobias; Tartakovsky, Alexandre M.
2017-11-01
In this work, we study gravity-driven flow of water in the presence of air on a synthetic surface intersected by a horizontal fracture and investigate the importance of droplet and rivulet flow modes on the partitioning behavior at the fracture intersection. We present laboratory experiments, three-dimensional smoothed particle hydrodynamics (SPH) simulations using a heavily parallelized code, and a theoretical analysis. The flow-rate-dependent mode switching from droplets to rivulets is observed in experiments and reproduced by the SPH model, and the transition ranges agree in SPH simulations and laboratory experiments. We show that flow modes heavily influence the "bypass" behavior of water flowing along a fracture junction. Flows favoring the formation of droplets exhibit a much stronger bypass capacity compared to rivulet flows, where nearly the whole fluid mass is initially stored within the horizontal fracture. The effect of fluid buffering within the horizontal fracture is presented in terms of dimensionless fracture inflow so that characteristic scaling regimes can be recovered. For both cases (rivulets and droplets), the flow within the horizontal fracture transitions into a Washburn regime until a critical threshold is reached and the bypass efficiency increases. For rivulet flows, the initial filling of the horizontal fracture is described by classical plug flow. Meanwhile, for droplet flows, a size-dependent partitioning behavior is observed, and the filling of the fracture takes longer. For the case of rivulet flow, we provide an analytical solution that demonstrates the existence of classical Washburn flow within the horizontal fracture.
Liu, Chen
2017-04-14
Here we report a method for visualization of volumetric structural information of live biological samples with no exogenous contrast agents. The process is made possible through a technique that involves generation, synthesis and analysis of three-dimensional (3D) Fourier components of light diffracted by the sample. This leads to the direct recovery of quantitative cellular morphology with no iterative procedures for reduced computational complexity. Combing with the fact that the technique is easily adaptive to any imaging platform and requires minimum sample preparation, our proposed method is particularly promising for observing fast, volumetric and dynamic events previously only accessible through staining methods.
Kim, Jinyong; Luo, Gang; Wang, Chao-Yang
2017-10-01
3D fine-mesh flow-fields recently developed by Toyota Mirai improved water management and mass transport in proton exchange membrane (PEM) fuel cell stacks, suggesting their potential value for robust and high-power PEM fuel cell stack performance. In such complex flow-fields, Forchheimer's inertial effect is dominant at high current density. In this work, a two-phase flow model of 3D complex flow-fields of PEMFCs is developed by accounting for Forchheimer's inertial effect, for the first time, to elucidate the underlying mechanism of liquid water behavior and mass transport inside 3D complex flow-fields and their adjacent gas diffusion layers (GDL). It is found that Forchheimer's inertial effect enhances liquid water removal from flow-fields and adds additional flow resistance around baffles, which improves interfacial liquid water and mass transport. As a result, substantial improvements in high current density cell performance and operational stability are expected in PEMFCs with 3D complex flow-fields, compared to PEMFCs with conventional flow-fields. Higher current density operation required to further reduce PEMFC stack cost per kW in the future will necessitate optimizing complex flow-field designs using the present model, in order to efficiently remove a large amount of product water and hence minimize the mass transport voltage loss.
Arakane, S.; Mizoshiri, M.; Sakurai, J.; Hata, S.
2017-05-01
We have demonstrated the fabrication of two types of thermal flow sensors with Cu-rich and Cu2O-rich microheaters using femtosecond laser-induced reduction of CuO nanoparticles. The microheaters in the shape of microbridge structures were formed to thermally isolate from the substrates by four layer-by-layer laminations of two-dimensional micropatterns. First, we evaluated the patterning properties such as dispensing coating conditions and degree of reduction for the selective fabrication of three-dimensional Cu-rich and Cu2O-rich microstructures. Then, a hot-film flow sensor with a Cu-rich microheater and a calorimetric flow sensor with a Cu2O-rich microheater were fabricated using their respective appropriate laser irradiation conditions. The hot-film sensor with the Cu-rich microbridge single heater enabled us to measure the flow rate in a wide range of 0-450 cc min-1. Although a large temperature dependence of the Cu2O-rich microbridge heaters caused a large error for the hot-film flow sensors with single heaters, they showed higher heat-resistance and generated heat with a lower drive power. The temperature coefficient of resistance of the Cu2O-rich microstructures had a semiconductor-like large absolute value and was less than -4.6 × 10-8 °C-1. The higher temperature sensitivity of the Cu2O-rich microstructures was useful for thermal detection. Based on these advantages, a calorimetric flow sensor composed of the Cu2O-rich microbridge single heater and two Cu2O-rich thermal detectors was proposed and fabricated. The calorimetric flow sensor was driven by a circuit for measuring the temperature difference. The Cu2O-rich flow sensor could detect bi-directional flow with a small output error.
Zhu, Y B; Liu, J S; Wang, L Q; Guan, X; Luo, Y J; Geng, J; Geng, Q G; Lin, Y J; Zhang, L X; Li, X X; Lu, Y P
2017-08-01
Objective: To investigate the feasibility and diagnostic value of preoperative transthoracic echocardiography guided three dimensional printing model (TTE Guided 3DPM) on the assessment of structural heart disease (SHD). Methods: From February 2016 to October 2016, 44 patients underwent cardiac surgery in Tianjin Chest Hospital, forty-four patients were assessed preoperatively using TTE Guided 3DPM, including 25 males and 19 females, aged 3-75 years, with an average of (44±22) years. compared to conventional three dimensional transthoracic echocardiography (3D-TTE), and took direct intraoperative findings as "Golden Standard" simultaneously. There are twelve patients with SHD, including four cases with mitral prolapse, two cases with partial endocardial cushion defect, two cases with secondary atrial septal defect, two cases with rheumatic mitral stenosis, one case with tetralogy of Fallot, one case with ventricular septal defect (VSD), thirty-two patients without SHD were designed as negative control. Results: The sensitivity and specificity of TTE Guided 3DPM were greater than or equal to 3D-TTE, P value of McNemar test of 3D-TTE was greater than 0.05, the difference was not statistically significant, kappa =0.745, P Guided 3DPM was greater than 0.05, the difference was not statistically significant, kappa =0.955, P Guided 3DPM and gold standards were consistent. Compared with 3D-TTE and TTE Guided 3DPM, P value was greater than 0.05, the difference was not statistically significant, kappa =0.879, P Guided 3DPM were consistent. TTE Guided 3DPM displayed the three-dimensional structure of SHD cardiac lesions clearly, which were consistent with intraoperative findings. Conclusion: TTE Guided 3DPM provides essential information for the preoperative evaluation and decision of SHD.
Dong, Di; Brandt, Peter; Chang, Ping; Schütte, Florian; Yang, Xiaofeng; Yan, Jinhui; Zeng, Jisheng
2017-12-01
The region encompassing the Kuroshio Extension (KE) in the Northwestern Pacific Ocean (25°N-45°N and 130°E-180°E) is one of the most eddy-energetic regions of the global ocean. The three-dimensional structures and transports of mesoscale eddies in this region are comprehensively investigated by combined use of satellite data and Argo profiles. With the allocation of Argo profiles inside detected eddies, the spatial variations of structures of eddy temperature and salinity anomalies are analyzed. The results show that eddies predominantly have subsurface (near-surface) intensified temperature and salinity anomalies south (north) of the KE jet, which is related to different background stratifications between these regions. A new method based on eddy trajectories and the inferred three-dimensional eddy structures is proposed to estimate heat and salt transports by eddy movements in a Lagrangian framework. Spatial distributions of eddy transports are presented over the vicinity of the KE for the first time. The magnitude of eddy-induced meridional heat (freshwater volume) transport is on the order of 0.01 PW (103 m3/s). The eddy heat transport divergence results in an oceanic heat loss south and heat gain north of the KE, thereby reinforcing and counteracting the oceanic heat loss from air-sea fluxes south and north of the KE jet, respectively. It also suggests a poleward heat transport across the KE jet due to eddy propagation.
International Nuclear Information System (INIS)
Ryu, Jeong-Soo; Seo, Choon-Gyo; Kim, Jae-Min; Yun, Chung-Bang
2010-01-01
This paper proposes a slightly new three-dimensional radial-shaped dynamic infinite elements fully coupled to finite elements for an analysis of soil-structure interaction system in a horizontally layered medium. We then deal with a seismic analysis technique for a three-dimensional soil-structure interactive system, based on the coupled finite-infinite method in frequency domain. The dynamic infinite elements are simulated for the unbounded domain with wave functions propagating multi-generated wave components. The accuracy of the dynamic infinite element and effectiveness of the seismic analysis technique may be demonstrated through a typical compliance analysis of square surface footing, an L-shaped mat concrete footing on layered soil medium and two kinds of practical seismic analysis tests. The practical analyses are (1) a site response analysis of the well-known Hualien site excited by all travelling wave components (primary, shear, Rayleigh waves) and (2) a generation of a floor response spectrum of a nuclear power plant. The obtained dynamic results show good agreement compared with the measured response data and numerical values of other soil-structure interaction analysis package.
Mir, Rafia; Jallu, Shais; Singh, T P
2015-06-01
The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.
Huang, M.; Bisht, G.; Zhou, T.; Chen, X.; Dai, H.; Hammond, G. E.; Riley, W. J.; Downs, J.; Liu, Y.; Zachara, J. M.
2016-12-01
A fully coupled three-dimensional surface and subsurface land model is developed and applied to a site along the Columbia River to simulate three-way interactions among river water, groundwater, and land surface processes. The model features the coupling of the Community Land Model version 4.5 (CLM4.5) and a massively-parallel multi-physics reactive tranport model (PFLOTRAN). The coupled model (CLM-PFLOTRAN) is applied to a 400m×400m study domain instrumented with groundwater monitoring wells in the Hanford 300 Area along the Columbia River. CLM-PFLOTRAN simulations are performed at three different spatial resolutions over the period 2011-2015 to evaluate the impact of spatial resolution on simulated variables. To demonstrate the difference in model simulations with and without lateral subsurface flow, a vertical-only CLM-PFLOTRAN simulation is also conducted for comparison. Results show that the coupled model is skillful in simulating stream-aquifer interactions, and the land-surface energy partitioning can be strongly modulated by groundwater-river water interactions in high water years due to increased soil moisture availability caused by elevated groundwater table. In addition, spatial resolution does not seem to impact the land surface energy flux simulations, although it is a key factor for accurately estimating the mass exchange rates at the boundaries and associated biogeochemical reactions in the aquifer. The coupled model developed in this study establishes a solid foundation for understanding co-evolution of hydrology and biogeochemistry along the river corridors under historical and future hydro-climate changes.
Decker, Jeremy D.; Swain, Eric D.; Stith, Bradley M.; Langtimm, Catherine A.
2013-01-01
Everglades restoration activities may cause changes to temperature and salinity stratification at the Port of the Islands (POI) marina, which could affect its suitability as a cold weather refuge for manatees. To better understand how the Picayune Strand Restoration Project (PSRP) may alter this important resource in Collier County in southwestern Florida, the USGS has developed a three-dimensional hydrodynamic model for the marina and canal system at POI. Empirical data suggest that manatees aggregate at the site during winter because of thermal inversions that provide warmer water near the bottom that appears to only occur in the presence of salinity stratification. To study these phenomena, the environmental fluid dynamics code simulator was used to represent temperature and salinity transport within POI. Boundary inputs were generated using a larger two-dimensional model constructed with the flow and transport in a linked overland-aquifer density-dependent system simulator. Model results for a representative winter period match observed trends in salinity and temperature fluctuations and produce temperature inversions similar to observed values. Modified boundary conditions, representing proposed PSRP alterations, were also tested to examine the possible effect on the salinity stratification and temperature inversion within POI. Results show that during some periods, salinity stratification is reduced resulting in a subsequent reduction in temperature inversion compared with the existing conditions simulation. This may have an effect on POI’s suitability as a passive thermal refuge for manatees and other temperature-sensitive species. Additional testing was completed to determine the important physical relationships affecting POI’s suitability as a refuge.
Directory of Open Access Journals (Sweden)
M. Nawaz
Full Text Available In this article, we developed a computer code of Galerikan Finite Element method (GFEM for three dimensional flow equations of nano-plasma fluid (blood in the presence of uniform applied magnetic field when Hall and ion slip current are significant. Lorentz force is calculated through generalized Ohmâs law with Maxwell equations. A series of numerical simulations are carried out to search Î·max and algebraic equations are solved by Gauss-Seidel method with simulation tolerance 10-8. Simulated results for special case have an excellent agreement with the already published results. Velocity components and temperature of the nano-plasma (blood are influenced significantly by the inclusion of nano-particles of Copper (Cu and Silver (Ag. Heat enhancement is observed when copper and silver nonmagnetic nanoparticles are used instead of simple base fluid (conventional fluid. Radiative nature of nano-plasma in the presence of magnetic field causes a decrease in the temperature due to the transfer of heat by the electromagnetic waves. In contrast to this, due to heat dissipated by Joule heating and viscous dissipation phenomena, temperature of nano-plasmaincreases as thermal radiation parameter is increased. Thermal boundary layer thickness can be controlled by using radiative fluid instead of non-radiative fluid. Momentum boundary layer thickness can be reduced by increasing the intensity of the applied magnetic field. Temperature of plasma in the presence magnetic field is higher than the plasma in the absence of magnetic field. Keywords: Nanofluid, Grid independent study, Convergence, Error analysis, Skin friction, Joule heating, Viscous dissipation, Hall and ion currents
International Nuclear Information System (INIS)
Meloni, S.
1998-01-01
To simulate transmitted radiation in agroforestry systems, radiative transfer models usually require a detailed three-dimensional description of the tree canopy. We propose here a simplification of the description of the three-dimensional structure of wild cherry trees (Prunus avium). The simplified tree description was tested against the detailed one for five-year-old wild cherry. It allowed accurate simulation of transmitted radiation and avoided tedious measurements of tree structure. The simplified description was then applied to older trees. Allometric relationships were used to compute the parameters not available on free-grown trees. The transmitted radiation in an agroforestry system was simulated at four different ages: 5, 10, 15 and 20 years. The trees were planted on a 5 m square grid. Two row orientations, chosen to provide different transmitted radiation patterns, were tested: north/south and north- east/south-west. The simulations showed that the daily mean transmitted radiation was reduced from 92% of incident radiation under five-year-old trees to 37% under 20-year-old trees. The variability of transmitted radiation increased with tree growth. The row orientation had only small effects on the shaded area at the beginning and end of the day when solar elevation was low. (author)
Energy Technology Data Exchange (ETDEWEB)
Finn, John M., E-mail: finn@lanl.gov [T-5, Applied Mathematics and Plasma Physics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2015-03-15
Properties of integration schemes for solenoidal fields in three dimensions are studied, with a focus on integrating magnetic field lines in a plasma using adaptive time stepping. It is shown that implicit midpoint (IM) and a scheme we call three-dimensional leapfrog (LF) can do a good job (in the sense of preserving KAM tori) of integrating fields that are reversible, or (for LF) have a “special divergence-free” (SDF) property. We review the notion of a self-adjoint scheme, showing that such schemes are at least second order accurate and can always be formed by composing an arbitrary scheme with its adjoint. We also review the concept of reversibility, showing that a reversible but not exactly volume-preserving scheme can lead to a fractal invariant measure in a chaotic region, although this property may not often be observable. We also show numerical results indicating that the IM and LF schemes can fail to preserve KAM tori when the reversibility property (and the SDF property for LF) of the field is broken. We discuss extensions to measure preserving flows, the integration of magnetic field lines in a plasma and the integration of rays for several plasma waves. The main new result of this paper relates to non-uniform time stepping for volume-preserving flows. We investigate two potential schemes, both based on the general method of Feng and Shang [Numer. Math. 71, 451 (1995)], in which the flow is integrated in split time steps, each Hamiltonian in two dimensions. The first scheme is an extension of the method of extended phase space, a well-proven method of symplectic integration with non-uniform time steps. This method is found not to work, and an explanation is given. The second method investigated is a method based on transformation to canonical variables for the two split-step Hamiltonian systems. This method, which is related to the method of non-canonical generating functions of Richardson and Finn [Plasma Phys. Controlled Fusion 54, 014004 (2012
Use of three-dimensional parameters in the analysis of crystal structures under compression
DEFF Research Database (Denmark)
Balic Zunic, Tonci
2007-01-01
. For a complete understanding of structural changes, the behaviour of all coordination polyhedra plus the voids that separate them must be investigated. The structural voids in a framework are identified by a Voronoi tessellation. It can be performed e.g. on the anionic framework alone to find the centres...... of the coordination polyhedra of cations and the voids that separate them. Analysis of individual compressional characteristics of structural components gives clues for the strong and weak parts of structures under high pressures and paths for structural transformations. The expected behaviour of distortion...
Weed, Richard Allen; Sankar, L. N.
1994-01-01
An increasing amount of research activity in computational fluid dynamics has been devoted to the development of efficient algorithms for parallel computing systems. The increasing performance to price ratio of engineering workstations has led to research to development procedures for implementing a parallel computing system composed of distributed workstations. This thesis proposal outlines an ongoing research program to develop efficient strategies for performing three-dimensional flow analysis on distributed computing systems. The PVM parallel programming interface was used to modify an existing three-dimensional flow solver, the TEAM code developed by Lockheed for the Air Force, to function as a parallel flow solver on clusters of workstations. Steady flow solutions were generated for three different wing and body geometries to validate the code and evaluate code performance. The proposed research will extend the parallel code development to determine the most efficient strategies for unsteady flow simulations.
Winzen, A; Roidl, B; Schröder, W
2016-04-01
Low-speed aerodynamics has gained increasing interest due to its relevance for the design process of small flying air vehicles. These small aircraft operate at similar aerodynamic conditions as, e.g. birds which therefore can serve as role models of how to overcome the well-known problems of low Reynolds number flight. The flight of the barn owl is characterized by a very low flight velocity in conjunction with a low noise emission and a high level of maneuverability at stable flight conditions. To investigate the complex three-dimensional flow field and the corresponding local structural deformation in combination with their influence on the resulting aerodynamic forces, time-resolved stereoscopic particle-image velocimetry and force and moment measurements are performed on a prepared natural barn owl wing. Several spanwise positions are measured via PIV in a range of angles of attack [Formula: see text] 6° and Reynolds numbers 40 000 [Formula: see text] 120 000 based on the chord length. Additionally, the resulting forces and moments are recorded for -10° ≤ α ≤ 15° at the same Reynolds numbers. Depending on the spanwise position, the angle of attack, and the Reynolds number, the flow field on the wing's pressure side is characterized by either a region of flow separation, causing large-scale vortical structures which lead to a time-dependent deflection of the flexible wing structure or wing regions showing no instantaneous deflection but a reduction of the time-averaged mean wing curvature. Based on the force measurements the three-dimensional fluid-structure interaction is assumed to considerably impact the aerodynamic forces acting on the wing leading to a strong mechanical loading of the interface between the wing and body. These time-depending loads which result from the flexibility of the wing should be taken into consideration for the design of future small flying air vehicles using flexible wing structures.
Kawasaki, Takeshi; Tanaka, Hajime
2010-06-16
The physical understanding of glass transition remains a major challenge of physics and materials science. Among various glass-forming liquids, a colloidal liquid interacting with hard-core repulsion is now regarded as one of the most ideal model systems. Here we study the structure and dynamics of three-dimensional polydisperse colloidal liquids by Brownian dynamics simulations. We reveal that medium-range crystalline bond orientational order of the hexagonal close packed structure grows in size and lifetime with increasing packing fraction. We show that dynamic heterogeneity may be a direct consequence of this transient structural ordering, which suggests its origin is thermodynamic rather than kinetic. We also reveal that nucleation of crystals preferentially occurs in regions of high medium-range order, reflecting the low crystal-liquid interfacial energy there. These findings may shed new light not only on the fundamental nature of the glass transition, but also the mechanism of crystal nucleation.
King, Justin T.; Kumar, Rajeev; Green, Melissa A.
2018-03-01
The effects of changing Strouhal number on the three-dimensional wake produced by a rigid, bioinspired trapezoidal pitching panel are analyzed through the use of stereoscopic particle image velocimetry over a Strouhal number range of 0.17-0.56. The results show that for all cases, at least some section of the wake comprises an alternating series of interacting vortex rings. The behavior of the flows induced by these vortex rings is consistent with the wake phenomena of spanwise compression and transverse expansion. Increases in Strouhal number correspond to an increased rate of spanwise compression, a greater amount of transverse expansion, and the movement of the location of wake breakdown onset upstream.
International Nuclear Information System (INIS)
Cole, C.R.; Wurstner, S.K.; Williams, M.D.; Thorne, P.D.; Bergeron, M.P.
1997-12-01
A three-dimensional numerical model of groundwater flow and transport, based on the Coupled Fluid Energy, and Solute Transport (CFEST) code, was developed for the Hanford Site to support the Hanford Groundwater Project (HGWP), managed by Pacific Northwest National Laboratory. The model was developed to increase the understanding and better forecast the migration of several contaminant plumes being monitored by the HGWP, and to support the Hanford Site Composite Analysis for low-level waste disposal in the 200-Area Plateau. Recent modeling efforts have focused on continued refinement of an initial version of the three-dimensional model developed in 1995 and its application to simulate future transport of selected contaminant plumes in the aquifer system. This version of the model was updated using a more current version of the CFEST code called CFEST96. Prior to conducting simulations of contaminant transport with the three-dimensional model, a previous steady-state, two-dimensional model of the unconfined aquifer system was recalibrated to 1979 water-table conditions with a statistical inverse method implemented in the CFEST-INV computer code. The results of the recalibration were used to refine the three-dimensional conceptual model and to calibrate it with a conceptualization that preserves the two-dimensional hydraulic properties and knowledge of the aquifer's three-dimensional properties for the same 1979 water-table conditions. The transient behavior of the three-dimensional flow model was also calibrated by adjusting model storage properties (specific yield) until transient water-table predictions approximated observed water-table elevations between 1979 and 1996
Energy Technology Data Exchange (ETDEWEB)
Cole, C.R.; Wurstner, S.K.; Williams, M.D.; Thorne, P.D.; Bergeron, M.P.
1997-12-01
A three-dimensional numerical model of groundwater flow and transport, based on the Coupled Fluid Energy, and Solute Transport (CFEST) code, was developed for the Hanford Site to support the Hanford Groundwater Project (HGWP), managed by Pacific Northwest National Laboratory. The model was developed to increase the understanding and better forecast the migration of several contaminant plumes being monitored by the HGWP, and to support the Hanford Site Composite Analysis for low-level waste disposal in the 200-Area Plateau. Recent modeling efforts have focused on continued refinement of an initial version of the three-dimensional model developed in 1995 and its application to simulate future transport of selected contaminant plumes in the aquifer system. This version of the model was updated using a more current version of the CFEST code called CFEST96. Prior to conducting simulations of contaminant transport with the three-dimensional model, a previous steady-state, two-dimensional model of the unconfined aquifer system was recalibrated to 1979 water-table conditions with a statistical inverse method implemented in the CFEST-INV computer code. The results of the recalibration were used to refine the three-dimensional conceptual model and to calibrate it with a conceptualization that preserves the two-dimensional hydraulic properties and knowledge of the aquifer`s three-dimensional properties for the same 1979 water-table conditions. The transient behavior of the three-dimensional flow model was also calibrated by adjusting model storage properties (specific yield) until transient water-table predictions approximated observed water-table elevations between 1979 and 1996.
3did: a catalog of domain-based interactions of known three-dimensional structure.
Mosca, Roberto; Céol, Arnaud; Stein, Amelie; Olivella, Roger; Aloy, Patrick
2014-01-01
The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into 'interaction topologies'. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.
Canine hippocampal formation composited into three-dimensional structure using MPRAGE.
Jung, Mi-Ae; Nahm, Sang-Soep; Lee, Min-Su; Lee, In-Hye; Lee, Ah-Ra; Jang, Dong-Pyo; Kim, Young-Bo; Cho, Zang-Hee; Eom, Ki-Dong
2010-07-01
This study was performed to anatomically illustrate the living canine hippocampal formation in three-dimensions (3D), and to evaluate its relationship to surrounding brain structures. Three normal beagle dogs were scanned on a MR scanner with inversion recovery segmented 3D gradient echo sequence (known as MP-RAGE: Magnetization Prepared Rapid Gradient Echo). The MRI data was manually segmented and reconstructed into a 3D model using the 3D slicer software tool. From the 3D model, the spatial relationships between hippocampal formation and surrounding structures were evaluated. With the increased spatial resolution and contrast of the MPRAGE, the canine hippocampal formation was easily depicted. The reconstructed 3D image allows easy understanding of the hippocampal contour and demonstrates the structural relationship of the hippocampal formation to surrounding structures in vivo.
International Nuclear Information System (INIS)
Zhu, H P; Yu, A B
2004-01-01
Granular flow in a cylindrical hopper with flat bottom is investigated based on the results generated by the discrete element method. The dependence of flow behaviour on the geometric and physical parameters of the hopper and particles, such as the orifice size and wall roughness of hoppers, and frictional and damping coefficients between particles, is analysed to establish the spatial and statistical distributions of microdynamic variables related to flow and force structures such as velocity, porosity, coordination number, and interaction forces between particles and between particles and walls. It is shown from the velocity field that there are four different zones in the hopper flow: a stagnant zone, a plug flow zone, a converging flow zone, and a transition zone from plug flow to converging flow. The Beverloo equation can describe the relationship between discharge rate and orifice size; however, the constants in the equation may vary with the wall friction coefficient, particle friction and damping coefficients. The flow and force structures of particles in the hopper are spatially non-uniform. In particular, porosity is high in the region near the orifice and low in the upper part and around the bottom corner of the hopper, whilst the coordination number has an opposite distribution. Large contact forces are experienced by particles around the bottom corner whereas small forces are experienced by particles in the upper part and the region near the orifice. However, there is a region above the orifice where particles experience the maximum total interaction forces between particles; the forces gradually propagate from this region into the bed and have a minimum value in the central upper part. The velocity distribution, flow and force structures are affected by the geometric and physical parameters of the hopper and particles
Ghelardi, Stefano; Rizzo, Cesare; Villa, Diego
2017-12-01
In this paper, we report our study on a numerical fluid-structure interaction problem originally presented by Mok et al. (2001) in two dimensions and later studied in three dimensions by Valdés Vazquez (2007), Lombardi (2012), and Trimarchi (2012). We focus on a 3D test case in which we evaluated the sensitivity of several input parameters on the fluid and structural results. In particular, this analysis provides a starting point from which we can look deeper into specific aspects of these simulations and analyze more realistic cases, e.g., in sails design. In this study, using the commercial software ADINA™, we addressed a well-known unsteadiness problem comprising a square box representing the fluid domain with a flexible bottom modeled with structural shell elements. We compared data from previously published work whose authors used the same numerical approach, i.e., a partitioned approach coupling a finite volume solver (for the fluid domain) and a finite element solver (for the solid domain). Specifically, we established several benchmarks and made comparisons with respect to fluid and solid meshes, structural element types, and structural damping, as well as solution algorithms. Moreover, we compared our method with a monolithic finite element solution method. Our comparisons of new and old results provide an outline of best practices for such simulations.
Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Directory of Open Access Journals (Sweden)
Vidya Mangala Prasad
2017-06-01
Full Text Available Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.
Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G
2017-06-01
Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.
Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy
International Nuclear Information System (INIS)
Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G
2002-01-01
The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.
Energy Technology Data Exchange (ETDEWEB)
Timofeev, V. I., E-mail: inna@ns.crys.ras.ru, E-mail: tostars@mail.ru, E-mail: ugama@yandex.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Abramchik, Yu. A. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Zhukhlistova, N. E. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Muravieva, T. I.; Esipov, R. S. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)
2016-01-15
Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sites were shown to be identical in both proteins.
Lukeš, Tomáš; Křížek, Pavel; Švindrych, Zdeněk; Benda, Jakub; Ovesný, Martin; Fliegel, Karel; Klíma, Miloš; Hagen, Guy M
2014-12-01
We introduce and demonstrate a new high performance image reconstruction method for super-resolution structured illumination microscopy based on maximum a posteriori probability estimation (MAP-SIM). Imaging performance is demonstrated on a variety of fluorescent samples of different thickness, labeling density and noise levels. The method provides good suppression of out of focus light, improves spatial resolution, and allows reconstruction of both 2D and 3D images of cells even in the case of weak signals. The method can be used to process both optical sectioning and super-resolution structured illumination microscopy data to create high quality super-resolution images.
Three-dimensional quantification of structures in trabecular bone using measures of complexity
DEFF Research Database (Denmark)
Marwan, Norbert; Kurths, Jürgen; Thomsen, Jesper Skovhus
2009-01-01
evaluate different aspects of organization and complexity of 3D structures, such as complexity of its surface or shape variability. We apply these measures to 3D data acquired by high-resolution microcomputed tomography (µCT) from human proximal tibiae and lumbar vertebrae at different stages...... of osteoporotic bone loss. The outcome is compared to the results of conventional static histomorphometry and exhibits clear relationships between the analyzed geometrical features of trabecular bone and loss of bone density, but also indicate that the measures reveal additional information about the structural...
International Nuclear Information System (INIS)
Chaturvedi, Ashutosh; Lee, Zhenghong
2005-01-01
Quantitative analysis of intrathoracic airway tree geometry is important for objective evaluation of bronchial tree structure and function. Currently, there is more human data than small animal data on airway morphometry. In this study, we implemented a semi-automatic approach to quantitatively describe airway tree geometry by using high-resolution computed tomography (CT) images to build a tree data structure for small animals such as rats and mice. Silicon lung casts of the excised lungs from a canine and a mouse were used for micro-CT imaging of the airway trees. The programming language IDL was used to implement a 3D region-growing threshold algorithm for segmenting out the airway lung volume from the CT data. Subsequently, a fully-parallel 3D thinning algorithm was implemented in order to complete the skeletonization of the segmented airways. A tree data structure was then created and saved by parsing through the skeletonized volume using the Python programming language. Pertinent information such as the length of all airway segments was stored in the data structure. This approach was shown to be accurate and efficient for up to six generations for the canine lung cast and ten generations for the mouse lung cast
Large-Pore Mesoporous Silica with Three-Dimensional Wormhole Framework Structures.
Park, In; Pinnavaia, Thomas J
2009-02-01
Large-pore mesoporous silica with 3D wormhole framework structures (denoted MSU-J) are prepared through a supramolecular hydrogen-bonding assembly pathway from low-cost sodium silicate as the silica source and commercially available mono- and triamine Jeffamine and Surfonamine surfactants as structure-directing porogens. The calcined mesostructures exhibit large pore sizes (up to 8.2 nm), surface areas (632-1030 m(2)/g) and pore volumes (0.5-2.0 cm(3)/g), depending on the surfactant chain length and synthesis temperature (25-65 °C). The textural properties of these new wormhole mesostructures are comparable to those of hexagonal SBA-15 derivatives and large pore MCM-48. However, unlike the SBA-15 structure type, wherein the 3D pore network is formed by connecting 1D cylindrical mesopores through micropores, MSU-J mesophases have wormhole framework structures containing fully interconnected 3D mesopores that can minimize the diffusion limitations often encountered in adsorption and chemical catalysis. Also, unlike large pore MCM-48, which requires cost-intensive tetraethylorthosilicate as a silica source and the use of a co-surfactant as a pore expander under strong acid conditions, MSU-J mesostructures are assembled from low cost sodium silicate in the presence of a single Jeffamine or Surfonamine porogen at near-neutral pH.
High power microwave source with a three dimensional printed metamaterial slow-wave structure
International Nuclear Information System (INIS)
French, David M.; Shiffler, Don
2016-01-01
For over the last decade, the concept of metamaterials has led to new approaches for considering the interaction of radiation with complex structures. However, practical manifestations of such a device operating at high power densities have proven difficult to achieve due to the resonant nature of metamaterials and the resultant high electric fields, which place severe constraints on manufacturing the slow wave structures. In this paper, we describe the first experimental manifestation of a high power microwave device utilizing a metallic slow wave structure (metamaterial-like) fabricated using additive manufacturing. The feasibility of utilizing additive manufacturing as a technique for building these relatively complicated structures has thus been demonstrated. The MW class microwave source operates in the C-band and shows frequency tunablility with electron beam voltage. The basic electromagnetic characteristics of this device, the construction using additive manufacturing, and the basic performance as a microwave oscillator are considered. Due to the tunable nature of the device, it shows promise not only as an oscillator but also as a microwave amplifier. Therefore, the dispersive characteristics and a discussion of the anticipated gain is included as it relates to an amplifier configuration.
Three-dimensional Morphology and X-ray Scattering Structure of ...
Indian Academy of Sciences (India)
Abstract. It is well established that water-alcohol mixtures exhibit anomalous properties at very low as well as at very high alcohol concentrations. Almost all the studies in this regard intend to link these anomalies to the microscopic structural changes as water (or alcohol) concentration increases in the mixture. However, it is.
Goffart, D.; Wal, D.J. van der; Klomp, E.M.; Hoogstraten, H.W.; Janssen, L.P.B.M.; Breysse, L.; Trolez, Y.
1996-01-01
A three-dimensional modeling of the transporting elements in a self-wiping corotating twin-screw extruder has been carried out by using the finite element package Sepran. This simulation uses the 3D geometry of the channel rolled over the twin-screw, which consists of the intermeshing and normal
Cai, M; Gong, Y; Kao, J L; Krishnamoorthi, R
1995-04-18
The solution structure of Cucurbita maxima trypsin inhibitor-V (CMTI-V), which is also a specific inhibitor of the blood coagulation protein, factor XIIa, was determined by 1H NMR spectroscopy in combination with a distance-geometry and simulated annealing algorithm. Sequence-specific resonance assignments were made for all the main-chain and most of the side-chain hydrogens. Stereospecific assignments were also made for some of the beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens. The ring conformations of all six prolines in the inhibitor were determined on the basis of 1H-1H vicinal coupling constant patterns; most of the proline ring hydrogens were stereospecifically assigned on the basis of vicinal coupling constant and intraresidue nuclear Overhauser effect (NOE) patterns. Distance constraints were determined on the basis of NOEs between pairs of hydrogens. Dihedral angle constraints were determined from estimates of scalar coupling constants and intraresidue NOEs. On the basis of 727 interproton distance and 111 torsion angle constraints, which included backbone phi angles and side-chain chi 1, chi 2, chi 3, and chi 4 angles, 22 structures were calculated by a distance geometry algorithm and refined by energy minimization and simulated annealing methods. Both main-chain and side-chain atoms are well-defined, except for a loop region, two terminal residues, and some side-chain atoms located on the molecular surface. The average root mean squared deviation in the position for equivalent atoms between the 22 individual structures and the mean structure obtained by averaging their coordinates is 0.58 +/- 0.06 A for the main-chain atoms and 1.01 +/- 0.07 A for all the non-hydrogen atoms of residues 3-40 and 49-67. These structures were compared to the X-ray crystallographic structure of another protein of the same inhibitor family-chymotrypsin inhibitor-2 from barley seeds [CI-2; McPhalen, C. A., & James, M. N. G. (1987) Biochemistry 26
Three-dimensional structure of the Upper Scorpius association with the Gaia first data release
Galli, Phillip A. B.; Joncour, Isabelle; Moraux, Estelle
2018-03-01
Using new proper motion data from recently published catalogs, we revisit the membership of previously identified members of the Upper Scorpius association. We confirmed 750 of them as cluster members based on the convergent point method, compute their kinematic parallaxes and combined them with Gaia parallaxes to investigate the 3D structure and geometry of the association using a robust covariance method. We find a mean distance of 146 ± 3 ± 6 pc and show that the morphology of the association defined by the brightest (and most massive) stars yields a prolate ellipsoid with dimensions of 74 × 38 × 32 pc3, while the faintest cluster members define a more elongated structure with dimensions of 98 × 24 × 18 pc3. We suggest that the different properties of both populations is an imprint of the star formation history in this region.
Three-dimensionality of space in the structure of the periodic table of chemical elements
International Nuclear Information System (INIS)
Veremeichik, T. F.
2006-01-01
The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed
Three-dimensional stacked structured ASIC devices and methods of fabrication thereof
Shinde, Subhash L.; Teifel, John; Flores, Richard S.; Jarecki Jr., Robert L.; Bauer, Todd
2015-11-19
A 3D stacked sASIC is provided that includes a plurality of 2D reconfigurable structured structured ASIC (sASIC) levels interconnected through hard-wired arrays of 3D vias. The 2D sASIC levels may contain logic, memory, analog functions, and device input/output pad circuitry. During fabrication, these 2D sASIC levels are stacked on top of each other and fused together with 3D metal vias. Such 3D vias may be fabricated as through-silicon vias (TSVs). They may connect to the back-side of the 2D sASIC level, or they may be connected to top metal pads on the front-side of the 2D sASIC level.
Three-dimensional Structure of a Viral Genome-delivery Portal Vertex
Energy Technology Data Exchange (ETDEWEB)
A Olia; P Prevelige Jr.; J Johnson; G Cingolani
2011-12-31
DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Here, we report two snapshots of the dodecameric portal protein of bacteriophage P22. The 3.25-{angstrom}-resolution structure of the portal-protein core bound to 12 copies of gene product 4 (gp4) reveals a {approx}1.1-MDa assembly formed by 24 proteins. Unexpectedly, a lower-resolution structure of the full-length portal protein unveils the unique topology of the C-terminal domain, which forms a {approx}200-{angstrom}-long {alpha}-helical barrel. This domain inserts deeply into the virion and is highly conserved in the Podoviridae family. We propose that the barrel domain facilitates genome spooling onto the interior surface of the capsid during genome packaging and, in analogy to a rifle barrel, increases the accuracy of genome ejection into the host cell.
[Three dimensional structure of the connective tissue papillae of the tongue in Suncus murinus].
Kobayashi, K; Miyata, K; Iwasaki, S; Takahashi, K
1989-08-01
The surface structure of the connective tissue papillae (CP) of Suncus murinus tongue was observed by SEM after fixing with Karnovsky's fixative and removal of the epithelial cell layer with 3N or 8N HCl. On the surface of the slender conical tongue, there are densely distributed filiform papillae among which fungiform papillae are seen sporadically. A pair of vallate papillae are situated in the posterior region of the tongue. Filiform papillae appear somewhat different externally depending on the dorsal surface of the anterior tongue. At the tip of the tongue, filiform papillae are of a slender conical shape and have a slight depression in the anterior basal portion. The CP of these is seen as a spherical protrusion on which a shallow groove runs in the anteroposterior direction. In the middle region, somewhat large filiform papillae contain CP having one or two small round head-like structures on each spherical protrusion. These head-like structures are increased in number in the posterior region. In the most posterior region of the anterior tongue, there are distributed large filiform papillae having several slender protrusions that surround a basal anterior depression. These large branched filiform papillae have a glove finger like CP. Small conical filiform papillae are distributed in the posterior marginal region of the anterior tongue which have CP of a horse-shoe like protrusion that opens in the anterior direction. Spherical fungiform papillae have CP which are thick columnar in shape with many lateral thin folds running vertically and having a round depression on the top of each. CP of the vallate papillae appear as a beehive like structure.(ABSTRACT TRUNCATED AT 250 WORDS)
Rosenthal, Eric I; Holt, Amanda L; Sweeney, Alison M
2017-05-01
The largest habitat by volume on Earth is the oceanic midwater, which is also one of the least understood in terms of animal ecology. The organisms here exhibit a spectacular array of optical adaptations for living in a visual void that have only barely begun to be described. We describe a complex pattern of broadband scattering from the skin of Argyropelecus sp., a hatchetfish found in the mesopelagic zone of the world's oceans. Hatchetfish skin superficially resembles the unpolished side of aluminium foil, but on closer inspection contains a complex composite array of subwavelength-scale dielectric structures. The superficial layer of this array contains dielectric stacks that are rectangular in cross-section, while the deeper layer contains dielectric bundles that are elliptical in cross-section; the cells in both layers have their longest dimension running parallel to the dorsal-ventral axis of the fish. Using the finite-difference time-domain approach and photographic radiometry, we explored the structural origins of this scattering behaviour and its environmental consequences. When the fish's flank is illuminated from an arbitrary incident angle, a portion of the scattered light exits in an arc parallel to the fish's anterior-posterior axis. Simultaneously, some incident light is also scattered downwards through the complex birefringent skin structure and exits from the ventral photophores. We show that this complex scattering pattern will provide camouflage simultaneously against the horizontal radially symmetric solar radiance in this habitat, and the predatory bioluminescent searchlights that are common here. The structure also directs light incident on the flank of the fish into the downwelling, silhouette-hiding counter-illumination of the ventral photophores. © 2017 The Authors.
Vemareddy, P.; Demóulin, P.
2018-04-01
We study the magnetic structure of a successively erupting sigmoid in active region 12371 by modeling the quasi-static coronal field evolution with nonlinear force-free field (NLFFF) equilibria. Helioseismic and Magnetic Imager/Solar Dynamic Observatory vector magnetograms are used as input to the NLFFF model. In all eruption events, the modeled structure resembles the observed pre-eruptive coronal sigmoid and the NLFFF core field is a combination of double inverse-J-shaped and inverse-S field lines with dips touching the photosphere. Such field lines are formed by the flux cancellation reconnection of opposite-J field lines at bald-patch locations, which in turn implies the formation of a weakly twisted flux-rope (FR) from large-scale sheared arcade field lines. Later on, this FR undergoes coronal tether-cutting reconnection until a coronal mass ejection is triggered. The modeled structure captured these major features of sigmoid-to-arcade-to-sigmoid transformation, which is reoccuring under continuous photospheric flux motions. Calculations of the field line twist reveal a fractional increase followed by a decrease of the number of pixels having a range of twist. This traces the buildup process of a twisted core field by slow photospheric motions and the relaxation after eruption, respectively. Our study infers that the large eruptivity of this AR is due to a steep decrease of the background coronal field meeting the torus instability criteria at a low height (≈40 Mm) in contrast to noneruptive ARs.
Energy Technology Data Exchange (ETDEWEB)
Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)
2012-06-01
The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.
Directory of Open Access Journals (Sweden)
Fatemeh Zafarani
2013-01-01
Full Text Available Structural intrauterine abnormalities are an important cause of infertility, recurrentpregnancy loss and bleeding or pain associated with a poor reproductive outcome. Variousdiagnostic methods have been applied to detect these lesions such as hysterosalpingography,hysteroscopy and sonohysterography. More recently, three-dimensionalextended imaging (3DXI provides the ability to obtain sequential sections of acquiredvolume scans in A, B and C planes. Here, we briefly discuss the technique of salineinfusion sonography, followed by a review of sonohysterographic characteristics ofintracavitary pathologies with more focus on some definitions and measurements.
Three-dimensional (3D) printing of mouse primary hepatocytes to generate 3D hepatic structure.
Kim, Yohan; Kang, Kyojin; Jeong, Jaemin; Paik, Seung Sam; Kim, Ji Sook; Park, Su A; Kim, Wan Doo; Park, Jisun; Choi, Dongho
2017-02-01
The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6-8 weeks old mice by a 2-step collagenase method. Samples of 4 × 10 7 hepatocytes with 80%-90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin , HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers.
Three-dimensional structure and cyanobacterial activity within a desert biological soil crust.
Raanan, Hagai; Felde, Vincent J M N L; Peth, Stephan; Drahorad, Sylvie; Ionescu, Danny; Eshkol, Gil; Treves, Haim; Felix-Henningsen, Peter; Berkowicz, Simon M; Keren, Nir; Horn, Rainer; Hagemann, Martin; Kaplan, Aaron
2016-02-01
Desert biological soil crusts (BSCs) are formed by adhesion of soil particles to polysaccharides excreted by filamentous cyanobacteria, the pioneers and main producers in this habitat. Biological soil crust destruction is a central factor leading to land degradation and desertification. We study the effect of BSC structure on cyanobacterial activity. Micro-scale structural analysis using X-ray microtomography revealed a vesiculated layer 1.5-2.5 mm beneath the surface in close proximity to the cyanobacterial location. Light profiles showed attenuation with depth of 1%-5% of surface light within 1 mm but also revealed the presence of 'light pockets', coinciding with the vesiculated layer, where the irradiance was 10-fold higher than adjacent crust parts at the same depth. Maximal photosynthetic activity, examined by O2 concentration profiles, was observed 1 mm beneath the surface and another peak in association with the 'light pockets'. Thus, photosynthetic activity may not be visible to currently used remote sensing techniques, suggesting that BSCs' contribution to terrestrial productivity is underestimated. Exposure to irradiance higher than 10% full sunlight diminished chlorophyll fluorescence, whereas O2 evolution and CO2 uptake rose, indicating that fluorescence did not reflect cyanobacterial photosynthetic activity. Our data also indicate that although resistant to high illumination, the BSC-inhabiting cyanobacteria function as 'low-light adapted' organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.
Polesky, Sandra P.; Dechaumphai, Pramote; Glass, Christopher E.; Pandey, Ajay K.
1990-01-01
A three-dimensional flux-based thermal analysis method has been developed and its capability is demonstrated by predicting the transient nonlinear temperature response of a swept cowl leading edge subjected to intense three-dimensional aerodynamic heating. The predicted temperature response from the transient thermal analysis is used in a linear elastic structural analysis to determine thermal stresses. Predicted thermal stresses are compared with those obtained from a two-dimensional analysis which represents conditions along the chord where maximum heating occurs. Results indicate a need for a three-dimensional analysis to predict accurately the leading edge thermal stress response.
Kiyan, Duygu; Hogg, Colin; Rath, Volker; Byrdina, Svetlana; Vandemeulebrouck, Jean; Revil, Andre; Silva, Catarina; Viveiros, Fatima; Ferreira, Teresa; Carmo, Rita
2017-04-01
The Furnas volcano is the eastern-most of the three active central volcanoes of Sao Miguel Island. The main caldera formed about 30 ka BP, followed by a younger eruption at 10-12 ka BP, which is responsible for the steep topography of more than 200 m in the target area. It contains several very young eruptive centers, and a shallow caldera lake. Tectonic features of varying directions have been identified in the caldera and its vicinity (Carmo et al., 2015). In the northern part of the caldera, containing the fumarole field of Caldeiras das Furnas, a detailed map of surface CO2 emissions was recently made available (Viveiros et al., 2010). Following a pilot survey of 13 AudioMagnetoTelluric soundings (AMT) and Electrical Resistivity Tomography (ERT) data collected along two profiles in the eastern part of Furnas caldera in 2015, a second campaign was completed in June 2016, yielding a total of 39 separate soundings including 15 broad-band magnetotelluric (MT) soundings to image the electrical conductivity of the subsurface. The data quality achieved by both techniques is very good, and initial results indicate a general correlation between regions of elevated conductivity at depth and the mapped surface CO2 emissions, suggesting that they may both be caused by the presence hydrothermal fluids. Dimensionality and directionality analysis using the WALDIM (Marti et al., 2009) approach in conjunction with Phase Tensor (Caldwell et al., 2004) indicate that the geo-electrical structure needs to be inverted in 3-D. Indicators of directionality derived from the analysis follow the general geological, fault dominated structural trend of NE-SW of Sao Miguel Island. A quantitative analysis of the potential influence of the Atlantic Ocean indicates that MT data up to 1 second period can be used in inversions with confidence without including the ocean. The 3-D inversions thus have been performed including only high-resolution topography and the Furnas lake bathymetry data
DHMPIV and Tomo-PIV measurements of three-dimensional structures in a turbulent boundary layer
Amili, O.; Atkinson, C.; Soria, J.
In turbulent boundary layers, a large portion of total turbulence production happens in the near wall region, y/δ memory intensive reconstruction algorithm. It is based on a multiplicative line-of-sight (MLOS) estimation that determines possible particle locations in the volume, followed by simultaneous iterative correction. Application of MLOS-SART and MART to a turbulent boundary layer at Refθ=2200 using a 4 camera Tomo-PIV system with a volume of 1000×1000×160 voxels is discussed. In addition, near wall velocity measurement attempt made by digital holographic microscopic particle image velocimetry (DHMPIV). The technique provides a solution to overcome the poor axial accuracy and the low spatial resolution which are common problems in digital holography [5]. By reducing the depth of focus by at least one order of magnitude as well as increasing the lateral spatial resolution, DHMPIV provides the opportunity to resolve the small-scale structures existing in near wall layers.
Saibil, Helen R; Seybert, Anja; Habermann, Anja; Winkler, Juliane; Eltsov, Mikhail; Perkovic, Mario; Castaño-Diez, Daniel; Scheffer, Margot P; Haselmann, Uta; Chlanda, Petr; Lindquist, Susan; Tyedmers, Jens; Frangakis, Achilleas S
2012-09-11
Yeast prions constitute a "protein-only" mechanism of inheritance that is widely deployed by wild yeast to create diverse phenotypes. One of the best-characterized prions, [PSI(+)], is governed by a conformational change in the prion domain of Sup35, a translation-termination factor. When this domain switches from its normal soluble form to an insoluble amyloid, the ensuing change in protein synthesis creates new traits. Two factors make these traits heritable: (i) the amyloid conformation is self-templating; and (ii) the protein-remodeling factor heat-shock protein (Hsp)104 (acting together with Hsp70 chaperones) partitions the template to daughter cells with high fidelity. Prions formed by several other yeast proteins create their own phenotypes but share the same mechanistic basis of inheritance. Except for the amyloid fibril itself, the cellular architecture underlying these protein-based elements of inheritance is unknown. To study the 3D arrangement of prion assemblies in their cellular context, we examined yeast [PSI(+)] prions in the native, hydrated state in situ, taking advantage of recently developed methods for cryosectioning of vitrified cells. Cryo-electron tomography of the vitrified sections revealed the prion assemblies as aligned bundles of regularly spaced fibrils in the cytoplasm with no bounding structures. Although the fibers were widely spaced, other cellular complexes, such as ribosomes, were excluded from the fibril arrays. Subtomogram image averaging, made possible by the organized nature of the assemblies, uncovered the presence of an additional array of densities between the fibers. We suggest these structures constitute a self-organizing mechanism that coordinates fiber deposition and the regulation of prion inheritance.
Suzuki, Motohiro; Kim, Kab-Jin; Kim, Sanghoon; Yoshikawa, Hiroki; Tono, Takayuki; Yamada, Kihiro T.; Taniguchi, Takuya; Mizuno, Hayato; Oda, Kent; Ishibashi, Mio; Hirata, Yuushou; Li, Tian; Tsukamoto, Arata; Chiba, Daichi; Ono, Teruo
2018-03-01
An X-ray tomographic technique was developed to investigate the internal magnetic domain structure in a micrometer-sized ferromagnetic sample. The technique is based on a scanning hard X-ray nanoprobe using X-ray magnetic circular dichroism (XMCD). From transmission XMCD images at the Gd L3 edge as a function of the sample rotation angle, the three-dimensional (3D) distribution of a single component of the magnetic vector in a GdFeCo microdisc was reconstructed with a spatial resolution of 360 nm, using a modified algebraic reconstruction algorithm. The method is applicable to practical magnetic materials and can be extended to 3D visualization of the magnetic domain formation process under external magnetic fields.
Energy Technology Data Exchange (ETDEWEB)
Popovic, Svetozar; Upadhyay, Janardan; Vuskovic, Leposava; Phillips, H. Lawrence; Valente-Feliciano, Anne-Marie
2017-12-26
A method for efficient plasma etching of surfaces inside three-dimensional structures can include positioning an inner electrode within the chamber cavity; evacuating the chamber cavity; adding a first inert gas to the chamber cavity; regulating the pressure in the chamber; generating a plasma sheath along the inner wall of the chamber cavity; adjusting a positive D.C. bias on the inner electrode to establish an effective plasma sheath voltage; adding a first electronegative gas to the chamber cavity; optionally readjusting the positive D.C. bias on the inner electrode reestablish the effective plasma sheath voltage at the chamber cavity; etching the inner wall of the chamber cavity; and polishing the inner wall to a desired surface roughness.
Three-dimensional band structure of LaSb and CeSb: Absence of band inversion
Oinuma, H.; Souma, S.; Takane, D.; Nakamura, T.; Nakayama, K.; Mitsuhashi, T.; Horiba, K.; Kumigashira, H.; Yoshida, M.; Ochiai, A.; Takahashi, T.; Sato, T.
2017-07-01
We have performed angle-resolved photoemission spectroscopy (ARPES) of LaSb and CeSb, a candidate of topological insulators. Using soft-x-ray photons, we have accurately determined the three-dimensional bulk band structure and revealed that the band inversion at the Brillouin-zone corner, a prerequisite for realizing the topological-insulator phase, is absent in both LaSb and CeSb. Moreover, unlike the ARPES data obtained with soft-x-ray photons, those with VUV photons were found to suffer significant kz broadening. These results suggest that LaSb and CeSb are topologically trivial semimetals, and unusual Dirac-cone-like states observed with VUV photons are not of the topological origin.
Benavides-Piccione, Ruth; Fernaud-Espinosa, Isabel; Robles, Victor; Yuste, Rafael; DeFelipe, Javier
2013-01-01
Dendritic spines of pyramidal neurons are targets of most excitatory synapses in the cerebral cortex. Recent evidence suggests that the morphology of the dendritic spine could determine its synaptic strength and learning rules. However, unfortunately, there are scant data available regarding the detailed morphology of these structures for the human cerebral cortex. In the present study, we analyzed over 8900 individual dendritic spines that were completely 3D reconstructed along the length of apical and basal dendrites of layer III pyramidal neurons in the cingulate cortex of 2 male humans (aged 40 and 85 years old), using intracellular injections of Lucifer Yellow in fixed tissue. We assembled a large, quantitative database, which revealed a major reduction in spine densities in the aged case. Specifically, small and short spines of basal dendrites and long spines of apical dendrites were lost, regardless of the distance from the soma. Given the age difference between the cases, our results suggest selective alterations in spines with aging in humans and indicate that the spine volume and length are regulated by different biological mechanisms. PMID:22710613
Multiscale Pressure-Balanced Structures in Three-dimensional Magnetohydrodynamic Turbulence
Energy Technology Data Exchange (ETDEWEB)
Yang, Liping; Zhang, Lei; Feng, Xueshang [SIGMA Weather Group, State Key Laboratory for Space Weather, National Space Science Center, Chinese Academy of Sciences, 100190, Beijing (China); He, Jiansen; Tu, Chuanyi; Wang, Linghua [School of Earth and Space Sciences, Peking University, 100871 Beijing (China); Li, Shengtai [Theoretical Division, MS B284, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Marsch, Eckart [Institute for Experimental and Applied Physics, Christian Albrechts University at Kiel, D-24118 Kiel (Germany); Wang, Xin, E-mail: jshept@gmail.com [School of Space and Environment, Beihang University, 100191 Beijing (China)
2017-02-10
Observations of solar wind turbulence indicate the existence of multiscale pressure-balanced structures (PBSs) in the solar wind. In this work, we conduct a numerical simulation to investigate multiscale PBSs and in particular their formation in compressive magnetohydrodynamic turbulence. By the use of the higher-order Godunov code Athena, a driven compressible turbulence with an imposed uniform guide field is simulated. The simulation results show that both the magnetic pressure and the thermal pressure exhibit a turbulent spectrum with a Kolmogorov-like power law, and that in many regions of the simulation domain they are anticorrelated. The computed wavelet cross-coherence spectra of the magnetic pressure and the thermal pressure, as well as their space series, indicate the existence of multiscale PBSs, with the small PBSs being embedded in the large ones. These multiscale PBSs are likely to be related to the highly oblique-propagating slow-mode waves, as the traced multiscale PBS is found to be traveling in a certain direction at a speed consistent with that predicted theoretically for a slow-mode wave propagating in the same direction.
Three-dimensional Imaging Reveals New Compartments and Structural Adaptations in Odontoblasts.
Khatibi Shahidi, M; Krivanek, J; Kaukua, N; Ernfors, P; Hladik, L; Kostal, V; Masich, S; Hampl, A; Chubanov, V; Gudermann, T; Romanov, R A; Harkany, T; Adameyko, I; Fried, K
2015-07-01
In organized tissues, the precise geometry and the overall shape are critical for the specialized functions that the cells carry out. Odontoblasts are major matrix-producing cells of the tooth and have also been suggested to participate in sensory transmission. However, refined morphologic data on these important cells are limited, which hampers the analysis and understanding of their cellular functions. We took advantage of fluorescent color-coding genetic tracing to visualize and reconstruct in 3 dimensions single odontoblasts, pulp cells, and their assemblages. Our results show distinct structural features and compartments of odontoblasts at different stages of maturation, with regard to overall cellular shape, formation of the main process, orientation, and matrix deposition. We demonstrate previously unanticipated contacts between the processes of pulp cells and odontoblasts. All reported data are related to mouse incisor tooth. We also show that odontoblasts express TRPM5 and Piezo2 ion channels. Piezo2 is expressed ubiquitously, while TRPM5 is asymmetrically distributed with distinct localization to regions proximal to and within odontoblast processes. © International & American Associations for Dental Research 2015.
Energy Technology Data Exchange (ETDEWEB)
Hao, Yanna; Wu, Chao, E-mail: wuchao27@126.com; Zhao, Zongzhe; Zhao, Ying; Xu, Jie; Qiu, Yang; Jiang, Jie; Yu, Tong; Ma, Chunyu; Zhou, Buyun
2016-01-01
In this study, silica nanospheres with different particle sizes were used as hard template for synthesis of a starch with a novel three-dimensional ordered macroporous structure (3DOMTS). As a pharmaceutical adjuvant, 3DOMTS was used to improve the dissolution rate and oral relative bioavailability of water-insoluble drugs. Felodipine (FDP) was chosen as a model drug and was loaded into the 3DOMTS by solvent evaporation. FDP loading into 3DOMTS with different pore sizes was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), differential scanning calorimeter (DSC), powder X-ray diffractometer (PXRD) and Fourier-Transform Infrared (FTIR). The results obtained showed that FDP was present in the pores in an amorphic or microcrystalline state. The in vitro dissolution results showed that 3DOMTS could effectively improve the dissolution rate of FDP in comparison with commercial common tablets. Pharmacokinetic results indicated that the oral relative bioavailability of self-made FDP–3DOMTS tablets were 184%, showing that 3DOMTS produced a significantly increased oral absorption of FDP. In conclusion, 3DOMTS exhibits the dual potential of improving the dissolution rate of poorly water soluble drugs and the novel filler produced by direct compression technology confirming that 3DOMTS will be useful for many applications in the field of pharmaceutics. - Highlights: • We successfully prepared a starch with a novel three-dimensional ordered macroporous structure (3DOMTS). • 3DOMTS can suppress the crystallinity of the drug to maintain it at amorphous state. • In vivo and in vitro experiments proved that 3DOMTS can improve the solubility and bioavailability of felodipine.
McElrone, Andrew J; Choat, Brendan; Parkinson, Dilworth Y; MacDowell, Alastair A; Brodersen, Craig R
2013-04-05
High resolutio