Slat Cove Unsteadiness Effect of 3D Flow Structures
NASA Technical Reports Server (NTRS)
Choudhari, Meelan M.; Khorrami, Mehdi R.
2006-01-01
Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.
Laser direct writing 3D structures for microfluidic channels: flow meter and mixer
NASA Astrophysics Data System (ADS)
Lin, Chih-Lang; Liu, Yi-Jui; Lin, Zheng-Da; Wu, Bo-Long; Lee, Yi-Hsiung; Shin, Chow-Shing; Baldeck, Patrice L.
2015-03-01
The 3D laser direct-writing technology is aimed at the modeling of arbitrary three-dimensional (3D) complex microstructures by scanning a laser-focusing point along predetermined trajectories. Through the perspective technique, the details of designed 3D structures can be properly fabricated in a microchannel. This study introduces a direct reading flow meter and a 3D passive mixer fabricated by laser direct writing for microfluidic applications. The flow meter consists of two rod-shaped springs, a pillar, an anchor, and a wedge-shaped indicator, installed inside a microfluidic channel. The indicator is deflected by the flowing fluid while restrained by the spring to establish an equilibrium indication according to the flow rate. The measurement is readily carried out by optical microscopy observation. The 3D passive Archimedes-screw-shaped mixer is designed to disturb the laminar flow 3D direction for enhancing the mixing efficiency. The simulation results indicate that the screw provides 3D disturbance of streamlines in the microchannel. The mixing demonstration for fluids flowing in the micrchannel approximately agrees with the simulation result. Thanks to the advantage of the laser direct writing technology, this study performs the ingenious applications of 3D structures for microchannels.
NASA Astrophysics Data System (ADS)
Timmerman, B. H.; Watt, D. W.; Bryanston-Cross, P. J.
1999-02-01
Using holographic interferometry the three-dimensional structure of unsteady and large-scale motions within subsonic and transonic turbulent jet flows has been studied. The instantaneous 3D flow structure is obtained by tomographic reconstruction techniques from quantitative phase maps recorded using a rapid-switching, double reference beam, double pulse laser system. The reconstruction of the jets studied here reveal a three-dimensional nature of the flow. In particular an increasing complexity can be seen in the turbulence as the flow progresses from the jet nozzle. Furthermore, a coherent three-dimensional, possibly rotating, structure can be seen to exist within these jets. The type of flow features illustrated here are not just of fundamental importance for understanding the behavior of free jet flows, but are also common to a number of industrial applications, ranging from the combustion flow within an IC engine to the transonic flow through the stages of a gas turbine.
NASA Technical Reports Server (NTRS)
Fleming, J. L.; Simpson, R. L.
1997-01-01
Laser Doppler velocimetry (LDV) measurements and hydrogen bubble flow visualization techniques were used to examine the near-wall flow structure of 2D and 3D turbulent boundary layers (TBLs) over a range of low Reynolds numbers. The goals of this research were (1) an increased understanding of the flow physics in the near wall region of turbulent boundary layers,(2) to observe and quantify differences between 2D and 3D TBL flow structures, and (3) to document Reynolds number effects for 3D TBLs. The LDV data have provided results detailing the turbulence structure of the 2D and 3D TBLs. These results include mean Reynolds stress distributions, flow skewing results, and U and V spectra. Effects of Reynolds number for the 3D flow were also examined. Comparison to results with the same 3D flow geometry but at a significantly higher Reynolds number provided unique insight into the structure of 3D TBLs. While the 3D mean and fluctuating velocities were found to be highly dependent on Reynolds number, a previously defined shear stress parameter was discovered to be invariant with Reynolds number. The hydrogen bubble technique was used as a flow visualization tool to examine the near-wall flow structure of 2D and 3D TBLs. Both the quantitative and qualitative results displayed larger turbulent fluctuations with more highly concentrated vorticity regions for the 2D flow.
Segmentation of bone structures in 3D CT images based on continuous max-flow optimization
NASA Astrophysics Data System (ADS)
Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.
2015-03-01
In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.
The mantle wedge's transient 3-D flow regime and thermal structure
NASA Astrophysics Data System (ADS)
Davies, D. R.; Le Voci, G.; Goes, S.; Kramer, S. C.; Wilson, C. R.
2016-01-01
Arc volcanism, volatile cycling, mineralization, and continental crust formation are likely regulated by the mantle wedge's flow regime and thermal structure. Wedge flow is often assumed to follow a regular corner-flow pattern. However, studies that incorporate a hydrated rheology and thermal buoyancy predict internal small-scale-convection (SSC). Here, we systematically explore mantle-wedge dynamics in 3-D simulations. We find that longitudinal "Richter-rolls" of SSC (with trench-perpendicular axes) commonly occur if wedge hydration reduces viscosities to Pa s, although transient transverse rolls (with trench-parallel axes) can dominate at viscosities of Pa s. Rolls below the arc and back arc differ. Subarc rolls have similar trench-parallel and trench-perpendicular dimensions of 100-150 km and evolve on a 1-5 Myr time-scale. Subback-arc instabilities, on the other hand, coalesce into elongated sheets, usually with a preferential trench-perpendicular alignment, display a wavelength of 150-400 km and vary on a 5-10 Myr time scale. The modulating influence of subback-arc ridges on the subarc system increases with stronger wedge hydration, higher subduction velocity, and thicker upper plates. We find that trench-parallel averages of wedge velocities and temperature are consistent with those predicted in 2-D models. However, lithospheric thinning through SSC is somewhat enhanced in 3-D, thus expanding hydrous melting regions and shifting dehydration boundaries. Subarc Richter-rolls generate time-dependent trench-parallel temperature variations of up to K, which exceed the transient 50-100 K variations predicted in 2-D and may contribute to arc-volcano spacing and the variable seismic velocity structures imaged beneath some arcs.
3D Structure and Internal Circulation of Pancake Vortices in Rotating Stratified Flows
NASA Astrophysics Data System (ADS)
Hassanzadeh, Pedram; Marcus, Philip; Aubert, Oriane; Le Bars, Michael; Le Gal, Patrice
2011-11-01
Jovian vortices, Atlantic meddies, and vortices of the protoplanetrary disks are examples of weakly-forced or unforced long-lived vortices in rotating stratified flows. Knowing the 3D structure and internal circulation of these vortices is essential in understanding their physics, which is not well-understood. For example, the aspect ratio of these vortices has been long thought to be f / N where f is the Coriolis parameter and N is the Brunt-Vaisala frequency. However, our recent theoretical and experimental study has shown that the aspect ratio in fact depends not only on f and N but also on the Rossby number and density mixing inside the vortex. The new scaling law also agrees with the available measurements of the meddies and Jupiter's Great Red Spot. High resolution 3D numerical simulations of the Navier-Stokes equation are carried out to confirm this new scaling law for a slowly (viscously) decaying anticyclonic vortex in which the Rossby number and stratification inside the vortex evolve in time. For a wide range of parameters and different distributions of density anomaly, the secondary circulations within the vortices are studied. The effect of a non-uniform background stratification is investigated, and the small cyclonic vortices that form above and below the anticyclone are studied.
NASA Astrophysics Data System (ADS)
Wada, Ikuko; He, Jiangheng; Hasegawa, Akira; Nakajima, Junichi
2015-09-01
We develop a 3-D thermal model for the Northeast Japan subduction margin, using a realistic slab geometry for the subducting Pacific plate, and investigate the effects of oblique subduction and 3-D slab geometry on the mantle wedge flow pattern and the thermal structure. In the Tohoku region, the mantle wedge flow pattern is nearly two-dimensional resulting in a thermal structure similar to those obtained by a 2-D model, owing to the simple slab geometry and subduction nearly perpendicular to the margin. However, in Hokkaido, oblique subduction leads to 3-D mantle wedge flow with northerly inflow and west-northwestward outflow and also results in lower temperatures in the shallow part of the mantle wedge than in Tohoku due to lower sinking rate of the slab. Between Hokkaido and Tohoku, the slab has a hinge-like shape due to a relatively sharp change in the dip direction. In this hinge zone, northerly mantle inflow from Hokkaido and westerly mantle inflow from Tohoku converge, discouraging inflow from northwest and resulting in a cooler mantle wedge. The model-predicted mantle wedge flow patterns are consistent with observed seismic anisotropy and may explain the orientations of volcanic cross-chains. The predicted 3-D thermal structure correlates well with the along-arc variations in the location of the frontal arc volcanoes and help to provide new insights into the surface heat flow pattern and the down-dip extent of interplate earthquakes.
Topology method for analyses of 3-D viscous flow structure in transonic turbomachinery
NASA Astrophysics Data System (ADS)
Guo, Yanhu; Wang, Baoguo; Shen, Mengyu
1997-12-01
A topology method is presented in this paper to reveal flow structure occurring inside turbomachinery, in which near wall flow structure is revealed by using wall limiting streamlines and space flow feature is revealed by using space streamlines and cross-section streamlines. As an example, a computational three-dimensional viscous flow field inside a transonic turbine cascade is studied. Through the analysis, the form and evolution of vortex system and the whole process of separation occurring within this cascade are revealed. The application of topology method for analyze flow structure inside turbomachinery is very important for understanding flow features and mechanism of flow loss even for improving the design of turbomachinery and increasing its efficiency.
Quaini, A.; Canic, S.; Glowinski, R.; Igo, S.; Hartley, C.J.; Zoghbi, W.; Little, S.
2011-01-01
This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194
Quaini, A; Canic, S; Glowinski, R; Igo, S; Hartley, C J; Zoghbi, W; Little, S
2012-01-10
This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194
Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis
NASA Astrophysics Data System (ADS)
Bulusu, Kartik V.; Plesniak, Michael W.
2015-11-01
In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.
3D Flow Visualization Using Texture Advection
NASA Technical Reports Server (NTRS)
Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)
2001-01-01
Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.
Investigation on 3D t wake flow structures of swimming bionic fish
NASA Astrophysics Data System (ADS)
Shen, G.-X.; Tan, G.-K.; Lai, G.-J.
2012-10-01
A bionic experimental platform was designed for the purpose of investigating time accurate three-dimensional flow field, using digital particle image velocimetry (DSPIV). The wake behind the flapping trail of a robotic fish model was studied at high spatial resolution. The study was performed in a water channel. A robot fish model was designed and built. The model was fixed onto a rigid support framework using a cable-supporting method, with twelve stretched wires. The entire tail of the model can perform prescribed motions in two degrees of freedom, mainly in carangiform mode, by driving its afterbody and lunate caudal fin respectively. The DSPIV system was set up to operate in a translational manner, measuring velocity field in a series of parallel slices. Phase locked measurements were repeated for a number of runs, allowing reconstruction of phase average flow field. Vortex structures with phase history of the wake were obtained. The study reveals some new and complex three-dimensional flow structures in the wake of the fish, including "reverse hairpin vortex" and "reverse Karman S-H vortex rings", allowing insight into physics of this complex flow.
NASA Astrophysics Data System (ADS)
Domitner, J.; Hölzl, C.; Kharicha, A.; Wu, M.; Ludwig, A.; Köhler, M.; Ratke, L.
2012-01-01
A central parameter to describe the formation of porosity and macrosegregation during casting processes is the permeability of the dendritic mushy zone. To determine this specific feature for a binary Al-18wt.%Cu alloy, flow simulations based on the Lattice Boltz-mann (LB) method were performed. The LB method allows an efficient solving of fluid flow problems dealing with complex shapes within an acceptable period of time. The 3D structure required as input for the simulations was captured with X-ray microtomography, which enables the generation of representative geometries for permeability investigations. Removing the eutectic phase from the measured dataset generated a remaining network of solid primary dendrites. In the simulations, a pressure gradient was applied to force the liquid through the free interdendritic channels. The permeability of the structure was then calculated from the resulting flow velocity pattern using Darcy's law. To examine the influence of different boundary conditions on the results obtained, several simulations were conducted.
Belenkov, E. A. Ali-Pasha, V. A.
2011-01-15
The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.
NASA Astrophysics Data System (ADS)
Gao, Jian; Katz, Joseph
2015-11-01
In studies of turbulent flows over rough walls, considerable efforts have been put on the overall effects of roughness parameters such as roughness height and spatial arrangement on the mean profiles and turbulence statistics. However there is very little experimental data on the generation, evolution, and interaction among roughness-initiated turbulent structures, which are essential for elucidating the near-wall turbulence production. As a first step, we approach this problem experimentally by applying digital holographic microscopy (DHM) to measure the flow and turbulence around a pair of cubic roughness elements embedded in the inner part of a high Reynolds number turbulent channel flow (Reτ = 2000 - 5000). The ratio of half-channel height (h) to cube height (a) is 25, and the cubes are aligned in the spanwise direction, and separated by 1.5 a. DHM provides high-resolution three-dimensional (3D) three-component (3C) velocity distributions. The presentation discusses methods to improve the data accuracy, both during the hologram acquisition and particle tracking phases. First, we compare and mutually validate velocity fields obtained from a two-view DHM system. Subsequently, during data processing, the seven criteria used for particle tracking is validated and augmented by planar tracking of particle image projections. Sample results reveal instantaneous 3D velocity fields and vortical structures resolved in fine details of several wall units. Funded by NSF and ONR.
Zeinali, Soheila; Çetin, Barbaros; Oliaei, Samad Nadimi Bavil; Karpat, Yiğit
2015-07-01
Microfluidics is the combination of micro/nano fabrication techniques with fluid flow at microscale to pursue powerful techniques in controlling and manipulating chemical and biological processes. Sorting and separation of bio-particles are highly considered in diagnostics and biological analyses. Dielectrophoresis (DEP) has offered unique advantages for microfluidic devices. In DEP devices, asymmetric pair of planar electrodes could be employed to generate non-uniform electric fields. In DEP applications, facing 3D sidewall electrodes is considered to be one of the key solutions to increase device throughput due to the generated homogeneous electric fields along the height of microchannels. Despite the advantages, fabrication of 3D vertical electrodes requires a considerable challenge. In this study, two alternative fabrication techniques have been proposed for the fabrication of a microfluidic device with 3D sidewall electrodes. In the first method, both the mold and the electrodes are fabricated using high precision machining. In the second method, the mold with tilted sidewalls is fabricated using high precision machining and the electrodes are deposited on the sidewall using sputtering together with a shadow mask fabricated by electric discharge machining. Both fabrication processes are assessed as highly repeatable and robust. Moreover, the two methods are found to be complementary with respect to the channel height. Only the manipulation of particles with negative-DEP is demonstrated in the experiments, and the throughput values up to 105 particles / min is reached in a continuous flow. The experimental results are compared with the simulation results and the limitations on the fabrication techniques are also discussed. PMID:25808433
NASA Astrophysics Data System (ADS)
Gubchenko, V. M.
2015-12-01
In part I of the work, the physical effects responsible for the formation of low-speed flows in plasma coronas, coupled with formation of coronas magnetosphere-like structures, are described qualitatively. Coronal domain structures form if we neglect scales of spatial plasma dispersion: high-speed flows are accumulated in magnetic tubes of the open domains, while magnetic structures and low-speed flows are concentrated within boundaries of domains. The inductive electromagnetic process occurring in flows of the hot collisionless plasma is shown to underlie the formation of magnetosphere-like structures. Depending on the form of the velocity distribution function of particles (PDF), a hot flow differently reveals its electromagnetic properties, which are expressed by the induction of resistive and diamagnetic scales of spatial dispersion. These determine the magnetic structure scales and structure reconstruction. The inductive electromagnetic process located in lines of the plasma nontransparency and absorption, in which the structures of excited fields are spatially aperiodic and skinned to the magnetic field sources. The toroidal and dipole magnetic sources of different configurations are considered for describing the corona structures during the solar maximum and solar minimum.
Multigrid calculations of 3-D turbulent viscous flows
NASA Technical Reports Server (NTRS)
Yokota, Jeffrey W.
1989-01-01
Convergence properties of a multigrid algorithm, developed to calculate compressible viscous flows, are analyzed by a vector sequence eigenvalue estimate. The full 3-D Reynolds-averaged Navier-Stokes equations are integrated by an implicit multigrid scheme while a k-epsilon turbulence model is solved, uncoupled from the flow equations. Estimates of the eigenvalue structure for both single and multigrid calculations are compared in an attempt to analyze the process as well as the results of the multigrid technique. The flow through an annular turbine is used to illustrate the scheme's ability to calculate complex 3-D flows.
NASA Technical Reports Server (NTRS)
Hassan, M. I.; Kuwana, K.; Saito, K.
2001-01-01
In the past, we measured three-D flow structure in the liquid and gas phases that were created by a spreading flame over liquid fuels. In that effort, we employed several different techniques including our original laser sheet particle tracking (LSPT) technique, which is capable of measuring transient 2-D flow structures. Recently we obtained a state-of-the-art integrated particle image velocimetry (IPIV), whose function is similar to LSPT, but it has an integrated data recording and processing system. To evaluate the accuracy of our IPIV system, we conducted a series of flame spread tests using the same experimental apparatus that we used in our previous flame spread studies and obtained a series of 2-D flow profiles corresponding to our previous LSPT measurements. We confirmed that both LSPT and IPIV techniques produced similar data, but IPIV data contains more detailed flow structures than LSPT data. Here we present some of newly obtained IPIV flow structure data, and discuss the role of gravity in the flame-induced flow structures. Note that the application of IPIV to our flame spread problems is not straightforward, and it required several preliminary tests for its accuracy including this IPIV comparison to LSPT.
USM3D Predictions of Supersonic Nozzle Flow
NASA Technical Reports Server (NTRS)
Carter, Melissa B.; Elmiligui, Alaa A.; Campbell, Richard L.; Nayani, Sudheer N.
2014-01-01
This study focused on the NASA Tetrahedral Unstructured Software System CFD code (USM3D) capability to predict supersonic plume flow. Previous studies, published in 2004 and 2009, investigated USM3D's results versus historical experimental data. This current study continued that comparison however focusing on the use of the volume souring to capture the shear layers and internal shock structure of the plume. This study was conducted using two benchmark axisymmetric supersonic jet experimental data sets. The study showed that with the use of volume sourcing, USM3D was able to capture and model a jet plume's shear layer and internal shock structure.
NASA Astrophysics Data System (ADS)
Le Voci, Giuseppe; Davies, Rhodri; Goes, Saskia; Kramer, Stephan; Wilson, Cian
2014-05-01
Arc volcanism at subduction zones is likely regulated by the mantle wedge's flow regime and thermal structure and, hence, numerous studies have attempted to quantify the principal controls on mantle wedge conditions. Here, we build on these previous studies by undertaking the first systematic 2-D and 3-D numerical investigation, across a wide parameter-space, into how hydration and thermal buoyancy influence the wedge's flow regime and associated thermal structure, above a kinematically driven subducting plate. We find that small-scale convection (SSC), resulting from Rayleigh-Taylor instabilities, or drips, off the base of the overriding lithosphere, is a typical occurrence, if: (i) viscosities are < 5×1018 Pa s; and (ii) hydrous weakening of wedge rheology extends at least 100-150 km from the trench. In 2-D models, instabilities generally take the form of 'drips'. Although along-strike averages of wedge velocities and temperature in 3-D structure are consistent with those in 2-D, fluctuations are larger in 3-D. Furthermore, in 3-D, two separate, but interacting, longitudinal Richter roll systems form (with their axes aligned perpendicular to the trench), the first below the arc region and the second below the back-arc region. These instabilities result in transient and spatial temperature fluctuations of 100-150K, which are sufficient to influence melting, the stability of hydrous minerals and the dehydration of crustal material. Furthermore, they are efficient at eroding the overriding lithosphere, particularly in 3-D and, thus, provide a means to explain observations of high heat flow and thin back-arc lithosphere at many subduction zones, if back-arc mantle is hydrated.
Jeong, J.Y.; Ryou, H.S.
1997-03-01
Heat transfer characteristics and flow structure in turbulent flows through a flat plate three-dimensional turbulent boundary layer containing built-in vortex generators have been analyzed by means of the space marching Crank-Nicolson finite difference method. The method solves the slender flow approximation of the steady three-dimensional Navier-Stokes and energy equations. This study used the eddy diffusivity model and standard {kappa}-{epsilon} model to predict heat transfer and flow field in the turbulent flow with imbedded longitudinal vortex. The results show boundary layer distortion due to vortices, such as strong spanwise flow divergence and boundary layer thinning. The heat transfer and skin friction show relatively good results in comparison with experimental data. The vortex core moves slightly away from the wall and grows slowly; consequently, the vortex influences the flow over a very long distance downstream. The enhancement of the heat transfer in the vicinity of the wall is due to the increasing spanwise separation of the vortices as they develop in the streamwise direction.
NASA Technical Reports Server (NTRS)
Banks, D. W.; Hafez, M. M.
1996-01-01
Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.
XML3D and Xflow: combining declarative 3D for the Web with generic data flows.
Klein, Felix; Sons, Kristian; Rubinstein, Dmitri; Slusallek, Philipp
2013-01-01
Researchers have combined XML3D, which provides declarative, interactive 3D scene descriptions based on HTML5, with Xflow, a language for declarative, high-performance data processing. The result lets Web developers combine a 3D scene graph with data flows for dynamic meshes, animations, image processing, and postprocessing. PMID:24808080
3-D Flow Visualization with a Light-field Camera
NASA Astrophysics Data System (ADS)
Thurow, B.
2012-12-01
Light-field cameras have received attention recently due to their ability to acquire photographs that can be computationally refocused after they have been acquired. In this work, we describe the development of a light-field camera system for 3D visualization of turbulent flows. The camera developed in our lab, also known as a plenoptic camera, uses an array of microlenses mounted next to an image sensor to resolve both the position and angle of light rays incident upon the camera. For flow visualization, the flow field is seeded with small particles that follow the fluid's motion and are imaged using the camera and a pulsed light source. The tomographic MART algorithm is then applied to the light-field data in order to reconstruct a 3D volume of the instantaneous particle field. 3D, 3C velocity vectors are then determined from a pair of 3D particle fields using conventional cross-correlation algorithms. As an illustration of the concept, 3D/3C velocity measurements of a turbulent boundary layer produced on the wall of a conventional wind tunnel are presented. Future experiments are planned to use the camera to study the influence of wall permeability on the 3-D structure of the turbulent boundary layer.Schematic illustrating the concept of a plenoptic camera where each pixel represents both the position and angle of light rays entering the camera. This information can be used to computationally refocus an image after it has been acquired. Instantaneous 3D velocity field of a turbulent boundary layer determined using light-field data captured by a plenoptic camera.
Structured light field 3D imaging.
Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Yin, Yongkai; Li, Ameng; Wu, Jiachen; Gao, Bruce Z
2016-09-01
In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces. PMID:27607639
The 3D Flow Field Around an Embedded Planet
NASA Astrophysics Data System (ADS)
Fung, Jeffrey; Artymowicz, Pawel; Wu, Yanqin
2015-10-01
3D modifications to the well-studied 2D flow topology around an embedded planet have the potential to resolve long-standing problems in planet formation theory. We present a detailed analysis of the 3D isothermal flow field around a 5 Earth-mass planet on a fixed circular orbit, simulated using our graphics processing unit hydrodynamics code PEnGUIn. We find that, overall, the horseshoe region has a columnar structure extending vertically much beyond the Hill sphere of the planet. This columnar structure is only broken for some of the widest horseshoe streamlines, along which high altitude fluid descends rapidly into the planet’s Bondi sphere, performs one horseshoe turn, and exits the Bondi sphere radially in the midplane. A portion of this flow exits the horseshoe region altogether, which we refer to as the “transient” horseshoe flow. The flow continues as it rolls up into a pair of up-down symmetric horizontal vortex lines shed into the wake of the planet. This flow, unique to 3D, affects both planet accretion and migration. It prevents the planet from sustaining a hydrostatic atmosphere due to its intrusion into the Bondi sphere, and leads to a significant corotation torque on the planet, unanticipated by 2D analysis. In the reported simulation, starting with a {{Σ }}˜ {r}-3/2 radial surface density profile, this torque is positive and partially cancels with the negative differential Lindblad torque, resulting in a factor of three slower planet migration rate. Finally, we report 3D effects can be suppressed by a sufficiently large disk viscosity, leading to results similar to 2D.
3D flow focusing for microfluidic flow cytometry with ultrasonics
NASA Astrophysics Data System (ADS)
Gnyawali, Vaskar; Strohm, Eric M.; Daghighi, Yasaman; van de Vondervoort, Mia; Kolios, Michael C.; Tsai, Scott S. H.
2015-11-01
We are developing a flow cytometer that detects unique acoustic signature waves generated from single cells due to interactions between the cells and ultrasound waves. The generated acoustic waves depend on the size and biomechanical properties of the cells and are sufficient for identifying cells in the medium. A microfluidic system capable of focusing cells through a 10 x 10 μm ultrasound beam cross section was developed to facilitate acoustic measurements of single cells. The cells are streamlined in a hydro-dynamically 3D focused flow in a 300 x 300 μm channel made using PDMS. 3D focusing is realized by lateral sheath flows and an inlet needle (inner diameter 100 μm). The accuracy of the 3D flow focusing is measured using a dye and detecting its localization using confocal microscopy. Each flowing cell would be probed by an ultrasound pulse, which has a center frequency of 375 MHz and bandwidth of 250 MHz. The same probe would also be used for recording the scattered waves from the cells, which would be processed to distinguish the physical and biomechanical characteristics of the cells, eventually identifying them. This technique has potential applications in detecting circulating tumor cells, blood cells and blood-related diseases.
Finite element solver for 3-D compressible viscous flows
NASA Technical Reports Server (NTRS)
Reddy, K. C.; Reddy, J. N.
1986-01-01
The space shuttle main engine (SSME) has extremely complex internal flow structure. The geometry of the flow domain is three-dimensional with complicated topology. The flow is compressible, viscous, and turbulent with large gradients in flow quantities and regions of recirculations. The analysis of the flow field in SSME involves several tedious steps. One is the geometrical modeling of the particular zone of the SSME being studied. Accessing the geometry definition, digitalizing it, and developing surface interpolations suitable for an interior grid generator require considerable amount of manual labor. There are several types of grid generators available with some general-purpose finite element programs. An efficient and robust computational scheme for solving 3D Navier-Stokes equations has to be implemented. Post processing software has to be adapted to visualize and analyze the computed 3D flow field. The progress made in a project to develop software for the analysis of the flow is discussed. The technical approach to the development of the finite element scheme and the relaxation procedure are discussed. The three dimensional finite element code for the compressible Navier-Stokes equations is listed.
NASA Astrophysics Data System (ADS)
Gubchenko, Vladimir
The task was to provide an analytical elementary magnetosphere-like model in kinetics for verification of the 3D EM PIC codes created for space/aerospace and HED plasmas applications. Kinetic approach versus cold MHD approach takes into account different behavior in the EM fields of resonant and non resonant particles in the velocity phase space, which appears via shape characteristics of the particle velocity distribution function (PVDF) and via the spatial dispersion effect forming the collisionless dissipation in the EM fields. The external flow is a hot collisionless plasma characterized by the particle velocity distribution function (PVDF) with different shapes: Maxwellian, kappa, etc. The flow is in a “hot regime”: it can be supersonic but its velocity remains less the thermal velocity of the electrons. The “internal” part of the magnetosphere formed by trapped particles is the prescribed 3D stationary magnetization considered as a spherical “quasiparticle” with internal magnetodipole and toroidal moments represented as a broadband EM driver. We obtain after the linearization of Vlasov/Maxwell equations a self-consistent 3D large scale kinetic solution of the classic problem. Namely, we: model the “outer” part of the magnetosphere formed by external hot plasma flow of the flyby particles. Solution of the Vlasov equation expressed via a tensor of dielectric permittivity of nonmagnetized and magnetized flowing plasma. Here, we obtain the direct kinetic dissipative effect of the magnetotail formation and the opposite diamagnetic effect of the magnetosphere “dipolization”. We get MHD wave cone in flow magnetized by external guiding magnetic (GM) field. Magnetosphere in our consideration is a 3D dissipative “wave” package structure of the skinned EM fields formed by the “waves” excited at frequency bands where we obtain negative values and singularities (resonances) of squared EM refractive index of the cold plasma. The hot regime
Magnetosheath Flow Anomalies in 3-D
NASA Technical Reports Server (NTRS)
Vaisberg, O. L.; Burch, J. L.; Smirnov, V. N.; Avanov, L. A.; Moore, T. E.; Waite, J. H., Jr.; Skalsky, A. A.; Borodkova, N. L.; Coffey, V. N.; Gallagher, D. L.; Rose, M. Franklin (Technical Monitor)
2000-01-01
Measurements of the plasma and magnetic field with high temporal resolution on the Interball Tail probe reveal many flow anomalies in the magnetosheath. They are usually seen as flow direction and number density variations, accompanied by magnetic field discontinuities. Large flow anomalies with number density variations of factor of 2 or more and velocity variations of 100 km/s or more are seen with periodicity of about I per hour. The cases of flow anomalies following in succession are also observed, and suggest their decay while propagating through the magnetosheath. Some magnetospheric disturbances observed in the outer magnetosphere after the satellite has crossed the magnetopause on the inbound orbit suggest their association with magnetosheath flow anomalies observed in the magnetosheath prior to magnetopause crossing.
Inferential modeling of 3D chromatin structure
Wang, Siyu; Xu, Jinbo; Zeng, Jianyang
2015-01-01
For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen. PMID:25690896
NASA Astrophysics Data System (ADS)
Fullea, J.; Muller, M. R.; Jones, A. G.
2012-04-01
Little is known of Ireland's deep, low-enthalpy geothermal resources and the potential for space heating and/or electricity generation based on geothermal energy to displace Ireland's significant reliance on carbon-based fuels. IRETHERM (www.iretherm.ie) is a four-and-a-half year, all-island, academic-government-industry collaborative project, initiated in 2011, with the overarching objective of developing a strategic and holistic understanding of Ireland's geothermal energy potential through integrated modelling of new and existing geophysical and geological data. One of the challenges in searching for deep geothermal resources in the relatively unexplored setting of Ireland lies in identifying those areas most likely to support significantly elevated temperatures at depth. Available borehole data, although sparse and clustered around areas of mineral and hydrocarbon interest, suggest a marked regional increase in surface heat-flow across Ireland, from ~40 mW/m2 in the south to >80 mW/m2 in the north. The origins of both the observed regional heat-flow trend and local temperature anomalies have not been investigated and are not currently understood. Although variations in the structure of the crust and lithosphere have been revealed by a number of active-source seismic and teleseismic experiments, their effects on surface heat-flow have not been modelled. Bulk 3-D variation in crustal heat-production across Ireland, which may contribute significantly to the observed regional and local temperature variations, has also not been determined. We investigate the origins of Ireland's regional heat-flow trend and regional and local temperature variations using the software package LitMod. This software combines petrological and geophysical modelling of the lithosphere and sub-lithospheric upper mantle within an internally consistent thermodynamic-geophysical framework, where all relevant properties are functions of temperature, pressure and chemical composition. The major
Optic flow aided navigation and 3D scene reconstruction
NASA Astrophysics Data System (ADS)
Rollason, Malcolm
2013-10-01
An important enabler for low cost airborne systems is the ability to exploit low cost inertial instruments. An Inertial Navigation System (INS) can provide a navigation solution, when GPS is denied, by integrating measurements from inertial sensors. However, the gyrometer and accelerometer biases of low cost inertial sensors cause compound errors in the integrated navigation solution. This paper describes experiments to establish whether (and to what extent) the navigation solution can be aided by fusing measurements from an on-board video camera with measurements from the inertial sensors. The primary aim of the work was to establish whether optic flow aided navigation is beneficial even when the 3D structure within the observed scene is unknown. A further aim was to investigate whether an INS can help to infer 3D scene content from video. Experiments with both real and synthetic data have been conducted. Real data was collected using an AR Parrot quadrotor. Empirical results illustrate that optic flow provides a useful aid to navigation even when the 3D structure of the observed scene is not known. With optic flow aiding of the INS, the computed trajectory is consistent with the true camera motion, whereas the unaided INS yields a rapidly increasing position error (the data represents ~40 seconds, after which the unaided INS is ~50 metres in error and has passed through the ground). The results of the Monte Carlo simulation concur with the empirical result. Position errors, which grow as a quadratic function of time when unaided, are substantially checked by the availability of optic flow measurements.
Challenges in Lagrangian transport and predictability in 3D flows
NASA Astrophysics Data System (ADS)
Branicki, M.; Wiggins, S.; Kirwan, A. D.; Malek-Madani, R.
2011-12-01
The interplay between the geometrical theory of dynamical systems and the trajectory-based description of aperiodically time-dependent fluid flows has led to significant advances in understanding the role of chaotic transport in geophysical flows at scales dominated by advection. Lagrangian transport analysis utilizing either the time-dependent geometry of intersecting stable and unstable manifolds of the so-called Distinguished Hyperbolic Trajectories (DHT), or ridges of finite-time Lyapunov exponent fields (LCS), provide a much needed and complementary insight into ephemeral mechanisms responsible for the existence of `leaky' transport barriers and 'leaky' mesoscale eddies. However, to date most oceanic applications have been confined to 2D analysis of near surface regions in 'perfect' flows not accounting for model or measurement error, and with the tacit assumption of negligible vertical velocities. I will systematically address issues concerning the regimes of applicability of two-dimensional analysis in 3D aperiodically time-dependent flows, as well as outstanding challenges in fully 3D Lagrangian transport analysis. Even for perfect horizontal velocities, little is known about the vertical extent of stable/unstable manifolds associated with DHTs and/or other special structures relevant to stratified 3D flows. In particular, their sensitivity to errors in the vertical velocities and data assimilation methods has been little studied. Rigorous results regarding the above issues will be illustrated by revealing and mathematically tractable toy models, as well as examples from a detailed study in an eddy-rich region from the Gulf of Mexico and the Mediterranean. New ways of quantifying the uncertainty in Lagrangian predictions will also be presented.
Recent Advances in Visualizing 3D Flow with LIC
NASA Technical Reports Server (NTRS)
Interrante, Victoria; Grosch, Chester
1998-01-01
Line Integral Convolution (LIC), introduced by Cabral and Leedom in 1993, is an elegant and versatile technique for representing directional information via patterns of correlation in a texture. Although most commonly used to depict 2D flow, or flow over a surface in 3D, LIC methods can equivalently be used to portray 3D flow through a volume. However, the popularity of LIC as a device for illustrating 3D flow has historically been limited both by the computational expense of generating and rendering such a 3D texture and by the difficulties inherent in clearly and effectively conveying the directional information embodied in the volumetric output textures that are produced. In an earlier paper, we briefly discussed some of the factors that may underlie the perceptual difficulties that we can encounter with dense 3D displays and outlined several strategies for more effectively visualizing 3D flow with volume LIC. In this article, we review in more detail techniques for selectively emphasizing critical regions of interest in a flow and for facilitating the accurate perception of the 3D depth and orientation of overlapping streamlines, and we demonstrate new methods for efficiently incorporating an indication of orientation into a flow representation and for conveying additional information about related scalar quantities such as temperature or vorticity over a flow via subtle, continuous line width and color variations.
3D Flow reconstruction using ultrasound PIV
NASA Astrophysics Data System (ADS)
Poelma, C.; Mari, J. M.; Foin, N.; Tang, M.-X.; Krams, R.; Caro, C. G.; Weinberg, P. D.; Westerweel, J.
2011-04-01
Ultrasound particle image velocimetry (PIV) can be used to obtain velocity fields in non-transparent geometries and/or fluids. In the current study, we use this technique to document the flow in a curved tube, using ultrasound contrast bubbles as flow tracer particles. The performance of the technique is first tested in a straight tube, with both steady laminar and pulsatile flows. Both experiments confirm that the technique is capable of reliable measurements. A number of adaptations are introduced that improve the accuracy and applicability of ultrasound PIV. Firstly, due to the method of ultrasound image acquisition, a correction is required for the estimation of velocities from tracer displacements. This correction accounts for the fact that columns in the image are recorded at slightly different instances. The second improvement uses a slice-by-slice scanning approach to obtain three-dimensional velocity data. This approach is here demonstrated in a strongly curved tube. The resulting flow profiles and wall shear stress distribution shows a distinct asymmetry. To meaningfully interpret these three-dimensional results, knowledge of the measurement thickness is required. Our third contribution is a method to determine this quantity, using the correlation peak heights. The latter method can also provide the third (out-of-plane) component if the measurement thickness is known, so that all three velocity components are available using a single probe.
3D structure and nuclear targets
NASA Astrophysics Data System (ADS)
Dupré, Raphaël; Scopetta, Sergio
2016-06-01
Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three-dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non-nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse-momentum-dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.
Slope instability in complex 3D topography promoted by convergent 3D groundwater flow
NASA Astrophysics Data System (ADS)
Reid, M. E.; Brien, D. L.
2012-12-01
Slope instability in complex topography is generally controlled by the interaction between gravitationally induced stresses, 3D strengths, and 3D pore-fluid pressure fields produced by flowing groundwater. As an example of this complexity, coastal bluffs sculpted by landsliding commonly exhibit a progression of undulating headlands and re-entrants. In this landscape, stresses differ between headlands and re-entrants and 3D groundwater flow varies from vertical rainfall infiltration to lateral groundwater flow on lower permeability layers with subsequent discharge at the curved bluff faces. In plan view, groundwater flow converges in the re-entrant regions. To investigate relative slope instability induced by undulating topography, we couple the USGS 3D limit-equilibrium slope-stability model, SCOOPS, with the USGS 3D groundwater flow model, MODFLOW. By rapidly analyzing the stability of millions of potential failures, the SCOOPS model can determine relative slope stability throughout the 3D domain underlying a digital elevation model (DEM), and it can utilize both fully 3D distributions of pore-water pressure and material strength. The two models are linked by first computing a groundwater-flow field in MODFLOW, and then computing stability in SCOOPS using the pore-pressure field derived from groundwater flow. Using these two models, our analyses of 60m high coastal bluffs in Seattle, Washington showed augmented instability in topographic re-entrants given recharge from a rainy season. Here, increased recharge led to elevated perched water tables with enhanced effects in the re-entrants owing to convergence of groundwater flow. Stability in these areas was reduced about 80% compared to equivalent dry conditions. To further isolate these effects, we examined groundwater flow and stability in hypothetical landscapes composed of uniform and equally spaced, oscillating headlands and re-entrants with differing amplitudes. The landscapes had a constant slope for both
Lattice Boltzmann Method for 3-D Flows with Curved Boundary
NASA Technical Reports Server (NTRS)
Mei, Renwei; Shyy, Wei; Yu, Dazhi; Luo, Li-Shi
2002-01-01
In this work, we investigate two issues that are important to computational efficiency and reliability in fluid dynamics applications of the lattice, Boltzmann equation (LBE): (1) Computational stability and accuracy of different lattice Boltzmann models and (2) the treatment of the boundary conditions on curved solid boundaries and their 3-D implementations. Three athermal 3-D LBE models (D3QI5, D3Ql9, and D3Q27) are studied and compared in terms of efficiency, accuracy, and robustness. The boundary treatment recently developed by Filippova and Hanel and Met et al. in 2-D is extended to and implemented for 3-D. The convergence, stability, and computational efficiency of the 3-D LBE models with the boundary treatment for curved boundaries were tested in simulations of four 3-D flows: (1) Fully developed flows in a square duct, (2) flow in a 3-D lid-driven cavity, (3) fully developed flows in a circular pipe, and (4) a uniform flow over a sphere. We found that while the fifteen-velocity 3-D (D3Ql5) model is more prone to numerical instability and the D3Q27 is more computationally intensive, the 63Q19 model provides a balance between computational reliability and efficiency. Through numerical simulations, we demonstrated that the boundary treatment for 3-D arbitrary curved geometry has second-order accuracy and possesses satisfactory stability characteristics.
Flow over bio-inspired 3D herringbone wall riblets
NASA Astrophysics Data System (ADS)
Chen, Huawei; Rao, Fugang; Shang, Xiaopeng; Zhang, Deyuan; Hagiwara, Ichiro
2014-03-01
Under the inspiration of small riblets of shark skin, the microgroove drag reduction riblets whose direction set along fluid flow have been widely investigated. Herringbone-type riblets of bird flight feather are seldom exploited although bird also has excellent flight performance. Inspired from the flight feather, novel bio-inspired plane-3D (p-3D) and spatial-3D (s-3D) herringbone wall riblets are proposed. Through experiment measurement of drag reduction in water tunnel, maximum drag reduction of p-3D and s-3D herringbone riblets was about 17 and 20 %, higher than traditional microgroove riblets. Moreover, significant change of drag reduction was also found by change of the angle between herringbone riblets. In particular, maximum drag reduction occurred as angle between herringbone riblets was about 60° close to real flight feather, which indicates that microstructure of bird flight feather has great impact on flight performance.
Discovering Structural Regularity in 3D Geometry
Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.
2010-01-01
We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292
Supersonic turbulence in 3D isothermal flow collision
NASA Astrophysics Data System (ADS)
Folini, Doris; Walder, Rolf; Favre, Jean M.
2014-02-01
Large scale supersonic bulk flows are present in a wide range of astrophysical objects, from O-star winds to molecular clouds, galactic sheets, accretion, or γ-ray bursts. Associated flow collisions shape observable properties and internal physics alike. Our goal is to shed light on the interplay between large scale aspects of such collision zones and the characteristics of the compressible turbulence they harbor. Our model setup is as simple as can be: 3D hydrodynamical simulations of two head-on colliding, isothermal, and homogeneous flows with identical upstream (subscript u) flow parameters and Mach numbers 2 < Mu < 43. The turbulence in the collision zone is driven by the upstream flows, whose kinetic energy is partly dissipated and spatially modulated by the shocks confining the zone. Numerical results are in line with expectations from self-similarity arguments. The spatial scale of modulation grows with the collision zone. The fraction of energy dissipated at the confining shocks decreases with increasing Mu. The mean density is ρm ≈ 20ρu, independent of Mu. The root mean square Mach number is Mrms ≈ 0.25Mu. Deviations toward weaker turbulence are found as the collision zone thickens and for small Mu. The density probability function is not log-normal. The turbulence is inhomogeneous, weaker in the center of the zone than close to the confining shocks. It is also anisotropic: transverse to the upstream flows Mrms is always subsonic. We argue that uniform, head-on colliding flows generally disfavor turbulence that is at the same time isothermal, supersonic, and isotropic. The anisotropy carries over to other quantities like the density variance - Mach number relation. Line-of-sight effects thus exist. Structure functions differ depending on whether they are computed along a line-of-sight perpendicular or parallel to the upstream flow. Turbulence characteristics generally deviate markedly from those found for uniformly driven, supersonic, isothermal
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.
Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B
2008-01-01
New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose
Numerical analysis of 3-D potential flow in centrifugal turbomachines
NASA Astrophysics Data System (ADS)
Daiguji, H.
1983-09-01
A numerical method is developed for analysing a three-dimensional steady incompressible potential flow through an impeller in centrifugal turbomachines. The method is the same as the previous method which was developed for the axial flow turbomachines, except for some treatments in the downstream region. In order to clarify the validity and limitation of the method, a comparison with the existing experimental data and numerical results is made for radial flow compressor impellers. The calculated blade surface pressure distributions almost coincide with the quasi-3-D calculation by Krimerman and Adler (1978), but are different partly from the quasi-3-D calculation using one meridional flow analysis. It is suggested from this comparison that the flow through an impeller with high efficiency near the design point can be predicted by this fully 3-D numerical method.
NASA Astrophysics Data System (ADS)
González-Torre, Iván; Losada, Juan Carlos; Falconer, Ruth; Hapca, Simona; Tarquis, Ana M.
2015-04-01
Soil structure may be defined as the spatial arrangement of soil particles, aggregates and pores. The geometry of each one of these elements, as well as their spatial arrangement, has a great influence on the transport of fluids and solutes through the soil. Fractal/Multifractal methods have been increasingly applied to quantify soil structure thanks to the advances in computer technology (Tarquis et al., 2003). There is no doubt that computed tomography (CT) has provided an alternative for observing intact soil structure. These CT techniques reduce the physical impact to sampling, providing three-dimensional (3D) information and allowing rapid scanning to study sample dynamics in near real-time (Houston et al., 2013a). However, several authors have dedicated attention to the appropriate pore-solid CT threshold (Elliot and Heck, 2007; Houston et al., 2013b) and the better method to estimate the multifractal parameters (Grau et al., 2006; Tarquis et al., 2009). The aim of the present study is to evaluate the effect of the algorithm applied in the multifractal method (box counting and box gliding) and the cube size on the calculation of generalized fractal dimensions (Dq) in grey images without applying any threshold. To this end, soil samples were extracted from different areas plowed with three tools (moldboard, chissel and plow). Soil samples for each of the tillage treatment were packed into polypropylene cylinders of 8 cm diameter and 10 cm high. These were imaged using an mSIMCT at 155keV and 25 mA. An aluminium filter (0.25 mm) was applied to reduce beam hardening and later several corrections where applied during reconstruction. References Elliot, T.R. and Heck, R.J. 2007. A comparison of 2D and 3D thresholding of CT imagery. Can. J. Soil Sci., 87(4), 405-412. Grau, J, Médez, V.; Tarquis, A.M., Saa, A. and Díaz, M.C.. 2006. Comparison of gliding box and box-counting methods in soil image analysis. Geoderma, 134, 349-359. González-Torres, Iván. Theory and
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures
Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.
2010-01-01
New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs
3-D structures of planetary nebulae
NASA Astrophysics Data System (ADS)
Steffen, W.
2016-07-01
Recent advances in the 3-D reconstruction of planetary nebulae are reviewed. We include not only results for 3-D reconstructions, but also the current techniques in terms of general methods and software. In order to obtain more accurate reconstructions, we suggest to extend the widely used assumption of homologous nebula expansion to map spectroscopically measured velocity to position along the line of sight.
An elliptic calculation procedure for 3-D viscous flow
NASA Astrophysics Data System (ADS)
Moore, J. G.
1985-05-01
The computation of 3-D internal transonic flows by means of a 3-D Euler Code is discussed. A multidomain approach for time hyperbolic system is presented. This technique, based on the decomposition of the computational domain into several subdomains which may overlap one another, makes it possible to simplify some mesh generation problems and to fit discontinuities such as shocks and slip surfaces. A description of the 3-D Euler Code is given. The space discretization method and the treatment of boundary conditions are emphasized. Various applications of this code in turbomachinery are discussed.
STAR3D: a stack-based RNA 3D structural alignment tool
Ge, Ping; Zhang, Shaojie
2015-01-01
The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875
STAR3D: a stack-based RNA 3D structural alignment tool.
Ge, Ping; Zhang, Shaojie
2015-11-16
The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875
Modeling Electric Current Flow in 3D Fractured Media
NASA Astrophysics Data System (ADS)
Demirel, S.; Roubinet, D.; Irving, J.
2014-12-01
The study of fractured rocks is extremely important in a variety of research fields and applications such as hydrogeology, hydrocarbon extraction and long-term storage of toxic waste. As fractures are highly conductive structures in comparison to the surrounding rock, their presence can be either an advantage or a drawback. For hydrocarbon extraction, fractures allow for quick and easy access to the resource whereas for toxic waste storage their presence increases the risk of leakage and migration of pollutants. In both cases, the identification of fracture network characteristics is an essential step. Recently, we have developed an approach for modeling electric current flow in 2D fractured media. This approach is based on a discrete-dual-porosity model where fractures are represented explicitly, the matrix is coarsely discretized into blocks, and current flow exchange between the fractures and matrix is analytically evaluated at the fracture-scale and integrated at the block-scale [1]. Although this approach has shown much promise and has proven its efficiency for 2D simulations, its extension to 3D remains to be addressed. To this end, we assume that fractures can be represented as two-dimensional finite planes embedded in the surrounding matrix, and we express analytically the distribution of electric potential at the fracture scale. This fracture-scale expression takes into account the electric-current-flow exchange with the surrounding matrix and flow conservation is enforced at the fracture intersections. The fracture-matrix exchange is then integrated at the matrix-block scale where the electric current flow conservation at the block boundaries is formulated with a modified finite volume method. With the objective of providing a low-computational-cost modeling approach adapted to 3D simulations in fractured media, our model is (i) validated and compared to existing modeling approaches and, (ii) used to evaluate the impact of the presence of fractures on
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles
2015-07-01
The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server
Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles
2015-01-01
The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960
NASA Astrophysics Data System (ADS)
Mottyll, S.; Skoda, R.
2015-12-01
A compressible inviscid flow solver with barotropic cavitation model is applied to two different ultrasonic horn set-ups and compared to hydrophone, shadowgraphy as well as erosion test data. The statistical analysis of single collapse events in wall-adjacent flow regions allows the determination of the flow aggressiveness via load collectives (cumulative event rate vs collapse pressure), which show an exponential decrease in agreement to studies on hydrodynamic cavitation [1]. A post-processing projection of event rate and collapse pressure on a reference grid reduces the grid dependency significantly. In order to evaluate the erosion-sensitive areas a statistical analysis of transient wall loads is utilised. Predicted erosion sensitive areas as well as temporal pressure and vapour volume evolution are in good agreement to the experimental data.
3D-GNOME: an integrated web service for structural modeling of the 3D genome
Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz
2016-01-01
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892
3D-GNOME: an integrated web service for structural modeling of the 3D genome.
Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz
2016-07-01
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892
3D Printed Micro Free-Flow Electrophoresis Device.
Anciaux, Sarah K; Geiger, Matthew; Bowser, Michael T
2016-08-01
The cost, time, and restrictions on creative flexibility associated with current fabrication methods present significant challenges in the development and application of microfluidic devices. Additive manufacturing, also referred to as three-dimensional (3D) printing, provides many advantages over existing methods. With 3D printing, devices can be made in a cost-effective manner with the ability to rapidly prototype new designs. We have fabricated a micro free-flow electrophoresis (μFFE) device using a low-cost, consumer-grade 3D printer. Test prints were performed to determine the minimum feature sizes that could be reproducibly produced using 3D printing fabrication. Microfluidic ridges could be fabricated with dimensions as small as 20 μm high × 640 μm wide. Minimum valley dimensions were 30 μm wide × 130 μm wide. An acetone vapor bath was used to smooth acrylonitrile-butadiene-styrene (ABS) surfaces and facilitate bonding of fully enclosed channels. The surfaces of the 3D-printed features were profiled and compared to a similar device fabricated in a glass substrate. Stable stream profiles were obtained in a 3D-printed μFFE device. Separations of fluorescent dyes in the 3D-printed device and its glass counterpart were comparable. A μFFE separation of myoglobin and cytochrome c was also demonstrated on a 3D-printed device. Limits of detection for rhodamine 110 were determined to be 2 and 0.3 nM for the 3D-printed and glass devices, respectively. PMID:27377354
Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe
2015-07-15
X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844
Mottyll, Stephan; Skoda, Romuald
2016-07-01
As a contribution to a better understanding of cavitation erosion mechanisms, a compressible inviscid finite volume flow solver with barotropic homogeneous liquid-vapor mixture cavitation model is applied to ultrasonic horn set-ups with and without stationary specimen, that exhibit attached cavitation at the horn tip. Void collapses and shock waves, which are closely related to cavitation erosion, are resolved. The computational results are compared to hydrophone, shadowgraphy and erosion test data. At the horn tip, vapor volume and topology, subharmonic oscillation frequency as well as the amplitude of propagating pressure waves are in good agreement with experimental data. For the evaluation of flow aggressiveness and the assessment of erosion sensitive wall zones, statistical analyses of wall loads and of the multiplicity of distinct collapses in wall-adjacent flow regions are applied to the horn tip and the stationary specimen. An a posteriori projection of load collectives, i.e. cumulative collapse rate vs. collapse pressure, onto a reference grid eliminates the grid dependency effectively for attached cavitation at the horn tip, whereas a significant grid dependency remains at the stationary specimen. The load collectives show an exponential decrease towards higher collapse pressures. Erosion sensitive wall zones are well predicted for both, horn tip and stationary specimen, and load profiles are in good qualitative agreement with measured topography profiles of eroded duplex stainless steel samples after long-term runs. For the considered amplitude and gap width according to ASTM G32-10 standard, the analysis of load collectives reveals that the distinctive erosive ring shape at the horn tip can be attributed to frequent breakdown and re-development of a small portion of the tip-attached cavity. This partial breakdown of the attached cavity repeats at each driving cycle and is associated with relatively moderate collapse peak pressures, whereas the
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures
Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador
2015-01-01
Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144
Vertical Flow Lithography for Fabrication of 3D Anisotropic Particles.
Habasaki, Shohei; Lee, Won Chul; Yoshida, Shotaro; Takeuchi, Shoji
2015-12-22
A microfluidics-based method for the 3D fabrication of anisotropic particles is reported. The method uses a vertical microchannel where tunable light patterns solidify photocurable resins for stacking multiple layers of the resins, thus enabling an application of stereolithography concepts to conventional flow lithography. Multilayered, tapered, and angular compartmental microparticles are demonstrated. PMID:26551590
Joint 3d Estimation of Vehicles and Scene Flow
NASA Astrophysics Data System (ADS)
Menze, M.; Heipke, C.; Geiger, A.
2015-08-01
driving. While much progress has been made in recent years, imaging conditions in natural outdoor environments are still very challenging for current reconstruction and recognition methods. In this paper, we propose a novel unified approach which reasons jointly about 3D scene flow as well as the pose, shape and motion of vehicles in the scene. Towards this goal, we incorporate a deformable CAD model into a slanted-plane conditional random field for scene flow estimation and enforce shape consistency between the rendered 3D models and the parameters of all superpixels in the image. The association of superpixels to objects is established by an index variable which implicitly enables model selection. We evaluate our approach on the challenging KITTI scene flow dataset in terms of object and scene flow estimation. Our results provide a prove of concept and demonstrate the usefulness of our method.
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions
Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.
2010-01-01
Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913
Two-equation turbulence modeling for 3-D hypersonic flows
NASA Technical Reports Server (NTRS)
Bardina, J. E.; Coakley, T. J.; Marvin, J. G.
1992-01-01
An investigation to verify, incorporate and develop two-equation turbulence models for three-dimensional high speed flows is presented. The current design effort of hypersonic vehicles has led to an intensive study of turbulence models for compressible hypersonic flows. This research complements an extensive review of experimental data and the current development of 2D turbulence models. The review of experimental data on 2D and 3D flows includes complex hypersonic flows with pressure profiles, skin friction, wall heat transfer, and turbulence statistics data. In a parallel effort, turbulence models for high speed flows have been tested against flat plate boundary layers, and are being tested against the 2D database. In the present paper, we present the results of 3D Navier-Stokes numerical simulations with an improved k-omega two-equation turbulence model against experimental data and empirical correlations of an adiabatic flat plate boundary layer, a cold wall flat plate boundary layer, and a 3D database flow, the interaction of an oblique shock wave and a thick turbulent boundary layer with a free stream Mach number = 8.18 and Reynolds number = 5 x 10 to the 6th.
An annotation system for 3D fluid flow visualization
NASA Technical Reports Server (NTRS)
Loughlin, Maria M.; Hughes, John F.
1995-01-01
Annotation is a key activity of data analysis. However, current systems for data analysis focus almost exclusively on visualization. We propose a system which integrates annotations into a visualization system. Annotations are embedded in 3D data space, using the Post-it metaphor. This embedding allows contextual-based information storage and retrieval, and facilitates information sharing in collaborative environments. We provide a traditional database filter and a Magic Lens filter to create specialized views of the data. The system has been customized for fluid flow applications, with features which allow users to store parameters of visualization tools and sketch 3D volumes.
Complex flow dynamics around 3D microbot prototypes.
Martínez-Aranda, Sergio; Galindo-Rosales, Francisco J; Campo-Deaño, Laura
2016-02-28
A new experimental setup for the study of the complex flow dynamics around 3D microbot prototypes in a straight microchannel has been developed and assessed. The ultimate aim of this work is focused on the analysis of the morphology of different microbot prototypes to get a better insight into their efficiency when they swim through the main conduits of the human circulatory system. The setup consists of a fused silica straight microchannel with a 3D microbot prototype fastened in the center of the channel cross-section by an extremely thin support. Four different prototypes were considered: a cube, a sphere and two ellipsoids with aspect ratios of 1 : 2 and 1 : 4, respectively. Flow visualization and micro-particle image velocimetry (μPIV) measurements were performed using Newtonian and viscoelastic blood analogue fluids. An efficiency parameter, ℑ, to discriminate the prototypes in terms of flow disturbance has been proposed. PMID:26790959
Implementation of Flow Tripping Capability in the USM3D Unstructured Flow Solver
NASA Technical Reports Server (NTRS)
Pandya, Mohagna J.; Abdol-Hamid, Khaled S.; Campbell, Richard L.; Frink, Neal T.
2006-01-01
A flow tripping capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. The capability is based on prescribing an appropriate profile of turbulence model variables to energize the boundary layer in a plane normal to a specified trip region on the body surface. We demonstrate this approach using the k-epsilon two-equation turbulence model of USM3D. Modification to the solution procedure primarily consists of developing a data structure to identify all unstructured tetrahedral grid cells located in the plane normal to a specified surface trip region and computing a function based on the mean flow solution to specify the modified profile of the turbulence model variables. We leverage this data structure and also show an adjunct approach that is based on enforcing a laminar flow condition on the otherwise fully turbulent flow solution in user-specified region. The latter approach is applied for the solutions obtained using other one-and two-equation turbulence models of USM3D. A key ingredient of the present capability is the use of a graphical user-interface tool PREDISC to define a trip region on the body surface in an existing grid. Verification of the present modifications is demonstrated on three cases, namely, a flat plate, the RAE2822 airfoil, and the DLR F6 wing-fuselage configuration.
Implementation of Flow Tripping Capability in the USM3D Unstructured Flow Solver
NASA Technical Reports Server (NTRS)
Pandya, Mohagna J.; Abdol-Harrid, Khaled S.; Campbell, Richard L.; Frink, Neal T.
2006-01-01
A flow tripping capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. The capability is based on prescribing an appropriate profile of turbulence model variables to energize the boundary layer in a plane normal to a specified trip region on the body surface. We demonstrate this approach using the k-e two-equation turbulence model of USM3D. Modification to the solution procedure primarily consists of developing a data structure to identify all unstructured tetrahedral grid cells located in the plane normal to a specified surface trip region and computing a function based on the mean flow solution to specify the modified profile of the turbulence model variables. We leverage this data structure and also show an adjunct approach that is based on enforcing a laminar flow condition on the otherwise fully turbulent flow solution in user specified region. The latter approach is applied for the solutions obtained using other one- and two-equation turbulence models of USM3D. A key ingredient of the present capability is the use of a graphical user-interface tool PREDISC to define a trip region on the body surface in an existing grid. Verification of the present modifications is demonstrated on three cases, namely, a flat plate, the RAE2822 airfoil, and the DLR F6 wing-fuselage configuration.
Computational modeling of RNA 3D structures and interactions.
Dawson, Wayne K; Bujnicki, Janusz M
2016-04-01
RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling. PMID:26689764
Measuring Actin Flow in 3D Cell Protrusions
Chiu, Chi-Li; Digman, Michelle A.; Gratton, Enrico
2013-01-01
Actin dynamics is important in determining cell shape, tension, and migration. Methods such as fluorescent speckle microscopy and spatial temporal image correlation spectroscopy have been used to capture high-resolution actin turnover dynamics within cells in two dimensions. However, these methods are not directly applicable in 3D due to lower resolution and poor contrast. Here, we propose to capture actin flow in 3D with high spatial-temporal resolution by combining nanoscale precise imaging by rapid beam oscillation and fluctuation spectroscopy techniques. To measure the actin flow along cell protrusions in cell expressing actin-eGFP cultured in a type I collagen matrix, the laser was orbited around the protrusion and its trajectory was modulated in a clover-shaped pattern perpendicularly to the protrusion. Orbits were also alternated at two positions closely spaced along the protrusion axis. The pair cross-correlation function was applied to the fluorescence fluctuation from these two positions to capture the flow of actin. Measurements done on nonmoving cellular protrusion tips showed no pair-correlation at two orbital positions indicating a lack of flow of F-actin bundles. However, in some protrusions, the pair-correlation approach revealed directional flow of F-actin bundles near the protrusion surface with flow rates in the range of ∼1 μm/min, comparable to results in two dimensions using fluorescent speckle microscopy. Furthermore, we found that the actin flow rate is related to the distance to the protrusion tip. We also observed collagen deformation by concomitantly detecting collagen fibers with reflectance detection during these actin motions. The implementation of the nanoscale precise imaging by rapid beam oscillation method with a cloverleaf-shaped trajectory in conjunction with the pair cross-correlation function method provides a quantitative way of capturing dynamic flows and organization of proteins during cell migration in 3D in conditions of
Advancements in 3D Structural Analysis of Geothermal Systems
Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David
2013-06-23
Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1
A finite element solver for 3-D compressible viscous flows
NASA Technical Reports Server (NTRS)
Reddy, K. C.; Reddy, J. N.; Nayani, S.
1990-01-01
Computation of the flow field inside a space shuttle main engine (SSME) requires the application of state of the art computational fluid dynamic (CFD) technology. Several computer codes are under development to solve 3-D flow through the hot gas manifold. Some algorithms were designed to solve the unsteady compressible Navier-Stokes equations, either by implicit or explicit factorization methods, using several hundred or thousands of time steps to reach a steady state solution. A new iterative algorithm is being developed for the solution of the implicit finite element equations without assembling global matrices. It is an efficient iteration scheme based on a modified nonlinear Gauss-Seidel iteration with symmetric sweeps. The algorithm is analyzed for a model equation and is shown to be unconditionally stable. Results from a series of test problems are presented. The finite element code was tested for couette flow, which is flow under a pressure gradient between two parallel plates in relative motion. Another problem that was solved is viscous laminar flow over a flat plate. The general 3-D finite element code was used to compute the flow in an axisymmetric turnaround duct at low Mach numbers.
Unsteady 3D Turbulent Flow Separation around a ROV Body
NASA Astrophysics Data System (ADS)
Ungureanu, Costel; Lungu, Adrian
2009-09-01
Turbulent separated flows around ellipsoids of various aspect ratios are investigated using a numerical method. The Reynolds averaged equations for continuity and momentum are solved by cell-centered finite-volume method for the primitive variables to describe the 3D turbulent incompressible flow. The objectives of the study are: (a) to investigate the propulsive performances of a moving Remotely Operated Vehicle (ROV hereafter) ellipsoidal body; (b) to validate the computational solutions through comparisons with the experimental data; (c) to investigate the effects of the angle of attack on the separation pattern as well as on the hydrodynamic forces and moments.
Unit cell geometry of 3-D braided structures
NASA Technical Reports Server (NTRS)
Du, Guang-Wu; Ko, Frank K.
1993-01-01
The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.
NASA Astrophysics Data System (ADS)
Li, Qiang; Yu, Guichang; Liu, Shulian; Zheng, Shuiying
2012-09-01
Journal bearings are important parts to keep the high dynamic performance of rotor machinery. Some methods have already been proposed to analysis the flow field of journal bearings, and in most of these methods simplified physical model and classic Reynolds equation are always applied. While the application of the general computational fluid dynamics (CFD)-fluid structure interaction (FSI) techniques is more beneficial for analysis of the fluid field in a journal bearing when more detailed solutions are needed. This paper deals with the quasi-coupling calculation of transient fluid dynamics of oil film in journal bearings and rotor dynamics with CFD-FSI techniques. The fluid dynamics of oil film is calculated by applying the so-called "dynamic mesh" technique. A new mesh movement approach is presented while the dynamic mesh models provided by FLUENT are not suitable for the transient oil flow in journal bearings. The proposed mesh movement approach is based on the structured mesh. When the journal moves, the movement distance of every grid in the flow field of bearing can be calculated, and then the update of the volume mesh can be handled automatically by user defined function (UDF). The journal displacement at each time step is obtained by solving the moving equations of the rotor-bearing system under the known oil film force condition. A case study is carried out to calculate the locus of the journal center and pressure distribution of the journal in order to prove the feasibility of this method. The calculating results indicate that the proposed method can predict the transient flow field of a journal bearing in a rotor-bearing system where more realistic models are involved. The presented calculation method provides a basis for studying the nonlinear dynamic behavior of a general rotor-bearing system.
3D visualization of middle ear structures
NASA Astrophysics Data System (ADS)
Vogel, Uwe; Schmitt, Thomas
1998-06-01
The achievement of volume geometry data from middle ear structures and surrounding components performs a necessary supposition for the finite element simulation of the vibrational and transfer characteristics of the ossicular chain. So far those models base on generalized figures and size data from anatomy textbooks or particular manual and one- or two-dimensional distance measurements of single ossicles, mostly obtained by light microscopy, respectively. Therefore the goal of this study is to create a procedure for complete three-dimensional imaging of real middle ear structures (tympanic membrane, ossicles, ligaments) in vitro or even in vivo. The main problems are their microscopic size with relevant structures from 10 micrometer to 5 mm, representing various tissue properties (bone, soft tissue). Additionally, these structures are surrounded by the temporal bone, the most solid bone of the human body. Generally there exist several established diagnostic tools for medical imaging that could be used for geometry data acquisition, e.g., X-ray computed tomography and magnetic resonance imaging. Basically they image different tissue parameters, either bony structures (ossicles), or soft tissue (tympanic membrane, ligaments). But considering this application those standard techniques allow low spatial resolution only, usually in the 0.5 - 1mm range, at least in one spatial direction. Thus particular structures of the middle ear region could even be missed completely because of their spatial location. In vitro there is a way out by collecting three complete data sets, each distinguished by 90 degree rotation of a cube-shaped temporal bone specimen. That allows high-resolution imaging in three orthogonal planes, which essentially supports the three-dimensional interpolation of the unknown elements, starting from the regularly set elements of the cubic grid with an edge extension given by the original two-dimensional matrix. A different approach represents the
Acetylcholinesterase: From 3D Structure to Function
Dvir, Hay; Silman, Israel; Harel, Michal; Rosenberry, Terrone L.; Sussman, Joel L.
2010-01-01
By rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase terminates neurotransmission at cholinergic synapses. Acetylcholinesterase is a very fast enzyme, functioning at a rate approaching that of a diffusion-controlled reaction. The powerful toxicity of organophosphate poisons is attributed primarily to their potent inhibition of acetylcholinesterase. Acetylcholinesterase inhibitors are utilized in the treatment of various neurological disorders, and are the principal drugs approved thus far by the FDA for management of Alzheimer’s disease. Many organophosphates and carbamates serve as potent insecticides, by selectively inhibiting insect acetylcholinesterase. The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine. It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues. The crystal structure of recombinant human acetylcholinesterase in its apo-state is similar in its overall features to that of the Torpedo enzyme; however, the unique crystal packing reveals a novel peptide sequence which blocks access to the active-site gorge. PMID:20138030
Patterns of 3D flow in a rotating cylinder array
NASA Astrophysics Data System (ADS)
Craig, Anna; Dabiri, John; Koseff, Jeffrey
2015-11-01
Experimental data are presented for large arrays of rotating, finite-height cylinders, which show that the three-dimensional flows are strongly dependent on the geometric and rotational configurations of the array. Two geometric configurations of the cylinders, each with two rotational configurations, were examined for a total of four arrays. 2D PIV was conducted in multiple intersecting horizontal and vertical sheets at a location far downstream of the leading edge of the array in order to build up a picture of the 3D developed flow patterns. It was found that the rotation of the cylinders drives the formation of streamwise and transverse flow patterns between cylinders. These horizontal flow patterns, by conservation of mass, drive vertical flows through the top of the array. As the array of rotating cylinders may provide insight into the flow kinematics of an array of vertical axis wind turbines, this planform flux is of particular interest as it would bring down into the array high kinetic energy fluid from above the array, thus increasing the energy resource available to turbines far downstream of the leading edge of the array.
The computation of steady 3-D separated flows over aerodynamic bodies at incidence and yaw
NASA Technical Reports Server (NTRS)
Pulliam, T. H.; Pan, D.
1986-01-01
This paper describes the implementation of a general purpose 3-D NS code and its application to simulated 3-D separated vortical flows over aerodynamic bodies. The thin-layer Reynolds-averaged NS equations are solved by an implicit approximate factorization scheme. The pencil data structure enables the code to run on very fine grids using only limited incore memories. Solutions of a low subsonic flow over an inclined ellipsoid are compared with experimental data to validate the code. Transonic flows over a yawed elliptical wing at incidence are computed and separations occurred at different yaw angles are discussed.
3D Shape and Indirect Appearance by Structured Light Transport.
OToole, Matthew; Mather, John; Kutulakos, Kiriakos N
2016-07-01
We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture. PMID:27295455
3d Modelling of Convective Flow In The Rhine Graben
NASA Astrophysics Data System (ADS)
Bächler, D.; Kohl, T.; Rybach, L.
Detailed investigations of the temperature distribution in the Rhine Graben indi- cate regular pattern of thermal anomalies following major north-south striking faults. These anomalies remain unexplained by conventional Rhine Graben studies based on 2D east-west striking sections. First analytical solutions for convective flow in vertical faults are applied for a clearly observable anomalous temperature pattern along ma- jor Rhine Graben faults. By these calculations the fault height, fault aperture, minimal fault permeability and time to convective onset is derived from the observed distances. Since analytical solutions are limited to simple model geometries further improvement was achieved by numerical model simulations, which allow to assume more com- plex initial and boundary conditions. Using the finite volume code TOUGH2 series of anomalies following the same fault were simulated by a 3D numerical model. Fo- cussing on the predominant north-south permeability structure the model consists of a vertical north-south striking fault and surrounding matrix. The fault geometries are based on the analytically predicted fault geometries (aperture=200m, height=3500m) and on the observed temperatures. Comparison of simulation results with observed temperatures shows that the fault is situated between 500 to 600m and 4200m. The fault permeability is taken as 5*10-13m2 and the fluid velocity in the fault is calcu- lated as 10-9 to 10-10 m/s. These results indicate the importance of our considerations since mass flux is much higher in the faults than across them. The minimal age of the anomaly is considered to be 77'000 years, since steady state is reached after this time span. The study proves that the observed temperature anomaly pattern along the gamma fault at Landau can be explained by north-south striking convection systems within fault zones. Similar situations have been found at Soultz. This may be a hint on a general feature of the major north-south striking
Comparison of protein structures using 3D profile alignment.
Suyama, M; Matsuo, Y; Nishikawa, K
1997-01-01
A novel method for protein structure comparison using 3D profile alignment is presented. The 3D profile is a position-dependent scoring matrix derived from three-dimensional structures and is basically used to estimate sequence-structure compatibility for prediction of protein structure. Our idea is to compare two 3D profiles using a dynamic programming algorithm to obtain optimal alignment and a similarity score between them. When the 3D profile of hemoglobin was compared with each of the profiles in the library, which contained 325 profiles of representative structures, all the profiles of other globins were detected with relatively high scores, and proteins in the same structural class followed the globins. Exhaustive comparison of 3D profiles in the library was also performed to depict protein relatedness in the structure space. Using multidimensional scaling, a planar projection of points in the protein structure space revealed an overall grouping in terms of structural classes, i.e., all-alpha, all-beta, alpha/beta, and alpha+beta. These results differ in implication from those obtained by the conventional structure-structure comparison method. Differences are discussed with respect to the structural divergence of proteins in the course of molecular evolution. PMID:9071025
MPSalsa 3D Simulations of Chemically Reacting Flows
Many important scientific and engineering applications require a detailed analysis of complex systems with coupled fluid flow, thermal energy transfer, mass transfer and nonequilibrium chemical reactions. Currently, computer simulations of these complex reacting flow problems are limited to idealized systems in one or two spatial dimensions when coupled with a detailed, fundamental chemistry model. The goal of our research is to develop, analyze and implement advanced MP numerical algorithms that will allow high resolution 3D simulations with an equal emphasis on fluid flow and chemical kinetics modeling. In our research, we focus on the development of new, fully coupled, implicit solution strategies that are based on robust MP iterative solution methods (copied from http://www.cs.sandia.gov/CRF/MPSalsa/). These simulations are needed for scientific and technical areas such as: combustion research for transportation, atmospheric chemistry modeling for pollution studies, chemically reacting flow models for analysis and control of manufacturing processes, surface catalytic reactors for methane to methanol conversion and chemical vapor deposition (CVD) process modeling for production of advanced semiconductor materials (http://www.cs.sandia.gov/CRF/MPSalsa/).
This project website provides six QuickTime videos of these simulations, along with a small image gallery and slideshow animations. A list of related publications and conference presentations is also made available.
Energy flow in passive and active 3D cochlear model
Wang, Yanli; Steele, Charles; Puria, Sunil
2015-12-31
Energy flow in the cochlea is an important characteristic of the cochlear traveling wave, and many investigators, such as von Békésy and Lighthill, have discussed this phenomenon. Particularly after the discovery of the motility of the outer hair cells (OHCs), the nature of the power gain of the cochlea has been a fundamental research question. In the present work, direct three-dimensional (3D) calculations of the power on cross sections of the cochlea and on the basilar membrane are performed based on a box model of the mouse cochlea. The distributions of the fluid pressure and fluid velocity in the scala vestibuli are presented. The power output from the OHCs and the power loss due to fluid viscous damping are calculated along the length of the cochlea. This work provides a basis for theoretical calculations of the power gain of the OHCs from mechanical considerations.
Energy flow in passive and active 3D cochlear model
NASA Astrophysics Data System (ADS)
Wang, Yanli; Puria, Sunil; Steele, Charles
2015-12-01
Energy flow in the cochlea is an important characteristic of the cochlear traveling wave, and many investigators, such as von Békésy and Lighthill, have discussed this phenomenon. Particularly after the discovery of the motility of the outer hair cells (OHCs), the nature of the power gain of the cochlea has been a fundamental research question. In the present work, direct three-dimensional (3D) calculations of the power on cross sections of the cochlea and on the basilar membrane are performed based on a box model of the mouse cochlea. The distributions of the fluid pressure and fluid velocity in the scala vestibuli are presented. The power output from the OHCs and the power loss due to fluid viscous damping are calculated along the length of the cochlea. This work provides a basis for theoretical calculations of the power gain of the OHCs from mechanical considerations.
Formal representation of 3D structural geological models
NASA Astrophysics Data System (ADS)
Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle
2016-05-01
The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.
3D separation over a wall-mounted hemisphere in steady and pulsatile flow
NASA Astrophysics Data System (ADS)
Carr, Ian A.; Plesniak, Michael W.
2014-11-01
Flow separation over a surface-mounted hemispheriod is prevalent in countless applications, both under steady (constant freestream velocity) and unsteady flow over the protuberance. Previous studies of 3D separation have been limited to steady inflow conditions. In biological and geophysical flows, pulsatile flow conditions are much more commonly observed, yet such conditions have not been well studied. Primarily motivated by previous studies of the flow observed in various human vocal fold pathologies, such as polyps, our research aims to fill the knowledge gap in unsteady 3D flow separation. This is achieved by characterizing surface pressure fields and velocity fields, focused primarily on the vortical flow structures and dynamics that occur around a hemispheroid protuberance under pulsatile flow conditions. Surface static pressure and two-dimensional, instantaneous and phase-averaged, particle image velocimetry data in steady and pulsatile flow are presented and compared. Coherent vortical flow structures have been identified using the λci vortex identification criterion. This analysis has revealed a novel set of flow structures dependent on the pulsatile flow forcing function. This material is based in part upon work supported by the National Science Foundation under Grant Number CBET-1236351.
Capacitance extraction from complex 3D interconnect structures
Cartwright, D.; Csanak, G.; George, D.; Walker, R.; Kuprat, A.; Dengi, A.; Grobman, W.
1999-06-01
A new tool has been developed for calculating the capacitance matrix for complex 3D interconnect structures involving multiple layers of irregularly shaped interconnect, imbedded in different dielectric materials. This method utilizes a new 3D adaptive unstructured grid capability, and a linear finite element algorithm. The capacitance is determined from the minimum in the total system energy as the nodes are varied to minimize the error in the electric field in the dielectric(s).
Simulations of soluble surfactants in 3D multiphase flow
NASA Astrophysics Data System (ADS)
Muradoglu, Metin; Tryggvason, Gretar
2014-10-01
A finite-difference/front-tracking method is developed for simulations of soluble surfactants in 3D multiphase flows. The interfacial and bulk surfactant concentration evolution equations are solved fully coupled with the incompressible Navier-Stokes equations. A non-linear equation of state is used to relate interfacial surface tension to surfactant concentration at the interface. Simple test cases are designed to validate different parts of the numerical algorithm and the computational results are found to be in a good agreement with the analytical solutions. The numerical algorithm is parallelized using a domain-decomposition method. It is then applied to study the effects of soluble surfactants on the motion of buoyancy-driven bubbles in a straight square channel in nearly undeformable (spherical) and deformable (ellipsoidal) regimes. Finally the method is used to examine the effects of soluble surfactants on the lateral migration of bubbles in a pressure-driven channel flow. It is found that surfactant-induced Marangoni stresses counteract the shear-induced lift force and can reverse the lateral bubble migration completely, i.e., the contaminated bubble drifts away from the channel wall and stabilizes at the center of the channel when the surfactant-induced Marangoni stresses are sufficiently large.
ICEd-ALE Treatment of 3-D Fluid Flow.
Energy Science and Technology Software Center (ESTSC)
1999-09-13
Version: 00 SALE3D calculates three-dimensional fluid flow at all speeds, from the incompressible limit to highly supersonic. An implicit treatment of the pressure calculation similar to that in the Implicit Continuous-fluid Eulerian (ICE) technique provides this flow speed flexibility. In addition, the computing mesh may move with the fluid in a typical Lagrangian fashion, be held in an Eulerian manner, or move in some arbitrarily specified way to provide a continuous rezoning capability. This latitudemore » results from use of an Arbitrary Lagrangian-Eulerian (ALE) treatment of the mesh. The partial differential equations solved are the Navier-Stokes equations and the mass and internal energy equations. The fluid pressure is determined from an equation of state and supplemented with an artificial viscous pressure for the computation of shock waves. The computing mesh consists of a three-dimensional network of arbitrarily shaped, six-sided deformable cells, and a variety of user-selectable boundary conditions are provided in the program.« less
3D annotation and manipulation of medical anatomical structures
NASA Astrophysics Data System (ADS)
Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim
2009-02-01
Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.
3D Ultrasonic Wave Simulations for Structural Health Monitoring
NASA Technical Reports Server (NTRS)
Campbell, Leckey Cara A/; Miler, Corey A.; Hinders, Mark K.
2011-01-01
Structural health monitoring (SHM) for the detection of damage in aerospace materials is an important area of research at NASA. Ultrasonic guided Lamb waves are a promising SHM damage detection technique since the waves can propagate long distances. For complicated flaw geometries experimental signals can be difficult to interpret. High performance computing can now handle full 3-dimensional (3D) simulations of elastic wave propagation in materials. We have developed and implemented parallel 3D elastodynamic finite integration technique (3D EFIT) code to investigate ultrasound scattering from flaws in materials. EFIT results have been compared to experimental data and the simulations provide unique insight into details of the wave behavior. This type of insight is useful for developing optimized experimental SHM techniques. 3D EFIT can also be expanded to model wave propagation and scattering in anisotropic composite materials.
3D Simulation of Velocity Profile of Turbulent Flow in Open Channel with Complex Geometry
NASA Astrophysics Data System (ADS)
Kamel, Benoumessad; Ilhem, Kriba; Ali, Fourar; Abdelbaki, Djebaili
Simulation of open channel flow or river flow presents unique challenge to numerical simulators, which is widely used in the applications of computational fluid dynamics. The prediction is extremely difficult because the flow in open channel is usually transient and turbulent, the geometry is irregular and curved, and the free-surface elevation is varying with time. The results from a 3D non-linear k- ɛ turbulence model are presented to investigate the flow structure, the velocity distribution and mass transport process in a meandering compound open channel and a straight open channel. The 3D numerical model for calculating flow is set up in cylinder coordinates in order to calculate the complex boundary channel. The finite volume method is used to disperse the governing equations and the SIMPLE algorithm is applied to acquire the coupling of velocity and pressure. The non-linear k- ɛ turbulent model has good useful value because of taking into account the anisotropy and not increasing the computational time. The main contributions of this study are developing a numerical method that can be applied to predict the flow in river bends with various bend curvatures and different width-depth ratios. This study demonstrates that the 3D non-linear k- ɛ turbulence model can be used for analyzing flow structures, the velocity distribution and pollutant transport in the complex boundary open channel, this model is applicable for real river and wetland problem.
Commercial turbofan engine exhaust nozzle flow analyses using PAB3D
NASA Technical Reports Server (NTRS)
Abdol-Hamid, Khaled S.; Uenishi, K.; Carlson, John R.; Keith, B. D.
1992-01-01
Recent developments of a three-dimensional (PAB3D) code have paved the way for a computational investigation of complex aircraft aerodynamic components. The PAB3D code was developed for solving the simplified Reynolds Averaged Navier-Stokes equations in a three-dimensional multiblock/multizone structured mesh domain. The present analysis was applied to commercial turbofan exhaust flow systems. Solution sensitivity to grid density is presented. Laminar flow solutions were developed for all grids and two-equation k-epsilon solutions were developed for selected grids. Static pressure distributions, mass flow and thrust quantities were calculated for on-design engine operating conditions. Good agreement between predicted surface static pressures and experimental data was observed at different locations. Mass flow was predicted within 0.2 percent of experimental data. Thrust forces were typically within 0.4 percent of experimental data.
New 3-D flow interpolation method on moving ADCP data
NASA Astrophysics Data System (ADS)
Tsubaki, R.; Kawahara, Y.; Muto, Y.; Fujita, I.
2012-05-01
A simple but accurate interpolation procedure for obtaining the three-dimensional distribution of three-component velocity data, from moving acoustic doppler current profiler (ADCP) observation data, is proposed. For understanding actual flow structure within a river with complex bathymetry, the three-dimensional mean velocity field provides a basic picture of the flow. For obtaining the three-dimensional distribution of three-component velocity data, in this work, anisotropic gridding was introduced in order to remove the random component of measured velocity data caused by the turbulence of the flow and measurement error. A continuity correction based on the pressure equation was used to reduce both random and systematic errors. The accuracy of the developed method was evaluated using three-dimensional flow simulation data from a detached-eddy simulation (DES). By using the procedure developed, the complex flow structure surrounding the spur dikes section in the Uji River was successfully visualized and explored. The proposed method shows superiorities in both accuracy and consistency for the interpolated velocity field, as compared to the kriging and inverse-distance weighted (IDW) methods.
Designing 3D Structure by 5-7 Kirigami
NASA Astrophysics Data System (ADS)
Gong, Xingting; Cho, Yigil; Castle, Toen; Sussman, Daniel; Kamien, Randall
2015-03-01
The purpose of this talk is to explore how one can create 3D structures from 2D materials through the art of kirigami. Kirigami expands upon origami by allowing not only folds, but also cuts, into materials. If we take an incompressible material such as paper and remove a hole from it, the paper will buckle into the third dimension once that hole is sealed in order to relieve strain. Thus, orienting cuts and folds in certain places throughout a sheet of paper can influence its ``pop-up,'' 3D structure. To narrow down the inverse design problem, we confined ourselves to making only one kind of cut (which we call the ``5-7 cut'') on a honeycomb grid, and we show how this single cut can give rise to arbitrarily complex three dimensional structures. A simple set of rules exists: (a) one 5-7 cut divides the material into 2 sections which can choose to pop-up or down independently of each other, (b) rows of uniform cuts must pop up or down in unison, giving (nearly) arbitrary 2D structure, and (c) the 5-7 cuts can be arranged in various ways to create 6 basic pop-up ``modes,'' which can then be arranged to give (nearly) arbitrary 3D structure. These simple rules allow a framework for designing targeted 3D structure from an initial 2D sheet of material. This work was supported by NSF EFRI-ODISSEI Grant EFRI 13-31583.
3D flow past transonic turbine cascade SE 1050 — Experiment and numerical simulations
NASA Astrophysics Data System (ADS)
Šimurda, D.; Fürst, J.; Luxa, M.
2013-08-01
This paper is concerned with experimental and numerical research on 3D flow past prismatic turbine cascade SE1050 (known in QNET network as open test case SE1050). The primary goal was to assess the influence of the inlet velocity profile on the flow structures in the interblade channel and on the flow field parameters at the cascade exit and to compare these findings to results of numerical simulations. Investigations of 3D flow past the cascade with non-uniform inlet velocity profile were carried out both experimentally and numerically at subsonic ( M 2is = 0.8) and at transonic ( M 2is = 1.2) regime at design angle of incidence. Experimental data was obtained using a traversing device with a five-hole conical probe. Numerically, the 3D flow was simulated by open source code OpenFOAM and in-house code. Analyses of experimental data and CFD simulations have revealed the development of distinctive vortex structures resulting from non-uniform inlet velocity profile. Origin of these structures results in increased loss of kinetic energy and spanwise shift of kinetic energy loss coefficient distribution. Differences found between the subsonic and the transonic case confirm earlier findings available in the literature. Results of CFD and experiments agree reasonably well.
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L
2013-07-01
The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures
Rahrig, Ryan R.; Petrov, Anton I.; Leontis, Neocles B.; Zirbel, Craig L.
2013-01-01
The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643
NASA Astrophysics Data System (ADS)
Vosnjak, S.; Mlacnik, J.
2009-04-01
The Drava Power Plants Utility company is the owner of all hydropower plants on the Drava River, Slovenia. On the flood waves relief structure of the Zlatoličje HPP headrace channel the construction of a turbine intake structure for the Melje small hydropower plant is planned. The Melje small HPP shall exploit the biological minimum discharge for electricity production. Since the structure shall be small, the price of a physical hydraulic model research, in comparison with the price of the structure itself, would be too high. Consequently, the client decided to test the designed structure in the cheapest possible way and ordered a 3D mathematical model of the turbine intake structure. By this mathematical model the designed form of the intake structure should be verified, or, in case of non-compliance, a modified form of such structure which would meet the required modes of the SHPP operation should be proposed. Since such a 3D mathematical model hasn't been used for a hydraulic modelling of this type yet, the project performers were slightly mistrustful of the results obtained by it. Regarding our long years' experiences with physical modelling we decided to construct also a physical hydraulic model in order to be able to verify the designed form of the intake structure and then to use the results for the 3D mathematical model calibration. A partial physical hydraulic model was constructed in the Laboratory for Hydraulic Research in Ljubljana in a model scale of 1:20. For construction and implementation of all the necessary research only 30 days were needed. Simultaneously with the physical model all the preparatory arrangements for the geometry of the mathematical model were going on. During the further development of the mathematical model, also some additional researches on the physical model were performed. Considering the time needed to fully establish the functionality of the mathematical model, it showed up to be very time consuming even in comparison to
Sydney-Gunnedah-Bowen Basin deep 3D structure
NASA Astrophysics Data System (ADS)
Danis, Cara
2012-01-01
Studies of the Sydney-Gunnedah-Bowen Basin (SGBB), one of the largest extensional rift sedimentary basins on the east coast of Australia, lack an understanding of the 3D upper crustal structure. Understanding of the subsurface structure is essential for many areas of resource exploration, development and management, as well as scientific research. Geological models provide a way to visualise and investigate the subsurface structure. The integrated regional scale gravity modelling approach, which uses boreholes and seismic data constraints, provides an understanding of the upper crustal structure and allows the development of a 3D geological model which can be used as the architectural framework for many different applications. This work presents a 3D geological model of the SGBB developed for application in high resolution thermal models. It is the culmination of geological surfaces derived from the interpolation of previous regional scale 2D gravity models and numerous borehole records. The model outlines the basement structure of the SGBB and provides information on depth to basement, depth to basal volcanics and thickness of overlying sediments. Through understanding the uncertainties, limitations, confidence and reliability of this model, the 3D geological model can provide the ideal framework for future research.
RNAComposer and RNA 3D structure prediction for nanotechnology.
Biesiada, Marcin; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W; Purzycka, Katarzyna J
2016-07-01
RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented. PMID:27016145
Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun
2016-05-10
Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant. PMID:27060701
Correlations of Surface Deformation and 3D Flow Field in a Compliant Wall Turbulent Channel Flow.
NASA Astrophysics Data System (ADS)
Wang, Jin; Zhang, Cao; Katz, Joseph
2015-11-01
This study focuses on the correlations between surface deformation and flow features, including velocity, vorticity and pressure, in a turbulent channel flow over a flat, compliant Polydimethylsiloxane (PDMS) wall. The channel centerline velocity is 2.5 m/s, and the friction Reynolds number is 2.3x103. Analysis is based on simultaneous measurements of the time resolved 3D velocity and surface deformation using tomographic PIV and Mach-Zehnder Interferometry. The volumetric pressure distribution is calculated plane by plane by spatially integrating the material acceleration using virtual boundary, omni-directional method. Conditional sampling based on local high/low pressure and deformation events reveals the primary flow structures causing the deformation. High pressure peaks appear at the interface between sweep and ejection, whereas the negative deformations peaks (dent) appear upstream, under the sweeps. The persistent phase lag between flow and deformations are presumably caused by internal damping within the PDMS. Some of the low pressure peaks and strong ejections are located under the head of hairpin vortices, and accordingly, are associated with positive deformation (bump). Others bumps and dents are correlated with some spanwise offset large inclined quasi-streamwise vortices that are not necessarily associated with hairpins. Sponsored by ONR.
Instability and Wave Propagation in Structured 3D Composites
NASA Astrophysics Data System (ADS)
Kaynia, Narges; Fang, Nicholas X.; Boyce, Mary C.
2014-03-01
Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the complex instability and wrinkling pattern arising in 3D structured composites and the effect of the buckling pattern on the overall structural response. The 3D structured composites consisted of stiffer plates supported by soft matrix on both sides. Compression beyond the critical strain led to complex buckling patterns in the initially straight plates. The motivation of our work is to elaborate the formation of a system of prescribed periodic scatterers (metamaterials) due to buckling, and their effect to interfere wave propagation through the metamaterial structures. Such metamaterials made from elastomers enable large reversible deformation and, as a result, significant changes of the wave propagation properties. We developed analytical and finite element models to capture various aspects of the instability mechanism. Mechanical experiments were designed to further explore the modeling results. The ability to actively alter the 3D composite structure can enable on-demand tunability of many different functions, such as active control of wave propagation to create band-gaps and waveguides.
Structured Light-Based 3D Reconstruction System for Plants
Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima
2015-01-01
Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701
Structured Light-Based 3D Reconstruction System for Plants.
Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima
2015-01-01
Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701
3D printed components with ultrasonically arranged microscale structure
NASA Astrophysics Data System (ADS)
Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.
2016-02-01
This paper shows the first application of in situ manipulation of discontinuous fibrous structure mid-print, within a 3D printed polymeric composite architecture. Currently, rapid prototyping methods (fused filament fabrication, stereolithography) are gaining increasing popularity within the engineering commnity to build structural components. Unfortunately, the full potential of these components is limited by the mechanical properties of the materials used. The aim of this study is to create and demonstrate a novel method to instantaneously orient micro-scale glass fibres within a selectively cured photocurable resin system, using ultrasonic forces to align the fibres in the desired 3D architecture. To achieve this we have mounted a switchable, focused laser module on the carriage of a three-axis 3D printing stage, above an in-house ultrasonic alignment rig containing a mixture of photocurable resin and discontinuous 14 μm diameter glass fibre reinforcement(50 μm length). In our study, a suitable print speed of 20 mm s-1 was used, which is comparable to conventional additive layer techniques. We show the ability to construct in-plane orthogonally aligned sections printed side by side, where the precise orientation of the configurations is controlled by switching the ultrasonic standing wave profile mid-print. This approach permits the realisation of complex fibrous architectures within a 3D printed landscape. The versatile nature of the ultrasonic manipulation technique also permits a wide range of particle types (diameters, aspect ratios and functions) and architectures (in-plane, and out-plane) to be patterned, leading to the creation of a new generation of fibrous reinforced composites for 3D printing.
Mitiche, Amar; Sekkati, Hicham
2006-11-01
This study investigates a variational, active curve evolution method for dense three-dimentional (3D) segmentation and interpretation of optical flow in an image sequence of a scene containing moving rigid objects viewed by a possibly moving camera. This method jointly performs 3D motion segmentation, 3D interpretation (recovery of 3D structure and motion), and optical flow estimation. The objective functional contains two data terms for each segmentation region, one based on the motion-only equation which relates the essential parameters of 3D rigid body motion to optical flow, and the other on the Horn and Schunck optical flow constraint. It also contains two regularization terms for each region, one for optical flow, the other for the region boundary. The necessary conditions for a minimum of the functional result in concurrent 3D-motion segmentation, by active curve evolution via level sets, and linear estimation of each region essential parameters and optical flow. Subsequently, the screw of 3D motion and regularized relative depth are recovered analytically for each region from the estimated essential parameters and optical flow. Examples are provided which verify the method and its implementation. PMID:17063686
All dispenser printed flexible 3D structured thermoelectric generators
NASA Astrophysics Data System (ADS)
Cao, Z.; Shi, J. J.; Torah, R. N.; Tudor, M. J.; Beeby, S. P.
2015-12-01
This work presents a vertically fabricated 3D thermoelectric generator (TEG) by dispenser printing on flexible polyimide substrate. This direct-write technology only involves printing of electrodes, thermoelectric active materials and structure material, which needs no masks to transfer the patterns onto the substrate. The dimension for single thermoelectric element is 2 mm × 2 mm × 0.5 mm while the distance between adjacent cubes is 1.2 mm. The polymer structure layer was used to support the electrodes which are printed to connect the top ends of the thermoelectric material and ensure the flexibility as well. The advantages and the limitations of the dispenser printed 3D TEGs will also be evaluated in this paper. The proposed method is potential to be a low-cost and scalable fabrication solution for TEGs.
The 3-D inelastic analyses for computational structural mechanics
NASA Technical Reports Server (NTRS)
Hopkins, D. A.; Chamis, C. C.
1989-01-01
The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.
3D reconstruction methods of coronal structures by radio observations
NASA Astrophysics Data System (ADS)
Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.
1992-11-01
The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.
3D reconstruction methods of coronal structures by radio observations
NASA Technical Reports Server (NTRS)
Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.
1992-01-01
The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.
Numerical simulation of internal and external inviscid and viscous 3-D flow fields
NASA Astrophysics Data System (ADS)
Leicher, Stefan
1986-11-01
A numerical method for solving the 3-D Euler equations in geometrical complex domains was developed. The approach divides the computational space into multiple blocks whose structure follows the natural lines of the conficuration. A systematic, multi-block grid generation scheme is used to produce the grid. The flow solutions are obtained by solving the Euler equations by a finite volume discretization and a Runge-Kutta time stepping scheme. The main advantage of this method is the applicability to complex geometries, for example complete aircraft configurations including wing, fuselage, canard and tail. The coupling with a 3-D boundary layer method allows to account for viscous effects. Another application for the method was the simulation of flows in the presence of a propeller.
Effects of Presence, Copresence, and Flow on Learning Outcomes in 3D Learning Spaces
ERIC Educational Resources Information Center
Hassell, Martin D.; Goyal, Sandeep; Limayem, Moez; Boughzala, Imed
2012-01-01
The level of satisfaction and effectiveness of 3D virtual learning environments were examined. Additionally, 3D virtual learning environments were compared with face-to-face learning environments. Students that experienced higher levels of flow and presence also experienced more satisfaction but not necessarily more effectiveness with 3D virtual…
Quasi 3D modeling of water flow in vadose zone and groundwater
NASA Astrophysics Data System (ADS)
Kuznetsov, M.; Yakirevich, A.; Pachepsky, Y. A.; Sorek, S.; Weisbrod, N.
2012-07-01
SummaryThe complexity of subsurface flow systems calls for a variety of concepts leading to the multiplicity of simplified flow models. One habitual simplification is based on the assumption that lateral flow and transport in unsaturated zone are not significant unless the capillary fringe is involved. In such cases the flow and transport in the unsaturated zone above groundwater level can be simulated as a 1D phenomenon, whereas the flow and transport through groundwater are viewed as 2D or 3D phenomena. A new approach for a numerical scheme for 3D variably saturated flow using quasi 3D Richards' equation and finite difference scheme is presented. The corresponding numerical algorithm and the QUASI-3D computer code were developed. Results of the groundwater level simulations were compared with transient laboratory experimental data for 2D data constant-flux infiltration, quasi-3D HYDRUS-MODFLOW numerical model and a FULL-3D numerical model using Richards' equation. Hypothetical 3D examples of infiltration, pumping and groundwater mound dissipation for different spatial-time scales are presented. Water flow simulation for the Alto Piura aquifer (Peru) demonstrates the QUASI-3D model application at the regional scale. Computationally the QUASI-3D code was found to be more efficient by an order of 10-300%, while being accurate with respect to the benchmark fully 3D variable saturation code, when the capillary fringe was considered.
Dynactin 3D structure: implications for assembly and dynein binding.
Imai, Hiroshi; Narita, Akihiro; Maéda, Yuichiro; Schroer, Trina A
2014-09-23
The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification. PMID:25046383
Recent Enhancements to USM3D Unstructured Flow Solver for Unsteady Flows
NASA Technical Reports Server (NTRS)
Pandya, Mohagna J.; Frink, Neal T.; Abdol-Hamid, Khaled S.; Chung, James J.
2004-01-01
The NASA USM3D unstructured flow solver is undergoing extensions to address dynamic flow problems in support of NASA and NAVAIR efforts to study the applicability of Computational Fluid Dynamics tools for the prediction of aircraft stability and control characteristics. The initial extensions reported herein include two second-order time stepping schemes, Detached-Eddy Simulation, and grid motion. This paper reports the initial code verification and validation assessment of the dynamic flow capabilities of USM3D. The cases considered are the classic inviscid shock-tube problem, low Reynolds number wake shedding from a NACA 0012 airfoil, high Reynolds number DES-based wake shedding from a 4-to-1 length-to-diameter cylinder, and forced pitch oscillation of a NACA 0012 airfoil with inviscid and turbulent flow.
3D precision surface measurement by dynamic structured light
NASA Astrophysics Data System (ADS)
Franke, Ernest A.; Magee, Michael J.; Mitchell, Joseph N.; Rigney, Michael P.
2004-02-01
This paper describes a 3-D imaging technique developed as an internal research project at Southwest Research Institute. The technique is based on an extension of structured light methods in which a projected pattern of parallel lines is rotated over the surface to be measured. A sequence of images is captured and the surface elevation at any location can then be determined from measurements of the temporal pattern, at any point, without considering any other points on the surface. The paper describes techniques for system calibration and surface measurement based on the method of projected quadric shells. Algorithms were developed for image and signal analysis and computer programs were written to calibrate the system and to calculate 3-D coordinates of points on a measured surface. A prototype of the Dynamic Structured Light (DSL) 3-D imaging system was assembled and typical parts were measured. The design procedure was verified and used to implement several different configurations with different measurement volumes and measurement accuracy. A small-parts measurement accuracy of 32 micrometers (.0012") RMS was verified by measuring the surface of a precision-machined plane. Large aircraft control surfaces were measured with a prototype setup that provided .02" depth resolution over a 4" by 8" field of view. Measurement times are typically less than three minutes for 300,000 points. A patent application has been filed.
Myosin filament 3D structure in mammalian cardiac muscle☆
AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.
2008-01-01
A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277
Simulation of a 3D unsteady flow in an axial turbine stage
NASA Astrophysics Data System (ADS)
Straka, Petr
2012-04-01
The contribution deals with a numerical simulation of an unsteady flow in an axial turbine stage. The solution is performed using an in-house numerical code developed in the Aeronautical and Test Institute, Plc. in Prague. The numerical code is based on a finite volume discretization of governing equations (Favre averaged Navier-Stokes equations) and a two-equations turbulence model. The temporal integration is based on the implicit second-order backward Euler formula, which is realized through the iteration process in dual time. The proposed numerical method is used for solution of the 3D, unsteady, viscous turbulent flow of a perfect gas in the axial turbine stage. The flow path consists of an input nozzle, stator blade-wheel, rotor blade-wheel, a shroud-seal gap and a diffuser. Attention is paid to the influence of a secondary flow structures, such as generated vortices and flow in shroud-seal gap.
Brien, Dianne L.; Reid, Mark E.
2007-01-01
Landslides are a common problem on coastal bluffs throughout the world. Along the coastal bluffs of the Puget Sound in Seattle, Washington, landslides range from small, shallow failures to large, deep-seated landslides. Landslides of all types can pose hazards to human lives and property, but deep-seated landslides are of significant concern because their large areal extent can cause extensive property damage. Although many geomorphic processes shape the coastal bluffs of Seattle, we focus on large (greater than 3,000 m3), deepseated, rotational landslides that occur on the steep bluffs along Puget Sound. Many of these larger failures occur in advance outwash deposits of the Vashon Drift (Qva); some failures extend into the underlying Lawton Clay Member of the Vashon Drift (Qvlc). The slope stability of coastal bluffs is controlled by the interplay of three-dimensional (3-D) variations in gravitational stress, strength, and pore-water pressure. We assess 3-D slope-stability using SCOOPS (Reid and others, 2000), a computer program that allows us to search a high-resolution digital-elevation model (DEM) to quantify the relative stability of all parts of the landscape by computing the stability and volume of thousands of potential spherical failures. SCOOPS incorporates topography, 3-D strength variations, and 3-D pore pressures. Initially, we use our 3-D analysis methods to examine the effects of topography and geology by using heterogeneous material properties, as defined by stratigraphy, without pore pressures. In this scenario, the least-stable areas are located on the steepest slopes, commonly in Qva or Qvlc. However, these locations do not agree well with observations of deep-seated landslides. Historically, both shallow colluvial landslides and deep-seated landslides have been observed near the contact between Qva and Qvlc, and commonly occur in Qva. The low hydraulic conductivity of Qvlc impedes ground-water flow, resulting in elevated pore pressures at the
3-D simulation of nanopore structure for DNA sequencing.
Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho
2012-07-01
In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538
3-D lookup: Fast protein structure database searches
Holm. L.; Sander, C.
1995-12-31
There are far fewer classes of three-dimensional protein folds than sequence families but the problem of detecting three-dimensional similarities is NP-complete. We present a novel heuristic for identifying 3-D similarities between a query structure and the database of known protein structures. Many methods for structure alignment use a bottom-up approach, identifying first local matches and then solving a combinatorial problem in building up larger clusters of matching substructures. Here the top-down approach is to start with the global comparison and select a rough superimposition using a fast 3-D lookup of secondary structure motifs. The superimposition is then extended to an alignment of C{sup {alpha}} atoms by an iterative dynamic programming step. An all-against-all comparison of 385-representative proteins (150,000 pair comparisons) took 1 day of computer time on a single R8000 processor. In other words, one query structure is scanned against the database in a matter of minutes. The method is rated at 90% reliability at capturing statistically significant similarities. It is useful as a rapid preprocessor to a comprehensive protein structure database search system.
Structure and magnetic exchange in heterometallic 3d-3d transition metal triethanolamine clusters.
Langley, Stuart K; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S
2012-01-21
Synthetic methods are described that have resulted in the formation of seven heterometallic complexes, all of which contain partially deprotonated forms of the ligand triethanolamine (teaH(3)). These compounds are [Mn(III)(4)Co(III)(2)Co(II)(2)O(2)(teaH(2))(2)(teaH)(0.82)(dea)(3.18)(O(2)CMe)(2)(OMe)(2)](BF(4))(2)(O(2)CMe)(2)·3.18MeOH·H(2)O (1), [Mn(II)(2)Mn(III)(2)Co(III)(2)(teaH)(4)(OMe)(2)(acac)(4)](NO(3))(2)·2MeOH (2), [Mn(III)(2)Ni(II)(4)(teaH)(4)(O(2)CMe)(6)]·2MeCN (3), [Mn(III)(2)Co(II)(2)(teaH)(2)(sal)(2)(acac)(2)(MeOH)(2)]·2MeOH (4), [Mn(II)(2)Fe(III)(2)(teaH)(2)(paa)(4)](NO(3))(2)·2MeOH·CH(2)Cl(2) (5), [Mn(II)Mn(III)(2)Co(III)(2)O(teaH)(2)(dea)(Iso)(OMe)(F)(2)(Phen)(2)](BF(4))(NO(3))·3MeOH (6) and [Mn(II)(2)Mn(III)Co(III)(2)(OH)(teaH)(3)(teaH(2))(acac)(3)](NO(3))(2)·3CH(2)Cl(2) (7). All of the compounds contain manganese, combined with 3d transition metal ions such as Fe, Co and Ni. The crystal structures are described and examples of 'rods', tetranuclear 'butterfly' and 'triangular' Mn(3) cluster motifs, flanked in some cases by diamagnetic cobalt(III) centres, are presented. Detailed DC and AC magnetic susceptibility and magnetization studies, combined with spin Hamiltonian analysis, have yielded J values and identified the spin ground states. In most cases, the energies of the low-lying excited states have also been obtained. The features of note include the 'inverse butterfly' spin arrangement in 2, 4 and 5. A S = 5/2 ground state occurs, for the first time, in the Mn(III)(2)Mn(II) triangular moiety within 6, the many other reported [Mn(3)O](6+) examples having S = ½ or 3/2 ground states. Compound 7 provides the first example of a Mn(II)(2)Mn(III) triangle, here within a pentanuclear Mn(3)Co(2) cluster. PMID:22113523
Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions
Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun
2013-01-01
Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state1. However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging2, due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-13-7, the resolution afforded by live-cell microscopy is limited (~ 200 nm). Our work was aimed at developing a correlation method that permits direct visualization of early events of HIV-1 infection by combining live-cell fluorescent light microscopy, cryo-fluorescent microscopy, and cryoET. In this manner, live-cell and cryo-fluorescent signals can be used to accurately guide the sampling in cryoET. Furthermore, structural information obtained from cryoET can be complemented with the dynamic functional data gained through live-cell imaging of fluorescent labeled target. In this video article, we provide detailed methods and protocols for structural investigation of HIV-1 and host-cell interactions using 3D correlative high-speed live-cell imaging and high-resolution cryoET structural analysis. HeLa cells infected with HIV-1 particles were characterized first by confocal live-cell microscopy, and the region containing the same viral particle was then analyzed by cryo-electron tomography for 3D structural details. The correlation between two sets of imaging data, optical imaging and electron imaging, was achieved using a home-built cryo-fluorescence light microscopy stage. The approach detailed here will be valuable, not only for study of virus-host cell interactions, but also for broader applications in cell biology, such as cell signaling, membrane receptor trafficking, and many other dynamic cellular processes. PMID:23852318
Navier-Stokes solutions for rotating 3-D duct flows
NASA Astrophysics Data System (ADS)
Srivastava, B. N.
1988-07-01
This paper deals with the computation of three-dimensional viscous turbulent flow in a rotating rectangular duct of low aspect ratio using thin-layer Navier-Stokes equations. Scalar form of an approximate factorization implicit scheme along with a modified q-omega turbulence model has been utilized for mean flow predictions. The predicted mean flow behavior has been favorably compared with the experimental data for mean axial velocity, channel pressure and cross-flow velocities at a flow Mach number of 0.05 and a rotational speed of 300 rpm.
Automatic structural matching of 3D image data
NASA Astrophysics Data System (ADS)
Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor
2015-10-01
A new image matching technique is described. It is implemented as an object-independent hierarchical structural juxtaposition algorithm based on an alphabet of simple object-independent contour structural elements. The structural matching applied implements an optimized method of walking through a truncated tree of all possible juxtapositions of two sets of structural elements. The algorithm was initially developed for dealing with 2D images such as the aerospace photographs, and it turned out to be sufficiently robust and reliable for matching successfully the pictures of natural landscapes taken in differing seasons from differing aspect angles by differing sensors (the visible optical, IR, and SAR pictures, as well as the depth maps and geographical vector-type maps). At present (in the reported version), the algorithm is enhanced based on additional use of information on third spatial coordinates of observed points of object surfaces. Thus, it is now capable of matching the images of 3D scenes in the tasks of automatic navigation of extremely low flying unmanned vehicles or autonomous terrestrial robots. The basic principles of 3D structural description and matching of images are described, and the examples of image matching are presented.
Verification of internal flow analyses in complex 3-D geometries
NASA Astrophysics Data System (ADS)
Choi, S. K.; Buggeln, R. C.
1992-11-01
Analysis of internal flow in advanced rocket propulsion systems is complicated by hardware geometry, high Reynolds numbers, rotation, high frequency phenomena, and near incompressibility. Typical of such a problem is the Space Shuttle Main Engine (SSME) hot gas manifold (HGM). Previous analyses of flow in the SSME HGM have been compared to air flow data and found to be inaccurate with respect to system losses, outer wall static pressures, and transfer duct environments. Such discrepancies could arise from flow measurement methodology, low order algorithms, turbulence modeling, and/or inadequate grid resolution. The objective of this work is to compare internal flow computational analyses to LDV flow measurements for the MSFC HGM pilot model configuration using two grids of different node density in the near wall region. Grids were generated with the EAGLE grid generator and calculations were made with the SRA MINT code. The calculated results were compared with HGM experimental data obtained in the MSFC water flow facility.
3D topographic correction of the BSR heat flow and detection of focused fluid flow
NASA Astrophysics Data System (ADS)
He, Tao; Li, Hong-Lin; Zou, Chang-Chun
2014-06-01
The bottom-simulating reflector (BSR) is a seismic indicator of the bottom of a gas hydrate stability zone. Its depth can be used to calculate the seafloor surface heat flow. The calculated BSR heat flow variations include disturbances from two important factors: (1) seafloor topography, which focuses the heat flow over regions of concave topography and defocuses it over regions of convex topography, and (2) the focused warm fluid flow within the accretionary prism coming from depths deeper than BSR. The focused fluid flow can be detected if the contribution of the topography to the BSR heat flow is removed. However, the analytical equation cannot solve the topographic effect at complex seafloor regions. We prove that 3D finite element method can model the topographic effect on the regional background heat flow with high accuracy, which can then be used to correct the topographic effect and obtain the BSR heat flow under the condition of perfectly flat topography. By comparing the corrected BSR heat flow with the regional background heat flow, focused fluid flow regions can be detected that are originally too small and cannot be detected using present-day equipment. This method was successfully applied to the midslope region of northern Cascadia subducting margin. The results suggest that the Cucumber Ridge and its neighboring area are positive heat flow anomalies, about 10%-20% higher than the background heat flow after 3D topographic correction. Moreover, the seismic imaging associated the positive heat flow anomaly areas with seabed fracture-cavity systems. This suggests flow of warm gas-carrying fluids along these high-permeability pathways, which could result in higher gas hydrate concentrations.
Automating the determination of 3D protein structure
Rayl, K.D.
1993-12-31
The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.
NASA Astrophysics Data System (ADS)
Kincaid, C. R.; MacDougall, J. G.; Druken, K. A.; Fischer, K. M.
2010-12-01
Understanding patterns in plate scale mantle flow in subduction zones is key to models of thermal structure, dehydration reactions, volatile distributions and magma generation and transport in convergent margins. Different patterns of flow in the mantle wedge can generate distinct signatures in seismological observables. Observed shear wave fast polarization directions in several subduction zones are inconsistent with predictions of simple 2-D wedge corner flow. Geochemical signatures in a number of subduction zones also indicate 3-D flow and entrainment patterns in the wedge. We report on a series of laboratory experiments on subduction driven flow to characterize spatial and temporal variability in 3-D patterns in flow and shear-induced finite strain. Cases focus on how rollback subduction, along-strike dip changes in subducting plates and evolving gaps or tears in subduction zones control temporal-spatial patterns in 3-D wedge flow. Models utilize a glucose working fluid with a temperature dependent viscosity to represent the upper 2000 km of the mantle. Subducting lithosphere is modeled with two rubber-reinforced continuous belts. Belts pass around trench and upper/lower mantle rollers. The deeper rollers can move laterally to allow for time varying dip angle. Each belt has independent speed control and dip adjustment, allowing for along-strike changes in convergence rate and the evolution of slab gaps. Rollback is modeled using a translation system to produce either uniform and asymmetric lateral trench motion. Neutral density finite strain markers are distributed throughout the fluid and used as proxies for tracking the evolution of anisotropy through space and time in the evolving flow fields. Particle image velocimetry methods are also used to track time varying 3-D velocity fields for directly calculating anisotropy patterns. Results show that complex plate motions (rollback, steepening) and morphologies (gaps) in convergent margins produce flows with
Gas flow environment and heat transfer nonrotating 3D program
NASA Technical Reports Server (NTRS)
Schulz, R. J.
1982-01-01
A complete set of benchmark quality data for the flow and heat transfer within a large rectangular turning duct is provided. These data are to be used to evaluate, and verify, three-dimensional internal viscous flow models and computational codes. The analytical contract objective is to select a computational code and define the capabilities of this code to predict the experimental results obtained. Details of the proper code operation will be defined and improvements to the code modeling capabilities will be formulated. Internal flow in a large rectangular cross-sectioned 90 deg. bend turning duct was studied. The duct construction was designed to allow detailed measurements to be made for the following three duct wall conditions: (1) an isothermal wall with isothermal flow; (2) an adiabatic wall with convective heat transfer by mixing between an unheated surrounding flow; and (3) an isothermal wall with heat transfer from a uniformly hot inlet flow.
Engineering extracellular matrix structure in 3D multiphase tissues
Gillette, Brian M.; Rossen, Ninna S.; Das, Nikkan; Leong, Debra; Wang, Meixin; Dugar, Arushi; Sia, Samuel K.
2011-01-01
In native tissues, microscale variations in the extracellular matrix (ECM) structure can drive different cellular behaviors. Although control over ECM structure could prove useful in tissue engineering and in studies of cellular behavior, isotropic 3D matrices poorly replicate variations in local microenvironments. In this paper, we demonstrate a method to engineer local variations in the density and size of collagen fibers throughout 3D tissues. The results showed that, in engineered multiphase tissues, the structures of collagen fibers in both the bulk ECM phases (as measured by mesh size and width of fibers) as well as at tissue interfaces (as measured by density of fibers and thickness of tissue interfaces) could be modulated by varying the collagen concentrations and gelling temperatures. As the method makes use of a previously published technique for tissue bonding, we also confirmed that significant adhesion strength at tissue interfaces was achieved under all conditions tested. Hence, this study demonstrates how collagen fiber structures can be engineered within all regions of a tightly integrated multiphase tissue scaffold by exploiting knowledge of collagen assembly. PMID:21840047
Complete Tem-Tomography: 3D Structure of Gems Cluster
NASA Technical Reports Server (NTRS)
Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.
2015-01-01
GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.
Characterizing 3D Vegetation Structure from Space: Mission Requirements
NASA Technical Reports Server (NTRS)
Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane
2012-01-01
Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral
Gas flow environmental and heat transfer nonrotating 3D program
NASA Technical Reports Server (NTRS)
Geil, T.; Steinhoff, J.
1983-01-01
A complete set of benchmark quality data for the flow and heat transfer within a large rectangular turning duct is being compiled. These data will be used to evaluate and verify three dimensional internal viscous flow models and computational codes. The analytical objective is to select such a computational code and define the capabilities of this code to predict the experimental results. Details of the proper code operation will be defined and improvements to the code modeling capabilities will be formulated.
Structural analysis of tropical cyclone using INSAT-3D observations
NASA Astrophysics Data System (ADS)
Jaiswal, Neeru; Kishtawal, C. M.
2016-05-01
The continuous observations from visible and thermal infrared (TIR) channels of geostationary satellites are highly useful for obtaining the features associated with the shape and dynamics of cloud structures within the tropical cyclones (TCs). As TC develops from an unstructured cloud cluster and intensifies, the cloud structures become more axisymmetric around the centre of the TC. To better understand the structure of TC during different stages of its evolution i.e. from its cyclogenesis to maturity and dissipation, the continuous satellite observations plays a key role. The high spatial and temporal resolution observations from geostationary satellites are very useful in order to analyze the cloud organization during the cyclogenesis. The gradient of the brightness temperatures measures the level of symmetry of each structure, which characterizes the degree of cloud organization of the TC. In the present work, the structural analysis of TC during its life period using the observations from Indian geostationary satellite INSAT-3D has been discussed. The visible and TIR observations from INSAT-3D satellite were used to fix the center position of the cyclone which is an input for the cyclone track and intensity prediction models. This data is also used to estimate the intensity of cyclone in the advanced Dvorak technique (ADT), and in the estimation of radius of maximum winds (Rmax) of TC which is an essential input parameter for the prediction of storm surge associated to the cyclones. The different patterns of cloud structure during the intensification stage, eye-wall formation and dissipation have been discussed. The early identification of these features helps in predicting the rapid intensification of TC which in turn improves the intensity predictions.
Protein 3D Structure Computed from Evolutionary Sequence Variation
Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris
2011-01-01
The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein
3D imaging of particle-scale rotational motion in cyclically driven granular flows
NASA Astrophysics Data System (ADS)
Harrington, Matt; Powers, Dylan; Cooper, Eric; Losert, Wolfgang
Recent experimental advances have enabled three-dimensional (3D) imaging of motion, structure, and failure within granular systems. 3D imaging allows researchers to directly characterize bulk behaviors that arise from particle- and meso-scale features. For instance, segregation of a bidisperse system of spheres under cyclic shear can originate from microscopic irreversibilities and the development of convective secondary flows. Rotational motion and frictional rotational coupling, meanwhile, have been less explored in such experimental 3D systems, especially under cyclic forcing. In particular, relative amounts of sliding and/or rolling between pairs of contacting grains could influence the reversibility of both trajectories, in terms of both position and orientation. In this work, we apply the Refractive Index Matched Scanning technique to a granular system that is cyclically driven and measure both translational and rotational motion of individual grains. We relate measured rotational motion to resulting shear bands and convective flows, further indicating the degree to which pairs and neighborhoods of grains collectively rotate.
On the growth of enstrophy in axisymmetric 3D Euler flows with swirl
NASA Astrophysics Data System (ADS)
Ayala, Diego; Doering, Charles
2015-11-01
By numerically solving suitable PDE-constrained optimization problems, we study a family of axisymmetric vector fields, having the structure of a pair of vortex rings with swirl, that maximize the instantaneous production of enstrophy in the context of 3-dimensional (3D) incompressible Euler flows. The axisymmetric fields are parametrized by their energy K , enstrophy E and helicity H . The imposed symmetry is justified by the results from the seminal work of Doering & Lu (2008), recently confirmed independently by Ayala & Protas (2015), where highly localized pairs of colliding vortex rings were found to be instantaneously optimal for enstrophy production in 3D Navier-Stokes flows. The axial symmetry allows for an exhaustive exploration of the parameter space (K , E , H , as the 3D problem is effectively reduced to a 2-dimensional system of partial differential equations for the modified azimuthal vorticity and the azimuthal circulation density, with the corresponding reduction in computational complexity. Possible connections between these optimal axisymmetric fields with swirl and the ``blow-up'' problem are discussed.
NASA Astrophysics Data System (ADS)
Harlander, U.; Wright, G. B.; Egbers, C.
2012-04-01
In the earth's atmosphere baroclinic instability is responsible for the heat and momentum transport from low to high latitudes. In the fifties, Raymond Hide used a rather simple laboratory experiment to study such vortices in the lab. The experiment is comprised by a cooled inner and heated outer cylinder mounted on a rotating platform, which mimics the heated tropical and cooled polar regions of the earth's atmosphere. The experiment shows rich dynamics that have been studied by varying the radial temperature difference and the rate of annulus revolution. At the Brandenburg University of Technology (BTU) Cottbus the differentially heated rotating annulus is a reference experiment of the DFG priority program 'MetStröm'. The 3D structure of the annulus flow field has been numerically simulated but, to our knowledge, has not been measured in the laboratory. In the present paper we use novel interpolation techniques to reconstruct the 3D annulus flow field from synchronous Particle Image Velocimetry (PIV) and Infrared Thermography (IRT) measurements. The PIV system is used to measure the horizontal velocity components at 40, 60, 80, 100, and 120 mm above the bottom. The uppermost level is thus 15 mm below the fluid's surface. The surface temperature is simultaneously measured by an infrared (IR) camera. The PIV and infrared cameras have been mounted above the annulus and they co-rotate with the annulus. From the PIV observations alone a coherent 3D picture of the flow cannot be constructed since the PIV measurements have been taken at different instants of time. Therefore a corresponding IR image has been recorded for each PIV measurement. These IR images can be used to reconstruct the correct phase of the measured velocity fields. Each IR and PIV image for which t>0 is rotated back to the position at t=0. Then all surface waves have the same phase. In contrast, the PIV velocity fields generally have different phases since they have been taken at different vertical
Eulerian and Lagrangian methods for vortex tracking in 2D and 3D flows
NASA Astrophysics Data System (ADS)
Huang, Yangzi; Green, Melissa
2014-11-01
Coherent structures are a key component of unsteady flows in shear layers. Improvement of experimental techniques has led to larger amounts of data and requires of automated procedures for vortex tracking. Many vortex criteria are Eulerian, and identify the structures by an instantaneous local swirling motion in the field, which are indicated by closed or spiral streamlines or pathlines in a reference frame. Alternatively, a Lagrangian Coherent Structures (LCS) analysis is a Lagrangian method based on the quantities calculated along fluid particle trajectories. In the current work, vortex detection is demonstrated on data from the simulation of two cases: a 2D flow with a flat plate undergoing a 45 ° pitch-up maneuver and a 3D wall-bounded turbulence channel flow. Vortices are visualized and tracked by their centers and boundaries using Γ1, the Q criterion, and LCS saddle points. In the cases of 2D flow, saddle points trace showed a rapid acceleration of the structure which indicates the shedding from the plate. For channel flow, saddle points trace shows that average structure convection speed exhibits a similar trend as a function of wall-normal distance as the mean velocity profile, and leads to statistical quantities of vortex dynamics. Dr. Jeff Eldredge and his research group at UCLA are gratefully acknowledged for sharing the database of simulation for the current research. This work was supported by the Air Force Office of Scientific Research under AFOSR Award No. FA9550-14-1-0210.
Segmented Domain Decomposition Multigrid For 3-D Turbomachinery Flows
NASA Technical Reports Server (NTRS)
Celestina, M. L.; Adamczyk, J. J.; Rubin, S. G.
2001-01-01
A Segmented Domain Decomposition Multigrid (SDDMG) procedure was developed for three-dimensional viscous flow problems as they apply to turbomachinery flows. The procedure divides the computational domain into a coarse mesh comprised of uniformly spaced cells. To resolve smaller length scales such as the viscous layer near a surface, segments of the coarse mesh are subdivided into a finer mesh. This is repeated until adequate resolution of the smallest relevant length scale is obtained. Multigrid is used to communicate information between the different grid levels. To test the procedure, simulation results will be presented for a compressor and turbine cascade. These simulations are intended to show the ability of the present method to generate grid independent solutions. Comparisons with data will also be presented. These comparisons will further demonstrate the usefulness of the present work for they allow an estimate of the accuracy of the flow modeling equations independent of error attributed to numerical discretization.
NASA Astrophysics Data System (ADS)
Maurer, Thomas; Brück, Yasemine; Hinz, Christoph; Gerke, Horst H.
2015-04-01
Structural heterogeneity, namely the spatial distribution of soils and sediments (represented by mineral particles), characterizes catchment hydrological behavior. In natural catchments, local geology and the specific geomorphic processes determine the characteristics and spatial distribution of structures. In constructed catchments, structural features are determined primarily by the construction processes and the geological origin of the parent material. Objectives are scenarios of 3D catchment structures in form of complete 3D description of soil hydraulic properties generated from the knowledge of the formation processes. The constructed hydrological catchment 'Hühnerwasser' (Lower Lusatia, Brandenburg, Germany) was used for the calibration and validation of model results due to its well-known conditions. For the modelling of structural features, a structure generator was used to model i) quasi-deterministic sediment distributions using input data from a geological model of the parent material excavation site; ii) sediment distributions that are conditioned to measurement data from soil sampling; and iii) stochastic component sediment distributions. All three approaches allow a randomization within definable limits. Furthermore, the spoil cone / spoil ridge orientation, internal layering, surface compaction and internal spoil cone compaction were modified. These generated structural models were incorporated in a gridded 3D volume model constructed with the GOCAD software. For selected scenarios, the impact of structure variation was assessed by hydrological modelling with HYDRUS 2D/3D software. For that purpose, 3D distributions of soil hydraulic properties were estimated based on generated sediment properties using adapted pedotransfer functions. Results from the hydrological model were compared them to measured discharges from the catchment. The impact of structural feature variation on flow behaviour was analysed by comparing different simulation scenarios
3-D Particle Tracking Velocimetry: Development and Applications in Small Scale Flows
NASA Astrophysics Data System (ADS)
Tien, Wei-Hsin
The thesis contains two parts of studies. In part I, a novel volumetric velocimetry technique is developed to measure the 3-D flow field of small-scale flows. The technique utilizes a color-coded pinhole plate with multiple light sources aligned to each pinhole to achieve high particle image density and large measurable depth on a single lens microscope system. A color separation algorithm and an improved particle identification algorithm are developed to identify individual particle images from each pinhole view. Furthermore, a calibration-based technique based on epi-polar line search method is developed to reconstruct the spatial coordinates of the particle, and a new two-frame tracking particle-tracking algorithm is developed to calculate the velocity field. The system was setup to achieve a magnification of 2.69, resulting in an imaging volume of 3.35 x 2.5 x 1.5 mm3 and showed satisfactory measurement accuracy. The technique was then further miniaturized to achieve a magnification of 10, resulting in a imaging volume of 600 x 600 x 600 microm3. The system was applied to a backward-facing step flow to test its ability to reconstruct the unsteady flow field with two-frame tracking. Finally, this technique was applied to a steady streaming flow field in a microfluidic device used to trap particles. The results revealed the three-dimensional flow structure that has not been observed in previous studies, and provided insights to the design of a more efficient trapping device. In part II, an in-vitro study was carried out to investigate the flow around a prosthetic venous valve. Using 2-D PIV, the dynamics of the valve motion was captured and the velocity fields were measured to investigate the effect of the sinus pocket and the coupling effect of a pair of valves. The PIV and hemodynamic results showed that the sinus pocket around the valve functioned as a flow regulator to smooth the entrained velocity profile and suppress the jet width. For current prosthetic
Dual multispectral and 3D structured light laparoscope
NASA Astrophysics Data System (ADS)
Clancy, Neil T.; Lin, Jianyu; Arya, Shobhit; Hanna, George B.; Elson, Daniel S.
2015-03-01
Intraoperative feedback on tissue function, such as blood volume and oxygenation would be useful to the surgeon in cases where current clinical practice relies on subjective measures, such as identification of ischaemic bowel or tissue viability during anastomosis formation. Also, tissue surface profiling may be used to detect and identify certain pathologies, as well as diagnosing aspects of tissue health such as gut motility. In this paper a dual modality laparoscopic system is presented that combines multispectral reflectance and 3D surface imaging. White light illumination from a xenon source is detected by a laparoscope-mounted fast filter wheel camera to assemble a multispectral image (MSI) cube. Surface shape is then calculated using a spectrally-encoded structured light (SL) pattern detected by the same camera and triangulated using an active stereo technique. Images of porcine small bowel were acquired during open surgery. Tissue reflectance spectra were acquired and blood volume was calculated at each spatial pixel across the bowel wall and mesentery. SL features were segmented and identified using a `normalised cut' algoritm and the colour vector of each spot. Using the 3D geometry defined by the camera coordinate system the multispectral data could be overlaid onto the surface mesh. Dual MSI and SL imaging has the potential to provide augmented views to the surgeon supplying diagnostic information related to blood supply health and organ function. Future work on this system will include filter optimisation to reduce noise in tissue optical property measurement, and minimise spot identification errors in the SL pattern.
NASA Astrophysics Data System (ADS)
Carlsohn, Matthias F.; Kemmling, André; Petersen, Arne; Wietzke, Lennart
2016-04-01
Cerebral aneurysms require endovascular treatment to eliminate potentially lethal hemorrhagic rupture by hemostasis of blood flow within the aneurysm. Devices (e.g. coils and flow diverters) promote homeostasis, however, measurement of blood flow within an aneurysm or cerebral vessel before and after device placement on a microscopic level has not been possible so far. This would allow better individualized treatment planning and improve manufacture design of devices. For experimental analysis, direct measurement of real-time microscopic cerebrovascular flow in micro-structures may be an alternative to computed flow simulations. An application of microscopic aneurysm flow measurement on a regular basis to empirically assess a high number of different anatomic shapes and the corresponding effect of different devices would require a fast and reliable method at low cost with high throughout assessment. Transparent three dimensional 3D models of brain vessels and aneurysms may be used for microscopic flow measurements by particle image velocimetry (PIV), however, up to now the size of structures has set the limits for conventional 3D-imaging camera set-ups. On line flow assessment requires additional computational power to cope with the processing large amounts of data generated by sequences of multi-view stereo images, e.g. generated by a light field camera capturing the 3D information by plenoptic imaging of complex flow processes. Recently, a fast and low cost workflow for producing patient specific three dimensional models of cerebral arteries has been established by stereo-lithographic (SLA) 3D printing. These 3D arterial models are transparent an exhibit a replication precision within a submillimeter range required for accurate flow measurements under physiological conditions. We therefore test the feasibility of microscopic flow measurements by PIV analysis using a plenoptic camera system capturing light field image sequences. Averaging across a sequence of
NASA Astrophysics Data System (ADS)
Izham, Mohamad Yusoff; Muhamad Uznir, Ujang; Alias, Abdul Rahman; Ayob, Katimon; Wan Ruslan, Ismail
2011-04-01
Existing 2D data structures are often insufficient for analysing the dynamism of saturation excess overland flow (SEOF) within a basin. Moreover, all stream networks and soil surface structures in GIS must be preserved within appropriate projection plane fitting techniques known as georeferencing. Inclusion of 3D volumetric structure of the current soft geo-objects simulation model would offer a substantial effort towards representing 3D soft geo-objects of SEOF dynamically within a basin by visualising saturated flow and overland flow volume. This research attempts to visualise the influence of a georeference system towards the dynamism of overland flow coverage and total overland flow volume generated from the SEOF process using VSG data structure. The data structure is driven by Green-Ampt methods and the Topographic Wetness Index (TWI). VSGs are analysed by focusing on spatial object preservation techniques of the conformal-based Malaysian Rectified Skew Orthomorphic (MRSO) and the equidistant-based Cassini-Soldner projection plane under the existing geodetic Malaysian Revised Triangulation 1948 (MRT48) and the newly implemented Geocentric Datum for Malaysia (GDM2000) datum. The simulated result visualises deformation of SEOF coverage under different georeference systems via its projection planes, which delineate dissimilar computation of SEOF areas and overland flow volumes. The integration of Georeference, 3D GIS and the saturation excess mechanism provides unifying evidence towards successful landslide and flood disaster management through envisioning the streamflow generating process (mainly SEOF) in a 3D environment.
Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media
NASA Astrophysics Data System (ADS)
Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben
2014-09-01
We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.
NASA Astrophysics Data System (ADS)
Meng, Hui; Hussain, Fazle
1991-10-01
To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.
Approximate analytic solutions to 3D unconfined groundwater flow within regional 2D models
NASA Astrophysics Data System (ADS)
Luther, K.; Haitjema, H. M.
2000-04-01
We present methods for finding approximate analytic solutions to three-dimensional (3D) unconfined steady state groundwater flow near partially penetrating and horizontal wells, and for combining those solutions with regional two-dimensional (2D) models. The 3D solutions use distributed singularities (analytic elements) to enforce boundary conditions on the phreatic surface and seepage faces at vertical wells, and to maintain fixed-head boundary conditions, obtained from the 2D model, at the perimeter of the 3D model. The approximate 3D solutions are analytic (continuous and differentiable) everywhere, including on the phreatic surface itself. While continuity of flow is satisfied exactly in the infinite 3D flow domain, water balance errors can occur across the phreatic surface.
A 3D visualization system for molecular structures
NASA Technical Reports Server (NTRS)
Green, Terry J.
1989-01-01
The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.
Large-eddy simulation of 3D turbulent flow past a complete marine hydrokinetic turbine
NASA Astrophysics Data System (ADS)
Kang, S.; Sotiropoulos, F.
2011-12-01
A high-resolution computational framework was recently developed by Kang et al (Adv. Water Resour., submitted) for simulating three-dimensional (3D), turbulent flow past real-life, complete marine hydrokinetic (MHK) turbine configurations. In this model the complex turbine geometry is resolved by employing the curvilinear immersed boundary (CURVIB) method, which solves the 3D unsteady incompressible Navier-Stokes equations in generalized curvilinear domains with embedded arbitrarily complex, moving and/or stationary immersed boundaries (Ge and Sotiropoulos, 2007). Turbulence is simulated using the large-eddy simulation (LES) approach adapted in the context of the CURVIB method, with a wall model based on solving the simplified boundary layer equations used to reconstruct boundary conditions near all solid surfaces (Kang et al., 2011). The model can resolve the flow patterns generated by the rotor and all stationary components of the turbine as well as the interactions of the flow structures with the channel bed. We apply this model to carry out LES of the flow past the model-size hydrokinetic turbine deployed in the St. Anthony Falls Laboratory main channel. The mean velocities and second-order turbulence statistics measured in the downstream wake using acoustic Doppler velocimetry (ADV) are compared with the LES results. The comparisons show that the computed mean velocities and turbulent stresses are in good agreement with the measurements. The high-resolution LES data are used to explore physically important downstream flow characteristics such as the time-averaged wake structure, recovery of cross-sectionally averaged power potential, near-bed scour potential, etc. This work is supported by Verdant Power.
3D Imaging with Structured Illumination for Advanced Security Applications
Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.
2015-09-01
Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.
An Efficient 3D Imaging using Structured Light Systems
NASA Astrophysics Data System (ADS)
Lee, Deokwoo
Structured light 3D surface imaging has been crucial in the fields of image processing and computer vision, particularly in reconstruction, recognition and others. In this dissertation, we propose the approaches to development of an efficient 3D surface imaging system using structured light patterns including reconstruction, recognition and sampling criterion. To achieve an efficient reconstruction system, we address the problem in its many dimensions. In the first, we extract geometric 3D coordinates of an object which is illuminated by a set of concentric circular patterns and reflected to a 2D image plane. The relationship between the original and the deformed shape of the light patterns due to a surface shape provides sufficient 3D coordinates information. In the second, we consider system efficiency. The efficiency, which can be quantified by the size of data, is improved by reducing the number of circular patterns to be projected onto an object of interest. Akin to the Shannon-Nyquist Sampling Theorem, we derive the minimum number of circular patterns which sufficiently represents the target object with no considerable information loss. Specific geometric information (e.g. the highest curvature) of an object is key to deriving the minimum sampling density. In the third, the object, represented using the minimum number of patterns, has incomplete color information (i.e. color information is given a priori along with the curves). An interpolation is carried out to complete the photometric reconstruction. The results can be approximately reconstructed because the minimum number of the patterns may not exactly reconstruct the original object. But the result does not show considerable information loss, and the performance of an approximate reconstruction is evaluated by performing recognition or classification. In an object recognition, we use facial curves which are deformed circular curves (patterns) on a target object. We simply carry out comparison between the
3D Seismic Imaging over a Potential Collapse Structure
NASA Astrophysics Data System (ADS)
Gritto, Roland; O'Connell, Daniel; Elobaid Elnaiem, Ali; Mohamed, Fathelrahman; Sadooni, Fadhil
2016-04-01
The Middle-East has seen a recent boom in construction including the planning and development of complete new sub-sections of metropolitan areas. Before planning and construction can commence, however, the development areas need to be investigated to determine their suitability for the planned project. Subsurface parameters such as the type of material (soil/rock), thickness of top soil or rock layers, depth and elastic parameters of basement, for example, comprise important information needed before a decision concerning the suitability of the site for construction can be made. A similar problem arises in environmental impact studies, when subsurface parameters are needed to assess the geological heterogeneity of the subsurface. Environmental impact studies are typically required for each construction project, particularly for the scale of the aforementioned building boom in the Middle East. The current study was conducted in Qatar at the location of a future highway interchange to evaluate a suite of 3D seismic techniques in their effectiveness to interrogate the subsurface for the presence of karst-like collapse structures. The survey comprised an area of approximately 10,000 m2 and consisted of 550 source- and 192 receiver locations. The seismic source was an accelerated weight drop while the geophones consisted of 3-component 10 Hz velocity sensors. At present, we analyzed over 100,000 P-wave phase arrivals and performed high-resolution 3-D tomographic imaging of the shallow subsurface. Furthermore, dispersion analysis of recorded surface waves will be performed to obtain S-wave velocity profiles of the subsurface. Both results, in conjunction with density estimates, will be utilized to determine the elastic moduli of the subsurface rock layers.
Improved hybrid optimization algorithm for 3D protein structure prediction.
Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang
2014-07-01
A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. PMID:25069136
The 3D structure of Coronal Mass Ejections
NASA Astrophysics Data System (ADS)
Patsourakos, Spiros
2016-07-01
Coronal Mass Ejections (CMEs) represent one of the most powerful energy release phenomena in the entire solar system and are a major driver of space weather. Prior to 2006, our observational access to CMEs was limited to single viewpoint remote sensing observations in the inner/outer corona, and in-situ observations further away, e.g. at 1 AU. Taking all these factors together, turned out to be a major obstacle in our understanding and characterizing of the 3D structure and evolution of CMEs. The situation improved dramatically with the availability of multi-viewpoint imaging observations of CMEs, all way through from the Sun to 1 AU, from the STEREO mission since 2006, combined with observations from other missions (SOHO, Hinode, SDO, IRIS). With this talk we will discuss several key recent results in CME science resulting from the analysis of multi-viewpoint observations. This includes: (1) shape and structure; (2) kinematics and energetics; (3) trajectories, deflections and rotations; (4) arrival times and velocities at 1 AU; (5) magnetic field structure; (6) relationships with coronal and interplanetary shocks and solar energetic particles. The implications of these results in terms of CME theories and models will be also addressed. We will conclude with a discussion of important open issues in our understanding of CMEs and how these could be addressed with upcoming (Solar Orbiter, Solar Probe Plus) and under-study missions (e.g., L5).
3D-Flow processor for a programmable Level-1 trigger (feasibility study)
Crosetto, D.
1992-10-01
A feasibility study has been made to use the 3D-Flow processor in a pipelined programmable parallel processing architecture to identify particles such as electrons, jets, muons, etc., in high-energy physics experiments.
CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins
Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu
2014-01-01
Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753
3D structures of membrane proteins from genomic sequencing
Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.
2012-01-01
Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045
NASA Technical Reports Server (NTRS)
Parikh, Paresh; Pirzadeh, Shahyar; Loehner, Rainald
1990-01-01
A set of computer programs for 3-D unstructured grid generation, fluid flow calculations, and flow field visualization was developed. The grid generation program, called VGRID3D, generates grids over complex configurations using the advancing front method. In this method, the point and element generation is accomplished simultaneously, VPLOT3D is an interactive, menudriven pre- and post-processor graphics program for interpolation and display of unstructured grid data. The flow solver, VFLOW3D, is an Euler equation solver based on an explicit, two-step, Taylor-Galerkin algorithm which uses the Flux Corrected Transport (FCT) concept for a wriggle-free solution. Using these programs, increasingly complex 3-D configurations of interest to aerospace community were gridded including a complete Space Transportation System comprised of the space-shuttle orbitor, the solid-rocket boosters, and the external tank. Flow solutions were obtained on various configurations in subsonic, transonic, and supersonic flow regimes.
Determining 3D Flow Fields via Multi-camera Light Field Imaging
Truscott, Tadd T.; Belden, Jesse; Nielson, Joseph R.; Daily, David J.; Thomson, Scott L.
2013-01-01
In the field of fluid mechanics, the resolution of computational schemes has outpaced experimental methods and widened the gap between predicted and observed phenomena in fluid flows. Thus, a need exists for an accessible method capable of resolving three-dimensional (3D) data sets for a range of problems. We present a novel technique for performing quantitative 3D imaging of many types of flow fields. The 3D technique enables investigation of complicated velocity fields and bubbly flows. Measurements of these types present a variety of challenges to the instrument. For instance, optically dense bubbly multiphase flows cannot be readily imaged by traditional, non-invasive flow measurement techniques due to the bubbles occluding optical access to the interior regions of the volume of interest. By using Light Field Imaging we are able to reparameterize images captured by an array of cameras to reconstruct a 3D volumetric map for every time instance, despite partial occlusions in the volume. The technique makes use of an algorithm known as synthetic aperture (SA) refocusing, whereby a 3D focal stack is generated by combining images from several cameras post-capture 1. Light Field Imaging allows for the capture of angular as well as spatial information about the light rays, and hence enables 3D scene reconstruction. Quantitative information can then be extracted from the 3D reconstructions using a variety of processing algorithms. In particular, we have developed measurement methods based on Light Field Imaging for performing 3D particle image velocimetry (PIV), extracting bubbles in a 3D field and tracking the boundary of a flickering flame. We present the fundamentals of the Light Field Imaging methodology in the context of our setup for performing 3DPIV of the airflow passing over a set of synthetic vocal folds, and show representative results from application of the technique to a bubble-entraining plunging jet. PMID:23486112
Coupled aeroelastic oscillations of a turbine blade row in 3D transonic flow
NASA Astrophysics Data System (ADS)
Gnesin, Vitaly; Kolodyazhnaya, Lyubov; Rzadkowski, Romuald
2001-10-01
This paper presents the mutual time - marching method to predict the aeroelastic stability of an oscillating blade row in 3D transonic flow. The ideal gas flow through a blade row is governed by the time dependent Euler equations in conservative form which are integrated by using the explicit monotonous second order accurate Godunov-Kolgan finite volume scheme and moving hybrid H-O grid. The structure analysis uses the modal approach and 3D finite element dynamic model of blade. The blade movement is assumed as a linear combination of the first modes of blade natural oscillations with the modal coefficients depending on time. To demonstrate the capability and correctness of the method, two experimentally investigated test cases have been selected, in which the blades had performed tuned harmonic bending or torsional vibrations (The 1st and 4th standard configurations of the “Workshop on Aeroelasticity in Turbomachines” by Bolcs and Fransson, 1986). The calculated results of aeroelastic behaviour of the blade row (4th standard configuration), are presented over a wide frequency range under different start regimes of interblade phase angle.
Fluid flow pathways study from the 3D seismic data offshore southwestern Taiwan
NASA Astrophysics Data System (ADS)
Chen, L.; Chi, W. C.; Chiang, H. T.; Lin, S.
2014-12-01
3D seismic reflection data provide detailed information on the physical properties of the crust, which can be used for hydrocarbon exploration. Recently, scientists from Taiwan and Germany are collaborating on a project to use a portable 3D seismic system, called P-Cable, to study gas hydrates offshore southwest Taiwan. We have collected 3 cubes, covering the active and passive margins. At these three sites, there is a wide-spread bottom-simulating reflector (BSR). We use the BSR to study the shallow thermal structures of these prospect sites, and use the temperature field information to study fluid migration patterns. We have also done in-situ heat flow measurements, and found similar results, showing focused fluid flow migrations in some pathways. Some of the high temperature fields also correlate with gas chimneys found through seismic attribute analyses. Preliminary results show that there might be active fluid migration above the BSR in the gas hydrate stability zone. In September and October of 2014, we will collect additional P-Cable datasets to be incorporated into this study. Such results will be used to evaluate some proposed sites for future drilling programs.
Brightness-compensated 3-D optical flow algorithm for monitoring cochlear motion patterns
NASA Astrophysics Data System (ADS)
von Tiedemann, Miriam; Fridberger, Anders; Ulfendahl, Mats; de Monvel, Jacques Boutet
2010-09-01
A method for three-dimensional motion analysis designed for live cell imaging by fluorescence confocal microscopy is described. The approach is based on optical flow computation and takes into account brightness variations in the image scene that are not due to motion, such as photobleaching or fluorescence variations that may reflect changes in cellular physiology. The 3-D optical flow algorithm allowed almost perfect motion estimation on noise-free artificial sequences, and performed with a relative error of <10% on noisy images typical of real experiments. The method was applied to a series of 3-D confocal image stacks from an in vitro preparation of the guinea pig cochlea. The complex motions caused by slow pressure changes in the cochlear compartments were quantified. At the surface of the hearing organ, the largest motion component was the transverse one (normal to the surface), but significant radial and longitudinal displacements were also present. The outer hair cell displayed larger radial motion at their basolateral membrane than at their apical surface. These movements reflect mechanical interactions between different cellular structures, which may be important for communicating sound-evoked vibrations to the sensory cells. A better understanding of these interactions is important for testing realistic models of cochlear mechanics.
Reacting Multi-Species Gas Capability for USM3D Flow Solver
NASA Technical Reports Server (NTRS)
Frink, Neal T.; Schuster, David M.
2012-01-01
The USM3D Navier-Stokes flow solver contributed heavily to the NASA Constellation Project (CxP) as a highly productive computational tool for generating the aerodynamic databases for the Ares I and V launch vehicles and Orion launch abort vehicle (LAV). USM3D is currently limited to ideal-gas flows, which are not adequate for modeling the chemistry or temperature effects of hot-gas jet flows. This task was initiated to create an efficient implementation of multi-species gas and equilibrium chemistry into the USM3D code to improve its predictive capabilities for hot jet impingement effects. The goal of this NASA Engineering and Safety Center (NESC) assessment was to implement and validate a simulation capability to handle real-gas effects in the USM3D code. This document contains the outcome of the NESC assessment.
ODTLES : a model for 3D turbulent flow based on one-dimensional turbulence modeling concepts.
McDermott, Randy; Kerstein, Alan R.; Schmidt, Rodney Cannon
2005-01-01
This report describes an approach for extending the one-dimensional turbulence (ODT) model of Kerstein [6] to treat turbulent flow in three-dimensional (3D) domains. This model, here called ODTLES, can also be viewed as a new LES model. In ODTLES, 3D aspects of the flow are captured by embedding three, mutually orthogonal, one-dimensional ODT domain arrays within a coarser 3D mesh. The ODTLES model is obtained by developing a consistent approach for dynamically coupling the different ODT line sets to each other and to the large scale processes that are resolved on the 3D mesh. The model is implemented computationally and its performance is tested and evaluated by performing simulations of decaying isotropic turbulence, a standard turbulent flow benchmarking problem.
Strategies for Effectively Visualizing a 3D Flow Using Volume Line Integral Convolution
NASA Technical Reports Server (NTRS)
Interrante, Victoria; Grosch, Chester
1997-01-01
This paper discusses strategies for effectively portraying 3D flow using volume line integral convolution. Issues include defining an appropriate input texture, clarifying the distinct identities and relative depths of the advected texture elements, and selectively highlighting regions of interest in both the input and output volumes. Apart from offering insights into the greater potential of 3D LIC as a method for effectively representing flow in a volume, a principal contribution of this work is the suggestion of a technique for generating and rendering 3D visibility-impeding 'halos' that can help to intuitively indicate the presence of depth discontinuities between contiguous elements in a projection and thereby clarify the 3D spatial organization of elements in the flow. The proposed techniques are applied to the visualization of a hot, supersonic, laminar jet exiting into a colder, subsonic coflow.
3D Soil Images Structure Quantification using Relative Entropy
NASA Astrophysics Data System (ADS)
Tarquis, A. M.; Gonzalez-Nieto, P. L.; Bird, N. R. A.
2012-04-01
Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice-Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.
A 3D velocimetry study of the flow through prosthetic heart valves
NASA Astrophysics Data System (ADS)
Ledesma, R.; Zenit, R.; Pulos, G.; Sanchez, E.; Juarez, A.
2006-11-01
Blood damage commonly appears in medical valve prothesis. It is a mayor concern for the designers and surgeons. It is well known that this damage and other complications result from the modified fluid dynamics through the replacement valve. To evaluate the performance of prosthetic heart valves, it is necessary to study the flow through them. To conduct this study , we have built a flow channel that emulates cardiac conditions and allows optical access such that a 3D-PIV velocimetry system could be used. The experiments are aimed to reconstruct the downstream structure of the flow through a mechanical and a bio-material tricuspid heart valve prothesis. Preliminary results show that the observed coherent structures can be related with haemolysis and trombosis, illnesses commonly found in valve prothesis recipients. The mean flow, the levels of strain rate and the turbulence intensity generated by the valves can also be directly related to blood damage. In general, bio-material made valves tend to reduce these complications.
NASA Astrophysics Data System (ADS)
Matsakos, T.; Chièze, J.-P.; Stehlé, C.; González, M.; Ibgui, L.; de Sá, L.; Lanz, T.; Orlando, S.; Bonito, R.; Argiroffi, C.; Reale, F.; Peres, G.
2014-08-01
The structure and dynamics of young stellar object (YSO) accretion shocks depend strongly on the local magnetic field strength and configuration, as well as on the radiative transfer effects responsible for the energy losses. We present the first 3D YSO shock simulations of the interior of the stream, assuming a uniform background magnetic field, a clumpy infalling gas, and an acoustic energy flux flowing at the base of the chromosphere. We study the dynamical evolution and the post-shock structure as a function of the plasma-beta (thermal pressure over magnetic pressure). We find that a strong magnetic field (~hundreds of Gauss) leads to the formation of fibrils in the shocked gas due to the plasma confinement within flux tubes. The corresponding emission is smooth and fully distinguishable from the case of a weak magnetic field (~tenths of Gauss) where the hot slab demonstrates chaotic motion and oscillates periodically.
Three-dimensional potential flows from functions of a 3D complex variable
NASA Technical Reports Server (NTRS)
Kelly, Patrick; Panton, Ronald L.; Martin, E. D.
1990-01-01
Potential, or ideal, flow velocities can be found from the gradient of an harmonic function. An ordinary complex valued analytic function can be written as the sum of two real valued functions, both of which are harmonic. Thus, 2D complex valued functions serve as a source of functions that describe two-dimensional potential flows. However, this use of complex variables has been limited to two-dimensions. Recently, a new system of three-dimensional complex variables has been developed at the NASA Ames Research Center. As a step toward application of this theory to the analysis of 3D potential flow, several functions of a three-dimensional complex variable have been investigated. The results for two such functions, the 3D exponential and 3D logarithm, are presented in this paper. Potential flows found from these functions are investigated. Important characteristics of these flows fields are noted.
NASA Astrophysics Data System (ADS)
Leigh, S. J.; Purssell, C. P.; Billson, D. R.; Hutchins, D. A.
2014-09-01
Flow sensing is an essential technique required for a wide range of application environments ranging from liquid dispensing to utility monitoring. A number of different methodologies and deployment strategies have been devised to cover the diverse range of potential application areas. The ability to easily create new bespoke sensors for new applications is therefore of natural interest. Fused deposition modelling is a 3D printing technology based upon the fabrication of 3D structures in a layer-by-layer fashion using extruded strands of molten thermoplastic. The technology was developed in the late 1980s but has only recently come to more wide-scale attention outside of specialist applications and rapid prototyping due to the advent of low-cost 3D printing platforms such as the RepRap. Due to the relatively low-cost of the printers and feedstock materials, these printers are ideal candidates for wide-scale installation as localized manufacturing platforms to quickly produce replacement parts when components fail. One of the current limitations with the technology is the availability of functional printing materials to facilitate production of complex functional 3D objects and devices beyond mere concept prototypes. This paper presents the formulation of a simple magnetite nanoparticle-loaded thermoplastic composite and its incorporation into a 3D printed flow-sensor in order to mimic the function of a commercially available flow-sensing device. Using the multi-material printing capability of the 3D printer allows a much smaller amount of functional material to be used in comparison to the commercial flow sensor by only placing the material where it is specifically required. Analysis of the printed sensor also revealed a much more linear response to increasing flow rate of water showing that 3D printed devices have the potential to at least perform as well as a conventionally produced sensor.
A 3-D implicit finite-volume model of shallow water flows
NASA Astrophysics Data System (ADS)
Wu, Weiming; Lin, Qianru
2015-09-01
A three-dimensional (3-D) model has been developed to simulate shallow water flows in large water bodies, such as coastal and estuarine waters. The eddy viscosity is determined using a newly modified mixing length model that uses different mixing length functions for the horizontal and vertical shear strain rates. The 3-D shallow water flow equations with the hydrostatic pressure assumption are solved using an implicit finite-volume method based on a quadtree (telescoping) rectangular mesh on the horizontal plane and the sigma coordinate in the vertical direction. The quadtree technique can locally refine the mesh around structures or in high-gradient regions by splitting a coarse cell into four child cells. The grid nodes are numbered with a one-dimensional index system that has unstructured grid feature for better grid flexibility. All the primary variables are arranged in a non-staggered grid system. Fluxes at cell faces are determined using a Rhie and Chow-type momentum interpolation, to avoid the possible spurious checkerboard oscillations caused by linear interpolation. Each of the discretized governing equations is solved iteratively using the flexible GMRES method with ILUT preconditioning, and coupling of water level and velocity among these equations is achieved by using the SIMPLEC algorithm with under-relaxation. The model has been tested in four cases, including steady flow near a spur-dyke, tidal flows in San Francisco Bay and Gironde Estuary, and wind-induced current in a flume. The calculated water levels and velocities are in good agreement with the measured values.
Potential for 3-D hyporheic exchange flow along a succession of pool-riffle sequences
NASA Astrophysics Data System (ADS)
Käser, Daniel; Binley, Andrew; Krause, Stefan; Heathwaite, Louise
2010-05-01
Pool-riffle sequences are key geomorphological features that can influence the ecology of streams by inducing a flow exchange between surface water and groundwater - a process called hyporheic exchange flow (HEF). The objective of this research was to test the suitability of a simple 3-D groundwater model for characterizing HEF induced by pool-riffle sequences that had been the focus of experimental study. Three reaches of 20 m were modelled separately. While the bed topography was surveyed and represented at a high resolution, the permeability distribution referred to a simple conceptual model consisting of two superposed layers. One hypothesis was that, despite its simplicity, the calibrated model would produce an acceptable fit between observed and simulated heads because its permeability structure resembled the natural system. The potential complexity of hyporheic flow patterns is well-known, yet this study highlights the usefulness of a simple conceptual model coupled to mechanistic flow equations for describing HEF in 3-D. The error structure of the calibrated model provides insight into various site-specific features. The root mean square error between computed and observed hydraulic heads (relative to the head drop over the structure) is comparable to other studies with more elaborate permeability structures. After calibration, a sensitivity analysis was conducted in order to determine the influence of permeability contrast between the layers, depth of the permeability interface, and basal flux on three HEF characteristics: residence time, lateral and vertical extent, and total flux. Results indicate that permeability characteristics can affect HEF in different ways. For example, the vertical extent is deepest in homogeneous conditions, whereas the lateral extent is not significantly affected by permeability contrast, or by the depth of the interface between the two layers. Thus bank piezometers may be insufficient to calibrate groundwater models of HEF
3D-printed devices for continuous-flow organic chemistry
Dragone, Vincenza; Sans, Victor; Rosnes, Mali H; Kitson, Philip J
2013-01-01
Summary We present a study in which the versatility of 3D-printing is combined with the processing advantages of flow chemistry for the synthesis of organic compounds. Robust and inexpensive 3D-printed reactionware devices are easily connected using standard fittings resulting in complex, custom-made flow systems, including multiple reactors in a series with in-line, real-time analysis using an ATR-IR flow cell. As a proof of concept, we utilized two types of organic reactions, imine syntheses and imine reductions, to show how different reactor configurations and substrates give different products. PMID:23766811
Inverse cascades sustained by the transfer rate of angular momentum in a 3D turbulent flow.
López-Caballero, Miguel; Burguete, Javier
2013-03-22
The existence of energy cascades as signatures of conserved magnitudes is one of the universal characteristics of turbulent flows. In homogeneous 3D turbulence, the energy conservation produces a direct cascade from large to small scales, although in 2D, it produces an inverse cascade pointing towards small wave numbers. In this Letter, we present the first evidence of an inverse cascade in a fully developed 3D experimental turbulent flow where the conserved magnitude is the angular momentum. Two counterrotating flows collide in a central region where very large fluctuations are produced, generating a turbulent drag that transfers the external torque between different fluid layers. PMID:25166809
Model studies of blood flow in basilar artery with 3D laser Doppler anemometer
NASA Astrophysics Data System (ADS)
Frolov, S. V.; Sindeev, S. V.; Liepsch, D.; Balasso, A.; Proskurin, S. G.; Potlov, A. Y.
2015-03-01
It is proposed an integrated approach to the study of basilar artery blood flow using 3D laser Doppler anemometer for identifying the causes of the formation and development of cerebral aneurysms. Feature of the work is the combined usage of both mathematical modeling and experimental methods. Described the experimental setup and the method of measurement of basilar artery blood flow, carried out in an interdisciplinary laboratory of Hospital Rechts der Isar of Technical University of Munich. The experimental setup used to simulate the blood flow in the basilar artery and to measure blood flow characteristics using 3D laser Doppler anemometer (3D LDA). Described a method of numerical studies carried out in Tambov State Technical University and the Bakoulev Center for Cardiovascular Surgery. Proposed an approach for sharing experimental and numerical methods of research to identify the causes of the basilar artery aneurysms.
3D vector flow using a row-column addressed CMUT array
NASA Astrophysics Data System (ADS)
Holbek, Simon; Christiansen, Thomas Lehrmann; Engholm, Mathias; Lei, Anders; Stuart, Mathias Bo; Beers, Christopher; Moesner, Lars Nordahl; Bagge, Jan Peter; Thomsen, Erik Vilain; Jensen, Jørgen Arendt
2016-04-01
This paper presents an in-house developed 2-D capacitive micromachined ultrasonic transducer (CMUT) applied for 3-D blood flow estimation. The probe breaks with conventional transducers in two ways; first, the ultrasonic pressure field is generated from thousands of small vibrating micromachined cells, and second, elements are accessed by row and/or column indices. The 62+62 2-D row-column addressed prototype CMUT probe was used for vector flow estimation by transmitting focused ultrasound into a flow-rig with a fully developed parabolic flow. The beam-to-flow angle was 90°. The received data was beamformed and processed offline. A transverse oscillation (TO) velocity estimator was used to estimate the 3-D vector flow along a line originating from the center of the transducer. The estimated velocities in the lateral and axial direction were close to zero as expected. In the transverse direction a characteristic parabolic velocity profile was estimated with a peak velocity of 0.48 m/s +/- 0.02 m/s in reference to the expected 0.54 m/s. The results presented are the first 3-D vector flow estimates obtained with a row-column CMUT probe, which demonstrates that the CMUT technology is feasible for 3-D flow estimation.
The performance & flow visualization studies of three-dimensional (3-D) wind turbine blade models
NASA Astrophysics Data System (ADS)
Sutrisno, Prajitno, Purnomo, W., Setyawan B.
2016-06-01
Recently, studies on the design of 3-D wind turbine blades have a less attention even though 3-D blade products are widely sold. In contrary, advanced studies in 3-D helicopter blade tip have been studied rigorously. Studies in wind turbine blade modeling are mostly assumed that blade spanwise sections behave as independent two-dimensional airfoils, implying that there is no exchange of momentum in the spanwise direction. Moreover, flow visualization experiments are infrequently conducted. Therefore, a modeling study of wind turbine blade with visualization experiment is needed to be improved to obtain a better understanding. The purpose of this study is to investigate the performance of 3-D wind turbine blade models with backward-forward swept and verify the flow patterns using flow visualization. In this research, the blade models are constructed based on the twist and chord distributions following Schmitz's formula. Forward and backward swept are added to the rotating blades. Based on this, the additional swept would enhance or diminish outward flow disturbance or stall development propagation on the spanwise blade surfaces to give better blade design. Some combinations, i. e., b lades with backward swept, provide a better 3-D favorable rotational force of the rotor system. The performance of the 3-D wind turbine system model is measured by a torque meter, employing Prony's braking system. Furthermore, the 3-D flow patterns around the rotating blade models are investigated by applying "tuft-visualization technique", to study the appearance of laminar, separated, and boundary layer flow patterns surrounding the 3-dimentional blade system.
Simulation of a Synthetic Jet in Quiescent Air Using TLNS3D Flow Code
NASA Technical Reports Server (NTRS)
Vatsa, Veer N.; Turkel, Eli
2007-01-01
Although the actuator geometry is highly three-dimensional, the outer flowfield is nominally two-dimensional because of the high aspect ratio of the rectangular slot. For the present study, this configuration is modeled as a two-dimensional problem. A multi-block structured grid available at the CFDVAL2004 website is used as a baseline grid. The periodic motion of the diaphragm is simulated by specifying a sinusoidal velocity at the diaphragm surface with a frequency of 450 Hz, corresponding to the experimental setup. The amplitude is chosen so that the maximum Mach number at the jet exit is approximately 0.1, to replicate the experimental conditions. At the solid walls zero slip, zero injection, adiabatic temperature and zero pressure gradient conditions are imposed. In the external region, symmetry conditions are imposed on the side (vertical) boundaries and far-field conditions are imposed on the top boundary. A nominal free-stream Mach number of 0.001 is imposed in the free stream to simulate incompressible flow conditions in the TLNS3D code, which solves compressible flow equations. The code was run in unsteady (URANS) mode until the periodicity was established. The time-mean quantities were obtained by running the code for at least another 15 periods and averaging the flow quantities over these periods. The phase-locked average of flow quantities were assumed to be coincident with their values during the last full time period.
Flow properties along field lines in a 3-D tilted-dipole geometry
NASA Technical Reports Server (NTRS)
Pizzo, V. J.
1995-01-01
A 3-D MHD simulation of a global, tilted-dipole solar wind flow pattern is analyzed to determine flow properties along individual magnetic field lines. In the model, flow conditions near the Sun are chosen to provide a reasonable match to the interplanetary configuration prevailing during the recent south polar passage by Ulysses, i.e., a streamer belt inclined approximately 30 deg to the solar equator and speeds ranging from 325-800 km/s. Field lines all across the stream pattern are traced from 1 to 10 AU by following the motion of marker particles embedded in the flow. It is found that those field lines threading the core of the interaction region are subject to significant latitudinal and relative longitudinal displacement over this range of heliocentric distance. Thus, observations taken at a fixed latitude in the inner solar system sample, over the course of a solar rotation, field lines which connect to a range of latitudes in the outer heliosphere. Maps of the field line displacements are presented to help visualize these connections. In addition, it is found that depending upon the location relative to the CIR structure, the radial evolution of fluid elements frozen to different field lines can deviate considerably from that of the canonical solar wind. That is, for selected subsets of field lines, large speed changes (not just at shocks) can be experienced; the density variation can be far from 1/r(exp 2), and the magnetic field intensity need not decay monotonically with distance.
Progress Toward Overset-Grid Moving Body Capability for USM3D Unstructured Flow Solver
NASA Technical Reports Server (NTRS)
Pandyna, Mohagna J.; Frink, Neal T.; Noack, Ralph W.
2005-01-01
A static and dynamic Chimera overset-grid capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. Modifications to the solver primarily consist of a few strategic calls to the Donor interpolation Receptor Transaction library (DiRTlib) to facilitate communication of solution information between various grids. The assembly of multiple overlapping grids into a single-zone composite grid is performed by the Structured, Unstructured and Generalized Grid AssembleR (SUGGAR) code. Several test cases are presented to verify the implementation, assess overset-grid solution accuracy and convergence relative to single-grid solutions, and demonstrate the prescribed relative grid motion capability.
Generation of 3D Spatially Variable Anisotropy for Groundwater Flow Simulations.
Borghi, Andrea; Renard, Philippe; Courrioux, Gabriel
2015-01-01
Sedimentary units generally present anisotropy in their hydraulic properties, with higher hydraulic conductivity along bedding planes, rather than perpendicular to them. This common property leads to a modeling challenge if the sedimentary structure is folded. In this paper, we show that the gradient of the geological potential used by implicit geological modeling techniques can be used to compute full hydraulic conductivity tensors varying in space according to the geological orientation. For that purpose, the gradient of the potential, a vector normal to the bedding, is used to construct a rotation matrix that allows the estimation of the 3D hydraulic conductivity tensor in a single matrix operation. A synthetic 2D cross section example is used to illustrate the method and show that flow simulations performed in such a folded environment are highly influenced by this rotating anisotropy. When using the proposed method, the streamlines follow very closely the folded formation. This is not the case with an isotropic model. PMID:25648610
NASA Astrophysics Data System (ADS)
Yang, L. M.; Shu, C.; Wang, Y.; Sun, Y.
2016-08-01
The sphere function-based gas kinetic scheme (GKS), which was presented by Shu and his coworkers [23] for simulation of inviscid compressible flows, is extended to simulate 3D viscous incompressible and compressible flows in this work. Firstly, we use certain discrete points to represent the spherical surface in the phase velocity space. Then, integrals along the spherical surface for conservation forms of moments, which are needed to recover 3D Navier-Stokes equations, are approximated by integral quadrature. The basic requirement is that these conservation forms of moments can be exactly satisfied by weighted summation of distribution functions at discrete points. It was found that the integral quadrature by eight discrete points on the spherical surface, which forms the D3Q8 discrete velocity model, can exactly match the integral. In this way, the conservative variables and numerical fluxes can be computed by weighted summation of distribution functions at eight discrete points. That is, the application of complicated formulations resultant from integrals can be replaced by a simple solution process. Several numerical examples including laminar flat plate boundary layer, 3D lid-driven cavity flow, steady flow through a 90° bending square duct, transonic flow around DPW-W1 wing and supersonic flow around NACA0012 airfoil are chosen to validate the proposed scheme. Numerical results demonstrate that the present scheme can provide reasonable numerical results for 3D viscous flows.
Postprocessing techniques for 3D non-linear structures
NASA Technical Reports Server (NTRS)
Gallagher, Richard S.
1987-01-01
How graphics postprocessing techniques are currently used to examine the results of 3-D nonlinear analyses, some new techniques which take advantage of recent technology, and how these results relate to both the finite element model and its geometric parent are reviewed.
Arbitrary and Parallel Nanofabrication of 3D Metal Structures with Polymer Brush Resists.
Chen, Chaojian; Xie, Zhuang; Wei, Xiaoling; Zheng, Zijian
2015-12-01
3D polymer brushes are reported for the first time as ideal resists for the alignment-free nanofabrication of complex 3D metal structures with sub-100 nm lateral resolution and sub-10 nm vertical resolution. Since 3D polymer brushes can be serially fabricated in parallel, this method is effective to generate arbitrary 3D metal structures over a large area at a high throughput. PMID:26439441
Implementation of Advanced Two Equation Turbulence Models in the USM3D Unstructured Flow Solver
NASA Technical Reports Server (NTRS)
Wang, Qun-Zhen; Massey, Steven J.; Abdol-Hamid, Khaled S.
2000-01-01
USM3D is a widely-used unstructured flow solver for simulating inviscid and viscous flows over complex geometries. The current version (version 5.0) of USM3D, however, does not have advanced turbulence models to accurately simulate complicated flow. We have implemented two modified versions of the original Jones and Launder k-epsilon "two-equation" turbulence model and the Girimaji algebraic Reynolds stress model in USM3D. Tests have been conducted for three flat plate boundary layer cases, a RAE2822 airfoil and an ONERA M6 wing. The results are compared with those from direct numerical simulation, empirical formulae, theoretical results, and the existing Spalart-Allmaras one-equation model.
A 3D moisture-stress FEM analysis for time dependent problems in timber structures
NASA Astrophysics Data System (ADS)
Fortino, Stefania; Mirianon, Florian; Toratti, Tomi
2009-11-01
This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.
3D Structured Grid Generation Codes for Turbomachinery
NASA Technical Reports Server (NTRS)
Loellbach, James; Tsung, Fu-Lin
1999-01-01
This report describes the research tasks during the past year. The research was mainly in the area of computational grid generation in support of CFD analyses of turbomachinery components. In addition to the grid generation work, a numerical simulation was obtained for the flow through a centrifugal gas compressor using an unstructured Navier-Stokes solver. Other tasks involved many different turbomachinery component analyses. These analyses were performed for NASA projects or for industrial applications. The work includes both centrifugal and axial machines, single and multiple blade rows, and steady and unsteady analyses. Over the past five years, a set of structured grid generation codes were developed that allow grids to be obtained fairly quickly for the large majority of configurations we encounter. These codes do not comprise a generalized grid generation package; they are noninteractive codes specifically designed for turbomachinery blade row geometries. But because of this limited scope, the codes are small, fast, and portable, and they can be run in the batch mode on small workstations. During the past year, these programs were used to generate computational grids were modified for a wide variety of configurations. In particular, the codes or wrote supplementary codes to improve our grid generation capabilities for multiple blade row configurations. This involves generating separate grids for each blade row, and then making them match and overlap by a few grid points at their common interface so that fluid properties are communicated across the interface. Unsteady rotor/stator analyses were performed for an axial turbine, a centrifugal compressor, and a centrifugal pump. Steady-state single-blade-row analyses were made for a study of blade sweep in transonic compressors. There was also cooperation on the application of an unstructured Navier-Stokes solver for turbomachinery flow simulations. In particular, the unstructured solver was used to analyze the
Designing self-assembling 3D structures of microcapsules
NASA Astrophysics Data System (ADS)
Li, Like; Shum, Henry; Shklyaev, Oleg; Yashin, Victor; Balazs, Anna
Self-assembly of complex, three-dimensional structures is commonly achieved by biological cells but difficult to realize in synthetic systems with micron-scale or larger components. Some previous modeling studies have considered only the planar self-assembly of microcapsules on a substrate. In this work, nanoparticles released from the capsules bind to the substrate and to the shells of nearby capsules. The non-uniform nanoparticle deposition on a capsule's surface leads to adhesion gradients, which drive the capsules to effectively ``climb'' on top of one another and self-organize in the vertical direction. We determine conditions that favor this structural organization. In particular, we study how the vertical structuring depends on the background fluid flow, the topography of the microcapsules and the underlying surface, the capsule-capsule interaction and that between the capsules and the substrate. The findings can provide design rules for the autonomous creation of novel nanocomposites, where the layers are formed from nanoparticle-containing and nanoparticle-decorated microcapsules.
NASA Astrophysics Data System (ADS)
Kim, Jong Young; Park, Jung Kyu; Hahn, Sei Kwang; Kwon, Tai Hun; Cho, Dong-Woo
2009-10-01
The flow behavior model for 3D scaffold fabrication in the polymer deposition process by the heating method was developed for enhanced efficiency of the deposition process. The analysis of the polymer flow property is very important in the fabrication process of precise micro-structures such as scaffolds. In this study, a deposition model considering fluid mechanics and heat transfer phenomena was built up and introduced for the estimation of the fluid behavior of molten polymer. The effectiveness of the simulation model was verified through comparison with the experimental result in the case of PCL biomaterial. In addition, the effects of various parameters, such as pressure, temperature and nozzle size, were predicted through simulation before experimental approaches. Through the fabrication of 3D scaffold, it is concluded that this model is useful in predicting the flow behavior characteristics in the micro-structure fabrication process, which is based on the heating method.
High fidelity digital inline holographic method for 3D flow measurements.
Toloui, Mostafa; Hong, Jiarong
2015-10-19
Among all the 3D optical flow diagnostic techniques, digital inline holographic particle tracking velocimetry (DIH-PTV) provides the highest spatial resolution with low cost, simple and compact optical setups. Despite these advantages, DIH-PTV suffers from major limitations including poor longitudinal resolution, human intervention (i.e. requirement for manually determined tuning parameters during tracer field reconstruction and extraction), limited tracer concentration, and expensive computations. These limitations prevent this technique from being widely used for high resolution 3D flow measurements. In this study, we present a novel holographic particle extraction method with the goal of overcoming all the major limitations of DIH-PTV. The proposed method consists of multiple steps involving 3D deconvolution, automatic signal-to-noise ratio enhancement and thresholding, and inverse iterative particle extraction. The entire method is implemented using GPU-based algorithm to increase the computational speed significantly. Validated with synthetic particle holograms, the proposed method can achieve particle extraction rate above 95% with fake particles less than 3% and maximum position error below 1.6 particle diameter for holograms with particle concentration above 3000 particles/mm^{3}. The applicability of the proposed method for DIH-PTV has been further validated using the experiment of laminar flow in a microchannel and the synthetic tracer flow fields generated using a DNS turbulent channel flow database. Such improvements will substantially enhance the implementation of DIH-PTV for 3D flow measurements and enable the potential commercialization of this technique. PMID:26480377
Time-lapse 3-D seismic imaging of shallow subsurface contaminant flow.
McKenna, J; Sherlock, D; Evans, B
2001-12-01
This paper presents a physical modelling study outlining a technique whereby buoyant contaminant flow within water-saturated unconsolidated sand was remotely monitored utilizing the time-lapse 3-D (TL3-D) seismic response. The controlled temperature and pressure conditions, along with the high level of acquisition repeatability attainable using sandbox physical models, allow the TL3-D seismic response to pore fluid movement to be distinguished from all other effects. TL3-D seismic techniques are currently being developed to monitor hydrocarbon reserves within producing reservoirs in an endeavour to improve overall recovery. However, in many ways, sandbox models under atmospheric conditions more accurately simulate the shallow subsurface than petroleum reservoirs. For this reason, perhaps the greatest application for analogue sandbox modelling is to improve our understanding of shallow groundwater and environmental flow mechanisms. Two fluid flow simulations were conducted whereby air and kerosene were injected into separate water-saturated unconsolidated sand models. In both experiments, a base 3-D seismic volume was recorded and compared with six later monitor surveys recorded while the injection program was conducted. Normal incidence amplitude and P-wave velocity information were extracted from the TL3-D seismic data to provide visualization of contaminant migration. Reflection amplitudes displayed qualitative areal distribution of fluids when a suitable impedance contrast existed between pore fluids. TL3-D seismic reflection tomography can potentially monitor the change in areal distribution of fluid contaminants over time, indicating flow patterns. However, other research and this current work have not established a quantifiable relationship between either normal reflection amplitudes and attenuation and fluid saturation. Generally, different pore fluids will have unique seismic velocities due to differences in compressibility and density. The predictable
Ergodic theory and experimental visualization of chaos in 3D flows
NASA Astrophysics Data System (ADS)
Sotiropoulos, Fotis; Mezic, Igor
2000-11-01
In his motivation for the ergodic hypothesis Gibbs invoked an analogy with fluid mixing: “…Yet no fact is more familiar to us than that stirring tends to bring a liquid to a state of uniform mixture, or uniform densities of its components…”. Although proof of the ergodic hypothesis is possible only for the simplest of systems using methods from ergodic theory, the use of the hypothesis has led to many accurate predictions in statistical mechanics. The problem of fluid mixing, however, turned out to be considerably more complicated than Gibbs envisioned. Chaotic advection can indeed lead to efficient mixing even in non-turbulent flows, but many non-mixed islands are known to persist within well-mixed regions. In numerical studies, Poincaré maps can be used to reveal the structure of such islands but their visualization in the laboratory requires laborious experimental procedures and is possible only for certain types of flows. Here we propose the first non-intrusive, simple to implement, and generally applicable technique for constructing experimental Poincaré maps and apply it to a steady, 3D, vortex breakdown bubble. We employ standard laser-induced fluorescence (LIF) and construct Poincaré maps by time averaging a sufficiently long sequence of instantaneous LIF images. We also show that ergodic theory methods provide a rigorous theoretical justification for this approach whose main objective is to reveal the non-ergodic regions of the flow.
A moving mesh algorithm for 3-D regional groundwater flow with water table and seepage face
NASA Astrophysics Data System (ADS)
Knupp, P.
A numerical algorithm is described for solving the free-surface groundwater flow equations in 3-D large-scale unconfined aquifers with strongly heterogeneous conductivity and surface recharge. The algorithm uses a moving mesh to track the water-table as it evolves according to kinematic and seepage face boundary conditions. Both steady-state and transient algorithms are implemented in the SECO-Flow 3-D code and demonstrated on stratigraphy based on the Delaware Basin of south-eastern New Mexico.
Using flow information to support 3D vessel reconstruction from rotational angiography
Waechter, Irina; Bredno, Joerg; Weese, Juergen; Barratt, Dean C.; Hawkes, David J.
2008-07-15
For the assessment of cerebrovascular diseases, it is beneficial to obtain three-dimensional (3D) morphologic and hemodynamic information about the vessel system. Rotational angiography is routinely used to image the 3D vascular geometry and we have shown previously that rotational subtraction angiography has the potential to also give quantitative information about blood flow. Flow information can be determined when the angiographic sequence shows inflow and possibly outflow of contrast agent. However, a standard volume reconstruction assumes that the vessel tree is uniformly filled with contrast agent during the whole acquisition. If this is not the case, the reconstruction exhibits artifacts. Here, we show how flow information can be used to support the reconstruction of the 3D vessel centerline and radii in this case. Our method uses the fast marching algorithm to determine the order in which voxels are analyzed. For every voxel, the rotational time intensity curve (R-TIC) is determined from the image intensities at the projection points of the current voxel. Next, the bolus arrival time of the contrast agent at the voxel is estimated from the R-TIC. Then, a measure of the intensity and duration of the enhancement is determined, from which a speed value is calculated that steers the propagation of the fast marching algorithm. The results of the fast marching algorithm are used to determine the 3D centerline by backtracking. The 3D radius is reconstructed from 2D radius estimates on the projection images. The proposed method was tested on computer simulated rotational angiography sequences with systematically varied x-ray acquisition, blood flow, and contrast agent injection parameters and on datasets from an experimental setup using an anthropomorphic cerebrovascular phantom. For the computer simulation, the mean absolute error of the 3D centerline and 3D radius estimation was 0.42 and 0.25 mm, respectively. For the experimental datasets, the mean absolute
Real-time structured light intraoral 3D measurement pipeline
NASA Astrophysics Data System (ADS)
Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman
2013-02-01
Computer aided design and manufacturing (CAD/CAM) is increasingly becoming a standard feature and service provided to patients in dentist offices and denture manufacturing laboratories. Although the quality of the tools and data has slowly improved in the last years, due to various surface measurement challenges, practical, accurate, invivo, real-time 3D high quality data acquisition and processing still needs improving. Advances in GPU computational power have allowed for achieving near real-time 3D intraoral in-vivo scanning of patient's teeth. We explore in this paper, from a real-time perspective, a hardware-software-GPU solution that addresses all the requirements mentioned before. Moreover we exemplify and quantify the hard and soft deadlines required by such a system and illustrate how they are supported in our implementation.
3-D structure and dynamics of microtubule self-organization
NASA Astrophysics Data System (ADS)
Wang, Jing; Ou-Yang, H. Daniel
2008-03-01
Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.
3-D model of a radial flow sub-watt methanol fuel processor
Holladay, J. D.; Wang, Y.
2015-10-01
A 3-D model is presented for a novel sub-watt packed bed reactor. The reactor uses an annular inlet flow combined with a radial flow packed bed reactor. The baseline reactor is compared to a reactor with multiple outlets and a reactor with 3 internal fins. Increasing the outlets from 1 to 4 did improve the flow distribution, but did not increase the performance in the simulation. However, inserting fins allowed a decrease in temperature with same inlet flow of approximately 35K. Or the inlet flow rate could be increased by a factor of 2.8x while maintaining >99% conversion.
NASA Astrophysics Data System (ADS)
Wang, ChengYue; Gao, Qi; Wei, RunJie; Li, Tian; Wang, JinJun
2016-06-01
Volumetric measurement for the leading-edge vortex (LEV) breakdown of a delta wing has been conducted by three-dimensional (3D) flow visualization and tomographic particle image velocimetry (TPIV). The 3D flow visualization is employed to show the vortex structures, which was recorded by four cameras with high resolution. 3D dye streaklines of the visualization are reconstructed using a similar way of particle reconstruction in TPIV. Tomographic PIV is carried out at the same time using same cameras with the dye visualization. Q criterion is employed to identify the LEV. Results of tomographic PIV agree well with the reconstructed 3D dye streaklines, which proves the validity of the measurements. The time-averaged flow field based on TPIV is shown and described by sections of velocity and streamwise vorticity. Combining the two measurement methods sheds light on the complex structures of both bubble type and spiral type of breakdown. The breakdown position is recognized by investigating both the streaklines and TPIV velocity fields. Proper orthogonal decomposition is applied to extract a pair of conjugated helical instability modes from TPIV data. Therefore, the dominant frequency of the instability modes is obtained from the corresponding POD coefficients of the modes based on wavelet transform analysis.
Combination 3D TOP with 2D PC MRA Techique for cerebral blood flow volume measurement.
Guo, G; Wu, R H; Zhang, Y P; Guan, J T; Guo, Y L; Cheng, Y; terBrugge, K; Mikulis, D J
2006-01-01
To demonstrate the discrepancy of cerebral blood flow volume (BFV) estimation with 2D phase-contrast (2D PC) MRA guided with 3D time-of-flight (3D TOF) MR localization by using an "internal" standard. 20 groups of the common (CCA), internal (ICA), and external (ECA) carotid arteries in 10 healthy subjects were examined with 2D PC MRA guided by 3D TOF MR angiograms. The sum BFV of the internal and external carotid arteries was then compared with the ipsilateral common carotid artery flow. An accurate technique would demonstrate no difference. The difference was therefore a measure of accuracy of the method. 3D TOF MRA localization is presented to allow the determination of a slice orientation to improve the accuracy of 2D PC MRA in estimate the BFV. By using the combined protocols, there was better correlation in BFV estimate between the sum of ICA+ECA with the ipsilateral CCA (R2=0.729, P=0.000). The inconsistency (mean +/- SD) was found to be 6.95 +/- 5.95% for estimate the BFV in ICA+ECA and ipsilateral CCA. The main inconsistency was contributed to the ECA and its branches. Guided with 3D TOF MRA localization, 2D PC MRA is more accurate in the determination of blood flow volume in the carotid arteries. PMID:17946401
Numerical Optimization Strategy for Determining 3D Flow Fields in Microfluidics
NASA Astrophysics Data System (ADS)
Eden, Alex; Sigurdson, Marin; Mezic, Igor; Meinhart, Carl
2015-11-01
We present a hybrid experimental-numerical method for generating 3D flow fields from 2D PIV experimental data. An optimization algorithm is applied to a theory-based simulation of an alternating current electrothermal (ACET) micromixer in conjunction with 2D PIV data to generate an improved representation of 3D steady state flow conditions. These results can be used to investigate mixing phenomena. Experimental conditions were simulated using COMSOL Multiphysics to solve the temperature and velocity fields, as well as the quasi-static electric fields. The governing equations were based on a theoretical model for ac electrothermal flows. A Nelder-Mead optimization algorithm was used to achieve a better fit by minimizing the error between 2D PIV experimental velocity data and numerical simulation results at the measurement plane. By applying this hybrid method, the normalized RMS velocity error between the simulation and experimental results was reduced by more than an order of magnitude. The optimization algorithm altered 3D fluid circulation patterns considerably, providing a more accurate representation of the 3D experimental flow field. This method can be generalized to a wide variety of flow problems. This research was supported by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office.
3D positional tracking of ellipsoidal particles in a microtube flow using holographic microscopy
NASA Astrophysics Data System (ADS)
Byeon, Hyeok Jun; Seo, Kyung Won; Lee, Sang Joon
2014-11-01
Understanding of micro-scale flow phenomena is getting large attention under advances in micro-scale measurement technologies. Especially, the dynamics of particles suspended in a fluid is essential in both scientific and industrial fields. Moreover, most particles handled in research and industrial fields have non-spherical shapes rather than a simple spherical shape. Under various flow conditions, these non-spherical particles exhibit unique dynamic behaviors. To analyze these dynamic behaviors in a fluid flow, 3D positional information of the particles should be measured accurately. In this study, digital holographic microscopy (DHM) is employed to measure the 3D positional information of non-spherical particles, which are fabricated by stretching spherical polystyrene particles. 3D motions of those particles are obtained by interpreting the holograms captured from particles. Ellipsoidal particles with known size and shape are observed to verify the performance of the DHM technique. In addition, 3D positions of particles in a microtube flow are traced. This DHM technique exhibits promising potential in the analysis of dynamic behaviors of non-spherical particles suspended in micro-scale fluid flows.
One-layer microfluidic device for hydrodynamic 3D self-flow-focusing operating in low flow speed
NASA Astrophysics Data System (ADS)
Daghighi, Yasaman; Gnyawali, Vaskar; Strohm, Eric M.; Tsai, Scott S. H.; Kolios, Michael C.
2016-03-01
Hydrodynamic 3D flow-focusing techniques in microfluidics are categorized as (a) sheathless techniques which require high flow rates and long channels, resulting in high operating cost and high flow rates which are inappropriate for applications with flow rate limitations, and (b) sheath-flow based techniques which usually require excessive sheath flow rate to achieve hydrodynamic 3D flow-focusing. Many devices based on these principles use complicated fabrication methods to create multi-layer microchannels. We have developed a sheath-flow based microfluidic device that is capable of hydrodynamic 3D self-flow-focusing. In this device the main flow (black ink) in a low speed, and a sheath flow, enter through two inlets and enter a 180 degree curved channel (300 × 300 μm cross-section). Main flow migrates outwards into the sheath-flow due to centrifugal effects and consequently, vertical focusing is achieved at the end of the curved channel. Then, two other sheath flows horizontally confine the main flow to achieve horizontal focusing. Thus, the core flow is three-dimensionally focused at the center of the channel at the downstream. Using centrifugal force for 3D flow-focusing in a single-layer fabricated microchannel has been previously investigated by few groups. However, their demonstrated designs required high flow speed (>1 m/s) which is not suitable for many applications that live biomedical specie are involved. Here, we introduce a new design which is operational in low flow speed (<0.05 m/s) and is suitable for applications involving live cells. This microfluidic device can be used in detecting, counting and isolating cells in many biomedical applications.
Reconstruction of 3D structure using stochastic methods: morphology and transport properties
NASA Astrophysics Data System (ADS)
Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena
2013-04-01
One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
Pei, Jimin; Tang, Ming; Grishin, Nick V
2008-07-01
Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087
Simultaneous Aerodynamic and Structural Design Optimization (SASDO) for a 3-D Wing
NASA Technical Reports Server (NTRS)
Gumbert, Clyde R.; Hou, Gene J.-W.; Newman, Perry A.
2001-01-01
The formulation and implementation of an optimization method called Simultaneous Aerodynamic and Structural Design Optimization (SASDO) is shown as an extension of the Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) method. It is extended by the inclusion of structure element sizing parameters as design variables and Finite Element Method (FEM) analysis responses as constraints. The method aims to reduce the computational expense. incurred in performing shape and sizing optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, FEM structural analysis and sensitivity analysis tools. SASDO is applied to a simple. isolated, 3-D wing in inviscid flow. Results show that the method finds the saine local optimum as a conventional optimization method with some reduction in the computational cost and without significant modifications; to the analysis tools.
Grinberg, L; Cheever, E; Anor, T; Madsen, J R; Karniadakis, G E
2011-01-01
We compare results from numerical simulations of pulsatile blood flow in two patient-specific intracranial arterial networks using one-dimensional (1D) and three-dimensional (3D) models. Specifically, we focus on the pressure and flowrate distribution at different segments of the network computed by the two models. Results obtained with 1D and 3D models with rigid walls show good agreement in massflow distribution at tens of arterial junctions and also in pressure drop along the arteries. The 3D simulations with the rigid walls predict higher amplitude of the flowrate and pressure temporal oscillations than the 1D simulations with compliant walls at various segments even for small time-variations in the arterial cross-sectional areas. Sensitivity of the flow and pressure with respect to variation in the elasticity parameters is investigated with the 1D model. PMID:20661645
NASA Astrophysics Data System (ADS)
Wada, I.; Wang, K.; He, J.
2013-12-01
In this study, we revisit the effects of along-strike variation in slab geometry and oblique subduction on subduction zone thermal structures. Along-strike variations in slab dip cause changes in the descending rate of the slab and generate trench-parallel pressure gradients that drive trench-parallel mantle flow (e.g., Kneller and van Keken, 2007). Oblique subduction also drives trench-parallel mantle flow. In this study, we use a finite element code PGCtherm3D and examine a range of generic subduction geometries and parameters to investigate the effects of the above two factors. This exercise is part of foundational work towards developing detailed 3-D thermal models for NE Japan, Nankai, and Cascadia to better constrain their 3-D thermal structures and to understand the role of temperature in controlling metamorphic, seismogenic, and volcanic processes. The 3-D geometry of the subducting slabs in the forearc and arc regions are well delineated at these three subduction zones. Further, relatively large compilations of surface heat flow data at these subduction zones make them excellent candidates for this study. At NE Japan, a megathrust earthquake occurred on March 11, 2011; at Nankai and Cascadia, there has been a great effort to constrain the scale of the next subduction thrust earthquake for the purpose of disaster prevention. Temperature influences the slip behavior of subduction faults by (1) affecting the rheology of the interface material and (2) controlling dehydration reactions, which can lead to elevated pore fluid pressure. Beyond the depths of subduction thrust earthquakes, the thermal structure is affected strongly by the pattern of mantle wedge flow. This flow is driven by viscous coupling between the subducting slab and the overriding mantle, and it brings in hot flowing mantle into the wedge. The trench-ward (up-dip) extent of the slab-mantle coupling is thus a key factor that controls the thermal structure. Slab-mantle decoupling at shallow
Dynamic coupling between fluid flow and vein growth in fractures: a 3D numerical model
NASA Astrophysics Data System (ADS)
Schwarz, J.-O.; Enzmann, F.
2012-04-01
chemical species to the growth site or by incorporation of material into the crystal structure. Hence a flexible growth rate is applied that adapts for both cases. After reaching a threshold value of generated vein material, the simulation is stopped and the generated geometry exported. Subsequently the fluid flow field for the new geometry is simulated by GeoDict, followed by simulation of vein growth. By iterative calculations of fluid flow and vein growth we couple the two processes and simulate dynamic vein growth. Although the model is very simplistic in the current state, we anticipate that it reproduces crucial characteristics of vein growth and hence yield further insights into vein generation in 3D. Ogilvie SR, Isakov E, Glover PWJ (2006) Fluid flow through rough fractures in rocks. II: A new matching model for rough rock fractures. Earth and Planetary Science Letters 241:454-465 Wiegmann A (2007) Computation of the permeability of porous materials from their microstructure by FFF-Stokes. In: Prätzel-Wolters D (ed) Berichte des Fraunhofer ITWM, vol. 129, Kaiserslautern, p 24
Numerical Simulations of High-Frequency Respiratory Flows in 2D and 3D Lung Bifurcation Models
NASA Astrophysics Data System (ADS)
Chen, Zixi; Parameswaran, Shamini; Hu, Yingying; He, Zhaoming; Raj, Rishi; Parameswaran, Siva
2014-07-01
To better understand the human pulmonary system and optimize the high-frequency oscillatory ventilation (HFOV) design, numerical simulations were conducted under normal breathing frequency and HFOV condition using a CFD code Ansys Fluent and its user-defined C programs. 2D and 3D double bifurcating lung models were created, and the geometry corresponds to fifth to seventh generations of airways with the dimensions based on the Weibel's pulmonary model. Computations were carried out for different Reynolds numbers (Re = 400 and 1000) and Womersley numbers (α = 4 and 16) to study the air flow fields, gas transportation, and wall shear stresses in the lung airways. Flow structure was compared with experimental results. Both 2D and 3D numerical models successfully reproduced many results observed in the experiment. The oxygen concentration distribution in the lung model was investigated to analyze the influence of flow oscillation on gas transport inside the lung model.
Finite volume and finite element methods applied to 3D laminar and turbulent channel flows
Louda, Petr; Příhoda, Jaromír; Sváček, Petr; Kozel, Karel
2014-12-10
The work deals with numerical simulations of incompressible flow in channels with rectangular cross section. The rectangular cross section itself leads to development of various secondary flow patterns, where accuracy of simulation is influenced by numerical viscosity of the scheme and by turbulence modeling. In this work some developments of stabilized finite element method are presented. Its results are compared with those of an implicit finite volume method also described, in laminar and turbulent flows. It is shown that numerical viscosity can cause errors of same magnitude as different turbulence models. The finite volume method is also applied to 3D turbulent flow around backward facing step and good agreement with 3D experimental results is obtained.
3D Reconstruction of virtual colon structures from colonoscopy images.
Hong, DongHo; Tavanapong, Wallapak; Wong, Johnny; Oh, JungHwan; de Groen, Piet C
2014-01-01
This paper presents the first fully automated reconstruction technique of 3D virtual colon segments from individual colonoscopy images. It is the basis of new software applications that may offer great benefits for improving quality of care for colonoscopy patients. For example, a 3D map of the areas inspected and uninspected during colonoscopy can be shown on request of the endoscopist during the procedure. The endoscopist may revisit the suggested uninspected areas to reduce the chance of missing polyps that reside in these areas. The percentage of the colon surface seen by the endoscopist can be used as a coarse objective indicator of the quality of the procedure. The derived virtual colon models can be stored for post-procedure training of new endoscopists to teach navigation techniques that result in a higher level of procedure quality. Our technique does not require a prior CT scan of the colon or any global positioning device. Our experiments on endoscopy images of an Olympus synthetic colon model reveal encouraging results with small average reconstruction errors (4.1 mm for the fold depths and 12.1 mm for the fold circumferences). PMID:24225230
Numerical simulation of a combined oxidation ditch flow using 3D k-epsilon turbulence model.
Luo, Lin; Li, Wei-min; Deng, Yong-sen; Wang, Tao
2005-01-01
The standard three dimensional(3D) k-epsilon turbulence model was applied to simulate the flow field of a small scale combined oxidation ditch. The moving mesh approach was used to model the rotor of the ditch. Comparison of the computed and the measured data is acceptable. A vertical reverse flow zone in the ditch was found, and it played a very important role in the ditch flow behavior. The flow pattern in the ditch is discussed in detail, and approaches are suggested to improve the hydrodynamic performance in the ditch. PMID:16313008
Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana
2016-05-01
On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations. PMID:27167030
Triangular framework mesh generation of 3D geological structure
NASA Astrophysics Data System (ADS)
Meng, Xianhai; Zhou, Kun; Li, Jigang; Yang, Qin
2013-03-01
The dynamic simulation of oil migration and accumulation is an important issue on the research of petroleum exploration, and it is a numerical simulation process with special requirement on the framework mesh of 3D geological models, which means that the mesh should have same geometry and topology relation near the intersected part of geological surfaces. In this paper, basing on the conforming Delaunay triangulation algorithm to construct mesh of individual geological stratum or fault, a novel link-Delaunay-triangulation method is presented to achieve the geometric and topological consistency in the intersected line between two surfaces, also with the analysis of termination of our algorithm. Finally, some examples of the geological framework mesh are provided and the experimental result proved that the algorithm's effectiveness in engineering practice.
NASA Astrophysics Data System (ADS)
Gnesin, V. I.; Kolodyazhnaya, L. V.; Rzadkowski, R.
2005-09-01
In this study presented the algorithm proposed involves the coupled solution of 3-D unsteady flow through a turbine stage and the dynamics problem for rotor-blade motion by the action of aerodynamic forces, without separating the outer and inner flow fluctuations. The partially integrated method involves the solution of the fluid and structural equations separately, but information is exchanged at each time step, so that solution from one domain is used as a boundary condition for the other domain. 3-D transonic gas flow through the stator and rotor blades in relative motion with periodicity on the whole annulus is described by the unsteady Euler conservation equations, which are integrated using the explicit monotonous finite-volume difference scheme of Godunov-Kolgan. The structural analysis uses the modal approach and a 3-D finite element model of a blade. A calculation has been done for the last stage of the steam turbine, under design and off-design regimes. It is shown that the amplitude-frequency spectrum of blade oscillations contains the high frequency harmonics, corresponding to the rotor moving past one stator blade pitch, and low frequency harmonics caused by blade oscillations and flow nonuniformity downstream from the blade row; moreover, the spectrum involves the harmonics which are not multiples of the rotation frequency.
3D Modelling of Magnetized Star-planet Interactions: Cometary-type Tails and In-spiraling Flows
NASA Astrophysics Data System (ADS)
Matsakos, T.; Uribe, A.; Konigl, A.
2015-01-01
Close-in exoplanets interact with their host stars not only gravitationally but also through magnetized plasma outflows. Here, we identify the different types of such interactions based on the physical parameters that characterize the system. We perform 3D magneto-hydrodynamic (MHD ) numerical simulations to model the evolution of a variety of possible star-planet configurations, incorporating realistic stellar and planetary outflows. We explore a wide range of parameters and analyze the flow structures and magnetic topologies that develop.
Image quality improvement for a 3D structure exhibiting multiple 2D patterns and its implementation.
Hirayama, Ryuji; Nakayama, Hirotaka; Shiraki, Atsushi; Kakue, Takashi; Shimobaba, Tomoyoshi; Ito, Tomoyoshi
2016-04-01
A three-dimensional (3D) structure designed by our proposed algorithm can simultaneously exhibit multiple two-dimensional patterns. The 3D structure provides multiple patterns having directional characteristics by distributing the effects of the artefacts. In this study, we proposed an iterative algorithm to improve the image quality of the exhibited patterns and have verified the effectiveness of the proposed algorithm using numerical simulations. Moreover, we fabricated different 3D glass structures (an octagonal prism, a cube and a sphere) using the proposed algorithm. All 3D structures exhibit four patterns, and different patterns can be observed depending on the viewing direction. PMID:27137021
NASA Astrophysics Data System (ADS)
Meheust, Y.; De Dreuzy, J.; Pichot, G.
2011-12-01
Flow channeling and permeability scaling in fractured media have been classically addressed either at the fracture- or at the network- scales. In the latter case they are linked to the topological structure of the network, while at the fracture scale they are controlled by the variability of the local aperture distribution inside individual fractures. In this study we analyze these two combined effects, investigating how flow localization below the scale of individual fractures influences that at the network scale and the resulting medium permeability. This is done by use of a new highly-resolved 3D discrete fracture network model (DFN). The local apertures of individual fractures are distributed according to a truncated Gaussian law, and exhibit self-affine spatial correlations that are bounded by an upper cutoff scale Lc; Lc and the fracture closure, defined as the ratio of the aperture fluctuations at scale Lc to the mean aperture, are considered homogeneous over the DFN. The network topology is controlled by a homogeneous scalar fracture density and a power law fracture length distribution. We have varied these features to investigate a large variety of DFN topologies, from sparse networks with varying degrees of fracture interconnections, flow bottlenecks and dead-ends (Fig. 1a), to dense well-connected networks (Fig. 1b). We have also investigated a large range of fracture closures, performing extensive simulations of about 105 different DFN realizations. At the fracture scale, accounting for local aperture fluctuations leads to a monotical deviation (which can exceed 50%) of the equivalent fracture transmissivity from the parallel plate behavior. At the network scale we observe a complex interaction between flow channeling within fracture planes and flow localization in the network. This interaction is controlled by the location of fracture interactions with respect to that of low local transmissivity zones (particularly the closed zones), in the fracture
NASA Astrophysics Data System (ADS)
Szekely, Gabor; Koller, Thomas; Kikinis, Ron; Gerig, Guido
1994-09-01
Medical image analysis has to support the clinicians ability to identify, manipulate and quantify anatomical structures. On scalar 2D image data, a human observer is often superior to computer assisted analysis, but the interpretation of vector- valued data or data combined from different modalities, especially in 3D, can benefit from computer assistance. The problem of how to convey the complex information to the clinician is often tackled by providing colored multimodality renderings. We propose to go a step beyond by supplying a suitable modelling of anatomical and functional structures encoding important shape features and physical properties. The multiple attributes regarding geometry, topology and function are carried by the symbolic description and can be interactively queried and edited. Integrated 3D rendering of object surfaces and symbolic representation acts as a visual interface to allow interactive communication between the observer and the complex data, providing new possibilities for quantification and therapy planning. The discussion is guided by the prototypical example of investigating the cerebral vasculature in MRA volume data. Geometric, topological and flow-related information can be assessed by interactive analysis on a computer workstation, providing otherwise hidden qualitative and quantitative information. Several case studies demonstrate the potential usage for structure identification, definition of landmarks, assessment of topology for catheterization, and local simulation of blood flow.
NASA Astrophysics Data System (ADS)
Sippel, Judith; Fuchs, Sven; Cacace, Mauro; Kastner, Oliver; Huenges, Ernst; Scheck-Wenderoth, Magdalena
2013-04-01
In the light of an aspired reduction of CO2 emissions for Germany's capital Berlin, one possible alternative for meeting the city's growing energy demands lies in deep geothermal energy. To minimise exploration risks, a profound knowledge about the subsurface temperature distribution is indispensable. We present a 3D structural model that is used for thermal modelling and thus correlates calculated subsurface temperatures with geothermally relevant structures in the deep subsurface of Berlin - an ideal base for improving the probability of finding adequate geothermal reservoirs. Berlin is located in the eastern part of the North German Basin which is filled with several thousand metres of Permian to Cenozoic sediments containing hot and water bearing aquifers to potentially be used as hydrothermal reservoirs. To characterise the geological underground, the 3D structural model integrates stratigraphical, petrophysical and well-log based information from local boreholes as well as stratigraphic trends from (seismic data based) regional 3D models. The model differentiates 21 geological units: 17 Permian-Cenozoic sedimentary layers, pre-Permian sediments, upper crust, lower crust and the lithospheric mantle. Based on this 3D geological model complemented by databased lithology-dependent thermal properties, two groups of numerical thermal simulations have been carried out: calculations of the steady-state conductive thermal field and simulations of coupled fluid and heat transport. The 3D thermal models predict large lateral variations in temperatures that are validated by high-precession temperature logs. These variations are mostly caused by three specific geological layers and their physical properties: the Permian Zechstein salt with its markedly high thermal conductivity and strong thickness variation (171-3442 m); the crystalline upper crustal layer with its high radiogenic heat production and decreasing thickness from east to west; and the Tertiary Rupelian
An improved parallel SPH approach to solve 3D transient generalized Newtonian free surface flows
NASA Astrophysics Data System (ADS)
Ren, Jinlian; Jiang, Tao; Lu, Weigang; Li, Gang
2016-08-01
In this paper, a corrected parallel smoothed particle hydrodynamics (C-SPH) method is proposed to simulate the 3D generalized Newtonian free surface flows with low Reynolds number, especially the 3D viscous jets buckling problems are investigated. The proposed C-SPH method is achieved by coupling an improved SPH method based on the incompressible condition with the traditional SPH (TSPH), that is, the improved SPH with diffusive term and first-order Kernel gradient correction scheme is used in the interior of the fluid domain, and the TSPH is used near the free surface. Thus the C-SPH method possesses the advantages of two methods. Meanwhile, an effective and convenient boundary treatment is presented to deal with 3D multiple-boundary problem, and the MPI parallelization technique with a dynamic cells neighbor particle searching method is considered to improve the computational efficiency. The validity and the merits of the C-SPH are first verified by solving several benchmarks and compared with other results. Then the viscous jet folding/coiling based on the Cross model is simulated by the C-SPH method and compared with other experimental or numerical results. Specially, the influences of macroscopic parameters on the flow are discussed. All the numerical results agree well with available data, and show that the C-SPH method has higher accuracy and better stability for solving 3D moving free surface flows over other particle methods.
High-Resolution 3D Seismic Imaging of Fluid Flow Anomalies in the Southwest Barents Sea
NASA Astrophysics Data System (ADS)
Planke, S.; Eriksen, F. N.; Eriksen, O. K.; Assad, M.; Stokke, H. H.
2014-12-01
Fluid flow features imaged as gas flares in the water column, pockmarks and mud volcanoes on the seabed, and high-amplitude cross-cutting reflections and bright spots in the sub-surface are abundant in the SW Barents Sea offshore northern Norway. This region is covered by extensive conventional 2D and 3D deep penetration seismic reflection data and multibeam bathymetry. High-resolution 3D P-Cable seismic data have been acquired in the SW Barents Sea over the past few years to image the uppermost ca. 500 m of the sub-surface. The P-Cable system consist of 12 to 16 short streamers (25 m) that are towed on a cross-cable perpendicular to the vessel's steaming direction. This configuration allows for acquisition of seismic data with high trace density, typically with 6 m in-line separation. The vertical resolution is a good as 1-2 m using conventional site survey air gun configurations. The sedimentary succession in the SW Barents Sea consists of upper Paleozoic evaporites overlaid by Mesozoic and Cenozoic clastic sediments. There are several organic-rich intervals in the sequence, including Paleozoic coals and Triassic and Jurassic marine source rocks that are locally in the oil or gas maturation windows. Glacial erosion has locally removed kilometer thick Cenozoic and Mesozoic successions, leaving the Mesozoic and Paleozoic strata in shallow sub-surface. The new high-resolution 3D surveys have targeted shallow fluid anomalies in the subsurface. These are imaged as high-amplitude reflections in fault blocks and structural highs, locally cross-cutting well-defined Mesozoic reflections. Commonly, disturbed reflections are present in overlying sequences, or high-amplitude reflections are imaged in the glacial overburden sediments. Locally, hundreds of pockmarks are imaged by the seafloor reflection. The deep cross-cutting reflections are interpreted as hydrocarbon accumulations that locally migrate towards the surface. The fluids are stored in shallow gas pockets or
Intuitive Visualization of Transient Flow: Towards a Full 3D Tool
NASA Astrophysics Data System (ADS)
Michel, Isabel; Schröder, Simon; Seidel, Torsten; König, Christoph
2015-04-01
Visualization of geoscientific data is a challenging task especially when targeting a non-professional audience. In particular, the graphical presentation of transient vector data can be a significant problem. With STRING Fraunhofer ITWM (Kaiserslautern, Germany) in collaboration with delta h Ingenieurgesellschaft mbH (Witten, Germany) developed a commercial software for intuitive 2D visualization of 3D flow problems. Through the intuitive character of the visualization experts can more easily transport their findings to non-professional audiences. In STRING pathlets moving with the flow provide an intuition of velocity and direction of both steady-state and transient flow fields. The visualization concept is based on the Lagrangian view of the flow which means that the pathlets' movement is along the direction given by pathlines. In order to capture every detail of the flow an advanced method for intelligent, time-dependent seeding of the pathlets is implemented based on ideas of the Finite Pointset Method (FPM) originally conceived at and continuously developed by Fraunhofer ITWM. Furthermore, by the same method pathlets are removed during the visualization to avoid visual cluttering. Additional scalar flow attributes, for example concentration or potential, can either be mapped directly to the pathlets or displayed in the background of the pathlets on the 2D visualization plane. The extensive capabilities of STRING are demonstrated with the help of different applications in groundwater modeling. We will discuss the strengths and current restrictions of STRING which have surfaced during daily use of the software, for example by delta h. Although the software focusses on the graphical presentation of flow data for non-professional audiences its intuitive visualization has also proven useful to experts when investigating details of flow fields. Due to the popular reception of STRING and its limitation to 2D, the need arises for the extension to a full 3D tool
A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows
NASA Astrophysics Data System (ADS)
Bijleveld, H. A.; Veldman, A. E. P.
2014-12-01
A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.
Parallel Adaptive Computation of Blood Flow in a 3D ``Whole'' Body Model
NASA Astrophysics Data System (ADS)
Zhou, M.; Figueroa, C. A.; Taylor, C. A.; Sahni, O.; Jansen, K. E.
2008-11-01
Accurate numerical simulations of vascular trauma require the consideration of a larger portion of the vasculature than previously considered, due to the systemic nature of the human body's response. A patient-specific 3D model composed of 78 connected arterial branches extending from the neck to the lower legs is constructed to effectively represent the entire body. Recently developed outflow boundary conditions that appropriately represent the downstream vasculature bed which is not included in the 3D computational domain are applied at 78 outlets. In this work, the pulsatile blood flow simulations are started on a fairly uniform, unstructured mesh that is subsequently adapted using a solution-based approach to efficiently resolve the flow features. The adapted mesh contains non-uniform, anisotropic elements resulting in resolution that conforms with the physical length scales present in the problem. The effects of the mesh resolution on the flow field are studied, specifically on relevant quantities of pressure, velocity and wall shear stress.
Numerical modelling of gravel unconstrained flow experiments with the DAN3D and RASH3D codes
NASA Astrophysics Data System (ADS)
Sauthier, Claire; Pirulli, Marina; Pisani, Gabriele; Scavia, Claudio; Labiouse, Vincent
2015-12-01
Landslide continuum dynamic models have improved considerably in the last years, but a consensus on the best method of calibrating the input resistance parameter values for predictive analyses has not yet emerged. In the present paper, numerical simulations of a series of laboratory experiments performed at the Laboratory for Rock Mechanics of the EPF Lausanne were undertaken with the RASH3D and DAN3D numerical codes. They aimed at analysing the possibility to use calibrated ranges of parameters (1) in a code different from that they were obtained from and (2) to simulate potential-events made of a material with the same characteristics as back-analysed past-events, but involving a different volume and propagation path. For this purpose, one of the four benchmark laboratory tests was used as past-event to calibrate the dynamic basal friction angle assuming a Coulomb-type behaviour of the sliding mass, and this back-analysed value was then used to simulate the three other experiments, assumed as potential-events. The computational findings show good correspondence with experimental results in terms of characteristics of the final deposits (i.e., runout, length and width). Furthermore, the obtained best fit values of the dynamic basal friction angle for the two codes turn out to be close to each other and within the range of values measured with pseudo-dynamic tilting tests.
Delft3D-FLOW on PRACE infrastructures for real life hydrodynamic applications.
NASA Astrophysics Data System (ADS)
Donners, John; Genseberger, Menno; Jagers, Bert; de Goede, Erik; Mourits, Adri
2013-04-01
PRACE, the Partnership for Advanced Computing in Europe, offers access to the largest high-performance computing systems in Europe. PRACE invites and helps industry to increase their innovative potential through the use of the PRACE infrastructure. This poster describes different efforts to assist Deltares with porting the open-source simulation software Delft3D-FLOW to PRACE infrastructures. Analysis of the performance on these infrastructures has been done for real life flow applications. Delft3D-FLOW is a 2D and 3D shallow water solver which calculates non-steady flow and transport phenomena resulting from tidal and meteorological forcing on a curvilinear, boundary fitted grid in Cartesian or spherical coordinates. It also includes a module which sediment transport (both suspended and bed total load) and morphological changes for an arbitrary number of cohesive and non-cohesive fractions. As Delft3D-FLOW has been developed over several decades, with a variety of functionality and over 350k lines of source code, porting to PRACE infrastructures needs some effort. At the moment Delft3D-FLOW uses MPI with domain decomposition in one direction as its parallellisation approach. Because it is hard to identify scaling issues if one immediately starts with a complex case with many features enabled, different cases with increasing complexity have been used to investigate scaling of this parallellisation approach on several PRACE platforms. As a base reference case we started with a schematic high-resolution 2D hydrodynamic model of the river Waal that turned out to be surprisingly well-suited to the highly-parallel PRACE machines. Although Delft3D-FLOW employs a sophisticated build system, several modifications were required to port it to most PRACE systems due to the use of specific, highly-tuned compilers and MPI-libraries. After this we moved to a 3D hydrodynamic model of Rotterdam harbour that includes sections of the rivers Rhine and Meuse and a part of the North
3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.
Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana
2016-05-01
Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system. PMID:26992060
3D Modeling of Branching Structures for Anatomical Instruction
Mattingly, William A.; Chariker, Julia H.; Paris, Richard; Chang, Dar-jen; Pani, John R.
2015-01-01
Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices. PMID:27087764
3-D High-Lift Flow-Physics Experiment - Transition Measurements
NASA Technical Reports Server (NTRS)
McGinley, Catherine B.; Jenkins, Luther N.; Watson, Ralph D.; Bertelrud, Arild
2005-01-01
An analysis of the flow state on a trapezoidal wing model from the NASA 3-D High Lift Flow Physics Experiment is presented. The objective of the experiment was to characterize the flow over a non-proprietary semi-span three-element high-lift configuration to aid in assessing the state of the art in the computation of three-dimensional high-lift flows. Surface pressures and hot-film sensors are used to determine the flow conditions on the slat, main, and flap. The locations of the attachments lines and the values of the attachment line Reynolds number are estimated based on the model surface pressures. Data from the hot-films are used to determine if the flow is laminar, transitional, or turbulent by examining the hot-film time histories, statistics, and frequency spectra.
UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation
Zhu, Jinhao; Wei, Bryan; Yuan, Yuan; Mi, Yongli
2009-01-01
A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 × 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions. PMID:19228709
3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site
NASA Astrophysics Data System (ADS)
Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco
2015-04-01
each other, water flow is high. Our 3D structural model allows the recognition of such intersections in 3D space and the prediction of their spatial extent. The structural model developed with the introduction of the locally known hydraulic permeabilities and in combination with the results of on-going hydrochemical investigations will allow to estimate the location of the recently active water pathways. References Wehrens, P., Baumberger, R., Berger, A., & Herwegh, M. (in prep.). How is strain localized in a mid-crustal basement section? Spatial distribution of deformation in the Aar massif (Switzerland).
3D Crustal Structure and 3D-b-value in AbuDabbab Seismogenic Source, Northern Red Sea.
NASA Astrophysics Data System (ADS)
Al-Arifi, Nassir; El Kherpy, Sami; Koulakov, Ivan
2014-05-01
Abu Dabbab seismogenic source region is of unique seismic activity located on the Egyptian Red Sea coast. It's known as earthquake Cannons where the earthquakes are accompanied by a sound of distinct rumbling similar to the sound of a distant quarry blast which is heard by humans for several generations. Seismic activity of Abu Dabbab becomes very well determined after establishing of the Egyptian National Seismic Network 1997. Joint earthquake tomography inversion of local and regional data has been performed in order to image the crustal heterogeneity and the origin of the cannons earthquakes. Most previous studies suggested that this activity is of magmatic origin. We found the seismicity forms an arc shaped cluster that surrounds an aseismic block. This aseismic block has high velocities and a low Vp/Vs ratio. The origin of this seismic activity is probably due an active fault below the non-deformed block of Precambrian Igneous rock reaching a depth of ~10 km. Spatial mapping of the frequency magnitude distribution of the earthquakes and 3D-b-value indicate a strong variation moreover high b-value (1.4) at depth downward the rigid block. The Combined interpretation of the seismic imaging and 3D b-value in addition to the seismological and the geophysical observations revealed the tectonic origin of the earthquake activity in this area which is related strongly to the evolution of the crust in the Red Sea and its tectonic activity. KEYWARD:Three dimensional Crustal Structure - Seismic activity -Three-D b-value- Red Sea tectonics- Tectonic activity
Simulation of 3-D Nonequilibrium Seeded Air Flow in the NASA-Ames MHD Channel
NASA Technical Reports Server (NTRS)
Gupta, Sumeet; Tannehill, John C.; Mehta, Unmeel B.
2004-01-01
The 3-D nonequilibrium seeded air flow in the NASA-Ames experimental MHD channel has been numerically simulated. The channel contains a nozzle section, a center section, and an accelerator section where magnetic and electric fields can be imposed on the flow. In recent tests, velocity increases of up to 40% have been achieved in the accelerator section. The flow in the channel is numerically computed us ing a 3-D parabolized Navier-Stokes (PNS) algorithm that has been developed to efficiently compute MHD flows in the low magnetic Reynolds number regime: The MHD effects are modeled by introducing source terms into the PNS equations which can then be solved in a very efficient manner. The algorithm has been extended in the present study to account for nonequilibrium seeded air flows. The electrical conductivity of the flow is determined using the program of Park. The new algorithm has been used to compute two test cases that match the experimental conditions. In both cases, magnetic and electric fields are applied to the seeded flow. The computed results are in good agreement with the experimental data.
Evaluation of the 3-D channeling flow in a fractured type of oil/gas reservoir
NASA Astrophysics Data System (ADS)
Ishibashi, T.; Watanabe, N.; Tsuchiya, N.; Tamagawa, T.
2013-12-01
An understanding of the flow and transport characteristics through rock fracture networks is of critical importance in many engineering and scientific applications. These include effective recovery of targeted fluid such as oil/gas, geothermal, or potable waters, and isolation of hazardous materials. Here, the formation of preferential flow path (i.e. channeling flow) is one of the most significant characteristics in considering fluid flow through rock fracture networks; however, the impact of channeling flow remains poorly understood. In order to deepen our understanding of channeling flow, the authors have developed a novel discrete fracture network (DFN) model simulator, GeoFlow. Different from the conventional DFN model simulators, we can characterize each fracture not by a single aperture value but by a heterogeneous aperture distribution in GeoFlow [Ishibashi et al., 2012]. As a result, the formation of 3-D preferential flow paths within fracture network can be considered by using this simulator. Therefore, we would challenge to construct the precise fracture networks whose fractures have heterogeneous aperture distributions in field scale, and to analyze fluid flows through the fracture networks by GeoFlow. In the present study, the Yufutsu oil/gas field in Hokkaido, Japan is selected as the subject area for study. This field is known as the fractured type of reservoir, and reliable DFN models can be constructed for this field based on the 3-D seismic data, well logging, in-situ stress measurement, and acoustic emission data [Tamagawa et al., 2012]. Based on these DFN models, new DFN models for 1,080 (East-West) × 1,080 (North-South) × 1,080 (Depth) m^3, where fractures are represented by squares of 44-346 m on a side, are re-constructed. In these new models, scale-dependent aperture distributions are considered for all fractures constructing the fracture networks. Note that the multi-scale modeling of fracture flow has been developed by the authors
Quasi 3D modeling of water flow and solute transport in vadose zone and groundwater
NASA Astrophysics Data System (ADS)
Yakirevich, A.; Kuznetsov, M.; Weisbrod, N.; Pachepsky, Y. A.
2013-12-01
The complexity of subsurface flow systems calls for a variety of concepts leading to the multiplicity of simplified flow models. One commonly used simplification is based on the assumption that lateral flow and transport in unsaturated zone is insignificant unless the capillary fringe is involved. In such cases the flow and transport in the unsaturated zone above groundwater level can be simulated as a 1D phenomenon, whereas through groundwater they are viewed as 2D or 3D phenomena. A new approach for a numerical scheme for 3D variably saturated flow and transport is presented. A Quasi-3D approach allows representing flow in the 'vadose zone - aquifer' system by a series of 1D Richards' equations solved in variably-saturated zone and by 3D-saturated flow equation in groundwater (modified MODFLOW code). The 1D and 3D equations are coupled at the phreatic surface in a way that aquifer replenishment is calculated using the Richards' equation, and solving for the moving water table does not require definition of the specific yield parameter. The 3D advection-dispersion equation is solved in the entire domain by the MT3D code. Using implicit finite differences approximation to couple processes in the vadose zone and groundwater provides mass conservation and increase of computational efficiency. The above model was applied to simulate the impact of irrigation on groundwater salinity in the Alto Piura aquifer (Northern Peru). Studies on changing groundwater quality in arid and semi-arid lands show that irrigation return flow is one of the major factors contributing to aquifer salinization. Existing mathematical models do not account explicitly for the solute recycling during irrigation on a daily scale. Recycling occurs throughout the unsaturated and saturated zones, as function of the solute mass extracted from pumping wells. Salt concentration in irrigation water is calculated at each time step as a function of concentration of both surface water and groundwater
Pei, Jimin; Grishin, Nick V.
2015-01-01
SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408
Pei, Jimin; Grishin, Nick V
2014-01-01
Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408
GMOL: An Interactive Tool for 3D Genome Structure Visualization.
Nowotny, Jackson; Wells, Avery; Oluwadare, Oluwatosin; Xu, Lingfei; Cao, Renzhi; Trieu, Tuan; He, Chenfeng; Cheng, Jianlin
2016-01-01
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function. PMID:26868282
Characterizing 3D RNA structure by single molecule FRET.
Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L
2016-07-01
The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327
A 3-D Vortex Code for Parachute Flow Predictions: VIPAR Version 1.0
STRICKLAND, JAMES H.; HOMICZ, GREGORY F.; PORTER, VICKI L.; GOSSLER, ALBERT A.
2002-07-01
This report describes a 3-D fluid mechanics code for predicting flow past bluff bodies whose surfaces can be assumed to be made up of shell elements that are simply connected. Version 1.0 of the VIPAR code (Vortex Inflation PARachute code) is described herein. This version contains several first order algorithms that we are in the process of replacing with higher order ones. These enhancements will appear in the next version of VIPAR. The present code contains a motion generator that can be used to produce a large class of rigid body motions. The present code has also been fully coupled to a structural dynamics code in which the geometry undergoes large time dependent deformations. Initial surface geometry is generated from triangular shell elements using a code such as Patran and is written into an ExodusII database file for subsequent input into VIPAR. Surface and wake variable information is output into two ExodusII files that can be post processed and viewed using software such as EnSight{trademark}.
SAFAS: Unifying Form and Structure through Interactive 3D Simulation
ERIC Educational Resources Information Center
Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.
2015-01-01
There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…