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Sample records for 3t 3d dynamic

  1. [3D emulation of epicardium dynamic mapping].

    PubMed

    Lu, Jun; Yang, Cui-Wei; Fang, Zu-Xiang

    2005-03-01

    In order to realize epicardium dynamic mapping of the whole atria, 3-D graphics are drawn with OpenGL. Some source codes are introduced in the paper to explain how to produce, read, and manipulate 3-D model data.

  2. Neuroradiologic applications of dynamic MR angiography at 3 T.

    PubMed

    Parmar, Hemant; Ivancevic, Marko K; Dudek, Nancy; Gandhi, Dheeraj; Geerts, Liesbeth; Hoogeveen, R; Mukherji, S K; Chenevert, Thomas L

    2009-02-01

    Four-dimensional time-resolved MR angiography (4D-MRA) using keyhole imaging techniques is a new method of performing contrastenhanced vascular imaging. Combining parallel imaging and keyhole imaging techniques, it is possible to obtain dynamic MRA scans up to 60 times faster, thereby achieving subsecond sampling of the contrast hemodynamics. Furthermore, imaging at 3 T gives higher signal, thus affording higher spatial resolution and allowing dynamic 3D MRA to approach the diagnostic performance of conventional digital subtraction angiography. This article presents the authors' clinical experience using 4D-MRA to evaluate various vascular abnormalities in the brain, spine, orbits, and neck at 3 T, demonstrates the imaging findings of this novel technique, and discusses its advantages and use in current neuroradiology practice.

  3. Static & Dynamic Response of 3D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

    NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.

  4. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect

    Steven R Prescott; Curtis Smith

    2011-07-01

    provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  5. Dynamics of 3D isolated thermal filaments

    NASA Astrophysics Data System (ADS)

    Walkden, N. R.; Easy, L.; Militello, F.; Omotani, J. T.

    2016-11-01

    Simulations have been carried out to establish how electron thermal physics, introduced in the form of a dynamic electron temperature, affects isolated filament motion and dynamics in 3D. It is found that thermal effects impact filament motion in two major ways when the pressure perturbation within the filament is supported primarily through a temperature increase as opposed to density: they lead to a strong increase in filament propagation in the bi-normal direction and a significant decrease in net radial propagation. Both effects arise from the temperature dependence of the sheath current which leads to a non-uniform floating potential, with the latter effect supplemented by faster pressure loss. The reduction in radial velocity can only occur when the filament cross-section loses angular symmetry. The behaviour is observed across different filament sizes and suggests that filaments with much larger temperature perturbations than density perturbations are more strongly confined to the near SOL region.

  6. 3D Hall MHD Reconnection Dynamics

    NASA Astrophysics Data System (ADS)

    Huba, J. D.; Rudakov, L.

    2002-05-01

    A 3D Hall MHD simulation code (VooDoo) has recently been developed at the Naval Research Laboratory. We present preliminary results of a fully 3D magnetic reconnection study using this code. The initial configuration of the plasma system is as follows. The ambient, reversed magnetic field is in the x-direction and is proportional to B0 tanh(y/Ly) where Ly is the scale length of the current sheet. Perturbation fields δ Bx and δ By are introduced to initiate the reconnection process. This initial configuration is similar to that used in the 2D GEM reconnection study. However, the perturbation fields are localized in the z-direction. We consider two cases: no guide field (Bz = 0) and a weak guide field (Bz = 0.1B0). We find that the reconnection process is not stationary in the z-direction but propagates in the B x ∇ n direction consistent with Hall drift physics. Hence, an asymmetric disruption of the current sheet ensues. The flow structure of the plasma in the vicinity of the X-point is complex. We find that the `neutral line' (i.e, along the z-direction) is not an ignorable coordinate and is not periodic in Hall MHD reconnection dynamics; two assumptions that are often made in reconnection studies. \\ Research supported by NASA and ONR

  7. Time Efficient 3D Radial UTE Sampling with Fully Automatic Delay Compensation on a Clinical 3T MR Scanner

    PubMed Central

    Reichenbach, Jürgen R.

    2016-01-01

    This work’s aim was to minimize the acquisition time of a radial 3D ultra-short echo-time (UTE) sequence and to provide fully automated, gradient delay compensated, and therefore artifact free, reconstruction. The radial 3D UTE sequence (echo time 60 μs) was implemented as single echo acquisition with center-out readouts and improved time efficient spoiling on a clinical 3T scanner without hardware modifications. To assess the sequence parameter dependent gradient delays each acquisition contained a quick calibration scan and utilized the phase of the readouts to detect the actual k-space center. This calibration scan does not require any user interaction. To evaluate the robustness of this automatic delay estimation phantom experiments were performed and 19 in vivo imaging data of the head, tibial cortical bone, feet and lung were acquired from 6 volunteers. As clinical application of this fast 3D UTE acquisition single breath-hold lung imaging is demonstrated. The proposed sequence allowed very short repetition times (TR~1ms), thus reducing total acquisition time. The proposed, fully automated k-phase based gradient delay calibration resulted in accurate delay estimations (difference to manually determined optimal delay −0.13 ± 0.45 μs) and allowed unsupervised reconstruction of high quality images for both phantom and in vivo data. The employed fast spoiling scheme efficiently suppressed artifacts caused by incorrectly refocused echoes. The sequence proved to be quite insensitive to motion, flow and susceptibility artifacts and provides oversampling protection against aliasing foldovers in all directions. Due to the short TR, acquisition times are attractive for a wide range of clinical applications. For short T2* mapping this sequence provides free choice of the second TE, usually within less scan time as a comparable dual echo UTE sequence. PMID:26975051

  8. Time Efficient 3D Radial UTE Sampling with Fully Automatic Delay Compensation on a Clinical 3T MR Scanner.

    PubMed

    Herrmann, Karl-Heinz; Krämer, Martin; Reichenbach, Jürgen R

    2016-01-01

    This work's aim was to minimize the acquisition time of a radial 3D ultra-short echo-time (UTE) sequence and to provide fully automated, gradient delay compensated, and therefore artifact free, reconstruction. The radial 3D UTE sequence (echo time 60 μs) was implemented as single echo acquisition with center-out readouts and improved time efficient spoiling on a clinical 3T scanner without hardware modifications. To assess the sequence parameter dependent gradient delays each acquisition contained a quick calibration scan and utilized the phase of the readouts to detect the actual k-space center. This calibration scan does not require any user interaction. To evaluate the robustness of this automatic delay estimation phantom experiments were performed and 19 in vivo imaging data of the head, tibial cortical bone, feet and lung were acquired from 6 volunteers. As clinical application of this fast 3D UTE acquisition single breath-hold lung imaging is demonstrated. The proposed sequence allowed very short repetition times (TR~1ms), thus reducing total acquisition time. The proposed, fully automated k-phase based gradient delay calibration resulted in accurate delay estimations (difference to manually determined optimal delay -0.13 ± 0.45 μs) and allowed unsupervised reconstruction of high quality images for both phantom and in vivo data. The employed fast spoiling scheme efficiently suppressed artifacts caused by incorrectly refocused echoes. The sequence proved to be quite insensitive to motion, flow and susceptibility artifacts and provides oversampling protection against aliasing foldovers in all directions. Due to the short TR, acquisition times are attractive for a wide range of clinical applications. For short T2* mapping this sequence provides free choice of the second TE, usually within less scan time as a comparable dual echo UTE sequence.

  9. NIKE3D96. Static & Dynamic Response of 3D Solids

    SciTech Connect

    Maker, B.; Hallquist, J.O.; Ferencz, R.M.

    1991-02-01

    NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.

  10. DYNAMIC 3D QSAR TECHNIQUES: APPLICATIONS IN TOXICOLOGY

    EPA Science Inventory

    Two dynamic techniques recently developed to account for conformational flexibility of chemicals in 3D QSARs are presented. In addition to the impact of conformational flexibility of chemicals in 3D QSAR models, the applicability of various molecular descriptors is discussed. The...

  11. 3D Protein Dynamics in the Cell Nucleus.

    PubMed

    Singh, Anand P; Galland, Rémi; Finch-Edmondson, Megan L; Grenci, Gianluca; Sibarita, Jean-Baptiste; Studer, Vincent; Viasnoff, Virgile; Saunders, Timothy E

    2017-01-10

    The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line.

  12. Real-time motion- and B0-correction for LASER-localized spiral-accelerated 3D-MRSI of the brain at 3T.

    PubMed

    Bogner, Wolfgang; Hess, Aaron T; Gagoski, Borjan; Tisdall, M Dylan; van der Kouwe, Andre J W; Trattnig, Siegfried; Rosen, Bruce; Andronesi, Ovidiu C

    2014-03-01

    The full potential of magnetic resonance spectroscopic imaging (MRSI) is often limited by localization artifacts, motion-related artifacts, scanner instabilities, and long measurement times. Localized adiabatic selective refocusing (LASER) provides accurate B1-insensitive spatial excitation even at high magnetic fields. Spiral encoding accelerates MRSI acquisition, and thus, enables 3D-coverage without compromising spatial resolution. Real-time position- and shim/frequency-tracking using MR navigators correct motion- and scanner instability-related artifacts. Each of these three advanced MRI techniques provides superior MRSI data compared to commonly used methods. In this work, we integrated in a single pulse sequence these three promising approaches. Real-time correction of motion, shim, and frequency-drifts using volumetric dual-contrast echo planar imaging-based navigators were implemented in an MRSI sequence that uses low-power gradient modulated short-echo time LASER localization and time efficient spiral readouts, in order to provide fast and robust 3D-MRSI in the human brain at 3T. The proposed sequence was demonstrated to be insensitive to motion- and scanner drift-related degradations of MRSI data in both phantoms and volunteers. Motion and scanner drift artifacts were eliminated and excellent spectral quality was recovered in the presence of strong movement. Our results confirm the expected benefits of combining a spiral 3D-LASER-MRSI sequence with real-time correction. The new sequence provides accurate, fast, and robust 3D metabolic imaging of the human brain at 3T. This will further facilitate the use of 3D-MRSI for neuroscience and clinical applications.

  13. An Evaluative Review of Simulated Dynamic Smart 3d Objects

    NASA Astrophysics Data System (ADS)

    Romeijn, H.; Sheth, F.; Pettit, C. J.

    2012-07-01

    Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.

  14. Multitasking the code ARC3D. [for computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Barton, John T.; Hsiung, Christopher C.

    1986-01-01

    The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

  15. Fractal dimension as a measure of altered actin cytoskeleton in MC3T3-E1 cells under simulated microgravity using 3-D/2-D clinostats.

    PubMed

    Qian, A R; Li, D; Han, J; Gao, X; Di, S M; Zhang, W; Hu, L F; Shang, Peng

    2012-05-01

    Osteoblasts, the bone-forming cells, respond to various mechanical forces, such as stretch and fluid shear force in essentially similar ways. The cytoskeleton, as the load-bearing architecture of the cell, is sensitive to altered inertial forces. Disruption of the cytoskeleton will result in alteration of cellular structure and function. However, it is difficult to quantitatively illustrate cytoskeletal rearrangement because of the complexity of cytoskeletal structure. Usually, the morphological changes in actin organization caused by external stimulus are basically descriptive. In this study, fractal dimensions (D) analysis was used to quantify the morphological changes in the actin cytoskeleton of osteoblast-like cells (MC3T3-E1) under simulated microgravity using 3-D/2-D clinostats. The ImageJ software was used to count the fractal dimension of actin cytoskeleton by box-counting methods. Real-time PCR and immunofluroscent assays were used to further confirm the results obtained by fractal dimension analysis. The results showed significant decreases in D value of actin cytoskeleton, β-actin mRNA expression, and the mean fluorescence intensity of F-actin in osteoblast-like cells after 24 or 48 h of incubation under 3-D/2-D clinorotation condition compared with control. The findings indicate that 3-D/2-D clinorotation affects both actin cytoskeleton architecture and mRNA expression, and fractal may be a promising approach for quantitative analysis of the changes in cytoskeleton in different environments.

  16. The Vibrational Dynamics of 3D HOCl Above Dissociation

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Der; Reichl, Linda; Jung, Christof

    2015-03-01

    We have analyzed the vibrational dynamics of HOCl above dissociation using a 3D energy surface which governs the vibrational dynamics of HOCl above dissociation. The dynamics is dominated by an invariant manifold which is transversally unstable for small spacing between Cl and HO complex, and stable for large spacing. Above dissociation, the InM separates two mirror image periodic orbits, embedded in a large chaotic sea, that can hold a large number of quantum states. These periodic orbits have the capability of forming significant quasibound states of the molecule above dissociation. Welch Foundation.

  17. Nanoimaging of Focal Adhesion Dynamics in 3D

    PubMed Central

    Chiu, Chi-Li; Aguilar, Jose S.; Tsai, Connie Y.; Wu, GuiKai; Gratton, Enrico; Digman, Michelle A.

    2014-01-01

    Organization and dynamics of focal adhesion proteins have been well characterized in cells grown on two-dimensional (2D) cell culture surfaces. However, much less is known about the dynamic association of these proteins in the 3D microenvironment. Limited imaging technologies capable of measuring protein interactions in real time and space for cells grown in 3D is a major impediment in understanding how proteins function under different environmental cues. In this study, we applied the nano-scale precise imaging by rapid beam oscillation (nSPIRO) technique and combined the scaning-fluorescence correlation spectroscopy (sFCS) and the number and molecular brightness (N&B) methods to investigate paxillin and actin dynamics at focal adhesions in 3D. Both MDA-MB-231 cells and U2OS cells produce elongated protrusions with high intensity regions of paxillin in cell grown in 3D collagen matrices. Using sFCS we found higher percentage of slow diffusing proteins at these focal spots, suggesting assembling/disassembling processes. In addition, the N&B analysis shows paxillin aggregated predominantly at these focal contacts which are next to collagen fibers. At those sites, actin showed slower apparent diffusion rate, which indicated that actin is either polymerizing or binding to the scaffolds in these locals. Our findings demonstrate that by multiplexing these techniques we have the ability to spatially and temporally quantify focal adhesion assembly and disassembly in 3D space and allow the understanding tumor cell invasion in a more complex relevant environment. PMID:24959851

  18. Dynamic deformable models for 3D MRI heart segmentation

    NASA Astrophysics Data System (ADS)

    Zhukov, Leonid; Bao, Zhaosheng; Gusikov, Igor; Wood, John; Breen, David E.

    2002-05-01

    Automated or semiautomated segmentation of medical images decreases interstudy variation, observer bias, and postprocessing time as well as providing clincally-relevant quantitative data. In this paper we present a new dynamic deformable modeling approach to 3D segmentation. It utilizes recently developed dynamic remeshing techniques and curvature estimation methods to produce high-quality meshes. The approach has been implemented in an interactive environment that allows a user to specify an initial model and identify key features in the data. These features act as hard constraints that the model must not pass through as it deforms. We have employed the method to perform semi-automatic segmentation of heart structures from cine MRI data.

  19. 3D Dynamic Earthquake Fracture Simulation (Test Case)

    NASA Astrophysics Data System (ADS)

    Korkusuz Öztürk, Yasemin; Meral Özel, Nurcan; Ando, Ryosuke

    2016-04-01

    A 3D dynamic earthquake fracture simulation is being developed for the fault structures which are non-planar to understand heterogeneous stress states in the Marmara Sea. Locating in a seismic gap, a large earthquake is expected in the center of the Sea of Marmara. Concerning the fact that more than 14 million inhabitants of İstanbul, located very closely to the Marmara Sea, the importance of the analysis of the Central Marmara Sea is extremely high. A few 3D dynamic earthquake fracture studies have been already done in the Sea of Marmara for pure right lateral strike-slip stress regimes (Oglesby and Mai, 2012; Aochi and Ulrich, 2015). In this study, a 3D dynamic earthquake fracture model with heterogeneous stress patches from the TPV5, a SCEC code validation case, is adapted. In this test model, the fault and the ground surfaces are gridded by a scalene triangulation technique using GMSH program. For a grid size changing between 0.616 km and 1.050 km the number of elements for the fault surface is 1984 and for the ground surface is 1216. When these results are compared with Kaneko's results for TPV5 from SPECFEM3D, reliable findings could be observed for the first 6.5 seconds (stations on the fault) although a stability problem is encountered after this time threshold. To solve this problem grid sizes are made smaller, so the number of elements increase 7986 for the fault surface and 4867 for the ground surface. On the other hand, computational problems arise in that case, since the computation time is directly proportional to the number of total elements and the required memory also increases with the square of that. Therefore, it is expected that this method can be adapted for less coarse grid cases, regarding the main difficulty coming from the necessity of an effective supercomputer and run time limitations. The main objective of this research is to obtain 3D dynamic earthquake rupture scenarios, concerning not only planar and non-planar faults but also

  20. Modeling tree crown dynamics with 3D partial differential equations

    PubMed Central

    Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

    2014-01-01

    We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth toward light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications. PMID:25101095

  1. 3D dynamic holographic display by modulating complex amplitude experimentally.

    PubMed

    Li, Xin; Liu, Juan; Jia, Jia; Pan, Yijie; Wang, Yongtian

    2013-09-09

    Complex amplitude modulation method is presented theoretically and performed experimentally for three-dimensional (3D) dynamic holographic display with reduced speckle using a single phase-only spatial light modulator. The determination of essential factors is discussed based on the basic principle and theory. The numerical simulations and optical experiments are performed, where the static and animated objects without refinement on the surfaces and without random initial phases are reconstructed successfully. The results indicate that this method can reduce the speckle in reconstructed images effectively; furthermore, it will not cause the internal structure in the reconstructed pixels. Since the complex amplitude modulation is based on the principle of phase-only hologram, it does not need the stringent alignment of pixels. This method can be used for high resolution imaging or measurement in various optical areas.

  2. A skinning prediction scheme for dynamic 3D mesh compression

    NASA Astrophysics Data System (ADS)

    Mamou, Khaled; Zaharia, Titus; Prêteux, Françoise

    2006-08-01

    This paper presents a new prediction-based compression technique for dynamic 3D meshes with constant connectivity and time-varying geometry. The core of the proposed algorithm is a skinning model used for motion compensation. The mesh is first partitioned within vertex clusters that can be described by a single affine motion model. The proposed segmentation technique automatically determines the number of clusters and relays on a decimation strategy privileging the simplification of vertices exhibiting the same affine motion over the whole animation sequence. The residual prediction errors are finally compressed using a temporal-DCT representation. The performances of our encoder are objectively evaluated on a data set of eight animation sequences with various sizes, geometries and topologies, and exhibiting both rigid and elastic motions. The experimental evaluation shows that the proposed compression scheme outperforms state of the art techniques such as MPEG-4/AFX, Dynapack, RT, GV, MCGV, TDCT, PCA and RT compression schemes.

  3. Effects of in-pulse transverse relaxation in 3D ultrashort echo time sequences: analytical derivation, comparison to numerical simulation and experimental application at 3T.

    PubMed

    Springer, Fabian; Steidle, Günter; Martirosian, Petros; Claussen, Claus D; Schick, Fritz

    2010-09-01

    The introduction of ultrashort-echo-time-(UTE)-sequences to clinical whole-body MR scanners has opened up the field of MR characterization of materials or tissues with extremely fast signal decay. If the transverse relaxation time is in the range of the RF-pulse duration, approximation of the RF-pulse by an instantaneous rotation applied at the middle of the RF-pulse and immediately followed by free relaxation will lead to a distinctly underestimated echo signal. Thus, the regular Ernst equation is not adequate to correctly describe steady state signal under those conditions. The paper presents an analytically derived modified Ernst equation, which correctly describes in-pulse relaxation of transverse magnetization under typical conditions: The equation is valid for rectangular excitation pulses, usually applied in 3D UTE sequences. Longitudinal relaxation time of the specimen must be clearly longer than RF-pulse duration, which is fulfilled for tendons and bony structures as well as many solid materials. Under these conditions, the proposed modified Ernst equation enables adequate and relatively simple calculation of the magnetization of materials or tissues. Analytically derived data are compared to numerical results obtained by using an established Runge-Kutta-algorithm based on the Bloch equations. Validity of the new approach was also tested by systematical measurements of a solid polymeric material on a 3T whole-body MR scanner. Thus, the presented modified Ernst equation provides a suitable basis for T1 measurements, even in tissues with T2 values as short as the RF-pulse duration: independent of RF-pulse duration, the 'variable flip angle method' led to consistent results of longitudinal relaxation time T1, if the T2 relaxation time of the material of interest is known as well.

  4. Computer acquisition of 3D images utilizing dynamic speckles

    NASA Astrophysics Data System (ADS)

    Kamshilin, Alexei A.; Semenov, Dmitry V.; Nippolainen, Ervin; Raita, Erik

    2006-05-01

    We present novel technique for fast non-contact and continuous profile measurements of rough surfaces by use of dynamic speckles. The dynamic speckle pattern is generated when the laser beam scans the surface under study. The most impressive feature of the proposed technique is its ability to work at extremely high scanning speed of hundreds meters per second. The technique is based on the continuous frequency measurements of the light-power modulation after spatial filtering of the scattered light. The complete optical-electronic system was designed and fabricated for fast measurement of the speckles velocity, its recalculation into the distance, and further data acquisition into computer. The measured surface profile is displayed in a PC monitor in real time. The response time of the measuring system is below 1 μs. Important parameters of the system such as accuracy, range of measurements, and spatial resolution are analyzed. Limits of the spatial filtering technique used for continuous tracking of the speckle-pattern velocity are shown. Possible ways of further improvement of the measurements accuracy are demonstrated. Owing to its extremely fast operation, the proposed technique could be applied for online control of the 3D-shape of complex objects (e.g., electronic circuits) during their assembling.

  5. Flexible 3D pharmacophores as descriptors of dynamic biological space.

    PubMed

    Nettles, James H; Jenkins, Jeremy L; Williams, Chris; Clark, Alex M; Bender, Andreas; Deng, Zhan; Davies, John W; Glick, Meir

    2007-10-01

    Development of a pharmacophore hypothesis related to small-molecule activity is pivotal to chemical optimization of a series, since it defines features beneficial or detrimental to activity. Although crystal structures may provide detailed 3D interaction information for one molecule with its receptor, docking a different ligand to that model often leads to unreliable results due to protein flexibility. Graham Richards' lab was one of the first groups to utilize "fuzzy" pattern recognition algorithms taken from the field of image processing to solve problems in protein modeling. Thus, descriptor "fuzziness" was partly able to emulate conformational flexibility of the target while simultaneously enhancing the speed of the search. In this work, we extend these developments to a ligand-based method for describing and aligning molecules in flexible chemical space termed FEature POint PharmacophoreS (FEPOPS), which allows exploration of dynamic biological space. We develop a novel, combinatorial algorithm for molecular comparisons and evaluate it using the WOMBAT dataset. The new approach shows superior retrospective virtual screening performance than earlier shape-based or charge-based algorithms. Additionally, we use target prediction to evaluate how FEPOPS alignments match the molecules biological activity by identifying the atoms and features that make the key contributions to overall chemical similarity. Overall, we find that FEPOPS are sufficiently fuzzy and flexible to find not only new ligand scaffolds, but also challenging molecules that occupy different conformational states of dynamic biological space as from induced fits.

  6. Analysis and dynamic 3D visualization of cerebral blood flow combining 3D and 4D MR image sequences

    NASA Astrophysics Data System (ADS)

    Forkert, Nils Daniel; Säring, Dennis; Fiehler, Jens; Illies, Till; Möller, Dietmar; Handels, Heinz

    2009-02-01

    In this paper we present a method for the dynamic visualization of cerebral blood flow. Spatio-temporal 4D magnetic resonance angiography (MRA) image datasets and 3D MRA datasets with high spatial resolution were acquired for the analysis of arteriovenous malformations (AVMs). One of the main tasks is the combination of the information of the 3D and 4D MRA image sequences. Initially, in the 3D MRA dataset the vessel system is segmented and a 3D surface model is generated. Then, temporal intensity curves are analyzed voxelwise in the 4D MRA image sequences. A curve fitting of the temporal intensity curves to a patient individual reference curve is used to extract the bolus arrival times in the 4D MRA sequences. After non-linear registration of both MRA datasets the extracted hemodynamic information is transferred to the surface model where the time points of inflow can be visualized color coded dynamically over time. The dynamic visualizations computed using the curve fitting method for the estimation of the bolus arrival times were rated superior compared to those computed using conventional approaches for bolus arrival time estimation. In summary the procedure suggested allows a dynamic visualization of the individual hemodynamic situation and better understanding during the visual evaluation of cerebral vascular diseases.

  7. Vortex dynamics in 3D shock-bubble interaction

    NASA Astrophysics Data System (ADS)

    Hejazialhosseini, Babak; Rossinelli, Diego; Koumoutsakos, Petros

    2013-11-01

    The dynamics of shock-bubble interaction involve an interplay of vortex stretching, dilation, and baroclinic vorticity generation. Here, we quantify the interplay of these contributions through high resolution 3D simulations for several Mach and Atwood numbers. We present a volume rendering of density and vorticity magnitude fields of shock-bubble interaction at M = 3 and air/helium density ratio η = 7.25 to elucidate the evolution of the flow structures. We distinguish the vorticity growth rates due to baroclinicity, stretching, and dilatation at low and high Mach numbers as well as the late time evolution of the circulation. The results demonstrate that a number of analytical models need to be revised in order to predict the late time circulation of shock-bubble interactions at high Mach numbers. To this effect, we propose a simple model for the dependence of the circulation to Mach number and ambient to bubble density ratio for air/helium shock-bubble interactions.

  8. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2004-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  9. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2001-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  10. Gamified Assessment Supported by a Dynamic 3D Collaborative Game

    ERIC Educational Resources Information Center

    Mavridis, Apostolos; Tsiatsos, Thrasyvoulos; Chatzakis, Michalis; Kitsikoudis, Konstantinos; Lazarou, Efthymios

    2015-01-01

    This study examined whether a 3D collaborative gave can be used as a midterm examination method and investigated the impact of this game on students' attitude towards collaboration. A total of 89 students and one coordinating professor participated in this study. The intervention lasted five weeks and took place in a computer science department.…

  11. Face recognition based on matching of local features on 3D dynamic range sequences

    NASA Astrophysics Data System (ADS)

    Echeagaray-Patrón, B. A.; Kober, Vitaly

    2016-09-01

    3D face recognition has attracted attention in the last decade due to improvement of technology of 3D image acquisition and its wide range of applications such as access control, surveillance, human-computer interaction and biometric identification systems. Most research on 3D face recognition has focused on analysis of 3D still data. In this work, a new method for face recognition using dynamic 3D range sequences is proposed. Experimental results are presented and discussed using 3D sequences in the presence of pose variation. The performance of the proposed method is compared with that of conventional face recognition algorithms based on descriptors.

  12. DREAM3D simulations of inner-belt dynamics

    SciTech Connect

    Cunningham, Gregory Scott

    2015-05-26

    A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere, where the loss to the atmosphere is enabled by pitch-angle scattering from Coulomb and wave-particle interactions. In the 1973 paper, equilibrium solutions to a decoupled set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium two-belt structure. Each 1D radial diffusion equation incorporated an L-and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This decoupling of the problem is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering. However, for some values of μ and L the lifetime associated with pitch-angle scattering is comparable to the timescale associated with radial diffusion, suggesting that the true equilibrium solutions might reflect `coupled modes' involving pitch-angle scattering and radial diffusion and thus requiring a 3D diffusion model. In the work we show here, we have computed the equilibrium solutions using our 3D diffusion model, DREAM3D, that allows for such coupling. We find that the 3D equilibrium solutions are quite similar to the solutions shown in the 1973 paper when we use the same physical models for radial diffusion and pitch-angle scattering from hiss. However, we show that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to understand the two-belt structure.

  13. Comparison of accelerated 3-D spiral chemical shift imaging and single-voxel spectroscopy at 3T in the pediatric age group.

    PubMed

    Yazbek, Sandrine; Prabhu, Sanjay P; Connaughton, Pauline; Grant, Patricia E; Gagoski, Borjan

    2015-08-01

    Single-voxel spectroscopy (SVS) is usually used in the pediatric population when a short acquisition time is crucial. To overcome the long acquisition time of 3-D phase-encoded chemical shift imaging (CSI) and lack of spatial coverage of single-voxel spectroscopy, efficient encoding schemes using spiral k-space trajectories have been successfully deployed, enabling acquisition of volumetric CSI in <5 min. We assessed feasibility of using 3-D spiral CSI sequence routinely in pediatric clinical settings by comparing its reconstructed spectra against SVS spectra. Volumetric spiral CSI obtained spectra from 2-cc isotropic voxels over a 16×16×10-cm region. SVS acquisition encoded a 3.4-cc (1.5-mm) isotropic voxel. Acquisition time was 3 min for every technique. Data were gathered prospectively from 11 random pediatric patients. Spectra from left basal ganglia were obtained using both techniques and were processed with post-processing software. The following metabolite ratios were calculated: N-acetylaspartate/creatine (NAA/Cr), choline/creatine (Cho/Cr), lactate/creatine (Lac/Cr) and N-acetylapartate/choline (NAA/Cho). We collected data on 11 children ages 4 days to 10 years. In 10/11 cases, spectral quality of both methods was acceptable. Considering 10/11 cases, we found a statistically significant difference between SVS and 3-D spiral CSI for all three ratios. However, this difference was fixed and was probably caused by a fixed bias. This means that 3-D spiral CSI can be used instead of SVS by removing the mean difference between the methods for each ratio. Accelerated 3-D CSI is feasible in pediatric patients and can potentially substitute for SVS.

  14. The vibrational dynamics of 3D HOCl above dissociation

    SciTech Connect

    Lin, Yi-Der; Reichl, L. E.; Jung, Christof

    2015-03-28

    We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.

  15. The vibrational dynamics of 3D HOCl above dissociation

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Der; Reichl, L. E.; Jung, Christof

    2015-03-01

    We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.

  16. Recent results on photonic devices made by laser writing: 3D 3T near IR waveguides, mid-IR spectrometers and electro-optic beam combiners

    NASA Astrophysics Data System (ADS)

    Martin, G.; Vázquez de Aldana, J. R.; Rodenas, A.; d'Amico, C.; Stoian, R.

    2016-07-01

    Direct laser writing is a powerful technique for the development of astrophotonic devices, namely by allowing 3D structuring of waveguides and structures. One of the main interests is the possibility to avoid in-plane crossings of waveguides that can induce losses and crosstalk in future multi-telescope beam combiners. We will present our results in 3D three telescope beam combiners in the near infrared, that allow for phase closure studies. Besides, laser writing can be used to inscribe a grating over long distances along the waveguide direction. This can be used as an on-chip diffraction grating or as a way to sample a stationary wave that can be obtained in the waveguide. Thus, integrated optics spectrometers based on the SWIFTS concept (stationary wave integrated Fourier transform spectrometer) have been realized and characterized in the near and mid infrared using commercial chalcogenide glasses. Finally, we will also present our results on laser writing on electro-optic materials, that allow to obtain waveguides and beam combiners that can be phase-modulated using electrodes. We have focused our work on two well-known materials: Lithium Niobate, that allows for TM waveguides and has a high electro-optical coefficient, and BGO, that has a lower coefficient, but presents the advantage of being isotropic, guiding both TE and TM polarizations identically.

  17. First 3-D simulations of meteor plasma dynamics and turbulence

    NASA Astrophysics Data System (ADS)

    Oppenheim, Meers M.; Dimant, Yakov S.

    2015-02-01

    Millions of small but detectable meteors hit the Earth's atmosphere every second, creating trails of hot plasma that turbulently diffuse into the background atmosphere. For over 60 years, radars have detected meteor plasmas and used these signals to infer characteristics of the meteoroid population and upper atmosphere, but, despite the importance of meteor radar measurements, the complex processes by which these plasmas evolve have never been thoroughly explained or modeled. In this paper, we present the first fully 3-D simulations of meteor evolution, showing meteor plasmas developing instabilities, becoming turbulent, and inhomogeneously diffusing into the background ionosphere. These instabilities explain the characteristics and strength of many radar observations, in particular the high-resolution nonspecular echoes made by large radars. The simulations reveal how meteors create strong electric fields that dig out deep plasma channels along the Earth's magnetic fields. They also allow researchers to explore the impacts of the intense winds and wind shears, commonly found at these altitudes, on meteor plasma evolution. This study will allow the development of more sophisticated models of meteor radar signals, enabling the extraction of detailed information about the properties of meteoroid particles and the atmosphere.

  18. Measurement of dynamic cell-induced 3D displacement fields in vitro for traction force optical coherence microscopy

    PubMed Central

    Mulligan, Jeffrey A.; Bordeleau, François; Reinhart-King, Cynthia A.; Adie, Steven G.

    2017-01-01

    Traction force microscopy (TFM) is a method used to study the forces exerted by cells as they sense and interact with their environment. Cell forces play a role in processes that take place over a wide range of spatiotemporal scales, and so it is desirable that TFM makes use of imaging modalities that can effectively capture the dynamics associated with these processes. To date, confocal microscopy has been the imaging modality of choice to perform TFM in 3D settings, although multiple factors limit its spatiotemporal coverage. We propose traction force optical coherence microscopy (TF-OCM) as a novel technique that may offer enhanced spatial coverage and temporal sampling compared to current methods used for volumetric TFM studies. Reconstructed volumetric OCM data sets were used to compute time-lapse extracellular matrix deformations resulting from cell forces in 3D culture. These matrix deformations revealed clear differences that can be attributed to the dynamic forces exerted by normal versus contractility-inhibited NIH-3T3 fibroblasts embedded within 3D Matrigel matrices. Our results are the first step toward the realization of 3D TF-OCM, and they highlight the potential use of OCM as a platform for advancing cell mechanics research. PMID:28271010

  19. Dynamics of 3D view invariance in monkey inferotemporal cortex.

    PubMed

    Ratan Murty, N Apurva; Arun, Sripati P

    2015-04-01

    Rotations in depth are challenging for object vision because features can appear, disappear, be stretched or compressed. Yet we easily recognize objects across views. Are the underlying representations view invariant or dependent? This question has been intensely debated in human vision, but the neuronal representations remain poorly understood. Here, we show that for naturalistic objects, neurons in the monkey inferotemporal (IT) cortex undergo a dynamic transition in time, whereby they are initially sensitive to viewpoint and later encode view-invariant object identity. This transition depended on two aspects of object structure: it was strongest when objects foreshortened strongly across views and were similar to each other. View invariance in IT neurons was present even when objects were reduced to silhouettes, suggesting that it can arise through similarity between external contours of objects across views. Our results elucidate the viewpoint debate by showing that view invariance arises dynamically in IT neurons out of a representation that is initially view dependent.

  20. Introducing a New 3D Dynamical Model for Barred Galaxies

    NASA Astrophysics Data System (ADS)

    Jung, Christof; Zotos, Euaggelos E.

    2015-11-01

    The regular or chaotic dynamics of an analytical realistic three dimensional model composed of a spherically symmetric central nucleus, a bar and a flat disk is investigated. For describing the properties of the bar, we introduce a new simple dynamical model and we explore the influence on the character of orbits of all the involved parameters of it, such as the mass and the scale length of the bar, the major semi-axis and the angular velocity of the bar, as well as the energy. Regions of phase space with ordered and chaotic motion are identified in dependence on these parameters and for breaking the rotational symmetry. First, we study in detail the dynamics in the invariant plane z = pz = 0 using the Poincaré map as a basic tool and then study the full three-dimensional case using the Smaller Alignment index method as principal tool for distinguishing between order and chaos. We also present strong evidence obtained through the numerical simulations that our new bar model can realistically describe the formation and the evolution of the observed twin spiral structure in barred galaxies.

  1. Quasi-3D Cytoskeletal Dynamics of Osteocytes under Fluid Flow

    PubMed Central

    Baik, Andrew D.; Lu, X. Lucas; Qiu, Jun; Huo, Bo; Hillman, Elizabeth M.C.; Dong, Cheng; Guo, X. Edward

    2010-01-01

    Osteocytes respond to dynamic fluid shear loading by activating various biochemical pathways, mediating a dynamic process of bone formation and resorption. Whole-cell deformation and regional deformation of the cytoskeleton may be able to directly regulate this process. Attempts to image cellular deformation by conventional microscopy techniques have been hindered by low temporal or spatial resolution. In this study, we developed a quasi-three-dimensional microscopy technique that enabled us to simultaneously visualize an osteocyte's traditional bottom-view profile and a side-view profile at high temporal resolution. Quantitative analysis of the plasma membrane and either the intracellular actin or microtubule (MT) cytoskeletal networks provided characterization of their deformations over time. Although no volumetric dilatation of the whole cell was observed under flow, both the actin and MT networks experienced primarily tensile strains in all measured strain components. Regional heterogeneity in the strain field of normal strains was observed in the actin networks, especially in the leading edge to flow, but not in the MT networks. In contrast, side-view shear strains exhibited similar subcellular distribution patterns in both networks. Disruption of MT networks caused actin normal strains to decrease, whereas actin disruption had little effect on the MT network strains, highlighting the networks' mechanical interactions in osteocytes. PMID:21044578

  2. 3D Probed Lipid Dynamics in Small Unilamellar Vesicles.

    PubMed

    Chao, Meng-Hsuan; Lin, Yen-Ting; Dhenadhayalan, Namasivayam; Lee, Hsin-Lung; Lee, Hsin-Yen; Lin, King-Chuen

    2017-04-01

    Single-molecule fluorescence correlation spectroscopy overcomes the resolution barrier of optical microscopy (10≈-20 nm) and is utilized to look into lipid dynamics in small unilamellar vesicles (SUVs; diameter < 100 nm). The fluorescence trajectories of lipid-like tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine (DiD) in the membrane bilayers are acquired at a single-molecule level. The autocorrelation analysis yields the kinetic information on lipid organization, oxygen transport, and lateral diffusion in SUVs' membrane. First, the isomerization feasibility may be restricted by the addition of cholesterols, which form structure conjugation with DiD chromophore. Second, the oxygen transport is prevented from the ultrasmall cluster and cholesterol-rich regions, whereas it can pass through the membrane region with liquid-disordered phase (Ld ) and defects. Third, by analyzing 2D spectra correlating the lipid diffusion coefficient and triplet-state lifetime, the heterogeneity in lipid bilayer can be precisely visualized such as lipid domain with different phases, the defects of lipid packing, and DiD-induced "bouquet" ultrasmall clusters.

  3. 3D numerical simulations of vesicle and inextensible capsule dynamics

    NASA Astrophysics Data System (ADS)

    Farutin, Alexander; Biben, Thierry; Misbah, Chaouqi

    2014-10-01

    Vesicles are locally-inextensible fluid membranes, capsules are endowed with in-plane shear elasticity mimicking the cytoskeleton of red blood cells (RBCs), but are extensible, while RBCs are inextensible. We use boundary integral (BI) methods based on the Green function techniques to model and solve numerically their dynamics. We regularize the single layer integral by subtraction of exact identities for the terms involving the normal and the tangential components of the force. The stability and precision of BI calculation is enhanced by taking advantage of additional quadrature nodes located in vertices of an auxiliary mesh, constructed by a standard refinement procedure from the main mesh. We extend the partition of unity technique to boundary integral calculation on triangular meshes. The proposed algorithm offers the same treatment of near-singular integration regardless whether the source and the target points belong to the same surface or not. Bending forces are calculated by using expressions derived from differential geometry. Membrane incompressibility is handled by using two penalization parameters per suspended entity: one for deviation of the global area from prescribed value and another for the sum of squares of local strains defined on each vertex. Extensible or inextensible capsules, a model of RBC, are studied by storing the position in the reference configuration for each vertex. The elastic force is then calculated by direct variation of the elastic energy. Various nonequilibrium physical examples on vesicles and capsules will be presented and the convergence and precision tests highlighted. Overall, a good convergence is observed with numerical error inversely proportional to the number of vertices used for surface discretization, the highest order of convergence allowed by piece-wise linear interpolation of the surface.

  4. Synthesis and display of dynamic holographic 3D scenes with real-world objects.

    PubMed

    Paturzo, Melania; Memmolo, Pasquale; Finizio, Andrea; Näsänen, Risto; Naughton, Thomas J; Ferraro, Pietro

    2010-04-26

    A 3D scene is synthesized combining multiple optically recorded digital holograms of different objects. The novel idea consists of compositing moving 3D objects in a dynamic 3D scene using a process that is analogous to stop-motion video. However in this case the movie has the exciting attribute that it can be displayed and observed in 3D. We show that 3D dynamic scenes can be projected as an alternative to complicated and heavy computations needed to generate realistic-looking computer generated holograms. The key tool for creating the dynamic action is based on a new concept that consists of a spatial, adaptive transformation of digital holograms of real-world objects allowing full control in the manipulation of the object's position and size in a 3D volume with very high depth-of-focus. A pilot experiment to evaluate how viewers perceive depth in a conventional single-view display of the dynamic 3D scene has been performed.

  5. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    PubMed Central

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-01-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils. PMID:26548801

  6. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions.

    PubMed

    Doyle, Andrew D; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M

    2015-11-09

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

  7. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    NASA Astrophysics Data System (ADS)

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-11-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

  8. On the dynamics of jellyfish locomotion via 3D particle tracking velocimetry

    NASA Astrophysics Data System (ADS)

    Piper, Matthew; Kim, Jin-Tae; Chamorro, Leonardo P.

    2016-11-01

    The dynamics of jellyfish (Aurelia aurita) locomotion is experimentally studied via 3D particle tracking velocimetry. 3D locations of the bell tip are tracked over 1.5 cycles to describe the jellyfish path. Multiple positions of the jellyfish bell margin are initially tracked in 2D from four independent planes and individually projected in 3D based on the jellyfish path and geometrical properties of the setup. A cubic spline interpolation and the exponentially weighted moving average are used to estimate derived quantities, including velocity and acceleration of the jellyfish locomotion. We will discuss distinctive features of the jellyfish 3D motion at various swimming phases, and will provide insight on the 3D contraction and relaxation in terms of the locomotion, the steadiness of the bell margin eccentricity, and local Reynolds number based on the instantaneous mean diameter of the bell.

  9. Dynamic visual image modeling for 3D synthetic scenes in agricultural engineering

    NASA Astrophysics Data System (ADS)

    Gao, Li; Yan, Juntao; Li, Xiaobo; Ji, Yatai; Li, Xin

    The dynamic visual image modeling for 3D synthetic scenes by using dynamic multichannel binocular visual image based on the mobile self-organizing network. Technologies of 3D modeling synthetic scenes have been widely used in kinds of industries. The main purpose of this paper is to use multiple networks of dynamic visual monitors and sensors to observe an unattended area, to use the advantages of mobile network in rural areas for improving existing mobile network information service further and providing personalized information services. The goal of displaying is to provide perfect representation of synthetic scenes. Using low-power dynamic visual monitors and temperature/humidity sensor or GPS installed in the node equipment, monitoring data will be sent at scheduled time. Then through the mobile self-organizing network, 3D model is rebuilt by synthesizing the returned images. On this basis, we formalize a novel algorithm for multichannel binocular visual 3D images based on fast 3D modeling. Taking advantage of these low prices mobile, mobile self-organizing networks can get a large number of video from where is not suitable for human observation or unable to reach, and accurately synthetic 3D scene. This application will play a great role in promoting its application in agriculture.

  10. Investigation of Dynamic Crack Coalescence Using a Gypsum-Like 3D Printing Material

    NASA Astrophysics Data System (ADS)

    Jiang, Chao; Zhao, Gao-Feng; Zhu, Jianbo; Zhao, Yi-Xin; Shen, Luming

    2016-10-01

    Dynamic crack coalescence attracts great attention in rock mechanics. However, specimen preparation in experimental study is a time-consuming and difficult procedure. In this work, a gypsum-like material by powder bed and inkjet 3D printing technique was applied to produce specimens with preset cracks for split Hopkinson pressure bar (SHPB) test. From micro X-ray CT test, it was found that the 3D printing technique could successfully prepare specimens that contain preset cracks with width of 0.2 mm. Basic mechanical properties of the 3D printing material, i.e., the elastic modulus, the Poisson's ratio, the density, the compressive strength, the indirect tensile strength, and the fracture toughness, were obtained and reported. Unlike 3D printed specimens using polylactic acid, these gypsum-like specimens can produce failure patterns much closer to those observed in classical rock mechanical tests. Finally, the dynamic crack coalescence of the 3D printed specimens with preset cracks were captured using a high-speed camera during SHPB tests. Failure patterns of these 3D printed specimens are similar to the specimens made by Portland cement concrete. Our results indicate that sample preparation by 3D printing is highly competitive due to its quickness in prototyping, precision and flexibility on the geometry, and high material homogeneity.

  11. Nonrigid registration and classification of the kidneys in 3D dynamic contrast enhanced (DCE) MR images

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Ghafourian, Pegah; Sharma, Puneet; Salman, Khalil; Martin, Diego; Fei, Baowei

    2012-02-01

    We have applied image analysis methods in the assessment of human kidney perfusion based on 3D dynamic contrast-enhanced (DCE) MRI data. This approach consists of 3D non-rigid image registration of the kidneys and fuzzy C-mean classification of kidney tissues. The proposed registration method reduced motion artifacts in the dynamic images and improved the analysis of kidney compartments (cortex, medulla, and cavities). The dynamic intensity curves show the successive transition of the contrast agent through kidney compartments. The proposed method for motion correction and kidney compartment classification may be used to improve the validity and usefulness of further model-based pharmacokinetic analysis of kidney function.

  12. Evolution, Interaction, and Intrinsic Properties of Dislocations in Intermetallics: Anisotropic 3D Dislocation Dynamics Approach

    SciTech Connect

    Chen, Qian

    2008-01-01

    The generation, motion, and interaction of dislocations play key roles during the plastic deformation process of crystalline solids. 3D Dislocation Dynamics has been employed as a mesoscale simulation algorithm to investigate the collective and cooperative behavior of dislocations. Most current research on 3D Dislocation Dynamics is based on the solutions available in the framework of classical isotropic elasticity. However, due to some degree of elastic anisotropy in almost all crystalline solids, it is very necessary to extend 3D Dislocation Dynamics into anisotropic elasticity. In this study, first, the details of efficient and accurate incorporation of the fully anisotropic elasticity into 3D discrete Dislocation Dynamics by numerically evaluating the derivatives of Green's functions are described. Then the intrinsic properties of perfect dislocations, including their stability, their core properties and disassociation characteristics, in newly discovered rare earth-based intermetallics and in conventional intermetallics are investigated, within the framework of fully anisotropic elasticity supplemented with the atomistic information obtained from the ab initio calculations. Moreover, the evolution and interaction of dislocations in these intermetallics as well as the role of solute segregation are presented by utilizing fully anisotropic 3D dislocation dynamics. The results from this work clearly indicate the role and the importance of elastic anisotropy on the evolution of dislocation microstructures, the overall ductility and the hardening behavior in these systems.

  13. The AFDD International Dynamic Stall Workshop on Correlation of Dynamic Stall Models with 3-D Dynamic Stall Data

    NASA Technical Reports Server (NTRS)

    Tan, C. M.; Carr, L. W.

    1996-01-01

    A variety of empirical and computational fluid dynamics two-dimensional (2-D) dynamic stall models were compared to recently obtained three-dimensional (3-D) dynamic stall data in a workshop on modeling of 3-D dynamic stall of an unswept, rectangular wing, of aspect ratio 10. Dynamic stall test data both below and above the static stall angle-of-attack were supplied to the participants, along with a 'blind' case where only the test conditions were supplied in advance, with results being compared to experimental data at the workshop itself. Detailed graphical comparisons are presented in the report, which also includes discussion of the methods and the results. The primary conclusion of the workshop was that the 3-D effects of dynamic stall on the oscillating wing studied in the workshop can be reasonably reproduced by existing semi-empirical models once 2-D dynamic stall data have been obtained. The participants also emphasized the need for improved quantification of 2-D dynamic stall.

  14. Dynamics of Capillary-Driven Flow in 3D Printed Open Microchannels.

    PubMed

    Lade, Robert K; Hippchen, Erik J; Macosko, Christopher W; Francis, Lorraine F

    2017-03-28

    Microchannels have applications in microfluidic devices, patterns for micromolding, and even flexible electronic devices. Three-dimensional (3D) printing presents a promising alternative manufacturing route for these microchannels due to the technology's relative speed and the design freedom it affords its users. However, the roughness of 3D printed surfaces can significantly influence flow dynamics inside of a microchannel. In this work, open microchannels are fabricated using four different 3D printing techniques: fused deposition modeling (FDM), stereolithography (SLA), selective laser sintering, and multi jet modeling. Microchannels printed with each technology are evaluated with respect to their surface roughness, morphology, and how conducive they are to spontaneous capillary filling. Based on this initial assessment, microchannels printed with FDM and SLA are chosen as models to study spontaneous, capillary-driven flow dynamics in 3D printed microchannels. Flow dynamics are investigated over short (∼10(-3) s), intermediate (∼1 s), and long (∼10(2) s) time scales. Surface roughness causes a start-stop motion down the channel due to contact line pinning, while the cross-sectional shape imparted onto the channels during the printing process is shown to reduce the expected filling velocity. A significant delay in the onset of Lucas-Washburn dynamics (a long-time equilibrium state where meniscus position advances proportionally to the square root of time) is also observed. Flow dynamics are assessed as a function of printing technology, print orientation, channel dimensions, and liquid properties. This study provides the first in-depth investigation of the effect of 3D printing on microchannel flow dynamics as well as a set of rules on how to account for these effects in practice. The extension of these effects to closed microchannels and microchannels fabricated with other 3D printing technologies is also discussed.

  15. Numerical simulations and vorticity dynamics of self-propelled swimming of 3D bionic fish

    NASA Astrophysics Data System (ADS)

    Xin, ZhiQiang; Wu, ChuiJie

    2012-02-01

    Numerical simulations and the control of self-propelled swimming of three-dimensional bionic fish in a viscous flow and the mechanism of fish swimming are carried out in this study, with a 3D computational fluid dynamics package, which includes the immersed boundary method and the volume of fluid method, the adaptive multi-grid finite volume method, and the control strategy of fish swimming. Firstly, the mechanism of 3D fish swimming was studied and the vorticity dynamics root was traced to the moving body surface by using the boundary vorticity-flux theory. With the change of swimming speed, the contributions of the fish body and caudal fin to thrust are analyzed quantitatively. The relationship between vortex structures of fish swimming and the forces exerted on the fish body are also given in this paper. Finally, the 3D wake structure of self-propelled swimming of 3D bionic fish is presented. The in-depth analysis of the 3D vortex structure in the role of 3D biomimetic fish swimming is also performed.

  16. Dynamic 3d Modeling of a Canal-Tunnel Using Photogrammetric and Bathymetric Data

    NASA Astrophysics Data System (ADS)

    Moisan, E.; Heinkele, C.; Charbonnier, P.; Foucher, P.; Grussenmeyer, P.; Guillemin, S.; Koehl, M.

    2017-02-01

    This contribution introduces an original method for dynamically surveying the vault and underwater parts of a canal-tunnel for 3D modeling. The recording system, embedded on a barge, is composed of cameras that provide images of the above-water part of the tunnel, and a sonar that acquires underwater 3D profiles. In this contribution we propose to fully exploit the capacities of photogrammetry to deal with the issue of geo-referencing data in the absence of global positioning system (GPS) data. More specifically, we use it both for reconstructing the vault and side walls of the tunnel in 3D and for estimating the trajectory of the boat, which is necessary to rearrange sonar profiles to form the 3D model of the canal. We report on a first experimentation carried out inside a canal-tunnel and show promising preliminary results that illustrate the potentialities of the proposed approach.

  17. Development and applications of 4-D ultrasound (dynamic 3-D) in neurosonology.

    PubMed

    Delcker, A; Schürks, M; Polz, H

    1999-10-01

    The development and application of color-coded data in three-dimensional (3-D) reconstruction or four-dimensional (4-D) imaging (equal to dynamic 3-D) are demonstrated. In 4-D imaging, electrocardiography-triggered data acquisition of consecutive phases during the heart cycle are stored to form a multiphase 3-D data set. The option of color-coded data gives a new insight into such hemodynamic information. In the past, 3-D reconstructions were simple unicolor images, as in power mode, and the color-coded hemodynamic information was lost. These new options are presented here, along with color-coded data in examples of angiographically controlled pathologic results in extracranial and intracranial vessels.

  18. First application of the 3D-MHB on dynamic compressive behavior of UHPC

    NASA Astrophysics Data System (ADS)

    Cadoni, Ezio; Dotta, Matteo; Forni, Daniele; Riganti, Gianmario; Albertini, Carlo

    2015-09-01

    In order to study the dynamic behaviour of material in confined conditions a new machine was conceived and called 3D-Modified Hopkinson Bar (3D-MHB). It is a Modified Hopkinson Bar apparatus designed to apply dynamic loading in materials having a tri-axial stress state. It consists of a pulse generator system (with pre-tensioned bar and brittle joint), 1 input bar, and 5 output bars. The first results obtained on Ultra High Performance Concrete in compression with three different mono-axial compression states are presented. The results show how the pre-stress states minimize the boundary condition and a more uniform response is obtained.

  19. 3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

    PubMed Central

    Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, Jérôme; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

    2017-01-01

    We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume. PMID:28230188

  20. 3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

    NASA Astrophysics Data System (ADS)

    Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, Jérôme; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

    2017-02-01

    We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume.

  1. Introducing a Public Stereoscopic 3D High Dynamic Range (SHDR) Video Database

    NASA Astrophysics Data System (ADS)

    Banitalebi-Dehkordi, Amin

    2017-03-01

    High dynamic range (HDR) displays and cameras are paving their ways through the consumer market at a rapid growth rate. Thanks to TV and camera manufacturers, HDR systems are now becoming available commercially to end users. This is taking place only a few years after the blooming of 3D video technologies. MPEG/ITU are also actively working towards the standardization of these technologies. However, preliminary research efforts in these video technologies are hammered by the lack of sufficient experimental data. In this paper, we introduce a Stereoscopic 3D HDR database of videos that is made publicly available to the research community. We explain the procedure taken to capture, calibrate, and post-process the videos. In addition, we provide insights on potential use-cases, challenges, and research opportunities, implied by the combination of higher dynamic range of the HDR aspect, and depth impression of the 3D aspect.

  2. The optimizations of CGH generation algorithms based on multiple GPUs for 3D dynamic holographic display

    NASA Astrophysics Data System (ADS)

    Yang, Dan; Liu, Juan; Zhang, Yingxi; Li, Xin; Wang, Yongtian

    2016-10-01

    Holographic display has been considered as a promising display technology. Currently, low-speed generation of holograms with big holographic data is one of crucial bottlenecks for three dimensional (3D) dynamic holographic display. To solve this problem, the acceleration method computation platform is presented based on look-up table point source method. The computer generated holograms (CGHs) acquisition is sped up by offline file loading and inline calculation optimization, where a pure phase CGH with gigabyte data is encoded to record an object with 10 MB sampling data. Both numerical simulation and optical experiment demonstrate that the CGHs with 1920×1080 resolution by the proposed method can be applied to the 3D objects reconstruction with high quality successfully. It is believed that the CGHs with huge data can be generated by the proposed method with high speed for 3D dynamic holographic display in near future.

  3. Tunable nonuniform sampling method for fast calculation and intensity modulation in 3D dynamic holographic display.

    PubMed

    Zhang, Zhao; Liu, Juan; Jia, Jia; Li, Xin; Han, Jian; Hu, Bin; Wang, Yongtian

    2013-08-01

    Heavy computational load of computer-generated hologram (CGH) and imprecise intensity modulation of 3D images are crucial problems in dynamic holographic display. The nonuniform sampling method is proposed to speed up CGH generation and precisely modulate the reconstructed intensities of phase-only CGH. The proposed method can eliminate the redundant information properly, where 70% reduction in the storage amount can be reached when it is combined with the novel lookup table method. Multigrayscale modulation of reconstructed 3D images can be achieved successfully. Numerical simulations and optical experiments are performed, and both are in good agreement. It is believed that the proposed method can be used in 3D dynamic holographic display.

  4. 3D dynamic simulation of crack propagation in extracorporeal shock wave lithotripsy

    NASA Astrophysics Data System (ADS)

    Wijerathne, M. L. L.; Hori, Muneo; Sakaguchi, Hide; Oguni, Kenji

    2010-06-01

    Some experimental observations of Shock Wave Lithotripsy(SWL), which include 3D dynamic crack propagation, are simulated with the aim of reproducing fragmentation of kidney stones with SWL. Extracorporeal shock wave lithotripsy (ESWL) is the fragmentation of kidney stones by focusing an ultrasonic pressure pulse onto the stones. 3D models with fine discretization are used to accurately capture the high amplitude shear shock waves. For solving the resulting large scale dynamic crack propagation problem, PDS-FEM is used; it provides numerically efficient failure treatments. With a distributed memory parallel code of PDS-FEM, experimentally observed 3D photoelastic images of transient stress waves and crack patterns in cylindrical samples are successfully reproduced. The numerical crack patterns are in good agreement with the experimental ones, quantitatively. The results shows that the high amplitude shear waves induced in solid, by the lithotriptor generated shock wave, play a dominant role in stone fragmentation.

  5. Trans3D: a free tool for dynamical visualization of EEG activity transmission in the brain.

    PubMed

    Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

    2014-08-01

    The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/.

  6. Effect of Ductile Agents on the Dynamic Behavior of SiC3D Network Composites

    NASA Astrophysics Data System (ADS)

    Zhu, Jingbo; Wang, Yangwei; Wang, Fuchi; Fan, Qunbo

    2016-10-01

    Co-continuous SiC ceramic composites using pure aluminum, epoxy, and polyurethane (PU) as ductile agents were developed. The dynamic mechanical behavior and failure mechanisms were investigated experimentally using the split Hopkinson pressure bar (SHPB) method and computationally by finite element (FE) simulations. The results show that the SiC3D/Al composite has the best overall performance in comparison with SiC3D/epoxy and SiC3D/PU composites. FE simulations are generally consistent with experimental data. These simulations provide valuable help in predicting mechanical strength and in interpreting the experimental results and failure mechanisms. They may be combined with micrographs for fracture characterizations of the composites. We found that interactions between the SiC phase and ductile agents under dynamic compression in the SHPB method are complex, and that interfacial condition is an important parameter that determines the mechanical response of SiC3D composites with a characteristic interlocking structure during dynamic compression. However, the effect of the mechanical properties of ductile agents on dynamic behavior of the composites is a second consideration in the production of the composites.

  7. How Spatial Abilities and Dynamic Visualizations Interplay When Learning Functional Anatomy with 3D Anatomical Models

    ERIC Educational Resources Information Center

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material…

  8. On the Dynamic Programming Approach for the 3D Navier-Stokes Equations

    SciTech Connect

    Manca, Luigi

    2008-06-15

    The dynamic programming approach for the control of a 3D flow governed by the stochastic Navier-Stokes equations for incompressible fluid in a bounded domain is studied. By a compactness argument, existence of solutions for the associated Hamilton-Jacobi-Bellman equation is proved. Finally, existence of an optimal control through the feedback formula and of an optimal state is discussed.

  9. Modulation measuring profilometry with cross grating projection and single shot for dynamic 3D shape measurement

    NASA Astrophysics Data System (ADS)

    Lu, Mingteng; Su, Xianyu; Cao, Yiping; You, Zhisheng; Zhong, Min

    2016-12-01

    In order to determine Dynamic 3-D shape with vertical measurement mode, a fast modulation measuring profilometry (MMP) with a cross grating projection and single shot is proposed. Unlike the previous methods, in our current projection system, one cross grating is projected by a special projection lens consisting of a common projection lens and a cylindrical lens. Due to the characteristics of cylindrical lens, the image of the vertical component and the horizontal component of the cross grating is separated in the image space, and the measuring range is just the space between the two image planes. Through a beam splitter, the CCD camera can coaxially capture the fringe pattern of the cross grating modulated by the testing object's shape. In one fringe pattern, by applying Fourier transform, filtering and inverse Fourier transform, the modulation corresponding to the vertical and horizontal components of the cross grating can be obtained respectively. Then the 3-D shape of the object can be reconstructed according to the mapping relationship between modulation and height, which was established by calibration process in advance. So the 3-D shape information can be recorded at the same speed of the frame rate of the CCD camera. This paper gives the principle of the proposed method and the set-up for measuring experiment and system calibration. The 3-D shape of a still object and a dynamic process of liquid vortex were measured and reconstructed in the experiments, and the results proved the method's feasibility. The advantage of the proposed method is that only one fringe pattern is needed to extract the modulation distribution and to reconstruct the 3-D shape of the object. Therefore, the proposed method can achieve high speed measurement and vertical measurement without shadow and occlusion. It can be used in the dynamic 3-D shape measurement and vibration analysis.

  10. 3D dynamic computer model of the head-neck complex.

    PubMed

    Sierra, Daniel A; Enderle, John D

    2006-01-01

    A 3D dynamic computer model for the movement of the head is presented that incorporates anatomically correct information about the diverse elements forming the system. The skeleton is considered as a set of interconnected rigid 3D bodies following the Newton-Euler laws of movement. The muscles are modeled using Enderle's linear model. Finally, the soft tissues, namely the ligaments, intervertebral disks, and zigapophysial joints, are modeled using the finite elements approach. The model is intended to study the neural network that controls movement and maintains the balance of the head-neck complex during eye movements.

  11. A Bio-Inspired Approach to Task Assignment of Swarm Robots in 3-D Dynamic Environments.

    PubMed

    Yi, Xin; Zhu, Anmin; Yang, Simon X; Luo, Chaomin

    2016-03-15

    Intending to mimic the operating mechanism of biological neural systems, a self organizing map-based approach to task assignment of a swarm of robots in 3-D dynamic environments is proposed in this paper. This approach integrates the advantages and characteristics of biological neural systems. It is capable of dynamically planning the paths of a swarm of robots in 3-D environments under uncertain situations, such as when some robots are presented in or broken down or when more than one robot is needed for some special task locations. A Bezier path optimizing algorithm and a parameter adjusting algorithm are integrated in this paper. It is capable of reducing the complexity of the robot navigation control and limiting the number of convergence iterations. The simulation results with different environments demonstrate the effectiveness of the proposed approach.

  12. Integrated Navigation, Guidance, and Control of Missile Systems: 3-D Dynamic Model

    DTIC Science & Technology

    2013-02-01

    UNCLASSIFIED DSTO-TR-2805 Figure B.1: Aerodynamic variables for a missile and is the lift coefficient . LC  , represent respectively the...UNCLASSIFIED Integrated Navigation, Guidance, and Control of Missile Systems: 3-D Dynamic Model Farhan A. Faruqi Weapons...engagement kinematics is derived suitable for developing, implementing and testing modern missile guidance systems. The model developed here is

  13. Dynamical D4-D8 and D3-D7 branes in supergravity

    SciTech Connect

    Binetruy, Pierre; Sasaki, Misao; Uzawa, Kunihito

    2009-07-15

    We present a class of dynamical solutions for intersecting D4-D8 and D3-D7 brane systems in ten-dimensional type IIA and IIB supergravity. We discuss if these solutions can be recovered in lower-dimensional effective theories for the warped compactification of a general p-brane system. It is found that an effective p+1-dimensional description is not possible in general due to the entanglement of the transverse coordinates and the p+1-dimensional coordinates in the metric components. For the D4-D8 brane system, the dynamical solutions reduces to a static warped AdS{sub 6}xS{sup 4} geometry in a certain spacetime region. For the D3-D7 brane system, we find a dynamical solution whose metric form is similar to that of a D3-brane solution. The main difference is the existence of a nontrivial dilaton configuration in the D3-D7 solution. Then we discuss cosmology of these solutions. We find that they behave like a Kasner-type cosmological solution at {tau}{yields}{infinity}, while it reduces to a warped static solution at {tau}{yields}0, where {tau} is the cosmic time.

  14. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    SciTech Connect

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A.; Zadoks, R.I.

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  15. Dynamic WIFI-Based Indoor Positioning in 3D Virtual World

    NASA Astrophysics Data System (ADS)

    Chan, S.; Sohn, G.; Wang, L.; Lee, W.

    2013-11-01

    A web-based system based on the 3DTown project was proposed using Google Earth plug-in that brings information from indoor positioning devices and real-time sensors into an integrated 3D indoor and outdoor virtual world to visualize the dynamics of urban life within the 3D context of a city. We addressed limitation of the 3DTown project with particular emphasis on video surveillance camera used for indoor tracking purposes. The proposed solution was to utilize wireless local area network (WLAN) WiFi as a replacement technology for localizing objects of interest due to the wide spread availability and large coverage area of WiFi in indoor building spaces. Indoor positioning was performed using WiFi without modifying existing building infrastructure or introducing additional access points (AP)s. A hybrid probabilistic approach was used for indoor positioning based on previously recorded WiFi fingerprint database in the Petrie Science and Engineering building at York University. In addition, we have developed a 3D building modeling module that allows for efficient reconstruction of outdoor building models to be integrated with indoor building models; a sensor module for receiving, distributing, and visualizing real-time sensor data; and a web-based visualization module for users to explore the dynamic urban life in a virtual world. In order to solve the problems in the implementation of the proposed system, we introduce approaches for integration of indoor building models with indoor positioning data, as well as real-time sensor information and visualization on the web-based system. In this paper we report the preliminary results of our prototype system, demonstrating the system's capability for implementing a dynamic 3D indoor and outdoor virtual world that is composed of discrete modules connected through pre-determined communication protocols.

  16. 3D dosimetric validation of motion compensation concepts in radiotherapy using an anthropomorphic dynamic lung phantom.

    PubMed

    Mann, P; Witte, M; Moser, T; Lang, C; Runz, A; Johnen, W; Berger, M; Biederer, J; Karger, C P

    2017-01-21

    In this study, we developed a new setup for the validation of clinical workflows in adaptive radiation therapy, which combines a dynamic ex vivo porcine lung phantom and three-dimensional (3D) polymer gel dosimetry. The phantom consists of an artificial PMMA-thorax and contains a post mortem explanted porcine lung to which arbitrary breathing patterns can be applied. A lung tumor was simulated using the PAGAT (polyacrylamide gelatin gel fabricated at atmospheric conditions) dosimetry gel, which was evaluated in three dimensions by magnetic resonance imaging (MRI). To avoid bias by reaction with oxygen and other materials, the gel was collocated inside a BAREX(™) container. For calibration purposes, the same containers with eight gel samples were irradiated with doses from 0 to 7 Gy. To test the technical feasibility of the system, a small spherical dose distribution located completely within the gel volume was planned. Dose delivery was performed under static and dynamic conditions of the phantom with and without motion compensation by beam gating. To verify clinical target definition and motion compensation concepts, the entire gel volume was homogeneously irradiated applying adequate margins in case of the static phantom and an additional internal target volume in case of dynamically operated phantom without and with gated beam delivery. MR-evaluation of the gel samples and comparison of the resulting 3D dose distribution with the planned dose distribution revealed a good agreement for the static phantom. In case of the dynamically operated phantom without motion compensation, agreement was very poor while additional application of motion compensation techniques restored the good agreement between measured and planned dose. From these experiments it was concluded that the set up with the dynamic and anthropomorphic lung phantom together with 3D-gel dosimetry provides a valuable and versatile tool for geometrical and dosimetrical validation of motion compensated

  17. 3D dosimetric validation of motion compensation concepts in radiotherapy using an anthropomorphic dynamic lung phantom

    NASA Astrophysics Data System (ADS)

    Mann, P.; Witte, M.; Moser, T.; Lang, C.; Runz, A.; Johnen, W.; Berger, M.; Biederer, J.; Karger, C. P.

    2017-01-01

    In this study, we developed a new setup for the validation of clinical workflows in adaptive radiation therapy, which combines a dynamic ex vivo porcine lung phantom and three-dimensional (3D) polymer gel dosimetry. The phantom consists of an artificial PMMA-thorax and contains a post mortem explanted porcine lung to which arbitrary breathing patterns can be applied. A lung tumor was simulated using the PAGAT (polyacrylamide gelatin gel fabricated at atmospheric conditions) dosimetry gel, which was evaluated in three dimensions by magnetic resonance imaging (MRI). To avoid bias by reaction with oxygen and other materials, the gel was collocated inside a BAREX™ container. For calibration purposes, the same containers with eight gel samples were irradiated with doses from 0 to 7 Gy. To test the technical feasibility of the system, a small spherical dose distribution located completely within the gel volume was planned. Dose delivery was performed under static and dynamic conditions of the phantom with and without motion compensation by beam gating. To verify clinical target definition and motion compensation concepts, the entire gel volume was homogeneously irradiated applying adequate margins in case of the static phantom and an additional internal target volume in case of dynamically operated phantom without and with gated beam delivery. MR-evaluation of the gel samples and comparison of the resulting 3D dose distribution with the planned dose distribution revealed a good agreement for the static phantom. In case of the dynamically operated phantom without motion compensation, agreement was very poor while additional application of motion compensation techniques restored the good agreement between measured and planned dose. From these experiments it was concluded that the set up with the dynamic and anthropomorphic lung phantom together with 3D-gel dosimetry provides a valuable and versatile tool for geometrical and dosimetrical validation of motion compensated

  18. 3D-VAS--initial results from computerized visualization of dynamic occlusion.

    PubMed

    Ruge, S; Kordass, B

    2008-01-01

    Visualization of the dynamic occlusion is one of the central tasks in both clinical dentistry and dental engineering. Many aspects of dynamic occlusion, such as the interocclusal function in the posterior region, cannot be seen directly clinically and at best can be recorded with contact paper. Therefore, analyses of the dynamic occlusion using mounted models in the articulator are unavoidable in many cases for reproduction of dynamic occlusion. However, the reproduction of dynamic occlusion in the mechanical articulator has clear restrictions inherent to the process, but also caused by biological variability. Virtual articulators can expediently supplement mechanical articulators, since with them it is possible to display in relation to time unusual and extraordinary perspectives, such as sectional images and flowing, sliding contact points. One of the latest developments in the field of virtual articulation is the 3D virtual articulation system module of the Zebris company, D-Isny. By means of a specially developed coupling tray, 3D-scanned rows of teeth can be matched with computerized motion recordings of mandibular function. The software displays the movements of the 3D-scanned rows of teeth not only with jaw motion but also with chewing motion--therefore movements under chewing pressure--in real time and facilitates special analytical methods transcending mechanical occlusion analysis in conventional articulators: This includes displays of the strength of the contact points and surfaces, the occurrence of the contact points in relation to time, sectional images of the dentition, analyses of the interocclusal gap in the occlusal region, etc. This software and its possibilities are described and explained by reference to individual cases.

  19. How spatial abilities and dynamic visualizations interplay when learning functional anatomy with 3D anatomical models.

    PubMed

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material presentation formats, spatial abilities, and anatomical tasks. First, to understand the cognitive challenges a novice learner would be faced with when first exposed to 3D anatomical content, a six-step cognitive task analysis was developed. Following this, an experimental study was conducted to explore how presentation formats (dynamic vs. static visualizations) support learning of functional anatomy, and affect subsequent anatomical tasks derived from the cognitive task analysis. A second aim was to investigate the interplay between spatial abilities (spatial visualization and spatial relation) and presentation formats when the functional anatomy of a 3D scapula and the associated shoulder flexion movement are learned. Findings showed no main effect of the presentation formats on performances, but revealed the predictive influence of spatial visualization and spatial relation abilities on performance. However, an interesting interaction between presentation formats and spatial relation ability for a specific anatomical task was found. This result highlighted the influence of presentation formats when spatial abilities are involved as well as the differentiated influence of spatial abilities on anatomical tasks.

  20. Characterisation of dynamic couplings at lower limb residuum/socket interface using 3D motion capture.

    PubMed

    Tang, Jinghua; McGrath, Michael; Laszczak, Piotr; Jiang, Liudi; Bader, Dan L; Moser, David; Zahedi, Saeed

    2015-12-01

    Design and fitting of artificial limbs to lower limb amputees are largely based on the subjective judgement of the prosthetist. Understanding the science of three-dimensional (3D) dynamic coupling at the residuum/socket interface could potentially aid the design and fitting of the socket. A new method has been developed to characterise the 3D dynamic coupling at the residuum/socket interface using 3D motion capture based on a single case study of a trans-femoral amputee. The new model incorporated a Virtual Residuum Segment (VRS) and a Socket Segment (SS) which combined to form the residuum/socket interface. Angular and axial couplings between the two segments were subsequently determined. Results indicated a non-rigid angular coupling in excess of 10° in the quasi-sagittal plane and an axial coupling of between 21 and 35 mm. The corresponding angular couplings of less than 4° and 2° were estimated in the quasi-coronal and quasi-transverse plane, respectively. We propose that the combined experimental and analytical approach adopted in this case study could aid the iterative socket fitting process and could potentially lead to a new socket design.

  1. Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

    PubMed Central

    Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

    2014-01-01

    Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports

  2. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji

    2016-03-01

    Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.

  3. Radial electric field 3D modeling for wire arrays driving dynamic hohlraums on Z.

    SciTech Connect

    Mock, Raymond Cecil

    2007-06-01

    The anode-cathode structure of the Z-machine wire array results in a higher negative radial electric field (Er) on the wires near the cathode relative to the anode. The magnitude of this field has been shown to anti-correlate with the axial radiation top/bottom symmetry in the DH (Dynamic Hohlraum). Using 3D modeling, the structure of this field is revealed for different wire-array configurations and for progressive mechanical alterations, providing insight for minimizing the negative Er on the wire array in the anode-to-cathode region of the DH. Also, the 3D model is compared to Sasorov's approximation, which describes Er at the surface of the wire in terms of wire-array parameters.

  4. The computer simulation of 3d gas dynamics in a gas centrifuge

    NASA Astrophysics Data System (ADS)

    Borman, V. D.; Bogovalov, S. V.; Borisevich, V. D.; Tronin, I. V.; Tronin, V. N.

    2016-09-01

    We argue on the basis of the results of 2D analysis of the gas flow in gas centrifuges that a reliable calculation of the circulation of the gas and gas content in the gas centrifuge is possible only in frameworks of 3D numerical simulation of gas dynamics in the gas centrifuge (hereafter GC). The group from National research nuclear university, MEPhI, has created a computer code for 3D simulation of the gas flow in GC. The results of the computer simulations of the gas flows in GC are presented. A model Iguassu centrifuge is explored for the simulations. A nonaxisymmetric gas flow is produced due to interaction of the hypersonic rotating flow with the scoops for extraction of the product and waste flows from the GC. The scoops produce shock waves penetrating into a working camera of the GC and form spiral waves there.

  5. Blob Dynamics in 3D BOUT Simulations of Tokamak Edge Turbulence

    SciTech Connect

    Russell, D; D'Ippolito, D; Myra, J; Nevins, W; Xu, X

    2004-08-23

    Propagating filaments of enhanced plasma density, or blobs, observed in 3D numerical simulations of a diverted, neutral-fueled tokamak are studied. Fluctuations of vorticity, electrical potential {phi}, temperature T{sub e} and current density J{sub {parallel}} associated with the blobs have a dipole structure perpendicular to the magnetic field and propagate radially with large E {center_dot} B drift velocities (> 1 km/s). The simulation results are consistent with a 3D blob dynamics model that incorporates increased parallel plasma resistivity (from neutral cooling of the X-point region), blob disconnection from the divertor sheath, X-point closure of the current loops, and collisional physics to sustain the {phi}, T{sub e}, J{sub {parallel}} dipoles.

  6. User's manuals for DYNA3D and DYNAP: nonlinear dynamic analysis of solids in three dimensions

    SciTech Connect

    Hallquist, J.O.

    1981-07-01

    This report provides a user's manual for DYNA3D, an explicit three-dimensional finite element code for analyzing the large deformation dynamic response of inelastic solids. A contact-impact algorithm permits gaps and sliding along material interfaces. By a specialization of this algorithm, such interfaces can be rigidly tied to admit variable zoning without the need of transition regions. Spatial discretization is achieved by the use of 8-node solid elements, and the equations-of-motion are integrated by the central difference method. Post-processors for DYNA3D include GRAPE for plotting deformed shapes and stress contours and DYNAP for plotting time histories. A user's manual for DYNAP is also provided in this report.

  7. Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI

    PubMed Central

    Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C. A.; van Doorn, Pieter A.; Tiddens, Harm A. W. M.; van der Ploeg, Ans T.; de Bruijne, Marleen

    2016-01-01

    Background Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. Methods The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Conclusion Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response. PMID:27391236

  8. Obstacle avoidance using predictive vision based on a dynamic 3D world model

    NASA Astrophysics Data System (ADS)

    Benjamin, D. Paul; Lyons, Damian; Achtemichuk, Tom

    2006-10-01

    We have designed and implemented a fast predictive vision system for a mobile robot based on the principles of active vision. This vision system is part of a larger project to design a comprehensive cognitive architecture for mobile robotics. The vision system represents the robot's environment with a dynamic 3D world model based on a 3D gaming platform (Ogre3D). This world model contains a virtual copy of the robot and its environment, and outputs graphics showing what the virtual robot "sees" in the virtual world; this is what the real robot expects to see in the real world. The vision system compares this output in real time with the visual data. Any large discrepancies are flagged and sent to the robot's cognitive system, which constructs a plan for focusing on the discrepancies and resolving them, e.g. by updating the position of an object or by recognizing a new object. An object is recognized only once; thereafter its observed data are monitored for consistency with the predictions, greatly reducing the cost of scene understanding. We describe the implementation of this vision system and how the robot uses it to locate and avoid obstacles.

  9. Representation and coding of large-scale 3D dynamic maps

    NASA Astrophysics Data System (ADS)

    Cohen, Robert A.; Tian, Dong; Krivokuća, Maja; Sugimoto, Kazuo; Vetro, Anthony; Wakimoto, Koji; Sekiguchi, Shunichi

    2016-09-01

    combined with depth and color measurements of the surrounding environment. Localization could be achieved with GPS, inertial measurement units (IMU), cameras, or combinations of these and other devices, while the depth measurements could be achieved with time-of-flight, radar or laser scanning systems. The resulting 3D maps, which are composed of 3D point clouds with various attributes, could be used for a variety of applications, including finding your way around indoor spaces, navigating vehicles around a city, space planning, topographical surveying or public surveying of infrastructure and roads, augmented reality, immersive online experiences, and much more. This paper discusses application requirements related to the representation and coding of large-scale 3D dynamic maps. In particular, we address requirements related to different types of acquisition environments, scalability in terms of progressive transmission and efficiently rendering different levels of details, as well as key attributes to be included in the representation. Additionally, an overview of recently developed coding techniques is presented, including an assessment of current performance. Finally, technical challenges and needs for future standardization are discussed.

  10. Salinity effects on cracking morphology and dynamics in 3-D desiccating clays

    NASA Astrophysics Data System (ADS)

    DeCarlo, Keita F.; Shokri, Nima

    2014-04-01

    Saline conditions induce not only chemical but physical changes in swelling clays, and have a significant influence on the crack dynamics and morphology of desiccating clays. In this study, we used X-ray microtomography to experimentally investigate the effects of sodium chloride on the morphology and dynamics of desiccation cracks in three-dimensional mixtures of sand-bentonite slurry under varying rheological conditions. Rectangular glass containers were packed with slurries of different salt concentrations, with the top boundary exposed to air for evaporation. The growth and propagation of the cracking network that subsequently formed was visualized in 3-D at multiple intervals. The characterization of cracking and branching behavior shows a high extent of localized surficial crack networks at low salinity, with a transition to less extensive but more centralized crack networks with increased salinity. The observed behavior was described in the context of the physicochemical properties of the montmorillonite clay, where shifts from an "entangled" (large platelet spacing, small pore structure) to a "stacked" (small platelet spacing, open pore structure) network influence fluid distribution and thus extent of cracking and branching behavior. This is further corroborated by vertical profiles of water distribution, which shows localized desiccation fronts that shift to uniform desaturation with increasing salt concentration. Our results provide new insights regarding the formation, dynamics, and patterns of desiccation cracks formed during evaporation from 3-D saline clay structures, which will be useful in hydrological applications including water management, land surface evaporation, and subsurface contaminant transport.

  11. Semi-automatic segmentation for 3D motion analysis of the tongue with dynamic MRI.

    PubMed

    Lee, Junghoon; Woo, Jonghye; Xing, Fangxu; Murano, Emi Z; Stone, Maureen; Prince, Jerry L

    2014-12-01

    Dynamic MRI has been widely used to track the motion of the tongue and measure its internal deformation during speech and swallowing. Accurate segmentation of the tongue is a prerequisite step to define the target boundary and constrain the tracking to tissue points within the tongue. Segmentation of 2D slices or 3D volumes is challenging because of the large number of slices and time frames involved in the segmentation, as well as the incorporation of numerous local deformations that occur throughout the tongue during motion. In this paper, we propose a semi-automatic approach to segment 3D dynamic MRI of the tongue. The algorithm steps include seeding a few slices at one time frame, propagating seeds to the same slices at different time frames using deformable registration, and random walker segmentation based on these seed positions. This method was validated on the tongue of five normal subjects carrying out the same speech task with multi-slice 2D dynamic cine-MR images obtained at three orthogonal orientations and 26 time frames. The resulting semi-automatic segmentations of a total of 130 volumes showed an average dice similarity coefficient (DSC) score of 0.92 with less segmented volume variability between time frames than in manual segmentations.

  12. Determination of the material fracture toughness by numerical analysis of 3D elastoplastic dynamic deformation

    NASA Astrophysics Data System (ADS)

    Bogdanov, V. R.; Sulim, G. T.

    2016-03-01

    We develop a technique for calculating the plastic strain and fracture toughness fields of a material by solving dynamical 3D problems of determining the stress-strain state in the elastoplastic statement with possible unloading of the material taken into account. The numerical solution was obtained by a finite difference scheme applied to the three-point shock bending tests of parallelepiped-shaped bars made of different materials with plane crack-notches in the middle. The fracture toughness coefficient was determined for reactor steel. The numerically calculated stress tensor components, mean stresses, the Odquist parameter characterizing the accumulated plastic strain, and the fracture toughness are illustrated by graphs.

  13. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  14. ClC-3 Promotes Osteogenic Differentiation in MC3T3-E1 Cell After Dynamic Compression.

    PubMed

    Wang, Dawei; Wang, Hao; Gao, Feng; Wang, Kun; Dong, Fusheng

    2017-06-01

    ClC-3 chloride channel has been proved to have a relationship with the expression of osteogenic markers during osteogenesis, persistent static compression can upregulate the expression of ClC-3 and regulate osteodifferentiation in osteoblasts. However, there was no study about the relationship between the expression of ClC-3 and osteodifferentiation after dynamic compression. In this study, we applied dynamic compression on MC3T3-E1 cells to detect the expression of ClC-3, runt-related transcription factor 2 (Runx2), bone morphogenic protein-2 (BMP-2), osteopontin (OPN), nuclear-associated antigen Ki67 (Ki67), and proliferating cell nuclear antigen (PCNA) in biopress system, then we investigated the expression of these genes after dynamic compression with Chlorotoxin (specific ClC-3 chloride channel inhibitor) added. Under transmission electron microscopy, there were more cell surface protrusions, rough surfaced endoplasmic reticulum, mitochondria, Golgi apparatus, abundant glycogen, and lysosomes scattered in the cytoplasm in MC3T3-E1 cells after dynamic compression. The nucleolus was more obvious. We found that ClC-3 was significantly up-regulated after dynamic compression. The compressive force also up-regulated Runx2, BMP-2, and OPN after dynamic compression for 2, 4 and 8 h. The proliferation gene Ki67 and PCNA did not show significantly change after dynamic compression for 8 h. Chlorotoxin did not change the expression of ClC-3 but reduced the expression of Runx2, BMP-2, and OPN after dynamic compression compared with the group without Cltx added. The data from the current study suggested that ClC-3 may promotes osteogenic differentiation in MC3T3-E1 cell after dynamic compression. J. Cell. Biochem. 118: 1606-1613, 2017. © 2016 Wiley Periodicals, Inc.

  15. An Experimental Study of Mixing Dynamics in 3D Granular Flows

    NASA Astrophysics Data System (ADS)

    Zaman, Zafir

    Compared with the mixing of fluids, the mixing and segregation of granular materials remains one of the big questions of science. Unlike fluids, granular materials segregate based on differences in particle properties, such as density and size. For 2D granular flows, a dynamical systems framework has been effective in describing regions of mixing and segregation. However, computational and theoretical results are just starting to form a framework for 3D granular flows, such as the bi-axial spherical tumbler (BST) flow. This thesis builds on this emerging framework through a series of experimental studies with theoretical and model support with the goal of better understanding 3D mixing. The first study tests the commonly used assumption in continuum models of granular flow that single axis tumbler flow is two dimensional. Utilizing both surface and destructive subsurface imaging, this study shows that weak 3D deviations occur in the form of an axial drift within single axis tumbler flow of varying material spanwise depth. Afterward, this thesis focuses on the development of a custom-built X-ray imaging system to non-destructively visualize the tumbler subsurface. The second study revisits the axial drift and demonstrates that wall roughness impacts the curvature and overall displacement of particle trajectories throughout the tumbler domain using subsurface particle trajectories provided by the X-ray imaging system. Finally, mixing in the fully 3D BST flow is studied. In particular, 3D persistent mixing barriers that are predicted by the dynamical systems framework are shown to exist. Some barriers are remarkably persistent for as much as 500 protocol iterations despite the presence of collisional diffusion. The structures arise from two competing effects, the cutting and shuffling action of the protocol and the stretching from the flowing layer. The tumbling protocol controls the mixing behavior as well as the types of non-mixing barriers observed. Supplementary

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

    PubMed Central

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

    2016-01-01

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

  17. Development and validation of a 3-D model to predict knee joint loading during dynamic movement.

    PubMed

    McLean, S G; Su, A; van den Bogert, A J

    2003-12-01

    The purpose of this study was to develop a subject-specific 3-D model of the lower extremity to predict neuromuscular control effects on 3-D knee joint loading during movements that can potentially cause injury to the anterior cruciate ligament (ACL) in the knee. The simulation consisted of a forward dynamic 3-D musculoskeletal model of the lower extremity, scaled to represent a specific subject. Inputs of the model were the initial position and velocity of the skeletal elements, and the muscle stimulation patterns. Outputs of the model were movement and ground reaction forces, as well as resultant 3-D forces and moments acting across the knee joint. An optimization method was established to find muscle stimulation patterns that best reproduced the subject's movement and ground reaction forces during a sidestepping task. The optimized model produced movements and forces that were generally within one standard deviation of the measured subject data. Resultant knee joint loading variables extracted from the optimized model were comparable to those reported in the literature. The ability of the model to successfully predict the subject's response to altered initial conditions was quantified and found acceptable for use of the model to investigate the effect of altered neuromuscular control on knee joint loading during sidestepping. Monte Carlo simulations (N = 100,000) using randomly perturbed initial kinematic conditions, based on the subject's variability, resulted in peak anterior force, valgus torque and internal torque values of 378 N, 94 Nm and 71 Nm, respectively, large enough to cause ACL rupture. We conclude that the procedures described in this paper were successful in creating valid simulations of normal movement, and in simulating injuries that are caused by perturbed neuromuscular control.

  18. Insights from 3D numerical simulations on the dynamics of the India-Asia collision zone

    NASA Astrophysics Data System (ADS)

    Pusok, A. E.; Kaus, B.; Popov, A.

    2013-12-01

    The dynamics of the India-Asia collision zone remains one of the most remarkable topics of the current research interest: the transition from subduction to collision and uplift, followed by the rise of the abnormally thick Tibetan plateau, and the deformation at its Eastern and Western syntaxes, are processes still not fully understood. Models that have addressed this topic include wholescale underthrusting of Indian lithospheric mantle under Tibet, distributed homogeneous shortening or the thin-sheet model, slip-line field model for lateral extrusion or lower crustal flow models for the exhumation of the Himalayan units and lateral spreading of the Tibetan plateau. Of these, the thin-sheet model has successfully illustrated some of the basic physics of continental collision and has the advantage of a 3D model being reduced to 2D, but one of its major shortcomings is that it cannot simultaneously represent channel flow and gravitational collapse of the mantle lithosphere, since these mechanisms require the lithosphere to interact with the underlying mantle, or to have a vertically non-homogeneous rheology. As a consequence, 3D models are emerging as powerful tools to understand the dynamics of coupled systems. However, because of yet recent developments and various complexities, the current 3D models simulating the dynamics of continent collision zones have relied on certain explicit assumptions, such as replacing part of the asthenosphere with various types of boundary conditions that mimic the effect of mantle flow, in order to focus on the lithospheric/crustal deformation. Here, we employ the parallel 3D code LaMEM (Lithosphere and Mantle Evolution Model), with a finite difference staggered grid solver, which is capable of simulating lithospheric deformation while simultaneously taking mantle flow and a free surface into account. We present qualitative results on lithospheric and upper-mantle scale simulations in which the Indian lithosphere is subducted and

  19. Rapid 3D dynamic arterial spin labeling with a sparse model-based image reconstruction.

    PubMed

    Zhao, Li; Fielden, Samuel W; Feng, Xue; Wintermark, Max; Mugler, John P; Meyer, Craig H

    2015-11-01

    Dynamic arterial spin labeling (ASL) MRI measures the perfusion bolus at multiple observation times and yields accurate estimates of cerebral blood flow in the presence of variations in arterial transit time. ASL has intrinsically low signal-to-noise ratio (SNR) and is sensitive to motion, so that extensive signal averaging is typically required, leading to long scan times for dynamic ASL. The goal of this study was to develop an accelerated dynamic ASL method with improved SNR and robustness to motion using a model-based image reconstruction that exploits the inherent sparsity of dynamic ASL data. The first component of this method is a single-shot 3D turbo spin echo spiral pulse sequence accelerated using a combination of parallel imaging and compressed sensing. This pulse sequence was then incorporated into a dynamic pseudo continuous ASL acquisition acquired at multiple observation times, and the resulting images were jointly reconstructed enforcing a model of potential perfusion time courses. Performance of the technique was verified using a numerical phantom and it was validated on normal volunteers on a 3-Tesla scanner. In simulation, a spatial sparsity constraint improved SNR and reduced estimation errors. Combined with a model-based sparsity constraint, the proposed method further improved SNR, reduced estimation error and suppressed motion artifacts. Experimentally, the proposed method resulted in significant improvements, with scan times as short as 20s per time point. These results suggest that the model-based image reconstruction enables rapid dynamic ASL with improved accuracy and robustness.

  20. Innovative LIDAR 3D Dynamic Measurement System to estimate fruit-tree leaf area.

    PubMed

    Sanz-Cortiella, Ricardo; Llorens-Calveras, Jordi; Escolà, Alexandre; Arnó-Satorra, Jaume; Ribes-Dasi, Manel; Masip-Vilalta, Joan; Camp, Ferran; Gràcia-Aguilá, Felip; Solanelles-Batlle, Francesc; Planas-DeMartí, Santiago; Pallejà-Cabré, Tomàs; Palacin-Roca, Jordi; Gregorio-Lopez, Eduard; Del-Moral-Martínez, Ignacio; Rosell-Polo, Joan R

    2011-01-01

    In this work, a LIDAR-based 3D Dynamic Measurement System is presented and evaluated for the geometric characterization of tree crops. Using this measurement system, trees were scanned from two opposing sides to obtain two three-dimensional point clouds. After registration of the point clouds, a simple and easily obtainable parameter is the number of impacts received by the scanned vegetation. The work in this study is based on the hypothesis of the existence of a linear relationship between the number of impacts of the LIDAR sensor laser beam on the vegetation and the tree leaf area. Tests performed under laboratory conditions using an ornamental tree and, subsequently, in a pear tree orchard demonstrate the correct operation of the measurement system presented in this paper. The results from both the laboratory and field tests confirm the initial hypothesis and the 3D Dynamic Measurement System is validated in field operation. This opens the door to new lines of research centred on the geometric characterization of tree crops in the field of agriculture and, more specifically, in precision fruit growing.

  1. Stability and 3-D spatial dynamics analysis of a three cable crane

    NASA Technical Reports Server (NTRS)

    Yang, Li-Farn; Mikulas, Martin M., Jr.; Chiou, Jin-Chern

    1992-01-01

    A 3-cable crane mechanism has been designed for incorporation into a highly loaded Lunar crane for planetary construction. This 3-cable crane must maintain a positive stability margin in all phases of the loading/unloading, assembly, or installation operations. A 2D kinematic curvature theory is applied to: (1) derive a general stability criterion to prevent the 3-cable crane from instability; and (2) determine a simple equation of natural frequency for two planar models of 3-cable crane. Investigation of the 2D vibrational characteristics of the planar models provides valuable insight toward understanding of 3D dynamic behavior of the 3-cable crane. Also, precision in natural frequency from this simple kinematic equation due to the exclusion of the radius-of-gyration of a suspended article is discussed. Multibody dynamics of the 3D 3-cable crane is presented and simulated to study the resulting vibrational characteristics under external disturbances and to verify the feasibility of the stability criterion for the 3-cable crane.

  2. Dynamic 3-D virtual fixtures for minimally invasive beating heart procedures.

    PubMed

    Ren, Jing; Patel, Rajni V; McIsaac, Kenneth A; Guiraudon, Gerard; Peters, Terry M

    2008-08-01

    Two-dimensional or 3-D visual guidance is often used for minimally invasive cardiac surgery and diagnosis. This visual guidance suffers from several drawbacks such as limited field of view, loss of signal from time to time, and in some cases, difficulty of interpretation. These limitations become more evident in beating-heart procedures when the surgeon has to perform a surgical procedure in the presence of heart motion. In this paper, we propose dynamic 3-D virtual fixtures (DVFs) to augment the visual guidance system with haptic feedback, to provide the surgeon with more helpful guidance by constraining the surgeon's hand motions thereby protecting sensitive structures. DVFs can be generated from preoperative dynamic magnetic resonance (MR) or computed tomograph (CT) images and then mapped to the patient during surgery. We have validated the feasibility of the proposed method on several simulated surgical tasks using a volunteer's cardiac image dataset. Validation results show that the integration of visual and haptic guidance can permit a user to perform surgical tasks more easily and with reduced error rate. We believe this is the first work presented in the field of virtual fixtures that explicitly considers heart motion.

  3. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    SciTech Connect

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-04

    This paper presents results from an explanatory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected in the resulting steady-state analyses using NASA's FUN3D CFD software.

  4. Semi-brittle rheology and ice dynamics in DynEarthSol3D

    NASA Astrophysics Data System (ADS)

    Logan, Liz C.; Lavier, Luc L.; Choi, Eunseo; Tan, Eh; Catania, Ginny A.

    2017-01-01

    We present a semi-brittle rheology and explore its potential for simulating glacier and ice sheet deformation using a numerical model, DynEarthSol3D (DES), in simple, idealized experiments. DES is a finite-element solver for the dynamic and quasi-static simulation of continuous media. The experiments within demonstrate the potential for DES to simulate ice failure and deformation in dynamic regions of glaciers, especially at quickly changing boundaries like glacier termini in contact with the ocean. We explore the effect that different rheological assumptions have on the pattern of flow and failure. We find that the use of a semi-brittle constitutive law is a sufficient material condition to form the characteristic pattern of basal crevasse-aided pinch-and-swell geometry, which is observed globally in floating portions of ice and can often aid in eroding the ice sheet margins in direct contact with oceans.

  5. A portable instrument for 3-D dynamic robot measurements using triangulation and laser tracking

    SciTech Connect

    Mayer, J.R.R. . Mechanical Engineering Dept.); Parker, G.A. . Dept. of Mechanical Engineering)

    1994-08-01

    The paper describes the development and validation of a 3-D measurement instrument capable of determining the static and dynamic performance of industrial robots to ISO standards. Using two laser beams to track an optical target attached to the robot end-effector, the target position coordinates may be estimated, relative to the instrument coordinate frame, to a high accuracy using triangulation principles. The effect of variations in the instrument geometry from the nominal model is evaluated through a kinematic model of the tracking head. Significant improvements of the measurement accuracy are then obtained by a simple adjustment of the main parameters. Extensive experimental test results are included to demonstrate the instrument performance. Finally typical static and dynamic measurement results for an industrial robot are presented to illustrate the effectiveness and usefulness of the instrument.

  6. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    NASA Technical Reports Server (NTRS)

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-01

    This paper presents results from an exploratory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected and the resulting steady-state analyses using NASA's FUN3D CFD software.

  7. 3D microscale laser dynamic forming: Multiscale modeling and experimental validation

    SciTech Connect

    Gao Huang; Cheng, Gary J.

    2011-05-15

    Microscale laser dynamic forming ({mu}LDF) shows great potential in fabricating robust and high-aspect-ratio metallic microcomponents. Experiments revealed that strain rate and sample size play important roles in determining the dynamic plasticity and final results of {mu}LDF. To further understand these effects, a multiscale modeling methodology is adopted to characterize the microscale dynamic plasticity considering the evolutions of nano-to-submicron dislocations avalanches under shock loading. In this methodology, 3D discrete dislocation dynamics simulations are implemented to derive the yield strength and the initial strain hardening dependence on size and strain rate. It is observed that there exist three dynamic stages during deformation process. The initial strain hardening rate in Stage II increases with strain rate. The mechanical threshold stress model, intrinsically equipped with strain-rate-dependent flow stress and initial hardening, is chosen and modified to incorporate size effect quantitatively. This scale-dependent model, implemented in abaqus/explicit, provides deformation depths and thickness variations in good agreement with experimental results in {mu}LDF.

  8. Geological evolution of the North Sea: a dynamic 3D model including petroleum system elements

    NASA Astrophysics Data System (ADS)

    Sabine, Heim; Rüdiger, Lutz; Dirk, Kaufmann; Lutz, Reinhardt

    2013-04-01

    This study investigates the sedimentary basin evolution of the German North Sea with a focus on petroleum generation, migration and accumulation. The study is conducted within the framework of the project "Geoscientific Potential of the German North Sea (GPDN)", a joint project of federal (BGR, BSH) and state authorities (LBEG) with partners from industry and scientific institutions. Based on the structural model of the "Geotektonischer Atlas 3D" (GTA3D, LBEG), this dynamic 3D model contains additionally the northwestern part ("Entenschnabel" area) of the German North Sea. Geological information, e.g. lithostratigraphy, facies and structural data, provided by industry, was taken from published research projects, or literature data such as the Southern Permian Basin Atlas (SPBA; Doornenbal et al., 2010). Numerical modeling was carried out for a sedimentary succession containing 17 stratigraphic layers and several sublayers, representing the sedimentary deposition from the Devonian until Present. Structural details have been considered in terms of simplified faults and salt structures, as well as main erosion and salt movement events. Lithology, facies and the boundary conditions e.g. heat flow, paleo water-depth and sediment water interface temperature were assigned. The system calibration is based on geochemical and petrological data, such as maturity of organic matter (VRr) and present day temperature. Due to the maturity of the sedimentary organic matter Carboniferous layers are the major source rocks for gas generation. Main reservoir rocks are the Rotliegend sandstones, furthermore, sandstones of the Lower Triassic and Jurassic can serve as reservoir rocks in areas where the Zechstein salts are absent. The model provides information on the temperature and maturity distribution within the main source rock layers as well as information of potential hydrocarbon generation based on kinetic data for gas liberation. Finally, this dynamic 3D model offers a first

  9. Observing molecular dynamics with time-resolved 3D momentum imaging

    NASA Astrophysics Data System (ADS)

    Sturm, F. P.; Wright, T.; Bocharova, I.; Ray, D.; Shivaram, N.; Cryan, J.; Belkacem, A.; Weber, T.; Dörner, R.

    2014-05-01

    Photo-excitation and ionization trigger rich dynamics in molecular systems which play a key role in many important processes in nature such as vision, photosynthesis or photoprotection. Observing those reactions in real-time without significantly disturbing the molecules by a strong electric field has been a great challenge. Recent experiments using Time-of-Flight and Velocity Map Imaging techniques have revealed important information on the dynamics of small molecular systems upon photo-excitation. We have developed an apparatus for time-resolved momentum imaging of electrons and ions in all three spatial dimensions that employs two-color femtosecond laser pulses in the vacuum and extreme ultraviolet (VUV, XUV) for probing molecular dynamics. Our COLTRIMS style reaction microscope can measure electrons and ions in coincidence and reconstruct the momenta of the reaction fragments in 3D. We use a high power 800 nm laser in a loose focusing geometry gas cell to efficinetly drive High Harmonic Generation. The resulting photon flux is sufficient to perform 2-photon pump-probe experiments using VUV and XUV pulses for both pump and probe. With this setup we investigate non-Born-Oppenheimer dynamics in small molecules such as C2H4 and CO2 on a femtosecond time scale. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  10. Defragmented image based autostereoscopic 3D displays with dynamic eye tracking

    NASA Astrophysics Data System (ADS)

    Kim, Sung-Kyu; Yoon, Ki-Hyuk; Yoon, Seon Kyu; Ju, Heongkyu

    2015-12-01

    We studied defragmented image based autostereoscopic 3D displays with dynamic eye tracking. Specifically, we examined the impact of parallax barrier (PB) angular orientation on their image quality. The 3D display system required fine adjustment of PB angular orientation with respect to a display panel. This was critical for both image color balancing and minimizing image resolution mismatch between horizontal and vertical directions. For evaluating uniformity of image brightness, we applied optical ray tracing simulations. The simulations took effects of PB orientation misalignment into account. The simulation results were then compared with recorded experimental data. Our optimal simulated system produced significantly enhanced image uniformity at around sweet spots in viewing zones. However this was contradicted by real experimental results. We offer quantitative treatment of illuminance uniformity of view images to estimate misalignment of PB orientation, which could account for brightness non-uniformity observed experimentally. Our study also shows that slight imperfection in the adjustment of PB orientation due to practical restrictions of adjustment accuracy can induce substantial non-uniformity of view images' brightness. We find that image brightness non-uniformity critically depends on misalignment of PB angular orientation, for example, as slight as ≤ 0.01 ° in our system. This reveals that reducing misalignment of PB angular orientation from the order of 10-2 to 10-3 degrees can greatly improve the brightness uniformity.

  11. Description of patellar movement by 3D parameters obtained from dynamic CT acquisition

    NASA Astrophysics Data System (ADS)

    de Sá Rebelo, Marina; Moreno, Ramon Alfredo; Gobbi, Riccardo Gomes; Camanho, Gilberto Luis; de Ávila, Luiz Francisco Rodrigues; Demange, Marco Kawamura; Pecora, Jose Ricardo; Gutierrez, Marco Antonio

    2014-03-01

    The patellofemoral joint is critical in the biomechanics of the knee. The patellofemoral instability is one condition that generates pain, functional impairment and often requires surgery as part of orthopedic treatment. The analysis of the patellofemoral dynamics has been performed by several medical image modalities. The clinical parameters assessed are mainly based on 2D measurements, such as the patellar tilt angle and the lateral shift among others. Besides, the acquisition protocols are mostly performed with the leg laid static at fixed angles. The use of helical multi slice CT scanner can allow the capture and display of the joint's movement performed actively by the patient. However, the orthopedic applications of this scanner have not yet been standardized or widespread. In this work we present a method to evaluate the biomechanics of the patellofemoral joint during active contraction using multi slice CT images. This approach can greatly improve the analysis of patellar instability by displaying the physiology during muscle contraction. The movement was evaluated by computing its 3D displacements and rotations from different knee angles. The first processing step registered the images in both angles based on the femuŕs position. The transformation matrix of the patella from the images was then calculated, which provided the rotations and translations performed by the patella from its position in the first image to its position in the second image. Analysis of these parameters for all frames provided real 3D information about the patellar displacement.

  12. Brownian nanoimaging of interface dynamics and ligand-receptor binding at cell surfaces in 3-D.

    PubMed

    Kuznetsov, Igor R; Evans, Evan A

    2013-04-01

    We describe a method for nanoimaging interfacial dynamics and ligand-receptor binding at surfaces of live cells in 3-D. The imaging probe is a 1-μm diameter glass bead confined by a soft laser trap to create a "cloud" of fluctuating states. Using a facile on-line method of video image analysis, the probe displacements are reported at ~10 ms intervals with bare precisions (±SD) of 4-6 nm along the optical axis (elevation) and 2 nm in the transverse directions. We demonstrate how the Brownian distributions are analyzed to characterize the free energy potential of each small probe in 3-D taking into account the blur effect of its motions during CCD image capture. Then, using the approach to image interactions of a labeled probe with lamellae of leukocytic cells spreading on cover-glass substrates, we show that deformations of the soft distribution in probe elevations provide both a sensitive long-range sensor for defining the steric topography of a cell lamella and a fast telemetry for reporting rare events of probe binding with its surface receptors. Invoking established principles of Brownian physics and statistical thermodynamics, we describe an off-line method of super resolution that improves precision of probe separations from a non-reactive steric boundary to ~1 nm.

  13. Effects of haptic information on the perception of dynamic 3-D movement.

    PubMed

    Umemura, Hiroyuki

    2014-01-01

    This study examined effects of hand movement on visual perception of 3-D movement. I used an apparatus in which a cursor position in a simulated 3-D space and the position of a stylus on a haptic device could coincide using a mirror. In three experiments, participants touched the center of a rectangle in the visual display with the stylus of the force-feedback device. Then the rectangle's surface stereoscopically either protruded toward a participant or indented away from the participant. Simultaneously, the stylus either pushed back participant's hand, pulled away, or remained static. Visual and haptic information were independently manipulated. Participants judged whether the rectangle visually protruded or dented. Results showed that when the hand was pulled away, subjects were biased to perceive rectangles indented; however, when the hand was pushed back, no effect of haptic information was observed (Experiment 1). This effect persisted even when the cursor position was spatially separated from the hand position (Experiment 2). But, when participants touched an object different from the visual stimulus, this effect disappeared (Experiment 3). These results suggest that the visual system tried to integrate the dynamic visual and haptic information when they coincided cognitively, and the effect of haptic information on visually perceived depth was direction-dependent.

  14. Segmentation of whole cells and cell nuclei from 3-D optical microscope images using dynamic programming.

    PubMed

    McCullough, D P; Gudla, P R; Harris, B S; Collins, J A; Meaburn, K J; Nakaya, M A; Yamaguchi, T P; Misteli, T; Lockett, S J

    2008-05-01

    Communications between cells in large part drive tissue development and function, as well as disease-related processes such as tumorigenesis. Understanding the mechanistic bases of these processes necessitates quantifying specific molecules in adjacent cells or cell nuclei of intact tissue. However, a major restriction on such analyses is the lack of an efficient method that correctly segments each object (cell or nucleus) from 3-D images of an intact tissue specimen. We report a highly reliable and accurate semi-automatic algorithmic method for segmenting fluorescence-labeled cells or nuclei from 3-D tissue images. Segmentation begins with semi-automatic, 2-D object delineation in a user-selected plane, using dynamic programming (DP) to locate the border with an accumulated intensity per unit length greater that any other possible border around the same object. Then the two surfaces of the object in planes above and below the selected plane are found using an algorithm that combines DP and combinatorial searching. Following segmentation, any perceived errors can be interactively corrected. Segmentation accuracy is not significantly affected by intermittent labeling of object surfaces, diffuse surfaces, or spurious signals away from surfaces. The unique strength of the segmentation method was demonstrated on a variety of biological tissue samples where all cells, including irregularly shaped cells, were accurately segmented based on visual inspection.

  15. 3D Plasma Clusters: Analysis of dynamical evolution and individual particle interaction

    SciTech Connect

    Antonova, T.; Thomas, H. M.; Morfill, G. E.; Annaratone, B. M.

    2008-09-07

    3D plasma clusters (up to 100 particles) have been built inside small (32 mm{sup 3}) plasma volume in gravity. It has been estimated that the external confinement has a negligible influence on the processes inside the clusters. At such conditions the analysis of dynamical evolution and individual particle interactions have shown that the binary interaction among particles in addition to the repelling Coulomb force exhibits also an attractive part. The tendency of the systems to approach the state with minimum energy by rearranging particles inside has been detected. The measured 63 particles' cluster vibrations are in close agreement with vibrations of a drop with surface tension. This indicates that even a 63 particle cluster already exhibits properties normally associated with the cooperative regime.

  16. Self-Consistent 3D Modeling of Electron Cloud Dynamics and Beam Response

    SciTech Connect

    Furman, Miguel; Furman, M.A.; Celata, C.M.; Kireeff-Covo, M.; Sonnad, K.G.; Vay, J.-L.; Venturini, M.; Cohen, R.; Friedman, A.; Grote, D.; Molvik, A.; Stoltz, P.

    2007-04-02

    We present recent advances in the modeling of beam electron-cloud dynamics, including surface effects such as secondary electron emission, gas desorption, etc, and volumetric effects such as ionization of residual gas and charge-exchange reactions. Simulations for the HCX facility with the code WARP/POSINST will be described and their validity demonstrated by benchmarks against measurements. The code models a wide range of physical processes and uses a number of novel techniques, including a large-timestep electron mover that smoothly interpolates between direct orbit calculation and guiding-center drift equations, and a new computational technique, based on a Lorentz transformation to a moving frame, that allows the cost of a fully 3D simulation to be reduced to that of a quasi-static approximation.

  17. 3D time dependent thermo-fluid dynamic model of ground deformation at Campi Flegrei caldera

    NASA Astrophysics Data System (ADS)

    Castaldo, R.; Tizzani, P.; Manconi, A.; Manzo, M.; Pepe, S.; Pepe, A.; Lanari, R.

    2012-04-01

    In active volcanic areas deformation signals are generally characterized by non-linear spatial and temporal variations [Tizzani P. et al., 2007]. This behaviour has been revealed in the last two decades by the so-called advanced DInSAR processing algorithms, developed to analyze surface deformation phenomena [Berardino P. et al., 2002; Ferretti C. et al., 2001]. Notwithstanding, most of the inverse modelling attempts to characterize the evolution of the volcanic sources are based on the assumption that the Earth's crust behaves as a homogeneous linear elastic material. However, the behaviour of the upper lithosphere in thermally anomalous regions (as active volcanoes are) might be well described as a non-Newtonian fluid, where some of the material proprieties of the rocks (i.e., apparent viscosities) can change over time [Pinkerton H. et al., 1995]. In this context, we considered the thermal proprieties and mechanical heterogeneities of the upper crust in order to develop a new 3D time dependent thermo-fluid dynamic model of Campi Flegrei (CF) caldera, Southern Italy. More specifically, according to Tizzani P. et al. (2010), we integrated in a FEM environment geophysical information (gravimetric, seismic, and borehole data) available for the considered area and performed two FEM optimization procedures to constrain the 3D distribution of unknown physical parameters (temperature and viscosity distributions) that might help explaining the data observed at surface (geothermal wells and DInSAR measurements). First, we searched for the heat production, the volume source distribution and surface emissivity parameters providing the best-fit of the geothermal profiles data measured at six boreholes [Agip ESGE, 1986], by solving the Fourier heat equation over time (about 40 kys). The 3D thermal field resulting from this optimization was used to calculate the 3D brittle-ductile transition. This analysis revealed the presence of a ductile region, located beneath the centre of

  18. Enhanced high dynamic range 3D shape measurement based on generalized phase-shifting algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Minmin; Du, Guangliang; Zhou, Canlin; Zhang, Chaorui; Si, Shuchun; Li, Hui; Lei, Zhenkun; Li, YanJie

    2017-02-01

    Measuring objects with large reflectivity variations across their surface is one of the open challenges in phase measurement profilometry (PMP). Saturated or dark pixels in the deformed fringe patterns captured by the camera will lead to phase fluctuations and errors. Jiang et al. proposed a high dynamic range real-time three-dimensional (3D) shape measurement method (Jiang et al., 2016) [17] that does not require changing camera exposures. Three inverted phase-shifted fringe patterns are used to complement three regular phase-shifted fringe patterns for phase retrieval whenever any of the regular fringe patterns are saturated. Nonetheless, Jiang's method has some drawbacks: (1) the phases of saturated pixels are estimated by different formulas on a case by case basis; in other words, the method lacks a universal formula; (2) it cannot be extended to the four-step phase-shifting algorithm, because inverted fringe patterns are the repetition of regular fringe patterns; (3) for every pixel in the fringe patterns, only three unsaturated intensity values can be chosen for phase demodulation, leaving the other unsaturated ones idle. We propose a method to enhance high dynamic range 3D shape measurement based on a generalized phase-shifting algorithm, which combines the complementary techniques of inverted and regular fringe patterns with a generalized phase-shifting algorithm. Firstly, two sets of complementary phase-shifted fringe patterns, namely the regular and the inverted fringe patterns, are projected and collected. Then, all unsaturated intensity values at the same camera pixel from two sets of fringe patterns are selected and employed to retrieve the phase using a generalized phase-shifting algorithm. Finally, simulations and experiments are conducted to prove the validity of the proposed method. The results are analyzed and compared with those of Jiang's method, demonstrating that our method not only expands the scope of Jiang's method, but also improves

  19. 3D Reconstruction of Human Laryngeal Dynamics Based on Endoscopic High-Speed Recordings.

    PubMed

    Semmler, Marion; Kniesburges, Stefan; Birk, Veronika; Ziethe, Anke; Patel, Rita; Dollinger, Michael

    2016-07-01

    Standard laryngoscopic imaging techniques provide only limited two-dimensional insights into the vocal fold vibrations not taking the vertical component into account. However, previous experiments have shown a significant vertical component in the vibration of the vocal folds. We present a 3D reconstruction of the entire superior vocal fold surface from 2D high-speed videoendoscopy via stereo triangulation. In a typical camera-laser set-up the structured laser light pattern is projected on the vocal folds and captured at 4000 fps. The measuring device is suitable for in vivo application since the external dimensions of the miniaturized set-up barely exceed the size of a standard rigid laryngoscope. We provide a conservative estimate on the resulting resolution based on the hardware components and point out the possibilities and limitations of the miniaturized camera-laser set-up. In addition to the 3D vocal fold surface, we extended previous approaches with a G2-continuous model of the vocal fold edge. The clinical applicability was successfully established by the reconstruction of visual data acquired from 2D in vivo high-speed recordings of a female and a male subject. We present extracted dynamic parameters like maximum amplitude and velocity in the vertical direction. The additional vertical component reveals deeper insights into the vibratory dynamics of the vocal folds by means of a non-invasive method. The successful miniaturization allows for in vivo application giving access to the most realistic model available and hence enables a comprehensive understanding of the human phonation process.

  20. Quantifying Key Climate Parameter Uncertainties Using an Earth System Model with a Dynamic 3D Ocean

    NASA Astrophysics Data System (ADS)

    Olson, R.; Sriver, R. L.; Goes, M. P.; Urban, N.; Matthews, D.; Haran, M.; Keller, K.

    2011-12-01

    Climate projections hinge critically on uncertain climate model parameters such as climate sensitivity, vertical ocean diffusivity and anthropogenic sulfate aerosol forcings. Climate sensitivity is defined as the equilibrium global mean temperature response to a doubling of atmospheric CO2 concentrations. Vertical ocean diffusivity parameterizes sub-grid scale ocean vertical mixing processes. These parameters are typically estimated using Intermediate Complexity Earth System Models (EMICs) that lack a full 3D representation of the oceans, thereby neglecting the effects of mixing on ocean dynamics and meridional overturning. We improve on these studies by employing an EMIC with a dynamic 3D ocean model to estimate these parameters. We carry out historical climate simulations with the University of Victoria Earth System Climate Model (UVic ESCM) varying parameters that affect climate sensitivity, vertical ocean mixing, and effects of anthropogenic sulfate aerosols. We use a Bayesian approach whereby the likelihood of each parameter combination depends on how well the model simulates surface air temperature and upper ocean heat content. We use a Gaussian process emulator to interpolate the model output to an arbitrary parameter setting. We use Markov Chain Monte Carlo method to estimate the posterior probability distribution function (pdf) of these parameters. We explore the sensitivity of the results to prior assumptions about the parameters. In addition, we estimate the relative skill of different observations to constrain the parameters. We quantify the uncertainty in parameter estimates stemming from climate variability, model and observational errors. We explore the sensitivity of key decision-relevant climate projections to these parameters. We find that climate sensitivity and vertical ocean diffusivity estimates are consistent with previously published results. The climate sensitivity pdf is strongly affected by the prior assumptions, and by the scaling

  1. 3D structure and dynamics of prominences in IRIS-Hinode collaborative observations

    NASA Astrophysics Data System (ADS)

    Okamoto, J.; De Pontieu, B.; Tarbell, T. D.; Title, A. M.

    2013-12-01

    A new solar physics satellite, Interface Region Imaging Spectrograph (IRIS), was launched on June 27, 2013. IRIS obtains UV spectra and images with high spatial resolution (0.33 arcsec) and high time cadence (1 sec / slit) of the chromosphere and transition region of the Sun. The chromosphere is located between the photosphere and the corona. Recently, the Hinode satellite has revealed that the chromosphere is highly active and suggested that it is a very important region in terms of energy deposit and transfer for coronal heating and solar wind acceleration. However, we cannot have further chromospheric information by Hinode because the Hinode Solar Optical Telescope has only a filtergraph for chromospheric observations. Now we have IRIS. IRIS performs spectroscopic observations to get the missing physical quantities of the dynamic chromosphere. Moreover, IRIS and Hinode is the most powerful collaboration to understand chromospheric activities. Hinode observes extremely high-cadence (1.6 sec) and high-spatial (0.2 arcsec) 2-D images, while IRIS measures line-of-sight velocity and Doppler width of fine structures with temperature dependence. This combination provides information about 3-D structures and dynamic phenomena of chromospheric features. Here we focus on prominence observations performed by IRIS and Hinode, and introduce the initial results of prominence dynamics and magnetic structures such as helical configurations, propagating waves and their damping mechanisms, and formation processes.

  2. A novel time dependent gamma evaluation function for dynamic 2D and 3D dose distributions.

    PubMed

    Podesta, Mark; Persoon, Lucas C G G; Verhaegen, Frank

    2014-10-21

    Modern external beam radiotherapy requires detailed verification and quality assurance so that confidence can be placed on both the delivery of a single treatment fraction and on the consistency of delivery throughout the treatment course. To verify dose distributions, a comparison between prediction and measurement must be made. Comparisons between two dose distributions are commonly performed using a Gamma evaluation which is a calculation of two quantities on a pixel by pixel basis; the dose difference, and the distance to agreement. By providing acceptance criteria (e.g. 3%, 3 mm), the function will find the most appropriate match within its two degrees of freedom. For complex dynamic treatments such as IMRT or VMAT it is important to verify the dose delivery in a time dependent manner and so a gamma evaluation that includes a degree of freedom in the time domain via a third parameter, time to agreement, is presented here. A C++ (mex) based gamma function was created that could be run on either CPU and GPU computing platforms that would allow a degree of freedom in the time domain. Simple test cases were created in both 2D and 3D comprising of simple geometrical shapes with well-defined boundaries varying over time. Changes of varying magnitude in either space or time were introduced and repeated gamma analyses were performed varying the criteria. A clinical VMAT case was also included, artificial air bubbles of varying size were introduced to a patient geometry, along with shifts of varying magnitude in treatment time. For all test cases where errors in distance, dose or time were introduced, the time dependent gamma evaluation could accurately highlight the errors.The time dependent gamma function presented here allows time to be included as a degree of freedom in gamma evaluations. The function allows for 2D and 3D data sets which are varying over time to be compared using appropriate criteria without penalising minor offsets of subsequent radiation fields

  3. Toroidal Rotation and 3D Nonlinear Dynamics in the Peeling-Ballooning Model of ELMs

    NASA Astrophysics Data System (ADS)

    Snyder, P. B.

    2004-11-01

    Maximizing the height of the edge transport barrier (or ``pedestal'') while maintaining acceptably small edge localized modes (ELMs) is a critical issue for tokamak performance. The peeling-ballooning model proposes that intermediate wavelength MHD instabilities are responsible for ELMs and impose constraints on the pedestal. Recent studies of linear peeling-ballooning stability have found encouraging agreement with observations [e.g. 1]. To allow more detailed prediction of mode characteristics, including eventually predictions of the ELM energy loss and its deposition, we consider effects of sheared toroidal rotation, as well as 3D nonlinear dynamics. An eigenmode formulation for toroidal rotation shear is developed and incorporated into the framework of the ELITE stability code [2], resolving the low rotation discontinuity in previous high-n results. Rotation shear is found to impact the structure of peeling-ballooning modes, causing radial narrowing and mode shearing. The calculated mode frequency is found to agree with observed rotation in the edge region in the early stages of the ELM crash. Nonlinear studies with the 3D BOUT and NIMROD codes reveal detailed characteristics of the early evolution of these edge instabilities, including the impact of non-ideal effects. The expected linear growth phase is followed by a fast crash event in which poloidally narrow, filamentary structures propagate radially outward from the pedestal region, closely resembling observed ELM events. Comparisons with ELM observations will be discussed. \\vspace0.25em [1] P.B. Snyder et al., Nucl. Fusion 44, 320 (2004); P.B. Snyder et al., Phys. Plasmas 9, 2037 (2002). [2] H.R. Wilson et al., Phys. Plasmas 9, 1277 (2002).

  4. Compressible magma/mantle dynamics: 3-D, adaptive simulations in ASPECT

    NASA Astrophysics Data System (ADS)

    Dannberg, Juliane; Heister, Timo

    2016-12-01

    Melt generation and migration are an important link between surface processes and the thermal and chemical evolution of the Earth's interior. However, their vastly different timescales make it difficult to study mantle convection and melt migration in a unified framework, especially for 3-D global models. And although experiments suggest an increase in melt volume of up to 20 per cent from the depth of melt generation to the surface, previous computations have neglected the individual compressibilities of the solid and the fluid phase. Here, we describe our extension of the finite element mantle convection code ASPECT that adds melt generation and migration. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in areas where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. Together with a high-performance, massively parallel implementation, this allows for high-resolution, 3-D, compressible, global mantle convection simulations coupled with melt migration. We evaluate the functionality and potential of this method using a series of benchmarks and model setups, compare results of the compressible and incompressible formulation, and show the effectiveness of adaptive mesh refinement when applied to melt migration. Our model of magma dynamics provides a framework for modelling processes on different scales and investigating links between processes occurring in the deep mantle and melt generation and migration. This approach could prove particularly useful applied to modelling the generation of komatiites or other melts originating in greater depths. The implementation is available in the Open Source ASPECT repository.

  5. Crustal deformation dynamics and stress evolution during seamount subduction: High-resolution 3-D numerical modeling

    NASA Astrophysics Data System (ADS)

    Ruh, Jonas B.; Sallarès, Valentí; Ranero, César R.; Gerya, Taras

    2016-09-01

    Seamounts or submarine volcanoes frequently collide with the overriding crust along presently active subduction zones locally modifying stress and permanent deformation patterns. Dynamics of this process is not fully understood, and several end-member scenarios of seamount-crust interaction are proposed. Here we use high-resolution 3-D numerical models to investigate evolution of crustal deformation and stress distribution within the upper plate induced by the underthrusting of subducting seamounts. The dynamical effects of the upper plate strength, subduction interface strength, and strain weakening of the crust are investigated. Experiment results demonstrate that characteristic crustal fracturing patterns formed in response to different seamount-crust interaction scenarios. Indenting seamounts strongly deform the overriding plate along a corridor as wide as the underthrusting seamount by constantly shifting subvertical shear zones rooted at the seamount extensions. A reentrant develops during initial seamount collision. A topographic bulge atop the seamount and lateral ridges emerge from further seamount subduction. Obtained stress pattern shows areas of large overpressure above the rearward and large underpressure above the trenchward flank of the seamount. Results of numerical experiments are consistent with seismic reflection images and seismic velocity models of the upper plate in areas of seamount subduction along the Middle America Trench and give important insights into the long-lasting question, whether subducting seamounts and rough seafloor act as barriers or asperities for megathrust earthquakes.

  6. A digital holography set-up for 3D vortex flow dynamics

    NASA Astrophysics Data System (ADS)

    Lebon, Benoît; Perret, Gaële; Coëtmellec, Sébastien; Godard, Gilles; Gréhan, Gérard; Lebrun, Denis; Brossard, Jérôme

    2016-06-01

    In the present paper, a digital in-line holography (DIH) set-up, with a converging beam, is used to take three-dimensional (3D) velocity measurements of vortices. The vortices are formed periodically at the edges of a submerged horizontal plate submitted to regular waves. They take the form of vortex filaments that extend from side to side of the channel. They undergo strongly three-dimensional instability mechanisms that remain very complicated to characterize experimentally. The experiments are performed in a 10 × 0.3 × 0.3 m3 wave flume. The DIH set-up is performed using a modulated laser diode emitting at the wavelength of 640 nm and a lensless CCD camera. The beam crosses the channel side to side. To reveal the flow dynamics, 30-μm hydrogen bubbles are generated at the edge of the plate to serve as tracers. Their locations are recorded on the holograms multiple times to access the dynamics of the flow. This method leads to an accuracy in the order of 100 μm on the axial location. Those measurements have been validated with stereo-PIV measurements. A very good agreement is found on time-averaged velocity fields between the two techniques.

  7. Fibrillogenesis from nanosurfaces: multiphoton imaging and stereological analysis of collagen 3D self-assembly dynamics.

    PubMed

    Bancelin, Stéphane; Decencière, Etienne; Machairas, Vaïa; Albert, Claire; Coradin, Thibaud; Schanne-Klein, Marie-Claire; Aimé, Carole

    2014-09-21

    The assembly of proteins into fibrillar structures is an important process that concerns different biological contexts, including molecular medicine and functional biomaterials. Engineering of hybrid biomaterials can advantageously provide synergetic interactions of the biopolymers with an inorganic component to ensure specific supramolecular organization and dynamics. To this aim, we designed hybrid systems associating collagen and surface-functionalized silica particles and we built a new strategy to investigate fibrillogenesis processes in such multicomponents systems, working at the crossroads of chemistry, physics and mathematics. The self-assembly process was investigated by bimodal multiphoton imaging coupling second harmonic generation (SHG) and 2 photon excited fluorescence (2PEF). The in-depth spatial characterization of the system was further achieved using the three-dimensional analysis of the SHG/2PEF data via mathematical morphology processing. Quantitation of collagen distribution around particles offers strong evidence that the chemically induced confinement of the protein on the silica nanosurfaces has a key influence on the spatial extension of fibrillogenesis. This new approach is unique in the information it can provide on 3D dynamic hybrid systems and may be extended to other associations of fibrillar molecules with optically responsive nano-objects.

  8. 3D Simulations of Helmet Streamer Dynamics and Implications for the Slow Solar Wind

    NASA Astrophysics Data System (ADS)

    Higginson, Aleida K.; Antiochos, Spiro K.; DeVore, C. R.; Zurbuchen, Thomas H.

    2015-04-01

    The source of the slow solar wind at the Sun is still an issue of intense debate in solar and heliospheric physics. Because the majority of the solar wind observed at Earth is slow wind, understanding its origin is essential for understanding and predicting Earth’s space weather environment. In-situ and remote observations show that, when compared to the fast wind, the slow solar wind corresponds to higher freeze-in temperatures, as indicated by charge-state ratios, and more corona-like elemental abundance ratios. These results indicate that the most likely source for the slow wind is the hot plasma in the closed-field corona, but the release mechanism(s) for the wind from the closed-field regions is far from understood. We perform fully dynamic, 3D MHD simulations in order to the study the opening and closing of the Sun’s magnetic field that leads to the escape of the slow solar wind. In particular, we calculate the dynamics of helmet streamers that are driven by photospheric motions such as supergranular flows. We determine in detail the opening and closing of coronal flux, and discuss the implications of our results for theories of slow wind origin, especially the S-Web model. We also determine observational signatures for the upcoming inner heliosphere missions Solar Orbiter and Solar Probe Plus.This work was supported by the NASA SR&T and TR&T Programs.

  9. Holographic display system for dynamic synthesis of 3D light fields with increased space bandwidth product.

    PubMed

    Agour, Mostafa; Falldorf, Claas; Bergmann, Ralf B

    2016-06-27

    We present a new method for the generation of a dynamic wave field with high space bandwidth product (SBP). The dynamic wave field is generated from several wave fields diffracted by a display which comprises multiple spatial light modulators (SLMs) each having a comparably low SBP. In contrast to similar approaches in stereoscopy, we describe how the independently generated wave fields can be coherently superposed. A major benefit of the scheme is that the display system may be extended to provide an even larger display. A compact experimental configuration which is composed of four phase-only SLMs to realize the coherent combination of independent wave fields is presented. Effects of important technical parameters of the display system on the wave field generated across the observation plane are investigated. These effects include, e.g., the tilt of the individual SLM and the gap between the active areas of multiple SLMs. As an example of application, holographic reconstruction of a 3D object with parallax effects is demonstrated.

  10. Analysis of Wnt signalling dynamics during colon crypt development in 3D culture

    PubMed Central

    Tan, Chin Wee; Hirokawa, Yumiko; Burgess, Antony W.

    2015-01-01

    Many systems biology studies lack context-relevant data and as a consequence the predictive capabilities can be limited in developing targeted cancer therapeutics. Production of colon crypt in vitro is ideal for studying colon systems biology. This report presents the first production of, to our knowledge, physiologically-shaped, functional colon crypts in vitro (i.e. single crypts with cells expressing Mucin 2 and Chromogranin A). Time-lapsed monitoring of crypt formation revealed an increased frequency of single-crypt formation in the absence of noggin. Using quantitative 3D immunofluorescence of β-catenin and E-cadherin, spatial-temporal dynamics of these proteins in normal colon crypt cells stimulated with Wnt3A or inhibited by cycloheximide has been measured. Colon adenoma cultures established from APCmin/+ mouse have developmental differences and β-catenin spatial localization compared to normal crypts. Quantitative data describing the effects of signalling pathways and proteins dynamics for both normal and adenomatous colon crypts is now within reach to inform a systems approach to colon crypt biology. PMID:26087250

  11. The Shock Dynamics of Heterogeneous YSO Jets: 3D Simulations Meet Multi-epoch Observations

    NASA Astrophysics Data System (ADS)

    Hansen, E. C.; Frank, A.; Hartigan, P.; Lebedev, S. V.

    2017-03-01

    High-resolution observations of young stellar object (YSO) jets show them to be composed of many small-scale knots or clumps. In this paper, we report results of 3D numerical simulations designed to study how such clumps interact and create morphologies and kinematic patterns seen in emission line observations. Our simulations focus on clump scale dynamics by imposing velocity differences between spherical, over-dense regions, which then lead to the formation of bow shocks as faster clumps overtake slower material. We show that much of the spatial structure apparent in emission line images of jets arises from the dynamics and interactions of these bow shocks. Our simulations show a variety of time-dependent features, including bright knots associated with Mach stems where the shocks intersect, a “frothy” emission structure that arises from the presence of the Nonlinear Thin Shell Instability along the surfaces of the bow shocks, and the merging and fragmentation of clumps. Our simulations use a new non-equilibrium cooling method to produce synthetic emission maps in Hα and [S ii]. These are directly compared to multi-epoch Hubble Space Telescope observations of Herbig–Haro jets. We find excellent agreement between features seen in the simulations and the observations in terms of both proper motion and morphologies. Thus we conclude that YSO jets may be dominated by heterogeneous structures and that interactions between these structures and the shocks they produce can account for many details of YSO jet evolution.

  12. Real-time automated 3D sensing, detection, and recognition of dynamic biological micro-organic events

    NASA Astrophysics Data System (ADS)

    Javidi, Bahram; Yeom, Seokwon; Moon, Inkyu; Daneshpanah, Mehdi

    2006-05-01

    In this paper, we present an overview of three-dimensional (3D) optical imaging techniques for real-time automated sensing, visualization, and recognition of dynamic biological microorganisms. Real time sensing and 3D reconstruction of the dynamic biological microscopic objects can be performed by single-exposure on-line (SEOL) digital holographic microscopy. A coherent 3D microscope-based interferometer is constructed to record digital holograms of dynamic micro biological events. Complex amplitude 3D images of the biological microorganisms are computationally reconstructed at different depths by digital signal processing. Bayesian segmentation algorithms are applied to identify regions of interest for further processing. A number of pattern recognition approaches are addressed to identify and recognize the microorganisms. One uses 3D morphology of the microorganisms by analyzing 3D geometrical shapes which is composed of magnitude and phase. Segmentation, feature extraction, graph matching, feature selection, and training and decision rules are used to recognize the biological microorganisms. In a different approach, 3D technique is used that are tolerant to the varying shapes of the non-rigid biological microorganisms. After segmentation, a number of sampling patches are arbitrarily extracted from the complex amplitudes of the reconstructed 3D biological microorganism. These patches are processed using a number of cost functions and statistical inference theory for the equality of means and equality of variances between the sampling segments. Also, we discuss the possibility of employing computational integral imaging for 3D sensing, visualization, and recognition of biological microorganisms illuminated under incoherent light. Experimental results with several biological microorganisms are presented to illustrate detection, segmentation, and identification of micro biological events.

  13. Dynamic stress-strain states for metal foams using a 3D cellular model

    NASA Astrophysics Data System (ADS)

    Zheng, Zhijun; Wang, Changfeng; Yu, Jilin; Reid, Stephen R.; Harrigan, John J.

    2014-12-01

    Dynamic uniaxial impact behaviour of metal foams using a 3D cell-based finite element model is examined. At sufficiently high loading rates, these materials respond by forming ‘shock or consolidation waves' (Tan et al., 2005a, 2005b). However, the existing dynamic experimental methods have limitations in fully informing this behaviour, particularly for solving boundary/initial value problems. Recently, the problem of the shock-like response of an open-cell foam has been examined by Barnes et al. (2014) using the Hugoniot-curve representations. The present study is somewhat complementary to that approach and additionally aims to provide insight into the ‘rate sensitivity' mechanism applicable to cellular materials. To assist our understanding of the ‘loading rate sensitivity' behaviour of cellular materials, a virtual ‘test' method based on the direct impact technique is explored. Following a continuum representation of the response, the strain field calculation method is employed to determine the local strains ahead of and behind the resulting ‘shock front'. The dynamic stress-strain states in the densification stage are found to be different from the quasi-static ones. It is evident that the constitutive behaviour of the cellular material is deformation-mode dependent. The nature of the ‘rate sensitivity' revealed for cellular materials in this paper is different from the strain-rate sensitivity of dense metals. It is shown that the dynamic stress-strain states behind a shock front of the cellular material lie on a unique curve and each point on the curve corresponds to a particular ‘impact velocity', referred as the velocity upstream of the shock in this study. The dynamic stress-strain curve is related to a layer-wise collapse mode, whilst the equivalent quasi-static curve is related to a random shear band collapse mode. The findings herein are aimed at improving the experimental test techniques used to characterise the rate-sensitivity behaviour

  14. Dynamic earthquake rupture simulations on nonplanar faults embedded in 3D geometrically complex, heterogeneous elastic solids

    SciTech Connect

    Duru, Kenneth; Dunham, Eric M.

    2016-01-15

    Dynamic propagation of shear ruptures on a frictional interface in an elastic solid is a useful idealization of natural earthquakes. The conditions relating discontinuities in particle velocities across fault zones and tractions acting on the fault are often expressed as nonlinear friction laws. The corresponding initial boundary value problems are both numerically and computationally challenging. In addition, seismic waves generated by earthquake ruptures must be propagated for many wavelengths away from the fault. Therefore, reliable and efficient numerical simulations require both provably stable and high order accurate numerical methods. We present a high order accurate finite difference method for: a) enforcing nonlinear friction laws, in a consistent and provably stable manner, suitable for efficient explicit time integration; b) dynamic propagation of earthquake ruptures along nonplanar faults; and c) accurate propagation of seismic waves in heterogeneous media with free surface topography. We solve the first order form of the 3D elastic wave equation on a boundary-conforming curvilinear mesh, in terms of particle velocities and stresses that are collocated in space and time, using summation-by-parts (SBP) finite difference operators in space. Boundary and interface conditions are imposed weakly using penalties. By deriving semi-discrete energy estimates analogous to the continuous energy estimates we prove numerical stability. The finite difference stencils used in this paper are sixth order accurate in the interior and third order accurate close to the boundaries. However, the method is applicable to any spatial operator with a diagonal norm satisfying the SBP property. Time stepping is performed with a 4th order accurate explicit low storage Runge–Kutta scheme, thus yielding a globally fourth order accurate method in both space and time. We show numerical simulations on band limited self-similar fractal faults revealing the complexity of rupture

  15. 3D airflow dynamics over transverse ridges Mpekweni, South Africa: implications for dune field migration behaviour

    NASA Astrophysics Data System (ADS)

    Jackson, Derek; Cooper, Andrew; Green, Andrew; Beyers, Meiring; Wiles, Errol; Benallack, Keegan

    2016-04-01

    Un-vegetated dune fields provide excellent opportunities to examine airflow dynamics over various types and scales of dune landforms. The three dimensional surface over which lower boundary layers travel, help adjust surface airflow and consequently the aeolian response of the dunes themselves. The use of computational fluid dynamic (CFD) modelling in recent studies now enables investigation of the 3D behaviour of airflow over complex terrain, providing new insights into heterogeneous surface flow and aeolian response of dune surfaces on a large (dunefield) scale. Using a largely un-vegetated coastal dune field site at Mpekweni, Eastern Cape, South Africa, a detailed (0.1m gridded) terrestrial laser scanning survey was conducted to create a high resolution topographical surface. Using local wind flow measurements and local met station records as input, CFD modelling was performed for a number of scenarios involving variable direction and magnitude to examine surface flow patterns across multiple dune forms. Near surface acceleration, expansion and separation of airflow inducing convergence and divergence (steering) of flow velocity streamlines are investigated. Flow acceleration over dune crests/brink lines is a key parameter in driving dune migration and slip face dynamics. Dune aspect ratio (height to length) is also important in determining the degree of crestal flow acceleration, with an increase in flow associated with increasing aspect ratios. Variations in dune height appear to be the most important parameter in driving general flow acceleration. The results from the study provide new insights into dune migration behaviour at this site as well as surface flow behaviour across multiple dune configurations and length scales within un-vegetated dune fields.

  16. 3D Dynamics of Freshwater Lenses in the Near-Surface Layer of the Tropical Ocean

    NASA Astrophysics Data System (ADS)

    Soloviev, Alexander; Dean, Cayla

    2015-04-01

    Convective rains in the Intertropical Convergence Zone (ITCZ) produce lenses of freshened water on the ocean surface. These lenses are localized in space and typically involve both salinity and temperature anomalies. Due to significant density anomalies, strong pressure gradients develop, which result in lateral spreading of freshwater lenses in a form resembling gravity currents. Gravity currents inherently involve three-dimensional dynamics. As a type of organized structure, gravity currents in the upper layer of the ocean may also interact with, and be shaped by, the ambient oceanic environment and atmospheric conditions. Among the important factors are the background stratification, wind stress, wind/wave mixing and spatially coherent organized motions in the near-surface layer of the ocean. Under certain conditions, a resonant interaction between a propagating freshwater lens and internal waves in the underlying pycnocline (e.g., barrier layer) may develop, whereas interaction with wind stress may produce an asymmetry in the freshwater lens and associated mixing. These two types of interactions working in concert may explain the series of sharp frontal interfaces, which have been observed in association with freshwater lenses during TOGA COARE. In this work, we have conducted a series of numerical experiments using computational fluid dynamics tools. These numerical simulations were designed to elucidate the relationship between vertical mixing and horizontal advection of salinity under various environmental conditions and potential impact on the Aquarius and SMOS satellite image formation. Available near-surface data from field experiments served as a guidance for numerical simulations. The results of this study indicate that 3D dynamics of freshwater lenses are essential within a certain range of wind/wave conditions and the freshwater influx in the surface layer of the ocean.

  17. Diagnostic Value of 3D Fast Low-Angle Shot Dynamic MRI of Breast Papillomas

    PubMed Central

    Kim, Eun-Kyung; Kim, Jeong-Ah; Kwak, Jin Young; Jeong, Joon

    2009-01-01

    Purpose To evaluate the value of breast MRI in analysis of papillomas of the breast. Materials and Methods From 1996 to 2004, 94 patients underwent surgery due to papillomas of the breast. Among them, 21 patients underwent 3D fast low angle shot (FLASH) dynamic breast MRI. Eight masses were palpable and 11 of 21 patients had nipple discharge. Two radiologists indifferently analyzed the location, size of the lesions and shape, margin of the masses, multiplicity and ductal relation. The MRI findings were categorized according to breast imaging reporting and data system (BI-RADS) lexicon. The amount and pattern of enhancement and associated findings were also evaluated according to BI-RADS. We then compared the MRI findings with galactography, mammography and breast ultrasonography (US) and examined histopathologic correlation. Results On breast MRI, the lesion size was 0.4-1.59 cm, and 18 patients showed subareolar location. On 4.25 cm (mean 1.54) dynamic enhanced images, imaging findings showed mass (n = 10), intracystic mass (n = 3), focus (n = 5), ductal enhancement (n = 2), and segmental enhancement (n = 1). In cases of the masses, the shapes of the masses were round (n = 4), lobulated (n = 3), and irregular (n = 6), and margins were circumscribed (n = 6), microlobulated (n = 5), and indistinct (n = 2). The enhancement patterns were homogeneous enhancement (n = 7), heterogeneous (n = 3) or rim enhancement (n = 3). Conclusion The contrast enhanced dynamic breast MRI was highly sensitive for diagnosis of breast papillomas. MRI could play a key role in the pre-operative work-up for multiple papillomas and papillomatosis. PMID:20046427

  18. Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

    SciTech Connect

    B. Philip; Z. Wang; M.A. Berrill; M. Birke; M. Pernice

    2014-04-01

    The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton–Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

  19. Dynamic 3-D computer graphics for designing a diagnostic tool for patients with schizophrenia.

    PubMed

    Farkas, Attila; Papathomas, Thomas V; Silverstein, Steven M; Kourtev, Hristiyan; Papayanopoulos, John F

    2016-11-01

    We introduce a novel procedure that uses dynamic 3-D computer graphics as a diagnostic tool for assessing disease severity in schizophrenia patients, based on their reduced influence of top-down cognitive processes in interpreting bottom-up sensory input. Our procedure uses the hollow-mask illusion, in which the concave side of the mask is misperceived as convex, because familiarity with convex faces dominates sensory cues signaling a concave mask. It is known that schizophrenia patients resist this illusion and their resistance increases with illness severity. Our method uses virtual masks rendered with two competing textures: (a) realistic features that enhance the illusion; (b) random-dot visual noise that reduces the illusion. We control the relative weights of the two textures to obtain psychometric functions for controls and patients and assess illness severity. The primary novelty is the use of a rotating mask that is easy to implement on a wide variety of portable devices and avoids the use of elaborate stereoscopic devices that have been used in the past. Thus our method, which can also be used to assess the efficacy of treatments, provides clinicians the advantage to bring the test to the patient's own environment, instead of having to bring patients to the clinic.

  20. 3D dynamic model of healthy and pathologic arteries for ultrasound technique evaluation.

    PubMed

    Balocco, Simone; Basset, Olivier; Azencot, Jacques; Tortoli, Piero; Cachard, Christian

    2008-12-01

    A 3D model reproducing the biomechanical behavior of human blood vessels is presented. The model, based on a multilayer geometry composed of right generalized cylinders, enables the representation of different vessel morphologies, including bifurcations, either healthy or affected by stenoses. Using a finite element approach, blood flow is simulated by considering a dynamic displacement of the scatterers (erythrocytes), while arterial pulsation due to the hydraulic pressure is taken into account through a fluid-structure interaction based on a wall model. Each region is acoustically characterized using FIELD II software, which produces the radio frequency echo signals corresponding to echographic scans. Three acoustic physiological phantoms of carotid arteries surrounded by elastic tissue are presented to illustrate the model's capability. The first corresponds to a healthy blood vessel, the second includes a 50% stenosis, and the third represents a carotid bifurcation. Examples of M mode, B mode and color Doppler images derived from these phantoms are shown. Two examples of M-mode image segmentation and the identification of the atherosclerotic plaque boundaries on Doppler color images are reported. The model could be used as a tool for the preliminary evaluation of ultrasound signal processing and visualization techniques.

  1. Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

    NASA Astrophysics Data System (ADS)

    Philip, B.; Wang, Z.; Berrill, M. A.; Birke, M.; Pernice, M.

    2014-04-01

    The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

  2. Two-phase DNS of evaporating drops with 3D phenomena and contact-line dynamics

    NASA Astrophysics Data System (ADS)

    Valluri, Prashant; Sáenz, Pedro J.; Sefiane, Khellil; Matar, Omar K.

    2014-11-01

    A novel 3D two-phase model based on the diffuse-interface method is developed to investigate the fully-coupled two-phase dynamics of a sessile drop undergoing evaporation on a heated substrate. General transient advection-diffusion transport equations are implemented to address the conservation of energy and vapour in the gas phase, which also allows the more realistic modelling of interface mass and energy transport based on local conditions. The emphasis of this investigation is on addressing three-dimensional phenomena during evaporation of drops with non-circular contact area. Irregular drops lead to complex interface shapes with intricate contract-angle distributions along the triple line and with a three-dimensional flow which previous axisymmetric approaches cannot show. The versatility of this model also allows the simulation of the more complex case of drops evaporating with a moving contact line. Both constant-angle (CA) and constant-radius (CR) modes of pure evaporation are successfully simulated and validated against experiments. ThermaPOWER project (EU IRSES-PIRSES GA-2011-294905).

  3. Monitoring an eruption fissure in 3D: video recording, particle image velocimetry and dynamics

    NASA Astrophysics Data System (ADS)

    Witt, Tanja; Walter, Thomas R.

    2015-04-01

    The processes during an eruption are very complex. To get a better understanding several parameters are measured. One of the measured parameters is the velocity of particles and patterns, as ash and emitted magma, and of the volcano itself. The resulting velocity field provides insights into the dynamics of a vent. Here we test our algorithm for 3 dimensional velocity fields on videos of the second fissure eruption of Bárdarbunga 2014. There we acquired videos from lava fountains of the main fissure with 2 high speed cameras with small angles between the cameras. Additionally we test the algorithm on videos from the geyser Strokkur, where we had 3 cameras and larger angles between the cameras. The velocity is calculated by a correlation in the Fourier space of contiguous images. Considering that we only have the velocity field of the surface smaller angles result in a better resolution of the existing velocity field in the near field. For general movements also larger angles can be useful, e.g. to get the direction, height and velocity of eruption clouds. In summary, it can be stated that 3D velocimetry can be used for several application and with different setup due to the application.

  4. Foot roll-over evaluation based on 3D dynamic foot scan.

    PubMed

    Samson, William; Van Hamme, Angèle; Sanchez, Stéphane; Chèze, Laurence; Van Sint Jan, Serge; Feipel, Véronique

    2014-01-01

    Foot roll-over is commonly analyzed to evaluate gait pathologies. The current study utilized a dynamic foot scanner (DFS) to analyze foot roll-over. The right feet of ten healthy subjects were assessed during gait trials with a DFS system integrated into a walkway. A foot sole picture was computed by vertically projecting points from the 3D foot shape which were lower than a threshold height of 15 mm. A 'height' value of these projected points was determined; corresponding to the initial vertical coordinates prior to projection. Similar to pedobarographic analysis, the foot sole picture was segmented into anatomical regions of interest (ROIs) to process mean height (average of height data by ROI) and projected surface (area of the projected foot sole by ROI). Results showed that these variables evolved differently to plantar pressure data previously reported in the literature, mainly due to the specificity of each physical quantity (millimeters vs Pascals). Compared to plantar pressure data arising from surface contact by the foot, the current method takes into account the whole plantar aspect of the foot, including the parts that do not make contact with the support surface. The current approach using height data could contribute to a better understanding of specific aspects of foot motion during walking, such as plantar arch height and the windlass mechanism. Results of this study show the underlying method is reliable. Further investigation is required to validate the DFS measurements within a clinical context, prior to implementation into clinical practice.

  5. Dynamic 3D reconstructions of the heart wall from tomographic imaging

    NASA Astrophysics Data System (ADS)

    Lange, Joerg; von Smekal, Alexander

    1994-05-01

    We present a dynamic reconstruction of the left ventricle (LV) of the human heart. LV surface is represented by a set of points. The coordinates of these points are iterated by an artificial neural network while optimizing the match between the reconstruction based on these coordinates and the signal data. The input for the network are the segment's positions which represent the surface within the original data. The output is a set of real-valued coordinates quantifying the location of the LV surface points. The reconstruction is simultaneously developed in 3-D space and temporal domain. A topological constraint during training of the network gives corresponding vertices in space and time with global correctness. At any phase of the heart beat the network develops a map among the surface points which is highly ordered. This results in very regular wire-frames, that can be displayed rapidly on even small graphic workstations. Without time and third dimension this is very similar to Durbin's algorithm for solving the traveling salesman problem (TSP). To achieve a smooth representation we keep our network from developing the full TSP optimal solution.

  6. On the unsteady wake dynamics behind a circular disk using fully 3D proper orthogonal decomposition

    NASA Astrophysics Data System (ADS)

    Yang, Jianzhi; Liu, Minghou; Wu, Guang; Gu, Hailin; Yao, Mengyun

    2017-02-01

    In the present work, the wakes behind a circular disk at various transitional regimes are numerically explored using fully 3D proper orthogonal decomposition (POD). The Reynolds numbers considered in this study (Re = 152, 170, 300 and 3000) cover four transitional states, i.e. the reflectional-symmetry-breaking (RSB) mode, the standing wave (SW) mode, a weakly chaotic state, and a higher-Reynolds-number state. Through analysis of the spatial POD modes at different wake states, it is found that a planar-symmetric vortex shedding mode characterized by the first mode pair is persistent in all the states. When the wake develops into a weakly chaotic state, a new vortex shedding mode characterized by the second mode pair begins to appear and completely forms at the higher-Reynolds-number state of Re = 3000, i.e. planar-symmetry-breaking vortex shedding mode. On the other hand, the coherent structure at Re = 3000 extracted from the first two POD modes shows a good resemblance to the wake configuration in the SW mode, while the coherent structure reconstructed from the first four POD modes shows a good resemblance to the wake configuration in the RSB mode. The present results indicate that the dynamics or flow instabilities observed at transitional RSB and SW modes are still preserved in a higher-Reynolds-number regime.

  7. Integration of Libration Point Orbit Dynamics into a Universal 3-D Autonomous Formation Flying Algorithm

    NASA Technical Reports Server (NTRS)

    Folta, David; Bauer, Frank H. (Technical Monitor)

    2001-01-01

    The autonomous formation flying control algorithm developed by the Goddard Space Flight Center (GSFC) for the New Millennium Program (NMP) Earth Observing-1 (EO-1) mission is investigated for applicability to libration point orbit formations. In the EO-1 formation-flying algorithm, control is accomplished via linearization about a reference transfer orbit with a state transition matrix (STM) computed from state inputs. The effect of libration point orbit dynamics on this algorithm architecture is explored via computation of STMs using the flight proven code, a monodromy matrix developed from a N-body model of a libration orbit, and a standard STM developed from the gravitational and coriolis effects as measured at the libration point. A comparison of formation flying Delta-Vs calculated from these methods is made to a standard linear quadratic regulator (LQR) method. The universal 3-D approach is optimal in the sense that it can be accommodated as an open-loop or closed-loop control using only state information.

  8. 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

    Fluid flow is one of the main mass transport mechanisms in the Earth's crust and abundant mineral vein networks are important indicators for fluid flow and fluid rock interaction. These systems are dynamic and part of the so called RTM processes (reaction-transport-mechanics). Understanding of mineral vein systems requires coupling of these processes. Here we present a conceptional model for dynamic vein growth of syntaxial, posttectonic veins generated by advective fluid flow and show first results of a numerical model for this scenario. Vein generation requires three processes to occur: (i) fracture generation by mechanical stress e.g. hydro-fracturing, (ii) flow of a supersaturated fluid on that fracture and (iii) crystallization of phase(s) on or in the fracture. 3D synthetic fractures are generated with the SynFrac code (Ogilvie, et al. 2006). Subsequently solutions of the Navier-Stokes equation for this fracture are computed by a computational fluid dynamics code called GeoDict (Wiegmann 2007). Transport (advective and diffusive) of chemical species to growth sites in the fracture and vein growth are computed by a self-written MATLAB script. The numerical model discretizes the wall rock and fracture geometry by volumetric pixels (voxels). Based on this representation, the model computes the three basic functions for vein generation: (a) nucleation, (b) fluid flow with transport of chemical species and (c) growth. The following conditions were chosen for these three modules. Nucleation is heterogeneous and occurs instantaneously at the wall rock/fracture interface. Advective and diffusive flow of a supersaturated fluid and related transport of chemical species occurs according to the computed fluid flow field by GeoDict. Concentration of chemical species at the inflow is constant, representing external fluid buffering. Changes/decrease in the concentration of chemical species occurs only due to vein growth. Growth of nuclei is limited either by transport of

  9. A Hybrid Geophysical Fluid Dynamics and Fully 3D Fluid Dynamics Approach to Simulate Multiphysics Coastal Flows

    NASA Astrophysics Data System (ADS)

    Tang, H.; Qu, K.

    2014-12-01

    A hybrid method that couples a geophysical fluid dynamics model to a fully 3D fluid dynamics model is the most feasible and promising approach to simulate coastal ocean flow phenomena that involve multiple types of physics spanning a vast range of temporal and spatial scales. We propose such a hybrid method that couples the Finite Volume Coastal Ocean Model (FVCOM) with the Solver for Incompressible Flow on Overset Meshes (SIFOM); the former is used to simulate large-scale estuary flows, and the latter is employed to capture small-scale local processes. The coupling involves distinct governing equations, different numerical algorithms, and dissimilar grids, and it is two-way and realized using the Schwartz alternative iteration. In this presentation, the proposed method will be outlined, and a few applications that are newly produced by it but cannot be handled by other conventional approaches will be presented.

  10. 3D dynamic rupture simulation and local tomography studies following the 2010 Haiti earthquake

    NASA Astrophysics Data System (ADS)

    Douilly, Roby

    The 2010 M7.0 Haiti earthquake was the first major earthquake in southern Haiti in 250 years. As this event could represent the beginning of a new period of active seismicity in the region, and in consideration of how vulnerable the population is to earthquake damage, it is important to understand the nature of this event and how it has influenced seismic hazards in the region. Most significantly, the 2010 earthquake occurred on the secondary Leogâne thrust fault (two fault segments), not the Enriquillo Fault, the major strike-slip fault in the region, despite it being only a few kilometers away. We first use a finite element model to simulate rupture along the Leogâne fault. We varied friction and background stress to investigate the conditions that best explain observed surface deformations and why the rupture did not to jump to the nearby Enriquillo fault. Our model successfully replicated rupture propagation along the two segments of the Leogâne fault, and indicated that a significant stress increase occurred on the top and to the west of the Enriquillo fault. We also investigated the potential ground shaking level in this region if a rupture similar to the Mw 7.0 2010 Haiti earthquake were to occur on the Enriquillo fault. We used a finite element method and assumptions on regional stress to simulate low frequency dynamic rupture propagation for the segment of the Enriquillo fault closer to the capital. The high-frequency ground motion components were calculated using the specific barrier model, and the hybrid synthetics were obtained by combining the low-frequencies ( 1Hz) from the stochastic simulation using matched filtering at a crossover frequency of 1 Hz. The average horizontal peak ground acceleration, computed at several sites of interest through Port-au-Prince (the capital), has a value of 0.35g. Finally, we investigated the 3D local tomography of this region. We considered 897 high-quality records from the earthquake catalog as recorded by

  11. 3D Visualization of "Frozen" Dynamic Magma Chambers in the Duluth Complex, Northeastern Minnesota

    NASA Astrophysics Data System (ADS)

    Peterson, D. M.; Hauck, S. A.

    2005-12-01

    The Mesoproterozoic Duluth Complex and associated intrusions of the Midcontinent Rift in northeastern Minnesota constitute one of the largest, semi-continuous, mafic intrusive complexes in the world, second only to the Bushveld Complex of South Africa. These rocks cover an arcuate area of over 5,000 square kilometers and give rise to two strong gravity anomalies (+50 & +70 mgal) that imply intrusive roots to more than 13 km depth. The geometry of three large mafic intrusions within the Duluth Complex have been modeled by the integration of field mapping and drill hole data with maps of gravity and magnetic anomalies. The igneous bodies include the South Kawishiwi, Partridge River, and Bald Eagle intrusions that collectively outcrop over an area of > 800 square kilometers. The South Kawishiwi and Partridge River intrusions host several billion tons of low-grade Cu-Ni-PGE mineralization near their base, while the geophysical expressions of the Bald Eagle intrusion have the same shape and dimensions as the "bulls eye" pattern of low velocity seismic reflection anomalies along the East Pacific Rise. These anomalies are interpreted to define regions of melt concentrations, i.e., active magma chambers. This suggests that the funnel-shaped Bald Eagle intrusion could be an example of a "frozen" dynamic magma chamber. In support of this analogy we note that the magmatic systems of intracontinental rifts, mid-ocean ridges, extensional regimes in back-arc environments, and ophiolites have a common characteristic: the emplacement of magma in extensional environments, and the common products in all four are varieties of layered intrusions, dikes and sills, and overlying volcanic rocks. 3D visualization of these intrusions is integral to the understanding of the Duluth Complex magmatic system and associated mineralization, and can be used as a proxy for study of similar systems, such as the Antarctic Ferrar dolerites, worldwide.

  12. Velocity Measurement in Carotid Artery: Quantitative Comparison of Time-Resolved 3D Phase-Contrast MRI and Image-based Computational Fluid Dynamics

    PubMed Central

    Sarrami-Foroushani, Ali; Nasr Esfahany, Mohsen; Nasiraei Moghaddam, Abbas; Saligheh Rad, Hamidreza; Firouznia, Kavous; Shakiba, Madjid; Ghanaati, Hossein; Wilkinson, Iain David; Frangi, Alejandro Federico

    2015-01-01

    Background: Understanding hemodynamic environment in vessels is important for realizing the mechanisms leading to vascular pathologies. Objectives: Three-dimensional velocity vector field in carotid bifurcation is visualized using TR 3D phase-contrast magnetic resonance imaging (TR 3D PC MRI) and computational fluid dynamics (CFD). This study aimed to present a qualitative and quantitative comparison of the velocity vector field obtained by each technique. Subjects and Methods: MR imaging was performed on a 30-year old male normal subject. TR 3D PC MRI was performed on a 3 T scanner to measure velocity in carotid bifurcation. 3D anatomical model for CFD was created using images obtained from time-of-flight MR angiography. Velocity vector field in carotid bifurcation was predicted using CFD and PC MRI techniques. A statistical analysis was performed to assess the agreement between the two methods. Results: Although the main flow patterns were the same for the both techniques, CFD showed a greater resolution in mapping the secondary and circulating flows. Overall root mean square (RMS) errors for all the corresponding data points in PC MRI and CFD were 14.27% in peak systole and 12.91% in end diastole relative to maximum velocity measured at each cardiac phase. Bland-Altman plots showed a very good agreement between the two techniques. However, this study was not aimed to validate any of methods, instead, the consistency was assessed to accentuate the similarities and differences between Time-resolved PC MRI and CFD. Conclusion: Both techniques provided quantitatively consistent results of in vivo velocity vector fields in right internal carotid artery (RCA). PC MRI represented a good estimation of main flow patterns inside the vasculature, which seems to be acceptable for clinical use. However, limitations of each technique should be considered while interpreting results. PMID:26793288

  13. Dynamic diffusion tensor measurements in muscle tissue using Single Line Multiple Echo Diffusion Tensor Acquisition Technique at 3T

    PubMed Central

    Baete, Steven H.; Cho, Gene; Sigmund, Eric E.

    2015-01-01

    When diffusion biomarkers display transient changes, i.e. in muscle following exercise, traditional diffusion tensor imaging (DTI) methods lack temporal resolution to resolve the dynamics. This paper presents an MRI method for dynamic diffusion tensor acquisitions on a clinical 3T scanner. This method, SL-MEDITATE (Single Line Multiple Echo Diffusion Tensor Acquisition Technique) achieves a high temporal resolution (4s) (1) by rapid diffusion encoding through the acquisition of multiple echoes with unique diffusion sensitization and (2) by limiting the readout to a single line volume. The method is demonstrated in a rotating anisotropic phantom, in a flow phantom with adjustable flow speed, and in in vivo skeletal calf muscle of healthy volunteers following a plantar flexion exercise. The rotating and flow-varying phantom experiments show that SL-MEDITATE correctly identifies the rotation of the first diffusion eigenvector and the changes in diffusion tensor parameter magnitudes, respectively. Immediately following exercise, the in vivo mean diffusivity (MD) time-courses show, before the well-known increase, an initial decrease which is not typically observed in traditional DTI. In conclusion, SL-MEDITATE can be used to capture transient changes in tissue anisotropy in a single line. Future progress might allow for dynamic DTI when combined with appropriate k-space trajectories and compressed sensing reconstruction. PMID:25900166

  14. 3D dynamic rupture with anelastic wave propagation using an hp-adaptive Discontinuous Galerkin method

    NASA Astrophysics Data System (ADS)

    Tago, J.; Cruz-Atienza, V. M.; Etienne, V.; Virieux, J.; Benjemaa, M.; Sanchez-Sesma, F. J.

    2010-12-01

    Simulating any realistic seismic scenario requires incorporating physical basis into the model. Considering both the dynamics of the rupture process and the anelastic attenuation of seismic waves is essential to this purpose and, therefore, we choose to extend the hp-adaptive Discontinuous Galerkin finite-element method to integrate these physical aspects. The 3D elastodynamic equations in an unstructured tetrahedral mesh are solved with a second-order time marching approach in a high-performance computing environment. The first extension incorporates the viscoelastic rheology so that the intrinsic attenuation of the medium is considered in terms of frequency dependent quality factors (Q). On the other hand, the extension related to dynamic rupture is integrated through explicit boundary conditions over the crack surface. For this visco-elastodynamic formulation, we introduce an original discrete scheme that preserves the optimal code performance of the elastodynamic equations. A set of relaxation mechanisms describes the behavior of a generalized Maxwell body. We approximate almost constant Q in a wide frequency range by selecting both suitable relaxation frequencies and anelastic coefficients characterizing these mechanisms. In order to do so, we solve an optimization problem which is critical to minimize the amount of relaxation mechanisms. Two strategies are explored: 1) a least squares method and 2) a genetic algorithm (GA). We found that the improvement provided by the heuristic GA method is negligible. Both optimization strategies yield Q values within the 5% of the target constant Q mechanism. Anelastic functions (i.e. memory variables) are introduced to efficiently evaluate the time convolution terms involved in the constitutive equations and thus to minimize the computational cost. The incorporation of anelastic functions implies new terms with ordinary differential equations in the mathematical formulation. We solve these equations using the same order

  15. Magnitude subtraction vs. complex subtraction in dynamic contrast-enhanced 3D-MR angiography: basic experiments and clinical evaluation.

    PubMed

    Naganawa, S; Ito, T; Iwayama, E; Fukatsu, H; Ishiguchi, T; Ishigaki, T; Ichinose, N

    1999-11-01

    Magnitude subtraction and complex subtraction in dynamic contrast-enhanced three-dimensional magnetic resonance (3D-MR) angiography were compared using a phantom and 23 human subjects. In phantom studies, complex subtraction showed far better performance than magnitude subtraction, especially for longer echo times, with thicker slices, and without fat suppression. With complex subtraction, non-fat-suppressed studies showed contrast-to-noise ratios comparable to those in fat-suppressed studies. In human subjects, complex subtraction was superior to magnitude subtraction in 9 subjects, but comparable to magnitude subtraction in 14 subjects. There were no cases in which magnitude subtraction was superior to complex subtraction. Although the differences observed in human studies when complex subtraction was applied with thinner slices, shorter echo times, and the fat-suppression technique were not as pronounced as those seen in phantom studies, complex subtraction should be performed in dynamic contrast-enhanced 3D-MR angiography because there are no drawbacks in complex subtraction. Further research is necessary to assess the feasibility of dynamic contrast-enhanced 3D-MR angiography without fat suppression in human subjects using complex subtraction, as suggested by the results of phantom studies. If it is found to be feasible, dynamic contrast-enhanced 3D-MR angiography without fat suppression using complex subtraction may prove to be a robust technique that eliminates the need for shimming and can reduce the acquisition time. J. Magn. Reson. Imaging 1999;10:813-820.

  16. 3D-seismic observations of Late Pleistocene glacial dynamics on the central West Greenland margin

    NASA Astrophysics Data System (ADS)

    Hofmann, Julia; Knutz, Paul; Cofaigh, Colm Ó.

    2016-04-01

    Fast-flowing ice streams and outlet glaciers exert a major control on glacial discharge from contemporary and palaeo ice sheets. Improving our understanding of the extent and dynamic behaviour of these palaeo-ice streams is therefore crucial for predictions of the response of ice sheets to present and future climate warming and the associated implications for global sea level. This poster presents results from two 3D-seismic surveys located on the shelf adjoining the Disko Bay trough-mouth fan (TMF), one of the largest glacial outlet systems in Greenland. Located at the seaward terminus of the c. 370 km long cross-shelf Disko Trough, the Disko Bay TMF was generated by highly efficient subglacial sediment delivery onto the continental slopes during repeated ice-stream advances. A variety of submarine glacial landform assemblages are recognised on the seabed reflecting past ice-stream activity presumably related to glacial-interglacial cycles. The 3D-seismic volumes cover the shallow banks located north and south of the Disko Trough. The focus of this study is the seabed and the uppermost stratigraphic interval associated with the Late Stage of TMF development, presumably covering the late Pleistocene (Hofmann et al., submitted). Seabed morphologies include multiple sets of ridges up to 20 m high that extend in NW-SE direction for c. 30 km, and cross-cutting curvilinear furrows with maximum lengths of c. 9 km and average depths of c. 4.5 m. Back-stepping, arcuate scarps facing NW define the shelf break on the northern survey, comprising average widths of c. 4.5 km and incision depths of c. 27.5 m. The large transverse ridge features on the southern survey are likely ice-marginal and are interpreted as terminal moraine ridges recording the existence of a shelf-edge terminating, grounded Late Weichselian ice sheet. The furrows, most prominent on the outer shelf adjoining the shallow banks and partly incising the moraine ridges, are interpreted as iceberg ploughmarks

  17. Quantifying Transient 3D Dynamical Phenomena of Single mRNA Particles in Live Yeast Cell Measurements

    PubMed Central

    Calderon, Christopher P.; Thompson, Michael A.; Casolari, Jason M.; Paffenroth, Randy C.; Moerner, W. E.

    2013-01-01

    Single-particle tracking (SPT) has been extensively used to obtain information about diffusion and directed motion in a wide range of biological applications. Recently, new methods have appeared for obtaining precise (10s of nm) spatial information in three dimensions (3D) with high temporal resolution (measurements obtained every 4ms), which promise to more accurately sense the true dynamical behavior in the natural 3D cellular environment. Despite the quantitative 3D tracking information, the range of mathematical methods for extracting information about the underlying system has been limited mostly to mean-squared displacement analysis and other techniques not accounting for complex 3D kinetic interactions. There is a great need for new analysis tools aiming to more fully extract the biological information content from in vivo SPT measurements. High-resolution SPT experimental data has enormous potential to objectively scrutinize various proposed mechanistic schemes arising from theoretical biophysics and cell biology. At the same time, methods for rigorously checking the statistical consistency of both model assumptions and estimated parameters against observed experimental data (i.e. goodness-of-fit tests) have not received great attention. We demonstrate methods enabling (1) estimation of the parameters of 3D stochastic differential equation (SDE) models of the underlying dynamics given only one trajectory; and (2) construction of hypothesis tests checking the consistency of the fitted model with the observed trajectory so that extracted parameters are not over-interpreted (the tools are applicable to linear or nonlinear SDEs calibrated from non-stationary time series data). The approach is demonstrated on high-resolution 3D trajectories of single ARG3 mRNA particles in yeast cells in order to show the power of the methods in detecting signatures of transient directed transport. The methods presented are generally relevant to a wide variety of 2D and 3D SPT

  18. Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d.

    PubMed

    Wan, Hua; Hu, Jian-ping; Tian, Xu-hong; Chang, Shan

    2013-01-28

    The interaction between human complement receptor type 2 (CR2) and antigen-bound C3d can bridge the innate and adaptive immune systems. The recently determined structure of the CR2(SCR1-2):C3d complex has revealed the expected binding interface of CR2-C3d. In this article, wild type (WT) and three mutants of the new structure are studied by molecular dynamics (MD) simulations. The differently decreased structural stabilities of the mutants relative to WT are shown to be consistent with the experimental data, which can be explained by the different hydrogen bond patterns at the interfaces. It is also found that two clusters of residues (D36/E37/E39 and E160/D163/E166) in the acidic pocket of C3d are important for CR2-C3d interactions, which is in good agreement with previous mutagenesis study. In addition, functional dynamics and the conformational change of CR2 are explored by using domain cross-correlation map (DCCM), principal component analysis (PCA), and free energy landscape (FEL) methods. The conformational change mainly corresponds to the opening of a V-shaped structure of CR2, which is consistent with the previously reported high interdomain flexibility of CR2. We further suppose that the opening of a V-shaped structure of CR2 may favor the binding stability of CR2(SCR1-2):C3d. This study would provide some new insights into the understanding of the CR2-C3d interaction mechanism.

  19. Multiview holographic 3D dynamic display by combining a nano-grating patterned phase plate and LCD.

    PubMed

    Wan, Wenqiang; Qiao, Wen; Huang, Wenbin; Zhu, Ming; Ye, Yan; Chen, Xiangyu; Chen, Linsen

    2017-01-23

    Limited by the refreshable data volume of commercial spatial light modulator (SLM), electronic holography can hardly provide satisfactory 3D live video. Here we propose a holography based multiview 3D display by separating the phase information of a lightfield from the amplitude information. In this paper, the phase information was recorded by a 5.5-inch 4-view phase plate with a full coverage of pixelated nano-grating arrays. Because only amplitude information need to be updated, the refreshing data volume in a 3D video display was significantly reduced. A 5.5 inch TFT-LCD with a pixel size of 95 μm was used to modulate the amplitude information of a lightfield at a rate of 20 frames per second. To avoid crosstalk between viewing points, the spatial frequency and orientation of each nano-grating in the phase plate was fine tuned. As a result, the transmission light converged to the viewing points. The angular divergence was measured to be 1.02 degrees (FWHM) by average, slightly larger than the diffraction limit of 0.94 degrees. By refreshing the LCD, a series of animated sequential 3D images were dynamically presented at 4 viewing points. The resolution of each view was 640 × 360. Images for each viewing point were well separated and no ghost images were observed. The resolution of the image and the refreshing rate in the 3D dynamic display can be easily improved by employing another SLM. The recoded 3D videos showed the great potential of the proposed holographic 3D display to be used in mobile electronics.

  20. Multiplexing encoding method for full-color dynamic 3D holographic display.

    PubMed

    Xue, Gaolei; Liu, Juan; Li, Xin; Jia, Jia; Zhang, Zhao; Hu, Bin; Wang, Yongtian

    2014-07-28

    The multiplexing encoding method is proposed and demonstrated for reconstructing colorful images accurately by using single phase-only spatial light modulator (SLM). It will encode the light waves at different wavelengths into one pure-phase hologram at the same time based on the analytic formulas. The three-dimensional (3D) images can be reconstructed clearly when the light waves at different wavelengths are incident into the encoding hologram. Numerical simulations and optical experiments for 2D and 3D colorful images are performed. The results show that the colorful reconstructed images with high quality are achieved successfully. The proposed multiplexing method is a simple and fast encoding approach and the size of the system is small and compact. It is expected to be used for realizing full-color 3D holographic display in future.

  1. Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

    PubMed Central

    Taly, Jean-François; Marin, Antoine; Gibrat, Jean-François

    2008-01-01

    Background Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potential functions and a reduced representation of the polypeptide chain. These simplifications facilitate the exploration of the protein conformational space but do not permit to capture entirely the subtle relationship that exists between the amino acid sequence and its native structure. It has been proposed that physics-based energy functions together with techniques for sampling the conformational space, e.g., Monte Carlo or molecular dynamics (MD) simulations, are better suited to the task of modelling proteins at higher resolutions than those of models obtained with the former type of methods. In this study we monitor different protein structural properties along MD trajectories to discriminate correct from erroneous models. These models are based on the sequence-structure alignments provided by our fold recognition method, FROST. We define correct models as being built from alignments of sequences with structures similar to their native structures and erroneous models from alignments of sequences with structures unrelated to their native structures. Results For three test sequences whose native structures belong to the all-α, all-β and αβ classes we built a set of models intended to cover the whole spectrum: from a perfect model, i.e., the native structure, to a very poor model, i.e., a random alignment of the test sequence with a structure belonging to another structural class, including several intermediate models based on fold recognition alignments. We submitted these models to 11 ns of MD simulations at three different temperatures. We monitored along the corresponding trajectories the mean of the Root-Mean-Square deviations (RMSd) with respect to the initial conformation, the RMSd fluctuations, the number of conformation clusters, the evolution of secondary structures and the

  2. Analysis of thoracic aorta hemodynamics using 3D particle tracking velocimetry and computational fluid dynamics.

    PubMed

    Gallo, Diego; Gülan, Utku; Di Stefano, Antonietta; Ponzini, Raffaele; Lüthi, Beat; Holzner, Markus; Morbiducci, Umberto

    2014-09-22

    Parallel to the massive use of image-based computational hemodynamics to study the complex flow establishing in the human aorta, the need for suitable experimental techniques and ad hoc cases for the validation and benchmarking of numerical codes has grown more and more. Here we present a study where the 3D pulsatile flow in an anatomically realistic phantom of human ascending aorta is investigated both experimentally and computationally. The experimental study uses 3D particle tracking velocimetry (PTV) to characterize the flow field in vitro, while finite volume method is applied to numerically solve the governing equations of motion in the same domain, under the same conditions. Our findings show that there is an excellent agreement between computational and measured flow fields during the forward flow phase, while the agreement is poorer during the reverse flow phase. In conclusion, here we demonstrate that 3D PTV is very suitable for a detailed study of complex unsteady flows as in aorta and for validating computational models of aortic hemodynamics. In a future step, it will be possible to take advantage from the ability of 3D PTV to evaluate velocity fluctuations and, for this reason, to gain further knowledge on the process of transition to turbulence occurring in the thoracic aorta.

  3. Dynamics of electron emission in double photoionization processes near the krypton 3d threshold

    NASA Astrophysics Data System (ADS)

    Penent, F.; Sheinerman, S.; Andric, L.; Lablanquie, P.; Palaudoux, J.; Becker, U.; Braune, M.; Viefhaus, J.; Eland, J. H. D.

    2008-02-01

    Two-electron emission following photoabsorption near the Kr 3d threshold is investigated both experimentally and theoretically. On the experimental side, electron/electron coincidences using a magnetic bottle time-of-flight spectrometer allow us to observe the complete double photo ionization (DPI) continua of selected Kr2+ final states, and to see how these continua are affected by resonant processes in the vicinity of the Kr 3d threshold. The analysis is based on a quantum mechanical approach that takes into account the contribution of three different processes: (A) Auger decay of the inner 3d vacancy with the associated post-collision interaction (PCI) effects, (B) capture of slow photoelectrons into discrete states followed by valence multiplet decay (VMD) of the excited ionic states and (C) valence shell DPI. The dominant process for each Kr2+(4p-2) final state is the photoionization of the inner shell followed by Auger decay of the 3d vacancies. Moreover, for the 4p-2(3P) and 4p-2(1D) final ionic states an important contribution comes from the processes of slow photoelectron capture followed by VMD as well as from double ionization of the outer shell involving also VMD.

  4. In vivo-in vitro comparison of acute respiratory tract toxicity using human 3D airway epithelial models and human A549 and murine 3T3 monolayer cell systems.

    PubMed

    Sauer, Ursula G; Vogel, Sandra; Hess, Annemarie; Kolle, Susanne N; Ma-Hock, Lan; van Ravenzwaay, Bennard; Landsiedel, Robert

    2013-02-01

    The usefulness of in vitro systems to predict acute inhalation toxicity was investigated. Nineteen substances were tested in three-dimensional human airway epithelial models, EpiAirway™ and MucilAir™, and in A549 and 3T3 monolayer cell cultures. IC(50) values were compared to rat four-hour LC(50) values classified according to EPA and GHS hazard categories. Best results were achieved with a prediction model distinguishing toxic from non-toxic substances, with satisfactory specificities and sensitivities. Using a self-made four-level prediction model to classify substances into four in vitro hazard categories, in vivo-in vitro concordance was mediocre, but could be improved by excluding substances causing pulmonary edema and emphysema in vivo. None of the test systems was outstanding, and there was no evidence that tissue or monolayer systems using respiratory tract cells provide an added value. However, the test systems only reflected bronchiole epithelia and alveolar cells and investigated cytotoxicity. Effects occurring in other cells by other mechanisms could not be recognised. Further work should optimise test protocols and expand the set of substances tested to define applicability domains. In vivo respiratory toxicity data for in vitro comparisons should distinguish different modes of action, and their relevance for human health effects should be ensured.

  5. 3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research.

    PubMed

    Fang, Suqin; Yan, Xiaolong; Liao, Hong

    2009-12-01

    Root architecture plays important roles in plant water and nutrient acquisition. However, accurate modeling of the root system that provides a realistic representation of roots in the soil is limited by a lack of appropriate tools for the non-destructive and precise measurement of the root system architecture in situ. Here we describe a root growth system in which the roots grow in a solid gel matrix that was used to reconstruct 3D root architecture in situ and dynamically simulate its changes under various nutrient conditions with a high degree of precision. A 3D laser scanner combined with a transparent gel-based growth system was used to capture 3D images of roots. The root system skeleton was extracted using a skeleton extraction method based on the Hough transformation, and mesh modeling using Ball-B spline was employed. We successfully used this system to reconstruct rice and soybean root architectures and determine their changes under various phosphorus (P) supply conditions. Our results showed that the 3D root architecture parameters that were dynamically calculated based on the skeletonization and simulation of root systems were significantly correlated with the biomass and P content of rice and soybean based on both the simulation system and previous reports. Therefore, this approach provides a novel technique for the study of crop root growth and its adaptive changes to various environmental conditions.

  6. Using 3-D OFEM for movement correction and quantitative evaluation in dynamic cardiac NH3 PET images

    NASA Astrophysics Data System (ADS)

    Lin, Hong-Dun; Yang, Bang-Hung; Chen, Chih-Hao; Wu, Liang-Chih; Liu, Ren-Shyan; Chung, Being-Tau; Lin, Kang-Ping

    2005-04-01

    Various forms of cardiac pathology, such as myocardial ischemia and infarction, can be characterized with 13NH3-PET images. In clinical situation, polar map (bullseye image), which derived by combining images from multiple planes (designated by the circle around the myocardium in the above images), so that information of the entire myocardium can be displayed in a single image for diagnosis. However, image artifact problem always arises from body movement or breathing motion in image acquisition period and results in indefinite myocardium disorder region shown in bullseye image. In this study, a 3-D motion and movement correction method is developed to solve the image artifact problem to improve the accuracy of diagnostic bullseye image. The proposed method is based on 3-D optical flow estimation method (OFEM) and cooperates with the particular dynamic imaging protocol, which snaps serial PET images (5 frames) in later half imaging period. The 3-D OFEM assigns to each image point in the visual 3-D flow velocity field, which associates with the non-rigid motion of the time-varying brightness of a sequence of images. It presents vectors of corresponding images position between frames for motion correction. To validate the performance of proposed method, 10 normal and 20 abnormal whole-body dynamic PET imaging studies were applied, and the results show that the bullseye images, which generated by corrected images, present clear and definite tissue region for clinical diagnosis.

  7. Nonlinear dynamics of 3D beams of fast magnetosonic waves propagating in the ionospheric and magnetospheric plasma

    NASA Astrophysics Data System (ADS)

    Belashov, V. Yu.; Belashova, E. S.

    2016-11-01

    On the basis of the model of the three-dimensional (3D) generalized Kadomtsev-Petviashvili equation for magnetic field h = B / B the formation, stability, and dynamics of 3D soliton-like structures, such as the beams of fast magnetosonic (FMS) waves generated in ionospheric and magnetospheric plasma at a low-frequency branch of oscillations when β = 4 πnT/ B 2 ≪ 1 and β > 1, are studied. The study takes into account the highest dispersion correction determined by values of the plasma parameters and the angle θ = ( B, k), which plays a key role in the FMS beam propagation at those angles to the magnetic field that are close to π/2. The stability of multidimensional solutions is studied by an investigation of the Hamiltonian boundness under its deformations on the basis of solving of the corresponding variational problem. The evolution and dynamics of the 3D FMS wave beam are studied by the numerical integration of equations with the use of specially developed methods. The results can be interpreted in terms of the self-focusing phenomenon, as the formation of a stationary beam and the scattering and self-focusing of the solitary beam of FMS waves. These cases were studied with a detailed investigation of all evolutionary stages of the 3D FMS wave beams in the ionospheric and magnetospheric plasma.

  8. Repercussion of geometric and dynamic constraints on the 3D rendering quality in structurally adaptive multi-view shooting systems

    NASA Astrophysics Data System (ADS)

    Ali-Bey, Mohamed; Moughamir, Saïd; Manamanni, Noureddine

    2011-12-01

    in this paper a simulator of a multi-view shooting system with parallel optical axes and structurally variable configuration is proposed. The considered system is dedicated to the production of 3D contents for auto-stereoscopic visualization. The global shooting/viewing geometrical process, which is the kernel of this shooting system, is detailed and the different viewing, transformation and capture parameters are then defined. An appropriate perspective projection model is afterward derived to work out a simulator. At first, this latter is used to validate the global geometrical process in the case of a static configuration. Next, the simulator is used to show the limitations of a static configuration of this shooting system type by considering the case of dynamic scenes and then a dynamic scheme is achieved to allow a correct capture of this kind of scenes. After that, the effect of the different geometrical capture parameters on the 3D rendering quality and the necessity or not of their adaptation is studied. Finally, some dynamic effects and their repercussions on the 3D rendering quality of dynamic scenes are analyzed using error images and some image quantization tools. Simulation and experimental results are presented throughout this paper to illustrate the different studied points. Some conclusions and perspectives end the paper. [Figure not available: see fulltext.

  9. Dynamic 3D MR Visualization and Detection of Upper Airway Obstruction during Sleep using Region Growing Segmentation

    PubMed Central

    Kim, Yoon-Chul; Khoo, Michael C.K.; Davidson Ward, Sally L.; Nayak, Krishna S.

    2016-01-01

    Goal We demonstrate a novel and robust approach for visualization of upper airway dynamics and detection of obstructive events from dynamic 3D magnetic resonance imaging (MRI) scans of the pharyngeal airway. Methods This approach uses 3D region growing, where the operator selects a region of interest that includes the pharyngeal airway, places two seeds in the patent airway, and determines a threshold for the first frame. Results This approach required 5 sec/frame of CPU time compared to 10 min/frame of operator time for manual segmentation. It compared well with manual segmentation, resulting in Dice Coefficients of 0.84 to 0.94, whereas the Dice Coefficients for two manual segmentations by the same observer were 0.89 to 0.97. It was also able to automatically detect 83% of collapse events. Conclusion Use of this simple semi-automated segmentation approach improves the workflow of novel dynamic MRI studies of the pharyngeal airway and enables visualization and detection of obstructive events. Significance Obstructive sleep apnea is a significant public health issue affecting 4-9% of adults and 2% of children. Recently, 3D dynamic MRI of the upper airway has been demonstrated during natural sleep, with sufficient spatio-temporal resolution to non-invasively study patterns of airway obstruction in young adults with OSA. This work makes it practical to analyze these long scans and visualize important factors in an MRI sleep study, such as the time, site, and extent of airway collapse. PMID:26258929

  10. Versatile, Immersive, Creative and Dynamic Virtual 3-D Healthcare Learning Environments: A Review of the Literature

    PubMed Central

    2008-01-01

    The author provides a critical overview of three-dimensional (3-D) virtual worlds and “serious gaming” that are currently being developed and used in healthcare professional education and medicine. The relevance of this e-learning innovation for teaching students and professionals is debatable and variables influencing adoption, such as increased knowledge, self-directed learning, and peer collaboration, by academics, healthcare professionals, and business executives are examined while looking at various Web 2.0/3.0 applications. There is a need for more empirical research in order to unearth the pedagogical outcomes and advantages associated with this e-learning technology. A brief description of Roger’s Diffusion of Innovations Theory and Siemens’ Connectivism Theory for today’s learners is presented as potential underlying pedagogical tenets to support the use of virtual 3-D learning environments in higher education and healthcare. PMID:18762473

  11. Modeling and 3-D Simulation of Biofilm Dynamics in Aqueous Environment

    NASA Astrophysics Data System (ADS)

    Wang, Qi

    2011-11-01

    We present a complex fluid model for biofilms growing in an aqueous environment. The modeling approach represents a new paradigm to develop models for biofilm-environment interaction that can be used to systematically incorporate refined chemical and physiological mechanisms. Special solutions of the model are presented and analyzed. 3-D numerical simulations in aqueous environment with emphasis on biofilm- ambient fluid interaction will be discussed in detail.

  12. Migration dynamics of breast cancer cells in a tunable 3D interstitial flow chamber.

    PubMed

    Haessler, Ulrike; Teo, Jeremy C M; Foretay, Didier; Renaud, Philippe; Swartz, Melody A

    2012-04-01

    The migration of cells such as leukocytes, tumor cells, and fibroblasts through 3D matrices is critical for regulating homeostasis and immunity and for driving pathogenesis. Interstitial flow through the extracellular matrix, which can substantially increase during inflammation and in the tumor microenvironment, can influence cell migration in multiple ways. Leukocytes and tumor cells are heterogeneous in their migration responses to flow, yet most 3D migration studies use endpoint measurements representing average characteristics. Here we present a robust new microfluidic device for 3D culture with live imaging under well-controlled flow conditions, along with a comparison of analytical methods for describing the migration behavior of heterogeneous cell populations. We then use the model to provide new insight on how interstitial flow affects MDA-MB-231 breast cancer cell invasion, phenomena that are not seen from averaged or endpoint measurements. Specifically, we find that interstitial flow increases the percentage of cells that become migratory, and increases migrational speed in about 20% of the cells. It also increases the migrational persistence of a subpopulation (5-10% of cells) in the positive or negative flow direction. Cells that migrated upstream moved faster but with less directedness, whereas cells that migrated in the direction of flow moved at slower speeds but with higher directedness. These findings demonstrate how fluid flow in the tumor microenvironment can enhance tumor cell invasion by directing a subpopulation of tumor cells in the flow direction; i.e., towards the draining lymphatic vessels, a major route of metastasis.

  13. Motion field estimation for a dynamic scene using a 3D LiDAR.

    PubMed

    Li, Qingquan; Zhang, Liang; Mao, Qingzhou; Zou, Qin; Zhang, Pin; Feng, Shaojun; Ochieng, Washington

    2014-09-09

    This paper proposes a novel motion field estimation method based on a 3D light detection and ranging (LiDAR) sensor for motion sensing for intelligent driverless vehicles and active collision avoidance systems. Unlike multiple target tracking methods, which estimate the motion state of detected targets, such as cars and pedestrians, motion field estimation regards the whole scene as a motion field in which each little element has its own motion state. Compared to multiple target tracking, segmentation errors and data association errors have much less significance in motion field estimation, making it more accurate and robust. This paper presents an intact 3D LiDAR-based motion field estimation method, including pre-processing, a theoretical framework for the motion field estimation problem and practical solutions. The 3D LiDAR measurements are first projected to small-scale polar grids, and then, after data association and Kalman filtering, the motion state of every moving grid is estimated. To reduce computing time, a fast data association algorithm is proposed. Furthermore, considering the spatial correlation of motion among neighboring grids, a novel spatial-smoothing algorithm is also presented to optimize the motion field. The experimental results using several data sets captured in different cities indicate that the proposed motion field estimation is able to run in real-time and performs robustly and effectively.

  14. Motion Field Estimation for a Dynamic Scene Using a 3D LiDAR

    PubMed Central

    Li, Qingquan; Zhang, Liang; Mao, Qingzhou; Zou, Qin; Zhang, Pin; Feng, Shaojun; Ochieng, Washington

    2014-01-01

    This paper proposes a novel motion field estimation method based on a 3D light detection and ranging (LiDAR) sensor for motion sensing for intelligent driverless vehicles and active collision avoidance systems. Unlike multiple target tracking methods, which estimate the motion state of detected targets, such as cars and pedestrians, motion field estimation regards the whole scene as a motion field in which each little element has its own motion state. Compared to multiple target tracking, segmentation errors and data association errors have much less significance in motion field estimation, making it more accurate and robust. This paper presents an intact 3D LiDAR-based motion field estimation method, including pre-processing, a theoretical framework for the motion field estimation problem and practical solutions. The 3D LiDAR measurements are first projected to small-scale polar grids, and then, after data association and Kalman filtering, the motion state of every moving grid is estimated. To reduce computing time, a fast data association algorithm is proposed. Furthermore, considering the spatial correlation of motion among neighboring grids, a novel spatial-smoothing algorithm is also presented to optimize the motion field. The experimental results using several data sets captured in different cities indicate that the proposed motion field estimation is able to run in real-time and performs robustly and effectively. PMID:25207868

  15. Dynamics of Quasi 2D and 3D Co-rotating Vortex Merger

    NASA Astrophysics Data System (ADS)

    Khandekar, Akshay; Jacob, Jamey

    2013-11-01

    Merger of vortices is examined experimentally to compare the merger of slender parallel vortices generated either coincidentally or continuously. It is known that like-sign vortices rotate around a common center of circulation and merger between the vortices may occur under certain conditions. This merger is dependent on the strength of the vortex circulation, distance of separation between the centers of the two vortices, ReΓ , and vorticity distribution. Quasi-2D and 3D experimental data is examined and merger relations are derived. The former uses high aspect ratio rotating paddles in a tank and while the latter are from wing-tip vortices in a wind tunnel. The vortex merger tank generates slender co-rotating vortices and are examined using PIV, while in the wind tunnel two opposing wings are arranged at opposite angles of attack to generate a pair of vortices that merge downstream. A 5-hole probe is used to obtain 3D velocity vectors via wake survey, along with PIV. The procedure is performed in the wake at different distances to observe merger under different conditions. Temporally and spatially dependent relations in quasi-2D and 3D vortex merger are derived. Merger behavior is generally similar between the cases, but instabilities along quasi-2D vortices may affect.

  16. Biologic response of inguinal hernia prosthetics: a comparative study of conventional static meshes versus 3D dynamic implants.

    PubMed

    Amato, Giuseppe; Romano, Giorgio; Agrusa, Antonino; Marasa, Salvatore; Cocorullo, Gianfranco; Gulotta, Gaspare; Goetze, Thorsten; Puleio, Roberto

    2015-01-01

    Despite improvements in prosthetics and surgical techniques, the rate of complications following inguinal hernia repair remains high. Among these, discomfort and chronic pain have become a source of increasing concern among surgeons. Poor quality of tissue ingrowth, such as thin scar plates or shrinking scars-typical results with conventional static implants and plugs-may contribute to these adverse events. Recently, a new type of 3D dynamically responsive implant was introduced to the market. This device, designed to be placed fixation-free, seems to induce ingrowth of viable and structured tissue instead of regressive fibrotic scarring. To elucidate the differences in biologic response between the conventional static meshes and this 3D dynamically responsive implant, a histological comparison was planned. The aim of this study was to determine the quality of tissue incorporation in both types of implants excised after short, medium, and long periods post-implantation. The results showed large differences in the biologic responses between the two implant types. Histologically, the 3D dynamic implant showed development of tissue elements more similar to natural abdominal wall structures, such as the ingrowth of loose and well-hydrated connective tissue, well-formed vascular structures, elastic fibers, and mature nerves, with negligible or absent inflammatory response. All these characteristics were completely absent in the conventional static implants, where a persistent inflammatory reaction was associated with thin, hardened, and shrunken fibrotic scar formation. Consequently, as herniation is a degenerative process, the 3D dynamic implants, which induce regeneration of the typical groin components, seem to address its pathogenesis.

  17. Dynamic Assessment of Fibroblast Mechanical Activity during Rac-induced Cell Spreading in 3-D Culture

    PubMed Central

    Petroll, W. Matthew; Ma, Lisha; Kim, Areum; Ly, Linda; Vishwanath, Mridula

    2009-01-01

    The goal of this study was to determine the morphological and sub-cellular mechanical effects of Rac activation on fibroblasts within 3-D collagen matrices. Corneal fibroblasts were plated at low density inside 100 μm thick fibrillar collagen matrices and cultured for 1 to 2 days in serum-free media. Time-lapse imaging was then performed using Nomarski DIC. After an acclimation period, perfusion was switched to media containing PDGF. In some experiments, Y-27632 or blebbistatin were used to inhibit Rho-kinase (ROCK) or myosin II, respectively. PDGF activated Rac and induced cell spreading, which resulted in an increase in cell length, cell area, and the number of pseudopodial processes. Tractional forces were generated by extending pseudopodia, as indicated by centripetal displacement and realignment of collagen fibrils. Interestingly, the pattern of pseudopodial extension and local collagen fibril realignment was highly dependent upon the initial orientation of fibrils at the leading edge. Following ROCK or myosin II inhibition, significant ECM relaxation was observed, but small displacements of collagen fibrils continued to be detected at the tips of pseudopodia. Taken together, the data suggests that during Rac-induced cell spreading within 3-D matrices, there is a shift in the distribution of forces from the center to the periphery of corneal fibroblasts. ROCK mediates the generation of large myosin II-based tractional forces during cell spreading within 3-D collagen matrices, however residual forces can be generated at the tips of extending pseudopodia that are both ROCK and myosin II-independent. PMID:18452153

  18. A 3D Optical Surface Profilometer Using a Dual-Frequency Liquid Crystal-Based Dynamic Fringe Pattern Generator

    PubMed Central

    Joo, Kyung-Il; Kim, Mugeon; Park, Min-Kyu; Park, Heewon; Kim, Byeonggon; Hahn, JoonKu; Kim, Hak-Rin

    2016-01-01

    We propose a liquid crystal (LC)-based 3D optical surface profilometer that can utilize multiple fringe patterns to extract an enhanced 3D surface depth profile. To avoid the optical phase ambiguity and enhance the 3D depth extraction, 16 interference patterns were generated by the LC-based dynamic fringe pattern generator (DFPG) using four-step phase shifting and four-step spatial frequency varying schemes. The DFPG had one common slit with an electrically controllable birefringence (ECB) LC mode and four switching slits with a twisted nematic LC mode. The spatial frequency of the projected fringe pattern could be controlled by selecting one of the switching slits. In addition, moving fringe patterns were obtainable by applying voltages to the ECB LC layer, which varied the phase difference between the common and the selected switching slits. Notably, the DFPG switching time required to project 16 fringe patterns was minimized by utilizing the dual-frequency modulation of the driving waveform to switch the LC layers. We calculated the phase modulation of the DFPG and reconstructed the depth profile of 3D objects using a discrete Fourier transform method and geometric optical parameters. PMID:27801812

  19. Network dynamics of 3D engineered neuronal cultures: a new experimental model for in-vitro electrophysiology

    PubMed Central

    Frega, Monica; Tedesco, Mariateresa; Massobrio, Paolo; Pesce, Mattia; Martinoia, Sergio

    2014-01-01

    Despite the extensive use of in-vitro models for neuroscientific investigations and notwithstanding the growing field of network electrophysiology, all studies on cultured cells devoted to elucidate neurophysiological mechanisms and computational properties, are based on 2D neuronal networks. These networks are usually grown onto specific rigid substrates (also with embedded electrodes) and lack of most of the constituents of the in-vivo like environment: cell morphology, cell-to-cell interaction and neuritic outgrowth in all directions. Cells in a brain region develop in a 3D space and interact with a complex multi-cellular environment and extracellular matrix. Under this perspective, 3D networks coupled to micro-transducer arrays, represent a new and powerful in-vitro model capable of better emulating in-vivo physiology. In this work, we present a new experimental paradigm constituted by 3D hippocampal networks coupled to Micro-Electrode-Arrays (MEAs) and we show how the features of the recorded network dynamics differ from the corresponding 2D network model. Further development of the proposed 3D in-vitro model by adding embedded functionalized scaffolds might open new prospects for manipulating, stimulating and recording the neuronal activity to elucidate neurophysiological mechanisms and to design bio-hybrid microsystems. PMID:24976386

  20. Network dynamics of 3D engineered neuronal cultures: a new experimental model for in-vitro electrophysiology.

    PubMed

    Frega, Monica; Tedesco, Mariateresa; Massobrio, Paolo; Pesce, Mattia; Martinoia, Sergio

    2014-06-30

    Despite the extensive use of in-vitro models for neuroscientific investigations and notwithstanding the growing field of network electrophysiology, all studies on cultured cells devoted to elucidate neurophysiological mechanisms and computational properties, are based on 2D neuronal networks. These networks are usually grown onto specific rigid substrates (also with embedded electrodes) and lack of most of the constituents of the in-vivo like environment: cell morphology, cell-to-cell interaction and neuritic outgrowth in all directions. Cells in a brain region develop in a 3D space and interact with a complex multi-cellular environment and extracellular matrix. Under this perspective, 3D networks coupled to micro-transducer arrays, represent a new and powerful in-vitro model capable of better emulating in-vivo physiology. In this work, we present a new experimental paradigm constituted by 3D hippocampal networks coupled to Micro-Electrode-Arrays (MEAs) and we show how the features of the recorded network dynamics differ from the corresponding 2D network model. Further development of the proposed 3D in-vitro model by adding embedded functionalized scaffolds might open new prospects for manipulating, stimulating and recording the neuronal activity to elucidate neurophysiological mechanisms and to design bio-hybrid microsystems.

  1. HBT-EP Program: MHD Dynamics and Active Control through 3D Fields and Currents

    NASA Astrophysics Data System (ADS)

    Navratil, G. A.; Abler, M. C.; Bialek, J.; Brooks, J. W.; Byrne, P. J.; Desanto, S.; Hughes, P. E.; Levesque, J. P.; Mauel, M. E.; Rhodes, D. J.; Hansen, C. J.

    2016-10-01

    The HBT-EP active mode control research program aims to: (i) advance understanding of the effects of 3D shaping on advanced tokamak fusion performance, (ii) resolve important MHD issues associated with disruptions, and (iii) measure and mitigate the effects of 3D scrape-off layer (SOL) currents through active and passive control of the plasma edge and conducting boundary structures. A GPU-based low latency control system uses 96 inputs and 64 outputs to control the plasma boundary. An in-vessel adjustable ferritic wall is used to study ferritic RWMs with increased growth rates, RMP response, and disruptivity. A quasi-linear sharp-boundary model is developed to study effects of toroidal curvature and plasma shaping on beta limits with resistive plasmas and walls. Measurement of currents between vessel sections reveals currents running from the plasma to the wall during wall-touching kink modes and disruptions. Asymmetries in plasma current are observed using segmented Rogowski coils. Biased electrodes in the plasma are used to control rotation of external kinks and drive currents in the SOL. An extensive array of SOL current monitors and edge drive electrodes will be installed for pioneering studies of helical edge current control. Supported by U.S. DOE Grant DE-FG02-86ER53222.

  2. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features.

    PubMed

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer's disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may be

  3. WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

    NASA Technical Reports Server (NTRS)

    Koppenhoefer, Kyle C.; Gullerud, Arne S.; Ruggieri, Claudio; Dodds, Robert H., Jr.; Healy, Brian E.

    1998-01-01

    This report describes theoretical background material and commands necessary to use the WARP3D finite element code. WARP3D is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of ductile fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, face loading), an element extinction facility to model crack growth, nonlinear material models including viscoplastic effects, and the Gurson-Tver-gaard dilatant plasticity model for void growth. The nonlinear, dynamic equilibrium equations are solved using an incremental-iterative, implicit formulation with full Newton iterations to eliminate residual nodal forces. The history integration of the nonlinear equations of motion is accomplished with Newmarks Beta method. A central feature of WARP3D involves the use of a linear-preconditioned conjugate gradient (LPCG) solver implemented in an element-by-element format to replace a conventional direct linear equation solver. This software architecture dramatically reduces both the memory requirements and CPU time for very large, nonlinear solid models since formation of the assembled (dynamic) stiffness matrix is avoided. Analyses thus exhibit the numerical stability for large time (load) steps provided by the implicit formulation coupled with the low memory requirements characteristic of an explicit code. In addition to the much lower memory requirements of the LPCG solver, the CPU time required for solution of the linear equations during each Newton iteration is generally one-half or less of the CPU time required for a traditional direct solver. All other computational aspects of the code (element stiffnesses, element strains, stress updating, element internal forces) are implemented in the element-by- element, blocked architecture. This greatly improves

  4. Quenching to unitarity: Quantum dynamics in a 3D Bose gas

    NASA Astrophysics Data System (ADS)

    Sykes, Andrew; Corson, John; D'Incao, Jose; Koller, Andrew; Bohn, John; Rey, Ana Maria; Hazzard, Kaden; Greene, Chris

    2014-03-01

    We study the dynamics of a zero temperature Bose condensate following a sudden quench of the scattering length from noninteracting to unitarity (infinite scattering length). In this talk we discuss how a qualitative understanding of the dynamics can be built up by understanding few-body physics under the same dynamical scenario. We calculate the coherent evolution of the momentum distribution, particularly focusing on the time dependence of the contact. By comparing the results to a many-body mean-field calculation, we gauge the qualitative and quantitative accuracy of this approach. We then discuss the results of a three-body calculation, in which loss dynamics occurs due to three-body recombination. One the key results of this work indicates that loss dynamics takes place over a much longer timescale than the coherent dynamics. This exciting result supports the idea that meta-stable degenerate unitary Bose gases may be experimentally observable in such a non-equilibrium scenario.

  5. Persistent and automatic intraoperative 3D digitization of surfaces under dynamic magnifications of an operating microscope.

    PubMed

    Kumar, Ankur N; Miga, Michael I; Pheiffer, Thomas S; Chambless, Lola B; Thompson, Reid C; Dawant, Benoit M

    2015-01-01

    One of the major challenges impeding advancement in image-guided surgical (IGS) systems is the soft-tissue deformation during surgical procedures. These deformations reduce the utility of the patient's preoperative images and may produce inaccuracies in the application of preoperative surgical plans. Solutions to compensate for the tissue deformations include the acquisition of intraoperative tomographic images of the whole organ for direct displacement measurement and techniques that combines intraoperative organ surface measurements with computational biomechanical models to predict subsurface displacements. The later solution has the advantage of being less expensive and amenable to surgical workflow. Several modalities such as textured laser scanners, conoscopic holography, and stereo-pair cameras have been proposed for the intraoperative 3D estimation of organ surfaces to drive patient-specific biomechanical models for the intraoperative update of preoperative images. Though each modality has its respective advantages and disadvantages, stereo-pair camera approaches used within a standard operating microscope is the focus of this article. A new method that permits the automatic and near real-time estimation of 3D surfaces (at 1 Hz) under varying magnifications of the operating microscope is proposed. This method has been evaluated on a CAD phantom object and on full-length neurosurgery video sequences (∼1 h) acquired intraoperatively by the proposed stereovision system. To the best of our knowledge, this type of validation study on full-length brain tumor surgery videos has not been done before. The method for estimating the unknown magnification factor of the operating microscope achieves accuracy within 0.02 of the theoretical value on a CAD phantom and within 0.06 on 4 clinical videos of the entire brain tumor surgery. When compared to a laser range scanner, the proposed method for reconstructing 3D surfaces intraoperatively achieves root mean square

  6. Optical measurement of the dynamic strain field of a fan blade using a 3D scanning vibrometer

    NASA Astrophysics Data System (ADS)

    Vuye, C.; Vanlanduit, S.; Presezniak, F.; Steenackers, G.; Guillaume, P.

    2011-07-01

    Understanding the origin of the stress and strain distribution is crucial to increase the durability of components under dynamic loading. Numerical simulations based on finite element (FE) models help with this understanding but must be validated by real measured data. Updating the FE model using the measured data is often the next step in the design process. In this paper the recently developed 3D-scanning laser doppler vibrometer (3D-SLDV) is used to measure the 3D-displacement of a fan blade, which is then used to calculate the dynamic strain distributions. The measurement principle and experimental setup are discussed thoroughly. The experimental results are validated by using a FE model on the one hand and strain gage measurements on the other. It is shown that this technique is capable of measuring normal strain far below 1 microstrain. This technique has the potential to fill in the gap of accurately measuring small (full-field) normal and shear strains at both low and high frequencies, where other optical techniques (and strain gages) would certainly fail.

  7. Fully 3D Multiple Beam Dynamics Processes Simulation for the Fermilab Tevatron

    SciTech Connect

    Stern, E.; Amundson, J.; Spentzouris, P; Valishev, A.; /Fermilab

    2010-06-01

    The Fermilab Tevatron has been, until 2010, the premier high-energy physics collider in the world. The data collected over the last decade by high-energy physics experiments running at the Tevatron have been analyzed to make important measurements in fundamental areas such as B meson masses and flavor oscillation, searches for the Higgs boson, and supersymmetry. Collecting these data at the limits of detectability has required the Tevatron to operate reliably at high beam intensities to maximize the number of collisions to analyze. This impressive achievement has been assisted by the use of HPC resources and software provided through the SciDAC program. This paper describes the enhancements to the BeamBeam3d code to realistically simulate the Tevatron, the validation of these simulations, and the improvement in equipment reliability and personal safety achieved with the aid of simulations.

  8. 3D Hall MHD Reconnection Dynamics in a Strongly Sheared System

    NASA Astrophysics Data System (ADS)

    Huba, J. D.; Rudakov, L. I.

    2002-12-01

    A 3D Hall MHD simulation code (VooDoo) has recently been developed at the Naval Research Laboratory. Recent results have demonstrated that magnetic shock-like structures [Rudakov and Huba, 2002] and a `reconnection wave' [Huba and Rudakov, 2002] can propagate in three dimensional, reversed field plasma layers. In this talk we present preliminary results of a fully 3D magnetic reconnection process in a reversed field plasma that includes a strong guide field, i.e., no magnetic nulls. The initial configuration of the plasma system is as follows. The ambient, reversed magnetic field is in the x-direction with Bx = B0 tanh(y/Ly) where Ly is the scale length of the current sheet. The ambient guide field is in the z-direction with Bz = B0. Perturbation fields δ Bx and δ By are introduced to initiate the reconnection process. This initial configuration is similar to that used in the 2D GEM reconnection study. However, the perturbation fields are localized in the z-direction. We find that the magnetic topology of the system is reconfigured via a process akin to `magnetic flipping' described by Priest and Forbes (1992). A high-density, magnetic flux-rope forms in the center of the plasma sheet. Magnetic flipping occurs between the center of the flux-tube and the boundaries in the x-direction. Associated with this magnetic flipping geometry, the reconnected magnetic field component By reverses sign 3 times in the x-direction, in contrast to only once in the no-guide field case. As in previous Hall MHD reconnection simulation studies, the system evolves asymmetrically along the current. Huba, J.D. and L.I. Rudakov, to be published in Phys. Plasmas, 2002. Priest, E.R. and T.G. Forbes, J. Geophys. Res. 97, 1521, 1992. Rudakov, L.I. and J.D. Huba, Phys. Rev. Lett. 89, 095002, 2002. Research supported by NASA and ONR.

  9. Tidal dynamics of the Terminos Lagoon, Mexico: observations and 3D numerical modelling

    NASA Astrophysics Data System (ADS)

    Contreras Ruiz Esparza, Adolfo; Douillet, Pascal; Zavala-Hidalgo, Jorge

    2014-09-01

    The tidal circulation patterns in the Terminos Lagoon were studied based on the analysis of 1 year of measurements and numerical simulations using a baroclinic 3D hydrodynamic model, the MARS3D. A gauging network was installed consisting of six self-recording pressure-temperature sensors, a tide gauge station and two current profilers, with pressure and temperature sensors moored in the main lagoon inlets. Model simulations were validated against current and sea level observations and were used to analyse the circulation patterns caused by the tidal forcing. The numerical model was forced with eight harmonic components, four diurnal ( K 1, O 1, P 1, Q 1) and four semi-diurnal ( M 2, S 2, N 2, K 2), extracted from the TPX0.7 database. The tidal patterns in the study area vary from mixed, mainly diurnal in the two main inlets of the lagoon, to diurnal in its interior. The tidal residual circulation inside the lagoon is dominated by a cyclonic gyre. The results indicate a net flux from the southwest Ciudad del Carmen inlet (CdC) towards the northeast Puerto Real inlet (PtR) along the southern side of the lagoon and the opposite in the northern side. The results indicate two areas of strong currents in the vicinity of the inlets and weak currents inside the lagoon. The area of strong currents in the vicinity of the CdC inlet is larger than that observed in the PtR inlet. Nevertheless, the current analysis indicates that the highest current speeds, which can reach a magnitude of 1.9 m s-1, occurred in PtR. A further analysis of the tide distortion in the inlets revealed that both passages are ebb dominated.

  10. Integrating Dynamic Data and Sensors with Semantic 3D City Models in the Context of Smart Cities

    NASA Astrophysics Data System (ADS)

    Chaturvedi, K.; Kolbe, T. H.

    2016-10-01

    Smart cities provide effective integration of human, physical and digital systems operating in the built environment. The advancements in city and landscape models, sensor web technologies, and simulation methods play a significant role in city analyses and improving quality of life of citizens and governance of cities. Semantic 3D city models can provide substantial benefits and can become a central information backbone for smart city infrastructures. However, current generation semantic 3D city models are static in nature and do not support dynamic properties and sensor observations. In this paper, we propose a new concept called Dynamizer allowing to represent highly dynamic data and providing a method for injecting dynamic variations of city object properties into the static representation. The approach also provides direct capability to model complex patterns based on statistics and general rules and also, real-time sensor observations. The concept is implemented as an Application Domain Extension for the CityGML standard. However, it could also be applied to other GML-based application schemas including the European INSPIRE data themes and national standards for topography and cadasters like the British Ordnance Survey Mastermap or the German cadaster standard ALKIS.

  11. Dynamical system of scalar field from 2-dimension to 3-D and its cosmological implications

    NASA Astrophysics Data System (ADS)

    Fang, Wei; Tu, Hong; Huang, Jiasheng; Shu, Chenggang

    2016-09-01

    We give the three-dimensional dynamical autonomous systems for most of the popular scalar field dark energy models including (phantom) quintessence, (phantom) tachyon, K-essence, and general non-canonical scalar field models, change the dynamical variables from variables (x, y, λ ) to observable related variables (w_{φ }, Ω _{φ }, λ ), and show the intimate relationships between those scalar fields that the three-dimensional system of K-essence can reduce to (phantom) tachyon, general non-canonical scalar field can reduce to (phantom) quintessence and K-essence can also reduce to (phantom) quintessence for some special cases. For the applications of the three-dimensional dynamical systems, we investigate several special cases and give the exactly dynamical solutions in detail. In the end of this paper, we argue that it is more convenient and also has more physical meaning to express the differential equations of dynamical systems in (w_{φ }, Ω _{φ }, λ ) instead of variables (x, y, λ ) and to investigate the dynamical system in three dimensions instead of two dimensions. We also raise a question about the possibility of the chaotic behavior in the spatially flat single scalar field FRW cosmological models in the presence of ordinary matter.

  12. Local and cluster critical dynamics of the 3d random-site Ising model

    NASA Astrophysics Data System (ADS)

    Ivaneyko, D.; Ilnytskyi, J.; Berche, B.; Holovatch, Yu.

    2006-10-01

    We present the results of Monte Carlo simulations for the critical dynamics of the three-dimensional site-diluted quenched Ising model. Three different dynamics are considered, these correspond to the local update Metropolis scheme as well as to the Swendsen-Wang and Wolff cluster algorithms. The lattice sizes of L=10-96 are analysed by a finite-size-scaling technique. The site dilution concentration p=0.85 was chosen to minimize the correction-to-scaling effects. We calculate numerical values of the dynamical critical exponents for the integrated and exponential autocorrelation times for energy and magnetization. As expected, cluster algorithms are characterized by lower values of dynamical critical exponent than the local one: also in the case of dilution critical slowing down is more pronounced for the Metropolis algorithm. However, the striking feature of our estimates is that they suggest that dilution leads to decrease of the dynamical critical exponent for the cluster algorithms. This phenomenon is quite opposite to the local dynamics, where dilution enhances critical slowing down.

  13. Dynamic 3-D chemical agent cloud mapping using a sensor constellation deployed on mobile platforms

    NASA Astrophysics Data System (ADS)

    Cosofret, Bogdan R.; Konno, Daisei; Rossi, David; Marinelli, William J.; Seem, Pete

    2014-05-01

    The need for standoff detection technology to provide early Chem-Bio (CB) threat warning is well documented. Much of the information obtained by a single passive sensor is limited to bearing and angular extent of the threat cloud. In order to obtain absolute geo-location, range to threat, 3-D extent and detailed composition of the chemical threat, fusion of information from multiple passive sensors is needed. A capability that provides on-the-move chemical cloud characterization is key to the development of real-time Battlespace Awareness. We have developed, implemented and tested algorithms and hardware to perform the fusion of information obtained from two mobile LWIR passive hyperspectral sensors. The implementation of the capability is driven by current Nuclear, Biological and Chemical Reconnaissance Vehicle operational tactics and represents a mission focused alternative of the already demonstrated 5-sensor static Range Test Validation System (RTVS).1 The new capability consists of hardware for sensor pointing and attitude information which is made available for streaming and aggregation as part of the data fusion process for threat characterization. Cloud information is generated using 2-sensor data ingested into a suite of triangulation and tomographic reconstruction algorithms. The approaches are amenable to using a limited number of viewing projections and unfavorable sensor geometries resulting from mobile operation. In this paper we describe the system architecture and present an analysis of results obtained during the initial testing of the system at Dugway Proving Ground during BioWeek 2013.

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

    PubMed

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

    2015-11-16

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

  15. The 1999 Izmit, Turkey, earthquake: A 3D dynamic stress transfer model of intraearthquake triggering

    USGS Publications Warehouse

    Harris, R.A.; Dolan, J.F.; Hartleb, R.; Day, S.M.

    2002-01-01

    Before the August 1999 Izmit (Kocaeli), Turkey, earthquake, theoretical studies of earthquake ruptures and geological observations had provided estimates of how far an earthquake might jump to get to a neighboring fault. Both numerical simulations and geological observations suggested that 5 km might be the upper limit if there were no transfer faults. The Izmit earthquake appears to have followed these expectations. It did not jump across any step-over wider than 5 km and was instead stopped by a narrower step-over at its eastern end and possibly by a stress shadow caused by a historic large earthquake at its western end. Our 3D spontaneous rupture simulations of the 1999 Izmit earthquake provide two new insights: (1) the west- to east-striking fault segments of this part of the North Anatolian fault are oriented so as to be low-stress faults and (2) the easternmost segment involved in the August 1999 rupture may be dipping. An interesting feature of the Izmit earthquake is that a 5-km-long gap in surface rupture and an adjacent 25° restraining bend in the fault zone did not stop the earthquake. The latter observation is a warning that significant fault bends in strike-slip faults may not arrest future earthquakes.

  16. A Novel Flow-Perfusion Bioreactor Supports 3D Dynamic Cell Culture

    PubMed Central

    Sailon, Alexander M.; Allori, Alexander C.; Davidson, Edward H.; Reformat, Derek D.; Allen, Robert J.; Warren, Stephen M.

    2009-01-01

    Background. Bone engineering requires thicker three-dimensional constructs than the maximum thickness supported by standard cell-culture techniques (2 mm). A flow-perfusion bioreactor was developed to provide chemotransportation to thick (6 mm) scaffolds. Methods. Polyurethane scaffolds, seeded with murine preosteoblasts, were loaded into a novel bioreactor. Control scaffolds remained in static culture. Samples were harvested at days 2, 4, 6, and 8 and analyzed for cellular distribution, viability, metabolic activity, and density at the periphery and core. Results. By day 8, static scaffolds had a periphery cell density of 67% ± 5.0%, while in the core it was 0.3% ± 0.3%. Flow-perfused scaffolds demonstrated peripheral cell density of 94% ± 8.3% and core density of 76% ± 3.1% at day 8. Conclusions. Flow perfusion provides chemotransportation to thick scaffolds. This system may permit high throughput study of 3D tissues in vitro and enable prefabrication of biological constructs large enough to solve clinical problems. PMID:20037739

  17. Intersegmental dynamics of 3D upper arm and forearm longitudinal axis rotations during baseball pitching.

    PubMed

    Naito, Kozo; Takagi, Hiroyasu; Yamada, Norimasa; Hashimoto, Shinichi; Maruyama, Takeo

    2014-12-01

    The shoulder internal rotation (IR) and forearm pronation (PR) are important elements for baseball pitching, however, how rapid rotations of IR and PR are produced by muscular torques and inter-segmental forces is not clear. The aim of this study is to clarify how IR and PR angular velocities are maximized, depending on muscular torque and interactive torque effects, and gain a detailed knowledge about inter-segmental interaction within a multi-joint linked chain. The throwing movements of eight collegiate baseball pitchers were recorded by a motion capture system, and induced-acceleration analysis was used to assess the respective contributions of the muscular (MUS) and interactive torques associated with gyroscopic moment (GYR), and Coriolis (COR) and centrifugal forces (CEN) to maximum angular velocities of IR (MIRV) and PR (MPRV). The results showed that the contribution of MUS account for 98.0% of MIRV, while that contribution to MPRV was indicated as negative (-48.1%). It was shown that MPRV depends primarily on the interactive torques associated with GYR and CEN, but the effects of GYR, COR and CEN on MIRV are negligible. In conclusion, rapid PR motion during pitching is created by passive-effect, and is likely a natural movement which arises from 3D throwing movement. Applying the current analysis to IR and PR motions is helpful in providing the implications for improving performance and considering conditioning methods for pitchers.

  18. Dynamic 3-D vortex structure of the laminar separation bubble on SD7003 airfoil

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Hain, Rainer; Kähler, Christian J.

    2008-11-01

    Recent increasing interest in laminar separation bubble (LSB) is aroused by the development of the micro air vehicles (MAVs), which normally cruise in the Reynolds number range of 50,000-200,000. This paper studies the LSB over the SD 7003 airfoil at the angle of attack α=4^o and at Re=60,000 using the time-resolved PIV technique. A Nd:Yag laser operated at 1000 Hz and a high speed CMOS camera was synchronized to capture the particle images with the full resolution of 1504 x 1128 pixels at 1000 fps. Measurements were carried out from two orthogonal views: in the stream-wise wall-normal plane and the quasi-surface-parallel plane. 3-D disturbance was observed to start even prior to the point of transition. Vortex shedding in transition near the reattachment region of the LSB was clearly identified in the span-wise wall-normal plane, with the dominant K-H frequency of around 10.7 Hz. And subsequent vortex evolution in the reattached turbulent boundary layer was found to be characterized by paired positive and negative vorticity packets transported downstream.

  19. Dynamic diffraction-limited light-coupling of 3D-maneuvered wave-guided optical waveguides.

    PubMed

    Villangca, Mark; Bañas, Andrew; Palima, Darwin; Glückstad, Jesper

    2014-07-28

    We have previously proposed and demonstrated the targeted-light delivery capability of wave-guided optical waveguides (WOWs). As the WOWs are maneuvered in 3D space, it is important to maintain efficient light coupling through the waveguides within their operating volume. We propose the use of dynamic diffractive techniques to create diffraction-limited spots that will track and couple to the WOWs during operation. This is done by using a spatial light modulator to encode the necessary diffractive phase patterns to generate the multiple and dynamic coupling spots. The method is initially tested for a single WOW and we have experimentally demonstrated dynamic tracking and coupling for both lateral and axial displacements.

  20. 3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

    SciTech Connect

    Sofronov, I.D.; Voronin, B.L.; Butnev, O.I.

    1997-12-31

    The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle. The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.

  1. Dynamic tracking of a deformable tissue based on 3D-2D MR-US image registration

    NASA Astrophysics Data System (ADS)

    Marami, Bahram; Sirouspour, Shahin; Fenster, Aaron; Capson, David W.

    2014-03-01

    Real-time registration of pre-operative magnetic resonance (MR) or computed tomography (CT) images with intra-operative Ultrasound (US) images can be a valuable tool in image-guided therapies and interventions. This paper presents an automatic method for dynamically tracking the deformation of a soft tissue based on registering pre-operative three-dimensional (3D) MR images to intra-operative two-dimensional (2D) US images. The registration algorithm is based on concepts in state estimation where a dynamic finite element (FE)- based linear elastic deformation model correlates the imaging data in the spatial and temporal domains. A Kalman-like filtering process estimates the unknown deformation states of the soft tissue using the deformation model and a measure of error between the predicted and the observed intra-operative imaging data. The error is computed based on an intensity-based distance metric, namely, modality independent neighborhood descriptor (MIND), and no segmentation or feature extraction from images is required. The performance of the proposed method is evaluated by dynamically deforming 3D pre-operative MR images of a breast phantom tissue based on real-time 2D images obtained from an US probe. Experimental results on different registration scenarios showed that deformation tracking converges in a few iterations. The average target registration error on the plane of 2D US images for manually selected fiducial points was between 0.3 and 1.5 mm depending on the size of deformation.

  2. Dynamic Characteristics Analysis of a Small-Sized Linear Oscillatory Actuator Employing the 3-D Finite Element Method

    NASA Astrophysics Data System (ADS)

    Shoji, Noritaka; Hirata, Katsuhiro; Ueyama, Kenji; Hashimoto, Eiichiro; Takagi, Takahiro

    Recently, linear oscillatory actuators have been used in a wide range of applications because of their advantages, such as high efficiency, simple structure, and easy control. Small linear oscillatory actuators are expected to be used in haptic devices and the vibration system of mobile phones. In this paper, we propose a new structure of a small linear oscillatory actuator. The static and dynamic characteristics of the actuator are calculated by the 3-D finite element method. The effectiveness of this method is shown by the comparison of the calculated results with the experimental results.

  3. 3D Case Studies of Monitoring Dynamic Structural Tests using Long Exposure Imagery

    NASA Astrophysics Data System (ADS)

    McCarthy, D. M. J.; Chandler, J. H.; Palmeri, A.

    2014-06-01

    Structural health monitoring uses non-destructive testing programmes to detect long-term degradation phenomena in civil engineering structures. Structural testing may also be carried out to assess a structure's integrity following a potentially damaging event. Such investigations are increasingly carried out with vibration techniques, in which the structural response to artificial or natural excitations is recorded and analysed from a number of monitoring locations. Photogrammetry is of particular interest here since a very high number of monitoring locations can be measured using just a few images. To achieve the necessary imaging frequency to capture the vibration, it has been necessary to reduce the image resolution at the cost of spatial measurement accuracy. Even specialist sensors are limited by a compromise between sensor resolution and imaging frequency. To alleviate this compromise, a different approach has been developed and is described in this paper. Instead of using high-speed imaging to capture the instantaneous position at each epoch, long-exposure images are instead used, in which the localised image of the object becomes blurred. The approach has been extended to create 3D displacement vectors for each target point via multiple camera locations, which allows the simultaneous detection of transverse and torsional mode shapes. The proposed approach is frequency invariant allowing monitoring of higher modal frequencies irrespective of a sampling frequency. Since there is no requirement for imaging frequency, a higher image resolution is possible for the most accurate spatial measurement. The results of a small scale laboratory test using off-the-shelf consumer cameras are demonstrated. A larger experiment also demonstrates the scalability of the approach.

  4. Estimation of Pulmonary Motion in Healthy Subjects and Patients with Intrathoracic Tumors Using 3D-Dynamic MRI: Initial Results

    PubMed Central

    Schoebinger, Max; Herth, Felix; Tuengerthal, Siegfried; Meinzer, Heinz-Peter; Kauczor, Hans-Ulrich

    2009-01-01

    Objective To estimate a new technique for quantifying regional lung motion using 3D-MRI in healthy volunteers and to apply the technique in patients with intra- or extrapulmonary tumors. Materials and Methods Intraparenchymal lung motion during a whole breathing cycle was quantified in 30 healthy volunteers using 3D-dynamic MRI (FLASH [fast low angle shot] 3D, TRICKS [time-resolved interpolated contrast kinetics]). Qualitative and quantitative vector color maps and cumulative histograms were performed using an introduced semiautomatic algorithm. An analysis of lung motion was performed and correlated with an established 2D-MRI technique for verification. As a proof of concept, the technique was applied in five patients with non-small cell lung cancer (NSCLC) and 5 patients with malignant pleural mesothelioma (MPM). Results The correlation between intraparenchymal lung motion of the basal lung parts and the 2D-MRI technique was significant (r = 0.89, p < 0.05). Also, the vector color maps quantitatively illustrated regional lung motion in all healthy volunteers. No differences were observed between both hemithoraces, which was verified by cumulative histograms. The patients with NSCLC showed a local lack of lung motion in the area of the tumor. In the patients with MPM, there was global diminished motion of the tumor bearing hemithorax, which improved siginificantly after chemotherapy (CHT) (assessed by the 2D- and 3D-techniques) (p < 0.01). Using global spirometry, an improvement could also be shown (vital capacity 2.9 ± 0.5 versus 3.4 L ± 0.6, FEV1 0.9 ± 0.2 versus 1.4 ± 0.2 L) after CHT, but this improvement was not significant. Conclusion A 3D-dynamic MRI is able to quantify intraparenchymal lung motion. Local and global parenchymal pathologies can be precisely located and might be a new tool used to quantify even slight changes in lung motion (e.g. in therapy monitoring, follow-up studies or even benign lung diseases). PMID:19885311

  5. 3D-SSF: A bio-inspired approach for dynamic multi-subject clustering of white matter tracts.

    PubMed

    Chekir, A; Hassas, S; Descoteaux, M; Côté, M; Garyfallidis, E; Oulebsir-Boumghar, F

    2017-01-27

    There is growing interest in the study of white matter (WM) variation across subjects, and in particular the analysis of specific WM bundles, to better understand brain development and aging, as well as to improve early detection of some diseases. Several WM multi-subject clustering methods have been proposed to study WM bundles. These methods aim to overcome the complexity of the problem, which includes the huge size of the WM tractography datasets generated from multiple subjects, the existence of various streamlines with different positions, lengths and geometric forms, as well as the presence of outliers. However, the current methods are not sufficiently flexible to address all of these constraints. Here we introduce a novel dynamic multi-subject clustering framework based on a distributed multiagent implementation of the Multiple Species Flocking model, that we name 3D-Streamlines Stream Flocking (3D-SSF). Specifically, we consider streamlines from different subjects as data streams, and each streamline is assigned to a mobile agent. Agents work together following flocking rules in order to form a flock. Thanks to a similarity function, the agents that are associated with similar streamlines form a flock, whereas the agents that are associated with dissimilar streamlines are considered outliers. We use various experiments performed on noisy synthetic and real human brain data to validate 3D-SSF and demonstrate that it is more efficient and robust to outliers compared to other classical approaches. 3D-SSF is able to extract WM bundles at a population level, while considering WM variation across subjects and eliminating outlier streamlines.

  6. Constraining the Absolute Orientation of eta Carinae's Binary Orbit: A 3-D Dynamical Model for the Broad [Fe III] Emission

    NASA Technical Reports Server (NTRS)

    Madura, T. I.; Gull, T. R.; Owocki, S. P.; Groh, J. H.; Okazaki, A. T.; Russell, C. M. P.

    2011-01-01

    We present a three-dimensional (3-D) dynamical model for the broad [Fe III] emission observed in Eta Carinae using the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS). This model is based on full 3-D Smoothed Particle Hydrodynamics (SPH) simulations of Eta Car's binary colliding winds. Radiative transfer codes are used to generate synthetic spectro-images of [Fe III] emission line structures at various observed orbital phases and STIS slit position angles (PAs). Through a parameter study that varies the orbital inclination i, the PA(theta) that the orbital plane projection of the line-of-sight makes with the apastron side of the semi-major axis, and the PA on the sky of the orbital axis, we are able, for the first time, to tightly constrain the absolute 3-D orientation of the binary orbit. To simultaneously reproduce the blue-shifted emission arcs observed at orbital phase 0.976, STIS slit PA = +38deg, and the temporal variations in emission seen at negative slit PAs, the binary needs to have an i approx. = 130deg to 145deg, Theta approx. = -15deg to +30deg, and an orbital axis projected on the sky at a P A approx. = 302deg to 327deg east of north. This represents a system with an orbital axis that is closely aligned with the inferred polar axis of the Homunculus nebula, in 3-D. The companion star, Eta(sub B), thus orbits clockwise on the sky and is on the observer's side of the system at apastron. This orientation has important implications for theories for the formation of the Homunculus and helps lay the groundwork for orbital modeling to determine the stellar masses.

  7. 3D shoulder kinematics for static vs dynamic and passive vs active testing conditions.

    PubMed

    Robert-Lachaine, Xavier; Allard, Paul; Godbout, Véronique; Begon, Mickael

    2015-09-18

    Shoulder motion analysis provides clinicians with references of normal joint rotations. Shoulder joints orientations assessment is often based on series of static positions, while clinicians perform either passive or active tests and exercises mostly in dynamic. These conditions of motion could modify joint coordination and lead to discrepancies with the established references. Hence, the objective was to evaluate the influence of static vs dynamic and passive vs active testing conditions on shoulder joints orientations. Twenty asymptomatic subjects setup with 45 markers on the upper limb and trunk were tracked by an optoelectronic system. Static positions (30°, 60°, 90° and 120° of thoracohumeral elevation) and dynamic motion both in active condition and passively mobilised by an examiner were executed. Three-dimensional sternoclavicular, acromioclavicular, scapulothoracic and glenohumeral joint angles (12 in total) representing the distal segment orientation relative to the proximal segment orientation were estimated using a shoulder kinematical chain model. Separate four-way repeated measures ANOVA were applied on the 12 joint angles with factors of static vs dynamic, passive vs active, thoracohumeral elevation angle (30°, 60°, 90° and 120°) and plane of elevation (frontal and sagittal). Scapulothoracic lateral rotation progressed more during arm elevation in static than in dynamic gaining 4.2° more, and also in passive than in active by 6.6°. Glenohumeral elevation increased more during arm elevation in active than in passive by 4.4°. Shoulder joints orientations are affected by the testing conditions, which should be taken into consideration for data acquisition, inter-study comparison or clinical applications.

  8. A method of improving the dynamic response of 3D force/torque sensors

    NASA Astrophysics Data System (ADS)

    Osypiuk, Rafał; Piskorowski, Jacek; Kubus, Daniel

    2016-02-01

    In the paper attention is drawn to adverse dynamic properties of filters implemented in commercial measurement systems, force/torque sensors, which are increasingly used in industrial robotics. To remedy the problem, it has been proposed to employ a time-variant filter with appropriately modulated parameters, owing to which it is possible to suppress the amplitude of the transient response and, at the same time, to increase the pulsation of damped oscillations; this results in the improvement of dynamic properties in terms of reducing the duration of transients. This property plays a key role in force control and in the fundamental problem of the robot establishing contact with rigid environment. The parametric filters have been verified experimentally and compared with filters available for force/torque sensors manufactured by JR3. The obtained results clearly indicate the advantages of the proposed solution, which may be an interesting alternative to the classic methods of filtration.

  9. Vorticity Dynamics of Self-Propelled Swimming of 3D Bionic Fish

    NASA Astrophysics Data System (ADS)

    Xin, Z. Q.; Wu, C. J.

    2011-09-01

    Numerical simulations and control of tail-swaying swim of three-dimensional biomimetic fish in a viscous flow and the vorticity dynamics of fish swimming have been investigated in this paper, with a computational fluid dynamics package, which combines the adaptive multi-grid finite volume method and the methods of immersed boundary and volume of fluid, and the control strategy of fish motion. Using boundary vorticity-flux (BVF) theory, we have studied the mechanism of fish swimming and trace the physical root to the moving body surface. With the change of swimming speed, the effects of fish body and caudalfin on thrust, is analysed quantitatively. Finally the relationship between the forces exerted on fish body and vortex structures of fish swimming has been presented in this paper.

  10. Foot deformation during walking: differences between static and dynamic 3D foot morphology in developing feet.

    PubMed

    Barisch-Fritz, Bettina; Schmeltzpfenning, Timo; Plank, Clemens; Grau, Stefan

    2014-01-01

    The complex functions of feet require a specific composition, which is progressively achieved by developmental processes. This development should take place without being affected by footwear. The aim of this study is to evaluate differences between static and dynamic foot morphology in developing feet. Feet of 2554 participants (6-16 years) were recorded using a new scanner system (DynaScan4D). Each foot was recorded in static half and full weight-bearing and during walking. Several foot measures corresponding to those used in last construction were calculated. The differences were identified by one-way ANOVA and paired Student's t-test. Static and dynamic values of each foot measure must be considered to improve the fit of footwear. In particular, footwear must account for the increase of forefoot width and the decrease of midfoot girth. Furthermore, the toe box should have a more rounded shape. The findings are important for the construction of footwear for developing feet.

  11. Pre-impact fall detection system using dynamic threshold and 3D bounding box

    NASA Astrophysics Data System (ADS)

    Otanasap, Nuth; Boonbrahm, Poonpong

    2017-02-01

    Fall prevention and detection system have to subjugate many challenges in order to develop an efficient those system. Some of the difficult problems are obtrusion, occlusion and overlay in vision based system. Other associated issues are privacy, cost, noise, computation complexity and definition of threshold values. Estimating human motion using vision based usually involves with partial overlay, caused either by direction of view point between objects or body parts and camera, and these issues have to be taken into consideration. This paper proposes the use of dynamic threshold based and bounding box posture analysis method with multiple Kinect cameras setting for human posture analysis and fall detection. The proposed work only uses two Kinect cameras for acquiring distributed values and differentiating activities between normal and falls. If the peak value of head velocity is greater than the dynamic threshold value, bounding box posture analysis will be used to confirm fall occurrence. Furthermore, information captured by multiple Kinect placed in right angle will address the skeleton overlay problem due to single Kinect. This work contributes on the fusion of multiple Kinect based skeletons, based on dynamic threshold and bounding box posture analysis which is the only research work reported so far.

  12. Haptic perception of force magnitude and its relation to postural arm dynamics in 3D

    PubMed Central

    van Beek, Femke E.; Bergmann Tiest, Wouter M.; Mugge, Winfred; Kappers, Astrid M. L.

    2015-01-01

    In a previous study, we found the perception of force magnitude to be anisotropic in the horizontal plane. In the current study, we investigated this anisotropy in three dimensional space. In addition, we tested our previous hypothesis that the perceptual anisotropy was directly related to anisotropies in arm dynamics. In experiment 1, static force magnitude perception was studied using a free magnitude estimation paradigm. This experiment revealed a significant and consistent anisotropy in force magnitude perception, with forces exerted perpendicular to the line between hand and shoulder being perceived as 50% larger than forces exerted along this line. In experiment 2, postural arm dynamics were measured using stochastic position perturbations exerted by a haptic device and quantified through system identification. By fitting a mass-damper-spring model to the data, the stiffness, damping and inertia parameters could be characterized in all the directions in which perception was also measured. These results show that none of the arm dynamics parameters were oriented either exactly perpendicular or parallel to the perceptual anisotropy. This means that endpoint stiffness, damping or inertia alone cannot explain the consistent anisotropy in force magnitude perception. PMID:26643041

  13. Critical Dynamics of The Classical 3-D Heisenberg Antiferromagnet with Anisotropy

    NASA Astrophysics Data System (ADS)

    Bunker, Alex; Chen, Kun; Landau, D. P.

    1997-03-01

    Using large scale Monte Carlo and spin-dynamics techniques^1 we studied the dynamic behavior of the body-centered cubic classical Heisenberg antiferromagnet with single site anisotropy. In order to directly compare our results to experiment, we set the anisotropy to match that found^2 in FeF2 (strong anisotropy) and MnF2 (weak anisotropy). We determined the form of the dynamic structure factor, S(q,ω), at Tc and found agreement with experiment^3 and theory^4 which indicate a strong diffusive longitudinal component that is critical and a weak, non-critical propagative transverse component. Supported in part by the NSF ^**current address: Solid State Division, ORNL ^1 K. Chen, D. P. Landau, Phys. Rev. B \\underline49, 3266, (1994) ^2 J. Als-Nielsen in Phase Transitions and Critical Phenomena, \\underline5A, C. Domb, M. S. Green, (Academic Press, 1976) ^3 M. P. Schulhof et. al., Phys. Rev. B \\underline1, 2304, (1970) ^4 S. W. Lovesey, E. Balcar, J. Phys. Cond. Matt. \\underline7, 2147, (1995)

  14. Haptic perception of force magnitude and its relation to postural arm dynamics in 3D.

    PubMed

    van Beek, Femke E; Bergmann Tiest, Wouter M; Mugge, Winfred; Kappers, Astrid M L

    2015-12-08

    In a previous study, we found the perception of force magnitude to be anisotropic in the horizontal plane. In the current study, we investigated this anisotropy in three dimensional space. In addition, we tested our previous hypothesis that the perceptual anisotropy was directly related to anisotropies in arm dynamics. In experiment 1, static force magnitude perception was studied using a free magnitude estimation paradigm. This experiment revealed a significant and consistent anisotropy in force magnitude perception, with forces exerted perpendicular to the line between hand and shoulder being perceived as 50% larger than forces exerted along this line. In experiment 2, postural arm dynamics were measured using stochastic position perturbations exerted by a haptic device and quantified through system identification. By fitting a mass-damper-spring model to the data, the stiffness, damping and inertia parameters could be characterized in all the directions in which perception was also measured. These results show that none of the arm dynamics parameters were oriented either exactly perpendicular or parallel to the perceptual anisotropy. This means that endpoint stiffness, damping or inertia alone cannot explain the consistent anisotropy in force magnitude perception.

  15. 2D and 3D Non-planar Dynamic Rupture by a Finite Volume Method

    NASA Astrophysics Data System (ADS)

    Benjemaa, M.; Glinsky-Olivier, N.; Cruz-Atienza, V. M.; Virieux, J.; Piperno, S.; Lanteri, S.

    2006-12-01

    Understanding the physics of the rupture process requires very sophisticated and accurate tools in which both the geometry of the fault surface and realistic frictional behaviours could interact during rupture propagation. New formulations have been recently proposed for modelling the dynamic shear rupture of non-planar faults (Ando et al., 2004; Cruz-Atienza &Virieux, 2004; Huang &Costanzo, 2004) providing highly accurate field estimates nearby the crack edges at the expanse of a simple medium description or high computational cost. We propose a new method based on the finite volume formulation to model the dynamic rupture propagation of non-planar faults. After proper transformations of the velocity-stress elastodynamic system of partial differential equations following an explicit conservative law, we construct an unstructured time-domain numerical formulation of the crack problem. As a result, arbitrary non-planar faults can be explicitly represented without extra computational cost. The analysis of the total discrete energy through the fault surface leads us to the specification of dynamic rupture boundary conditions which insure the correct discrete energy time variation and, therefore, the system stability. These boundary conditions are set on stress fluxes and not on stress values, which makes the fracture to have no thickness. Different shapes of cracks are analysed. We present an example of a bidimensional non-planar spontaneous fault growth in heterogeneous media as well as preliminary results of a highly efficient extension to the three dimensional rupture model based on the standard MPI.

  16. Numerical Modeling of 3-D Dynamics of Ultrasound Contrast Agent Microbubbles Using the Boundary Integral Method

    NASA Astrophysics Data System (ADS)

    Calvisi, Michael; Manmi, Kawa; Wang, Qianxi

    2014-11-01

    Ultrasound contrast agents (UCAs) are microbubbles stabilized with a shell typically of lipid, polymer, or protein and are emerging as a unique tool for noninvasive therapies ranging from gene delivery to tumor ablation. The nonspherical dynamics of contrast agents are thought to play an important role in both diagnostic and therapeutic applications, for example, causing the emission of subharmonic frequency components and enhancing the uptake of therapeutic agents across cell membranes and tissue interfaces. A three-dimensional model for nonspherical contrast agent dynamics based on the boundary integral method is presented. The effects of the encapsulating shell are approximated by adapting Hoff's model for thin-shell, spherical contrast agents to the nonspherical case. A high-quality mesh of the bubble surface is maintained by implementing a hybrid approach of the Lagrangian method and elastic mesh technique. Numerical analyses for the dynamics of UCAs in an infinite liquid and near a rigid wall are performed in parameter regimes of clinical relevance. The results show that the presence of a coating significantly reduces the oscillation amplitude and period, increases the ultrasound pressure amplitude required to incite jetting, and reduces the jet width and velocity.

  17. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features

    PubMed Central

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T.

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer’s disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may

  18. Dynamical History Of The Local Group In ΛCDM slowromancapii@ - Including External Perturbers In 3D

    NASA Astrophysics Data System (ADS)

    Banik, Indranil; Zhao, Hongsheng

    2017-01-01

    We attempt to fit the observed radial velocities (RVs) of ˜ 30 Local Group (LG) galaxies using a 3D dynamical model of it and its immediate environment within the context of the standard cosmological paradigm, ΛCDM. This extends and confirms the basic results of our previous axisymmetric investigation of the LG (MNRAS, 459, 2237). We find that there remains a tendency for observed RVs to exceed those predicted by our best-fitting model. The typical mismatch is slightly higher than in our 2D model, with a root mean square value of ˜ 50 km/s. Our main finding is that including the 3D distribution of massive perturbing dark matter halos is unlikely to help greatly with the high velocity galaxy problem. Nonetheless, the 2D and 3D results differ in several other ways such as which galaxies' RVs are most problematic and the preferred values of parameters common to both models. The anomalously high RVs of several LG dwarfs may be better explained if the Milky Way (MW) and Andromeda (M31) were once moving much faster than in our models. This would allow LG dwarfs to gain very high RVs via gravitational slingshot encounters with a massive fast-moving galaxy. Such a scenario is possible in some modified gravity theories, especially those which require the MW and M31 to have previously undergone a close flyby. In a ΛCDM context, however, this scenario is not feasible as the resulting dynamical friction would cause a rapid merger.

  19. KMOS3D: Dynamical Constraints on the Mass Budget in Early Star-forming Disks

    NASA Astrophysics Data System (ADS)

    Wuyts, Stijn; Förster Schreiber, Natascha M.; Wisnioski, Emily; Genzel, Reinhard; Burkert, Andreas; Bandara, Kaushala; Beifiori, Alessandra; Belli, Sirio; Bender, Ralf; Brammer, Gabriel B.; Chan, Jeffrey; Davies, Ric; Fossati, Matteo; Galametz, Audrey; Kulkarni, Sandesh K.; Lang, Philipp; Lutz, Dieter; Mendel, J. Trevor; Momcheva, Ivelina G.; Naab, Thorsten; Nelson, Erica J.; Saglia, Roberto P.; Seitz, Stella; Tacconi, Linda J.; Tadaki, Ken-ichi; Übler, Hannah; van Dokkum, Pieter G.; Wilman, David J.; Wuyts, Eva

    2016-11-01

    We exploit deep integral-field spectroscopic observations with KMOS/Very Large Telescope of 240 star-forming disks at 0.6\\lt z\\lt 2.6 to dynamically constrain their mass budget. Our sample consists of massive (≳ {10}9.8 {M}⊙ ) galaxies with sizes {R}e≳ 2 {kpc}. By contrasting the observed velocity and dispersion profiles with dynamical models, we find that on average the stellar content contributes {32}-7+8 % of the total dynamical mass, with a significant spread among galaxies (68th percentile range {f}{star}˜ 18 % {--}62 % ). Including molecular gas as inferred from CO- and dust-based scaling relations, the estimated baryonic mass adds up to {56}-12+17 % of the total for the typical galaxy in our sample, reaching ˜ 90 % at z\\gt 2. We conclude that baryons make up most of the mass within the disk regions of high-redshift star-forming disk galaxies, with typical disks at z\\gt 2 being strongly baryon-dominated within R e . Substantial object-to-object variations in both stellar and baryonic mass fractions are observed among the galaxies in our sample, larger than what can be accounted for by the formal uncertainties in their respective measurements. In both cases, the mass fractions correlate most strongly with measures of surface density. High-{{{Σ }}}{star} galaxies feature stellar mass fractions closer to unity, and systems with high inferred gas or baryonic surface densities leave less room for additional mass components other than stars and molecular gas. Our findings can be interpreted as more extended disks probing further (and more compact disks probing less far) into the dark matter halos that host them. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programs 092.A-0091, 093.A-0079, 094.A-0217, 095.A-0047, and 096.A-0025.

  20. Measuring dynamic cell-material interactions and remodeling during 3D human mesenchymal stem cell migration in hydrogels.

    PubMed

    Schultz, Kelly M; Kyburz, Kyle A; Anseth, Kristi S

    2015-07-21

    Biomaterials that mimic aspects of the extracellular matrix by presenting a 3D microenvironment that cells can locally degrade and remodel are finding increased applications as wound-healing matrices, tissue engineering scaffolds, and even substrates for stem cell expansion. In vivo, cells do not simply reside in a static microenvironment, but instead, they dynamically reengineer their surroundings. For example, cells secrete proteases that degrade extracellular components, attach to the matrix through adhesive sites, and can exert traction forces on the local matrix, causing its spatial reorganization. Although biomaterials scaffolds provide initially well-defined microenvironments for 3D culture of cells, less is known about the changes that occur over time, especially local matrix remodeling that can play an integral role in directing cell behavior. Here, we use microrheology as a quantitative tool to characterize dynamic cellular remodeling of peptide-functionalized poly(ethylene glycol) (PEG) hydrogels that degrade in response to cell-secreted matrix metalloproteinases (MMPs). This technique allows measurement of spatial changes in material properties during migration of encapsulated cells and has a sensitivity that identifies regions where cells simply adhere to the matrix, as well as the extent of local cell remodeling of the material through MMP-mediated degradation. Collectively, these microrheological measurements provide insight into microscopic, cellular manipulation of the pericellular region that gives rise to macroscopic tracks created in scaffolds by migrating cells. This quantitative and predictable information should benefit the design of improved biomaterial scaffolds for medically relevant applications.

  1. PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: NUMERICAL STUDIES OF 3D NONLINEAR ELM DYNAMICS

    SciTech Connect

    SNYDER,P.B; WILSON,H.R; XU,X.Q

    2004-11-01

    Nonlinear simulations with the 3D electromagnetic two-fluid BOUT code are employed to study the dynamics of edge localized modes (ELMs) driven by intermediate wavelength peeling-ballooning modes. It is found that the early behavior of the modes is similar to expectations from linear, ideal peeling-ballooning mode theory, with the modes growing linearly at a fraction of the Alfven frequency. In the nonlinear phase, the modes grow explosively, forming a number of extended filaments which propagate rapidly from the outer closed flux region into the open flux region toward the outboard wall. Similarities to non-linear ballooning theory, as well as additional complexities are observed. Comparison to observations reveals a number of similarities. Implications of the simulations and proposals for the dynamics of the full ELM crash are discussed.

  2. The 3D dynamics of the Cosserat rod as applied to continuum robotics

    NASA Astrophysics Data System (ADS)

    Jones, Charles Rees

    2011-12-01

    In the effort to simulate the biologically inspired continuum robot's dynamic capabilities, researchers have been faced with the daunting task of simulating---in real-time---the complete three dimensional dynamics of the "beam-like" structure which includes the three "stiff" degrees-of-freedom transverse and dilational shear. Therefore, researchers have traditionally limited the difficulty of the problem with simplifying assumptions. This study, however, puts forward a solution which makes no simplifying assumptions and trades off only the real-time requirement of the desired solution. The solution is a Finite Difference Time Domain method employing an explicit single step method with cheap right hands sides. The cheap right hand sides are the result of a rather ingenious formulation of the classical beam called the Cosserat rod by, first, the Cosserat brothers and, later, Stuart S. Antman which results in five nonlinear but uncoupled equations that require only multiplication and addition. The method is therefore suitable for hardware implementation thus moving the real-time requirement from a software solution to a hardware solution.

  3. MERIDIONAL CIRCULATION DYNAMICS FROM 3D MAGNETOHYDRODYNAMIC GLOBAL SIMULATIONS OF SOLAR CONVECTION

    SciTech Connect

    Passos, Dário; Charbonneau, Paul; Miesch, Mark

    2015-02-10

    The form of solar meridional circulation is a very important ingredient for mean field flux transport dynamo models. However, a shroud of mystery still surrounds this large-scale flow, given that its measurement using current helioseismic techniques is challenging. In this work, we use results from three-dimensional global simulations of solar convection to infer the dynamical behavior of the established meridional circulation. We make a direct comparison between the meridional circulation that arises in these simulations and the latest observations. Based on our results, we argue that there should be an equatorward flow at the base of the convection zone at mid-latitudes, below the current maximum depth helioseismic measures can probe (0.75 R{sub ⊙}). We also provide physical arguments to justify this behavior. The simulations indicate that the meridional circulation undergoes substantial changes in morphology as the magnetic cycle unfolds. We close by discussing the importance of these dynamical changes for current methods of observation which involve long averaging periods of helioseismic data. Also noteworthy is the fact that these topological changes indicate a rich interaction between magnetic fields and plasma flows, which challenges the ubiquitous kinematic approach used in the vast majority of mean field dynamo simulations.

  4. Dwarf ellipticals in the eye of SAURON: dynamical & stellar population analysis in 3D

    NASA Astrophysics Data System (ADS)

    Ryś, Agnieszka; Falcón-Barroso, Jesús; van de Ven, Glenn; Koleva, Mina

    2015-02-01

    We present the dynamical and stellar population analysis of 12 dwarf elliptical galaxies (dEs) observed using the SAURON IFU (WHT, La Palma). We demonstrate that dEs have lower angular momenta than their presumed late-type progenitors and we show that dE circular velocity curves are steeper than the rotation curves of galaxies with equal and up to an order of magnitude higher luminosity. Transformation due to tidal harassment is able to explain all of the above, unless the dE progenitors were already compact and had lower angular momenta at higher redshifts. We then look at the star formation histories (SFHs) of our galaxies and find that for the majority of them star formation activity was either still strong at a few Gyr of age or they experienced a secondary burst of star formation roughly at that time. This latter possibility would be in agreement with the scenario where tidal harassment drives the remaining gas inwards and induces a secondary star formation episode. Finally, one of our galaxies appears to be composed exclusively of an old population (>~12 Gyr). Combining this with our earlier dynamical results, we conclude that it either was ram-pressure stripped early on in its evolution in a group environment and subsequently tidally heated (which lowered its angular momentum and increased compactness), or that it evolved in situ in the cluster's central parts, compact enough to avoid tidal disruption.

  5. On the Estimation Accuracy of the 3D Body Center of Mass Trajectory during Human Locomotion: Inverse vs. Forward Dynamics

    PubMed Central

    Pavei, Gaspare; Seminati, Elena; Cazzola, Dario; Minetti, Alberto E.

    2017-01-01

    The dynamics of body center of mass (BCoM) 3D trajectory during locomotion is crucial to the mechanical understanding of the different gaits. Forward Dynamics (FD) obtains BCoM motion from ground reaction forces while Inverse Dynamics (ID) estimates BCoM position and speed from motion capture of body segments. These two techniques are widely used by the literature on the estimation of BCoM. Despite the specific pros and cons of both methods, FD is less biased and considered as the golden standard, while ID estimates strongly depend on the segmental model adopted to schematically represent the moving body. In these experiments a single subject walked, ran, (uni- and bi-laterally) skipped, and race-walked at a wide range of speeds on a treadmill with force sensors underneath. In all conditions a simultaneous motion capture (8 cameras, 36 markers) took place. 3D BCoM trajectories computed according to five marker set models of ID have been compared to the one obtained by FD on the same (about 2,700) strides. Such a comparison aims to check the validity of the investigated models to capture the “true” dynamics of gaits in terms of distance between paths, mechanical external work and energy recovery. Results allow to conclude that: (1) among gaits, race walking is the most critical in being described by ID, (2) among the investigated segmental models, those capturing the motion of four limbs and trunk more closely reproduce the subtle temporal and spatial changes of BCoM trajectory within the strides of most gaits, (3) FD-ID discrepancy in external work is speed dependent within a gait in the most unsuccessful models, and (4) the internal work is not affected by the difference in BCoM estimates. PMID:28337148

  6. On the Estimation Accuracy of the 3D Body Center of Mass Trajectory during Human Locomotion: Inverse vs. Forward Dynamics.

    PubMed

    Pavei, Gaspare; Seminati, Elena; Cazzola, Dario; Minetti, Alberto E

    2017-01-01

    The dynamics of body center of mass (BCoM) 3D trajectory during locomotion is crucial to the mechanical understanding of the different gaits. Forward Dynamics (FD) obtains BCoM motion from ground reaction forces while Inverse Dynamics (ID) estimates BCoM position and speed from motion capture of body segments. These two techniques are widely used by the literature on the estimation of BCoM. Despite the specific pros and cons of both methods, FD is less biased and considered as the golden standard, while ID estimates strongly depend on the segmental model adopted to schematically represent the moving body. In these experiments a single subject walked, ran, (uni- and bi-laterally) skipped, and race-walked at a wide range of speeds on a treadmill with force sensors underneath. In all conditions a simultaneous motion capture (8 cameras, 36 markers) took place. 3D BCoM trajectories computed according to five marker set models of ID have been compared to the one obtained by FD on the same (about 2,700) strides. Such a comparison aims to check the validity of the investigated models to capture the "true" dynamics of gaits in terms of distance between paths, mechanical external work and energy recovery. Results allow to conclude that: (1) among gaits, race walking is the most critical in being described by ID, (2) among the investigated segmental models, those capturing the motion of four limbs and trunk more closely reproduce the subtle temporal and spatial changes of BCoM trajectory within the strides of most gaits, (3) FD-ID discrepancy in external work is speed dependent within a gait in the most unsuccessful models, and (4) the internal work is not affected by the difference in BCoM estimates.

  7. MORPHOLOGY AND DYNAMICS OF SOLAR PROMINENCES FROM 3D MHD SIMULATIONS

    SciTech Connect

    Terradas, J.; Soler, R.; Oliver, R.; Ballester, J. L.; Luna, M.

    2015-01-20

    In this paper we present a numerical study of the time evolution of solar prominences embedded in sheared magnetic arcades. The prominence is represented by a density enhancement in a background-stratified atmosphere and is connected to the photosphere through the magnetic field. By solving the ideal magnetohydrodynamic equations in three dimensions, we study the dynamics for a range of parameters representative of real prominences. Depending on the parameters considered, we find prominences that are suspended above the photosphere, i.e., detached prominences, but also configurations resembling curtain or hedgerow prominences whose material continuously connects to the photosphere. The plasma-β is an important parameter that determines the shape of the structure. In many cases magnetic Rayleigh-Taylor instabilities and oscillatory phenomena develop. Fingers and plumes are generated, affecting the whole prominence body and producing vertical structures in an essentially horizontal magnetic field. However, magnetic shear is able to reduce or even to suppress this instability.

  8. Depth-kymography: high-speed calibrated 3D imaging of human vocal fold vibration dynamics.

    PubMed

    George, Nibu A; de Mul, Frits F M; Qiu, Qingjun; Rakhorst, Gerhard; Schutte, Harm K

    2008-05-21

    We designed and developed a laser line-triangulation endoscope compatible with any standard high-speed camera for a complete three-dimensional profiling of human vocal fold vibration dynamics. With this novel device we are able to measure absolute values of vertical and horizontal vibration amplitudes, length and width of vocal folds as well as the opening and closing velocities from a single in vivo measurement. We have studied, for the first time, the generation and propagation of mucosal waves by locating the position of its maximum vertical position and the propagation velocity. Precise knowledge about the absolute dimensions of human vocal folds and their vibration parameters has significant importance in clinical diagnosis and treatment as well as in fundamental research in voice. The new device can be used to investigate different kinds of pathological conditions including periodic or aperiodic vibrations. Consequently, the new device has significant importance in investigating vocal fold paralysis and in phonosurgical applications.

  9. Dynamic mineral clouds on HD 189733b. I. 3D RHD with kinetic, non-equilibrium cloud formation

    NASA Astrophysics Data System (ADS)

    Lee, G.; Dobbs-Dixon, I.; Helling, Ch.; Bognar, K.; Woitke, P.

    2016-10-01

    Context. Observations of exoplanet atmospheres have revealed the presence of cloud particles in their atmospheres. 3D modelling of cloud formation in atmospheres of extrasolar planets coupled to the atmospheric dynamics has long been a challenge. Aims: We investigate the thermo-hydrodynamic properties of cloud formation processes in the atmospheres of hot Jupiter exoplanets. Methods: We simulate the dynamic atmosphere of HD 189733b with a 3D model that couples 3D radiative-hydrodynamics with a kinetic, microphysical mineral cloud formation module designed for RHD/GCM exoplanet atmosphere simulations. Our simulation includes the feedback effects of cloud advection and settling, gas phase element advection and depletion/replenishment and the radiative effects of cloud opacity. We model the cloud particles as a mix of mineral materials which change in size and composition as they travel through atmospheric thermo-chemical environments. All local cloud properties such as number density, grain size and material composition are time-dependently calculated. Gas phase element depletion as a result of cloud formation is included in the model. In situ effective medium theory and Mie theory is applied to calculate the wavelength dependent opacity of the cloud component. Results: We present a 3D cloud structure of a chemically complex, gaseous atmosphere of the hot Jupiter HD 189733b. Mean cloud particle sizes are typically sub-micron (0.01-0.5 μm) at pressures less than 1 bar with hotter equatorial regions containing the smallest grains. Denser cloud structures occur near terminator regions and deeper (~1 bar) atmospheric layers. Silicate materials such as MgSiO3[s] are found to be abundant at mid-high latitudes, while TiO2[s] and SiO2[s] dominate the equatorial regions. Elements involved in the cloud formation can be depleted by several orders of magnitude. Conclusions: The interplay between radiative-hydrodynamics and cloud kinetics leads to an inhomogeneous, wavelength

  10. Dynamic rupture modeling of the 2011 M9 Tohoku earthquake with an unstructured 3D spectral element method

    NASA Astrophysics Data System (ADS)

    Galvez, P.; Ampuero, J. P.; Dalguer, L. A.; Nissen-Meyer, T.

    2011-12-01

    On March 11th 2011, a Mw 9 earthquake stroke Japan causing 28000 victims and triggering a devastating tsunami that caused severe damage along the Japanese coast. The exceptional amount of data recorded by this earthquake, with thousands of sensors located all over Japan, provides a great opportunity for seismologist and engineers to investigate in detail the rupture process in order to better understand the physics of this type of earthquakes and their associated effects, like tsunamis. Here we investigate, by means of dynamic rupture simulations, a plausible mechanism to explain key observations about the rupture process of the 2011 M9 Tohoku earthquake, including the spatial complementarity between high and low frequency aspects of slip (e.g, Simons et al, Science 2011, Meng et al, GRL 2011). To model the dynamic rupture of this event, we use a realistic non-planar fault geometry of the megathrust interface, using the unstructured 3D spectral element open source code SPECFEM3D-SESAME, in which we recently implemented the dynamic fault boundary conditions. This implementation follows the principles introduced by Ampuero (2002) and Kaneko et al. (2008) and involves encapsulated modules plugged into the code. Our current implementation provides the possibility of modeling dynamic rupture for multiple, non-planar faults governed by slip-weakening friction. We successfully verified the code in several SCEC benchmarks, including a 3D problem with branched faults, as well as modeling the rupture of subduction megathrust with a splay fault, finding results comparable to published results. Our first set of simulations is aimed at testing if the diversity of rupture phenomena during the 2011 M9 Tohoku earthquake (see Ampuero et al in this session) can be overall reproduced by assuming the most basic friction law, linear slip-weakening friction, but prescribing a spatially heterogeneous distribution of the critical slip weakening distance Dc and initial fault stresses. Our

  11. Capturing the 3D Motion of an Infalling Galaxy via Fluid Dynamics

    NASA Astrophysics Data System (ADS)

    Su, Yuanyuan; Kraft, Ralph P.; Nulsen, Paul E. J.; Roediger, Elke; Forman, William R.; Churazov, Eugene; Randall, Scott W.; Jones, Christine; Machacek, Marie E.

    2017-01-01

    The Fornax Cluster is the nearest (≤slant 20 Mpc) galaxy cluster in the southern sky. NGC 1404 is a bright elliptical galaxy falling through the intracluster medium (ICM) of the Fornax Cluster. The sharp leading edge of NGC 1404 forms a classical “cold front” that separates 0.6 keV dense interstellar medium and 1.5 keV diffuse ICM. We measure the angular pressure variation along the cold front using a very deep (670 ks) Chandra X-ray observation. We are taking the classical approach—using stagnation pressure to determine a substructure’s speed—to the next level by not only deriving a general speed but also directionality, which yields the complete velocity field as well as the distance of the substructure directly from the pressure distribution. We find a hydrodynamic model consistent with the pressure jump along NGC 1404's atmosphere measured in multiple directions. The best-fit model gives an inclination of 33° and a Mach number of 1.3 for the infall of NGC 1404, in agreement with complementary measurements of the motion of NGC 1404. Our study demonstrates the successful treatment of a highly ionized ICM as ideal fluid flow, in support of the hypothesis that magnetic pressure is not dynamically important over most of the virial region of galaxy clusters.

  12. Separation efficiency of a hydrodynamic separator using a 3D computational fluid dynamics multiscale approach.

    PubMed

    Schmitt, Vivien; Dufresne, Matthieu; Vazquez, Jose; Fischer, Martin; Morin, Antoine

    2014-01-01

    The aim of this study is to investigate the use of computational fluid dynamics (CFD) to predict the solid separation efficiency of a hydrodynamic separator. The numerical difficulty concerns the discretization of the geometry to simulate both the global behavior and the local phenomena that occur near the screen. In this context, a CFD multiscale approach was used: a global model (at the scale of the device) is used to observe the hydrodynamic behavior within the device; a local model (portion of the screen) is used to determine the local phenomena that occur near the screen. The Eulerian-Lagrangian approach was used to model the particle trajectories in both models. The global model shows the influence of the particles' characteristics on the trapping efficiency. A high density favors the sedimentation. In contrast, particles with small densities (1,040 kg/m(3)) are steered by the hydrodynamic behavior and can potentially be trapped by the separator. The use of the local model allows us to observe the particle trajectories near the screen. A comparison between two types of screens (perforated plate vs expanded metal) highlights the turbulent effects created by the shape of the screen.

  13. 3D direct impacts of urban aerosols on dynamics during the CAPITOUL field experiment

    NASA Astrophysics Data System (ADS)

    Aouizerats, B.; Tulet, P.; Gomes, L.

    2012-12-01

    Evaluating the radiative impacts of aerosol particles is of great interest for understanding atmospheric physics and processes feedbacks. To respond to such objectives, the online fully coupled model Meso-NH is applied to a real case during a two-day Intensive Observation Period (IOP) of the CAPITOUL campaign. The aerosol optical properties are computed from the chemical composition and the size distribution of the particle population, and are compared to observations and analysed at local and regional scales. The differences between two simulations are then studied in order to isolate the direct radiative impacts of aerosols on dynamics. Results show that the aerosol particles generate a forcing on shortwave flux by a decrease of the amount reaching the surface up to 30 Wm-2. The resulting feedbacks lead to a cooling up to 0.6 K on the 2-meter temperature over the city of Toulouse and over the larger 125 km by 125 km area around Toulouse. This cooling is also modeled along the whole boundary layer, leading to a decrease of the boundary layer height up to -50 m during the afternoon and a decrease of the vertical velocities with an average of -3 %.

  14. Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution.

    PubMed

    Miyata, Tatsuhiko; Hirata, Fumio

    2008-04-30

    We have developed an algorithm for sampling the conformational space of large flexible molecules in solution, which combines the molecular dynamics (MD) method and the three-dimensional reference interaction site model (3D-RISM) theory. The solvent-induced force acting on solute atoms was evaluated as the gradient of the solvation free energy with respect to the solute-atom coordinates. To enhance the computation speed, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator Algorithm) to the combined MD/3D-RISM method. By virtue of the algorithm, one can choose a longer timestep for renewing the solvent-induced force compared with that of the conformational update. To illustrate the present MD/3D-RISM simulation, we applied the method to a model of acetylacetone in aqueous solution. The multiple timestep algorithm succeeded in enhancing the computation speed by 3.4 times for this model case. Acetylacetone possesses an intramolecular hydrogen-bonding capability between the hydroxyl group and the carbonyl oxygen atom, and the molecule is significantly stabilized due to this hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of the MD simulation in gas phase, while in the aqueous solutions the bond is disrupted in a significant number of conformations. This result qualitatively agrees with the behavior on a free energy barrier lying upon the process for rotating a torsional degree of freedom of the hydroxyl group, where it is significantly reduced in aqueous solution by a cancellation between the electrostatic interaction and the solvation free energy.

  15. 3D Dynamic Rupture Simulations Across Interacting Faults: the Mw7.0, 2010, Haiti Earthquake

    NASA Astrophysics Data System (ADS)

    Douilly, R.; Aochi, H.; Calais, E.; Freed, A. M.; Aagaard, B.

    2014-12-01

    The mechanisms controlling rupture propagation between fault segments during an earthquake are key to the hazard posed by fault systems. Rupture initiation on a fault segment sometimes transfers to a larger fault, resulting in a significant event (e.g.i, 2002 M7.9Denali and 2010 M7.1 Darfield earthquakes). In other cases rupture is constrained to the initial segment and does not transfer to nearby faults, resulting in events of moderate magnitude. This is the case of the 1989 M6.9 Loma Prieta and 2010 M7.0 Haiti earthquakes which initiated on reverse faults abutting against a major strike-slip plate boundary fault but did not propagate onto it. Here we investigatethe rupture dynamics of the Haiti earthquake, seeking to understand why rupture propagated across two segments of the Léogâne fault but did not propagate to the adjacenent Enriquillo Plantain Garden Fault, the major 200 km long plate boundary fault cutting through southern Haiti. We use a Finite Element Model to simulate the nucleation and propagation of rupture on the Léogâne fault, varying friction and background stress to determine the parameter set that best explains the observed earthquake sequence. The best-fit simulation is in remarkable agreement with several finite fault inversions and predicts ground displacement in very good agreement with geodetic and geological observations. The two slip patches inferred from finite-fault inversions are explained by the successive rupture of two fault segments oriented favorably with respect to the rupture propagation, while the geometry of the Enriquillo fault did not allow shear stress to reach failure. Although our simulation results replicate well the ground deformation consistent with the geodetic surface observation but convolving the ground motion with the soil amplification from the microzonation study will correctly account for the heterogeneity of the PGA throughout the rupture area.

  16. PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: TOROIDAL ROTATION AND 3D NONLINEAR DYNAMICS

    SciTech Connect

    SNYDER,P.B; WILSON,H.R; XU,X.Q; WEBSTER,A.J

    2004-06-01

    Understanding the physics of the H-Mode pedestal and edge localized modes (ELMs) is very important to next-step fusion devices for two primary reasons: (1) The pressure at the top of the edge barrier (''pedestal height'') strongly impacts global confinement and fusion performance, and (2) large ELMs lead to localized transient heat loads on material surfaces that may constrain component lifetimes. The development of the peeling-ballooning model has shed light on these issues by positing a mechanism for ELM onset and constraints on the pedestal height. The mechanism involves instability of ideal coupled ''peeling-ballooning'' modes driven by the sharp pressure gradient and consequent large bootstrap current in the H-mode edge. It was first investigated in the local, high-n limit [1], and later quantified for non-local, finite-n modes in general toroidal geometry [2,3]. Important aspects are that a range of wavelengths may potentially be unstable, with intermediate n's (n {approx} 3-30) generally limiting in high performance regimes, and that stability bounds are strongly sensitive to shape [Fig l(a)], and to collisionality (i.e. temperature and density) [4] through the bootstrap current. The development of efficient MHD stability codes such as ELITE [3,2] and MISHKA [5] has allowed detailed quantification of peeling-ballooning stability bounds (e.g. [6]) and extensive and largely successful comparisons with observation (e.g. [2,6-9]). These previous calculations are ideal, static, and linear. Here we extend this work to incorporate the impact of sheared toroidal rotation, and the non-ideal, nonlinear dynamics which must be studied to quantify ELM size and heat deposition on material surfaces.

  17. Parallel phase-shifting digital holography and its application to high-speed 3D imaging of dynamic object

    NASA Astrophysics Data System (ADS)

    Awatsuji, Yasuhiro; Xia, Peng; Wang, Yexin; Matoba, Osamu

    2016-03-01

    Digital holography is a technique of 3D measurement of object. The technique uses an image sensor to record the interference fringe image containing the complex amplitude of object, and numerically reconstructs the complex amplitude by computer. Parallel phase-shifting digital holography is capable of accurate 3D measurement of dynamic object. This is because this technique can reconstruct the complex amplitude of object, on which the undesired images are not superimposed, form a single hologram. The undesired images are the non-diffraction wave and the conjugate image which are associated with holography. In parallel phase-shifting digital holography, a hologram, whose phase of the reference wave is spatially and periodically shifted every other pixel, is recorded to obtain complex amplitude of object by single-shot exposure. The recorded hologram is decomposed into multiple holograms required for phase-shifting digital holography. The complex amplitude of the object is free from the undesired images is reconstructed from the multiple holograms. To validate parallel phase-shifting digital holography, a high-speed parallel phase-shifting digital holography system was constructed. The system consists of a Mach-Zehnder interferometer, a continuous-wave laser, and a high-speed polarization imaging camera. Phase motion picture of dynamic air flow sprayed from a nozzle was recorded at 180,000 frames per second (FPS) have been recorded by the system. Also phase motion picture of dynamic air induced by discharge between two electrodes has been recorded at 1,000,000 FPS, when high voltage was applied between the electrodes.

  18. Nonlinear dynamics of the 3D FMS and Alfven wave beams propagating in plasma of ionosphere and magnetosphere

    NASA Astrophysics Data System (ADS)

    Belashov, Vasily

    We study the formation, structure, stability and dynamics of the multidimensional soliton-like beam structures forming on the low-frequency branch of oscillation in the ionospheric and magnetospheric plasma for cases when beta=4pinT/B(2) <<1 and beta>1. In first case with the conditions omegadynamics under conditions {k_{x}}(2) >>{k_{yz}}(2,) v_{x}$<3D Belashov-Karpman (BK) equation [1] for magnetic field h=B_{wave}/B with due account of the high order dispersive correction defined by values of plasma parameters and the angle Theta=(B,k) [2]. In another case the dynamics of the finite-amplitude Alfvén waves propagating in the ionosphere and magnetosphere near-to-parallel to the field B is described by the 3D derivative nonlinear Schrödinger (3-DNLS) equation for the magnetic field of the wave h=(B_{y}+iB_{z})/2B/1-beta/ [3]. To study the stability of multidimensional solitons in both cases we use the method developed in [2] and investigated the Hamiltonian bounding with its deformation conserving momentum by solving the corresponding variation problem. To study evolution of solitons and their collision dynamics the proper equations were being integrated numerically using the codes specially developed and described in detail in [3]. As a result, we have obtained that in both cases for a single solitons on a level with wave spreading and collapse the formation of multidimensional solitons can be observed. These results may be interpreted in terms of self-focusing phenomenon for the FMS and Alfvén waves’ beam as stationary beam formation, scattering and self-focusing of wave beam. The soliton collisions on a level with known elastic interaction can lead to formation of complex structures including the multisoliton bound states. For all cases the problem of multidimensional soliton dynamics in the ionospheric and

  19. Characterization of 3D MEMS structural dynamics with a conformal multi-channel fiber optic heterodyne vibrometer

    NASA Astrophysics Data System (ADS)

    Kilpatrick, James; Apostol, Adela; Markov, Vladimir

    Insight into transient structural interactions, including coupled vibrations and modal non-degeneracy (mode splitting) is important to the development of current and next generation vibratory gyroscopes and MEMS resonators. Device optimization based on characterization of these effects is currently time consuming and limited by the requirement to perform spatially distributed measurements with existing single point sensors. In addition, the effects of interest and the diagnosis of their underlying causes and dependences are not readily revealed by traditional modal and finite element analyses. This paper, accordingly, discusses the design of a novel multi-channel fiber-optic heterodyne vibrometer which addresses this requirement directly. We describe a fiber-optic interferometer design which incorporates many standard fiber-optic telecommunications components, configured to support dynamic imaging of the real-time structural behavior of macro and micro vibratory resonators, including planar and 3D micro electromechanical systems (MEMS). The capabilities of the new sensor are illustrated by representative data obtained from a variety of 3D vibratory MEMS structures currently under development.

  20. Dynamically coupled 3D pollutant dispersion model for assessing produced water discharges in the Canadian offshore area.

    PubMed

    Zhao, Lin; Chen, Zhi; Lee, Kenneth

    2013-02-05

    Produced water is the contaminated water that is brought to the surface in the process of recovering oil and gas. On the basis of discharge volume, this type of contaminated water is the largest contributor to the offshore waste stream. Modeling studies of large amounts of wastewater discharge into offshore areas have helped in the understanding of pollutant dispersion behaviors in marine environments and in further evaluating the potential environmental effects resulting from produced water discharges. This study presents an integrated three-dimensional (3D) approach for the simulation of produced water discharges in offshore areas. Specifically, an explicit second-order finite difference method was used to model the far-field pollutant dispersion behavior, and this method was coupled with the jet-plume model JETLAG with an extension of the 3D cross-flow conditions to simulate the near-field mixing processes. A dynamic coupling technique with full consideration of the interaction between the discharged fluids and receiving waters was employed in the model. A case study was conducted on the Grand Banks of Newfoundland, Canada. The field validation of the modeling results was conducted for both the near-field and far-field dispersion processes, and the modeling results were in good agreement with the field observations. This study provides an integrated system tool for the simulation of complex transport processes in offshore areas, and the results from such modeling systems can be further used for the risk assessment analysis of the surface water environment.

  1. Static and dynamic fatigue behavior of topology designed and conventional 3D printed bioresorbable PCL cervical interbody fusion devices.

    PubMed

    Knutsen, Ashleen R; Borkowski, Sean L; Ebramzadeh, Edward; Flanagan, Colleen L; Hollister, Scott J; Sangiorgio, Sophia N

    2015-09-01

    Recently, as an alternative to metal spinal fusion cages, 3D printed bioresorbable materials have been explored; however, the static and fatigue properties of these novel cages are not well known. Unfortunately, current ASTM testing standards used to determine these properties were designed prior to the advent of bioresorbable materials for cages. Therefore, the applicability of these standards for bioresorbable materials is unknown. In this study, an image-based topology and a conventional 3D printed bioresorbable poly(ε)-caprolactone (PCL) cervical cage design were tested in compression, compression-shear, and torsion, to establish their static and fatigue properties. Difficulties were in fact identified in establishing failure criteria and in particular determining compressive failure load. Given these limitations, under static loads, both designs withstood loads of over 650 N in compression, 395 N in compression-shear, and 0.25 Nm in torsion, prior to yielding. Under dynamic testing, both designs withstood 5 million (5M) cycles of compression at 125% of their respective yield forces. Geometry significantly affected both the static and fatigue properties of the cages. The measured compressive yield loads fall within the reported physiological ranges; consequently, these PCL bioresorbable cages would likely require supplemental fixation. Most importantly, supplemental testing methods may be necessary beyond the current ASTM standards, to provide more accurate and reliable results, ultimately improving preclinical evaluation of these devices.

  2. Static and Dynamic Fatigue Behavior of Topology Designed and Conventional 3D Printed Bioresorbable PCL Cervical Interbody Fusion Devices

    PubMed Central

    Knutsen, Ashleen R.; Borkowski, Sean L.; Ebramzadeh, Edward; Flanagan, Colleen L.; Hollister, Scott J.; Sangiorgio, Sophia N.

    2015-01-01

    Recently, as an alternative to metal spinal fusion cages, 3D printed bioresorbable materials have been explored; however, the static and fatigue properties of these novel cages are not well known. Unfortunately, current ASTM testing standards used to determine these properties were designed prior to the advent of bioresorbable materials for cages. Therefore, the applicability of these standards for bioresorbable materials is unknown. In this study, an image-based topology and a conventional 3D printed bioresorbable poly(ε)-caprolactone (PCL) cervical cage design were tested in compression, compression-shear, and torsion, to establish their static and fatigue properties. Difficulties were in fact identified in establishing failure criteria and in particular determining compressive failure load. Given these limitations, under static loads, both designs withstood loads of over 650N in compression, 395N in compression-shear, and 0.25Nm in torsion, prior to yielding. Under dynamic testing, both designs withstood 5 million (5M) cycles of compression at 125% of their respective yield forces. Geometry significantly affected both the static and fatigue properties of the cages. The measured compressive yield loads fall within the reported physiological ranges; consequently, these PCL bioresorbable cages would likely require supplemental fixation. Most importantly, supplemental testing methods may be necessary beyond the current ASTM standards, to provide more accurate and reliable results, ultimately improving preclinical evaluation of these devices. PMID:26072198

  3. Guided wave-based J-integral estimation for dynamic stress intensity factors using 3D scanning laser Doppler vibrometry

    NASA Astrophysics Data System (ADS)

    Ayers, J.; Owens, C. T.; Liu, K. C.; Swenson, E.; Ghoshal, A.; Weiss, V.

    2013-01-01

    The application of guided waves to interrogate remote areas of structural components has been researched extensively in characterizing damage. However, there exists a sparsity of work in using piezoelectric transducer-generated guided waves as a method of assessing stress intensity factors (SIF). This quantitative information enables accurate estimation of the remaining life of metallic structures exhibiting cracks, such as military and commercial transport vehicles. The proposed full wavefield approach, based on 3D laser vibrometry and piezoelectric transducer-generated guided waves, provides a practical means for estimation of dynamic stress intensity factors (DSIF) through local strain energy mapping via the J-integral. Strain energies and traction vectors can be conveniently estimated from wavefield data recorded using 3D laser vibrometry, through interpolation and subsequent spatial differentiation of the response field. Upon estimation of the Jintegral, it is possible to obtain the corresponding DSIF terms. For this study, the experimental test matrix consists of aluminum plates with manufactured defects representing canonical elliptical crack geometries under uniaxial tension that are excited by surface mounted piezoelectric actuators. The defects' major to minor axes ratios vary from unity to approximately 133. Finite element simulations are compared to experimental results and the relative magnitudes of the J-integrals are examined.

  4. Vortex dynamics in the near-wake of tabs with various geometries using 2D and 3D PIV

    NASA Astrophysics Data System (ADS)

    Pagan-Vazquez, Axy; Khovalyg, Dolaana; Marsh, Charles; Hamed, Ali M.; Chamorro, Leonardo P.

    2016-11-01

    The vortex dynamics and turbulence statistics in the near-wake of rectangular, trapezoidal, triangular, and ellipsoidal tabs were studied in a refractive-index-matching channel at Re = 2000 and 13000, based on the tab height. The tabs share the same bulk dimensions including a 17 mm height, a 28 mm base width, and a 24.5o angle. 3D PIV was used to study the mean flow and dominant large-scale vortices, while high-spatial resolution planar PIV was used to quantify high-order statistics. The results show the coexistence of counter-rotating vortex pair (CVP) and hairpin structures. These vortices exhibit distinctive topology and strength across Re and tab geometry. The CVP is a steady structure that grows in strength over a significantly longer distance at the low Re due to the lower turbulence levels and the delayed shedding of the hairpin vortices. These features at the low Re are associated with the presence of K-H instability that develops over three tab heights. The interaction between the hairpins and CVP is measured in 3D for the first time and shows complex coexistence. Although the CVP suffers deformation and splitting at times, it maintains its presence and leads to significant spanwise and wall-normal flows.

  5. NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics simulations.

    PubMed Central

    Strahan, G D; Keniry, M A; Shafer, R H

    1998-01-01

    The solution structure and dynamical properties of the potassium-stabilized, hairpin dimer quadruplex formed by the oligonucleotide d(G3T4G3) have been elucidated by a combination of high-resolution NMR and molecular dynamics simulations. Refinement calculations were carried out both in vacuo, without internally coordinated K+ cations, and in explicit water, with internally coordinated K+ cations. In the latter case, the electrostatic interactions were calculated using the particle mesh Ewald (PME) method. The NMR restraints indicate that the K+ quadruplex has a folding arrangement similar to that formed by the same oligonucleotide in the presence of sodium, but with significant local differences. Unlike the Na+ quadruplex, the thymine loops found in K+ exhibit considerable flexibility, and appear to interconvert between two preferred conformations. Furthermore, the NMR evidence points toward K+-stabilized guanine quartets of slightly larger diameter relative to the Na+-stabilized structure. The characteristics of the quartet stem are greatly affected by the modeling technique employed: caged cations alter the size and symmetry of the quartets, and explicit water molecules form hydration spines within the grooves. These results provide insight into those factors that determine the overall stability of hairpin dimer quadruplexes and the effects of different cations in modulating the relative stability of the dimeric hairpin and linear, four-stranded, quadruplex forms. PMID:9675197

  6. Using Parameters of Dynamic Pulse Function for 3d Modeling in LOD3 Based on Random Textures

    NASA Astrophysics Data System (ADS)

    Alizadehashrafi, B.

    2015-12-01

    The pulse function (PF) is a technique based on procedural preprocessing system to generate a computerized virtual photo of the façade with in a fixed size square(Alizadehashrafi et al., 2009, Musliman et al., 2010). Dynamic Pulse Function (DPF) is an enhanced version of PF which can create the final photo, proportional to real geometry. This can avoid distortion while projecting the computerized photo on the generated 3D model(Alizadehashrafi and Rahman, 2013). The challenging issue that might be handled for having 3D model in LoD3 rather than LOD2, is the final aim that have been achieved in this paper. In the technique based DPF the geometries of the windows and doors are saved in an XML file schema which does not have any connections with the 3D model in LoD2 and CityGML format. In this research the parameters of Dynamic Pulse Functions are utilized via Ruby programming language in SketchUp Trimble to generate (exact position and deepness) the windows and doors automatically in LoD3 based on the same concept of DPF. The advantage of this technique is automatic generation of huge number of similar geometries e.g. windows by utilizing parameters of DPF along with defining entities and window layers. In case of converting the SKP file to CityGML via FME software or CityGML plugins the 3D model contains the semantic database about the entities and window layers which can connect the CityGML to MySQL(Alizadehashrafi and Baig, 2014). The concept behind DPF, is to use logical operations to project the texture on the background image which is dynamically proportional to real geometry. The process of projection is based on two vertical and horizontal dynamic pulses starting from upper-left corner of the background wall in down and right directions respectively based on image coordinate system. The logical one/zero on the intersections of two vertical and horizontal dynamic pulses projects/does not project the texture on the background image. It is possible to define

  7. Complexity dynamics and Hopf bifurcation analysis based on the first Lyapunov coefficient about 3D IS-LM macroeconomics system

    NASA Astrophysics Data System (ADS)

    Ma, Junhai; Ren, Wenbo; Zhan, Xueli

    2017-04-01

    Based on the study of scholars at home and abroad, this paper improves the three-dimensional IS-LM model in macroeconomics, analyzes the equilibrium point of the system and stability conditions, focuses on the parameters and complex dynamic characteristics when Hopf bifurcation occurs in the three-dimensional IS-LM macroeconomics system. In order to analyze the stability of limit cycles when Hopf bifurcation occurs, this paper further introduces the first Lyapunov coefficient to judge the limit cycles, i.e. from a practical view of the business cycle. Numerical simulation results show that within the range of most of the parameters, the limit cycle of 3D IS-LM macroeconomics is stable, that is, the business cycle is stable; with the increase of the parameters, limit cycles becomes unstable, and the value range of the parameters in this situation is small. The research results of this paper have good guide significance for the analysis of macroeconomics system.

  8. Non-linear dynamics of viscous bilayers subjected to an electric field: 3D phase field simulations

    NASA Astrophysics Data System (ADS)

    Dritselis, Christos; Karapetsas, George; Bontozoglou, Vasilis

    2014-11-01

    The scope of this work is to investigate the non-linear dynamics of the electro-hydrodynamic instability of a bilayer of immiscible liquids. We consider the case of two viscous films which is separated from the top electrode by air. We assume that the liquids are perfect dielectrics and consider the case of both flat and patterned electrodes. We develop a computational model using the diffuse interface method and carry out 3D numerical simulations fully accounting for the flow and electric field in all phases. We perform a parametric study and investigate the influence of the electric properties of fluids, applied voltage and various geometrical characteristics of the mask. The authors acknowledge the support by the General Secretariat of Research and Technology of Greece under the action ``Supporting Postdoctoral Researchers'' (Grant Number PE8/906), co-funded by the European Social Fund and National Resources.

  9. The effect of rheological approximations on the dynamics and topography in 3D subduction-collision models

    NASA Astrophysics Data System (ADS)

    Pusok, Adina E.; Kaus, Boris J. P.; Popov, Anton A.

    2016-04-01

    Most of the major mountain belts and orogenic plateaus are found within the overlying plate of active or fossil subduction and/or collision zones. Moreover, they evolve differently from one another as the result of specific combinations of surface and mantle processes. These differences arise for several reasons, such as different rheological properties, different amounts of regional isostatic compensation, and different mechanisms by which forces are applied to the convergent plates. Previous 3D geodynamic models of subduction/collision processes have used various rheological approximations, making numerical results difficult to compare, since there is no clear image on the extent of these approximations on the dynamics. Here, we employ the code LaMEM to perform high-resolution long-term 3D simulations of subduction/continental collision in an integrated lithospheric and upper-mantle scale model. We test the effect of rheological approximations on mantle and lithosphere dynamics in a geometrically simplified model setup that resembles a tectonic map of the India-Asia collision zone. We use the "sticky-air" approach to allow for the development of topography and the dynamics of subduction and collision is entirely driven by slab-pull (i.e. "free subduction"). The models exhibit a wide range of behaviours depending on the rheological law employed: from linear to temperature-dependent visco-elasto-plastic rheology that takes into account both diffusion and dislocation creep. For example, we find that slab dynamics varies drastically between end member models: in viscous approximations, slab detachment is slow following a viscous thinning, while for a non-linear visco-elasto-plastic rheology, slab detachment is relatively fast, inducing strong mantle flow in the slab window. We also examine the stress states in the subducting and overriding plates and topography evolution in the upper plate, and we discuss the implications on lithosphere dynamics at convergent margins

  10. 3D Dynamics of the Near-Surface Layer of the Ocean in the Presence of Freshwater Influx

    NASA Astrophysics Data System (ADS)

    Dean, C.; Soloviev, A.

    2015-12-01

    Freshwater inflow due to convective rains or river runoff produces lenses of freshened water in the near surface layer of the ocean. These lenses are localized in space and typically involve both salinity and temperature anomalies. Due to significant density anomalies, strong pressure gradients develop, which result in lateral spreading of freshwater lenses in a form resembling gravity currents. Gravity currents inherently involve three-dimensional dynamics. The gravity current head can include the Kelvin-Helmholtz billows with vertical density inversions. In this work, we have conducted a series of numerical experiments using computational fluid dynamics tools. These numerical simulations were designed to elucidate the relationship between vertical mixing and horizontal advection of salinity under various environmental conditions and potential impact on the pollution transport including oil spills. The near-surface data from the field experiments in the Gulf of Mexico during the SCOPE experiment were available for validation of numerical simulations. In particular, we observed a freshwater layer within a few-meter depth range and, in some cases, a density inversion at the edge of the freshwater lens, which is consistent with the results of numerical simulations. In conclusion, we discuss applicability of these results to the interpretation of Aquarius and SMOS sea surface salinity satellite measurements. The results of this study indicate that 3D dynamics of the near-surface layer of the ocean are essential in the presence of freshwater inflow.

  11. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    NASA Astrophysics Data System (ADS)

    Dick, Jonathan; Tetzlaff, Doerthe; Bradford, John; Soulsby, Chris

    2016-04-01

    Soil moisture is a fundamental component of the water cycle that influences many hydrological processes, such as flooding, solute transport, biogeochemical processes, and land-atmosphere interactions. The relationship between vegetation and soil moisture is complex and reciprocal. Soil moisture may affect vegetation distribution due to its function as the primary source of water, in turn the structure of vegetation canopies regulate water partitioning into interception, throughfall and steam flow. Such spatial differences in inputs, together with complex patterns of water uptake from distributed root networks can create marked heterogeneity in soil moisture dynamics at small scales. Traditional methods of monitoring soil moisture have revolved around limited point measurements, but improved geophysical techniques have facilitated a trend towards more spatially distributed measurements to help understand this heterogeneity. Here, we present a study using 3D ERT surveys in a 3.2km upland catchment in the Scottish Highlands where increasing afforestation (for climate change adaptation, biofuels and conservation) has the potential to increase interception losses and reduce soil moisture storage. The study combined 3D surveys, traditional point measurements and laboratory analysis of soil cores to assess the plot scale soil moisture dynamics in podzolic soils under forest stands of 15m high Scots pine (Pinus sylvestris) and adjacent non-forest plots dominated by heather (Calluna vulgaris) shrubs (<0.5m high). These dominant species are typical of forest and non-forest vegetation communities the Scottish Highlands. Results showed differences in the soil moisture dynamics under the different vegetation types, with heterogeneous patterns in the forested site mainly correlated with canopy cover and mirroring interception losses. Temporal variability in the forested site was greater, probably due to the interception, and increased evapotranspiration losses relative to the

  12. Exploration of Novel Inhibitors for Bruton’s Tyrosine Kinase by 3D QSAR Modeling and Molecular Dynamics Simulation

    PubMed Central

    Choi, Light; Woo Lee, Keun

    2016-01-01

    Bruton’s tyrosine kinase (BTK) is a cytoplasmic, non-receptor tyrosine kinase which is expressed in most of the hematopoietic cells and plays an important role in many cellular signaling pathways. B cell malignancies are dependent on BCR signaling, thus making BTK an efficient therapeutic target. Over the last few years, significant efforts have been made in order to develop BTK inhibitors to treat B-cell malignancies, and autoimmunity or allergy/hypersensitivity but limited success has been achieved. Here in this study, 3D QSAR pharmacophore models were generated for Btk based on known IC50 values and experimental energy scores with extensive validations. The five features pharmacophore model, Hypo1, includes one hydrogen bond acceptor lipid, one hydrogen bond donor, and three hydrophobic features, which has the highest correlation coefficient (0.98), cost difference (112.87), and low RMS (1.68). It was further validated by the Fisher’s randomization method and test set. The well validated Hypo1 was used as a 3D query to search novel Btk inhibitors with different chemical scaffold using high throughput virtual screening technique. The screened compounds were further sorted by applying ADMET properties, Lipinski’s rule of five and molecular docking studies to refine the retrieved hits. Furthermore, molecular dynamic simulation was employed to study the stability of docked conformation and to investigate the binding interactions in detail. Several important hydrogen bonds with Btk were revealed, which includes the gatekeeper residues Glu475 and Met 477 at the hinge region. Overall, this study suggests that the proposed hits may be more effective inhibitors for cancer and autoimmune therapy. PMID:26784025

  13. Vertical Scan (V-SCAN) for 3-D Grid Adaptive Mesh Refinement for an atmospheric Model Dynamical Core

    NASA Astrophysics Data System (ADS)

    Andronova, N. G.; Vandenberg, D.; Oehmke, R.; Stout, Q. F.; Penner, J. E.

    2009-12-01

    One of the major building blocks of a rigorous representation of cloud evolution in global atmospheric models is a parallel adaptive grid MPI-based communication library (an Adaptive Blocks for Locally Cartesian Topologies library -- ABLCarT), which manages the block-structured data layout, handles ghost cell updates among neighboring blocks and splits a block as refinements occur. The library has several modules that provide a layer of abstraction for adaptive refinement: blocks, which contain individual cells of user data; shells - the global geometry for the problem, including a sphere, reduced sphere, and now a 3D sphere; a load balancer for placement of blocks onto processors; and a communication support layer which encapsulates all data movement. A major performance concern with adaptive mesh refinement is how to represent calculations that have need to be sequenced in a particular order in a direction, such as calculating integrals along a specific path (e.g. atmospheric pressure or geopotential in the vertical dimension). This concern is compounded if the blocks have varying levels of refinement, or are scattered across different processors, as can be the case in parallel computing. In this paper we describe an implementation in ABLCarT of a vertical scan operation, which allows computing along vertical paths in the correct order across blocks transparent to their resolution and processor location. We test this functionality on a 2D and a 3D advection problem, which tests the performance of the model’s dynamics (transport) and physics (sources and sinks) for different model resolutions needed for inclusion of cloud formation.

  14. Large Scale 3-D Dislocation Dynamics and Atomistic Simulations of Flow and Strain-Hardening Behavior of Metallic Micropillars

    NASA Astrophysics Data System (ADS)

    Rao, Satish

    2015-03-01

    Experimental studies show strong strengthening effects for micrometer-scale FCC as well as two-phase superalloy crystals, even at high initial dislocation densities. This talk shows results from large-scale 3-D discrete dislocation simulations (DDS) used to explicitly model the deformation behavior of FCC Ni (flow stress and strain-hardening) as well as superalloy microcrystals for diameters ranging from 1 - 20 microns. The work shows that two size-sensitive athermal hardening processes, beyond forest and precipitation hardening, are sufficient to develop the dimensional scaling of the flow stress, stochastic stress variation, flow intermittency and, high initial strain-hardening rates, similar to experimental observations for various materials. In addition, 3D dislocation dynamics simulations are used to investigate strain-hardening characteristics and dislocation microstructure evolution with strain in large 20 micron size Ni microcrystals (bulk-like) under three different loading axes: 111, 001 and 110. Three different multi-slip loading axes, < 111 > , < 001 > and < 110 > , are explored for shear strains of ~0.03 and final dislocation densities of ~1013/m2. The orientation dependence of initial strain hardening rates and dislocation microstructure evolution with strain are discussed. The simulated strain hardening results are compared with experimental data under similar loading conditions from bulk single-crystal Ni. Finally, atomistic simulation results on the operation of single arm sources in Ni bipillars with a large angle grain boundary is discussed. The atomistic simulation results are compared with experimental mechanical behavior data on Cu bipillars with a similar large angle grain boundary. This work was supported by AFOSR (Dr. David Stargel), and by a grant of computer time from the DOD High Performance Computing Modernization Program, at the Aeronautical Systems Center/Major Shared Resource Center.

  15. Mobile Biplane X-Ray Imaging System for Measuring 3D Dynamic Joint Motion During Overground Gait.

    PubMed

    Guan, Shanyuanye; Gray, Hans A; Keynejad, Farzad; Pandy, Marcus G

    2016-01-01

    Most X-ray fluoroscopy systems are stationary and impose restrictions on the measurement of dynamic joint motion; for example, knee-joint kinematics during gait is usually measured with the subject ambulating on a treadmill. We developed a computer-controlled, mobile, biplane, X-ray fluoroscopy system to track human body movement for high-speed imaging of 3D joint motion during overground gait. A robotic gantry mechanism translates the two X-ray units alongside the subject, tracking and imaging the joint of interest as the subject moves. The main aim of the present study was to determine the accuracy with which the mobile imaging system measures 3D knee-joint kinematics during walking. In vitro experiments were performed to measure the relative positions of the tibia and femur in an intact human cadaver knee and of the tibial and femoral components of a total knee arthroplasty (TKA) implant during simulated overground gait. Accuracy was determined by calculating mean, standard deviation and root-mean-squared errors from differences between kinematic measurements obtained using volumetric models of the bones and TKA components and reference measurements obtained from metal beads embedded in the bones. Measurement accuracy was enhanced by the ability to track and image the joint concurrently. Maximum root-mean-squared errors were 0.33 mm and 0.65° for translations and rotations of the TKA knee and 0.78 mm and 0.77° for translations and rotations of the intact knee, which are comparable to results reported for treadmill walking using stationary biplane systems. System capability for in vivo joint motion measurement was also demonstrated for overground gait.

  16. Ice-sheet dynamics through the Quaternary on the mid-Norwegian continental margin inferred from 3D seismic data.

    PubMed

    Montelli, A; Dowdeswell, J A; Ottesen, D; Johansen, S E

    2017-02-01

    Reconstructing the evolution of ice sheets is critical to our understanding of the global environmental system, but most detailed palaeo-glaciological reconstructions have hitherto focused on the very recent history of ice sheets. Here, we present a three-dimensional (3D) reconstruction of the changing nature of ice-sheet derived sedimentary architecture through the Quaternary Ice Age of almost 3 Ma. An extensive geophysical record documents a marine-terminating, calving Fennoscandian Ice Sheet (FIS) margin present periodically on the mid-Norwegian shelf since the beginning of the Quaternary. Spatial and temporal variability of the FIS is illustrated by the gradual development of fast-flowing ice streams and associated intensification of focused glacial erosion and sedimentation since that time. Buried subglacial landforms reveal a complex and dynamic ice sheet, with converging palaeo-ice streams and several flow-switching events that may reflect major changes in topography and basal thermal regime. Lack of major subglacial meltwater channels suggests a largely distributed drainage system beneath the marine-terminating part of the FIS. This palaeo-environmental examination of the FIS provides a useful framework for ice-sheet modelling and shows that fragmentary preservation of buried surfaces and variability of ice-sheet dynamics should be taken into account when reconstructing glacial history from spatially limited datasets.

  17. Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs.

    PubMed

    Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba

    2014-01-01

    Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non

  18. Atmospheric transport of persistent organic pollutants - development of a 3-d dynamical transport model covering the northern hemisphere

    NASA Astrophysics Data System (ADS)

    Hansen, K. M.; Christensen, J. H.; Geels, C.; Frohn, L. M.; Brandt, J.

    2003-04-01

    The Danish Eulerian Hemispheric Model (DEHM) is a 3-D dynamical atmospheric transport model originally developed to describe the atmospheric transport of sulphur, lead, and mercury to the Arctic. The model has been validated carefully for these compounds. A new version of DEHM is currently being developed to describe the atmospheric transport of persistent organic pollutants (POPs) which are toxic, lipophilic and bio-accumulating compounds showing great persistence in the environment. The model has a horizontal resolution of 150 km x 150 km and 18 vertical layers, and it is driven by meteorological data from the numerical weather prediction model MM5V2. During environmental cycling POPs can be deposited and re-emitted several times before reaching a final destination. A description of the exchange processes between the land/ocean surfaces and the atmosphere is included in the model to account for this multi-hop transport. The present model version describes the atmospheric transport of the pesticide alpha-hexachlorocyclohexane (alpha-HCH). Other POPs may be included when proper data on emissions and physical-chemical parameters becomes available. The model-processes and the first model results are presented. The atmospheric transport of alpha-HCH for the 1990s is well described by the model.

  19. Rapid Reconstitution Packages (RRPs) implemented by integration of computational fluid dynamics (CFD) and 3D printed microfluidics.

    PubMed

    Chi, Albert; Curi, Sebastian; Clayton, Kevin; Luciano, David; Klauber, Kameron; Alexander-Katz, Alfredo; D'hers, Sebastian; Elman, Noel M

    2014-08-01

    Rapid Reconstitution Packages (RRPs) are portable platforms that integrate microfluidics for rapid reconstitution of lyophilized drugs. Rapid reconstitution of lyophilized drugs using standard vials and syringes is an error-prone process. RRPs were designed using computational fluid dynamics (CFD) techniques to optimize fluidic structures for rapid mixing and integrating physical properties of targeted drugs and diluents. Devices were manufactured using stereo lithography 3D printing for micrometer structural precision and rapid prototyping. Tissue plasminogen activator (tPA) was selected as the initial model drug to test the RRPs as it is unstable in solution. tPA is a thrombolytic drug, stored in lyophilized form, required in emergency settings for which rapid reconstitution is of critical importance. RRP performance and drug stability were evaluated by high-performance liquid chromatography (HPLC) to characterize release kinetics. In addition, enzyme-linked immunosorbent assays (ELISAs) were performed to test for drug activity after the RRPs were exposed to various controlled temperature conditions. Experimental results showed that RRPs provided effective reconstitution of tPA that strongly correlated with CFD results. Simulation and experimental results show that release kinetics can be adjusted by tuning the device structural dimensions and diluent drug physical parameters. The design of RRPs can be tailored for a number of applications by taking into account physical parameters of the active pharmaceutical ingredients (APIs), excipients, and diluents. RRPs are portable platforms that can be utilized for reconstitution of emergency drugs in time-critical therapies.

  20. Radionuclide transport and uptake in coastal aquatic ecosystems: a comparison of a 3D dynamic model and a compartment model.

    PubMed

    Erichsen, Anders Christian; Konovalenko, Lena; Møhlenberg, Flemming; Closter, Rikke Margrethe; Bradshaw, Clare; Aquilonius, Karin; Kautsky, Ulrik

    2013-05-01

    In safety assessments of underground radioactive waste repositories, understanding radionuclide fate in ecosystems is necessary to determine the impacts of potential releases. Here, the reliability of two mechanistic models (the compartmental K-model and the 3D dynamic D-model) in describing the fate of radionuclides released into a Baltic Sea bay is tested. Both are based on ecosystem models that simulate the cycling of organic matter (carbon). Radionuclide transfer is linked to adsorption and flows of carbon in food chains. Accumulation of Th-230, Cs-135, and Ni-59 in biological compartments was comparable between the models and site measurements despite differences in temporal resolution, biological state variables, and partition coefficients. Both models provided confidence limits for their modeled concentration ratios, an improvement over models that only estimate means. The D-model enables estimates at high spatio-temporal resolution. The K-model, being coarser but faster, allows estimates centuries ahead. Future developments could integrate the two models to take advantage of their respective strengths.

  1. The Combination of Speckle Correlation and Fringe Projection for the Measurement of Dynamic 3-D Deformations of Airbag Caps

    NASA Astrophysics Data System (ADS)

    Weber, Herbert; Lichtenberger, Ralf; Wolf, Thomas

    Highly dynamic 3-D deformations of airbag caps in the time interval from the ignition of the airbag to the fracture of the covers have been studied optically. The large out-of-plane displacement compared to the in-plane displacements afforded that the measurement problem was solved by combining white light speckle correlation with fringe projection. In order to record the speckle patterns and the fringe patterns simultaneously by two high speed CCD cameras they had to be separated spectrally. The in-plane displacements yield from the speckle patterns by pattern recognition methods. The out-of-plane displacements can be calculated from the contour of the caps. They yield from the phase maps which are calculated from the fringe patterns. For each time instant only one image is available so that phase shifting procedures to evaluate the fringe patterns could not be applied. In this paper we present a method which is based on the simulation of a phase locked loop (PLL). This results in continuous phase maps without phase unwrapping.

  2. Use of magnetic micro-cantilevers to study the dynamics of 3D engineered smooth muscle constructs

    NASA Astrophysics Data System (ADS)

    Liu, Alan; Zhao, Ruogang; Copeland, Craig; Chen, Christopher; Reich, Daniel

    2013-03-01

    The normal and pathological response of arterial tissue to mechanical stimulus sheds important light on such conditions as atherosclerosis and hypertension. While most previous methods of determining the biomechanical properties of arteries have relied on excised tissue, we have devised a system that enables the growth and in situ application of forces to arrays of stable suspended microtissues consisting of arterial smooth muscle cells (SMCs). Briefly, this magnetic microtissue tester system consists of arrays of pairs of elastomeric magnetically actuated micro-cantilevers between which SMC-infused 3D collagen gels self-assemble and remodel into aligned microtissue constructs. These devices allow us to simultaneously apply force and track stress-strain relationships of multiple microtissues per substrate. We have studied the dilatory capacity and subsequent response of the tissues and find that the resulting stress-strain curves show viscoelastic behavior as well as a linear dynamic recovery. These results provide a foundation for elucidating the mechanical behavior of this novel model system as well as further experiments that simulate pathological conditions. Supported in part by NIH grant HL090747.

  3. 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors.

    PubMed

    Wang, Fangfang; Yang, Wei; Shi, Yonghui; Le, Guowei

    2015-09-01

    The discovery of clinically relevant inhibitors of retinoic acid receptor-related orphan receptor-gamma-t (RORγt) for autoimmune diseases therapy has proven to be a challenging task. In the present work, to find out the structural features required for the inhibitory activity, we show for the first time a three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for a series of novel thiazole/thiophene ketone amides with inhibitory activity at the RORγt receptor. The optimum CoMFA and CoMSIA models, derived from ligand-based superimposition I, exhibit leave-one-out cross-validated correlation coefficient (R(2)cv) of .859 and .805, respectively. Furthermore, the external predictive abilities of the models were evaluated by a test set, producing the predicted correlation coefficient (R(2)pred) of .7317 and .7097, respectively. In addition, molecular docking analysis was applied to explore the binding modes between the inhibitors and the receptor. MD simulation and MM/PBSA method were also employed to study the stability and rationality of the derived conformations, and the binding free energies in detail. The QSAR models and the results of molecular docking, MD simulation, binding free energies corroborate well with each other and further provide insights regarding the development of novel RORγt inhibitors with better activity.

  4. 3D Structure Generation, Molecular Dynamics and Docking Studies of IRHOM2 Protein Involved in Cancer & Rheumatoid Arthritis.

    PubMed

    Raj, Utkarsh; Kumar, Himansu; Varadwaj, Pritish Kumar

    2015-01-01

    A short-lived membrane protein IRHOM2 pedals a cascade of events by regulating Epidermal Growth Factor Receptor (EGFR) signalling in parallel with metalloproteases which results their involvement in cancer as well as in rheumatoid arthritis. Therefore, IRHOM2 is a potential therapeutic drug target for these diseases, but its 3D-structure has not been reported yet. In this study, the three-dimensional structure of the IRHOM2 protein was generated using I-TASSER (Iterative Threading Assembly Refinement) server. The modeled structure of IRHOM2 receptor was validated using various Structural Analysis and Verification Server (SAVES) in which 99.7% of amino acid residues are present in the favoured regions of the Ramachandran Plot. Further, the refined modeled structure was subjected to molecular dynamics simulation & docking analysis. Virtual screening studies were carried out using Glide with various selective libraries containing 24552 compounds and the analysis indicated extensive hydrogen bonding network and hydrophobic interactions which play a significant role in its binding. Docking results were analyzed for high ranking compounds using a consensus based docking score to calculate the binding affinity as a measure of protein-ligand interactions. The top ranking molecule against IRHOM2 active site has a glide g-score of -12.565 kcal/mol and glide e-model score of -74.967 with 3 hydrogen bonds and 11 hydrophobic contacts. This compound may act as probable inhibitor against these chronic diseases but further in vitro studies are required.

  5. Modelling of river plume dynamics in Öre estuary (Baltic Sea) with Telemac-3D hydrodynamic model

    NASA Astrophysics Data System (ADS)

    Sokolov, Alexander

    2016-04-01

    The main property of river plumes is their buoyancy, fresh water discharged by rivers is less dense than the receiving, saline waters. To study the processes of plume formation in case of river discharge into a brackish estuary where salinity is low (3.5 - 5 psu) a three dimensional hydrodynamic model was applied to the Öre estuary in the Baltic Sea. This estuary is a small fjord-like bay in the north part of the Baltic Sea. Size of the bay is about 8 by 8 km with maximum depth of 35 metres. River Öre has a small average freshwater discharge of 35 m3/s. But in spring during snowmelt the discharge can be many times higher. For example, in April 2015 the discharge increased from 8 m3/s to 160 m3/s in 18 days. To study river plume dynamics a finite element based three dimensional baroclinic model TELEMAC - 3D is used. The TELEMAC modelling suite is developed by the National Laboratory of Hydraulics and Environment (LNHE) of Electricité de France (EDF). Modelling domain was approximated by an unstructured mesh with element size varies from 50 to 500 m. In vertical direction a sigma-coordinate with 20 layers was used. Open sea boundary conditions were obtained from the Baltic Sea model HIROMB-BOOS using COPERNICUS marine environment monitoring service. Comparison of modelling results with observations obtained by BONUS COCOA project's field campaign in Öre estuary in 2015 shows that the model plausible simulate river plume dynamics. Modelling of age of freshwater is also discussed. This work resulted from the BONUS COCOA project was supported by BONUS (Art 185), funded jointly by the EU and the Swedish Research Council Formas.

  6. Dynamic deformation measurements of a rotating disc by twin-pulsed 3D digital holography and interpolation of phase maps

    NASA Astrophysics Data System (ADS)

    Perez-Lopez, Carlos; Mendoza Santoyo, Fernando

    2004-06-01

    This paper describes the application of twin-pulsed 3D digital holography to the measurement of the dynamic deformation of a disc while it rotates. Object rotation produces interferometric fringes that are related to deformations for instance, stress due to the centrifugal forces, out-to plane vibrations, and the object angular displacement. Furthermore an unbalanced disc that rotates may present a characteristic vibration amplitude pattern at a specific frequency. An optical arrangement that illuminates, with a twin pulsed laser, from three different positions the object was used to recover the x, y and z displacement components in a rotating object. The technique is able to distinguish the disc rotation from the displacement along the x-y plane and the out-of-plane z displacement. Two laser pulses are fired in order to take two digital holgrams with a time separation of 20 μs. This is done for each of the three object illumination positions. Triads of twin-pulsed digital holograms taken at different times during object rotation are processed independently, and their optical phase maps retrieved by the conventional Fourier transform method together with the combination of data from the three illumination positions. The phase term related to the deformation is found experimentally where the intrinsic sensitivity vector is related to the rotation via the vector cross product, forming parallel fringes. To recover the rotation and deformation data the unwrapped phase maps were used as 'tilt' phase planes an all three sensitivity vectors in order to recover the in-plane, and out-to plane displacements. An interpolation algorithm was developed to correlate the time depending phase maps, leading to obtain object vibration frequency data. Experimental results are presented, showing in particular that the rotating object has an unbalancing due to the detected vibration frequency.

  7. A Diffusion-Based and Dynamic 3D-Printed Device That Enables Parallel in Vitro Pharmacokinetic Profiling of Molecules

    PubMed Central

    Lockwood, Sarah Y.; Meisel, Jayda E.; Monsma, Frederick J.; Spence, Dana M.

    2016-01-01

    The process of bringing a drug to market involves many steps, including the preclinical stage, where various properties of the drug candidate molecule are determined. These properties, which include drug absorption, distribution, metabolism, and excretion, are often displayed in a pharmacokinetic (PK) profile. While PK profiles are determined in animal models, in vitro systems that model in vivo processes are available, although each possesses shortcomings. Here, we present a 3D-printed, diffusion-based, and dynamic in vitro PK device. The device contains six flow channels, each with integrated porous membrane-based insert wells. The pores of these membranes enable drugs to freely diffuse back and forth between the flow channels and the inserts, thus enabling both loading and clearance portions of a standard PK curve to be generated. The device is designed to work with 96-well plate technology and consumes single-digit milliliter volumes to generate multiple PK profiles, simultaneously. Generation of PK profiles by use of the device was initially performed with fluorescein as a test molecule. Effects of such parameters as flow rate, loading time, volume in the insert well, and initial concentration of the test molecule were investigated. A prediction model was generated from this data, enabling the user to predict the concentration of the test molecule at any point along the PK profile within a coefficient of variation of ~5%. Depletion of the analyte from the well was characterized and was determined to follow first-order rate kinetics, indicated by statistically equivalent (p > 0.05) depletion half-lives that were independent of the starting concentration. A PK curve for an approved antibiotic, levofloxacin, was generated to show utility beyond the fluorescein test molecule. PMID:26727249

  8. Comparison of 2D and 3D modeled tumor motion estimation/prediction for dynamic tumor tracking during arc radiotherapy.

    PubMed

    Liu, Wu; Ma, Xiangyu; Yan, Huagang; Chen, Zhe; Nath, Ravinder; Li, Haiyun

    2017-03-06

    Many real-time imaging techniques have been developed to localize the target in 3D space or in 2D beam's eye view (BEV) plane for intrafraction motion tracking in radiation therapy. With tracking system latency, 3D-modeled method is expected to be more accurate even in terms of 2D BEV tracking error. No quantitative analysis, however, has been reported. In this study, we simulated co-planar arc deliveries using respiratory motion data acquired from 42 patients to quantitatively compare the accuracy between 2D BEV and 3D-modeled tracking in arc therapy and determine whether 3D information is needed for motion tracking. We used our previously developed low kV dose adaptive MV-kV imaging and motion compensation framework as a representative of 3D-modeled methods. It optimizes the balance between additional kV imaging dose and 3D tracking accuracy and solves the MLC blockage issue. With simulated Gaussian marker detection errors (zero mean and 0.39 mm standard deviation) and ~155/310/460 ms tracking system latencies, the mean percentage of time that the target moved >2 mm from the predicted 2D BEV position are 1.1%/4.0%/7.8% and 1.3%/5.8%/11.6% for 3D-modeled and 2D-only tracking, respectively. The corresponding average BEV RMS errors are 0.67/0.90/1.13 mm and 0.79/1.10/1.37 mm. Compared to the 2D method, the 3D method reduced the average RMS unresolved motion along the beam direction from ~3 mm to ~1 mm, resulting on average only <1% dosimetric advantage in the depth direction. Only for a small fraction of the patients, when tracking latency is long, the 3D-modeled method showed significant improvement of BEV tracking accuracy, indicating potential dosimetric advantage. However, if the tracking latency is short (~150 ms or less), those improvements are limited. Therefore, 2D BEV tracking has sufficient targeting accuracy for most clinical cases. The 3D technique is, however, still important in solving the MLC blockage problem during 2D BEV tracking.

  9. Dynamics of Actin Stress Fibers and Focal Adhesions during Slow Migration in Swiss 3T3 Fibroblasts: Intracellular Mechanism of Cell Turning

    PubMed Central

    Miyoshi, Hiromi; Miura, Takuya; Tanaka, Hiroto; Tsubota, Ken-ichi; Liu, Hao

    2016-01-01

    To understand the mechanism regulating the spontaneous change in polarity that leads to cell turning, we quantitatively analyzed the dynamics of focal adhesions (FAs) coupling with the self-assembling actin cytoskeletal structure in Swiss 3T3 fibroblasts. Fluorescent images were acquired from cells expressing GFP-actin and RFP-zyxin by laser confocal microscopy. On the basis of the maximum area, duration, and relocation distance of FAs extracted from the RFP-zyxin images, the cells could be divided into 3 regions: the front region, intermediate lateral region, and rear region. In the intermediate lateral region, FAs appeared close to the leading edge and were stabilized gradually as its area increased. Simultaneously, bundled actin stress fibers (SFs) were observed vertically from the positions of these FAs, and they connected to the other SFs parallel to the leading edge. Finally, these connecting SFs fused to form a single SF with matured FAs at both ends. This change in SF organization with cell retraction in the first cycle of migration followed by a newly formed protrusion in the next cycle is assumed to lead to cell turning in migrating Swiss 3T3 fibroblasts. PMID:28119928

  10. EPR detected polarization transfer between Gd3+ and protons at low temperature and 3.3 T: The first step of dynamic nuclear polarization

    NASA Astrophysics Data System (ADS)

    Nagarajan, Vijayasarathi; Hovav, Yonatan; Feintuch, Akiva; Vega, Shimon; Goldfarb, Daniella

    2010-06-01

    Electron-electron double resonance pulsed electron paramagnetic resonance (EPR) at 95 GHz (3.3 T) is used to follow the dynamics of the electron spin polarization during the first stages of dynamic nuclear polarization in solids. The experiments were performed on a frozen solution of Gd+3 (S =7/2) in water/glycerol. Focusing on the central |-1/2⟩→|+1/2⟩ transition we measured the polarization transfer from the Gd3+ electron spin to the adjacent H1 protons. The dependence of the echo detected EPR signal on the length of the microwave irradiation at the EPR "forbidden" transition corresponding to an electron and a proton spin flip is measured for different powers, showing dynamics on the microsecond to millisecond time scales. A theoretical model based on the spin density matrix formalism is suggested to account for this dynamics. The central transition of the Gd3+ ion is considered as an effective S =1/2 system and is coupled to H1 (I =1/2) nuclei. Simulations based on a single electron-single nucleus four level system are shown to deviate from the experimental results and an alternative approach taking into account the more realistic multinuclei picture is shown to agree qualitatively with the experiments.

  11. Method for dose-reduced 3D catheter tracking on a scanning-beam digital x-ray system using dynamic electronic collimation

    PubMed Central

    Dunkerley, David A. P.; Funk, Tobias; Speidel, Michael A.

    2016-01-01

    Scanning-beam digital x-ray (SBDX) is an inverse geometry x-ray fluoroscopy system capable of tomosynthesis-based 3D catheter tracking. This work proposes a method of dose-reduced 3D tracking using dynamic electronic collimation (DEC) of the SBDX scanning x-ray tube. Positions in the 2D focal spot array are selectively activated to create a region-of-interest (ROI) x-ray field around the tracked catheter. The ROI position is updated for each frame based on a motion vector calculated from the two most recent 3D tracking results. The technique was evaluated with SBDX data acquired as a catheter tip inside a chest phantom was pulled along a 3D trajectory. DEC scans were retrospectively generated from the detector images stored for each focal spot position. DEC imaging of a catheter tip in a volume measuring 11.4 cm across at isocenter required 340 active focal spots per frame, versus 4473 spots in full-FOV mode. The dose-area-product (DAP) and peak skin dose (PSD) for DEC versus full field-of-view (FOV) scanning were calculated using an SBDX Monte Carlo simulation code. DAP was reduced to 7.4% to 8.4% of the full-FOV value, consistent with the relative number of active focal spots (7.6%). For image sequences with a moving catheter, PSD was 33.6% to 34.8% of the full-FOV value. The root-mean-squared-deviation between DEC-based 3D tracking coordinates and full-FOV 3D tracking coordinates was less than 0.1 mm. The 3D distance between the tracked tip and the sheath centerline averaged 0.75 mm. Dynamic electronic collimation can reduce dose with minimal change in tracking performance. PMID:27375314

  12. Development, Verification and Use of Gust Modeling in the NASA Computational Fluid Dynamics Code FUN3D

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.

    2012-01-01

    This paper presents the implementation of gust modeling capability in the CFD code FUN3D. The gust capability is verified by computing the response of an airfoil to a sharp edged gust. This result is compared with the theoretical result. The present simulations will be compared with other CFD gust simulations. This paper also serves as a users manual for FUN3D gust analyses using a variety of gust profiles. Finally, the development of an Auto-Regressive Moving-Average (ARMA) reduced order gust model using a gust with a Gaussian profile in the FUN3D code is presented. ARMA simulated results of a sequence of one-minus-cosine gusts is shown to compare well with the same gust profile computed with FUN3D. Proper Orthogonal Decomposition (POD) is combined with the ARMA modeling technique to predict the time varying pressure coefficient increment distribution due to a novel gust profile. The aeroelastic response of a pitch/plunge airfoil to a gust environment is computed with a reduced order model, and compared with a direct simulation of the system in the FUN3D code. The two results are found to agree very well.

  13. Dynamic particle accumulation structure (PAS) in half-zone liquid bridge Reconstruction of particle motion by 3-D PTV

    NASA Astrophysics Data System (ADS)

    Ueno, I.; Abe, Y.; Noguchi, K.; Kawamura, H.

    Three-dimensional (3-D) velocity field reconstruction of oscillatory thermocapillary convections in a half-zone liquid bridge with a radius of O (1 mm) was carried out by applying 3-D particle tracking velocimetry (PTV). Simultaneous observation of the particles suspended in the bridge by two CCD cameras was carried out by placing a small cubic beam splitter above a transparent top rod. The reconstruction of the 3-D trajectories and the velocity fields of the particles in the several types of oscillatory-flow regimes were conducted successfully for sufficiently long period without losing particle tracking. With this application the present authors conducted a series of experiments focusing upon the collapse and re-formation process of the PAS by mechanically disturbing fully developed PAS.

  14. 3D multidisciplinary numerical model of polychlorinated biphenyl dynamics on the Black Sea north-western shelf

    NASA Astrophysics Data System (ADS)

    Bagaiev, Andrii; Ivanov, Vitaliy

    2014-05-01

    The Black Sea north-western shelf plays a key role in economics of the developing countries such as Ukraine due to food supply, invaluable recreational potential and variety of the relevant maritime shipping routes. On the other hand, a shallow flat shelf is mostly affected by anthropogenic pollution, eutrophication, hypoxia and harmful algae blooms. The research is focused on modeling the transport and transformation of PCBs (PolyChlorinated Biphenyls) because they are exceedingly toxic and highly resistant to degradation, hence cumulatively affect marine ecosystems. Being lipophilic compounds, PCBs demonstrate the distinguishing sorption/desorption activity taking part in the biogeochemical fluxes via the organic matter particles and sediments. In the framework of the research, the coastal in-situ data on PCB concentration in the water column and sediments are processed, visualized and analyzed. It is concluded that the main sources of PCBs are related to the Danube discharge and resuspension from the shallow-water sediments. Developed 3D numerical model is aimed at simulation of PCB contamination of the water column and sediment. The model integrates the full physics hydrodynamic block as well as modules, which describe detritus transport and transformation and PCB dynamics. Three state variables are simulated in PCB transport module: concentration in solute, on the settling particles of detritus and in the top layer of sediments. PCB adsorption/desorption on detritus; the reversible PCB fluxes at the water-sediment boundary; destruction of detritus are taken into consideration. Formalization of PCB deposition/resuspension in the sediments is adapted from Van Rijn's model of the suspended sediment transport. The model was spun up to reconstruct the short term scenario of the instantaneous PCB release from the St. George Arm of Danube. It has been shown that PCB transport on sinking detritus represents the natural buffer mechanism damping the spreading PCB

  15. NIKE3D: an implicit, finite-deformation, finite element code for analyzing the static and dynamic response of three-dimensional solids

    SciTech Connect

    Hallquist, J.O.

    1981-01-01

    A user's manual is provided for NIKE3D, a fully implicit three-dimensional finite element code for analyzing the large deformation static and dynamic response of inelastic solids. A contact-impact algorithm permits gaps and sliding along material interfaces. By a specialization of this algorithm, such interfaces can be rigidly tied to admit variable zoning without the need of transition regions. Spatial discretization is achieved by the use of 8-node constant pressure solid elements. Bandwidth minimization is optional. Post-processors for NIKE3D include GRAPE for plotting deformed shapes and stress contours and DYNAP for plotting time histories.

  16. Dynamic MR urography in children with uropathic disease with a combined 2D and 3D acquisition protocol—comparison with MAG3 scintigraphy

    PubMed Central

    Martirosian, P; Fuchs, J; Obermayer, F; Tsiflikas, I; Schick, F; Schäfer, J F

    2014-01-01

    Objective: The aim of this study was to evaluate combined two-dimensional (2D) and three-dimensional (3D) dynamic MR urography with respiratory compensation in children with anomalies of the genitourinary tract, allowing for computation of split renal function and assessment of urinary tract obstruction. Methods: Dynamic MR urography was performed in 53 children (3 months–16 years of age) with anomalies of the urinary tract. A protocol for dynamic MR urography and nephrography was implemented at 1.5 T using a navigator-triggered 2D TurboFLASH sequence. Split renal function and contrast-medium excretion were assessed after the bolus injection of 0.05 mmol kg−1 body weight of gadolinium dimeglumine. In the excretory phase, a 3D gradient-echo data set with high spatial resolution was acquired. In all patients, mercaptoacetyltriglycine (MAG3) scintigraphy was obtained as a reference standard. Results: In all children, dynamic MR nephrography and urography could be performed with excellent compensation of breathing artefacts providing region of interest analysis in nearly identical kidney positions. The assessment of contrast-medium excretion into the ureter allowed for discrimination of functional from non-functional stenosis. Split renal function assessed by MRI showed an excellent agreement with the MAG3 reference standard with a correlation coefficient r = 0.95. Additionally recorded 3D data sets offered good depiction of anatomical anomalies in all patients. Conclusion: The proposed protocol provides a robust technique for assessment of ureteral obstruction and split renal function with compensation of breathing artefacts, short post-processing time and excellent 3D spatial resolution. Advances in knowledge: The combined protocol of 2D and 3D MR urography is an efficient technique for assessment of renal morphology and function. PMID:25270833

  17. Research on the Dynamic Problems of 3D Cross Coupling Quantum Harmonic Oscillator by Virtue of Intermediate Representation | x> λ, ν

    NASA Astrophysics Data System (ADS)

    Xu, Shi-Min; Xu, Xing-Lei; Li, Hong-Qi

    2008-06-01

    The intermediate representation (namely intermediate coordinate-momentum representation) | x> λ, ν are introduced and employed to research the expression of the operator tauhat{p}+σhat{x} in intermediate representation | x> λ, ν . The systematic Hamilton operator hat{H} of 3D cross coupling quantum harmonic oscillator was diagonalized by virtue of quadratic form theory. The quantity of λ, ν, τand σ were figured out. The dynamic problems of 3D cross coupling quantum harmonic oscillator are researched by virtue of intermediate representation. The energy eigen-value and eigenwave function of 3D cross coupling quantum harmonic oscillator were obtained in intermediate representation. The importance of intermediate representation was discussed. The results show that the Radon transformation of Wigner operator is just the projectional operator | x> λ, ν λ, ν < x|, and the Radon transformation of Wigner function is just a margin distribution.

  18. Multi-camera and structured-light vision system (MSVS) for dynamic high-accuracy 3D measurements of railway tunnels.

    PubMed

    Zhan, Dong; Yu, Long; Xiao, Jian; Chen, Tanglong

    2015-04-14

    Railway tunnel 3D clearance inspection is critical to guaranteeing railway operation safety. However, it is a challenge to inspect railway tunnel 3D clearance using a vision system, because both the spatial range and field of view (FOV) of such measurements are quite large. This paper summarizes our work on dynamic railway tunnel 3D clearance inspection based on a multi-camera and structured-light vision system (MSVS). First, the configuration of the MSVS is described. Then, the global calibration for the MSVS is discussed in detail. The onboard vision system is mounted on a dedicated vehicle and is expected to suffer from multiple degrees of freedom vibrations brought about by the running vehicle. Any small vibration can result in substantial measurement errors. In order to overcome this problem, a vehicle motion deviation rectifying method is investigated. Experiments using the vision inspection system are conducted with satisfactory online measurement results.

  19. Nonrigid Registration of 2-D and 3-D Dynamic Cell Nuclei Images for Improved Classification of Subcellular Particle Motion

    PubMed Central

    Kim, Il-Han; Chen, Yi-Chun M.; Spector, David L.; Eils, Roland; Rohr, Karl

    2012-01-01

    The observed motion of subcellular particles in fluorescence microscopy image sequences of live cells is generally a superposition of the motion and deformation of the cell and the motion of the particles. Decoupling the two types of movements to enable accurate classification of the particle motion requires the application of registration algorithms. We have developed an intensity-based approach for nonrigid registration of multi-channel microscopy image sequences of cell nuclei. First, based on 3-D synthetic images we demonstrate that cell nucleus deformations change the observed motion types of particles and that our approach allows to recover the original motion. Second, we have successfully applied our approach to register 2-D and 3-D real microscopy image sequences. A quantitative experimental comparison with previous approaches for nonrigid registration of cell microscopy has also been performed. PMID:20840894

  20. A stroboscopic structured illumination system used in dynamic 3D visualization of high-speed motion object

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Zhang, Qican; Li, Yong; Xiang, Liqun; Cao, Yiping; Chen, Wenjing

    2005-04-01

    A stroboscopic structured illumination system, which can be used in measurement for 3D shape and deformation of high-speed motion object, is proposed and verified by experiments. The system, present in this paper, can automatically detect the position of high-speed moving object and synchronously control the flash of LED to project a structured optical field onto surface of motion object and the shoot of imaging system to acquire an image of deformed fringe pattern, also can create a signal, set artificially through software, to synchronously control the LED and imaging system to do their job. We experiment on a civil electric fan, successful acquire a serial of instantaneous, sharp and clear images of rotation blade and reconstruct its 3D shapes in difference revolutions.

  1. Geo-Referenced Dynamic Pushbroom Stereo Mosaics for 3D and Moving Target Extraction - A New Geometric Approach

    DTIC Science & Technology

    2009-12-01

    different real video sequences of large-scale 3D scenes to show the accuracy and effectiveness of the representation. Applications include airborne or ground...a moving platform, we will have to naturally and effectively handle obvious motion parallax and object occlusions in order to be able to detect...stereo mosaics of static scenes. These results are mainly presented in Sections 3 and 4. Second, an effective and efficient patch-based stereo

  2. Linear and nonlinear instability and ligament dynamics in 3D laminar two-layer liquid/liquid flows

    NASA Astrophysics Data System (ADS)

    Ó Náraigh, Lennon; Valluri, Prashant; Scott, David; Bethune, Iain; Spelt, Peter

    2013-11-01

    We consider the linear and nonlinear stability of two-phase density-matched but viscosity contrasted fluids subject to laminar Poiseuille flow in a channel, paying particular attention to the formation of three-dimensional waves. The Orr-Sommerfeld-Squire analysis is used along with DNS of the 3D two-phase Navier-Stokes equations using our newly launched TPLS Solver (http://edin.ac/10cRKzS). For the parameter regimes considered, we demonstrate the existence of two distinct mechanisms whereby 3D waves enter the system, and dominate at late time. There exists a direct route, whereby 3D waves are amplified by the standard linear mechanism; for certain parameter classes, such waves grow at a rate less than but comparable to that of most-dangerous two-dimensional mode. Additionally, there is a weakly nonlinear route, whereby a purely spanwise wave couples to a streamwise mode and grows exponentially. We demonstrate these mechanisms in isolation and in concert. Consideration is also given to the ultimate state of these waves: persistent three-dimensional nonlinear waves are stretched and distorted by the base flow, thereby producing regimes of ligaments, ``sheets,'' or ``interfacial turbulence.'' HECToR RAP/dCSE Project e174, HPC-Europa 2.

  3. Analogy between a 10D model for nonlinear wave-wave interaction in a plasma and the 3D Lorenz dynamics

    NASA Astrophysics Data System (ADS)

    Letellier, C.; Aguirre, L. A.; Maquet, J.; Lefebvre, B.

    2003-05-01

    This paper investigates nonlinear wave-wave interactions in a system that describes a modified decay instability and consists of three Langmuir and one ion-sound waves. As a means to establish that the underlying dynamics exists in a 3D space and that it is of the Lorenz-type, both continuous and discrete-time multivariable global models were obtained from data. These data were obtained from a 10D dynamical system that describes the modified decay instability obtained from Zakharov’s equations which characterise Langmuir turbulence. This 10D model is equivariant under a continuous rotation symmetry and a discrete order-2 rotation symmetry. When the continuous rotation symmetry is modded out, that is, when the dynamics are represented with the continuous rotation symmetry removed under a local diffeomorphism, it is shown that a 3D system may describe the underlying dynamics. For certain parameter values, the models, obtained using global modelling techniques from three time series from the 10D dynamics with the continuous rotation symmetry modded out, generate attractors which are topologically equivalent. These models can be simulated easily and, due to their simplicity, are amenable for analysis of the original dynamics after symmetries have been modded out. Moreover, it is shown that all of these attractors are topologically equivalent to an attractor generated by the well-known Lorenz system.

  4. Dynamic characteristics of a pump-turbine during hydraulic transients of a model pumped-storage system: 3D CFD simulation

    NASA Astrophysics Data System (ADS)

    Zhang, X. X.; Cheng, Y. G.; Xia, L. S.; Yang, J. D.

    2014-03-01

    The runaway process in a model pumped-storage system was simulated for analyzing the dynamic characteristics of a pump-turbine. The simulation was adopted by coupling 1D (One Dimensional) pipeline MOC (Method of Characteristics) equations with a 3D (Three Dimensional) pump-turbine CFD (Computational Fluid Dynamics) model, in which the water hammer wave in the 3D zone was defined by giving a pressure dependent density. We found from the results that the dynamic performances of the pump-turbine do not coincide with the static operating points, especially in the S-shaped characteristics region, where the dynamic trajectories follow ring-shaped curves. Specifically, the transient operating points with the same Q11 and M11 in different moving directions of the dynamic trajectories give different n11. The main reason of this phenomenon is that the transient flow patterns inside the pump-turbine are influenced by the ones in the previous time step, which leads to different flow patterns between the points with the same Q11 and M11 in different moving directions of the dynamic trajectories.

  5. The dynamics of neutrino-driven supernova explosions after shock revival in 2D and 3D

    NASA Astrophysics Data System (ADS)

    Müller, B.

    2015-10-01

    We study the growth of the explosion energy after shock revival in neutrino-driven explosions in two and three dimensions (2D/3D) using multi-group neutrino hydrodynamics simulations of an 11.2 M⊙ star. The 3D model shows a faster and steadier growth of the explosion energy and already shows signs of subsiding accretion after one second. By contrast, the growth of the explosion energy in 2D is unsteady, and accretion lasts for several seconds as confirmed by additional long-time simulations of stars of similar masses. Appreciable explosion energies can still be reached, albeit at the expense of rather high neutron star masses. In 2D, the binding energy at the gain radius is larger because the strong excitation of downward-propagating g modes removes energy from the freshly accreted material in the downflows. Consequently, the mass outflow rate is considerably lower in 2D than in 3D. This is only partially compensated by additional heating by outward-propagating acoustic waves in 2D. Moreover, the mass outflow rate in 2D is reduced because much of the neutrino energy deposition occurs in downflows or bubbles confined by secondary shocks without driving outflows. Episodic constriction of outflows and vertical mixing of colder shocked material and hot, neutrino-heated ejecta due to Rayleigh-Taylor instability further hamper the growth of the explosion energy in 2D. Further simulations will be necessary to determine whether these effects are generic over a wider range of supernova progenitors.

  6. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  7. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chih; Lou, Xia; Zhang, Zhixiong; Ingram, Patrick; Yoon, Euisik

    2015-07-01

    Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional cancer chemotherapy. Yet to date, PDT efficacy has been mostly characterized using 2D cultures. Compared to 2D cultures, 3D sphere culture generates unique spatial distributions of nutrients and oxygen for the cells that better mimics the in-vivo conditions. Using a novel polyHEMA (non-adherent polymer) fabrication process, we developed a microfluidic sphere formation platform that can (1) generate 1,024 uniform (size variation <10%) cancer spheres within a 2 cm by 2 cm core area, (2) culture spheres for more than 2 weeks, and (3) allow the retrieval of spheres. Using the presented platform, we have successfully characterized the different responses in 2D and 3D cell culture to PDT. Furthermore, we investigated the treatment resistance effect in cancer cells induced by tumor associated fibroblasts (CAF). Although the CAFs can enhance the resistance to traditional chemotherapy agents, no significant difference in PDT was observed. The preliminary results suggest that the PDT can be an attractive alternative cancer therapy, which is less affected by the therapeutic resistance induced by cancer associated cells.

  8. CQL3D-Hybrid-FOW modeling of the temporal dynamics of NSTX NBI+HHFW discharges

    SciTech Connect

    Harvey, R. W.; Petrov, Yu. V.; Liu, D.; Heidbrink, W. W.; Taylor, G.; Bonoli, P. T.

    2014-02-12

    The CQL3D Fokker-Planck code[1] has been upgraded to include physics of finite-orbit-width (FOW) guiding-center orbits[2,3], as compared with the previous zero-orbit-width (ZOW) model, and a recent first-order orbit calculation[2]. The Fast Ion Diagnostic FIDA[4,5] signal resulting from neutral beam (NBI) and high harmonic fast wave (HHFW) RF power injected into the NSTX spherical tokamak can now be modeled quite accurately, using ion distributions from the CQL3D-Hybrid-FOW code, a rapidly executing variant that includes FOW+gyro-orbit losses to the plasma edge, FOW effects on NBI injection and HHFW diffusion, but does not include neoclassical radial diffusion. Accurate simulation of prompt fast ion (FI) losses is a key feature of the marked modeling improvement relative to previous ZOW results. By comparing NBI-only and NBI+HHFW shots, independent confirmation of the usual 35% edge loss of HHFW in NSTX is obtained. Further, HHFW prompt losses from the plasma core are shown to be 3X as large (>25%) as the NBI-only case. The modulated NBI and time-dependent background plasma variations and charge exchange losses of fast ions are accounted for, and the temporal neutron variation is in approximate agreement with NSTX observations.

  9. CQL3D-Hybrid-FOW modeling of the temporal dynamics of NSTX NBI+HHFW discharges

    NASA Astrophysics Data System (ADS)

    Harvey, R. W.; Petrov, Yu. V.; Liu, D.; Heidbrink, W. W.; Taylor, G.; Bonoli, P. T.

    2014-02-01

    The CQL3D Fokker-Planck code[1] has been upgraded to include physics of finite-orbit-width (FOW) guiding-center orbits[2,3], as compared with the previous zero-orbit-width (ZOW) model, and a recent first-order orbit calculation[2]. The Fast Ion Diagnostic FIDA[4,5] signal resulting from neutral beam (NBI) and high harmonic fast wave (HHFW) RF power injected into the NSTX spherical tokamak can now be modeled quite accurately, using ion distributions from the CQL3D-Hybrid-FOW code, a rapidly executing variant that includes FOW+gyro-orbit losses to the plasma edge, FOW effects on NBI injection and HHFW diffusion, but does not include neoclassical radial diffusion. Accurate simulation of prompt fast ion (FI) losses is a key feature of the marked modeling improvement relative to previous ZOW results. By comparing NBI-only and NBI+HHFW shots, independent confirmation of the usual 35% edge loss of HHFW in NSTX is obtained. Further, HHFW prompt losses from the plasma core are shown to be 3X as large (>25%) as the NBI-only case. The modulated NBI and time-dependent background plasma variations and charge exchange losses of fast ions are accounted for, and the temporal neutron variation is in approximate agreement with NSTX observations.

  10. Dynamic shape modeling of the mitral valve from real-time 3D ultrasound images using continuous medial representation

    NASA Astrophysics Data System (ADS)

    Pouch, Alison M.; Yushkevich, Paul A.; Jackson, Benjamin M.; Gorman, Joseph H., III; Gorman, Robert C.; Sehgal, Chandra M.

    2012-03-01

    Purpose: Patient-specific shape analysis of the mitral valve from real-time 3D ultrasound (rt-3DUS) has broad application to the assessment and surgical treatment of mitral valve disease. Our goal is to demonstrate that continuous medial representation (cm-rep) is an accurate valve shape representation that can be used for statistical shape modeling over the cardiac cycle from rt-3DUS images. Methods: Transesophageal rt-3DUS data acquired from 15 subjects with a range of mitral valve pathology were analyzed. User-initialized segmentation with level sets and symmetric diffeomorphic normalization delineated the mitral leaflets at each time point in the rt-3DUS data series. A deformable cm-rep was fitted to each segmented image of the mitral leaflets in the time series, producing a 4D parametric representation of valve shape in a single cardiac cycle. Model fitting accuracy was evaluated by the Dice overlap, and shape interpolation and principal component analysis (PCA) of 4D valve shape were performed. Results: Of the 289 3D images analyzed, the average Dice overlap between each fitted cm-rep and its target segmentation was 0.880+/-0.018 (max=0.912, min=0.819). The results of PCA represented variability in valve morphology and localized leaflet thickness across subjects. Conclusion: Deformable medial modeling accurately captures valve geometry in rt-3DUS images over the entire cardiac cycle and enables statistical shape analysis of the mitral valve.

  11. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures

    PubMed Central

    Chen, Yu-Chih; Lou, Xia; Zhang, Zhixiong; Ingram, Patrick; Yoon, Euisik

    2015-01-01

    Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional cancer chemotherapy. Yet to date, PDT efficacy has been mostly characterized using 2D cultures. Compared to 2D cultures, 3D sphere culture generates unique spatial distributions of nutrients and oxygen for the cells that better mimics the in-vivo conditions. Using a novel polyHEMA (non-adherent polymer) fabrication process, we developed a microfluidic sphere formation platform that can (1) generate 1,024 uniform (size variation <10%) cancer spheres within a 2 cm by 2 cm core area, (2) culture spheres for more than 2 weeks, and (3) allow the retrieval of spheres. Using the presented platform, we have successfully characterized the different responses in 2D and 3D cell culture to PDT. Furthermore, we investigated the treatment resistance effect in cancer cells induced by tumor associated fibroblasts (CAF). Although the CAFs can enhance the resistance to traditional chemotherapy agents, no significant difference in PDT was observed. The preliminary results suggest that the PDT can be an attractive alternative cancer therapy, which is less affected by the therapeutic resistance induced by cancer associated cells. PMID:26153550

  12. Full-field dynamic displacement and strain measurement using pulsed and high-speed 3D image correlation photogrammetry

    NASA Astrophysics Data System (ADS)

    Schmidt, Timothy; Tyson, John; Galanulis, Konstantin

    2004-02-01

    3D image correlation is a robust method for measuring full-field displacements and strains using a calibrated pair of video cameras. Underlying principles and benefits are reviewed, and the method is compared to both 3D ESPI and 2D image correlation. Several applications combining image correlation photogrammetry with stroboscopic illumination and/or high-speed video cameras are presented. Operational strains in ionic polymeric muscle samples and electro-restrictive actuators are determined. The use of short-duration white light pulses to study automobile tires on road wheels at speeds up to 150 miles per hour is demonstrated. Initial work measuring strains on an 18" flywheel in a spin pit at up to 35,000 rpm is described. A notched rubber dogbone sample is pulled to failure at 125% strain in 38 milliseconds, and hundreds of full-field strain maps are captured. This paper includes discussion of sample preparation methods and special lighting systems, including pulsed arc lamps and pulsed lasers. A matrix of capability using available high speed cameras is included.

  13. Development of the dynamic motion simulator of 3D micro-gravity with a combined passive/active suspension system

    NASA Technical Reports Server (NTRS)

    Yoshida, Kazuya; Hirose, Shigeo; Ogawa, Tadashi

    1994-01-01

    The establishment of those in-orbit operations like 'Rendez-Vous/Docking' and 'Manipulator Berthing' with the assistance of robotics or autonomous control technology, is essential for the near future space programs. In order to study the control methods, develop the flight models, and verify how the system works, we need a tool or a testbed which enables us to simulate mechanically the micro-gravity environment. There have been many attempts to develop the micro-gravity testbeds, but once the simulation goes into the docking and berthing operation that involves mechanical contacts among multi bodies, the requirement becomes critical. A group at the Tokyo Institute of Technology has proposed a method that can simulate the 3D micro-gravity producing a smooth response to the impact phenomena with relatively simple apparatus. Recently the group carried out basic experiments successfully using a prototype hardware model of the testbed. This paper will present our idea of the 3D micro-gravity simulator and report the results of our initial experiments.

  14. Dynamics of errors in 3D motion estimation and implications for strain-tensor imaging in acoustic elastography

    NASA Astrophysics Data System (ADS)

    Bilgen, Mehmet

    2000-06-01

    For the purpose of quantifying the noise in acoustic elastography, a displacement covariance matrix is derived analytically for the cross-correlation based 3D motion estimator. Static deformation induced in tissue from an external mechanical source is represented by a second-order strain tensor. A generalized 3D model is introduced for the ultrasonic echo signals. The components of the covariance matrix are related to the variances of the displacement errors and the errors made in estimating the elements of the strain tensor. The results are combined to investigate the dependences of these errors on the experimental and signal-processing parameters as well as to determine the effects of one strain component on the estimation of the other. The expressions are evaluated for special cases of axial strain estimation in the presence of axial, axial-shear and lateral-shear type deformations in 2D. The signals are shown to decorrelate with any of these deformations, with strengths depending on the reorganization and interaction of tissue scatterers with the ultrasonic point spread function following the deformation. Conditions that favour the improvements in motion estimation performance are discussed, and advantages gained by signal companding and pulse compression are illustrated.

  15. 3D numerical modeling of mantle flow, crustal dynamics and magma genesis associated with slab roll-back and tearing: The eastern Mediterranean case

    NASA Astrophysics Data System (ADS)

    Menant, Armel; Sternai, Pietro; Jolivet, Laurent; Guillou-Frottier, Laurent; Gerya, Taras

    2016-05-01

    Interactions between subduction dynamics and magma genesis have been intensely investigated, resulting in several conceptual models derived from geological, geochemical and geophysical data. To provide physico-chemical constraints on these conceptual models, self-consistent numerical simulations containing testable thermo-mechanical parameters are required, especially considering the three-dimensional (3D) natural complexity of subduction systems. Here, we use a 3D high-resolution petrological and thermo-mechanical numerical model to quantify the relative contribution of oceanic and continental subduction/collision, slab roll-back and tearing to magma genesis and transport processes. Our modeling results suggest that the space and time distribution and composition of magmas in the overriding plate is controlled by the 3D slab dynamics and related asthenospheric flow. Moreover, the decrease of the bulk lithospheric strength induced by mantle- and crust-derived magmas promotes the propagation of strike-slip and extensional fault zones through the overriding crust as response to slab roll-back and continental collision. Reduction of the lithosphere/asthenosphere rheological contrast by lithospheric weakening also favors the transmission of velocities from the flowing mantle to the crust. Similarities between our modeling results and the late Cenozoic tectonic and magmatic evolution across the eastern Mediterranean region suggest an efficient control of mantle flow on the magmatic activity in this region, which in turn promotes lithospheric deformation by mantle drag via melt-induced weakening effects.

  16. Self-assembled dynamic 3D fingerprints in liquid-crystal coatings towards controllable friction and adhesion.

    PubMed

    Liu, Danqing; Broer, Dirk J

    2014-04-25

    Chiral-nematic polymer network coatings form a "fingerprint" texture through self-assembly. For this purpose the molecular helix of the coating is oriented parallel to the substrate. The coating has a flat surface but when actuated by light in the presence of a copolymerized azobenzene compound, 3D fingerprint structures appear in the coating. The helix forms protrusions at the positions where the molecules are aligned parallel to the surface and withdraws at the positions where the orientation is perpendicular. This process proceeds rapidly and is reversible, that is, the fingerprint-shaped protrusions disappear when the light is switched off. The texture in the on-state resembles that of a human fingerprint and is used to manipulate the gripping friction of a robotic finger. The friction coefficient drops by a factor of four to five when the fingerprint switched on because of reduced surface contacts.

  17. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components.

    PubMed

    Gerling, Thomas; Wagenbauer, Klaus F; Neuner, Andrea M; Dietz, Hendrik

    2015-03-27

    We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components' interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

  18. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

    NASA Astrophysics Data System (ADS)

    Gerling, Thomas; Wagenbauer, Klaus F.; Neuner, Andrea M.; Dietz, Hendrik

    2015-03-01

    We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

  19. Dynamic analysis of angiogenesis in transgenic zebrafish embryos using a 3D multilayer chip-based technology

    NASA Astrophysics Data System (ADS)

    Akagi, Jin; Zhu, Feng; Hall, Chris J.; Khoshmanesh, Khashayar; Kalantar-Zadeh, Kourosh; Mitchell, Arnan; Crosier, Kathryn E.; Crosier, Philip S.; Wlodkowic, Donald

    2013-03-01

    Transgenic zebrafish (Danio rerio) models of human diseases have recently emerged as innovative experimental systems in drug discovery and molecular pathology. None of the currently available technologies, however, allow for automated immobilization and treatment of large numbers of spatially encoded transgenic embryos during real-time developmental analysis. This work describes the proof-of-concept design and validation of an integrated 3D microfluidic chip-based system fabricated directly in the poly(methyl methacrylate) transparent thermoplastic using infrared laser micromachining. At its core, the device utilizes an array of 3D micro-mechanical traps to actively capture and immobilize single embryos using a low-pressure suction. It also features built-in piezoelectric microdiaphragm pumps, embryo trapping suction manifold, drug delivery manifold and optically transparent indium tin oxide (ITO) heating element to provide optimal temperature during embryo development. Furthermore, we present design of the proof-of-concept off-chip electronic interface equipped with robotic servo actuator driven stage, innovative servomotor-actuated pinch valves and miniaturized fluorescent USB microscope. Our results show that the innovative device has 100% embryo trapping efficiency while supporting normal embryo development for up to 72 hours in a confined microfluidic environment. We also present data that this microfluidic system can be readily applied to kinetic analysis of a panel of investigational anti-angiogenic agents in transgenic zebrafish Tg(fli1a:EGFP) line. The optical transparency and embryo immobilization allow for convenient visualization of developing vasculature patterns in response to drug treatment without the need for specimen re-positioning. The integrated electronic interfaces bring the Lab-on-a-Chip systems a step closer to realization of complete analytical automation.

  20. Extension of the Optimized Virtual Fields Method to estimate viscoelastic material parameters from 3D dynamic displacement fields

    PubMed Central

    Connesson, N.; Clayton, E.H.; Bayly, P.V.; Pierron, F.

    2015-01-01

    In-vivo measurement of the mechanical properties of soft tissues is essential to provide necessary data in biomechanics and medicine (early cancer diagnosis, study of traumatic brain injuries, etc.). Imaging techniques such as Magnetic Resonance Elastography (MRE) can provide 3D displacement maps in the bulk and in vivo, from which, using inverse methods, it is then possible to identify some mechanical parameters of the tissues (stiffness, damping etc.). The main difficulties in these inverse identification procedures consist in dealing with the pressure waves contained in the data and with the experimental noise perturbing the spatial derivatives required during the processing. The Optimized Virtual Fields Method (OVFM) [1], designed to be robust to noise, present natural and rigorous solution to deal with these problems. The OVFM has been adapted to identify material parameter maps from Magnetic Resonance Elastography (MRE) data consisting of 3-dimensional displacement fields in harmonically loaded soft materials. In this work, the method has been developed to identify elastic and viscoelastic models. The OVFM sensitivity to spatial resolution and to noise has been studied by analyzing 3D analytically simulated displacement data. This study evaluates and describes the OVFM identification performances: different biases on the identified parameters are induced by the spatial resolution and experimental noise. The well-known identification problems in the case of quasi-incompressible materials also find a natural solution in the OVFM. Moreover, an a posteriori criterion to estimate the local identification quality is proposed. The identification results obtained on actual experiments are briefly presented. PMID:26146416

  1. Calculation of Local Water Densities in Biological Systems — A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

    PubMed Central

    Stumpe, Martin C.; Blinov, Nikolay; Wishart, David; Kovalenko, Andriy; Pande, Vijay S.

    2010-01-01

    Water plays a unique role in all living organisms. Not only is it nature’s ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules like proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces like the hydrophobic effect are relevant. Computational methods like molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are indeed the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods, MD simulations and the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH, and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems. PMID:21174421

  2. Combined 3D-QSAR, molecular docking and molecular dynamics study on thyroid hormone activity of hydroxylated polybrominated diphenyl ethers to thyroid receptors β

    SciTech Connect

    Li, Xiaolin; Ye, Li; Wang, Xiaoxiang; Wang, Xinzhou; Liu, Hongling; Zhu, Yongliang; Yu, Hongxia

    2012-12-15

    Several recent reports suggested that hydroxylated polybrominated diphenyl ethers (HO-PBDEs) may disturb thyroid hormone homeostasis. To illuminate the structural features for thyroid hormone activity of HO-PBDEs and the binding mode between HO-PBDEs and thyroid hormone receptor (TR), the hormone activity of a series of HO-PBDEs to thyroid receptors β was studied based on the combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) methods. The ligand- and receptor-based 3D-QSAR models were obtained using Comparative Molecular Similarity Index Analysis (CoMSIA) method. The optimum CoMSIA model with region focusing yielded satisfactory statistical results: leave-one-out cross-validation correlation coefficient (q{sup 2}) was 0.571 and non-cross-validation correlation coefficient (r{sup 2}) was 0.951. Furthermore, the results of internal validation such as bootstrapping, leave-many-out cross-validation, and progressive scrambling as well as external validation indicated the rationality and good predictive ability of the best model. In addition, molecular docking elucidated the conformations of compounds and key amino acid residues at the docking pocket, MD simulation further determined the binding process and validated the rationality of docking results. -- Highlights: ► The thyroid hormone activities of HO-PBDEs were studied by 3D-QSAR. ► The binding modes between HO-PBDEs and TRβ were explored. ► 3D-QSAR, molecular docking, and molecular dynamics (MD) methods were performed.

  3. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  4. From Dynamic Live Cell Imaging to 3D Ultrastructure: Novel Integrated Methods for High Pressure Freezing and Correlative Light-Electron Microscopy

    PubMed Central

    Spiegelhalter, Coralie; Tosch, Valérie; Hentsch, Didier; Koch, Marc; Kessler, Pascal; Schwab, Yannick; Laporte, Jocelyn

    2010-01-01

    Background In cell biology, the study of proteins and organelles requires the combination of different imaging approaches, from live recordings with light microscopy (LM) to electron microscopy (EM). Methodology To correlate dynamic events in adherent cells with both ultrastructural and 3D information, we developed a method for cultured cells that combines confocal time-lapse images of GFP-tagged proteins with electron microscopy. With laser micro-patterned culture substrate, we created coordinates that were conserved at every step of the sample preparation and visualization processes. Specifically designed for cryo-fixation, this method allowed a fast freezing of dynamic events within seconds and their ultrastructural characterization. We provide examples of the dynamic oligomerization of GFP-tagged myotubularin (MTM1) phosphoinositides phosphatase induced by osmotic stress, and of the ultrastructure of membrane tubules dependent on amphiphysin 2 (BIN1) expression. Conclusion Accessible and versatile, we show that this approach is efficient to routinely correlate functional and dynamic LM with high resolution morphology by EM, with immuno-EM labeling, with 3D reconstruction using serial immuno-EM or tomography, and with scanning-EM. PMID:20140253

  5. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  6. Time-Resolved MR Angiography of the Legs at 3 T Using a Low Dose of Gadolinium: Initial Experience and Contrast Dynamics

    PubMed Central

    Sandhu, Gurpreet Singh; Rezaee, Rod P.; Jesberger, John; Wright, Katherine; Griswold, Mark A.; Gulani, Vikas

    2014-01-01

    OBJECTIVE This article describes our initial clinical experience with time-resolved MR angiography (MRA) of the legs using the time-resolved imaging with stochastic trajectories (TWIST) technique with a half dose of gadolinium. MATERIALS AND METHODS Thirty-four patients underwent a TWIST examination of the legs at 3 T. Thirty-three patients also underwent a bolus-chase MRA examination in the same setting. Times elapsed between the start of contrast injection and the appearance of contrast material (tA) and peak enhancement of the arteries in the legs (tB) were analyzed. The number of patients with examinations affected by venous contamination was determined. The differences in tA and tB between cases in which venous contamination was present or absent were evaluated using a two-tailed Student t test. RESULTS The TWIST technique using a half dose of gadolinium provided diagnostic-quality images of all patients. The mean tA was 35.5 ± 8.8 (SD) seconds (range, 17.8–60.4 seconds), and the mean tB was 59.1 ± 15.1 seconds (range, 31–98.8 seconds). Venous contamination was observed in bolus-chase MRA images of 52.9% of patients. The relationship between venous contamination and tA was not statistically significant (p = 0.13). The incidence of venous contamination was higher in patients with lower values of tB (p = 0.01). CONCLUSION The described low-dose clinical experience with TWIST and the contrast dynamics information gained from this study could aid radiologists in planning protocols for leg MRA examinations. PMID:22358010

  7. Near-infrared spectro-interferometry of Mira variables and comparisons to 1D dynamic model atmospheres and 3D convection simulations

    NASA Astrophysics Data System (ADS)

    Wittkowski, M.; Chiavassa, A.; Freytag, B.; Scholz, M.; Höfner, S.; Karovicova, I.; Whitelock, P. A.

    2016-03-01

    Aims: We aim at comparing spectro-interferometric observations of Mira variable asymptotic giant branch (AGB) stars with the latest 1D dynamic model atmospheres based on self-excited pulsation models (CODEX models) and with 3D dynamic model atmospheres including pulsation and convection (CO5BOLD models) to better understand the processes that extend the molecular atmosphere to radii where dust can form. Methods: We obtained a total of 20 near-infrared K-band spectro-interferometric snapshot observations of the Mira variables o Cet, R Leo, R Aqr, X Hya, W Vel, and R Cnc with a spectral resolution of about 1500. We compared observed flux and visibility spectra with predictions by CODEX 1D dynamic model atmospheres and with azimuthally averaged intensities based on CO5BOLD 3D dynamic model atmospheres. Results: Our visibility data confirm the presence of spatially extended molecular atmospheres located above the continuum radii with large-scale inhomogeneities or clumps that contribute a few percent of the total flux. The detailed structure of the inhomogeneities or clumps show a variability on time scales of 3 months and above. Both modeling attempts provided satisfactory fits to our data. In particular, they are both consistent with the observed decrease in the visibility function at molecular bands of water vapor and CO, indicating a spatially extended molecular atmosphere. Observational variability phases are mostly consistent with those of the best-fit CODEX models, except for near-maximum phases, where data are better described by near-minimum models. Rosseland angular diameters derived from the model fits are broadly consistent between those based on the 1D and the 3D models and with earlier observations. We derived fundamental parameters including absolute radii, effective temperatures, and luminosities for our sources. Conclusions: Our results provide a first observational support for theoretical results that shocks induced by convection and pulsation in the

  8. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  9. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  10. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  11. Tracer diffusion in a polymer gel: simulations of static and dynamic 3D networks using spherical boundary conditions.

    PubMed

    Kamerlin, Natasha; Elvingson, Christer

    2016-11-30

    We have investigated an alternative to the standard periodic boundary conditions for simulating the diffusion of tracer particles in a polymer gel by performing Brownian dynamics simulations using spherical boundary conditions. The gel network is constructed by randomly distributing tetravalent cross-linking nodes and connecting nearest pairs. The final gel structure is characterised by the radial distribution functions, chain lengths and end-to-end distances, and the pore size distribution. We have looked at the diffusion of tracer particles with a wide range of sizes, diffusing in both static and dynamic networks of two different volume fractions. It is quantitatively shown that the dynamical effect of the network becomes more important in facilitating the diffusional transport for larger particle sizes, and that one obtains a finite diffusion also for particle sizes well above the maximum in the pore size distribution.

  12. An autonomous multisensor in situ metrology system for enabling high dynamic range measurement of 3D surfaces on precision machine tools

    NASA Astrophysics Data System (ADS)

    Liu, Samuel M. Y.; Cheung, Benny C. F.; Whitehouse, David; Cheng, Ching-Hsiang

    2016-11-01

    An in situ measurement is of prime importance when trying to maintain the position of the workpiece for further compensation processes in order to improve the accuracy and efficiency of the precision machining of three dimensional (3D) surfaces. However, the coordinates of most of the machine tools with closed machine interfaces and control system are not accessible for users, which make it difficult to use the motion axes of the machine tool for in situ measurements. This paper presents an autonomous multisensor in situ metrology system for enabling high dynamic range measurement of 3D surfaces on precision machine tools. It makes use of a designed tool path and an additional motion sensor to assist the registration of time-space data for the position estimation of a 2D laser scanner which measures the surface with a high lateral resolution and large area without the need to interface with the machine tool system. A prototype system was built and integrated into an ultra-precision polishing machine. Experimental results show that it measures the 3D surfaces with high resolution, high repeatability, and large measurement range. The system not only improves the efficiency and accuracy of the precision machining process but also extends the capability of machine tools.

  13. Caring in the Dynamics of Design and Languaging: Exploring Second Language Learning in 3D Virtual Spaces

    ERIC Educational Resources Information Center

    Zheng, Dongping

    2012-01-01

    This study provides concrete evidence of ecological, dialogical views of languaging within the dynamics of coordination and cooperation in a virtual world. Beginning level second language learners of Chinese engaged in cooperative activities designed to provide them opportunities to refine linguistic actions by way of caring for others, for the…

  14. 3d-3d correspondence revisited

    DOE PAGES

    Chung, Hee -Joong; Dimofte, Tudor; Gukov, Sergei; ...

    2016-04-21

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d N = 2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. As a result, we also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  15. Second-Order Inelastic Dynamic Analysis of 3D Semi-Rigid Steel Frames Under Earthquake Loads with Three Components

    SciTech Connect

    Ozakgul, Kadir

    2008-07-08

    In this study, it has been presented an algorithm for second-order elastoplastic dynamic time-history analysis of three dimensional frames that have steel members with semirigid joints. The proposed analysis accounts for material, geometric and connection nonlinearities. Material nonlinearity have been modeled by the Ramberg-Osgood relation. While the geometric nonlinearity caused by axial force has been described by the use of the geometric stiffness matrix, the nonlinearity caused by the interaction between the axial force and bending moment has been also described by the use of the stability functions. The independent hardening model has been used to describe the nonlinear behaviour of semi-rigid connections. Dynamic equation of motion has been solved by Newmark's constant acceleration method in time history domain.

  16. 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.

  17. Numerical modeling of the 3D dynamics of ultrasound contrast agent microbubbles using the boundary integral method

    NASA Astrophysics Data System (ADS)

    Wang, Qianxi; Manmi, Kawa; Calvisi, Michael L.

    2015-02-01

    Ultrasound contrast agents (UCAs) are microbubbles stabilized with a shell typically of lipid, polymer, or protein and are emerging as a unique tool for noninvasive therapies ranging from gene delivery to tumor ablation. While various models have been developed to describe the spherical oscillations of contrast agents, the treatment of nonspherical behavior has received less attention. However, the nonspherical dynamics of contrast agents are thought to play an important role in therapeutic applications, for example, enhancing the uptake of therapeutic agents across cell membranes and tissue interfaces, and causing tissue ablation. In this paper, a model for nonspherical contrast agent dynamics based on the boundary integral method is described. The effects of the encapsulating shell are approximated by adapting Hoff's model for thin-shell, spherical contrast agents. A high-quality mesh of the bubble surface is maintained by implementing a hybrid approach of the Lagrangian method and elastic mesh technique. The numerical model agrees well with a modified Rayleigh-Plesset equation for encapsulated spherical bubbles. Numerical analyses of the dynamics of UCAs in an infinite liquid and near a rigid wall are performed in parameter regimes of clinical relevance. The oscillation amplitude and period decrease significantly due to the coating. A bubble jet forms when the amplitude of ultrasound is sufficiently large, as occurs for bubbles without a coating; however, the threshold amplitude required to incite jetting increases due to the coating. When a UCA is near a rigid boundary subject to acoustic forcing, the jet is directed towards the wall if the acoustic wave propagates perpendicular to the boundary. When the acoustic wave propagates parallel to the rigid boundary, the jet direction has components both along the wave direction and towards the boundary that depend mainly on the dimensionless standoff distance of the bubble from the boundary. In all cases, the jet

  18. Non-linear dynamic analyses of 3D masonry structures by means of a homogenized rigid body and spring model (HRBSM)

    NASA Astrophysics Data System (ADS)

    Bertolesi, Elisa; Milani, Gabriele; Casolo, Siro

    2016-12-01

    A simple homogenized rigid body and spring model (HRBSM) is presented and applied for the non-linear dynamic analysis of 3D masonry structures. The approach, previously developed by the authors for the modeling of in-plane loaded walls is herein extended to real 3D buildings subjected to in- and out-of-plane deformation modes. The elementary cell is discretized by means of three-noded plane stress elements and non-linear interfaces. At a structural level, the non-linear analyses are performed replacing the homogenized orthotropic continuum with a rigid element and non-linear spring assemblage (RBSM) by means of which both in and out of plane mechanisms are allowed. All the simulations here presented are performed using the commercial software Abaqus. In order to validate the proposed model for the analyses of full scale structures subjected to seismic actions, two different examples are critically discussed, namely a church façade and an in-scale masonry building, both subjected to dynamic excitation. The results obtained are compared with experimental or numerical results available in literature.

  19. Dynamic pulse buckling of cylindrical shells under axial impact: A benchmark study of 2D and 3D finite element calculations

    SciTech Connect

    Hoffman, E.L.; Ammerman, D.J.

    1995-04-01

    A series of tests investigating dynamic pulse buckling of a cylindrical shell under axial impact is compared to several 2D and 3D finite element simulations of the event. The purpose of the work is to investigate the performance of various analysis codes and element types on a problem which is applicable to radioactive material transport packages, and ultimately to develop a benchmark problem to qualify finite element analysis codes for the transport package design industry. During the pulse buckling tests, a buckle formed at each end of the cylinder, and one of the two buckles became unstable and collapsed. Numerical simulations of the test were performed using PRONTO, a Sandia developed transient dynamics analysis code, and ABAQUS/Explicit with both shell and continuum elements. The calculations are compared to the tests with respect to deformed shape and impact load history.

  20. Dynamic topology and flux rope evolution during non-linear tearing of 3D null point current sheets

    SciTech Connect

    Wyper, P. F. Pontin, D. I.

    2014-10-15

    In this work, the dynamic magnetic field within a tearing-unstable three-dimensional current sheet about a magnetic null point is described in detail. We focus on the evolution of the magnetic null points and flux ropes that are formed during the tearing process. Generally, we find that both magnetic structures are created prolifically within the layer and are non-trivially related. We examine how nulls are created and annihilated during bifurcation processes, and describe how they evolve within the current layer. The type of null bifurcation first observed is associated with the formation of pairs of flux ropes within the current layer. We also find that new nulls form within these flux ropes, both following internal reconnection and as adjacent flux ropes interact. The flux ropes exhibit a complex evolution, driven by a combination of ideal kinking and their interaction with the outflow jets from the main layer. The finite size of the unstable layer also allows us to consider the wider effects of flux rope generation. We find that the unstable current layer acts as a source of torsional magnetohydrodynamic waves and dynamic braiding of magnetic fields. The implications of these results to several areas of heliophysics are discussed.

  1. 3-D localization of non-radioactive strontium in osteoarthritic bone: Role in the dynamic labeling of bone pathological changes.

    PubMed

    Panahifar, Arash; Cooper, David M L; Doschak, Michael R

    2015-11-01

    The study objective was to visualize regions of bone that undergo pathological mineralization and/or remodeling during pathogenesis of osteoarthritis, by employing non-radioactive strontium as a dynamic tracer of bone turnover. Post traumatic osteoarthritis was surgically induced in skeletally mature rats, followed by in vivo micro-CT imaging for 12 weeks to assess bone micro-structural changes. Rats either received strontium ranelate daily for the entire course of study or only last 10 days before euthanization. Distribution of strontium in bone was assessed in two and three dimensions, using electron probe micro-analysis (EPMA) and synchrotron dual energy K-edge subtraction micro-CT (SRμCT), respectively. Considerable early formation of osteophytes around the collateral ligament attachments and margins of articulating surfaces were observed, followed by subchondral sclerosis at the later stages. Accordingly, strontium was heavily incorporated by mineralizing osteophytes at 4, 8, and 12 weeks post-surgery, whereas subchondral bone only incorporated strontium between weeks 8-12.This study showed low dose stable strontium can effectively serve as a dynamic tracer of bone turnover to study pathological bone micro-structural changes, at resolution higher than nuclear medicine. Co-administration of strontium during therapeutic drug intervention may show enormous utility in assessing the efficacy of those compounds upon adaptive bone physiology.

  2. Study of 3-D Dynamic Roughness Effects on Flow Over a NACA 0012 Airfoil Using Large Eddy Simulations at Low Reynolds Numbers

    NASA Astrophysics Data System (ADS)

    Guda, Venkata Subba Sai Satish

    There have been several advancements in the aerospace industry in areas of design such as aerodynamics, designs, controls and propulsion; all aimed at one common goal i.e. increasing efficiency --range and scope of operation with lesser fuel consumption. Several methods of flow control have been tried. Some were successful, some failed and many were termed as impractical. The low Reynolds number regime of 104 - 105 is a very interesting range. Flow physics in this range are quite different than those of higher Reynolds number range. Mid and high altitude UAV's, MAV's, sailplanes, jet engine fan blades, inboard helicopter rotor blades and wind turbine rotors are some of the aerodynamic applications that fall in this range. The current study deals with using dynamic roughness as a means of flow control over a NACA 0012 airfoil at low Reynolds numbers. Dynamic 3-D surface roughness elements on an airfoil placed near the leading edge aim at increasing the efficiency by suppressing the effects of leading edge separation like leading edge stall by delaying or totally eliminating flow separation. A numerical study of the above method has been carried out by means of a Large Eddy Simulation, a mathematical model for turbulence in Computational Fluid Dynamics, owing to the highly unsteady nature of the flow. A user defined function has been developed for the 3-D dynamic roughness element motion. Results from simulations have been compared to those from experimental PIV data. Large eddy simulations have relatively well captured the leading edge stall. For the clean cases, i.e. with the DR not actuated, the LES was able to reproduce experimental results in a reasonable fashion. However DR simulation results show that it fails to reattach the flow and suppress flow separation compared to experiments. Several novel techniques of grid design and hump creation are introduced through this study.

  3. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  4. Distinct 3D Architecture and Dynamics of the Human HtrA2(Omi) Protease and Its Mutated Variants

    PubMed Central

    Gieldon, Artur; Zurawa-Janicka, Dorota; Jarzab, Miroslaw; Wenta, Tomasz; Golik, Przemyslaw; Dubin, Grzegorz; Lipinska, Barbara; Ciarkowski, Jerzy

    2016-01-01

    HtrA2(Omi) protease controls protein quality in mitochondria and plays a major role in apoptosis. Its HtrA2S306A mutant (with the catalytic serine routinely disabled for an X-ray study to avoid self-degradation) is a homotrimer whose subunits contain the serine protease domain (PD) and the regulatory PDZ domain. In the inactive state, a tight interdomain interface limits penetration of both PDZ-activating ligands and PD substrates into their respective target sites. We successfully crystalized HtrA2V226K/S306A, whose active counterpart HtrA2V226K has had higher proteolytic activity, suggesting higher propensity to opening the PD-PDZ interface than that of the wild type HtrA2. Yet, the crystal structure revealed the HtrA2V226K/S306A architecture typical of the inactive protein. To get a consistent interpretation of crystallographic data in the light of kinetic results, we employed molecular dynamics (MD). V325D inactivating mutant was used as a reference. Our simulations demonstrated that upon binding of a specific peptide ligand NH2-GWTMFWV-COOH, the PDZ domains open more dynamically in the wild type protease compared to the V226K mutant, whereas the movement is not observed in the V325D mutant. The movement relies on a PDZ vs. PD rotation which opens the PD-PDZ interface in a lid-like (budding flower-like in trimer) fashion. The noncovalent hinges A and B are provided by two clusters of interfacing residues, harboring V325D and V226K in the C- and N-terminal PD barrels, respectively. The opening of the subunit interfaces progresses in a sequential manner during the 50 ns MD simulation. In the systems without the ligand only minor PDZ shifts relative to PD are observed, but the interface does not open. Further activation-associated events, e.g. PDZ-L3 positional swap seen in any active HtrA protein (vs. HtrA2), were not observed. In summary, this study provides hints on the mechanism of activation of wtHtrA2, the dynamics of the inactive HtrA2V325D, but does not

  5. 3D Dynamic Rupture with Slip Reactivation and Ground Motion Simulations of the 2011 Mw 9.0 Tohoku Earthquake

    NASA Astrophysics Data System (ADS)

    Dalguer, Luis; Galvez, Percy

    2013-04-01

    Seismological, geodetic and tsunami observations, including kinematic source inversion and back-projection models of the giant megathrust 2011 Mw 9.0 Tohoku earthquake indicate that the earthquake featured complex rupture patterns, with multiple rupture fronts and rupture styles. The compilation of these studies reveals fundamentally three main feature: 1) spectacular large slip over 50m, 2) the existence of slip reactivation and 3) distinct regions of low and high frequency radiation. In this paper we investigate the possible mechanisms causing the slip reactivation. For this purpose we perform earthquakes dynamic rupture and strong ground motion simulations. We investigate two mechanisms as potential sources of slip reactivation: 1) The additional push to the earthquake rupture (slip reactivation) comes from the rupture front back propagating from the free-surface after rupturing the trench of the fault, a phenomena usually observed in dynamic rupture simulations of dipping faults (e.g. Dalguer et al. 2001). This mechanism produces smooth slip velocity reactivation with low frequency content. 2) Slip reactivation governed by the friction constitutive low (in the form given by Kanamori and Heaton, 2000) in which frictional strength drops initially to certain value, but then at large slips there is a second drop in frictional strength. The slip velocity caused by this mechanism is a sharp pulse capable to radiate stronger ground motion. Our simulations show that the second mechanism produces synthetic ground motion pattern along the Japanese cost of the Tohoku event consistent with the observed ground motion. In addition, the rupture pattern with slip reactivation is also consistent with kinematic source inversion models in which slip reactivation is observed. Therefore we propose that the slip reactivation observed in this earthquake is results of strong frictional strength drop, maybe caused by fault melting, pressurization, lubrication or other thermal weakening

  6. Construction of semi-dynamic model of subduction zone with given plate kinematics in 3D sphere

    NASA Astrophysics Data System (ADS)

    Morishige, M.; Honda, S.; Tackley, P. J.

    2010-09-01

    We present a semi-dynamic subduction zone model in a three-dimensional spherical shell. In this model, velocity is imposed on the top surface and in a small three-dimensional region around the shallow plate boundary while below this region, the slab is able to subduct under its own weight. Surface plate velocities are given by Euler's theorem of rigid plate rotation on a sphere. The velocity imposed in the region around the plate boundary is determined so that mass conservation inside the region is satisfied. A kinematic trench migration can be easily incorporated in this model. As an application of this model, mantle flow around slab edges is considered, and we find that the effect of Earth curvature is small by comparing our model with a similar one in a rectangular box, at least for the parameters used in this study. As a second application of the model, mantle flow around a plate junction is studied, and we find the existence of mantle return flow perpendicular to the plate boundary. Since this model can naturally incorporate the spherical geometry and plate movement on the sphere, it is useful for studying a specific subduction zone where the plate kinematics is well constrained.

  7. A 3D Hybrid Model for Tissue Growth: The Interplay between Cell Population and Mass Transport Dynamics

    PubMed Central

    Cheng, Gang; Markenscoff, Pauline; Zygourakis, Kyriacos

    2009-01-01

    Abstract To provide theoretical guidance for the design and in vitro cultivation of bioartificial tissues, we have developed a multiscale computational model that can describe the complex interplay between cell population and mass transport dynamics that governs the growth of tissues in three-dimensional scaffolds. The model has three components: a transient partial differential equation for the simultaneous diffusion and consumption of a limiting nutrient; a cellular automaton describing cell migration, proliferation, and collision; and equations that quantify how the varying nutrient concentration modulates cell division and migration. The hybrid discrete-continuous model was parallelized and solved on a distributed-memory multicomputer to study how transport limitations affect tissue regeneration rates under conditions encountered in typical bioreactors. Simulation results show that the severity of transport limitations can be estimated by the magnitude of two dimensionless groups: the Thiele modulus and the Biot number. Key parameters including the initial seeding mode, cell migration speed, and the hydrodynamic conditions in the bioreactor are shown to affect not only the overall rate, but also the pattern of tissue growth. This study lays the groundwork for more comprehensive models that can handle mixed cell cultures, multiple nutrients and growth factors, and other cellular processes, such as cell death. PMID:19619455

  8. Label-free fast 3D coherent imaging reveals pancreatic islet micro-vascularization and dynamic blood flow

    PubMed Central

    Berclaz, Corinne; Szlag, Daniel; Nguyen, David; Extermann, Jérôme; Bouwens, Arno; Marchand, Paul J.; Nilsson, Julia; Schmidt-Christensen, Anja; Holmberg, Dan; Grapin-Botton, Anne; Lasser, Theo

    2016-01-01

    In diabetes, pancreatic β-cells play a key role. These cells are clustered within structures called islets of Langerhans inside the pancreas and produce insulin, which is directly secreted into the blood stream. The dense vascularization of islets of Langerhans is critical for maintaining a proper regulation of blood glucose homeostasis and is known to be affected from the early stage of diabetes. The deep localization of these islets inside the pancreas in the abdominal cavity renders their in vivo visualization a challenging task. A fast label-free imaging method with high spatial resolution is required to study the vascular network of islets of Langerhans. Based on these requirements, we developed a label-free and three-dimensional imaging method for observing islets of Langerhans using extended-focus Fourier domain Optical Coherence Microscopy (xfOCM). In addition to structural imaging, this system provides three-dimensional vascular network imaging and dynamic blood flow information within islets of Langerhans. We propose our method to deepen the understanding of the interconnection between diabetes and the evolution of the islet vascular network. PMID:27895996

  9. Data-driven techniques for detecting dynamical state changes in noisily measured 3D single-molecule trajectories.

    PubMed

    Calderon, Christopher P

    2014-11-12

    Optical microscopes and nanoscale probes (AFM, optical tweezers, etc.) afford researchers tools capable of quantitatively exploring how molecules interact with one another in live cells. The analysis of in vivo single-molecule experimental data faces numerous challenges due to the complex, crowded, and time changing environments associated with live cells. Fluctuations and spatially varying systematic forces experienced by molecules change over time; these changes are obscured by "measurement noise" introduced by the experimental probe monitoring the system. In this article, we demonstrate how the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS) of Fox et al. [IEEE Transactions on Signal Processing 59] can be used to detect both subtle and abrupt state changes in time series containing "thermal" and "measurement" noise. The approach accounts for temporal dependencies induced by random and "systematic overdamped" forces. The technique does not require one to subjectively select the number of "hidden states" underlying a trajectory in an a priori fashion. The number of hidden states is simultaneously inferred along with change points and parameters characterizing molecular motion in a data-driven fashion. We use large scale simulations to study and compare the new approach to state-of-the-art Hidden Markov Modeling techniques. Simulations mimicking single particle tracking (SPT) experiments are the focus of this study.

  10. An approach for the 3D dynamic mathematical modelization of big structures with special respect to Ariane 5

    NASA Astrophysics Data System (ADS)

    Dieker, S.

    1993-10-01

    With special respect to Ariane 5, solutions are outlined that allow an improvement of the mathematical modeling and calculation in structural dynamics. Substructuring, and the application of modern component mode synthesis methods, are necessary. However, most of the methods result in modal degrees of freedom (DOF) of the interfaces and demand a high effort to couple the substructures. A general method is described that overcomes the disadvantages of the modal interface DOFs. As a result, the coupling of substructures is reduced to a simple addition of matrices. All reduced matrices of the substructures are real and symmetric. In a second section, special aspects of modeling are discussed. Structural aspects that are taken into account are the viscoelastic material behavior of the propellant of the solid rocket booster, the idealization of fluids and shells, and the fluid-structure-interaction. The coupling between axial, lateral and circumferential wave modes of Ariane 5 is no longer negligible; a hybrid description of the DOFs of the complete launcher by grid point displacements and Fourier series is possible, and offers an additional way to reduce the number of DOFs.

  11. Molecular dynamics studies of side chain effect on the beta-1,3-D-glucan triple helix in aqueous solution.

    PubMed

    Okobira, Tadashi; Miyoshi, Kentaro; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji

    2008-03-01

    beta-1,3-D-glucans have been isolated from fungi as right-handed 6(1) triple helices. They are categorized by the side chains bound to the main triple helix through beta-(1-->6)-D-glycosyl linkage. Indeed, since a glucose-based side chain is water soluble, the presence and frequency of glucose-based side chains give rise to significant variation in the physical properties of the glucan family. Curdlan has no side chains and self-assembles to form an water-insoluble triple helical structure, while schizophyllan, which has a 1,6-D-glucose side chain on every third glucose unit along the main chain, is completely water soluble. A thermal fluctuation in the optical rotatory dispersion is observed for the side chain, indicating probable co-operative interaction between the side chains and water molecules. This paper documents molecular dynamics simulations in aqueous solution for three models of the beta-1,3-D-glucan series: curdlan (no side chain), schizophyllan (a beta-(1-->6)-D-glycosyl side-chain at every third position), and a hypothetical triple helix with a side chain at every sixth main-chain glucose unit. A decrease was observed in the helical pitch as the population of the side chain increased. Two types of hydrogen bonding via water molecules, the side chain/main chain and the side chain/side chain hydrogen bonding, play an important role in determination of the triple helix conformation. The formation of a one-dimensional cavity of diameter about 3.5 A was observed in the schizophyllan triple helix, while curdlan showed no such cavity. The side chain/side chain hydrogen bonding in schizophyllan and the hypothetical beta-1,3-D-glucan triple helix could cause the tilt of the main-chain glucose residues to the helix.

  12. 3D simulation of boreal forests: structure and dynamics in complex terrain and in a changing climate

    NASA Astrophysics Data System (ADS)

    Brazhnik, Ksenia; Shugart, Herman H.

    2015-10-01

    To understand how the Siberian boreal forests may respond to near-future climate change, we employed a modeling approach and examined thresholds for significant and irreversible changes in forest structure and composition that are likely to be reached by mid-21st century. We applied the new spatially-explicit gap-dynamics model SIBBORK toward the understanding of how transition zones, namely treelines, which are notoriously undersampled and difficult to model, may change in the near future. We found that a 2 °C change in annual average air temperature significantly altered the structure, composition, and productivity of boreal forests stands both in the northern and the southern treeline ecotones. Treeline migration occurs at smaller temperature changes. Based on the current (1990-2014) observed warming trends, a 2 °C increase in annual average temperature compared to historical climate (1961-1990) is likely to be experienced at the northern treeline by 2040 and at the southern treeline by 2050. With regards to the forest biome, the most significant warming to date has been predicted and observed in Siberia. A 2 °C increase in annual average temperature compared to the second half of the 19th century is smaller than the predictions of even the most conservative RCP2.6 climate change scenario (IPCC 2013), and has previously been assumed to not likely result in dramatic changes to ecosystems or biome shifts. We show that at a +2 °C change, biome shifts from forest to steppe are likely to occur across a large area in southern Siberia. These changes in land cover will inevitably result in changes in the biodiversity, carbon storage, and the ecosystem services provided by the boreal forests of southern Siberia.

  13. Dynamic 3D visual analytic tools: a method for maintaining situational awareness during high tempo warfare or mass casualty operations

    NASA Astrophysics Data System (ADS)

    Lizotte, Todd E.

    2010-04-01

    Maintaining Situational Awareness (SA) is crucial to the success of high tempo operations, such as war fighting and mass casualty events (bioterrorism, natural disasters). Modern computer and software applications attempt to provide command and control manager's situational awareness via the collection, integration, interrogation and display of vast amounts of analytic data in real-time from a multitude of data sources and formats [1]. At what point does the data volume and displays begin to erode the hierarchical distributive intelligence, command and control structure of the operation taking place? In many cases, people tasked with making decisions, have insufficient experience in SA of high tempo operations and become overwhelmed easily as vast amounts of data begin to be displayed in real-time as an operation unfolds. In these situations, where data is plentiful and the relevance of the data changes rapidly, there is a chance for individuals to target fixate on those data sources they are most familiar. If these individuals fall into this type of pitfall, they will exclude other data that might be just as important to the success of the operation. To counter these issues, it is important that the computer and software applications provide a means for prompting its users to take notice of adverse conditions or trends that are critical to the operation. This paper will discuss a new method of displaying data called a Crisis ViewTM, that monitors critical variables that are dynamically changing and allows preset thresholds to be created to prompt the user when decisions need to be made and when adverse or positive trends are detected. The new method will be explained in basic terms, with examples of its attributes and how it can be implemented.

  14. Gender Dimorphic ACL Strain In Response to Combined Dynamic 3D Knee Joint Loading: Implications for ACL Injury Risk

    PubMed Central

    Mizuno, Kiyonori; Andrish, Jack T.; van den Bogert, Antonie J.; McLean, Scott G.

    2009-01-01

    While gender-based differences in knee joint anatomies/laxities are well documented, the potential for them to precipitate gender-dimorphic ACL loading and resultant injury risk has not been considered. To this end, we generated gender-specific models of ACL strain as a function of any six degrees of freedom (6DOF) knee joint load state via a combined cadaveric and analytical approach. Continuously varying joint forces and torques were applied to five male and five female cadaveric specimens and recorded along with synchronous knee flexion and ACL strain data. All data (~10,000 samples) were submitted to specimen-specific regression analyses, affording ACL strain predictions as a function of the combined 6 DOF knee loads. Following individual model verifications, generalized gender-specific models were generated and subjected to 6 DOF external load scenarios consistent with both a clinical examination and a dynamic sports maneuver. The ensuing model-based strain predictions were subsequently examined for gender-based discrepancies. Male and female specimen specific models predicted ACL strain within 0.51% ± 0.10% and 0.52% ± 0.07% of the measured data respectively, and explained more than 75% of the associated variance in each case. Predicted female ACL strains were also significantly larger than respective male values for both of simulated 6 DOF load scenarios. Outcomes suggest that the female ACL will rupture in response to comparatively smaller external load applications. Future work must address the underlying anatomical/laxity contributions to knee joint mechanical and resultant ACL loading, ultimately affording prevention strategies that may cater to individual joint vulnerabilities. PMID:19464897

  15. 3D Dynamic Rupture Simulation Across a Complex Fault System: the Mw7.0, 2010, Haiti Earthquake

    NASA Astrophysics Data System (ADS)

    Douilly, R.; Aochi, H.; Calais, E.; Freed, A. M.

    2013-12-01

    Earthquakes ruptures sometimes take place on a secondary fault and surprisingly do not activate an adjacent major one. The 1989 Loma Prieta earthquake is a classic case where rupture occurred on a blind thrust while the adjacent San Andreas Fault was not triggered during the process. Similar to Loma Prieta, the Mw7.0, January 12 2010, Haiti earthquake also ruptured a secondary blind thrust, the Léogâne fault, adjacent to the main plate boundary, the Enriquillo Plantain Garden Fault, which did not rupture during this event. Aftershock relocalizations delineate the Léogâne rupture with two north dipping segments with slightly different dip, where the easternmost segment had mostly dip-slip motion and the westernmost one had mostly strike-slip motion. In addition, an offshore south dipping structure inferred from the aftershocks to the west of the rupture zone coincides with the offshore Trois Baies reverse fault, a region of increase in Coulomb stress increase. In this study, we investigate the rupture dynamics of the Haiti earthquake in a complex fault system of multiple segments identified by the aftershock relocations. We suppose a background stress regime that is consistent with the type of motion of each fault and with the regional tectonic regime. We initiate a nucleation on the east segment of the Léogâne fault by defining a circular region with a 2 km radius where shear stress is slightly greater than the yield stress. By varying friction on faults and background stress, we find a range of plausible scenarios. In the absence of near-field seismic records of the event, we score the different models against the static deformation field derived from GPS and InSAR at the surface. All the plausible simulations show that the rupture propagates from the eastern to the western segment along the Léogâne fault, but not on the Enriquillo fault nor on the Trois Baies fault. The best-fit simulation shows a significant increase of shear stresses on the Trois Baies

  16. 3D Dynamic Rupture process ans Near Source Ground Motion Simulation Using the Discrete Element Method: Application to the 1999 Chi-chi and 2000 Tottori Earthquakes

    NASA Astrophysics Data System (ADS)

    Dalguer Gudiel, L. A.; Irikura, K.

    2001-12-01

    We performed a 3D model to simulate the dynamic rupture of a pre-existing fault and near-source ground motion of actual earthquakes solving the elastodynamic equation of motion using the 3D Discrete Element Method (DEM). The DEM is widely employed in engineering to designate lumped mass models in a truss arrangement, as opposed to FEM (Finite Element) models that may also consist of lumped masses, but normally require to mount a full stiffness matrix for response determination. The term has also been used for models of solids consisting of assemblies of discrete elements, such as spheres in elastic contact, employed in the analysis of perforation or penetration of concrete or rock. It should be noted that the designation Lattice Models, common in Physics, may be more adequate, although it omits reference to a fundamental property of the approach, which is the lumped-mass representation. In the present DEM formulation, the method models any orthotropic elastic solid. It is constructed by a three dimensional periodic truss-like structures using cubic elements that consists of lumping masses in nodal points, which are interconnected by unidimensional elements. The method was previously used in 2D to simulate in a simplified way the 1999 Chi-chi (Taiwan) earthquake (Dalguer et. al., 2000). Now the method was extended to resolve 3D problems. We apply the model to simulate the dynamic rupture process and near source ground motion of the 1999 Chi-chi (Taiwan) and the 2000 Tottori (Japan) earthquakes. The attractive feature in the problem under consideration is the possibility of introducing internal cracks or fractures with little computational effort and without increasing the number of degrees of freedom. For the 3D dynamic spontaneous rupture simulation of these eartquakes we need to know: the geometry of the fault, the initial stress distribution along the fault, the stress drop distribution, the strength of the fault to break and the critical slip (because slip

  17. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  18. In situ UV curable 3D printing of multi-material tri-legged soft bot with spider mimicked multi-step forward dynamic gait

    NASA Astrophysics Data System (ADS)

    Zeb Gul, Jahan; Yang, Bong-Su; Yang, Young Jin; Chang, Dong Eui; Choi, Kyung Hyun

    2016-11-01

    Soft bots have the expedient ability of adopting intricate postures and fitting in complex shapes compared to mechanical robots. This paper presents a unique in situ UV curing three-dimensional (3D) printed multi-material tri-legged soft bot with spider mimicked multi-step dynamic forward gait using commercial bio metal filament (BMF) as an actuator. The printed soft bot can produce controllable forward motion in response to external signals. The fundamental properties of BMF, including output force, contractions at different frequencies, initial loading rate, and displacement-rate are verified. The tri-pedal soft bot CAD model is designed inspired by spider’s legged structure and its locomotion is assessed by simulating strain and displacement using finite element analysis. A customized rotational multi-head 3D printing system assisted with multiple wavelength’s curing lasers is used for in situ fabrication of tri-pedal soft-bot using two flexible materials (epoxy and polyurethane) in three layered steps. The size of tri-pedal soft-bot is 80 mm in diameter and each pedal’s width and depth is 5 mm × 5 mm respectively. The maximum forward speed achieved is 2.7 mm s-1 @ 5 Hz with input voltage of 3 V and 250 mA on a smooth surface. The fabricated tri-pedal soft bot proved its power efficiency and controllable locomotion at three input signal frequencies (1, 2, 5 Hz).

  19. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    NASA Astrophysics Data System (ADS)

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

    2011-09-01

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

  20. Dynamical microstructure formation in 3D directional solidification of transparent model alloys: in situ characterization in DECLIC Directional Solidification Insert under diffusion transport in microgravity

    NASA Astrophysics Data System (ADS)

    Bergeon, N.; Mota, F. L.; Chen, L.; Tourret, D.; Debierre, J. M.; Guérin, R.; Karma, A.; Billia, B.; Trivedi, R.

    2015-06-01

    To clarify and characterize the fundamental physical mechanisms active in the dynamical formation of three-dimensional (3D) arrays of cells and dendrites under diffusive growth conditions, in situ monitoring of series of experiments on transparent model alloy succinonitrile - 0.24 wt% camphor was carried out under low gravity in the DECLIC Directional Solidification Insert on-board the International Space Station. These experiments offered the very unique opportunity to in situ observe and characterize the whole development of the microstructure in extended 3D patterns. The experimental methods will be first briefly described, including in particular the observation modes and the image analysis procedures developed to quantitatively characterize the patterns. Microgravity environment provided the conditions to get quantitative benchmark data: homogeneous patterns corresponding to homogeneous values of control parameters along the whole interface were obtained. The sequence of microstructure formation will be presented as well as the evolution of the primary spacing which is one of the most important pattern characteristic. Time evolution of this primary spacing during the microstructure development will be analysed to identify the mechanisms of spacing selection and adjustment; the importance of the macroscopic interfacial curvature will be pointed out.

  1. A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors.

    PubMed

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-11-01

    Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.

  2. Characterization of fracture reservoirs using static and dynamic data: From sonic and 3D seismic to permeability distribution. Annual report, March 1, 1996--February 28, 1997

    SciTech Connect

    Parra, J.O.; Collier, H.A.; Owen, T.E.

    1997-06-01

    In low porosity, low permeability zones, natural fractures are the primary source of permeability which affect both production and injection of fluids. The open fractures do not contribute much to porosity, but they provide an increased drainage network to any porosity. They also may connect the borehole to remote zones of better reservoir characteristics. An important approach to characterizing the fracture orientation and fracture permeability of reservoir formations is one based on the effects of such conditions on the propagation of acoustic and seismic waves in the rock. The project is a study directed toward the evaluation of acoustic logging and 3D-seismic measurement techniques as well as fluid flow and transport methods for mapping permeability anisotropy and other petrophysical parameters for the understanding of the reservoir fracture systems and associated fluid dynamics. The principal application of these measurement techniques and methods is to identify and investigate the propagation characteristics of acoustic and seismic waves in the Twin Creek hydrocarbon reservoir owned by Union Pacific Resources (UPR) and to characterize the fracture permeability distribution using production data. This site is located in the overthrust area of Utah and Wyoming. UPR drilled six horizontal wells, and presently UPR has two rigs running with many established drill hole locations. In addition, there are numerous vertical wells that exist in the area as well as 3D seismic surveys. Each horizontal well contains full FMS logs and MWD logs, gamma logs, etc.

  3. Vertical temperature dynamics in the Northern Baltic Sea based on 3D modelling and data from shallow-water Argo floats

    NASA Astrophysics Data System (ADS)

    Westerlund, Antti; Tuomi, Laura

    2016-06-01

    3D hydrodynamic models often produce errors in the depth of the mixed layer and the vertical density structure. We used the 3D hydrodynamic model NEMO to investigate the effect of vertical turbulence parameterisations on seasonal temperature dynamics in the Bothnian Sea, Baltic Sea for the years 2012 and 2013. We used vertical profiles from new shallow-water Argo floats, operational in the area since 2012, to validate our model. We found that NEMO was able to reproduce the general features of the seasonal temperature variations in the study area, when meteorological forcing was accurate. The k-ε and k-ω schemes were selected for a more detailed analysis. Both schemes showed clear differences, but neither proved superior. While sea surface temperature was better simulated with the k-ω scheme, thermocline depth was clearly better with the k-ε scheme. We investigated the effect of wave-breaking on the mixing of the surface layer. The Craig and Banner parameterisation clearly improved the representation of thermocline depth. However, further tuning of the mixing parameterisations for the Baltic Sea is needed to better simulate the vertical temperature structure. We found the autonomous Baltic Sea Argo floats valuable for model validation and performance evaluation.

  4. Comparison of Galunggung1982-83 and Eyjafjalla-2010 Eruptions: definition of eruption dynamics from 3D Ash Surface Morphology

    NASA Astrophysics Data System (ADS)

    Aydar, E.; Höskuldsson, A.; Ersoy, O.; Gourgaud, A.

    2012-04-01

    We consider that all works, concepts on aviation safety, security codes, establishment of warning systems etc begin in 1982, when two commercial jumbo jets en route to Australia across Indonesia suffered loss of engine thrust from ingesting volcanic ash from the erupting Galunggung Volcano, Java, and descended more than 20,000 ft before the engines could be restarted (Casadevall, 1991). It is not the only incident of this kind but this Galunggung eruption had a pionner character attracting attention on aviation safety against volcanic eruptions in international community. As the needs for precautions on aviation safety against volcanic ash encounters began with Galunggung 1982 eruption and as we all concerned by the measures taken by ICAO due to Eyjafjallajökull-2010 eruption, we aimed to investigate this last huge airspace perturbing eruption and compare the volcanic ashes produced by those two eruptions. Volcanic ash characterization should be most important parameter to understand how the eruption concerned unrolled. Galunggung 1982-83 eruption was exceptionally long, lasting about nine months between 5 April 1982-8 January 1983). During this well known eruption, the composition of the erupted magma evolved from andesite (58% SiO2) to Mg-rich basalt (47% SiO2), while the style of the eruption changed drastically through time (Katili and Sudrdajat, 1984; Sudrajat and Tilling, 1984; Gourgaud et al., 1989 gourgaud etal 2000). Paralel to chemical changes and water consumption, eruption dynamic was also changed and occured in three eruption phases with different eruptive styles as an initial Vulcanian phase (5 April-13 May), a phreatomagmatic phase (17 May-28 October) and a Strombolian phase (3 November-8 January), have been recognized (Katili and Sudradjat,1984). We examined the surficial morphological features of proximal tephra collected from Galunggung and Eyjafjalla volcanoes. Surface texture and morphology of volcanic ash particles change according to various

  5. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  6. Lagrangian advection scheme with shape matrix (LASM) v0.2: interparcel mixing, physics-dynamics coupling and 3-D extension

    NASA Astrophysics Data System (ADS)

    Dong, L.; Wang, B.; Liu, L.; Huang, Y.

    2015-08-01

    The interparcel mixing algorithm in the Lagrangian advection scheme with shape matrix (LASM) is updated to make the scheme more robust. The linear degeneration criterion is replaced by the maximum deviation of the skeleton points so that the new algorithm is more effective in controlling the shape of parcels, which is vital for long time simulation. LASM is inherently shape-preserving without any complicated filter or limiter, and it is linear. This fact contributes to the ability to preserve the sum of multiple tracers exactly on the parcels in LASM. A newly proposed terminator "toy"-chemistry test is used to test LASM, which shows that LASM can preserve the weighted sum of two reactive species precisely. The physics-dynamics coupling (i.e., tendency evaluation type) is also discussed. A flow generated by a WRF large-eddy simulation is also used to test the 3-D extension of LASM.

  7. Comparison of the transcriptomic profile of hepatic human induced pluripotent stem like cells cultured in plates and in a 3D microscale dynamic environment.

    PubMed

    Leclerc, Eric; Kimura, Keiichi; Shinohara, Marie; Danoy, Mathieu; Le Gall, Morgane; Kido, Taketomo; Miyajima, Atsushi; Fujii, Teruo; Sakai, Yasuyuki

    2017-01-01

    We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells. However, the overall tissue still presented characteristic of immature and foetal patterns. Nevertheless, the biochip culture provided a specific micro-environment in which a complex multicellular differentiation toward liver could be oriented.

  8. A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study.

    PubMed

    Choubey, Sanjay K; Jeyaraman, Jeyakanthan

    2016-11-01

    Deregulated epigenetic activity of Histone deacetylase 1 (HDAC1) in tumor development and carcinogenesis pronounces it as promising therapeutic target for cancer treatment. HDAC1 has recently captured the attention of researchers owing to its decisive role in multiple types of cancer. In the present study a multistep framework combining ligand based 3D-QSAR, molecular docking and Molecular Dynamics (MD) simulation studies were performed to explore potential compound with good HDAC1 binding affinity. Four different pharmacophore hypotheses Hypo1 (AADR), Hypo2 (AAAH), Hypo3 (AAAR) and Hypo4 (ADDR) were obtained. The hypothesis Hypo1 (AADR) with two hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatics ring (R) was selected to build 3D-QSAR model on the basis of statistical parameter. The pharmacophore hypothesis produced a statistically significant QSAR model, with co-efficient of correlation r(2)=0.82 and cross validation correlation co-efficient q(2)=0.70. External validation result displays high predictive power with r(2) (o) value of 0.88 and r(2) (m) value of 0.58 to carry out further in silico studies. Virtual screening result shows ZINC70450932 as the most promising lead where HDAC1 interacts with residues Asp99, His178, Tyr204, Phe205 and Leu271 forming seven hydrogen bonds. A high docking score (-11.17kcal/mol) and lower docking energy -37.84kcal/mol) displays the binding efficiency of the ligand. Binding free energy calculation was done using MM/GBSA to access affinity of ligands towards protein. Density Functional Theory was employed to explore electronic features of the ligands describing intramolcular charge transfer reaction. Molecular dynamics simulation studies at 50ns display metal ion (Zn)-ligand interaction which is vital to inhibit the enzymatic activity of the protein.

  9. Dynamic pulse buckling of cylindrical shells under axial impact: A comparison of 2D and 3D finite element calculations with experimental data

    SciTech Connect

    Hoffman, E.L.; Ammerman, D.J.

    1995-04-01

    A series of tests investigating dynamic pulse buckling of a cylindrical shell under axial impact is compared to several 2D and 3D finite element simulations of the event. The purpose of the work is to investigate the performance of various analysis codes and element types on a problem which is applicable to radioactive material transport packages, and ultimately to develop a benchmark problem to qualify finite element analysis codes for the transport package design industry. Four axial impact tests were performed on 4 in-diameter, 8 in-long, 304 L stainless steel cylinders with a 3/16 in wall thickness. The cylinders were struck by a 597 lb mass with an impact velocity ranging from 42.2 to 45.1 ft/sec. During the impact event, a buckle formed at each end of the cylinder, and one of the two buckles became unstable and collapsed. The instability occurred at the top of the cylinder in three tests and at the bottom in one test. Numerical simulations of the test were performed using the following codes and element types: PRONTO2D with axisymmetric four-node quadrilaterals; PRONTO3D with both four-node shells and eight-node hexahedrons; and ABAQUS/Explicit with axisymmetric two-node shells and four-node quadrilaterals, and 3D four-node shells and eight-node hexahedrons. All of the calculations are compared to the tests with respect to deformed shape and impact load history. As in the tests, the location of the instability is not consistent in all of the calculations. However, the calculations show good agreement with impact load measurements with the exception of an initial load spike which is proven to be the dynamic response of the load cell to the impact. Finally, the PRONIT02D calculation is compared to the tests with respect to strain and acceleration histories. Accelerometer data exhibited good qualitative agreement with the calculations. The strain comparisons show that measurements are very sensitive to gage placement.

  10. Reconstructing the retreat dynamics of the Bjørnøyrenna Ice Stream based on new 3D seismic data from the central Barents Sea

    NASA Astrophysics Data System (ADS)

    Piasecka, Emilia D.; Winsborrow, Monica C. M.; Andreassen, Karin; Stokes, Chris R.

    2016-11-01

    The stability of contemporary ice sheets is influenced by the discharge from ice streams - corridors of fast-flowing ice bounded by ice flowing an order of magnitude slower. Reconstructions of palaeo-ice stream dynamics contribute to our understanding of ice stream sensitivity to the ocean-climate system and can aid in the numerical modelling and prediction of future changes in contemporary ice sheets. Here we use 3D seismic data, covering 13,000 km2 in the central Bjørnøyrenna (Bear Island Trough), Barents Sea, to investigate the record of ice streaming preserved on the seafloor and on a buried palaeo-seafloor surface. The unusually broad coverage and high resolution of the dataset, as well as its location in the central area of the trough, enables improved reconstruction of dynamics of the former Bjørnøyrenna Ice Stream in terms of number of streaming events, their trajectory, and their relative age sequence during deglaciation. Our results reveal major changes in the configuration and flow dynamics of the ice stream, with up to 10 flow-switching events identified. For the first time, we also document ice streaming sourced from the eastern Barents Sea around the time of the LGM. This high degree of flow variability is suggested to have resulted from climate-driven changes in ice sheet geometry (and ice divide migration), and variations in topography that influenced calving at the ice stream terminus.

  11. 3D Reconstruction of Chick Embryo Vascular Geometries Using Non-invasive High-Frequency Ultrasound for Computational Fluid Dynamics Studies.

    PubMed

    Tan, Germaine Xin Yi; Jamil, Muhammad; Tee, Nicole Gui Zhen; Zhong, Liang; Yap, Choon Hwai

    2015-11-01

    Recent animal studies have provided evidence that prenatal blood flow fluid mechanics may play a role in the pathogenesis of congenital cardiovascular malformations. To further these researches, it is important to have an imaging technique for small animal embryos with sufficient resolution to support computational fluid dynamics studies, and that is also non-invasive and non-destructive to allow for subject-specific, longitudinal studies. In the current study, we developed such a technique, based on ultrasound biomicroscopy scans on chick embryos. Our technique included a motion cancelation algorithm to negate embryonic body motion, a temporal averaging algorithm to differentiate blood spaces from tissue spaces, and 3D reconstruction of blood volumes in the embryo. The accuracy of the reconstructed models was validated with direct stereoscopic measurements. A computational fluid dynamics simulation was performed to model fluid flow in the generated construct of a Hamburger-Hamilton (HH) stage 27 embryo. Simulation results showed that there were divergent streamlines and a low shear region at the carotid duct, which may be linked to the carotid duct's eventual regression and disappearance by HH stage 34. We show that our technique has sufficient resolution to produce accurate geometries for computational fluid dynamics simulations to quantify embryonic cardiovascular fluid mechanics.

  12. Intra-operative 2-D ultrasound and dynamic 3-D aortic model registration for magnetic navigation of transcatheter aortic valve implantation.

    PubMed

    Luo, Zhe; Cai, Junfeng; Peters, Terry M; Gu, Lixu

    2013-11-01

    We propose a navigation system for transcatheter aortic valve implantation that employs a magnetic tracking system (MTS) along with a dynamic aortic model and intra-operative ultrasound (US) images. This work is motivated by the desire of our cardiology and cardiac surgical colleagues to minimize or eliminate the use of radiation in the interventional suite or operating room. The dynamic 3-D aortic model is constructed from a preoperative 4-D computed tomography dataset that is animated in synchrony with the real time electrocardiograph input of patient, and then preoperative planning is performed to determine the target position of the aortic valve prosthesis. The contours of the aortic root are extracted automatically from short axis US images in real-time for registering the 2-D intra-operative US image to the preoperative dynamic aortic model. The augmented MTS guides the interventionist during positioning and deployment of the aortic valve prosthesis to the target. The results of the aortic root segmentation algorithm demonstrate an error of 0.92±0.85 mm with a computational time of 36.13±6.26 ms. The navigation approach was validated in porcine studies, yielding fiducial localization errors, target registration errors, deployment distance, and tilting errors of 3.02±0.39 mm, 3.31±1.55 mm, 3.23±0.94 mm, and 5.85±3.06(°) , respectively.

  13. Evaluation of the scale dependent dynamic SGS model in the open source code caffa3d.MBRi in wall-bounded flows

    NASA Astrophysics Data System (ADS)

    Draper, Martin; Usera, Gabriel

    2015-04-01

    The Scale Dependent Dynamic Model (SDDM) has been widely validated in large-eddy simulations using pseudo-spectral codes [1][2][3]. The scale dependency, particularly the potential law, has been proved also in a priori studies [4][5]. To the authors' knowledge there have been only few attempts to use the SDDM in finite difference (FD) and finite volume (FV) codes [6][7], finding some improvements with the dynamic procedures (scale independent or scale dependent approach), but not showing the behavior of the scale-dependence parameter when using the SDDM. The aim of the present paper is to evaluate the SDDM in the open source code caffa3d.MBRi, an updated version of the code presented in [8]. caffa3d.MBRi is a FV code, second-order accurate, parallelized with MPI, in which the domain is divided in unstructured blocks of structured grids. To accomplish this, 2 cases are considered: flow between flat plates and flow over a rough surface with the presence of a model wind turbine, taking for this case the experimental data presented in [9]. In both cases the standard Smagorinsky Model (SM), the Scale Independent Dynamic Model (SIDM) and the SDDM are tested. As presented in [6][7] slight improvements are obtained with the SDDM. Nevertheless, the behavior of the scale-dependence parameter supports the generalization of the dynamic procedure proposed in the SDDM, particularly taking into account that no explicit filter is used (the implicit filter is unknown). [1] F. Porté-Agel, C. Meneveau, M.B. Parlange. "A scale-dependent dynamic model for large-eddy simulation: application to a neutral atmospheric boundary layer". Journal of Fluid Mechanics, 2000, 415, 261-284. [2] E. Bou-Zeid, C. Meneveau, M. Parlante. "A scale-dependent Lagrangian dynamic model for large eddy simulation of complex turbulent flows". Physics of Fluids, 2005, 17, 025105 (18p). [3] R. Stoll, F. Porté-Agel. "Dynamic subgrid-scale models for momentum and scalar fluxes in large-eddy simulations of

  14. AE3D

    SciTech Connect

    Spong, Donald A

    2016-06-20

    AE3D solves for the shear Alfven eigenmodes and eigenfrequencies in a torodal magnetic fusion confinement device. The configuration can be either 2D (e.g. tokamak, reversed field pinch) or 3D (e.g. stellarator, helical reversed field pinch, tokamak with ripple). The equations solved are based on a reduced MHD model and sound wave coupling effects are not currently included.

  15. Studies of new fused benzazepine as selective dopamine D3 receptor antagonists using 3D-QSAR, molecular docking and molecular dynamics.

    PubMed

    Liu, Jing; Li, Yan; Zhang, Shuwei; Xiao, Zhengtao; Ai, Chunzhi

    2011-02-18

    In recent years, great interest has been paid to the development of compounds with high selectivity for central dopamine (DA) D3 receptors, an interesting therapeutic target in the treatment of different neurological disorders. In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), homology modeling, molecular docking and molecular dynamics (MD) were carried out to reveal the requisite 3D structural features for activity. Our results show that both the receptor-based (Q(2) = 0.603, R(2) (ncv) = 0.829, R(2) (pre) = 0.690, SEE = 0.316, SEP = 0.406) and ligand-based 3D-QSAR models (Q(2) = 0.506, R(2) (ncv) =0.838, R(2) (pre) = 0.794, SEE = 0.316, SEP = 0.296) are reliable with proper predictive capacity. In addition, a combined analysis between the CoMFA, CoMSIA contour maps and MD results with a homology DA receptor model shows that: (1) ring-A, position-2 and R(3) substituent in ring-D are crucial in the design of antagonists with higher activity; (2) more bulky R(1) substituents (at position-2 of ring-A) of antagonists may well fit in the binding pocket; (3) hydrophobicity represented by MlogP is important for building satisfactory QSAR models; (4) key amino acids of the binding pocket are CYS101, ILE105, LEU106, VAL151, PHE175, PHE184, PRO254 and ALA251. To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists. These results might provide information for a better understanding of the mechanism of antagonism and thus be helpful in designing new potent DA D3 antagonists.

  16. XML3D and Xflow: combining declarative 3D for the Web with generic data flows.

    PubMed

    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.

  17. Dynamics of pickup ion velocity distribution function in Titan's plasma environment (TA encounter): 3D hybrid kinetic modeling and comparison with CAPS observations

    NASA Astrophysics Data System (ADS)

    Simpson, D. G.; Lipatov, A. S.; Sittler, E. C.; Hartle, R. E.; Cooper, J. F.

    2013-12-01

    Wave-particle interactions play a very important role in the plasma dynamics near Titan: mass loading, excitation of the low-frequency waves and the formation of the particle velocity distribution function, e.g. ring/shell-like distributions, etc. The kinetic approach is important for estimation of the collision processes e.g. a charge exchange. The particle velocity distribution function also plays a key role for understanding the observed particle fluxes. In this report we discuss the ion velocity distribution function dynamics from 3D hybrid modeling. The modeling is based on recent analysis of the Cassini Plasma Spectrometer (CAPS) ion measurements during the TA flyby. In our model the background ions, all pickup ions, and ionospheric ions are considered as particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. The temperatures of the background electrons and pickup electrons were also included into the generalized Ohm's law. We also take into account the collisions between the ions and neutrals. We use Chamberlain profiles for the exosphere's components and include a simple ionosphere model with M=28 ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Our modeling shows that interaction between background plasma and pickup ions H+, H2+, CH4+ and N2+ has a more complicated structure than was observed in the T9 flyby and modeling due to the large gyroradius of the background O+ ions [1,2,3,4]. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS TA observations. We also compare our kinetic modeling with other hybrid and MHD modeling of Titan's environment. References [1] Sittler, E.C., et al., Energy Deposition Processes in Titan's Upper Atmosphere and Its Induced Magnetosphere. In: Titan from Cassini-Huygens, Brown, R.H., Lebreton J.P., Waite, J.H., Eds

  18. Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

    PubMed

    Saraee, Mahdieh B; Korayem, Moharam H

    2015-08-07

    Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle.

  19. Integrating focal adhesion dynamics, cytoskeleton remodeling, and actin motor activity for predicting cell migration on 3D curved surfaces of the extracellular matrix.

    PubMed

    Kim, Min-Cheol; Kim, Choong; Wood, Levi; Neal, Devin; Kamm, Roger D; Asada, H Harry

    2012-11-01

    An integrative cell migration model incorporating focal adhesion (FA) dynamics, cytoskeleton and nucleus remodeling and actin motor activity is developed for predicting cell migration behaviors on 3-dimensional curved surfaces, such as cylindrical lumens in the 3-D extracellular matrix (ECM). The work is motivated by 3-D microfluidic migration experiments suggesting that the migration speed and direction may vary depending on the cross sectional shape of the lumen along which the cell migrates. In this paper, the mechanical structure of the cell is modeled as double elastic membranes of cell and nucleus. The two elastic membranes are connected by stress fibers, which are extended from focal adhesions on the cell surface to the nuclear membrane. The cell deforms and gains traction as transmembrane integrins distributed over the outer cell membrane bind to ligands on the ECM, form focal adhesions, and activate stress fibers. Probabilities at which integrin ligand-receptor bonds are formed as well as ruptures are affected by the surface geometry, resulting in diverse migration behaviors that depend on the curvature of the surface. Monte Carlo simulations of the integrative model reveal that (a) the cell migration speed is dependent on the cross sectional area of the lumen with a maximum speed at a particular diameter or width, (b) as the lumen diameter increases, the cell tends to spread and migrate around the circumference of the lumen, while it moves in the longitudinal direction as the lumen diameter narrows, (c) once the cell moves in one direction, it tends to stay migrating in the same direction despite the stochastic nature of migration. The relationship between the cell migration speed and the lumen width agrees with microfluidic experimental data for cancer cell migration.

  20. Robust patella motion tracking using intensity-based 2D-3D registration on dynamic bi-plane fluoroscopy: towards quantitative assessment in MPFL reconstruction surgery

    NASA Astrophysics Data System (ADS)

    Otake, Yoshito; Esnault, Matthieu; Grupp, Robert; Kosugi, Shinichi; Sato, Yoshinobu

    2016-03-01

    The determination of in vivo motion of multiple-bones using dynamic fluoroscopic images and computed tomography (CT) is useful for post-operative assessment of orthopaedic surgeries such as medial patellofemoral ligament reconstruction. We propose a robust method to measure the 3D motion of multiple rigid objects with high accuracy using a series of bi-plane fluoroscopic images and a multi-resolution, intensity-based, 2D-3D registration. A Covariance Matrix Adaptation Evolution Strategy (CMA-ES) optimizer was used with a gradient correlation similarity metric. Four approaches to register three rigid objects (femur, tibia-fibula and patella) were implemented: 1) an individual bone approach registering one bone at a time, each with optimization of a six degrees of freedom (6DOF) parameter, 2) a sequential approach registering one bone at a time but using the previous bone results as the background in DRR generation, 3) a simultaneous approach registering all the bones together (18DOF) and 4) a combination of the sequential and the simultaneous approaches. These approaches were compared in experiments using simulated images generated from the CT of a healthy volunteer and measured fluoroscopic images. Over the 120 simulated frames of motion, the simultaneous approach showed improved registration accuracy compared to the individual approach: with less than 0.68mm root-mean-square error (RMSE) for translation and less than 1.12° RMSE for rotation. A robustness evaluation was conducted with 45 trials of a randomly perturbed initialization showed that the sequential approach improved robustness significantly (74% success rate) compared to the individual bone approach (34% success) for patella registration (femur and tibia-fibula registration had a 100% success rate with each approach).

  1. 3D discrete angiogenesis dynamic model and stochastic simulation for the assessment of blood perfusion coefficient and impact on heat transfer between nanoparticles and malignant tumors.

    PubMed

    Yifat, Jonathan; Gannot, Israel

    2015-03-01

    Early detection of malignant tumors plays a crucial role in the survivability chances of the patient. Therefore, new and innovative tumor detection methods are constantly searched for. Tumor-specific magnetic-core nano-particles can be used with an alternating magnetic field to detect and treat tumors by hyperthermia. For the analysis of the method effectiveness, the bio-heat transfer between the nanoparticles and the tissue must be carefully studied. Heat diffusion in biological tissue is usually analyzed using the Pennes Bio-Heat Equation, where blood perfusion plays an important role. Malignant tumors are known to initiate an angiogenesis process, where endothelial cell migration from neighboring vasculature eventually leads to the formation of a thick blood capillary network around them. This process allows the tumor to receive its extensive nutrition demands and evolve into a more progressive and potentially fatal tumor. In order to assess the effect of angiogenesis on the bio-heat transfer problem, we have developed a discrete stochastic 3D model & simulation of tumor-induced angiogenesis. The model elaborates other angiogenesis models by providing high resolution 3D stochastic simulation, capturing of fine angiogenesis morphological features, effects of dynamic sprout thickness functions, and stochastic parent vessel generator. We show that the angiogenesis realizations produced are well suited for numerical bio-heat transfer analysis. Statistical study on the angiogenesis characteristics was derived using Monte Carlo simulations. According to the statistical analysis, we provide analytical expression for the blood perfusion coefficient in the Pennes equation, as a function of several parameters. This updated form of the Pennes equation could be used for numerical and analytical analyses of the proposed detection and treatment method.

  2. A new back-and-forth iterative method for time-reversed convection modeling: Implications for the Cenozoic evolution of 3-D structure and dynamics of the mantle

    NASA Astrophysics Data System (ADS)

    Glišović, Petar; Forte, Alessandro M.

    2016-06-01

    The 3-D distribution of buoyancy in the convecting mantle drives a suite of convection-related manifestations. Although seismic tomography is providing increasingly resolved images of the present-day mantle heterogeneity, the distribution of mantle density variations in the geological past is unknown, and, by implication, this is true for the convection-related observables. The one major exception is tectonic plate motions, since geologic data are available to estimate their history and they currently provide the only available constraints on the evolution of 3-D mantle buoyancy in the past. We developed a new back-and-forth iterative method for time-reversed convection modeling with a procedure for matching plate velocity data at different instants in the past. The crucial aspect of this reconstruction methodology is to ensure that at all times plates are driven by buoyancy forces in the mantle and not vice versa. Employing tomography-based retrodictions over the Cenozoic, we estimate the global amplitude of the following observables: dynamic surface topography, the core-mantle boundary ellipticity, the free-air gravity anomalies, and the global divergence rates of tectonic plates. One of the major benefits of the new data assimilation method is the stable recovery of much shorter wavelength changes in heterogeneity than was possible in our previous work. We now resolve what appears to be two-stage subduction of the Farallon plate under the western U.S. and a deeply rooted East African Plume that is active under the Ethiopian volcanic fields during the Early Eocene.

  3. Use of RELAP5-3D for Dynamic Analysis of a Closed-Loop Brayton Cycle Coupled To a Nuclear Reactor

    NASA Astrophysics Data System (ADS)

    McCann, Larry D.

    2007-01-01

    This paper describes results of a dynamic system model for a pair of closed Brayton-cycle (CBC) loops running in parallel that are connected to a nuclear gas reactor. The model assumes direct coupling between the reactor and the Brayton-cycle loops. The RELAP5-3D (version 2.4.1) computer program was used to perform the analysis. Few reactors have ever been coupled to closed Brayton-cycle systems. As such their behavior under dynamically varying loads, startup and shut down conditions, and requirements for safe and autonomous operation are largely unknown. The model described in this paper represents the reactor, turbine, compressor, recuperator, heat rejection system and alternator. The initial results of the model indicate stable operation of the reactor-driven Brayton-cycle system. However, for analysts with mostly pressurized water reactor experience, the Brayton cycle loops coupled to a gas-cooled reactor also indicate some counter-intuitive behavior for the complete coupled system. This model has provided crucial information in evaluating the reactor design and would have been further developed for use in developing procedures for safe start up, shut down, safe-standby, and other autonomous operating modes had the plant development cycle been completed.

  4. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations.

    PubMed

    Gao, Xiaodong; Han, Liping; Ren, Yujie

    2016-05-05

    Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q² values (0.531, 0.726), fitted correlation r² coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.

  5. Use of RELAP5-3D for Dynamic Analysis of a Closed-Loop Brayton Cycle Coupled To a Nuclear Reactor

    SciTech Connect

    McCann, Larry D.

    2007-01-30

    This paper describes results of a dynamic system model for a pair of closed Brayton-cycle (CBC) loops running in parallel that are connected to a nuclear gas reactor. The model assumes direct coupling between the reactor and the Brayton-cycle loops. The RELAP5-3D (version 2.4.1) computer program was used to perform the analysis. Few reactors have ever been coupled to closed Brayton-cycle systems. As such their behavior under dynamically varying loads, startup and shut down conditions, and requirements for safe and autonomous operation are largely unknown. The model described in this paper represents the reactor, turbine, compressor, recuperator, heat rejection system and alternator. The initial results of the model indicate stable operation of the reactor-driven Brayton-cycle system. However, for analysts with mostly pressurized water reactor experience, the Brayton cycle loops coupled to a gas-cooled reactor also indicate some counter-intuitive behavior for the complete coupled system. This model has provided crucial information in evaluating the reactor design and would have been further developed for use in developing procedures for safe start up, shut down, safe-standby, and other autonomous operating modes had the plant development cycle been completed.

  6. Macrophage podosomes go 3D.

    PubMed

    Van Goethem, Emeline; Guiet, Romain; Balor, Stéphanie; Charrière, Guillaume M; Poincloux, Renaud; Labrousse, Arnaud; Maridonneau-Parini, Isabelle; Le Cabec, Véronique

    2011-01-01

    Macrophage tissue infiltration is a critical step in the immune response against microorganisms and is also associated with disease progression in chronic inflammation and cancer. Macrophages are constitutively equipped with specialized structures called podosomes dedicated to extracellular matrix (ECM) degradation. We recently reported that these structures play a critical role in trans-matrix mesenchymal migration mode, a protease-dependent mechanism. Podosome molecular components and their ECM-degrading activity have been extensively studied in two dimensions (2D), but yet very little is known about their fate in three-dimensional (3D) environments. Therefore, localization of podosome markers and proteolytic activity were carefully examined in human macrophages performing mesenchymal migration. Using our gelled collagen I 3D matrix model to obligate human macrophages to perform mesenchymal migration, classical podosome markers including talin, paxillin, vinculin, gelsolin, cortactin were found to accumulate at the tip of F-actin-rich cell protrusions together with β1 integrin and CD44 but not β2 integrin. Macrophage proteolytic activity was observed at podosome-like protrusion sites using confocal fluorescence microscopy and electron microscopy. The formation of migration tunnels by macrophages inside the matrix was accomplished by degradation, engulfment and mechanic compaction of the matrix. In addition, videomicroscopy revealed that 3D F-actin-rich protrusions of migrating macrophages were as dynamic as their 2D counterparts. Overall, the specifications of 3D podosomes resembled those of 2D podosome rosettes rather than those of individual podosomes. This observation was further supported by the aspect of 3D podosomes in fibroblasts expressing Hck, a master regulator of podosome rosettes in macrophages. In conclusion, human macrophage podosomes go 3D and take the shape of spherical podosome rosettes when the cells perform mesenchymal migration. This work

  7. Digital holography and 3-D imaging.

    PubMed

    Banerjee, Partha; Barbastathis, George; Kim, Myung; Kukhtarev, Nickolai

    2011-03-01

    This feature issue on Digital Holography and 3-D Imaging comprises 15 papers on digital holographic techniques and applications, computer-generated holography and encryption techniques, and 3-D display. It is hoped that future work in the area leads to innovative applications of digital holography and 3-D imaging to biology and sensing, and to the development of novel nonlinear dynamic digital holographic techniques.

  8. Dynamics of leaf gas exchange, xylem and phloem transport, water potential and carbohydrate concentration in a realistic 3-D model tree crown

    PubMed Central

    Nikinmaa, Eero; Sievänen, Risto; Hölttä, Teemu

    2014-01-01

    Background and Aims Tree models simulate productivity using general gas exchange responses and structural relationships, but they rarely check whether leaf gas exchange and resulting water and assimilate transport and driving pressure gradients remain within acceptable physical boundaries. This study presents an implementation of the cohesion–tension theory of xylem transport and the Münch hypothesis of phloem transport in a realistic 3-D tree structure and assesses the gas exchange and transport dynamics. Methods A mechanistic model of xylem and phloem transport was used, together with a tested leaf assimilation and transpiration model in a realistic tree architecture to simulate leaf gas exchange and water and carbohydrate transport within an 8-year-old Scots pine tree. The model solved the dynamics of the amounts of water and sucrose solute in the xylem, cambium and phloem using a fine-grained mesh with a system of coupled ordinary differential equations. Key Results The simulations predicted the observed patterns of pressure gradients and sugar concentration. Diurnal variation of environmental conditions influenced tree-level gradients in turgor pressure and sugar concentration, which are important drivers of carbon allocation. The results and between-shoot variation were sensitive to structural and functional parameters such as tree-level scaling of conduit size and phloem unloading. Conclusions Linking whole-tree-level water and assimilate transport, gas exchange and sink activity opens a new avenue for plant studies, as features that are difficult to measure can be studied dynamically with the model. Tree-level responses to local and external conditions can be tested, thus making the approach described here a good test-bench for studies of whole-tree physiology. PMID:24854169

  9. 3-D Seismic Interpretation

    NASA Astrophysics Data System (ADS)

    Moore, Gregory F.

    2009-05-01

    This volume is a brief introduction aimed at those who wish to gain a basic and relatively quick understanding of the interpretation of three-dimensional (3-D) seismic reflection data. The book is well written, clearly illustrated, and easy to follow. Enough elementary mathematics are presented for a basic understanding of seismic methods, but more complex mathematical derivations are avoided. References are listed for readers interested in more advanced explanations. After a brief introduction, the book logically begins with a succinct chapter on modern 3-D seismic data acquisition and processing. Standard 3-D acquisition methods are presented, and an appendix expands on more recent acquisition techniques, such as multiple-azimuth and wide-azimuth acquisition. Although this chapter covers the basics of standard time processing quite well, there is only a single sentence about prestack depth imaging, and anisotropic processing is not mentioned at all, even though both techniques are now becoming standard.

  10. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  11. Bootstrapping 3D fermions

    DOE PAGES

    Iliesiu, Luca; Kos, Filip; Poland, David; ...

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  12. Bootstrapping 3D fermions

    SciTech Connect

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  13. 3D change detection - Approaches and applications

    NASA Astrophysics Data System (ADS)

    Qin, Rongjun; Tian, Jiaojiao; Reinartz, Peter

    2016-12-01

    Due to the unprecedented technology development of sensors, platforms and algorithms for 3D data acquisition and generation, 3D spaceborne, airborne and close-range data, in the form of image based, Light Detection and Ranging (LiDAR) based point clouds, Digital Elevation Models (DEM) and 3D city models, become more accessible than ever before. Change detection (CD) or time-series data analysis in 3D has gained great attention due to its capability of providing volumetric dynamics to facilitate more applications and provide more accurate results. The state-of-the-art CD reviews aim to provide a comprehensive synthesis and to simplify the taxonomy of the traditional remote sensing CD techniques, which mainly sit within the boundary of 2D image/spectrum analysis, largely ignoring the particularities of 3D aspects of the data. The inclusion of 3D data for change detection (termed 3D CD), not only provides a source with different modality for analysis, but also transcends the border of traditional top-view 2D pixel/object-based analysis to highly detailed, oblique view or voxel-based geometric analysis. This paper reviews the recent developments and applications of 3D CD using remote sensing and close-range data, in support of both academia and industry researchers who seek for solutions in detecting and analyzing 3D dynamics of various objects of interest. We first describe the general considerations of 3D CD problems in different processing stages and identify CD types based on the information used, being the geometric comparison and geometric-spectral analysis. We then summarize relevant works and practices in urban, environment, ecology and civil applications, etc. Given the broad spectrum of applications and different types of 3D data, we discuss important issues in 3D CD methods. Finally, we present concluding remarks in algorithmic aspects of 3D CD.

  14. Molecular modeling study of CP-690550 derivatives as JAK3 kinase inhibitors through combined 3D-QSAR, molecular docking, and dynamics simulation techniques.

    PubMed

    Wang, Jing Li; Cheng, Li Ping; Wang, Tian Chi; Deng, Wei; Wu, Fan Hong

    2017-03-01

    To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives. Some new JAK3 kinase inhibitors were designed. Some of them have better inhibitory activity than the most potent Tofacitinib (CP-690550). Molecular docking was used to identify some key amino acid residues at the active site of JAK3 protein. 10ns MD simulations were successfully performed to confirm the detailed binding mode and validate the rationality of docking results. The calculation of the binding free energies by MMPBSA method gives a good correlation with the predicted biological activity. To our knowledge, this is the first report on MD simulations and free energy calculations for this series of compounds. The combination results of this study will be valuable for the development of potent and novel JAK3 kinase inhibitors.

  15. Background and Pickup Ion Velocity Distribution Dynamics in Titan's Plasma Environment: 3D Hybrid Simulation and Comparison with CAPS T9 Observations

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

    In this report we discuss the ion velocity distribution dynamics from the 3D hybrid simulation. In our model the background, pickup, and ionospheric ions are considered as a particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. We also take into account the collisions between the ions and neutrals. The current simulation shows that mass loading by pickup ions H(+); H2(+), CH4(+) and N2(+) is stronger than in the previous simulations when O+ ions are introduced into the background plasma. In our hybrid simulations we use Chamberlain profiles for the atmospheric components. We also include a simple ionosphere model with average mass M = 28 amu ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS T9 observations. Our simulation shows an asymmetry of the ion density distribution and the magnetic field, including the formation of the Alfve n wing-like structures. The simulation also shows that the ring-like velocity distribution for pickup ions relaxes to a Maxwellian core and a shell-like halo.

  16. Modeling the spatial and temporal population dynamics of the copepod Centropages typicus in the northwestern Mediterranean Sea during the year 2001 using a 3D ecosystem model

    NASA Astrophysics Data System (ADS)

    Carlotti, F.; Eisenhauer, L.; Campbell, R.; Diaz, F.

    2014-07-01

    The spatio-temporal dynamics of a simulated Centropages typicus (Kröyer) population during the year 2001 at the regional scale of the northwestern Mediterranean Sea are addressed using a 3D coupled physical-biogeochemical model. The setup of the coupled biological model comprises a pelagic plankton ecosystem model and a stage-structured population model forced by the 3D velocity and temperature fields provided by an eddy-resolving regional circulation model. The population model for C. typicus (C. t. below) represents demographic processes through five groups of developmental stages, which depend on underlying individual growth and development processes and are forced by both biotic (prey and predator fields) and abiotic (temperature, advection) factors from the coupled physical-biogeochemical model. The objective is to characterize C. t. ontogenic habitats driven by physical and trophic processes. The annual dynamics are presented for two of the main oceanographic stations in the Gulf of Lions, which are representative of shelf and open sea conditions, while the spatial distributions over the whole area are presented for three dates during the year, in early and late spring and in winter. The simulated spatial patterns of C. t. developmental stages are closely related to mesoscale hydrodynamic features and circulation patterns. The seasonal and spatial distributions on the Gulf of Lions shelf depend on the seasonal interplay between the Rhône river plume, the mesoscale eddies on the shelf and the Northern Current acting as either as a dynamic barrier between the shelf and the open sea or allowing cross-shelf exchanges. In the central gyre of the northwestern Mediterranean Sea, the patchiness of plankton is tightly linked to mesoscale frontal systems, surface eddies and filaments and deep gradients. Due to its flexibility in terms of its diet, C. t. succeeds in maintaining its population in both coastal and offshore areas year round. The simulations suggest that

  17. Molecular modeling studies on series of Btk inhibitors using docking, structure-based 3D-QSAR and molecular dynamics simulation: a combined approach.

    PubMed

    Balasubramanian, Pavithra K; Balupuri, Anand; Cho, Seung Joo

    2016-03-01

    Bruton tyrosine kinase (Btk) is a non-receptor tyrosine kinase. It is a crucial component in BCR pathway and expressed only in hematopoietic cells except T cells and Natural killer cells. BTK is a promising target because of its involvement in signaling pathways and B cell diseases such as autoimmune disorders and lymphoma. In this work, a combined molecular modeling study of molecular docking, 3D-QSAR and molecular dynamic (MD) simulation were performed on a series of 2,5-diaminopyrimidine compounds as inhibitors targeting Btk kinase to understand the interaction and key residues involved in the inhibition. A structure based CoMFA (q (2) = 0.675, NOC = 5, r (2) = 0.961) and COMSIA (q (2) = 0.704, NOC = 6, r (2) = 0.962) models were developed from the conformation obtained by docking. The developed models were subjected to various validation techniques such as leave-five-out, external test set, bootstrapping, progressive sampling and rm (2) metrics and found to have a good predictive ability in both internal and external validation. Our docking results showed the important residues that interacts in the active site residues in inhibition of Btk kinase. Furthermore, molecular dynamics simulation was employed to study the stability of the docked conformation and to investigate the binding interactions in detail. The MD simulation analyses identified several important hydrogen bonds with Btk, including the gatekeeper residue Thr474 and Met477 at the hinge region. Hydrogen bond with active site residues Leu408 and Arg525 were also recognized. A good correlation between the MD results, docking studies and the contour map analysis are observed. This indicates that the developed models are reliable. Our results from this study can provide insights in the designing and development of more potent Btk kinase inhibitors.

  18. Dynamics of Submarine Landslides in an Active Margin from Analysis of Particle Size, Cores, and 3D Seismic Data: Site C0021, IODP Expedition 338, Offshore Japan

    NASA Astrophysics Data System (ADS)

    Sawyer, D.; Moore, Z. T.

    2013-12-01

    The deposits of submarine landslides, termed mass transport deposits (MTDs), were drilled and cored at Site C0021 in the Nankai Trough during Integrated Ocean Drilling Program (IODP) Expedition 338. Two MTDs were identified at 94-117 mbsf and 133-176 mbsf. Each MTD includes mud clasts, tilted bedding, and/or chaotic bedding, an increase in shear strength, a decrease in porosity, the occurrence of shear zones/faults, and a semi-transparent seismic facies. We conducted laser particle size analyses of sediments throughout the entire cored interval at Site C0021 (0 - 5 mbsf and 90 - 194 mbsf). Particle size distributions show that sediments shallower than 155 mbsf are composed of approximately 80% silt-sized, 15% clay-sized, and 5% sand-sized particles. Sediments deeper than 155 mbsf are predominantly composed of approximately 65% silt-sized, 15% clay-sized, and 20% sand-sized particles. MTDs have no obvious differences from non-MTD particle size distributions. We are examining the MTDs to gain insight into their dynamic behavior by mapping them in 3D seismic data. We measure slope geometry, runout distance, and characterize the depositional features preserved within the MTDs in the basal surface, top surface, and internal body. We use slope geometry to calculate regional gravitational shear stress and we use runout distance and morphology as indicators of the dynamic behavior of the landslide. Future work will focus on back-analysis estimates of shear stress and shear strength parameters. Our goal is to distinguish whether these landslides occurred as relatively rapid-moving, low-viscosity events or relatively slow-moving, high-viscosity events. This is an important distinction to make given that initial acceleration of a landslide is a critical variable that determines amplitude of slide-generated tsunami.

  19. Stress evolution and dynamics of the lithosphere from 2-D and 3-D numerical models of long-term tectonic processes.

    NASA Astrophysics Data System (ADS)

    Kaus, B. J.

    2007-12-01

    The processes that generate stress in the lithosphere are incompletely understood. Whereas it is obvious that lithospheric deformation (and topography) is ultimately caused by cooling of the Earth from the time of formation, it is less clear how lithospheric deformation is coupled to mantle flow and how this affect stresses. Part of this is due to the somewhat complicated rheology of the lithosphere, which varies from brittle (elastoplastic) to ductile (viscous). In addition, vertical layering of the lithosphere may give rise to instabilities which affect its dynamics and stress evolution in a non-trivial manner. Obtaining a better insight in these processes thus requires numerical tools that can model the mantle-lithosphere system in a self-consistent manner (i.e. in a single computational domain) including topographic effects (i.e. free surface) and viscoelastoplastic rheologies. I have recently developed 2-D and 3-D numerical tools that incorporate the above mentioned features. Here I focus on a number of case studies to illustrate how differences in rheology and boundary conditions alter the dynamics and in particular the stress evolution of the lithosphere. Instabilities such as bending or buckling of compressed lithosphere reduce the average stress ('structural weakening"). Viscoelasticity results in time- dependencies, which are particularly pronounced in highly viscous parts of the lithosphere (e.g. the mantle lithosphere). Strong parts of the lithospere thus don't necessarily have large differential stresses (and earthquakes). The Christmas-tree approximation should therefore be used with care to infer stress levels in the lithosphere. Finally I will illustrate differences in stresses between "kinematically-driven" and "internally-driven" lithospheric- scale deformation models.

  20. Venus in 3D

    NASA Technical Reports Server (NTRS)

    Plaut, Jeffrey J.

    1993-01-01

    Stereographic images of the surface of Venus which enable geologists to reconstruct the details of the planet's evolution are discussed. The 120-meter resolution of these 3D images make it possible to construct digital topographic maps from which precise measurements can be made of the heights, depths, slopes, and volumes of geologic structures.

  1. 3D photoacoustic imaging

    NASA Astrophysics Data System (ADS)

    Carson, Jeffrey J. L.; Roumeliotis, Michael; Chaudhary, Govind; Stodilka, Robert Z.; Anastasio, Mark A.

    2010-06-01

    Our group has concentrated on development of a 3D photoacoustic imaging system for biomedical imaging research. The technology employs a sparse parallel detection scheme and specialized reconstruction software to obtain 3D optical images using a single laser pulse. With the technology we have been able to capture 3D movies of translating point targets and rotating line targets. The current limitation of our 3D photoacoustic imaging approach is its inability ability to reconstruct complex objects in the field of view. This is primarily due to the relatively small number of projections used to reconstruct objects. However, in many photoacoustic imaging situations, only a few objects may be present in the field of view and these objects may have very high contrast compared to background. That is, the objects have sparse properties. Therefore, our work had two objectives: (i) to utilize mathematical tools to evaluate 3D photoacoustic imaging performance, and (ii) to test image reconstruction algorithms that prefer sparseness in the reconstructed images. Our approach was to utilize singular value decomposition techniques to study the imaging operator of the system and evaluate the complexity of objects that could potentially be reconstructed. We also compared the performance of two image reconstruction algorithms (algebraic reconstruction and l1-norm techniques) at reconstructing objects of increasing sparseness. We observed that for a 15-element detection scheme, the number of measureable singular vectors representative of the imaging operator was consistent with the demonstrated ability to reconstruct point and line targets in the field of view. We also observed that the l1-norm reconstruction technique, which is known to prefer sparseness in reconstructed images, was superior to the algebraic reconstruction technique. Based on these findings, we concluded (i) that singular value decomposition of the imaging operator provides valuable insight into the capabilities of

  2. Applying 3D Dynamic Visualisation to (Palaeo) Geomorphic Reconstruction: Modelling a Tenth Century Jökulhlaup at Sólheimajökull Glacier, South Iceland.

    NASA Astrophysics Data System (ADS)

    Booth, Laura; Isaacs, John

    2014-05-01

    Models of the area with aerial photography to create a 3D virtual environment, which provides the basis for entering field data to the geomorphic reconstruction. The result is a visual simulation of Sólheimajökull's Tenth Century physical environment which places the flood into geomorphic and topographic context. The wider implications of developing this tool are many when considering its ease of use and first-person navigational controls. The animations allow immediate exposure to environments that are otherwise lost in reality. VolcVis is a powerful tool in bringing reconstructed palaeo-environments back to life, albeit in the virtual sphere. It allows a uniquely contemporary appreciation of an elapsed event; yet which was a critical episode in the geomorphic evolution of this dynamic region. When field data are pieced together into a simulation, they hold a greater cohesive strength, giving the results wider applicability and relevance to a range of users and decision-makers, serving both technical and nontechnical perspectives. VolcVis' ability to dynamically display field data presents new possibilities for generating hypotheses, and for data sharing with Icelandic hazard mitigation authorities and the general public.

  3. Flow dynamics and sedimentation of lateral accretion packages in sinuous deep-water channels: A 3D seismic case study from the northwestern South China Sea margin

    NASA Astrophysics Data System (ADS)

    Li, Shengli; Gong, Chenglin

    2016-07-01

    The current study uses 3D seismic data to document architectural styles and flow dynamics of lateral accretion packages (LAPs) associated with sinuous deep-water channels, contributing to a better understanding of flow processes and sedimentation associated with LAPs. The documented LAPs underwent three main stages of architectural evolution, including the early incision stages characterized by intense downcutting, active migration stages characterized by active migration and avulsion of the individual channels, and late abandonment stages characterized by the termination of sediment gravity-flows and LAP growth. These three stages of LAP growth repeated through time, yielding a fining-upward pattern from sandy channel-fill turbidites, into sand-mud couplets, all capped by muddy turbidites. A river-reversed helical flow circulation was created by an imbalance, through the flow depth, of inwardly directed pressure gradient forces near the bed and outwardly directed centrifugal forces near the surface. It consists of low-velocity cores near the outer banks and low-velocity cores along the inner banks. Such river-reversed helical flow pattern is evidenced by volumetrically extensive LAPs and toplap and downlap terminations along the gentle banks and by aerially restricted, seismically unresolvable levees and truncation terminations near the steep banks. This river-reversed helical flow circulation favors asymmetric intra-channel deposition characterized by inner bank deposition versus outer bank erosion, and which, in turn, forced individual channels to consistently migrate towards outer banks, resulting in significant asymmetric cross-channel profiles with aerially extensive LAPs along inner banks.

  4. Self consistent particles dynamics in/out of the cusp region by using back tracking technics; a global 3D PIC simulation approach

    NASA Astrophysics Data System (ADS)

    Esmaeili, A.; Cai, D.; Lembege, B.; Nishikawa, K.

    2013-12-01

    Large scale three dimensionbal PIC (particle in cell) simulations are presently used in order to analyze the global solar wind-terrestrial magnetosphere intreraction within a full self-consistent approach, and where both electrons and ions are treated as an assembly of individual particles. This 3D kinetic approach allows us to analyze in particular the dynamics and the fine structures of the cusp region when including self consistently not only its whole neighborhood (in the terrestrial magnetosphere) but also the impact of the solar wind and the interplanetary field (IMF) features. Herein, we focuss our attention on the cusp region and in particular on the acceleration and precipitation of particles (both ions and electrons) within the cusp. In present simulations, the IMF is chosen northward, (i.e. where the X -reconnection region is just above the cusp, in the meridian plane). Back-trackings of self-consistent particles are analyzed in details in order to determine (i) which particles (just above the cusp) are precipitated deeply into the cusp, (ii) which populations are injected from the cusp into the nearby tail, (iii) where the particles suffer the largest energisation along their self-consistent trajectories, (iv) where these populations accumulate, and (v) where the most energetic particles are originally coming from. This approach allows to make a traking of particles within the scenario "solar wind-magnetosheath- cusp -nearbytail"; moreover it strongly differs from the standard test particles technics and allows to provide informations not accessible when using full MHD approach. Keywords: Tracing Particles, Particle In Cell (PIC) simulation, double cusp, test particles method, IMF, Solar wind, Magnetosphere

  5. Atom-based 3D-QSAR, molecular docking and molecular dynamics simulation assessment of inhibitors for thyroid hormone receptor α and β.

    PubMed

    Gupta, Manish Kumar; Misra, Krishna

    2014-06-01

    The three-dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitors of thyroid hormone receptors (TR) α and (TR) β was studied. The training set of the TRα model generated a correlation coefficient (R(2)) =  0.9535, with standard deviation (SD) =  0.3016. From the test set of the TRα model, a Q(2) value for the predicted activities (= 0.4303), squared correlation (random selection R(2)-CV  =  0.6929), Pearson-R (= 0.7294) and root mean square error (RMSE  =  0.6342) were calculated. The P-value for TRα (= 1.411e-96) and TRβ (= 2.108e-165) models indicate a high degree of self-reliance. For the TRβ model, the training set yielded R(2) = 0.9424 with SD = 0.3719. From the test set of TRβ, Q(2) value (= 0.5336), the squared correlation (R(2)-CV  =  0.7201), the Pearson-R (= 0.7852) and RMSE for test set predictions (= 0.8630) all strengthen the good predictive competence of the QSAR model derived. Examination of internal as well as external validation supports the rationality and good predictive ability of the best model. Molecular docking explained the conformations of molecules and important amino acid residues at the docking pocket, and a molecular dynamics simulation study further uncovered the binding process and validated the rationality of docking results. The findings not only lead to a better understanding of interactions between these antagonists and thyroid hormone receptors α and β, but also provide valuable information about the impact of structure on activity that will be very beneficial in the design of novel antagonists with preferred activity.

  6. Twin Peaks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The two hills in the distance, approximately one to two kilometers away, have been dubbed the 'Twin Peaks' and are of great interest to Pathfinder scientists as objects of future study. 3D glasses are necessary to identify surface detail. The white areas on the left hill, called the 'Ski Run' by scientists, may have been formed by hydrologic processes.

    The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  7. 3D and beyond

    NASA Astrophysics Data System (ADS)

    Fung, Y. C.

    1995-05-01

    This conference on physiology and function covers a wide range of subjects, including the vasculature and blood flow, the flow of gas, water, and blood in the lung, the neurological structure and function, the modeling, and the motion and mechanics of organs. Many technologies are discussed. I believe that the list would include a robotic photographer, to hold the optical equipment in a precisely controlled way to obtain the images for the user. Why are 3D images needed? They are to achieve certain objectives through measurements of some objects. For example, in order to improve performance in sports or beauty of a person, we measure the form, dimensions, appearance, and movements.

  8. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  9. Martian terrain - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    An area of rocky terrain near the landing site of the Sagan Memorial Station can be seen in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. This image is part of a 3D 'monster' panorama of the area surrounding the landing site.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  10. River flood events as natural tracers for investigating the hydrological dynamics of a coupled river-aquifer system: preliminary results from 3D crosshole electrical resistivity monitoring

    NASA Astrophysics Data System (ADS)

    Coscia, I.; Greenhalgh, S. A.; Linde, N.; Doetsch, J.; Vogt, T.; Green, A. G.

    2009-12-01

    This research, on geoelectric monitoring of changing aquifer conditions associated with flood events of the River Thur in Switzerland, forms part of the much wider RECORD (REstored CORridor Dynamics) project. Major precipitation and snow-melt events cause rapid undamped fluctuations of discharge along the entire length of the river. River water that infiltrates the neighbouring aquifer normally has higher electrical resistivity than that of the groundwater during the early stages of flood events. This enables us to use infiltration during such events as a natural tracer in 3D time-lapse electrical resistivity tomography (ERT) experiments. Over a 10 x 15 m areal array, we have installed eighteen 12-m-deep monitoring boreholes spaced 3.5 m apart that completely penetrate the underlying 7-m-thick aquifer. Each borehole has been instrumented with ten 0.7-m-spaced electrodes that span the thickness of the aquifer. A multichannel resistivity meter, programmed to cycle through various 4-point electrode configurations of the 180 electrodes in a rolling sub-sequence, allows the collection of a 15,000-measurement data set every ~7 hours. Fourteen of these boreholes are also equipped with STS sensors that provide time-series of water-table depth and water temperature and electrical conductivity. Three-dimensional static ERT inversion at stable hydrological conditions was performed to investigate the resolving capability of our measuring sequence and to define the main lithological structures within the aquifer. Preliminary analyses of the ERT time series collected during a major flooding event this past summer suggest that the data are sensitive to three factors: water-level fluctuations in the aquifer, water-temperature variations, and electrical conductivity changes associated with changing salinity of the groundwater. The total changes in apparent resistivity are of the order of 20%. Since our primary interest is in the salinity effect that might be used to delineate

  11. SU-D-213-03: Towards An Optimized 3D Scintillation Dosimetry Tool for Quality Assurance of Dynamic Radiotherapy Techniques

    SciTech Connect

    Rilling, M; Goulet, M; Thibault, S; Archambault, L

    2015-06-15

    specifications. This work leads the way to improving the 3D dosimeter’s achievable resolution, efficiency and build for providing a quality assurance tool fully meeting clinical needs. M.R. is financially supported by a Master’s Canada Graduate Scholarship from the NSERC. This research is also supported by the NSERC Industrial Research Chair in Optical Design.

  12. A Parameter-Free Dynamic Alternative to Hyper-Viscosity for Coupled Transport Equations: Application to the Simulation of 3D Squall Lines Using Spectral Elements

    DTIC Science & Technology

    2015-06-04

    that involve physics coupling with phase change in the simulation of 3D deep convection . We show that the VMS+DC approach is a robust technique that can...of 3D deep convection . We show that the VMS+DC approach is a robust technique that can damp the high order modes characterizing the spectral element...of Spectral Elements, Deep Convection , Kessler Microphysics Preprint J. Comput. Phys. 283 (2015) 360-373 June 4, 2015 1. Introduction In the field of

  13. Synthesis, characterisation, conformational preferences, dynamic NMR studies and antimicrobial evaluation of N-nitroso- and N-formyl-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-ones

    NASA Astrophysics Data System (ADS)

    Ponnuswamy, S.; Akila, A.; Kiruthiga devi, D.; Maheshwaran, V.; Ponnuswamy, M. N.

    2016-04-01

    The stereochemical preferences of N-nitroso- and N-formyl-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-ones 3 & 4, respectively, have been determined using 1D and 2D NMR spectral techniques. Interestingly, the N-nitroso compound 3 is found to prefer an equilibrium between alternate chair conformations with diaxial phenyl groups, while the N-formyl compound 4 prefers flattened boat conformation. This is stereochemically a novel report on the flexible rings adopting a chair conformation with diaxial phenyl groups. The X-ray crystal structure of N-nitroso-c-3,t-3-dimethyl-r-2,c-7-diphenyl-1,4-diazepan-5-one (3) also supports the chair conformation with diaxial phenyl groups. Dynamic 1H NMR spectral studies have been carried out on the N-nitroso and N-formyl diazepan-5-ones 3 &4 and the energy barriers for N-NO and N-CO rotations are found to be 88.7 and 75.7 kJ/mol, respectively. The antimicrobial activities have been determined for the compounds 2-4 and it is found that all the compounds exhibit significant antibacterial and antifungal activities when compared to the standard chloramphenicol.

  14. FUN3D Manual: 12.5

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2014-01-01

    This manual describes the installation and execution of FUN3D version 12.5, including optional dependent packages. FUN3D is a suite of computational uid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables ecient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  15. FUN3D Manual: 12.4

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2014-01-01

    This manual describes the installation and execution of FUN3D version 12.4, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixedelement unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  16. FUN3D Manual: 12.6

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.6, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  17. FUN3D Manual: 12.9

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2016-01-01

    This manual describes the installation and execution of FUN3D version 12.9, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  18. FUN3D Manual: 13.1

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2017-01-01

    This manual describes the installation and execution of FUN3D version 13.1, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  19. FUN3D Manual: 12.7

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.7, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  20. FUN3D Manual: 13.0

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bill; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2016-01-01

    This manual describes the installation and execution of FUN3D version 13.0, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  1. FUN3D Manual: 12.8

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.8, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  2. Interactive 3D Mars Visualization

    NASA Technical Reports Server (NTRS)

    Powell, Mark W.

    2012-01-01

    The Interactive 3D Mars Visualization system provides high-performance, immersive visualization of satellite and surface vehicle imagery of Mars. The software can be used in mission operations to provide the most accurate position information for the Mars rovers to date. When integrated into the mission data pipeline, this system allows mission planners to view the location of the rover on Mars to 0.01-meter accuracy with respect to satellite imagery, with dynamic updates to incorporate the latest position information. Given this information so early in the planning process, rover drivers are able to plan more accurate drive activities for the rover than ever before, increasing the execution of science activities significantly. Scientifically, this 3D mapping information puts all of the science analyses to date into geologic context on a daily basis instead of weeks or months, as was the norm prior to this contribution. This allows the science planners to judge the efficacy of their previously executed science observations much more efficiently, and achieve greater science return as a result. The Interactive 3D Mars surface view is a Mars terrain browsing software interface that encompasses the entire region of exploration for a Mars surface exploration mission. The view is interactive, allowing the user to pan in any direction by clicking and dragging, or to zoom in or out by scrolling the mouse or touchpad. This set currently includes tools for selecting a point of interest, and a ruler tool for displaying the distance between and positions of two points of interest. The mapping information can be harvested and shared through ubiquitous online mapping tools like Google Mars, NASA WorldWind, and Worldwide Telescope.

  3. Hydroxyapatite scaffolds for bone tissue engineering made by 3D printing.

    PubMed

    Leukers, Barbara; Gülkan, Hülya; Irsen, Stephan H; Milz, Stefan; Tille, Carsten; Schieker, Matthias; Seitz, Hermann

    2005-12-01

    Nowadays, there is a significant need for synthetic bone replacement materials used in bone tissue engineering (BTE). Rapid prototyping and especially 3D printing is a suitable technique to create custom implants based on medical data sets. 3D printing allows to fabricate scaffolds based on Hydroxyapatite with complex internal structures and high resolution. To determine the in vitro behaviour of cells cultivated on the scaffolds, we designed a special test-part. MC3T3-E1 cells were seeded on the scaffolds and cultivated under static and dynamic setups. Histological evaluation was carried out to characterise the cell ingrowth. In summary, the dynamic cultivation method lead to a stronger population compared to the static cultivation method. The cells proliferated deep into the structure forming close contact to Hydroxyapatite granules.

  4. Intraoral 3D scanner

    NASA Astrophysics Data System (ADS)

    Kühmstedt, Peter; Bräuer-Burchardt, Christian; Munkelt, Christoph; Heinze, Matthias; Palme, Martin; Schmidt, Ingo; Hintersehr, Josef; Notni, Gunther

    2007-09-01

    Here a new set-up of a 3D-scanning system for CAD/CAM in dental industry is proposed. The system is designed for direct scanning of the dental preparations within the mouth. The measuring process is based on phase correlation technique in combination with fast fringe projection in a stereo arrangement. The novelty in the approach is characterized by the following features: A phase correlation between the phase values of the images of two cameras is used for the co-ordinate calculation. This works contrary to the usage of only phase values (phasogrammetry) or classical triangulation (phase values and camera image co-ordinate values) for the determination of the co-ordinates. The main advantage of the method is that the absolute value of the phase at each point does not directly determine the coordinate. Thus errors in the determination of the co-ordinates are prevented. Furthermore, using the epipolar geometry of the stereo-like arrangement the phase unwrapping problem of fringe analysis can be solved. The endoscope like measurement system contains one projection and two camera channels for illumination and observation of the object, respectively. The new system has a measurement field of nearly 25mm × 15mm. The user can measure two or three teeth at one time. So the system can by used for scanning of single tooth up to bridges preparations. In the paper the first realization of the intraoral scanner is described.

  5. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  6. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  7. Validation of Blood Volume Fraction Quantification with 3D Gradient Echo Dynamic Contrast-Enhanced Magnetic Resonance Imaging in Porcine Skeletal Muscle.

    PubMed

    Hindel, Stefan; Söhner, Anika; Maaß, Marc; Sauerwein, Wolfgang; Möllmann, Dorothe; Baba, Hideo Andreas; Kramer, Martin; Lüdemann, Lutz

    2017-01-01

    The purpose of this study was to assess the accuracy of fractional blood volume (vb) estimates in low-perfused and low-vascularized tissue using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). The results of different MRI methods were compared with histology to evaluate the accuracy of these methods under clinical conditions. vb was estimated by DCE-MRI using a 3D gradient echo sequence with k-space undersampling in five muscle groups in the hind leg of 9 female pigs. Two gadolinium-based contrast agents (CA) were used: a rapidly extravasating, extracellular, gadolinium-based, low-molecular-weight contrast agent (LMCA, gadoterate meglumine) and an extracellular, gadolinium-based, albumin-binding, slowly extravasating blood pool contrast agent (BPCA, gadofosveset trisodium). LMCA data were evaluated using the extended Tofts model (ETM) and the two-compartment exchange model (2CXM). The images acquired with administration of the BPCA were used to evaluate the accuracy of vb estimation with a bolus deconvolution technique (BD) and a method we call equilibrium MRI (EqMRI). The latter calculates the ratio of the magnitude of the relaxation rate change in the tissue curve at an approximate equilibrium state to the height of the same area of the arterial input function (AIF). Immunohistochemical staining with isolectin was used to label endothelium. A light microscope was used to estimate the fractional vascular area by relating the vascular region to the total tissue region (immunohistochemical vessel staining, IHVS). In addition, the percentage fraction of vascular volume was determined by multiplying the microvascular density (MVD) with the average estimated capillary lumen, [Formula: see text], where d = 8μm is the assumed capillary diameter (microvascular density estimation, MVDE). Except for ETM values, highly significant correlations were found between most of the MRI methods investigated. In the cranial thigh, for example, the vb medians

  8. Validation of Blood Volume Fraction Quantification with 3D Gradient Echo Dynamic Contrast-Enhanced Magnetic Resonance Imaging in Porcine Skeletal Muscle

    PubMed Central

    Söhner, Anika; Maaß, Marc; Sauerwein, Wolfgang; Möllmann, Dorothe; Baba, Hideo Andreas; Kramer, Martin; Lüdemann, Lutz

    2017-01-01

    The purpose of this study was to assess the accuracy of fractional blood volume (vb) estimates in low-perfused and low-vascularized tissue using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). The results of different MRI methods were compared with histology to evaluate the accuracy of these methods under clinical conditions. vb was estimated by DCE-MRI using a 3D gradient echo sequence with k-space undersampling in five muscle groups in the hind leg of 9 female pigs. Two gadolinium-based contrast agents (CA) were used: a rapidly extravasating, extracellular, gadolinium-based, low-molecular-weight contrast agent (LMCA, gadoterate meglumine) and an extracellular, gadolinium-based, albumin-binding, slowly extravasating blood pool contrast agent (BPCA, gadofosveset trisodium). LMCA data were evaluated using the extended Tofts model (ETM) and the two-compartment exchange model (2CXM). The images acquired with administration of the BPCA were used to evaluate the accuracy of vb estimation with a bolus deconvolution technique (BD) and a method we call equilibrium MRI (EqMRI). The latter calculates the ratio of the magnitude of the relaxation rate change in the tissue curve at an approximate equilibrium state to the height of the same area of the arterial input function (AIF). Immunohistochemical staining with isolectin was used to label endothelium. A light microscope was used to estimate the fractional vascular area by relating the vascular region to the total tissue region (immunohistochemical vessel staining, IHVS). In addition, the percentage fraction of vascular volume was determined by multiplying the microvascular density (MVD) with the average estimated capillary lumen, π(d2)2, where d = 8μm is the assumed capillary diameter (microvascular density estimation, MVDE). Except for ETM values, highly significant correlations were found between most of the MRI methods investigated. In the cranial thigh, for example, the vb medians (interquartile range

  9. Quantifying modes of 3D cell migration

    PubMed Central

    Driscoll, Meghan K.; Danuser, Gaudenz

    2015-01-01

    Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates. PMID:26603943

  10. Modeling cellular processes in 3D.

    PubMed

    Mogilner, Alex; Odde, David

    2011-12-01

    Recent advances in photonic imaging and fluorescent protein technology offer unprecedented views of molecular space-time dynamics in living cells. At the same time, advances in computing hardware and software enable modeling of ever more complex systems, from global climate to cell division. As modeling and experiment become more closely integrated we must address the issue of modeling cellular processes in 3D. Here, we highlight recent advances related to 3D modeling in cell biology. While some processes require full 3D analysis, we suggest that others are more naturally described in 2D or 1D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling.

  11. Quantifying Modes of 3D Cell Migration.

    PubMed

    Driscoll, Meghan K; Danuser, Gaudenz

    2015-12-01

    Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates.

  12. Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT.

    PubMed

    Maruyama, Yutaka; Yoshida, Norio; Tadano, Hiroto; Takahashi, Daisuke; Sato, Mitsuhisa; Hirata, Fumio

    2014-07-05

    A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems.

  13. Comparison of the 3D VERB Code Simulations of the Dynamic Evolution of the Outer and Inner Radiation Belts With the Reanalysis Obtained from Observations on Multiple Spacecraft

    NASA Astrophysics Data System (ADS)

    Shprits, Y.; Subbotin, D.; Ni, B.; Daae, M.; Kondrashov, D. A.; Hartinger, M.; Kim, K.; Orlova, K.; Nagai, T.; Friedel, R. H.; Chen, Y.

    2010-12-01

    In this study we present simulations of the inner and outer radiation belts using the Versatile Electron Radiation Belt (VERB) accounting for radial, pitch-angle, energy, and mixed diffusion. Qusi-linear diffusion coefficients are computed using the Full Diffusion Code (FDC) due to day-side and night-side chorus waves, magneto-sonic waves, phasmaspheric hiss waves, EMIC and hiss waves in the regions of plumes, lightning generated whistlers and anthropogenic whistlers. Sensitivity simulations show that the knowledge of wave spectral properties and spacial distribution of waves is crucially important for reproducing long term observations. The 3D VERB code simulations are compared to 3D reanalysis of the radiation belt fluxes obtained by blending the predictive model with observations from LANL GEO, CRRES, Akebono, and GPS. We also discuss the initial results of coupled RCM-VERB simulations. Finally, we present a statistical analysis of radiation belt phase space density obtained from reanalysis to explore sudden drop outs of the radiation belt fluxes and location of peaks in phase space density. The application of the developed tools to future measurements on board RBSP is discussed.

  14. Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations.

    PubMed

    Qian, Haiyan; Chen, Jiongjiong; Pan, Youlu; Chen, Jianzhong

    2016-09-19

    11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

  15. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  16. Spherical 3D isotropic wavelets

    NASA Astrophysics Data System (ADS)

    Lanusse, F.; Rassat, A.; Starck, J.-L.

    2012-04-01

    Context. Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D spherical Fourier-Bessel (SFB) analysis in spherical coordinates is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. Aims: The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the SFB decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. Methods: We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. (2006). We also present a new fast discrete spherical Fourier-Bessel transform (DSFBT) based on both a discrete Bessel transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and find we can successfully remove noise without much loss to the large scale structure. Results: We have described a new spherical 3D isotropic wavelet transform, ideally suited to analyse and denoise future 3D spherical cosmological surveys, which uses a novel DSFBT. We illustrate its potential use for denoising using a toy model. All the algorithms presented in this paper are available for download as a public code called MRS3D at http://jstarck.free.fr/mrs3d.html

  17. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-04-14

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  18. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    SciTech Connect

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  19. Application of computational fluid dynamics and fluid structure interaction techniques for calculating the 3D transient flow of journal bearings coupled with rotor 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.

  20. Terrain Dynamics Analysis Using Space-Time Domain Hypersurfaces and Gradient Trajectories Derived From Time Series of 3D Point Clouds

    DTIC Science & Technology

    2015-08-01

    CONTRACT NUMBER Form Approved OMB NO. 0704-0188 3. DATES COVERED (From - To) - UU UU UU UU 01-08-2015 1-Apr-2011 31- Mar -2014 Approved for Public Release...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 landscape dynamics, lidar time series, space time cube, tangible interface...2701 Sullivan Drive Suite 240 Raleigh, NC 27695 -7514 31- Mar -2014 ABSTRACT Terrain Dynamics Analysis Using Space-Time Domain Hypersurfaces and

  1. Analysis of Vertical Dynamics in the Northern Baltic Sea based on 3D Modelling and Data from Shallow-Water Argo Floats

    NASA Astrophysics Data System (ADS)

    Westerlund, Antti; Tuomi, Laura

    2016-04-01

    Vertical mixing is a challenge for ocean models. 3D hydrodynamic models often produce considerable errors in mixed layer depths and vertical temperature structure that can be related to the vertical turbulence parameterisation. These errors can be pronounced in areas with complex hydrography. In the Baltic Sea, for example, there are high horizontal and vertical salinity gradients. Furthermore, thermocline and halocline are located at different depths. This produces stratification conditions challenging for all ocean models. We studied vertical mixing with modelling experiments and new observational data. NEMO 3D ocean model has been set up at Finnish Meteorological Institute (FMI) for the Baltic Sea, based on the NEMO Nordic configuration. The model has been discretized on a Baltic Sea - North Sea grid with 2 nautical mile resolution and 56 vertical layers, using FMI-HIRLAM atmospheric forcing. The observational data for Baltic Sea off-shore areas is sparse and new methods are needed to collect data for model validation and development. FMI has been testing Argo floats in the Baltic Sea since 2011 in order to increase the amount of observed vertical profiles of salinity and temperature. This is the first time Argo floats have been successfully used in the brackish, shallow waters of the Baltic Sea. This new data set is well suited for evaluating the capability of hydrodynamic models to produce the vertical structure of temperature. It provides a time series of profiles from the area of interest with good temporal resolution, showing the structure of temperature in the water column throughout the summer. We found that NEMO was able to reproduce the general features of the seasonal temperature variations in the study area, when meteorological forcing was accurate. We ran the model with different vertical turbulence parameterisations. The k-ɛ and k-ω schemes showed clear differences, but neither proved superior. While sea surface temperature was better simulated

  2. Single-Crystal to Single-Crystal Phase Transition and Segmented Thermochromic Luminescence in a Dynamic 3D Interpenetrated Ag(I) Coordination Network.

    PubMed

    Yan, Zhi-Hao; Li, Xiao-Yu; Liu, Li-Wei; Yu, Si-Qi; Wang, Xing-Po; Sun, Di

    2016-02-01

    A new 3D Ag(I)-based coordination network, [Ag2(pz)(bdc)·H2O]n (1; pz = pyrazine and H2bdc = benzene-1,3-dicarboxylic acid), was constructed by one-pot assembly and structurally established by single-crystal X-ray diffraction at different temperatures. Upon cooling from 298 to 93 K, 1 undergo an interesting single-crystal to single-crystal phase transition from orthorhombic Ibca (Z = 16) to Pccn (Z = 32) at around 148 K. Both phases show a rare 2-fold-interpenetrated 4-connected lvt network but incorporate different [Ag2(COO)2] dimeric secondary building units. It is worth mentioning that complex 1 shows red- and blue-shifted luminescences in the 290-170 and 140-80 K temperature ranges, respectively. The variable-temperature single-crystal X-ray crystallographic studies suggest that the argentophilic interactions and rigidity of the structure dominated the luminescence chromism trends at the respective temperature ranges. Upon being mechanically ground, 1 exhibits a slight mechanoluminescence red shift from 589 to 604 nm at 298 K.

  3. A dynamic multi-organ-chip for long-term cultivation and substance testing proven by 3D human liver and skin tissue co-culture.

    PubMed

    Wagner, Ilka; Materne, Eva-Maria; Brincker, Sven; Süssbier, Ute; Frädrich, Caroline; Busek, Mathias; Sonntag, Frank; Sakharov, Dmitry A; Trushkin, Evgeny V; Tonevitsky, Alexander G; Lauster, Roland; Marx, Uwe

    2013-09-21

    Current in vitro and animal tests for drug development are failing to emulate the systemic organ complexity of the human body and, therefore, to accurately predict drug toxicity. In this study, we present a multi-organ-chip capable of maintaining 3D tissues derived from cell lines, primary cells and biopsies of various human organs. We designed a multi-organ-chip with co-cultures of human artificial liver microtissues and skin biopsies, each a (1)/100,000 of the biomass of their original human organ counterparts, and have successfully proven its long-term performance. The system supports two different culture modes: i) tissue exposed to the fluid flow, or ii) tissue shielded from the underlying fluid flow by standard Transwell® cultures. Crosstalk between the two tissues was observed in 14-day co-cultures exposed to fluid flow. Applying the same culture mode, liver microtissues showed sensitivity at different molecular levels to the toxic substance troglitazone during a 6-day exposure. Finally, an astonishingly stable long-term performance of the Transwell®-based co-cultures could be observed over a 28-day period. This mode facilitates exposure of skin at the air-liquid interface. Thus, we provide here a potential new tool for systemic substance testing.

  4. 3D World Building System

    ScienceCinema

    None

    2016-07-12

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  5. 3D Buckligami: Digital Matter

    NASA Astrophysics Data System (ADS)

    van Hecke, Martin; de Reus, Koen; Florijn, Bastiaan; Coulais, Corentin

    2014-03-01

    We present a class of elastic structures which exhibit collective buckling in 3D, and create these by a 3D printing/moulding technique. Our structures consist of cubic lattice of anisotropic unit cells, and we show that their mechanical properties are programmable via the orientation of these unit cells.

  6. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  7. LLNL-Earth3D

    SciTech Connect

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  8. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  9. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  10. 3D vision system assessment

    NASA Astrophysics Data System (ADS)

    Pezzaniti, J. Larry; Edmondson, Richard; Vaden, Justin; Hyatt, Bryan; Chenault, David B.; Kingston, David; Geulen, Vanilynmae; Newell, Scott; Pettijohn, Brad

    2009-02-01

    In this paper, we report on the development of a 3D vision system consisting of a flat panel stereoscopic display and auto-converging stereo camera and an assessment of the system's use for robotic driving, manipulation, and surveillance operations. The 3D vision system was integrated onto a Talon Robot and Operator Control Unit (OCU) such that direct comparisons of the performance of a number of test subjects using 2D and 3D vision systems were possible. A number of representative scenarios were developed to determine which tasks benefited most from the added depth perception and to understand when the 3D vision system hindered understanding of the scene. Two tests were conducted at Fort Leonard Wood, MO with noncommissioned officers ranked Staff Sergeant and Sergeant First Class. The scenarios; the test planning, approach and protocols; the data analysis; and the resulting performance assessment of the 3D vision system are reported.

  11. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery.

  12. Dynamics of 3D representation of interfaces in UV-induced chemical vapor deposition: experiments, modeling, and simulation for silicon nitride thin layers

    NASA Astrophysics Data System (ADS)

    Flicstein, Jean; Guillonneau, E.; Marquez, Jose; How Kee Chun, L. S.; Maisonneuve, D.; David, C.; Wang, Zh. Z.; Palmier, Jean F.; Courant, J. L.

    2001-06-01

    We study the surface dynamics of silicon nitride films deposited by UV-induced low pressure chemical vapor pressure. Atomic force microscopy measurements show that the surface reaches a scale invariant stationary state coherent wit the Kardar-Parisi-Zhang (KPZ) equation. Discrete geometry techniques are oriented to extra morphological characteristics of surface and bulk which corresponds to computer simulated photodeposit. This allows to determine the physical origin of KPZ scaling to be al ow value of the surface sticking probability, and connected to the surface concentration of activate charged centers, which permits to start the evaluation of the Monte Carlo-molecular dynamics simulator.

  13. 3D integral imaging with optical processing

    NASA Astrophysics Data System (ADS)

    Martínez-Corral, Manuel; Martínez-Cuenca, Raúl; Saavedra, Genaro; Javidi, Bahram

    2008-04-01

    Integral imaging (InI) systems are imaging devices that provide auto-stereoscopic images of 3D intensity objects. Since the birth of this new technology, InI systems have faced satisfactorily many of their initial drawbacks. Basically, two kind of procedures have been used: digital and optical procedures. The "3D Imaging and Display Group" at the University of Valencia, with the essential collaboration of Prof. Javidi, has centered its efforts in the 3D InI with optical processing. Among other achievements, our Group has proposed the annular amplitude modulation for enlargement of the depth of field, dynamic focusing for reduction of the facet-braiding effect, or the TRES and MATRES devices to enlarge the viewing angle.

  14. 3-D Mesh Generation Nonlinear Systems

    SciTech Connect

    Christon, M. A.; Dovey, D.; Stillman, D. W.; Hallquist, J. O.; Rainsberger, R. B

    1994-04-07

    INGRID is a general-purpose, three-dimensional mesh generator developed for use with finite element, nonlinear, structural dynamics codes. INGRID generates the large and complex input data files for DYNA3D, NIKE3D, FACET, and TOPAZ3D. One of the greatest advantages of INGRID is that virtually any shape can be described without resorting to wedge elements, tetrahedrons, triangular elements or highly distorted quadrilateral or hexahedral elements. Other capabilities available are in the areas of geometry and graphics. Exact surface equations and surface intersections considerably improve the ability to deal with accurate models, and a hidden line graphics algorithm is included which is efficient on the most complicated meshes. The primary new capability is associated with the boundary conditions, loads, and material properties required by nonlinear mechanics programs. Commands have been designed for each case to minimize user effort. This is particularly important since special processing is almost always required for each load or boundary condition.

  15. Using the Flow-3D General Moving Object Model to Simulate Coupled Liquid Slosh - Container Dynamics on the SPHERES Slosh Experiment: Aboard the International Space Station

    NASA Technical Reports Server (NTRS)

    Schulman, Richard; Kirk, Daniel; Marsell, Brandon; Roth, Jacob; Schallhorn, Paul

    2013-01-01

    The SPHERES Slosh Experiment (SSE) is a free floating experimental platform developed for the acquisition of long duration liquid slosh data aboard the International Space Station (ISS). The data sets collected will be used to benchmark numerical models to aid in the design of rocket and spacecraft propulsion systems. Utilizing two SPHERES Satellites, the experiment will be moved through different maneuvers designed to induce liquid slosh in the experiment's internal tank. The SSE has a total of twenty-four thrusters to move the experiment. In order to design slosh generating maneuvers, a parametric study with three maneuvers types was conducted using the General Moving Object (GMO) model in Flow-30. The three types of maneuvers are a translation maneuver, a rotation maneuver and a combined rotation translation maneuver. The effectiveness of each maneuver to generate slosh is determined by the deviation of the experiment's trajectory as compared to a dry mass trajectory. To fully capture the effect of liquid re-distribution on experiment trajectory, each thruster is modeled as an independent force point in the Flow-3D simulation. This is accomplished by modifying the total number of independent forces in the GMO model from the standard five to twenty-four. Results demonstrate that the most effective slosh generating maneuvers for all motions occurs when SSE thrusters are producing the highest changes in SSE acceleration. The results also demonstrate that several centimeters of trajectory deviation between the dry and slosh cases occur during the maneuvers; while these deviations seem small, they are measureable by SSE instrumentation.

  16. Quasi-Instantaneous Bacterial Inactivation on Cu-Ag Nanoparticulate 3D Catheters in the Dark and Under Light: Mechanism and Dynamics.

    PubMed

    Rtimi, Sami; Sanjines, Rosendo; Pulgarin, Cesar; Kiwi, John

    2016-01-13

    The first evidence for Cu-Ag (50%/50%) nanoparticulate hybrid coatings is presented leading to a complete and almost instantaneous bacterial inactivation in the dark (≤5 min). Dark bacterial inactivation times on Cu-Ag (50%/50%) were observed to coincide with the times required by actinic light irradiation. This provides the evidence that the bimetal Cu-Ag driven inactivation predominates over a CuO/Cu2O and Ag2O oxides inducing a semiconductor driven behavior. Cu- or Ag-coated polyurethane (PU) catheters led to bacterial inactivation needing about ∼30 min. The accelerated bacterial inactivation by Cu-Ag coated on 3D catheters sputtered was investigated in a detailed way. The release of Cu/Ag ions during bacterial inactivation was followed by inductively coupled plasma mass-spectrometry (ICP-MS) and the amount of Cu and Ag-ions released were below the cytotoxicity levels permitted by the sanitary regulations. By stereomicroscopy the amount of live/dead cells were followed during the bacterial inactivation time. By Fourier transform infrared spectroscopy (FTIR), the systematic shift of the -(CH2) band stretching of the outer lipo-polysaccharide bilayer (LPS) was followed to monitor the changes leading to cell lysis. A hydrophobic to hydrophilic transformation of the Cu-Ag PU catheter surface under light was observed within 30 min followed concomitantly to a longer back transformation to the hydrophobic initial state in the dark. Physical insight is provided for the superior performance of Cu-Ag films compared to Cu or Ag films in view of the drastic acceleration of the bacterial inactivation observed on bimetal Cu-Ag films coating PU catheters. A mechanism of bacterial inactivation is suggested that is consistent with the findings reported in this study.

  17. Application of Kolomogorov-Zurbenko Filter and the decoupled direct 3D method for the dynamic evaluation of a regional air quality model

    EPA Science Inventory

    Regional air quality models are being used in a policy-setting to estimate the response of air pollutant concentrations to changes in emissions and meteorology. Dynamic evaluation entails examination of a retrospective case(s) to assess whether an air quality model has properly p...

  18. 3D culture for cardiac cells.

    PubMed

    Zuppinger, Christian

    2016-07-01

    This review discusses historical milestones, recent developments and challenges in the area of 3D culture models with cardiovascular cell types. Expectations in this area have been raised in recent years, but more relevant in vitro research, more accurate drug testing results, reliable disease models and insights leading to bioartificial organs are expected from the transition to 3D cell culture. However, the construction of organ-like cardiac 3D models currently remains a difficult challenge. The heart consists of highly differentiated cells in an intricate arrangement.Furthermore, electrical “wiring”, a vascular system and multiple cell types act in concert to respond to the rapidly changing demands of the body. Although cardiovascular 3D culture models have been predominantly developed for regenerative medicine in the past, their use in drug screening and for disease models has become more popular recently. Many sophisticated 3D culture models are currently being developed in this dynamic area of life science. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

  19. 3D Spray Droplet Distributions in Sneezes

    NASA Astrophysics Data System (ADS)

    Techet, Alexandra; Scharfman, Barry; Bourouiba, Lydia

    2015-11-01

    3D spray droplet clouds generated during human sneezing are investigated using the Synthetic Aperture Feature Extraction (SAFE) method, which relies on light field imaging (LFI) and synthetic aperture (SA) refocusing computational photographic techniques. An array of nine high-speed cameras are used to image sneeze droplets and tracked the droplets in 3D space and time (3D + T). An additional high-speed camera is utilized to track the motion of the head during sneezing. In the SAFE method, the raw images recorded by each camera in the array are preprocessed and binarized, simplifying post processing after image refocusing and enabling the extraction of feature sizes and positions in 3D + T. These binary images are refocused using either additive or multiplicative methods, combined with thresholding. Sneeze droplet centroids, radii, distributions and trajectories are determined and compared with existing data. The reconstructed 3D droplet centroids and radii enable a more complete understanding of the physical extent and fluid dynamics of sneeze ejecta. These measurements are important for understanding the infectious disease transmission potential of sneezes in various indoor environments.

  20. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  1. Dynamic Assessment of the Vaginal High Pressure Zone using High Definition Manometery, 3D -Ultrasound and Magnetic Resonance Imaging of the Pelvic Floor Muscles

    PubMed Central

    Raizada, Varuna; Bhargava, Valmik; Jung, Sung-Ae; Karstens, Anna; Pretorius, Dolores; Krysl, Petr; Mittal, Ravinder K

    2010-01-01

    Aims We used a novel technique, high definition manometry (HDM) that utilizes 256 tactile sensitive micro-transducers to define the characteristics of vaginal high-pressure zone. Methods 16 nullipara asymptomatic women were studied using HDM, transperineal 2D dynamic ultrasound and dynamic magnetic resonance (MR) imaging. Results Vaginal high-pressure zone revealed higher contact pressures in anterior and posterior compared to lateral directions, both at rest and squeeze. At rest, anterior pressure cluster is located 10 mm cephalad to posterior pressure cluster; with squeeze the latter moves in the cranial direction by 7 mm. Ultrasound and MR images reveal that the anorectal angle moves cephalad and ventrally during squeeze. Cephalad movement of posterior pressure cluster during squeeze is similar to the cranial movement of anorectal angle. Conclusions We propose that the vaginal high-pressure zone represents the constrictor function and cranial movement of the posterior pressure cluster represents the elevator function of pelvic floor. PMID:20462564

  2. 3D Scan Systems Integration

    DTIC Science & Technology

    2007-11-02

    AGENCY USE ONLY (Leave Blank) 2. REPORT DATE 5 Feb 98 4. TITLE AND SUBTITLE 3D Scan Systems Integration REPORT TYPE AND DATES COVERED...2-89) Prescribed by ANSI Std. Z39-1 298-102 [ EDO QUALITY W3PECTEDI DLA-ARN Final Report for US Defense Logistics Agency on DDFG-T2/P3: 3D...SCAN SYSTEMS INTEGRATION Contract Number SPO100-95-D-1014 Contractor Ohio University Delivery Order # 0001 Delivery Order Title 3D Scan Systems

  3. Orbital and escape dynamics in barred galaxies - II. The 3D system: exploring the role of the normally hyperbolic invariant manifolds

    NASA Astrophysics Data System (ADS)

    Jung, Christof; Zotos, Euaggelos E.

    2016-12-01

    A three degrees of freedom (3-dof) barred galaxy model composed of a spherically symmetric nucleus, a bar, a flat disc and a spherically symmetric dark matter halo is used for investigating the dynamics of the system. We use colour-coded plots to demonstrate how the value of the semimajor axis of the bar influences the regular or chaotic dynamics of the 3-dof system. For distinguishing between ordered and chaotic motion, we use the Smaller ALingment Index (SALI) method, a fast yet very accurate tool. Undoubtedly, the most important elements of the dynamics are the normally hyperbolic invariant manifolds (NHIMs) located in the vicinity of the index 1 Lagrange points L2 and L3. These manifolds direct the flow of stars over the saddle points, while they also trigger the formation of rings and spirals. The dynamics in the neighbourhood of the saddle points is visualized by bifurcation diagrams of the Lyapunov orbits as well as by the restriction of the Poincaré map to the NHIMs. In addition, we reveal how the semimajor axis of the bar influences the structure of these manifolds which determine the final stellar structure (rings or spirals). Our numerical simulations suggest that in galaxies with weak bars the formation of R1 rings or R_1^' } pseudo-rings is favoured. In the case of galaxies with intermediate and strong bars, the invariant manifolds seem to give rise to R1R2 rings and twin spiral formations, respectively. We also compare our numerical outcomes with earlier related work and with observational data.

  4. A benchmark study of 2D and 3D finite element calculations simulating dynamic pulse buckling tests of cylindrical shells under axial impact

    SciTech Connect

    Hoffman, E.L.; Ammerman, D.J.

    1993-08-01

    A series of tests investigating dynamic pulse buckling of a cylindrical shell under axial impact is compared to several finite element simulations of the event. The purpose of the study is to compare the performance of the various analysis codes and element types with respect to a problem which is applicable to radioactive material transport packages, and ultimately to develop a benchmark problem to qualify finite element analysis codes for the transport package design industry.

  5. 3D quantification of dynamic fluid-fluid interfaces in porous media with fast x-ray microtomography: A comparison with quasi-equilibrium methods

    NASA Astrophysics Data System (ADS)

    Meisenheimer, D.; Brueck, C. L.; Wildenschild, D.

    2015-12-01

    X-ray microtomography imaging of fluid-fluid interfaces in three-dimensional porous media allows for the testing of thermodynamically derived predictions that seek a unique relationship between capillary pressure, fluid saturation, and specific interfacial area (Pc-Sw-Anw). Previous experimental studies sought to test this functional dependence under quasi-equilibrium conditions (assumed static on the imaging time-scale); however, applying predictive models developed under static conditions for dynamic scenarios can lead to substantial flaws in predicted outcomes. Theory and models developed using dynamic data can be verified using fast x-ray microtomography which allows for the unprecedented measurement of developing interfacial areas, curvatures, and trapping behaviors of fluid phases in three-dimensional systems. We will present results of drainage and imbibition experiments of air and water within a mixture of glass beads. The experiments were performed under both quasi-equilibrium and dynamic conditions at the Advanced Photon Source (APS) at Argonne National Laboratory. Fast x-ray microtomography was achieved by utilizing the high brilliance of the x-ray beam at the APS under pink-beam conditions where the white beam is modified with a 4 mm Al absorber and a 0.8 mrad Pt-coated mirror to eliminate low and high-energy photons, respectively. We present a comparison of the results from the quasi-equilibrium and dynamic experiments in an effort to determine if the Pc-Sw-Anw relationship is comparable under either experimental condition and to add to the discussion on whether the Pc-Sw-Anw relationship is unique as hypothesized by existing theory.

  6. 3D polymer scaffold arrays.

    PubMed

    Simon, Carl G; Yang, Yanyin; Dorsey, Shauna M; Ramalingam, Murugan; Chatterjee, Kaushik

    2011-01-01

    We have developed a combinatorial platform for fabricating tissue scaffold arrays that can be used for screening cell-material interactions. Traditional research involves preparing samples one at a time for characterization and testing. Combinatorial and high-throughput (CHT) methods lower the cost of research by reducing the amount of time and material required for experiments by combining many samples into miniaturized specimens. In order to help accelerate biomaterials research, many new CHT methods have been developed for screening cell-material interactions where materials are presented to cells as a 2D film or surface. However, biomaterials are frequently used to fabricate 3D scaffolds, cells exist in vivo in a 3D environment and cells cultured in a 3D environment in vitro typically behave more physiologically than those cultured on a 2D surface. Thus, we have developed a platform for fabricating tissue scaffold libraries where biomaterials can be presented to cells in a 3D format.

  7. Autofocus for 3D imaging

    NASA Astrophysics Data System (ADS)

    Lee-Elkin, Forest

    2008-04-01

    Three dimensional (3D) autofocus remains a significant challenge for the development of practical 3D multipass radar imaging. The current 2D radar autofocus methods are not readily extendable across sensor passes. We propose a general framework that allows a class of data adaptive solutions for 3D auto-focus across passes with minimal constraints on the scene contents. The key enabling assumption is that portions of the scene are sparse in elevation which reduces the number of free variables and results in a system that is simultaneously solved for scatterer heights and autofocus parameters. The proposed method extends 2-pass interferometric synthetic aperture radar (IFSAR) methods to an arbitrary number of passes allowing the consideration of scattering from multiple height locations. A specific case from the proposed autofocus framework is solved and demonstrates autofocus and coherent multipass 3D estimation across the 8 passes of the "Gotcha Volumetric SAR Data Set" X-Band radar data.

  8. Extracting full-field dynamic strain on a wind turbine rotor subjected to arbitrary excitations using 3D point tracking and a modal expansion technique

    NASA Astrophysics Data System (ADS)

    Baqersad, Javad; Niezrecki, Christopher; Avitabile, Peter

    2015-09-01

    Health monitoring of rotating structures such as wind turbines and helicopter rotors is generally performed using conventional sensors that provide a limited set of data at discrete locations near or on the hub. These sensors usually provide no data on the blades or inside them where failures might occur. Within this paper, an approach was used to extract the full-field dynamic strain on a wind turbine assembly subject to arbitrary loading conditions. A three-bladed wind turbine having 2.3-m long blades was placed in a semi-built-in boundary condition using a hub, a machining chuck, and a steel block. For three different test cases, the turbine was excited using (1) pluck testing, (2) random impacts on blades with three impact hammers, and (3) random excitation by a mechanical shaker. The response of the structure to the excitations was measured using three-dimensional point tracking. A pair of high-speed cameras was used to measure displacement of optical targets on the structure when the blades were vibrating. The measured displacements at discrete locations were expanded and applied to the finite element model of the structure to extract the full-field dynamic strain. The results of the paper show an excellent correlation between the strain predicted using the proposed approach and the strain measured with strain-gages for each of the three loading conditions. The approach used in this paper to predict the strain showed higher accuracy than the digital image correlation technique. The new expansion approach is able to extract dynamic strain all over the entire structure, even inside the structure beyond the line of sight of the measurement system. Because the method is based on a non-contacting measurement approach, it can be readily applied to a variety of structures having different boundary and operating conditions, including rotating blades.

  9. Molecular modeling studies of [6,6,5] Tricyclic Fused Oxazolidinones as FXa inhibitors using 3D-QSAR, Topomer CoMFA, molecular docking and molecular dynamics simulations.

    PubMed

    Xu, Cheng; Ren, Yujie

    2015-10-15

    Coagulation factor Xa (Factor Xa, FXa) is a particularly promising target for novel anticoagulant therapy. The first oral factor Xa inhibitor has been approved in the EU and Canada in 2008. In this work, 38 [6,6,5] Tricyclic Fused Oxazolidinones were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics and Topomer CoMFA (comparative molecular field analysis) were used to build 3D-QSAR models. The results show that the best CoMFA model has q(2)=0.511 and r(2)=0.984, the best CoMSIA (comparative molecular similarity indices analysis) model has q(2)=0.700 and r(2)=0.993 and the Topomer CoMFA analysis has q(2)=0.377 and r(2)=0.886. The results indicated the steric, hydrophobic, H-acceptor and electrostatic fields play key roles in models. Molecular docking and molecular dynamics explored the binding relationship of the ligand and the receptor protein.

  10. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  11. Measurement of 3-D Vibrational Motion by Dynamic Photogrammetry Using Least-Square Image Matching for Sub-Pixel Targeting to Improve Accuracy.

    PubMed

    Lee, Hyoseong; Rhee, Huinam; Oh, Jae Hong; Park, Jin Ho

    2016-03-11

    This paper deals with an improved methodology to measure three-dimensional dynamic displacements of a structure by digital close-range photogrammetry. A series of stereo images of a vibrating structure installed with targets are taken at specified intervals by using two daily-use cameras. A new methodology is proposed to accurately trace the spatial displacement of each target in three-dimensional space. This method combines the correlation and the least-square image matching so that the sub-pixel targeting can be obtained to increase the measurement accuracy. Collinearity and space resection theory are used to determine the interior and exterior orientation parameters. To verify the proposed method, experiments have been performed to measure displacements of a cantilevered beam excited by an electrodynamic shaker, which is vibrating in a complex configuration with mixed bending and torsional motions simultaneously with multiple frequencies. The results by the present method showed good agreement with the measurement by two laser displacement sensors. The proposed methodology only requires inexpensive daily-use cameras, and can remotely detect the dynamic displacement of a structure vibrating in a complex three-dimensional defection shape up to sub-pixel accuracy. It has abundant potential applications to various fields, e.g., remote vibration monitoring of an inaccessible or dangerous facility.

  12. Measurement of 3-D Vibrational Motion by Dynamic Photogrammetry Using Least-Square Image Matching for Sub-Pixel Targeting to Improve Accuracy

    PubMed Central

    Lee, Hyoseong; Rhee, Huinam; Oh, Jae Hong; Park, Jin Ho

    2016-01-01

    This paper deals with an improved methodology to measure three-dimensional dynamic displacements of a structure by digital close-range photogrammetry. A series of stereo images of a vibrating structure installed with targets are taken at specified intervals by using two daily-use cameras. A new methodology is proposed to accurately trace the spatial displacement of each target in three-dimensional space. This method combines the correlation and the least-square image matching so that the sub-pixel targeting can be obtained to increase the measurement accuracy. Collinearity and space resection theory are used to determine the interior and exterior orientation parameters. To verify the proposed method, experiments have been performed to measure displacements of a cantilevered beam excited by an electrodynamic shaker, which is vibrating in a complex configuration with mixed bending and torsional motions simultaneously with multiple frequencies. The results by the present method showed good agreement with the measurement by two laser displacement sensors. The proposed methodology only requires inexpensive daily-use cameras, and can remotely detect the dynamic displacement of a structure vibrating in a complex three-dimensional defection shape up to sub-pixel accuracy. It has abundant potential applications to various fields, e.g., remote vibration monitoring of an inaccessible or dangerous facility. PMID:26978366

  13. Phase and magnitude spatiotemporal dynamics of β oscillation in electrocorticography (ECoG) in the monkey motor cortex at the onset of 3D reaching movements.

    PubMed

    Watanabe, Hidenori; Takahashi, Kazutaka; Nishimura, Yukio; Isa, Tadashi

    2014-01-01

    β oscillations in local field potentials, electro-corticography (ECoG), and electroencephalograms (EEG) are ubiquitous in the motor cortex of monkeys and humans. However due to their lack of contributions, compared to other frequency ranges, to decode effector kinematics especially in ECoG signals, spatiotemporal dynamics of ECoG β oscillations has not been examined despite the larger areas that ECoG arrays can cover than standard intracortical multielectrode arrays. Here, we used ECoG grids to cover large areas of motor cortex and some somatosensory cortex in monkeys while they performed an unconstrained reaching and a lever pulling task at two force levels in three dimensional space. We showed that under the pulling task β power increased around movement onset. However, the β phases were locked around the movement onsets and their peak timings were spatially aligned in the motor cortex. These results may indicate that spatiotemporal dynamics of β oscillation conveys task relevant information and that ECoG arrays will be useful to study larger spatiotemporal patterns in the motor cortex, or any cortical areas in general, than intracortical multielectrode arrays.

  14. 3D Visualization of Cooperative Trajectories

    NASA Technical Reports Server (NTRS)

    Schaefer, John A.

    2014-01-01

    Aerodynamicists and biologists have long recognized the benefits of formation flight. When birds or aircraft fly in the upwash region of the vortex generated by leaders in a formation, induced drag is reduced for the trail bird or aircraft, and efficiency improves. The major consequence of this is that fuel consumption can be greatly reduced. When two aircraft are separated by a large enough longitudinal distance, the aircraft are said to be flying in a cooperative trajectory. A simulation has been developed to model autonomous cooperative trajectories of aircraft; however it does not provide any 3D representation of the multi-body system dynamics. The topic of this research is the development of an accurate visualization of the multi-body system observable in a 3D environment. This visualization includes two aircraft (lead and trail), a landscape for a static reference, and simplified models of the vortex dynamics and trajectories at several locations between the aircraft.

  15. Volumetric visualization of 3D data

    NASA Technical Reports Server (NTRS)

    Russell, Gregory; Miles, Richard

    1989-01-01

    In recent years, there has been a rapid growth in the ability to obtain detailed data on large complex structures in three dimensions. This development occurred first in the medical field, with CAT (computer aided tomography) scans and now magnetic resonance imaging, and in seismological exploration. With the advances in supercomputing and computational fluid dynamics, and in experimental techniques in fluid dynamics, there is now the ability to produce similar large data fields representing 3D structures and phenomena in these disciplines. These developments have produced a situation in which currently there is access to data which is too complex to be understood using the tools available for data reduction and presentation. Researchers in these areas are becoming limited by their ability to visualize and comprehend the 3D systems they are measuring and simulating.

  16. Faster Aerodynamic Simulation With Cart3D

    NASA Technical Reports Server (NTRS)

    2003-01-01

    A NASA-developed aerodynamic simulation tool is ensuring the safety of future space operations while providing designers and engineers with an automated, highly accurate computer simulation suite. Cart3D, co-winner of NASA's 2002 Software of the Year award, is the result of over 10 years of research and software development conducted by Michael Aftosmis and Dr. John Melton of Ames Research Center and Professor Marsha Berger of the Courant Institute at New York University. Cart3D offers a revolutionary approach to computational fluid dynamics (CFD), the computer simulation of how fluids and gases flow around an object of a particular design. By fusing technological advancements in diverse fields such as mineralogy, computer graphics, computational geometry, and fluid dynamics, the software provides a new industrial geometry processing and fluid analysis capability with unsurpassed automation and efficiency.

  17. Fast Domain Partitioning Method for dynamic boundary integral equations applicable to non-planar faults dipping in 3-D elastic half-space

    NASA Astrophysics Data System (ADS)

    Ando, Ryosuke

    2016-11-01

    The elastodynamic boundary integral equation method (BIEM) in real space and in the temporal domain is an accurate semi-analytical tool to investigate the earthquake rupture dynamics on non-planar faults. However, its heavy computational demand for a historic integral generally increases with a time complexity of O(MN3)for the number of time steps N and elements M due to volume integration in the causality cone. In this study, we introduce an efficient BIEM, termed the `Fast Domain Partitioning Method' (FDPM), which enables us to reduce the computation time to the order of the surface integral, O(MN2), without degrading the accuracy. The memory requirement is also reduced to O(M2) from O(M2N). FDPM uses the physical nature of Green's function for stress to partition the causality cone into the domains of the P and S wave fronts, the domain in-between the P and S wave fronts, and the domain of the static equilibrium, where the latter two domains exhibit simpler dependences on time and/or space. The scalability of this method is demonstrated on the large-scale par