Engineering 3D Models of Tumors and Bone to Understand Tumor-Induced Bone Disease and Improve Treatments

PubMed Central

Kwakwa, Kristin A.; Vanderburgh, Joseph P.; Guelcher, Scott A.

2018-01-01

Purpose of Review Bone is a structurally unique microenvironment that presents many challenges for the development of 3D models for studying bone physiology and diseases, including cancer. As researchers continue to investigate the interactions within the bone microenvironment, the development of 3D models of bone has become critical. Recent Findings 3D models have been developed that replicate some properties of bone, but have not fully reproduced the complex structural and cellular composition of the bone microenvironment. This review will discuss 3D models including polyurethane, silk, and collagen scaffolds that have been developed to study tumor-induced bone disease. In addition, we discuss 3D printing techniques used to better replicate the structure of bone. Summary 3D models that better replicate the bone microenvironment will help researchers better understand the dynamic interactions between tumors and the bone microenvironment, ultimately leading to better models for testing therapeutics and predicting patient outcomes. PMID:28646444

Fully 3D modeling of tokamak vertical displacement events with realistic parameters

NASA Astrophysics Data System (ADS)

Pfefferle, David; Ferraro, Nathaniel; Jardin, Stephen; Bhattacharjee, Amitava

2016-10-01

In this work, we model the complex multi-domain and highly non-linear physics of Vertical Displacement Events (VDEs), one of the most damaging off-normal events in tokamaks, with the implicit 3D extended MHD code M3D-C1. The code has recently acquired the capability to include finite thickness conducting structures within the computational domain. By exploiting the possibility of running a linear 3D calculation on top of a non-linear 2D simulation, we monitor the non-axisymmetric stability and assess the eigen-structure of kink modes as the simulation proceeds. Once a stability boundary is crossed, a fully 3D non-linear calculation is launched for the remainder of the simulation, starting from an earlier time of the 2D run. This procedure, along with adaptive zoning, greatly increases the efficiency of the calculation, and allows to perform VDE simulations with realistic parameters and high resolution. Simulations are being validated with NSTX data where both axisymmetric (toroidally averaged) and non-axisymmetric induced and conductive (halo) currents have been measured. This work is supported by US DOE Grant DE-AC02-09CH11466.

3D MHD Modeling of Prominence Formation by Plasma Evaporation and Condensation

NASA Astrophysics Data System (ADS)

Torok, T.; Lionello, R.; Mikic, Z.; Downs, C.; Titov, V. S.

2017-12-01

The formation of prominence material in the solar corona still belongs to the open questions of solar physics. There exists a consensus that prominence plasma has to be of chromospheric origin, but the mechanisms by which it accumulates in the corona are still not well understood. The presently most accepted scenario invokes the evaporation of chromospheric plasma via foot point heating and its subsequent condensation in the corona via thermal instabilities. This scenario has been successfully modeled in 1D hydrodynamic simulations along single field lines of a static magnetic field, but a more appropriate, fully 3D treatment of the thermodynamics in time-dependent magnetic fields was started just very recently by Xia et al. Our group at PSI has recently begun to engage in this challenging task as well, using our time-dependent, fully 3D thermodynamic MHD code MAS. For our investigation we consider two different coronal flux-rope configurations, using the analytical model by Titov and Démoulin and a model in which an elongated flux rope is constructed by photospheric flows. We investigate the plasma behavior for both configurations, using heating models of different complexity, and accompany our analysis by 1D loop simulations performed along selected field lines. In this presentation, we outline our modeling approach and discuss the results obtained so far.

Can CH-53K 3D Technical Data Support the Provisioning Process

DTIC Science & Technology

2017-05-01

contain the minimum required data characteristics and elements (Appendix A) and (2) are fully anno - tated, they can be converted to 3D PDF files that...were anno - tated as part of the original model development/creation process, the time to perform an annotation would be about 50 percent (about 1.5...files, after the fact. If the models had been anno - tated at the time they were created, we estimate that the cost to implement a 3D PDF solution for

A three-dimensional semianalytical model of hydraulic fracture growth through weak barriers

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

Luiskutty, C.T.; Tomutes, L.; Palmer, I.D.

1989-08-01

The goal of this research was to develop a fracture model for length/height ratio {le}4 that includes 2D flow (and a line source corresponding to the perforated interval) but makes approximations that allow a semianalytical solution, with large computer-time savings over the fully numerical mode. The height, maximum width, and pressure at the wellbore in this semianalytical model are calculated and compared with the results of the fully three-dimensional (3D) model. There is reasonable agreement in all parameters, the maximum discrepancy being 24%. Comparisons of fracture volume and leakoff volume also show reasonable agreement in volume and fluid efficiencies. Themore » values of length/height ratio, in the four cases in which agreement is found, vary from 1.5 to 3.7. The model offers a useful first-order (or screening) calculation of fracture-height growth through weak barriers (e.g., low stress contrasts). When coupled with the model developed for highly elongated fractures of length/height ratio {ge}4, which are also found to be in basic agreement with the fully numerical model, this new model provides the capability for approximating fracture-height growth through barriers for vertical fracture shapes that vary from penny to highly elongated. The computer time required is estimated to be less than the time required for the fully numerical model by a factor of 10 or more.« less

DYNA3D: A computer code for crashworthiness engineering

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

Hallquist, J.O.; Benson, D.J.

1986-09-01

A finite element program with crashworthiness applications has been developed at LLNL. DYNA3D, an explicit, fully vectorized, finite deformation structural dynamics program, has four capabilities that are critical for the efficient and realistic modeling crash phenomena: (1) fully optimized nonlinear solid, shell, and beam elements for representing a structure; (2) a broad range of constitutive models for simulating material behavior; (3) sophisticated contact algorithms for impact interactions; (4) a rigid body capability to represent the bodies away from the impact region at a greatly reduced cost without sacrificing accuracy in the momentum calculations. Basic methodologies of the program are brieflymore » presented along with several crashworthiness calculations. Efficiencies of the Hughes-Liu and Belytschko-Tsay shell formulations are considered.« less

Higher Rank ABJM Wilson Loops from Matrix Models

NASA Astrophysics Data System (ADS)

Cookmeyer, Jonathan; Liu, James; Zayas, Leopoldo

2017-01-01

We compute the expectation values of 1/6 supersymmetric Wilson Loops in ABJM theory in higher rank representations. Using standard matrix model techniques, we calculate the expectation value in the rank m fully symmetric and fully antisymmetric representation where m is scaled with N. To leading order, we find agreement with the classical action of D6 and D2 branes in AdS4 ×CP3 respectively. Further, we compute the first subleading order term, which, on the AdS side, makes a prediction for the one-loop effective action of the corresponding D6 and D2 branes. Supported by the National Science Foundation under Grant No. PHY 1559988 and the US Department of Energy under Grant No. DE-SC0007859.

High Cycle Fatigue Prediction for Mistuned Bladed Disks with Fully Coupled Fluid-Structural Interaction

DTIC Science & Technology

2006-06-01

response (time domain) structural vibration model for mistuned rotor bladed disk based on the efficient SNM model has been developed. The vi- bration...airfoil and 3D wing, unsteady vortex shedding of a stationary cylinder, induced vibration of a cylinder, forced vibration of a pitching airfoil, induced... vibration and flutter boundary of 2D NACA 64A010 transonic airfoil, 3D plate wing structural response. The predicted results agree well with benchmark

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

DOE PAGES

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.; ...

2016-09-18

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

A fully coupled method for massively parallel simulation of hydraulically driven fractures in 3-dimensions: FULLY COUPLED PARALLEL SIMULATION OF HYDRAULIC FRACTURES IN 3-D

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

Settgast, Randolph R.; Fu, Pengcheng; Walsh, Stuart D. C.

This study describes a fully coupled finite element/finite volume approach for simulating field-scale hydraulically driven fractures in three dimensions, using massively parallel computing platforms. The proposed method is capable of capturing realistic representations of local heterogeneities, layering and natural fracture networks in a reservoir. A detailed description of the numerical implementation is provided, along with numerical studies comparing the model with both analytical solutions and experimental results. The results demonstrate the effectiveness of the proposed method for modeling large-scale problems involving hydraulically driven fractures in three dimensions.

3D image processing architecture for camera phones

NASA Astrophysics Data System (ADS)

Atanassov, Kalin; Ramachandra, Vikas; Goma, Sergio R.; Aleksic, Milivoje

2011-03-01

Putting high quality and easy-to-use 3D technology into the hands of regular consumers has become a recent challenge as interest in 3D technology has grown. Making 3D technology appealing to the average user requires that it be made fully automatic and foolproof. Designing a fully automatic 3D capture and display system requires: 1) identifying critical 3D technology issues like camera positioning, disparity control rationale, and screen geometry dependency, 2) designing methodology to automatically control them. Implementing 3D capture functionality on phone cameras necessitates designing algorithms to fit within the processing capabilities of the device. Various constraints like sensor position tolerances, sensor 3A tolerances, post-processing, 3D video resolution and frame rate should be carefully considered for their influence on 3D experience. Issues with migrating functions such as zoom and pan from the 2D usage model (both during capture and display) to 3D needs to be resolved to insure the highest level of user experience. It is also very important that the 3D usage scenario (including interactions between the user and the capture/display device) is carefully considered. Finally, both the processing power of the device and the practicality of the scheme needs to be taken into account while designing the calibration and processing methodology.

A Novel Method for Dynamic Short-Beam Shear Testing of 3D Woven Composites

DTIC Science & Technology

2011-08-11

specimen was homogenized as an orthotropic elastic material with properties given in Table 1 [38]. The use of fully elastic model removes any material...impact event however after approximately 0.5 mm of deflection, equilibrium is reached. It is observed from Fig. 4(d) that equilibrium is never fully ...The public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing

Data-driven sampling method for building 3D anatomical models from serial histology

NASA Astrophysics Data System (ADS)

Salunke, Snehal Ulhas; Ablove, Tova; Danforth, Theresa; Tomaszewski, John; Doyle, Scott

2017-03-01

In this work, we investigate the effect of slice sampling on 3D models of tissue architecture using serial histopathology. We present a method for using a single fully-sectioned tissue block as pilot data, whereby we build a fully-realized 3D model and then determine the optimal set of slices needed to reconstruct the salient features of the model objects under biological investigation. In our work, we are interested in the 3D reconstruction of microvessel architecture in the trigone region between the vagina and the bladder. This region serves as a potential avenue for drug delivery to treat bladder infection. We collect and co-register 23 serial sections of CD31-stained tissue images (6 μm thick sections), from which four microvessels are selected for analysis. To build each model, we perform semi-automatic segmentation of the microvessels. Subsampled meshes are then created by removing slices from the stack, interpolating the missing data, and re-constructing the mesh. We calculate the Hausdorff distance between the full and subsampled meshes to determine the optimal sampling rate for the modeled structures. In our application, we found that a sampling rate of 50% (corresponding to just 12 slices) was sufficient to recreate the structure of the microvessels without significant deviation from the fullyrendered mesh. This pipeline effectively minimizes the number of histopathology slides required for 3D model reconstruction, and can be utilized to either (1) reduce the overall costs of a project, or (2) enable additional analysis on the intermediate slides.

1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time.

PubMed

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator-which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics.

Impact of vitamin D on the hospitalization rate of Crohn's disease patients seen at a tertiary care center

PubMed Central

Venkata, Krishna V R; Arora, Sumant S; Xie, Feng-Long; Malik, Talha A

2017-01-01

AIM To study the association between vitamin D level and hospitalization rate in Crohn’s disease (CD) patients. METHODS We designed a retrospective cohort study using adult patients (> 19 years) with CD followed for at least one year at our inflammatory bowel disease center. Vitamin D levels were divided into: low mean vitamin D level (< 30 ng/mL) vs appropriate mean vitamin D level (30-100 ng/mL). Generalized Poisson Regression Models (GPR) for Rate Data were used to estimate partially adjusted and fully adjusted incidence rate ratios (IRR) of hospitalization among CD patients. We also examined IRRs for vitamin D level as a continuous variable. RESULTS Of the 880 CD patients, 196 patients with vitamin D level during the observation period were included. Partially adjusted model demonstrated that CD patients with a low mean vitamin D level were almost twice more likely to be admitted (IRR = 1.76, 95%CI: 1.38-2.24) compared to those with an appropriate vitamin D level. The fully adjusted model confirmed this association (IRR = 1.44, 95%CI: 1.11-1.87). Partially adjusted model with vitamin D level as a continuous variable demonstrated, higher mean vitamin D level was associated with a 3% lower likelihood of admission with every unit (ng/mL) rise in mean vitamin D level (IRR = 0.97, 95%CI: 0.96-0.98). The fully adjusted model confirmed this association (IRR = 0.98, 95%CI: 0.97-0.99). CONCLUSION Normal or adequate vitamin D stores may be protective in the clinical course of CD. However, this role needs to be further characterized and understood. PMID:28465638

Anibamine and its Analogues as Novel Anti Prostate Cancer Agents

DTIC Science & Technology

2010-06-01

PC- 3, and DU-145 has been conducted continuously to evaluate the efficacy of more ligands. A molecular modeling study (3D QSAR ) protocol has been... Toxicology at Virginia Commonwealth University. Both the PI’s lab and Dr. 10 Selley’s lab have fully functional binding assay facility. The assays is...pursue the docking study and 3D QSAR study. 5.3 3D QSAR (Quantitative Structure-Activity Relationships) Study As proposed in our proposal, we will

1D-3D hybrid modeling—from multi-compartment models to full resolution models in space and time

PubMed Central

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M.; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics. PMID:25120463

Multigrid Method for Modeling Multi-Dimensional Combustion with Detailed Chemistry

NASA Technical Reports Server (NTRS)

Zheng, Xiaoqing; Liu, Chaoqun; Liao, Changming; Liu, Zhining; McCormick, Steve

1996-01-01

A highly accurate and efficient numerical method is developed for modeling 3-D reacting flows with detailed chemistry. A contravariant velocity-based governing system is developed for general curvilinear coordinates to maintain simplicity of the continuity equation and compactness of the discretization stencil. A fully-implicit backward Euler technique and a third-order monotone upwind-biased scheme on a staggered grid are used for the respective temporal and spatial terms. An efficient semi-coarsening multigrid method based on line-distributive relaxation is used as the flow solver. The species equations are solved in a fully coupled way and the chemical reaction source terms are treated implicitly. Example results are shown for a 3-D gas turbine combustor with strong swirling inflows.

Automatic pedicles detection using convolutional neural network in a 3D spine reconstruction from biplanar radiographs

NASA Astrophysics Data System (ADS)

Bakhous, Christine; Aubert, Benjamin; Vazquez, Carlos; Cresson, Thierry; Parent, Stefan; De Guise, Jacques

2018-02-01

The 3D analysis of the spine deformities (scoliosis) has a high potential in its clinical diagnosis and treatment. In a biplanar radiographs context, a 3D analysis requires a 3D reconstruction from a pair of 2D X-rays. Whether being fully-/semiautomatic or manual, this task is complex because of the noise, the structure superimposition and partial information due to a limited projections number. Being involved in the axial vertebra rotation (AVR), which is a fundamental clinical parameter for scoliosis diagnosis, pedicles are important landmarks for the 3D spine modeling and pre-operative planning. In this paper, we focus on the extension of a fully-automatic 3D spine reconstruction method where the Vertebral Body Centers (VBCs) are automatically detected using Convolutional Neural Network (CNN) and then regularized using a Statistical Shape Model (SSM) framework. In this global process, pedicles are inferred statistically during the SSM regularization. Our contribution is to add a CNN-based regression model for pedicle detection allowing a better pedicle localization and improving the clinical parameters estimation (e.g. AVR, Cobb angle). Having 476 datasets including healthy patients and Adolescent Idiopathic Scoliosis (AIS) cases with different scoliosis grades (Cobb angles up to 116°), we used 380 for training, 48 for testing and 48 for validation. Adding the local CNN-based pedicle detection decreases the mean absolute error of the AVR by 10%. The 3D mean Euclidian distance error between detected pedicles and ground truth decreases by 17% and the maximum error by 19%. Moreover, a general improvement is observed in the 3D spine reconstruction and reflected in lower errors on the Cobb angle estimation.

Standardized 3D Bioprinting of Soft Tissue Models with Human Primary Cells.

PubMed

Rimann, Markus; Bono, Epifania; Annaheim, Helene; Bleisch, Matthias; Graf-Hausner, Ursula

2016-08-01

Cells grown in 3D are more physiologically relevant than cells cultured in 2D. To use 3D models in substance testing and regenerative medicine, reproducibility and standardization are important. Bioprinting offers not only automated standardizable processes but also the production of complex tissue-like structures in an additive manner. We developed an all-in-one bioprinting solution to produce soft tissue models. The holistic approach included (1) a bioprinter in a sterile environment, (2) a light-induced bioink polymerization unit, (3) a user-friendly software, (4) the capability to print in standard labware for high-throughput screening, (5) cell-compatible inkjet-based printheads, (6) a cell-compatible ready-to-use BioInk, and (7) standard operating procedures. In a proof-of-concept study, skin as a reference soft tissue model was printed. To produce dermal equivalents, primary human dermal fibroblasts were printed in alternating layers with BioInk and cultured for up to 7 weeks. During long-term cultures, the models were remodeled and fully populated with viable and spreaded fibroblasts. Primary human dermal keratinocytes were seeded on top of dermal equivalents, and epidermis-like structures were formed as verified with hematoxylin and eosin staining and immunostaining. However, a fully stratified epidermis was not achieved. Nevertheless, this is one of the first reports of an integrative bioprinting strategy for industrial routine application. © 2015 Society for Laboratory Automation and Screening.

Numerical study of the 3-D effect on FEL performance and its application to the APS LEUTL FEL

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

Chae, Y.C.

A Low-Energy Undulator Test Line (LEUTL) is under construction at the Advanced Photon Source (APS). In LEUTL periodic focusing is provided by external quadrupoles. This results in an elliptical beam with its betatron oscillation envelope varying along the undulators. The free-electron laser (FEL) interaction with such a beam will exhibit truly 3-D effects. Thus the investigation of 3-D effects is important in optimizing the FEL performance. The programs GINGER and TDA3D, coupled with theoretically known facts, have been used for this purpose. Both programs are fully 3-D in moving the particle, but model the interaction between particles and axially symmetricmore » electromagnetic waves. Even though TDA3D can include a few azimuthal modes in the interaction, it is still not a fully 3-D FEL code. However, they show that these 2-D programs can still be used for an elliptical beam whose aspect ratio is within certain limits. The author presents numerical results of FEL performance for the circular beam, the elliptical beam, and finally for the beam in the realistic LEUTL lattice.« less

Simulating Water Flow in Variably Saturated Soils - Exploring the Advantage of Three-dimensional Models

NASA Astrophysics Data System (ADS)

Hopp, L.; Ivanov, V. Y.

2010-12-01

There is still a debate in rainfall-runoff modeling over the advantage of using three-dimensional models based on partial differential equations describing variably saturated flow vs. models with simpler infiltration and flow routing algorithms. Fully explicit 3D models are computationally demanding but allow the representation of spatially complex domains, heterogeneous soils, conditions of ponded infiltration, and solute transport, among others. Models with simpler infiltration and flow routing algorithms provide faster run times and are likely to be more versatile in the treatment of extreme conditions such as soil drying but suffer from underlying assumptions and ad-hoc parameterizations. In this numerical study, we explore the question of whether these two model strategies are competing approaches or if they complement each other. As a 3D physics-based model we use HYDRUS-3D, a finite element model that numerically solves the Richards equation for variably-saturated water flow. As an example of a simpler model, we use tRIBS+VEGGIE that solves the 1D Richards equation for vertical flow and applies Dupuit-Forchheimer approximation for saturated lateral exchange and gravity-driven flow for unsaturated lateral exchange. The flow can be routed using either the D-8 (steepest descent) or D-infinity flow routing algorithms. We study lateral subsurface stormflow and moisture dynamics at the hillslope-scale, using a zero-order basin topography, as a function of storm size, antecedent moisture conditions and slope angle. The domain and soil characteristics are representative of a forested hillslope with conductive soils in a humid environment, where the major runoff generating process is lateral subsurface stormflow. We compare spatially integrated lateral subsurface flow at the downslope boundary as well as spatial patterns of soil moisture. We illustrate situations where both model approaches perform equally well and identify conditions under which the application of a fully-explicit 3D model may be required for a realistic description of the hydrologic response.

3D-printed orthodontic brackets - proof of concept.

PubMed

Krey, Karl-Friedrich; Darkazanly, Nawras; Kühnert, Rolf; Ruge, Sebastian

Today, orthodontic treatment with fixed appliances is usually carried out using preprogrammed straight-wire brackets made of metal or ceramics. The goal of this study was to determine the possibility of clinically implementing a fully digital workflow with individually designed and three-dimensionally printed (3D-printed) brackets. Edgewise brackets were designed using computer-aided design (CAD) software for demonstration purposes. After segmentation of the malocclusion model generated based on intraoral scan data, the brackets were digitally positioned on the teeth and a target occlusion model created. The thus-defined tooth position was used to generate a template for an individualized arch form in the horizontal plane. The base contours of the brackets were modified to match the shape of the tooth surfaces, and a positioning guide (fabricated beforehand) was used to ensure that the brackets were bonded at the correct angle and position. The brackets, positioning guide, and retainer splint, digitally designed on the target occlusion model, were 3D printed using a Digital Light Processing (DLP) 3D printer. The archwires were individually pre-bent using the template. In the treatment sequence, it was shown for the first time that, in principle, it is possible to perform treatment with an individualized 3D-printed brackets system by using the proposed fully digital workflow. Technical aspects of the system, problems encountered in treatment, and possible future developments are discussed in this article.

Global fully kinetic models of planetary magnetospheres with iPic3D

NASA Astrophysics Data System (ADS)

Gonzalez, D.; Sanna, L.; Amaya, J.; Zitz, A.; Lembege, B.; Markidis, S.; Schriver, D.; Walker, R. J.; Berchem, J.; Peng, I. B.; Travnicek, P. M.; Lapenta, G.

2016-12-01

We report on the latest developments of our approach to model planetary magnetospheres, mini magnetospheres and the Earth's magnetosphere with the fully kinetic, electromagnetic particle in cell code iPic3D. The code treats electrons and multiple species of ions as full kinetic particles. We review: 1) Why a fully kinetic model and in particular why kinetic electrons are needed for capturing some of the most important aspects of the physics processes of planetary magnetospheres. 2) Why the energy conserving implicit method (ECIM) in its newest implementation [1] is the right approach to reach this goal. We consider the different electron scales and study how the new IECIM can be tuned to resolve only the electron scales of interest while averaging over the unresolved scales preserving their contribution to the evolution. 3) How with modern computing planetary magnetospheres, mini magnetosphere and eventually Earth's magnetosphere can be modeled with fully kinetic electrons. The path from petascale to exascale for iPiC3D is outlined based on the DEEP-ER project [2], using dynamic allocation of different processor architectures (Xeon and Xeon Phi) and innovative I/O technologies.Specifically results from models of Mercury are presented and compared with MESSENGER observations and with previous hybrid (fluid electrons and kinetic ions) simulations. The plasma convection around the planets includes the development of hydrodynamic instabilities at the flanks, the presence of the collisionless shocks, the magnetosheath, the magnetopause, reconnection zones, the formation of the plasma sheet and the magnetotail, and the variation of ion/electron plasma flows when crossing these frontiers. Given the full kinetic nature of our approach we focus on detailed particle dynamics and distribution at locations that can be used for comparison with satellite data. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint arXiv:1602.06326.[2] www.deep-er.eu

Generalized thick strip modelling for vortex-induced vibration of long flexible cylinders

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

Bao, Y., E-mail: ybao@sjtu.edu.cn; Department of Aeronautics, Imperial College London, South Kensington Campus, London; Palacios, R., E-mail: r.palacios@imperial.ac.uk

2016-09-15

We propose a generalized strip modelling method that is computationally efficient for the VIV prediction of long flexible cylinders in three-dimensional incompressible flow. In order to overcome the shortcomings of conventional strip-theory-based 2D models, the fluid domain is divided into “thick” strips, which are sufficiently thick to locally resolve the small scale turbulence effects and three dimensionality of the flow around the cylinder. An attractive feature of the model is that we independently construct a three-dimensional scale resolving model for individual strips, which have local spanwise scale along the cylinder's axial direction and are only coupled through the structural modelmore » of the cylinder. Therefore, this approach is able to cover the full spectrum for fully resolved 3D modelling to 2D strip theory. The connection between these strips is achieved through the calculation of a tensioned beam equation, which is used to represent the dynamics of the flexible body. In the limit, however, a single “thick” strip would fill the full 3D domain. A parallel Fourier spectral/hp element method is employed to solve the 3D flow dynamics in the strip-domain, and then the VIV response prediction is achieved through the strip–structure interactions. Numerical tests on both laminar and turbulent flows as well as the comparison against the fully resolved DNS are presented to demonstrate the applicability of this approach.« less

Cancer drug discovery: recent innovative approaches to tumor modeling.

PubMed

Lovitt, Carrie J; Shelper, Todd B; Avery, Vicky M

2016-09-01

Cell culture models have been at the heart of anti-cancer drug discovery programs for over half a century. Advancements in cell culture techniques have seen the rapid evolution of more complex in vitro cell culture models investigated for use in drug discovery. Three-dimensional (3D) cell culture research has become a strong focal point, as this technique permits the recapitulation of the tumor microenvironment. Biologically relevant 3D cellular models have demonstrated significant promise in advancing cancer drug discovery, and will continue to play an increasing role in the future. In this review, recent advances in 3D cell culture techniques and their application in tumor modeling and anti-cancer drug discovery programs are discussed. The topics include selection of cancer cells, 3D cell culture assays (associated endpoint measurements and analysis), 3D microfluidic systems and 3D bio-printing. Although advanced cancer cell culture models and techniques are becoming commonplace in many research groups, the use of these approaches has yet to be fully embraced in anti-cancer drug applications. Furthermore, limitations associated with analyzing information-rich biological data remain unaddressed.

Bioprinting technologies for disease modeling.

PubMed

Memic, Adnan; Navaei, Ali; Mirani, Bahram; Cordova, Julio Alvin Vacacela; Aldhahri, Musab; Dolatshahi-Pirouz, Alireza; Akbari, Mohsen; Nikkhah, Mehdi

2017-09-01

There is a great need for the development of biomimetic human tissue models that allow elucidation of the pathophysiological conditions involved in disease initiation and progression. Conventional two-dimensional (2D) in vitro assays and animal models have been unable to fully recapitulate the critical characteristics of human physiology. Alternatively, three-dimensional (3D) tissue models are often developed in a low-throughput manner and lack crucial native-like architecture. The recent emergence of bioprinting technologies has enabled creating 3D tissue models that address the critical challenges of conventional in vitro assays through the development of custom bioinks and patient derived cells coupled with well-defined arrangements of biomaterials. Here, we provide an overview on the technological aspects of 3D bioprinting technique and discuss how the development of bioprinted tissue models have propelled our understanding of diseases' characteristics (i.e. initiation and progression). The future perspectives on the use of bioprinted 3D tissue models for drug discovery application are also highlighted.

Semantic Building FAÇADE Segmentation from Airborne Oblique Images

NASA Astrophysics Data System (ADS)

Lin, Y.; Nex, F.; Yang, M. Y.

2018-05-01

With the introduction of airborne oblique camera systems and the improvement of photogrammetric techniques, high-resolution 2D and 3D data can be acquired in urban areas. This high-resolution data allows us to perform detailed investigations on building roofs and façades which can contribute to LoD3 city modeling. Normally, façade segmentation is achieved from terrestrial views. In this paper, we address the problem from aerial views by using high resolution oblique aerial images as the data source in urban areas. In addition to traditional image features, such as RGB and SIFT, normal vector and planarity are also extracted from dense matching point clouds. Then, these 3D geometrical features are projected back to 2D space to assist façade interpretation. Random forest is trained and applied to label façade pixels. Fully connected conditional random field (CRF), capturing long-range spatial interactions, is used as a post-processing to refine our classification results. Its pairwise potential is defined by a linear combination of Gaussian kernels and the CRF model is efficiently solved by mean field approximation. Experiments show that 3D features can significantly improve classification results. Also, fully connected CRF performs well in correcting noisy pixels.

Design and Implementation of a Self-Directed Stereochemistry Lesson Using Embedded Virtual Three-Dimensional Images in a Portable Document Format

ERIC Educational Resources Information Center

Cody, Jeremy A.; Craig, Paul A.; Loudermilk, Adam D.; Yacci, Paul M.; Frisco, Sarah L.; Milillo, Jennifer R.

2012-01-01

A novel stereochemistry lesson was prepared that incorporated both handheld molecular models and embedded virtual three-dimensional (3D) images. The images are fully interactive and eye-catching for the students; methods for preparing 3D molecular images in Adobe Acrobat are included. The lesson was designed and implemented to showcase the 3D…

Automated volumetric lung segmentation of thoracic CT images using fully convolutional neural network

NASA Astrophysics Data System (ADS)

Negahdar, Mohammadreza; Beymer, David; Syeda-Mahmood, Tanveer

2018-02-01

Deep Learning models such as Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance in 2D medical image analysis. In clinical practice; however, most analyzed and acquired medical data are formed of 3D volumes. In this paper, we present a fast and efficient 3D lung segmentation method based on V-net: a purely volumetric fully CNN. Our model is trained on chest CT images through volume to volume learning, which palliates overfitting problem on limited number of annotated training data. Adopting a pre-processing step and training an objective function based on Dice coefficient addresses the imbalance between the number of lung voxels against that of background. We have leveraged Vnet model by using batch normalization for training which enables us to use higher learning rate and accelerates the training of the model. To address the inadequacy of training data and obtain better robustness, we augment the data applying random linear and non-linear transformations. Experimental results on two challenging medical image data show that our proposed method achieved competitive result with a much faster speed.

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.

Modeling of power transmission and stress grading for corona protection

NASA Astrophysics Data System (ADS)

Zohdi, T. I.; Abali, B. E.

2017-11-01

Electrical high voltage (HV) machines are prone to corona discharges leading to power losses as well as damage of the insulating layer. Many different techniques are applied as corona protection and computational methods aid to select the best design. In this paper we develop a reduced-order model in 1D estimating electric field and temperature distribution of a conductor wrapped with different layers, as usual for HV-machines. Many assumptions and simplifications are undertaken for this 1D model, therefore, we compare its results to a direct numerical simulation in 3D quantitatively. Both models are transient and nonlinear, giving a possibility to quickly estimate in 1D or fully compute in 3D by a computational cost. Such tools enable understanding, evaluation, and optimization of corona shielding systems for multilayered coils.

Modeling Intrajunction Dispersion at a Well-Mixed Tidal River Junction

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

Wolfram, Phillip J.; Fringer, Oliver B.; Monsen, Nancy E.

In this paper, the relative importance of small-scale, intrajunction flow features such as shear layers, separation zones, and secondary flows on dispersion in a well-mixed tidal river junction is explored. A fully nonlinear, nonhydrostatic, and unstructured three-dimensional (3D) model is used to resolve supertidal dispersion via scalar transport at a well-mixed tidal river junction. Mass transport simulated in the junction is compared against predictions using a simple node-channel model to quantify the effects of small-scale, 3D intrajunction flow features on mixing and dispersion. The effects of three-dimensionality are demonstrated by quantifying the difference between two-dimensional (2D) and 3D model results.more » An intermediate 3D model that does not resolve the secondary circulation or the recirculating flow at the junction is also compared to the 3D model to quantify the relative sensitivity of mixing on intrajunction flow features. Resolution of complex flow features simulated by the full 3D model is not always necessary because mixing is primarily governed by bulk flow splitting due to the confluence–diffluence cycle. Finally, results in 3D are comparable to the 2D case for many flow pathways simulated, suggesting that 2D modeling may be reasonable for nonstratified and predominantly hydrostatic flows through relatively straight junctions, but not necessarily for the full junction network.« less

Modeling Intrajunction Dispersion at a Well-Mixed Tidal River Junction

DOE PAGES

Wolfram, Phillip J.; Fringer, Oliver B.; Monsen, Nancy E.; ...

2016-08-01

In this paper, the relative importance of small-scale, intrajunction flow features such as shear layers, separation zones, and secondary flows on dispersion in a well-mixed tidal river junction is explored. A fully nonlinear, nonhydrostatic, and unstructured three-dimensional (3D) model is used to resolve supertidal dispersion via scalar transport at a well-mixed tidal river junction. Mass transport simulated in the junction is compared against predictions using a simple node-channel model to quantify the effects of small-scale, 3D intrajunction flow features on mixing and dispersion. The effects of three-dimensionality are demonstrated by quantifying the difference between two-dimensional (2D) and 3D model results.more » An intermediate 3D model that does not resolve the secondary circulation or the recirculating flow at the junction is also compared to the 3D model to quantify the relative sensitivity of mixing on intrajunction flow features. Resolution of complex flow features simulated by the full 3D model is not always necessary because mixing is primarily governed by bulk flow splitting due to the confluence–diffluence cycle. Finally, results in 3D are comparable to the 2D case for many flow pathways simulated, suggesting that 2D modeling may be reasonable for nonstratified and predominantly hydrostatic flows through relatively straight junctions, but not necessarily for the full junction network.« less

Neutron and X-ray total scattering study of hydrogen disorder in fully hydrated hydrogrossular, Ca3Al2(O4H4)3

NASA Astrophysics Data System (ADS)

Keen, David A.; Keeble, Dean S.; Bennett, Thomas D.

2018-04-01

The structure of fully hydrated grossular, or katoite, contains an unusual arrangement of four O-H bonds within each O4 tetrahedra. Neutron and X-ray total scattering from a powdered deuterated sample have been measured to investigate the local arrangement of this O4D4 cluster. The O-D bond length determined directly from the pair distribution function is 0.954 Å, although the Rietveld-refined distance between average O and D positions was slightly smaller. Reverse Monte Carlo refinement of supercell models to the total scattering data show that other than the consequences of this correctly determined O-D bond length, there is little to suggest that the O4D4 structure is locally significantly different from that expected based on the average structure determined solely from Bragg diffraction.

3D deeply supervised network for automated segmentation of volumetric medical images.

PubMed

Dou, Qi; Yu, Lequan; Chen, Hao; Jin, Yueming; Yang, Xin; Qin, Jing; Heng, Pheng-Ann

2017-10-01

While deep convolutional neural networks (CNNs) have achieved remarkable success in 2D medical image segmentation, it is still a difficult task for CNNs to segment important organs or structures from 3D medical images owing to several mutually affected challenges, including the complicated anatomical environments in volumetric images, optimization difficulties of 3D networks and inadequacy of training samples. In this paper, we present a novel and efficient 3D fully convolutional network equipped with a 3D deep supervision mechanism to comprehensively address these challenges; we call it 3D DSN. Our proposed 3D DSN is capable of conducting volume-to-volume learning and inference, which can eliminate redundant computations and alleviate the risk of over-fitting on limited training data. More importantly, the 3D deep supervision mechanism can effectively cope with the optimization problem of gradients vanishing or exploding when training a 3D deep model, accelerating the convergence speed and simultaneously improving the discrimination capability. Such a mechanism is developed by deriving an objective function that directly guides the training of both lower and upper layers in the network, so that the adverse effects of unstable gradient changes can be counteracted during the training procedure. We also employ a fully connected conditional random field model as a post-processing step to refine the segmentation results. We have extensively validated the proposed 3D DSN on two typical yet challenging volumetric medical image segmentation tasks: (i) liver segmentation from 3D CT scans and (ii) whole heart and great vessels segmentation from 3D MR images, by participating two grand challenges held in conjunction with MICCAI. We have achieved competitive segmentation results to state-of-the-art approaches in both challenges with a much faster speed, corroborating the effectiveness of our proposed 3D DSN. Copyright © 2017 Elsevier B.V. All rights reserved.

Separation of Evans and Hiro currents in VDE of tokamak plasma

NASA Astrophysics Data System (ADS)

Galkin, Sergei A.; Svidzinski, V. A.; Zakharov, L. E.

2014-10-01

Progress on the Disruption Simulation Code (DSC-3D) development and benchmarking will be presented. The DSC-3D is one-fluid nonlinear time-dependent MHD code, which utilizes fully 3D toroidal geometry for the first wall, pure vacuum and plasma itself, with adaptation to the moving plasma boundary and accurate resolution of the plasma surface current. Suppression of fast magnetosonic scale by the plasma inertia neglecting will be demonstrated. Due to code adaptive nature, self-consistent plasma surface current modeling during non-linear dynamics of the Vertical Displacement Event (VDE) is accurately provided. Separation of the plasma surface current on Evans and Hiro currents during simulation of fully developed VDE, then the plasma touches in-vessel tiles, will be discussed. Work is supported by the US DOE SBIR Grant # DE-SC0004487.

A novel 2.5D finite difference scheme for simulations of resistivity logging in anisotropic media

NASA Astrophysics Data System (ADS)

Zeng, Shubin; Chen, Fangzhou; Li, Dawei; Chen, Ji; Chen, Jiefu

2018-03-01

The objective of this study is to develop a method to model 3D resistivity well logging problems in 2D formation with anisotropy, known as 2.5D modeling. The traditional 1D forward modeling extensively used in practice lacks the capability of modeling 2D formation. A 2.5D finite difference method (FDM) solving all the electric and magnetic field components simultaneously is proposed. Compared to other previous 2.5D FDM schemes, this method is more straightforward in modeling fully anisotropic media and easy to be implemented. Fourier transform is essential to this FDM scheme, and by employing Gauss-Legendre (GL) quadrature rule the computational time of this step can be greatly reduced. In the numerical examples, we first demonstrate the validity of the FDM scheme with GL rule by comparing with 1D forward modeling for layered anisotropic problems, and then we model a complicated 2D formation case and find that the proposed 2.5D FD scheme is much more efficient than 3D numerical methods.

A 3D human neural cell culture system for modeling Alzheimer’s disease

PubMed Central

Kim, Young Hye; Choi, Se Hoon; D’Avanzo, Carla; Hebisch, Matthias; Sliwinski, Christopher; Bylykbashi, Enjana; Washicosky, Kevin J.; Klee, Justin B.; Brüstle, Oliver; Tanzi, Rudolph E.; Kim, Doo Yeon

2015-01-01

Stem cell technologies have facilitated the development of human cellular disease models that can be used to study pathogenesis and test therapeutic candidates. These models hold promise for complex neurological diseases such as Alzheimer’s disease (AD) because existing animal models have been unable to fully recapitulate all aspects of pathology. We recently reported the characterization of a novel three-dimensional (3D) culture system that exhibits key events in AD pathogenesis, including extracellular aggregation of β-amyloid and accumulation of hyperphosphorylated tau. Here we provide instructions for the generation and analysis of 3D human neural cell cultures, including the production of genetically modified human neural progenitor cells (hNPCs) with familial AD mutations, the differentiation of the hNPCs in a 3D matrix, and the analysis of AD pathogenesis. The 3D culture generation takes 1–2 days. The aggregation of β-amyloid is observed after 6-weeks of differentiation followed by robust tau pathology after 10–14 weeks. PMID:26068894

An application of cascaded 3D fully convolutional networks for medical image segmentation.

PubMed

Roth, Holger R; Oda, Hirohisa; Zhou, Xiangrong; Shimizu, Natsuki; Yang, Ying; Hayashi, Yuichiro; Oda, Masahiro; Fujiwara, Michitaka; Misawa, Kazunari; Mori, Kensaku

2018-06-01

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ∼10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. 1 . Copyright © 2018 Elsevier Ltd. All rights reserved.

Fully-coupled analysis of jet mixing problems. Three-dimensional PNS model, SCIP3D

NASA Technical Reports Server (NTRS)

Wolf, D. E.; Sinha, N.; Dash, S. M.

1988-01-01

Numerical procedures formulated for the analysis of 3D jet mixing problems, as incorporated in the computer model, SCIP3D, are described. The overall methodology closely parallels that developed in the earlier 2D axisymmetric jet mixing model, SCIPVIS. SCIP3D integrates the 3D parabolized Navier-Stokes (PNS) jet mixing equations, cast in mapped cartesian or cylindrical coordinates, employing the explicit MacCormack Algorithm. A pressure split variant of this algorithm is employed in subsonic regions with a sublayer approximation utilized for treating the streamwise pressure component. SCIP3D contains both the ks and kW turbulence models, and employs a two component mixture approach to treat jet exhausts of arbitrary composition. Specialized grid procedures are used to adjust the grid growth in accordance with the growth of the jet, including a hybrid cartesian/cylindrical grid procedure for rectangular jets which moves the hybrid coordinate origin towards the flow origin as the jet transitions from a rectangular to circular shape. Numerous calculations are presented for rectangular mixing problems, as well as for a variety of basic unit problems exhibiting overall capabilities of SCIP3D.

Improved Range Estimation Model for Three-Dimensional (3D) Range Gated Reconstruction

PubMed Central

Chua, Sing Yee; Guo, Ningqun; Tan, Ching Seong; Wang, Xin

2017-01-01

Accuracy is an important measure of system performance and remains a challenge in 3D range gated reconstruction despite the advancement in laser and sensor technology. The weighted average model that is commonly used for range estimation is heavily influenced by the intensity variation due to various factors. Accuracy improvement in term of range estimation is therefore important to fully optimise the system performance. In this paper, a 3D range gated reconstruction model is derived based on the operating principles of range gated imaging and time slicing reconstruction, fundamental of radiant energy, Laser Detection And Ranging (LADAR), and Bidirectional Reflection Distribution Function (BRDF). Accordingly, a new range estimation model is proposed to alleviate the effects induced by distance, target reflection, and range distortion. From the experimental results, the proposed model outperforms the conventional weighted average model to improve the range estimation for better 3D reconstruction. The outcome demonstrated is of interest to various laser ranging applications and can be a reference for future works. PMID:28872589

3D virtual character reconstruction from projections: a NURBS-based approach

NASA Astrophysics Data System (ADS)

Triki, Olfa; Zaharia, Titus B.; Preteux, Francoise J.

2004-05-01

This work has been carried out within the framework of the industrial project, so-called TOON, supported by the French government. TOON aims at developing tools for automating the traditional 2D cartoon content production. This paper presents preliminary results of the TOON platform. The proposed methodology concerns the issues of 2D/3D reconstruction from a limited number of drawn projections, and 2D/3D manipulation/deformation/refinement of virtual characters. Specifically, we show that the NURBS-based modeling approach developed here offers a well-suited framework for generating deformable 3D virtual characters from incomplete 2D information. Furthermore, crucial functionalities such as animation and non-rigid deformation can be also efficiently handled and solved. Note that user interaction is enabled exclusively in 2D by achieving a multiview constraint specification method. This is fully consistent and compliant with the cartoon creator traditional practice and makes it possible to avoid the use of 3D modeling software packages which are generally complex to manipulate.

Development and validation of P-MODTRAN7 and P-MCScene, 1D and 3D polarimetric radiative transfer models

NASA Astrophysics Data System (ADS)

Hawes, Frederick T.; Berk, Alexander; Richtsmeier, Steven C.

2016-05-01

A validated, polarimetric 3-dimensional simulation capability, P-MCScene, is being developed by generalizing Spectral Sciences' Monte Carlo-based synthetic scene simulation model, MCScene, to include calculation of all 4 Stokes components. P-MCScene polarimetric optical databases will be generated by a new version (MODTRAN7) of the government-standard MODTRAN radiative transfer algorithm. The conversion of MODTRAN6 to a polarimetric model is being accomplished by (1) introducing polarimetric data, by (2) vectorizing the MODTRAN radiation calculations and by (3) integrating the newly revised and validated vector discrete ordinate model VDISORT3. Early results, presented here, demonstrate a clear pathway to the long-term goal of fully validated polarimetric models.

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

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

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

Testing of transition-region models: Test cases and data

NASA Technical Reports Server (NTRS)

Singer, Bart A.; Dinavahi, Surya; Iyer, Venkit

1991-01-01

Mean flow quantities in the laminar turbulent transition region and in the fully turbulent region are predicted with different models incorporated into a 3-D boundary layer code. The predicted quantities are compared with experimental data for a large number of different flows and the suitability of the models for each flow is evaluated.

Fully porous 3D printed titanium femoral stem to reduce stress-shielding following total hip arthroplasty.

PubMed

Arabnejad, Sajad; Johnston, Burnett; Tanzer, Michael; Pasini, Damiano

2017-08-01

Current hip replacement femoral implants are made of fully solid materials which all have stiffness considerably higher than that of bone. This mechanical mismatch can cause significant bone resorption secondary to stress shielding, which can lead to serious complications such as peri-prosthetic fracture during or after revision surgery. In this work, a high strength fully porous material with tunable mechanical properties is introduced for use in hip replacement design. The implant macro geometry is based off of a short stem taper-wedge implant compatible with minimally invasive hip replacement surgery. The implant micro-architecture is fine-tuned to locally mimic bone tissue properties which results in minimum bone resorption secondary to stress shielding. We present a systematic approach for the design of a 3D printed fully porous hip implant that encompasses the whole activity spectrum of implant development, from concept generation, multiscale mechanics of porous materials, material architecture tailoring, to additive manufacturing, and performance assessment via in vitro experiments in composite femurs. We show that the fully porous implant with an optimized material micro-structure can reduce the amount of bone loss secondary to stress shielding by 75% compared to a fully solid implant. This result also agrees with those of the in vitro quasi-physiological experimental model and the corresponding finite element model for both the optimized fully porous and fully solid implant. These studies demonstrate the merit and the potential of tuning material architecture to achieve a substantial reduction of bone resorption secondary to stress shielding. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1774-1783, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Getting in touch--3D printing in forensic imaging.

PubMed

Ebert, Lars Chr; Thali, Michael J; Ross, Steffen

2011-09-10

With the increasing use of medical imaging in forensics, as well as the technological advances in rapid prototyping, we suggest combining these techniques to generate displays of forensic findings. We used computed tomography (CT), CT angiography, magnetic resonance imaging (MRI) and surface scanning with photogrammetry in conjunction with segmentation techniques to generate 3D polygon meshes. Based on these data sets, a 3D printer created colored models of the anatomical structures. Using this technique, we could create models of bone fractures, vessels, cardiac infarctions, ruptured organs as well as bitemark wounds. The final models are anatomically accurate, fully colored representations of bones, vessels and soft tissue, and they demonstrate radiologically visible pathologies. The models are more easily understood by laypersons than volume rendering or 2D reconstructions. Therefore, they are suitable for presentations in courtrooms and for educational purposes. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Electro-mechanical response of a 3D nerve bundle model to mechanical loads leading to axonal injury.

PubMed

Cinelli, I; Destrade, M; Duffy, M; McHugh, P

2018-03-01

Traumatic brain injuries and damage are major causes of death and disability. We propose a 3D fully coupled electro-mechanical model of a nerve bundle to investigate the electrophysiological impairments due to trauma at the cellular level. The coupling is based on a thermal analogy of the neural electrical activity by using the finite element software Abaqus CAE 6.13-3. The model includes a real-time coupling, modulated threshold for spiking activation, and independent alteration of the electrical properties for each 3-layer fibre within a nerve bundle as a function of strain. Results of the coupled electro-mechanical model are validated with previously published experimental results of damaged axons. Here, the cases of compression and tension are simulated to induce (mild, moderate, and severe) damage at the nerve membrane of a nerve bundle, made of 4 fibres. Changes in strain, stress distribution, and neural activity are investigated for myelinated and unmyelinated nerve fibres, by considering the cases of an intact and of a traumatised nerve membrane. A fully coupled electro-mechanical modelling approach is established to provide insights into crucial aspects of neural activity at the cellular level due to traumatic brain injury. One of the key findings is the 3D distribution of residual stresses and strains at the membrane of each fibre due to mechanically induced electrophysiological impairments, and its impact on signal transmission. Copyright © 2017 John Wiley & Sons, Ltd.

GALFIT-CORSAIR: Implementing the Core-Sérsic Model Into GALFIT

NASA Astrophysics Data System (ADS)

Bonfini, Paolo

2014-10-01

We introduce GALFIT-CORSAIR: a publicly available, fully retro-compatible modification of the 2D fitting software GALFIT (v.3) which adds an implementation of the core-Sersic model. We demonstrate the software by fitting the images of NGC 5557 and NGC 5813, which have been previously identified as core-Sersic galaxies by their 1D radial light profiles. These two examples are representative of different dust obscuration conditions, and of bulge/disk decomposition. To perform the analysis, we obtained deep Hubble Legacy Archive (HLA) mosaics in the F555W filter (~V-band). We successfully reproduce the results of the previous 1D analysis, modulo the intrinsic differences between the 1D and the 2D fitting procedures. The code and the analysis procedure described here have been developed for the first coherent 2D analysis of a sample of core-Sersic galaxies, which will be presented in a forth-coming paper. As the 2D analysis provides better constraining on multi-component fitting, and is fully seeing-corrected, it will yield complementary constraints on the missing mass in depleted galaxy cores.

Easy and Fast Reconstruction of a 3D Avatar with an RGB-D Sensor.

PubMed

Mao, Aihua; Zhang, Hong; Liu, Yuxin; Zheng, Yinglong; Li, Guiqing; Han, Guoqiang

2017-05-12

This paper proposes a new easy and fast 3D avatar reconstruction method using an RGB-D sensor. Users can easily implement human body scanning and modeling just with a personal computer and a single RGB-D sensor such as a Microsoft Kinect within a small workspace in their home or office. To make the reconstruction of 3D avatars easy and fast, a new data capture strategy is proposed for efficient human body scanning, which captures only 18 frames from six views with a close scanning distance to fully cover the body; meanwhile, efficient alignment algorithms are presented to locally align the data frames in the single view and then globally align them in multi-views based on pairwise correspondence. In this method, we do not adopt shape priors or subdivision tools to synthesize the model, which helps to reduce modeling complexity. Experimental results indicate that this method can obtain accurate reconstructed 3D avatar models, and the running performance is faster than that of similar work. This research offers a useful tool for the manufacturers to quickly and economically create 3D avatars for products design, entertainment and online shopping.

Arterial waveguide model for shear wave elastography: implementation and in vitro validation

NASA Astrophysics Data System (ADS)

Vaziri Astaneh, Ali; Urban, Matthew W.; Aquino, Wilkins; Greenleaf, James F.; Guddati, Murthy N.

2017-07-01

Arterial stiffness is found to be an early indicator of many cardiovascular diseases. Among various techniques, shear wave elastography has emerged as a promising tool for estimating local arterial stiffness through the observed dispersion of guided waves. In this paper, we develop efficient models for the computational simulation of guided wave dispersion in arterial walls. The models are capable of considering fluid-loaded tubes, immersed in fluid or embedded in a solid, which are encountered in in vitro/ex vivo, and in vivo experiments. The proposed methods are based on judiciously combining Fourier transformation and finite element discretization, leading to a significant reduction in computational cost while fully capturing complex 3D wave propagation. The developed methods are implemented in open-source code, and verified by comparing them with significantly more expensive, fully 3D finite element models. We also validate the models using the shear wave elastography of tissue-mimicking phantoms. The computational efficiency of the developed methods indicates the possibility of being able to estimate arterial stiffness in real time, which would be beneficial in clinical settings.

Automatic Building Abstraction from Aerial Photogrammetry

NASA Astrophysics Data System (ADS)

Ley, A.; Hänsch, R.; Hellwich, O.

2017-09-01

Multi-view stereo has been shown to be a viable tool for the creation of realistic 3D city models. Nevertheless, it still states significant challenges since it results in dense, but noisy and incomplete point clouds when applied to aerial images. 3D city modelling usually requires a different representation of the 3D scene than these point clouds. This paper applies a fully-automatic pipeline to generate a simplified mesh from a given dense point cloud. The mesh provides a certain level of abstraction as it only consists of relatively large planar and textured surfaces. Thus, it is possible to remove noise, outlier, as well as clutter, while maintaining a high level of accuracy.

3D Proximal Tubule Tissues Recapitulate Key Aspects of Renal Physiology to Enable Nephrotoxicity Testing

PubMed Central

King, Shelby M.; Higgins, J. William; Nino, Celina R.; Smith, Timothy R.; Paffenroth, Elizabeth H.; Fairbairn, Casey E.; Docuyanan, Abigail; Shah, Vishal D.; Chen, Alice E.; Presnell, Sharon C.; Nguyen, Deborah G.

2017-01-01

Due to its exposure to high concentrations of xenobiotics, the kidney proximal tubule is a primary site of nephrotoxicity and resulting attrition in the drug development pipeline. Current pre-clinical methods using 2D cell cultures and animal models are unable to fully recapitulate clinical drug responses due to limited in vitro functional lifespan, or species-specific differences. Using Organovo's proprietary 3D bioprinting platform, we have developed a fully cellular human in vitro model of the proximal tubule interstitial interface comprising renal fibroblasts, endothelial cells, and primary human renal proximal tubule epithelial cells to enable more accurate prediction of tissue-level clinical outcomes. Histological characterization demonstrated formation of extensive microvascular networks supported by endogenous extracellular matrix deposition. The epithelial cells of the 3D proximal tubule tissues demonstrated tight junction formation and expression of renal uptake and efflux transporters; the polarized localization and function of P-gp and SGLT2 were confirmed. Treatment of 3D proximal tubule tissues with the nephrotoxin cisplatin induced loss of tissue viability and epithelial cells in a dose-dependent fashion, and cimetidine rescued these effects, confirming the role of the OCT2 transporter in cisplatin-induced nephrotoxicity. The tissues also demonstrated a fibrotic response to TGFβ as assessed by an increase in gene expression associated with human fibrosis and histological verification of excess extracellular matrix deposition. Together, these results suggest that the bioprinted 3D proximal tubule model can serve as a test bed for the mechanistic assessment of human nephrotoxicity and the development of pathogenic states involving epithelial-interstitial interactions, making them an important adjunct to animal studies. PMID:28337147

Services Oriented Smart City Platform Based On 3d City Model Visualization

NASA Astrophysics Data System (ADS)

Prandi, F.; Soave, M.; Devigili, F.; Andreolli, M.; De Amicis, R.

2014-04-01

The rapid technological evolution, which is characterizing all the disciplines involved within the wide concept of smart cities, is becoming a key factor to trigger true user-driven innovation. However to fully develop the Smart City concept to a wide geographical target, it is required an infrastructure that allows the integration of heterogeneous geographical information and sensor networks into a common technological ground. In this context 3D city models will play an increasingly important role in our daily lives and become an essential part of the modern city information infrastructure (Spatial Data Infrastructure). The work presented in this paper describes an innovative Services Oriented Architecture software platform aimed at providing smartcities services on top of 3D urban models. 3D city models are the basis of many applications and can became the platform for integrating city information within the Smart-Cites context. In particular the paper will investigate how the efficient visualisation of 3D city models using different levels of detail (LODs) is one of the pivotal technological challenge to support Smart-Cities applications. The goal is to provide to the final user realistic and abstract 3D representations of the urban environment and the possibility to interact with a massive amounts of semantic information contained into the geospatial 3D city model. The proposed solution, using OCG standards and a custom service to provide 3D city models, lets the users to consume the services and interact with the 3D model via Web in a more effective way.

A 3D THz image processing methodology for a fully integrated, semi-automatic and near real-time operational system

NASA Astrophysics Data System (ADS)

Brook, A.; Cristofani, E.; Vandewal, M.; Matheis, C.; Jonuscheit, J.; Beigang, R.

2012-05-01

The present study proposes a fully integrated, semi-automatic and near real-time mode-operated image processing methodology developed for Frequency-Modulated Continuous-Wave (FMCW) THz images with the center frequencies around: 100 GHz and 300 GHz. The quality control of aeronautics composite multi-layered materials and structures using Non-Destructive Testing is the main focus of this work. Image processing is applied on the 3-D images to extract useful information. The data is processed by extracting areas of interest. The detected areas are subjected to image analysis for more particular investigation managed by a spatial model. Finally, the post-processing stage examines and evaluates the spatial accuracy of the extracted information.

Fully Implicit, Nonlinear 3D Extended Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Chacon, Luis; Knoll, Dana

2003-10-01

Extended magnetohydrodynamics (XMHD) includes nonideal effects such as nonlinear, anisotropic transport and two-fluid (Hall) effects. XMHD supports multiple, separate time scales that make explicit time differencing approaches extremely inefficient. While a fully implicit implementation promises efficiency without sacrificing numerical accuracy,(D. A. Knoll et al., phJ. Comput. Phys.) 185 (2), 583-611 (2003) the nonlinear nature of the XMHD system and the numerical stiffness associated with the fast waves make this endeavor difficult. Newton-Krylov methods are, however, ideally suited for such a task. These synergistically combine Newton's method for nonlinear convergence, and Krylov techniques to solve the associated Jacobian (linear) systems. Krylov methods can be implemented Jacobian-free and can be preconditioned for efficiency. Successful preconditioning strategies have been developed for 2D incompressible resistive(L. Chacón et al., phJ. Comput. Phys). 178 (1), 15- 36 (2002) and Hall(L. Chacón and D. A. Knoll, phJ. Comput. Phys.), 188 (2), 573-592 (2003) MHD models. These are based on ``physics-based'' ideas, in which knowledge of the physics is exploited to derive well-conditioned (diagonally-dominant) approximations to the original system that are amenable to optimal solver technologies (multigrid). In this work, we will describe the status of the extension of the 2D preconditioning ideas for a 3D compressible, single-fluid XMHD model.

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches

NASA Astrophysics Data System (ADS)

Ragno, Rino; Ballante, Flavio; Pirolli, Adele; Wickersham, Richard B.; Patsilinakos, Alexandros; Hesse, Stéphanie; Perspicace, Enrico; Kirsch, Gilbert

2015-08-01

Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors.

Observable Signatures of Wind-driven Chemistry with a Fully Consistent Three-dimensional Radiative Hydrodynamics Model of HD 209458b

NASA Astrophysics Data System (ADS)

Drummond, B.; Mayne, N. J.; Manners, J.; Carter, A. L.; Boutle, I. A.; Baraffe, I.; Hébrard, É.; Tremblin, P.; Sing, D. K.; Amundsen, D. S.; Acreman, D.

2018-03-01

We present a study of the effect of wind-driven advection on the chemical composition of hot-Jupiter atmospheres using a fully consistent 3D hydrodynamics, chemistry, and radiative transfer code, the Met Office Unified Model (UM). Chemical modeling of exoplanet atmospheres has primarily been restricted to 1D models that cannot account for 3D dynamical processes. In this work, we couple a chemical relaxation scheme to the UM to account for the chemical interconversion of methane and carbon monoxide. This is done consistently with the radiative transfer meaning that departures from chemical equilibrium are included in the heating rates (and emission) and hence complete the feedback between the dynamics, thermal structure, and chemical composition. In this Letter, we simulate the well studied atmosphere of HD 209458b. We find that the combined effect of horizontal and vertical advection leads to an increase in the methane abundance by several orders of magnitude, which is directly opposite to the trend found in previous works. Our results demonstrate the need to include 3D effects when considering the chemistry of hot-Jupiter atmospheres. We calculate transmission and emission spectra, as well as the emission phase curve, from our simulations. We conclude that gas-phase nonequilibrium chemistry is unlikely to explain the model–observation discrepancy in the 4.5 μm Spitzer/IRAC channel. However, we highlight other spectral regions, observable with the James Webb Space Telescope, where signatures of wind-driven chemistry are more prominant.

Alzheimer’s in 3D culture: Challenges and perspectives

PubMed Central

D'Avanzo, Carla; Aronson, Jenna; Kim, Young Hye; Choi, Se Hoon; Tanzi, Rudolph E.; Kim, Doo Yeon

2015-01-01

Summary Alzheimer’s disease (AD) is the most common cause of dementia, and there is currently no cure. The “β-amyloid cascade hypothesis” of AD is the basis of current understanding of AD pathogenesis and drug discovery. However, no AD models have fully validated this hypothesis. We recently developed a human stem cell culture model of AD by cultivating genetically modified human neural stem cells in a three-dimensional (3D) cell culture system. These cells were able to recapitulate key events of AD pathology including β-amyloid plaques and neurofibrillary tangles. In this review, we will discuss the progress and current limitations of AD mouse models and human stem cell models as well as explore the breakthroughs of 3D cell culture systems. We will also share our perspective on the potential of dish models of neurodegenerative diseases for studying pathogenic cascades and therapeutic drug discovery. PMID:26252541

Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

Assessment of MARMOT Grain Growth Model

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

Fromm, B.; Zhang, Y.; Schwen, D.

2015-12-01

This report assesses the MARMOT grain growth model by comparing modeling predictions with experimental results from thermal annealing. The purpose here is threefold: (1) to demonstrate the validation approach of using thermal annealing experiments with non-destructive characterization, (2) to test the reconstruction capability and computation efficiency in MOOSE, and (3) to validate the grain growth model and the associated parameters that are implemented in MARMOT for UO 2. To assure a rigorous comparison, the 2D and 3D initial experimental microstructures of UO 2 samples were characterized using non-destructive Synchrotron x-ray. The same samples were then annealed at 2273K for grainmore » growth, and their initial microstructures were used as initial conditions for simulated annealing at the same temperature using MARMOT. After annealing, the final experimental microstructures were characterized again to compare with the results from simulations. So far, comparison between modeling and experiments has been done for 2D microstructures, and 3D comparison is underway. The preliminary results demonstrated the usefulness of the non-destructive characterization method for MARMOT grain growth model validation. A detailed analysis of the 3D microstructures is in progress to fully validate the current model in MARMOT.« less

Bioprinting of 3D Convoluted Renal Proximal Tubules on Perfusable Chips

NASA Astrophysics Data System (ADS)

Homan, Kimberly A.; Kolesky, David B.; Skylar-Scott, Mark A.; Herrmann, Jessica; Obuobi, Humphrey; Moisan, Annie; Lewis, Jennifer A.

2016-10-01

Three-dimensional models of kidney tissue that recapitulate human responses are needed for drug screening, disease modeling, and, ultimately, kidney organ engineering. Here, we report a bioprinting method for creating 3D human renal proximal tubules in vitro that are fully embedded within an extracellular matrix and housed in perfusable tissue chips, allowing them to be maintained for greater than two months. Their convoluted tubular architecture is circumscribed by proximal tubule epithelial cells and actively perfused through the open lumen. These engineered 3D proximal tubules on chip exhibit significantly enhanced epithelial morphology and functional properties relative to the same cells grown on 2D controls with or without perfusion. Upon introducing the nephrotoxin, Cyclosporine A, the epithelial barrier is disrupted in a dose-dependent manner. Our bioprinting method provides a new route for programmably fabricating advanced human kidney tissue models on demand.

Bioprinting of 3D Convoluted Renal Proximal Tubules on Perfusable Chips

PubMed Central

Homan, Kimberly A.; Kolesky, David B.; Skylar-Scott, Mark A.; Herrmann, Jessica; Obuobi, Humphrey; Moisan, Annie; Lewis, Jennifer A.

2016-01-01

Three-dimensional models of kidney tissue that recapitulate human responses are needed for drug screening, disease modeling, and, ultimately, kidney organ engineering. Here, we report a bioprinting method for creating 3D human renal proximal tubules in vitro that are fully embedded within an extracellular matrix and housed in perfusable tissue chips, allowing them to be maintained for greater than two months. Their convoluted tubular architecture is circumscribed by proximal tubule epithelial cells and actively perfused through the open lumen. These engineered 3D proximal tubules on chip exhibit significantly enhanced epithelial morphology and functional properties relative to the same cells grown on 2D controls with or without perfusion. Upon introducing the nephrotoxin, Cyclosporine A, the epithelial barrier is disrupted in a dose-dependent manner. Our bioprinting method provides a new route for programmably fabricating advanced human kidney tissue models on demand. PMID:27725720

The impacts of the axial-to-radial airflow quantity ratio and suction distance on air curtain dust control in a fully mechanized coal face.

PubMed

Wang, Hao; Cheng, Weimin; Sun, Biao; Yu, Haiming; Jin, Hu

2018-03-01

To understand the impacts of the axial-to-radial airflow quantity ratio (denoted as R) and the suction distance (denoted as D s ) on air curtain dust control in a fully mechanized coal face, the 3 down 610 coal face in Jiangzhuang coal mine was numerically simulated in this study. A mathematic model was established to describe the airflow migration and dust diffusion in a coal face, and a scaled physical model was constructed. The comparison between simulation results and field measurements validated the model and the parameter settings. Furthermore, the airflow migration and dust diffusion at various R and D s are analyzed using Ansys CFD. The results show that a reduction of R and D s is conducive to the formation of an effective axial dust control air curtain; the dust diffusion distance decreases with the decrease of both R and D s . By analyzing the simulation results, the optimal parameter for air curtain dust control in the 3 down 610 coal face and those faces with similar production conditions is determined as R = 1/9 and D s  = 2 m. Under the optimal parameter condition, the high-concentration dust can be confined in front of the mining driver within a space 5.8 m away from the coal face.

Effect of Freeze-Thaw Cycles on Soil Nitrogen Reactive Transport in a Polygonal Arctic Tundra Ecosystem at Barrow AK Using 3-D Coupled ALM-PFLOTRAN

NASA Astrophysics Data System (ADS)

Yuan, F.; Wang, G.; Painter, S. L.; Tang, G.; Xu, X.; Kumar, J.; Bisht, G.; Hammond, G. E.; Mills, R. T.; Thornton, P. E.; Wullschleger, S. D.

2017-12-01

In Arctic tundra ecosystem soil freezing-thawing is one of dominant physical processes through which biogeochemical (e.g., carbon and nitrogen) cycles are tightly coupled. Besides hydraulic transport, freezing-thawing can cause pore water movement and aqueous species gradients, which are additional mechanisms for soil nitrogen (N) reactive-transport in Tundra ecosystem. In this study, we have fully coupled an in-development ESM(i.e., Advanced Climate Model for Energy, ACME)'s Land Model (ALM) aboveground processes with a state-of-the-art massively parallel 3-D subsurface thermal-hydrology and reactive transport code, PFLOTRAN. The resulting coupled ALM-PFLOTRAN model is a Land Surface Model (LSM) capable of resolving 3-D soil thermal-hydrological-biogeochemical cycles. This specific version of PFLOTRAN has incorporated CLM-CN Converging Trophic Cascade (CTC) model and a full and simple but robust soil N cycle. It includes absorption-desorption for soil NH4+ and gas dissolving-degasing process as well. It also implements thermal-hydrology mode codes with three newly-modified freezing-thawing algorithms which can greatly improve computing performance in regarding to numerical stiffness at freezing-point. Here we tested the model in fully 3-D coupled mode at the Next Generation Ecosystem Experiment-Arctic (NGEE-Arctic) field intensive study site at the Barrow Environmental Observatory (BEO), AK. The simulations show that: (1) synchronous coupling of soil thermal-hydrology and biogeochemistry in 3-D can greatly impact ecosystem dynamics across polygonal tundra landscape; and (2) freezing-thawing cycles can add more complexity to the system, resulting in greater mobility of soil N vertically and laterally, depending upon local micro-topography. As a preliminary experiment, the model is also implemented for Pan-Arctic region in 1-D column mode (i.e. no lateral connection), showing significant differences compared to stand-alone ALM. The developed ALM-PFLOTRAN coupling codes embeded within ESM will be used for Pan-Arctic regional evaluation of climate change-caused ecosystem responses and their feedbacks to climate system at various scales.

Dense Plasma Focus Modeling

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

Li, Hui; Li, Shengtai; Jungman, Gerard

2016-08-31

The mechanisms for pinch formation in Dense Plasma Focus (DPF) devices, with the generation of high-energy ions beams and subsequent neutron production over a relatively short distance, are not fully understood. Here we report on high-fidelity 2D and 3D numerical magnetohydrodynamic (MHD) simulations using the LA-COMPASS code to study the pinch formation dynamics and its associated instabilities and neutron production.

3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study.

PubMed

Dolz, Jose; Desrosiers, Christian; Ben Ayed, Ismail

2018-04-15

This study investigates a 3D and fully convolutional neural network (CNN) for subcortical brain structure segmentation in MRI. 3D CNN architectures have been generally avoided due to their computational and memory requirements during inference. We address the problem via small kernels, allowing deeper architectures. We further model both local and global context by embedding intermediate-layer outputs in the final prediction, which encourages consistency between features extracted at different scales and embeds fine-grained information directly in the segmentation process. Our model is efficiently trained end-to-end on a graphics processing unit (GPU), in a single stage, exploiting the dense inference capabilities of fully CNNs. We performed comprehensive experiments over two publicly available datasets. First, we demonstrate a state-of-the-art performance on the ISBR dataset. Then, we report a large-scale multi-site evaluation over 1112 unregistered subject datasets acquired from 17 different sites (ABIDE dataset), with ages ranging from 7 to 64 years, showing that our method is robust to various acquisition protocols, demographics and clinical factors. Our method yielded segmentations that are highly consistent with a standard atlas-based approach, while running in a fraction of the time needed by atlas-based methods and avoiding registration/normalization steps. This makes it convenient for massive multi-site neuroanatomical imaging studies. To the best of our knowledge, our work is the first to study subcortical structure segmentation on such large-scale and heterogeneous data. Copyright © 2017 Elsevier Inc. All rights reserved.

Modeling of Hydraulic Fracture Propagation at the kISMET Site Using a Fully Coupled 3D Network-Flow and Quasi- Static Discrete Element Model

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

Zhou, Jing; Huang, Hai; Mattson, Earl

Aimed at supporting the design of hydraulic fracturing experiments at the kISMET site, ~1500 m below ground in a deep mine, we performed pre-experimental hydraulic fracturing simulations in order to estimate the breakdown pressure, propagation pressure, fracture geometry, and the magnitude of induced seismicity using a newly developed fully coupled three-dimensional (3D) network flow and quasi-static discrete element model (DEM). The quasi-static DEM model, which is constructed by Delaunay tessellation of the rock volume, considers rock fabric heterogeneities by using the “disordered” DEM mesh and adding random perturbations to the stiffness and tensile/shear strengths of individual DEM elements and themore » elastic beams between them. A conjugate 3D flow network based on the DEM lattice is constructed to calculate the fluid flow in both the fracture and porous matrix. One distinctive advantage of the model is that fracturing is naturally described by the breakage of elastic beams between DEM elements. It is also extremely convenient to introduce mechanical anisotropy into the model by simply assigning orientation-dependent tensile/shear strengths to the elastic beams. In this paper, the 3D hydraulic fracturing model was verified against the analytic solution for a penny-shaped crack model. We applied the model to simulate fracture propagation from a vertical open borehole based on initial estimates of rock mechanical properties and in-situ stress conditions. The breakdown pressure and propagation pressure are directly obtained from the simulation. In addition, the released elastic strain energies of individual fracturing events were calculated and used as a conservative estimate for the magnitudes of the potential induced seismic activities associated with fracturing. The comparisons between model predictions and experimental results are still ongoing.« less

An object oriented fully 3D tomography visual toolkit.

PubMed

Agostinelli, S; Paoli, G

2001-04-01

In this paper we present a modern object oriented component object model (COMM) C + + toolkit dedicated to fully 3D cone-beam tomography. The toolkit allows the display and visual manipulation of analytical phantoms, projection sets and volumetric data through a standard Windows graphical user interface. Data input/output is performed using proprietary file formats but import/export of industry standard file formats, including raw binary, Windows bitmap and AVI, ACR/NEMA DICOMM 3 and NCSA HDF is available. At the time of writing built-in implemented data manipulators include a basic phantom ray-tracer and a Matrox Genesis frame grabbing facility. A COMM plug-in interface is provided for user-defined custom backprojector algorithms: a simple Feldkamp ActiveX control, including source code, is provided as an example; our fast Feldkamp plug-in is also available.

3D printed electromagnetic transmission and electronic structures fabricated on a single platform using advanced process integration techniques

NASA Astrophysics Data System (ADS)

Deffenbaugh, Paul Issac

3D printing has garnered immense attention from many fields including in-office rapid prototyping of mechanical parts, outer-space satellite replication, garage functional firearm manufacture, and NASA rocket engine component fabrication. 3D printing allows increased design flexibility in the fabrication of electronics, microwave circuits and wireless antennas and has reached a level of maturity which allows functional parts to be printed. Much more work is necessary in order to perfect the processes of 3D printed electronics especially in the area of automation. Chapter 1 shows several finished prototypes of 3D printed electronics as well as newly developed techniques in fabrication. Little is known about the RF and microwave properties and applications of the standard materials which have been developed for 3D printing. Measurement of a wide variety of materials over a broad spectrum of frequencies up to 10 GHz using a variety of well-established measurement methods is performed throughout chapter 2. Several types of high frequency RF transmission lines are fabricated and valuable model-matched data is gathered and provided in chapter 3 for future designers' use. Of particular note is a fully 3D printed stripline which was automatically fabricated in one process on one machine. Some core advantages of 3D printing RF/microwave components include rapid manufacturing of complex, dimensionally sensitive circuits (such as antennas and filters which are often iteratively tuned) and the ability to create new devices that cannot be made using standard fabrication techniques. Chapter 4 describes an exemplary fully 3D printed curved inverted-F antenna.

Multidimensional, fully implicit, exactly conserving electromagnetic particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Chacon, Luis

2015-09-01

We discuss a new, conservative, fully implicit 2D-3V particle-in-cell algorithm for non-radiative, electromagnetic kinetic plasma simulations, based on the Vlasov-Darwin model. Unlike earlier linearly implicit PIC schemes and standard explicit PIC schemes, fully implicit PIC algorithms are unconditionally stable and allow exact discrete energy and charge conservation. This has been demonstrated in 1D electrostatic and electromagnetic contexts. In this study, we build on these recent algorithms to develop an implicit, orbit-averaged, time-space-centered finite difference scheme for the Darwin field and particle orbit equations for multiple species in multiple dimensions. The Vlasov-Darwin model is very attractive for PIC simulations because it avoids radiative noise issues in non-radiative electromagnetic regimes. The algorithm conserves global energy, local charge, and particle canonical-momentum exactly, even with grid packing. The nonlinear iteration is effectively accelerated with a fluid preconditioner, which allows efficient use of large timesteps, O(√{mi/me}c/veT) larger than the explicit CFL. In this presentation, we will introduce the main algorithmic components of the approach, and demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 1D and 2D. Support from the LANL LDRD program and the DOE-SC ASCR office.

Seismic Wave Propagation in Fully Anisotropic Axisymmetric Media: Applications and Practical Considerations

NASA Astrophysics Data System (ADS)

van Driel, Martin; Nissen-Meyer, Tarje; Stähler, Simon; Waszek, Lauren; Hempel, Stefanie; Auer, Ludwig; Deuss, Arwen

2014-05-01

We present a numerical method to compute high-frequency 3D elastic waves in fully anisotropic axisymmetric media. The method is based on a decomposition of the wavefield into a series of uncoupled 2D equations, for which the dependence of the wavefield on the azimuth can be solved analytically. The remaining 2D problems are then solved using a spectral element method (AxiSEM). AxiSEM was recently published open-source (Nissen-Meyer et al. 2014) as a production ready code capable to compute global seismic wave propagation up to frequencies of ~2Hz. It accurately models visco-elastic dissipation and anisotropy (van Driel et al., submitted to GJI) and runs efficiently on HPC resources using up to 10K cores. At very short period, the Fresnel Zone of body waves is narrow and sensitivity is focused around the geometrical ray. In cases where the azimuthal variations of structural heterogeneity exhibit long spatial wavelengths, so called 2.5D simulations (3D wavefields in 2D models) provide a good approximation. In AxiSEM, twodimensional variations in the source-receiver plane are effectively modelled as ringlike structures extending in the out-of-plane direction. In contrast to ray-theory, which is widely used in high-frequency applications, AxiSEM provides complete waveforms, thus giving access to frequency dependency, amplitude variations, and peculiar wave effects such as diffraction and caustics. Here we focus on the practical implications of the inherent axisymmetric geometry and show how the 2.5D-features of our method method can be used to model realistic anisotropic structures, by applying it to problems such as the D" region and the inner core.

WE-AB-BRA-05: Fully Automatic Segmentation of Male Pelvic Organs On CT Without Manual Intervention

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

Gao, Y; Lian, J; Chen, R

Purpose: We aim to develop a fully automatic tool for accurate contouring of major male pelvic organs in CT images for radiotherapy without any manual initialization, yet still achieving superior performance than the existing tools. Methods: A learning-based 3D deformable shape model was developed for automatic contouring. Specifically, we utilized a recent machine learning method, random forest, to jointly learn both image regressor and classifier for each organ. In particular, the image regressor is trained to predict the 3D displacement from each vertex of the 3D shape model towards the organ boundary based on the local image appearance around themore » location of this vertex. The predicted 3D displacements are then used to drive the 3D shape model towards the target organ. Once the shape model is deformed close to the target organ, it is further refined by an organ likelihood map estimated by the learned classifier. As the organ likelihood map provides good guideline for the organ boundary, the precise contouring Result could be achieved, by deforming the 3D shape model locally to fit boundaries in the organ likelihood map. Results: We applied our method to 29 previously-treated prostate cancer patients, each with one planning CT scan. Compared with manually delineated pelvic organs, our method obtains overlap ratios of 85.2%±3.74% for the prostate, 94.9%±1.62% for the bladder, and 84.7%±1.97% for the rectum, respectively. Conclusion: This work demonstrated feasibility of a novel machine-learning based approach for accurate and automatic contouring of major male pelvic organs. It shows the potential to replace the time-consuming and inconsistent manual contouring in the clinic. Also, compared with the existing works, our method is more accurate and also efficient since it does not require any manual intervention, such as manual landmark placement. Moreover, our method obtained very similar contouring results as the clinical experts. Project is partially support by a grant from NCI 1R01CA140413.« less

Automatic bladder segmentation from CT images using deep CNN and 3D fully connected CRF-RNN.

PubMed

Xu, Xuanang; Zhou, Fugen; Liu, Bo

2018-03-19

Automatic approach for bladder segmentation from computed tomography (CT) images is highly desirable in clinical practice. It is a challenging task since the bladder usually suffers large variations of appearance and low soft-tissue contrast in CT images. In this study, we present a deep learning-based approach which involves a convolutional neural network (CNN) and a 3D fully connected conditional random fields recurrent neural network (CRF-RNN) to perform accurate bladder segmentation. We also propose a novel preprocessing method, called dual-channel preprocessing, to further advance the segmentation performance of our approach. The presented approach works as following: first, we apply our proposed preprocessing method on the input CT image and obtain a dual-channel image which consists of the CT image and an enhanced bladder density map. Second, we exploit a CNN to predict a coarse voxel-wise bladder score map on this dual-channel image. Finally, a 3D fully connected CRF-RNN refines the coarse bladder score map and produce final fine-localized segmentation result. We compare our approach to the state-of-the-art V-net on a clinical dataset. Results show that our approach achieves superior segmentation accuracy, outperforming the V-net by a significant margin. The Dice Similarity Coefficient of our approach (92.24%) is 8.12% higher than that of the V-net. Moreover, the bladder probability maps performed by our approach present sharper boundaries and more accurate localizations compared with that of the V-net. Our approach achieves higher segmentation accuracy than the state-of-the-art method on clinical data. Both the dual-channel processing and the 3D fully connected CRF-RNN contribute to this improvement. The united deep network composed of the CNN and 3D CRF-RNN also outperforms a system where the CRF model acts as a post-processing method disconnected from the CNN.

Landslide/reservoir interaction: 3D numerical modelling of the Vajont rockslide and generated water wave

NASA Astrophysics Data System (ADS)

Crosta, G.; Imposimato, S.; Roddeman, D.; Frattini, P.

2012-04-01

Fast moving landslides can be originated along slopes in mountainous terrains with natural and artificial lakes, or fjords at the slope foot. This landslides can reach extremely high speed and the impact with the immobile reservoir water can be influenced by the local topography and the landslide mass profile. The impact can generate large impulse waves and landslide tsunami. Initiation, propagation and runup are the three phases that need to be considered. The landslide evolution and the consequent wave can be controlled by the initial mass position (subaerial, partially or completely submerged), the landslide speed, the type of material, the subaerial and subaqueous slope geometry, the landslide depth and length at the impact, and the water depth. Extreme events have been caused by subaerial landslides: the 1963 Vajont rockslide (Italy), the 1958 Lituya Bay event (Alaska), the Tafjord and the Loen multiple events event (Norway), also from volcanic collapses (Hawaii and Canary islands). Various researchers completed a systematic experimental work on 2D and 3D wave generation and propagation (Kamphuis and Bowering, 1970; Huber, 1980; Müller, 1995; Huber and Hager, 1997; Fritz, 2002; Zweifel, 2004; Panizzo et al., 2005; Heller, 2007; Heller and Kinnear, 2010; Sælevik et al., 2009), using both rigid blocks and deformable granular" masses. Model data and results have been used to calibrate and validate numerical modelling tools (Harbitz, 1992; Jiang and LeBlond, 1993; Grilli et al., 2002; Grilli and Watts, 2005; Lynett and Liu, 2005; Tinti et al., 2006; Abadie et al., 2010) generally considering simplified rheologies (e.g. viscous rheologies) for subaerial subaqueous spreading. We use a FEM code (Roddeman, 2011; Crosta et al., 2006, 2009, 2010, 2011) adopting an Eulerian-Lagrangian approach to give accurate results for large deformations. We model both 2D and fully 3D events considering different settings. The material is considered as a fully deformable elasto-plastic continuum and water as nearly incompressible. In particular we modeled the Vajont rockslide both in 2D and 3D considering the landslide water interaction. More simulations have been performed to validate the model against 2D and 3D tank experiments considering different slope geometries and water depth.

Augmented Articles: The Future of Peer-Reviewed Publications?

NASA Astrophysics Data System (ADS)

Madura, Thomas Ignatius; Clementel, Nicola; Gull, Theodore R.

2015-08-01

The predominance of 2D figures and animations in the literature is clearly driven by the need to display data in a classic paper-journal format. However, there is no real reason that researchers should be limited to 2D graphics when presenting their results in peer-reviewed publications. This is especially true since all major astrophysical journals are now published online. So-called ‘augmented articles’ are possible, in which 3D interactive models, images, sound, and video can be included directly within an Adobe Portable Document Format (PDF) article. The inclusion of 3D interactive models in the astrophysics literature is slowly becoming popular, and several journals now fully support the inclusion of 3D interactive figures and movies. I present examples of recently published augmented articles in astronomy (e.g. Madura et al. 2015, arXiv:1503.00716) and discuss their perceived benefits and limitations. Such articles may become the norm in astronomy as data and numerical simulations increasingly become multidimensional (see http://www.technologyreview.com/view/535796/astronomers-create-3-d-printed-model-of-colliding-stellar-winds/).

3D culture models of Alzheimer's disease: a road map to a "cure-in-a-dish".

PubMed

Choi, Se Hoon; Kim, Young Hye; Quinti, Luisa; Tanzi, Rudolph E; Kim, Doo Yeon

2016-12-09

Alzheimer's disease (AD) transgenic mice have been used as a standard AD model for basic mechanistic studies and drug discovery. These mouse models showed symbolic AD pathologies including β-amyloid (Aβ) plaques, gliosis and memory deficits but failed to fully recapitulate AD pathogenic cascades including robust phospho tau (p-tau) accumulation, clear neurofibrillary tangles (NFTs) and neurodegeneration, solely driven by familial AD (FAD) mutation(s). Recent advances in human stem cell and three-dimensional (3D) culture technologies made it possible to generate novel 3D neural cell culture models that recapitulate AD pathologies including robust Aβ deposition and Aβ-driven NFT-like tau pathology. These new 3D human cell culture models of AD hold a promise for a novel platform that can be used for mechanism studies in human brain-like environment and high-throughput drug screening (HTS). In this review, we will summarize the current progress in recapitulating AD pathogenic cascades in human neural cell culture models using AD patient-derived induced pluripotent stem cells (iPSCs) or genetically modified human stem cell lines. We will also explain how new 3D culture technologies were applied to accelerate Aβ and p-tau pathologies in human neural cell cultures, as compared the standard two-dimensional (2D) culture conditions. Finally, we will discuss a potential impact of the human 3D human neural cell culture models on the AD drug-development process. These revolutionary 3D culture models of AD will contribute to accelerate the discovery of novel AD drugs.

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

Rodgers, Arthur J.; Dreger, Douglas S.; Pitarka, Arben

We performed three-dimensional (3D) anelastic ground motion simulations of the South Napa earthquake to investigate the performance of different finite rupture models and the effects of 3D structure on the observed wavefield. We considered rupture models reported by Dreger et al. (2015), Ji et al., (2015), Wei et al. (2015) and Melgar et al. (2015). We used the SW4 anelastic finite difference code developed at Lawrence Livermore National Laboratory (Petersson and Sjogreen, 2013) and distributed by the Computational Infrastructure for Geodynamics. This code can compute the seismic response for fully 3D sub-surface models, including surface topography and linear anelasticity. Wemore » use the 3D geologic/seismic model of the San Francisco Bay Area developed by the United States Geological Survey (Aagaard et al., 2008, 2010). Evaluation of earlier versions of this model indicated that the structure can reproduce main features of observed waveforms from moderate earthquakes (Rodgers et al., 2008; Kim et al., 2010). Simulations were performed for a domain covering local distances (< 25 km) and resolution providing simulated ground motions valid to 1 Hz.« less

Slope instability in complex 3D topography promoted by convergent 3D groundwater flow

NASA Astrophysics Data System (ADS)

Reid, M. E.; Brien, D. L.

2012-12-01

Slope instability in complex topography is generally controlled by the interaction between gravitationally induced stresses, 3D strengths, and 3D pore-fluid pressure fields produced by flowing groundwater. As an example of this complexity, coastal bluffs sculpted by landsliding commonly exhibit a progression of undulating headlands and re-entrants. In this landscape, stresses differ between headlands and re-entrants and 3D groundwater flow varies from vertical rainfall infiltration to lateral groundwater flow on lower permeability layers with subsequent discharge at the curved bluff faces. In plan view, groundwater flow converges in the re-entrant regions. To investigate relative slope instability induced by undulating topography, we couple the USGS 3D limit-equilibrium slope-stability model, SCOOPS, with the USGS 3D groundwater flow model, MODFLOW. By rapidly analyzing the stability of millions of potential failures, the SCOOPS model can determine relative slope stability throughout the 3D domain underlying a digital elevation model (DEM), and it can utilize both fully 3D distributions of pore-water pressure and material strength. The two models are linked by first computing a groundwater-flow field in MODFLOW, and then computing stability in SCOOPS using the pore-pressure field derived from groundwater flow. Using these two models, our analyses of 60m high coastal bluffs in Seattle, Washington showed augmented instability in topographic re-entrants given recharge from a rainy season. Here, increased recharge led to elevated perched water tables with enhanced effects in the re-entrants owing to convergence of groundwater flow. Stability in these areas was reduced about 80% compared to equivalent dry conditions. To further isolate these effects, we examined groundwater flow and stability in hypothetical landscapes composed of uniform and equally spaced, oscillating headlands and re-entrants with differing amplitudes. The landscapes had a constant slope for both headlands and re-entrants to minimize slope effects on stability. Despite these equal slopes, our analyses, given dry conditions, illustrated that the headlands can be 5-7% less stable than the re-entrants, owing to the geometry of the 3D failure mass with the lowest stability. We then simulated groundwater flow in these landscapes; flow was caused by recharge perching on a horizontal low permeability layer with discharge at the bluff faces. By systematically varying recharge, hydraulic conductivity of the material, and conductance at the bluffs, we created different 3D pore-pressure fields. Recharge rates and hydraulic conductivities controlled the height of the water table, whereas bluff conductance influenced the gradient of the water table near the bluff face. Given elevated water tables with steep gradients, bluffs in the re-entrants became unstable where flow converged. Thus, with progressively stronger effects from water flow, overall instability evolved from relatively unstable headlands to more uniform stability to relatively unstable re-entrants. Larger re-entrants led to more 3D flow convergence and greater localized instability. One- or two-dimensional models cannot fully characterize slope instability in complex topography.

Method of transition from 3D model to its ontological representation in aircraft design process

NASA Astrophysics Data System (ADS)

Govorkov, A. S.; Zhilyaev, A. S.; Fokin, I. V.

2018-05-01

This paper proposes the method of transition from a 3D model to its ontological representation and describes its usage in the aircraft design process. The problems of design for manufacturability and design automation are also discussed. The introduced method is to aim to ease the process of data exchange between important aircraft design phases, namely engineering and design control. The method is also intended to increase design speed and 3D model customizability. This requires careful selection of the complex systems (CAD / CAM / CAE / PDM), providing the basis for the integration of design and technological preparation of production and more fully take into account the characteristics of products and processes for their manufacture. It is important to solve this problem, as investment in the automation define the company's competitiveness in the years ahead.

Fully Coupled Thermomechanical Finite Element Analysis of Material Evolution During Friction-Stir Welding of AA5083

DTIC Science & Technology

2009-09-03

coefficients are set to a value of 0.3. The stick/slip critical shear stress level is defined using a modified Coulomb friction law. Within this law, there...Modified Johnson Cook Model Equivalent Plastic Strain a P M,htgnert S d lei Y 1 2 3 4 5 6 7 420 440 460 480 500 520 540 560 Original Johnson Cook Model...Lett., 2005, 59, 3315–3318. 7 Thomas, W. M. and Nicholas, E. D. Friction stir welding for the transportation industries. Mater. Des ., 1997, 18, 269

The Concurrent Engineering Design Paradigm Is Now Fully Functional for Graphics Education

ERIC Educational Resources Information Center

Krueger, Thomas J.; Barr, Ronald E.

2007-01-01

Engineering design graphics education has come a long way in the past two decades. The emergence of solid geometric modeling technology has become the focal point for the graphical development of engineering design ideas. The main attraction of this 3-D modeling approach is the downstream application of the data base to analysis and…

SU-F-J-140: Using Handheld Stereo Depth Cameras to Extend Medical Imaging for Radiation Therapy Planning

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

Jenkins, C; Xing, L; Yu, S

Purpose: A correct body contour is essential for the accuracy of dose calculation in radiation therapy. While modern medical imaging technologies provide highly accurate representations of body contours, there are times when a patient’s anatomy cannot be fully captured or there is a lack of easy access to CT/MRI scanning. Recently, handheld cameras have emerged that are capable of performing three dimensional (3D) scans of patient surface anatomy. By combining 3D camera and medical imaging data, the patient’s surface contour can be fully captured. Methods: A proof-of-concept system matches a patient surface model, created using a handheld stereo depth cameramore » (DC), to the available areas of a body contour segmented from a CT scan. The matched surface contour is then converted to a DICOM structure and added to the CT dataset to provide additional contour information. In order to evaluate the system, a 3D model of a patient was created by segmenting the body contour with a treatment planning system (TPS) and fabricated with a 3D printer. A DC and associated software were used to create a 3D scan of the printed phantom. The surface created by the camera was then registered to a CT model that had been cropped to simulate missing scan data. The aligned surface was then imported into the TPS and compared with the originally segmented contour. Results: The RMS error for the alignment between the camera and cropped CT models was 2.26 mm. Mean distance between the aligned camera surface and ground truth model was −1.23 +/−2.47 mm. Maximum deviations were < 1 cm and occurred in areas of high concavity or where anatomy was close to the couch. Conclusion: The proof-of-concept study shows an accurate, easy and affordable method to extend medical imaging for radiation therapy planning using 3D cameras without additional radiation. Intel provided the camera hardware used in this study.« less

Vertically-Integrated Dual-Continuum Models for CO2 Injection in Fractured Aquifers

NASA Astrophysics Data System (ADS)

Tao, Y.; Guo, B.; Bandilla, K.; Celia, M. A.

2017-12-01

Injection of CO2 into a saline aquifer leads to a two-phase flow system, with supercritical CO2 and brine being the two fluid phases. Various modeling approaches, including fully three-dimensional (3D) models and vertical-equilibrium (VE) models, have been used to study the system. Almost all of that work has focused on unfractured formations. 3D models solve the governing equations in three dimensions and are applicable to generic geological formations. VE models assume rapid and complete buoyant segregation of the two fluid phases, resulting in vertical pressure equilibrium and allowing integration of the governing equations in the vertical dimension. This reduction in dimensionality makes VE models computationally more efficient, but the associated assumptions restrict the applicability of VE model to formations with moderate to high permeability. In this presentation, we extend the VE and 3D models for CO2 injection in fractured aquifers. This is done in the context of dual-continuum modeling, where the fractured formation is modeled as an overlap of two continuous domains, one representing the fractures and the other representing the rock matrix. Both domains are treated as porous media continua and can be modeled by either a VE or a 3D formulation. The transfer of fluid mass between rock matrix and fractures is represented by a mass transfer function connecting the two domains. We have developed a computational model that combines the VE and 3D models, where we use the VE model in the fractures, which typically have high permeability, and the 3D model in the less permeable rock matrix. A new mass transfer function is derived, which couples the VE and 3D models. The coupled VE-3D model can simulate CO2 injection and migration in fractured aquifers. Results from this model compare well with a full-3D model in which both the fractures and rock matrix are modeled with 3D models, with the hybrid VE-3D model having significantly reduced computational cost. In addition to the VE-3D model, we explore simplifications of the rock matrix domain by using sugar-cube and matchstick conceptualizations and develop VE-dual porosity and VE-matchstick models. These vertically-integrated dual-permeability and dual-porosity models provide a range of computationally efficient tools to model CO2 storage in fractured saline aquifers.

Fast carotid artery MR angiography with compressed sensing based three-dimensional time-of-flight sequence.

PubMed

Li, Bo; Li, Hao; Dong, Li; Huang, Guofu

2017-11-01

In this study, we sought to investigate the feasibility of fast carotid artery MR angiography (MRA) by combining three-dimensional time-of-flight (3D TOF) with compressed sensing method (CS-3D TOF). A pseudo-sequential phase encoding order was developed for CS-3D TOF to generate hyper-intense vessel and suppress background tissues in under-sampled 3D k-space. Seven healthy volunteers and one patient with carotid artery stenosis were recruited for this study. Five sequential CS-3D TOF scans were implemented at 1, 2, 3, 4 and 5-fold acceleration factors for carotid artery MRA. Blood signal-to-tissue ratio (BTR) values for fully-sampled and under-sampled acquisitions were calculated and compared in seven subjects. Blood area (BA) was measured and compared between fully sampled acquisition and each under-sampled one. There were no significant differences between the fully-sampled dataset and each under-sampled in BTR comparisons (P>0.05 for all comparisons). The carotid vessel BAs measured from the images of CS-3D TOF sequences with 2, 3, 4 and 5-fold acceleration scans were all highly correlated with that of the fully-sampled acquisition. The contrast between blood vessels and background tissues of the images at 2 to 5-fold acceleration is comparable to that of fully sampled images. The images at 2× to 5× exhibit the comparable lumen definition to the corresponding images at 1×. By combining the pseudo-sequential phase encoding order, CS reconstruction, and 3D TOF sequence, this technique provides excellent visualizations for carotid vessel and calcifications in a short scan time. It has the potential to be integrated into current multiple blood contrast imaging protocol. Copyright © 2017. Published by Elsevier Inc.

On the local well-posedness and a Prodi-Serrin-type regularity criterion of the three-dimensional MHD-Boussinesq system without thermal diffusion

NASA Astrophysics Data System (ADS)

Larios, Adam; Pei, Yuan

2017-07-01

We prove a Prodi-Serrin-type global regularity condition for the three-dimensional Magnetohydrodynamic-Boussinesq system (3D MHD-Boussinesq) without thermal diffusion, in terms of only two velocity and two magnetic components. To the best of our knowledge, this is the first Prodi-Serrin-type criterion for such a 3D hydrodynamic system which is not fully dissipative, and indicates that such an approach may be successful on other systems. In addition, we provide a constructive proof of the local well-posedness of solutions to the fully dissipative 3D MHD-Boussinesq system, and also the fully inviscid, irresistive, non-diffusive MHD-Boussinesq equations. We note that, as a special case, these results include the 3D non-diffusive Boussinesq system and the 3D MHD equations. Moreover, they can be extended without difficulty to include the case of a Coriolis rotational term.

Comparative 1D and 3D numerical investigation of open-channel junction flows and energy losses

NASA Astrophysics Data System (ADS)

Luo, Hao; Fytanidis, Dimitrios K.; Schmidt, Arthur R.; García, Marcelo H.

2018-07-01

The complexity of open channel confluences stems from flow mixing, secondary circulation, post-confluence flow separation, contraction and backwater effects. These effects in turn result in a large number of parameters required to adequately quantify the junction induced hydraulic resistance and describe mean flow pattern and turbulent flow structures due to flow merging. The recent development in computing power advances the application of 3D Computational Fluid Dynamics (CFD) codes to visualize and understand the Confluence Hydrodynamic Zone (CHZ). Nevertheless, 1D approaches remain the mainstay in large drainage network or waterway system modeling considering computational efficiency and data availability. This paper presents (i) a modified 1D nonlinear dynamic model; (ii) a fully 3D non-hydrostatic, Reynolds-averaged Navier-Stokes Equations (RANS)-based, Computational Fluid Dynamics (CFD) model; (iii) an analysis of changing confluence hydrodynamics and 3D turbulent flow structure under various controls; (iv) a comparison of flow features (i.e. upstream water depths, energy losses and post-confluence contraction) predicted by 1D and 3D models; and (v) parameterization of 3D flow characteristics in 1D modeling through the computation of correction coefficients associated with contraction, energy and momentum. The present comprehensive 3D numerical investigation highlights the driving mechanisms for junction induced energy losses. Moreover, the comparative 1D and 3D study quantifies the deviation of 1D approximations and associated underlying assumptions from the 'true' resultant flow field. The study may also shed light on improving the accuracy of the 1D large network modeling through the parameterization of the complex 3D feature of the flow field and correction of interior boundary conditions at junctions of larger angles and/or with substantial lateral inflows. Moreover, the enclosed numerical investigations may enhance the understanding of the primary mechanisms contributing to hydraulic structure induced turbulent flow behavior and increased hydraulic resistance.

Computation of Coupled Thermal-Fluid Problems in Distributed Memory Environment

NASA Technical Reports Server (NTRS)

Wei, H.; Shang, H. M.; Chen, Y. S.

2001-01-01

The thermal-fluid coupling problems are very important to aerospace and engineering applications. Instead of analyzing heat transfer and fluid flow separately, this study merged two well-accepted engineering solution methods, SINDA for thermal analysis and FDNS for fluid flow simulation, into a unified multi-disciplinary thermal fluid prediction method. A fully conservative patched grid interface algorithm for arbitrary two-dimensional and three-dimensional geometry has been developed. The state-of-the-art parallel computing concept was used to couple SINDA and FDNS for the communication of boundary conditions through PVM (Parallel Virtual Machine) libraries. Therefore, the thermal analysis performed by SINDA and the fluid flow calculated by FDNS are fully coupled to obtain steady state or transient solutions. The natural convection between two thick-walled eccentric tubes was calculated and the predicted results match the experiment data perfectly. A 3-D rocket engine model and a real 3-D SSME geometry were used to test the current model, and the reasonable temperature field was obtained.

Numerical and experimental analysis of a ducted propeller designed by a fully automated optimization process under open water condition

NASA Astrophysics Data System (ADS)

Yu, Long; Druckenbrod, Markus; Greve, Martin; Wang, Ke-qi; Abdel-Maksoud, Moustafa

2015-10-01

A fully automated optimization process is provided for the design of ducted propellers under open water conditions, including 3D geometry modeling, meshing, optimization algorithm and CFD analysis techniques. The developed process allows the direct integration of a RANSE solver in the design stage. A practical ducted propeller design case study is carried out for validation. Numerical simulations and open water tests are fulfilled and proved that the optimum ducted propeller improves hydrodynamic performance as predicted.

Comparison of 2D numerical models for river flood hazard assessment: simulation of the Secchia River flood in January, 2014

NASA Astrophysics Data System (ADS)

Shustikova, Iuliia; Domeneghetti, Alessio; Neal, Jeffrey; Bates, Paul; Castellarin, Attilio

2017-04-01

Hydrodynamic modeling of inundation events still brings a large array of uncertainties. This effect is especially evident in the models run for geographically large areas. Recent studies suggest using fully two-dimensional (2D) models with high resolution in order to avoid uncertainties and limitations coming from the incorrect interpretation of flood dynamics and an unrealistic reproduction of the terrain topography. This, however, affects the computational efficiency increasing the running time and hardware demands. Concerning this point, our study evaluates and compares numerical models of different complexity by testing them on a flood event that occurred in the basin of the Secchia River, Northern Italy, on 19th January, 2014. The event was characterized by a levee breach and consequent flooding of over 75 km2 of the plain behind the dike within 48 hours causing population displacement, one death and economic losses in excess of 400 million Euro. We test the well-established TELEMAC 2D, and LISFLOOD-FP codes, together with the recently launched HEC-RAS 5.0.3 (2D model), all models are implemented using different grid size (2-200 m) based on the 1 m digital elevation model resolution. TELEMAC is a fully 2D hydrodynamic model which is based on the finite-element or finite-volume approach. Whereas HEC-RAS 5.0.3 and LISFLOOD-FP are both coupled 1D-2D models. All models are calibrated against observed inundation extent and maximum water depths, which are retrieved from remotely sensed data and field survey reports. Our study quantitatively compares the three modeling strategies highlighting differences in terms of the ease of implementation, accuracy of representation of hydraulic processes within floodplains and computational efficiency. Additionally, we look into the different grid resolutions in terms of the results accuracy and computation time. Our study is a preliminary assessment that focuses on smaller areas in order to identify potential modeling schemes that would be efficient for simulating flooding scenarios for large and very large floodplains. This research aims at contributing to the reduction of uncertainties and limitations in hazard and risk assessment.

The Value of 3D Printing Models of Left Atrial Appendage Using Real-Time 3D Transesophageal Echocardiographic Data in Left Atrial Appendage Occlusion: Applications toward an Era of Truly Personalized Medicine.

PubMed

Liu, Peng; Liu, Rijing; Zhang, Yan; Liu, Yingfeng; Tang, Xiaoming; Cheng, Yanzhen

The objective of this study was to assess the clinical feasibility of generating 3D printing models of left atrial appendage (LAA) using real-time 3D transesophageal echocardiogram (TEE) data for preoperative reference of LAA occlusion. Percutaneous LAA occlusion can effectively prevent patients with atrial fibrillation from stroke. However, the anatomical structure of LAA is so complicated that adequate information of its structure is essential for successful LAA occlusion. Emerging 3D printing technology has the demonstrated potential to structure more accurately than conventional imaging modalities by creating tangible patient-specific models. Typically, 3D printing data sets are acquired from CT and MRI, which may involve intravenous contrast, sedation, and ionizing radiation. It has been reported that 3D models of LAA were successfully created by the data acquired from CT. However, 3D printing of the LAA using real-time 3D TEE data has not yet been explored. Acquisition of 3D transesophageal echocardiographic data from 8 patients with atrial fibrillation was performed using the Philips EPIQ7 ultrasound system. Raw echocardiographic image data were opened in Philips QLAB and converted to 'Cartesian DICOM' format and imported into Mimics® software to create 3D models of LAA, which were printed using a rubber-like material. The printed 3D models were then used for preoperative reference and procedural simulation in LAA occlusion. We successfully printed LAAs of 8 patients. Each LAA costs approximately CNY 800-1,000 and the total process takes 16-17 h. Seven of the 8 Watchman devices predicted by preprocedural 2D TEE images were of the same sizes as those placed in the real operation. Interestingly, 3D printing models were highly reflective of the shape and size of LAAs, and all device sizes predicted by the 3D printing model were fully consistent with those placed in the real operation. Also, the 3D printed model could predict operating difficulty and the presence of a peridevice leak. 3D printing of the LAA using real-time 3D transesophageal echocardiographic data has a perfect and rapid application in LAA occlusion to assist with physician planning and decision making. © 2016 S. Karger AG, Basel.

Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging

DTIC Science & Technology

2009-10-01

molecular breast imaging, with the ability to dynamically contour any sized breast, will improve detection and potentially in vivo characterization of...Having flexible 3D positioning about the breast yielded minimal RMSD differences, which is important for high resolution molecular emission imaging. This...TITLE: Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging PRINCIPAL

Recovering the 3d Pose and Shape of Vehicles from Stereo Images

NASA Astrophysics Data System (ADS)

Coenen, M.; Rottensteiner, F.; Heipke, C.

2018-05-01

The precise reconstruction and pose estimation of vehicles plays an important role, e.g. for autonomous driving. We tackle this problem on the basis of street level stereo images obtained from a moving vehicle. Starting from initial vehicle detections, we use a deformable vehicle shape prior learned from CAD vehicle data to fully reconstruct the vehicles in 3D and to recover their 3D pose and shape. To fit a deformable vehicle model to each detection by inferring the optimal parameters for pose and shape, we define an energy function leveraging reconstructed 3D data, image information, the vehicle model and derived scene knowledge. To minimise the energy function, we apply a robust model fitting procedure based on iterative Monte Carlo model particle sampling. We evaluate our approach using the object detection and orientation estimation benchmark of the KITTI dataset (Geiger et al., 2012). Our approach can deal with very coarse pose initialisations and we achieve encouraging results with up to 82 % correct pose estimations. Moreover, we are able to deliver very precise orientation estimation results with an average absolute error smaller than 4°.

The cranial nerve skywalk: A 3D tutorial of cranial nerves in a virtual platform.

PubMed

Richardson-Hatcher, April; Hazzard, Matthew; Ramirez-Yanez, German

2014-01-01

Visualization of the complex courses of the cranial nerves by students in the health-related professions is challenging through either diagrams in books or plastic models in the gross laboratory. Furthermore, dissection of the cranial nerves in the gross laboratory is an extremely meticulous task. Teaching and learning the cranial nerve pathways is difficult using two-dimensional (2D) illustrations alone. Three-dimensional (3D) models aid the teacher in describing intricate and complex anatomical structures and help students visualize them. The study of the cranial nerves can be supplemented with 3D, which permits the students to fully visualize their distribution within the craniofacial complex. This article describes the construction and usage of a virtual anatomy platform in Second Life™, which contains 3D models of the cranial nerves III, V, VII, and IX. The Cranial Nerve Skywalk features select cranial nerves and the associated autonomic pathways in an immersive online environment. This teaching supplement was introduced to groups of pre-healthcare professional students in gross anatomy courses at both institutions and student feedback is included. © 2014 American Association of Anatomists.

i3Drive, a 3D interactive driving simulator.

PubMed

Ambroz, Miha; Prebil, Ivan

2010-01-01

i3Drive, a wheeled-vehicle simulator, can accurately simulate vehicles of various configurations with up to eight wheels in real time on a desktop PC. It presents the vehicle dynamics as an interactive animation in a virtual 3D environment. The application is fully GUI-controlled, giving users an easy overview of the simulation parameters and letting them adjust those parameters interactively. It models all relevant vehicle systems, including the mechanical models of the suspension, power train, and braking and steering systems. The simulation results generally correspond well with actual measurements, making the system useful for studying vehicle performance in various driving scenarios. i3Drive is thus a worthy complement to other, more complex tools for vehicle-dynamics simulation and analysis.

3D CFD Modeling of the LMF System: Desulfurization Kinetics

NASA Astrophysics Data System (ADS)

Cao, Qing; Pitts, April; Zhang, Daojie; Nastac, Laurentiu; Williams, Robert

A fully transient 3D CFD modeling approach capable of predicting the three phase (gas, slag and steel) fluid flow characteristics and behavior of the slag/steel interface in the argon gas bottom stirred ladle with two off-centered porous plugs (Ladle Metallurgical Furnace or LMF) has been recently developed. The model predicts reasonably well the fluid flow characteristics in the LMF system and the observed size of the slag eyes for both the high-stirring and low-stirring conditions. A desulfurization reaction kinetics model considering metal/slag interface characteristics is developed in conjunction with the CFD modeling approach. The model is applied in this study to determine the effects of processing time, and gas flow rate on the efficiency of desulfurization in the studied LMF system.

Neural patterning of human induced pluripotent stem cells in 3-D cultures for studying biomolecule-directed differential cellular responses.

PubMed

Yan, Yuanwei; Bejoy, Julie; Xia, Junfei; Guan, Jingjiao; Zhou, Yi; Li, Yan

2016-09-15

Appropriate neural patterning of human induced pluripotent stem cells (hiPSCs) is critical to generate specific neural cells/tissues and even mini-brains that are physiologically relevant to model neurological diseases. However, the capacity of signaling factors that regulate 3-D neural tissue patterning in vitro and differential responses of the resulting neural populations to various biomolecules have not yet been fully understood. By tuning neural patterning of hiPSCs with small molecules targeting sonic hedgehog (SHH) signaling, this study generated different 3-D neuronal cultures that were mainly comprised of either cortical glutamatergic neurons or motor neurons. Abundant glutamatergic neurons were observed following the treatment with an antagonist of SHH signaling, cyclopamine, while Islet-1 and HB9-expressing motor neurons were enriched by an SHH agonist, purmorphamine. In neurons derived with different neural patterning factors, whole-cell patch clamp recordings showed similar voltage-gated Na(+)/K(+) currents, depolarization-evoked action potentials and spontaneous excitatory post-synaptic currents. Moreover, these different neuronal populations exhibited differential responses to three classes of biomolecules, including (1) matrix metalloproteinase inhibitors that affect extracellular matrix remodeling; (2) N-methyl-d-aspartate that induces general neurotoxicity; and (3) amyloid β (1-42) oligomers that cause neuronal subtype-specific neurotoxicity. This study should advance our understanding of hiPSC self-organization and neural tissue development and provide a transformative approach to establish 3-D models for neurological disease modeling and drug discovery. Appropriate neural patterning of human induced pluripotent stem cells (hiPSCs) is critical to generate specific neural cells, tissues and even mini-brains that are physiologically relevant to model neurological diseases. However, the capability of sonic hedgehog-related small molecules to tune different neuronal subtypes in 3-D differentiation from hiPSCs and the differential cellular responses of region-specific neuronal subtypes to various biomolecules have not been fully investigated. By tuning neural patterning of hiPSCs with small molecules targeting sonic hedgehog signaling, this study provides knowledge on the differential susceptibility of region-specific neuronal subtypes derived from hiPSCs to different biomolecules in extracellular matrix remodeling and neurotoxicity. The findings are significant for understanding 3-D neural patterning of hiPSCs for the applications in brain organoid formation, neurological disease modeling, and drug discovery. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Formation and Reconnection of Three-Dimensional Current Sheets in the Solar Corona

NASA Technical Reports Server (NTRS)

Edmondson, J. K.; Antiochos, S. K.; DeVore, C. R.; Zurbuchen, T. H.

2010-01-01

Current-sheet formation and magnetic reconnection are believed to be the basic physical processes responsible for much of the activity observed in astrophysical plasmas, such as the Sun s corona. We investigate these processes for a magnetic configuration consisting of a uniform background field and an embedded line dipole, a topology that is expected to be ubiquitous in the corona. This magnetic system is driven by a uniform horizontal flow applied at the line-tied photosphere. Although both the initial field and the driver are translationally symmetric, the resulting evolution is calculated using a fully three-dimensional magnetohydrodynamic (3D MHD) simulation with adaptive mesh refinement that resolves the current sheet and reconnection dynamics in detail. The advantage of our approach is that it allows us to apply directly the vast body of knowledge gained from the many studies of 2D reconnection to the fully 3D case. We find that a current sheet forms in close analogy to the classic Syrovatskii 2D mechanism, but the resulting evolution is different than expected. The current sheet is globally stable, showing no evidence for a disruption or a secondary instability even for aspect ratios as high as 80:1. The global evolution generally follows the standard Sweet- Parker 2D reconnection model except for an accelerated reconnection rate at a very thin current sheet, due to the tearing instability and the formation of magnetic islands. An interesting conclusion is that despite the formation of fully 3D structures at small scales, the system remains close to 2D at global scales. We discuss the implications of our results for observations of the solar corona. Subject Headings: Sun: corona Sun: magnetic fields Sun: reconnection

Transthoracic 3D echocardiographic left heart chamber quantification in patients with bicuspid aortic valve disease.

PubMed

van den Hoven, Allard T; Mc-Ghie, Jackie S; Chelu, Raluca G; Duijnhouwer, Anthonie L; Baggen, Vivan J M; Coenen, Adriaan; Vletter, Wim B; Dijkshoorn, Marcel L; van den Bosch, Annemien E; Roos-Hesselink, Jolien W

2017-12-01

Integration of volumetric heart chamber quantification by 3D echocardiography into clinical practice has been hampered by several factors which a new fully automated algorithm (Left Heart Model, (LHM)) may help overcome. This study therefore aims to evaluate the feasibility and accuracy of the LHM software in quantifying left atrial and left ventricular volumes and left ventricular ejection fraction in a cohort of patients with a bicuspid aortic valve. Patients with a bicuspid aortic valve were prospectively included. All patients underwent 2D and 3D transthoracic echocardiography and computed tomography. Left atrial and ventricular volumes were obtained using the automated program, which did not require manual contour detection. For comparison manual and semi-automated measurements were performed using conventional 2D and 3D datasets. 53 patients were included, in four of those patients no 3D dataset could be acquired. Additionally, 12 patients were excluded based on poor imaging quality. Left ventricular end-diastolic and end-systolic volumes and ejection fraction calculated by the LHM correlated well with manual 2D and 3D measurements (Pearson's r between 0.43 and 0.97, p < 0.05). Left atrial volume (LAV) also correlated significantly although LHM did estimate larger LAV compared to both 2DE and 3DE (Pearson's r between 0.61 and 0.81, p < 0.01). The fully automated software works well in a real-world setting and helps to overcome some of the major hurdles in integrating 3D analysis into daily practice, as it is user-independent and highly reproducible in a group of patients with a clearly defined and well-studied valvular abnormality.

The potential of 3D techniques for cultural heritage object documentation

NASA Astrophysics Data System (ADS)

Bitelli, Gabriele; Girelli, Valentina A.; Remondino, Fabio; Vittuari, Luca

2007-01-01

The generation of 3D models of objects has become an important research point in many fields of application like industrial inspection, robotics, navigation and body scanning. Recently the techniques for generating photo-textured 3D digital models have interested also the field of Cultural Heritage, due to their capability to combine high precision metrical information with a qualitative and photographic description of the objects. In fact this kind of product is a fundamental support for documentation, studying and restoration of works of art, until a production of replicas by fast prototyping techniques. Close-range photogrammetric techniques are nowadays more and more frequently used for the generation of precise 3D models. With the advent of automated procedures and fully digital products in the 1990s, it has become easier to use and cheaper, and nowadays a wide range of commercial software is available to calibrate, orient and reconstruct objects from images. This paper presents the complete process for the derivation of a photorealistic 3D model of an important basalt stela (about 70 x 60 x 25 cm) discovered in the archaeological site of Tilmen Höyük, in Turkey, dating back to 2nd mill. BC. We will report the modeling performed using passive and active sensors and the comparison of the achieved results.

A discriminative model-constrained graph cuts approach to fully automated pediatric brain tumor segmentation in 3-D MRI.

PubMed

Wels, Michael; Carneiro, Gustavo; Aplas, Alexander; Huber, Martin; Hornegger, Joachim; Comaniciu, Dorin

2008-01-01

In this paper we present a fully automated approach to the segmentation of pediatric brain tumors in multi-spectral 3-D magnetic resonance images. It is a top-down segmentation approach based on a Markov random field (MRF) model that combines probabilistic boosting trees (PBT) and lower-level segmentation via graph cuts. The PBT algorithm provides a strong discriminative observation model that classifies tumor appearance while a spatial prior takes into account the pair-wise homogeneity in terms of classification labels and multi-spectral voxel intensities. The discriminative model relies not only on observed local intensities but also on surrounding context for detecting candidate regions for pathology. A mathematically sound formulation for integrating the two approaches into a unified statistical framework is given. The proposed method is applied to the challenging task of detection and delineation of pediatric brain tumors. This segmentation task is characterized by a high non-uniformity of both the pathology and the surrounding non-pathologic brain tissue. A quantitative evaluation illustrates the robustness of the proposed method. Despite dealing with more complicated cases of pediatric brain tumors the results obtained are mostly better than those reported for current state-of-the-art approaches to 3-D MR brain tumor segmentation in adult patients. The entire processing of one multi-spectral data set does not require any user interaction, and takes less time than previously proposed methods.

Parallel numerical modeling of hybrid-dimensional compositional non-isothermal Darcy flows in fractured porous media

NASA Astrophysics Data System (ADS)

Xing, F.; Masson, R.; Lopez, S.

2017-09-01

This paper introduces a new discrete fracture model accounting for non-isothermal compositional multiphase Darcy flows and complex networks of fractures with intersecting, immersed and non-immersed fractures. The so called hybrid-dimensional model using a 2D model in the fractures coupled with a 3D model in the matrix is first derived rigorously starting from the equi-dimensional matrix fracture model. Then, it is discretized using a fully implicit time integration combined with the Vertex Approximate Gradient (VAG) finite volume scheme which is adapted to polyhedral meshes and anisotropic heterogeneous media. The fully coupled systems are assembled and solved in parallel using the Single Program Multiple Data (SPMD) paradigm with one layer of ghost cells. This strategy allows for a local assembly of the discrete systems. An efficient preconditioner is implemented to solve the linear systems at each time step and each Newton type iteration of the simulation. The numerical efficiency of our approach is assessed on different meshes, fracture networks, and physical settings in terms of parallel scalability, nonlinear convergence and linear convergence.

Feasibility of rapid and automated importation of 3D echocardiographic left ventricular (LV) geometry into a finite element (FEM) analysis model

PubMed Central

Verhey, Janko F; Nathan, Nadia S

2004-01-01

Background Finite element method (FEM) analysis for intraoperative modeling of the left ventricle (LV) is presently not possible. Since 3D structural data of the LV is now obtainable using standard transesophageal echocardiography (TEE) devices intraoperatively, the present study describes a method to transfer this data into a commercially available FEM analysis system: ABAQUS©. Methods In this prospective study TomTec LV Analysis TEE© Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. A newly developed software program MVCP FemCoGen©, written in Delphi, reformats the TomTec file structures in five patients for use in ABAQUS and allows visualization of regional deformation of the LV. Results This study demonstrates that a fully automated importation of 3D TEE data into FEM modeling is feasible and can be efficiently accomplished in the operating room. Conclusion For complete intraoperative 3D LV finite element analysis, three input elements are necessary: 1. time-gaited, reality-based structural information, 2. continuous LV pressure and 3. instantaneous tissue elastance. The first of these elements is now available using the methods presented herein. PMID:15473901

Evaluation of Full Reynolds Stress Turbulence Models in FUN3D

NASA Technical Reports Server (NTRS)

Dudek, Julianne C.; Carlson, Jan-Renee

2017-01-01

Full seven-equation Reynolds stress turbulence models are promising tools for today’s aerospace technology challenges. This paper examines two such models for computing challenging turbulent flows including shock-wave boundary layer interactions, separation and mixing layers. The Wilcox and the SSG/LRR full second-moment Reynolds stress models have been implemented into the FUN3D (Fully Unstructured Navier-Stokes Three Dimensional) unstructured Navier-Stokes code and were evaluated for four problems: a transonic two-dimensional diffuser, a supersonic axisymmetric compression corner, a compressible planar shear layer, and a subsonic axisymmetric jet. Simulation results are compared with experimental data and results computed using the more commonly used Spalart-Allmaras (SA) one-equation and the Menter Shear Stress Transport (SST-V) two-equation turbulence models.

Evaluation of Full Reynolds Stress Turbulence Models in FUN3D

NASA Technical Reports Server (NTRS)

Dudek, Julianne C.; Carlson, Jan-Renee

2017-01-01

Full seven-equation Reynolds stress turbulence models are a relatively new and promising tool for todays aerospace technology challenges. This paper uses two stress-omega full Reynolds stress models to evaluate challenging flows including shock-wave boundary layer interactions, separation and mixing layers. The Wilcox and the SSG/LRR full second-moment Reynolds stress models have been implemented into the FUN3D (Fully Unstructured Navier-Stokes Three Dimensional) unstructured Navier-Stokes code and are evaluated for four problems: a transonic two-dimensional diffuser, a supersonic axisymmetric compression corner, a compressible planar shear layer, and a subsonic axisymmetric jet. Simulation results are compared with experimental data and results using the more commonly used Spalart-Allmaras (SA) one-equation and the Menter Shear Stress Transport (SST-V) two-equation turbulence models.

A Large-Scale Design Integration Approach Developed in Conjunction with the Ares Launch Vehicle Program

NASA Technical Reports Server (NTRS)

Redmon, John W.; Shirley, Michael C.; Kinard, Paul S.

2012-01-01

This paper presents a method for performing large-scale design integration, taking a classical 2D drawing envelope and interface approach and applying it to modern three dimensional computer aided design (3D CAD) systems. Today, the paradigm often used when performing design integration with 3D models involves a digital mockup of an overall vehicle, in the form of a massive, fully detailed, CAD assembly; therefore, adding unnecessary burden and overhead to design and product data management processes. While fully detailed data may yield a broad depth of design detail, pertinent integration features are often obscured under the excessive amounts of information, making them difficult to discern. In contrast, the envelope and interface method results in a reduction in both the amount and complexity of information necessary for design integration while yielding significant savings in time and effort when applied to today's complex design integration projects. This approach, combining classical and modern methods, proved advantageous during the complex design integration activities of the Ares I vehicle. Downstream processes, benefiting from this approach by reducing development and design cycle time, include: Creation of analysis models for the Aerodynamic discipline; Vehicle to ground interface development; Documentation development for the vehicle assembly.

Determination of orthotropic mechanical properties of 3D printed parts for structural health monitoring

NASA Astrophysics Data System (ADS)

Poissenot-Arrigoni, Bastien; Scheyer, Austin; Anton, Steven R.

2017-04-01

The evolution of additive manufacturing has allowed engineers to use 3D printing for many purposes. As a natural consequence of the 3D printing process, the printed object is anisotropic. As part of an ongoing project to embed piezoelectric devices in 3D printed structures for structural health monitoring (SHM), this study aims to find the mechanical properties of the 3D printed material and the influence of different external factors on those properties. The orthotropic mechanical properties of a 3D printed structure are dependent on the printing parameters used to create the structure. In order to develop an orthotropic material model, mechanical properties will be found experimentally from additively manufactured samples created from polylactic acid (PLA) using a consumer-level fused deposition modeling (FDM) printer; the Lulzbot TAZ 6. Nine mechanical constants including three Young's moduli, three Poisson's ratios, and three shear moduli are needed to fully describe the 3D elastic behavior of the material. Printed specimens with different raster orientations and print orientations allow calculation of the different material constants. In this work, seven of the nine mechanical constants were found. Two shear moduli were unable to be measured due to difficulties in printing two of the sample orientations. These mechanical properties are needed in order to develop orthotropic material models of systems employing 3D printed PLA. The results from this paper will be used to create a model of a piezoelectric transducer embedded in a 3D printed structure for structural health monitoring.

AxiSEM3D: a new fast method for global wave propagation in 3-D Earth models with undulating discontinuities

NASA Astrophysics Data System (ADS)

Leng, K.; Nissen-Meyer, T.; van Driel, M.; Al-Attar, D.

2016-12-01

We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models with laterally heterogeneous media and finite boundary perturbations. Our method is a hybrid of pseudo-spectral and spectral element methods (SEM). We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridional equations, which can be solved by a 2-D spectral element method (based on www.axisem.info). Computational efficiency of our method stems from lateral smoothness of global Earth models (with respect to wavelength) as well as axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. All boundary perturbations that violate geometric spherical symmetry, including Earth's ellipticity, topography and bathymetry, undulations of internal discontinuities such as Moho and CMB, are uniformly considered by means of a Particle Relabeling Transformation.The MPI-based high performance C++ code AxiSEM3D, is now available for forward simulations upon 3-D Earth models with fluid outer core, ellipticity, and both mantle and crustal structures. We show novel benchmarks for global wave solutions in 3-D mantle structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period going down to 5s. It is shown that our method runs up to two orders of magnitude faster than the 3-D SEM for such settings, and such computational advantage scales favourably with seismic frequency. By examining wavefields passing through hypothetical Gaussian plumes of varying sharpness, we identify in model-wavelength space the limits where our method may lose its advantage.

Accuracy of 1D microvascular flow models in the limit of low Reynolds numbers.

PubMed

Pindera, Maciej Z; Ding, Hui; Athavale, Mahesh M; Chen, Zhijian

2009-05-01

We describe results of numerical simulations of steady flows in tubes with branch bifurcations using fully 3D and reduced 1D geometries. The intent is to delineate the range of validity of reduced models used for simulations of flows in microcapillary networks, as a function of the flow Reynolds number Re. Results from model problems indicate that for Re less than 1 and possibly as high as 10, vasculatures may be represented by strictly 1D Poiseuille flow geometries with flow variation in the axial dimensions only. In that range flow rate predictions in the different branches generated by 1D and 3D models differ by a constant factor, independent of Re. When the cross-sectional areas of the branches are constant these differences are generally small and appear to stem from an uncertainty of how the individual branch lengths are defined. This uncertainty can be accounted for by a simple geometrical correction. For non-constant cross-sections the differences can be much more significant. If additional corrections for the presence of branch junctions and flow area variations are not taken into account in 1D models of complex vasculatures, the resultant flow predictions should be interpreted with caution.

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data

PubMed Central

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-01-01

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for Photogrammetry and Remote Sensing (ISPRS) benchmark datasets. The results show that the proposed method can robustly produce accurate regularized 3D building rooftop models. PMID:28335486

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data.

PubMed

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-03-19

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for Photogrammetry and Remote Sensing (ISPRS) benchmark datasets. The results show that the proposed method can robustly produce accurate regularized 3D building rooftop models.

UT simulation using a fully automated 3D hybrid model: Application to planar backwall breaking defects inspection

NASA Astrophysics Data System (ADS)

Imperiale, Alexandre; Chatillon, Sylvain; Darmon, Michel; Leymarie, Nicolas; Demaldent, Edouard

2018-04-01

The high frequency models gathered in the CIVA software allow fast computations and provide satisfactory quantitative predictions in a wide range of situations. However, the domain of validity of these models is limited since they do not accurately predict the ultrasound response in configurations involving subwavelength complex phenomena. In addition, when modelling backwall breaking defects inspection, an important challenge remains to capture the propagation of the creeping waves that are generated at the critical angle. Hybrid models combining numerical and asymptotic methods have already been shown to be an effective strategy to overcome these limitations in 2D [1]. However, 3D simulations remain a crucial issue for industrial applications because of the computational cost of the numerical solver. A dedicated three dimensional high order finite element model combined with a domain decomposition method has been recently proposed to tackle 3D limitations [2]. In this communication, we will focus on the specific case of planar backwall breaking defects, with an adapted coupling strategy in order to efficiently model the propagation of creeping waves. Numerical and experimental validations will be proposed on various configurations.

Getting AM Up to Speed Across the Army Life Cycle

DTIC Science & Technology

2016-12-01

acquisition domain, more engi- neering work is needed to better define what standards should be used in Data Item Descriptions (DID) and Contract Data... compared to traditional parts replacement using procurement. While cold spray AM technology does not necessarily require the use of 3D models, to fully

SPH calculations of asteroid disruptions: The role of pressure dependent failure models

NASA Astrophysics Data System (ADS)

Jutzi, Martin

2015-03-01

We present recent improvements of the modeling of the disruption of strength dominated bodies using the Smooth Particle Hydrodynamics (SPH) technique. The improvements include an updated strength model and a friction model, which are successfully tested by a comparison with laboratory experiments. In the modeling of catastrophic disruptions of asteroids, a comparison between old and new strength models shows no significant deviation in the case of targets which are initially non-porous, fully intact and have a homogeneous structure (such as the targets used in the study by Benz and Asphaug, 1999). However, for many cases (e.g. initially partly or fully damaged targets and rubble-pile structures) we find that it is crucial that friction is taken into account and the material has a pressure dependent shear strength. Our investigations of the catastrophic disruption threshold Q D * as a function of target properties and target sizes up to a few 100 km show that a fully damaged target modeled without friction has a Q D * which is significantly (5-10 times) smaller than in the case where friction is included. When the effect of the energy dissipation due to compaction (pore crushing) is taken into account as well, the targets become even stronger ( Q D * is increased by a factor of 2-3). On the other hand, cohesion is found to have an negligible effect at large scales and is only important at scales ≲ 1 km. Our results show the relative effects of strength, friction and porosity on the outcome of collisions among small (≲ 1000 km) bodies. These results will be used in a future study to improve existing scaling laws for the outcome of collisions (e.g. Leinhardt and Stewart, 2012).

3D lens-free time-lapse microscopy for 3D cell culture

NASA Astrophysics Data System (ADS)

Berdeu, Anthony; Momey, Fabien; Laperrousaz, Bastien; Bordy, Thomas; Gidrol, Xavier; Dinten, Jean-Marc; Picollet-D'hahan, Nathalie; Allier, Cédric

2017-07-01

We propose a new imaging platform based on lens-free time-lapse microscopy for 3D cell culture and its dedicated algorithm lying on a fully 3D regularized inverse problem approach. First 3D+t results are presented

Objective and subjective comparison of standard 2-D and fully 3-D reconstructed data on a PET/CT system.

PubMed

Strobel, Klaus; Rüdy, Matthias; Treyer, Valerie; Veit-Haibach, Patrick; Burger, Cyrill; Hany, Thomas F

2007-07-01

The relative advantage of fully 3-D versus 2-D mode for whole-body imaging is currently the focus of considerable expert debate. The nature of 3-D PET acquisition for FDG PET/CT theoretically allows a shorter scan time and improved efficiency of FDG use than in the standard 2-D acquisition. We therefore objectively and subjectively compared standard 2-D and fully 3-D reconstructed data for FDG PET/CT on a research PET/CT system. In a total of 36 patients (mean 58.9 years, range 17.3-78.9 years; 21 male, 15 female) referred for known or suspected malignancy, FDG PET/CT was performed using a research PET/CT system with advanced detector technology with improved sensitivity and spatial resolution. After 45 min uptake, a low-dose CT (40 mAs) from head to thigh was performed followed by 2-D PET (emission 3 min per field) and 3-D PET (emission 1.5 min per field) with both seven slices overlap to cover the identical anatomical region. Acquisition time was therefore 50% less (seven fields; 21 min vs. 10.5 min). PET data was acquired in a randomized fashion, so in 50% of the cases 2-D data was acquired first. CT data was used for attenuation correction. 2-D (OSEM) and 3-D PET images were iteratively reconstructed. Subjective analysis of 2-D and 3-D images was performed by two readers in a blinded, randomized fashion evaluating the following criteria: sharpness of organs (liver, chest wall/lung), overall image quality and detectability and dignity of each identified lesion. Objective analysis of PET data was investigated measuring maximum standard uptake value with lean body mass (SUV(max,LBM)) of identified lesions. On average, per patient, the SUV(max) was 7.86 (SD 7.79) for 2-D and 6.96 (SD 5.19) for 3-D. On a lesion basis, the average SUV(max) was 7.65 (SD 7.79) for 2-D and 6.75 (SD 5.89) for 3-D. The absolute difference on a paired t-test of SUV 3-D-2-D based on each measured lesion was significant with an average of -0.956 (P=0.002) and an average of -0.884 on a patient base (P<0.05). With 3-D the SUV(max) decreased by an average of 5.2% for each lesion, and an average of 6.0% for each patient. Subjective analysis showed fair inter-observer agreement regarding detectability (kappa=0.24 for 3-D; 0.36 for 3-D) and dignity (kappa=0.44 for 3-D and 0.4 for 2-D) of the lesions. There was no significant diagnostic difference between 3-D and 2-D. Only in one patient, a satellite liver metastasis of a colon cancer was missed in 3-D and detected only in 2-D. On average, the overall image quality for 3-D images was equal (in 24%) or inferior (in 76%) compared to 2-D. A possible major advantage of 3-D data acquisition is the faster patient throughput with a 50% reduction in scan time. The fully 3-D reconstruction technique has overcome the technical drawbacks of current 3-D imaging technique. In our limited number of patients there was no significant diagnostic difference between 2-D and fully 3-D.

The 3D Reference Earth Model: Status and Preliminary Results

NASA Astrophysics Data System (ADS)

Moulik, P.; Lekic, V.; Romanowicz, B. A.

2017-12-01

In the 20th century, seismologists constructed models of how average physical properties (e.g. density, rigidity, compressibility, anisotropy) vary with depth in the Earth's interior. These one-dimensional (1D) reference Earth models (e.g. PREM) have proven indispensable in earthquake location, imaging of interior structure, understanding material properties under extreme conditions, and as a reference in other fields, such as particle physics and astronomy. Over the past three decades, new datasets motivated more sophisticated efforts that yielded models of how properties vary both laterally and with depth in the Earth's interior. Though these three-dimensional (3D) models exhibit compelling similarities at large scales, differences in the methodology, representation of structure, and dataset upon which they are based, have prevented the creation of 3D community reference models. As part of the REM-3D project, we are compiling and reconciling reference seismic datasets of body wave travel-time measurements, fundamental mode and overtone surface wave dispersion measurements, and normal mode frequencies and splitting functions. These reference datasets are being inverted for a long-wavelength, 3D reference Earth model that describes the robust long-wavelength features of mantle heterogeneity. As a community reference model with fully quantified uncertainties and tradeoffs and an associated publically available dataset, REM-3D will facilitate Earth imaging studies, earthquake characterization, inferences on temperature and composition in the deep interior, and be of improved utility to emerging scientific endeavors, such as neutrino geoscience. Here, we summarize progress made in the construction of the reference long period dataset and present a preliminary version of REM-3D in the upper-mantle. In order to determine the level of detail warranted for inclusion in REM-3D, we analyze the spectrum of discrepancies between models inverted with different subsets of the reference dataset. This procedure allows us to evaluate the extent of consistency in imaging heterogeneity at various depths and between spatial scales.

Improved Large-Scale Inundation Modelling by 1D-2D Coupling and Consideration of Hydrologic and Hydrodynamic Processes - a Case Study in the Amazon

NASA Astrophysics Data System (ADS)

Hoch, J. M.; Bierkens, M. F.; Van Beek, R.; Winsemius, H.; Haag, A.

2015-12-01

Understanding the dynamics of fluvial floods is paramount to accurate flood hazard and risk modeling. Currently, economic losses due to flooding constitute about one third of all damage resulting from natural hazards. Given future projections of climate change, the anticipated increase in the World's population and the associated implications, sound knowledge of flood hazard and related risk is crucial. Fluvial floods are cross-border phenomena that need to be addressed accordingly. Yet, only few studies model floods at the large-scale which is preferable to tiling the output of small-scale models. Most models cannot realistically model flood wave propagation due to a lack of either detailed channel and floodplain geometry or the absence of hydrologic processes. This study aims to develop a large-scale modeling tool that accounts for both hydrologic and hydrodynamic processes, to find and understand possible sources of errors and improvements and to assess how the added hydrodynamics affect flood wave propagation. Flood wave propagation is simulated by DELFT3D-FM (FM), a hydrodynamic model using a flexible mesh to schematize the study area. It is coupled to PCR-GLOBWB (PCR), a macro-scale hydrological model, that has its own simpler 1D routing scheme (DynRout) which has already been used for global inundation modeling and flood risk assessments (GLOFRIS; Winsemius et al., 2013). A number of model set-ups are compared and benchmarked for the simulation period 1986-1996: (0) PCR with DynRout; (1) using a FM 2D flexible mesh forced with PCR output and (2) as in (1) but discriminating between 1D channels and 2D floodplains, and, for comparison, (3) and (4) the same set-ups as (1) and (2) but forced with observed GRDC discharge values. Outputs are subsequently validated against observed GRDC data at Óbidos and flood extent maps from the Dartmouth Flood Observatory. The present research constitutes a first step into a globally applicable approach to fully couple hydrologic with hydrodynamic computations while discriminating between 1D-channels and 2D-floodplains. Such a fully-fledged set-up would be able to provide higher-order flood hazard information, e.g. time to flooding and flood duration, ultimately leading to improved flood risk assessment and management at the large scale.

Electro-mechanical response of a 3D nerve bundle model to mechanical loads leading to axonal injury.

PubMed

Cinelli, I; Destrade, M; Duffy, M; McHugh, P

2017-07-01

Axonal damage is one of the most common pathological features of traumatic brain injury, leading to abnormalities in signal propagation for nervous systems. We present a 3D fully coupled electro-mechanical model of a nerve bundle, made with the finite element software Abaqus 6.13-3. The model includes a real-time coupling, modulated threshold for spiking activation and independent alteration of the electrical properties for each 3-layer fibre within the bundle. Compression and tension are simulated to induce damage at the nerve membrane. Changes in strain, stress distribution and neural activity are investigated for myelinated and unmyelinated nerve fibres, by considering the cases of an intact and of a traumatized nerve membrane. Results show greater changes in transmitting action potential in the myelinated fibre.

Limitations of the hCMEC/D3 cell line as a model for Aβ clearance by the human blood-brain barrier.

PubMed

Biemans, Elisanne A L M; Jäkel, Lieke; de Waal, Robert M W; Kuiperij, H Bea; Verbeek, Marcel M

2017-07-01

Alzheimer's disease and cerebral amyloid angiopathy are characterized by accumulation of amyloid-β (Aβ) at the cerebrovasculature due to decreased clearance at the blood-brain barrier (BBB). However, the exact mechanism of Aβ clearance across this barrier has not been fully elucidated. The hCMEC/D3 cell line has been characterized as a valid model for the BBB. In this study we evaluated the use of this model to study Aβ clearance across the BBB, with an emphasis on brain-to-blood directional permeability. Barrier integrity of hCMEC/D3 monolayers was confirmed for large molecules in both the apical to basolateral and the reverse direction. However, permeability for smaller molecules was substantially higher, especially in basolateral to apical direction, and barrier formation for Aβ was completely absent in this direction. In addition, hCMEC/D3 cells failed to develop a high TEER, possibly caused by incomplete formation of tight junctions. We conclude that the hCMEC/D3 model has several limitations to study the cerebral clearance of Aβ. Therefore, the model needs further characterization before this cell system can be generally applied as a model to study cerebral Aβ clearance. © 2016 The Authors Journal of Neuroscience Research Published by Wiley Periodicals, Inc. © 2016 The Authors Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

Modulation of cortical activity in 2D versus 3D virtual reality environments: an EEG study.

PubMed

Slobounov, Semyon M; Ray, William; Johnson, Brian; Slobounov, Elena; Newell, Karl M

2015-03-01

There is a growing empirical evidence that virtual reality (VR) is valuable for education, training, entertaining and medical rehabilitation due to its capacity to represent real-life events and situations. However, the neural mechanisms underlying behavioral confounds in VR environments are still poorly understood. In two experiments, we examined the effect of fully immersive 3D stereoscopic presentations and less immersive 2D VR environments on brain functions and behavioral outcomes. In Experiment 1 we examined behavioral and neural underpinnings of spatial navigation tasks using electroencephalography (EEG). In Experiment 2, we examined EEG correlates of postural stability and balance. Our major findings showed that fully immersive 3D VR induced a higher subjective sense of presence along with enhanced success rate of spatial navigation compared to 2D. In Experiment 1 power of frontal midline EEG (FM-theta) was significantly higher during the encoding phase of route presentation in the 3D VR. In Experiment 2, the 3D VR resulted in greater postural instability and modulation of EEG patterns as a function of 3D versus 2D environments. The findings support the inference that the fully immersive 3D enriched-environment requires allocation of more brain and sensory resources for cognitive/motor control during both tasks than 2D presentations. This is further evidence that 3D VR tasks using EEG may be a promising approach for performance enhancement and potential applications in clinical/rehabilitation settings. Copyright © 2014 Elsevier B.V. All rights reserved.

Footprint Map Partitioning Using Airborne Laser Scanning Data

NASA Astrophysics Data System (ADS)

Xiong, B.; Oude Elberink, S.; Vosselman, G.

2016-06-01

Nowadays many cities and countries are creating their 3D building models for a better daily management and smarter decision making. The newly created 3D models are required to be consistent with existing 2D footprint maps. Thereby the 2D maps are usually combined with height data for the task of 3D reconstruction. Many buildings are often composed by parts that are discontinuous over height. Building parts can be reconstructed independently and combined into a complete building. Therefore, most of the state-of-the-art work on 3D building reconstruction first decomposes a footprint map into parts. However, those works usually change the footprint maps for easier partitioning and cannot detect building parts that are fully inside the footprint polygon. In order to solve those problems, we introduce two methodologies, one more dependent on height data, and the other one more dependent on footprints. We also experimentally evaluate the two methodologies and compare their advantages and disadvantages. The experiments use Airborne Laser Scanning (ALS) data and two vector maps, one with 1:10,000 scale and another one with 1:500 scale.

The 3D Reference Earth Model (REM-3D): Update and Outlook

NASA Astrophysics Data System (ADS)

Lekic, V.; Moulik, P.; Romanowicz, B. A.; Dziewonski, A. M.

2016-12-01

Elastic properties of the Earth's interior (e.g. density, rigidity, compressibility, anisotropy) vary spatially due to changes in temperature, pressure, composition, and flow. In the 20th century, seismologists have constructed reference models of how these quantities vary with depth, notably the PREM model of Dziewonski and Anderson (1981). These 1D reference earth models have proven indispensable in earthquake location, imaging of interior structure, understanding material properties under extreme conditions, and as a reference in other fields, such as particle physics and astronomy. Over the past three decades, more sophisticated efforts by seismologists have yielded several generations of models of how properties vary not only with depth, but also laterally. Yet, though these three-dimensional (3D) models exhibit compelling similarities at large scales, differences in the methodology, representation of structure, and dataset upon which they are based, have prevented the creation of 3D community reference models. We propose to overcome these challenges by compiling, reconciling, and distributing a long period (>15 s) reference seismic dataset, from which we will construct a 3D seismic reference model (REM-3D) for the Earth's mantle, which will come in two flavors: a long wavelength smoothly parameterized model and a set of regional profiles. Here, we summarize progress made in the construction of the reference long period dataset, and present preliminary versions of the REM-3D in order to illustrate the two flavors of REM-3D and their relative advantages and disadvantages. As a community reference model and with fully quantified uncertainties and tradeoffs, REM-3D will facilitate Earth imaging studies, earthquake characterization, inferences on temperature and composition in the deep interior, and be of improved utility to emerging scientific endeavors, such as neutrino geoscience. In this presentation, we outline the outlook for setting up advisory community working groups and the community workshop that would assess progress, evaluate model and dataset performance, identify avenues for improvement, and recommend strategies for maximizing model adoption in and utility for the deep Earth community.

Interactive 3D Models and Simulations for Nuclear Security Education, Training, and Analysis.

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

Warner, David K.; Dickens, Brian Scott; Heimer, Donovan J.

By providing examples of products that have been produced in the past, it is the hopes of the authors that the audience will have a more thorough understanding of 3D modeling tools, potential applications, and capabilities that they can provide. Truly the applications and capabilities of these types of tools are only limited by one’s imagination. The future of three-dimensional models lies in the expansion into the world of virtual reality where one will experience a fully immersive first-person environment. The use of headsets and hand tools will allow students and instructors to have a more thorough spatial understanding ofmore » facilities and scenarios that they will encounter in the real world.« less

Fully Coupled Simulation of Lithium Ion Battery Cell Performance

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

Trembacki, Bradley L.; Murthy, Jayathi Y.; Roberts, Scott Alan

Lithium-ion battery particle-scale (non-porous electrode) simulations applied to resolved electrode geometries predict localized phenomena and can lead to better informed decisions on electrode design and manufacturing. This work develops and implements a fully-coupled finite volume methodology for the simulation of the electrochemical equations in a lithium-ion battery cell. The model implementation is used to investigate 3D battery electrode architectures that offer potential energy density and power density improvements over traditional layer-by-layer particle bed battery geometries. Advancement of micro-scale additive manufacturing techniques has made it possible to fabricate these 3D electrode microarchitectures. A variety of 3D battery electrode geometries are simulatedmore » and compared across various battery discharge rates and length scales in order to quantify performance trends and investigate geometrical factors that improve battery performance. The energy density and power density of the 3D battery microstructures are compared in several ways, including a uniform surface area to volume ratio comparison as well as a comparison requiring a minimum manufacturable feature size. Significant performance improvements over traditional particle bed electrode designs are observed, and electrode microarchitectures derived from minimal surfaces are shown to be superior. A reduced-order volume-averaged porous electrode theory formulation for these unique 3D batteries is also developed, allowing simulations on the full-battery scale. Electrode concentration gradients are modeled using the diffusion length method, and results for plate and cylinder electrode geometries are compared to particle-scale simulation results. Additionally, effective diffusion lengths that minimize error with respect to particle-scale results for gyroid and Schwarz P electrode microstructures are determined.« less

Turbulence Model Behavior in Low Reynolds Number Regions of Aerodynamic Flowfields

NASA Technical Reports Server (NTRS)

Rumsey, Christopher L.; Spalart, Philippe R.

2008-01-01

The behaviors of the widely-used Spalart-Allmaras (SA) and Menter shear-stress transport (SST) turbulence models at low Reynolds numbers and under conditions conducive to relaminarization are documented. The flows used in the investigation include 2-D zero pressure gradient flow over a flat plate from subsonic to hypersonic Mach numbers, 2-D airfoil flow from subsonic to supersonic Mach numbers, 2-D subsonic sink-flow, and 3-D subsonic flow over an infinite swept wing (particularly its leading-edge region). Both models exhibit a range over which they behave transitionally in the sense that the flow is neither laminar nor fully turbulent, but these behaviors are different: the SST model typically has a well-defined transition location, whereas the SA model does not. Both models are predisposed to delayed activation of turbulence with increasing freestream Mach number. Also, both models can be made to achieve earlier activation of turbulence by increasing their freestream levels, but too high a level can disturb the turbulent solution behavior. The technique of maintaining freestream levels of turbulence without decay in the SST model, introduced elsewhere, is shown here to be useful in reducing grid-dependence of the model's transitional behavior. Both models are demonstrated to be incapable of predicting relaminarization; eddy viscosities remain weakly turbulent in accelerating or laterally-strained boundary layers for which experiment and direct simulations indicate turbulence suppression. The main conclusion is that these models are intended for fully turbulent high Reynolds number computations, and using them for transitional (e.g., low Reynolds number) or relaminarizing flows is not appropriate.

Turbulence Model Behavior in Low Reynolds Number Regions of Aerodynamic Flowfields

NASA Technical Reports Server (NTRS)

Rumsey, Christopher L.; Spalart, Philippe R.

2008-01-01

The behaviors of the widely-used Spalart-Allmaras (SA) and Menter shear-stress transport (SST) turbulence models at low Reynolds numbers and under conditions conducive to relaminarization are documented. The flows used in the investigation include 2-D zero pressure gradient flow over a flat plate from subsonic to hypersonic Mach numbers, 2-D airfoil flow from subsonic to supersonic Mach numbers, 2-D subsonic sink-flow, and 3-D subsonic flow over an infinite swept wing (particularly its leading-edge region). Both models exhibit a range over which they behave 'transitionally' in the sense that the flow is neither laminar nor fully turbulent, but these behaviors are different: the SST model typically has a well-defined transition location, whereas the SA model does not. Both models are predisposed to delayed activation of turbulence with increasing freestream Mach number. Also, both models can be made to achieve earlier activation of turbulence by increasing their freestream levels, but too high a level can disturb the turbulent solution behavior. The technique of maintaining freestream levels of turbulence without decay in the SST model, introduced elsewhere, is shown here to be useful in reducing grid-dependence of the model's transitional behavior. Both models are demonstrated to be incapable of predicting relaminarization; eddy viscosities remain weakly turbulent in accelerating or laterally-strained boundary layers for which experiment and direct simulations indicate turbulence suppression. The main conclusion is that these models are intended for fully turbulent high Reynolds number computations, and using them for transitional (e.g., low Reynolds number) or relaminarizing flows is not appropriate.

Barriers to front propagation in laminar, three-dimensional fluid flows

NASA Astrophysics Data System (ADS)

Doan, Minh; Simons, J. J.; Lilienthal, Katherine; Solomon, Tom; Mitchell, Kevin A.

2018-03-01

We present experiments on one-way barriers that block reaction fronts in a fully three-dimensional (3D) fluid flow. Fluorescent Belousov-Zhabotinsky reaction fronts are imaged with laser-scanning in a laminar, overlapping vortex flow. The barriers are analyzed with a 3D extension to burning invariant manifold (BIM) theory that was previously applied to two-dimensional advection-reaction-diffusion processes. We discover tube and sheet barriers that guide the front evolution. The experimentally determined barriers are explained by BIMs calculated from a model of the flow.

Whole lung morphometry with 3D multiple b-value hyperpolarized gas MRI and compressed sensing.

PubMed

Chan, Ho-Fung; Stewart, Neil J; Parra-Robles, Juan; Collier, Guilhem J; Wild, Jim M

2017-05-01

To demonstrate three-dimensional (3D) multiple b-value diffusion-weighted (DW) MRI of hyperpolarized 3 He gas for whole lung morphometry with compressed sensing (CS). A fully-sampled, two b-value, 3D hyperpolarized 3 He DW-MRI dataset was acquired from the lungs of a healthy volunteer and retrospectively undersampled in the k y and k z phase-encoding directions for CS simulations. Optimal k-space undersampling patterns were determined by minimizing the mean absolute error between reconstructed and fully-sampled 3 He apparent diffusion coefficient (ADC) maps. Prospective three-fold, undersampled, 3D multiple b-value 3 He DW-MRI datasets were acquired from five healthy volunteers and one chronic obstructive pulmonary disease (COPD) patient, and the mean values of maps of ADC and mean alveolar dimension (Lm D ) were validated against two-dimensional (2D) and 3D fully-sampled 3 He DW-MRI experiments. Reconstructed undersampled datasets showed no visual artifacts and good preservation of the main image features and quantitative information. A good agreement between fully-sampled and prospective undersampled datasets was found, with a mean difference of +3.4% and +5.1% observed in mean global ADC and Lm D values, respectively. These differences were within the standard deviation range and consistent with values reported from healthy and COPD lungs. Accelerated CS acquisition has facilitated 3D multiple b-value 3 He DW-MRI scans in a single breath-hold, enabling whole lung morphometry mapping. Magn Reson Med 77:1916-1925, 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 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Emergence of fully gapped s++-wave and nodal d-wave states mediated by orbital and spin fluctuations in a ten-orbital model of KFe2Se2

NASA Astrophysics Data System (ADS)

Saito, Tetsuro; Onari, Seiichiro; Kontani, Hiroshi

2011-04-01

We study the superconducting state in recently discovered high-Tc superconductor KxFe2Se2 based on the ten-orbital Hubbard-Holstein model without hole pockets. When the Coulomb interaction is large, a spin-fluctuation-mediated d-wave state appears due to the nesting between electron pockets. Interestingly, the symmetry of the body-centered tetragonal structure in KxFe2Se2 requires the existence of nodes in the d-wave gap, although a fully gapped d-wave state is realized in the case of a simple tetragonal structure. In the presence of moderate electron-phonon interaction due to Fe-ion optical modes, however, orbital fluctuations give rise to the fully gapped s++-wave state without sign reversal. Therefore, both superconducting states are distinguishable by careful measurements of the gap structure or the impurity effect on Tc.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code

NASA Astrophysics Data System (ADS)

Chacon, Luis

2006-10-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field to machine precision, non-dissipative, and linearly and nonlinearly stable in the absence of physical dissipation. PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, second-order implicit schemes such as Crank-Nicolson and BDF2 (2^nd order backward differentiation formula) are available. PIXIE3D is fully parallel (employs PETSc for parallelism), and exhibits excellent parallel scalability. A parallel, scalable, MG preconditioning strategy, based on physics-based preconditioning ideas, has been developed for resistive MHD, and is currently being extended to Hall MHD. In this poster, we will report on progress in the algorithmic formulation for extended MHD, as well as the the serial and parallel performance of PIXIE3D in a variety of problems and geometries. L. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004) L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002); J. Comput. Phys., 188 (2), 573-592 (2003) L. Chac'on, 32nd EPS Conf. Plasma Physics, Tarragona, Spain, 2005 L. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006

Fully anisotropic 3-D EM modelling on a Lebedev grid with a multigrid pre-conditioner

NASA Astrophysics Data System (ADS)

Jaysaval, Piyoosh; Shantsev, Daniil V.; de la Kethulle de Ryhove, Sébastien; Bratteland, Tarjei

2016-12-01

We present a numerical algorithm for 3-D electromagnetic (EM) simulations in conducting media with general electric anisotropy. The algorithm is based on the finite-difference discretization of frequency-domain Maxwell's equations on a Lebedev grid, in which all components of the electric field are collocated but half a spatial step staggered with respect to the magnetic field components, which also are collocated. This leads to a system of linear equations that is solved using a stabilized biconjugate gradient method with a multigrid preconditioner. We validate the accuracy of the numerical results for layered and 3-D tilted transverse isotropic (TTI) earth models representing typical scenarios used in the marine controlled-source EM method. It is then demonstrated that not taking into account the full anisotropy of the conductivity tensor can lead to misleading inversion results. For synthetic data corresponding to a 3-D model with a TTI anticlinal structure, a standard vertical transverse isotropic (VTI) inversion is not able to image a resistor, while for a 3-D model with a TTI synclinal structure it produces a false resistive anomaly. However, if the VTI forward solver used in the inversion is replaced by the proposed TTI solver with perfect knowledge of the strike and dip of the dipping structures, the resulting resistivity images become consistent with the true models.

EBM regeneration and changes in EBM component mRNA expression in stromal cells after corneal injury

PubMed Central

Santhanam, Abirami; Marino, Gustavo K.; Torricelli, Andre A. M.

2017-01-01

Purpose To investigate the production of the epithelial basement membrane (EBM) component mRNAs at time points before lamina lucida and lamina densa regeneration in anterior stromal cells after corneal injury that would heal with and without fibrosis. Methods Rabbit corneas were removed from 2 to 19 days after −4.5D or −9.0D photorefractive keratectomy (PRK) with the VISX S4 IR laser. Corneas were evaluated with transmission electron microscopy (TEM) for full regeneration of the lamina lucida and the lamina densa. Laser capture microdissection (LCM) based quantitative real-time (RT)–PCR was used to quantitate the expression of mRNAs for laminin α-3 (LAMA3), perlecan, nidogen-1, and nidogen-2 in the anterior stroma. Results After −4.5D PRK, EBM was found to be fully regenerated at 8 to 10 days after surgery. At 4 days after PRK, the nidogen-2 and LAMA3 mRNAs levels were detected at statistically significantly lower levels in the anterior stroma of the −9.0D PRK corneas (where the EBM would not fully regenerate) compared to the −4.5D PRK corneas (where the EBM was destined to fully regenerate). At 7 days after PRK, nidogen-2 and LAMA3 mRNAs continued to be statistically significantly lower in the anterior stroma of the −9.0D PRK corneas compared to their expression in the anterior stroma of the −4.5D PRK corneas. Conclusions Key EBM components LAMA3 and nidogen-2 mRNAs are expressed at higher levels in the anterior stroma during EBM regeneration in the −4.5D PRK corneas where the EBM is destined to fully regenerate and no haze developed compared to the −9.0D PRK corneas where the EBM will not fully regenerate and myofibroblast-related stromal fibrosis (haze) will develop. PMID:28275314

Automatic Assessment of 3D Modeling Exams

ERIC Educational Resources Information Center

Sanna, A.; Lamberti, F.; Paravati, G.; Demartini, C.

2012-01-01

Computer-based assessment of exams provides teachers and students with two main benefits: fairness and effectiveness in the evaluation process. This paper proposes a fully automatic evaluation tool for the Graphic and Virtual Design (GVD) curriculum at the First School of Architecture of the Politecnico di Torino, Italy. In particular, the tool is…

Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI.

PubMed

Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

2015-01-01

Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. Copyright © 2014. Published by Elsevier Inc.

Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI

PubMed Central

Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

2016-01-01

Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

Grounding line dynamics inferred from a 3D full-Stokes model solving the contact problem

NASA Astrophysics Data System (ADS)

Favier, Lionel; Gagliardini, Olivier; Durand, Gael; Zwinger, Thomas

2010-05-01

The mass balance of marine ice-sheets, such as the West Antarctic Ice Sheet, is mostly controlled by their grounding line dynamics. Most numerical models simulating marine ice-sheets involve simplifications and do not include all the stress gradients. First results obtained with a 3D full-Stokes model for the grounded ice-sheet / floating ice-shelf transition, using the finite-element code Elmer/Ice, are presented. The initial geometry, which takes into account a dome and a calving front, has been laterally extruded from a previously investigated 2D flowline geometry. The grounding line migration is computed by solving the contact problem between the ice and the rigid downward sloping bedrock, where a non linear friction law is applied in the two horizontal directions. The evolutions of the sea-air and sea-ice interfaces are determined by the solution of a local transport equation. The consistency between the 3D model and the analogous results of the flowline model is shown by comparing the results in the basic extruded case, with no normal flux through lateral boundaries. Thereafter, spatially non uniform perturbations are introduced, to simulate the grounding line dynamics under fully three-dimensional perturbations.

Almost but not quite 2D, Non-linear Bayesian Inversion of CSEM Data

NASA Astrophysics Data System (ADS)

Ray, A.; Key, K.; Bodin, T.

2013-12-01

The geophysical inverse problem can be elegantly stated in a Bayesian framework where a probability distribution can be viewed as a statement of information regarding a random variable. After all, the goal of geophysical inversion is to provide information on the random variables of interest - physical properties of the earth's subsurface. However, though it may be simple to postulate, a practical difficulty of fully non-linear Bayesian inversion is the computer time required to adequately sample the model space and extract the information we seek. As a consequence, in geophysical problems where evaluation of a full 2D/3D forward model is computationally expensive, such as marine controlled source electromagnetic (CSEM) mapping of the resistivity of seafloor oil and gas reservoirs, Bayesian studies have largely been conducted with 1D forward models. While the 1D approximation is indeed appropriate for exploration targets with planar geometry and geological stratification, it only provides a limited, site-specific idea of uncertainty in resistivity with depth. In this work, we extend our fully non-linear 1D Bayesian inversion to a 2D model framework, without requiring the usual regularization of model resistivities in the horizontal or vertical directions used to stabilize quasi-2D inversions. In our approach, we use the reversible jump Markov-chain Monte-Carlo (RJ-MCMC) or trans-dimensional method and parameterize the subsurface in a 2D plane with Voronoi cells. The method is trans-dimensional in that the number of cells required to parameterize the subsurface is variable, and the cells dynamically move around and multiply or combine as demanded by the data being inverted. This approach allows us to expand our uncertainty analysis of resistivity at depth to more than a single site location, allowing for interactions between model resistivities at different horizontal locations along a traverse over an exploration target. While the model is parameterized in 2D, we efficiently evaluate the forward response using 1D profiles extracted from the model at the common-midpoints of the EM source-receiver pairs. Since the 1D approximation is locally valid at different midpoint locations, the computation time is far lower than is required by a full 2D or 3D simulation. We have applied this method to both synthetic and real CSEM survey data from the Scarborough gas field on the Northwest shelf of Australia, resulting in a spatially variable quantification of resistivity and its uncertainty in 2D. This Bayesian approach results in a large database of 2D models that comprise a posterior probability distribution, which we can subset to test various hypotheses about the range of model structures compatible with the data. For example, we can subset the model distributions to examine the hypothesis that a resistive reservoir extends overs a certain spatial extent. Depending on how this conditions other parts of the model space, light can be shed on the geological viability of the hypothesis. Since tackling spatially variable uncertainty and trade-offs in 2D and 3D is a challenging research problem, the insights gained from this work may prove valuable for subsequent full 2D and 3D Bayesian inversions.

Esophagus segmentation in CT via 3D fully convolutional neural network and random walk.

PubMed

Fechter, Tobias; Adebahr, Sonja; Baltas, Dimos; Ben Ayed, Ismail; Desrosiers, Christian; Dolz, Jose

2017-12-01

Precise delineation of organs at risk is a crucial task in radiotherapy treatment planning for delivering high doses to the tumor while sparing healthy tissues. In recent years, automated segmentation methods have shown an increasingly high performance for the delineation of various anatomical structures. However, this task remains challenging for organs like the esophagus, which have a versatile shape and poor contrast to neighboring tissues. For human experts, segmenting the esophagus from CT images is a time-consuming and error-prone process. To tackle these issues, we propose a random walker approach driven by a 3D fully convolutional neural network (CNN) to automatically segment the esophagus from CT images. First, a soft probability map is generated by the CNN. Then, an active contour model (ACM) is fitted to the CNN soft probability map to get a first estimation of the esophagus location. The outputs of the CNN and ACM are then used in conjunction with a probability model based on CT Hounsfield (HU) values to drive the random walker. Training and evaluation were done on 50 CTs from two different datasets, with clinically used peer-reviewed esophagus contours. Results were assessed regarding spatial overlap and shape similarity. The esophagus contours generated by the proposed algorithm showed a mean Dice coefficient of 0.76 ± 0.11, an average symmetric square distance of 1.36 ± 0.90 mm, and an average Hausdorff distance of 11.68 ± 6.80, compared to the reference contours. These results translate to a very good agreement with reference contours and an increase in accuracy compared to existing methods. Furthermore, when considering the results reported in the literature for the publicly available Synapse dataset, our method outperformed all existing approaches, which suggests that the proposed method represents the current state-of-the-art for automatic esophagus segmentation. We show that a CNN can yield accurate estimations of esophagus location, and that the results of this model can be refined by a random walk step taking pixel intensities and neighborhood relationships into account. One of the main advantages of our network over previous methods is that it performs 3D convolutions, thus fully exploiting the 3D spatial context and performing an efficient volume-wise prediction. The whole segmentation process is fully automatic and yields esophagus delineations in very good agreement with the gold standard, showing that it can compete with previously published methods. © 2017 American Association of Physicists in Medicine.

A computationally efficient method for full-core conjugate heat transfer modeling of sodium fast reactors

DOE PAGES

Hu, Rui; Yu, Yiqi

2016-09-08

For efficient and accurate temperature predictions of sodium fast reactor structures, a 3-D full-core conjugate heat transfer modeling capability is developed for an advanced system analysis tool, SAM. The hexagon lattice core is modeled with 1-D parallel channels representing the subassembly flow, and 2-D duct walls and inter-assembly gaps. The six sides of the hexagon duct wall and near-wall coolant region are modeled separately to account for different temperatures and heat transfer between coolant flow and each side of the duct wall. The Jacobian Free Newton Krylov (JFNK) solution method is applied to solve the fluid and solid field simultaneouslymore » in a fully coupled fashion. The 3-D full-core conjugate heat transfer modeling capability in SAM has been demonstrated by a verification test problem with 7 fuel assemblies in a hexagon lattice layout. In addition, the SAM simulation results are compared with RANS-based CFD simulations. Very good agreements have been achieved between the results of the two approaches.« less

Burning invariant manifolds for reaction fronts in three-dimensional fluid flows

NASA Astrophysics Data System (ADS)

Mitchell, Kevin; Solomon, Tom

2017-11-01

The geometry of reaction fronts that propagate in fully three-dimensional (3D) fluid flows is studied using the tools of dynamical systems theory. The evolution of an infinitesimal front element is modeled as a six-dimensional ODE-three dimensions for the position of the front element and three for the orientation of its unit normal. This generalizes an earlier approach to understanding front propagation in two-dimensional (2D) fluid flows. As in 2D, the 3D system exhibits prominent burning invariant manifolds (BIMs). In 3D, BIMs are two-dimensional dynamically defined surfaces that form one-way barriers to the propagation of reaction fronts within the fluid. Due to the third dimension, BIMs in 3D exhibit a richer topology than their cousins in 2D. In particular, whereas BIMs in both 2D and 3D can originate from fixed points of the dynamics, BIMs in 3D can also originate from limit cycles. Such BIMs form robust tube-like channels that guide and constrain the evolution of the front within the bulk of the fluid. Supported by NSF Grant CMMI-1201236.

Program Package for 3d PIC Model of Plasma Fiber

NASA Astrophysics Data System (ADS)

Kulhánek, Petr; Břeň, David

2007-08-01

A fully three dimensional Particle in Cell model of the plasma fiber had been developed. The code is written in FORTRAN 95, implementation CVF (Compaq Visual Fortran) under Microsoft Visual Studio user interface. Five particle solvers and two field solvers are included in the model. The solvers have relativistic and non-relativistic variants. The model can deal both with periodical and non-periodical boundary conditions. The mechanism of the surface turbulences generation in the plasma fiber was successfully simulated with the PIC program package.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

PubMed

Lounnas, Valère; Wedler, Henry B; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

Sensitivity analysis for the coupling of a subglacial hydrology model with a 3D ice-sheet model.

NASA Astrophysics Data System (ADS)

Bertagna, L.; Perego, M.; Gunzburger, M.; Hoffman, M. J.; Price, S. F.

2017-12-01

When studying the movement of ice sheets, one of the most important factors that influence the velocity of the ice is the amount of friction against the bedrock. Usually, this is modeled by a friction coefficient that may depend on the bed geometry and other quantities, such as the temperature and/or water pressure at the ice-bedrock interface. These quantities are often assumed to be known (either by indirect measurements or by means of parameter estimation) and constant in time. Here, we present a 3D computational model for the simulation of the ice dynamics which incorporates a 2D model proposed by Hewitt (2011) for the subglacial water pressure. The hydrology model is fully coupled with the Blatter-Pattyn model for the ice sheet flow, as the subglacial water pressure appears in the expression for the ice friction coefficient, and the ice velocity appears as a source term in the hydrology model. We will present results on real geometries, and perform a sensitivity analysis with respect to the hydrology model parameters.

Three-Dimensional Human iPSC-Derived Artificial Skeletal Muscles Model Muscular Dystrophies and Enable Multilineage Tissue Engineering.

PubMed

Maffioletti, Sara Martina; Sarcar, Shilpita; Henderson, Alexander B H; Mannhardt, Ingra; Pinton, Luca; Moyle, Louise Anne; Steele-Stallard, Heather; Cappellari, Ornella; Wells, Kim E; Ferrari, Giulia; Mitchell, Jamie S; Tyzack, Giulia E; Kotiadis, Vassilios N; Khedr, Moustafa; Ragazzi, Martina; Wang, Weixin; Duchen, Michael R; Patani, Rickie; Zammit, Peter S; Wells, Dominic J; Eschenhagen, Thomas; Tedesco, Francesco Saverio

2018-04-17

Generating human skeletal muscle models is instrumental for investigating muscle pathology and therapy. Here, we report the generation of three-dimensional (3D) artificial skeletal muscle tissue from human pluripotent stem cells, including induced pluripotent stem cells (iPSCs) from patients with Duchenne, limb-girdle, and congenital muscular dystrophies. 3D skeletal myogenic differentiation of pluripotent cells was induced within hydrogels under tension to provide myofiber alignment. Artificial muscles recapitulated characteristics of human skeletal muscle tissue and could be implanted into immunodeficient mice. Pathological cellular hallmarks of incurable forms of severe muscular dystrophy could be modeled with high fidelity using this 3D platform. Finally, we show generation of fully human iPSC-derived, complex, multilineage muscle models containing key isogenic cellular constituents of skeletal muscle, including vascular endothelial cells, pericytes, and motor neurons. These results lay the foundation for a human skeletal muscle organoid-like platform for disease modeling, regenerative medicine, and therapy development. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Management Sciences Division Annual Report (10th)

DTIC Science & Technology

1993-01-01

of the Weapon System Management Information System (WSMIS). TheI Aircraft Sustainability Model ( ASM ) is the computational technique employed by...provisioning. We enhanced the capabilities of RBIRD by using the Aircraft Sustainability Model ( ASM ) for the spares calculation. ASM offers many... ASM for several years to 3 compute spares for war. It is also fully compatible with the Air Force’s peacetime spares computation system (D041). This

Universality and depinning models for plastic yield in amorphous materials

NASA Astrophysics Data System (ADS)

Budrikis, Zoe; Fernandez Castellano, David; Sandfeld, Stefan; Zaiser, Michael; Zapperi, Stefano

Plastic yield in amorphous materials occurs as a result of complex collective dynamics of local reorganizations, which gives rise to rich phenomena such as strain localization, intermittent dynamics and power-law distributed avalanches. While such systems have received considerable attention, both theoretical and experimental, controversy remains over the nature of the yielding transition. We present a new fully-tensorial coarsegrained model in 2D and 3D, and demonstrate that the exponents describing avalanche distributions are universal under a variety of loading conditions, system dimensionality and size, and boundary conditions. Our results show that while depinning-type models in general are apt to describe the system, mean field depinning models are not.

Effects of perturbations and radial profiles on ignition of inertial confinement fusion hotspots

NASA Astrophysics Data System (ADS)

Taylor, S.; Chittenden, J. P.

2014-06-01

Perturbations of inertial confinement fusion hotspots from spherical symmetry cause an increase in the implosion velocity required for ignition, as investigated analytically by [R. Kishony and D. Shvarts, Phys. Plasmas 8, 4925 (2001)] and in numerical studies by many authors. In this paper, we analyse the mechanisms behind this effect by comparing fully 3D fluid simulations of National Ignition Facility targets to a novel analytic model of the thermal energy balance of the hotspot. The analytic model takes into account the radial variation of the state variables within the hotspot and provides an accurate relationship between the hotspot's 0D parameters (ρc, Tc, R , uR, and q) and its heating and cooling rates. The dominant effect of perturbations appears to be an increase in the inflow velocity at the hotspot's surface due to transverse flow of material between perturbation structures, causing premature thermalisation of kinetic energy before the hotspot is fully compressed. In hotspots with a broad perturbation spectrum, thermalisation of energy is inhibited by nonradial motion introduced by mode-mode interaction, reducing the yield further.

CFD Modeling of Helium Pressurant Effects on Cryogenic Tank Pressure Rise Rates in Normal Gravity

NASA Technical Reports Server (NTRS)

Grayson, Gary; Lopez, Alfredo; Chandler, Frank; Hastings, Leon; Hedayat, Ali; Brethour, James

2007-01-01

A recently developed computational fluid dynamics modeling capability for cryogenic tanks is used to simulate both self-pressurization from external heating and also depressurization from thermodynamic vent operation. Axisymmetric models using a modified version of the commercially available FLOW-3D software are used to simulate actual physical tests. The models assume an incompressible liquid phase with density that is a function of temperature only. A fully compressible formulation is used for the ullage gas mixture that contains both condensable vapor and a noncondensable gas component. The tests, conducted at the NASA Marshall Space Flight Center, include both liquid hydrogen and nitrogen in tanks with ullage gas mixtures of each liquid's vapor and helium. Pressure and temperature predictions from the model are compared to sensor measurements from the tests and a good agreement is achieved. This further establishes the accuracy of the developed FLOW-3D based modeling approach for cryogenic systems.

The 3D model control of image processing

NASA Technical Reports Server (NTRS)

Nguyen, An H.; Stark, Lawrence

1989-01-01

Telerobotics studies remote control of distant robots by a human operator using supervisory or direct control. Even if the robot manipulators has vision or other senses, problems arise involving control, communications, and delay. The communication delays that may be expected with telerobots working in space stations while being controlled from an Earth lab have led to a number of experiments attempting to circumvent the problem. This delay in communication is a main motivating factor in moving from well understood instantaneous hands-on manual control to less well understood supervisory control; the ultimate step would be the realization of a fully autonomous robot. The 3-D model control plays a crucial role in resolving many conflicting image processing problems that are inherent in resolving in the bottom-up approach of most current machine vision processes. The 3-D model control approach is also capable of providing the necessary visual feedback information for both the control algorithms and for the human operator.

Numerical simulation of evolutionary erodible bedforms using the particle finite element method

NASA Astrophysics Data System (ADS)

Bravo, Rafael; Becker, Pablo; Ortiz, Pablo

2017-07-01

This paper presents a numerical strategy for the simulation of flows with evolutionary erodible boundaries. The fluid equations are fully resolved in 3D, while the sediment transport is modelled using the Exner equation and solved with an explicit Lagrangian procedure based on a fixed 2D mesh. Flow and sediment are coupled in geometry by deforming the fluid mesh in the vertical direction and in velocities with the experimental sediment flux computed using the Meyer Peter Müller model. A comparison with real experiments on channels is performed, giving good agreement.

Evaluation of an operational water cycle prediction system for the Laurentian Great Lakes and St. Lawrence River

NASA Astrophysics Data System (ADS)

Fortin, Vincent; Durnford, Dorothy; Smith, Gregory; Dyck, Sarah; Martinez, Yosvany; Mackay, Murray; Winter, Barbara

2017-04-01

Environment and Climate Change Canada (ECCC) is implementing new numerical guidance products based on fully coupled numerical models to better inform the public as well as specialized users on the current and future state of various components of the water cycle, including stream flow and water levels. Outputs from this new system, named the Water Cycle Prediction System (WCPS), have been available for the Great Lakes and St. Lawrence River watershed since June 2016. WCPS links together ECCC's weather forecasting model, GEM, the 2-D ice model C-ICE, the 3-D lake and ocean model NEMO, and a 2-D hydrological model, WATROUTE. Information concerning the water cycle is passed between the models at intervals varying from a few minutes to one hour. It currently produces two forecasts per day for the next three days of the complete water cycle in the Great Lakes region, the largest freshwater lake system in the world. Products include spatially-varying precipitation, evaporation, river discharge, water level anomalies, surface water temperatures, ice coverage, and surface currents. These new products are of interest to water resources and management authority, flood forecasters, hydroelectricity producers, navigation, environmental disaster managers, search and rescue teams, agriculture, and the general public. This presentation focuses on the evaluation of various elements forecasted by the system, and weighs the advantages and disadvantages of running the system fully coupled.

Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model

PubMed Central

Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

2014-01-01

Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method. PMID:27170866

Fully automatic segmentation of the femur from 3D-CT images using primitive shape recognition and statistical shape models.

PubMed

Ben Younes, Lassad; Nakajima, Yoshikazu; Saito, Toki

2014-03-01

Femur segmentation is well established and widely used in computer-assisted orthopedic surgery. However, most of the robust segmentation methods such as statistical shape models (SSM) require human intervention to provide an initial position for the SSM. In this paper, we propose to overcome this problem and provide a fully automatic femur segmentation method for CT images based on primitive shape recognition and SSM. Femur segmentation in CT scans was performed using primitive shape recognition based on a robust algorithm such as the Hough transform and RANdom SAmple Consensus. The proposed method is divided into 3 steps: (1) detection of the femoral head as sphere and the femoral shaft as cylinder in the SSM and the CT images, (2) rigid registration between primitives of SSM and CT image to initialize the SSM into the CT image, and (3) fitting of the SSM to the CT image edge using an affine transformation followed by a nonlinear fitting. The automated method provided good results even with a high number of outliers. The difference of segmentation error between the proposed automatic initialization method and a manual initialization method is less than 1 mm. The proposed method detects primitive shape position to initialize the SSM into the target image. Based on primitive shapes, this method overcomes the problem of inter-patient variability. Moreover, the results demonstrate that our method of primitive shape recognition can be used for 3D SSM initialization to achieve fully automatic segmentation of the femur.

Fully automated MR liver volumetry using watershed segmentation coupled with active contouring.

PubMed

Huynh, Hieu Trung; Le-Trong, Ngoc; Bao, Pham The; Oto, Aytek; Suzuki, Kenji

2017-02-01

Our purpose is to develop a fully automated scheme for liver volume measurement in abdominal MR images, without requiring any user input or interaction. The proposed scheme is fully automatic for liver volumetry from 3D abdominal MR images, and it consists of three main stages: preprocessing, rough liver shape generation, and liver extraction. The preprocessing stage reduced noise and enhanced the liver boundaries in 3D abdominal MR images. The rough liver shape was revealed fully automatically by using the watershed segmentation, thresholding transform, morphological operations, and statistical properties of the liver. An active contour model was applied to refine the rough liver shape to precisely obtain the liver boundaries. The liver volumes calculated by the proposed scheme were compared to the "gold standard" references which were estimated by an expert abdominal radiologist. The liver volumes computed by using our developed scheme excellently agreed (Intra-class correlation coefficient was 0.94) with the "gold standard" manual volumes by the radiologist in the evaluation with 27 cases from multiple medical centers. The running time was 8.4 min per case on average. We developed a fully automated liver volumetry scheme in MR, which does not require any interaction by users. It was evaluated with cases from multiple medical centers. The liver volumetry performance of our developed system was comparable to that of the gold standard manual volumetry, and it saved radiologists' time for manual liver volumetry of 24.7 min per case.

Microfluidic vascularized bone tissue model with hydroxyapatite-incorporated extracellular matrix.

PubMed

Jusoh, Norhana; Oh, Soojung; Kim, Sudong; Kim, Jangho; Jeon, Noo Li

2015-10-21

Current in vitro systems mimicking bone tissues fail to fully integrate the three-dimensional (3D) microvasculature and bone tissue microenvironments, decreasing their similarity to in vivo conditions. Here, we propose 3D microvascular networks in a hydroxyapatite (HA)-incorporated extracellular matrix (ECM) for designing and manipulating a vascularized bone tissue model in a microfluidic device. Incorporation of HA of various concentrations resulted in ECM with varying mechanical properties. Sprouting angiogenesis was affected by mechanically modulated HA-extracellular matrix interactions, generating a model of vascularized bone microenvironment. Using this platform, we observed that hydroxyapatite enhanced angiogenic properties such as sprout length, sprouting speed, sprout number, and lumen diameter. This new platform integrates fibrin ECM with the synthetic bone mineral HA to provide in vivo-like microenvironments for bone vessel sprouting.

A Quantitative Evaluation of SCEC Community Velocity Model Version 3.0

NASA Astrophysics Data System (ADS)

Chen, P.; Zhao, L.; Jordan, T. H.

2003-12-01

We present a systematic methodology for evaluating and improving 3D seismic velocity models using broadband waveform data from regional earthquakes. The operator that maps a synthetic waveform into an observed waveform is expressed in the Rytov form D(ω ) = {exp}[{i} ω δ τ {p}(ω ) - ω δ τ {q}(ω )]. We measure the phase delay time δ τ p(ω ) and the amplitude reduction time δ τ q(ω ) as a function of frequency ω using Gee & Jordan's [1992] isolation-filter technique, and we correct the data for frequency-dependent interference and frequency-independent source statics. We have applied this procedure to a set of small events in Southern California. Synthetic seismograms were computed using three types of velocity models: the 1D Standard Southern California Crustal Model (SoCaL) [Dreger & Helmberger, 1993], the 3D SCEC Community Velocity Model, Version 3.0 (CVM3.0) [Magistrale et al., 2000], and a set of path-averaged 1D models (A1D) extracted from CVM3.0 by horizontally averaging wave slownesses along source-receiver paths. The 3D synthetics were computed using K. Olsen's finite difference code. More than 1000 measurements were made on both P and S waveforms at frequencies ranging from 0.2 to 1 Hz. Overall, the 3D model provided a substantially better fit to the waveform data than either laterally homogeneous or path-dependent 1D models. Relative to SoCaL, CVM3.0 provided a variance reduction of about 64% in δ τ p, and 41% in δ τ q. Relative to A1D, the variance reduction is about 46% and 20%, respectively. The same set of measurements can be employed to invert for both seismic source properties and seismic velocity structures. Fully numerical methods are being developed to compute the Fréchet kernels for these measurements [L. Zhao et. al., this meeting]. This methodology thus provides a unified framework for regional studies of seismic sources and Earth structure in Southern California and elsewhere.

Nonlinear 3D MHD verification study: SpeCyl and PIXIE3D codes for RFP and Tokamak plasmas

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Cappello, S.; Chacon, L.

2010-11-01

A strong emphasis is presently placed in the fusion community on reaching predictive capability of computational models. An essential requirement of such endeavor is the process of assessing the mathematical correctness of computational tools, termed verification [1]. We present here a successful nonlinear cross-benchmark verification study between the 3D nonlinear MHD codes SpeCyl [2] and PIXIE3D [3]. Excellent quantitative agreement is obtained in both 2D and 3D nonlinear visco-resistive dynamics for reversed-field pinch (RFP) and tokamak configurations [4]. RFP dynamics, in particular, lends itself as an ideal non trivial test-bed for 3D nonlinear verification. Perspectives for future application of the fully-implicit parallel code PIXIE3D to RFP physics, in particular to address open issues on RFP helical self-organization, will be provided. [4pt] [1] M. Greenwald, Phys. Plasmas 17, 058101 (2010) [0pt] [2] S. Cappello and D. Biskamp, Nucl. Fusion 36, 571 (1996) [0pt] [3] L. Chac'on, Phys. Plasmas 15, 056103 (2008) [0pt] [4] D. Bonfiglio, L. Chac'on and S. Cappello, Phys. Plasmas 17 (2010)

Magnetosphere - Ionosphere - Thermosphere (MIT) Coupling at Jupiter

NASA Astrophysics Data System (ADS)

Yates, J. N.; Ray, L. C.; Achilleos, N.

2017-12-01

Jupiter's upper atmospheric temperature is considerably higher than that predicted by Solar Extreme Ultraviolet (EUV) heating alone. Simulations incorporating magnetosphere-ionosphere coupling effects into general circulation models have, to date, struggled to reproduce the observed atmospheric temperatures under simplifying assumptions such as azimuthal symmetry and a spin-aligned dipole magnetic field. Here we present the development of a full three-dimensional thermosphere model coupled in both hemispheres to an axisymmetric magnetosphere model. This new coupled model is based on the two-dimensional MIT model presented in Yates et al., 2014. This coupled model is a critical step towards to the development of a fully coupled 3D MIT model. We discuss and compare the resulting thermospheric flows, energy balance and MI coupling currents to those presented in previous 2D MIT models.

Externally Calibrated Parallel Imaging for 3D Multispectral Imaging Near Metallic Implants Using Broadband Ultrashort Echo Time Imaging

PubMed Central

Wiens, Curtis N.; Artz, Nathan S.; Jang, Hyungseok; McMillan, Alan B.; Reeder, Scott B.

2017-01-01

Purpose To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. Theory and Methods A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Results Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. Conclusion A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. PMID:27403613

Modeling Three-Dimensional Shock Initiation of PBX 9501 in ALE3D

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

Leininger, L; Springer, H K; Mace, J

A recent SMIS (Specific Munitions Impact Scenario) experimental series performed at Los Alamos National Laboratory has provided 3-dimensional shock initiation behavior of the HMX-based heterogeneous high explosive, PBX 9501. A series of finite element impact calculations have been performed in the ALE3D [1] hydrodynamic code and compared to the SMIS results to validate and study code predictions. These SMIS tests used a powder gun to shoot scaled NATO standard fragments into a cylinder of PBX 9501, which has a PMMA case and a steel impact cover. This SMIS real-world shot scenario creates a unique test-bed because (1) SMIS tests facilitatemore » the investigation of 3D Shock to Detonation Transition (SDT) within the context of a considerable suite of diagnostics, and (2) many of the fragments arrive at the impact plate off-center and at an angle of impact. A particular goal of these model validation experiments is to demonstrate the predictive capability of the ALE3D implementation of the Tarver-Lee Ignition and Growth reactive flow model [2] within a fully 3-dimensional regime of SDT. The 3-dimensional Arbitrary Lagrange Eulerian (ALE) hydrodynamic model in ALE3D applies the Ignition and Growth (I&G) reactive flow model with PBX 9501 parameters derived from historical 1-dimensional experimental data. The model includes the off-center and angle of impact variations seen in the experiments. Qualitatively, the ALE3D I&G calculations reproduce observed 'Go/No-Go' 3D Shock to Detonation Transition (SDT) reaction in the explosive, as well as the case expansion recorded by a high-speed optical camera. Quantitatively, the calculations show good agreement with the shock time of arrival at internal and external diagnostic pins. This exercise demonstrates the utility of the Ignition and Growth model applied for the response of heterogeneous high explosives in the SDT regime.« less

Learning normalized inputs for iterative estimation in medical image segmentation.

PubMed

Drozdzal, Michal; Chartrand, Gabriel; Vorontsov, Eugene; Shakeri, Mahsa; Di Jorio, Lisa; Tang, An; Romero, Adriana; Bengio, Yoshua; Pal, Chris; Kadoury, Samuel

2018-02-01

In this paper, we introduce a simple, yet powerful pipeline for medical image segmentation that combines Fully Convolutional Networks (FCNs) with Fully Convolutional Residual Networks (FC-ResNets). We propose and examine a design that takes particular advantage of recent advances in the understanding of both Convolutional Neural Networks as well as ResNets. Our approach focuses upon the importance of a trainable pre-processing when using FC-ResNets and we show that a low-capacity FCN model can serve as a pre-processor to normalize medical input data. In our image segmentation pipeline, we use FCNs to obtain normalized images, which are then iteratively refined by means of a FC-ResNet to generate a segmentation prediction. As in other fully convolutional approaches, our pipeline can be used off-the-shelf on different image modalities. We show that using this pipeline, we exhibit state-of-the-art performance on the challenging Electron Microscopy benchmark, when compared to other 2D methods. We improve segmentation results on CT images of liver lesions, when contrasting with standard FCN methods. Moreover, when applying our 2D pipeline on a challenging 3D MRI prostate segmentation challenge we reach results that are competitive even when compared to 3D methods. The obtained results illustrate the strong potential and versatility of the pipeline by achieving accurate segmentations on a variety of image modalities and different anatomical regions. Copyright © 2017 Elsevier B.V. All rights reserved.

3D patient-specific models for left atrium characterization to support ablation in atrial fibrillation patients.

PubMed

Valinoti, Maddalena; Fabbri, Claudio; Turco, Dario; Mantovan, Roberto; Pasini, Antonio; Corsi, Cristiana

2018-01-01

Radiofrequency ablation (RFA) is an important and promising therapy for atrial fibrillation (AF) patients. Optimization of patient selection and the availability of an accurate anatomical guide could improve RFA success rate. In this study we propose a unified, fully automated approach to build a 3D patient-specific left atrium (LA) model including pulmonary veins (PVs) in order to provide an accurate anatomical guide during RFA and without PVs in order to characterize LA volumetry and support patient selection for AF ablation. Magnetic resonance data from twenty-six patients referred for AF RFA were processed applying an edge-based level set approach guided by a phase-based edge detector to obtain the 3D LA model with PVs. An automated technique based on the shape diameter function was designed and applied to remove PVs and compute LA volume. 3D LA models were qualitatively compared with 3D LA surfaces acquired during the ablation procedure. An expert radiologist manually traced the LA on MR images twice. LA surfaces from the automatic approach and manual tracing were compared by mean surface-to-surface distance. In addition, LA volumes were compared with volumes from manual segmentation by linear and Bland-Altman analyses. Qualitative comparison of 3D LA models showed several inaccuracies, in particular PVs reconstruction was not accurate and left atrial appendage was missing in the model obtained during RFA procedure. LA surfaces were very similar (mean surface-to-surface distance: 2.3±0.7mm). LA volumes were in excellent agreement (y=1.03x-1.4, r=0.99, bias=-1.37ml (-1.43%) SD=2.16ml (2.3%), mean percentage difference=1.3%±2.1%). Results showed the proposed 3D patient-specific LA model with PVs is able to better describe LA anatomy compared to models derived from the navigation system, thus potentially improving electrograms and voltage information location and reducing fluoroscopic time during RFA. Quantitative assessment of LA volume derived from our 3D LA model without PVs is also accurate and may provide important information for patient selection for RFA. Copyright © 2017 Elsevier Inc. All rights reserved.

Investigating the capabilities of semantic enrichment of 3D CityEngine data

NASA Astrophysics Data System (ADS)

Solou, Dimitra; Dimopoulou, Efi

2016-08-01

In recent years the development of technology and the lifting of several technical limitations, has brought the third dimension to the fore. The complexity of urban environments and the strong need for land administration, intensify the need of using a three-dimensional cadastral system. Despite the progress in the field of geographic information systems and 3D modeling techniques, there is no fully digital 3D cadastre. The existing geographic information systems and the different methods of three-dimensional modeling allow for better management, visualization and dissemination of information. Nevertheless, these opportunities cannot be totally exploited because of deficiencies in standardization and interoperability in these systems. Within this context, CityGML was developed as an international standard of the Open Geospatial Consortium (OGC) for 3D city models' representation and exchange. CityGML defines geometry and topology for city modeling, also focusing on semantic aspects of 3D city information. The scope of CityGML is to reach common terminology, also addressing the imperative need for interoperability and data integration, taking into account the number of available geographic information systems and modeling techniques. The aim of this paper is to develop an application for managing semantic information of a model generated based on procedural modeling. The model was initially implemented in CityEngine ESRI's software, and then imported to ArcGIS environment. Final goal was the original model's semantic enrichment and then its conversion to CityGML format. Semantic information management and interoperability seemed to be feasible by the use of the 3DCities Project ESRI tools, since its database structure ensures adding semantic information to the CityEngine model and therefore automatically convert to CityGML for advanced analysis and visualization in different application areas.

The Vajont disaster: a 3D numerical simulation for the slide and the waves

NASA Astrophysics Data System (ADS)

Rubino, Angelo; Androsov, Alexey; Vacondio, Renato; Zanchettin, Davide; Voltzinger, Naum

2016-04-01

A very high resolution O(5 m), 3D hydrostatic nonlinear numerical model was used to simulate the dynamics of both the slide and the surface waves produced during the Vajont disaster (north Italy, 1963), one of the major landslide-induced tsunamis ever documented. Different simulated wave phenomena like, e.g., maximum run-up on the opposite shore, maximum height, and water velocity were analyzed and compared with data available in literature, including the results of a fully 3D simulation obtained with a Smoothed Particle Hydrodynamic code. The difference between measured and simulated after-slide bathymetries was calculated and used in an attempt to quantify the relative magnitude and extension of rigid and fluid motion components during the event.

Resistivity Image from 2D Inversion of Magnetotelluric Data in the Northern Cascadia Subduction Zone (United States)

NASA Astrophysics Data System (ADS)

Gultom, F. B.; Niasari, S. W.; Hartantyo, E.

2018-04-01

Cascadia Subduction Zone (CSZ) lies between Pacific margin and North America plate. The purpose of this research is to identify the CSZ along Oregon, Idaho, Wyoming from conductivity (σ) contrast in the subsurface by using the magnetotelluric (MT) method. MT is an electromagnetic method that use frequency between 10-4 Hz and 104 Hz. We obtained the MT data from the EarthScope USArray in the form of EDI-File (five components of the electromagnetic field). We analyzed the MT data using phase tensor and modeled the data using 2D inversion. From the phase tensor analysis, the 3D data dominated the eastern regions. Global data misfit is 6,88, where WYI18 (close to Yellowstone) contributes misfit of 29,3. This means that the model response does not fit the data, which implies the data is not fully 2D. The 2D inversion results are found high resistivity anomalies (more than 500 ohm.m) at shallow depth beneath Oregon and Wyoming, which coresspond to high density anomalies. This high resistivity anomalies might correspond to the north American plate. Thus, it can be concluded that 2D inversion model can be used for most 3D MT data to illustrate the resistivity distribution in the Cascadia Subduction Zone.

System Design, Calibration and Performance Analysis of a Novel 360° Stereo Panoramic Mobile Mapping System

NASA Astrophysics Data System (ADS)

Blaser, S.; Nebiker, S.; Cavegn, S.

2017-05-01

Image-based mobile mapping systems enable the efficient acquisition of georeferenced image sequences, which can later be exploited in cloud-based 3D geoinformation services. In order to provide a 360° coverage with accurate 3D measuring capabilities, we present a novel 360° stereo panoramic camera configuration. By using two 360° panorama cameras tilted forward and backward in combination with conventional forward and backward looking stereo camera systems, we achieve a full 360° multi-stereo coverage. We furthermore developed a fully operational new mobile mapping system based on our proposed approach, which fulfils our high accuracy requirements. We successfully implemented a rigorous sensor and system calibration procedure, which allows calibrating all stereo systems with a superior accuracy compared to that of previous work. Our study delivered absolute 3D point accuracies in the range of 4 to 6 cm and relative accuracies of 3D distances in the range of 1 to 3 cm. These results were achieved in a challenging urban area. Furthermore, we automatically reconstructed a 3D city model of our study area by employing all captured and georeferenced mobile mapping imagery. The result is a very high detailed and almost complete 3D city model of the street environment.

The role of 3-D interactive visualization in blind surveys of H I in galaxies

NASA Astrophysics Data System (ADS)

Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

2015-09-01

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

A Study of Grid Resolution, Transition and Turbulence Model Using the Transonic Simple Straked Delta Wing

NASA Technical Reports Server (NTRS)

Bartels, Robert E.

2001-01-01

Three-dimensional transonic flow over a delta wing is investigated using several turbulence models. The performance of linear eddy viscosity models and an explicit algebraic stress model is assessed at the start of vortex flow, and the results compared with experimental data. To assess the effect of transition location, computations that either fix transition aft of the leading edge or are fully turbulent are performed. These computations show that grid resolution, transition location and turbulence model significantly affect the 3D flowfield.

Novel and simple route to fabricate fully biocompatible plasmonic mushroom arrays adhered on silk biopolymer

NASA Astrophysics Data System (ADS)

Park, Joonhan; Choi, Yunkyoung; Lee, Myungjae; Jeon, Heonsu; Kim, Sunghwan

2014-12-01

A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures.A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures. Electronic supplementary information (ESI) available: The incident angle dependence of reflectance spectra and the atomic force microscopy image of the Au nanoparticle array on a silk film after 1 hour of ultrasonication. See DOI: 10.1039/c4nr05172f

Electromagnetic particle-in-cell simulations of the solar wind interaction with lunar magnetic anomalies.

PubMed

Deca, J; Divin, A; Lapenta, G; Lembège, B; Markidis, S; Horányi, M

2014-04-18

We present the first three-dimensional fully kinetic and electromagnetic simulations of the solar wind interaction with lunar crustal magnetic anomalies (LMAs). Using the implicit particle-in-cell code iPic3D, we confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface forming a mini-magnetosphere, as suggested by spacecraft observations and theory. In contrast to earlier magnetohydrodynamics and hybrid simulations, the fully kinetic nature of iPic3D allows us to investigate the space charge effects and in particular the electron dynamics dominating the near-surface lunar plasma environment. We describe for the first time the interaction of a dipole model centered just below the lunar surface under plasma conditions such that only the electron population is magnetized. The fully kinetic treatment identifies electromagnetic modes that alter the magnetic field at scales determined by the electron physics. Driven by strong pressure anisotropies, the mini-magnetosphere is unstable over time, leading to only temporal shielding of the surface underneath. Future human exploration as well as lunar science in general therefore hinges on a better understanding of LMAs.

Progress report on PIXIE3D, a fully implicit 3D extended MHD solver

NASA Astrophysics Data System (ADS)

Chacon, Luis

2008-11-01

Recently, invited talk at DPP07 an optimal, massively parallel implicit algorithm for 3D resistive magnetohydrodynamics (PIXIE3D) was demonstrated. Excellent algorithmic and parallel results were obtained with up to 4096 processors and 138 million unknowns. While this is a remarkable result, further developments are still needed for PIXIE3D to become a 3D extended MHD production code in general geometries. In this poster, we present an update on the status of PIXIE3D on several fronts. On the physics side, we will describe our progress towards the full Braginskii model, including: electron Hall terms, anisotropic heat conduction, and gyroviscous corrections. Algorithmically, we will discuss progress towards a robust, optimal, nonlinear solver for arbitrary geometries, including preconditioning for the new physical effects described, the implementation of a coarse processor-grid solver (to maintain optimal algorithmic performance for an arbitrarily large number of processors in massively parallel computations), and of a multiblock capability to deal with complicated geometries. L. Chac'on, Phys. Plasmas 15, 056103 (2008);

Numerical Validation of the N3S-NATUR Code for Supersonic Nozzles and Afterbody Flows

NASA Astrophysics Data System (ADS)

Perrot, Y.; Hadjadj, A.

2005-02-01

A numerical investigation was conducted to assess the ability of the three-dimensional Navier-Stokes solver, N3S-Natur [1], using the k-ω SST turbulence model when computing nozzle-afterbody flows with propulsive jets. Three nozzle configurations were selected as test cases for the computational method: the first is the ONERA TIC nozzle, the second is an axisymmetric boat-tailed afterbody configuration and the third is a fully 3D transonic nozzle. In most situations, internal and external flow-field regions are modeled. The obtained results are carefully analyzed and compared to the experimental data. A three-dimensional computation was done to make evidence of 3D phenomena which are not negligible. A particular attention was payed to the appearance of a recirculation zone on the afterbody.

Multifunction of Chrysin in Parkinson's Model: Anti-Neuronal Apoptosis, Neuroprotection via Activation of MEF2D, and Inhibition of Monoamine Oxidase-B.

PubMed

Guo, Baojian; Zheng, Chengyou; Cai, Wei; Cheng, Jiehong; Wang, Hongyu; Li, Haitao; Sun, Yewei; Cui, Wei; Wang, Yuqiang; Han, Yifan; Lee, Simon Ming-Yuen; Zhang, Zaijun

2016-07-06

Chrysin, a flavonoid compound existing in several plants, is applied as a dietary supplement because of its beneficial effects on general human health and alleviation of neurological disorders. However, mechanisms underlying neuroprotection of chrysin has not been fully elucidated, and the effects of chrysin on the Parkinson's disease (PD) model in vivo have not been investigated. It is here shown that chrysin protects primary granular neurons against 1-methyl-4-phenylpyridinium ion insult via antiapoptosis by reversing the dysregulated expression of Bcl-2, Bax, and caspase 3. The mechanisms also involved activating transcriptional factor myocyte enhancer factor 2D (MEF2D) via regulation of AKT-GSK3β signaling. In this in vivo model of PD, chrysin rescued the dopaminergic neurons loss and alleviated the decrease in dopamine level induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine in mice. Moreover, chrysin markedly inhibited monoamine oxidase-B activity in vitro and in vivo. In conclusion, chrysin exerts beneficial effects to PD, possibly through multitarget mechanisms including antineuronal apoptosis, activation of the AKT-GSK3β/MEF2D pathway, and inhibition of the MAO-B activity.

Differences in growth properties of endometrial cancer in three dimensional (3D) culture and 2D cell monolayer

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

Chitcholtan, Kenny, E-mail: kenny.chitcholtan@otago.ac.nz; Asselin, Eric, E-mail: Eric.Asselin@uqtr.ca; Parent, Sophie, E-mail: Sophie.Parent@uqtr.ca

2013-01-01

Three-dimensional (3D) in vitro models have an invaluable role in understanding the behaviour of tumour cells in a well defined microenvironment. This is because some aspects of tumour characteristics cannot be fully recapitulated in a cell monolayer (2D). In the present study, we compared growth patterns, expression of signalling molecules, and metabolism-associated proteins of endometrial cancer cell lines in 3D and 2D cell cultures. Cancer cells formed spherical structures in 3D reconstituted basement membrane (3D rBM), and the morphological appearance was cell line dependent. Cell differentiation was observed after 8 days in the 3D rBM. There was reduced proliferation, detectedmore » by less expression of PCNA in 3D rBM than in 2D cell monolayers. The addition of exogenous epidermal growth factor (EGF) to cancer cells induced phosphorylation of EGFR and Akt in both cell culture conditions. The uptake of glucose was selectively altered in the 3D rBM, but there was a lack of association with Glut-1 expression. The secretion of vascular endothelial growth factor (VEGF) and prostaglandin E{sub 2} (PGE{sub 2}) was selectively altered in 3D rBM, and it was cell line dependent. Our data demonstrated that 3D rBM as an in vitro model can influence proliferation and metabolism of endometrial cancer cell behaviour compared to 2D cell monolayer. Changes are specific to individual cell types. The use of 3D rBM is, therefore, important in the in vitro study of targeted anticancer therapies.« less

Novel and simple route to fabricate fully biocompatible plasmonic mushroom arrays adhered on silk biopolymer.

PubMed

Park, Joonhan; Choi, Yunkyoung; Lee, Myungjae; Jeon, Heonsu; Kim, Sunghwan

2015-01-14

A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures.

3D Hall MHD-EPIC Simulations of Ganymede's Magnetosphere

NASA Astrophysics Data System (ADS)

Zhou, H.; Toth, G.; Jia, X.

2017-12-01

Fully kinetic modeling of a complete 3D magnetosphere is still computationally expensive and not feasible on current computers. While magnetohydrodynamic (MHD) models have been successfully applied to a wide range of plasma simulation, they cannot capture some important kinetic effects. We have recently developed a new modeling tool to embed the implicit particle-in-cell (PIC) model iPIC3D into the Block-Adaptive-Tree-Solarwind-Roe-Upwind-Scheme (BATS-R-US) magnetohydrodynamic model. This results in a kinetic model of the regions where kinetic effects are important. In addition to the MHD-EPIC modeling of the magnetosphere, the improved model presented here is now able to represent the moon as a resistive body. We use a stretched spherical grid with adaptive mesh refinement (AMR) to capture the resistive body and its boundary. A semi-implicit scheme is employed for solving the magnetic induction equation to allow time steps that are not limited by the resistivity. We have applied the model to Ganymede, the only moon in the solar system known to possess a strong intrinsic magnetic field, and included finite resistivity beneath the moon`s surface to model the electrical properties of the interior in a self-consistent manner. The kinetic effects of electrons and ions on the dayside magnetopause and tail current sheet are captured with iPIC3D. Magnetic reconnections under different upstream background conditions of several Galileo flybys are simulated to study the global reconnection rate and the magnetospheric dynamics

Full 3-dimensional digital workflow for multicomponent dental appliances: A proof of concept.

PubMed

van der Meer, W Joerd; Vissink, Arjan; Ren, Yijin

2016-04-01

The authors used a 3-dimensional (3D) printer and a bending robot to produce a multicomponent dental appliance to assess whether 3D digital models of the dentition are applicable for a full digital workflow. The authors scanned a volunteer's dentition with an intraoral scanner (Lava Chairside Oral Scanner C.O.S., 3M). A digital impression was used to design 2 multicomponent orthodontic appliances. Biocompatible acrylic baseplates were produced with the aid of a 3D printer. The metal springs and clasps were produced by a bending robot. The fit of the 2 appliances was assessed by 2 experienced orthodontists. The authors assessed both orthodontic appliances with the volunteer's dentition and found the fit to be excellent. Clinicians can fully produce a multicomponent dental appliance consisting of both an acrylic baseplate and other parts, such as clasps, springs, or screws, using a digital workflow process without the need for a physical model of the patient's dentition. Plaster models can be superfluous for orthodontic treatment as digital models can be used in all phases of a full digital workflow in orthodontics. The arduous task of making a multicomponent dental appliance that involves bending wires can possibly be replaced by a computer, design software, a 3D printer, and a bending robot. Copyright © 2016 American Dental Association. Published by Elsevier Inc. All rights reserved.

Dynamic tracking of prosthetic valve motion and deformation from bi-plane x-ray views: feasibility study

NASA Astrophysics Data System (ADS)

Hatt, Charles R.; Wagner, Martin; Raval, Amish N.; Speidel, Michael A.

2016-03-01

Transcatheter aortic valve replacement (TAVR) requires navigation and deployment of a prosthetic valve within the aortic annulus under fluoroscopic guidance. To support improved device visualization in this procedure, this study investigates the feasibility of frame-by-frame 3D reconstruction of a moving and expanding prosthetic valve structure from simultaneous bi-plane x-ray views. In the proposed method, a dynamic 3D model of the valve is used in a 2D/3D registration framework to obtain a reconstruction of the valve. For each frame, valve model parameters describing position, orientation, expansion state, and deformation are iteratively adjusted until forward projections of the model match both bi-plane views. Simulated bi-plane imaging of a valve at different signal-difference-to-noise ratio (SDNR) levels was performed to test the approach. 20 image sequences with 50 frames of valve deployment were simulated at each SDNR. The simulation achieved a target registration error (TRE) of the estimated valve model of 0.93 +/- 2.6 mm (mean +/- S.D.) for the lowest SDNR of 2. For higher SDNRs (5 to 50) a TRE of 0.04 mm +/- 0.23 mm was achieved. A tabletop phantom study was then conducted using a TAVR valve. The dynamic 3D model was constructed from high resolution CT scans and a simple expansion model. TRE was 1.22 +/- 0.35 mm for expansion states varying from undeployed to fully deployed, and for moderate amounts of inter-frame motion. Results indicate that it is feasible to use bi-plane imaging to recover the 3D structure of deformable catheter devices.

Dynamic tracking of prosthetic valve motion and deformation from bi-plane x-ray views: feasibility study.

PubMed

Hatt, Charles R; Wagner, Martin; Raval, Amish N; Speidel, Michael A

2016-01-01

Transcatheter aortic valve replacement (TAVR) requires navigation and deployment of a prosthetic valve within the aortic annulus under fluoroscopic guidance. To support improved device visualization in this procedure, this study investigates the feasibility of frame-by-frame 3D reconstruction of a moving and expanding prosthetic valve structure from simultaneous bi-plane x-ray views. In the proposed method, a dynamic 3D model of the valve is used in a 2D/3D registration framework to obtain a reconstruction of the valve. For each frame, valve model parameters describing position, orientation, expansion state, and deformation are iteratively adjusted until forward projections of the model match both bi-plane views. Simulated bi-plane imaging of a valve at different signal-difference-to-noise ratio (SDNR) levels was performed to test the approach. 20 image sequences with 50 frames of valve deployment were simulated at each SDNR. The simulation achieved a target registration error (TRE) of the estimated valve model of 0.93 ± 2.6 mm (mean ± S.D.) for the lowest SDNR of 2. For higher SDNRs (5 to 50) a TRE of 0.04 mm ± 0.23 mm was achieved. A tabletop phantom study was then conducted using a TAVR valve. The dynamic 3D model was constructed from high resolution CT scans and a simple expansion model. TRE was 1.22 ± 0.35 mm for expansion states varying from undeployed to fully deployed, and for moderate amounts of inter-frame motion. Results indicate that it is feasible to use bi-plane imaging to recover the 3D structure of deformable catheter devices.

3D nozzle flow simulations including state-to-state kinetics calculation

NASA Astrophysics Data System (ADS)

Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.

2014-12-01

In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.

Nonlinear interaction between underwater explosion bubble and structure based on fully coupled model

NASA Astrophysics Data System (ADS)

Zhang, A. M.; Wu, W. B.; Liu, Y. L.; Wang, Q. X.

2017-08-01

The interaction between an underwater explosion bubble and an elastic-plastic structure is a complex transient process, accompanying violent bubble collapsing, jet impact, penetration through the bubble, and large structural deformation. In the present study, the bubble dynamics are modeled using the boundary element method and the nonlinear transient structural response is modeled using the explicit finite element method. A new fully coupled 3D model is established through coupling the equations for the state variables of the fluid and structure and solving them as a set of coupled linear algebra equations. Based on the acceleration potential theory, the mutual dependence between the hydrodynamic load and the structural motion is decoupled. The pressure distribution in the flow field is calculated with the Bernoulli equation, where the partial derivative of the velocity potential in time is calculated using the boundary integral method to avoid numerical instabilities. To validate the present fully coupled model, the experiments of small-scale underwater explosion near a stiffened plate are carried out. High-speed imaging is used to capture the bubble behaviors and strain gauges are used to measure the strain response. The numerical results correspond well with the experimental data, in terms of bubble shapes and structural strain response. By both the loosely coupled model and the fully coupled model, the interaction between a bubble and a hollow spherical shell is studied. The bubble patterns vary with different parameters. When the fully coupled model and the loosely coupled model are advanced with the same time step, the error caused by the loosely coupled model becomes larger with the coupling effect becoming stronger. The fully coupled model is more stable than the loosely coupled model. Besides, the influences of the internal fluid on the dynamic response of the spherical shell are studied. At last, the case that the bubble interacts with an air-backed stiffened plate is simulated. The associated interesting physical phenomenon is obtained and expounded.

A Semi-implicit Treatment of Porous Media in Steady-State CFD.

PubMed

Domaingo, Andreas; Langmayr, Daniel; Somogyi, Bence; Almbauer, Raimund

There are many situations in computational fluid dynamics which require the definition of source terms in the Navier-Stokes equations. These source terms not only allow to model the physics of interest but also have a strong impact on the reliability, stability, and convergence of the numerics involved. Therefore, sophisticated numerical approaches exist for the description of such source terms. In this paper, we focus on the source terms present in the Navier-Stokes or Euler equations due to porous media-in particular the Darcy-Forchheimer equation. We introduce a method for the numerical treatment of the source term which is independent of the spatial discretization and based on linearization. In this description, the source term is treated in a fully implicit way whereas the other flow variables can be computed in an implicit or explicit manner. This leads to a more robust description in comparison with a fully explicit approach. The method is well suited to be combined with coarse-grid-CFD on Cartesian grids, which makes it especially favorable for accelerated solution of coupled 1D-3D problems. To demonstrate the applicability and robustness of the proposed method, a proof-of-concept example in 1D, as well as more complex examples in 2D and 3D, is presented.

DYNA3D, INGRID, and TAURUS: an integrated, interactive software system for crashworthiness engineering

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

Benson, D.J.; Hallquist, J.O.; Stillman, D.W.

1985-04-01

Crashworthiness engineering has always been a high priority at Lawrence Livermore National Laboratory because of its role in the safe transport of radioactive material for the nuclear power industry and military. As a result, the authors have developed an integrated, interactive set of finite element programs for crashworthiness analysis. The heart of the system is DYNA3D, an explicit, fully vectorized, large deformation structural dynamics code. DYNA3D has the following four capabilities that are critical for the efficient and accurate analysis of crashes: (1) fully nonlinear solid, shell, and beam elements for representing a structure, (2) a broad range of constitutivemore » models for representing the materials, (3) sophisticated contact algorithms for the impact interactions, and (4) a rigid body capability to represent the bodies away from the impact zones at a greatly reduced cost without sacrificing any accuracy in the momentum calculations. To generate the large and complex data files for DYNA3D, INGRID, a general purpose mesh generator, is used. It runs on everything from IBM PCs to CRAYS, and can generate 1000 nodes/minute on a PC. With its efficient hidden line algorithms and many options for specifying geometry, INGRID also doubles as a geometric modeller. TAURUS, an interactive post processor, is used to display DYNA3D output. In addition to the standard monochrome hidden line display, time history plotting, and contouring, TAURUS generates interactive color displays on 8 color video screens by plotting color bands superimposed on the mesh which indicate the value of the state variables. For higher quality color output, graphic output files may be sent to the DICOMED film recorders. We have found that color is every bit as important as hidden line removal in aiding the analyst in understanding his results. In this paper the basic methodologies of the programs are presented along with several crashworthiness calculations.« less

Reverse engineering--rapid prototyping of the skull in forensic trauma analysis.

PubMed

Kettner, Mattias; Schmidt, Peter; Potente, Stefan; Ramsthaler, Frank; Schrodt, Michael

2011-07-01

Rapid prototyping (RP) comprises a variety of automated manufacturing techniques such as selective laser sintering (SLS), stereolithography, and three-dimensional printing (3DP), which use virtual 3D data sets to fabricate solid forms in a layer-by-layer technique. Despite a growing demand for (virtual) reconstruction models in daily forensic casework, maceration of the skull is frequently assigned to ensure haptic evidence presentation in the courtroom. Owing to the progress in the field of forensic radiology, 3D data sets of relevant cases are usually available to the forensic expert. Here, we present a first application of RP in forensic medicine using computed tomography scans for the fabrication of an SLS skull model in a case of fatal hammer impacts to the head. The report is intended to show that this method fully respects the dignity of the deceased and is consistent with medical ethics but nevertheless provides an excellent 3D impression of anatomical structures and injuries. © 2011 American Academy of Forensic Sciences.

Forward Monte Carlo Computations of Polarized Microwave Radiation

NASA Technical Reports Server (NTRS)

Battaglia, A.; Kummerow, C.

2000-01-01

Microwave radiative transfer computations continue to acquire greater importance as the emphasis in remote sensing shifts towards the understanding of microphysical properties of clouds and with these to better understand the non linear relation between rainfall rates and satellite-observed radiance. A first step toward realistic radiative simulations has been the introduction of techniques capable of treating 3-dimensional geometry being generated by ever more sophisticated cloud resolving models. To date, a series of numerical codes have been developed to treat spherical and randomly oriented axisymmetric particles. Backward and backward-forward Monte Carlo methods are, indeed, efficient in this field. These methods, however, cannot deal properly with oriented particles, which seem to play an important role in polarization signatures over stratiform precipitation. Moreover, beyond the polarization channel, the next generation of fully polarimetric radiometers challenges us to better understand the behavior of the last two Stokes parameters as well. In order to solve the vector radiative transfer equation, one-dimensional numerical models have been developed, These codes, unfortunately, consider the atmosphere as horizontally homogeneous with horizontally infinite plane parallel layers. The next development step for microwave radiative transfer codes must be fully polarized 3-D methods. Recently a 3-D polarized radiative transfer model based on the discrete ordinate method was presented. A forward MC code was developed that treats oriented nonspherical hydrometeors, but only for plane-parallel situations.

An automated 3D reconstruction method of UAV images

NASA Astrophysics Data System (ADS)

Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

2015-10-01

In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

Shutdown Dose Rate Analysis for the long-pulse D-D Operation Phase in KSTAR

NASA Astrophysics Data System (ADS)

Park, Jin Hun; Han, Jung-Hoon; Kim, D. H.; Joo, K. S.; Hwang, Y. S.

2017-09-01

KSTAR is a medium size fully superconducting tokamak. The deuterium-deuterium (D-D) reaction in the KSTAR tokamak generates neutrons with a peak yield of 3.5x1016 per second through a pulse operation of 100 seconds. The effect of neutron generation from full D-D high power KSTAR operation mode to the machine, such as activation, shutdown dose rate, and nuclear heating, are estimated for an assurance of safety during operation, maintenance, and machine upgrade. The nuclear heating of the in-vessel components, and neutron activation of the surrounding materials have been investigated. The dose rates during operation and after shutdown of KSTAR have been calculated by a 3D CAD model of KSTAR with the Monte Carlo code MCNP5 (neutron flux and decay photon), the inventory code FISPACT (activation and decay photon) and the FENDL 2.1 nuclear data library.

Fully implicit Particle-in-cell algorithms for multiscale plasma simulation

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

Chacon, Luis

The outline of the paper is as follows: Particle-in-cell (PIC) methods for fully ionized collisionless plasmas, explicit vs. implicit PIC, 1D ES implicit PIC (charge and energy conservation, moment-based acceleration), and generalization to Multi-D EM PIC: Vlasov-Darwin model (review and motivation for Darwin model, conservation properties (energy, charge, and canonical momenta), and numerical benchmarks). The author demonstrates a fully implicit, fully nonlinear, multidimensional PIC formulation that features exact local charge conservation (via a novel particle mover strategy), exact global energy conservation (no particle self-heating or self-cooling), adaptive particle orbit integrator to control errors in momentum conservation, and canonical momenta (EM-PICmore » only, reduced dimensionality). The approach is free of numerical instabilities: ω peΔt >> 1, and Δx >> λ D. It requires many fewer dofs (vs. explicit PIC) for comparable accuracy in challenging problems. Significant CPU gains (vs explicit PIC) have been demonstrated. The method has much potential for efficiency gains vs. explicit in long-time-scale applications. Moment-based acceleration is effective in minimizing N FE, leading to an optimal algorithm.« less

A Comparative Study of Shock Structures for the Halloween 2003 and the 23 July 2012 CME Events

NASA Astrophysics Data System (ADS)

Wu, C. C.; Liou, K.

2015-12-01

Interplanetary (IP) shocks driven by coronal mass ejections (CMEs) play an important role in space weather. For example, solar energetic particles are accelerated at the shock and storm sudden commencements are produced by the impingement of the Earth by the shocks. Here, we study shocks associated with two major CME events - the Halloween 2003 and the 23 July 2012 CME events, using a three-dimensional (3D) magnetohydrodynamics model (H3DMHD). The H3DMHD (Wu et al. 2007, JGR) combines the kinematic solar wind model (HAF) for regions near the solar surface (2.5-18 Rs) and a 3D magnetohydrodynamics model (Han et al. 1988), which takes output from HAF at 18 Rs and propagates outward up to 1.7 AU. The H3DMHD code has been fully tested and is capable of simulating disturbances propagating in the solar wind. We will focus on the temporal and spatial structure of the CME-driven shocks, including the shock type and strength.

The Thistle Field - Analysis of its past performance and optimisation of its future development

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

Bayat, M.G.; Tehrani, D.H.

1985-01-01

The Thistle Field geology and its reservoir performance over the past six years have been reviewed. The latest reservoir simulation study of the field, covering the performance history-matching, and the conclusions of various prediction cases are reported. The special features of PORES, Britoil in-house 3D 3-phase fully implicit numerical simulator and its modeling aids as applied to the Thistle Field are presented.

Three-dimensional fully-coupled electrical and thermal transport model of dynamic switching in oxide memristors

DOE PAGES

Gao, Xujiao; Mamaluy, Denis; Mickel, Patrick R.; ...

2015-09-08

In this paper, we present a fully-coupled electrical and thermal transport model for oxide memristors that solves simultaneously the time-dependent continuity equations for all relevant carriers, together with the time-dependent heat equation including Joule heating sources. The model captures all the important processes that drive memristive switching and is applicable to simulate switching behavior in a wide range of oxide memristors. The model is applied to simulate the ON switching in a 3D filamentary TaOx memristor. Simulation results show that, for uniform vacancy density in the OFF state, vacancies fill in the conduction filament till saturation, and then fill outmore » a gap formed in the Ta electrode during ON switching; furthermore, ON-switching time strongly depends on applied voltage and the ON-to-OFF current ratio is sensitive to the filament vacancy density in the OFF state.« less

3D CAFE modeling of grain structures: application to primary dendritic and secondary eutectic solidification

NASA Astrophysics Data System (ADS)

Carozzani, T.; Digonnet, H.; Gandin, Ch-A.

2012-01-01

A three-dimensional model is presented for the prediction of grain structures formed in casting. It is based on direct tracking of grain boundaries using a cellular automaton (CA) method. The model is fully coupled with a solution of the heat flow computed with a finite element (FE) method. Several unique capabilities are implemented including (i) the possibility to track the development of several types of grain structures, e.g. dendritic and eutectic grains, (ii) a coupling scheme that permits iterations between the FE method and the CA method, and (iii) tabulated enthalpy curves for the solid and liquid phases that offer the possibility to work with multicomponent alloys. The present CAFE model is also fully parallelized and runs on a cluster of computers. Demonstration is provided by direct comparison between simulated and recorded cooling curves for a directionally solidified aluminum-7 wt% silicon alloy.

Approximation of a foreign object using x-rays, reference photographs and 3D reconstruction techniques.

PubMed

Briggs, Matt; Shanmugam, Mohan

2013-12-01

This case study describes how a 3D animation was created to approximate the depth and angle of a foreign object (metal bar) that had become embedded into a patient's head. A pre-operative CT scan was not available as the patient could not fit though the CT scanner, therefore a post surgical CT scan, x-ray and photographic images were used. A surface render was made of the skull and imported into Blender (a 3D animation application). The metal bar was not available, however images of a similar object that was retrieved from the scene by the ambulance crew were used to recreate a 3D model. The x-ray images were then imported into Blender and used as background images in order to align the skull reconstruction and metal bar at the correct depth/angle. A 3D animation was then created to fully illustrate the angle and depth of the iron bar in the skull.

Externally calibrated parallel imaging for 3D multispectral imaging near metallic implants using broadband ultrashort echo time imaging.

PubMed

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Reeder, Scott B

2017-06-01

To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. Magn Reson Med 77:2303-2309, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Fully automated, real-time 3D ultrasound segmentation to estimate first trimester placental volume using deep learning.

PubMed

Looney, Pádraig; Stevenson, Gordon N; Nicolaides, Kypros H; Plasencia, Walter; Molloholli, Malid; Natsis, Stavros; Collins, Sally L

2018-06-07

We present a new technique to fully automate the segmentation of an organ from 3D ultrasound (3D-US) volumes, using the placenta as the target organ. Image analysis tools to estimate organ volume do exist but are too time consuming and operator dependant. Fully automating the segmentation process would potentially allow the use of placental volume to screen for increased risk of pregnancy complications. The placenta was segmented from 2,393 first trimester 3D-US volumes using a semiautomated technique. This was quality controlled by three operators to produce the "ground-truth" data set. A fully convolutional neural network (OxNNet) was trained using this ground-truth data set to automatically segment the placenta. OxNNet delivered state-of-the-art automatic segmentation. The effect of training set size on the performance of OxNNet demonstrated the need for large data sets. The clinical utility of placental volume was tested by looking at predictions of small-for-gestational-age babies at term. The receiver-operating characteristics curves demonstrated almost identical results between OxNNet and the ground-truth). Our results demonstrated good similarity to the ground-truth and almost identical clinical results for the prediction of SGA.

Representation and Reconconstruction of Triangular Irregular Networks with Vertical Walls

NASA Astrophysics Data System (ADS)

Gorte, B.; Lesparre, J.

2012-06-01

Point clouds obtained by aerial laser scanning are a convenient input source for high resolution 2.5d elevation models, such as the Dutch AHN-2. More challenging is the fully automatic reconstruction of 3d city models. An actual demand for a combined 2.5d terrain and 3d city model for an urban hydrology application led to the design of an extension to the well-known Delaunay triangulated irregular networks (TINs) as to accommodate vertical walls. In addition we introduce methods to generate and refine models adhering to our data structure. These are based on combining two approaches: a representation of the TIN using stars of vertices and triangles, together with segmenting the TIN on the basis of coplanarity of adjacent triangles. The approach is supposed to deliver the complete model including walls at the correct locations, without relying on additional map data, as these often lack completeness, actuality and accuracy, and moreover most of the time do not account for parts facades not going down to street level. However, automatic detection of height discontinuities to obtain the exact location of the walls is currently still under implementation.

Galerkin CFD solvers for use in a multi-disciplinary suite for modeling advanced flight vehicles

NASA Astrophysics Data System (ADS)

Moffitt, Nicholas J.

This work extends existing Galerkin CFD solvers for use in a multi-disciplinary suite. The suite is proposed as a means of modeling advanced flight vehicles, which exhibit strong coupling between aerodynamics, structural dynamics, controls, rigid body motion, propulsion, and heat transfer. Such applications include aeroelastics, aeroacoustics, stability and control, and other highly coupled applications. The suite uses NASA STARS for modeling structural dynamics and heat transfer. Aerodynamics, propulsion, and rigid body dynamics are modeled in one of the five CFD solvers below. Euler2D and Euler3D are Galerkin CFD solvers created at OSU by Cowan (2003). These solvers are capable of modeling compressible inviscid aerodynamics with modal elastics and rigid body motion. This work reorganized these solvers to improve efficiency during editing and at run time. Simple and efficient propulsion models were added, including rocket, turbojet, and scramjet engines. Viscous terms were added to the previous solvers to create NS2D and NS3D. The viscous contributions were demonstrated in the inertial and non-inertial frames. Variable viscosity (Sutherland's equation) and heat transfer boundary conditions were added to both solvers but not verified in this work. Two turbulence models were implemented in NS2D and NS3D: Spalart-Allmarus (SA) model of Deck, et al. (2002) and Menter's SST model (1994). A rotation correction term (Shur, et al., 2000) was added to the production of turbulence. Local time stepping and artificial dissipation were adapted to each model. CFDsol is a Taylor-Galerkin solver with an SA turbulence model. This work improved the time accuracy, far field stability, viscous terms, Sutherland?s equation, and SA model with NS3D as a guideline and added the propulsion models from Euler3D to CFDsol. Simple geometries were demonstrated to utilize current meshing and processing capabilities. Air-breathing hypersonic flight vehicles (AHFVs) represent the ultimate application of the suite. The current models are accurate at low supersonic speed and reasonable for engineering approximation at hypersonic speeds. Improvements to extend the models fully into the hypersonic regime are given in the Recommendations section.

Automatic Testing and Assessment of Neuroanatomy Using a Digital Brain Atlas: Method and Development of Computer- and Mobile-Based Applications

ERIC Educational Resources Information Center

Nowinski, Wieslaw L.; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G.; Marchenko, Yevgen; Volkau, Ihar

2009-01-01

Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to "Terminologia…

Reconstructing liver shape and position from MR image slices using an active shape model

NASA Astrophysics Data System (ADS)

Fenchel, Matthias; Thesen, Stefan; Schilling, Andreas

2008-03-01

We present an algorithm for fully automatic reconstruction of 3D position, orientation and shape of the human liver from a sparsely covering set of n 2D MR slice images. Reconstructing the shape of an organ from slice images can be used for scan planning, for surgical planning or other purposes where 3D anatomical knowledge has to be inferred from sparse slices. The algorithm is based on adapting an active shape model of the liver surface to a given set of slice images. The active shape model is created from a training set of liver segmentations from a group of volunteers. The training set is set up with semi-manual segmentations of T1-weighted volumetric MR images. Searching for the optimal shape model that best fits to the image data is done by maximizing a similarity measure based on local appearance at the surface. Two different algorithms for the active shape model search are proposed and compared: both algorithms seek to maximize the a-posteriori probability of the grey level appearance around the surface while constraining the surface to the space of valid shapes. The first algorithm works by using grey value profile statistics in normal direction. The second algorithm uses average and variance images to calculate the local surface appearance on the fly. Both algorithms are validated by fitting the active shape model to abdominal 2D slice images and comparing the shapes, which have been reconstructed, to the manual segmentations and to the results of active shape model searches from 3D image data. The results turn out to be promising and competitive to active shape model segmentations from 3D data.

Three-dimensional joint inversion for magnetotelluric resistivity and static shift distributions in complex media

NASA Astrophysics Data System (ADS)

Sasaki, Yutaka; Meju, Max A.

2006-05-01

Accurate interpretation of magnetotelluric (MT) data in the presence of static shift arising from near-surface inhomogeneities is an unresolved problem in three-dimensional (3-D) inversion. While it is well known in 1-D and 2-D studies that static shift can lead to erroneous interpretation, how static shift can influence the result of 3-D inversion is not fully understood and is relevant to improved subsurface analysis. Using the synthetic data generated from 3-D models with randomly distributed heterogeneous overburden and elongate homogeneous overburden that are consistent with geological observations, this paper examines the effects of near-surface inhomogeneity on the accuracy of 3-D inversion models. It is found that small-scale and shallow depth structures are severely distorted while the large-scale structure is marginally distorted in 3-D inversion not accounting for static shift; thus the erroneous near-surface structure does degrade the reconstruction of smaller-scale structure at any depth. However, 3-D joint inversion for resistivity and static shift significantly reduces the artifacts caused by static shifts and improves the overall resolution, irrespective of whether a zero-sum or Gaussian distribution of static shifts is assumed. The 3-D joint inversion approach works equally well for situations where the shallow bodies are of small size or long enough to allow some induction such that the effects of near-surface inhomogeneity are manifested as a frequency-dependent shift rather than a constant shift.

Nonlinear three-dimensional verification of the SPECYL and PIXIE3D magnetohydrodynamics codes for fusion plasmas

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Chacón, L.; Cappello, S.

2010-08-01

With the increasing impact of scientific discovery via advanced computation, there is presently a strong emphasis on ensuring the mathematical correctness of computational simulation tools. Such endeavor, termed verification, is now at the center of most serious code development efforts. In this study, we address a cross-benchmark nonlinear verification study between two three-dimensional magnetohydrodynamics (3D MHD) codes for fluid modeling of fusion plasmas, SPECYL [S. Cappello and D. Biskamp, Nucl. Fusion 36, 571 (1996)] and PIXIE3D [L. Chacón, Phys. Plasmas 15, 056103 (2008)], in their common limit of application: the simple viscoresistive cylindrical approximation. SPECYL is a serial code in cylindrical geometry that features a spectral formulation in space and a semi-implicit temporal advance, and has been used extensively to date for reversed-field pinch studies. PIXIE3D is a massively parallel code in arbitrary curvilinear geometry that features a conservative, solenoidal finite-volume discretization in space, and a fully implicit temporal advance. The present study is, in our view, a first mandatory step in assessing the potential of any numerical 3D MHD code for fluid modeling of fusion plasmas. Excellent agreement is demonstrated over a wide range of parameters for several fusion-relevant cases in both two- and three-dimensional geometries.

Nonlinear three-dimensional verification of the SPECYL and PIXIE3D magnetohydrodynamics codes for fusion plasmas

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

Bonfiglio, Daniele; Chacon, Luis; Cappello, Susanna

2010-01-01

With the increasing impact of scientific discovery via advanced computation, there is presently a strong emphasis on ensuring the mathematical correctness of computational simulation tools. Such endeavor, termed verification, is now at the center of most serious code development efforts. In this study, we address a cross-benchmark nonlinear verification study between two three-dimensional magnetohydrodynamics (3D MHD) codes for fluid modeling of fusion plasmas, SPECYL [S. Cappello and D. Biskamp, Nucl. Fusion 36, 571 (1996)] and PIXIE3D [L. Chacon, Phys. Plasmas 15, 056103 (2008)], in their common limit of application: the simple viscoresistive cylindrical approximation. SPECYL is a serial code inmore » cylindrical geometry that features a spectral formulation in space and a semi-implicit temporal advance, and has been used extensively to date for reversed-field pinch studies. PIXIE3D is a massively parallel code in arbitrary curvilinear geometry that features a conservative, solenoidal finite-volume discretization in space, and a fully implicit temporal advance. The present study is, in our view, a first mandatory step in assessing the potential of any numerical 3D MHD code for fluid modeling of fusion plasmas. Excellent agreement is demonstrated over a wide range of parameters for several fusion-relevant cases in both two- and three-dimensional geometries.« less

Biological properties of solid free form designed ceramic scaffolds with BMP-2: in vitro and in vivo evaluation.

PubMed

Abarrategi, Ander; Moreno-Vicente, Carolina; Martínez-Vázquez, Francisco Javier; Civantos, Ana; Ramos, Viviana; Sanz-Casado, José Vicente; Martínez-Corriá, Ramón; Perera, Fidel Hugo; Mulero, Francisca; Miranda, Pedro; López-Lacomba, José Luís

2012-01-01

Porous ceramic scaffolds are widely studied in the tissue engineering field due to their potential in medical applications as bone substitutes or as bone-filling materials. Solid free form (SFF) fabrication methods allow fabrication of ceramic scaffolds with fully controlled pore architecture, which opens new perspectives in bone tissue regeneration materials. However, little experimentation has been performed about real biological properties and possible applications of SFF designed 3D ceramic scaffolds. Thus, here the biological properties of a specific SFF scaffold are evaluated first, both in vitro and in vivo, and later scaffolds are also implanted in pig maxillary defect, which is a model for a possible application in maxillofacial surgery. In vitro results show good biocompatibility of the scaffolds, promoting cell ingrowth. In vivo results indicate that material on its own conducts surrounding tissue and allow cell ingrowth, thanks to the designed pore size. Additional osteoinductive properties were obtained with BMP-2, which was loaded on scaffolds, and optimal bone formation was observed in pig implantation model. Collectively, data show that SFF scaffolds have real application possibilities for bone tissue engineering purposes, with the main advantage of being fully customizable 3D structures.

Biological Properties of Solid Free Form Designed Ceramic Scaffolds with BMP-2: In Vitro and In Vivo Evaluation

PubMed Central

Abarrategi, Ander; Moreno-Vicente, Carolina; Martínez-Vázquez, Francisco Javier; Civantos, Ana; Ramos, Viviana; Sanz-Casado, José Vicente; Martínez-Corriá, Ramón; Perera, Fidel Hugo; Mulero, Francisca; Miranda, Pedro; López-Lacomba, José Luís

2012-01-01

Porous ceramic scaffolds are widely studied in the tissue engineering field due to their potential in medical applications as bone substitutes or as bone-filling materials. Solid free form (SFF) fabrication methods allow fabrication of ceramic scaffolds with fully controlled pore architecture, which opens new perspectives in bone tissue regeneration materials. However, little experimentation has been performed about real biological properties and possible applications of SFF designed 3D ceramic scaffolds. Thus, here the biological properties of a specific SFF scaffold are evaluated first, both in vitro and in vivo, and later scaffolds are also implanted in pig maxillary defect, which is a model for a possible application in maxillofacial surgery. In vitro results show good biocompatibility of the scaffolds, promoting cell ingrowth. In vivo results indicate that material on its own conducts surrounding tissue and allow cell ingrowth, thanks to the designed pore size. Additional osteoinductive properties were obtained with BMP-2, which was loaded on scaffolds, and optimal bone formation was observed in pig implantation model. Collectively, data show that SFF scaffolds have real application possibilities for bone tissue engineering purposes, with the main advantage of being fully customizable 3D structures. PMID:22470527

A curvilinear, fully implicit, conservative electromagnetic PIC algorithm in multiple dimensions

DOE PAGES

Chacon, L.; Chen, G.

2016-04-19

Here, we extend a recently proposed fully implicit PIC algorithm for the Vlasov–Darwin model in multiple dimensions (Chen and Chacón (2015) [1]) to curvilinear geometry. As in the Cartesian case, the approach is based on a potential formulation (Φ, A), and overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. Conservation theorems for local charge and global energy are derived in curvilinear representation, and then enforced discretely by a careful choice of the discretization of field and particle equations. Additionally, the algorithm conserves canonical-momentum in any ignorable direction, and preserves the Coulomb gauge ∇ • A = 0 exactly. Anmore » asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. We demonstrate the accuracy and efficiency properties of the algorithm with numerical experiments in mapped meshes in 1D-3V and 2D-3V.« less

A curvilinear, fully implicit, conservative electromagnetic PIC algorithm in multiple dimensions

NASA Astrophysics Data System (ADS)

Chacón, L.; Chen, G.

2016-07-01

We extend a recently proposed fully implicit PIC algorithm for the Vlasov-Darwin model in multiple dimensions (Chen and Chacón (2015) [1]) to curvilinear geometry. As in the Cartesian case, the approach is based on a potential formulation (ϕ, A), and overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. Conservation theorems for local charge and global energy are derived in curvilinear representation, and then enforced discretely by a careful choice of the discretization of field and particle equations. Additionally, the algorithm conserves canonical-momentum in any ignorable direction, and preserves the Coulomb gauge ∇ ṡ A = 0 exactly. An asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. We demonstrate the accuracy and efficiency properties of the algorithm with numerical experiments in mapped meshes in 1D-3V and 2D-3V.

A curvilinear, fully implicit, conservative electromagnetic PIC algorithm in multiple dimensions

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

Chacon, L.; Chen, G.

Here, we extend a recently proposed fully implicit PIC algorithm for the Vlasov–Darwin model in multiple dimensions (Chen and Chacón (2015) [1]) to curvilinear geometry. As in the Cartesian case, the approach is based on a potential formulation (Φ, A), and overcomes many difficulties of traditional semi-implicit Darwin PIC algorithms. Conservation theorems for local charge and global energy are derived in curvilinear representation, and then enforced discretely by a careful choice of the discretization of field and particle equations. Additionally, the algorithm conserves canonical-momentum in any ignorable direction, and preserves the Coulomb gauge ∇ • A = 0 exactly. Anmore » asymptotically well-posed fluid preconditioner allows efficient use of large cell sizes, which are determined by accuracy considerations, not stability, and can be orders of magnitude larger than required in a standard explicit electromagnetic PIC simulation. We demonstrate the accuracy and efficiency properties of the algorithm with numerical experiments in mapped meshes in 1D-3V and 2D-3V.« less

Open source 3D visualization and interaction dedicated to hydrological models

NASA Astrophysics Data System (ADS)

Richard, Julien; Giangola-Murzyn, Agathe; Gires, Auguste; Tchiguirinskaia, Ioulia; Schertzer, Daniel

2014-05-01

Climate change and surface urbanization strongly modify the hydrological cycle in urban areas, increasing the consequences of extreme events such as floods or draughts. These issues lead to the development of the Multi-Hydro model at the Ecole des Ponts ParisTech (A. Giangola-Murzyn et al., 2012). This fully distributed model allows to compute the hydrological response of urban and peri-urban areas. Unfortunately such models are seldom user friendly. Indeed generating the inputs before launching a new simulation is usually a tricky tasks, and understanding and interpreting the outputs remains specialist tasks not accessible to the wider public. The MH-AssimTool was developed to overcome these issues. To enable an easier and improved understanding of the model outputs, we decided to convert the raw output data (grids file in ascii format) to a 3D display. Some commercial paying models provide a 3D visualization. Because of the cost of their licenses, this kind of tools may not be accessible to the most concerned stakeholders. So, we are developing a new tool based on C++ for the computation, Qt for the graphic user interface, QGIS for the geographical side and OpenGL for the 3D display. All these languages and libraries are open source and multi-platform. We will discuss some preprocessing issues for the data conversion from 2.5D to 3D. Indeed, the GIS data, is considered as a 2.5D (e.i. 2D polygon + one height) and the its transform to 3D display implies a lot of algorithms. For example,to visualize in 3D one building, it is needed to have for each point the coordinates and the elevation according to the topography. Furthermore one have to create new points to represent the walls. Finally the interactions between the model and stakeholders through this new interface and how this helps converting a research tool into a an efficient operational decision tool will be discussed. This ongoing research on the improvement of the visualization methods is supported by the KIC-Climate Blue Green Dream project.

Large-scale 3D inversion of marine controlled source electromagnetic data using the integral equation method

NASA Astrophysics Data System (ADS)

Zhdanov, M. S.; Cuma, M.; Black, N.; Wilson, G. A.

2009-12-01

The marine controlled source electromagnetic (MCSEM) method has become widely used in offshore oil and gas exploration. Interpretation of MCSEM data is still a very challenging problem, especially if one would like to take into account the realistic 3D structure of the subsurface. The inversion of MCSEM data is complicated by the fact that the EM response of a hydrocarbon-bearing reservoir is very weak in comparison with the background EM fields generated by an electric dipole transmitter in complex geoelectrical structures formed by a conductive sea-water layer and the terranes beneath it. In this paper, we present a review of the recent developments in the area of large-scale 3D EM forward modeling and inversion. Our approach is based on using a new integral form of Maxwell’s equations allowing for an inhomogeneous background conductivity, which results in a numerically effective integral representation for 3D EM field. This representation provides an efficient tool for the solution of 3D EM inverse problems. To obtain a robust inverse model of the conductivity distribution, we apply regularization based on a focusing stabilizing functional which allows for the recovery of models with both smooth and sharp geoelectrical boundaries. The method is implemented in a fully parallel computer code, which makes it possible to run large-scale 3D inversions on grids with millions of inversion cells. This new technique can be effectively used for active EM detection and monitoring of the subsurface targets.

Precise photorealistic visualization for restoration of historic buildings based on tacheometry data

NASA Astrophysics Data System (ADS)

Ragia, Lemonia; Sarri, Froso; Mania, Katerina

2018-03-01

This paper puts forward a 3D reconstruction methodology applied to the restoration of historic buildings taking advantage of the speed, range and accuracy of a total geodetic station. The measurements representing geo-referenced points produced an interactive and photorealistic geometric mesh of a monument named `Neoria.' `Neoria' is a Venetian building located by the old harbor at Chania, Crete, Greece. The integration of tacheometry acquisition and computer graphics puts forward a novel integrated software framework for the accurate 3D reconstruction of a historical building. The main technical challenge of this work was the production of a precise 3D mesh based on a sufficient number of tacheometry measurements acquired fast and at low cost, employing a combination of surface reconstruction and processing methods. A fully interactive application based on game engine technologies was developed. The user can visualize and walk through the monument and the area around it as well as photorealistically view it at different times of day and night. Advanced interactive functionalities are offered to the user in relation to identifying restoration areas and visualizing the outcome of such works. The user could visualize the coordinates of the points measured, calculate distances and navigate through the complete 3D mesh of the monument. The geographical data are stored in a database connected with the application. Features referencing and associating the database with the monument are developed. The goal was to utilize a small number of acquired data points and present a fully interactive visualization of a geo-referenced 3D model.

Precise photorealistic visualization for restoration of historic buildings based on tacheometry data

NASA Astrophysics Data System (ADS)

Ragia, Lemonia; Sarri, Froso; Mania, Katerina

2018-04-01

This paper puts forward a 3D reconstruction methodology applied to the restoration of historic buildings taking advantage of the speed, range and accuracy of a total geodetic station. The measurements representing geo-referenced points produced an interactive and photorealistic geometric mesh of a monument named `Neoria.' `Neoria' is a Venetian building located by the old harbor at Chania, Crete, Greece. The integration of tacheometry acquisition and computer graphics puts forward a novel integrated software framework for the accurate 3D reconstruction of a historical building. The main technical challenge of this work was the production of a precise 3D mesh based on a sufficient number of tacheometry measurements acquired fast and at low cost, employing a combination of surface reconstruction and processing methods. A fully interactive application based on game engine technologies was developed. The user can visualize and walk through the monument and the area around it as well as photorealistically view it at different times of day and night. Advanced interactive functionalities are offered to the user in relation to identifying restoration areas and visualizing the outcome of such works. The user could visualize the coordinates of the points measured, calculate distances and navigate through the complete 3D mesh of the monument. The geographical data are stored in a database connected with the application. Features referencing and associating the database with the monument are developed. The goal was to utilize a small number of acquired data points and present a fully interactive visualization of a geo-referenced 3D model.

Use of fused deposit modeling for additive manufacturing in hospital facilities: European certification directives.

PubMed

Otero, Joel J; Vijverman, An; Mommaerts, Maurice Y

2017-09-01

The goal of this study was to identify current European Union regulations governing hospital-based use of fused deposit modeling (FDM), as implemented via desktop three-dimensional (3D) printers. Literature and Internet sources were screened, searching for official documents, regulations/legislation, and views of specialized attorneys or consultants regarding European regulations for 3D printing or additive manufacturing (AM) in a healthcare facility. A detailed review of the latest amendment (2016) of the European Parliament and Council legislation for medical devices and its classification was performed, which has regularly updated published guidelines for medical devices, that are classified by type and duration of patient contact. As expected, regulations increase in accordance with the level (I-III) of classification. Custom-made medical devices are subject to different regulations than those controlling serially mass-produced items, as originally specified in 98/79/EC European Parliament and Council legislation (1993) and again recently amended (2016). Healthcare facilities undertaking in-house custom production are not obliged to fully follow the directives as stipulated, given an exception for this scenario (Article 4.4a, 98/79/EC). Patient treatment and diagnosis with the aid of customized 3D printing in a healthcare facility can be performed without fully meeting the European Parliament and Council legislation if the materials used are ISO 10993 certified and article 4.4a applies. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Recent advancements in mechanical characterisation of 3D woven composites

NASA Astrophysics Data System (ADS)

Saleh, Mohamed Nasr; Soutis, Constantinos

2017-12-01

Three dimensional (3D) woven composites have attracted the interest of academia and industry thanks to their damage tolerance characteristics and automated fabric manufacturing. Although much research has been conducted to investigate their out-of-plane "through thickness" properties, still their in-plane properties are not fully understood and rely on extensive experimentation. To date, the literature lacks an inclusive summary of the mechanical characterisation for 3D woven composites. Therefore, the objective of this paper is to provide a comprehensive review of the available research studies on 3D woven composites mechanical characterisation, with less emphasis on the out-of-plane response, but an in-depth review of the in-plane response "un-notched vs. notched". The paper highlights the knowledge gap in the literature of 3D woven composites, suggesting opportunities for future research in this field and a room for improvement in utilising Non-Destructive Techniques (NDT), such as Digital Image Correlation (DIC), Acoustic Emission (AE) and X-ray Computed Tomography (CT), for observing damage initiation and evolution in 3D woven composites that could be used to calibrate and evaluate analytical and numerical models.

An Effective Construction Method of Modular Manipulator 3D Virtual Simulation Platform

NASA Astrophysics Data System (ADS)

Li, Xianhua; Lv, Lei; Sheng, Rui; Sun, Qing; Zhang, Leigang

2018-06-01

This work discusses about a fast and efficient method of constructing an open 3D manipulator virtual simulation platform which make it easier for teachers and students to learn about positive and inverse kinematics of a robot manipulator. The method was carried out using MATLAB. In which, the Robotics Toolbox, MATLAB GUI and 3D animation with the help of modelling using SolidWorks, were fully applied to produce a good visualization of the system. The advantages of using quickly build is its powerful function of the input and output and its ability to simulate a 3D manipulator realistically. In this article, a Schunk six DOF modular manipulator was constructed by the author's research group to be used as example. The implementation steps of this method was detailed described, and thereafter, a high-level open and realistic visualization manipulator 3D virtual simulation platform was achieved. With the graphs obtained from simulation, the test results show that the manipulator 3D virtual simulation platform can be constructed quickly with good usability and high maneuverability, and it can meet the needs of scientific research and teaching.

Hybrid graphene-copper UWB array sensor for brain tumor detection via scattering parameters in microwave detection system

NASA Astrophysics Data System (ADS)

Jamlos, Mohd Aminudin; Ismail, Abdul Hafiizh; Jamlos, Mohd Faizal; Narbudowicz, Adam

2017-01-01

Hybrid graphene-copper ultra-wideband array sensor applied to microwave imaging technique is successfully used in detecting and visualizing tumor inside human brain. The sensor made of graphene coated film for the patch while copper for both the transmission line and parasitic element. The hybrid sensor performance is better than fully copper sensor. Hybrid sensor recorded wider bandwidth of 2.0-10.1 GHz compared with fully copper sensor operated from 2.5 to 10.1 GHz. Higher gain of 3.8-8.5 dB is presented by hybrid sensor, while fully copper sensor stated lower gain ranging from 2.6 to 6.7 dB. Both sensors recorded excellent total efficiency averaged at 97 and 94%, respectively. The sensor used for both transmits equivalent signal and receives backscattering signal from stratified human head model in detecting tumor. Difference in the data of the scattering parameters recorded from the head model with presence and absence of tumor is used as the main data to be further processed in confocal microwave imaging algorithm in generating image. MATLAB software is utilized to analyze S-parameter signals obtained from measurement. Tumor presence is indicated by lower S-parameter values compared to higher values recorded by tumor absence.

3D CFD Quantification of the Performance of a Multi-Megawatt Wind Turbine

NASA Astrophysics Data System (ADS)

Laursen, J.; Enevoldsen, P.; Hjort, S.

2007-07-01

This paper presents the results of 3D CFD rotor computations of a Siemens SWT-2.3-93 variable speed wind turbine with 45m blades. In the paper CFD is applied to a rotor at stationary wind conditions without wind shear, using the commercial multi-purpose CFD-solvers ANSYS CFX 10.0 and 11.0. When comparing modelled mechanical effects with findings from other models and measurements, good agreement is obtained. Similarly the computed force distributions compare very well, whereas some discrepancies are found when comparing with an in-house BEM model. By applying the reduced axial velocity method the local angle of attack has been derived from the CFD solutions, and from this knowledge and the computed force distributions, local airfoil profile coefficients have been computed and compared to BEM airfoil coefficients. Finally, the transition model of Langtry and Menter is tested on the rotor, and the results are compared with the results from the fully turbulent setup.

Fully implicit moving mesh adaptive algorithm

NASA Astrophysics Data System (ADS)

Chacon, Luis

2005-10-01

In many problems of interest, the numerical modeler is faced with the challenge of dealing with multiple time and length scales. The former is best dealt with with fully implicit methods, which are able to step over fast frequencies to resolve the dynamical time scale of interest. The latter requires grid adaptivity for efficiency. Moving-mesh grid adaptive methods are attractive because they can be designed to minimize the numerical error for a given resolution. However, the required grid governing equations are typically very nonlinear and stiff, and of considerably difficult numerical treatment. Not surprisingly, fully coupled, implicit approaches where the grid and the physics equations are solved simultaneously are rare in the literature, and circumscribed to 1D geometries. In this study, we present a fully implicit algorithm for moving mesh methods that is feasible for multidimensional geometries. A crucial element is the development of an effective multilevel treatment of the grid equation.ootnotetextL. Chac'on, G. Lapenta, A fully implicit, nonlinear adaptive grid strategy, J. Comput. Phys., accepted (2005) We will show that such an approach is competitive vs. uniform grids both from the accuracy (due to adaptivity) and the efficiency standpoints. Results for a variety of models 1D and 2D geometries, including nonlinear diffusion, radiation-diffusion, Burgers equation, and gas dynamics will be presented.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol

NASA Astrophysics Data System (ADS)

Lounnas, Valère; Wedler, Henry B.; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G.; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J.; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

The modular approach enables a fully ab initio simulation of the contacts between 3D and 2D materials.

PubMed

Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio

2016-10-05

Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.

Online fully automated three-dimensional surface reconstruction of unknown objects

NASA Astrophysics Data System (ADS)

Khalfaoui, Souhaiel; Aigueperse, Antoine; Fougerolle, Yohan; Seulin, Ralph; Fofi, David

2015-04-01

This paper presents a novel scheme for automatic and intelligent 3D digitization using robotic cells. The advantage of our procedure is that it is generic since it is not performed for a specific scanning technology. Moreover, it is not dependent on the methods used to perform the tasks associated with each elementary process. The comparison of results between manual and automatic scanning of complex objects shows that our digitization strategy is very efficient and faster than trained experts. The 3D models of the different objects are obtained with a strongly reduced number of acquisitions while moving efficiently the ranging device.

Pixel-Level Deep Segmentation: Artificial Intelligence Quantifies Muscle on Computed Tomography for Body Morphometric Analysis.

PubMed

Lee, Hyunkwang; Troschel, Fabian M; Tajmir, Shahein; Fuchs, Georg; Mario, Julia; Fintelmann, Florian J; Do, Synho

2017-08-01

Pretreatment risk stratification is key for personalized medicine. While many physicians rely on an "eyeball test" to assess whether patients will tolerate major surgery or chemotherapy, "eyeballing" is inherently subjective and difficult to quantify. The concept of morphometric age derived from cross-sectional imaging has been found to correlate well with outcomes such as length of stay, morbidity, and mortality. However, the determination of the morphometric age is time intensive and requires highly trained experts. In this study, we propose a fully automated deep learning system for the segmentation of skeletal muscle cross-sectional area (CSA) on an axial computed tomography image taken at the third lumbar vertebra. We utilized a fully automated deep segmentation model derived from an extended implementation of a fully convolutional network with weight initialization of an ImageNet pre-trained model, followed by post processing to eliminate intramuscular fat for a more accurate analysis. This experiment was conducted by varying window level (WL), window width (WW), and bit resolutions in order to better understand the effects of the parameters on the model performance. Our best model, fine-tuned on 250 training images and ground truth labels, achieves 0.93 ± 0.02 Dice similarity coefficient (DSC) and 3.68 ± 2.29% difference between predicted and ground truth muscle CSA on 150 held-out test cases. Ultimately, the fully automated segmentation system can be embedded into the clinical environment to accelerate the quantification of muscle and expanded to volume analysis of 3D datasets.

Direct 3D cell-printing of human skin with functional transwell system.

PubMed

Kim, Byoung Soo; Lee, Jung-Seob; Gao, Ge; Cho, Dong-Woo

2017-06-06

Three-dimensional (3D) cell-printing has been emerging as a promising technology with which to build up human skin models by enabling rapid and versatile design. Despite the technological advances, challenges remain in the development of fully functional models that recapitulate complexities in the native tissue. Moreover, although several approaches have been explored for the development of biomimetic human skin models, the present skin models based on multistep fabrication methods using polydimethylsiloxane chips and commercial transwell inserts could be tackled by leveraging 3D cell-printing technology. In this paper, we present a new 3D cell-printing strategy for engineering a 3D human skin model with a functional transwell system in a single-step process. A hybrid 3D cell-printing system was developed, allowing for the use of extrusion and inkjet modules at the same time. We began by revealing the significance of each module in engineering human skin models; by using the extrusion-dispensing module, we engineered a collagen-based construct with polycaprolactone (PCL) mesh that prevented the contraction of collagen during tissue maturation; the inkjet-based dispensing module was used to uniformly distribute keratinocytes. Taking these features together, we engineered a human skin model with a functional transwell system; the transwell system and fibroblast-populated dermis were consecutively fabricated by using the extrusion modules. Following this process, keratinocytes were uniformly distributed onto the engineered dermis by the inkjet module. Our transwell system indicates a supportive 3D construct composed of PCL, enabling the maturation of a skin model without the aid of commercial transwell inserts. This skin model revealed favorable biological characteristics that included a stabilized fibroblast-stretched dermis and stratified epidermis layers after 14 days. It was also observed that a 50 times reduction in cost was achieved and 10 times less medium was used than in a conventional culture. Collectively, because this single-step process opens up chances for versatile designs, we envision that our cell-printing strategy could provide an attractive platform in engineering various human skin models.

Bayesian convolutional neural network based MRI brain extraction on nonhuman primates.

PubMed

Zhao, Gengyan; Liu, Fang; Oler, Jonathan A; Meyerand, Mary E; Kalin, Ned H; Birn, Rasmus M

2018-07-15

Brain extraction or skull stripping of magnetic resonance images (MRI) is an essential step in neuroimaging studies, the accuracy of which can severely affect subsequent image processing procedures. Current automatic brain extraction methods demonstrate good results on human brains, but are often far from satisfactory on nonhuman primates, which are a necessary part of neuroscience research. To overcome the challenges of brain extraction in nonhuman primates, we propose a fully-automated brain extraction pipeline combining deep Bayesian convolutional neural network (CNN) and fully connected three-dimensional (3D) conditional random field (CRF). The deep Bayesian CNN, Bayesian SegNet, is used as the core segmentation engine. As a probabilistic network, it is not only able to perform accurate high-resolution pixel-wise brain segmentation, but also capable of measuring the model uncertainty by Monte Carlo sampling with dropout in the testing stage. Then, fully connected 3D CRF is used to refine the probability result from Bayesian SegNet in the whole 3D context of the brain volume. The proposed method was evaluated with a manually brain-extracted dataset comprising T1w images of 100 nonhuman primates. Our method outperforms six popular publicly available brain extraction packages and three well-established deep learning based methods with a mean Dice coefficient of 0.985 and a mean average symmetric surface distance of 0.220 mm. A better performance against all the compared methods was verified by statistical tests (all p-values < 10 -4 , two-sided, Bonferroni corrected). The maximum uncertainty of the model on nonhuman primate brain extraction has a mean value of 0.116 across all the 100 subjects. The behavior of the uncertainty was also studied, which shows the uncertainty increases as the training set size decreases, the number of inconsistent labels in the training set increases, or the inconsistency between the training set and the testing set increases. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular Packing of Amphiphilic Nanosheets Resolved by X-ray Scattering

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

Harutyunyan, Boris; Dannenhoffer, Adam; Kewalramani, Sumit

2016-12-29

Molecular packing in light harvesting 2D assemblies of photocatalytic materials is a critical factor for solar-to-fuel conversion efficiency. However, structure–function correlations have yet to be fully established. This is partly due to the difficulties in extracting the molecular arrangements from the complex 3D powder averaged diffraction patterns of 2D lattices, obtained via in situ wide-angle X-ray scattering. Here, we develop a scattering theory formalism and couple it with a simple geometrical model for the molecular shape of chromophore 9-methoxy-N-(sodium hexanoate)perylene-3,4-dicarboximide (MeO-PMI) used in our study. This generally applicable method fully reproduces the measured diffraction pattern including the asymmetric line shapesmore » for the Bragg reflections and yields the molecular packing arrangement within a 2D crystal structure with a remarkable degree of detail. We find an approximate edge-centered herringbone structure for the PMI fused aromatic rings and ordering of the carboxypentyl chains above and below the nanosheets. Such a packing arrangement differs from the more symmetric face-to-face orientation of the unsubstituted PMI rings. This structural difference is correlated to our measurement of the reduced catalytic performance of MeO-PMI nanosheets as compared to the mesoscopically similar unsubstituted PMI assemblies.« less

Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model.

PubMed

Nicholson, Daren T; Chalk, Colin; Funnell, W Robert J; Daniel, Sam J

2006-11-01

The use of computer-generated 3-dimensional (3-D) anatomical models to teach anatomy has proliferated. However, there is little evidence that these models are educationally effective. The purpose of this study was to test the educational effectiveness of a computer-generated 3-D model of the middle and inner ear. We reconstructed a fully interactive model of the middle and inner ear from a magnetic resonance imaging scan of a human cadaver ear. To test the model's educational usefulness, we conducted a randomised controlled study in which 28 medical students completed a Web-based tutorial on ear anatomy that included the interactive model, while a control group of 29 students took the tutorial without exposure to the model. At the end of the tutorials, both groups were asked a series of 15 quiz questions to evaluate their knowledge of 3-D relationships within the ear. The intervention group's mean score on the quiz was 83%, while that of the control group was 65%. This difference in means was highly significant (P < 0.001). Our findings stand in contrast to the handful of previous randomised controlled trials that evaluated the effects of computer-generated 3-D anatomical models on learning. The equivocal and negative results of these previous studies may be due to the limitations of these studies (such as small sample size) as well as the limitations of the models that were studied (such as a lack of full interactivity). Given our positive results, we believe that further research is warranted concerning the educational effectiveness of computer-generated anatomical models.

Automated abdominal plane and circumference estimation in 3D US for fetal screening

NASA Astrophysics Data System (ADS)

Lorenz, C.; Brosch, T.; Ciofolo-Veit, C.; Klinder, T.; Lefevre, T.; Cavallaro, A.; Salim, I.; Papageorghiou, A. T.; Raynaud, C.; Roundhill, D.; Rouet, L.; Schadewaldt, N.; Schmidt-Richberg, A.

2018-03-01

Ultrasound is increasingly becoming a 3D modality. Mechanical and matrix array transducers are able to deliver 3D images with good spatial and temporal resolution. The 3D imaging facilitates the application of automated image analysis to enhance workflows, which has the potential to make ultrasound a less operator dependent modality. However, the analysis of the more complex 3D images and definition of all examination standards on 2D images pose barriers to the use of 3D in daily clinical practice. In this paper, we address a part of the canonical fetal screening program, namely the localization of the abdominal cross-sectional plane with the corresponding measurement of the abdominal circumference in this plane. For this purpose, a fully automated pipeline has been designed starting with a random forest based anatomical landmark detection. A feature trained shape model of the fetal torso including inner organs with the abdominal cross-sectional plane encoded into the model is then transformed into the patient space using the landmark localizations. In a free-form deformation step, the model is individualized to the image, using a torso probability map generated by a convolutional neural network as an additional feature image. After adaptation, the abdominal plane and the abdominal torso contour in that plane are directly obtained. This allows the measurement of the abdominal circumference as well as the rendering of the plane for visual assessment. The method has been trained on 126 and evaluated on 42 abdominal 3D US datasets. An average plane offset error of 5.8 mm and an average relative circumference error of 4.9 % in the evaluation set could be achieved.

Turbulent mixing of a critical fluid: The non-perturbative renormalization

NASA Astrophysics Data System (ADS)

Hnatič, M.; Kalagov, G.; Nalimov, M.

2018-01-01

Non-perturbative Renormalization Group (NPRG) technique is applied to a stochastical model of a non-conserved scalar order parameter near its critical point, subject to turbulent advection. The compressible advecting flow is modeled by a random Gaussian velocity field with zero mean and correlation function 〈υjυi 〉 ∼ (Pji⊥ + αPji∥) /k d + ζ. Depending on the relations between the parameters ζ, α and the space dimensionality d, the model reveals several types of scaling regimes. Some of them are well known (model A of equilibrium critical dynamics and linear passive scalar field advected by a random turbulent flow), but there is a new nonequilibrium regime (universality class) associated with new nontrivial fixed points of the renormalization group equations. We have obtained the phase diagram (d, ζ) of possible scaling regimes in the system. The physical point d = 3, ζ = 4 / 3 corresponding to three-dimensional fully developed Kolmogorov's turbulence, where critical fluctuations are irrelevant, is stable for α ≲ 2.26. Otherwise, in the case of "strong compressibility" α ≳ 2.26, the critical fluctuations of the order parameter become relevant for three-dimensional turbulence. Estimations of critical exponents for each scaling regime are presented.

Automated Recovery of Three-Dimensional Models of Plant Shoots from Multiple Color Images1[C][W][OPEN

PubMed Central

Pound, Michael P.; French, Andrew P.; Murchie, Erik H.; Pridmore, Tony P.

2014-01-01

Increased adoption of the systems approach to biological research has focused attention on the use of quantitative models of biological objects. This includes a need for realistic three-dimensional (3D) representations of plant shoots for quantification and modeling. Previous limitations in single-view or multiple-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present a fully automatic approach to image-based 3D plant reconstruction that can be achieved using a single low-cost camera. The reconstructed plants are represented as a series of small planar sections that together model the more complex architecture of the leaf surfaces. The boundary of each leaf patch is refined using the level-set method, optimizing the model based on image information, curvature constraints, and the position of neighboring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed and, as such, is applicable to a wide variety of plant species and topologies and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on data sets of wheat (Triticum aestivum) and rice (Oryza sativa) plants as well as a unique virtual data set that allows us to compute quantitative measures of reconstruction accuracy. The output is a 3D mesh structure that is suitable for modeling applications in a format that can be imported in the majority of 3D graphics and software packages. PMID:25332504

Two-component dark-bright solitons in three-dimensional atomic Bose-Einstein condensates.

PubMed

Wang, Wenlong; Kevrekidis, P G

2017-03-01

In the present work, we revisit two-component Bose-Einstein condensates in their fully three-dimensional (3D) form. Motivated by earlier studies of dark-bright solitons in the 1D case, we explore the stability of these structures in their fully 3D form in two variants. In one the dark soliton is planar and trapping a planar bright (disk) soliton. In the other case, a dark spherical shell soliton creates an effective potential in which a bright spherical shell of atoms is trapped in the second component. We identify these solutions as numerically exact states (up to a prescribed accuracy) and perform a Bogolyubov-de Gennes linearization analysis that illustrates that both structures can be dynamically stable in suitable intervals of sufficiently low chemical potentials. We corroborate this finding theoretically by analyzing the stability via degenerate perturbation theory near the linear limit of the system. When the solitary waves are found to be unstable, we explore their dynamical evolution via direct numerical simulations which, in turn, reveal wave forms that are more robust. Finally, using the SO(2) symmetry of the model, we produce multi-dark-bright planar or shell solitons involved in pairwise oscillatory motion.

Automatic orientation and 3D modelling from markerless rock art imagery

NASA Astrophysics Data System (ADS)

Lerma, J. L.; Navarro, S.; Cabrelles, M.; Seguí, A. E.; Hernández, D.

2013-02-01

This paper investigates the use of two detectors and descriptors on image pyramids for automatic image orientation and generation of 3D models. The detectors and descriptors replace manual measurements and are used to detect, extract and match features across multiple imagery. The Scale-Invariant Feature Transform (SIFT) and the Speeded Up Robust Features (SURF) will be assessed based on speed, number of features, matched features, and precision in image and object space depending on the adopted hierarchical matching scheme. The influence of applying in addition Area Based Matching (ABM) with normalised cross-correlation (NCC) and least squares matching (LSM) is also investigated. The pipeline makes use of photogrammetric and computer vision algorithms aiming minimum interaction and maximum accuracy from a calibrated camera. Both the exterior orientation parameters and the 3D coordinates in object space are sequentially estimated combining relative orientation, single space resection and bundle adjustment. The fully automatic image-based pipeline presented herein to automate the image orientation step of a sequence of terrestrial markerless imagery is compared with manual bundle block adjustment and terrestrial laser scanning (TLS) which serves as ground truth. The benefits of applying ABM after FBM will be assessed both in image and object space for the 3D modelling of a complex rock art shelter.

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

Markidis, S.; Rizwan, U.

The use of virtual nuclear control room can be an effective and powerful tool for training personnel working in the nuclear power plants. Operators could experience and simulate the functioning of the plant, even in critical situations, without being in a real power plant or running any risk. 3D models can be exported to Virtual Reality formats and then displayed in the Virtual Reality environment providing an immersive 3D experience. However, two major limitations of this approach are that 3D models exhibit static textures, and they are not fully interactive and therefore cannot be used effectively in training personnel. Inmore » this paper we first describe a possible solution for embedding the output of a computer application in a 3D virtual scene, coupling real-world applications and VR systems. The VR system reported here grabs the output of an application running on an X server; creates a texture with the output and then displays it on a screen or a wall in the virtual reality environment. We then propose a simple model for providing interaction between the user in the VR system and the running simulator. This approach is based on the use of internet-based application that can be commanded by a laptop or tablet-pc added to the virtual environment. (authors)« less

Advances in the steady-state hybrid regime in DIII-D – a fully non-inductive, ELM-suppressed scenario for ITER

DOE PAGES

Petty, Craig C.; Nazikian, Raffi; Park, Jin Myung; ...

2017-07-19

Here, the hybrid regime with beta, collisionality, safety factor and plasma shape relevant to the ITER steady-state mission has been successfully integrated with ELM suppression by applying an odd parity n=3 resonant magnetic perturbation (RMP). Fully non-inductive hybrids in the DIII-D tokamak with high beta (β ≤ 2.8%) and high confinement (98y2 ≤ 1.4) in the ITER similar shape have achieved zero surface loop voltage for up to two current relaxation times using efficient central current drive from ECCD and NBCD. The n=3 RMP causes surprisingly little increase in thermal transport during ELM suppression. Poloidal magnetic flux pumping in hybridmore » plasmas maintains q above 1 without loss of current drive efficiency, except that experiments show that extremely peaked ECCD profiles can create sawteeth. During ECCD, Alfvén eigenmode (AE) activity is replaced by a more benign fishbone-like mode, reducing anomalous beam ion diffusion by a factor of 2. While the electron and ion thermal diffusivities substantially increase with higher ECCD power, the loss of confinement can be offset by the decreased fast ion transport resulting from AE suppression. Extrapolations from DIII-D along a dimensionless parameter scaling path as well as those using self-consistent theory-based modeling show that these ELM-suppressed, fully non-inductive hybrids can achieve the Q = 5 ITER steady-state mission.« less

a Semi-Automated Point Cloud Processing Methodology for 3d Cultural Heritage Documentation

NASA Astrophysics Data System (ADS)

Kıvılcım, C. Ö.; Duran, Z.

2016-06-01

The preliminary phase in any architectural heritage project is to obtain metric measurements and documentation of the building and its individual elements. On the other hand, conventional measurement techniques require tremendous resources and lengthy project completion times for architectural surveys and 3D model production. Over the past two decades, the widespread use of laser scanning and digital photogrammetry have significantly altered the heritage documentation process. Furthermore, advances in these technologies have enabled robust data collection and reduced user workload for generating various levels of products, from single buildings to expansive cityscapes. More recently, the use of procedural modelling methods and BIM relevant applications for historic building documentation purposes has become an active area of research, however fully automated systems in cultural heritage documentation still remains open. In this paper, we present a semi-automated methodology, for 3D façade modelling of cultural heritage assets based on parametric and procedural modelling techniques and using airborne and terrestrial laser scanning data. We present the contribution of our methodology, which we implemented in an open source software environment using the example project of a 16th century early classical era Ottoman structure, Sinan the Architect's Şehzade Mosque in Istanbul, Turkey.

On the explicit versus family solution of the fully diurnal photochemical equations of the stratosphere

NASA Technical Reports Server (NTRS)

Austin, John

1991-01-01

The family approach used to solve chemical equations is examined by integrating a heirarchy of versions of a 2D model of stratospheric chemistry and transport on an isentropic surface. Errors of up to 20 percent in radical concentrations can result from the use of a small number of families; the use of more families increases the accuracy of the solutions. The minimum number of families which can be used to provide an accurate solution is discussed, and the parameterization of long-time-scale species is recommended for making the model more efficient. The most pervasive errors are found in calculations of the concentrations of radical species, a problem which can lead to errors in predicting O3 over the long run. Methods for improving the schemes are presented, emphasizing the possibility of producing an improved 3D model.

Modeling The Shock Initiation of PBX-9501 in ALE3D

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

Leininger, L; Springer, H K; Mace, J

The SMIS (Specific Munitions Impact Scenario) experimental series performed at Los Alamos National Laboratory has determined the 3-dimensional shock initiation behavior of the HMX-based heterogeneous high explosive, PBX 9501. A series of finite element impact calculations have been performed in the ALE3D [1] hydrodynamic code and compared to the SMIS results to validate the code predictions. The SMIS tests use a powder gun to shoot scaled NATO standard fragments at a cylinder of PBX 9501, which has a PMMA case and a steel impact cover. The SMIS real-world shot scenario creates a unique test-bed because many of the fragments arrivemore » at the impact plate off-center and at an angle of impact. The goal of this model validation experiments is to demonstrate the predictive capability of the Tarver-Lee Ignition and Growth (I&G) reactive flow model [2] in this fully 3-dimensional regime of Shock to Detonation Transition (SDT). The 3-dimensional Arbitrary Lagrange Eulerian hydrodynamic model in ALE3D applies the Ignition and Growth (I&G) reactive flow model with PBX 9501 parameters derived from historical 1-dimensional experimental data. The model includes the off-center and angle of impact variations seen in the experiments. Qualitatively, the ALE3D I&G calculations accurately reproduce the 'Go/No-Go' threshold of the Shock to Detonation Transition (SDT) reaction in the explosive, as well as the case expansion recorded by a high-speed optical camera. Quantitatively, the calculations show good agreement with the shock time of arrival at internal and external diagnostic pins. This exercise demonstrates the utility of the Ignition and Growth model applied in a predictive fashion for the response of heterogeneous high explosives in the SDT regime.« less

Hydrostratigraphic and structural controls on streamflow generation in the Chuska Mountains, Navajo Nation, AZ/NM

NASA Astrophysics Data System (ADS)

Tsinnajinnie, L.; Frisbee, M. D.; Wilson, J. L.

2017-12-01

A conceptual model of hydrostratigraphic and structural influences on 3D streamflow generation processes is tested in the Whiskey Creek watershed located in the Chuska Mountains of the Navajo Nation along the northern NM/AZ border. The role of hydrostratigraphy and structure in groundwater processes has been well studied. However, influences of heterogeneity due to geologic structure and stratigraphy of mountain blocks on 3D streamflow generation has received less attention. Three-dimensional flow in mountainous watersheds, such as Saguache Creek (CO) and Rio Hondo (NM), contributes significant amounts of groundwater from deep circulation to streamflow. This fully 3D conceptual model is fundamentally different than watersheds characterized as 2D, those dominated by surface and shallow subsurface runoff, because 3D watersheds can have much longer flowpaths and mean residence times (up to 1000s of years). In contrast to Saguache Creek (volcanic bedrock) and Rio Hondo (crystalline metamorphic), the bedrock geology of the watersheds draining the Chuska Mountains is primarily comprised of sedimentary bedrock capped by extrusive volcanics. We test this conceptual model using a combination of stream gauging, tritium analyses, and endmember mixing analysis (EMMA) on the general ion chemistry and stable isotope composition of water samples collected in 2013-2016. Springs that emerge from the Chuska Sandstone are tritium dead indicative of a large component of pre-bomb pulse water in discharge and deeper 3D flow. EMMA indicates that most streamflow is generated from groundwater emerging from the Chuska Sandstone. Gaining/losing conditions in Whiskey Creek are strongly related to hydrostratigraphy as evidenced by a transition from gaining conditions largely found in the Chuska Sandstone to losing conditions where the underlying Chinle Formation outcrops. Although tritium in Whiskey Creek suggests 3D interactions are present, hydrostratigraphic and structural controls may limit the occurrence of longer residence times and longer flow paths. Mountainous watersheds similar to the 3D hydrostratigraphic and structurally controlled models will exhibit different responses to perturbations, such as climate change, than watersheds that fit existing 2D and 3D conceptual models.

Implementation of Flow Tripping Capability in the USM3D Unstructured Flow Solver

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Abdol-Harrid, Khaled S.; Campbell, Richard L.; Frink, Neal T.

2006-01-01

A flow tripping capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. The capability is based on prescribing an appropriate profile of turbulence model variables to energize the boundary layer in a plane normal to a specified trip region on the body surface. We demonstrate this approach using the k-e two-equation turbulence model of USM3D. Modification to the solution procedure primarily consists of developing a data structure to identify all unstructured tetrahedral grid cells located in the plane normal to a specified surface trip region and computing a function based on the mean flow solution to specify the modified profile of the turbulence model variables. We leverage this data structure and also show an adjunct approach that is based on enforcing a laminar flow condition on the otherwise fully turbulent flow solution in user specified region. The latter approach is applied for the solutions obtained using other one- and two-equation turbulence models of USM3D. A key ingredient of the present capability is the use of a graphical user-interface tool PREDISC to define a trip region on the body surface in an existing grid. Verification of the present modifications is demonstrated on three cases, namely, a flat plate, the RAE2822 airfoil, and the DLR F6 wing-fuselage configuration.

Implementation of Flow Tripping Capability in the USM3D Unstructured Flow Solver

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Abdol-Hamid, Khaled S.; Campbell, Richard L.; Frink, Neal T.

2006-01-01

A flow tripping capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. The capability is based on prescribing an appropriate profile of turbulence model variables to energize the boundary layer in a plane normal to a specified trip region on the body surface. We demonstrate this approach using the k-epsilon two-equation turbulence model of USM3D. Modification to the solution procedure primarily consists of developing a data structure to identify all unstructured tetrahedral grid cells located in the plane normal to a specified surface trip region and computing a function based on the mean flow solution to specify the modified profile of the turbulence model variables. We leverage this data structure and also show an adjunct approach that is based on enforcing a laminar flow condition on the otherwise fully turbulent flow solution in user-specified region. The latter approach is applied for the solutions obtained using other one-and two-equation turbulence models of USM3D. A key ingredient of the present capability is the use of a graphical user-interface tool PREDISC to define a trip region on the body surface in an existing grid. Verification of the present modifications is demonstrated on three cases, namely, a flat plate, the RAE2822 airfoil, and the DLR F6 wing-fuselage configuration.

Influence of aerosols, clouds, and sunglint on polarization spectra of Earthshine

NASA Astrophysics Data System (ADS)

Emde, Claudia; Buras-Schnell, Robert; Sterzik, Michael; Bagnulo, Stefano

2017-08-01

Context. Ground-based observations of the Earthshine, I.e., the light scattered by Earth to the Moon, and then reflected back to Earth, simulate space observations of our planet and represent a powerful benchmark for the studies of Earth-like planets. Earthshine spectra are strongly linearly polarized, owing to scattering by molecules and small particles in the atmosphere of the Earth and surface reflection, and may allow us to measure global atmospheric and surface properties of planet Earth. Aims: We aim to interpret already published spectropolarimetric observations of the Earthshine by comparing them with new radiative transfer model simulations including a fully realistic three-dimensional (3D) surface-atmosphere model for planet Earth. Methods: We used the highly advanced Monte Carlo radiative transfer model MYSTIC to simulate polarized radiative transfer in the atmosphere of the Earth without approximations regarding the geometry, taking into account the polarization from surface reflection and multiple scattering by molecules, aerosol particles, cloud droplets, and ice crystals. Results: We have shown that Earth spectropolarimetry is highly sensitive to all these input parameters, and we have presented simulations of a fully realistic Earth atmosphere-surface model including 3D cloud fields and two-dimensional (2D) surface property maps. Our modeling results show that scattering in high ice water clouds and reflection from the ocean surface are crucial to explain the continuum polarization at longer wavelengths as has been reported in Earthshine observations taken at the Very Large Telescope in 2011 (3.8% and 6.6% at 800 nm, depending on which part of Earth was visible from the Moon at the time of the observations). We found that the relatively high degree of polarization of 6.6% can be attributed to light reflected by the ocean surface in the sunglint region. High ice-water clouds reduce the amount of absorption in the O2A band and thus explain the weak O2A band feature in the observations.

Use of micro computed-tomography and 3D printing for reverse engineering of mouse embryo nasal capsule

NASA Astrophysics Data System (ADS)

Tesařová, M.; Zikmund, T.; Kaucká, M.; Adameyko, I.; Jaroš, J.; Paloušek, D.; Škaroupka, D.; Kaiser, J.

2016-03-01

Imaging of increasingly complex cartilage in vertebrate embryos is one of the key tasks of developmental biology. This is especially important to study shape-organizing processes during initial skeletal formation and growth. Advanced imaging techniques that are reflecting biological needs give a powerful impulse to push the boundaries of biological visualization. Recently, techniques for contrasting tissues and organs have improved considerably, extending traditional 2D imaging approaches to 3D . X-ray micro computed tomography (μCT), which allows 3D imaging of biological objects including their internal structures with a resolution in the micrometer range, in combination with contrasting techniques seems to be the most suitable approach for non-destructive imaging of embryonic developing cartilage. Despite there are many software-based ways for visualization of 3D data sets, having a real solid model of the studied object might give novel opportunities to fully understand the shape-organizing processes in the developing body. In this feasibility study we demonstrated the full procedure of creating a real 3D object of mouse embryo nasal capsule, i.e. the staining, the μCT scanning combined by the advanced data processing and the 3D printing.

Generating 3D and 3D-like animations of strongly uneven surface microareas of bloodstains from small series of partially out-of-focus digital SEM micrographs.

PubMed

Hortolà, Policarp

2010-01-01

When dealing with microscopic still images of some kinds of samples, the out-of-focus problem represents a particularly serious limiting factor for the subsequent generation of fully sharp 3D animations. In order to produce fully-focused 3D animations of strongly uneven surface microareas, a vertical stack of six digital secondary-electron SEM micrographs of a human bloodstain microarea was acquired. Afterwards, single combined images were generated using a macrophotography and light microscope image post-processing software. Subsequently, 3D animations of texture and topography were obtained in different formats using a combination of software tools. Finally, a 3D-like animation of a texture-topography composite was obtained in different formats using another combination of software tools. By one hand, results indicate that the use of image post-processing software not concerned primarily with electron micrographs allows to obtain, in an easy way, fully-focused images of strongly uneven surface microareas of bloodstains from small series of partially out-of-focus digital SEM micrographs. On the other hand, results also indicate that such small series of electron micrographs can be utilized for generating 3D and 3D-like animations that can subsequently be converted into different formats, by using certain user-friendly software facilities not originally designed for use in SEM, that are easily available from Internet. Although the focus of this study was on bloodstains, the methods used in it well probably are also of relevance for studying the surface microstructures of other organic or inorganic materials whose sharp displaying is difficult of obtaining from a single SEM micrograph.

UFCN: a fully convolutional neural network for road extraction in RGB imagery acquired by remote sensing from an unmanned aerial vehicle

NASA Astrophysics Data System (ADS)

Kestur, Ramesh; Farooq, Shariq; Abdal, Rameen; Mehraj, Emad; Narasipura, Omkar; Mudigere, Meenavathi

2018-01-01

Road extraction in imagery acquired by low altitude remote sensing (LARS) carried out using an unmanned aerial vehicle (UAV) is presented. LARS is carried out using a fixed wing UAV with a high spatial resolution vision spectrum (RGB) camera as the payload. Deep learning techniques, particularly fully convolutional network (FCN), are adopted to extract roads by dense semantic segmentation. The proposed model, UFCN (U-shaped FCN) is an FCN architecture, which is comprised of a stack of convolutions followed by corresponding stack of mirrored deconvolutions with the usage of skip connections in between for preserving the local information. The limited dataset (76 images and their ground truths) is subjected to real-time data augmentation during training phase to increase the size effectively. Classification performance is evaluated using precision, recall, accuracy, F1 score, and brier score parameters. The performance is compared with support vector machine (SVM) classifier, a one-dimensional convolutional neural network (1D-CNN) model, and a standard two-dimensional CNN (2D-CNN). The UFCN model outperforms the SVM, 1D-CNN, and 2D-CNN models across all the performance parameters. Further, the prediction time of the proposed UFCN model is comparable with SVM, 1D-CNN, and 2D-CNN models.

Structured Finite Volume Modeling of U.S. Navy Aircraft Engine Test Cells Task 2: Turboprop Engine Vol 1

DTIC Science & Technology

1993-06-01

propeller was modeled using an actuator disk model, where in all of the net results of the propeller (wash, swirl, turbulence) are modeled as source...8217)DUCTI* ~ hVAILJZL TV D0*C) ME.UUT FULLY’ LEGIBLE FREPROI)UCTIM 𔃾S \\JiA~v~r (r7, CL w4 bj4 APPENDIX B COPY AVAUAEL TO e MonC DO* IOT flR=1 VULL...dynamics HVAC systems, energy loss measurement, power ARMY FlAP generation) BDG Shore Faciltes 3B Controls and electrical conservation (electrical systems

A 3.2-GHz fully integrated low-phase noise CMOS VCO with self-biasing current source for the IEEE 802.11a/hiperLAN WLAN standard

NASA Astrophysics Data System (ADS)

Quemada, C.; Adin, I.; Bistue, G.; Berenguer, R.; Mendizabal, J.

2005-06-01

A 3.3V, fully integrated 3.2-GHz voltage-controlled oscillator (VCO) is designed in a 0.18μm CMOS technology for the IEE 802.11a/HiperLAN WLAN standard for the UNII band from 5.15 to 5.35 GHz. The VCO is tunable between 2.85 GHz and 3.31 GHz. NMOS architecture with self-biasing current of the tank source is chosen. A startup circuit has been employed to avoid zero initial current. Current variation is lower than 1% for voltage supply variations of 10%. The use of a self-biasing current source in the tank provides a greater safety in the transconductance value and allows running along more extreme point operation The designed VCO displays a phase noise and output power of -98dBc/Hz (at 100 KHz offset frequency) and 0dBm respectively. This phase noise has been obtained with inductors of 2.2nH and quality factor of 12 at 3.2 GHz, and P-N junction varactors whose quality factor is estimated to exceed 40 at 3.2 GHz. These passive components have been fabricated, measured and modeled previously. The core of the VCO consumes 33mW DC power.

2-D inversion of VES data in Saqqara archaeological area, Egypt

NASA Astrophysics Data System (ADS)

El-Qady, Gad; Sakamoto, Chika; Ushijima, Keisuke

1999-10-01

The interpretation of actual geophysical field data still has a problem for obtaining a unique solution. In order to investigate the groundwater potentials in Saqqara archaeological area, vertical electrical soundings with Schlumberger array have been carried out. In the interpretation of VES data, 1D resistivity inversion has been performed based on a horizontally layered earth model by El-Qady (1995). However, some results of 1D inversion are not fully satisfied for actual 3D structures such as archaeological tombs. Therefore, we have carried out 2D inversion based on ABIC least squares method for Schlumberger VES data obtained in Saqqara area. Although the results of 2D cross sections were correlated with the previous interpretation, the 2D inversion still shows a rough spatial resistivity distribution, which is the abrupt change in resistivity between two neighboring blocks of the computed region. It is concluded that 3D interpretation is recommended for visualizing ground water distribution with depth in the Saqqara area.

Finite-element 3D simulation tools for high-current relativistic electron beams

NASA Astrophysics Data System (ADS)

Humphries, Stanley; Ekdahl, Carl

2002-08-01

The DARHT second-axis injector is a challenge for computer simulations. Electrons are subject to strong beam-generated forces. The fields are fully three-dimensional and accurate calculations at surfaces are critical. We describe methods applied in OmniTrak, a 3D finite-element code suite that can address DARHT and the full range of charged-particle devices. The system handles mesh generation, electrostatics, magnetostatics and self-consistent particle orbits. The MetaMesh program generates meshes of conformal hexahedrons to fit any user geometry. The code has the unique ability to create structured conformal meshes with cubic logic. Organized meshes offer advantages in speed and memory utilization in the orbit and field solutions. OmniTrak is a versatile charged-particle code that handles 3D electric and magnetic field solutions on independent meshes. The program can update both 3D field solutions from the calculated beam space-charge and current-density. We shall describe numerical methods for orbit tracking on a hexahedron mesh. Topics include: 1) identification of elements along the particle trajectory, 2) fast searches and adaptive field calculations, 3) interpolation methods to terminate orbits on material surfaces, 4) automatic particle generation on multiple emission surfaces to model space-charge-limited emission and field emission, 5) flexible Child law algorithms, 6) implementation of the dual potential model for 3D magnetostatics, and 7) assignment of charge and current from model particle orbits for self-consistent fields.

Fully Closed-Loop Multiple Model Probabilistic Predictive Controller Artificial Pancreas Performance in Adolescents and Adults in a Supervised Hotel Setting.

PubMed

Forlenza, Gregory P; Cameron, Faye M; Ly, Trang T; Lam, David; Howsmon, Daniel P; Baysal, Nihat; Kulina, Georgia; Messer, Laurel; Clinton, Paula; Levister, Camilla; Patek, Stephen D; Levy, Carol J; Wadwa, R Paul; Maahs, David M; Bequette, B Wayne; Buckingham, Bruce A

2018-05-01

Initial Food and Drug Administration-approved artificial pancreas (AP) systems will be hybrid closed-loop systems that require prandial meal announcements and will not eliminate the burden of premeal insulin dosing. Multiple model probabilistic predictive control (MMPPC) is a fully closed-loop system that uses probabilistic estimation of meals to allow for automated meal detection. In this study, we describe the safety and performance of the MMPPC system with announced and unannounced meals in a supervised hotel setting. The Android phone-based AP system with remote monitoring was tested for 72 h in six adults and four adolescents across three clinical sites with daily exercise and meal challenges involving both three announced (manual bolus by patient) and six unannounced (no bolus by patient) meals. Safety criteria were predefined. Controller aggressiveness was adapted daily based on prior hypoglycemic events. Mean 24-h continuous glucose monitor (CGM) was 157.4 ± 14.4 mg/dL, with 63.6 ± 9.2% of readings between 70 and 180 mg/dL, 2.9 ± 2.3% of readings <70 mg/dL, and 9.0 ± 3.9% of readings >250 mg/dL. Moderate hyperglycemia was relatively common with 24.6 ± 6.2% of readings between 180 and 250 mg/dL, primarily within 3 h after a meal. Overnight mean CGM was 139.6 ± 27.6 mg/dL, with 77.9 ± 16.4% between 70 and 180 mg/dL, 3.0 ± 4.5% <70 mg/dL, 17.1 ± 14.9% between 180 and 250 mg/dL, and 2.0 ± 4.5%> 250 mg/dL. Postprandial hyperglycemia was more common for unannounced meals compared with announced meals (4-h postmeal CGM 197.8 ± 44.1 vs. 140.6 ± 35.0 mg/dL; P < 0.001). No participants met safety stopping criteria. MMPPC was safe in a supervised setting despite meal and exercise challenges. Further studies are needed in a less supervised environment.

Methodology of modeling and measuring computer architectures for plasma simulations

NASA Technical Reports Server (NTRS)

Wang, L. P. T.

1977-01-01

A brief introduction to plasma simulation using computers and the difficulties on currently available computers is given. Through the use of an analyzing and measuring methodology - SARA, the control flow and data flow of a particle simulation model REM2-1/2D are exemplified. After recursive refinements the total execution time may be greatly shortened and a fully parallel data flow can be obtained. From this data flow, a matched computer architecture or organization could be configured to achieve the computation bound of an application problem. A sequential type simulation model, an array/pipeline type simulation model, and a fully parallel simulation model of a code REM2-1/2D are proposed and analyzed. This methodology can be applied to other application problems which have implicitly parallel nature.

A Semi-Automatic Image-Based Close Range 3D Modeling Pipeline Using a Multi-Camera Configuration

PubMed Central

Rau, Jiann-Yeou; Yeh, Po-Chia

2012-01-01

The generation of photo-realistic 3D models is an important task for digital recording of cultural heritage objects. This study proposes an image-based 3D modeling pipeline which takes advantage of a multi-camera configuration and multi-image matching technique that does not require any markers on or around the object. Multiple digital single lens reflex (DSLR) cameras are adopted and fixed with invariant relative orientations. Instead of photo-triangulation after image acquisition, calibration is performed to estimate the exterior orientation parameters of the multi-camera configuration which can be processed fully automatically using coded targets. The calibrated orientation parameters of all cameras are applied to images taken using the same camera configuration. This means that when performing multi-image matching for surface point cloud generation, the orientation parameters will remain the same as the calibrated results, even when the target has changed. Base on this invariant character, the whole 3D modeling pipeline can be performed completely automatically, once the whole system has been calibrated and the software was seamlessly integrated. Several experiments were conducted to prove the feasibility of the proposed system. Images observed include that of a human being, eight Buddhist statues, and a stone sculpture. The results for the stone sculpture, obtained with several multi-camera configurations were compared with a reference model acquired by an ATOS-I 2M active scanner. The best result has an absolute accuracy of 0.26 mm and a relative accuracy of 1:17,333. It demonstrates the feasibility of the proposed low-cost image-based 3D modeling pipeline and its applicability to a large quantity of antiques stored in a museum. PMID:23112656

A semi-automatic image-based close range 3D modeling pipeline using a multi-camera configuration.

PubMed

Rau, Jiann-Yeou; Yeh, Po-Chia

2012-01-01

The generation of photo-realistic 3D models is an important task for digital recording of cultural heritage objects. This study proposes an image-based 3D modeling pipeline which takes advantage of a multi-camera configuration and multi-image matching technique that does not require any markers on or around the object. Multiple digital single lens reflex (DSLR) cameras are adopted and fixed with invariant relative orientations. Instead of photo-triangulation after image acquisition, calibration is performed to estimate the exterior orientation parameters of the multi-camera configuration which can be processed fully automatically using coded targets. The calibrated orientation parameters of all cameras are applied to images taken using the same camera configuration. This means that when performing multi-image matching for surface point cloud generation, the orientation parameters will remain the same as the calibrated results, even when the target has changed. Base on this invariant character, the whole 3D modeling pipeline can be performed completely automatically, once the whole system has been calibrated and the software was seamlessly integrated. Several experiments were conducted to prove the feasibility of the proposed system. Images observed include that of a human being, eight Buddhist statues, and a stone sculpture. The results for the stone sculpture, obtained with several multi-camera configurations were compared with a reference model acquired by an ATOS-I 2M active scanner. The best result has an absolute accuracy of 0.26 mm and a relative accuracy of 1:17,333. It demonstrates the feasibility of the proposed low-cost image-based 3D modeling pipeline and its applicability to a large quantity of antiques stored in a museum.

A 2D-3D strategy for resolving tsunami-generated debris flow in urban environments

NASA Astrophysics Data System (ADS)

Birjukovs Canelas, Ricardo; Conde, Daniel; Garcia-Feal, Orlando; João Telhado, Maria; Ferreira, Rui M. L.

2017-04-01

The incorporation of solids, either sediment from the natural environment or remains from buildings or infrastructures is a relevant feature of tsunami run-up in urban environments, greatly increasing the destructive potential of tsunami propagation. Two-dimensional (2D) models have been used to assess the propagation of the bore, even in dense urban fronts. Computational advances are introduced in this work, namely a fully lagrangian, 3D description of the fluid-solid flow, coupled with a high performance meshless implementation capable of dealing with large domains and fine discretizations. A Smoothed Particle Hydrodynamics (SPH) Navier-Stokes discretization and a Distributed Contact Discrete Element Method (DCDEM) description of solid-solid interactions provide a state-of the-art fluid-solid flow description. Together with support for arbitrary geometries, centimetre scale resolution simulations of a city section in Lisbon downtown are presented. 2D results are used as boundary conditions for the 3D model, characterizing the incoming wave as it approaches the coast. It is shown that the incoming bore is able to mobilize and incorporate standing vehicles and other urban hardware. Such fully featured simulation provides explicit description of the interactions among fluid, floating debris (vehicles and urban furniture), the buildings and the pavement. The proposed model presents both an innovative research tool for the study of these flows and a powerful and robust approach to study, design and test mitigation solutions at the local scale. At the same time, due to the high time and space resolution of these methodologies, new questions are raised: scenario-building and initial configurations play a crucial role but they do not univocally determine the final configuration of the simulation, as the solution of the Navier-Stokes equations for high Reynolds numbers possesses a high number of degrees of freedom. This calls for conducting the simulations in a statistical framework, involving both initial conditions generation and interpretation of results, which is only attainable under very high standards of computational efficiency. This research as partially supported by Portuguese and European funds, within programs COMPETE2020 and PORL-FEDER, through project PTDC/ECM-HID/6387/2014 granted by the National Foundation for Science and Technology (FCT).

Assessment of critical path analyses of the relationship between permeability and electrical conductivity of pore networks

NASA Astrophysics Data System (ADS)

Skaggs, Todd H.

2011-10-01

Critical path analysis (CPA) is a method for estimating macroscopic transport coefficients of heterogeneous materials that are highly disordered at the micro-scale. Developed originally to model conduction in semiconductors, numerous researchers have noted that CPA might also have relevance to flow and transport processes in porous media. However, the results of several numerical investigations of critical path analysis on pore network models raise questions about the applicability of CPA to porous media. Among other things, these studies found that (i) in well-connected 3D networks, CPA predictions were inaccurate and became worse when heterogeneity was increased; and (ii) CPA could not fully explain the transport properties of 2D networks. To better understand the applicability of CPA to porous media, we made numerical computations of permeability and electrical conductivity on 2D and 3D networks with differing pore-size distributions and geometries. A new CPA model for the relationship between the permeability and electrical conductivity was found to be in good agreement with numerical data, and to be a significant improvement over a classical CPA model. In sufficiently disordered 3D networks, the new CPA prediction was within ±20% of the true value, and was nearly optimal in terms of minimizing the squared prediction errors across differing network configurations. The agreement of CPA predictions with 2D network computations was similarly good, although 2D networks are in general not well-suited for evaluating CPA. Numerical transport coefficients derived for regular 3D networks of slit-shaped pores were found to be in better agreement with experimental data from rock samples than were coefficients derived for networks of cylindrical pores.

A model for helicopter guidance on spiral trajectories

NASA Technical Reports Server (NTRS)

Mendenhall, S.; Slater, G. L.

1980-01-01

A point mass model is developed for helicopter guidance on spiral trajectories. A fully coupled set of state equations is developed and perturbation equations suitable for 3-D and 4-D guidance are derived and shown to be amenable to conventional state variable feedback methods. Control variables are chosen to be the magnitude and orientation of the net rotor thrust. Using these variables reference controls for nonlevel accelerating trajectories are easily determined. The effects of constant wind are shown to require significant feedforward correction to some of the reference controls and to the time. Although not easily measured themselves, the controls variables chosen are shown to be easily related to the physical variables available in the cockpit.

Assessment of predictive capabilities for aerodynamic heating in hypersonic flow

NASA Astrophysics Data System (ADS)

Knight, Doyle; Chazot, Olivier; Austin, Joanna; Badr, Mohammad Ali; Candler, Graham; Celik, Bayram; Rosa, Donato de; Donelli, Raffaele; Komives, Jeffrey; Lani, Andrea; Levin, Deborah; Nompelis, Ioannis; Panesi, Marco; Pezzella, Giuseppe; Reimann, Bodo; Tumuklu, Ozgur; Yuceil, Kemal

2017-04-01

The capability for CFD prediction of hypersonic shock wave laminar boundary layer interaction was assessed for a double wedge model at Mach 7.1 in air and nitrogen at 2.1 MJ/kg and 8 MJ/kg. Simulations were performed by seven research organizations encompassing both Navier-Stokes and Direct Simulation Monte Carlo (DSMC) methods as part of the NATO STO AVT Task Group 205 activity. Comparison of the CFD simulations with experimental heat transfer and schlieren visualization suggest the need for accurate modeling of the tunnel startup process in short-duration hypersonic test facilities, and the importance of fully 3-D simulations of nominally 2-D (i.e., non-axisymmmetric) experimental geometries.

Impact of two chemistry mechanisms fully coupled with mesoscale model on the atmospheric pollutants distribution

NASA Astrophysics Data System (ADS)

Arteta, J.; Cautenet, S.; Taghavi, M.; Audiffren, N.

Air quality models (AQM) consist of many modules (meteorology, emission, chemistry, deposition), and in some conditions such as: vicinity of clouds or aerosols plumes, complex local circulations (mountains, sea breezes), fully coupled models (online method) are necessary. In order to study the impact of lumped chemical mechanisms in AQM simulations, we examine the ability of both different chemical mechanisms: (i) simplified: Condensed Version of the MOdèle de Chimie Atmosphérique 2.2 (CV-MOCA2.2), and (ii) reference: Regional Atmospheric Chemistry Model (RACM), which are coupled online with the Regional Atmospheric Modeling Systems (RAMS) model, on the distribution of pollutants. During the ESCOMPTE experiment (Expérience sur Site pour COntraindre les Modèles de Pollution et de Transport d'Emissions) conducted over Southern France (including urban and industrial zones), Intensive observation periods (IOP) characterized by various meteorological and mixed chemical conditions are simulated. For both configurations of modeling, numerical results are compared with surface measurements (75 stations) for primary (NO x) and secondary (O 3) species. We point out the impact of the two different chemical mechanisms on the production of species involved in the oxidizing capacity such as ozone and radicals within urban and industrial areas. We highlight that both chemical mechanisms produce very similar results for the main pollutants (NO x and O 3) in three-dimensional (3D) distribution, despite large discrepancies in 0D modeling. For ozone concentration, we found sometimes small differences (5-10 ppb) between the mechanisms under study according to the cases (polluted or not). The relative difference between the two mechanisms over the whole domain is only -7% for ozone from CV-MOCA 2.2 versus RACM. When the order of magnitude is needed rather than an accurate estimate, a reduced mechanism is satisfactory. It has the advantage of running faster (four times less than CPU time on SGI 3800 with 30 processors). Simplified mechanisms are really important to study cases for which an online coupling is necessary between meso-scale and chemistry models (clouds or aerosols plumes impacts, highly variable meteorology).

Virtual Vents: A Microbathymetrical Survey of the Niua South Hydrothermal Field, NE Lau Basin, Tonga

NASA Astrophysics Data System (ADS)

Kwasnitschka, T.; Köser, K.; Duda, A.; Jamieson, J. W.; Boschen, R.; Gartman, A.; Hannington, M. D.; Funganitao, C.

2016-12-01

At a diameter of 200 m, the 1100 m deep Niua South hydrothermal field (NE Lau Basin) was studied in an interdisciplinary approach during the SOI funded Virtual Vents cruise in March of 2016. On the grounds of a previously generated 50 cm resolution AUV multi beam map, the projects backbone is formed by a fully color textured, 5 cm resolution photogrammetrical 3D model. Several hundred smaller and about 15 chimneys larger than 3 m were surveyed including their basal mounds and surrounding environment interconnecting to each other. This model was populated through exhaustive geological, biological and fluid sampling as well as continuous Eh measurements, forming the basis for highly detailed geological structural and biological studies resulting in 3D maps of the entire field. At a reasonable effort, such surveys form the basis for repetitive time series analysis and have the potential of a new standard in seafloor monitoring.

Coupling Hydrodynamic and Wave Propagation Codes for Modeling of Seismic Waves recorded at the SPE Test.

NASA Astrophysics Data System (ADS)

Larmat, C. S.; Rougier, E.; Delorey, A.; Steedman, D. W.; Bradley, C. R.

2016-12-01

The goal of the Source Physics Experiment (SPE) is to bring empirical and theoretical advances to the problem of detection and identification of underground nuclear explosions. For this, the SPE program includes a strong modeling effort based on first principles calculations with the challenge to capture both the source and near-source processes and those taking place later in time as seismic waves propagate within complex 3D geologic environments. In this paper, we report on results of modeling that uses hydrodynamic simulation codes (Abaqus and CASH) coupled with a 3D full waveform propagation code, SPECFEM3D. For modeling the near source region, we employ a fully-coupled Euler-Lagrange (CEL) modeling capability with a new continuum-based visco-plastic fracture model for simulation of damage processes, called AZ_Frac. These capabilities produce high-fidelity models of various factors believed to be key in the generation of seismic waves: the explosion dynamics, a weak grout-filled borehole, the surrounding jointed rock, and damage creation and deformations happening around the source and the free surface. SPECFEM3D, based on the Spectral Element Method (SEM) is a direct numerical method for full wave modeling with mathematical accuracy. The coupling interface consists of a series of grid points of the SEM mesh situated inside of the hydrodynamic code's domain. Displacement time series at these points are computed using output data from CASH or Abaqus (by interpolation if needed) and fed into the time marching scheme of SPECFEM3D. We will present validation tests with the Sharpe's model and comparisons of waveforms modeled with Rg waves (2-8Hz) that were recorded up to 2 km for SPE. We especially show effects of the local topography, velocity structure and spallation. Our models predict smaller amplitudes of Rg waves for the first five SPE shots compared to pure elastic models such as Denny &Johnson (1991).

Comparison of full 3-D, thin-film 3-D, and thin-film plate analyses of a postbuckled embedded delamination

NASA Technical Reports Server (NTRS)

Whitcomb, John D.

1989-01-01

Strain-energy release rates are often used to predict when delamination growth will occur in laminates under compression. Because of the inherently high computational cost of performing such analyses, less rigorous analyses such as thin-film plate analysis were used. The assumptions imposed by plate theory restrict the analysis to the calculation of total strain energy, G(sub t). The objective is to determine the accuracy of thin-film plate analysis by comparing the distribution of G(sub t) calculated using fully three dimensional (3D), thin-film 3D, and thin-film plate analyses. Thin-film 3D analysis is the same as thin-film plate analysis, except 3D analysis is used to model the sublaminate. The 3D stress analyses were performed using the finite element program NONLIN3D. The plate analysis results were obtained from published data, which used STAGS. Strain-energy release rates were calculated using variations of the virtual crack closure technique. The results demonstrate that thin-film plate analysis can predict the distribution of G(sub t) quite well, at least for the configurations considered. Also, these results verify the accuracy of the strain-energy release rate procedure for plate analysis.

Emergence of 3D Printed Dosage Forms: Opportunities and Challenges.

PubMed

Alhnan, Mohamed A; Okwuosa, Tochukwu C; Sadia, Muzna; Wan, Ka-Wai; Ahmed, Waqar; Arafat, Basel

2016-08-01

The recent introduction of the first FDA approved 3D-printed drug has fuelled interest in 3D printing technology, which is set to revolutionize healthcare. Since its initial use, this rapid prototyping (RP) technology has evolved to such an extent that it is currently being used in a wide range of applications including in tissue engineering, dentistry, construction, automotive and aerospace. However, in the pharmaceutical industry this technology is still in its infancy and its potential yet to be fully explored. This paper presents various 3D printing technologies such as stereolithographic, powder based, selective laser sintering, fused deposition modelling and semi-solid extrusion 3D printing. It also provides a comprehensive review of previous attempts at using 3D printing technologies on the manufacturing dosage forms with a particular focus on oral tablets. Their advantages particularly with adaptability in the pharmaceutical field have been highlighted, which enables the preparation of dosage forms with complex designs and geometries, multiple actives and tailored release profiles. An insight into the technical challenges facing the different 3D printing technologies such as the formulation and processing parameters is provided. Light is also shed on the different regulatory challenges that need to be overcome for 3D printing to fulfil its real potential in the pharmaceutical industry.

In vitro activation of the neuro-transduction mechanism in sensitive organotypic human skin model.

PubMed

Martorina, Francesca; Casale, Costantino; Urciuolo, Francesco; Netti, Paolo A; Imparato, Giorgia

2017-01-01

Recent advances in tissue engineering have encouraged researchers to endeavor the production of fully functional three-dimensional (3D) thick human tissues in vitro. Here, we report the fabrication of a fully innervated human skin tissue in vitro that recapitulates and replicates skin sensory function. Previous attempts to innervate in vitro 3D skin models did not demonstrate an effective functionality of the nerve network. In our approach, we initially engineer functional human skin tissue based on fibroblast-generated dermis and differentiated epidermis; then, we promote rat dorsal root ganglion (DRG) neurons axon ingrowth in the de-novo developed tissue. Neurofilaments network infiltrates the entire native dermis extracellular matrix (ECM), as demonstrated by immunofluorescence and second harmonic generation (SHG) imaging. To prove sensing functionality of the tissue, we use topical applications of capsaicin, an agonist of transient receptor protein-vanilloid 1 (TRPV1) channel, and quantify calcium currents resulting from variations of Ca ++ concentration in DRG neurons innervating our model. Calcium currents generation demonstrates functional cross-talking between dermis and epidermis compartments. Moreover, through a computational fluid dynamic (CFD) analysis, we set fluid dynamic conditions for a non-planar skin equivalent growth, as proof of potential application in creating skin grafts tailored on-demand for in vivo wound shape. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mapping Land and Water Surface Topography with instantaneous Structure from Motion

NASA Astrophysics Data System (ADS)

Dietrich, J.; Fonstad, M. A.

2012-12-01

Structure from Motion (SfM) has given researchers an invaluable tool for low-cost, high-resolution 3D mapping of the environment. These SfM 3D surface models are commonly constructed from many digital photographs collected with one digital camera (either handheld or attached to aerial platform). This method works for stationary or very slow moving objects. However, objects in motion are impossible to capture with one-camera SfM. With multiple simultaneously triggered cameras, it becomes possible to capture multiple photographs at the same time which allows for the construction 3D surface models of moving objects and surfaces, an instantaneous SfM (ISfM) surface model. In river science, ISfM provides a low-cost solution for measuring a number of river variables that researchers normally estimate or are unable to collect over large areas. With ISfM and sufficient coverage of the banks and RTK-GPS control it is possible to create a digital surface model of land and water surface elevations across an entire channel and water surface slopes at any point within the surface model. By setting the cameras to collect time-lapse photography of a scene it is possible to create multiple surfaces that can be compared using traditional digital surface model differencing. These water surface models could be combined the high-resolution bathymetry to create fully 3D cross sections that could be useful in hydrologic modeling. Multiple temporal image sets could also be used in 2D or 3D particle image velocimetry to create 3D surface velocity maps of a channel. Other applications in earth science include anything where researchers could benefit from temporal surface modeling like mass movements, lava flows, dam removal monitoring. The camera system that was used for this research consisted of ten pocket digital cameras (Canon A3300) equipped with wireless triggers. The triggers were constructed with an Arduino-style microcontroller and off-the-shelf handheld radios with a maximum range of several kilometers. The cameras are controlled from another microcontroller/radio combination that allows for manual or automatic triggering of the cameras. The total cost of the camera system was approximately 1500 USD.

Two- and three-dimensional folding of thin film single-crystalline silicon for photovoltaic power applications

PubMed Central

Guo, Xiaoying; Li, Huan; Yeop Ahn, Bok; Duoss, Eric B.; Hsia, K. Jimmy; Lewis, Jennifer A.; Nuzzo, Ralph G.

2009-01-01

Fabrication of 3D electronic structures in the micrometer-to-millimeter range is extremely challenging due to the inherently 2D nature of most conventional wafer-based fabrication methods. Self-assembly, and the related method of self-folding of planar patterned membranes, provide a promising means to solve this problem. Here, we investigate self-assembly processes driven by wetting interactions to shape the contour of a functional, nonplanar photovoltaic (PV) device. A mechanics model based on the theory of thin plates is developed to identify the critical conditions for self-folding of different 2D geometrical shapes. This strategy is demonstrated for specifically designed millimeter-scale silicon objects, which are self-assembled into spherical, and other 3D shapes and integrated into fully functional light-trapping PV devices. The resulting 3D devices offer a promising way to efficiently harvest solar energy in thin cells using concentrator microarrays that function without active light tracking systems. PMID:19934059

Two- and three-dimensional folding of thin film single-crystalline silicon for photovoltaic power applications.

PubMed

Guo, Xiaoying; Li, Huan; Ahn, Bok Yeop; Duoss, Eric B; Hsia, K Jimmy; Lewis, Jennifer A; Nuzzo, Ralph G

2009-12-01

Fabrication of 3D electronic structures in the micrometer-to-millimeter range is extremely challenging due to the inherently 2D nature of most conventional wafer-based fabrication methods. Self-assembly, and the related method of self-folding of planar patterned membranes, provide a promising means to solve this problem. Here, we investigate self-assembly processes driven by wetting interactions to shape the contour of a functional, nonplanar photovoltaic (PV) device. A mechanics model based on the theory of thin plates is developed to identify the critical conditions for self-folding of different 2D geometrical shapes. This strategy is demonstrated for specifically designed millimeter-scale silicon objects, which are self-assembled into spherical, and other 3D shapes and integrated into fully functional light-trapping PV devices. The resulting 3D devices offer a promising way to efficiently harvest solar energy in thin cells using concentrator microarrays that function without active light tracking systems.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0043: Deformation and Texture Development During Hot Working of Titanium

DTIC Science & Technology

2008-04-01

Hot Working of Titanium 5a. CONTRACT NUMBER F33615-03-D-5801-0043 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61202F 6 . AUTHOR(S) A.A...micrographs and thus to correlate microstructural features and texture data [3- 6 ]. For instance, Germain, et al. [3, 4 ] linked local orientations...microstructures can be developed in alpha/beta titanium alloys by TMP [2- 4 ], namely, fully lamellar, fully equiaxed, and duplex (bi-modal). A mixture

Towards dense volumetric pancreas segmentation in CT using 3D fully convolutional networks

NASA Astrophysics Data System (ADS)

Roth, Holger; Oda, Masahiro; Shimizu, Natsuki; Oda, Hirohisa; Hayashi, Yuichiro; Kitasaka, Takayuki; Fujiwara, Michitaka; Misawa, Kazunari; Mori, Kensaku

2018-03-01

Pancreas segmentation in computed tomography imaging has been historically difficult for automated methods because of the large shape and size variations between patients. In this work, we describe a custom-build 3D fully convolutional network (FCN) that can process a 3D image including the whole pancreas and produce an automatic segmentation. We investigate two variations of the 3D FCN architecture; one with concatenation and one with summation skip connections to the decoder part of the network. We evaluate our methods on a dataset from a clinical trial with gastric cancer patients, including 147 contrast enhanced abdominal CT scans acquired in the portal venous phase. Using the summation architecture, we achieve an average Dice score of 89.7 +/- 3.8 (range [79.8, 94.8])% in testing, achieving the new state-of-the-art performance in pancreas segmentation on this dataset.

Intersymbol Interference Investigations Using a 3D Time-Dependent Traveling Wave Tube Model

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Andro, Monty; Downey, Alan (Technical Monitor)

2001-01-01

For the first time, a physics based computational model has been used to provide a direct description of the effects of the TWT (Traveling Wave Tube) on modulated digital signals. The TWT model comprehensively takes into account the effects of frequency dependent AM/AM and AM/PM conversion; gain and phase ripple; drive-induced oscillations; harmonic generation; intermodulation products; and backward waves. Thus, signal integrity can be investigated in the presence of these sources of potential distortion as a function of the physical geometry of the high power amplifier and the operational digital signal. This method promises superior predictive fidelity compared to methods using TWT models based on swept amplitude and/or swept frequency data. The fully three-dimensional (3D), time-dependent, TWT interaction model using the electromagnetic code MAFIA is presented. This model is used to investigate assumptions made in TWT black box models used in communication system level simulations. In addition, digital signal performance, including intersymbol interference (ISI), is compared using direct data input into the MAFIA model and using the system level analysis tool, SPW (Signal Processing Worksystem).

A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

NASA Astrophysics Data System (ADS)

Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

2017-04-01

3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

2.5D Modeling of TEM Data Applied to Hidrogeological Studies in PARANÁ Basin, Brazil

NASA Astrophysics Data System (ADS)

Bortolozo, C. A.; Porsani, J. L.; Santos, F. M.

2013-12-01

The transient electromagnetic method (TEM) is used all over the world and has shown great potential in hydrological, hazardous waste site characterization, mineral exploration, general geological mapping, and geophysical reconnaissance. However, the behavior of TEM fields are very complex and is not yet fully understood. Forward modeling is one of the most common and effective methods to understand the physical behavior and significance of the electromagnetics responses of a TEM sounding. Until now, there are a limited number of solutions for the 2D forward problem for TEM. More rare are the descriptions of a three-component response of a 3D source over 2D earth, which is the so-called 2.5D. The 2.5D approach is more realistic than the conventional 2D source previous used, once normally the source cannot be realistic represented for a 2D approximation (normally source are square loops). At present the 2.5D model represents the only way of interpreting TEM data in terms of a complex earth, due to the prohibitive amount of computer time and storage required for a full 3D model. In this work we developed a TEM modeling program for understanding the different responses and how the magnetic and electric fields, produced by loop sources at air-earth interface, behave in different geoelectrical distributions. The models used in the examples are proposed focusing hydrogeological studies, once the main objective of this work is for detecting different kinds of aquifers in Paraná sedimentary basin, in São Paulo State - Brazil. The program was developed in MATLAB, a widespread language very common in the scientific community.

Theoretical Bounds for the Influence of Tissue-Level Ductility on the Apparent-Level Strength of Human Trabecular Bone

PubMed Central

Nawathe, Shashank; Juillard, Frédéric; Keaveny, Tony M.

2015-01-01

The role of tissue-level post-yield behavior on the apparent-level strength of trabecular bone is a potentially important aspect of bone quality. To gain insight into this issue, we compared the apparent-level strength of trabecular bone for the hypothetical cases of fully brittle versus fully ductile failure behavior of the trabecular tissue. Twenty human cadaver trabecular bone specimens (5 mm cube; BV/TV = 6–36%) were scanned with micro-CT to create 3D finite element models (22-micron element size). For each model, apparent-level strength was computed assuming either fully brittle (fracture with no tissue ductility) or fully ductile (yield with no tissue fracture) tissue-level behaviors. We found that the apparent-level ultimate strength for the brittle behavior was only about half the value of the apparent-level 0.2%-offset yield strength for the ductile behavior, and the ratio of these brittle to ductile strengths was almost constant (mean ± SD = 0.56 ± 0.02; n=20; R2 = 0.99 between the two measures). As a result of this small variation, although the ratio of brittle to ductile strengths was positively correlated with the bone volume fraction (R2=0.44, p=0.01) and structure model index (SMI, R2=0.58, p<0.01), these effects were small. Mechanistically, the fully ductile behavior resulted in a much higher apparent-level strength because in this case about 16-fold more tissue was required to fail than for the fully brittle behavior; also, there was more tensile- than compressive-mode of failure at the tissue level for the fully brittle behavior. We conclude that, in theory, the apparent-level strength behavior of human trabecular bone can vary appreciably depending on whether the tissue fails in a fully ductile versus fully brittle manner, and this effect is largely constant despite appreciable variations in bone volume fraction and microarchitecture. PMID:23497799

Virtual hydrology observatory: an immersive visualization of hydrology modeling

NASA Astrophysics Data System (ADS)

Su, Simon; Cruz-Neira, Carolina; Habib, Emad; Gerndt, Andreas

2009-02-01

The Virtual Hydrology Observatory will provide students with the ability to observe the integrated hydrology simulation with an instructional interface by using a desktop based or immersive virtual reality setup. It is the goal of the virtual hydrology observatory application to facilitate the introduction of field experience and observational skills into hydrology courses through innovative virtual techniques that mimic activities during actual field visits. The simulation part of the application is developed from the integrated atmospheric forecast model: Weather Research and Forecasting (WRF), and the hydrology model: Gridded Surface/Subsurface Hydrologic Analysis (GSSHA). Both the output from WRF and GSSHA models are then used to generate the final visualization components of the Virtual Hydrology Observatory. The various visualization data processing techniques provided by VTK are 2D Delaunay triangulation and data optimization. Once all the visualization components are generated, they are integrated into the simulation data using VRFlowVis and VR Juggler software toolkit. VR Juggler is used primarily to provide the Virtual Hydrology Observatory application with fully immersive and real time 3D interaction experience; while VRFlowVis provides the integration framework for the hydrologic simulation data, graphical objects and user interaction. A six-sided CAVETM like system is used to run the Virtual Hydrology Observatory to provide the students with a fully immersive experience.

A tool for teaching three-dimensional dermatomes combined with distribution of cutaneous nerves on the limbs.

PubMed

Kooloos, Jan G M; Vorstenbosch, Marc A T M

2013-01-01

A teaching tool that facilitates student understanding of a three-dimensional (3D) integration of dermatomes with peripheral cutaneous nerve field distributions is described. This model is inspired by the confusion in novice learners between dermatome maps and nerve field distribution maps. This confusion leads to the misconception that these two distribution maps fully overlap, and may stem from three sources: (1) the differences in dermatome maps in anatomical textbooks, (2) the limited views in the figures of dermatome maps and cutaneous nerve field maps, hampering the acquisition of a 3D picture, and (3) the lack of figures showing both maps together. To clarify this concept, the learning process can be facilitated by transforming the 2D drawings in textbooks to a 3D hands-on model and by merging the information from the separate maps. Commercially available models were covered with white cotton pantyhose, and borders between dermatomes were marked using the drawings from the students' required study material. Distribution maps of selected peripheral nerves were cut out from color transparencies. Both the model and the cut-out nerve fields were then at the students' disposal during a laboratory exercise. The students were instructed to affix the transparencies in the right place according to the textbook's figures. This model facilitates integrating the spatial relationships of the two types of nerve distributions. By highlighting the spatial relationship and aiming to provoke student enthusiasm, this model follows the advantages of other low-fidelity models. © 2013 American Association of Anatomists.

3D printing for orthopedic applications: from high resolution cone beam CT images to life size physical models

NASA Astrophysics Data System (ADS)

Jackson, Amiee; Ray, Lawrence A.; Dangi, Shusil; Ben-Zikri, Yehuda K.; Linte, Cristian A.

2017-03-01

With increasing resolution in image acquisition, the project explores capabilities of printing toward faithfully reflecting detail and features depicted in medical images. To improve safety and efficiency of orthopedic surgery and spatial conceptualization in training and education, this project focused on generating virtual models of orthopedic anatomy from clinical quality computed tomography (CT) image datasets and manufacturing life-size physical models of the anatomy using 3D printing tools. Beginning with raw micro CT data, several image segmentation techniques including thresholding, edge recognition, and region-growing algorithms available in packages such as ITK-SNAP, MITK, or Mimics, were utilized to separate bone from surrounding soft tissue. After converting the resulting data to a standard 3D printing format, stereolithography (STL), the STL file was edited using Meshlab, Netfabb, and Meshmixer. The editing process was necessary to ensure a fully connected surface (no loose elements), positive volume with manifold geometry (geometry possible in the 3D physical world), and a single, closed shell. The resulting surface was then imported into a "slicing" software to scale and orient for printing on a Flashforge Creator Pro. In printing, relationships between orientation, print bed volume, model quality, material use and cost, and print time were considered. We generated anatomical models of the hand, elbow, knee, ankle, and foot from both low-dose high-resolution cone-beam CT images acquired using the soon to be released scanner developed by Carestream, as well as scaled models of the skeletal anatomy of the arm and leg, together with life-size models of the hand and foot.

The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Dobbs-Dixon, Ian; Greene, Thomas

2017-10-01

Using the atmospheric structure from a 3D global radiation-hydrodynamic simulation of HD 189733b and the open-source Bayesian Atmospheric Radiative Transfer (BART) code, we investigate the difference between the secondary-eclipse temperature structure produced with a 3D simulation and the best-fit 1D retrieved model. Synthetic data are generated by integrating the 3D models over the Spitzer, the Hubble Space Telescope (HST), and the James Web Space Telescope (JWST) bandpasses, covering the wavelength range between 1 and 11 μm where most spectroscopically active species have pronounced features. Using the data from different observing instruments, we present detailed comparisons between the temperature-pressure profiles recovered by BART and those from the 3D simulations. We calculate several averages of the 3D thermal structure and explore which particular thermal profile matches the retrieved temperature structure. We implement two temperature parameterizations that are commonly used in retrieval to investigate different thermal profile shapes. To assess which part of the thermal structure is best constrained by the data, we generate contribution functions for our theoretical model and each of our retrieved models. Our conclusions are strongly affected by the spectral resolution of the instruments included, their wavelength coverage, and the number of data points combined. We also see some limitations in each of the temperature parametrizations, as they are not able to fully match the complex curvatures that are usually produced in hydrodynamic simulations. The results show that our 1D retrieval is recovering a temperature and pressure profile that most closely matches the arithmetic average of the 3D thermal structure. When we use a higher resolution, more data points, and a parametrized temperature profile that allows more flexibility in the middle part of the atmosphere, we find a better match between the retrieved temperature and pressure profile and the arithmetic average. The Spitzer and HST simulated observations sample deep parts of the planetary atmosphere and provide fewer constraints on the temperature and pressure profile, while the JWST observations sample the middle part of the atmosphere, providing a good match with the middle and most complex part of the arithmetic average of the 3D temperature structure.

Investigation of non-thermal plasma effects on lung cancer cells within 3D collagen matrices

NASA Astrophysics Data System (ADS)

Karki, Surya B.; Thapa Gupta, Tripti; Yildirim-Ayan, Eda; Eisenmann, Kathryn M.; Ayan, Halim

2017-08-01

Recent breakthroughs in plasma medicine have identified a potential application for the non-thermal plasma in cancer therapy. Most studies on the effects of non-thermal plasma on cancer cells have used traditional two-dimensional (2D) monolayer cell culture. However, very few studies are conducted employing non-thermal plasma in animal models. Two dimensional models do not fully mimic the three-dimensional (3D) tumor microenvironment and animal models are expensive and time-consuming. Therefore, we used 3D collagen matrices that closely resemble the native geometry of cancer tissues and provide more physiologically relevant results than 2D models, while providing a more cost effective and efficient precursor to animal studies. We previously demonstrated a role for non-thermal plasma application in promoting apoptotic cell death and reducing the viability of A549 lung adenocarcinoma epithelial cells cultured upon 2D matrices. In this study, we wished to determine the efficacy of non-thermal plasma application in driving apoptotic cell death of A549 lung cancer cells encapsulated within a 3D collagen matrix. The percentage of apoptosis increased as treatment time increased and was time dependent. In addition, the anti-viability effect of plasma was demonstrated. Twenty-four hours post-plasma treatment, 38% and 99% of cell death occurred with shortest (15 s) and longest treatment time (120 s) respectively at the plasma-treated region. We found that plasma has a greater effect on the viability of A549 lung cancer cells on the superficial surface of 3D matrices and has diminishing effects as it penetrates the 3D matrix. We also identified the nitrogen and oxygen species generated by plasma and characterized their penetration in vertical and lateral directions within the 3D matrix from the center of the plasma-treated region. Therefore, the utility of non-thermal dielectric barrier discharge plasma in driving apoptosis and reducing the viability of lung cancer cells in 3D collagen matrix indicates a therapeutic potential that warrants further research.

Modeling the Hot Tensile Flow Behaviors at Ultra-High-Strength Steel and Construction of Three-Dimensional Continuous Interaction Space for Forming Parameters

NASA Astrophysics Data System (ADS)

Quan, Guo-zheng; Zhan, Zong-yang; Wang, Tong; Xia, Yu-feng

2017-01-01

The response of true stress to strain rate, temperature and strain is a complex three-dimensional (3D) issue, and the accurate description of such constitutive relationships significantly contributes to the optimum process design. To obtain the true stress-strain data of ultra-high-strength steel, BR1500HS, a series of isothermal hot tensile tests were conducted in a wide temperature range of 973-1,123 K and a strain rate range of 0.01-10 s-1 on a Gleeble 3800 testing machine. Then the constitutive relationships were modeled by an optimally constructed and well-trained backpropagation artificial neural network (BP-ANN). The evaluation of BP-ANN model revealed that it has admirable performance in characterizing and predicting the flow behaviors of BR1500HS. A comparison on improved Arrhenius-type constitutive equation and BP-ANN model shows that the latter has higher accuracy. Consequently, the developed BP-ANN model was used to predict abundant stress-strain data beyond the limited experimental conditions. Then a 3D continuous interaction space for temperature, strain rate, strain and stress was constructed based on these predicted data. The developed 3D continuous interaction space for hot working parameters contributes to fully revealing the intrinsic relationships of BR1500HS steel.

Inner and outer coronary vessel wall segmentation from CCTA using an active contour model with machine learning-based 3D voxel context-aware image force

NASA Astrophysics Data System (ADS)

Sivalingam, Udhayaraj; Wels, Michael; Rempfler, Markus; Grosskopf, Stefan; Suehling, Michael; Menze, Bjoern H.

2016-03-01

In this paper, we present a fully automated approach to coronary vessel segmentation, which involves calcification or soft plaque delineation in addition to accurate lumen delineation, from 3D Cardiac Computed Tomography Angiography data. Adequately virtualizing the coronary lumen plays a crucial role for simulating blood ow by means of fluid dynamics while additionally identifying the outer vessel wall in the case of arteriosclerosis is a prerequisite for further plaque compartment analysis. Our method is a hybrid approach complementing Active Contour Model-based segmentation with an external image force that relies on a Random Forest Regression model generated off-line. The regression model provides a strong estimate of the distance to the true vessel surface for every surface candidate point taking into account 3D wavelet-encoded contextual image features, which are aligned with the current surface hypothesis. The associated external image force is integrated in the objective function of the active contour model, such that the overall segmentation approach benefits from the advantages associated with snakes and from the ones associated with machine learning-based regression alike. This yields an integrated approach achieving competitive results on a publicly available benchmark data collection (Rotterdam segmentation challenge).

Fast Flows in the Magnetotail and Energetic Particle Transport: Multiscale Coupling in the Magnetosphere

NASA Astrophysics Data System (ADS)

Lin, Y.; Wang, X.; Fok, M. C. H.; Buzulukova, N.; Perez, J. D.; Chen, L. J.

2017-12-01

The interaction between the Earth's inner and outer magnetospheric regions associated with the tail fast flows is calculated by coupling the Auburn 3-D global hybrid simulation code (ANGIE3D) to the Comprehensive Inner Magnetosphere/Ionosphere (CIMI) model. The global hybrid code solves fully kinetic equations governing the ions and a fluid model for electrons in the self-consistent electromagnetic field of the dayside and night side outer magnetosphere. In the integrated computation model, the hybrid simulation provides the CIMI model with field data in the CIMI 3-D domain and particle data at its boundary, and the transport in the inner magnetosphere is calculated by the CIMI model. By joining the two existing codes, effects of the solar wind on particle transport through the outer magnetosphere into the inner magnetosphere are investigated. Our simulation shows that fast flows and flux ropes are localized transients in the magnetotail plasma sheet and their overall structures have a dawn-dusk asymmetry. Strong perpendicular ion heating is found at the fast flow braking, which affects the earthward transport of entropy-depleted bubbles. We report on the impacts from the temperature anisotropy and non-Maxwellian ion distributions associated with the fast flows on the ring current and the convection electric field.

The cathode plasma simulation

NASA Astrophysics Data System (ADS)

Suksila, Thada

Since its invention at the University of Stuttgart, Germany in the mid-1960, scientists have been trying to understand and explain the mechanism of the plasma interaction inside the magnetoplasmadynamics (MPD) thruster. Because this thruster creates a larger level of efficiency than combustion thrusters, this MPD thruster is the primary cadidate thruster for a long duration (planetary) spacecraft. However, the complexity of this thruster make it difficult to fully understand the plasma interaction in an MPD thruster while operating the device. That is, there is a great deal of physics involved: the fluid dynamics, the electromagnetics, the plasma dynamics, and the thermodynamics. All of these physics must be included when an MPD thruster operates. In recent years, a computer simulation helped scientists to simulate the experiments by programing the physics theories and comparing the simulation results with the experimental data. Many MPD thruster simulations have been conducted: E. Niewood et al.[5], C. K. J. Hulston et al.[6], K. D. Goodfellow[3], J Rossignol et al.[7]. All of these MPD computer simulations helped the scientists to see how quickly the system responds to the new design parameters. For this work, a 1D MPD thruster simulation was developed to find the voltage drop between the cathode and the plasma regions. Also, the properties such as thermal conductivity, electrical conductivity and heat capacity are temperature and pressure dependent. These two conductivity and heat capacity are usually definded as constant values in many other models. However, this 1D and 2D cylindrical symmetry MPD thruster simulations include both temperature and pressure effects to the electrical, thermal conductivities and heat capacity values interpolated from W. F. Ahtye [4]. Eventhough, the pressure effect is also significant; however, in this study the pressure at 66 Pa was set as a baseline. The 1D MPD thruster simulation includes the sheath region, which is the interface between the plasma and the cathode regions. This sheath model [3] has been fully combined in the 1D simulation. That is, the sheath model calculates the heat flux and the sheath voltage by giving the temperature and the current density. This sheath model must be included in the simulation, as the sheath region is treated differently from the main plasma region. For our 2D cylindrical symmetry simulation, the dimensions of the cathode, the anode, the total current, the pressure, the type of gases, the work function can be changed in the input process as needed for particular interested. Also, the sheath model is still included and fully integrated in this 2D cylindrical symmetry simulation at the cathode surface grids. In addition, the focus of the 2D cylindrical symmetry simulation is to connect the properties on the plasma and the cathode regions on the cathode surface until the MPD thruster reach steady state and estimate the plasma arc attachement edge, electroarc edge, on the cathode surface. Finally, we can understand more about the behavior of an MPD thruster under many different conditions of 2D cylindrical symmetry MPD thruster simulations.

3D Visualization of Cultural Heritage Artefacts with Virtual Reality devices

NASA Astrophysics Data System (ADS)

Gonizzi Barsanti, S.; Caruso, G.; Micoli, L. L.; Covarrubias Rodriguez, M.; Guidi, G.

2015-08-01

Although 3D models are useful to preserve the information about historical artefacts, the potential of these digital contents are not fully accomplished until they are not used to interactively communicate their significance to non-specialists. Starting from this consideration, a new way to provide museum visitors with more information was investigated. The research is aimed at valorising and making more accessible the Egyptian funeral objects exhibited in the Sforza Castle in Milan. The results of the research will be used for the renewal of the current exhibition, at the Archaeological Museum in Milan, by making it more attractive. A 3D virtual interactive scenario regarding the "path of the dead", an important ritual in ancient Egypt, was realized to augment the experience and the comprehension of the public through interactivity. Four important artefacts were considered for this scope: two ushabty, a wooden sarcophagus and a heart scarab. The scenario was realized by integrating low-cost Virtual Reality technologies, as the Oculus Rift DK2 and the Leap Motion controller, and implementing a specific software by using Unity. The 3D models were implemented by adding responsive points of interest in relation to important symbols or features of the artefact. This allows highlighting single parts of the artefact in order to better identify the hieroglyphs and provide their translation. The paper describes the process for optimizing the 3D models, the implementation of the interactive scenario and the results of some test that have been carried out in the lab.

Design and implementation of an online systemic human anatomy course with laboratory.

PubMed

Attardi, Stefanie M; Rogers, Kem A

2015-01-01

Systemic Human Anatomy is a full credit, upper year undergraduate course with a (prosection) laboratory component at Western University Canada. To meet enrollment demands beyond the physical space of the laboratory facility, a fully online section was developed to run concurrently with the traditional face to face (F2F) course. Lectures given to F2F students are simultaneously broadcasted to online students using collaborative software (Blackboard Collaborate). The same collaborative software is used by a teaching assistant to deliver laboratory demonstrations in which three-dimensional (3D) virtual anatomical models are manipulated. Ten commercial software programs were reviewed to determine their suitability for demonstrating the virtual models, resulting in the selection of Netter's 3D Interactive Anatomy. Supplementary online materials for the central nervous system were developed by creating 360° images of plastinated prosected brain specimens and a website through which they could be accessed. This is the first description of a fully online undergraduate anatomy course with a live, interactive laboratory component. Preliminary data comparing the online and F2F student grades suggest that previous student academic performance, and not course delivery format, predicts performance in anatomy. Future qualitative studies will reveal student perceptions about their learning experiences in both of the course delivery formats. © 2014 American Association of Anatomists.

Neutron Angular Scatter Effects in 3DHZETRN: Quasi-Elastic

NASA Technical Reports Server (NTRS)

Wilson, John W.; Werneth, Charles M.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

2017-01-01

The current 3DHZETRN code has a detailed three dimensional (3D) treatment of neutron transport based on a forward/isotropic assumption and has been compared to Monte Carlo (MC) simulation codes in various geometries. In most cases, it has been found that 3DHZETRN agrees with the MC codes to the extent they agree with each other. However, a recent study of neutron leakage from finite geometries revealed that further improvements to the 3DHZETRN formalism are needed. In the present report, angular scattering corrections to the neutron fluence are provided in an attempt to improve fluence estimates from a uniform sphere. It is found that further developments in the nuclear production models are required to fully evaluate the impact of transport model updates. A model for the quasi-elastic neutron production spectra is therefore developed and implemented into 3DHZETRN.

Performance of new automated transthoracic three-dimensional echocardiographic software for left ventricular volumes and function assessment in routine clinical practice: Comparison with 3 Tesla cardiac magnetic resonance.

PubMed

Levy, Franck; Dan Schouver, Elie; Iacuzio, Laura; Civaia, Filippo; Rusek, Stephane; Dommerc, Carinne; Marechaux, Sylvestre; Dor, Vincent; Tribouilloy, Christophe; Dreyfus, Gilles

2017-11-01

Three-dimensional (3D) transthoracic echocardiography (TTE) is superior to two-dimensional Simpson's method for assessment of left ventricular (LV) volumes and LV ejection fraction (LVEF). Nevertheless, 3D TTE is not incorporated into everyday practice, as current LV chamber quantification software products are time-consuming. To evaluate the feasibility, accuracy and reproducibility of new fully automated fast 3D TTE software (HeartModel A.I. ; Philips Healthcare, Andover, MA, USA) for quantification of LV volumes and LVEF in routine practice; to compare the 3D LV volumes and LVEF obtained with a cardiac magnetic resonance (CMR) reference; and to optimize automated default border settings with CMR as reference. Sixty-three consecutive patients, who had comprehensive 3D TTE and CMR examinations within 24hours, were eligible for inclusion. Nine patients (14%) were excluded because of insufficient echogenicity in the 3D TTE. Thus, 54 patients (40 men; mean age 63±13 years) were prospectively included into the study. The inter- and intraobserver reproducibilities of 3D TTE were excellent (coefficient of variation<10%) for end-diastolic volume (EDV), end-systolic volume (ESV) and LVEF. Despite a slight underestimation of EDV using 3D TTE compared with CMR (bias=-22±34mL; P<0.0001), a significant correlation was found between the two measurements (r=0.93; P=0.0001). Enlarging default border detection settings leads to frequent volume overestimation in the general population, but improved agreement with CMR in patients with LVEF≤50%. Correlations between 3D TTE and CMR for ESV and LVEF were excellent (r=0.93 and r=0.91, respectively; P<0.0001). 3D TTE using new-generation fully automated software is a feasible, fast, reproducible and accurate imaging modality for LV volumetric quantification in routine practice. Optimization of border detection settings may increase agreement with CMR for EDV assessment in dilated ventricles. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Automatic Segmentation of the Eye in 3D Magnetic Resonance Imaging: A Novel Statistical Shape Model for Treatment Planning of Retinoblastoma

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

Ciller, Carlos, E-mail: carlos.cillerruiz@unil.ch; Ophthalmic Technology Group, ARTORG Center of the University of Bern, Bern; Centre d’Imagerie BioMédicale, University of Lausanne, Lausanne

Purpose: Proper delineation of ocular anatomy in 3-dimensional (3D) imaging is a big challenge, particularly when developing treatment plans for ocular diseases. Magnetic resonance imaging (MRI) is presently used in clinical practice for diagnosis confirmation and treatment planning for treatment of retinoblastoma in infants, where it serves as a source of information, complementary to the fundus or ultrasonographic imaging. Here we present a framework to fully automatically segment the eye anatomy for MRI based on 3D active shape models (ASM), and we validate the results and present a proof of concept to automatically segment pathological eyes. Methods and Materials: Manualmore » and automatic segmentation were performed in 24 images of healthy children's eyes (3.29 ± 2.15 years of age). Imaging was performed using a 3-T MRI scanner. The ASM consists of the lens, the vitreous humor, the sclera, and the cornea. The model was fitted by first automatically detecting the position of the eye center, the lens, and the optic nerve, and then aligning the model and fitting it to the patient. We validated our segmentation method by using a leave-one-out cross-validation. The segmentation results were evaluated by measuring the overlap, using the Dice similarity coefficient (DSC) and the mean distance error. Results: We obtained a DSC of 94.90 ± 2.12% for the sclera and the cornea, 94.72 ± 1.89% for the vitreous humor, and 85.16 ± 4.91% for the lens. The mean distance error was 0.26 ± 0.09 mm. The entire process took 14 seconds on average per eye. Conclusion: We provide a reliable and accurate tool that enables clinicians to automatically segment the sclera, the cornea, the vitreous humor, and the lens, using MRI. We additionally present a proof of concept for fully automatically segmenting eye pathology. This tool reduces the time needed for eye shape delineation and thus can help clinicians when planning eye treatment and confirming the extent of the tumor.« less

Automatic Segmentation of the Eye in 3D Magnetic Resonance Imaging: A Novel Statistical Shape Model for Treatment Planning of Retinoblastoma.

PubMed

Ciller, Carlos; De Zanet, Sandro I; Rüegsegger, Michael B; Pica, Alessia; Sznitman, Raphael; Thiran, Jean-Philippe; Maeder, Philippe; Munier, Francis L; Kowal, Jens H; Cuadra, Meritxell Bach

2015-07-15

Proper delineation of ocular anatomy in 3-dimensional (3D) imaging is a big challenge, particularly when developing treatment plans for ocular diseases. Magnetic resonance imaging (MRI) is presently used in clinical practice for diagnosis confirmation and treatment planning for treatment of retinoblastoma in infants, where it serves as a source of information, complementary to the fundus or ultrasonographic imaging. Here we present a framework to fully automatically segment the eye anatomy for MRI based on 3D active shape models (ASM), and we validate the results and present a proof of concept to automatically segment pathological eyes. Manual and automatic segmentation were performed in 24 images of healthy children's eyes (3.29 ± 2.15 years of age). Imaging was performed using a 3-T MRI scanner. The ASM consists of the lens, the vitreous humor, the sclera, and the cornea. The model was fitted by first automatically detecting the position of the eye center, the lens, and the optic nerve, and then aligning the model and fitting it to the patient. We validated our segmentation method by using a leave-one-out cross-validation. The segmentation results were evaluated by measuring the overlap, using the Dice similarity coefficient (DSC) and the mean distance error. We obtained a DSC of 94.90 ± 2.12% for the sclera and the cornea, 94.72 ± 1.89% for the vitreous humor, and 85.16 ± 4.91% for the lens. The mean distance error was 0.26 ± 0.09 mm. The entire process took 14 seconds on average per eye. We provide a reliable and accurate tool that enables clinicians to automatically segment the sclera, the cornea, the vitreous humor, and the lens, using MRI. We additionally present a proof of concept for fully automatically segmenting eye pathology. This tool reduces the time needed for eye shape delineation and thus can help clinicians when planning eye treatment and confirming the extent of the tumor. Copyright © 2015 Elsevier Inc. All rights reserved.

BIMOS transistor solutions for ESD protection in FD-SOI UTBB CMOS technology

NASA Astrophysics Data System (ADS)

Galy, Philippe; Athanasiou, S.; Cristoloveanu, S.

2016-01-01

We evaluate the Electro-Static Discharge (ESD) protection capability of BIpolar MOS (BIMOS) transistors integrated in ultrathin silicon film for 28 nm Fully Depleted SOI (FD-SOI) Ultra Thin Body and BOX (UTBB) high-k metal gate technology. Using as a reference our measurements in hybrid bulk-SOI structures, we extend the BIMOS design towards the ultrathin silicon film. Detailed study and pragmatic evaluations are done based on 3D TCAD simulation with standard physical models using Average Current Slope (ACS) method and quasi-static DC stress (Average Voltage Slope AVS method). These preliminary 3D TACD results are very encouraging in terms of ESD protection efficiency in advanced FD-SOI CMOS.

Design and application of 3D-printed stepless beam modulators in proton therapy

NASA Astrophysics Data System (ADS)

Lindsay, C.; Kumlin, J.; Martinez, D. M.; Jirasek, A.; Hoehr, C.

2016-06-01

A new method for the design of stepless beam modulators for proton therapy is described and verified. Simulations of the classic designs are compared against the stepless method for various modulation widths which are clinically applicable in proton eye therapy. Three modulator wheels were printed using a Stratasys Objet30 3D printer. The resulting depth dose distributions showed improved uniformity over the classic stepped designs. Simulated results imply a possible improvement in distal penumbra width; however, more accurate measurements are needed to fully verify this effect. Lastly, simulations were done to model bio-equivalence to Co-60 cell kill. A wheel was successfully designed to flatten this metric.

Numerical MHD codes for modeling astrophysical flows

NASA Astrophysics Data System (ADS)

Koldoba, A. V.; Ustyugova, G. V.; Lii, P. S.; Comins, M. L.; Dyda, S.; Romanova, M. M.; Lovelace, R. V. E.

2016-05-01

We describe a Godunov-type magnetohydrodynamic (MHD) code based on the Miyoshi and Kusano (2005) solver which can be used to solve various astrophysical hydrodynamic and MHD problems. The energy equation is in the form of entropy conservation. The code has been implemented on several different coordinate systems: 2.5D axisymmetric cylindrical coordinates, 2D Cartesian coordinates, 2D plane polar coordinates, and fully 3D cylindrical coordinates. Viscosity and diffusivity are implemented in the code to control the accretion rate in the disk and the rate of penetration of the disk matter through the magnetic field lines. The code has been utilized for the numerical investigations of a number of different astrophysical problems, several examples of which are shown.

Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education

PubMed Central

Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M.

2017-01-01

Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce a new dimension into veterinary education and training. PMID:28192461

Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education.

PubMed

Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M

2017-01-01

Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce a new dimension into veterinary education and training.

Investigation of unsteadiness in Shock-particle cloud interaction: Fully resolved two-dimensional simulation and one-dimensional modeling

NASA Astrophysics Data System (ADS)

Hosseinzadeh-Nik, Zahra; Regele, Jonathan D.

2015-11-01

Dense compressible particle-laden flow, which has a complex nature, exists in various engineering applications. Shock waves impacting a particle cloud is a canonical problem to investigate this type of flow. It has been demonstrated that large flow unsteadiness is generated inside the particle cloud from the flow induced by the shock passage. It is desirable to develop models for the Reynolds stress to capture the energy contained in vortical structures so that volume-averaged models with point particles can be simulated accurately. However, the previous work used Euler equations, which makes the prediction of vorticity generation and propagation innacurate. In this work, a fully resolved two dimensional (2D) simulation using the compressible Navier-Stokes equations with a volume penalization method to model the particles has been performed with the parallel adaptive wavelet-collocation method. The results still show large unsteadiness inside and downstream of the particle cloud. A 1D model is created for the unclosed terms based upon these 2D results. The 1D model uses a two-phase simple low dissipation AUSM scheme (TSLAU) developed by coupled with the compressible two phase kinetic energy equation.

The Formation of Coronal Loops by Thermal Instability in Three Dimensions

NASA Technical Reports Server (NTRS)

Mok, Yung; Mikic, Zoran; Lionello, Roberto; Linker, Jon A.

2008-01-01

Plasma loops in solar active regions have been observed in EUV and soft X-rays for decades. Their formation mechanism and properties, however, are still not fully understood. Predictions by early models, based on 1D hydrostatic equilibria with uniform plasma heating, are not consistent with high-resolution measurements. In this Letter, we demonstrate, via 3D simulations, that a class of heating models can lead to the dynamic formation of plasma loops provided the plasma is heated sufficiently to match SXT soft X-ray measurements. We show that individual flux tubes in a 3D magnetic structure tend to stand out against their neighbors. The loops have large aspect ratios and nearly uniform cross sections in the corona, similar to those observed by EIT and TRACE. The coronal EUV emission from these thermally unstable solutions is roughly consistent with EIT measurements. The solution oscillates in time through a large-amplitude, nonlinear cycle, leading to repeated brightening and fading of the loops.

High temporal resolution dynamic contrast-enhanced MRI using compressed sensing-combined sequence in quantitative renal perfusion measurement.

PubMed

Chen, Bin; Zhao, Kai; Li, Bo; Cai, Wenchao; Wang, Xiaoying; Zhang, Jue; Fang, Jing

2015-10-01

To demonstrate the feasibility of the improved temporal resolution by using compressed sensing (CS) combined imaging sequence in dynamic contrast-enhanced MRI (DCE-MRI) of kidney, and investigate its quantitative effects on renal perfusion measurements. Ten rabbits were included in the accelerated scans with a CS-combined 3D pulse sequence. To evaluate the image quality, the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were compared between the proposed CS strategy and the conventional full sampling method. Moreover, renal perfusion was estimated by using the separable compartmental model in both CS simulation and realistic CS acquisitions. The CS method showed DCE-MRI images with improved temporal resolution and acceptable image contrast, while presenting significantly higher SNR than the fully sampled images (p<.01) at 2-, 3- and 4-X acceleration. In quantitative measurements, renal perfusion results were in good agreement with the fully sampled one (concordance correlation coefficient=0.95, 0.91, 0.88) at 2-, 3- and 4-X acceleration in CS simulation. Moreover, in realistic acquisitions, the estimated perfusion by the separable compartmental model exhibited no significant differences (p>.05) between each CS-accelerated acquisition and the full sampling method. The CS-combined 3D sequence could improve the temporal resolution for DCE-MRI in kidney while yielding diagnostically acceptable image quality, and it could provide effective measurements of renal perfusion. Copyright © 2015 Elsevier Inc. All rights reserved.

Homogenization Issues in the Combustion of Heterogeneous Solid Propellants

NASA Technical Reports Server (NTRS)

Chen, M.; Buckmaster, J.; Jackson, T. L.; Massa, L.

2002-01-01

We examine random packs of discs or spheres, models for ammonium-perchlorate-in-binder propellants, and discuss their average properties. An analytical strategy is described for calculating the mean or effective heat conduction coefficient in terms of the heat conduction coefficients of the individual components, and the results are verified by comparison with those of direct numerical simulations (dns) for both 2-D (disc) and 3-D (sphere) packs across which a temperature difference is applied. Similarly, when the surface regression speed of each component is related to the surface temperature via a simple Arrhenius law, an analytical strategy is developed for calculating an effective Arrhenius law for the combination, and these results are verified using dns in which a uniform heat flux is applied to the pack surface, causing it to regress. These results are needed for homogenization strategies necessary for fully integrated 2-D or 3-D simulations of heterogeneous propellant combustion.

Modeling Ultra-fast assembly and sintering of gold nanostructures

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Salerno, K. Michael; Grest, Gary S.; Fan, Hongyou

We use fully atomistic simulations to understand the role of extreme pressure in the assembly and sintering of fcc superlattices of alkanethiol-coated gold nanocrystals into larger nanostructures. Recent quasi-isentropic experiments have shown that 1D, 2D and 3D nanostructures can be formed and recovered from dynamic compression experiments on Sandia's Veloce pulsed power accelerator. Here, we describe the role of coating properties, such as ligand length and grafting density, on ligand migration and deformation processes during pressure-driven coalescence of metal nano cores into permanent nanowires, nanosheets and 3D structures. The role of uniaxial vs isotropic pressure and the effects of compression along various superlattice orientations will be discussed. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

RELAP5-3D Results for Phase I (Exercise 2) of the OECD/NEA MHTGR-350 MW Benchmark

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

Gerhard Strydom

2012-06-01

The coupling of the PHISICS code suite to the thermal hydraulics system code RELAP5-3D has recently been initiated at the Idaho National Laboratory (INL) to provide a fully coupled prismatic Very High Temperature Reactor (VHTR) system modeling capability as part of the NGNP methods development program. The PHISICS code consists of three modules: INSTANT (performing 3D nodal transport core calculations), MRTAU (depletion and decay heat generation) and a perturbation/mixer module. As part of the verification and validation activities, steady state results have been obtained for Exercise 2 of Phase I of the newly-defined OECD/NEA MHTGR-350 MW Benchmark. This exercise requiresmore » participants to calculate a steady-state solution for an End of Equilibrium Cycle 350 MW Modular High Temperature Reactor (MHTGR), using the provided geometry, material, and coolant bypass flow description. The paper provides an overview of the MHTGR Benchmark and presents typical steady state results (e.g. solid and gas temperatures, thermal conductivities) for Phase I Exercise 2. Preliminary results are also provided for the early test phase of Exercise 3 using a two-group cross-section library and the Relap5-3D model developed for Exercise 2.« less

RELAP5-3D results for phase I (Exercise 2) of the OECD/NEA MHTGR-350 MW benchmark

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

Strydom, G.; Epiney, A. S.

2012-07-01

The coupling of the PHISICS code suite to the thermal hydraulics system code RELAP5-3D has recently been initiated at the Idaho National Laboratory (INL) to provide a fully coupled prismatic Very High Temperature Reactor (VHTR) system modeling capability as part of the NGNP methods development program. The PHISICS code consists of three modules: INSTANT (performing 3D nodal transport core calculations), MRTAU (depletion and decay heat generation) and a perturbation/mixer module. As part of the verification and validation activities, steady state results have been obtained for Exercise 2 of Phase I of the newly-defined OECD/NEA MHTGR-350 MW Benchmark. This exercise requiresmore » participants to calculate a steady-state solution for an End of Equilibrium Cycle 350 MW Modular High Temperature Reactor (MHTGR), using the provided geometry, material, and coolant bypass flow description. The paper provides an overview of the MHTGR Benchmark and presents typical steady state results (e.g. solid and gas temperatures, thermal conductivities) for Phase I Exercise 2. Preliminary results are also provided for the early test phase of Exercise 3 using a two-group cross-section library and the Relap5-3D model developed for Exercise 2. (authors)« less

a Low-Cost and Lightweight 3d Interactive Real Estate-Purposed Indoor Virtual Reality Application

NASA Astrophysics Data System (ADS)

Ozacar, K.; Ortakci, Y.; Kahraman, I.; Durgut, R.; Karas, I. R.

2017-11-01

Interactive 3D architectural indoor design have been more popular after it benefited from Virtual Reality (VR) technologies. VR brings computer-generated 3D content to real life scale and enable users to observe immersive indoor environments so that users can directly modify it. This opportunity enables buyers to purchase a property off-the-plan cheaper through virtual models. Instead of showing property through 2D plan or renders, this visualized interior architecture of an on-sale unbuilt property is demonstrated beforehand so that the investors have an impression as if they were in the physical building. However, current applications either use highly resource consuming software, or are non-interactive, or requires specialist to create such environments. In this study, we have created a real-estate purposed low-cost high quality fully interactive VR application that provides a realistic interior architecture of the property by using free and lightweight software: Sweet Home 3D and Unity. A preliminary study showed that participants generally liked proposed real estate-purposed VR application, and it satisfied the expectation of the property buyers.

Effective count rates for PET scanners with reduced and extended axial field of view

NASA Astrophysics Data System (ADS)

MacDonald, L. R.; Harrison, R. L.; Alessio, A. M.; Hunter, W. C. J.; Lewellen, T. K.; Kinahan, P. E.

2011-06-01

We investigated the relationship between noise equivalent count (NEC) and axial field of view (AFOV) for PET scanners with AFOVs ranging from one-half to twice those of current clinical scanners. PET scanners with longer or shorter AFOVs could fulfill different clinical needs depending on exam volumes and site economics. Using previously validated Monte Carlo simulations, we modeled true, scattered and random coincidence counting rates for a PET ring diameter of 88 cm with 2, 4, 6, and 8 rings of detector blocks (AFOV 7.8, 15.5, 23.3, and 31.0 cm). Fully 3D acquisition mode was compared to full collimation (2D) and partial collimation (2.5D) modes. Counting rates were estimated for a 200 cm long version of the 20 cm diameter NEMA count-rate phantom and for an anthropomorphic object based on a patient scan. We estimated the live-time characteristics of the scanner from measured count-rate data and applied that estimate to the simulated results to obtain NEC as a function of object activity. We found NEC increased as a quadratic function of AFOV for 3D mode, and linearly in 2D mode. Partial collimation provided the highest overall NEC on the 2-block system and fully 3D mode provided the highest NEC on the 8-block system for clinically relevant activities. On the 4-, and 6-block systems 3D mode NEC was highest up to ~300 MBq in the anthropomorphic phantom, above which 3D NEC dropped rapidly, and 2.5D NEC was highest. Projected total scan time to achieve NEC-density that matches current clinical practice in a typical oncology exam averaged 9, 15, 24, and 61 min for the 8-, 6-, 4-, and 2-block ring systems, when using optimal collimation. Increasing the AFOV should provide a greater than proportional increase in NEC, potentially benefiting patient throughput-to-cost ratio. Conversely, by using appropriate collimation, a two-ring (7.8 cm AFOV) system could acquire whole-body scans achieving NEC-density levels comparable to current standards within long, but feasible, scan times.

Fully automated reconstruction of three-dimensional vascular tree structures from two orthogonal views using computational algorithms and productionrules

NASA Astrophysics Data System (ADS)

Liu, Iching; Sun, Ying

1992-10-01

A system for reconstructing 3-D vascular structure from two orthogonally projected images is presented. The formidable problem of matching segments between two views is solved using knowledge of the epipolar constraint and the similarity of segment geometry and connectivity. The knowledge is represented in a rule-based system, which also controls the operation of several computational algorithms for tracking segments in each image, representing 2-D segments with directed graphs, and reconstructing 3-D segments from matching 2-D segment pairs. Uncertain reasoning governs the interaction between segmentation and matching; it also provides a framework for resolving the matching ambiguities in an iterative way. The system was implemented in the C language and the C Language Integrated Production System (CLIPS) expert system shell. Using video images of a tree model, the standard deviation of reconstructed centerlines was estimated to be 0.8 mm (1.7 mm) when the view direction was parallel (perpendicular) to the epipolar plane. Feasibility of clinical use was shown using x-ray angiograms of a human chest phantom. The correspondence of vessel segments between two views was accurate. Computational time for the entire reconstruction process was under 30 s on a workstation. A fully automated system for two-view reconstruction that does not require the a priori knowledge of vascular anatomy is demonstrated.

Empirical Reconstruction and Numerical Modeling of the First Geoeffective Coronal Mass Ejection of Solar Cycle 24

NASA Astrophysics Data System (ADS)

Wood, B. E.; Wu, C.-C.; Howard, R. A.; Socker, D. G.; Rouillard, A. P.

2011-03-01

We analyze the kinematics and morphology of a coronal mass ejection (CME) from 2010 April 3, which was responsible for the first significant geomagnetic storm of solar cycle 24. The analysis utilizes coronagraphic and heliospheric images from the two STEREO spacecraft, and coronagraphic images from SOHO/LASCO. Using an empirical three-dimensional (3D) reconstruction technique, we demonstrate that the CME can be reproduced reasonably well at all times with a 3D flux rope shape, but the case for a flux rope being the correct interpretation is not as strong as some events studied with STEREO in the past, given that we are unable to infer a unique orientation for the flux rope. A model with an orientation angle of -80° from the ecliptic plane (i.e., nearly N-S) works best close to the Sun, but a model at 10° (i.e., nearly E-W) works better far from the Sun. Both interpretations require the cross section of the flux rope to be significantly elliptical rather than circular. In addition to our empirical modeling, we also present a fully 3D numerical MHD model of the CME. This physical model appears to effectively reproduce aspects of the shape and kinematics of the CME's leading edge. It is particularly encouraging that the model reproduces the amount of interplanetary deceleration observed for the CME during its journey from the Sun to 1 AU.

Data Assimilation and Propagation of Uncertainty in Multiscale Cardiovascular Simulation

NASA Astrophysics Data System (ADS)

Schiavazzi, Daniele; Marsden, Alison

2015-11-01

Cardiovascular modeling is the application of computational tools to predict hemodynamics. State-of-the-art techniques couple a 3D incompressible Navier-Stokes solver with a boundary circulation model and can predict local and peripheral hemodynamics, analyze the post-operative performance of surgical designs and complement clinical data collection minimizing invasive and risky measurement practices. The ability of these tools to make useful predictions is directly related to their accuracy in representing measured physiologies. Tuning of model parameters is therefore a topic of paramount importance and should include clinical data uncertainty, revealing how this uncertainty will affect the predictions. We propose a fully Bayesian, multi-level approach to data assimilation of uncertain clinical data in multiscale circulation models. To reduce the computational cost, we use a stable, condensed approximation of the 3D model build by linear sparse regression of the pressure/flow rate relationship at the outlets. Finally, we consider the problem of non-invasively propagating the uncertainty in model parameters to the resulting hemodynamics and compare Monte Carlo simulation with Stochastic Collocation approaches based on Polynomial or Multi-resolution Chaos expansions.

The ins and outs of modelling vertical displacement events

NASA Astrophysics Data System (ADS)

Pfefferle, David

2017-10-01

Of the many reasons a plasma discharge disrupts, Vertical Displacement Events (VDEs) lead to the most severe forces and stresses on the vacuum vessel and Plasma Facing Components (PFCs). After loss of positional control, the plasma column drifts across the vacuum vessel and comes in contact with the first wall, at which point the stored magnetic and thermal energy is abruptly released. The vessel forces have been extensively modelled in 2D but, with the constraint of axisymmetry, the fundamental 3D effects that lead to toroidal peaking, sideways forces, field-line stochastisation and halo current rotation have been vastly overlooked. In this work, we present the main results of an intense VDE modelling activity using the implicit 3D extended MHD code M3D-C1 and share our experience with the multi-domain and highly non-linear physics encountered. At the culmination of code development by the M3D-C1 group over the last decade, highlighted by the inclusion of a finite-thickness resistive vacuum vessel within the computational domain, a series of fully 3D non-linear simulations are performed using realistic transport coefficients based on the reconstruction of so-called NSTX frozen VDEs, where the feedback control was purposely switched off to trigger a vertical instability. The vertical drift phase, the evolution of the current quench and the onset of 3D halo/eddy currents are diagnosed and investigated in detail. The sensitivity of the current quench to parameter changes is assessed via 2D non-linear runs. The growth of individual toroidal modes is monitored via linear-complex runs. The intricate evolution of the plasma, which is decaying to large extent in force-balance with induced halo/wall currents, is carefully resolved via 3D non-linear runs. The location, amplitude and rotation of normal currents and wall forces are analysed and compared with experimental traces.

A recommended workflow methodology in the creation of an educational and training application incorporating a digital reconstruction of the cerebral ventricular system and cerebrospinal fluid circulation to aid anatomical understanding.

PubMed

Manson, Amy; Poyade, Matthieu; Rea, Paul

2015-10-19

The use of computer-aided learning in education can be advantageous, especially when interactive three-dimensional (3D) models are used to aid learning of complex 3D structures. The anatomy of the ventricular system of the brain is difficult to fully understand as it is seldom seen in 3D, as is the flow of cerebrospinal fluid (CSF). This article outlines a workflow for the creation of an interactive training tool for the cerebral ventricular system, an educationally challenging area of anatomy. This outline is based on the use of widely available computer software packages. Using MR images of the cerebral ventricular system and several widely available commercial and free software packages, the techniques of 3D modelling, texturing, sculpting, image editing and animations were combined to create a workflow in the creation of an interactive educational and training tool. This was focussed on cerebral ventricular system anatomy, and the flow of cerebrospinal fluid. We have successfully created a robust methodology by using key software packages in the creation of an interactive education and training tool. This has resulted in an application being developed which details the anatomy of the ventricular system, and flow of cerebrospinal fluid using an anatomically accurate 3D model. In addition to this, our established workflow pattern presented here also shows how tutorials, animations and self-assessment tools can also be embedded into the training application. Through our creation of an established workflow in the generation of educational and training material for demonstrating cerebral ventricular anatomy and flow of cerebrospinal fluid, it has enormous potential to be adopted into student training in this field. With the digital age advancing rapidly, this has the potential to be used as an innovative tool alongside other methodologies for the training of future healthcare practitioners and scientists. This workflow could be used in the creation of other tools, which could be developed for use not only on desktop and laptop computers but also smartphones, tablets and fully immersive stereoscopic environments. It also could form the basis on which to build surgical simulations enhanced with haptic interaction.

Using a 3D profiler and infrared camera to monitor oven loading in fully cooked meat operations

NASA Astrophysics Data System (ADS)

Stewart, John; Giorges, Aklilu

2009-05-01

Ensuring meat is fully cooked is an important food safety issue for operations that produce "ready to eat" products. In order to kill harmful pathogens like Salmonella, all of the product must reach a minimum threshold temperature. Producers typically overcook the majority of the product to ensure meat in the most difficult scenario reaches the desired temperature. A difficult scenario can be caused by an especially thick piece of meat or by a surge of product into the process. Overcooking wastes energy, degrades product quality, lowers the maximum throughput rate of the production line and decreases product yield. At typical production rates of 6000lbs/hour, these losses from overcooking can have a significant cost impact on producers. A wide area 3D camera coupled with a thermal camera was used to measure the thermal mass variability of chicken breasts in a cooking process. Several types of variability are considered including time varying thermal mass (mass x temperature / time), variation in individual product geometry and variation in product temperature. The automatic identification of product arrangement issues that affect cooking such as overlapping product and folded products is also addressed. A thermal model is used along with individual product geometry and oven cook profiles to predict the percentage of product that will be overcooked and to identify products that may not fully cook in a given process.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code.

NASA Astrophysics Data System (ADS)

Chacon, L.; Knoll, D. A.

2004-11-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended primitive-variable MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field, non-dissipative, and stable in the absence of physical dissipation.(L. Chacón , phComput. Phys. Comm.) submitted (2004) PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, first and second-order implicit schemes are available, although higher-order temporal implicit schemes can be effortlessly implemented within the Newton-Krylov framework. A successful, scalable, MG physics-based preconditioning strategy, similar in concept to previous 2D MHD efforts,(L. Chacón et al., phJ. Comput. Phys). 178 (1), 15- 36 (2002); phJ. Comput. Phys., 188 (2), 573-592 (2003) has been developed. We are currently in the process of parallelizing the code using the PETSc library, and a Newton-Krylov-Schwarz approach for the parallel treatment of the preconditioner. In this poster, we will report on both the serial and parallel performance of PIXIE3D, focusing primarily on scalability and CPU speedup vs. an explicit approach.

A 3D network of helicates fully assembled by pi-stacking interactions.

PubMed

Vázquez, Miguel; Taglietti, Angelo; Gatteschi, Dante; Sorace, Lorenzo; Sangregorio, Claudio; González, Ana M; Maneiro, Marcelino; Pedrido, Rosa M; Bermejo, Manuel R

2003-08-07

The neutral dinuclear dihelicate [Cu2(L)2] x 2CH3CN (1) forms a unique 3D network in the solid state due to pi-stacking interactions, which are responsible for intermolecular antiferromagnetic coupling between Cu(II) ions.

Silicon photonics plasma-modulators with advanced transmission line design.

PubMed

Merget, Florian; Azadeh, Saeed Sharif; Mueller, Juliana; Shen, Bin; Nezhad, Maziar P; Hauck, Johannes; Witzens, Jeremy

2013-08-26

We have investigated two novel concepts for the design of transmission lines in travelling wave Mach-Zehnder interferometer based Silicon Photonics depletion modulators overcoming the analog bandwidth limitations arising from cross-talk between signal lines in push-pull modulators and reducing the linear losses of the transmission lines. We experimentally validate the concepts and demonstrate an E/O -3 dBe bandwidth of 16 GHz with a 4V drive voltage (in dual drive configuration) and 8.8 dB on-chip insertion losses. Significant bandwidth improvements result from suppression of cross-talk. An additional bandwidth enhancement of ~11% results from a reduction of resistive transmission line losses. Frequency dependent loss models for loaded transmission lines and E/O bandwidth modeling are fully verified.

A Spectral Element Ocean Model on the Cray T3D: the interannual variability of the Mediterranean Sea general circulation

NASA Astrophysics Data System (ADS)

Molcard, A. J.; Pinardi, N.; Ansaloni, R.

A new numerical model, SEOM (Spectral Element Ocean Model, (Iskandarani et al, 1994)), has been implemented in the Mediterranean Sea. Spectral element methods combine the geometric flexibility of finite element techniques with the rapid convergence rate of spectral schemes. The current version solves the shallow water equations with a fifth (or sixth) order accuracy spectral scheme and about 50.000 nodes. The domain decomposition philosophy makes it possible to exploit the power of parallel machines. The original MIMD master/slave version of SEOM, written in F90 and PVM, has been ported to the Cray T3D. When critical for performance, Cray specific high-performance one-sided communication routines (SHMEM) have been adopted to fully exploit the Cray T3D interprocessor network. Tests performed with highly unstructured and irregular grid, on up to 128 processors, show an almost linear scalability even with unoptimized domain decomposition techniques. Results from various case studies on the Mediterranean Sea are shown, involving realistic coastline geometry, and monthly mean 1000mb winds from the ECMWF's atmospheric model operational analysis from the period January 1987 to December 1994. The simulation results show that variability in the wind forcing considerably affect the circulation dynamics of the Mediterranean Sea.

Parameterized code SHARM-3D for radiative transfer over inhomogeneous surfaces.

PubMed

Lyapustin, Alexei; Wang, Yujie

2005-12-10

The code SHARM-3D, developed for fast and accurate simulations of the monochromatic radiance at the top of the atmosphere over spatially variable surfaces with Lambertian or anisotropic reflectance, is described. The atmosphere is assumed to be laterally uniform across the image and to consist of two layers with aerosols contained in the bottom layer. The SHARM-3D code performs simultaneous calculations for all specified incidence-view geometries and multiple wavelengths in one run. The numerical efficiency of the current version of code is close to its potential limit and is achieved by means of two innovations. The first is the development of a comprehensive precomputed lookup table of the three-dimensional atmospheric optical transfer function for various atmospheric conditions. The second is the use of a linear kernel model of the land surface bidirectional reflectance factor (BRF) in our algorithm that has led to a fully parameterized solution in terms of the surface BRF parameters. The code is also able to model inland lakes and rivers. The water pixels are described with the Nakajima-Tanaka BRF model of wind-roughened water surface with a Lambertian offset, which is designed to model approximately the reflectance of suspended matter and of a shallow lake or river bottom.

Parameterized code SHARM-3D for radiative transfer over inhomogeneous surfaces

NASA Astrophysics Data System (ADS)

Lyapustin, Alexei; Wang, Yujie

2005-12-01

The code SHARM-3D, developed for fast and accurate simulations of the monochromatic radiance at the top of the atmosphere over spatially variable surfaces with Lambertian or anisotropic reflectance, is described. The atmosphere is assumed to be laterally uniform across the image and to consist of two layers with aerosols contained in the bottom layer. The SHARM-3D code performs simultaneous calculations for all specified incidence-view geometries and multiple wavelengths in one run. The numerical efficiency of the current version of code is close to its potential limit and is achieved by means of two innovations. The first is the development of a comprehensive precomputed lookup table of the three-dimensional atmospheric optical transfer function for various atmospheric conditions. The second is the use of a linear kernel model of the land surface bidirectional reflectance factor (BRF) in our algorithm that has led to a fully parameterized solution in terms of the surface BRF parameters. The code is also able to model inland lakes and rivers. The water pixels are described with the Nakajima-Tanaka BRF model of wind-roughened water surface with a Lambertian offset, which is designed to model approximately the reflectance of suspended matter and of a shallow lake or river bottom.

Accelerator Technology Division: Annual Report FY 1990

DTIC Science & Technology

1991-05-01

new version of PARMTEQ that includes 3-D space - charge and image- charge effects in the Figure 2.4. Preliminary concept for the SSC RFQ Linac 25...developing a better space - charge model based on the work of Sachercr. We have successfully demonstrated the ability to include off-axis effects in...a way fully consistent with the space - charge forces. Modifying BEDLAM to include these effects will leave almost all of the code (the integrator

A three-dimensional human neural cell culture model of Alzheimer's disease.

PubMed

Choi, Se Hoon; Kim, Young Hye; Hebisch, Matthias; Sliwinski, Christopher; Lee, Seungkyu; D'Avanzo, Carla; Chen, Hechao; Hooli, Basavaraj; Asselin, Caroline; Muffat, Julien; Klee, Justin B; Zhang, Can; Wainger, Brian J; Peitz, Michael; Kovacs, Dora M; Woolf, Clifford J; Wagner, Steven L; Tanzi, Rudolph E; Kim, Doo Yeon

2014-11-13

Alzheimer's disease is the most common form of dementia, characterized by two pathological hallmarks: amyloid-β plaques and neurofibrillary tangles. The amyloid hypothesis of Alzheimer's disease posits that the excessive accumulation of amyloid-β peptide leads to neurofibrillary tangles composed of aggregated hyperphosphorylated tau. However, to date, no single disease model has serially linked these two pathological events using human neuronal cells. Mouse models with familial Alzheimer's disease (FAD) mutations exhibit amyloid-β-induced synaptic and memory deficits but they do not fully recapitulate other key pathological events of Alzheimer's disease, including distinct neurofibrillary tangle pathology. Human neurons derived from Alzheimer's disease patients have shown elevated levels of toxic amyloid-β species and phosphorylated tau but did not demonstrate amyloid-β plaques or neurofibrillary tangles. Here we report that FAD mutations in β-amyloid precursor protein and presenilin 1 are able to induce robust extracellular deposition of amyloid-β, including amyloid-β plaques, in a human neural stem-cell-derived three-dimensional (3D) culture system. More importantly, the 3D-differentiated neuronal cells expressing FAD mutations exhibited high levels of detergent-resistant, silver-positive aggregates of phosphorylated tau in the soma and neurites, as well as filamentous tau, as detected by immunoelectron microscopy. Inhibition of amyloid-β generation with β- or γ-secretase inhibitors not only decreased amyloid-β pathology, but also attenuated tauopathy. We also found that glycogen synthase kinase 3 (GSK3) regulated amyloid-β-mediated tau phosphorylation. We have successfully recapitulated amyloid-β and tau pathology in a single 3D human neural cell culture system. Our unique strategy for recapitulating Alzheimer's disease pathology in a 3D neural cell culture model should also serve to facilitate the development of more precise human neural cell models of other neurodegenerative disorders.

Interactions between human osteoblasts and prostate cancer cells in a novel 3D in vitro model

PubMed Central

Sieh, Shirly; Lubik, Amy A; Clements, Judith A; Nelson, Colleen C

2010-01-01

Cell-cell and cell-matrix interactions play a major role in tumor morphogenesis and cancer metastasis. Therefore, it is crucial to create a model with a biomimetic microenvironment that allows such interactions to fully represent the pathophysiology of a disease for an in vitro study. This is achievable by using three-dimensional (3D) models instead of conventional two-dimensional (2D) cultures with the aid of tissue engineering technology. We are now able to better address the complex intercellular interactions underlying prostate cancer (CaP) bone metastasis through such models. In this study, we assessed the interaction of CaP cells and human osteoblasts (hOBs) within a tissue engineered bone (TEB) construct. Consistent with other in vivo studies, our findings show that intercellular and CaP cell-bone matrix interactions lead to elevated levels of matrix metalloproteinases, steroidogenic enzymes and the CaP biomarker, prostate specific antigen (PSA); all associated with CaP metastasis. Hence, it highlights the physiological relevance of this model. We believe that this model will provide new insights for understanding of the previously poorly understood molecular mechanisms of bone metastasis, which will foster further translational studies, and ultimately offer a potential tool for drug screening. PMID:21197221

A two dimensional analytical modeling of surface potential in triple metal gate (TMG) fully-depleted Recessed-Source/Drain (Re-S/D) SOI MOSFET

NASA Astrophysics Data System (ADS)

Priya, Anjali; Mishra, Ram Awadh

2016-04-01

In this paper, analytical modeling of surface potential is proposed for new Triple Metal Gate (TMG) fully depleted Recessed-Source/Dain Silicon On Insulator (SOI) Metal Oxide Semiconductor Field Effect Transistor (MOSFET). The metal with the highest work function is arranged near the source region and the lowest one near the drain. Since Recessed-Source/Drain SOI MOSFET has higher drain current as compared to conventional SOI MOSFET due to large source and drain region. The surface potential model developed by 2D Poisson's equation is verified by comparison to the simulation result of 2-dimensional ATLAS simulator. The model is compared with DMG and SMG devices and analysed for different device parameters. The ratio of metal gate length is varied to optimize the result.

Beyond Point Clouds and Virtual Reality. Innovative Methods and Technologies for the Protection and Promotion of Cultural Heritage

NASA Astrophysics Data System (ADS)

Canevese, E. P.; De Gottardo, T.

2017-05-01

The morphometric and photogrammetric knowledge, combined with the historical research, are the indispensable prerequisites for the protection and enhancement of historical, architectural and cultural heritage. Nowadays the use of BIM (Building Information Modeling) as a supporting tool for restoration and conservation purposes is becoming more and more popular. However this tool is not fully adequate in this context because of its simplified representation of three-dimensional models, resulting from solid modelling techniques (mostly used in virtual reality) causing the loss of important morphometric information. One solution to this problem is imagining new advanced tools and methods that enable the building of effective and efficient three-dimensional representations backing the correct geometric analysis of the built model. Twenty-year of interdisciplinary research activities implemented by Virtualgeo focused on developing new methods and tools for 3D modeling that go beyond the simplified digital-virtual reconstruction used in standard solid modeling. Methods and tools allowing the creation of informative and true to life three-dimensional representations, that can be further used by various academics or industry professionals to carry out diverse analysis, research and design activities. Virtualgeo applied research activities, in line with the European Commission 2013's directives of Reflective 7 - Horizon 2020 Project, gave birth to GeomaticsCube Ecosystem, an ecosystem resulting from different technologies based on experiences garnered from various fields, metrology in particular, a discipline used in the automotive and aviation industry, and in general mechanical engineering. The implementation of the metrological functionality is only possible if the 3D model is created with special modeling techniques, based on surface modeling that allow, as opposed to solid modeling, a 3D representation of the manufact that is true to life. The advantages offered by metrological analysis are varied and important because they permit a precise and detailed overview of the 3D model's characteristics, and especially the over time monitoring of the model itself, these informations are impossible to obtain from a three-dimensional representation produced with solid modelling techniques. The applied research activities are also focused on the possibility of obtaining a photogrammetric and informative 3D model., Two distinct applications have been developed for this purpose, the first allows the classification of each individual element and the association of its material characteristics during the 3D modelling phase, whilst the second allows segmentations of the photogrammetric 3D model in its diverse aspects (materic, related to decay, chronological) with the possibility to make use and to populate the database, associated with the 3D model, with all types of multimedia contents.

Simulating Mass Removal of Groundwater Contaminant Plumes with Complex and Simple Models

NASA Astrophysics Data System (ADS)

Lopez, J.; Guo, Z.; Fogg, G. E.

2016-12-01

Chlorinated solvents used in industrial, commercial, and other applications continue to pose significant threats to human health through contamination of groundwater resources. A recent National Research Council report concludes that it is unlikely that remediation of these complex sites will be achieved in a time frame of 50-100 years under current methods and standards (NRC, 2013). Pump and treat has been a common strategy at many sites to contain and treat groundwater contamination. In these sites, extensive retention of contaminant mass in low-permeability materials (tailing) has been observed after years or decades of pumping. Although transport models can be built that contain enough of the complex, 3D heterogeneity to simulate the tailing and long cleanup times, this is seldom done because of the large data and computational burdens. Hence, useful, reliable models to simulate various cleanup strategies are rare. The purpose of this study is to explore other potential ways to simulate the mass-removal processes with shorter time and less cost but still produce robust results by capturing effects of the heterogeneity and long-term retention of mass. A site containing a trichloroethylene groundwater plume was selected as the study area. The plume is located within alluvial sediments in the Tucson Basin. A fully heterogeneous domain is generated first and MODFLOW is used to simulate the flow field. Contaminant transport is simulated using both MT3D and RWHet for the fully heterogeneous model. Other approaches, including dual-domain mass transfer and heterogeneous chemical reactions, are manipulated to simulate the mass removal in a less heterogeneous, or homogeneous, domain and results are compared to the results obtained from complex models. The capability of these simpler models to simulate remediation processes, especially capture the late-time tailing, are examined.

3D-FE Modeling of 316 SS under Strain-Controlled Fatigue Loading and CFD Simulation of PWR Surge Line

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

Mohanty, Subhasish; Barua, Bipul; Listwan, Joseph

In financial year 2017, we are focusing on developing a mechanistic fatigue model of surge line pipes for pressurized water reactors (PWRs). To that end, we plan to perform the following tasks: (1) conduct stress- and strain-controlled fatigue testing of surge-line base metal such as 316 stainless steel (SS) under constant, variable, and random fatigue loading, (2) develop cyclic plasticity material models of 316 SS, (3) develop one-dimensional (1D) analytical or closed-form model to validate the material models and to understand the mechanics associated with 316 SS cyclic hardening and/or softening, (4) develop three-dimensional (3D) finite element (FE) models withmore » implementation of evolutionary cyclic plasticity, and (5) develop computational fluid dynamics (CFD) model for thermal stratification, thermal-mechanical stress, and fatigue of example reactor components, such as a PWR surge line under plant heat-up, cool-down, and normal operation with/without grid-load-following. This semi-annual progress report presents the work completed on the above tasks for a 316 SS laboratory-scale specimen subjected to strain-controlled cyclic loading with constant, variable, and random amplitude. This is the first time that the accurate 3D-FE modeling of the specimen for its entire fatigue life, including the hardening and softening behavior, has been achieved. We anticipate that this work will pave the way for the development of a fully mechanistic-computer model that can be used for fatigue evaluation of safety-critical metallic components, which are traditionally evaluated by heavy reliance on time-consuming and costly test-based approaches. This basic research will not only help the nuclear reactor industry for fatigue evaluation of reactor components in a cost effective and less time-consuming way, but will also help other safety-related industries, such as aerospace, which is heavily dependent on test-based approaches, where a single full-scale fatigue test can cost millions of dollars and require years of effort to conduct. Toward our goal of demonstration of fully mechanistic fatigue evaluation of reactor components, we also started work on developing a component-level computer model of reactor components, such as 316 SS surge line pipe. This requires developing a thermal-mechanical stress analysis model of the reactor surge line, which, in turn, requires time-dependent temperature and stratification information along the boundary of the pipe. Toward that goal, CFD models of surge lines are being developed. In this report, we also present some preliminary results showing the temperature conditions along the surge line wall under reactor heat-up, cool-down, and steady-state power operation.« less

Spectral Invariance Principles Observed in Spectral Radiation Measurements of the Transition Zone

NASA Technical Reports Server (NTRS)

Marshak, Alexander

2011-01-01

The main theme for our research is the understanding and closure of the surface spectral shortwave radiation problem in fully 3D cloud situations by combining the new ARM scanning radars, shortwave spectrometers, and microwave radiometers with the arsenal of radiative transfer tools developed by our group. In particular, we define first a large number of cloudy test cases spanning all 3D possibilities not just the customary uniform-overcast ones. Second, for each case, we define a "Best Estimate of Clouds That Affect Shortwave Radiation" using all relevant ARM instruments, notably the new scanning radars, and contribute this to the ARM Archive. Third, we test the ASR-signature radiative transfer model RRTMG_SW for those cases, focusing on the near-IR because of long-standing problems in this spectral region, and work with the developers to improve RRTMG_SW in order to increase its penetration into the modeling community.

Implementation of a kappa-epsilon turbulence model to RPLUS3D code

NASA Technical Reports Server (NTRS)

Chitsomboon, Tawit

1992-01-01

The RPLUS3D code has been developed at the NASA Lewis Research Center to support the National Aerospace Plane (NASP) project. The code has the ability to solve three dimensional flowfields with finite rate combustion of hydrogen and air. The combustion process of the hydrogen-air system are simulated by an 18 reaction path, 8 species chemical kinetic mechanism. The code uses a Lower-Upper (LU) decomposition numerical algorithm as its basis, making it a very efficient and robust code. Except for the Jacobian matrix for the implicit chemistry source terms, there is no inversion of a matrix even though a fully implicit numerical algorithm is used. A k-epsilon turbulence model has recently been incorporated into the code. Initial validations have been conducted for a flow over a flat plate. Results of the validation studies are shown. Some difficulties in implementing the k-epsilon equations to the code are also discussed.

Implementation of a kappa-epsilon turbulence model to RPLUS3D code

NASA Astrophysics Data System (ADS)

Chitsomboon, Tawit

1992-02-01

The RPLUS3D code has been developed at the NASA Lewis Research Center to support the National Aerospace Plane (NASP) project. The code has the ability to solve three dimensional flowfields with finite rate combustion of hydrogen and air. The combustion process of the hydrogen-air system are simulated by an 18 reaction path, 8 species chemical kinetic mechanism. The code uses a Lower-Upper (LU) decomposition numerical algorithm as its basis, making it a very efficient and robust code. Except for the Jacobian matrix for the implicit chemistry source terms, there is no inversion of a matrix even though a fully implicit numerical algorithm is used. A k-epsilon turbulence model has recently been incorporated into the code. Initial validations have been conducted for a flow over a flat plate. Results of the validation studies are shown. Some difficulties in implementing the k-epsilon equations to the code are also discussed.

Simulation and optimization of ammonia removal at low temperature for a double channel oxidation ditch based on fully coupled activated sludge model (FCASM): a full-scale study.

PubMed

Yang, Min; Sun, Peide; Wang, Ruyi; Han, Jingyi; Wang, Jianqiao; Song, Yingqi; Cai, Jing; Tang, Xiudi

2013-09-01

An optimal operating condition for ammonia removal at low temperature, based on fully coupled activated sludge model (FCASM), was determined in a full-scale oxidation ditch process wastewater treatment plant (WWTP). The FCASM-based mechanisms model was calibrated and validated with the data measured on site. Several important kinetic parameters of the modified model were tested through respirometry experiment. Validated model was used to evaluate the relationship between ammonia removal and operating parameters, such as temperature (T), dissolved oxygen (DO), solid retention time (SRT) and hydraulic retention time of oxidation ditch (HRT). The simulated results showed that low temperature have a negative effect on the ammonia removal. Through orthogonal simulation tests of the last three factors and combination with the analysis of variance, the optimal operating mode acquired of DO, SRT, HRT for the WWTP at low temperature were 3.5 mg L(-1), 15 d and 14 h, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

LES-based filter-matrix lattice Boltzmann model for simulating fully developed turbulent channel flow

NASA Astrophysics Data System (ADS)

Zhuo, Congshan; Zhong, Chengwen

2016-11-01

In this paper, a three-dimensional filter-matrix lattice Boltzmann (FMLB) model based on large eddy simulation (LES) was verified for simulating wall-bounded turbulent flows. The Vreman subgrid-scale model was employed in the present FMLB-LES framework, which had been proved to be capable of predicting turbulent near-wall region accurately. The fully developed turbulent channel flows were performed at a friction Reynolds number Reτ of 180. The turbulence statistics computed from the present FMLB-LES simulations, including mean stream velocity profile, Reynolds stress profile and root-mean-square velocity fluctuations greed well with the LES results of multiple-relaxation-time (MRT) LB model, and some discrepancies in comparison with those direct numerical simulation (DNS) data of Kim et al. was also observed due to the relatively low grid resolution. Moreover, to investigate the influence of grid resolution on the present LES simulation, a DNS simulation on a finer gird was also implemented by present FMLB-D3Q19 model. Comparisons of detailed computed various turbulence statistics with available benchmark data of DNS showed quite well agreement.

A new heat transfer analysis in machining based on two steps of 3D finite element modelling and experimental validation

NASA Astrophysics Data System (ADS)

Haddag, B.; Kagnaya, T.; Nouari, M.; Cutard, T.

2013-01-01

Modelling machining operations allows estimating cutting parameters which are difficult to obtain experimentally and in particular, include quantities characterizing the tool-workpiece interface. Temperature is one of these quantities which has an impact on the tool wear, thus its estimation is important. This study deals with a new modelling strategy, based on two steps of calculation, for analysis of the heat transfer into the cutting tool. Unlike the classical methods, considering only the cutting tool with application of an approximate heat flux at the cutting face, estimated from experimental data (e.g. measured cutting force, cutting power), the proposed approach consists of two successive 3D Finite Element calculations and fully independent on the experimental measurements; only the definition of the behaviour of the tool-workpiece couple is necessary. The first one is a 3D thermomechanical modelling of the chip formation process, which allows estimating cutting forces, chip morphology and its flow direction. The second calculation is a 3D thermal modelling of the heat diffusion into the cutting tool, by using an adequate thermal loading (applied uniform or non-uniform heat flux). This loading is estimated using some quantities obtained from the first step calculation, such as contact pressure, sliding velocity distributions and contact area. Comparisons in one hand between experimental data and the first calculation and at the other hand between measured temperatures with embedded thermocouples and the second calculation show a good agreement in terms of cutting forces, chip morphology and cutting temperature.

Trans-Dimensional Bayesian Imaging of 3-D Crustal and Upper Mantle Structure in Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.

2016-12-01

Imaging 3-D structures using stepwise inversions of ambient noise and receiver function data is now a routine work. Here, we carry out the inversion in the trans-dimensional and hierarchical extension of the Bayesian framework to obtain rigorous estimates of uncertainty and high-resolution images of crustal and upper mantle structures beneath Northeast (NE) Asia. The methods inherently account for data sensitivities by means of using adaptive parameterizations and treating data noise as free parameters. Therefore, parsimonious results from the methods are balanced out between model complexity and data fitting. This allows fully exploiting data information, preventing from over- or under-estimation of the data fit, and increases model resolution. In addition, the reliability of results is more rigorously checked through the use of Bayesian uncertainties. It is shown by various synthetic recovery tests that complex and spatially variable features are well resolved in our resulting images of NE Asia. Rayleigh wave phase and group velocity tomograms (8-70 s), a 3-D shear-wave velocity model from depth inversions of the estimated dispersion maps, and regional 3-D models (NE China, the Korean Peninsula, and the Japanese islands) from joint inversions with receiver function data of dense networks are presented. High-resolution models are characterized by a number of tectonically meaningful features. We focus our interpretation on complex patterns of sub-lithospheric low velocity structures that extend from back-arc regions to continental margins. We interpret the anomalies in conjunction with distal and distributed intraplate volcanoes in NE Asia. Further discussion on other imaged features will be presented.

3D digital anatomy modelling - Practical or pretty?

PubMed

Murgitroyd, Ellen; Madurska, Marta; Gonzalez, Jasmina; Watson, Angus

2015-06-01

With an increasing move towards digitalisation of medical records and medical teaching, such as online exams and webinars, one of the questions that persists asks 'is there a place for digital anatomy teaching and can it effectively replace the traditional teaching methods such as cadaveric dissection?' Cadaveric dissection has a number of benefits as a teaching method but it also has its limitations. Although these can be partially addressed by prosections and new more "life-like" fixatives, it does not address the lack of resources and the increasing pressure to be able to study and learn at home. This paper reviews the literature with regards to the suitability of digital models for teaching and the wider uses a 3D digital anatomy model could have, such as postgraduate teaching, patient education and surgical planning. It also looks briefly at the learning model that anatomy as art contributes. The literature has scattered examples of digital models used for teaching at both undergraduate and postgraduate level, which demonstrate a number of positive outcomes, mostly surrounding user satisfaction and convenience. 3D modelling for patient education and operation planning has less exploration, and these papers generate a number of discussion points, mostly surrounding the practicality of digital models, which can be more time consuming and require the technology to be widely available and reliable. 3D digital anatomy is a useful adjunct to teaching and its use in patient education and operation planning have interesting possibilities still to be fully explored. Copyright © 2014 Royal College of Surgeons of Edinburgh (Scottish charity number SC005317) and Royal College of Surgeons in Ireland. Published by Elsevier Ltd. All rights reserved.

Helical core reconstruction of a DIII-D hybrid scenario tokamak discharge

DOE PAGES

Cianciosa, Mark; Wingen, Andreas; Hirshman, Steven P.; ...

2017-05-18

Our paper presents the first fully 3-dimensional (3D) equilibrium reconstruction of a helical core in a tokamak device. Using a new parallel implementation of the Variational Moments Equilibrium Code (PARVMEC) coupled to V3FIT, 3D reconstructions can be performed at resolutions necessary to produce helical states in nominally axisymmetric tokamak equilibria. In a flux pumping experiment performed on DIII-D, an external n=1 field was applied while a 3/2 neoclassical tearing mode was suppressed using ECCD. The externally applied field was rotated past a set of fixed diagnostics at a 20 Hz frequency. Furthermore, the modulation, were found to be strongest in the core SXR and MSE channels, indicates a localized rotating 3D structure locked in phase with the applied field. Signals from multiple time slices are converted to a virtual rotation of modeled diagnostics adding 3D signal information. In starting from an axisymmetric equilibrium reconstruction solution, the reconstructed broader current profile flattens the q-profile, resulting in an m=1, n=1 perturbation of the magnetic axis that ismore » $$\\sim 50\\times $$ larger than the applied n=1 deformation of the edge. Error propagation confirms that the displacement of the axis is much larger than the uncertainty in the axis position validating the helical equilibrium.« less

Helical core reconstruction of a DIII-D hybrid scenario tokamak discharge

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

Cianciosa, Mark; Wingen, Andreas; Hirshman, Steven P.

Our paper presents the first fully 3-dimensional (3D) equilibrium reconstruction of a helical core in a tokamak device. Using a new parallel implementation of the Variational Moments Equilibrium Code (PARVMEC) coupled to V3FIT, 3D reconstructions can be performed at resolutions necessary to produce helical states in nominally axisymmetric tokamak equilibria. In a flux pumping experiment performed on DIII-D, an external n=1 field was applied while a 3/2 neoclassical tearing mode was suppressed using ECCD. The externally applied field was rotated past a set of fixed diagnostics at a 20 Hz frequency. Furthermore, the modulation, were found to be strongest in the core SXR and MSE channels, indicates a localized rotating 3D structure locked in phase with the applied field. Signals from multiple time slices are converted to a virtual rotation of modeled diagnostics adding 3D signal information. In starting from an axisymmetric equilibrium reconstruction solution, the reconstructed broader current profile flattens the q-profile, resulting in an m=1, n=1 perturbation of the magnetic axis that ismore » $$\\sim 50\\times $$ larger than the applied n=1 deformation of the edge. Error propagation confirms that the displacement of the axis is much larger than the uncertainty in the axis position validating the helical equilibrium.« less

Agricultural Recharge Practices for Managing Nitrate in Regional Groundwater: Time-Resolution Assessment of Numerical Modeling Approach

NASA Astrophysics Data System (ADS)

Bastani, M.; Harter, T.

2017-12-01

Intentional recharge practices in irrigated landscapes are promising options to control and remediate groundwater quality degradation with respect to nitrate. To better understand the effect of these practices, a fully 3D transient heterogeneous transport model simulation is developed using MODFLOW and MT3D. The model is developed for a long-term study of nitrate improvements in an alluvial groundwater basin in Eastern San Joaquin Valley, CA. Different scenarios of agricultural recharge strategies including crop type change and winter flood flows are investigated. Transient simulations with high spatio-temporal resolutions are performed. We then consider upscaling strategies that would allow us to simplify the modeling process such that it can be applied at a very large basin-scale (1000s of square kilometers) for scenario analysis. We specifically consider upscaling of time-variant boundary conditions (both internal and external) that have significant influence on calculation cost of the model. We compare monthly transient stresses to upscaled annual and further upscaled average steady-state stresses on nitrate transport in groundwater under recharge scenarios.

The role of three-dimensional visualization in robotics-assisted cardiac surgery

NASA Astrophysics Data System (ADS)

Currie, Maria; Trejos, Ana Luisa; Rayman, Reiza; Chu, Michael W. A.; Patel, Rajni; Peters, Terry; Kiaii, Bob

2012-02-01

Objectives: The purpose of this study was to determine the effect of three-dimensional (3D) versus two-dimensional (2D) visualization on the amount of force applied to mitral valve tissue during robotics-assisted mitral valve annuloplasty, and the time to perform the procedure in an ex vivo animal model. In addition, we examined whether these effects are consistent between novices and experts in robotics-assisted cardiac surgery. Methods: A cardiac surgery test-bed was constructed to measure forces applied by the da Vinci surgical system (Intuitive Surgical, Sunnyvale, CA) during mitral valve annuloplasty. Both experts and novices completed roboticsassisted mitral valve annuloplasty with 2D and 3D visualization. Results: The mean time for both experts and novices to suture the mitral valve annulus and to tie sutures using 3D visualization was significantly less than that required to suture the mitral valve annulus and to tie sutures using 2D vision (p∠0.01). However, there was no significant difference in the maximum force applied by novices to the mitral valve during suturing (p = 0.3) and suture tying (p = 0.6) using either 2D or 3D visualization. Conclusion: This finding suggests that 3D visualization does not fully compensate for the absence of haptic feedback in robotics-assisted cardiac surgery. Keywords: Robotics-assisted surgery, visualization, cardiac surgery

Remote sensing of Earth terrain

NASA Technical Reports Server (NTRS)

Kong, Jin AU; Yueh, Herng-Aung

1990-01-01

The layered random medium model is used to investigate the fully polarimetric scattering of electromagnetic waves from vegetation. The vegetation canopy is modeled as an anisotropic random medium containing nonspherical scatterers with preferred alignment. The underlying medium is considered as a homogeneous half space. The scattering effect of the vegetation canopy are characterized by 3-D correlation functions with variances and correlation lengths respectively corresponding to the fluctuation strengths and the physical geometries of the scatterers. The strong fluctuation theory is used to calculate the anisotropic effective permittivity tensor of the random medium and the distorted Born approximation is then applied to obtain the covariance matrix which describes the fully polarimetric scattering properties of the vegetation field. This model accounts for all the interaction processes between the boundaries and the scatterers and includes all the coherent effects due to wave propagation in different directions such as the constructive and destructive interferences. For a vegetation canopy with low attenuation, the boundary between the vegetation and the underlying medium can give rise to significant coherent effects.

Invariant Theory for Dispersed Transverse Isotropy: An Efficient Means for Modeling Fiber Splay

NASA Technical Reports Server (NTRS)

Freed, alan D.; Einstein, Daniel R.; Vesely, Ivan

2004-01-01

Most soft tissues possess an oriented architecture of collagen fiber bundles, conferring both anisotropy and nonlinearity to their elastic behavior. Transverse isotropy has often been assumed for a subset of these tissues that have a single macroscopically-identifiable preferred fiber direction. Micro-structural studies, however, suggest that, in some tissues, collagen fibers are approximately normally distributed about a mean preferred fiber direction. Structural constitutive equations that account for this dispersion of fibers have been shown to capture the mechanical complexity of these tissues quite well. Such descriptions, however, are computationally cumbersome for two-dimensional (2D) fiber distributions, let alone for fully three-dimensional (3D) fiber populations. In this paper, we develop a new constitutive law for such tissues, based on a novel invariant theory for dispersed transverse isotropy. The invariant theory is based on a novel closed-form splay invariant that can easily handle 3D fiber populations, and that only requires a single parameter in the 2D case. The model is polyconvex and fits biaxial data for aortic valve tissue as accurately as the standard structural model. Modification of the fiber stress-strain law requires no re-formulation of the constitutive tangent matrix, making the model flexible for different types of soft tissues. Most importantly, the model is computationally expedient in a finite-element analysis.

3D chromosome rendering from Hi-C data using virtual reality

NASA Astrophysics Data System (ADS)

Zhu, Yixin; Selvaraj, Siddarth; Weber, Philip; Fang, Jennifer; Schulze, Jürgen P.; Ren, Bing

2015-01-01

Most genome browsers display DNA linearly, using single-dimensional depictions that are useful to examine certain epigenetic mechanisms such as DNA methylation. However, these representations are insufficient to visualize intrachromosomal interactions and relationships between distal genome features. Relationships between DNA regions may be difficult to decipher or missed entirely if those regions are distant in one dimension but could be spatially proximal when mapped to three-dimensional space. For example, the visualization of enhancers folding over genes is only fully expressed in three-dimensional space. Thus, to accurately understand DNA behavior during gene expression, a means to model chromosomes is essential. Using coordinates generated from Hi-C interaction frequency data, we have created interactive 3D models of whole chromosome structures and its respective domains. We have also rendered information on genomic features such as genes, CTCF binding sites, and enhancers. The goal of this article is to present the procedure, findings, and conclusions of our models and renderings.

Density functional plus dynamical mean-field theory of the metal-insulator transition in early transition-metal oxides

NASA Astrophysics Data System (ADS)

Dang, Hung T.; Ai, Xinyuan; Millis, Andrew J.; Marianetti, Chris A.

2014-09-01

The combination of density functional theory and single-site dynamical mean-field theory, using both Hartree and full continuous-time quantum Monte Carlo impurity solvers, is used to study the metal-insulator phase diagram of perovskite transition-metal oxides of the form ABO3 with a rare-earth ion A =Sr, La, Y and transition metal B =Ti, V, Cr. The correlated subspace is constructed from atomiclike d orbitals defined using maximally localized Wannier functions derived from the full p-d manifold; for comparison, results obtained using a projector method are also given. Paramagnetic DFT + DMFT computations using full charge self-consistency along with the standard "fully localized limit" (FLL) double counting are shown to incorrectly predict that LaTiO3, YTiO3, LaVO3, and SrMnO3 are metals. A more general examination of the dependence of physical properties on the mean p-d energy splitting, the occupancy of the correlated d states, the double-counting correction, and the lattice structure demonstrates the importance of charge-transfer physics even in the early transition-metal oxides and elucidates the factors underlying the failure of the standard approximations. If the double counting is chosen to produce a p-d splitting consistent with experimental spectra, single-site dynamical mean-field theory provides a reasonable account of the materials properties. The relation of the results to those obtained from "d-only" models in which the correlation problem is based on the frontier orbital p-d antibonding bands is determined. It is found that if an effective interaction U is properly chosen the d-only model provides a good account of the physics of the d1 and d2 materials.

Developing an integrated 3D-hydrodynamic and emerging contaminant model for assessing water quality in a Yangtze Estuary Reservoir.

PubMed

Xu, Cong; Zhang, Jingjie; Bi, Xiaowei; Xu, Zheng; He, Yiliang; Gin, Karina Yew-Hoong

2017-12-01

An integrated 3D-hydrodynamic and emerging contaminant model was developed for better understanding of the fate and transport of emerging contaminants in Qingcaosha Reservoir. The reservoir, which supplies drinking water for nearly half of Shanghai's population, is located in Yangtze Delta. The integrated model was built by Delft3D suite, a fully integrated multidimensional modeling software. Atrazine and Bisphenol A (BPA) were selected as two representative emerging contaminants for the study in this reservoir. The hydrodynamic model was calibrated and validated against observations from 2011 to 2015 while the integrated model was calibrated against observations from 2014 to 2015 and then applied to explore the potential risk of high atrazine concentrations in the reservoir driven by agriculture activities. Our results show that the model is capable of describing the spatial and temporal patterns of water temperature, salinity and the dynamic distributions of two representative emerging contaminants (i.e. atrazine and BPA) in the reservoir. The physical and biodegradation processes in this study were found to play a crucial role in determining the fate and transport of atrazine and BPA in the reservoir. The model also provides an insight into the potential risk of emerging contaminants and possible mitigation thresholds. The integrated approach can be a very useful tool to support policy-makers in the future management of Qingcaosha Reservoir. Copyright © 2017 Elsevier Ltd. All rights reserved.

Integration of 3D anatomical data obtained by CT imaging and 3D optical scanning for computer aided implant surgery

PubMed Central

2011-01-01

Background A precise placement of dental implants is a crucial step to optimize both prosthetic aspects and functional constraints. In this context, the use of virtual guiding systems has been recognized as a fundamental tool to control the ideal implant position. In particular, complex periodontal surgeries can be performed using preoperative planning based on CT data. The critical point of the procedure relies on the lack of accuracy in transferring CT planning information to surgical field through custom-made stereo-lithographic surgical guides. Methods In this work, a novel methodology is proposed for monitoring loss of accuracy in transferring CT dental information into periodontal surgical field. The methodology is based on integrating 3D data of anatomical (impression and cast) and preoperative (radiographic template) models, obtained by both CT and optical scanning processes. Results A clinical case, relative to a fully edentulous jaw patient, has been used as test case to assess the accuracy of the various steps concurring in manufacturing surgical guides. In particular, a surgical guide has been designed to place implants in the bone structure of the patient. The analysis of the results has allowed the clinician to monitor all the errors, which have been occurring step by step manufacturing the physical templates. Conclusions The use of an optical scanner, which has a higher resolution and accuracy than CT scanning, has demonstrated to be a valid support to control the precision of the various physical models adopted and to point out possible error sources. A case study regarding a fully edentulous patient has confirmed the feasibility of the proposed methodology. PMID:21338504

Search at BaBar for D^0--\\overlineD^0 Mixing using Semileptonic Decays.

NASA Astrophysics Data System (ADS)

Flood, Kevin

2004-05-01

Based on a 87 fb-1 dataset acquired by the Babar experiment running on and near the Υ(4S) from 1999-2002, a new upper limit is set on the rate of D^0--\\overlineD^0 mixing using the decay modes D^*+ arrow π^+ D^0, D^0 arrow [K / K^*]eν (+c.c.). These modes offer unambiguous initial and final-state charm flavor tags, and allow the combined use of the D^0 lifetime and D^*+--D^0 mass difference (Δ M) in a global likelihood fit. The high-statistics sample of reconstructed unmixed semileptonic D^0 decays is used to model Δ M and the time-dependence of mixed events directly from the data. Neural networks are used both to select events and to fully reconstruct the D^0. The current world-best published limit on semileptonic charm mixing is 5x10-3 (90% C.L.) (E791).

Quantitative wound healing measurement and monitoring system based on an innovative 3D imaging system

NASA Astrophysics Data System (ADS)

Yi, Steven; Yang, Arthur; Yin, Gongjie; Wen, James

2011-03-01

In this paper, we report a novel three-dimensional (3D) wound imaging system (hardware and software) under development at Technest Inc. System design is aimed to perform accurate 3D measurement and modeling of a wound and track its healing status over time. Accurate measurement and tracking of wound healing enables physicians to assess, document, improve, and individualize the treatment plan given to each wound patient. In current wound care practices, physicians often visually inspect or roughly measure the wound to evaluate the healing status. This is not an optimal practice since human vision lacks precision and consistency. In addition, quantifying slow or subtle changes through perception is very difficult. As a result, an instrument that quantifies both skin color and geometric shape variations would be particularly useful in helping clinicians to assess healing status and judge the effect of hyperemia, hematoma, local inflammation, secondary infection, and tissue necrosis. Once fully developed, our 3D imaging system will have several unique advantages over traditional methods for monitoring wound care: (a) Non-contact measurement; (b) Fast and easy to use; (c) up to 50 micron measurement accuracy; (d) 2D/3D Quantitative measurements;(e) A handheld device; and (f) Reasonable cost (< $1,000).

A fully integrated direct-conversion digital satellite tuner in 0.18 μm CMOS

NASA Astrophysics Data System (ADS)

Si, Chen; Zengwang, Yang; Mingliang, Gu

2011-04-01

A fully integrated direct-conversion digital satellite tuner for DVB-S/S2 and ABS-S applications is presented. A broadband noise-canceling Balun-LNA and passive quadrature mixers provided a high-linearity low noise RF front-end, while the synthesizer integrated the loop filter to reduce the solution cost and system debug time. Fabricated in 0.18 μm CMOS, the chip achieves a less than 7.6 dB noise figure over a 900-2150 MHz L-band, while the measured sensitivity for 4.42 MS/s QPSK-3/4 mode is -91 dBm at the PCB connector. The fully integrated integer-N synthesizer operating from 2150 to 4350 MHz achieves less than 1 °C integrated phase error. The chip consumes about 145 mA at a 3.3 V supply with internal integrated LDOs.

MobileFusion: real-time volumetric surface reconstruction and dense tracking on mobile phones.

PubMed

Ondrúška, Peter; Kohli, Pushmeet; Izadi, Shahram

2015-11-01

We present the first pipeline for real-time volumetric surface reconstruction and dense 6DoF camera tracking running purely on standard, off-the-shelf mobile phones. Using only the embedded RGB camera, our system allows users to scan objects of varying shape, size, and appearance in seconds, with real-time feedback during the capture process. Unlike existing state of the art methods, which produce only point-based 3D models on the phone, or require cloud-based processing, our hybrid GPU/CPU pipeline is unique in that it creates a connected 3D surface model directly on the device at 25Hz. In each frame, we perform dense 6DoF tracking, which continuously registers the RGB input to the incrementally built 3D model, minimizing a noise aware photoconsistency error metric. This is followed by efficient key-frame selection, and dense per-frame stereo matching. These depth maps are fused volumetrically using a method akin to KinectFusion, producing compelling surface models. For each frame, the implicit surface is extracted for live user feedback and pose estimation. We demonstrate scans of a variety of objects, and compare to a Kinect-based baseline, showing on average ∼ 1.5cm error. We qualitatively compare to a state of the art point-based mobile phone method, demonstrating an order of magnitude faster scanning times, and fully connected surface models.

Connection between plasma response and resonant magnetic perturbation (RMP) edge localized mode (ELM) suppression in DIII-D [Connection between plasma response and RMP ELM suppression in DIII-D

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

Wingen, Andreas; Ferraro, Nathaniel M.; Shafer, Morgan W.

Calculations of the plasma response to applied non-axisymmetric fields in several DIII-D discharges show that predicted displacements depend strongly on the edge current density. This result is found using both a linear two-fluid-MHD model (M3D-C1) and a nonlinear ideal-MHD model (VMEC). Furthermore, it is observed that the probability of a discharge being edge localized mode (ELM)-suppressed is most closely related to the edge current density, as opposed to the pressure gradient. It is found that discharges with a stronger kink response are closer to the peeling–ballooning stability limit in ELITE simulations and eventually cross into the unstable region, causing ELMsmore » to reappear. Thus for effective ELM suppression, the RMP has to prevent the plasma from generating a large kink response, associated with ELM instability. Experimental observations are in agreement with the finding; discharges which have a strong kink response in the MHD simulations show ELMs or ELM mitigation during the RMP phase of the experiment, while discharges with a small kink response in the MHD simulations are fully ELM suppressed in the experiment by the applied resonant magnetic perturbation. The results are cross-checked against modeled 3D ideal MHD equilibria using the VMEC code. The procedure of constructing optimal 3D equilibria for diverted H-mode discharges using VMEC is presented. As a result, kink displacements in VMEC are found to scale with the edge current density, similar to M3D-C1, but the displacements are smaller. A direct correlation in the flux surface displacements to the bootstrap current is shown.« less

Connection between plasma response and resonant magnetic perturbation (RMP) edge localized mode (ELM) suppression in DIII-D [Connection between plasma response and RMP ELM suppression in DIII-D

DOE PAGES

Wingen, Andreas; Ferraro, Nathaniel M.; Shafer, Morgan W.; ...

2015-09-03

Calculations of the plasma response to applied non-axisymmetric fields in several DIII-D discharges show that predicted displacements depend strongly on the edge current density. This result is found using both a linear two-fluid-MHD model (M3D-C1) and a nonlinear ideal-MHD model (VMEC). Furthermore, it is observed that the probability of a discharge being edge localized mode (ELM)-suppressed is most closely related to the edge current density, as opposed to the pressure gradient. It is found that discharges with a stronger kink response are closer to the peeling–ballooning stability limit in ELITE simulations and eventually cross into the unstable region, causing ELMsmore » to reappear. Thus for effective ELM suppression, the RMP has to prevent the plasma from generating a large kink response, associated with ELM instability. Experimental observations are in agreement with the finding; discharges which have a strong kink response in the MHD simulations show ELMs or ELM mitigation during the RMP phase of the experiment, while discharges with a small kink response in the MHD simulations are fully ELM suppressed in the experiment by the applied resonant magnetic perturbation. The results are cross-checked against modeled 3D ideal MHD equilibria using the VMEC code. The procedure of constructing optimal 3D equilibria for diverted H-mode discharges using VMEC is presented. As a result, kink displacements in VMEC are found to scale with the edge current density, similar to M3D-C1, but the displacements are smaller. A direct correlation in the flux surface displacements to the bootstrap current is shown.« less

Near-Infrared Light-Sensitive Polyvinyl Alcohol Hydrogel Photoresist for Spatiotemporal Control of Cell-Instructive 3D Microenvironments.

PubMed

Qin, Xiao-Hua; Wang, Xiaopu; Rottmar, Markus; Nelson, Bradley J; Maniura-Weber, Katharina

2018-03-01

Advanced hydrogel systems that allow precise control of cells and their 3D microenvironments are needed in tissue engineering, disease modeling, and drug screening. Multiphoton lithography (MPL) allows true 3D microfabrication of complex objects, but its biological application requires a cell-compatible hydrogel resist that is sufficiently photosensitive, cell-degradable, and permissive to support 3D cell growth. Here, an extremely photosensitive cell-responsive hydrogel composed of peptide-crosslinked polyvinyl alcohol (PVA) is designed to expand the biological applications of MPL. PVA hydrogels are formed rapidly by ultraviolet light within 1 min in the presence of cells, providing fully synthetic matrices that are instructive for cell-matrix remodeling, multicellular morphogenesis, and protease-mediated cell invasion. By focusing a multiphoton laser into a cell-laden PVA hydrogel, cell-instructive extracellular cues are site-specifically attached to the PVA matrix. Cell invasion is thus precisely guided in 3D with micrometer-scale spatial resolution. This robust hydrogel enables, for the first time, ultrafast MPL of cell-responsive synthetic matrices at writing speeds up to 50 mm s -1 . This approach should enable facile photochemical construction and manipulation of 3D cellular microenvironments with unprecedented flexibility and precision. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fully compressible solutions for early stage Richtmyer–Meshkov instability

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael

2016-10-27

Here, we will consider the effects of compressibility and viscosity on the early dynamics of the Richtmyer–Meshkov instability (RMI). In particular, we will combine theory, scaling, and high resolution simulation of RMI to probe the details of the initial compression and the subsequent viscous damping as a shock interacts with a density discontinuity. We will propose a refinement of the classic 1D model for the linear regime of RMI that, for small initial perturbation wavelengths, more accurately reproduces the 2D dynamics of a fully resolved numerical simulation.

Dynamics of tokamak plasma surface current in 3D ideal MHD model

NASA Astrophysics Data System (ADS)

Galkin, Sergei A.; Svidzinski, V. A.; Zakharov, L. E.

2013-10-01

Interest in the surface current which can arise on perturbed sharp plasma vacuum interface in tokamaks was recently generated by a few papers (see and references therein). In dangerous disruption events with plasma-touching-wall scenarios, the surface current can be shared with the wall leading to the strong, damaging forces acting on the wall A relatively simple analytic definition of δ-function surface current proportional to a jump of tangential component of magnetic field nevertheless leads to a complex computational problem on the moving plasma-vacuum interface, requiring the incorporation of non-linear 3D plasma dynamics even in one-fluid ideal MHD. The Disruption Simulation Code (DSC), which had recently been developed in a fully 3D toroidal geometry with adaptation to the moving plasma boundary, is an appropriate tool for accurate self-consistent δfunction surface current calculation. Progress on the DSC-3D development will be presented. Self-consistent surface current calculation under non-linear dynamics of low m kink mode and VDE will be discussed. Work is supported by the US DOE SBIR grant #DE-SC0004487.

Design method of freeform light distribution lens for LED automotive headlamp based on DMD

NASA Astrophysics Data System (ADS)

Ma, Jianshe; Huang, Jianwei; Su, Ping; Cui, Yao

2018-01-01

We propose a new method to design freeform light distribution lens for light-emitting diode (LED) automotive headlamp based on digital micro mirror device (DMD). With the Parallel optical path architecture, the exit pupil of the illuminating system is set in infinity. Thus the principal incident rays of micro lens in DMD is parallel. DMD is made of high speed digital optical reflection array, the function of distribution lens is to distribute the emergent parallel rays from DMD and get a lighting pattern that fully comply with the national regulation GB 25991-2010.We use DLP 4500 to design the light distribution lens, mesh the target plane regulated by the national regulation GB 25991-2010 and correlate the mesh grids with the active mirror array of DLP4500. With the mapping relations and the refraction law, we can build the mathematics model and get the parameters of freeform light distribution lens. Then we import its parameter into the three-dimensional (3D) software CATIA to construct its 3D model. The ray tracing results using Tracepro demonstrate that the Illumination value of target plane is easily adjustable and fully comply with the requirement of the national regulation GB 25991-2010 by adjusting the exit brightness value of DMD. The theoretical optical efficiencies of the light distribution lens designed using this method could be up to 92% without any other auxiliary lens.

Automatic testing and assessment of neuroanatomy using a digital brain atlas: method and development of computer- and mobile-based applications.

PubMed

Nowinski, Wieslaw L; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G; Marchenko, Yevgen; Volkau, Ihar

2009-10-01

Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to Terminologia Anatomica. Because the cerebral models are fully segmented and labeled, our approach enables automatic and random atlas-derived generation of questions to test location and naming of cerebral structures. This is done in four steps: test individualization by the instructor, test taking by the students at their convenience, automatic student assessment by the application, and communication of the individual assessment to the instructor. A computer-based application with an interactive 3D atlas and a preliminary mobile-based application were developed to realize this approach. The application works in two test modes: instructor and student. In the instructor mode, the instructor customizes the test by setting the scope of testing and student performance criteria, which takes a few seconds. In the student mode, the student is tested and automatically assessed. Self-testing is also feasible at any time and pace. Our approach is automatic both with respect to test generation and student assessment. It is also objective, rapid, and customizable. We believe that this approach is novel from computer-based, mobile-based, and atlas-assisted standpoints.

The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

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

Blecic, Jasmina; Dobbs-Dixon, Ian; Greene, Thomas, E-mail: jasmina@nyu.edu

Using the atmospheric structure from a 3D global radiation-hydrodynamic simulation of HD 189733b and the open-source Bayesian Atmospheric Radiative Transfer (BART) code, we investigate the difference between the secondary-eclipse temperature structure produced with a 3D simulation and the best-fit 1D retrieved model. Synthetic data are generated by integrating the 3D models over the Spitzer , the Hubble Space Telescope ( HST ), and the James Web Space Telescope ( JWST ) bandpasses, covering the wavelength range between 1 and 11 μ m where most spectroscopically active species have pronounced features. Using the data from different observing instruments, we present detailedmore » comparisons between the temperature–pressure profiles recovered by BART and those from the 3D simulations. We calculate several averages of the 3D thermal structure and explore which particular thermal profile matches the retrieved temperature structure. We implement two temperature parameterizations that are commonly used in retrieval to investigate different thermal profile shapes. To assess which part of the thermal structure is best constrained by the data, we generate contribution functions for our theoretical model and each of our retrieved models. Our conclusions are strongly affected by the spectral resolution of the instruments included, their wavelength coverage, and the number of data points combined. We also see some limitations in each of the temperature parametrizations, as they are not able to fully match the complex curvatures that are usually produced in hydrodynamic simulations. The results show that our 1D retrieval is recovering a temperature and pressure profile that most closely matches the arithmetic average of the 3D thermal structure. When we use a higher resolution, more data points, and a parametrized temperature profile that allows more flexibility in the middle part of the atmosphere, we find a better match between the retrieved temperature and pressure profile and the arithmetic average. The Spitzer and HST simulated observations sample deep parts of the planetary atmosphere and provide fewer constraints on the temperature and pressure profile, while the JWST observations sample the middle part of the atmosphere, providing a good match with the middle and most complex part of the arithmetic average of the 3D temperature structure.« less

A continuous mixing model for pdf simulations and its applications to combusting shear flows

NASA Technical Reports Server (NTRS)

Hsu, A. T.; Chen, J.-Y.

1991-01-01

The problem of time discontinuity (or jump condition) in the coalescence/dispersion (C/D) mixing model is addressed in this work. A C/D mixing model continuous in time is introduced. With the continuous mixing model, the process of chemical reaction can be fully coupled with mixing. In the case of homogeneous turbulence decay, the new model predicts a pdf very close to a Gaussian distribution, with finite higher moments also close to that of a Gaussian distribution. Results from the continuous mixing model are compared with both experimental data and numerical results from conventional C/D models.

Choice of Tuning Parameters on 3D IC Engine Simulations Using G-Equation

DOE PAGES

Liu, Jinlong; Szybist, James; Dumitrescu, Cosmin

2018-04-03

3D CFD spark-ignition IC engine simulations are extremely complex for the regular user. Truly-predictive CFD simulations for the turbulent flame combustion that solve fully coupled transport/chemistry equations may require large computational capabilities unavailable to regular CFD users. A solution is to use a simpler phenomenological model such as the G-equation that decouples transport/chemistry result. Such simulation can still provide acceptable and faster results at the expense of predictive capabilities. While the G-equation is well understood within the experienced modeling community, the goal of this paper is to document some of them for a novice or less experienced CFD user whomore » may not be aware that phenomenological models of turbulent flame combustion usually require heavy tuning and calibration from the user to mimic experimental observations. This study used ANSYS® Forte, Version 17.2, and the built-in G-equation model, to investigate two tuning constants that influence flame propagation in 3D CFD SI engine simulations: the stretch factor coefficient, Cms and the flame development coefficient, Cm2. After identifying several Cm2-Cms pairs that matched experimental data at one operating conditions, simulation results showed that engine models that used different Cm2-Cms sets predicted similar combustion performance, when the spark timing, engine load, and engine speed were changed from the operating condition used to validate the CFD simulation. A dramatic shift was observed when engine speed was doubled, which suggested that the flame stretch coefficient, Cms, had a much larger influence at higher engine speeds compared to the flame development coefficient, Cm2. Therefore, the Cm2-Cms sets that predicted a higher turbulent flame under higher in-cylinder pressure and temperature increased the peak pressure and efficiency. This suggest that the choice of the Cm2-Cms will affect the G-equation-based simulation accuracy when engine speed increases from the one used to validate the model. As a result, for the less-experienced CFD user and in the absence of enough experimental data that would help retune the tuning parameters at various operating conditions, the purpose of a good G-equation-based 3D engine simulation is to guide and/or complement experimental investigations, not the other way around. Only a truly-predictive simulation that fully couples the turbulence/chemistry equations can help reduce the amount of experimental work.« less

Choice of Tuning Parameters on 3D IC Engine Simulations Using G-Equation

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

Liu, Jinlong; Szybist, James; Dumitrescu, Cosmin

3D CFD spark-ignition IC engine simulations are extremely complex for the regular user. Truly-predictive CFD simulations for the turbulent flame combustion that solve fully coupled transport/chemistry equations may require large computational capabilities unavailable to regular CFD users. A solution is to use a simpler phenomenological model such as the G-equation that decouples transport/chemistry result. Such simulation can still provide acceptable and faster results at the expense of predictive capabilities. While the G-equation is well understood within the experienced modeling community, the goal of this paper is to document some of them for a novice or less experienced CFD user whomore » may not be aware that phenomenological models of turbulent flame combustion usually require heavy tuning and calibration from the user to mimic experimental observations. This study used ANSYS® Forte, Version 17.2, and the built-in G-equation model, to investigate two tuning constants that influence flame propagation in 3D CFD SI engine simulations: the stretch factor coefficient, Cms and the flame development coefficient, Cm2. After identifying several Cm2-Cms pairs that matched experimental data at one operating conditions, simulation results showed that engine models that used different Cm2-Cms sets predicted similar combustion performance, when the spark timing, engine load, and engine speed were changed from the operating condition used to validate the CFD simulation. A dramatic shift was observed when engine speed was doubled, which suggested that the flame stretch coefficient, Cms, had a much larger influence at higher engine speeds compared to the flame development coefficient, Cm2. Therefore, the Cm2-Cms sets that predicted a higher turbulent flame under higher in-cylinder pressure and temperature increased the peak pressure and efficiency. This suggest that the choice of the Cm2-Cms will affect the G-equation-based simulation accuracy when engine speed increases from the one used to validate the model. As a result, for the less-experienced CFD user and in the absence of enough experimental data that would help retune the tuning parameters at various operating conditions, the purpose of a good G-equation-based 3D engine simulation is to guide and/or complement experimental investigations, not the other way around. Only a truly-predictive simulation that fully couples the turbulence/chemistry equations can help reduce the amount of experimental work.« less

Genotoxic Effects of Low- and High-LET Radiation on Human Epithelial Cells Grown in 2-D Versus 3-D Culture

NASA Technical Reports Server (NTRS)

Patel, Z. S.; Cucinotta, F. A.; Huff, J. L.

2011-01-01

Risk estimation for radiation-induced cancer relies heavily on human epidemiology data obtained from terrestrial irradiation incidents from sources such as medical and occupational exposures as well as from the atomic bomb survivors. No such data exists for exposures to the types and doses of high-LET radiation that will be encountered during space travel; therefore, risk assessment for space radiation requires the use of data derived from cell culture and animal models. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. This work compares the genotoxic effects of radiation on normal human epithelial cells grown in standard 2-D monolayer culture compared to 3-D organotypic co-culture conditions. These 3-D organotypic models mimic the morphological features, differentiation markers, and growth characteristics of fully-differentiated normal human tissue and are reproducible using defined components. Cultures were irradiated with 2 Gy low-LET gamma rays or varying doses of high-LET particle radiation and genotoxic damage was measured using a modified cytokinesis block micronucleus assay. Our results revealed a 2-fold increase in residual damage in 2 Gy gamma irradiated cells grown under organotypic culture conditions compared to monolayer culture. Irradiation with high-LET particle radiation gave similar results, while background levels of damage were comparable under both scenarios. These observations may be related to the phenomenon of "multicellular resistance" where cancer cells grown as 3-D spheroids or in vivo exhibit an increased resistance to killing by chemotherapeutic agents compared to the same cells grown in 2-D culture. A variety of factors are likely involved in mediating this process, including increased cell-cell communication, microenvironment influences, and changes in cell cycle kinetics that may promote survival of damaged cells in 3-D culture that would otherwise die or be rendered reproductively inactive in 2-D culture.

SU-D-213-03: Towards An Optimized 3D Scintillation Dosimetry Tool for Quality Assurance of Dynamic Radiotherapy Techniques

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

Rilling, M; Centre de Recherche sur le Cancer, Hôtel-Dieu de Québec, Quebec City, QC; Département de radio-oncologie, CHU de Québec, Quebec City, QC

2015-06-15

Purpose: The purpose of this work is to simulate a multi-focus plenoptic camera used as the measuring device in a real-time three-dimensional scintillation dosimeter. Simulating and optimizing this realistic optical system will bridge the technological gap between concept validation and a clinically viable tool that can provide highly efficient, accurate and precise measurements for dynamic radiotherapy techniques. Methods: The experimental prototype, previously developed for proof of concept purposes, uses an off-the-shelf multi-focus plenoptic camera. With an array of interleaved microlenses of different focal lengths, this camera records spatial and angular information of light emitted by a plastic scintillator volume. Themore » three distinct microlens focal lengths were determined experimentally for use as baseline parameters by measuring image-to-object magnification for different distances in object space. A simulated plenoptic system was implemented using the non-sequential ray tracing software Zemax: this tool allows complete simulation of multiple optical paths by modeling interactions at interfaces such as scatter, diffraction, reflection and refraction. The active sensor was modeled based on the camera manufacturer specifications by a 2048×2048, 5 µm-pixel pitch sensor. Planar light sources, simulating the plastic scintillator volume, were employed for ray tracing simulations. Results: The microlens focal lengths were determined to be 384, 327 and 290 µm. A realistic multi-focus plenoptic system, with independently defined and optimizable specifications, was fully simulated. A f/2.9 and 54 mm-focal length Double Gauss objective was modeled as the system’s main lens. A three-focal length hexagonal microlens array of 250-µm thickness was designed, acting as an image-relay system between the main lens and sensor. Conclusion: Simulation of a fully modeled multi-focus plenoptic camera enables the decoupled optimization of the main lens and microlens 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.« less

Additive Manufacturing in the Marine Corps

DTIC Science & Technology

2015-06-01

commonly referred to as 3D printing. This thesis answers the question of how additive manufacturing can improve the effectiveness of Marine Corps...analysis of current and future 3D -printing processes, examination of several civilian and military examples, and examination of the impact across...fully integrating 3D printers, such as the lack of certification and qualification standards, unreliable end product results, and determining ownership

A statistical shape modelling framework to extract 3D shape biomarkers from medical imaging data: assessing arch morphology of repaired coarctation of the aorta.

PubMed

Bruse, Jan L; McLeod, Kristin; Biglino, Giovanni; Ntsinjana, Hopewell N; Capelli, Claudio; Hsia, Tain-Yen; Sermesant, Maxime; Pennec, Xavier; Taylor, Andrew M; Schievano, Silvia

2016-05-31

Medical image analysis in clinical practice is commonly carried out on 2D image data, without fully exploiting the detailed 3D anatomical information that is provided by modern non-invasive medical imaging techniques. In this paper, a statistical shape analysis method is presented, which enables the extraction of 3D anatomical shape features from cardiovascular magnetic resonance (CMR) image data, with no need for manual landmarking. The method was applied to repaired aortic coarctation arches that present complex shapes, with the aim of capturing shape features as biomarkers of potential functional relevance. The method is presented from the user-perspective and is evaluated by comparing results with traditional morphometric measurements. Steps required to set up the statistical shape modelling analyses, from pre-processing of the CMR images to parameter setting and strategies to account for size differences and outliers, are described in detail. The anatomical mean shape of 20 aortic arches post-aortic coarctation repair (CoA) was computed based on surface models reconstructed from CMR data. By analysing transformations that deform the mean shape towards each of the individual patient's anatomy, shape patterns related to differences in body surface area (BSA) and ejection fraction (EF) were extracted. The resulting shape vectors, describing shape features in 3D, were compared with traditionally measured 2D and 3D morphometric parameters. The computed 3D mean shape was close to population mean values of geometric shape descriptors and visually integrated characteristic shape features associated with our population of CoA shapes. After removing size effects due to differences in body surface area (BSA) between patients, distinct 3D shape features of the aortic arch correlated significantly with EF (r = 0.521, p = .022) and were well in agreement with trends as shown by traditional shape descriptors. The suggested method has the potential to discover previously unknown 3D shape biomarkers from medical imaging data. Thus, it could contribute to improving diagnosis and risk stratification in complex cardiac disease.

Motion compensation for fully 4D PET reconstruction using PET superset data

NASA Astrophysics Data System (ADS)

Verhaeghe, J.; Gravel, P.; Mio, R.; Fukasawa, R.; Rosa-Neto, P.; Soucy, J.-P.; Thompson, C. J.; Reader, A. J.

2010-07-01

Fully 4D PET image reconstruction is receiving increasing research interest due to its ability to significantly reduce spatiotemporal noise in dynamic PET imaging. However, thus far in the literature, the important issue of correcting for subject head motion has not been considered. Specifically, as a direct consequence of using temporally extensive basis functions, a single instance of movement propagates to impair the reconstruction of multiple time frames, even if no further movement occurs in those frames. Existing 3D motion compensation strategies have not yet been adapted to 4D reconstruction, and as such the benefits of 4D algorithms have not yet been reaped in a clinical setting where head movement undoubtedly occurs. This work addresses this need, developing a motion compensation method suitable for fully 4D reconstruction methods which exploits an optical tracking system to measure the head motion along with PET superset data to store the motion compensated data. List-mode events are histogrammed as PET superset data according to the measured motion, and a specially devised normalization scheme for motion compensated reconstruction from the superset data is required. This work proceeds to propose the corresponding time-dependent normalization modifications which are required for a major class of fully 4D image reconstruction algorithms (those which use linear combinations of temporal basis functions). Using realistically simulated as well as real high-resolution PET data from the HRRT, we demonstrate both the detrimental impact of subject head motion in fully 4D PET reconstruction and the efficacy of our proposed modifications to 4D algorithms. Benefits are shown both for the individual PET image frames as well as for parametric images of tracer uptake and volume of distribution for 18F-FDG obtained from Patlak analysis.

Motion compensation for fully 4D PET reconstruction using PET superset data.

PubMed

Verhaeghe, J; Gravel, P; Mio, R; Fukasawa, R; Rosa-Neto, P; Soucy, J-P; Thompson, C J; Reader, A J

2010-07-21

Fully 4D PET image reconstruction is receiving increasing research interest due to its ability to significantly reduce spatiotemporal noise in dynamic PET imaging. However, thus far in the literature, the important issue of correcting for subject head motion has not been considered. Specifically, as a direct consequence of using temporally extensive basis functions, a single instance of movement propagates to impair the reconstruction of multiple time frames, even if no further movement occurs in those frames. Existing 3D motion compensation strategies have not yet been adapted to 4D reconstruction, and as such the benefits of 4D algorithms have not yet been reaped in a clinical setting where head movement undoubtedly occurs. This work addresses this need, developing a motion compensation method suitable for fully 4D reconstruction methods which exploits an optical tracking system to measure the head motion along with PET superset data to store the motion compensated data. List-mode events are histogrammed as PET superset data according to the measured motion, and a specially devised normalization scheme for motion compensated reconstruction from the superset data is required. This work proceeds to propose the corresponding time-dependent normalization modifications which are required for a major class of fully 4D image reconstruction algorithms (those which use linear combinations of temporal basis functions). Using realistically simulated as well as real high-resolution PET data from the HRRT, we demonstrate both the detrimental impact of subject head motion in fully 4D PET reconstruction and the efficacy of our proposed modifications to 4D algorithms. Benefits are shown both for the individual PET image frames as well as for parametric images of tracer uptake and volume of distribution for (18)F-FDG obtained from Patlak analysis.

Investigation of surface wave amplitudes in 3-D velocity and 3-D Q models

NASA Astrophysics Data System (ADS)

Ruan, Y.; Zhou, Y.

2010-12-01

It has been long recognized that seismic amplitudes depend on both wave speed structures and anelasticity (Q) structures. However, the effects of lateral heterogeneities in wave speed and Q structures on seismic amplitudes has not been well understood. We investigate the effects of 3-D wave speed and 3-D anelasticity (Q) structures on surface-wave amplitudes based upon wave propagation simulations of twelve globally-distributed earthquakes and 801 stations in Earth models with and without lateral heterogeneities in wave speed and anelasticity using a Spectral Element Method (SEM). Our tomographic-like 3-D Q models are converted from a velocity model S20RTS using a set of reasonable mineralogical parameters, assuming lateral perturbations in both velocity and Q are due to temperature perturbations. Surface-wave amplitude variations of SEM seismograms are measured in the period range of 50--200 s using boxcar taper, cosine taper and Slepian multi-tapers. We calculate ray-theoretical predictions of surface-wave amplitude perturbations due to elastic focusing, attenuation, and anelastic focusing which respectively depend upon the second spatial derivative (''roughness'') of perturbations in phase velocity, 1/Q, and the roughness of perturbations in 1/Q. Both numerical experiments and theoretical calculations show that (1) for short-period (~ 50 s) surface waves, the effects of amplitude attenuation due to 3-D Q structures are comparable with elastic focusing effects due to 3-D wave speed structures; and (2) for long-period (> 100 s) surface waves, the effects of attenuation become much weaker than elastic focusing; and (3) elastic focusing effects are correlated with anelastic focusing at all periods due to the correlation between velocity and Q models; and (4) amplitude perturbations are depend on measurement techniques and therefore cannot be directly compared with ray-theoretical predictions because ray theory does not account for the effects of measurement techniques. We calculate 3-D finite-frequency sensitivity of surface-wave amplitude to perturbations in wave speed and anelasticity (Q) which fully account for the effects of elastic focusing, attenuation, anelastic focusing as well as measurement techniques. We show that amplitude perturbations calculated using wave speed and Q sensitivity kernels agree reasonably well with SEM measurements and therefore the sensitivity kernels can be used in a joint inversion of seismic phase delays and amplitudes to simultaneously image high resolution 3-D wave speed and 3-D Q structures in the upper mantle.

Can Computational Sediment Transport Models Reproduce the Observed Variability of Channel Networks in Modern Deltas?

NASA Astrophysics Data System (ADS)

Nesvold, E.; Mukerji, T.

2017-12-01

River deltas display complex channel networks that can be characterized through the framework of graph theory, as shown by Tejedor et al. (2015). Deltaic patterns may also be useful in a Bayesian approach to uncertainty quantification of the subsurface, but this requires a prior distribution of the networks of ancient deltas. By considering subaerial deltas, one can at least obtain a snapshot in time of the channel network spectrum across deltas. In this study, the directed graph structure is semi-automatically extracted from satellite imagery using techniques from statistical processing and machine learning. Once the network is labeled with vertices and edges, spatial trends and width and sinuosity distributions can also be found easily. Since imagery is inherently 2D, computational sediment transport models can serve as a link between 2D network structure and 3D depositional elements; the numerous empirical rules and parameters built into such models makes it necessary to validate the output with field data. For this purpose we have used a set of 110 modern deltas, with average water discharge ranging from 10 - 200,000 m3/s, as a benchmark for natural variability. Both graph theoretic and more general distributions are established. A key question is whether it is possible to reproduce this deltaic network spectrum with computational models. Delft3D was used to solve the shallow water equations coupled with sediment transport. The experimental setup was relatively simple; incoming channelized flow onto a tilted plane, with varying wave and tidal energy, sediment types and grain size distributions, river discharge and a few other input parameters. Each realization was run until a delta had fully developed: between 50 and 500 years (with a morphology acceleration factor). It is shown that input parameters should not be sampled independently from the natural ranges, since this may result in deltaic output that falls well outside the natural spectrum. Since we are interested in studying the patterns occurring in nature, ideas are proposed for how to sample computer realizations that match this distribution. By establishing a link between surface based patterns from the field with the associated subsurface structure from physics-based models, this is a step towards a fully Bayesian workflow in subsurface simulation.

Fully implicit moving mesh adaptive algorithm

NASA Astrophysics Data System (ADS)

Serazio, C.; Chacon, L.; Lapenta, G.

2006-10-01

In many problems of interest, the numerical modeler is faced with the challenge of dealing with multiple time and length scales. The former is best dealt with with fully implicit methods, which are able to step over fast frequencies to resolve the dynamical time scale of interest. The latter requires grid adaptivity for efficiency. Moving-mesh grid adaptive methods are attractive because they can be designed to minimize the numerical error for a given resolution. However, the required grid governing equations are typically very nonlinear and stiff, and of considerably difficult numerical treatment. Not surprisingly, fully coupled, implicit approaches where the grid and the physics equations are solved simultaneously are rare in the literature, and circumscribed to 1D geometries. In this study, we present a fully implicit algorithm for moving mesh methods that is feasible for multidimensional geometries. Crucial elements are the development of an effective multilevel treatment of the grid equation, and a robust, rigorous error estimator. For the latter, we explore the effectiveness of a coarse grid correction error estimator, which faithfully reproduces spatial truncation errors for conservative equations. We will show that the moving mesh approach is competitive vs. uniform grids both in accuracy (due to adaptivity) and efficiency. Results for a variety of models 1D and 2D geometries will be presented. L. Chac'on, G. Lapenta, J. Comput. Phys., 212 (2), 703 (2006) G. Lapenta, L. Chac'on, J. Comput. Phys., accepted (2006)

Compensated Row-Column Ultrasound Imaging System Using Fisher Tippett Multilayered Conditional Random Field Model

PubMed Central

Ben Daya, Ibrahim; Chen, Albert I. H.; Shafiee, Mohammad Javad; Wong, Alexander; Yeow, John T. W.

2015-01-01

3-D ultrasound imaging offers unique opportunities in the field of non destructive testing that cannot be easily found in A-mode and B-mode images. To acquire a 3-D ultrasound image without a mechanically moving transducer, a 2-D array can be used. The row column technique is preferred over a fully addressed 2-D array as it requires a significantly lower number of interconnections. Recent advances in 3-D row-column ultrasound imaging systems were largely focused on sensor design. However, these imaging systems face three intrinsic challenges that cannot be addressed by improving sensor design alone: speckle noise, sparsity of data in the imaged volume, and the spatially dependent point spread function of the imaging system. In this paper, we propose a compensated row-column ultrasound image reconstruction system using Fisher-Tippett multilayered conditional random field model. Tests carried out on both simulated and real row-column ultrasound images show the effectiveness of our proposed system as opposed to other published systems. Visual assessment of the results show our proposed system’s potential at preserving detail and reducing speckle. Quantitative analysis shows that our proposed system outperforms previously published systems when evaluated with metrics such as Peak Signal to Noise Ratio, Coefficient of Correlation, and Effective Number of Looks. These results show the potential of our proposed system as an effective tool for enhancing 3-D row-column imaging. PMID:26658577

A fully automatic three-step liver segmentation method on LDA-based probability maps for multiple contrast MR images.

PubMed

Gloger, Oliver; Kühn, Jens; Stanski, Adam; Völzke, Henry; Puls, Ralf

2010-07-01

Automatic 3D liver segmentation in magnetic resonance (MR) data sets has proven to be a very challenging task in the domain of medical image analysis. There exist numerous approaches for automatic 3D liver segmentation on computer tomography data sets that have influenced the segmentation of MR images. In contrast to previous approaches to liver segmentation in MR data sets, we use all available MR channel information of different weightings and formulate liver tissue and position probabilities in a probabilistic framework. We apply multiclass linear discriminant analysis as a fast and efficient dimensionality reduction technique and generate probability maps then used for segmentation. We develop a fully automatic three-step 3D segmentation approach based upon a modified region growing approach and a further threshold technique. Finally, we incorporate characteristic prior knowledge to improve the segmentation results. This novel 3D segmentation approach is modularized and can be applied for normal and fat accumulated liver tissue properties. Copyright 2010 Elsevier Inc. All rights reserved.

Some practical turbulence modeling options for Reynolds-averaged full Navier-Stokes calculations of three-dimensional flows

NASA Technical Reports Server (NTRS)

Bui, Trong T.

1993-01-01

New turbulence modeling options recently implemented for the 3-D version of Proteus, a Reynolds-averaged compressible Navier-Stokes code, are described. The implemented turbulence models include: the Baldwin-Lomax algebraic model, the Baldwin-Barth one-equation model, the Chien k-epsilon model, and the Launder-Sharma k-epsilon model. Features of this turbulence modeling package include: well documented and easy to use turbulence modeling options, uniform integration of turbulence models from different classes, automatic initialization of turbulence variables for calculations using one- or two-equation turbulence models, multiple solid boundaries treatment, and fully vectorized L-U solver for one- and two-equation models. Validation test cases include the incompressible and compressible flat plate turbulent boundary layers, turbulent developing S-duct flow, and glancing shock wave/turbulent boundary layer interaction. Good agreement is obtained between the computational results and experimental data. Sensitivity of the compressible turbulent solutions with the method of y(sup +) computation, the turbulent length scale correction, and some compressibility corrections are examined in detail. The test cases show that the highly optimized one-and two-equation turbulence models can be used in routine 3-D Navier-Stokes computations with no significant increase in CPU time as compared with the Baldwin-Lomax algebraic model.

Laboratory Measurements for H3+ Deuteration Reactions

NASA Astrophysics Data System (ADS)

Bowen, Kyle; Hillenbrand, Pierre-Michel; Urbain, Xavier; Savin, Daniel Wolf

2018-06-01

Deuterated molecules are important chemical tracers of protostellar cores. At the ~106 cm-3 particle densities and ~20 K temperatures typical for protostellar cores, most molecules freeze onto dust grains. A notable exception is H3+ and its isotopologues. These become important carriers of positive charge in the gas, can couple to any ambient magnetic field, and can thereby alter the cloud dynamics. Knowing the total abundance of H3+ and its isotopologues is important for studying the evolution of protostellar cores. However, H3+ and D3+ have no dipole moment. They lack a pure rotational spectrum and are not observable at protostellar core temperatures. Fortunately H2D+ and D2H+ have dipole moments and a pure rotational spectrum that can be excited in protostellar cores. Observations of these two molecules, combined with astrochemical models, provide information about the total abundance of H3+ and all its isotopologues. The inferred abundances, though, rely on accurate astrochemical data for the deuteration of H3+ and its isotopologues.Here we present laboratory measurements of the rate coefficients for three important deuterating reactions, namely D + H3+/H2D+/D2H+ → H + H2D+/ D2H+/D3+. Astrochemical models currently rely on rate coefficients from classical (Langevin) or semi-classical methods for these reactions, as fully quantum-mechanical calculations are beyond current computational capabilities. Laboratory studies are the most tractable means of providing the needed data. For our studies we used our novel dual-source, merged fast-beams apparatus, which enables us to study reactions of neutral atoms and molecular ions. Co-propagating beams allow us to measure experimental rate coefficients as a function of collision energy. We extract cross section data from these results, which we then convolve with a Maxwell-Boltzmann distribution to generate thermal rate coefficients. Here we present our results for these three reactions and discuss some implications.

Volumetric image classification using homogeneous decomposition and dictionary learning: A study using retinal optical coherence tomography for detecting age-related macular degeneration.

PubMed

Albarrak, Abdulrahman; Coenen, Frans; Zheng, Yalin

2017-01-01

Three-dimensional (3D) (volumetric) diagnostic imaging techniques are indispensable with respect to the diagnosis and management of many medical conditions. However there is a lack of automated diagnosis techniques to facilitate such 3D image analysis (although some support tools do exist). This paper proposes a novel framework for volumetric medical image classification founded on homogeneous decomposition and dictionary learning. In the proposed framework each image (volume) is recursively decomposed until homogeneous regions are arrived at. Each region is represented using a Histogram of Oriented Gradients (HOG) which is transformed into a set of feature vectors. The Gaussian Mixture Model (GMM) is then used to generate a "dictionary" and the Improved Fisher Kernel (IFK) approach is used to encode feature vectors so as to generate a single feature vector for each volume, which can then be fed into a classifier generator. The principal advantage offered by the framework is that it does not require the detection (segmentation) of specific objects within the input data. The nature of the framework is fully described. A wide range of experiments was conducted with which to analyse the operation of the proposed framework and these are also reported fully in the paper. Although the proposed approach is generally applicable to 3D volumetric images, the focus for the work is 3D retinal Optical Coherence Tomography (OCT) images in the context of the diagnosis of Age-related Macular Degeneration (AMD). The results indicate that excellent diagnostic predictions can be produced using the proposed framework. Copyright © 2016 Elsevier Ltd. All rights reserved.

Testing a 1-D Analytical Salt Intrusion Model and the Predictive Equation in Malaysian Estuaries

NASA Astrophysics Data System (ADS)

Gisen, Jacqueline Isabella; Savenije, Hubert H. G.

2013-04-01

Little is known about the salt intrusion behaviour in Malaysian estuaries. Study on this topic sometimes requires large amounts of data especially if a 2-D or 3-D numerical models are used for analysis. In poor data environments, 1-D analytical models are more appropriate. For this reason, a fully analytical 1-D salt intrusion model, based on the theory of Savenije in 2005, was tested in three Malaysian estuaries (Bernam, Selangor and Muar) because it is simple and requires minimal data. In order to achieve that, site surveys were conducted in these estuaries during the dry season (June-August) at spring tide by moving boat technique. Data of cross-sections, water levels and salinity were collected, and then analysed with the salt intrusion model. This paper demonstrates a good fit between the simulated and observed salinity distribution for all three estuaries. Additionally, the calibrated Van der Burgh's coefficient K, Dispersion coefficient D0, and salt intrusion length L, for the estuaries also displayed a reasonable correlations with those calculated from the predictive equations. This indicates that not only is the salt intrusion model valid for the case studies in Malaysia but also the predictive model. Furthermore, the results from this study describe the current state of the estuaries with which the Malaysian water authority in Malaysia can make decisions on limiting water abstraction or dredging. Keywords: salt intrusion, Malaysian estuaries, discharge, predictive model, dispersion

Towards large-scale mapping of urban three-dimensional structure using Landsat imagery and global elevation datasets

NASA Astrophysics Data System (ADS)

Wang, P.; Huang, C.

2017-12-01

The three-dimensional (3D) structure of buildings and infrastructures is fundamental to understanding and modelling of the impacts and challenges of urbanization in terms of energy use, carbon emissions, and earthquake vulnerabilities. However, spatially detailed maps of urban 3D structure have been scarce, particularly in fast-changing developing countries. We present here a novel methodology to map the volume of buildings and infrastructures at 30 meter resolution using a synergy of Landsat imagery and openly available global digital surface models (DSMs), including the Shuttle Radar Topography Mission (SRTM), ASTER Global Digital Elevation Map (GDEM), ALOS World 3D - 30m (AW3D30), and the recently released global DSM from the TanDEM-X mission. Our method builds on the concept of object-based height profile to extract height metrics from the DSMs and use a machine learning algorithm to predict height and volume from the height metrics. We have tested this algorithm in the entire England and assessed our result using Lidar measurements in 25 England cities. Our initial assessments achieved a RMSE of 1.4 m (R2 = 0.72) for building height and a RMSE of 1208.7 m3 (R2 = 0.69) for building volume, demonstrating the potential of large-scale applications and fully automated mapping of urban structure.

Jupiter Environment Tool

NASA Technical Reports Server (NTRS)

Sturm, Erick J.; Monahue, Kenneth M.; Biehl, James P.; Kokorowski, Michael; Ngalande, Cedrick,; Boedeker, Jordan

2012-01-01

The Jupiter Environment Tool (JET) is a custom UI plug-in for STK that provides an interface to Jupiter environment models for visualization and analysis. Users can visualize the different magnetic field models of Jupiter through various rendering methods, which are fully integrated within STK s 3D Window. This allows users to take snapshots and make animations of their scenarios with magnetic field visualizations. Analytical data can be accessed in the form of custom vectors. Given these custom vectors, users have access to magnetic field data in custom reports, graphs, access constraints, coverage analysis, and anywhere else vectors are used within STK.

3D Cryo-Imaging: A Very High-Resolution View of the Whole Mouse

PubMed Central

Roy, Debashish; Steyer, Grant J.; Gargesha, Madhusudhana; Stone, Meredith E.; Wilson, David L.

2009-01-01

We developed the Case Cryo-imaging system that provides information rich, very high-resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section-and-image block-face imaging technology. The system consists of a mouse-sized, motorized cryo-microtome with special features for imaging, a modified, brightfield/ fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 µm over the block face of a whole mouse sectioned at 40 µm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo-imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo-imaging, we could obtain 3D vasculature down to 10 µm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field-of-view, depth of field, contrast, and resolution, the Case Cryo-imaging system fills the gap between whole animal in vivo imaging and histology. PMID:19248166

A density functional theory study on the active center of Fe-only hydrogenase: characterization and electronic structure of the redox states.

PubMed

Liu, Zhi-Pan; Hu, P

2002-05-08

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z)() (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fe(d) at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(I) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(I)-Fe(I) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride. Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(I) species, but cannot bond with the Fe(I)-Fe(I) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2 pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (i) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2 pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(I)-Fe(I) complexes; and (iii) in the e(g)-2 pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).

Fusion of Terrestrial and Airborne Laser Data for 3D modeling Applications

NASA Astrophysics Data System (ADS)

Mohammed, Hani Mahmoud

This thesis deals with the 3D modeling phase of the as-built large BIM projects. Among several means of BIM data capturing, such as photogrammetric or range tools, laser scanners have been one of the most efficient and practical tool for a long time. They can generate point clouds with high resolution for 3D models that meet nowadays' market demands. The current 3D modeling projects of as-built BIMs are mainly focused on using one type of laser scanner data, such as Airborne or Terrestrial. According to the literatures, no significant (few) efforts were made towards the fusion of heterogeneous laser scanner data despite its importance. The importance of the fusion of heterogeneous data arises from the fact that no single type of laser data can provide all the information about BIM, especially for large BIM projects that are existing on a large area, such as university buildings, or Heritage places. Terrestrial laser scanners are able to map facades of buildings and other terrestrial objects. However, they lack the ability to map roofs or higher parts in the BIM project. Airborne laser scanner on the other hand, can map roofs of the buildings efficiently and can map only small part of the facades. Short range laser scanners can map the interiors of the BIM projects, while long range scanners are used for mapping wide exterior areas in BIM projects. In this thesis the long range laser scanner data obtained in the Stop-and-Go mapping mode, the short range laser scanner data, obtained in a fully static mapping mode, and the airborne laser data are all fused together to bring a complete effective solution for a large BIM project. Working towards the 3D modeling of BIM projects, the thesis framework starts with the registration of the data, where a new fast automatic registration algorithm were developed. The next step is to recognize the different objects in the BIM project (classification), and obtain 3D models for the buildings. The last step is the development of an occlusion removal algorithm to efficiently retain parts of the buildings occluded by surrounding objects such as trees, vehicles, or street poles.

Polarimetric Calibration and Assessment of GF-3 Images in Steppe

NASA Astrophysics Data System (ADS)

Chang, Y.; Yang, J.; Li, P.; Shi, L.; Zhao, L.

2018-04-01

The GaoFen-3 (GF-3) satellite is the first fully polarimetric synthetic aperture radar (PolSAR) satellite in China. It has three fully polarimetric imaging modes and is available for many applications. The system has been taken on several calibration experiments after the launch in Inner Mongolia by the Institute of Electronics, Chinese Academy of Sciences (IECAS), and the polarimetric calibration (PolCAL) strategy of GF-3 are also improved. Therefore, it is necessary to assess the image quality before any further applications. In this paper, we evaluated the polarimetric residual errors of GF-3 images that acquired in July 2017 in a steppe site. The results shows that the crosstalk of these images varies from -36 dB to -46 dB, and the channel imbalance varies from -0.43 dB to 0.55 dB with angle varying from -1.6 to 3.6 degree. We also made a PolCAL experiment to restrain the polarimetric distortion afterwards, and the polarimetric quality of the image got better after the PolCAL processing.

PIV Measurement of Wall Shear Stress and Flow Structures within an Intracranial Aneurysm Model

NASA Astrophysics Data System (ADS)

Chow, Ricky; Sparrow, Eph; Campbell, Gary; Divani, Afshin; Sheng, Jian

2012-11-01

The formation and rupture of an intracranial aneurysm (IA) is a debilitating and often lethal event. Geometric features of the aneurysm bulb and upstream artery, such as bulb size, bulb shape, and curvature of the artery, are two groups of factors that define the flow and stresses within an IA. Abnormal flow stresses are related to rupture. This presentation discusses the development of a quasi-3D PIV technique and its application in various glass models at Re = 275 and 550 to experimentally assess at a preliminary level the impact of geometry and flow rate. Some conclusions are to be drawn linking geometry of the flow domain to rupture risk. The extracted results also serve as the baseline case and as a precursor to a companion presentation by the authors discussing the impact of flow diverters, a new class of medical devices. The PIV experiments were performed in a fully index-matched flow facility, allowing for unobstructed observations over complex geometry. A reconstruction and analysis method was devised to obtain 3D mean wall stress distributions and flow fields. The quasi 3D measurements were reconstructed from orthogonal planes encompassing the entire glass model, spaced 0.4mm apart. Wall shear stresses were evaluated from the near-wall flow viscous stresses.

Exploring time-resolved photoluminescence for nanowires using a three-dimensional computational transient model.

PubMed

Ren, Dingkun; Scofield, Adam C; Farrell, Alan C; Rong, Zixuan; Haddad, Michael A; Laghumavarapu, Ramesh B; Liang, Baolai; Huffaker, Diana L

2018-04-26

Time-resolved photoluminescence (TRPL) has been implemented experimentally to measure the carrier lifetime of semiconductors for decades. For the characterization of nanowires, the rich information embedded in TRPL curves has not been fully interpreted and meaningfully mapped to the respective material properties. This is because their three-dimensional (3-D) geometries result in more complicated mechanisms of carrier recombination than those in thin films and analytical solutions cannot be found for those nanostructures. In this work, we extend the intrinsic power of TRPL by developing a full 3-D transient model, which accounts for different material properties and drift-diffusion, to simulate TRPL curves for nanowires. To show the capability of the model, we perform TRPL measurements on a set of GaAs nanowire arrays grown on silicon substrates and then fit the measured data by tuning various material properties, including carrier mobility, Shockley-Read-Hall recombination lifetime, and surface recombination velocity at the GaAs-Si heterointerface. From the resultant TRPL simulations, we numerically identify the lifetime characteristics of those material properties. In addition, we computationally map the spatial and temporal electron distributions in nanowire segments and reveal the underlying carrier dynamics. We believe this study provides a theoretical foundation for interpretation of TRPL measurements to unveil the complex carrier recombination mechanisms in 3-D nanostructured materials.

Combinatorial Drug Testing in 3D Microtumors Derived from GBM Patient-Derived Xenografts Reveals Cytotoxic Synergy in Pharmacokinomics-informed Pathway Interactions.

PubMed

Gilbert, Ashley N; Anderson, Joshua C; Duarte, Christine W; Shevin, Rachael S; Langford, Catherine P; Singh, Raj; Gillespie, G Yancey; Willey, Christopher D

2018-05-30

Glioblastoma multiforme (GBM), the most common form of primary malignant brain cancer in adults, is a devastating disease for which effective treatment has remained elusive for over 75 years. One reason for the minimal progress during this time is the lack of accurate preclinical models to represent the patient's tumor's in vivo environment, causing a disconnect in drug therapy effectiveness between the laboratory and clinic. While patient-derived xenografts (PDX's or xenolines) are excellent human tumor representations, they are not amenable to high throughput testing. Therefore, we developed a miniaturized xenoline system (microtumors) for drug testing. Nineteen GBM xenolines were profiled for global kinase (kinomic) activity revealing actionable kinase targets associated with intracranial tumor growth rate. Kinase inhibitors for these targets (WP1066, selumetinib, crizotinib, and cediranib) were selected for single and combination therapy using a fully human-derived three-dimensional (3D) microtumor model of GBM xenoline cells embedded in HuBiogel for subsequent molecular and phenotype assays. GBM microtumors closely resembled orthotopically-implanted tumors based on immunohistochemical analysis and displayed kinomic and morphological diversity. Drug response testing could be reproducibly performed in a 96-well format identifying several synergistic combinations. Our findings indicate that 3D microtumors can provide a suitable high-throughput model for combination drug testing.

3D Monte Carlo simulation of light propagation for laser acupuncture and optimization of illumination parameters

NASA Astrophysics Data System (ADS)

Zhong, Fulin; Li, Ting; Pan, Boan; Wang, Pengbo

2017-02-01

Laser acupuncture is an effective photochemical and nonthermal stimulation of traditional acupuncture points with lowintensity laser irradiation, which is advantageous in painless, sterile, and safe compared to traditional acupuncture. Laser diode (LD) provides single wavelength and relatively-higher power light for phototherapy. The quantitative effect of illumination parameters of LD in use of laser acupuncture is crucial for practical operation of laser acupuncture. However, this issue is not fully demonstrated, especially since experimental methodologies with animals or human are pretty hard to address to this issue. For example, in order to protect viability of cells and tissue, and get better therapeutic effect, it's necessary to control the output power varied at 5mW 10mW range, while the optimized power is still not clear. This study aimed to quantitatively optimize the laser output power, wavelength, and irradiation direction with highly realistic modeling of light transport in acupunctured tissue. A Monte Carlo Simulation software for 3D vowelized media and the highest-precision human anatomical model Visible Chinese Human (VCH) were employed. Our 3D simulation results showed that longer wavelength/higher illumination power, larger absorption in laser acupuncture; the vertical direction emission of the acupuncture laser results in higher amount of light absorption in both the acupunctured voxel of tissue and muscle layer. Our 3D light distribution of laser acupuncture within VCH tissue model is potential to be used in optimization and real time guidance in clinical manipulation of laser acupuncture.

Vitamin D levels and menopause-related symptoms

PubMed Central

LeBlanc, Erin S.; Desai, Manisha; Perrin, Nancy; Wactawski-Wende, Jean; Manson, JoAnn E.; Cauley, Jane A.; Michael, Yvonne L.; Tang, Jean; Womack, Catherine; Song, Yiqing; Johnson, Karen C.; O’Sullivan, Mary J.; Woods, Nancy; Stefanick, Marcia L.

2015-01-01

Objective To determine whether vitamin D levels are associated with menopause-related symptoms in older women. Methods A randomly selected subset of 1,407 women, among 26,104 potentially eligible participants of the Women’s Health Initiative Calcium and Vitamin D (CaD) trial of postmenopausal women aged 51-80 years, had 25-hydroxyvitamin D [25(OH)D] levels measured at the CaD trial baseline visit. Information about menopause-related symptoms at baseline was obtained by questionnaire and included overall number of symptoms and composite measures of sleep disturbance, emotional well-being, and energy/fatigue, as well as individual symptoms. After exclusions for missing data, 530 women [mean age 66.2 years (SD 6.8)] were included in these analyses. Results There were borderline significant associations between 25(OH)D levels and total number of menopausal symptoms (p values ranging from 0.05 to 0.06 for fully adjusted models); however, the effect was clinically insignificant and disappeared with correction for multiple testing. There were no associations between 25(OH)D levels and composite measures of sleep disturbance, emotional well-being, or energy/fatigue (p’s > 0.10 for fully adjusted models). Conclusions There was no evidence of a clinically important association between serum 25(OH)D levels and menopause-related symptoms in postmenopausal women. PMID:24736200

Computational identification of a phospholipidosis toxicophore using (13)C and (15)N NMR-distance based fingerprints.

PubMed

Slavov, Svetoslav H; Wilkes, Jon G; Buzatu, Dan A; Kruhlak, Naomi L; Willard, James M; Hanig, Joseph P; Beger, Richard D

2014-12-01

Modified 3D-SDAR fingerprints combining (13)C and (15)N NMR chemical shifts augmented with inter-atomic distances were used to model the potential of chemicals to induce phospholipidosis (PLD). A curated dataset of 328 compounds (some of which were cationic amphiphilic drugs) was used to generate 3D-QSDAR models based on tessellations of the 3D-SDAR space with grids of different density. Composite PLS models averaging the aggregated predictions from 100 fully randomized individual models were generated. On each of the 100 runs, the activities of an external blind test set comprised of 294 proprietary chemicals were predicted and averaged to provide composite estimates of their PLD-inducing potentials (PLD+ if PLD is observed, otherwise PLD-). The best performing 3D-QSDAR model utilized a grid with a density of 8ppm×8ppm in the C-C region, 8ppm×20ppm in the C-N region and 20ppm×20ppm in the N-N region. The classification predictive performance parameters of this model evaluated on the basis of the external test set were as follows: accuracy=0.70, sensitivity=0.73 and specificity=0.66. A projection of the most frequently occurring bins on the standard coordinate space suggested a toxicophore composed of an aromatic ring with a centroid 3.5-7.5Å distant from an amino-group. The presence of a second aromatic ring separated by a 4-5Å spacer from the first ring and at a distance of between 5.5Å and 7Å from the amino-group was also associated with a PLD+ effect. These models provide comparable predictive performance to previously reported models for PLD with the added benefit of being based entirely on non-confidential, publicly available training data and with good predictive performance when tested in a rigorous, external validation exercise. Published by Elsevier Ltd.

MO-B-BRD-01: Creation of 3D Printed Phantoms for Clinical Radiation Therapy

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

Ehler, E.

This session is designed so that the learning objectives are practical. The intent is that the attendee may take home an understanding of not just the technology, but also the logistical steps necessary to execute these 3D printing techniques in the clinic. Four practical 3D printing topics will be discussed: (i) Creating bolus and compensators for photon machines; (ii) tools for proton therapy; (iii) clinical applications in imaging; (iv) custom phantom design for clinic and research use. The use of 3D printers within the radiation oncology setting is proving to be a useful tool for creating patient specific bolus andmore » compensators with the added benefit of cost savings. Creating the proper protocol is essential to ensuring that the desired effect is achieved and modeled in the treatment planning system. The critical choice of printer material (since it determines the interaction with the radiation) will be discussed. Selection of 3D printer type, design methods, verification of dose calculation, and the printing process will be detailed to give the basis for establishing your own protocol for electron and photon fields. A practical discussion of likely obstacles that may be encountered will be included. The diversity of systems and techniques in proton facilities leads to different facilities having very different requirements for beam modifying hardware and quality assurance devices. Many departments find the need to design and fabricate facility-specific equipment, making 3D printing an attractive technology. 3D printer applications in proton therapy will be discussed, including beam filters and compensators, and the design of proton therapy specific quality assurance tools. Quality control specific to 3D printing in proton therapy will be addressed. Advantages and disadvantages of different printing technology for these applications will also be discussed. 3D printing applications using high-resolution radiology-based imaging data will be presented. This data is used to 3D print individualized physical models of patient’s unique anatomy for aid in planning complex and challenging surgical procedures. Methods, techniques and imaging requirements for 3D printing anatomic models from imaging data will be discussed. Specific applications currently being used in the radiology clinic will be detailed. Standardized phantoms for radiation therapy are abundant. However, custom phantom designs can be advantageous for both clinical tasks and research. 3D printing is a useful method of custom fabrication that allows one to construct custom objects relatively quickly. Possibilities for custom radiotherapy phantoms range from 3D printing a hollow shell and filling the shell with tissue equivalent materials to fully printing the entire phantom with materials that are tissue equivalent as well as suitable for 3D printing. A range of materials available for use in radiotherapy phantoms and in the case of phantoms for dosimetric measurements, this choice is critical. The necessary steps required will be discussed including: modalities of 3D model generation, 3D model requirements for 3D printing, generation of machine instructions from the 3D model, and 3D printing techniques, choice of phantoms material, and troubleshooting techniques for each step in the process. Case examples of 3D printed phantoms will be shown. Learning Objectives: Understand the types of 3D modeling software required to design your device, the file formats required for data transfer from design software to 3D printer, and general troubleshooting techniques for each step of the process. Learn the differences between materials and design for photons vs. electrons vs. protons. Understand the importance of material choice and design geometries for your custom phantoms. Learn specific steps of quality assurance and quality control for 3D printed beam filters and compensators for proton therapy. Learn of special 3D printing applications for imaging. Cunha: Research support from Phillips Healthcare.« less

MO-B-BRD-03: Principles, Pitfalls and Techniques of 3D Printing for Bolus and Compensators

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

Baker, J.

This session is designed so that the learning objectives are practical. The intent is that the attendee may take home an understanding of not just the technology, but also the logistical steps necessary to execute these 3D printing techniques in the clinic. Four practical 3D printing topics will be discussed: (i) Creating bolus and compensators for photon machines; (ii) tools for proton therapy; (iii) clinical applications in imaging; (iv) custom phantom design for clinic and research use. The use of 3D printers within the radiation oncology setting is proving to be a useful tool for creating patient specific bolus andmore » compensators with the added benefit of cost savings. Creating the proper protocol is essential to ensuring that the desired effect is achieved and modeled in the treatment planning system. The critical choice of printer material (since it determines the interaction with the radiation) will be discussed. Selection of 3D printer type, design methods, verification of dose calculation, and the printing process will be detailed to give the basis for establishing your own protocol for electron and photon fields. A practical discussion of likely obstacles that may be encountered will be included. The diversity of systems and techniques in proton facilities leads to different facilities having very different requirements for beam modifying hardware and quality assurance devices. Many departments find the need to design and fabricate facility-specific equipment, making 3D printing an attractive technology. 3D printer applications in proton therapy will be discussed, including beam filters and compensators, and the design of proton therapy specific quality assurance tools. Quality control specific to 3D printing in proton therapy will be addressed. Advantages and disadvantages of different printing technology for these applications will also be discussed. 3D printing applications using high-resolution radiology-based imaging data will be presented. This data is used to 3D print individualized physical models of patient’s unique anatomy for aid in planning complex and challenging surgical procedures. Methods, techniques and imaging requirements for 3D printing anatomic models from imaging data will be discussed. Specific applications currently being used in the radiology clinic will be detailed. Standardized phantoms for radiation therapy are abundant. However, custom phantom designs can be advantageous for both clinical tasks and research. 3D printing is a useful method of custom fabrication that allows one to construct custom objects relatively quickly. Possibilities for custom radiotherapy phantoms range from 3D printing a hollow shell and filling the shell with tissue equivalent materials to fully printing the entire phantom with materials that are tissue equivalent as well as suitable for 3D printing. A range of materials available for use in radiotherapy phantoms and in the case of phantoms for dosimetric measurements, this choice is critical. The necessary steps required will be discussed including: modalities of 3D model generation, 3D model requirements for 3D printing, generation of machine instructions from the 3D model, and 3D printing techniques, choice of phantoms material, and troubleshooting techniques for each step in the process. Case examples of 3D printed phantoms will be shown. Learning Objectives: Understand the types of 3D modeling software required to design your device, the file formats required for data transfer from design software to 3D printer, and general troubleshooting techniques for each step of the process. Learn the differences between materials and design for photons vs. electrons vs. protons. Understand the importance of material choice and design geometries for your custom phantoms. Learn specific steps of quality assurance and quality control for 3D printed beam filters and compensators for proton therapy. Learn of special 3D printing applications for imaging. Cunha: Research support from Phillips Healthcare.« less

MO-B-BRD-00: Clinical Applications of 3D Printing

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

NONE

This session is designed so that the learning objectives are practical. The intent is that the attendee may take home an understanding of not just the technology, but also the logistical steps necessary to execute these 3D printing techniques in the clinic. Four practical 3D printing topics will be discussed: (i) Creating bolus and compensators for photon machines; (ii) tools for proton therapy; (iii) clinical applications in imaging; (iv) custom phantom design for clinic and research use. The use of 3D printers within the radiation oncology setting is proving to be a useful tool for creating patient specific bolus andmore » compensators with the added benefit of cost savings. Creating the proper protocol is essential to ensuring that the desired effect is achieved and modeled in the treatment planning system. The critical choice of printer material (since it determines the interaction with the radiation) will be discussed. Selection of 3D printer type, design methods, verification of dose calculation, and the printing process will be detailed to give the basis for establishing your own protocol for electron and photon fields. A practical discussion of likely obstacles that may be encountered will be included. The diversity of systems and techniques in proton facilities leads to different facilities having very different requirements for beam modifying hardware and quality assurance devices. Many departments find the need to design and fabricate facility-specific equipment, making 3D printing an attractive technology. 3D printer applications in proton therapy will be discussed, including beam filters and compensators, and the design of proton therapy specific quality assurance tools. Quality control specific to 3D printing in proton therapy will be addressed. Advantages and disadvantages of different printing technology for these applications will also be discussed. 3D printing applications using high-resolution radiology-based imaging data will be presented. This data is used to 3D print individualized physical models of patient’s unique anatomy for aid in planning complex and challenging surgical procedures. Methods, techniques and imaging requirements for 3D printing anatomic models from imaging data will be discussed. Specific applications currently being used in the radiology clinic will be detailed. Standardized phantoms for radiation therapy are abundant. However, custom phantom designs can be advantageous for both clinical tasks and research. 3D printing is a useful method of custom fabrication that allows one to construct custom objects relatively quickly. Possibilities for custom radiotherapy phantoms range from 3D printing a hollow shell and filling the shell with tissue equivalent materials to fully printing the entire phantom with materials that are tissue equivalent as well as suitable for 3D printing. A range of materials available for use in radiotherapy phantoms and in the case of phantoms for dosimetric measurements, this choice is critical. The necessary steps required will be discussed including: modalities of 3D model generation, 3D model requirements for 3D printing, generation of machine instructions from the 3D model, and 3D printing techniques, choice of phantoms material, and troubleshooting techniques for each step in the process. Case examples of 3D printed phantoms will be shown. Learning Objectives: Understand the types of 3D modeling software required to design your device, the file formats required for data transfer from design software to 3D printer, and general troubleshooting techniques for each step of the process. Learn the differences between materials and design for photons vs. electrons vs. protons. Understand the importance of material choice and design geometries for your custom phantoms. Learn specific steps of quality assurance and quality control for 3D printed beam filters and compensators for proton therapy. Learn of special 3D printing applications for imaging. Cunha: Research support from Phillips Healthcare.« less

MO-B-BRD-04: Sterilization for 3D Printed Brachytherapy Applicators

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

Cunha, J.

This session is designed so that the learning objectives are practical. The intent is that the attendee may take home an understanding of not just the technology, but also the logistical steps necessary to execute these 3D printing techniques in the clinic. Four practical 3D printing topics will be discussed: (i) Creating bolus and compensators for photon machines; (ii) tools for proton therapy; (iii) clinical applications in imaging; (iv) custom phantom design for clinic and research use. The use of 3D printers within the radiation oncology setting is proving to be a useful tool for creating patient specific bolus andmore » compensators with the added benefit of cost savings. Creating the proper protocol is essential to ensuring that the desired effect is achieved and modeled in the treatment planning system. The critical choice of printer material (since it determines the interaction with the radiation) will be discussed. Selection of 3D printer type, design methods, verification of dose calculation, and the printing process will be detailed to give the basis for establishing your own protocol for electron and photon fields. A practical discussion of likely obstacles that may be encountered will be included. The diversity of systems and techniques in proton facilities leads to different facilities having very different requirements for beam modifying hardware and quality assurance devices. Many departments find the need to design and fabricate facility-specific equipment, making 3D printing an attractive technology. 3D printer applications in proton therapy will be discussed, including beam filters and compensators, and the design of proton therapy specific quality assurance tools. Quality control specific to 3D printing in proton therapy will be addressed. Advantages and disadvantages of different printing technology for these applications will also be discussed. 3D printing applications using high-resolution radiology-based imaging data will be presented. This data is used to 3D print individualized physical models of patient’s unique anatomy for aid in planning complex and challenging surgical procedures. Methods, techniques and imaging requirements for 3D printing anatomic models from imaging data will be discussed. Specific applications currently being used in the radiology clinic will be detailed. Standardized phantoms for radiation therapy are abundant. However, custom phantom designs can be advantageous for both clinical tasks and research. 3D printing is a useful method of custom fabrication that allows one to construct custom objects relatively quickly. Possibilities for custom radiotherapy phantoms range from 3D printing a hollow shell and filling the shell with tissue equivalent materials to fully printing the entire phantom with materials that are tissue equivalent as well as suitable for 3D printing. A range of materials available for use in radiotherapy phantoms and in the case of phantoms for dosimetric measurements, this choice is critical. The necessary steps required will be discussed including: modalities of 3D model generation, 3D model requirements for 3D printing, generation of machine instructions from the 3D model, and 3D printing techniques, choice of phantoms material, and troubleshooting techniques for each step in the process. Case examples of 3D printed phantoms will be shown. Learning Objectives: Understand the types of 3D modeling software required to design your device, the file formats required for data transfer from design software to 3D printer, and general troubleshooting techniques for each step of the process. Learn the differences between materials and design for photons vs. electrons vs. protons. Understand the importance of material choice and design geometries for your custom phantoms. Learn specific steps of quality assurance and quality control for 3D printed beam filters and compensators for proton therapy. Learn of special 3D printing applications for imaging. Cunha: Research support from Phillips Healthcare.« less

MO-B-BRD-02: 3D Printing in the Clinic

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

Remmes, N.

This session is designed so that the learning objectives are practical. The intent is that the attendee may take home an understanding of not just the technology, but also the logistical steps necessary to execute these 3D printing techniques in the clinic. Four practical 3D printing topics will be discussed: (i) Creating bolus and compensators for photon machines; (ii) tools for proton therapy; (iii) clinical applications in imaging; (iv) custom phantom design for clinic and research use. The use of 3D printers within the radiation oncology setting is proving to be a useful tool for creating patient specific bolus andmore » compensators with the added benefit of cost savings. Creating the proper protocol is essential to ensuring that the desired effect is achieved and modeled in the treatment planning system. The critical choice of printer material (since it determines the interaction with the radiation) will be discussed. Selection of 3D printer type, design methods, verification of dose calculation, and the printing process will be detailed to give the basis for establishing your own protocol for electron and photon fields. A practical discussion of likely obstacles that may be encountered will be included. The diversity of systems and techniques in proton facilities leads to different facilities having very different requirements for beam modifying hardware and quality assurance devices. Many departments find the need to design and fabricate facility-specific equipment, making 3D printing an attractive technology. 3D printer applications in proton therapy will be discussed, including beam filters and compensators, and the design of proton therapy specific quality assurance tools. Quality control specific to 3D printing in proton therapy will be addressed. Advantages and disadvantages of different printing technology for these applications will also be discussed. 3D printing applications using high-resolution radiology-based imaging data will be presented. This data is used to 3D print individualized physical models of patient’s unique anatomy for aid in planning complex and challenging surgical procedures. Methods, techniques and imaging requirements for 3D printing anatomic models from imaging data will be discussed. Specific applications currently being used in the radiology clinic will be detailed. Standardized phantoms for radiation therapy are abundant. However, custom phantom designs can be advantageous for both clinical tasks and research. 3D printing is a useful method of custom fabrication that allows one to construct custom objects relatively quickly. Possibilities for custom radiotherapy phantoms range from 3D printing a hollow shell and filling the shell with tissue equivalent materials to fully printing the entire phantom with materials that are tissue equivalent as well as suitable for 3D printing. A range of materials available for use in radiotherapy phantoms and in the case of phantoms for dosimetric measurements, this choice is critical. The necessary steps required will be discussed including: modalities of 3D model generation, 3D model requirements for 3D printing, generation of machine instructions from the 3D model, and 3D printing techniques, choice of phantoms material, and troubleshooting techniques for each step in the process. Case examples of 3D printed phantoms will be shown. Learning Objectives: Understand the types of 3D modeling software required to design your device, the file formats required for data transfer from design software to 3D printer, and general troubleshooting techniques for each step of the process. Learn the differences between materials and design for photons vs. electrons vs. protons. Understand the importance of material choice and design geometries for your custom phantoms. Learn specific steps of quality assurance and quality control for 3D printed beam filters and compensators for proton therapy. Learn of special 3D printing applications for imaging. Cunha: Research support from Phillips Healthcare.« less

Resolving the Tevatron Top Quark Forward-Backward Asymmetry Puzzle: Fully Differential Next-to-Next-to-Leading-Order Calculation.

PubMed

Czakon, Michal; Fiedler, Paul; Mitov, Alexander

2015-07-31

We determine the dominant missing standard model (SM) contribution to the top quark pair forward-backward asymmetry at the Tevatron. Contrary to past expectations, we find a large, around 27%, shift relative to the well-known value of the inclusive asymmetry in next-to-leading order QCD. Combining all known standard model corrections, we find that A(FB)(SM)=0.095±0.007. This value is in agreement with the latest DØ measurement [V. M. Abazov et al. (D0 Collaboration), Phys. Rev. D 90, 072011 (2014)] A(FB)(D∅)=0.106±0.03 and about 1.5σ below that of CDF [T. Aaltonen et al. (CDF Collaboration), Phys. Rev. D 87, 092002 (2013)] A(FB)(CDF)=0.164±0.047. Our result is derived from a fully differential calculation of the next-to-next-to leading order (NNLO) QCD corrections to inclusive top pair production at hadron colliders and includes-without any approximation-all partonic channels contributing to this process. This is the first complete fully differential calculation in NNLO QCD of a two-to-two scattering process with all colored partons.

Resolving the Tevatron Top Quark Forward-Backward Asymmetry Puzzle: Fully Differential Next-to-Next-to-Leading-Order Calculation

NASA Astrophysics Data System (ADS)

Czakon, Michal; Fiedler, Paul; Mitov, Alexander

2015-07-01

We determine the dominant missing standard model (SM) contribution to the top quark pair forward-backward asymmetry at the Tevatron. Contrary to past expectations, we find a large, around 27%, shift relative to the well-known value of the inclusive asymmetry in next-to-leading order QCD. Combining all known standard model corrections, we find that AF BS M = 0.095 ±0.007 . This value is in agreement with the latest DØ measurement [V. M. Abazov et al. (D0 Collaboration), Phys. Rev. D 90, 072011 (2014)] AFBD ∅=0.106 ±0.03 and about 1.5 σ below that of CDF [T. Aaltonen et al. (CDF Collaboration), Phys. Rev. D 87, 092002 (2013)] AFBCDF=0.164 ±0.047 . Our result is derived from a fully differential calculation of the next-to-next-to leading order (NNLO) QCD corrections to inclusive top pair production at hadron colliders and includes—without any approximation—all partonic channels contributing to this process. This is the first complete fully differential calculation in NNLO QCD of a two-to-two scattering process with all colored partons.

Geographic Video 3d Data Model And Retrieval

NASA Astrophysics Data System (ADS)

Han, Z.; Cui, C.; Kong, Y.; Wu, H.

2014-04-01

Geographic video includes both spatial and temporal geographic features acquired through ground-based or non-ground-based cameras. With the popularity of video capture devices such as smartphones, the volume of user-generated geographic video clips has grown significantly and the trend of this growth is quickly accelerating. Such a massive and increasing volume poses a major challenge to efficient video management and query. Most of the today's video management and query techniques are based on signal level content extraction. They are not able to fully utilize the geographic information of the videos. This paper aimed to introduce a geographic video 3D data model based on spatial information. The main idea of the model is to utilize the location, trajectory and azimuth information acquired by sensors such as GPS receivers and 3D electronic compasses in conjunction with video contents. The raw spatial information is synthesized to point, line, polygon and solid according to the camcorder parameters such as focal length and angle of view. With the video segment and video frame, we defined the three categories geometry object using the geometry model of OGC Simple Features Specification for SQL. We can query video through computing the spatial relation between query objects and three categories geometry object such as VFLocation, VSTrajectory, VSFOView and VFFovCone etc. We designed the query methods using the structured query language (SQL) in detail. The experiment indicate that the model is a multiple objective, integration, loosely coupled, flexible and extensible data model for the management of geographic stereo video.

Activation of dopamine D3 receptors inhibits reward-related learning induced by cocaine.

PubMed

Kong, H; Kuang, W; Li, S; Xu, M

2011-03-10

Memories of learned associations between the rewarding properties of drugs and environmental cues contribute to craving and relapse in humans. The mesocorticolimbic dopamine (DA) system is involved in reward-related learning induced by drugs of abuse. DA D3 receptors are preferentially expressed in mesocorticolimbic DA projection areas. Genetic and pharmacological studies have shown that DA D3 receptors suppress locomotor-stimulant effects of cocaine and reinstatement of cocaine-seeking behaviors. Activation of the extracellular signal-regulated kinase (ERK) induced by acute cocaine administration is also inhibited by D3 receptors. How D3 receptors modulate cocaine-induced reward-related learning and associated changes in cell signaling in reward circuits in the brain, however, have not been fully investigated. In the present study, we show that D3 receptor mutant mice exhibit potentiated acquisition of conditioned place preference (CPP) at low doses of cocaine compared to wild-type mice. Activation of ERK and CaMKIIα, but not the c-Jun N-terminal kinase and p38, in the nucleus accumbens, amygdala and prefrontal cortex is also potentiated in D3 receptor mutant mice compared to that in wild-type mice following CPP expression. These results support a model in which D3 receptors modulate reward-related learning induced by low doses of cocaine by inhibiting activation of ERK and CaMKIIα in reward circuits in the brain. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Re-examining the effect of low and intermediate mode number perturbations on Ignition Metrics Scaling Laws

NASA Astrophysics Data System (ADS)

Malka, Elad; Shvarts, Dov

2017-10-01

We re-examine the way 2/3D effects on scaling laws for ignition metrics, such as the generalized Lawson Criterion (GLC) and the Ignition Threshold Factor (ITF). These scaling laws were derived for 1D symmetrical case and 2/3D perturbations [Hann et al. PoP 2010; Lindl et al., PoP 2014; Betti et al., PoP 2010]. The main cause for the difference between the 1D and the 2/3D scaling laws in those works, is heat conduction losses from the hot-spot bubbles to the cold shell [Kishony and Shvarts, PoP 2001]. This ``dry out'' of the bubbles is the dominant mechanism for intermediate mode number perturbations (6

Utility of 3D Reconstruction of 2D Liver Computed Tomography/Magnetic Resonance Images as a Surgical Planning Tool for Residents in Liver Resection Surgery.

PubMed

Yeo, Caitlin T; MacDonald, Andrew; Ungi, Tamas; Lasso, Andras; Jalink, Diederick; Zevin, Boris; Fichtinger, Gabor; Nanji, Sulaiman

A fundamental aspect of surgical planning in liver resections is the identification of key vessel tributaries to preserve healthy liver tissue while fully resecting the tumor(s). Current surgical planning relies primarily on the surgeon's ability to mentally reconstruct 2D computed tomography/magnetic resonance (CT/MR) images into 3D and plan resection margins. This creates significant cognitive load, especially for trainees, as it relies on image interpretation, anatomical and surgical knowledge, experience, and spatial sense. The purpose of this study is to determine if 3D reconstruction of preoperative CT/MR images will assist resident-level trainees in making appropriate operative plans for liver resection surgery. Ten preoperative patient CT/MR images were selected. Images were case-matched, 5 to 2D planning and 5 to 3D planning. Images from the 3D group were segmented to create interactive digital models that the resident can manipulate to view the tumor(s) in relation to landmark hepatic structures. Residents were asked to evaluate the images and devise a surgical resection plan for each image. The resident alternated between 2D and 3D planning, in a randomly generated order. The primary outcome was the accuracy of resident's plan compared to expert opinion. Time to devise each surgical plan was the secondary outcome. Residents completed a prestudy and poststudy questionnaire regarding their experience with liver surgery and the 3D planning software. Senior level surgical residents from the Queen's University General Surgery residency program were recruited to participate. A total of 14 residents participated in the study. The median correct response rate was 2 of 5 (40%; range: 0-4) for the 2D group, and 3 of 5 (60%; range: 1-5) for the 3D group (p < 0.01). The average time to complete each plan was 156 ± 107 seconds for the 2D group, and 84 ± 73 seconds for the 3D group (p < 0.01). A total 13 of 14 residents found the 3D model easier to use than the 2D. Most residents noticed a difference between the 2 modalities and found that the 3D model improved their confidence with the surgical plan proposed. The results of this study show that 3D reconstruction for liver surgery planning increases accuracy of resident surgical planning and decreases amount of time required. 3D reconstruction would be a useful model for improving trainee understanding of liver anatomy and surgical resection, and would serve as an adjunct to current 2D planning methods. This has the potential to be developed into a module for teaching liver surgery in a competency-based medical curriculum. Copyright © 2017 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Lithospheric Stress and Geodynamics: History, Accomplishments and Challenges

NASA Astrophysics Data System (ADS)

Richardson, R. M.

2016-12-01

The kinematics of plate tectonics was established in the 1960s, and shortly thereafter the Earth's stress field was recognized as an important constraint on the dynamics of plate tectonics. Forty years ago the 1976 Chapman Conference on the Stress in the Lithosphere, which I was fortunate to attend as a graduate student, and the ensuing 1977 PAGEOPH Stress in the Earth publication's 28 articles highlighted a range of datasets and approaches that established fertile ground for geodynamic research ever since. What are the most useful indicators of stress? Do they measure residual or tectonic stresses? Local or far field sources? What role does rheology play in concentrating deformation? Great progress was made with the first World Stress Map in 1991 by Zoback and Zoback, and the current version (2016 release with 42,348 indicators) remains a tremendous resource for geodynamic research. Modeling sophistication has seen significant progress over the past 40 years. Early applications of stress to dynamics involved simple lithospheric flexure, particularly at subduction zones, Hawaii, and continental foreland basin systems. We have progressed to full 3-D finite element models for calculating the flexure and stress associated with loads on a crust and mantle with realistic non-linear viscoelastic rheology, including frictional sliding, low-temperature plasticity, and high-temperature creep. Initial efforts to use lithospheric stresses to constrain plate driving forces focused on a "top-down" view of the lithosphere. Such efforts have evolved to better include asthenosphere-lithosphere interactions, have gone from simple to complicated rheologies, from 2-D to 3-D, and seek to obtain a fully thermo-mechanical model that avoids relying on artificial boundary conditions to model plate dynamics. Still, there are a number of important issues in geodynamics, from philosophy (when are more complicated models necessary? can one hope to identify "the" answer with modeling, or only possible/"impossible" solutions?), to better including realistic boundary conditions, to a fully thermo-mechanical model of the system, to including multiple data sets beyond stress. The 1976 Chapman Conference truly opened the door to a rich stress data set, and identified challenges, many of which remain 40 years later.

Scalable implicit incompressible resistive MHD with stabilized FE and fully-coupled Newton–Krylov-AMG

DOE PAGES

Shadid, J. N.; Pawlowski, R. P.; Cyr, E. C.; ...

2016-02-10

Here, we discuss that the computational solution of the governing balance equations for mass, momentum, heat transfer and magnetic induction for resistive magnetohydrodynamics (MHD) systems can be extremely challenging. These difficulties arise from both the strong nonlinear, nonsymmetric coupling of fluid and electromagnetic phenomena, as well as the significant range of time- and length-scales that the interactions of these physical mechanisms produce. This paper explores the development of a scalable, fully-implicit stabilized unstructured finite element (FE) capability for 3D incompressible resistive MHD. The discussion considers the development of a stabilized FE formulation in context of the variational multiscale (VMS) method,more » and describes the scalable implicit time integration and direct-to-steady-state solution capability. The nonlinear solver strategy employs Newton–Krylov methods, which are preconditioned using fully-coupled algebraic multilevel preconditioners. These preconditioners are shown to enable a robust, scalable and efficient solution approach for the large-scale sparse linear systems generated by the Newton linearization. Verification results demonstrate the expected order-of-accuracy for the stabilized FE discretization. The approach is tested on a variety of prototype problems, that include MHD duct flows, an unstable hydromagnetic Kelvin–Helmholtz shear layer, and a 3D island coalescence problem used to model magnetic reconnection. Initial results that explore the scaling of the solution methods are also presented on up to 128K processors for problems with up to 1.8B unknowns on a CrayXK7.« less

Non-rigid registration of 3D ultrasound for neurosurgery using automatic feature detection and matching.

PubMed

Machado, Inês; Toews, Matthew; Luo, Jie; Unadkat, Prashin; Essayed, Walid; George, Elizabeth; Teodoro, Pedro; Carvalho, Herculano; Martins, Jorge; Golland, Polina; Pieper, Steve; Frisken, Sarah; Golby, Alexandra; Wells, William

2018-06-04

The brain undergoes significant structural change over the course of neurosurgery, including highly nonlinear deformation and resection. It can be informative to recover the spatial mapping between structures identified in preoperative surgical planning and the intraoperative state of the brain. We present a novel feature-based method for achieving robust, fully automatic deformable registration of intraoperative neurosurgical ultrasound images. A sparse set of local image feature correspondences is first estimated between ultrasound image pairs, after which rigid, affine and thin-plate spline models are used to estimate dense mappings throughout the image. Correspondences are derived from 3D features, distinctive generic image patterns that are automatically extracted from 3D ultrasound images and characterized in terms of their geometry (i.e., location, scale, and orientation) and a descriptor of local image appearance. Feature correspondences between ultrasound images are achieved based on a nearest-neighbor descriptor matching and probabilistic voting model similar to the Hough transform. Experiments demonstrate our method on intraoperative ultrasound images acquired before and after opening of the dura mater, during resection and after resection in nine clinical cases. A total of 1620 automatically extracted 3D feature correspondences were manually validated by eleven experts and used to guide the registration. Then, using manually labeled corresponding landmarks in the pre- and post-resection ultrasound images, we show that our feature-based registration reduces the mean target registration error from an initial value of 3.3 to 1.5 mm. This result demonstrates that the 3D features promise to offer a robust and accurate solution for 3D ultrasound registration and to correct for brain shift in image-guided neurosurgery.

Parallel CARLOS-3D code development

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

Putnam, J.M.; Kotulski, J.D.

1996-02-01

CARLOS-3D is a three-dimensional scattering code which was developed under the sponsorship of the Electromagnetic Code Consortium, and is currently used by over 80 aerospace companies and government agencies. The code has been extensively validated and runs on both serial workstations and parallel super computers such as the Intel Paragon. CARLOS-3D is a three-dimensional surface integral equation scattering code based on a Galerkin method of moments formulation employing Rao- Wilton-Glisson roof-top basis for triangular faceted surfaces. Fully arbitrary 3D geometries composed of multiple conducting and homogeneous bulk dielectric materials can be modeled. This presentation describes some of the extensions tomore » the CARLOS-3D code, and how the operator structure of the code facilitated these improvements. Body of revolution (BOR) and two-dimensional geometries were incorporated by simply including new input routines, and the appropriate Galerkin matrix operator routines. Some additional modifications were required in the combined field integral equation matrix generation routine due to the symmetric nature of the BOR and 2D operators. Quadrilateral patched surfaces with linear roof-top basis functions were also implemented in the same manner. Quadrilateral facets and triangular facets can be used in combination to more efficiently model geometries with both large smooth surfaces and surfaces with fine detail such as gaps and cracks. Since the parallel implementation in CARLOS-3D is at high level, these changes were independent of the computer platform being used. This approach minimizes code maintenance, while providing capabilities with little additional effort. Results are presented showing the performance and accuracy of the code for some large scattering problems. Comparisons between triangular faceted and quadrilateral faceted geometry representations will be shown for some complex scatterers.« less

Fully automatic three-dimensional visualization of intravascular optical coherence tomography images: methods and feasibility in vivo

PubMed Central

Ughi, Giovanni J; Adriaenssens, Tom; Desmet, Walter; D’hooge, Jan

2012-01-01

Intravascular optical coherence tomography (IV-OCT) is an imaging modality that can be used for the assessment of intracoronary stents. Recent publications pointed to the fact that 3D visualizations have potential advantages compared to conventional 2D representations. However, 3D imaging still requires a time consuming manual procedure not suitable for on-line application during coronary interventions. We propose an algorithm for a rapid and fully automatic 3D visualization of IV-OCT pullbacks. IV-OCT images are first processed for the segmentation of the different structures. This also allows for automatic pullback calibration. Then, according to the segmentation results, different structures are depicted with different colors to visualize the vessel wall, the stent and the guide-wire in details. Final 3D rendering results are obtained through the use of a commercial 3D DICOM viewer. Manual analysis was used as ground-truth for the validation of the segmentation algorithms. A correlation value of 0.99 and good limits of agreement (Bland Altman statistics) were found over 250 images randomly extracted from 25 in vivo pullbacks. Moreover, 3D rendering was compared to angiography, pictures of deployed stents made available by the manufacturers and to conventional 2D imaging corroborating visualization results. Computational time for the visualization of an entire data sets resulted to be ~74 sec. The proposed method allows for the on-line use of 3D IV-OCT during percutaneous coronary interventions, potentially allowing treatments optimization. PMID:23243578

Nonlinear 3D visco-resistive MHD modeling of fusion plasmas: a comparison between numerical codes

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Chacon, L.; Cappello, S.

2008-11-01

Fluid plasma models (and, in particular, the MHD model) are extensively used in the theoretical description of laboratory and astrophysical plasmas. We present here a successful benchmark between two nonlinear, three-dimensional, compressible visco-resistive MHD codes. One is the fully implicit, finite volume code PIXIE3D [1,2], which is characterized by many attractive features, notably the generalized curvilinear formulation (which makes the code applicable to different geometries) and the possibility to include in the computation the energy transport equation and the extended MHD version of Ohm's law. In addition, the parallel version of the code features excellent scalability properties. Results from this code, obtained in cylindrical geometry, are compared with those produced by the semi-implicit cylindrical code SpeCyl, which uses finite differences radially, and spectral formulation in the other coordinates [3]. Both single and multi-mode simulations are benchmarked, regarding both reversed field pinch (RFP) and ohmic tokamak magnetic configurations. [1] L. Chacon, Computer Physics Communications 163, 143 (2004). [2] L. Chacon, Phys. Plasmas 15, 056103 (2008). [3] S. Cappello, Plasma Phys. Control. Fusion 46, B313 (2004) & references therein.

Assay to mechanically tune and optically probe fibrillar fibronectin conformations from fully relaxed to breakage

PubMed Central

Little, William C.; Smith, Michael L.; Ebneter, Urs; Vogel, Viola

2013-01-01

In response to growing needs for quantitative biochemical and cellular assays that address whether the extracellular matrix (ECM) acts as a mechanochemical signal converter to co-regulate cellular mechanotransduction processes, a new assay is presented where plasma fibronectin fibers are manually deposited onto elastic sheets, while force-induced changes in protein conformation are monitored by fluorescence resonance energy transfer (FRET). Fully relaxed assay fibers can be stretched at least 5–6 fold, which involves Fn domain unfolding, before the fibers break. In native fibroblast ECM, this full range of stretch-regulated conformations coexists in every field of view confirming that the assay fibers are physiologically relevant model systems. Since alterations of protein function will directly correlate with their extension in response to force, the FRET vs. strain curves presented herein enable the mapping of fibronectin strain distributions in 2D and 3D cell cultures with high spatial resolution. Finally, cryptic sites for fibronectin’s N-terminal 70-kD fragment were found to be exposed at relatively low strain, demonstrating the assay’s potential to analyze stretch-regulated protein-rotein interactions. PMID:18417335

Seismic Waves, 4th order accurate

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

2013-08-16

SW4 is a program for simulating seismic wave propagation on parallel computers. SW4 colves the seismic wave equations in Cartesian corrdinates. It is therefore appropriate for regional simulations, where the curvature of the earth can be neglected. SW4 implements a free surface boundary condition on a realistic topography, absorbing super-grid conditions on the far-field boundaries, and a kinematic source model consisting of point force and/or point moment tensor source terms. SW4 supports a fully 3-D heterogeneous material model that can be specified in several formats. SW4 can output synthetic seismograms in an ASCII test format, or in the SAC finarymore » format. It can also present simulation information as GMT scripts, whixh can be used to create annotated maps. Furthermore, SW4 can output the solution as well as the material model along 2-D grid planes.« less

Fully resolved simulations of expansion waves propagating into particle beds

NASA Astrophysics Data System (ADS)

Marjanovic, Goran; Hackl, Jason; Annamalai, Subramanian; Jackson, Thomas; Balachandar, S.

2017-11-01

There is a tremendous amount of research that has been done on compression waves and shock waves moving over particles but very little concerning expansion waves. Using 3-D direct numerical simulations, this study will explore expansion waves propagating into fully resolved particle beds of varying volume fractions and geometric arrangements. The objectives of these simulations are as follows: 1) To fully resolve all (1-way coupled) forces on the particles in a time varying flow and 2) to verify state-of-the-art drag models for such complex flows. We will explore a range of volume fractions, from very low ones that are similar to single particle flows, to higher ones where nozzling effects are observed between neighboring particles. Further, we will explore two geometric arrangements: body centered cubic and face centered cubic. We will quantify the effects that volume fraction and geometric arrangement plays on the drag forces and flow fields experienced by the particles. These results will then be compared to theoretical predictions from a model based on the generalized Faxen's theorem. This work was supported in part by the U.S. Department of Energy under the Predictive Science Academic Alliance Program, under Contract No. DE-NA0002378.

Three dimensional numerical prediction of icing related power and energy losses on a wind turbine

NASA Astrophysics Data System (ADS)

Sagol, Ece

Regions of Canada experience harsh winter conditions that may persist for several months. Consequently, wind turbines located in these regions are exposed to ice accretion and its adverse effects, from loss of power to ceasing to function altogether. Since the weather-related annual energy production loss of a turbine may be as high as 16% of the nominal production for Canada, estimating these losses before the construction of a wind farm is essential for investors. A literature survey shows that most icing prediction methods and codes are developed for aircraft, and, as this information is mostly considered corporate intellectual property, it is not accessible to researchers in other domains. Moreover, aircraft icing is quite different from wind turbine icing. Wind turbines are exposed to icing conditions for much longer periods than aircraft, perhaps for several days in a harsh climate, whereas the maximum length of exposure of an aircraft is about 3-4 hours. In addition, wind turbine blades operate at subsonic speeds, at lower Reynolds numbers than aircraft, and their physical characteristics are different. A few icing codes have been developed for wind turbine icing nevertheless. However, they are either in 2D, which does not consider the 3D characteristics of the flow field, or they focus on simulating each rotation in a time-dependent manner, which is not practical for computing long hours of ice accretion. Our objective in this thesis is to develop a 3D numerical methodology to predict rime ice shape and the power loss of a wind turbine as a function of wind farm icing conditions. In addition, we compute the Annual Energy Production of a sample turbine under both clean and icing conditions. The sample turbine we have selected is the NREL Phase VI experimental wind turbine installed on a wind farm in Sweden, the icing events at which have been recorded and published. The proposed method is based on computing and validating the clean performance of the turbine, and then computing the ice shape and iced blade performance, under icing conditions. The first step is to compute the performance of the NREL Phase VI using the commercial ANSYSFLUENT computational fluid dynamics (CFD) tool. In order to reduce the computational cost, we use a rotating reference frame model which computes the flow properties as time-averaged quantities. A grid sensitivity study has been performed to eliminate the effect of mesh on the results. Of the existing models for characterizing turbulence, we have selected the two-equation SST k-pi model. In general, the computed pressure coefficients and bending moment have shown good agreement with the experimental data, particularly at pre-stall speeds. Although the torque deviates from the experimental data, the trend with respect to the wind speed is similar. After the clean power curve has been computed, collection efficiency, which is directly proportional to the rate of icing of a surface, is analyzed. A multiphase analysis, for the air and water phases, is necessary to compute the rate of accumulation of the droplets on the blade surfaces. We study two different approaches that are found in the literature -- Eulerian and Lagrangian -- and determine the most suitable one for our study case. The former applies the governing equations to the liquid phase, while the latter computes the trajectory of each droplet present in the air. We eventually decided on the Eulerian model for our study, as it can be adapted to handle large and complex meshes better than the Lagrangian model. This step is validated on a NACA 0012 airfoil, as experimental data for 3D flows are not available in the literature. The ice accretion on the sample wind turbine blades is computed using both a Quasi-3D and a Fully-3D method, which have a similar theoretical background, but a different order of modeling. In the former, all the steps are carried out in 2D and the overall power is computed using the Blade Element Momentum method, while the latter performs all the steps in the 3D domain. The Fully-3D method yields more accurate predictions for a clean blade. For icing conditions, a validation is not possible, owing to the lack of experimental data. However, the two methods produce quite different results for the performance of the ice shape and the iced blade. A critical analysis of the results shows that, although the computational cost of the Fully-3D method is much higher, icing analyses in 2D may lack accuracy, because the ice shape and the related power loss are compromised by not considering the 3D features of rotational flow. While performing the CFD computations on the iced blade, the rough surface of the ice is smoothed to a degree, in order to prevent numerical instability and to keep the mesh size within a reasonable limit. However, roughness effects cannot be excluded altogether, as they contribute significantly to performance reduction. We consider roughness through a modification in the CFD code, and assess its effect on performance for the clean blade.

Nucleon-nucleon scattering from fully dynamical lattice QCD.

PubMed

Beane, S R; Bedaque, P F; Orginos, K; Savage, M J

2006-07-07

We present results of the first fully dynamical lattice QCD determination of nucleon-nucleon scattering lengths in the 1S0 channel and 3S1 - 3D1 coupled channels. The calculations are performed with domain-wall valence quarks on the MILC staggered configurations with a lattice spacing of b = 0.125 fm in the isospin-symmetric limit, and in the absence of electromagnetic interactions.

A Novel Methodology to Validate the Accuracy of Extraoral Dental Scanners and Digital Articulation Systems.

PubMed

Ellakwa, A; Elnajar, S; Littlefair, D; Sara, G

2018-05-03

The aim of the current study is to develop a novel method to investigate the accuracy of 3D scanners and digital articulation systems. An upper and a lower poured stone model were created by taking impression of fully dentate male (fifty years old) participant. Titanium spheres were added to the models to allow for an easily recognisable geometric shape for measurement after scanning and digital articulation. Measurements were obtained using a Coordinate Measuring Machine to record volumetric error, articulation error and clinical effect error. Three scanners were compared, including the Imetric 3D iScan d104i, Shining 3D AutoScan-DS100 and 3Shape D800, as well as their respective digital articulation software packages. Stoneglass Industries PDC digital articulation system was also applied to the Imetric scans for comparison with the CMM measurements. All the scans displayed low volumetric error (p⟩0.05), indicating that the scanners themselves had a minor contribution to the articulation and clinical effect errors. The PDC digital articulation system was found to deliver the lowest average errors, with good repeatability of results. The new measuring technique in the current study was able to assess the scanning and articulation accuracy of the four systems investigated. The PDC digital articulation system using Imetric scans was recommended as it displayed the lowest articulation error and clinical effect error with good repeatability. The low errors from the PDC system may have been due to its use of a 3D axis for alignment rather than the use of a best fit. Copyright© 2018 Dennis Barber Ltd.

An efficient flexible-order model for 3D nonlinear water waves

NASA Astrophysics Data System (ADS)

Engsig-Karup, A. P.; Bingham, H. B.; Lindberg, O.

2009-04-01

The flexible-order, finite difference based fully nonlinear potential flow model described in [H.B. Bingham, H. Zhang, On the accuracy of finite difference solutions for nonlinear water waves, J. Eng. Math. 58 (2007) 211-228] is extended to three dimensions (3D). In order to obtain an optimal scaling of the solution effort multigrid is employed to precondition a GMRES iterative solution of the discretized Laplace problem. A robust multigrid method based on Gauss-Seidel smoothing is found to require special treatment of the boundary conditions along solid boundaries, and in particular on the sea bottom. A new discretization scheme using one layer of grid points outside the fluid domain is presented and shown to provide convergent solutions over the full physical and discrete parameter space of interest. Linear analysis of the fundamental properties of the scheme with respect to accuracy, robustness and energy conservation are presented together with demonstrations of grid independent iteration count and optimal scaling of the solution effort. Calculations are made for 3D nonlinear wave problems for steep nonlinear waves and a shoaling problem which show good agreement with experimental measurements and other calculations from the literature.

Fully automatic segmentation of arbitrarily shaped fiducial markers in cone-beam CT projections

NASA Astrophysics Data System (ADS)

Bertholet, J.; Wan, H.; Toftegaard, J.; Schmidt, M. L.; Chotard, F.; Parikh, P. J.; Poulsen, P. R.

2017-02-01

Radio-opaque fiducial markers of different shapes are often implanted in or near abdominal or thoracic tumors to act as surrogates for the tumor position during radiotherapy. They can be used for real-time treatment adaptation, but this requires a robust, automatic segmentation method able to handle arbitrarily shaped markers in a rotational imaging geometry such as cone-beam computed tomography (CBCT) projection images and intra-treatment images. In this study, we propose a fully automatic dynamic programming (DP) assisted template-based (TB) segmentation method. Based on an initial DP segmentation, the DPTB algorithm generates and uses a 3D marker model to create 2D templates at any projection angle. The 2D templates are used to segment the marker position as the position with highest normalized cross-correlation in a search area centered at the DP segmented position. The accuracy of the DP algorithm and the new DPTB algorithm was quantified as the 2D segmentation error (pixels) compared to a manual ground truth segmentation for 97 markers in the projection images of CBCT scans of 40 patients. Also the fraction of wrong segmentations, defined as 2D errors larger than 5 pixels, was calculated. The mean 2D segmentation error of DP was reduced from 4.1 pixels to 3.0 pixels by DPTB, while the fraction of wrong segmentations was reduced from 17.4% to 6.8%. DPTB allowed rejection of uncertain segmentations as deemed by a low normalized cross-correlation coefficient and contrast-to-noise ratio. For a rejection rate of 9.97%, the sensitivity in detecting wrong segmentations was 67% and the specificity was 94%. The accepted segmentations had a mean segmentation error of 1.8 pixels and 2.5% wrong segmentations.

Overview of 3D-TRACE, a NASA Initiative in Three-Dimensional Tomography of the Aerosol-Cloud Environment

NASA Astrophysics Data System (ADS)

Davis, Anthony; Diner, David; Yanovsky, Igor; Garay, Michael; Xu, Feng; Bal, Guillaume; Schechner, Yoav; Aides, Amit; Qu, Zheng; Emde, Claudia

2013-04-01

Remote sensing is a key tool for sorting cloud ensembles by dynamical state, aerosol environments by source region, and establishing causal relationships between aerosol amounts, type, and cloud microphysics-the so-called indirect aerosol climate impacts, and one of the main sources of uncertainty in current climate models. Current satellite imagers use data processing approaches that invariably start with cloud detection/masking to isolate aerosol air-masses from clouds, and then rely on one-dimensional (1D) radiative transfer (RT) to interpret the aerosol and cloud measurements in isolation. Not only does this lead to well-documented biases for the estimates of aerosol radiative forcing and cloud optical depths in current missions, but it is fundamentally inadequate for future missions such as EarthCARE where capturing the complex, three-dimensional (3D) interactions between clouds and aerosols is a primary objective. In order to advance the state of the art, the next generation of satellite information processing systems must incorporate technologies that will enable the treatment of the atmosphere as a fully 3D environment, represented more realistically as a continuum. At one end, there is an optically thin background dominated by aerosols and molecular scattering that is strongly stratified and relatively homogeneous in the horizontal. At the other end, there are optically thick embedded elements, clouds and aerosol plumes, which can be more or less uniform and quasi-planar or else highly 3D with boundaries in all directions; in both cases, strong internal variability may be present. To make this paradigm shift possible, we propose to combine the standard models for satellite signal prediction physically grounded in 1D and 3D RT, both scalar and vector, with technologies adapted from biomedical imaging, digital image processing, and computer vision. This will enable us to demonstrate how the 3D distribution of atmospheric constituents, and their associated microphysical properties, can be reconstructed from multi-angle/multi-spectral imaging radiometry and, more and more, polarimetry. Specific technologies of interest are computed tomography (reconstruction from projections), optical tomography (using cross-pixel radiation transport in the diffusion limit), stereoscopy (depth/height retrievals), blind source and scale separation (signal unmixing), and disocclusion (information recovery in the presence of obstructions). Later on, these potentially powerful inverse problem solutions will be fully integrated in a versatile satellite data analysis toolbox. At present, we can report substantial progress at the component level. Specifically, we will focus on the most elementary problems in atmospheric tomography with an emphasis on the vastly under-exploited class of multi-pixel techniques. One basic problem is to infer the outer shape and mean opacity of 3D clouds, along with a bulk measure of cloud particle size. Another is to separate high and low cloud layers based on their characteristically different spatial textures. Yet another is to reconstruct the 3D spatial distribution of aerosol density based on passive imaging. This suite of independent feasibility studies amounts to a compelling proofof- concept for the ambitious 3D-Tomographic Reconstruction of the Aerosol-Cloud Environment (3D-TRACE) project as a whole.

3-D Object Recognition from Point Cloud Data

NASA Astrophysics Data System (ADS)

Smith, W.; Walker, A. S.; Zhang, B.

2011-09-01

The market for real-time 3-D mapping includes not only traditional geospatial applications but also navigation of unmanned autonomous vehicles (UAVs). Massively parallel processes such as graphics processing unit (GPU) computing make real-time 3-D object recognition and mapping achievable. Geospatial technologies such as digital photogrammetry and GIS offer advanced capabilities to produce 2-D and 3-D static maps using UAV data. The goal is to develop real-time UAV navigation through increased automation. It is challenging for a computer to identify a 3-D object such as a car, a tree or a house, yet automatic 3-D object recognition is essential to increasing the productivity of geospatial data such as 3-D city site models. In the past three decades, researchers have used radiometric properties to identify objects in digital imagery with limited success, because these properties vary considerably from image to image. Consequently, our team has developed software that recognizes certain types of 3-D objects within 3-D point clouds. Although our software is developed for modeling, simulation and visualization, it has the potential to be valuable in robotics and UAV applications. The locations and shapes of 3-D objects such as buildings and trees are easily recognizable by a human from a brief glance at a representation of a point cloud such as terrain-shaded relief. The algorithms to extract these objects have been developed and require only the point cloud and minimal human inputs such as a set of limits on building size and a request to turn on a squaring option. The algorithms use both digital surface model (DSM) and digital elevation model (DEM), so software has also been developed to derive the latter from the former. The process continues through the following steps: identify and group 3-D object points into regions; separate buildings and houses from trees; trace region boundaries; regularize and simplify boundary polygons; construct complex roofs. Several case studies have been conducted using a variety of point densities, terrain types and building densities. The results have been encouraging. More work is required for better processing of, for example, forested areas, buildings with sides that are not at right angles or are not straight, and single trees that impinge on buildings. Further work may also be required to ensure that the buildings extracted are of fully cartographic quality. A first version will be included in production software later in 2011. In addition to the standard geospatial applications and the UAV navigation, the results have a further advantage: since LiDAR data tends to be accurately georeferenced, the building models extracted can be used to refine image metadata whenever the same buildings appear in imagery for which the GPS/IMU values are poorer than those for the LiDAR.

Incorporating Floating Surface Objects into a Fully Dispersive Surface Wave Model

DTIC Science & Technology

2016-04-19

surface objects Sigma -coordinate Navier-Stokes Finite volume Immersed boundary a b s t r a c t The shock-capturing, non-hydrostatic, three...ontaining object or fluid, respectively. A 3D object with geometry escribed in Cartesian coordinates ( x, y, z ) was first projected onto he NHWAVE...17) . Specifically, the mask values re assigned by ASK = 0 if object projection includes u , v point (i, j) and k = k b ∼ k t ASK = 1 otherwise

Generalized pipeline for preview and rendering of synthetic holograms

NASA Astrophysics Data System (ADS)

Pappu, Ravikanth; Sparrell, Carlton J.; Underkoffler, John S.; Kropp, Adam B.; Chen, Benjie; Plesniak, Wendy J.

1997-04-01

We describe a general pipeline for the computation and display of either fully-computed holograms or holographic stereograms using the same 3D database. A rendering previewer on a Silicon Graphics Onyx allows a user to specify viewing geometry, database transformations, and scene lighting. The previewer then generates one of two descriptions of the object--a series of perspective views or a polygonal model--which is then used by a fringe rendering engine to compute fringes specific to hologram type. The images are viewed on the second generation MIT Holographic Video System. This allows a viewer to compare holographic stereograms with fully-computed holograms originating from the same database and comes closer to the goal of a single pipeline being able to display the same data in different formats.

Drift turbulence, particle transport, and anomalous dissipation at the reconnecting magnetopause

NASA Astrophysics Data System (ADS)

Le, A.; Daughton, W.; Ohia, O.; Chen, L.-J.; Liu, Y.-H.; Wang, S.; Nystrom, W. D.; Bird, R.

2018-06-01

Using fully kinetic 3D simulations, the reconnection dynamics of asymmetric current sheets are examined at the Earth's magnetopause. The plasma parameters are selected to model MMS magnetopause diffusion region crossings with guide fields of 0.1, 0.4, and 1 of the reconnecting magnetosheath field. In each case, strong drift-wave fluctuations are observed in the lower-hybrid frequency range at the steep density gradient across the magnetospheric separatrix. These fluctuations give rise to cross-field electron particle transport. In addition, this turbulent mixing leads to significantly enhanced electron parallel heating in comparison to 2D simulations. We study three different methods of quantifying the anomalous dissipation produced by the drift fluctuations, based on spatial averaging, temporal averaging, and temporal averaging followed by integrating along magnetic field lines. A comparison of different methods reveals complications in identifying and measuring the anomalous dissipation. Nevertheless, the anomalous dissipation from short wavelength drift fluctuations appears weak for each case, and the reconnection rates observed in 3D are nearly the same as in 2D models. The 3D simulations feature a number of interesting new features that are consistent with recent MMS observations, including cold beams of magnetosheath electrons that penetrate into the hotter magnetospheric inflow, the related observation of decreasing temperature in regions of increasing total density, and an effective turbulent diffusion coefficient that agrees with predictions from quasi-linear theory.

Vitamin D levels and menopause-related symptoms.

PubMed

LeBlanc, Erin S; Desai, Manisha; Perrin, Nancy; Wactawski-Wende, Jean; Manson, JoAnn E; Cauley, Jane A; Michael, Yvonne L; Tang, Jean; Womack, Catherine; Song, Yiqing; Johnson, Karen C; O'Sullivan, Mary J; Woods, Nancy; Stefanick, Marcia L

2014-11-01

This study aims to determine whether vitamin D levels are associated with menopause-related symptoms in older women. A randomly selected subset of 1,407 women, among 26,104 potentially eligible participants of the Women's Health Initiative Calcium and Vitamin D trial of postmenopausal women aged 51 to 80 years, had 25-hydroxyvitamin D [25(OH)D] levels measured at the Women's Health Initiative Calcium and Vitamin D trial baseline visit. Information about menopause-related symptoms at baseline was obtained by questionnaire and included overall number of symptoms and composite measures of sleep disturbance, emotional well-being, and energy/fatigue, as well as individual symptoms. After exclusions for missing data, 530 women (mean [SD] age, 66.2 [6.8] y) were included in these analyses. Borderline significant associations between 25(OH)D levels and total number of menopausal symptoms were observed (with P values ranging from 0.05 to 0.06 for fully adjusted models); however, the effect was clinically insignificant and disappeared with correction for multiple testing. No associations between 25(OH)D levels and composite measures of sleep disturbance, emotional well-being, or energy/fatigue were observed (P's > 0.10 for fully adjusted models). There is no evidence for a clinically important association between serum 25(OH)D levels and menopause-related symptoms in postmenopausal women.

Modeling mantle convection in the spherical annulus

NASA Astrophysics Data System (ADS)

Hernlund, John W.; Tackley, Paul J.

2008-12-01

Most methods for modeling mantle convection in a two-dimensional (2D) circular annular domain suffer from innate shortcomings in their ability to capture several characteristics of the spherical shell geometry of planetary mantles. While methods such as rescaling the inner and outer radius to reduce anomalous effects in a 2D polar cylindrical coordinate system have been introduced and widely implemented, such fixes may have other drawbacks that adversely affect the outcome of some kinds of mantle convection studies. Here we propose a new approach that we term the "spherical annulus," which is a 2D slice that bisects the spherical shell and is quantitatively formulated at the equator of a spherical polar coordinate system after neglecting terms in the governing equations related to variations in latitude. Spherical scaling is retained in this approximation since the Jacobian function remains proportional to the square of the radius. We present example calculations to show that the behavior of convection in the spherical annulus compares favorably against calculations performed in other 2D annular domains when measured relative to those in a fully three-dimensional (3D) spherical shell.

An Advanced simulation Code for Modeling Inductive Output Tubes

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

Thuc Bui; R. Lawrence Ives

2012-04-27

During the Phase I program, CCR completed several major building blocks for a 3D large signal, inductive output tube (IOT) code using modern computer language and programming techniques. These included a 3D, Helmholtz, time-harmonic, field solver with a fully functional graphical user interface (GUI), automeshing and adaptivity. Other building blocks included the improved electrostatic Poisson solver with temporal boundary conditions to provide temporal fields for the time-stepping particle pusher as well as the self electric field caused by time-varying space charge. The magnetostatic field solver was also updated to solve for the self magnetic field caused by time changing currentmore » density in the output cavity gap. The goal function to optimize an IOT cavity was also formulated, and the optimization methodologies were investigated.« less

Tetherless mobile micrograsping using a magnetic elastic composite material

NASA Astrophysics Data System (ADS)

Zhang, Jiachen; Diller, Eric

2016-11-01

In this letter, we propose and characterize a new type of tetherless mobile microgripper for micrograsping that is made of a magnetic elastic composite material. Its magnetically-programmable material and structures make it the first three-dimensional (3D) mobile microgripper that is directly actuated and controlled by magnetic forces and torques. With a symmetric four-limb structure, the microgripper is 3.5 mm long from tip to tip when it is open and 30 μm thick. It forms an approximate 700 μm cube when it is closed. The orientation and 3D shape of the microgripper are determined by the direction and strength of the applied magnetic field, respectively. As a mobile device, the microgripper can be moved through aqueous environments for precise grasping and transportation of micro-objects, pulled by magnetic gradients directly or rolled in rotating magnetic fields. The deformation of the microgripper under magnetic actuation is characterized by modeling and confirmed experimentally. Being directly controlled by magnetic forces and torques, the microgripper is easier and more intuitive to control than other magnetic microgrippers that require other inputs such as thermal and chemical responses. In addition, the microgripper is capable of performing fast repeatable grasping motions, requiring no more than 25 ms to change from fully open to fully closed in water at room temperature. As a result of its large-amplitude 3D deformation, the microgripper can accommodate cargoes with a wide range of geometries and dimensions. A pick-and-place experiment demonstrates the efficacy of the microgripper and its potentials in biomedical, microfluidic, and microrobotic applications.

Multi-dimensional, fully implicit, exactly conserving electromagnetic particle-in-cell simulations in curvilinear geometry

NASA Astrophysics Data System (ADS)

Chen, Guangye; Chacon, Luis

2015-11-01

We discuss a new, conservative, fully implicit 2D3V Vlasov-Darwin particle-in-cell algorithm in curvilinear geometry for non-radiative, electromagnetic kinetic plasma simulations. Unlike standard explicit PIC schemes, fully implicit PIC algorithms are unconditionally stable and allow exact discrete energy and charge conservation. Here, we extend these algorithms to curvilinear geometry. The algorithm retains its exact conservation properties in curvilinear grids. The nonlinear iteration is effectively accelerated with a fluid preconditioner for weakly to modestly magnetized plasmas, which allows efficient use of large timesteps, O (√{mi/me}c/veT) larger than the explicit CFL. In this presentation, we will introduce the main algorithmic components of the approach, and demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 1D (slow shock) and 2D (island coalescense).

On generation and evolution of seaward propagating internal solitary waves in the northwestern South China Sea

NASA Astrophysics Data System (ADS)

Xu, Jiexin; Chen, Zhiwu; Xie, Jieshuo; Cai, Shuqun

2016-03-01

In this paper, the generation and evolution of seaward propagating internal solitary waves (ISWs) detected by satellite image in the northwestern South China Sea (SCS) are investigated by a fully nonlinear, non-hydrostatic, three-dimensional Massachusetts Institute of Technology general circulation model (MITgcm). The three-dimensional (3D) modeled ISWs agree favorably with those by satellite image, indicating that the observed seaward propagating ISWs may be generated by the interaction of barotropic tidal flow with the arc-like continental slope south of Hainan Island. Though the tidal current is basically in east-west direction, different types of internal waves are generated by tidal currents flowing over the slopes with different shaped shorelines. Over the slope where the shoreline is straight, only weak internal tides are generated; over the slope where the shoreline is seaward concave, large-amplitude internal bores are generated, and since the concave isobaths of the arc-like continental slope tend to focus the baroclinic tidal energy which is conveyed to the internal bores, the internal bores can efficiently disintegrate into a train of rank-ordered ISWs during their propagation away from the slope; while over the slope where the shoreline is seaward convex, no distinct internal tides are generated. It is also implied that the internal waves over the slope are generated due to mixed lee wave mechanism. Furthermore, the effects of 3D model, continental slope curvature, stratification, rotation and tidal forcing on the generation of ISWs are discussed, respectively. It is shown that, the amplitude and phase speed of ISWs derived from a two-dimensional (2D) model are smaller than those from the 3D one, and the 3D model has an advantage over 2D one in simulating the ISWs generated by the interaction between tidal currents and 3D curved continental slope; the reduced continental slope curvature hinders the extension of ISW crestline; both weaker stratification and rotation suppress the generation of ISWs; and the width of ISW crestline generated by K1 tidal harmonic is longer than that by M2 tidal harmonic.

3D critical layers in fully-developed turbulent flows

NASA Astrophysics Data System (ADS)

Saxton-Fox, Theresa; McKeon, Beverley

2016-11-01

Recent work has shown that 3D critical layers drive self-sustaining behavior of exact coherent solutions of the Navier-Stokes equations (Wang et al. 2007; Hall and Sherwin 2010; Park and Graham 2015). This study investigates the role of 3D critical layers in fully-developed turbulent flows. 3D critical layer effects are identified in instantaneous snapshots of turbulent boundary layers in both experimental and DNS data (Wu et al. 2014). Additionally, a 3D critical layer effect is demonstrated to appear using only a few resolvent response modes from the resolvent analysis of McKeon and Sharma 2010, with phase relationships appropriately chosen. Connections are sought to the thin shear layers observed in turbulent boundary layers (Klewicki and Hirschi 2004; Eisma et al. 2015) and to amplitude modulation observations (Mathis et al. 2009; Duvvuri and McKeon 2014). This research is made possible by the Department of Defense through the National Defense & Engineering Graduate Fellowship (NDSEG) Program and by the Air Force Office of Scientific Research Grant # FA9550-12-1-0060. The support of the Center for Turbulence Research (CTR) summer program at Stanford is gratefully acknowledged.

Anelastic Models of Fully-Convective Stars: Differential Rotation, Meridional Circulation and Residual Entropy

NASA Astrophysics Data System (ADS)

Sainsbury-Martinez, Felix; Browning, Matthew; Miesch, Mark; Featherstone, Nicholas A.

2018-01-01

Low-Mass stars are typically fully convective, and as such their dynamics may differ significantly from sun-like stars. Here we present a series of 3D anelastic HD and MHD simulations of fully convective stars, designed to investigate how the meridional circulation, the differential rotation, and residual entropy are affected by both varying stellar parameters, such as the luminosity or the rotation rate, and by the presence of a magnetic field. We also investigate, more specifically, a theoretical model in which isorotation contours and residual entropy (σ‧ = σ ‑ σ(r)) are intrinsically linked via the thermal wind equation (as proposed in the Solar context by Balbus in 2009). We have selected our simulation parameters in such as way as to span the transition between Solar-like differential rotation (fast equator + slow poles) and ‘anti-Solar’ differential rotation (slow equator + fast poles), as characterised by the convective Rossby number and △Ω. We illustrate the transition from single-celled to multi-celled MC profiles, and from positive to negative latitudinal entropy gradients. We show that an extrapolation involving both TWB and the σ‧/Ω link provides a reasonable estimate for the interior profile of our fully convective stars. Finally, we also present a selection of MHD simulations which exhibit an almost unsuppressed differential rotation profile, with energy balances remaining dominated by kinetic components.

Controls on sediment entrainment shear stress determined from X-Ray CT scans and a 3D moment-balance model

NASA Astrophysics Data System (ADS)

Hodge, R. A.; Voepel, H.; Leyland, J.; Sear, D. A.; Ahmed, S. I.

2017-12-01

The shear stress at which a grain is entrained is determined by the balance between the applied fluid forces, and the resisting forces of the grain. Recent research has tended to focus on the applied fluid forces; calculating the resisting forces requires measurement of the geometry of in-situ sediment grains which has previously been very difficult to measure. We have used CT scanning to measure the grain geometry of in-situ water-worked grains, and from these data have calculated metrics that are relevant to grain entrainment. We use these metrics to parameterise a new, fully 3D, moment-balance model of grain entrainment. Inputs to the model are grain dimensions, exposed area, elevation relative to the velocity profile, the location of grain-grain contact points, and contact area with fine matrix sediment. The new CT data and model mean that assumptions of previous grain-entrainment models (e.g. spherical grains, 1D measurements of protrusion, entrainment in the downstream direction) are no longer necessary. The model calculates the critical shear stress for each possible set of contact points, and outputs the lowest value. Consequently, metrics including pivot angle and the direction of grain entrainment are now model outputs, rather than having to be pre-determined. We use the CT data and model to calculate the critical shear stress of 1092 in-situ grains from baskets that were buried and water-worked in a flume prior to scanning. We find that there is no consistent relationship between relative grain size (D/D50) and pivot angle, whereas there is a negative relationship between D/D50 and protrusion. Out of all measured metrics, critical shear stress is most strongly controlled by protrusion. This finding suggests that grain-scale topographic data could be used to estimate grain protrusion and hence improve estimates of critical shear stress.

Modeling and design of Galfenol unimorph energy harvesters

NASA Astrophysics Data System (ADS)

Deng, Zhangxian; Dapino, Marcelo J.

2015-12-01

This article investigates the modeling and design of vibration energy harvesters that utilize iron-gallium (Galfenol) as a magnetoelastic transducer. Galfenol unimorphs are of particular interest; however, advanced models and design tools are lacking for these devices. Experimental measurements are presented for various unimorph beam geometries. A maximum average power density of 24.4 {mW} {{cm}}-3 and peak power density of 63.6 {mW} {{cm}}-3 are observed. A modeling framework with fully coupled magnetoelastic dynamics, formulated as a 2D finite element model, and lumped-parameter electrical dynamics is presented and validated. A comprehensive parametric study considering pickup coil dimensions, beam thickness ratio, tip mass, bias magnet location, and remanent flux density (supplied by bias magnets) is developed for a 200 Hz, 9.8 {{m}} {{{s}}}-2 amplitude harmonic base excitation. For the set of optimal parameters, the maximum average power density and peak power density computed by the model are 28.1 and 97.6 {mW} {{cm}}-3, respectively.

Modeling Liquid Rocket Engine Atomization and Swirl/Coaxial Injectors

DTIC Science & Technology

2008-02-27

47-61, 2004. 2. Yoon, S . S ., and Heister, S . D., "A Fully Nonlinear Model for Atomization of High - Speed Jets," Engineering Analysis with... Power , V20, pp 468-479, 2004. 5. Yoon, S . S ., and Heister, S . D., "Analytic Solutions for Computing Velocities Induced from Potential Vortex Ring...Heister, S . D., "Three Dimensional Flow Simulations in Recessed Region of a Coaxial Injector," J. Propulsion and Power , V21, No.4, pp. 728-742

Comparison Between Laser Scanning and Automated 3d Modelling Techniques to Reconstruct Complex and Extensive Cultural Heritage Areas

NASA Astrophysics Data System (ADS)

Fassi, F.; Fregonese, L.; Ackermann, S.; De Troia, V.

2013-02-01

In Cultural Heritage field, the necessity to survey objects in a fast manner, with the ability to repeat the measurements several times for deformation or degradation monitoring purposes, is increasing. In this paper, two significant cases, an architectonical one and an archaeological one, are presented. Due to different reasons and emergency situations, the finding of the optimal solution to enable quick and well-timed survey for a complete digital reconstruction of the object is required. In both cases, two survey methods have been tested and used: a laser scanning approach that allows to obtain high-resolution and complete scans within a short time and a photogrammetric one that allows the three-dimensional reconstruction of the object from images. In the last months, several methodologies, including free or low cost techniques, have arisen. These kinds of software allow the fully automatically three-dimensional reconstruction of objects from images, giving back a dense point cloud and, in some case, a surfaced mesh model. In this paper some comparisons between the two methodologies above mentioned are presented, using the example of some real cases of study. The surveys have been performed by employing both photogrammetry and laser scanner techniques. The methodological operational choices, depending on the required goal, the difficulties encountered during the survey with these methods, the execution time (that is the key parameter), and finally the obtained results, are fully described and examinated. On the final 3D model, an analytical comparison has been made, to analyse the differences, the tolerances, the possibility of accuracy improvement and the future developments.

Direct laser writing of microstructures on optically opaque and reflective surfaces

NASA Astrophysics Data System (ADS)

Rekštytė, S.; Jonavičius, T.; Malinauskas, M.

2014-02-01

Direct laser writing (DLW) based on ultra-localized polymerization is an efficient way to produce three-dimensional (3D) micro/nano-structures for diverse applications in science and industry. It is attractive for its flexibility to materialize CAD models out of wide spectrum of materials on the desired substrates. In case of direct laser lithography, photo-crosslinking can be achieved by tightly focusing ultrashort laser pulses to a photo- or thermo-polymers. Selectively exposing material to laser radiation allows creating fully 3D structures with submicrometer spatial resolution. In this paper we present DLW results of hybrid organic-inorganic material SZ2080 on optically opaque and reflective surfaces, such as silicon and various metals (Cr, Ti, Au). Our studies prove that one can precisely fabricate 2D and 3D structures with lower than 1 μm spatial resolution even on glossy or rough surfaces (surface roughness rms 0.068-0.670 μm) using sample translation velocities of up to 1 mm/s. Using femtosecond high pulse repetition rate laser, sample translation velocity can reach over 1 mm/s ensuring repeatable submicrometer structuring resolution.

Structure of gel phase DMPC determined by X-ray diffraction.

PubMed Central

Tristram-Nagle, Stephanie; Liu, Yufeng; Legleiter, Justin; Nagle, John F

2002-01-01

The structure of fully hydrated gel phase dimyristoylphosphatidylcholine lipid bilayers was obtained at 10 degrees C. Oriented lipid multilayers were used to obtain high signal-to-noise intensity data. The chain tilt angle and an estimate of the methylene electron density were obtained from wide angle reflections. The chain tilt angle is measured to be 32.3 +/- 0.6 degrees near full hydration, and it does not change as the sample is mildly dehydrated from a repeat spacing of D = 59.9 A to D = 56.5 A. Low angle diffraction peaks were obtained up to the tenth order for 17 samples with variable D and prepared by three different methods with different geometries. In addition to the usual Fourier reconstructions of the electron density profiles, model electron density profiles were fit to all the low angle data simultaneously while constraining the model to include the wide-angle data and the measured lipid volume. Results are obtained for area/lipid (A = 47.2 +/- 0.5 A(2)), the compressibility modulus (K(A) = 500 +/- 100 dyn/cm), various thicknesses, such as the hydrocarbon thickness (2D(C) = 30.3 +/- 0.2 A), and the head-to-head spacing (D(HH) = 40.1 +/- 0.1 A). PMID:12496100

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

Weston, Brian T.

This dissertation focuses on the development of a fully-implicit, high-order compressible ow solver with phase change. The work is motivated by laser-induced phase change applications, particularly by the need to develop large-scale multi-physics simulations of the selective laser melting (SLM) process in metal additive manufacturing (3D printing). Simulations of the SLM process require precise tracking of multi-material solid-liquid-gas interfaces, due to laser-induced melting/ solidi cation and evaporation/condensation of metal powder in an ambient gas. These rapid density variations and phase change processes tightly couple the governing equations, requiring a fully compressible framework to robustly capture the rapid density variations ofmore » the ambient gas and the melting/evaporation of the metal powder. For non-isothermal phase change, the velocity is gradually suppressed through the mushy region by a variable viscosity and Darcy source term model. The governing equations are discretized up to 4th-order accuracy with our reconstructed Discontinuous Galerkin spatial discretization scheme and up to 5th-order accuracy with L-stable fully implicit time discretization schemes (BDF2 and ESDIRK3-5). The resulting set of non-linear equations is solved using a robust Newton-Krylov method, with the Jacobian-free version of the GMRES solver for linear iterations. Due to the sti nes associated with the acoustic waves and thermal and viscous/material strength e ects, preconditioning the GMRES solver is essential. A robust and scalable approximate block factorization preconditioner was developed, which utilizes the velocity-pressure (vP) and velocity-temperature (vT) Schur complement systems. This multigrid block reduction preconditioning technique converges for high CFL/Fourier numbers and exhibits excellent parallel and algorithmic scalability on classic benchmark problems in uid dynamics (lid-driven cavity ow and natural convection heat transfer) as well as for laser-induced phase change problems in 2D and 3D.« less

3D Visualization of Hydrological Model Outputs For a Better Understanding of Multi-Scale Phenomena

NASA Astrophysics Data System (ADS)

Richard, J.; Schertzer, D. J. M.; Tchiguirinskaia, I.

2014-12-01

During the last decades, many hydrological models has been created to simulate extreme events or scenarios on catchments. The classical outputs of these models are 2D maps, time series or graphs, which are easily understood by scientists, but not so much by many stakeholders, e.g. mayors or local authorities, and the general public. One goal of the Blue Green Dream project is to create outputs that are adequate for them. To reach this goal, we decided to convert most of the model outputs into a unique 3D visualization interface that combines all of them. This conversion has to be performed with an hydrological thinking to keep the information consistent with the context and the raw outputs.We focus our work on the conversion of the outputs of the Multi-Hydro (MH) model, which is physically based, fully distributed and with a GIS data interface. MH splits the urban water cycle into 4 components: the rainfall, the surface runoff, the infiltration and the drainage. To each of them, corresponds a modeling module with specific inputs and outputs. The superimposition of all this information will highlight the model outputs and help to verify the quality of the raw input data. For example, the spatial and the time variability of the rain generated by the rainfall module will be directly visible in 4D (3D + time) before running a full simulation. It is the same with the runoff module: because the result quality depends of the resolution of the rasterized land use, it will confirm or not the choice of the cell size.As most of the inputs and outputs are GIS files, two main conversions will be applied to display the results into 3D. First, a conversion from vector files to 3D objects. For example, buildings are defined in 2D inside a GIS vector file. Each polygon can be extruded with an height to create volumes. The principle is the same for the roads but an intrusion, instead of an extrusion, is done inside the topography file. The second main conversion is the raster conversion. Several files, such as the topography, the land use, the water depth, etc., are defined by geo-referenced grids. The corresponding grids are converted into a list of triangles to be displayed inside the 3D window. For the water depth, the display in pixels will not longer be the only solution. Creation of water contours will be done to more easily delineate the flood inside the catchment.

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

Manley, M. E.; Abernathy, D. L.; Sahul, R.

A long-standing controversy for relaxor ferroelectrics has been the origin of the waterfall effect in the phonon dispersion curves, in which low-energy transverse phonons cascade into vertical columns. Originally interpreted as phonons interacting with polar nanoregions (PNRs), it was later explained as an interference effect of coupling damped optic and acoustic phonons. In light of a recently discovered PNR vibrational mode near the waterfall wavevector [M. E. Manley, J. W. Lynn, D. L. Abernathy, E. D. Specht, O. Delaire, A. R. Bishop, R. Sahul, and J. D. Budai, Nat. Commun. 5, 3683 (2014)] we have reexamined this feature using neutronmore » scattering on [100]-poled PMN-30%PT (0.6Pb(Mg 1/3Nb 2/3)O 3 0.3PbTiO 3). In addition, we find that the PNR mode couples to both optic and acoustic phonons, and that this results in complex patterns in the dynamic structure factor, including intensity pockets and peaks localized in momentum-energy space. These features are fully explained by extending the mode-coupling model to include three coupled damped harmonic oscillators representing the transverse optic, acoustic, and PNR modes.« less

Ultra-Portable Solar-Powered 3D Printers for Onsite Manufacturing of Medical Resources.

PubMed

Wong, Julielynn Y

2015-09-01

The first space-based fused deposition modeling (FDM) 3D printer is powered by solar photovoltaics. This study seeks to demonstrate the feasibility of using solar energy to power a FDM 3D printer to manufacture medical resources at the Mars Desert Research Station and to design an ultra-portable solar-powered 3D printer for off-grid environments. Six solar panels in a 3×2 configuration, a voltage regulator/capacitor improvised from a power adapter, and two 12V batteries in series were connected to power a FDM 3D printer. Three designs were printed onsite and evaluated by experts post analogue mission. A solar-powered 3D printer composed of off-the-shelf components was designed to be transported in airline carry-on luggage. During the analogue mission, the solar-powered printer could only be operated for <1 h/d, but was able to fabricate a functional dental tool, scalpel handle, and customized mallet splint over 2 d. Post analogue mission, an ultra-portable plug-and-play solar-powered 3D printer was designed that could print an estimated 16 dental tools or 8 mallet finger splints or 7 scalpel handles on one fully charged 12V 150Wh battery with a 110V AC converter. It is feasible to use solar energy to power a 3D printer to manufacture functional and personalized medical resources at a Mars analogue research station. Based on these findings, a solar-powered suitcase 3D printing system containing solar panels, 12V battery with charge controller and AC inverter, and back-up solar charge controller and inverter was designed for transport to and use in off-grid communities.

[The importance of full graphic display in a graphic organizer to facilitate discourse comprehension].

PubMed

Akio, Suzuki; Shunji, Awazu

2010-04-01

In order to examine the importance of fully representing graphic information items in graphic aids to facilitate comprehension of explanatory texts, we established and randomly assigned fifty university students into the following four groups: (a) participants who study the text without the aid, (b) participants who study the text with the aid, whose literal (key words) and graphic (arrows, boxes, etc.) information items are fully displayed, (c) participants who study the text with the aid, whose graphic information items are fully displayed but whose literal information items are partially displayed, and (d) participants who study the text with the aid, whose literal and graphic information items are partially displayed. The results of two kinds of comprehension tests "textbase and situation model" revealed that groups (b) and (c) outperformed groups (a) and (d). These findings suggest that graphic aids can facilitate students' text comprehension when graphic information items are fully displayed and literal information items are displayed either fully or partially; however, the aid cannot facilitate comprehension when both literal and graphic elements are displayed partially.

Numerical Analysis of AHSS Fracture in a Stretch-bending Test

NASA Astrophysics Data System (ADS)

Luo, Meng; Chen, Xiaoming; Shi, Ming F.; Shih, Hua-Chu

2010-06-01

Advanced High Strength Steels (AHSS) are increasingly used in the automotive industry due to their superior strength and substantial weight reduction advantage. However, their limited ductility gives rise to numerous manufacturing issues. One of them is the so-called `shear fracture' often observed on tight radii during stamping processes. Since traditional approaches, such as the Forming Limit Diagram (FLD), are unable to predict this type of fracture, efforts have been made to develop failure criteria that can predict shear fractures. In this paper, a recently developed Modified Mohr-Coulomb (MMC) ductile fracture criterion[1] is adopted to analyze the failure behavior of a Dual Phase (DP) steel sheet during stretch bending operations. The plasticity and ductile fracture of the present sheet are fully characterized by the Hill'48 orthotropic model and the MMC fracture model respectively. Finite Element models with three different element types (3D, shell and plane strain) were built for a Stretch Forming Simulator (SFS) test and numerical simulations with four different R/t ratios (die radius normalized by sheet thickness) were performed. It has been shown that the 3D and shell element models can accurately predict the failure location/mode, the upper die load-displacement responses as well as the wall stress and wrap angle at the onset of fracture for all R/t ratios. Furthermore, a series of parametric studies were conducted on the 3D element model, and the effects of tension level (clamping distance) and tooling friction on the failure modes/locations were investigated.

An alternative to fully coupled reactive transport simulations for long-term prediction of chemical reactions in complex geological systems

NASA Astrophysics Data System (ADS)

De Lucia, Marco; Kempka, Thomas; Kühn, Michael

2014-05-01

Fully-coupled reactive transport simulations involving multiphase hydrodynamics and chemical reactions in heterogeneous settings are extremely challenging from a computational point of view. This often leads to oversimplification of the investigated system: coarse spatial discretization, to keep the number of elements in the order of few thousands; simplified chemistry, disregarding many potentially important reactions. A novel approach for coupling non-reactive hydrodynamic simulations with the outcome of single batch geochemical simulations was therefore introduced to assess the potential long-term mineral trapping at the Ketzin pilot site for underground CO2 storage in Germany [1],[2]. The advantage of the coupling is the ability to use multi-million grid non-reactive hydrodynamics simulations on one side and few batch 0D geochemical simulations on the other, so that the complexity of both systems does not need to be reduced. This contribution shows the approach which was taken to validate this simplified coupling scheme. The procedure involved batch simulations of the reference geochemical model, then performing both non-reactive and fully coupled 1D and 3D reactive transport simulations and finally applying the simplified coupling scheme based on the non-reactive and geochemical batch model. The TOUGHREACT/ECO2N [3] simulator was adopted for the validation. The degree of refinement of the spatial grid and the complexity and velocity of the mineral reactions, along with a cut-off value for the minimum concentration of dissolved CO2 allowed to originate precipitates in the simplified approach were found out to be the governing parameters for the convergence of the two schemes. Systematic discrepancies between the approaches are not reducible, simply because there is no feedback between chemistry and hydrodynamics, and can reach 20 % - 30 % in unfavourable cases. However, even such discrepancy is completely acceptable, in our opinion, given the amount of uncertainty underlying the geochemical models. References [1] Klein, E., De Lucia, M., Kempka, T. Kühn, M. 2013. Evaluation of longterm mineral trapping at the Ketzin pilot site for CO2 storage: an integrative approach using geochemical modelling and reservoir simulation. International Journal of Greenhouse Gas Control 19: 720-730, doi:10.1016/j.ijggc.2013.05.014 [2] Kempka, T., Klein, E., De Lucia, M., Tillner, E. Kühn, M. 2013. Assessment of Long-term CO2 Trapping Mechanisms at the Ketzin Pilot Site (Germany) by Coupled Numerical Modelling. Energy Procedia 37: 5419-5426, doi:10.1016/j.egypro.2013.06.460 [3] Xu, T., Spycher, N., Sonnenthal, E., Zhang, G., Zheng, L., Pruess, K. 2010. TOUGHREACT Version 2.0: A simulator for subsurface reactive transport under non-isothermal multiphase flow conditions, Computers & Geosciences 37(6), doi:10.1016/j.cageo.2010.10.007

Evaluation of a Fully 3-D Bpf Method for Small Animal PET Images on Mimd Architectures

NASA Astrophysics Data System (ADS)

Bevilacqua, A.

Positron Emission Tomography (PET) images can be reconstructed using Fourier transform methods. This paper describes the performance of a fully 3-D Backprojection-Then-Filter (BPF) algorithm on the Cray T3E machine and on a cluster of workstations. PET reconstruction of small animals is a class of problems characterized by poor counting statistics. The low-count nature of these studies necessitates 3-D reconstruction in order to improve the sensitivity of the PET system: by including axially oblique Lines Of Response (LORs), the sensitivity of the system can be significantly improved by the 3-D acquisition and reconstruction. The BPF method is widely used in clinical studies because of its speed and easy implementation. Moreover, the BPF method is suitable for on-time 3-D reconstruction as it does not need any sinogram or rearranged data. In order to investigate the possibility of on-line processing, we reconstruct a phantom using the data stored in the list-mode format by the data acquisition system. We show how the intrinsically parallel nature of the BPF method makes it suitable for on-line reconstruction on a MIMD system such as the Cray T3E. Lastly, we analyze the performance of this algorithm on a cluster of workstations.

Nanocellulosic materials as bioinks for 3D bioprinting.

PubMed

Piras, Carmen C; Fernández-Prieto, Susana; De Borggraeve, Wim M

2017-09-26

3D bioprinting is a new developing technology with lots of promise in tissue engineering and regenerative medicine. Being biocompatible, biodegradable, renewable and cost-effective, cellulosic nanomaterials have recently captured the attention of researchers due to their applicability as inks for 3D bioprinting. Although a number of cellulose-based bioinks have been reported, the potential of cellulose nanofibrils and nanocrystals has not been fully explored yet. This minireview aims at highlighting the use of nanocellulosic materials for 3D bioprinting as an emerging, promising, new research field.

Advanced EUV mask and imaging modeling

NASA Astrophysics Data System (ADS)

Evanschitzky, Peter; Erdmann, Andreas

2017-10-01

The exploration and optimization of image formation in partially coherent EUV projection systems with complex source shapes requires flexible, accurate, and efficient simulation models. This paper reviews advanced mask diffraction and imaging models for the highly accurate and fast simulation of EUV lithography systems, addressing important aspects of the current technical developments. The simulation of light diffraction from the mask employs an extended rigorous coupled wave analysis (RCWA) approach, which is optimized for EUV applications. In order to be able to deal with current EUV simulation requirements, several additional models are included in the extended RCWA approach: a field decomposition and a field stitching technique enable the simulation of larger complex structured mask areas. An EUV multilayer defect model including a database approach makes the fast and fully rigorous defect simulation and defect repair simulation possible. A hybrid mask simulation approach combining real and ideal mask parts allows the detailed investigation of the origin of different mask 3-D effects. The image computation is done with a fully vectorial Abbe-based approach. Arbitrary illumination and polarization schemes and adapted rigorous mask simulations guarantee a high accuracy. A fully vectorial sampling-free description of the pupil with Zernikes and Jones pupils and an optimized representation of the diffraction spectrum enable the computation of high-resolution images with high accuracy and short simulation times. A new pellicle model supports the simulation of arbitrary membrane stacks, pellicle distortions, and particles/defects on top of the pellicle. Finally, an extension for highly accurate anamorphic imaging simulations is included. The application of the models is demonstrated by typical use cases.

Distributed Observer Network (DON), Version 3.0, User's Guide

NASA Technical Reports Server (NTRS)

Mazzone, Rebecca A.; Conroy, Michael P.

2015-01-01

The Distributed Observer Network (DON) is a data presentation tool developed by the National Aeronautics and Space Administration (NASA) to distribute and publish simulation results. Leveraging the display capabilities inherent in modern gaming technology, DON places users in a fully navigable 3-D environment containing graphical models and allows the users to observe how those models evolve and interact over time in a given scenario. Each scenario is driven with data that has been generated by authoritative NASA simulation tools and exported in accordance with a published data interface specification. This decoupling of the data from the source tool enables DON to faithfully display a simulator's results and ensure that every simulation stakeholder will view the exact same information every time.

The development of a 3D immunocompetent model of human skin.

PubMed

Chau, David Y S; Johnson, Claire; MacNeil, Sheila; Haycock, John W; Ghaemmaghami, Amir M

2013-09-01

As the first line of defence, skin is regularly exposed to a variety of biological, physical and chemical insults. Therefore, determining the skin sensitization potential of new chemicals is of paramount importance from the safety assessment and regulatory point of view. Given the questionable biological relevance of animal models to human as well as ethical and regulatory pressure to limit or stop the use of animal models for safety testing, there is a need for developing simple yet physiologically relevant models of human skin. Herein, we describe the construction of a novel immunocompetent 3D human skin model comprising of dendritic cells co-cultured with keratinocytes and fibroblasts. This model culture system is simple to assemble with readily-available components and importantly, can be separated into its constitutive individual layers to allow further insight into cell-cell interactions and detailed studies of the mechanisms of skin sensitization. In this study, using non-degradable microfibre scaffolds and a cell-laden gel, we have engineered a multilayer 3D immunocompetent model comprised of keratinocytes and fibroblasts that are interspersed with dendritic cells. We have characterized this model using a combination of confocal microscopy, immuno-histochemistry and scanning electron microscopy and have shown differentiation of the epidermal layer and formation of an epidermal barrier. Crucially the immune cells in the model are able to migrate and remain responsive to stimulation with skin sensitizers even at low concentrations. We therefore suggest this new biologically relevant skin model will prove valuable in investigating the mechanisms of allergic contact dermatitis and other skin pathologies in human. Once fully optimized, this model can also be used as a platform for testing the allergenic potential of new chemicals and drug leads.

Operational and theoretical temperature considerations in a Penning surface plasma source

NASA Astrophysics Data System (ADS)

Faircloth, D. C.; Lawrie, S. R.; Pereira Da Costa, H.; Dudnikov, V.

2015-04-01

A fully detailed 3D thermal model of the ISIS Penning surface plasma source is developed in ANSYS. The proportion of discharge power applied to the anode and cathode is varied until the simulation matches the operational temperature observations. The range of possible thermal contact resistances are modelled, which gives an estimation that between 67% and 85% of the discharge power goes to the cathode. Transient models show the electrode surface temperature rise during the discharge pulse for a range of duty cycles. The implications of these measurements are discussed and a mechanism for governing cesium coverage proposed. The requirements for the design of a high current long pulse source are stated.

SOLPS modeling of the effect on plasma detachment of closing the lower divertor in DIII-D

DOE PAGES

Sang, C. F.; Stangeby, P. C.; Guo, H. Y.; ...

2016-12-15

SOLPS modeling has been carried out to assess the effect of tightly closing the lower divertor in DIII-D, which at present is almost fully open, on the achievement of cold dissipative/detached divertor conditions. To isolate the impact of other factors on the divertor plasma solution and to make direct comparisons, most of the parameters including the meshes were kept as similar as possible. Only the neutral baffling was modified to compare a fully open divertor with a tightly closed one. The modeling shows that the tightly closed divertor greatly improves trapping of recycling neutrals, thereby increasing radiative and charge exchangemore » losses in the divertor and reducing the electron temperature T et and deposited power density q dep at the target plate. Furthermore, the closed structure enables the divertor plasma to enter into highly dissipative and detached divertor conditions at a significantly lower upstream density. The effects of divertor closure on the neutral density and pressure, and their correlation with the divertor plasma conditions are also demonstrated. The effect of molecular D 2- ion D + elastic collisions and neutral-neutral collisions on the divertor plasma solution are assessed.« less

Xenobiotic metabolism capacities of human skin in comparison with a 3D-epidermis model and keratinocyte-based cell culture as in vitro alternatives for chemical testing: phase II enzymes.

PubMed

Götz, Christine; Pfeiffer, Roland; Tigges, Julia; Ruwiedel, Karsten; Hübenthal, Ulrike; Merk, Hans F; Krutmann, Jean; Edwards, Robert J; Abel, Josef; Pease, Camilla; Goebel, Carsten; Hewitt, Nicola; Fritsche, Ellen

2012-05-01

The 7th Amendment to the EU Cosmetics Directive prohibits the use of animals in cosmetic testing for certain endpoints, such as genotoxicity. Therefore, skin in vitro models have to replace chemical testing in vivo. However, the metabolic competence neither of human skin nor of alternative in vitro models has so far been fully characterized, although skin is the first-pass organ for accidentally or purposely (cosmetics and pharmaceuticals) applied chemicals. Thus, there is an urgent need to understand the xenobiotic-metabolizing capacities of human skin and to compare these activities to models developed to replace animal testing. We have measured the activity of the phase II enzymes glutathione S-transferase, UDP-glucuronosyltransferase and N-acetyltransferase in ex vivo human skin, the 3D epidermal model EpiDerm 200 (EPI-200), immortalized keratinocyte-based cell lines (HaCaT and NCTC 2544) and primary normal human epidermal keratinocytes. We show that all three phase II enzymes are present and highly active in skin as compared to phase I. Human skin, therefore, represents a more detoxifying than activating organ. This work systematically compares the activities of three important phase II enzymes in four different in vitro models directly to human skin. We conclude from our studies that 3D epidermal models, like the EPI-200 employed here, are superior over monolayer cultures in mimicking human skin xenobiotic metabolism and thus better suited for dermatotoxicity testing. © 2012 John Wiley & Sons A/S.

A rigidity transition and glassy dynamics in a model for confluent 3D tissues

NASA Astrophysics Data System (ADS)

Merkel, Matthias; Manning, M. Lisa

The origin of rigidity in disordered materials is an outstanding open problem in statistical physics. Recently, a new type of rigidity transition was discovered in a family of models for 2D biological tissues, but the mechanisms responsible for rigidity remain unclear. This is not just a statistical physics problem, but also relevant for embryonic development, cancer growth, and wound healing. To gain insight into this rigidity transition and make new predictions about biological bulk tissues, we have developed a fully 3D self-propelled Voronoi (SPV) model. The model takes into account shape, elasticity, and self-propelled motion of the individual cells. We find that in the absence of self-propulsion, this model exhibits a rigidity transition that is controlled by a dimensionless model parameter describing the preferred cell shape, with an accompanying structural order parameter. In the presence of self-propulsion, the rigidity transition appears as a glass-like transition featuring caging and aging effects. Given the similarities between this transition and jamming in particulate solids, it is natural to ask if the two transitions are related. By comparing statistics of Voronoi geometries, we show the transitions are surprisingly close but demonstrably distinct. Furthermore, an index theorem used to identify topologically protected mechanical modes in jammed systems can be extended to these vertex-type models. In our model, residual stresses govern the transition and enter the index theorem in a different way compared to jammed particles, suggesting the origin of rigidity may be different between the two.

Combining coherent hard X-ray tomographies with phase retrieval to generate three-dimensional models of forming bone

NASA Astrophysics Data System (ADS)

Bortel, Emely L.; Langer, Max; Rack, Alexander; Forien, Jean-Baptiste; Duda, Georg N.; Fratzl, Peter; Zaslansky, Paul

2017-11-01

Holotomography, a phase sensitive synchrotron-based μCT modality, is a quantitative 3D imaging method. By exploiting partial spatial X-ray coherence, bones can be imaged volumetrically with high resolution coupled with impressive density sensitivity. This tomographic method reveals the main characteristics of the important tissue compartments in forming bones, including the rapidly-changing soft tissue and the partially or fully mineralized bone regions, while revealing subtle density differences in 3D. Here we show typical results observed within the growing femur bone midshafts of healthy mice that are 1, 3, 7, 10 and 14 days old (postpartum). Our results make use of partially-coherent synchrotron radiation employing inline Fresnel-propagation in multiple tomographic datasets obtained in the imaging beamline ID19 of the ESRF. The exquisite detail creates maps of the juxtaposed soft, partially mineralized and highly mineralized bone revealing the environment in which bone cells create and shape the matrix. This high resolution 3D data is a step towards creating realistic computational models that may be used to study the dynamic processes involved in bone tissue formation and adaptation. Such data will enhance our understanding of the important biomechanical interactions directing maturation and shaping of the bone micro- and macro-geometries.

On demand manufacturing of patient-specific liquid capsules via co-ordinated 3D printing and liquid dispensing.

PubMed

Okwuosa, Tochukwu C; Soares, Cindy; Gollwitzer, Verena; Habashy, Rober; Timmins, Peter; Alhnan, Mohamed A

2018-06-15

A method for the production of liquid capsules with the potential of modifying drug dose and release is presented. For the first time, the co-ordinated use of fused deposition modelling (FDM), 3D printing and liquid dispensing to fabricate individualised dosage form on demand in a fully automated fashion has been demonstrated. Polymethacrylate shells (Eudragit EPO and RL) for immediate and extended release were fabricated using FDM 3D printing and simultaneously filled using a computer-controlled liquid dispenser loaded with model drug solution (theophylline) or suspension (dipyridamole). The impact of printing modes: simultaneous shell printing and filling (single-phase) or sequential 3D printing of shell bottom, filling and shell cap (multi-phase), nozzle size, syringe volume, and shell structure has been reported. The use of shell thickness of 1.6 mm, and concentric architecture allowed successful containment of liquid core whilst maintaining the release properties of the 3D printed liquid capsule. The linear relationship between the theoretical and the actual volumes from the dispenser reflected its potential for accurate dosing (R 2  = 0.9985). Modifying the shell thickness of Eudragit RL capsule allowed a controlled extended drug release without the need for formulation change. Owing to its low cost and versatility, this approach can be adapted to wide spectrum of liquid formulations such as small and large molecule solutions and obviate the need for compatibility with the high temperature of FDM 3D printing process. In a clinical setting, health care staff will be able to instantly manufacture in small volumes liquid capsules with individualised dose contents and release pattern in response to specific patient's needs. Copyright © 2018 Elsevier B.V. All rights reserved.

A 3D Human Renal Cell Carcinoma-on-a-Chip for the Study of Tumor Angiogenesis.

PubMed

Miller, Chris P; Tsuchida, Connor; Zheng, Ying; Himmelfarb, Jonathan; Akilesh, Shreeram

2018-06-01

Tractable human tissue-engineered 3D models of cancer that enable fine control of tumor growth, metabolism, and reciprocal interactions between different cell types in the tumor microenvironment promise to accelerate cancer research and pharmacologic testing. Progress to date mostly reflects the use of immortalized cancer cell lines, and progression to primary patient-derived tumor cells is needed to realize the full potential of these platforms. For the first time, we report endothelial sprouting induced by primary patient tumor cells in a 3D microfluidic system. Specifically, we have combined primary human clear cell renal cell carcinoma (ccRCC) cells from six independent donors with human endothelial cells in a vascularized, flow-directed, 3D culture system ("ccRCC-on-a-chip"). The upregulation of key angiogenic factors in primary human ccRCC cells, which exhibited unique patterns of donor variation, was further enhanced when they were cultured in 3D clusters. When embedded in the matrix surrounding engineered human vessels, these ccRCC tumor clusters drove potent endothelial cell sprouting under continuous flow, thus recapitulating the critical angiogenic signaling axis between human ccRCC cells and endothelial cells. Importantly, this phenotype was driven by a primary tumor cell-derived biochemical gradient of angiogenic growth factor accumulation that was subject to pharmacological blockade. Our novel 3D system represents a vascularized tumor model that is easy to image and quantify and is fully tunable in terms of input cells, perfusate, and matrices. We envision that this ccRCC-on-a-chip will be valuable for mechanistic studies, for studying tumor-vascular cell interactions, and for developing novel and personalized antitumor therapies. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Exploring the Inner Edge of the Habitable Zone with Fully Coupled Oceans

NASA Technical Reports Server (NTRS)

Way, M.J; Del Genio, A.D.; Kelley, M.; Aleinov, I.; Clune, T.

2015-01-01

The role of rotation in planetary atmospheres plays an important role in regulating atmospheric and oceanic heat flow, cloud formation and precipitation. Using the Goddard Institute for Space Studies (GISS) three dimension General Circulation Model (3D-GCM) we demonstrate how varying rotation rate and increasing the incident solar flux on a planet are related to each other and may allow the inner edge of the habitable zone to be much closer than many previous habitable zone studies have indicated. This is shown in particular for fully coupled ocean runs -- some of the first that have been utilized in this context. Results with a 100m mixed layer depth and our fully coupled ocean runs are compared with those of Yang et al. 2014, which demonstrates consistency across models. However, there are clear differences for rotations rates of 1-16x present earth day lengths between the mixed layer and fully couple ocean models, which points to the necessity of using fully coupled oceans whenever possible. The latter was recently demonstrated quite clearly by Hu & Yang 2014 in their aquaworld study with a fully coupled ocean when compared with similar mixed layer ocean studies and by Cullum et al. 2014. Atmospheric constituent amounts were also varied alongside adjustments to cloud parameterizations (results not shown here). While the latter have an effect on what a planet's global mean temperature is once the oceans reach equilibrium they do not qualitatively change the overall relationship between the globally averaged surface temperature and incident solar flux for rotation rates ranging from 1 to 256 times the present Earth day length. At the same time this study demonstrates that given the lack of knowledge about the atmospheric constituents and clouds on exoplanets there is still a large uncertainty as to where a planet will sit in a given star's habitable zone.

Fully 3D refraction correction dosimetry system.

PubMed

Manjappa, Rakesh; Makki, S Sharath; Kumar, Rajesh; Vasu, Ram Mohan; Kanhirodan, Rajan

2016-02-21

The irradiation of selective regions in a polymer gel dosimeter results in an increase in optical density and refractive index (RI) at those regions. An optical tomography-based dosimeter depends on rayline path through the dosimeter to estimate and reconstruct the dose distribution. The refraction of light passing through a dose region results in artefacts in the reconstructed images. These refraction errors are dependant on the scanning geometry and collection optics. We developed a fully 3D image reconstruction algorithm, algebraic reconstruction technique-refraction correction (ART-rc) that corrects for the refractive index mismatches present in a gel dosimeter scanner not only at the boundary, but also for any rayline refraction due to multiple dose regions inside the dosimeter. In this study, simulation and experimental studies have been carried out to reconstruct a 3D dose volume using 2D CCD measurements taken for various views. The study also focuses on the effectiveness of using different refractive-index matching media surrounding the gel dosimeter. Since the optical density is assumed to be low for a dosimeter, the filtered backprojection is routinely used for reconstruction. We carry out the reconstructions using conventional algebraic reconstruction (ART) and refractive index corrected ART (ART-rc) algorithms. The reconstructions based on FDK algorithm for cone-beam tomography has also been carried out for comparison. Line scanners and point detectors, are used to obtain reconstructions plane by plane. The rays passing through dose region with a RI mismatch does not reach the detector in the same plane depending on the angle of incidence and RI. In the fully 3D scanning setup using 2D array detectors, light rays that undergo refraction are still collected and hence can still be accounted for in the reconstruction algorithm. It is found that, for the central region of the dosimeter, the usable radius using ART-rc algorithm with water as RI matched medium is 71.8%, an increase of 6.4% compared to that achieved using conventional ART algorithm. Smaller diameter dosimeters are scanned with dry air scanning by using a wide-angle lens that collects refracted light. The images reconstructed using cone beam geometry is seen to deteriorate in some planes as those regions are not scanned. Refraction correction is important and needs to be taken in to consideration to achieve quantitatively accurate dose reconstructions. Refraction modeling is crucial in array based scanners as it is not possible to identify refracted rays in the sinogram space.

Crustal structure of Australia from ambient seismic noise tomography

NASA Astrophysics Data System (ADS)

Saygin, Erdinc; Kennett, B. L. N.

2012-01-01

Surface wave tomography for Australian crustal structure has been carried out using group velocity measurements in the period range 1-32 s extracted from stacked correlations of ambient noise between station pairs. Both Rayleigh wave and Love wave group velocity maps are constructed for each period using the vertical and transverse component of the Green's function estimates from the ambient noise. The full suite of portable broadband deployments and permanent stations on the continent have been used with over 250 stations in all and up to 7500 paths. The permanent stations provide a useful link between the various shorter-term portable deployments. At each period the group velocity maps are constructed with a fully nonlinear tomographic inversion exploiting a subspace technique and the Fast Marching Method for wavefront tracking. For Rayleigh waves the continental coverage is good enough to allow the construction of a 3D shear wavespeed model in a two stage approach. Local group dispersion information is collated for a distribution of points across the continent and inverted for a 1D SV wavespeed profile using a Neighbourhood Algorithm method. The resulting set of 1D models are then interpolated to produce the final 3D wavespeed model. The group velocity maps show the strong influence of thick sediments at shorter periods, and distinct fast zones associated with cratonic regions. Below the sediments the 3D shear wavespeed model displays significant heterogeneity with only moderate correlation with surface tectonic features. For example, there is no evident expression of the Tasman Line marking the eastern edge of Precambrian outcrop. The large number of available inter-station paths extracted from the ambient noise analysis provide detailed shear wavespeed information for crustal structure across the Australian continent for the first time, including regions where there was no prior sampling because of difficult logistics.

High-Content Monitoring of Drug Effects in a 3D Spheroid Model

PubMed Central

Mittler, Frédérique; Obeïd, Patricia; Rulina, Anastasia V.; Haguet, Vincent; Gidrol, Xavier; Balakirev, Maxim Y.

2017-01-01

A recent decline in the discovery of novel medications challenges the widespread use of 2D monolayer cell assays in the drug discovery process. As a result, the need for more appropriate cellular models of human physiology and disease has renewed the interest in spheroid 3D culture as a pertinent model for drug screening. However, despite technological progress that has significantly simplified spheroid production and analysis, the seeming complexity of the 3D approach has delayed its adoption in many laboratories. The present report demonstrates that the use of a spheroid model may be straightforward and can provide information that is not directly available with a standard 2D approach. We describe a cost-efficient method that allows for the production of an array of uniform spheroids, their staining with vital dyes, real-time monitoring of drug effects, and an ATP-endpoint assay, all in the same 96-well U-bottom plate. To demonstrate the method performance, we analyzed the effect of the preclinical anticancer drug MLN4924 on spheroids formed by VCaP and LNCaP prostate cancer cells. The drug has different outcomes in these cell lines, varying from cell cycle arrest and protective dormancy to senescence and apoptosis. We demonstrate that by using high-content analysis of spheroid arrays, the effect of the drug can be described as a series of EC50 values that clearly dissect the cytostatic and cytotoxic drug actions. The method was further evaluated using four standard cancer chemotherapeutics with different mechanisms of action, and the effect of each drug is described as a unique multi-EC50 diagram. Once fully validated in a wider range of conditions, this method could be particularly valuable for phenotype-based drug discovery. PMID:29322028

Towards full-Braginskii implicit extended MHD

NASA Astrophysics Data System (ADS)

Chacon, Luis

2009-05-01

Recently, viable algorithms have been proposed for the scalable, fully-implicit temporal integration of 3D resistive MHD and cold-ion extended MHD models. While significant, these achievements must be tempered by the fact that such models lack predictive capabilities in regimes of interest for magnetic fusion. Short of including kinetic closures, a natural evolution path towards predictability starts by considering additional terms as described in Braginskii's fluid closures in the collisional regime. Here, we focus on the inclusion of two fundamental elements of relevance for fusion plasmas: anisotropic parallel electron transport, and warm-ion physics (i.e., ion finite Larmor radius effects, included via gyroviscosity). Both these elements introduce significant numerical difficulties, due to the strong anisotropy in the former, and the presence of dispersive waves in the latter. In this presentation, we will discuss progress in our fully implicit algorithmic formulation towards the inclusion of both these elements. L. Chac'on, Phys. Plasmas, 15, 056103 (2008) L. Chac'on, J. Physics: Conf. Series, 125, 012041 (2008)

Three-dimensional mesostructures as high-temperature growth templates, electronic cellular scaffolds, and self-propelled microrobots

PubMed Central

Yan, Zheng; Han, Mengdi; Shi, Yan; Badea, Adina; Yang, Yiyuan; Kulkarni, Ashish; Hanson, Erik; Kandel, Mikhail E.; Wen, Xiewen; Zhang, Fan; Luo, Yiyue; Lin, Qing; Zhang, Hang; Guo, Xiaogang; Huang, Yuming; Nan, Kewang; Jia, Shuai; Oraham, Aaron W.; Mevis, Molly B.; Lim, Jaeman; Guo, Xuelin; Gao, Mingye; Ryu, Woomi; Yu, Ki Jun; Nicolau, Bruno G.; Petronico, Aaron; Rubakhin, Stanislav S.; Lou, Jun; Ajayan, Pulickel M.; Thornton, Katsuyo; Popescu, Gabriel; Fang, Daining; Sweedler, Jonathan V.; Braun, Paul V.; Zhang, Haixia; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

2017-01-01

Recent work demonstrates that processes of stress release in prestrained elastomeric substrates can guide the assembly of sophisticated 3D micro/nanostructures in advanced materials. Reported application examples include soft electronic components, tunable electromagnetic and optical devices, vibrational metrology platforms, and other unusual technologies, each enabled by uniquely engineered 3D architectures. A significant disadvantage of these systems is that the elastomeric substrates, while essential to the assembly process, can impose significant engineering constraints in terms of operating temperatures and levels of dimensional stability; they also prevent the realization of 3D structures in freestanding forms. Here, we introduce concepts in interfacial photopolymerization, nonlinear mechanics, and physical transfer that bypass these limitations. The results enable 3D mesostructures in fully or partially freestanding forms, with additional capabilities in integration onto nearly any class of substrate, from planar, hard inorganic materials to textured, soft biological tissues, all via mechanisms quantitatively described by theoretical modeling. Illustrations of these ideas include their use in 3D structures as frameworks for templated growth of organized lamellae from AgCl–KCl eutectics and of atomic layers of WSe2 from vapor-phase precursors, as open-architecture electronic scaffolds for formation of dorsal root ganglion (DRG) neural networks, and as catalyst supports for propulsive systems in 3D microswimmers with geometrically controlled dynamics. Taken together, these methodologies establish a set of enabling options in 3D micro/nanomanufacturing that lie outside of the scope of existing alternatives. PMID:29078394

Three-dimensional mesostructures as high-temperature growth templates, electronic cellular scaffolds, and self-propelled microrobots

NASA Astrophysics Data System (ADS)

Yan, Zheng; Han, Mengdi; Shi, Yan; Badea, Adina; Yang, Yiyuan; Kulkarni, Ashish; Hanson, Erik; Kandel, Mikhail E.; Wen, Xiewen; Zhang, Fan; Luo, Yiyue; Lin, Qing; Zhang, Hang; Guo, Xiaogang; Huang, Yuming; Nan, Kewang; Jia, Shuai; Oraham, Aaron W.; Mevis, Molly B.; Lim, Jaeman; Guo, Xuelin; Gao, Mingye; Ryu, Woomi; Yu, Ki Jun; Nicolau, Bruno G.; Petronico, Aaron; Rubakhin, Stanislav S.; Lou, Jun; Ajayan, Pulickel M.; Thornton, Katsuyo; Popescu, Gabriel; Fang, Daining; Sweedler, Jonathan V.; Braun, Paul V.; Zhang, Haixia; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

2017-11-01

Recent work demonstrates that processes of stress release in prestrained elastomeric substrates can guide the assembly of sophisticated 3D micro/nanostructures in advanced materials. Reported application examples include soft electronic components, tunable electromagnetic and optical devices, vibrational metrology platforms, and other unusual technologies, each enabled by uniquely engineered 3D architectures. A significant disadvantage of these systems is that the elastomeric substrates, while essential to the assembly process, can impose significant engineering constraints in terms of operating temperatures and levels of dimensional stability; they also prevent the realization of 3D structures in freestanding forms. Here, we introduce concepts in interfacial photopolymerization, nonlinear mechanics, and physical transfer that bypass these limitations. The results enable 3D mesostructures in fully or partially freestanding forms, with additional capabilities in integration onto nearly any class of substrate, from planar, hard inorganic materials to textured, soft biological tissues, all via mechanisms quantitatively described by theoretical modeling. Illustrations of these ideas include their use in 3D structures as frameworks for templated growth of organized lamellae from AgCl-KCl eutectics and of atomic layers of WSe2 from vapor-phase precursors, as open-architecture electronic scaffolds for formation of dorsal root ganglion (DRG) neural networks, and as catalyst supports for propulsive systems in 3D microswimmers with geometrically controlled dynamics. Taken together, these methodologies establish a set of enabling options in 3D micro/nanomanufacturing that lie outside of the scope of existing alternatives.

Automatic 2D-to-3D image conversion using 3D examples from the internet

NASA Astrophysics Data System (ADS)

Konrad, J.; Brown, G.; Wang, M.; Ishwar, P.; Wu, C.; Mukherjee, D.

2012-03-01

The availability of 3D hardware has so far outpaced the production of 3D content. Although to date many methods have been proposed to convert 2D images to 3D stereopairs, the most successful ones involve human operators and, therefore, are time-consuming and costly, while the fully-automatic ones have not yet achieved the same level of quality. This subpar performance is due to the fact that automatic methods usually rely on assumptions about the captured 3D scene that are often violated in practice. In this paper, we explore a radically different approach inspired by our work on saliency detection in images. Instead of relying on a deterministic scene model for the input 2D image, we propose to "learn" the model from a large dictionary of stereopairs, such as YouTube 3D. Our new approach is built upon a key observation and an assumption. The key observation is that among millions of stereopairs available on-line, there likely exist many stereopairs whose 3D content matches that of the 2D input (query). We assume that two stereopairs whose left images are photometrically similar are likely to have similar disparity fields. Our approach first finds a number of on-line stereopairs whose left image is a close photometric match to the 2D query and then extracts depth information from these stereopairs. Since disparities for the selected stereopairs differ due to differences in underlying image content, level of noise, distortions, etc., we combine them by using the median. We apply the resulting median disparity field to the 2D query to obtain the corresponding right image, while handling occlusions and newly-exposed areas in the usual way. We have applied our method in two scenarios. First, we used YouTube 3D videos in search of the most similar frames. Then, we repeated the experiments on a small, but carefully-selected, dictionary of stereopairs closely matching the query. This, to a degree, emulates the results one would expect from the use of an extremely large 3D repository. While far from perfect, the presented results demonstrate that on-line repositories of 3D content can be used for effective 2D-to-3D image conversion. With the continuously increasing amount of 3D data on-line and with the rapidly growing computing power in the cloud, the proposed framework seems a promising alternative to operator-assisted 2D-to-3D conversion.

Membrane Interaction of Antimicrobial Peptides Using E. coli Lipid Extract as Model Bacterial Cell Membranes and SFG Spectroscopy

PubMed Central

Soblosky, Lauren; Ramamoorthy, Ayyalusamy; Chen, Zhan

2015-01-01

Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/E. coli polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties. PMID:25707312

CFD Computations for a Generic High-Lift Configuration Using TetrUSS

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Abdol-Hamid, Khaled S.; Parlette, Edward B.

2011-01-01

Assessment of the accuracy of computational results for a generic high-lift trapezoidal wing with a single slotted flap and slat is presented. The paper is closely aligned with the focus of the 1st AIAA CFD High Lift Prediction Workshop (HiLiftPW-1) which was to assess the accuracy of CFD methods for multi-element high-lift configurations. The unstructured grid Reynolds-Averaged Navier-Stokes solver TetrUSS/USM3D is used for the computational results. USM3D results are obtained assuming fully turbulent flow using the Spalart-Allmaras (SA) and Shear Stress Transport (SST) turbulence models. Computed solutions have been obtained at seven different angles-of-attack ranging from 6 -37 . Three grids providing progressively higher grid resolution are used to quantify the effect of grid resolution on the lift, drag, pitching moment, surface pressure and stall angle. SA results, as compared to SST results, exhibit better agreement with the measured data. However, both turbulence models under-predict upper surface pressures near the wing tip region.

Jump events in a 3D Edwards-Anderson spin glass

NASA Astrophysics Data System (ADS)

Mártin, Daniel A.; Iguain, José Luis

2017-11-01

The statistical properties of infrequent particle displacements, greater than a certain distance, are known as jump dynamics in the context of structural glass formers. We generalize the concept of a jump to the case of a spin glass, by dividing the system into small boxes, and considering the infrequent cooperative spin flips in each box. Jumps defined this way share similarities with jumps in structural glasses. We perform numerical simulations for the 3D Edwards-Anderson model, and study how the properties of these jumps depend on the waiting time after a quench. Similar to the results for structural glasses, we find that while jump frequency depends strongly on time, the jump duration and jump length are roughly stationary. At odds with some results reported on studies of structural glass formers, at long enough times, the rest time between jumps varies as the inverse of jump frequency. We give a possible explanation for this discrepancy. We also find that our results are qualitatively reproduced by a fully-connected trap model.

Biomaterials for integration with 3-D bioprinting.

PubMed

Skardal, Aleksander; Atala, Anthony

2015-03-01

Bioprinting has emerged in recent years as an attractive method for creating 3-D tissues and organs in the laboratory, and therefore is a promising technology in a number of regenerative medicine applications. It has the potential to (i) create fully functional replacements for damaged tissues in patients, and (ii) rapidly fabricate small-sized human-based tissue models, or organoids, for diagnostics, pathology modeling, and drug development. A number of bioprinting modalities have been explored, including cellular inkjet printing, extrusion-based technologies, soft lithography, and laser-induced forward transfer. Despite the innovation of each of these technologies, successful implementation of bioprinting relies heavily on integration with compatible biomaterials that are responsible for supporting the cellular components during and after biofabrication, and that are compatible with the bioprinting device requirements. In this review, we will evaluate a variety of biomaterials, such as curable synthetic polymers, synthetic gels, and naturally derived hydrogels. Specifically we will describe how they are integrated with the bioprinting technologies above to generate bioprinted constructs with practical application in medicine.

3-d finite element model development for biomechanics: a software demonstration

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

Hollerbach, K.; Hollister, A.M.; Ashby, E.

1997-03-01

Finite element analysis is becoming an increasingly important part of biomechanics and orthopedic research, as computational resources become more powerful, and data handling algorithms become more sophisticated. Until recently, tools with sufficient power did not exist or were not accessible to adequately model complicated, three-dimensional, nonlinear biomechanical systems. In the past, finite element analyses in biomechanics have often been limited to two-dimensional approaches, linear analyses, or simulations of single tissue types. Today, we have the resources to model fully three-dimensional, nonlinear, multi-tissue, and even multi-joint systems. The authors will present the process of developing these kinds of finite element models,more » using human hand and knee examples, and will demonstrate their software tools.« less

The effect of topography of upper-mantle discontinuities on SS precursors

NASA Astrophysics Data System (ADS)

Koroni, Maria; Trampert, Jeannot

2016-01-01

Using the spectral-element method, we explored the effect of topography of upper-mantle discontinuities on the traveltimes of SS precursors recorded on transverse component seismograms. The latter are routinely used to infer the topography of mantle transition zone discontinuities. The step from precursory traveltimes to topographic changes is mainly done using linearised ray theory, or sometimes using finite-frequency kernels. We simulated exact seismograms in 1-D and 3-D elastic models of the mantle. In a second simulation, we added topography to the discontinuities. We compared the waveforms obtained with and without topography by cross correlation of the SS precursors. Since we did not add noise, the precursors are visible in individual seismograms without the need of stacking. The resulting time anomalies were then converted into topographic variations and compared to the original topographic models. Based on the correlation between initial and inferred models, and provided that ray coverage is good, we found that linearised ray theory gives a relatively good idea on the location of the uplifts and depressions of the discontinuities. It seriously underestimates the amplitude of the topographic variations by a factor ranging between 2 and 7. Real data depend on the 3-D elastic structure and the topography. All studies to date correct for the 3-D elastic effects assuming that the traveltimes can be linearly decomposed into a structure and a discontinuity part. We found a strong non-linearity in this decomposition which cannot be modelled without a fully non-linear inversion for elastic structure and discontinuities simultaneously.

Particle-induced osteolysis in three-dimensional micro-computed tomography.

PubMed

Wedemeyer, Christian; Xu, Jie; Neuerburg, Carl; Landgraeber, Stefan; Malyar, Nasser M; von Knoch, Fabian; Gosheger, Georg; von Knoch, Marius; Löer, Franz; Saxler, Guido

2007-11-01

Small-animal models are useful for the in vivo study of particle-induced osteolysis, the most frequent cause of aseptic loosening after total joint replacement. Microstructural changes associated with particle-induced osteolysis have been extensively explored using two-dimensional (2D) techniques. However, relatively little is known regarding the 3D dynamic microstructure of particle-induced osteolysis. Therefore, we tested micro-computed tomography (micro-CT) as a novel tool for 3D analysis of wear debris-mediated osteolysis in a small-animal model of particle-induced osteolysis. The murine calvarial model based on polyethylene particles was utilized in 14 C57BL/J6 mice randomly divided into two groups. Group 1 received sham surgery, and group 2 was treated with polyethylene particles. We performed 3D micro-CT analysis and histological assessment. Various bone morphometric parameters were assessed. Regression was used to examine the relation between the results achieved by the two methods. Micro-CT analysis provides a fully automated means to quantify bone destruction in a mouse model of particle-induced osteolysis. This method revealed that the osteolytic lesions in calvaria in the experimental group were affected irregularly compared to the rather even distribution of osteolysis in the control group. This is an observation which would have been missed if histomorphometric analysis only had been performed, leading to false assessment of the actual situation. These irregularities seen by micro-CT analysis provide new insight into individual bone changes which might otherwise be overlooked by histological analysis and can be used as baseline information on which future studies can be designed.

A fully consistent and conservative vertically adaptive coordinate system for SLIM 3D v0.4 with an application to the thermocline oscillations of Lake Tanganyika

NASA Astrophysics Data System (ADS)

Delandmeter, Philippe; Lambrechts, Jonathan; Legat, Vincent; Vallaeys, Valentin; Naithani, Jaya; Thiery, Wim; Remacle, Jean-François; Deleersnijder, Eric

2018-03-01

The discontinuous Galerkin (DG) finite element method is well suited for the modelling, with a relatively small number of elements, of three-dimensional flows exhibiting strong velocity or density gradients. Its performance can be highly enhanced by having recourse to r-adaptivity. Here, a vertical adaptive mesh method is developed for DG finite elements. This method, originally designed for finite difference schemes, is based on the vertical diffusion of the mesh nodes, with the diffusivity controlled by the density jumps at the mesh element interfaces. The mesh vertical movement is determined by means of a conservative arbitrary Lagrangian-Eulerian (ALE) formulation. Though conservativity is naturally achieved, tracer consistency is obtained by a suitable construction of the mesh vertical velocity field, which is defined in such a way that it is fully compatible with the tracer and continuity equations at a discrete level. The vertically adaptive mesh approach is implemented in the three-dimensional version of the geophysical and environmental flow Second-generation Louvain-la-Neuve Ice-ocean Model (SLIM 3D; www.climate.be/slim). Idealised benchmarks, aimed at simulating the oscillations of a sharp thermocline, are dealt with. Then, the relevance of the vertical adaptivity technique is assessed by simulating thermocline oscillations of Lake Tanganyika. The results are compared to measured vertical profiles of temperature, showing similar stratification and outcropping events.

Developing of operational hydro-meteorological simulating and displaying system

NASA Astrophysics Data System (ADS)

Wang, Y.; Shih, D.; Chen, C.

2010-12-01

Hydrological hazards, which often occur in conjunction with extreme precipitation events, are the most frequent type of natural disaster in Taiwan. Hence, the researchers at the Taiwan Typhoon and Flood Research Institute (TTFRI) are devoted to analyzing and gaining a better understanding of the causes and effects of natural disasters, and in particular, typhoons and floods. The long-term goal of the TTFRI is to develop a unified weather-hydrological-oceanic model suitable for simulations with local parameterizations in Taiwan. The development of a fully coupled weather-hydrology interaction model is not yet completed but some operational hydro-meteorological simulations are presented as a step in the direction of completing a full model. The predicted rainfall data from Weather Research Forecasting (WRF) are used as our meteorological forcing on watershed modeling. The hydrology and hydraulic modeling are conducted by WASH123D numerical model. And the WRF/WASH123D coupled system is applied to simulate floods during the typhoon landfall periods. The daily operational runs start at 04UTC, 10UTC, 16UTC and 22UTC, about 4 hours after data downloaded from NCEP GFS. This system will execute 72-hr weather forecasts. The simulation of WASH123D will sequentially trigger after receiving WRF rainfall data. This study presents the preliminary framework of establishing this system, and our goal is to build this earlier warning system to alert the public form dangerous. The simulation results are further display by a 3D GIS web service system. This system is established following the Open Geospatial Consortium (OGC) standardization process for GIS web service, such as Web Map Service (WMS) and Web Feature Service (WFS). The traditional 2D GIS data, such as high resolution aerial photomaps and satellite images are integrated into 3D landscape model. The simulated flooding and inundation area can be dynamically mapped on Wed 3D world. The final goal of this system is to real-time forecast flood and the results can be visually displayed on the virtual catchment. The policymaker can easily and real-time gain visual information for decision making at any site through internet.

Towards a new multiscale air quality transport model using the fully unstructured anisotropic adaptive mesh technology of Fluidity (version 4.1.9)

NASA Astrophysics Data System (ADS)

Zheng, J.; Zhu, J.; Wang, Z.; Fang, F.; Pain, C. C.; Xiang, J.

2015-10-01

An integrated method of advanced anisotropic hr-adaptive mesh and discretization numerical techniques has been, for first time, applied to modelling of multiscale advection-diffusion problems, which is based on a discontinuous Galerkin/control volume discretization on unstructured meshes. Over existing air quality models typically based on static-structured grids using a locally nesting technique, the advantage of the anisotropic hr-adaptive model has the ability to adapt the mesh according to the evolving pollutant distribution and flow features. That is, the mesh resolution can be adjusted dynamically to simulate the pollutant transport process accurately and effectively. To illustrate the capability of the anisotropic adaptive unstructured mesh model, three benchmark numerical experiments have been set up for two-dimensional (2-D) advection phenomena. Comparisons have been made between the results obtained using uniform resolution meshes and anisotropic adaptive resolution meshes. Performance achieved in 3-D simulation of power plant plumes indicates that this new adaptive multiscale model has the potential to provide accurate air quality modelling solutions effectively.

Two dimensional model for coherent synchrotron radiation

NASA Astrophysics Data System (ADS)

Huang, Chengkun; Kwan, Thomas J. T.; Carlsten, Bruce E.

2013-01-01

Understanding coherent synchrotron radiation (CSR) effects in a bunch compressor requires an accurate model accounting for the realistic beam shape and parameters. We extend the well-known 1D CSR analytic model into two dimensions and develop a simple numerical model based on the Liénard-Wiechert formula for the CSR field of a coasting beam. This CSR numerical model includes the 2D spatial dependence of the field in the bending plane and is accurate for arbitrary beam energy. It also removes the singularity in the space charge field calculation present in a 1D model. Good agreement is obtained with 1D CSR analytic result for free electron laser (FEL) related beam parameters but it can also give a more accurate result for low-energy/large spot size beams and off-axis/transient fields. This 2D CSR model can be used for understanding the limitation of various 1D models and for benchmarking fully electromagnetic multidimensional particle-in-cell simulations for self-consistent CSR modeling.

Electronic Polarizability and the Effective Pair Potentials of Water

PubMed Central

Leontyev, I. V.; Stuchebrukhov, A. A.

2014-01-01

Employing the continuum dielectric model for electronic polarizability, we have developed a new consistent procedure for parameterization of the effective nonpolarizable potential of liquid water. The model explains the striking difference between the value of water dipole moment μ~3D reported in recent ab initio and experimental studies with the value μeff~2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the consistency of the parameterization scheme can be achieved if the magnitude of the effective dipole of water is understood as a scaled value μeff=μ∕εel, where εel =1.78 is the electronic (high-frequency) dielectric constant of water, and a new electronic polarization energy term, missing in the previous theories, is included. The new term is evaluated by using Kirkwood - Onsager theory. The new scheme is fully consistent with experimental data on enthalpy of vaporization, density, diffusion coefficient, and static dielectric constant. The new theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes. PMID:25383062

Polymerization and oscillation stuttering in a filamentous model of the subcellular Min oscillation

NASA Astrophysics Data System (ADS)

Rutenberg, Andrew; Sengupta, Supratim; Sain, Anirban; Derr, Julien

2011-03-01

We present a computational model of the E. coli Min oscillation that involves polymerization of MinD filaments followed by depolymerization stimulated by filament-end zones of MinE. Our stochastic model is fully three-dimensional, and tracks the diffusion and interactions of every MinD and MinE molecule. We recover self-organized Min oscillations. We investigate the experimental phenomenon of oscillation stuttering, which we relate to the disruption of MinE tip-binding at the filament scale.

Correlating confocal microscopy and atomic force indentation reveals metastatic cancer cells stiffen during invasion into collagen I matrices

NASA Astrophysics Data System (ADS)

Staunton, Jack R.; Doss, Bryant L.; Lindsay, Stuart; Ros, Robert

2016-01-01

Mechanical interactions between cells and their microenvironment dictate cell phenotype and behavior, calling for cell mechanics measurements in three-dimensional (3D) extracellular matrices (ECM). Here we describe a novel technique for quantitative mechanical characterization of soft, heterogeneous samples in 3D. The technique is based on the integration of atomic force microscopy (AFM) based deep indentation, confocal fluorescence microscopy, finite element (FE) simulations and analytical modeling. With this method, the force response of a cell embedded in 3D ECM can be decoupled from that of its surroundings, enabling quantitative determination of the elastic properties of both the cell and the matrix. We applied the technique to the quantification of the elastic properties of metastatic breast adenocarcinoma cells invading into collagen hydrogels. We found that actively invading and fully embedded cells are significantly stiffer than cells remaining on top of the collagen, a clear example of phenotypical change in response to the 3D environment. Treatment with Rho-associated protein kinase (ROCK) inhibitor significantly reduces this stiffening, indicating that actomyosin contractility plays a major role in the initial steps of metastatic invasion.

Automated 3D structure composition for large RNAs

PubMed Central

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

2012-01-01

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

Two Methods of Automatic Evaluation of Speech Signal Enhancement Recorded in the Open-Air MRI Environment

NASA Astrophysics Data System (ADS)

Přibil, Jiří; Přibilová, Anna; Frollo, Ivan

2017-12-01

The paper focuses on two methods of evaluation of successfulness of speech signal enhancement recorded in the open-air magnetic resonance imager during phonation for the 3D human vocal tract modeling. The first approach enables to obtain a comparison based on statistical analysis by ANOVA and hypothesis tests. The second method is based on classification by Gaussian mixture models (GMM). The performed experiments have confirmed that the proposed ANOVA and GMM classifiers for automatic evaluation of the speech quality are functional and produce fully comparable results with the standard evaluation based on the listening test method.

Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A.

1998-01-01

In a previous study using a fully three-dimensional (3D) helical slow-wave circuit cold- test model it was found, contrary to classical helical circuit analyses, that transverse FF electric fields have significant amplitudes compared with the longitudinal component. The RF fields obtained using this helical cold-test model have been scaled to correspond to those of an actual TWT. At the output of the tube, RF field forces reach 61%, 26% and 132% for radial, azimuthal and longitudinal components, respectively, compared to radial space charge forces indicating the importance of considering them in the design of electron beam focusing.

Intervertebral disc segmentation in MR images with 3D convolutional networks

NASA Astrophysics Data System (ADS)

Korez, Robert; Ibragimov, Bulat; Likar, Boštjan; Pernuš, Franjo; Vrtovec, Tomaž

2017-02-01

The vertebral column is a complex anatomical construct, composed of vertebrae and intervertebral discs (IVDs) supported by ligaments and muscles. During life, all components undergo degenerative changes, which may in some cases cause severe, chronic and debilitating low back pain. The main diagnostic challenge is to locate the pain generator, and degenerated IVDs have been identified to act as such. Accurate and robust segmentation of IVDs is therefore a prerequisite for computer-aided diagnosis and quantification of IVD degeneration, and can be also used for computer-assisted planning and simulation in spinal surgery. In this paper, we present a novel fully automated framework for supervised segmentation of IVDs from three-dimensional (3D) magnetic resonance (MR) spine images. By considering global intensity appearance and local shape information, a landmark-based approach is first used for the detection of IVDs in the observed image, which then initializes the segmentation of IVDs by coupling deformable models with convolutional networks (ConvNets). For this purpose, a 3D ConvNet architecture was designed that learns rich high-level appearance representations from a training repository of IVDs, and then generates spatial IVD probability maps that guide deformable models towards IVD boundaries. By applying the proposed framework to 15 3D MR spine images containing 105 IVDs, quantitative comparison of the obtained against reference IVD segmentations yielded an overall mean Dice coefficient of 92.8%, mean symmetric surface distance of 0.4 mm and Hausdorff surface distance of 3.7 mm.

Imaging lidar technology: development of a 3D-lidar elegant breadboard for rendezvous and docking, test results, and prospect to future sensor application

NASA Astrophysics Data System (ADS)

Moebius, B.; Pfennigbauer, M.; Pereira do Carmo, J.

2017-11-01

During the previous 15 years, Rendezvous and Docking Sensors (RVS) were developed, manufactured and qualified. In the mean time they were successfully applied in some space missions: For automatic docking of the European ATV "Jules Verne" on the International Space Station in 2008; for automatic berthing of the first Japanese HTV in 2009, and even the precursor model ARP-RVS for measurements during Shuttle Atlantis flights STS-84 and STS-86 to the MIR station. Up to now, about twenty RVS Flight Models for application on ATV, HTV and the American Cygnus Spacecraft were manufactured and delivered to the respective customers. RVS is designed for tracking of customer specific, cooperative targets (i.e. retro reflectors that are arranged in specific geometries). Once RVS has acquired the target, the sensor measures the distance to the target by timeof- flight determination of a pulsed laser beam. Any echo return provokes an interrupt signal and thus the readout of the according encoder positions of the two scan mirrors that represent Azimuth and Elevation measurement direction to the target. [2], [3]. The capability of the RVS for 3D mapping of the scene makes the fully space qualified RVS to be real 3D Lidar sensors; thus they are a sound technical base for the compact 3D Lidar breadboard that was developed in the course of the Imaging Lidar Technology (ILT) project.

a Low-Cost and Portable System for 3d Reconstruction of Texture-Less Objects

NASA Astrophysics Data System (ADS)

Hosseininaveh, A.; Yazdan, R.; Karami, A.; Moradi, M.; Ghorbani, F.

2015-12-01

The optical methods for 3D modelling of objects can be classified into two categories including image-based and range-based methods. Structure from Motion is one of the image-based methods implemented in commercial software. In this paper, a low-cost and portable system for 3D modelling of texture-less objects is proposed. This system includes a rotating table designed and developed by using a stepper motor and a very light rotation plate. The system also has eight laser light sources with very dense and strong beams which provide a relatively appropriate pattern on texture-less objects. In this system, regarding to the step of stepper motor, images are semi automatically taken by a camera. The images can be used in structure from motion procedures implemented in Agisoft software.To evaluate the performance of the system, two dark objects were used. The point clouds of these objects were obtained by spraying a light powders on the objects and exploiting a GOM laser scanner. Then these objects were placed on the proposed turntable. Several convergent images were taken from each object while the laser light sources were projecting the pattern on the objects. Afterward, the images were imported in VisualSFM as a fully automatic software package for generating an accurate and complete point cloud. Finally, the obtained point clouds were compared to the point clouds generated by the GOM laser scanner. The results showed the ability of the proposed system to produce a complete 3D model from texture-less objects.

Intermittency, coherent structures and dissipation in plasma turbulence

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

Wan, M.; Matthaeus, W. H.; Parashar, T. N.

Collisionless dissipation in turbulent plasmas such as the solar wind and the solar corona has been an intensively studied subject recently, with new insights often emerging from numerical simulation. Here we report results from high resolution, fully kinetic simulations of plasma turbulence in both two (2D) and three (3D) dimensions, studying the relationship between intermittency and dissipation. The simulations show development of turbulent coherent structures, characterized by sheet-like current density structures spanning a range of scales. An approximate dissipation measure is employed, based on work done by the electromagnetic field in the local electron fluid frame. This surrogate dissipation measuremore » is highly concentrated in small subvolumes in both 2D and 3D simulations. Fully kinetic simulations are also compared with magnetohydrodynamics (MHD) simulations in terms of coherent structures and dissipation. The interesting result emerges that the conditional averages of dissipation measure scale very similarly with normalized current density J in 2D and 3D particle-in-cell and in MHD. To the extent that the surrogate dissipation measure is accurate, this result implies that on average dissipation scales as ∼J{sup 2} in turbulent kinetic plasma. Multifractal intermittency is seen in the inertial range in both 2D and 3D, but at scales ∼ion inertial length, the scaling is closer to monofractal.« less

Lossy to lossless object-based coding of 3-D MRI data.

PubMed

Menegaz, Gloria; Thiran, Jean-Philippe

2002-01-01

We propose a fully three-dimensional (3-D) object-based coding system exploiting the diagnostic relevance of the different regions of the volumetric data for rate allocation. The data are first decorrelated via a 3-D discrete wavelet transform. The implementation via the lifting steps scheme allows to map integer-to-integer values, enabling lossless coding, and facilitates the definition of the object-based inverse transform. The coding process assigns disjoint segments of the bitstream to the different objects, which can be independently accessed and reconstructed at any up-to-lossless quality. Two fully 3-D coding strategies are considered: embedded zerotree coding (EZW-3D) and multidimensional layered zero coding (MLZC), both generalized for region of interest (ROI)-based processing. In order to avoid artifacts along region boundaries, some extra coefficients must be encoded for each object. This gives rise to an overheading of the bitstream with respect to the case where the volume is encoded as a whole. The amount of such extra information depends on both the filter length and the decomposition depth. The system is characterized on a set of head magnetic resonance images. Results show that MLZC and EZW-3D have competitive performances. In particular, the best MLZC mode outperforms the others state-of-the-art techniques on one of the datasets for which results are available in the literature.

Fully probabilistic seismic source inversion - Part 2: Modelling errors and station covariances

NASA Astrophysics Data System (ADS)

Stähler, Simon C.; Sigloch, Karin

2016-11-01

Seismic source inversion, a central task in seismology, is concerned with the estimation of earthquake source parameters and their uncertainties. Estimating uncertainties is particularly challenging because source inversion is a non-linear problem. In a companion paper, Stähler and Sigloch (2014) developed a method of fully Bayesian inference for source parameters, based on measurements of waveform cross-correlation between broadband, teleseismic body-wave observations and their modelled counterparts. This approach yields not only depth and moment tensor estimates but also source time functions. A prerequisite for Bayesian inference is the proper characterisation of the noise afflicting the measurements, a problem we address here. We show that, for realistic broadband body-wave seismograms, the systematic error due to an incomplete physical model affects waveform misfits more strongly than random, ambient background noise. In this situation, the waveform cross-correlation coefficient CC, or rather its decorrelation D = 1 - CC, performs more robustly as a misfit criterion than ℓp norms, more commonly used as sample-by-sample measures of misfit based on distances between individual time samples. From a set of over 900 user-supervised, deterministic earthquake source solutions treated as a quality-controlled reference, we derive the noise distribution on signal decorrelation D = 1 - CC of the broadband seismogram fits between observed and modelled waveforms. The noise on D is found to approximately follow a log-normal distribution, a fortunate fact that readily accommodates the formulation of an empirical likelihood function for D for our multivariate problem. The first and second moments of this multivariate distribution are shown to depend mostly on the signal-to-noise ratio (SNR) of the CC measurements and on the back-azimuthal distances of seismic stations. By identifying and quantifying this likelihood function, we make D and thus waveform cross-correlation measurements usable for fully probabilistic sampling strategies, in source inversion and related applications such as seismic tomography.

Design and properties of 3D scaffolds for bone tissue engineering.

PubMed

Gómez, S; Vlad, M D; López, J; Fernández, E

2016-09-15

In this study, the Voronoi tessellation method has been used to design novel bone like three dimension (3D) porous scaffolds. The Voronoi method has been processed with computer design software to obtain 3D virtual isotropic porous interconnected models, exactly matching the main histomorphometric indices of trabecular bone (trabecular thickness, trabecular separation, trabecular number, bone volume to total volume ratio, bone surface to bone volume ratio, etc.). These bone like models have been further computed for mechanical (elastic modulus) and fluid mass transport (permeability) properties. The results show that the final properties of the scaffolds can be controlled during their microstructure and histomorphometric initial design stage. It is also shown that final properties can be tuned during the design stage to exactly match those of trabecular natural bone. Moreover, identical total porosity models can be designed with quite different specific bone surface area and thus, this specific microstructural feature can be used to favour cell adhesion, migration and, ultimately, new bone apposition (i.e. osteoconduction). Once the virtual models are fully characterized and optimized, these can be easily 3D printed by additive manufacturing and/or stereolitography technologies. The significance of this article goes far beyond the specific objectives on which it is focussed. In fact, it shows, in a guided way, the entire novel process that can be followed to design graded porous implants, whatever its external shape and geometry, but internally tuned to the exact histomorphometric indices needed to match natural human tissues microstructures and, consequently, their mechanical and fluid properties, among others. The significance is even more relevant nowadays thanks to the available new computing and design software that is easily linked to the 3D printing new technologies. It is this transversality, at the frontier of different disciplines, the main characteristic that gives this article a high scientific impact and interest to a broaden audience. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Segmentation of skin lesions in chronic graft versus host disease photographs with fully convolutional networks

NASA Astrophysics Data System (ADS)

Wang, Jianing; Chen, Fuyao; Dellalana, Laura E.; Jagasia, Madan H.; Tkaczyk, Eric R.; Dawant, Benoit M.

2018-02-01

Chronic graft-versus-host disease (cGVHD) is a frequent and potentially life-threatening complication of allogeneic hematopoietic stem cell transplantation (HCT) and commonly affects the skin, resulting in distressing patient morbidity. The percentage of involved body surface area (BSA) is commonly used for diagnosing and scoring the severity of cGVHD. However, the segmentation of the involved BSA from patient whole body serial photography is challenging because (1) it is difficult to design traditional segmentation method that rely on hand crafted features as the appearance of cGVHD lesions can be drastically different from patient to patient; (2) to the best of our knowledge, currently there is no publicavailable labelled image set of cGVHD skin for training deep networks to segment the involved BSA. In this preliminary study we create a small labelled image set of skin cGVHD, and we explore the possibility to use a fully convolutional neural network (FCN) to segment the skin lesion in the images. We use a commercial stereoscopic Vectra H1 camera (Canfield Scientific) to acquire 400 3D photographs of 17 cGVHD patients aged between 22 and 72. A rotational data augmentation process is then applied, which rotates the 3D photos through 10 predefined angles, producing one 2D projection image at each position. This results in 4000 2D images that constitute our cGVHD image set. A FCN model is trained and tested using our images. We show that our method achieves encouraging results for segmenting cGVHD skin lesion in photographic images.

Study of High Lift Configurations

NASA Technical Reports Server (NTRS)

Edward, Jack R.; Hassan, Hassan A.

2000-01-01

This project focus on the implementation of the Warren-Hassan transition / turbulence model (Journal of Aircraft, Vol. 35, No. 5) into the NASA code CFL3D and its testing for multi-element airfoils in landing configuration at different angles of attack. The Warren-Hassan transition model solves an evolution equation for a kinetic energy characteristic of non-turbulent fluctuations. This is combined with an empirical estimate of the frequency of the most amplified first-mode disturbance to yield an expression for an eddy viscosity characteristic of non-turbulent fluctuations. This is combined with the k - zeta model for fully turbulent flow to yield a unified approach capable of predicting both transition onset and extent. Blending of the non-turbulent and turbulent components of the model is accomplished by an intermittency function based on the work of Dhawan and Narasimha (Journal of Fluid Mechanics, Vol. 3, No. 4).

Untangling Slab Dynamics Using 3-D Numerical and Analytical Models

NASA Astrophysics Data System (ADS)

Holt, A. F.; Royden, L.; Becker, T. W.

2016-12-01

Increasingly sophisticated numerical models have enabled us to make significant strides in identifying the key controls on how subducting slabs deform. For example, 3-D models have demonstrated that subducting plate width, and the related strength of toroidal flow around the plate edge, exerts a strong control on both the curvature and the rate of migration of the trench. However, the results of numerical subduction models can be difficult to interpret, and many first order dynamics issues remain at least partially unresolved. Such issues include the dominant controls on trench migration, the interdependence of asthenospheric pressure and slab dynamics, and how nearby slabs influence each other's dynamics. We augment 3-D, dynamically evolving finite element models with simple, analytical force-balance models to distill the physics associated with subduction into more manageable parts. We demonstrate that for single, isolated subducting slabs much of the complexity of our fully numerical models can be encapsulated by simple analytical expressions. Rates of subduction and slab dip correlate strongly with the asthenospheric pressure difference across the subducting slab. For double subduction, an additional slab gives rise to more complex mantle pressure and flow fields, and significantly extends the range of plate kinematics (e.g., convergence rate, trench migration rate) beyond those present in single slab models. Despite these additional complexities, we show that much of the dynamics of such multi-slab systems can be understood using the physics illuminated by our single slab study, and that a force-balance method can be used to relate intra-plate stress to viscous pressure in the asthenosphere and coupling forces at plate boundaries. This method has promise for rapid modeling of large systems of subduction zones on a global scale.

DREAM3D simulations of inner-belt dynamics

NASA Astrophysics Data System (ADS)

Cunningham, G.

2015-12-01

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 due to pitch-angle scattering from Coulomb and VLF wave-particle interactions. In this paper, equilibrium solutions to a set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium structure. Each diffusion equation incorporated an L- and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This model is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering, and that there is no acceleration caused by the VLF wave-particle interactions. We have revisited this model using our DREAM3D 3D diffusion code, which allows the user to explicitly model the diffusion in pitch-angle and momentum rather than using a lifetime. We find that a) replacing the lifetimes with an explicit model of pitch-angle diffusion, thus allowing for coupling between radial and pitch-angle diffusion, affects the equilibrium structure, and b) over the long time scales needed to reach equilibrium, significant acceleration due to VLF wave particle interactions takes place due to the 'cross-terms' in pitch-angle and momentum and the sharp gradient in the equilibrium pitch-angle distributions. We also find 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 fully understand the equilibirum nature of the trapped electron radiation belts.

Fully automatic detection and visualization of patient specific coronary supply regions

NASA Astrophysics Data System (ADS)

Fritz, Dominik; Wiedemann, Alexander; Dillmann, Ruediger; Scheuering, Michael

2008-03-01

Coronary territory maps, which associate myocardial regions with the corresponding coronary artery that supply them, are a common visualization technique to assist the physician in the diagnosis of coronary artery disease. However, the commonly used visualization is based on the AHA-17-segment model, which is an empirical population based model. Therefore, it does not necessarily cope with the often highly individual coronary anatomy of a specific patient. In this paper we introduce a novel fully automatic approach to compute the patient individual coronary supply regions in CTA datasets. This approach is divided in three consecutive steps. First, the aorta is fully automatically located in the dataset with a combination of a Hough transform and a cylindrical model matching approach. Having the location of the aorta, a segmentation and skeletonization of the coronary tree is triggered. In the next step, the three main branches (LAD, LCX and RCX) are automatically labeled, based on the knowledge of the pose of the aorta and the left ventricle. In the last step the labeled coronary tree is projected on the left ventricular surface, which can afterward be subdivided into the coronary supply regions, based on a Voronoi transform. The resulting supply regions can be either shown in 3D on the epicardiac surface of the left ventricle, or as a subdivision of a polarmap.

A fully parallel in time and space algorithm for simulating the electrical activity of a neural tissue.

PubMed

Bedez, Mathieu; Belhachmi, Zakaria; Haeberlé, Olivier; Greget, Renaud; Moussaoui, Saliha; Bouteiller, Jean-Marie; Bischoff, Serge

2016-01-15

The resolution of a model describing the electrical activity of neural tissue and its propagation within this tissue is highly consuming in term of computing time and requires strong computing power to achieve good results. In this study, we present a method to solve a model describing the electrical propagation in neuronal tissue, using parareal algorithm, coupling with parallelization space using CUDA in graphical processing unit (GPU). We applied the method of resolution to different dimensions of the geometry of our model (1-D, 2-D and 3-D). The GPU results are compared with simulations from a multi-core processor cluster, using message-passing interface (MPI), where the spatial scale was parallelized in order to reach a comparable calculation time than that of the presented method using GPU. A gain of a factor 100 in term of computational time between sequential results and those obtained using the GPU has been obtained, in the case of 3-D geometry. Given the structure of the GPU, this factor increases according to the fineness of the geometry used in the computation. To the best of our knowledge, it is the first time such a method is used, even in the case of neuroscience. Parallelization time coupled with GPU parallelization space allows for drastically reducing computational time with a fine resolution of the model describing the propagation of the electrical signal in a neuronal tissue. Copyright © 2015 Elsevier B.V. All rights reserved.